Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold471
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: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 143812 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1113111 original size:24 final size:24
Alignment explanation
Indices: 1113080--1113176 Score: 158
Period size: 24 Copynumber: 4.0 Consensus size: 24
1113070 AATGGAAAAG
*
1113080 AAGGATCTAGTGCTACTTTGAATA
1 AAGGATCTAGTGCTACTCTGAATA
1113104 AAGGATCTAGTGCTACTCTGAATA
1 AAGGATCTAGTGCTACTCTGAATA
1113128 AAGGATCTAGTGCTACTCTGAATA
1 AAGGATCTAGTGCTACTCTGAATA
* * *
1113152 AAGGATCAAATGCTACCCTGAATA
1 AAGGATCTAGTGCTACTCTGAATA
1113176 A
1 A
1113177 GAGTGAAGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (24 bp):
AAGGATCTAGTGCTACTCTGAATA
Found at i:1118555 original size:2 final size:2
Alignment explanation
Indices: 1118548--1118596 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1118538 ACGGGTTGTT
1118548 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
1118590 GA GA GA G
1 GA GA GA G
1118597 TAAATAGAAT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1121335 original size:28 final size:28
Alignment explanation
Indices: 1121304--1121358 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1121294 GAAAAAATAA
* *
1121304 AATGAAGGATAAGAATGAATTAAAAATG
1 AATGAAGGAAAAGAATGAATAAAAAATG
1121332 AATGAAGGAAAAGAATGAATAAAAAAT
1 AATGAAGGAAAAGAATGAATAAAAAAT
1121359 AACTGTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (28 bp):
AATGAAGGAAAAGAATGAATAAAAAATG
Found at i:1121356 original size:13 final size:13
Alignment explanation
Indices: 1121314--1121356 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1121304 AATGAAGGAT
1121314 AAGAATGAATTAAA
1 AAGAATGAA-TAAA
**
1121328 AATGAATGAAGGAA
1 AA-GAATGAATAAA
1121342 AAGAATGAATAAA
1 AAGAATGAATAAA
1121355 AA
1 AA
1121357 ATAACTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.46
14 6 0.25
15 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (13 bp):
AAGAATGAATAAA
Found at i:1122268 original size:2 final size:2
Alignment explanation
Indices: 1122261--1122297 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1122251 TTGATCAAAG
1122261 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1122298 GATACAACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1135431 original size:13 final size:12
Alignment explanation
Indices: 1135412--1135447 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
1135402 CCATTAATTT
1135412 TGATAGATTTGA
1 TGATAGATTTGA
1135424 TAGATAGATTT-A
1 T-GATAGATTTGA
1135436 TGATAGATTTGA
1 TGATAGATTTGA
1135448 CTTTATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (12 bp):
TGATAGATTTGA
Found at i:1135463 original size:11 final size:11
Alignment explanation
Indices: 1135408--1135445 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1135398 TCAACCATTA
1135408 ATTT-TGATAG
1 ATTTATGATAG
1135418 ATTTGATAGATAG
1 ATTT-AT-GATAG
1135431 ATTTATGATAG
1 ATTTATGATAG
1135442 ATTT
1 ATTT
1135446 GACTTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 9 0.36
12 3 0.12
13 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTTATGATAG
Found at i:1142561 original size:2 final size:2
Alignment explanation
Indices: 1142554--1142581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1142544 ATTAATAAAC
1142554 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
1142582 GAATCTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1143010 original size:36 final size:35
Alignment explanation
Indices: 1142977--1143052 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 35
1142967 TGGATATTAT
* *
1142977 ATTAAT-TATTTAA-ATATAATTATATATTTATATTA
1 ATTAATATAATTAATATAAAATTA-AT-TTTATATTA
1143012 ATTATATATAATTAATATAAAATTAATTTTATATTA
1 ATTA-ATATAATTAATATAAAATTAATTTTATATTA
1143048 ATTAA
1 ATTAA
