Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold591
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1432801
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 160147 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:353192 original size:20 final size:20
Alignment explanation
Indices: 353167--353204 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
353157 GTAACATATA
*
353167 ATATTGTATCATATGATACG
1 ATATTGTATAATATGATACG
353187 ATATTGTATAATATGATA
1 ATATTGTATAATATGATA
353205 TTAGTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
ATATTGTATAATATGATACG
Found at i:353204 original size:50 final size:48
Alignment explanation
Indices: 353147--353309 Score: 146
Period size: 50 Copynumber: 3.3 Consensus size: 48
353137 ATGCTATTTC
* * *
353147 ATATGATATTGTAACATATAATATTGTATCATATGATACGATATTGTATA
1 ATATGATATTGTAA-ATATAATATT-TATTATATAATACGAAATTGTATA
** * * * *
353197 ATATGATATTAGTTTATATAATATATTATTATATCATATGAAAATGTATG
1 ATATGATATT-GTAAATATAATAT-TTATTATATAATACGAAATTGTATA
* * * *
353247 ATATGATATTGTATAATGTGATATTATATTATATAATACAAAATAGTATA
1 ATATGATATTGTA-AATATAATATT-TATTATATAATACGAAATTGTATA
*
353297 CTATGATATTGTA
1 ATATGATATTGTA
353310 TGATAAAATA
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
49 3 0.03
50 84 0.93
51 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (48 bp):
ATATGATATTGTAAATATAATATTTATTATATAATACGAAATTGTATA
Found at i:353206 original size:15 final size:15
Alignment explanation
Indices: 353095--353271 Score: 78
Period size: 15 Copynumber: 11.3 Consensus size: 15
353085 TTATGATACA
353095 ATATTGTATAATATG
1 ATATTGTATAATATG
*
353110 ATAATGTATAATAT-
1 ATATTGTATAATATG
* * *
353124 ACTATTTTATCACATG
1 A-TATTGTATAATATG
* *
353140 CTA-T-T-TCATATG
1 ATATTGTATAATATG
*
353152 ATATTGTA-ACATATA
1 ATATTGTATA-ATATG
353167 ATATTGTATCATATGATACG
1 ATATTGTAT-A-AT-AT--G
353187 ATATTGTATAATATG
1 ATATTGTATAATATG
353202 ATATTAGTTTATATAATAT-
1 ATATT-G----TATAATATG
* *
353221 ATTATTATATCATATG
1 A-TATTGTATAATATG
* * *
353237 AAAATGTATGATATG
1 ATATTGTATAATATG
*
353252 ATATTGTATAATGTG
1 ATATTGTATAATATG
353267 ATATT
1 ATATT
353272 ATATTATATA
Statistics
Matches: 122, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
12 8 0.07
13 2 0.02
14 3 0.02
15 75 0.61
16 2 0.02
17 5 0.04
18 4 0.03
19 2 0.02
20 21 0.17
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:353268 original size:20 final size:20
Alignment explanation
Indices: 353245--353283 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
353235 TGAAAATGTA
*
353245 TGATATGATATTGTATAATG
1 TGATATGATATTATATAATG
*
353265 TGATATTATATTATATAAT
1 TGATATGATATTATATAAT
353284 ACAAAATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TGATATGATATTATATAATG
Found at i:353302 original size:65 final size:65
Alignment explanation
Indices: 353178--353314 Score: 163
Period size: 65 Copynumber: 2.1 Consensus size: 65
353168 TATTGTATCA
* * *
353178 TATGATACGATATTGTATAATATGATATTAGTTTATATAATATATTATTATATCATATGAAAATG
1 TATGATACGATATTGTATAATATGATATTAGTTTATATAATAAAATAGTATATCATATGAAAATG
* * *
353243 TATGATATGATATTGTATAATGTGATATTA-TATTATATAATACAAAATAGTATA-C-TATGATA
1 TATGATACGATATTGTATAATATGATATTAGT-TTATATAAT--AAAATAGTATATCATATGAAA
*
353305 TTG
63 ATG
353308 TATGATA
1 TATGATA
353315 AAATATAGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
64 1 0.02
65 52 0.84
66 1 0.02
67 8 0.13
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.44
Consensus pattern (65 bp):
TATGATACGATATTGTATAATATGATATTAGTTTATATAATAAAATAGTATATCATATGAAAATG
Found at i:353450 original size:13 final size:14
Alignment explanation
Indices: 353413--353464 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
353403 TTATGTATCA
* *
353413 AATATGATACAATAC
1 AATATCATAC-ATAT
353428 AATATCATAC-TAT
1 AATATCATACATAT
*
353441 AATATTATACAATAT
1 AATATCATAC-ATAT
353456 AATATCATA
1 AATATCATA
353465 TGTTACAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.35
15 20 0.65
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (14 bp):
AATATCATACATAT
Found at i:353915 original size:16 final size:16
Alignment explanation
Indices: 353894--353926 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
353884 AAGGTGGTCA
*
353894 CATAAAGGTGATTCCT
1 CATAAAGGTGATGCCT
353910 CATAAAGGTGATGCCT
1 CATAAAGGTGATGCCT
353926 C
1 C
353927 GTCTCAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (16 bp):
CATAAAGGTGATGCCT
Found at i:355380 original size:2 final size:2
Alignment explanation
Indices: 355373--355401 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
355363 CAACAGTTCT
355373 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
355402 ATGAAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:357014 original size:21 final size:21
Alignment explanation
Indices: 356979--357019 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
356969 AAACCTTACC
**
356979 GTGCAAGAAGTGAACAGTACT
1 GTGCAAGAAACGAACAGTACT
*
357000 GTGCAAGAAACGAACCGTAC
1 GTGCAAGAAACGAACAGTAC
357020 CATTCATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.15
Consensus pattern (21 bp):
GTGCAAGAAACGAACAGTACT
Found at i:357034 original size:21 final size:21
Alignment explanation
Indices: 357010--357053 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
357000 GTGCAAGAAA
*
357010 CGAACCGTACCATTCATAAAG
1 CGAACCGTACCATTCAAAAAG
*
357031 CGAACCGTACCGTTCAAAAAG
1 CGAACCGTACCATTCAAAAAG
357052 CG
1 CG
357054 TGATGCACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (21 bp):
CGAACCGTACCATTCAAAAAG
Found at i:357132 original size:2 final size:2
Alignment explanation
Indices: 357127--357169 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
357117 ATATATATAT
357127 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
357169 A
1 A
357170 GAATAGTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:360937 original size:11 final size:11
Alignment explanation
Indices: 360921--360965 Score: 90
Period size: 11 Copynumber: 4.1 Consensus size: 11
360911 AGATAGTGTA
360921 GATTTTAAATC
1 GATTTTAAATC
360932 GATTTTAAATC
1 GATTTTAAATC
360943 GATTTTAAATC
1 GATTTTAAATC
360954 GATTTTAAATC
1 GATTTTAAATC
360965 G
1 G
360966 TGAAAACTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (11 bp):
GATTTTAAATC
Found at i:362150 original size:2 final size:2
Alignment explanation
Indices: 362143--362196 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
362133 TTTAAACATT
362143 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
362184 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
362197 TTTTAAGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:362680 original size:4 final size:4
Alignment explanation
Indices: 362673--362707 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
362663 CATATAAAGA
362673 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
362708 ACACATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:367541 original size:28 final size:28
Alignment explanation
Indices: 367496--367549 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
367486 GAACATTTTA
367496 GAAGAAACTACTACAGATAAGCAAGACT
1 GAAGAAACTACTACAGATAAGCAAGACT
* * *
367524 GAAGAAACTGCTAGAGATGAGCAAGA
1 GAAGAAACTACTACAGATAAGCAAGA
367550 GAAAATTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (28 bp):
GAAGAAACTACTACAGATAAGCAAGACT
Found at i:368556 original size:20 final size:21
Alignment explanation
Indices: 368531--368619 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
368521 TTAACATATA
*
368531 TTCAAAT-ATTTGTACCTATC
1 TTCAAATCAATTGTACCTATC
368551 TTCAAAT-AATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
*
368571 TTCAATTCAATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
*
368592 TTCAATTCAATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
368613 TTCAAAT
1 TTCAAAT
368620 TGAATTAGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 25 0.38
21 40 0.62
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (21 bp):
TTCAAATCAATTGTACCTATC
Found at i:368584 original size:21 final size:21
Alignment explanation
Indices: 368540--368617 Score: 140
Period size: 21 Copynumber: 3.8 Consensus size: 21
368530 ATTCAAATAT
*
368540 TTGTACCTATCTTCAAAT-AA
1 TTGTACCTATCTTCAATTCAA
368560 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
368581 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
368602 TTGTACCTATCTTCAA
1 TTGTACCTATCTTCAA
368618 ATTGAATTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
20 17 0.30
21 39 0.70
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
TTGTACCTATCTTCAATTCAA
Found at i:368646 original size:21 final size:22
Alignment explanation
Indices: 368617--368756 Score: 83
Period size: 21 Copynumber: 6.4 Consensus size: 22
368607 CCTATCTTCA
*
368617 AATTGAATTAG-AGATAGGTAC
1 AATTCAATTAGAAGATAGGTAC
* * ** **
368638 AATTCAATTA-TACATATCTTT
1 AATTCAATTAGAAGATAGGTAC
*
368659 AATTC-ATTTGAAGATAGGTAC
1 AATTCAATTAGAAGATAGGTAC
* *
368680 AATT-GATTTGAAGATAGGTAC
1 AATTCAATTAGAAGATAGGTAC
* *
368701 AAATGCAATGAATTGAAGATAGGTAC
1 -AATTCAAT---TAGAAGATAGGTAC
*
368727 AATTGAATTA-AAGATAGGTAC
1 AATTCAATTAGAAGATAGGTAC
*
368748 AATTGAATT
1 AATTCAATT
368757 GAACGTATCT
Statistics
Matches: 93, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
20 3 0.03
21 64 0.69
22 4 0.04
23 2 0.02
25 6 0.06
26 14 0.15
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (22 bp):
AATTCAATTAGAAGATAGGTAC
Found at i:368656 original size:43 final size:42
Alignment explanation
Indices: 368594--368683 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 42
