Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1301
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: 1559340
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 165545 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1405690 original size:33 final size:32
Alignment explanation
Indices: 1405599--1405677 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
1405589 CCTAGCCATC
1405599 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
1405631 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1405663 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
1405678 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:1408135 original size:17 final size:17
Alignment explanation
Indices: 1408102--1408135 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1408092 AGGTTTTCCG
*
1408102 GGGGGAAAATCTACTAT
1 GGGGGAAAAACTACTAT
*
1408119 GGGGGAAAAACTGCTAT
1 GGGGGAAAAACTACTAT
1408136 ACAACACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (17 bp):
GGGGGAAAAACTACTAT
Found at i:1410378 original size:55 final size:55
Alignment explanation
Indices: 1410269--1410379 Score: 145
Period size: 55 Copynumber: 2.0 Consensus size: 55
1410259 CGGAATGTAA
* * * *
1410269 AAAAAGGGGGAAAATCCACTATATAGTAGGTTTTCCGTGGGGGTAATCTGGCTAT
1 AAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGTAAACTGGCTAT
*
1410324 AAAAAGGGGGAAAGCCCACTATATAGTCA-GCTTTCCCTGGGGGTAAAACT-GCTAT
1 AAAAAGGGGGAAAACCCACTATATAGT-AGGCTTTCCCTGGGGGT-AAACTGGCTAT
1410379 A
1 A
1410380 TAGCCATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 44 0.90
56 5 0.10
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (55 bp):
AAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGTAAACTGGCTAT
Found at i:1410379 original size:33 final size:32
Alignment explanation
Indices: 1410342--1410432 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
1410332 GGAAAGCCCA
* *
1410342 CTATATAGTCAGCTTTCCCTGGGGGTAA-AACTG
1 CTATATAGCCA-CTTTCCC-GGGGGGAAGAACTG
* *
1410375 CTATATAGCCATTTTTCCGGGGGGAAGAACTG
1 CTATATAGCCACTTTCCCGGGGGGAAGAACTG
* *
1410407 CTATATAGCCATTTTTCCGGGGGGAA
1 CTATATAGCCACTTTCCCGGGGGGAA
1410433 AGATGGCTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 7 0.13
32 36 0.68
33 10 0.19
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (32 bp):
CTATATAGCCACTTTCCCGGGGGGAAGAACTG
Found at i:1410406 original size:32 final size:32
Alignment explanation
Indices: 1410370--1410432 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1410360 CTGGGGGTAA
1410370 AACTGCTATATAGCCATTTTTCCGGGGGGAAG
1 AACTGCTATATAGCCATTTTTCCGGGGGGAAG
1410402 AACTGCTATATAGCCATTTTTCCGGGGGGAA
1 AACTGCTATATAGCCATTTTTCCGGGGGGAA
1410433 AGATGGCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (32 bp):
AACTGCTATATAGCCATTTTTCCGGGGGGAAG
Found at i:1414280 original size:2 final size:2
Alignment explanation
Indices: 1414273--1414324 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1414263 GGCCAATTTC
1414273 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
1414315 AG AG AG AG AG
1 AG AG AG AG AG
1414325 GGTGTGTGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1414331 original size:2 final size:2
Alignment explanation
Indices: 1414326--1414359 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1414316 GAGAGAGAGG
1414326 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1414360 ACCACACCAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1415902 original size:27 final size:27
Alignment explanation
Indices: 1415870--1415925 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1415860 ACAATGAAAG
1415870 GTTAACGTTTTTAACAACTTTAAAGAA
1 GTTAACGTTTTTAACAACTTTAAAGAA
1415897 GTTAACGTTTTTAACAACTTTAAAGAA
1 GTTAACGTTTTTAACAACTTTAAAGAA
1415924 GT
1 GT
1415926 ATCATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (27 bp):
GTTAACGTTTTTAACAACTTTAAAGAA
Found at i:1418384 original size:234 final size:233
Alignment explanation
Indices: 1417975--1418442 Score: 927
Period size: 234 Copynumber: 2.0 Consensus size: 233
1417965 GCCAAAAATG
1417975 AGGCCTGTTTAATCCTTCCCCATTTATTTAATTATACAAGAACACATTACATATTTTGATTTTAT
1 AGGCCTGTTTAATCCTTCCCCATTTATTTAATTATACAAGAACACATTACATATTTTGATTTTAT
1418040 ACAGTACTATTTTGATTCCTAAGTGTTCTTACGACAACGGATCAATTTGAGCTCTAAATACCATA
66 ACAGTACTATTTTGATTCCTAAGTGTTCTTACGACAACGGATCAATTTGAGCTCTAAATACCATA
1418105 CTCATATTCATATTACAATCATTCGGTTTTGATATAAATGTAATCAATATTTGGAAAAAATTCAT
131 CTCATATTCATATTACAATCATTCGGTTTTGATATAAATGTAATCAATATTTGGAAAAAATTCAT
1418170 ACAACAGTGCCTGCTGGCTTTATACTAAACAATACGTC
196 ACAACAGTGCCTGCTGGCTTTATACTAAACAATACGTC
1418208 NAGGCCTGTTTAATCCTTCCCCATTTATTTAATTATACAAGAACACATTACATATTTTGATTTTA
1 -AGGCCTGTTTAATCCTTCCCCATTTATTTAATTATACAAGAACACATTACATATTTTGATTTTA
1418273 TACAGTACTATTTTGATTCCTAAGTGTTCTTACGACAACGGATCAATTTGAGCTCTAAATACCAT
65 TACAGTACTATTTTGATTCCTAAGTGTTCTTACGACAACGGATCAATTTGAGCTCTAAATACCAT