1143053 GCTTGTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 5 0.14
36 15 0.42
37 8 0.22
38 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
ATTAATATAATTAATATAAAATTAATTTTATATTA
Found at i:1143029 original size:11 final size:10
Alignment explanation
Indices: 1142990--1143031 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
1142980 AATTATTTAA
1142990 ATATAATTAT
1 ATATAATTAT
1143000 ATAT--TTAT
1 ATATAATTAT
1143008 AT-TAATTAT
1 ATATAATTAT
1143017 ATATAATTA-
1 ATATAATTAT
1143026 ATATAA
1 ATATAA
1143032 AATTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 1 0.03
8 6 0.21
9 12 0.41
10 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATAATTAT
Found at i:1151693 original size:16 final size:16
Alignment explanation
Indices: 1151672--1151702 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1151662 AAGAAATTAC
1151672 TTCGTTATATCCGTAA
1 TTCGTTATATCCGTAA
1151688 TTCGTTATATCCGTA
1 TTCGTTATATCCGTA
1151703 TAAGAAATTC
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:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (16 bp):
TTCGTTATATCCGTAA
Found at i:1166988 original size:18 final size:18
Alignment explanation
Indices: 1166965--1167003 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1166955 TAAGTCTTAA
1166965 TTTAATTACATTATTTGG
1 TTTAATTACATTATTTGG
1166983 TTTAATTACATTATTTGG
1 TTTAATTACATTATTTGG
1167001 TTT
1 TTT
1167004 CAAAAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (18 bp):
TTTAATTACATTATTTGG
Found at i:1172976 original size:65 final size:65
Alignment explanation
Indices: 1172762--1173108 Score: 490
Period size: 65 Copynumber: 5.3 Consensus size: 65
1172752 ATTGAACCCA
* * * *
1172762 GGTTCAATATTTTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTACTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
* * *
1172827 GGTTCAAAATATTATGGCTGCGATATATTGAA-CCCCCTACCT-TTTTCCCATT-CTCATTGGAG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT--CTATTTT-TCATTGCT-ATTGGAG
1172889 AGGG
62 AGGG
1172893 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
* *
1172958 GGTTCAAAATATTATGGCCGCGATATATTGAA-CCCCCTACCT-TTTTCCAATT-CTCATTGGAG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT--CTATTTTTC-ATTGCT-ATTGGAG
1173020 AGGG
62 AGGG
*
1173024 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
1173089 GGTTCAAAATATTATGGCCG
1 GGTTCAAAATATTATGGCCG
1173109 NGTGTACCTT
Statistics
Matches: 253, Mismatches: 15, Indels: 28
0.85 0.05 0.09
Matches are distributed among these distances:
64 12 0.05
65 124 0.49
66 105 0.42
67 12 0.05
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (65 bp):
GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
Found at i:1172981 original size:131 final size:131
Alignment explanation
Indices: 1172762--1173108 Score: 640
Period size: 131 Copynumber: 2.6 Consensus size: 131
1172752 ATTGAACCCA
* * *
1172762 GGTTCAATATTTTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTACTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
* *
1172827 GGTTCAAAATATTATGGCTGCGATATATTGAACCCCCTACCTTTTTCCCATTCTCATTGGAGAGG
66 GGTTCAAAATATTATGGCCGCGATATATTGAACCCCCTACCTTTTTCCAATTCTCATTGGAGAGG
1172892 G
131 G
*
1172893 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
1172958 GGTTCAAAATATTATGGCCGCGATATATTGAACCCCCTACCTTTTTCCAATTCTCATTGGAGAGG
66 GGTTCAAAATATTATGGCCGCGATATATTGAACCCCCTACCTTTTTCCAATTCTCATTGGAGAGG
1173023 G
131 G
1173024 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
1 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
1173089 GGTTCAAAATATTATGGCCG
66 GGTTCAAAATATTATGGCCG
1173109 NGTGTACCTT
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 209 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (131 bp):
GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGGTATTGGAGAGGG
GGTTCAAAATATTATGGCCGCGATATATTGAACCCCCTACCTTTTTCCAATTCTCATTGGAGAGG