368584 TACCTATCTT
* *
368594 CAATTCAATTGTACCTATCTTCAAATTGAATTAG-AGATAGGTA
1 CAATTCAATTATACATATCTT-AAATT-AATTAGAAGATAGGTA
* * *
368637 CAATTCAATTATACATATCTTTAATTCATTTGAAGATAGGTA
1 CAATTCAATTATACATATCTTAAATTAATTAGAAGATAGGTA
368679 CAATT
1 CAATT
368684 GATTTGAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 4 0.10
42 18 0.44
43 19 0.46
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (42 bp):
CAATTCAATTATACATATCTTAAATTAATTAGAAGATAGGTA
Found at i:368756 original size:42 final size:42
Alignment explanation
Indices: 368617--368759 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 42
368607 CCTATCTTCA
* * * ** **
368617 AATTGAATT-AGAGATAGGTACAATTCAATTATACATATCTTT
1 AATTGAATTGA-AGATAGGTACAATTGAATTAAAGATAGGTAC
* * * *
368659 AATTCATTTGAAGATAGGTACAATTGATTTGAAGATAGGTAC
1 AATTGAATTGAAGATAGGTACAATTGAATTAAAGATAGGTAC
368701 AAATGCAATGAATTGAAGATAGGTACAATTGAATTAAAGATAGGTAC
1 -AAT----TGAATTGAAGATAGGTACAATTGAATTAAAGATAGGTAC
368748 AATTGAATTGAA
1 AATTGAATTGAA
368760 CGTATCTTCA
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
42 38 0.47
43 4 0.05
46 3 0.04
47 35 0.44
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (42 bp):
AATTGAATTGAAGATAGGTACAATTGAATTAAAGATAGGTAC
Found at i:369196 original size:17 final size:17
Alignment explanation
Indices: 369174--369207 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
369164 GTATATAGTG
369174 ACCCTAACTACGTCACT
1 ACCCTAACTACGTCACT
*
369191 ACCCTAACTCCGTCACT
1 ACCCTAACTACGTCACT
369208 TTTGGGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.44, G:0.06, T:0.24
Consensus pattern (17 bp):
ACCCTAACTACGTCACT
Found at i:369509 original size:21 final size:21
Alignment explanation
Indices: 369445--369513 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
369435 TAGATATGTC
*
369445 TGAATTGAACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* * *
369466 TCAATAGTACCTATCTTTAAA
1 TGAATTGTACCTATCTTCAAA
*
369487 TGAATTTTACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
369508 TGAATT
1 TGAATT
369514 AGAGATAGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:369545 original size:21 final size:21
Alignment explanation
Indices: 369519--369571 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
369509 GAATTAGAGA
369519 TAGGTATAATTCATTCGTACC
1 TAGGTATAATTCATTCGTACC
*
369540 TAGGTATAATTCATTTGTACC
1 TAGGTATAATTCATTCGTACC
369561 TAGGTATAATT
1 TAGGTATAATT
369572 ATTTAGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (21 bp):
TAGGTATAATTCATTCGTACC
Found at i:369584 original size:20 final size:22
Alignment explanation
Indices: 369518--369596 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 22
369508 TGAATTAGAG
*
369518 ATAGGTATAATTCA-TTCGTAC
1 ATAGGTATAATTCATTTAGTAC
*
369539 CTAGGTATAATTCATTT-GTAC
1 ATAGGTATAATTCATTTAGTAC
* *
369560 CTAGGTATAATT-ATTTAG-AG
1 ATAGGTATAATTCATTTAGTAC
369580 ATAGGTATAATT-ATTTA
1 ATAGGTATAATTCATTTA
369597 CACCTATCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
20 21 0.40
21 30 0.57
22 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
ATAGGTATAATTCATTTAGTAC
Found at i:369622 original size:21 final size:21
Alignment explanation
Indices: 369598--369671 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
369588 AATTATTTAC
369598 ACCTATCTTCAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
369619 ACCTATCTTCAAAT-AATTGT
1 ACCTATCTTCAATTCAATTGT
*
369639 ACCTATCTTTAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
369660 ACCTATCTTCAA
1 ACCTATCTTCAA
369672 ATGATTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.38
21 30 0.62
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (21 bp):
ACCTATCTTCAATTCAATTGT
Found at i:369700 original size:20 final size:20
Alignment explanation
Indices: 369669--369721 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
369659 TACCTATCTT
369669 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
*
369690 CAATTATTTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
369710 CAAATATTTGAA
1 CAAATATTTGAA
369722 TATATGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:372941 original size:23 final size:23
Alignment explanation
Indices: 372915--372961 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
372905 GGCAATCAAA
* *
372915 ATACATATATGTAGTACATGTAT
1 ATACATACATGTAATACATGTAT
372938 ATACATACATGTAATACATGTAT
1 ATACATACATGTAATACATGTAT
372961 A
1 A
372962 ACCGAAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (23 bp):
ATACATACATGTAATACATGTAT
Found at i:377662 original size:167 final size:160
Alignment explanation
Indices: 377397--377864 Score: 446
Period size: 158 Copynumber: 2.9 Consensus size: 160
377387 AAAAACCATT
* * * * * *
377397 TGGCCAGAAAAGCTGAAACTTGTGTGAAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAA
1 TGGCCAGAAAAGCTGTAACTTGTGTG-AAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAA
* * * *
377462 TCATGTTTCCC-GGGGATAAGGT-GGGGCCACAATGGGGGGTCGAAGTTTTACACAGGAATA-TA
65 TTATG-ATCCCTGGGGATAGGGTAGGGG-CACAAT--GGGGTC-----TTTACAAAGGAATAGTA
* *
377524 AAGAGAAAT-TTTAT-TTT-TAAA-TTTTCTACTAAGAACACGA
121 AAGAAAAATCTTT-TCTTTAAAAACTTTTCTACTAAGAA-A--A
377564 CTGGCCAGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAA
1 -TGGCCAGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAA
**
377629 TTATGATCCCTGGGGATAGGGTAGGGGCACAAT--GGTCTTTACAAAGGAATATGTGGAGAAAAA
65 TTATGATCCCTGGGGATAGGGTAGGGGCACAATGGGGTCTTTACAAAGGAATA-GTAAAGAAAAA
* ** *
377692 TCTTTTCTTTAAAAAAAAACTTTTTTTTTTAGAAAA
129 TCTTTTCTTT----AAAAACTTTTCTACTAAGAAAA
*
377728 --G---NAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAAT
1 TGGCCAGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAAT
**
377788 TATGATCCCTGGGGATAGGGTAGGGGCACAAT--GGTCTTTACAAAGGAATATGTGGAGAAAAAT
66 TATGATCCCTGGGGATAGGGTAGGGGCACAATGGGGTCTTTACAAAGGAATA-GTAAAGAAAAAT
377851 CTTTTCTTTAAAAA
130 CTTTTCTTTAAAAA
377865 AAACACTTTT
Statistics
Matches: 269, Mismatches: 19, Indels: 38
0.83 0.06 0.12
Matches are distributed among these distances:
154 5 0.02
158 143 0.53
160 9 0.03
161 7 0.03
163 4 0.01
164 1 0.00
166 8 0.03
167 63 0.23
168 29 0.11
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (160 bp):
TGGCCAGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAAT
TATGATCCCTGGGGATAGGGTAGGGGCACAATGGGGTCTTTACAAAGGAATAGTAAAGAAAAATC
TTTTCTTTAAAAACTTTTCTACTAAGAAAA
Found at i:377747 original size:158 final size:158
Alignment explanation
Indices: 377570--377887 Score: 620
Period size: 158 Copynumber: 2.0 Consensus size: 158
377560 ACGACTGGCC
377570 AGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAATTATGA
1 AGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAATTATGA
377635 TCCCTGGGGATAGGGTAGGGGCACAATGGTCTTTACAAAGGAATATGTGGAGAAAAATCTTTTCT
66 TCCCTGGGGATAGGGTAGGGGCACAATGGTCTTTACAAAGGAATATGTGGAGAAAAATCTTTTCT
377700 TTAAAAAAAA-ACTTTTTTTTTTAGAAA
131 TTAAAAAAAACACTTTTTTTTTTAGAAA
377727 AGNAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAATTATG
1 AG-AAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAATTATG
377792 ATCCCTGGGGATAGGGTAGGGGCACAATGGTCTTTACAAAGGAATATGTGGAGAAAAATCTTTTC
65 ATCCCTGGGGATAGGGTAGGGGCACAATGGTCTTTACAAAGGAATATGTGGAGAAAAATCTTTTC
377857 TTTAAAAAAAACACTTTTTTTTTTAGAAA
130 TTTAAAAAAAACACTTTTTTTTTTAGAAA
377886 AG
1 AG
377888 TTGCAACATT
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
157 2 0.01
158 138 0.87
159 19 0.12
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (158 bp):
AGAAAAGCTGTAACTTGTGTGAAGTATCATCAGGTAGGGTAGATTCAAGTTTGGTCAAATTATGA
TCCCTGGGGATAGGGTAGGGGCACAATGGTCTTTACAAAGGAATATGTGGAGAAAAATCTTTTCT
TTAAAAAAAACACTTTTTTTTTTAGAAA
Found at i:383288 original size:8 final size:7
Alignment explanation
Indices: 383277--383392 Score: 53
Period size: 8 Copynumber: 16.0 Consensus size: 7
383267 TGGGCGAAAA
383277 TGCGAGAG
1 TGCGA-AG
383285 TGCGAAG
1 TGCGAAG
383292 TTGCGAAG
1 -TGCGAAG
383300 -GCGAAAG
1 TGCG-AAG
*
383307 TGCAAAGG
1 TGCGAA-G
*
383315 TGCGACG
1 TGCGAAG
383322 T-CGAAGG
1 TGCGAA-G
*
383329 AGCGAAAG
1 TGCG-AAG
383337 TGCGAAG
1 TGCGAAG
*
383344 ATGCGACG
1 -TGCGAAG
383352 -GCGAAG
1 TGCGAAG
* *
383358 CGCAAAG
1 TGCGAAG
*
383365 ATGCGATG
1 -TGCGAAG
383373 -GCGAAAG
1 TGCG-AAG
383380 TGCGAAG
1 TGCGAAG
383387 -GCGAAG
1 TGCGAAG
383393 AAGCGATACT
Statistics
Matches: 83, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
6 20 0.24
7 23 0.28
8 38 0.46
9 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.41, T:0.10
Consensus pattern (7 bp):
TGCGAAG
Found at i:383308 original size:22 final size:22
Alignment explanation
Indices: 383278--383319 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
383268 GGGCGAAAAT
* * *
383278 GCGAGAGTGCGAAGTTGCGAAG
1 GCGAAAGTGCAAAGGTGCGAAG
383300 GCGAAAGTGCAAAGGTGCGA
1 GCGAAAGTGCAAAGGTGCGA
383320 CGTCGAAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.43, T:0.12
Consensus pattern (22 bp):
GCGAAAGTGCAAAGGTGCGAAG
Found at i:383350 original size:30 final size:30
Alignment explanation
Indices: 383300--383357 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
383290 AGTTGCGAAG
* *
383300 GCGAAAGTGCAAAGGTGCGACGTCGAAGGA
1 GCGAAAGTGCAAAGATGCGACGGCGAAGGA
*
383330 GCGAAAGTGCGAAGATGCGACGGCGAAG
1 GCGAAAGTGCAAAGATGCGACGGCGAAG
383358 CGCAAAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.41, T:0.09
Consensus pattern (30 bp):
GCGAAAGTGCAAAGATGCGACGGCGAAGGA
Found at i:384527 original size:14 final size:14
Alignment explanation
Indices: 384486--384520 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