1418338 ACTCATATTCATATTACAATCATTCGGTTTTGATATAAATGTAATCAATATTTGGAAAAAATTCA
130 ACTCATATTCATATTACAATCATTCGGTTTTGATATAAATGTAATCAATATTTGGAAAAAATTCA
1418403 TACAACAGTGCCTGCTGGCTTTATACTAAACAATACGTC
195 TACAACAGTGCCTGCTGGCTTTATACTAAACAATACGTC
1418442 A
1 A
1418443 TACGACTTAT
Statistics
Matches: 234, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
233 1 0.00
234 233 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (233 bp):
AGGCCTGTTTAATCCTTCCCCATTTATTTAATTATACAAGAACACATTACATATTTTGATTTTAT
ACAGTACTATTTTGATTCCTAAGTGTTCTTACGACAACGGATCAATTTGAGCTCTAAATACCATA
CTCATATTCATATTACAATCATTCGGTTTTGATATAAATGTAATCAATATTTGGAAAAAATTCAT
ACAACAGTGCCTGCTGGCTTTATACTAAACAATACGTC
Found at i:1429202 original size:15 final size:14
Alignment explanation
Indices: 1429179--1429208 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1429169 ACTGAAATGC
1429179 AAAAAAAAAAAAAT
1 AAAAAAAAAAAAAT
1429193 AAAAATAAAAAAAAT
1 AAAAA-AAAAAAAAT
1429208 A
1 A
1429209 TACTTACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:1443553 original size:24 final size:21
Alignment explanation
Indices: 1443496--1443544 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1443486 GTCACACTGG
1443496 CACCACCCACCCACCTCACGT
1 CACCACCCACCCACCTCACGT
*
1443517 CACCACCCACCCACCTCATGT
1 CACCACCCACCCACCTCACGT
1443538 CACCACC
1 CACCACC
1443545 ACAGTCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.61, G:0.04, T:0.10
Consensus pattern (21 bp):
CACCACCCACCCACCTCACGT
Found at i:1447471 original size:28 final size:28
Alignment explanation
Indices: 1447431--1447486 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1447421 GTTATATGGA
1447431 TATTCCTAGTTAGCTATATTTTAATGAG
1 TATTCCTAGTTAGCTATATTTTAATGAG
1447459 TATTCCTAGTTAGCTATATTTTAATGAG
1 TATTCCTAGTTAGCTATATTTTAATGAG
1447487 ATAAAATTCA
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:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (28 bp):
TATTCCTAGTTAGCTATATTTTAATGAG
Found at i:1455890 original size:13 final size:13
Alignment explanation
Indices: 1455872--1455898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1455862 TGAAACACAA
1455872 AAGAACGCATTTT
1 AAGAACGCATTTT
1455885 AAGAACGCATTTT
1 AAGAACGCATTTT
1455898 A
1 A
1455899 TGGTTTAAAA
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:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AAGAACGCATTTT
Found at i:1465636 original size:2 final size:2
Alignment explanation
Indices: 1465629--1465717 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
1465619 AGCTCAATAT
1465629 GA GA 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 GA GA
1465671 GA GA 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 GA GA
1465713 GA GA G
1 GA GA G
1465718 GGAGGGAGTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1466139 original size:17 final size:17
Alignment explanation
Indices: 1466119--1466155 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1466109 GTTTTAACAT
1466119 TAATTTCAATGTAACCA
1 TAATTTCAATGTAACCA
*
1466136 TAATTTTAATGTAACCA
1 TAATTTCAATGTAACCA
1466153 TAA
1 TAA
1466156 ATAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (17 bp):
TAATTTCAATGTAACCA
Found at i:1469574 original size:54 final size:54
Alignment explanation
Indices: 1469492--1469609 Score: 164
Period size: 54 Copynumber: 2.2 Consensus size: 54
1469482 CTCCTTTAGC
* * *
1469492 GTTAGCGCGACGGCGTGTTGTACAAAGTTGTGTCAGCGCAACGGCGTGTTGTAT
1 GTTAGCGCGACAGCGTGTCGTACAAAGTTGCGTCAGCGCAACGGCGTGTTGTAT
* * * * *
1469546 GTTAGCGCGACAGCGTGTCGTGCAAAGTTGCGTTATCGCGACGGCGTGTTGTGT
1 GTTAGCGCGACAGCGTGTCGTACAAAGTTGCGTCAGCGCAACGGCGTGTTGTAT
1469600 GTTAGCGCGA
1 GTTAGCGCGA
1469610 TGGCGTATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.27
Consensus pattern (54 bp):
GTTAGCGCGACAGCGTGTCGTACAAAGTTGCGTCAGCGCAACGGCGTGTTGTAT
Found at i:1469603 original size:23 final size:23
Alignment explanation
Indices: 1469577--1469644 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1469567 GCAAAGTTGC
*
1469577 GTTATCGCGACGGCGTGTTGTGT
1 GTTAGCGCGACGGCGTGTTGTGT
* *
1469600 GTTAGCGCGATGGCGTATTGTGT
1 GTTAGCGCGACGGCGTGTTGTGT
* *
1469623 -TCTAGCACGACGGCGCGTTGTG
1 GT-TAGCGCGACGGCGTGTTGTG
1469645 AAAATGTGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.12, C:0.19, G:0.38, T:0.31
Consensus pattern (23 bp):
GTTAGCGCGACGGCGTGTTGTGT
Found at i:1472528 original size:21 final size:21
Alignment explanation
Indices: 1472504--1472555 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1472494 CACACTCGTT
1472504 TGCAAAACCAACAGA-CACCGA
1 TGCAAAACCAACA-ACCACCGA
* *
1472525 TGCAGAACAAACAACCACCGA
1 TGCAAAACCAACAACCACCGA
1472546 TGCAAAACCA
1 TGCAAAACCA
1472556 TCATCGGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.48, C:0.33, G:0.13, T:0.06
Consensus pattern (21 bp):
TGCAAAACCAACAACCACCGA