G
Found at i:1173789 original size:16 final size:15
Alignment explanation
Indices: 1173759--1173795 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1173749 AAAAAAAGTG
1173759 ACATT-TATTACAGC
1 ACATTGTATTACAGC
1173773 ACATTGTATTAACAGC
1 ACATTGTATT-ACAGC
1173789 ACATTGT
1 ACATTGT
1173796 GTTTACAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 4 0.19
16 12 0.57
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (15 bp):
ACATTGTATTACAGC
Found at i:1173803 original size:16 final size:16
Alignment explanation
Indices: 1173766--1173803 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1173756 GTGACATTTA
1173766 TTACAGCACATTGTAT
1 TTACAGCACATTGTAT
* *
1173782 TAACAGCACATTGTGT
1 TTACAGCACATTGTAT
1173798 TTACAG
1 TTACAG
1173804 TACGAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (16 bp):
TTACAGCACATTGTAT
Found at i:1174808 original size:49 final size:50
Alignment explanation
Indices: 1174751--1174860 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
1174741 TGAAAAAAAA
* * *
1174751 TTTCAAAGTGCATTATATTTTGGA-CAAAATCACACACTTTGAAA-TTTTT
1 TTTCAAAGTGCATTAAATTTTGGACCAAAATAACACAATTT-AAATTTTTT
* ** *
1174800 TTTCAAAGTGCCTTAAATTTTGGACCAAGTTAACCCAATTTAAATTTTTT
1 TTTCAAAGTGCATTAAATTTTGGACCAAAATAACACAATTTAAATTTTTT
1174850 TTTCAAAGTGC
1 TTTCAAAGTGC
1174861 GTTCTGAAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 25 0.48
50 27 0.52
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (50 bp):
TTTCAAAGTGCATTAAATTTTGGACCAAAATAACACAATTTAAATTTTTT
Found at i:1177313 original size:59 final size:59
Alignment explanation
Indices: 1177241--1177387 Score: 213
Period size: 59 Copynumber: 2.4 Consensus size: 59
1177231 GAAACCACAG
* *
1177241 TATGACAATAAAAGTGATTGTCTTTTAAATTATTTAATTGTGACATGGTTGTTGATGAA
1 TATGACAATAAAAGTGATTGTCCTTTAAATTATCTAATTGTGACATGGTTGTTGATGAA
**
1177300 TATGACAATAAAAGTTTTTGTCCTTTAAATTATCTAATTGTGACATGGTTGTTGATGAA
1 TATGACAATAAAAGTGATTGTCCTTTAAATTATCTAATTGTGACATGGTTGTTGATGAA
1177359 TATGAATTCAAAATAAAAGTGATTGTCCT
1 TATG-A--C--AATAAAAGTGATTGTCCT
1177388 CTATACCATT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
59 59 0.77
60 1 0.01
62 1 0.01
64 16 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (59 bp):
TATGACAATAAAAGTGATTGTCCTTTAAATTATCTAATTGTGACATGGTTGTTGATGAA
Found at i:1195211 original size:2 final size:2
Alignment explanation
Indices: 1195204--1195235 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1195194 ATTTCTAGTG
1195204 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1195236 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1215607 original size:2 final size:2
Alignment explanation
Indices: 1215600--1215625 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1215590 TTGCTTAATA
1215600 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
1215626 ACAACTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1215647 original size:4 final size:4
Alignment explanation
Indices: 1215638--1215687 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
1215628 AACTGACAAG
1215638 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1215686 TA
1 TA
1215688 CTCTTTATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:1217997 original size:2 final size:2
Alignment explanation
Indices: 1217990--1218017 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1217980 TTAAATAATA
1217990 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
1218018 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1218848 original size:16 final size:16
Alignment explanation
Indices: 1218824--1218855 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1218814 TATGCGGGAC
*
1218824 ATACTAAAGACCTGAA
1 ATACGAAAGACCTGAA
1218840 ATACGAAAGACCTGAA
1 ATACGAAAGACCTGAA
1218856 TGTCATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
ATACGAAAGACCTGAA