384476 GCCGTCGCAT
*
384486 CTTCACACTTTCGC
1 CTTCGCACTTTCGC
384500 CTTCGCACTTTCGC
1 CTTCGCACTTTCGC
384514 CTTCGCA
1 CTTCGCA
384521 ACTTCGCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.43, G:0.11, T:0.34
Consensus pattern (14 bp):
CTTCGCACTTTCGC
Found at i:392574 original size:13 final size:13
Alignment explanation
Indices: 392556--392582 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
392546 TTTTTTTTTA
392556 AAAACTTGTGACC
1 AAAACTTGTGACC
392569 AAAACTTGTGACC
1 AAAACTTGTGACC
392582 A
1 A
392583 TTAAAGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
AAAACTTGTGACC
Found at i:392994 original size:14 final size:14
Alignment explanation
Indices: 392975--393002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
392965 TTAGCCAATC
392975 AAATAGGAATTTAA
1 AAATAGGAATTTAA
392989 AAATAGGAATTTAA
1 AAATAGGAATTTAA
393003 TTTTAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
AAATAGGAATTTAA
Found at i:396446 original size:11 final size:12
Alignment explanation
Indices: 396430--396462 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
396420 GATATTCAAA
396430 TAATTCAAAAT-
1 TAATTCAAAATG
*
396441 TAATTCAAAGTG
1 TAATTCAAAATG
396453 TAATTCAAAA
1 TAATTCAAAA
396463 CTCTGATACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (12 bp):
TAATTCAAAATG
Found at i:422635 original size:20 final size:20
Alignment explanation
Indices: 422610--422647 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
422600 ACACAATCAA
422610 TAATGCTTCATATATTTGGG
1 TAATGCTTCATATATTTGGG
422630 TAATGCTTCATATATTTG
1 TAATGCTTCATATATTTG
422648 AGGGCATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (20 bp):
TAATGCTTCATATATTTGGG
Found at i:423390 original size:166 final size:165
Alignment explanation
Indices: 423177--423778 Score: 803
Period size: 166 Copynumber: 3.7 Consensus size: 165
423167 GCAAAGTCGA
* * * *
423177 CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAAC
1 CATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAAC
* * * *
423242 AAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCCTTGAGGAAAATT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGAGGAAAATT
423307 TGTTTGAAAATTTTGGCTAAAAATAAACAAAATCTT
131 TGTTTGAAAATTTTGGCTAAAAATAAACAAAATC-T
* * * *
423343 TATTTAACAGGAAGTTGACATCTGATTGATACAAAAATATATCCCACAATATGGCATGCCAAAAC
1 CATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAAC
* * *
423408 AAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATATTTGCTGAGAAATCTTTGACGG-AAAT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA-GGAAAAT
*
423472 TTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACT
130 TTGTTTGAAAATTTTGGCTAAAAATAAACAAAAT-CT
* * *
423509 CATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTATAC
1 CATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAAC
* **
423574 AAATACTGTGTAAAAATTTCAAGCA--T-C------T-GTTGCTGAGAATTCTTTGACAAAAATT
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGAGGAAAATT
* * *
423629 TGTTTGAAAATTTTGGTTAAAATATAAGCAAAGTCGT
131 TGTTTGAAAATTTTGGCTAAAA-ATAAACAAAATC-T
** * *
423666 CATTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAAC
1 CATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAAC
* *
423731 AAACACTGTGTAAAAATTTCAAGCATCTGCTATAAATAGTTGCTGAGA
66 AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
423779 TAAATGCGAC
Statistics
Matches: 385, Mismatches: 36, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
156 44 0.11
157 93 0.24
159 1 0.00
160 1 0.00
163 1 0.00
164 1 0.00
166 231 0.60
167 13 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (165 bp):
CATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAAAC
AAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGAGGAAAATT
TGTTTGAAAATTTTGGCTAAAAATAAACAAAATCT
Found at i:423718 original size:157 final size:156
Alignment explanation
Indices: 423447--423759 Score: 477
Period size: 157 Copynumber: 2.0 Consensus size: 156
423437 CGATAAATAT
**
423447 TTGCTGAGAAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCAT
1 TTGCTGAGAAATCTTTGACAAAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCAT
423512 TAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCC-TATACAA
66 TAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTTA-ACAA
*
423576 ATACTGTGTAAAAATTTCAAGCATCTG
130 ACACTGTGTAAAAATTTCAAGCATCTG
* * * *
423603 TTGCTGAGAATTCTTTGACAAAAATTTGTTTGAAAATTTTGGTTAAAATATAAGCAAAGT-CGTC
1 TTGCTGAGAAATCTTTGACAAAAATTTGTTTGAAAATTTTGGCTAAAA-ATAAACAAACTAC-TC
* ** * *
423667 ATTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACA
64 ATTAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTTAACA
423732 AACACTGTGTAAAAATTTCAAGCATCTG
129 AACACTGTGTAAAAATTTCAAGCATCTG
423760 CTATAAATAG
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
156 45 0.32
157 95 0.67
158 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (156 bp):
TTGCTGAGAAATCTTTGACAAAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCAT
TAAACAGGAAGTTGACATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTTAACAAA
CACTGTGTAAAAATTTCAAGCATCTG
Found at i:423796 original size:323 final size:325
Alignment explanation
Indices: 423195--423796 Score: 825
Period size: 323 Copynumber: 1.8 Consensus size: 325
423185 AGAAAGCTGG
* * * *
423195 CATCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAACAAATAGTGTGTTAAAATT
1 CATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTAAACAAATACTGTGTAAAAATT
**
423260 TCAAGCATCTGCGATAAATAGCTGCTGAGAAATCCTTGAGGAAAATTTGTTTGAAAATTTTGGCT
66 TCAAGCATCT-CG----ATA--TGCTGAGAAATCCTTGACAAAAATTTGTTTGAAAATTTTGGCT
* * *
423325 AAAAATAAACAAAATCTTTATTTAACAGGAAGTTGACATCTGATTGATACAAAAATATATCCCAC
124 AAAAATAAACAAAATCGTCATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCAC
* * * *
423390 AATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATATTTGCTGAG
189 AATATGGCATGCCAAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* ** *
423455 AAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCATTAAACAGG
254 AAATATGCGACAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCATTAAACAGG
423520 AAGTTGA
319 AAGTTGA
*
423527 CATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTATACAAATACTGTGTAAAAATT
1 CATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTAAACAAATACTGTGTAAAAATT
* * *
423592 TCAAGCATCT-G-T-TGCTGAGAATTCTTTGACAAAAATTTGTTTGAAAATTTTGGTTAAAATAT
66 TCAAGCATCTCGATATGCTGAGAAATCCTTGACAAAAATTTGTTTGAAAATTTTGGCTAAAA-AT
* * ** * *
423654 AAGCAAAGTCGTCATTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCACGATATG
130 AAACAAAATCGTCATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCACAATATG
** *
423719 GCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCTATAAATAGTTGCTGAGATAA-A
195 GCATGCCAAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA-AATA
423783 TGCGACAGAAATTT
259 TGCGACAGAAATTT
423797 TTGTTATGGA
Statistics
Matches: 238, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
322 42 0.18
323 122 0.51
324 2 0.01
325 1 0.00
330 1 0.00
332 70 0.29
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (325 bp):
CATCCGATTGGTACAAAAATACATCCCACAATATGGCATGCCTAAACAAATACTGTGTAAAAATT
TCAAGCATCTCGATATGCTGAGAAATCCTTGACAAAAATTTGTTTGAAAATTTTGGCTAAAAATA
AACAAAATCGTCATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCACAATATGG
CATGCCAAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATATG
CGACAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAACTACTCATTAAACAGGAAGTTGA
Found at i:430897 original size:98 final size:93
Alignment explanation
Indices: 430713--430902 Score: 317
Period size: 98 Copynumber: 2.0 Consensus size: 93
430703 GTTCACGTGC
*
430713 TTGAGTGAACTCAGAACTTTCGGGCGTGATCGTTTATCAAACAACAACATTTTTGTATTCTTTTT
1 TTGAGTGAACGCAGAACTTTCGGGCGTGATCGTTTATCAAACAACAACATTTTTGTATTCTTTTT
430778 TAAAGAAAGGTGACGTGCGCTAAAATAT
66 TAAAGAAAGGTGACGTGCGCTAAAATAT
*
430806 NTTGAGTGAACGCAGAACTAAATTTGGGCGTGATCGTTTATCAAACAACAACATTTTTTGTATTC
1 -TTGAGTGAACGCAGAACT---TTCGGGCGTGATCGTTTATCAAACAACAACA-TTTTTGTATTC
430871 TTTTTTAAAGAAAGGTGACGTGCGCTAAAATA
61 TTTTTTAAAGAAAGGTGACGTGCGCTAAAATA
430903 CAATTGCACC
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
94 17 0.19
97 30 0.33
98 43 0.48
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (93 bp):
TTGAGTGAACGCAGAACTTTCGGGCGTGATCGTTTATCAAACAACAACATTTTTGTATTCTTTTT
TAAAGAAAGGTGACGTGCGCTAAAATAT
Found at i:432784 original size:160 final size:160
Alignment explanation
Indices: 432607--433036 Score: 635
Period size: 172 Copynumber: 2.6 Consensus size: 160
432597 GTATCGAGTC
* ** *
432607 TATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTAGTGGTATAAATATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
* *
432672 TAATGAGAATCTGTCAAAATTTGTAGGCATGAGGTCAATTTTTGGATAAAACGGAGTCATTATTG
66 TAATGAAAATCTGTCAAAATTTGTAGGCATGAGGTCAATTTTTGGATAAAAAGGAGTCATTATTG
*
432737 TGGTCAAAGTCCAATAACTCCAACAAAAAG
131 TGGTCAAAGTCCAATAACGCCAACAAAAAG
*
432767 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
432832 TAATGAAAATCTGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAAG
66 TAATGAAAATCTGTCAAAATTTGTAGGCAT------G------AGGTCAATTTTTGGATAAAAAG
*
432897 GAGTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
119 GAGTCATTATTGTGGTCAAAGTCCAATAACGCCAACAAAAAG
* * *
432939 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGATATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
*
433004 TAATGAAAATCCGTCAAAATTTGTAGGCATGAG
66 TAATGAAAATCTGTCAAAATTTGTAGGCATGAG
433037 AGCGCTTACA
Statistics
Matches: 244, Mismatches: 14, Indels: 24