Found at i:1472594 original size:15 final size:15
Alignment explanation
Indices: 1472571--1472600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1472561 GGATACCTGT
*
1472571 AAAATGAAACGAAAC
1 AAAAAGAAACGAAAC
1472586 AAAAAGAAACGAAAC
1 AAAAAGAAACGAAAC
1472601 GGAATCTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAGAAACGAAAC
Found at i:1482731 original size:20 final size:21
Alignment explanation
Indices: 1482708--1482747 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1482698 CAGCAAAAAC
1482708 GGCACAA-TAACAA-AAATGAT
1 GGCACAACT-ACAAGAAATGAT
1482728 GGCACAACTACAAGAAATGA
1 GGCACAACTACAAGAAATGA
1482748 AATTTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (21 bp):
GGCACAACTACAAGAAATGAT
Found at i:1515382 original size:30 final size:30
Alignment explanation
Indices: 1515346--1515428 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
1515336 TAATTGAATC
*
1515346 ACATAATATTATATCATATGATAATGAAAT
1 ACATAATATTTTATCATATGATAATGAAAT
*
1515376 GA-ATAATATTTTATCATACGATAATGAAAT
1 -ACATAATATTTTATCATATGATAATGAAAT
*
1515406 ACATAATATTTTATTATATGATA
1 ACATAATATTTTATCATATGATA
1515429 CCATATTGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (30 bp):
ACATAATATTTTATCATATGATAATGAAAT
Found at i:1515630 original size:15 final size:15
Alignment explanation
Indices: 1515561--1515630 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
1515551 TTCATGTGAA
* *
1515561 ATGATATCGTATAAT
1 ATGATATTGTATCAT
*
1515576 ATGATATTGTATTAT
1 ATGATATTGTATCAT
* *
1515591 AT-ATTATTGCATCAC
1 ATGA-TATTGTATCAT
*
1515606 ATGAAATTGTATCAT
1 ATGATATTGTATCAT
1515621 ATGATATTGT
1 ATGATATTGT
1515631 GAAATATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
14 1 0.02
15 42 0.95
16 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (15 bp):
ATGATATTGTATCAT
Found at i:1524581 original size:2 final size:2
Alignment explanation
Indices: 1524574--1524604 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1524564 TGATATGAAT
1524574 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1524605 GGGGTGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1524907 original size:12 final size:12
Alignment explanation
Indices: 1524883--1524915 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1524873 ATCACATTTT
1524883 GTCTGTC-GTCC
1 GTCTGTCTGTCC
1524894 GTCTGTCTGTCC
1 GTCTGTCTGTCC
1524906 GTCTGTCTGT
1 GTCTGTCTGT
1524916 AAACTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.30, G:0.27, T:0.42
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:1525365 original size:166 final size:166
Alignment explanation
Indices: 1525114--1526457 Score: 1969
Period size: 166 Copynumber: 8.0 Consensus size: 166
1525104 AACCATAAGA
* * *
1525114 CCAGGAGAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAACTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * *
1525179 TGACCCCCGGGGGAAGGGTGGGGCCACAATGGGGGGTCGAAGGTTTACATATGAATATACAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
1525244 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
*
1525280 CCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * *
1525345 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTAACAAAGGAATATATAGAAT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
1525410 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* *
1525446 CCAGGAAAGCTGAAACTTGTATGGAAGTAT-CTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * *
1525510 TGACCCCTGGGGGTAGGGAAGGATGGGGCCACAAT-GAGAGTTGAAGTTTTACATAGGAATATAT
66 TGACCCCCGGGGGTA--G--GG-TGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATAT
** *
1525574 AGAGTAAAAATTAAAAAATCTTCTTCTCAGAAACTAATCAG
126 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* *
1525615 ACAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * *
1525680 T-AACCCCGGGGGTAGGGTGAGGCCACATTGGGGGGTCGAAGTTTTACATAGGAATTTATATATA
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGG-A---ATATATA
*
1525744 GAGTAAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAG
127 GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * *
1525784 CCAGGAAAGTTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAGATTCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * *
1525849 TGACCCCCAGGGGTAGGCTGGGTCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
*
1525914 AAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * * *
1525950 CCAGGAAAGTTTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAGATTCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * *
1526015 TGACCCCCAGGGGTAGGCTGGGTCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
*
1526080 AAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* * *
1526116 CCAGGAAAGTTTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATTA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
*** * *
1526181 TGATTGCTGGGGGTAGGGTGGGG-CACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