0.87 0.05 0.09
Matches are distributed among these distances:
160 91 0.37
166 2 0.01
172 151 0.62
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (160 bp):
TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCTGTCAAAATTTGTAGGCATGAGGTCAATTTTTGGATAAAAAGGAGTCATTATTG
TGGTCAAAGTCCAATAACGCCAACAAAAAG
Found at i:437722 original size:21 final size:21
Alignment explanation
Indices: 437696--437738 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
437686 ATGTGGCTTA
437696 TAAAGCAGAAGCTTCATAATT
1 TAAAGCAGAAGCTTCATAATT
437717 TAAAGCAGAAGCTTCATAATT
1 TAAAGCAGAAGCTTCATAATT
437738 T
1 T
437739 TCTTTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
TAAAGCAGAAGCTTCATAATT
Found at i:439461 original size:2 final size:2
Alignment explanation
Indices: 439454--439510 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
439444 TAACAAGCAA
439454 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
439496 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
439511 TGTGGTAGGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:439986 original size:9 final size:9
Alignment explanation
Indices: 439972--440117 Score: 62
Period size: 9 Copynumber: 16.2 Consensus size: 9
439962 AAAACAGGTT
439972 TCCTGCTCC
1 TCCTGCTCC
439981 TCCTGCTCC
1 TCCTGCTCC
* * *
439990 T-GTTCACCC
1 TCCTGC-TCC
* *
439999 TCCTCCTGC
1 TCCTGCTCC
*
440008 TCCTGTTCAC
1 TCCTGCTC-C
*
440018 -CCTCCTCC
1 TCCTGCTCC
* *
440026 TGCTCCTCC
1 TCCTGCTCC
* *
440035 TGCTGCTGC
1 TCCTGCTCC
* *
440044 TGCTGCTGC
1 TCCTGCTCC
*
440053 TCCTCCTCC
1 TCCTGCTCC
*
440062 TCCTGCTGC
1 TCCTGCTCC
* *
440071 TGCTGCTGC
1 TCCTGCTCC
* *
440080 TGCTGCTGC
1 TCCTGCTCC
*
440089 TGCTGCTCC
1 TCCTGCTCC
*
440098 TCCTCCTCC
1 TCCTGCTCC
*
440107 TCCTCCTCC
1 TCCTGCTCC
440116 TC
1 TC
440118 GTTACAATGT
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
8 3 0.03
9 103 0.94
10 3 0.03
ACGTcount: A:0.01, C:0.50, G:0.15, T:0.34
Consensus pattern (9 bp):
TCCTGCTCC
Found at i:440003 original size:21 final size:21
Alignment explanation
Indices: 439977--440032 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
439967 AGGTTTCCTG
439977 CTCCTCCTGCTCCTGTTCACC
1 CTCCTCCTGCTCCTGTTCACC
439998 CTCCTCCTGCTCCTGTTCACC
1 CTCCTCCTGCTCCTGTTCACC
440019 CTCCTCCTGCTCCT
1 CTCCTCCTGCTCCT
440033 CCTGCTGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.04, C:0.54, G:0.09, T:0.34
Consensus pattern (21 bp):
CTCCTCCTGCTCCTGTTCACC
Found at i:440031 original size:6 final size:6
Alignment explanation
Indices: 440022--440116 Score: 64
Period size: 6 Copynumber: 15.8 Consensus size: 6
440012 GTTCACCCTC
* * * * * * *
440022 CTCCTG CTCCTC CTGCTG CTGCTG CTGCTG CTCCTC CTCCTC CTGCTG
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
* * * * * * *
440070 CTGCTG CTGCTG CTGCTG CTGCTG CTCCTC CTCCTC CTCCTC CTCCT
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
440117 CGTTACAATG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.00, C:0.48, G:0.18, T:0.34
Consensus pattern (6 bp):
CTCCTG
Found at i:440070 original size:3 final size:3
Alignment explanation
Indices: 440034--440095 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
440024 CCTGCTCCTC
* * * *
440034 CTG CTG CTG CTG CTG CTG CTC CTC CTC CTC CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
440082 CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CT
440096 CCTCCTCCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:457076 original size:49 final size:49
Alignment explanation
Indices: 457020--457119 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
457010 TTGGATAATT
457020 ATAAATCAATGTTAGAAAAGTTAAAACACTATTTTGAAATTATCATAAC
1 ATAAATCAATGTTAGAAAAGTTAAAACACTATTTTGAAATTATCATAAC
*
457069 ATAAATCAATGTTAGAAAAGTTAACACACTATTTTGAAATTATCATAAC
1 ATAAATCAATGTTAGAAAAGTTAAAACACTATTTTGAAATTATCATAAC
457118 AT
1 AT
457120 TATTACAAGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (49 bp):
ATAAATCAATGTTAGAAAAGTTAAAACACTATTTTGAAATTATCATAAC
Found at i:473031 original size:2 final size:2
Alignment explanation
Indices: 473026--473059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
473016 TTATTCTCTC
473026 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
473060 TATTAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:475791 original size:24 final size:24
Alignment explanation
Indices: 475745--475793 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
475735 ATGTATGTAC
* **
475745 TGCACTTTTGATGAACATTATAAA
1 TGCACTTTTGATGAAAAAAATAAA
*
475769 TGCACTTTTGATTAAAAAAATAAA
1 TGCACTTTTGATGAAAAAAATAAA
475793 T
1 T
475794 ATATTTCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (24 bp):
TGCACTTTTGATGAAAAAAATAAA
Found at i:476396 original size:2 final size:2
Alignment explanation
Indices: 476389--476415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
476379 NNNNNNNNNN
476389 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
476416 TCGTGGCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:483543 original size:172 final size:172
Alignment explanation
Indices: 483257--483604 Score: 678
Period size: 172 Copynumber: 2.0 Consensus size: 172
483247 NGTAATTATT
483257 ATCATCTTCTGAAGGGCTGTACTTCCCAAAGTTAAATAAACATACTAATAGTCCCTAGTTAATTT
1 ATCATCTTCTGAAGGGCTGTACTTCCCAAAGTTAAATAAACATACTAATAGTCCCTAGTTAATTT
483322 CTGTCGGTTTAAAGTTTGTATTCTTTTTTAATTTTTTAGTTTGGATGAGTAATATGAGCAAAAAA
66 CTGTCGGTTTAAAGTTTGTATTCTTTTTTAATTTTTTAGTTTGGATGAGTAATATGAGCAAAAAA
* *
483387 TCTACTTTAATTTTGACAGTAGTAAATAAATAGCACATTCGG
131 TCTACTTTAATTTTGACAGTAGGAAATAAATAGCACATCCGG
483429 ATCATCTTCTGAAGGGCTGTACTTCCCAAAGTTAAATAAACATACTAATAGTCCCTAGTTAATTT
1 ATCATCTTCTGAAGGGCTGTACTTCCCAAAGTTAAATAAACATACTAATAGTCCCTAGTTAATTT
483494 CTGTCGGTTTAAAGTTTGTATTCTTTTTTAATTTTTTAGTTTGGATGAGTAATATGAGCAAAAAA
66 CTGTCGGTTTAAAGTTTGTATTCTTTTTTAATTTTTTAGTTTGGATGAGTAATATGAGCAAAAAA
483559 TCTACTTTAATTTTGACAGTAGGAAATAAATAGCACATCCGG
131 TCTACTTTAATTTTGACAGTAGGAAATAAATAGCACATCCGG
483601 ATCA
1 ATCA
483605 GTCCTATATT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 174 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (172 bp):
ATCATCTTCTGAAGGGCTGTACTTCCCAAAGTTAAATAAACATACTAATAGTCCCTAGTTAATTT
CTGTCGGTTTAAAGTTTGTATTCTTTTTTAATTTTTTAGTTTGGATGAGTAATATGAGCAAAAAA
TCTACTTTAATTTTGACAGTAGGAAATAAATAGCACATCCGG
Found at i:493041 original size:20 final size:20
Alignment explanation
Indices: 492993--493047 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
492983 AAAAAAAATT
* * * *
492993 ACAGACAGACAGACGAACGG
1 ACAGACGGACGGACAAACAG
*
493013 ACGGACGGACGGACAAACAG
1 ACAGACGGACGGACAAACAG
493033 ACAGACGGACGGACA
1 ACAGACGGACGGACA
493048 CCGGACAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.33, T:0.00
Consensus pattern (20 bp):
ACAGACGGACGGACAAACAG
Found at i:493404 original size:41 final size:41
Alignment explanation
Indices: 493343--493424 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
493333 GTTTCAACAC
*
493343 ATTCACTTAGTTTGATGACATGAAATAATTGAACACATTGT
1 ATTCACTTAGTTTGACGACATGAAATAATTGAACACATTGT
*
493384 ATTCACTTAGTTTGACGACATGATATAATTGAACACATTGT
1 ATTCACTTAGTTTGACGACATGAAATAATTGAACACATTGT
493425 TTATTATACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (41 bp):
ATTCACTTAGTTTGACGACATGAAATAATTGAACACATTGT
Found at i:497350 original size:22 final size:22
Alignment explanation
Indices: 497322--497363 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
497312 TCTTCTCTAG
497322 GTAATTCGTTAAATATAGCCAA
1 GTAATTCGTTAAATATAGCCAA
497344 GTAATTCGTTAAATATAGCC
1 GTAATTCGTTAAATATAGCC
497364 CGAAATTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
GTAATTCGTTAAATATAGCCAA
Found at i:497372 original size:21 final size:22
Alignment explanation
Indices: 497324--497372 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
497314 TTCTCTAGGT
*
497324 AATTCGTTAAATATAGCCAAGT
1 AATTCGTTAAATATAGCCAAGA
*
497346 AATTCGTTAAATATAGCC-CGA
1 AATTCGTTAAATATAGCCAAGA
497367 AATTCG
1 AATTCG
497373 GCTCAGACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (22 bp):
AATTCGTTAAATATAGCCAAGA
Found at i:498229 original size:20 final size:20
Alignment explanation
Indices: 498204--498280 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
498194 ATTGTGCGCG
498204 CGCGCGCGCACACACACGCA
1 CGCGCGCGCACACACACGCA
* *
498224 CGCGCGCGCACACGCACGCG
1 CGCGCGCGCACACACACGCA
498244 CGCGCGCGCACACACACGCA
1 CGCGCGCGCACACACACGCA
*
498264 CGCACGCGCACACACAC
1 CGCGCGCGCACACACAC
498281 ACACACACGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.23, C:0.51, G:0.26, T:0.00
Consensus pattern (20 bp):
CGCGCGCGCACACACACGCA
Found at i:498235 original size:16 final size:16
Alignment explanation
Indices: 498216--498248 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
498206 CGCGCGCACA
498216 CACACGCACGCGCGCG
1 CACACGCACGCGCGCG
498232 CACACGCACGCGCGCG
1 CACACGCACGCGCGCG
498248 C
1 C
498249 GCGCACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.52, G:0.30, T:0.00
Consensus pattern (16 bp):
CACACGCACGCGCGCG
Found at i:500590 original size:32 final size:32
Alignment explanation
Indices: 500553--500620 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
500543 AAAGTGTTTA
500553 ATACCAGTTTGAGGACTCGTCATTCATGTAAT
1 ATACCAGTTTGAGGACTCGTCATTCATGTAAT
*
500585 ATACCAGTTTGAGGACTCGTCATTTATGTAAT
1 ATACCAGTTTGAGGACTCGTCATTCATGTAAT
500617 ATAC
1 ATAC
500621 TTGAACCCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
ATACCAGTTTGAGGACTCGTCATTCATGTAAT
Found at i:506653 original size:2 final size:2
Alignment explanation
Indices: 506646--506678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
506636 ATCGCCTGTC
506646 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
506679 ATTCGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:513399 original size:15 final size:15
Alignment explanation
Indices: 513379--513409 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
513369 AGAAACTTTT
513379 AGCCAAATTTTCAAA
1 AGCCAAATTTTCAAA
513394 AGCCAAATTTTCAAA
1 AGCCAAATTTTCAAA
513409 A
1 A
513410 ACCTTCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
AGCCAAATTTTCAAA
Found at i:515972 original size:31 final size:31
Alignment explanation
Indices: 515934--516068 Score: 169
Period size: 31 Copynumber: 4.6 Consensus size: 31
515924 GCTAACACAT
515934 AACACGCCGTCGCGCTAACGCAACTTTGCAC
1 AACACGCCGTCGCGCTAACGCAACTTTGCAC
515965 AACACGCCGTCGCGCTAA--C-A---T--AC
1 AACACGCCGTCGCGCTAACGCAACTTTGCAC
*
515988 AACACGCCGTCGCGCGAACGCAACTTTGCAC
1 AACACGCCGTCGCGCTAACGCAACTTTGCAC
* *
516019 AACACGCCGTCGCGCTAACACAACTTCGCAC
1 AACACGCCGTCGCGCTAACGCAACTTTGCAC
* *
516050 AACATGCCATCGCGCTAAC
1 AACACGCCGTCGCGCTAAC
516069 ATACAACACA
Statistics
Matches: 90, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
23 19 0.21
25 2 0.02
26 1 0.01
28 1 0.01
29 2 0.02
31 65 0.72
ACGTcount: A:0.28, C:0.39, G:0.19, T:0.14
Consensus pattern (31 bp):
AACACGCCGTCGCGCTAACGCAACTTTGCAC
Found at i:516002 original size:54 final size:54
Alignment explanation
Indices: 515920--516040 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
515910 AAACGAGACA
* *
515920 TCGCGCTAACACATAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG
1 TCGCGCTAACACACAACACGCCGTCGCGCGAACGCAACTTTGCACAACACGCCG
*
515974 TCGCGCTAACATACAACACGCCGTCGCGCGAACGCAACTTTGCACAACACGCCG
1 TCGCGCTAACACACAACACGCCGTCGCGCGAACGCAACTTTGCACAACACGCCG
516028 TCGCGCTAACACA
1 TCGCGCTAACACA
516041 ACTTCGCACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.28, C:0.39, G:0.19, T:0.14
Consensus pattern (54 bp):
TCGCGCTAACACACAACACGCCGTCGCGCGAACGCAACTTTGCACAACACGCCG
Found at i:516289 original size:16 final size:16
Alignment explanation
Indices: 516268--516298 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
516258 TTATTTTCAT
516268 TTATTATCAATACATA
1 TTATTATCAATACATA
516284 TTATTATCAATACAT
1 TTATTATCAATACAT
516299 TGAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTATCAATACATA
Found at i:517616 original size:2 final size:2
Alignment explanation
Indices: 517611--517635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
517601 ACGATATCAG
517611 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
517636 AGTTAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:521086 original size:1 final size:1
Alignment explanation
Indices: 521082--521106 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
521072 ATACACCCTA
521082 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
521107 TTCACAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:532278 original size:146 final size:146
Alignment explanation
Indices: 531693--532341 Score: 860
Period size: 146 Copynumber: 4.5 Consensus size: 146
531683 TTAAACCGTT
* * * *
531693 GGTCAGAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGAAAAATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
*
531756 CCAGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* *
531821 GATCATGACACACCCTTT
129 GGTCATGACACACCCTTA
* * * * * *
531839 GGTCCTAAGCAATATTTGTGTTAAGTTAGACCATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
* * **
531902 CCGGGCACGAATTTTGCA-TTATTT-TCCCA---A-C--GACCTTGCCCAAATGACCTTGTATCA
64 CCGGACACGAATTTTGCACTT-TTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCA
531959 AGGTCATGACACACCCTTA
128 AGGTCATGACACACCCTTA
* * * * *
531978 GGTCATTAGCAATCTCTGTGTAAATTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGGCC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
*
532043 GGACAC-AAATTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCTC-AATGACCTTGGGTCAAG
66 GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAG
532106 GTCATGACACACCCTTA
130 GTCATGACACACCCTTA
* *
532123 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTTTCAATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
532188 GGACACGAATTTTGTA-TTTTTCCTGCCAGTGACCTTGTCCTTGCCCGAATGACCTTGGGTCAAG
66 GGACACGAATTTTGCACTTTTT-CTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
532252 GTCATGACACAACCTTA
130 GTCATGACACACCCTTA
532269 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
*
532334 GGATACGA
66 GGACACGA
532342 TTGCACAGAC
Statistics
Matches: 446, Mismatches: 42, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
138 15 0.03
139 101 0.23
141 1 0.00
142 2 0.00
143 1 0.00
145 117 0.26
146 209 0.47
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (146 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTA
Found at i:532366 original size:12 final size:12
Alignment explanation
Indices: 532349--532383 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
532339 CGATTGCACA
532349 GACAGACGGACG
1 GACAGACGGACG
532361 GACAGACGGACG
1 GACAGACGGACG
532373 GACAGACGGAC
1 GACAGACGGAC
532384 AAGGTGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:533879 original size:31 final size:31
Alignment explanation
Indices: 533844--533911 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
533834 ACAATGGTAA
533844 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
533875 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
533906 CATTCT
1 CATTCT
533912 TATGCATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.16, C:0.32, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:537364 original size:168 final size:168
Alignment explanation
Indices: 537086--537422 Score: 656
Period size: 168 Copynumber: 2.0 Consensus size: 168
537076 AATGTGCAGG
*
537086 CAATTTGTGAGCACAAACTTAAAATAACCAATGCTGTGGTACGATGGCCTGGCATTACCCATGAC
1 CAATTTGTGAGCACAAACTTAAAATAACCAATGCTGTGGTACGATGGCCTGGCAGTACCCATGAC
537151 AATCGCATTTTAGAAAATTCTAATGTTTGAGCGCCGAGAAATAAATGGAATTTTGCTGGGTGACA
66 AATCGCATTTTAGAAAATTCTAATGTTTGAGCGCCGAGAAATAAATGGAATTTTGCTGGGTGACA
537216 ATGGATACCCCTTGAGATCATATCTTATTACGCCAGTC
131 ATGGATACCCCTTGAGATCATATCTTATTACGCCAGTC
537254 CAATTTGTGAGCACAAACTTAAAATAACCAATGCTGTGGTACGATGGCCTGGCAGTACCCATGAC
1 CAATTTGTGAGCACAAACTTAAAATAACCAATGCTGTGGTACGATGGCCTGGCAGTACCCATGAC
*
537319 AGTCGCATTTTAGAAAATTCTAATGTTTGAGCGCCGAGAAATAAATGGAATTTTGCTGGGTGACA
66 AATCGCATTTTAGAAAATTCTAATGTTTGAGCGCCGAGAAATAAATGGAATTTTGCTGGGTGACA
537384 ATGGATACCCCTTGAGATCATATCTTATTACGCCAGTC
131 ATGGATACCCCTTGAGATCATATCTTATTACGCCAGTC
537422 C
1 C
537423 TCACGCCAAA
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (168 bp):
CAATTTGTGAGCACAAACTTAAAATAACCAATGCTGTGGTACGATGGCCTGGCAGTACCCATGAC
AATCGCATTTTAGAAAATTCTAATGTTTGAGCGCCGAGAAATAAATGGAATTTTGCTGGGTGACA
ATGGATACCCCTTGAGATCATATCTTATTACGCCAGTC
Found at i:538645 original size:141 final size:142
Alignment explanation
Indices: 538455--538771 Score: 306
Period size: 142 Copynumber: 2.2 Consensus size: 142
538445 ATATGAATTG
* * * * * ** * * *
538455 GACACAATTTTTGCACTTTTCCTGCCAGAGACATTGATTTTGCCAAAATAACATTGGGTC-AAGG
1 GACACAAATTTTGCACTTTTCCCGCCAGTGACCTAGACCTTACCCAAATAACATTAGGTCTAAGG
*
538519 TCATGACACA-CCA-GCCCATAAGCAATCATTGTGTAAAGTAAGATCAACCAATGATTATCCA-T
66 -CACGACACATCCATG-CCATAAGCAATCATTGTGTAAAGTAA-A--AACCAATGATTATCCATT
*
538581 T-AAAA-ATA-AGAACCG
126 TAAAAAGATATA-AACCA
* * * * *
538596 GACACGAATTTTGCATTTTTCCCGCCAGTGACCTAGACCTTACCCAAATATCCTTAGGTCTATGG
1 GACACAAATTTTGCACTTTTCCCGCCAGTGACCTAGACCTTACCCAAATAACATTAGGTCTAAGG
* * * * * *
538661 CACGATACATTCATGTCATATGCAATCATTGTGTGAAGTAAAAACCAATGTTTATCCATTTAAAA
66 CACGACACATCCATGCCATAAGCAATCATTGTGTAAAGTAAAAACCAATGATTATCCATTTAAAA
538726 AGATATAAACCA
131 AGATATAAACCA
* *
538738 GACACAAATTTTGCACTTTTCCTGCCATTGACCT
1 GACACAAATTTTGCACTTTTCCCGCCAGTGACCT
538772 TGCCCGAATG
Statistics
Matches: 142, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
139 15 0.11
140 2 0.01
141 58 0.41
142 65 0.46
143 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (142 bp):
GACACAAATTTTGCACTTTTCCCGCCAGTGACCTAGACCTTACCCAAATAACATTAGGTCTAAGG
CACGACACATCCATGCCATAAGCAATCATTGTGTAAAGTAAAAACCAATGATTATCCATTTAAAA
AGATATAAACCA
Found at i:548533 original size:23 final size:23
Alignment explanation
Indices: 548503--548551 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
548493 CAAAAACTTT
548503 GTTTGCGGGGGGTATAATTAATG
1 GTTTGCGGGGGGTATAATTAATG
*
548526 GTTTGCGGGGGGTATAATTACTG
1 GTTTGCGGGGGGTATAATTAATG
548549 GTT
1 GTT
548552 CTAATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.06, G:0.39, T:0.37
Consensus pattern (23 bp):
GTTTGCGGGGGGTATAATTAATG
Found at i:550199 original size:19 final size:19
Alignment explanation
Indices: 550170--550258 Score: 124
Period size: 19 Copynumber: 4.6 Consensus size: 19
550160 ATAAGACTGT
550170 AAAGTCCGATGGTCACGCC
1 AAAGTCCGATGGTCACGCC
**
550189 AAAGTTTGATGGTCACGCC
1 AAAGTCCGATGGTCACGCC
*
550208 AAAGTCCGATGGTCACGCT
1 AAAGTCCGATGGTCACGCC
* *
550227 AAAGTCCGACGGTCTACACC
1 AAAGTCCGATGGTC-ACGCC
550247 AAAGTCCGATGG
1 AAAGTCCGATGG
550259 GTTGTTGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 46 0.77
20 14 0.23
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (19 bp):
AAAGTCCGATGGTCACGCC
Found at i:551839 original size:180 final size:180
Alignment explanation
Indices: 551537--551903 Score: 576
Period size: 180 Copynumber: 2.0 Consensus size: 180
551527 GTGAAATGGA
* *