* * *
1526245 AAATATTAAAAAATCATCTTCTCAGAAACTAATCAG
131 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* *
1526281 CCAGGAAAGCCGAAACTTGTGTGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * *
1526346 TGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGGGGGGT-GTTAAAGTTTTACATAGGAATA
66 TGACCCCCGGGGGTAGGGTGGGGCCACAAT-----GGGGGGTCG---AAGTTTTACATAGGAATA
1526410 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
123 TATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
1526454 CCAG
1 CCAG
1526458 ATTATTCTTT
Statistics
Matches: 1076, Mismatches: 81, Indels: 35
0.90 0.07 0.03
Matches are distributed among these distances:
164 10 0.01
165 221 0.21
166 477 0.44
167 2 0.00
169 205 0.19
170 92 0.09
171 6 0.01
173 63 0.06
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (166 bp):
CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
Found at i:1525893 original size:335 final size:332
Alignment explanation
Indices: 1525114--1526457 Score: 1971
Period size: 335 Copynumber: 4.0 Consensus size: 332
1525104 AACCATAAGA
* * *
1525114 CCAGGAGAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAACTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * * *
1525179 TGACCCCCGGGGGAAGGGTGGGGCCACAATGGGGGGTCGAAGGTTTACATATGAATATACAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
* * *
1525244 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCA
131 AAATATTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
*
1525309 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
196 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
* * * *
1525374 TGGGGGGTCAAAGTTTAACAAAGGAATATATAGAATAAATCTTTAAAAATCTTCTTCTCAGAAAC
261 TGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAAC
1525439 TAATCAG
326 TAATCAG
* *
1525446 CCAGGAAAGCTGAAACTTGTATGGAAGTAT-CTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * *
1525510 TGACCCCTGGGGGTAGGGAAGGATGGGGCCACAAT-GAGAGTTGAAGTTTTACATAGGAATATAT
66 TGACCCCCGGGGGTA--G--GG-TGGGGCCACAATGGAGGGTCGAAGTTTTACATAGGAATATAT
* *
1525574 AGAGTAAAAATTAAAAAATCTTCTTCTCAGAAACTAATCAGACAGGAAAGCTGAAACTTGTGTGG
126 AGAGTAAATATTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGG
* *
1525639 AAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAATCAT-AACCCCGGGGGTAGGGTGAGGC
191 AAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGC
*
1525703 CACATTGGGGGGTCGAAGTTTTACATAGGAATTTATATATAGAGTAAATCTTTAAAAATCTTCTT
256 CACAATGGGGGGTCGAAGTTTTACATAGG-A---ATATATAGAGTAAATCTTTAAAAATCTTCTT
*
1525768 TTCAGAAACTAATCAG
317 CTCAGAAACTAATCAG
* * *
1525784 CCAGGAAAGTTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAGATTCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
* * * *
1525849 TGACCCCCAGGGGTAGGCTGGGTCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
* * * * *
1525914 AAATCTTTAAAAATCTTCTTTTCAGAAACTAATCAGCCAGGAAAGTTTAAACTTGTGTGGAAGCA
131 AAATATTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
* * * *
1525979 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAGATTCATGACCCCCAGGGGTAGGCTG-GGTCCACA
196 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGG-CCACA
*
1526043 ATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTTTCAGAAA
260 ATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAA
1526108 CTAATCAG
325 CTAATCAG
* * *
1526116 CCAGGAAAGTTTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATTA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
*** *
1526181 TGATTGCTGGGGGTAGGGTGGGG-CACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
* * *
1526245 AAATATTAAAAAATCATCTTCTCAGAAACTAATCAGCCAGGAAAGCCGAAACTTGTGTGGAAGTA
131 AAATATTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
* * *
1526310 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACAT
196 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
1526375 TGGGGGGGGGGGT-GTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTC
261 T-----GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTC
1526439 TCAGAAACTAATCAG
318 TCAGAAACTAATCAG
1526454 CCAG
1 CCAG
1526458 ATTATTCTTT
Statistics
Matches: 909, Mismatches: 81, Indels: 38
0.88 0.08 0.04
Matches are distributed among these distances:
331 199 0.22
332 152 0.17
333 1 0.00
334 56 0.06
335 255 0.28
336 63 0.07
337 1 0.00
338 137 0.15
339 45 0.05
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (332 bp):
CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
TGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGT
AAATATTAAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
TGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAAC
TAATCAG
Found at i:1527992 original size:131 final size:131
Alignment explanation
Indices: 1527758--1528016 Score: 518
Period size: 131 Copynumber: 2.0 Consensus size: 131
1527748 TTCAATATTT