551537 GTACCCTATATGCAACATTTTGCCTAAAAATGACTAAGTTCAAAAGCAAGTATTTTTTTCATAAA
1 GTACCCTATATGCAACATTTTGCCGAAAAATGACAAAGTTCAAAAGCAAGTATTTTTTTCATAAA
*
551602 TTATTGGAAATCAAAATACTAGCAATATGCACACTTCTAATATAAGTACAATTGATCTGCAAAAG
66 TTATTGGAAATCAAAATACTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAG
* *
551667 AACAA-TTCCCTATCTTGAGAACTGTAGGAGGAGTTATCTGTACAATGAGG
131 AACAACTT-CCTATCTTGAAAACTGTAGGAGGAGTTATCTGTAAAATGAGG
* **
551717 GTACCCTATATGCAATATTTTGCCGAAAAATGACAAAGTTCAAAAGCTGGTA-TTTTTTCAATAA
1 GTACCCTATATGCAACATTTTGCCGAAAAATGACAAAGTTCAAAAGCAAGTATTTTTTTC-ATAA
* * * *
551781 ATTATTGGAAATCAAAATCCTTGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAA
65 ATTATTGGAAATCAAAATACTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAA
* *
551846 GAACAACTTCCTGTCTTGAAAACTGTAGGAGGAGTTATCTTTAAAATGAGG
130 GAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCTGTAAAATGAGG
551897 GTACCCT
1 GTACCCT
551904 TTTGGCAGCC
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
179 7 0.04
180 162 0.95
181 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (180 bp):
GTACCCTATATGCAACATTTTGCCGAAAAATGACAAAGTTCAAAAGCAAGTATTTTTTTCATAAA
TTATTGGAAATCAAAATACTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAG
AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCTGTAAAATGAGG
Found at i:559645 original size:10 final size:11
Alignment explanation
Indices: 559630--559669 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
559620 GGTTGTATAG
*
559630 CCTTTAAG-CT
1 CCTTTAAGCCA
*
559640 CCTTTAAGTCA
1 CCTTTAAGCCA
559651 CCTTTAAGCCA
1 CCTTTAAGCCA
559662 CCTTTAAG
1 CCTTTAAG
559670 GACTTGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:563429 original size:15 final size:15
Alignment explanation
Indices: 563409--563440 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
563399 AGTACAATGT
563409 AAGTTACATTGTAGC
1 AAGTTACATTGTAGC
563424 AAGTTACATTGTAGC
1 AAGTTACATTGTAGC
563439 AA
1 AA
563441 CATGTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (15 bp):
AAGTTACATTGTAGC
Found at i:574697 original size:20 final size:20
Alignment explanation
Indices: 574652--574698 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
574642 CTTTCAAAGT
* *
574652 TTTATATATATATCTATCTA
1 TTTATATATACATCTATATA
*
574672 TCTATATATACA-CTATTATA
1 TTTATATATACATCTA-TATA
574692 TTTATAT
1 TTTATAT
574699 GTTGTAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATATATACATCTATATA
Found at i:575420 original size:12 final size:12
Alignment explanation
Indices: 575400--575440 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
575390 AACTGAAGTG
*
575400 GGACAGACAGAC
1 GGACGGACAGAC
575412 GGACGGACAGAC
1 GGACGGACAGAC
* *
575424 AGACGGACTGAC
1 GGACGGACAGAC
575436 GGACG
1 GGACG
575441 CAGAGGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.39, T:0.02
Consensus pattern (12 bp):
GGACGGACAGAC
Found at i:575421 original size:16 final size:16
Alignment explanation
Indices: 575400--575431 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
575390 AACTGAAGTG
575400 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
575416 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
575432 TGACGGACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:576686 original size:89 final size:89
Alignment explanation
Indices: 576577--576744 Score: 284
Period size: 89 Copynumber: 1.9 Consensus size: 89
576567 CGTATCATTA
*
576577 GATTTTCCGGTGTCAACCGTGGAAAATAATCCGTAGTAGAACC-TAGGAGTTGATCTGTGAATGT
1 GATTTTCCGGTGTCAACCGTGGAAAATAATCCGTAGTAGAACCGT-GGAGTTGATCCGTGAATGT
576641 GTGACTGGGGCATTAACGATTATTT
65 GTGACTGGGGCATTAACGATTATTT
* * *
576666 GATTTTCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAGCCGTGGAGTTGATCCGTGGATGTG
1 GATTTTCCGGTGTCAACCGTGGAAAATAATCCGTAGTAGAACCGTGGAGTTGATCCGTGAATGTG
576731 TGACTGGGGCATTA
66 TGACTGGGGCATTA
576745 GTAATGATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
89 73 0.99
90 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (89 bp):
GATTTTCCGGTGTCAACCGTGGAAAATAATCCGTAGTAGAACCGTGGAGTTGATCCGTGAATGTG
TGACTGGGGCATTAACGATTATTT
Found at i:580355 original size:316 final size:316
Alignment explanation
Indices: 579782--580416 Score: 1234
Period size: 316 Copynumber: 2.0 Consensus size: 316
579772 GAATTACAAA
579782 TGAAATACAAAGAATATTGGTTTATGGCATTAAAGAATAAATCTGCAATGCATGAAACCTATACT
1 TGAAATACAAAGAATATTGGTTTATGGCATTAAAGAATAAATCTGCAATGCATGAAACCTATACT
*
579847 GGCTACAGTTAAAGCTTATACTTCAGTTGAATCAAAACTGTTTGACAAGGTGCATCTAATTACTA
66 GGCTACAGTTAAAGCTTATACTTCAGCTGAATCAAAACTGTTTGACAAGGTGCATCTAATTACTA
579912 TCGCGCTTGATATTTCTCGACATTATTGTAAGCGATGATGCTTTAAAAGTAAAGAACAATCGACG
131 TCGCGCTTGATATTTCTCGACATTATTGTAAGCGATGATGCTTTAAAAGTAAAGAACAATCGACG
579977 TCATTTGAGTGTTTCATTACGGGAAGATTTTACAAGAAATAAAAGAGATGAGATGGACGCGCGGG
196 TCATTTGAGTGTTTCATTACGGGAAGATTTTACAAGAAATAAAAGAGATGAGATGGACGCGCGGG
* *
580042 CGCGCCGACGCGCTGAATACAATTAGCCTGCTTAGGAACTCAATTTTTTCTCAGAT
261 CGCGCCGACGCACTGAATACAATTAGCCTGCTAAGGAACTCAATTTTTTCTCAGAT
580098 TGAAATACAAAGAATATTGGTTTATGGCATTAAAGAATAAATCTGCAATGCATGAAACCTATACT
1 TGAAATACAAAGAATATTGGTTTATGGCATTAAAGAATAAATCTGCAATGCATGAAACCTATACT
*
580163 GGCTACCGTTAAAGCTTATACTTCAGCTGAATCAAAACTGTTTGACAAGGTGCATCTAATTACTA
66 GGCTACAGTTAAAGCTTATACTTCAGCTGAATCAAAACTGTTTGACAAGGTGCATCTAATTACTA
580228 TCGCGCTTGATATTTCTCGACATTATTGTAAGCGATGATGCTTTAAAAGTAAAGAACAATCGACG
131 TCGCGCTTGATATTTCTCGACATTATTGTAAGCGATGATGCTTTAAAAGTAAAGAACAATCGACG
580293 TCATTTGAGTGTTTCATTACGGGAAGATTTTACAAGAAATAAAAGAGATGAGATGGACGCGCGGG
196 TCATTTGAGTGTTTCATTACGGGAAGATTTTACAAGAAATAAAAGAGATGAGATGGACGCGCGGG
580358 CGCGCCGACGCACTGAATACAATTAGCCTGCTAAGGAACTCAATTTTTTCTCAGAT
261 CGCGCCGACGCACTGAATACAATTAGCCTGCTAAGGAACTCAATTTTTTCTCAGAT
580414 TGA
1 TGA
580417 CAGAAGTTTA
Statistics
Matches: 315, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
316 315 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (316 bp):
TGAAATACAAAGAATATTGGTTTATGGCATTAAAGAATAAATCTGCAATGCATGAAACCTATACT
GGCTACAGTTAAAGCTTATACTTCAGCTGAATCAAAACTGTTTGACAAGGTGCATCTAATTACTA
TCGCGCTTGATATTTCTCGACATTATTGTAAGCGATGATGCTTTAAAAGTAAAGAACAATCGACG
TCATTTGAGTGTTTCATTACGGGAAGATTTTACAAGAAATAAAAGAGATGAGATGGACGCGCGGG
CGCGCCGACGCACTGAATACAATTAGCCTGCTAAGGAACTCAATTTTTTCTCAGAT
Found at i:584955 original size:14 final size:14
Alignment explanation
Indices: 584936--584963 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
584926 AATTAAAGAG
584936 ATTAATAAACAAAT
1 ATTAATAAACAAAT
584950 ATTAATAAACAAAT
1 ATTAATAAACAAAT
584964 GTTCAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAATAAACAAAT
Found at i:590715 original size:2 final size:2
Alignment explanation
Indices: 590708--590745 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
590698 TGAAGGTGAG
590708 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
590746 TTAACTGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:598195 original size:28 final size:28
Alignment explanation
Indices: 598155--598210 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
598145 TTGAGGGATT
598155 TCCATATCGTCATATATTTGTACTGGCC
1 TCCATATCGTCATATATTTGTACTGGCC
598183 TCCATATCGTCATATATTTGTACTGGCC
1 TCCATATCGTCATATATTTGTACTGGCC
598211 ATGGAGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (28 bp):
TCCATATCGTCATATATTTGTACTGGCC
Found at i:605299 original size:2 final size:2
Alignment explanation
Indices: 605292--605340 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
605282 CGATGAATCA
605292 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
605334 CT CT CT C
1 CT CT CT C
605341 CGCTCATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:609692 original size:29 final size:29
Alignment explanation
Indices: 609637--609692 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
609627 TTTTATTTAG
* * *
609637 ATATTTTACAATAATAGTGCATGTATACT
1 ATATTTTACAATAAAAGAGAATGTATACT
*
609666 ATATTTTACAATAAAAGAGAATTTATA
1 ATATTTTACAATAAAAGAGAATGTATA
609693 AATCACAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (29 bp):
ATATTTTACAATAAAAGAGAATGTATACT
Found at i:629882 original size:2 final size:2
Alignment explanation
Indices: 629877--629906 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
629867 AAAAGTGTTT
629877 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
629907 TTAAAGGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:632157 original size:2 final size:2
Alignment explanation
Indices: 632152--632199 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
632142 ACACTCATAT
632152 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
632194 TC TC TC
1 TC TC TC
632200 AATGTAGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:634634 original size:4 final size:4
Alignment explanation
Indices: 634625--634653 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
634615 AAAACAAAAT
634625 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
634654 CAGCCAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:635138 original size:13 final size:13
Alignment explanation
Indices: 635120--635146 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
635110 AATAACGATT
635120 TTGCAGAAGATAA
1 TTGCAGAAGATAA
635133 TTGCAGAAGATAA
1 TTGCAGAAGATAA
635146 T
1 T
635147 CGGCAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (13 bp):
TTGCAGAAGATAA
Found at i:635625 original size:2 final size:2
Alignment explanation
Indices: 635618--635655 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
635608 TATCTAGAAC
635618 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
635656 AGGGGCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:644284 original size:58 final size:61
Alignment explanation
Indices: 644172--644294 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 61
644162 ATTGTTAACT
*
644172 TACATTATTATTATTTTCATACCTTATAACTATGAGGAGTGTGTATGTACATGTACTTGATATC
1 TACATTATTATTATTATCATACCTTATAACTATGAGGAG-GTG-ATGTA-ATGTACTTGATATC
644236 TACATTATTATTATTATCATACCTTATAACTATGAGGA-GTG-TGT-ATGTACTTGATATC
1 TACATTATTATTATTATCATACCTTATAACTATGAGGAGGTGATGTAATGTACTTGATATC
644294 T
1 T
644295 GTTAACTGCG
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
58 15 0.26
60 3 0.05
62 3 0.05
64 37 0.64
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (61 bp):
TACATTATTATTATTATCATACCTTATAACTATGAGGAGGTGATGTAATGTACTTGATATC
Found at i:651563 original size:2 final size:2
Alignment explanation
Indices: 651556--651600 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
651546 TACAAGACCC
651556 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
651598 CT C
1 CT C
651601 AGTTTAGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:651921 original size:44 final size:44
Alignment explanation
Indices: 651872--652374 Score: 927
Period size: 44 Copynumber: 11.4 Consensus size: 44
651862 AACAGCCAAC
*
651872 TACTGAGATGTCAGCTCAACAAACTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
651916 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
651960 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
652004 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
652048 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
652092 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
*
652136 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACCACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
652180 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
*
652224 TACTGAGATGTCAGCTCAATAAGCTACAGGTATGTACAACACCT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
* *
652268 TACTGAGGTGTCAGCTCAACGAGCTACAGGTATGTACAACA-CT
1 TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
* *
652311 ATACTGAGATGTCAACTCAACAAGCTACATGTATGTACAACACCT
1 -TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
652356 TACTGAGATGTCAGCTCAA
1 TACTGAGATGTCAGCTCAA
652375 AAAAATACAG
Statistics
Matches: 445, Mismatches: 12, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
43 2 0.00
44 441 0.99
45 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (44 bp):
TACTGAGATGTCAGCTCAACAAGCTACAGGTATGTACAACACCT
Found at i:652714 original size:11 final size:11
Alignment explanation
Indices: 652694--652746 Score: 70
Period size: 11 Copynumber: 4.8 Consensus size: 11
652684 GTGGCCCCCA
652694 AAAGTAAACCC
1 AAAGTAAACCC
*
652705 AAATTAAACCC
1 AAAGTAAACCC
652716 AAAGTAAACCC
1 AAAGTAAACCC
** *
652727 TGAGTAGACCC
1 AAAGTAAACCC
652738 AAAGTAAAC
1 AAAGTAAAC
652747 TCCGAGTGGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.11, T:0.13
Consensus pattern (11 bp):
AAAGTAAACCC
Found at i:652753 original size:22 final size:22
Alignment explanation
Indices: 652712--652762 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
652702 CCCAAATTAA
652712 ACCCAAAGTAAACCCTGAGTAG
1 ACCCAAAGTAAACCCTGAGTAG
*
652734 ACCCAAAGTAAACTCC-GAGTGG
1 ACCCAAAGTAAAC-CCTGAGTAG
652756 ACCCAAA
1 ACCCAAA
652763 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (22 bp):
ACCCAAAGTAAACCCTGAGTAG
Found at i:660351 original size:19 final size:19
Alignment explanation
Indices: 660327--660366 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
660317 AAAAGATGGT
660327 AAGCAAAACTTATCTATTA
1 AAGCAAAACTTATCTATTA
660346 AAGCAAAACTTATCTATTA
1 AAGCAAAACTTATCTATTA
660365 AA
1 AA
660367 ACTGTCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (19 bp):
AAGCAAAACTTATCTATTA
Found at i:681760 original size:17 final size:17
Alignment explanation
Indices: 681738--681771 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
681728 ACTTTGGGGG
681738 GTGCGTATTATACACGA
1 GTGCGTATTATACACGA
681755 GTGCGTATTATACACGA
1 GTGCGTATTATACACGA
681772 TACATTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
GTGCGTATTATACACGA
Found at i:699118 original size:12 final size:12
Alignment explanation
Indices: 699101--699176 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 12
699091 CAGGCTGAGA
699101 CAACCACAGAGT
1 CAACCACAGAGT
699113 CAACCACTGAGATGT
1 CAACCAC--AGA-GT
*
699128 CTACCACAGAGT
1 CAACCACAGAGT
*
699140 CAACCACTGAAATGT
1 CAACCAC--AGA-GT
* *
699155 CTACCACAGAAT
1 CAACCACAGAGT
699167 CAACCACAGA
1 CAACCACAGA
699177 AATGGAGACC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 25 0.49
13 5 0.10
14 5 0.10
15 16 0.31
ACGTcount: A:0.39, C:0.32, G:0.14, T:0.14
Consensus pattern (12 bp):
CAACCACAGAGT
Found at i:699135 original size:27 final size:27
Alignment explanation
Indices: 699103--699180 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
699093 GGCTGAGACA
*
699103 ACCACAGAGTCAACCACTGAGATGTCT
1 ACCACAGAGTCAACCACTGAAATGTCT
699130 ACCACAGAGTCAACCACTGAAATGTCT
1 ACCACAGAGTCAACCACTGAAATGTCT
* *
699157 ACCACAGAATCAACCACAGAAATG
1 ACCACAGAGTCAACCACTGAAATG
699181 GAGACCAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.15
Consensus pattern (27 bp):
ACCACAGAGTCAACCACTGAAATGTCT
Found at i:699187 original size:27 final size:27
Alignment explanation
Indices: 699130--699187 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
699120 TGAGATGTCT
* * ***
699130 ACCACAGAGTCAACCACTGAAATGTCT
1 ACCACAGAATCAACCACAGAAATGGAG
699157 ACCACAGAATCAACCACAGAAATGGAG
1 ACCACAGAATCAACCACAGAAATGGAG
699184 ACCA
1 ACCA
699188 GTACCCTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.12
Consensus pattern (27 bp):
ACCACAGAATCAACCACAGAAATGGAG
Found at i:700521 original size:21 final size:21
Alignment explanation
Indices: 700496--700616 Score: 74
Period size: 21 Copynumber: 5.9 Consensus size: 21
700486 AACTACCACT
*
700496 ACTGAGCTAGAGACAACAAGC
1 ACTGAGCAAGAGACAACAAGC
* * *
700517 ACTGAACAAGAAACAACAACC
1 ACTGAGCAAGAGACAACAAGC
* *
700538 A-TGATGCCAGAGTCAACAAGC
1 ACTGA-GCAAGAGACAACAAGC
* *
700559 AC-AATCACAGAGACAAC-A--
1 ACTGAGCA-AGAGACAACAAGC
*
700577 ACTGTA-CAACAGACAACAAGC
1 ACTG-AGCAAGAGACAACAAGC
* *
700598 ACTGAACAAGATACAACAA
1 ACTGAGCAAGAGACAACAA
700617 CAATGAAACC
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
18 10 0.14
19 3 0.04
20 7 0.09
21 54 0.73
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (21 bp):
ACTGAGCAAGAGACAACAAGC
Found at i:700555 original size:42 final size:42
Alignment explanation
Indices: 700504--700740 Score: 124
Period size: 42 Copynumber: 5.8 Consensus size: 42
700494 CTACTGAGCT
* *
700504 AGAGACAACAAGCACTGAACAAGAAACAACAACCATGATGCC
1 AGAGACAACAAGCACTGAACAAGAAACAACAACCATGATACA
* *
700546 AGAGTCAACAAGCAC--AATCACAGAGACAACAA-C-TG-TACA
1 AGAGACAACAAGCACTGAA-CA-AGAAACAACAACCATGATACA
* * *
700585 ACAGACAACAAGCACTGAACAAGATACAACAACAATGA-A-A
1 AGAGACAACAAGCACTGAACAAGAAACAACAACCATGATACA
** * *
700625 CCAGA-AACAAGCACTGTCACAGAGACAACGACAA-C-TGA-ACA
1 AGAGACAACAAGCACTG-AACA-AGA-AACAACAACCATGATACA
* * * * *
700666 ACAGACAAC-AGTCACTGAACCAA-AGACAACCACAAGTGA-ACC
1 AGAGACAACAAG-CACTGAA-CAAGAAACAACAACCA-TGATACA
* ** *
700708 AGAAACAACAAGCACTTTACCAGAAACAACAAC
1 AGAGACAACAAGCACTGAACAAGAAACAACAAC
700741 AACAGTTCAA
Statistics
Matches: 149, Mismatches: 27, Indels: 38
0.70 0.13 0.18
Matches are distributed among these distances:
39 41 0.28
40 19 0.13
41 22 0.15
42 65 0.44
43 2 0.01
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (42 bp):
AGAGACAACAAGCACTGAACAAGAAACAACAACCATGATACA
Found at i:700594 original size:39 final size:38
Alignment explanation
Indices: 700551--700675 Score: 105
Period size: 39 Copynumber: 3.1 Consensus size: 38
700541 ATGCCAGAGT
700551 CAACAAGCACAATCACAGAGACAACAACTGTACAACAGA
1 CAACAAGCACAATCACAGAGACAACAACTG-ACAACAGA
*
700590 CAACAAGCACTGAA-CA-AGATACAACAACAATGA-AACCAGA
1 CAACAAGCAC--AATCACAGAGACAACAAC--TGACAA-CAGA
**
700630 -AACAAGCACTGTCACAGAGACAACGACAACTGAACAACAGA
1 CAACAAGCACAATCACAGAGAC-A--ACAACTG-ACAACAGA
700671 CAACA
1 CAACA
700676 GTCACTGAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
38 2 0.03
39 37 0.54
40 10 0.14
41 9 0.13
42 11 0.16
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.07
Consensus pattern (38 bp):
CAACAAGCACAATCACAGAGACAACAACTGACAACAGA
Found at i:700617 original size:81 final size:80
Alignment explanation
Indices: 700506--700715 Score: 241
Period size: 81 Copynumber: 2.6 Consensus size: 80
700496 ACTGAGCTAG
* **
700506 AGACAACAAGCACTGAACAAGAAACAACAACCATGATGCCAGAGTCAACAAGCACAATCACAGAG
1 AGACAACAAGCACTGAACAAGAAACAACAACAATGAAACCAGA---AACAAGCACAATCACAGAG
*
700571 AC-A-ACAACTGTACAAC
63 ACAACACAACTGAACAAC
* **
700587 AGACAACAAGCACTGAACAAGATACAACAACAATGAAACCAGAAACAAGCACTGTCACAGAGACA
1 AGACAACAAGCACTGAACAAGAAACAACAACAATGAAACCAGAAACAAGCACAATCACAGAGACA
700652 ACGACAACTGAACAAC
66 AC-ACAACTGAACAAC
* *
700668 AGACAAC-AGTCACTGAACCAA-AGACAACCACAAGTG-AACCAGAAACAA
1 AGACAACAAG-CACTGAA-CAAGAAACAACAACAA-TGAAACCAGAAACAA
700716 CAAGCACTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
78 19 0.17
79 1 0.01
80 2 0.02
81 87 0.76
82 5 0.04
ACGTcount: A:0.51, C:0.27, G:0.15, T:0.08
Consensus pattern (80 bp):
AGACAACAAGCACTGAACAAGAAACAACAACAATGAAACCAGAAACAAGCACAATCACAGAGACA
ACACAACTGAACAAC
Found at i:700671 original size:21 final size:20
Alignment explanation
Indices: 700647--700706 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
700637 ACTGTCACAG
700647 AGACAACGACAACTGAACAA
1 AGACAACGACAACTGAACAA
*
700667 CAGACAACAGTC-ACTGAACCAA