1527758 TAGGATAAAGAAAGATAACTCTTGTTGATCGAAGCATTTTTTTGTTACAAACCTATTTTACAAAA
1 TAGGATAAAGAAAGATAACTCTTGTTGATCGAAGCATTTTTTTGTTACAAACCTATTTTACAAAA
1527823 TGCTATTCTGAACTCAAAACCATCACTTCACTATGTTTATTAATATGAATTATCAATGTATATGT
66 TGCTATTCTGAACTCAAAACCATCACTTCACTATGTTTATTAATATGAATTATCAATGTATATGT
1527888 G
131 G
1527889 TAGGATAAAGAAAGATAACTCTTGTTGATCGAAGCATTTTTTTGTTACAAACCTATTTTACAAAA
1 TAGGATAAAGAAAGATAACTCTTGTTGATCGAAGCATTTTTTTGTTACAAACCTATTTTACAAAA
1527954 TGCTATTCTGAACTCAAAACCATCACTTCACTATGTTTATTAATATGAATTATCAATGTATAT
66 TGCTATTCTGAACTCAAAACCATCACTTCACTATGTTTATTAATATGAATTATCAATGTATAT
1528017 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (131 bp):
TAGGATAAAGAAAGATAACTCTTGTTGATCGAAGCATTTTTTTGTTACAAACCTATTTTACAAAA
TGCTATTCTGAACTCAAAACCATCACTTCACTATGTTTATTAATATGAATTATCAATGTATATGT
G
Found at i:1532878 original size:16 final size:16
Alignment explanation
Indices: 1532852--1532884 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1532842 TGATCACAAT
1532852 TTGTCCGTTGTCTGTCG
1 TTGTCCGTTGTC-GTCG
1532869 TTGT-CGTTGTCGTCG
1 TTGTCCGTTGTCGTCG
1532884 T
1 T
1532885 CGTTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.00, C:0.21, G:0.30, T:0.48
Consensus pattern (16 bp):
TTGTCCGTTGTCGTCG
Found at i:1533390 original size:166 final size:166
Alignment explanation
Indices: 1533043--1534400 Score: 1685
Period size: 166 Copynumber: 8.2 Consensus size: 166
1533033 GGTATTTTTC
* * * ** *
1533043 AAAAATCTTCTTCTCAAAAACTATTTGGCCTGAAAAGCTAAAACTTG-TGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAAATGGAAGCATCCTCAG
* * *
1533107 GTAGTGTAGAATT-AAGTTTGTTCAAATCATGG-CCCCGGGGGAAGGGAGGGGCCACAA-GAAGG
65 GTAGTGTAG-ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATG-GGG
1533169 GGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
128 GGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
1533208 AAAAATCTTCTTCTCAAAAACTATTGGGCAAGGAAAGCTCAAATTGAAATGGAAGCATCCACAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAAATGGAAGCATCCTCAGG
* * *
1533273 TAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCTGGTGGTAGGGTGGGGCCACAATGGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
* *
1533338 TGAAGTTTTACATAGGAATATAGAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1533374 AAAAATCTTATTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-ATAATGGAATCATCTTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGA-AATGGAAGCATCCTCAG
* ** * * * * *
1533438 GTAGTGTAGATTCAAGCTCATTCTAATCATGGTCCGCAGGGGTAGGGTGGGGCAAAAAATGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGC-CACAAT---GG
*
1533503 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTAT
126 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
1533544 AAAAATCTTCTTCTCAAAAACAATTAGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCCACAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAAATGGAAGCATCCTCAGG
* * * * *
1533609 AAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTTGGGTCACAATTGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
* *
1533674 TCAAGTTTTATAGAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
1533710 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAACCTGAAATTTG-AGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAAATGGAAGCATCCTCAG
* * *
1533774 GTAGTGTAGATTCAAGTTTGTTTAAATCATGGTCCCCGGGGGTAGGGTGGGGTCACAATAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* * * *
1533839 ATGAATTTTTACATAGGAATATATAGAGGAAATCTTA
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1533876 AAAAATCTTCTTCTCAAAAACTTTTAGGCCAG-AAAGCTCAAATT-ATAATGGAATCATCTTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGA-AATGGAAGCATCCTCAG
* ** ** * * *
1533939 GTAGTGTAGATTCAAGCTCATTCAAATCATGGTTTCCAGGGGTAGGGTGGGGCAAAAATGGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* * *
1534004 ATCAAGTTTAACATAGGAATATATAAAGAAAATCTAT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
1534041 AAAAATCTTCTTCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATGGGAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAAATGGAAGCATCCTCAGG
* * * *
1534106 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCTCTGGGGGTAGGGCGGGGCCACAATGGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
1534171 TCAAGTTTTACATAGGAATATAT-------A---TT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
1534197 AAAAATCTCCATCTCAAATACTATTAGGCCAG-AAAGCTTAAATTTG-AATAGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAAATGGAAGCATCCTCAG
* * *
1534260 GTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATTGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
1534325 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
1534362 AAAAATCTTCTTTTTAAAGACCATTTGGCCAGAAAAGCT
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCT
1534401 TTAACTTGTG
Statistics
Matches: 1022, Mismatches: 144, Indels: 53
0.84 0.12 0.04