1 -AGACAAC-GACAACTGAA-CAA
* *
700689 AGACAACCACAAGTGAAC
1 AGACAACGACAACTGAAC
700707 CAGAAACAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 2 0.06
21 25 0.78
22 5 0.16
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (20 bp):
AGACAACGACAACTGAACAA
Found at i:700740 original size:81 final size:80
Alignment explanation
Indices: 700506--700740 Score: 214
Period size: 81 Copynumber: 2.9 Consensus size: 80
700496 ACTGAGCTAG
* * ** **
700506 AGACAACAAGCACTGAACAAGAAACAACAACCATGATGCCAGAGTCAACAAGCACAAT--CACAG
1 AGACAACAAGCACTGAACAAGAGACAACAACAATGAAACCAGA---AACAAGCACTGTCACACAG
* *
700569 AGACAACAACTGTACAAC
63 AAACAACAACTGAACAAC
* *
700587 AGACAACAAGCACTGAACAAGATACAACAACAATGAAACCAGAAACAAGCACTGTCACAGAGACA
1 AGACAACAAGCACTGAACAAGAGACAACAACAATGAAACCAGAAACAAGCACTGTCACACAGA-A
*
700652 ACGACAACTGAACAAC
65 ACAACAACTGAACAAC
* *
700668 AGACAAC-AGTCACTGAACCAA-AGACAACCACAAGTG-AACCAGAAACAACAAGCACT-TTAC-
1 AGACAACAAG-CACTGAA-CAAGAGACAACAACAA-TGAAACCAG--A-AACAAGCACTGTCACA
700728 CAGAAACAACAAC
60 CAGAAACAACAAC
700741 AACAGTTCAA
Statistics
Matches: 130, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
78 10 0.08
80 7 0.05
81 91 0.70
82 8 0.06
83 4 0.03
84 10 0.08
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (80 bp):
AGACAACAAGCACTGAACAAGAGACAACAACAATGAAACCAGAAACAAGCACTGTCACACAGAAA
CAACAACTGAACAAC
Found at i:700891 original size:36 final size:36
Alignment explanation
Indices: 700849--700984 Score: 182
Period size: 36 Copynumber: 4.0 Consensus size: 36
700839 CCACAACATT
* **
700849 ACAGACACAATCCACAAAACAACAAACACAGACAAC
1 ACAGACACAATCTACTGAACAACAAACACAGACAAC
700885 ACAGACACAATCTACTG---AAC--A-AC--A-AAC
1 ACAGACACAATCTACTGAACAACAAACACAGACAAC
700912 ACAGACACAATCTACTGAACAACAAACACAGACAAC
1 ACAGACACAATCTACTGAACAACAAACACAGACAAC
700948 ACAGACACAATCTACTGAACAACAAACACAGACAAC
1 ACAGACACAATCTACTGAACAACAAACACAGACAAC
700984 A
1 A
700985 GAACAACAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 18
0.81 0.03 0.17
Matches are distributed among these distances:
27 20 0.23
28 1 0.01
30 5 0.06
31 1 0.01
32 1 0.01
33 5 0.06
35 1 0.01
36 54 0.61
ACGTcount: A:0.54, C:0.31, G:0.07, T:0.07
Consensus pattern (36 bp):
ACAGACACAATCTACTGAACAACAAACACAGACAAC
Found at i:700909 original size:15 final size:15
Alignment explanation
Indices: 700891--700936 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
700881 CAACACAGAC
700891 ACAATCTACTGAACA
1 ACAATCTACTGAACA
* *
700906 ACAAAC-ACAG-AC-
1 ACAATCTACTGAACA
700918 ACAATCTACTGAACA
1 ACAATCTACTGAACA
700933 ACAA
1 ACAA
700937 ACACAGACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
14 5 0.21
15 9 0.38
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.13
Consensus pattern (15 bp):
ACAATCTACTGAACA
Found at i:700917 original size:27 final size:27
Alignment explanation
Indices: 700882--700945 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
700872 AAACACAGAC
700882 AACACAGACACAATCTACTGAACAACA
1 AACACAGACACAATCTACTGAACAACA
700909 AACACAGACACAATCTACTGAACAACA
1 AACACAGACACAATCTACTGAACAACA
700936 AACACAGACA
1 AACACAGACA
700946 ACACAGACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.53, C:0.30, G:0.08, T:0.09
Consensus pattern (27 bp):
AACACAGACACAATCTACTGAACAACA
Found at i:700917 original size:63 final size:62
Alignment explanation
Indices: 700849--701035 Score: 276
Period size: 63 Copynumber: 3.1 Consensus size: 62
700839 CCACAACATT
*
700849 ACAGACACAATCCACAAAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
1 ACAGACACAAT-CACAGAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
*
700912 ACAGACACAATCTACTGAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
1 ACAGACACAATC-ACAGAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
* * *
700975 ACAG--AC-A--ACAGAACAACAAACACAGACAACACATACACAATCCACAGAACAACAAAC
1 ACAGACACAATCACAGAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
701032 ACAG
1 ACAG
701036 TTGTCAACTA
Statistics
Matches: 117, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
57 50 0.43
60 1 0.01
61 2 0.02
62 1 0.01
63 63 0.54
ACGTcount: A:0.55, C:0.31, G:0.07, T:0.06
Consensus pattern (62 bp):
ACAGACACAATCACAGAACAACAAACACAGACAACACAGACACAATCTACTGAACAACAAAC
Found at i:700976 original size:21 final size:20
Alignment explanation
Indices: 700916--700998 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
700906 ACAAACACAG
700916 ACACAATCTACTGAACAACAA
1 ACACAA-CTACTGAACAACAA
* *
700937 ACAC-A-GAC--AAC-ACAG
1 ACACAACTACTGAACAACAA
700952 ACACAATCTACTGAACAACAA
1 ACACAA-CTACTGAACAACAA
* *
700973 ACACAGACAACAGAACAACAA
1 ACACA-ACTACTGAACAACAA
700994 ACACA
1 ACACA
700999 GACAACACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
15 7 0.14
16 4 0.08
18 4 0.08
20 4 0.08
21 29 0.59
22 1 0.02
ACGTcount: A:0.55, C:0.30, G:0.07, T:0.07
Consensus pattern (20 bp):
ACACAACTACTGAACAACAA
Found at i:700999 original size:21 final size:21
Alignment explanation
Indices: 700964--701005 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
700954 ACAATCTACT
700964 GAACAACAAACACAGACAACA
1 GAACAACAAACACAGACAACA
700985 GAACAACAAACACAGACAACA
1 GAACAACAAACACAGACAACA
701006 CATACACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.29, G:0.10, T:0.00
Consensus pattern (21 bp):
GAACAACAAACACAGACAACA
Found at i:701014 original size:21 final size:21
Alignment explanation
Indices: 700965--701032 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
700955 CAATCTACTG
*
700965 AACAACAAACACAGACAACAG
1 AACAACAAACACAGACAACAC
700986 AACAACAAACACAGACAACAC
1 AACAACAAACACAGACAACAC
*
701007 ATAC-ACAATCCACAGAACAACA-
1 A-ACAACAA-ACACAG-ACAACAC
701029 AACA
1 AACA
701033 CAGTTGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 27 0.66
22 8 0.20
23 6 0.15
ACGTcount: A:0.60, C:0.31, G:0.06, T:0.03
Consensus pattern (21 bp):
AACAACAAACACAGACAACAC
Found at i:705831 original size:21 final size:21
Alignment explanation
Indices: 705807--705898 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
705797 CGATAATCCT
* *
705807 GATAGGATTAACGCACAATAG
1 GATAGGATTAACACACGATAG
705828 GATAGGATTAACACACGATAG
1 GATAGGATTAACACACGATAG
* * * * * *
705849 AACAGTA-TACACGCACCATAC
1 GATAGGATTA-ACACACGATAG
* *
705870 GATAGGATTGATACACGATAG
1 GATAGGATTAACACACGATAG
705891 GATAGGAT
1 GATAGGAT
705899 AGGATTGTAA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.94
22 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (21 bp):
GATAGGATTAACACACGATAG
Found at i:713650 original size:16 final size:16
Alignment explanation
Indices: 713629--713673 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
713619 CTAGGAAGTG
713629 GGTACGTTTTCTCTT-
1 GGTACGTTTTCTCTTA
713644 GGATACGTTTTCTCTTA
1 GG-TACGTTTTCTCTTA
713661 GGTACGTTTTCTC
1 GGTACGTTTTCTC
713674 CAGCATTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (16 bp):
GGTACGTTTTCTCTTA
Found at i:731577 original size:64 final size:64
Alignment explanation
Indices: 731474--731691 Score: 375
Period size: 64 Copynumber: 3.4 Consensus size: 64
731464 ATGATAATGC
731474 TGATTACAAAACTCAGGAACACCACAATGTAATTAATGGGGATCCTGTCAAAAGTCAACATAAT
1 TGATTACAAAACTCAGGAACACCACAATGTAATTAATGGGGATCCTGTCAAAAGTCAACATAAT
* * *
731538 TGATTACACAACTCAGGAACACCACAACGTAATTCATGGGGATCCTGTCAAAAGTCAACATAAT
1 TGATTACAAAACTCAGGAACACCACAATGTAATTAATGGGGATCCTGTCAAAAGTCAACATAAT
* *
731602 TGATTACAAAACTCAGGAACACCACAATGTTATTTGA-GGGGATCCTGTCAAAAGTCAACATAAT
1 TGATTACAAAACTCAGGAACACCACAATG-TAATTAATGGGGATCCTGTCAAAAGTCAACATAAT
731666 TGATTACAAAACTCAGGAACACCACA
1 TGATTACAAAACTCAGGAACACCACA
731692 GTTACTGTAG
Statistics
Matches: 146, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
64 141 0.97
65 5 0.03
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (64 bp):
TGATTACAAAACTCAGGAACACCACAATGTAATTAATGGGGATCCTGTCAAAAGTCAACATAAT
Found at i:733215 original size:38 final size:38
Alignment explanation
Indices: 733170--733335 Score: 181
Period size: 34 Copynumber: 4.6 Consensus size: 38
733160 ACAAACTTAC
*
733170 AGTCTCATTCTTTGCACTAATAAAACACCCACTTACAG
1 AGTCTCATTCTTTACACTAATAAAACACCCACTTACAG
* *
733208 AGTCTCATTTTTTACACTAATACAAAGCA--CACTTACTG
1 AGTCTCATTCTTTACACTAATA-AAA-CACCCACTTACAG
* * * *
733246 AG--TC--TCTTTACACTAATACAACGCACACTTACGG
1 AGTCTCATTCTTTACACTAATAAAACACCCACTTACAG
733280 AG--TC-TT-TTTACACTAATAAAACACCCACTTACAG
1 AGTCTCATTCTTTACACTAATAAAACACCCACTTACAG
733314 AGTCTCATTCTTTACACTAATA
1 AGTCTCATTCTTTACACTAATA
733336 CAACGCAAAC
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
32 1 0.01
33 2 0.02
34 51 0.47
35 1 0.01
36 4 0.04
37 2 0.02
38 42 0.39
39 3 0.03
40 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (38 bp):
AGTCTCATTCTTTACACTAATAAAACACCCACTTACAG
Found at i:733261 original size:34 final size:34
Alignment explanation
Indices: 733218--733372 Score: 163
Period size: 34 Copynumber: 4.4 Consensus size: 34
733208 AGTCTCATTT
733218 TTTACACTAATACAAAGCACACTTACTGAGTCTC
1 TTTACACTAATACAAAGCACACTTACTGAGTCTC
* * *
733252 TTTACACTAATACAACGCACACTTACGGAGTCTT
1 TTTACACTAATACAAAGCACACTTACTGAGTCTC
*
733286 TTTACACTAATA-AAA-CACCCACTTACAGAGTCTCATTC
1 TTTACACTAATACAAAGCA--CACTTACTGAG--TC--TC
* *
733324 TTTACACTAATACAACGCAAACTTA-TGGAGTCTC
1 TTTACACTAATACAAAGCACACTTACT-GAGTCTC
*
733358 TTTACATTAATACAA
1 TTTACACTAATACAA
733373 TGAGCACTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.02
33 2 0.02
34 69 0.68
36 4 0.04
38 21 0.21
39 2 0.02
40 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.30
Consensus pattern (34 bp):
TTTACACTAATACAAAGCACACTTACTGAGTCTC
Done.