Matches are distributed among these distances:
155 107 0.10
156 31 0.03
159 1 0.00
162 1 0.00
164 8 0.01
165 241 0.24
166 481 0.47
167 8 0.01
169 4 0.00
170 139 0.14
171 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAAATGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1534046 original size:331 final size:331
Alignment explanation
Indices: 1533043--1534440 Score: 1700
Period size: 331 Copynumber: 4.2 Consensus size: 331
1533033 GGTATTTTTC
* * * * *
1533043 AAAAATCTTCTTCTCAAAAACTATTTGGCCTGAAAAGCTAAAACTTGTGTGGAGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAGGCATCCTCAGG
* * * *
1533108 TAGTGTAGAATT-AAGTTTGTTCAAATCATGG-CCCCGGGGGAAGGGAGGGGCCACAAGAAGGGG
66 TAGTGTAG-ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGG
* *
1533171 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTGGG
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAAACTATTAGG
*
1533236 CAAGGAAAGCTCAAATTGA-AATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCAAATC
195 CCA-GAAAGCTCAAATT-ATAATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCAAATC
* * *
1533300 ATGG-TCCCTGGTGGTAGGGTGGGGCCACAATGGGGGGATGAAGTTTTACATAGGAATATAGAGA
258 ATGGTTCCC-GGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGA
1533364 GAAAATCTTT
322 GAAAATCTTT
* * ** *
1533374 AAAAATCTTATTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAT-AATGGAATCATCTTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-TGAGTGGAGGCATCCTCAG
* ** * * * * * *
1533438 GTAGTGTAGATTCAAGCTCATTCTAATCATGGTCCGCAGGGGTAGGGTGGGGCAAAAAATGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGC-CACAAT---AG
*
1533503 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC-TATAAAAATCTTCTTCTCAAAAACAA
126 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTA-AAAAATCTTCTTCTCAAAAACTA
* * *
1533567 TTAGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCCACAGGAAGTGTAGATTCAAATTTGTTCA
190 TTAGGCCAG-AAAGCTCAAATTATAATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCA
* * * * * *
1533632 AATCATGGTCCCCGGGGGTAGGGTTGGGTCACAATTGGGGGATCAAGTTTTATAGAGGAATATAT
254 AATCATGGTTCCCGGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATAT
1533697 AGAGAAAATCTTT
319 AGAGAAAATCTTT
* * *
1533710 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAACCTGAAATTTGAGTGGAGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAGGCATCCTCAGG
* *
1533775 TAGTGTAGATTCAAGTTTGTTTAAATCATGGTCCCCGGGGGTAGGGTGGGGTCACAATAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGA
* * * *
1533840 TGAATTTTTACATAGGAATATATAGAGGAAATCTTAAAAAATCTTCTTCTCAAAAACTTTTAGGC
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAAACTATTAGGC
* ** ** **
1533905 CAGAAAGCTCAAATTATAATGGAATCATCTTCAGGTAGTGTAGATTCAAGCTCATTCAAATCATG
196 CAGAAAGCTCAAATTATAATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCAAATCATG
* * * * * *
1533970 GTTTCCAGGGGTAGGGTGGGGCAAAAATGGGGGGATCAAGTTTAACATAGGAATATATAAAGAAA
261 GTTCCCGGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAA
*
1534035 ATCTAT
326 ATCTTT
* * ** *
1534041 AAAAATCTTCTTCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATGG-GAGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAG-GCATCCTCAG
* * * * *
1534105 GTAGTGTAGATTCAAGTTTGTTCAAATCATAGTCTCTGGGGGTAGGGCGGGGCCACAATGGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGG
* * *
1534170 ATCAAGTTTTACATAGGAATATAT-------A--TT-AAAAATCTCCATCTCAAATACTATTAGG
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAAACTATTAGG
* * * *
1534225 CCAGAAAGCTTAAATT-TGAATAGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
195 CCAGAAAGCTCAAATTAT-AATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCAAATCA
* *
1534289 T-GATCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG
259 TGGTTCCC-GGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAG
1534353 AAAATCTTT
323 AAAATCTTT
* * * * * ** * * * *
1534362 AAAAATCTTCTTTTTAAAGACCATTTGGCCAGAAAAGCTTTAACTTGTGTAGAGGCATCCTCGGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAGGCATCCTCAGG
*
1534427 TAGTGTAAATTCAA
66 TAGTGTAGATTCAA
1534441 AATCACAGTC
Statistics
Matches: 912, Mismatches: 138, Indels: 44
0.83 0.13 0.04
Matches are distributed among these distances:
320 5 0.01
321 199 0.22
322 3 0.00
324 1 0.00
330 4 0.00
331 320 0.35
332 83 0.09
333 5 0.01
335 8 0.01
336 281 0.31
337 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (331 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAGGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAAACTATTAGGC
CAGAAAGCTCAAATTATAATGGAAGCATCCACAGGTAGTGTAGATTCAAATTTGTTCAAATCATG
GTTCCCGGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAA
ATCTTT
Found at i:1534273 original size:155 final size:156
Alignment explanation
Indices: 1534040--1534349 Score: 480
Period size: 155 Copynumber: 2.0 Consensus size: 156
1534030 AGAAAATCTA
* * * *
1534040 TAAAAATCTTCTTCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATGGGAGCATCCTCAG
1 TAAAAATCTCCATCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATAGAAGCATCCTCAG
*
1534105 GTAGTGTAGATTCAAGTTTGTTCAAATCAT-AGTCTCTGGGGGTAGGGCGGGGCCACAATGGGGG
66 GTAGTGTAGATTCAAGTTTGTTCAAATCATGA-TCCCTGGGGGTAGGGCGGGGCCACAATGGGGG
1534169 GATCAAGTTTTACATAGGAATATATAT
130 GATCAAGTTTTACATAGGAATATATAT
* * * * **
1534196 TAAAAATCTCCATCTCAAATACTATTAGGCCAG-AAAGCTTAAATTTGAATAGAAGCATCCTCAG
1 TAAAAATCTCCATCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATAGAAGCATCCTCAG
* *
1534260 GTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATTGGGGG
66 GTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTGGGGGTAGGGCGGGGCCACAATGGGGGG
1534325 ATCAAGTTTTACATAGGAATATATA
131 ATCAAGTTTTACATAGGAATATATA
1534350 GAGAAAATCT
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
155 110 0.79
156 30 0.21
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (156 bp):
TAAAAATCTCCATCTCAAAAACAATTAGGCCAGAAAAGATCAAATTAAAATAGAAGCATCCTCAG
GTAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTGGGGGTAGGGCGGGGCCACAATGGGGGG
ATCAAGTTTTACATAGGAATATATAT
Found at i:1541506 original size:167 final size:167
Alignment explanation
Indices: 1540831--1541837 Score: 1553
Period size: 165 Copynumber: 6.0 Consensus size: 167
1540821 GAATCATCTT
*
1540831 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTTTATATATTCCTATGTAAAACTTTA
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT-
* *
1540896 ACATCCCCCCCA-TGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTAC
65 -CA-CCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTAC
* *
1540960 ACTACCTGAGGATACTTCCACACAAGTTTCAGCTCTCCTG
128 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
*
1541000 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTC
*
1541065 A-CCCCCAATTGT-GCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACACT
66 ACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACACT
*
1541128 ACCTGAGGATGCTACCACACAAGTTTCAGCTTTCCTG
131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * * *
1541165 GCTGTTTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTTCTATGTAAAATTTTA
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT-
* * * *
1541230 ACACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCT
65 -CA---CCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCT
*
1541295 ACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTTCCTG
126 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
1541337 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA-TTTC
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTC
* * * *
1541401 GACCCCCCCATTGTGGCCCCACCATAACCCCGGGGATCATGATTTTCACAACTTTGAATCTACAC
66 -ACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACAC
*
1541466 TACCTGAGGATGATTCCACACAAGTTTCAGCTTTCCTG
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* *
1541504 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATGCCTATGTAAAAC-TTC
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTC
* * *
1541568 AACCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGAATTTCACAACTTTGAATCTACACT
66 ACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACACT
**
1541632 ACCTGAGGATGCTTCCACATTAGTTTCAGCTTTCCTG
131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
*
1541669 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TTC
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTC
* * * *
1541733 GA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACGTTAAATCTACAC
66 -ACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACAC
*
1541797 TACCTGAGGATGCCTCCACACAAGTTTCAGCTTTCCTG
130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
1541835 GCT
1 GCT
1541838 TTCTGGTTCT
Statistics
Matches: 780, Mismatches: 46, Indels: 27
0.91 0.05 0.03
Matches are distributed among these distances:
165 306 0.39
166 101 0.13
167 156 0.20
169 64 0.08
170 1 0.00
171 12 0.02
172 140 0.18
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (167 bp):
GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTC
ACCCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACACT
ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
Found at i:1541575 original size:337 final size:334
Alignment explanation
Indices: 1540831--1541871 Score: 1614
Period size: 337 Copynumber: 3.1 Consensus size: 334
1540821 GAATCATCTT
* *
1540831 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTTTATATATTCCTATGTAAAACTTTA
1 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TTA
*
1540896 ACATCCCCCCC-ATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTAC
65 A-ACCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTAC
* *
1540960 ACTACCTGAGGATACTTCCACACAAGTTTCAGCTCTCCTGGCTGATTAGTTTCTGAGAAGAAGAT
129 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGAT
*
1541025 TTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT-GACCCCCAATTGT-GCCCCACCCTA
194 TTTTAAAGATTTACTCTATATATTCCTATGTAAAA-TTTCGACCCCCCATTGTGGCCCCACCCTA
* *
1541088 CCCCCAGGGATCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTACCACACAAGTT
258 CCCCCGGGGATCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTT
1541153 TCAGCTTTCCTG
323 TCAGCTTTCCTG
* * *
1541165 GCTGTTTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTTCTATGTAAAATTTTA
1 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA-CTTA
*
1541230 ACACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCT
65 A-A--CCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCT
*
1541295 ACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAG
127 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAG
*
1541360 ATTTTTAAAGATTTACTCTATATATTCCTATGTAAAATTTCGACCCCCCCATTGTGGCCCCACCA
192 ATTTTTAAAGATTTACTCTATATATTCCTATGTAAAATTTCGA-CCCCCCATTGTGGCCCCACCC
* * *
1541425 TAACCCCGGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGATTCCACACAAG
256 TACCCCCGGGGATCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAG
1541490 TTTCAGCTTTCCTG
321 TTTCAGCTTTCCTG
* *
1541504 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATGCCTATGTAAAACTTCA
1 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTAA
* * * * *
1541569 A--CCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGAATTTCACAACTTTGAATCTACAC
66 ACCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACAC
** *
1541631 TACCTGAGGATGCTTCCACATTAGTTTCAGCTTTCCTGGCTGTTTAGTTTCTGAGAAGAAGATTT
131 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTT
*
1541696 TTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCC
196 TTAAAGATTTACTCTATATATTCCTATGTAAAATTTCGACCCCCCATTGTGGCCCCACCCTACCC
* * * *
1541761 CCGGGGGTCATGAATTTCACAACGTTAAATCTACACTACCTGAGGATGCCTCCACACAAGTTTCA
261 CCGGGGATCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCA
1541826 GCTTTCCTG
326 GCTTTCCTG
* *
1541835 GCT-TTCT-GGTTCTTGAGAAGAATATTTTTGAAA-ATTT
1 GCTGTT-TAGTTTC-TGAGAAGAAGATTTTT-AAAGATTT
1541872 CTCGAAATTT
Statistics
Matches: 654, Mismatches: 43, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
330 6 0.01
331 115 0.18
332 137 0.21
333 20 0.03
334 62 0.09
336 10 0.02
337 152 0.23
338 13 0.02
339 139 0.21
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (334 bp):
GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTAA
ACCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTT
TTAAAGATTTACTCTATATATTCCTATGTAAAATTTCGACCCCCCATTGTGGCCCCACCCTACCC
CCGGGGATCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCA
GCTTTCCTG
Found at i:1542050 original size:12 final size:12
Alignment explanation
Indices: 1542033--1542065 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1542023 TGAAAAGTTT
1542033 ACGGACAGACGG
1 ACGGACAGACGG
1542045 ACGGACAGACGG
1 ACGGACAGACGG
1542057 AC-GACAGAC
1 ACGGACAGAC
1542066 AAAATGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.36, C:0.27, G:0.36, T:0.00
Consensus pattern (12 bp):
ACGGACAGACGG
Found at i:1542215 original size:12 final size:12
Alignment explanation
Indices: 1542198--1542227 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1542188 AGGGGGAAAG
1542198 TTGACCAAAATC
1 TTGACCAAAATC
1542210 TTGACCAAAATC
1 TTGACCAAAATC
*
1542222 GTGACC
1 TTGACC
1542228 GTGCCCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (12 bp):
TTGACCAAAATC
Found at i:1547715 original size:34 final size:34
Alignment explanation
Indices: 1547677--1547745 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1547667 AAAGAGAATT
1547677 ATCTCGTTATATAGATATTTTTAACAAACAAAAA
1 ATCTCGTTATATAGATATTTTTAACAAACAAAAA
1547711 ATCTCGTTATATAGATATTTTTAACAAACAAAAA
1 ATCTCGTTATATAGATATTTTTAACAAACAAAAA
1547745 A
1 A
1547746 CAAGATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (34 bp):
ATCTCGTTATATAGATATTTTTAACAAACAAAAA
Found at i:1548579 original size:40 final size:40
Alignment explanation
Indices: 1548524--1548729 Score: 331
Period size: 40 Copynumber: 5.2 Consensus size: 40
1548514 ATTCCACACT
* * *
1548524 ACATGTTCACTGATATTTAACAGAGAGTACAGGTCCAATA
1 ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
*
1548564 ACATGTTTATTGATATTTTACAGAGAGTATAGGTCCAATA
1 ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
* *
1548604 ACATGTTCATTGATATTTTACAGAGAGTACAGGCCCAATA
1 ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
* *
1548644 CCATGTTAATTGATATTTTACAGAGAGTATAGGTCCAATA
1 ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
*
1548684 ACATGTTCATTGATATTTTACAAAGAGTATAGGTCCAATA
1 ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
1548724 ACATGT
1 ACATGT
1548730 NACCACGTCC
Statistics
Matches: 152, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 152 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
ACATGTTCATTGATATTTTACAGAGAGTATAGGTCCAATA
Done.