Found at i:1225283 original size:11 final size:11
Alignment explanation
Indices: 1225246--1225340 Score: 162
Period size: 11 Copynumber: 9.0 Consensus size: 11
1225236 AACGCCTTTT
1225246 TACCCCAATGA
1 TACCCCAATGA
1225257 -ACCCCAATGA
1 TACCCCAATGA
1225267 -ACCCCAATGA
1 TACCCCAATGA
1225277 TACCCCAATGA
1 TACCCCAATGA
1225288 -ACCCCAATGA
1 TACCCCAATGA
1225298 TACCCCAATGA
1 TACCCCAATGA
1225309 TACCCCAATGA
1 TACCCCAATGA
1225320 -ACCCCAATGA
1 TACCCCAATGA
1225330 TACCCCAATGA
1 TACCCCAATGA
1225341 ACTCGTAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
10 40 0.49
11 41 0.51
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:1225283 original size:21 final size:21
Alignment explanation
Indices: 1225246--1225342 Score: 162
Period size: 21 Copynumber: 4.6 Consensus size: 21
1225236 AACGCCTTTT
1225246 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
1225267 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGA-ACCCCAATGA
1225288 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGA-ACCCCAATGA
1225309 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
1225330 TACCCCAATGAAC
1 TACCCCAATGAAC
1225343 TCGTAAATAC
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.14
21 54 0.73
22 10 0.14
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.14
Consensus pattern (21 bp):
TACCCCAATGAACCCCAATGA
Found at i:1225308 original size:32 final size:32
Alignment explanation
Indices: 1225246--1225340 Score: 183
Period size: 32 Copynumber: 3.0 Consensus size: 32
1225236 AACGCCTTTT
1225246 TACCCCAATGAACCCCAATGA-ACCCCAATGA
1 TACCCCAATGAACCCCAATGATACCCCAATGA
1225277 TACCCCAATGAACCCCAATGATACCCCAATGA
1 TACCCCAATGAACCCCAATGATACCCCAATGA
1225309 TACCCCAATGAACCCCAATGATACCCCAATGA
1 TACCCCAATGAACCCCAATGATACCCCAATGA
1225341 ACTCGTAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 21 0.33
32 42 0.67
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (32 bp):
TACCCCAATGAACCCCAATGATACCCCAATGA
Found at i:1234719 original size:2 final size:2
Alignment explanation
Indices: 1234712--1234764 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1234702 AGGGACCGGG
*
1234712 CT CT CT CT CT CT CT CT TT 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
1234754 CT CT CT CT CT C
1 CT CT CT CT CT C
1234765 AGGATAGGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1237640 original size:21 final size:21
Alignment explanation
Indices: 1237615--1237691 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
1237605 ATGTTGTGTT
1237615 CACCGCATATAATGTTAGAA-
1 CACCGCATATAATGTTAGAAG
1237635 CGACCGCATATAATGTTAGAAG
1 C-ACCGCATATAATGTTAGAAG
* *
1237657 CACCCCATATAATGTTGGAAG
1 CACCGCATATAATGTTAGAAG
*
1237678 CACCTCATATAATG
1 CACCGCATATAATG
1237692 ATAAATGTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (21 bp):
CACCGCATATAATGTTAGAAG
Found at i:1239517 original size:2 final size:2
Alignment explanation
Indices: 1239510--1239579 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
1239500 TTCAGTTTTC
*
1239510 AG AG AG AG AG AG AA 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
1239552 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
1239580 TGTGTGTGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1240089 original size:2 final size:2
Alignment explanation
Indices: 1240084--1240135 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1240074 GGCCGCCCCC
1240084 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
1240126 CT CT CT CT CT
1 CT CT CT CT CT
1240136 AATTTATACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1241738 original size:21 final size:21
Alignment explanation
Indices: 1241722--1241902 Score: 271
Period size: 21 Copynumber: 8.7 Consensus size: 21
1241712 GATATCATTT
*
1241722 GGTATCATAGGGGTATCATTAGG
1 GGTATCATTGGGGT-TCATT-GG
*
1241745 TGTAT--TT-GGGTATCATTGG
1 GGTATCATTGGGGT-TCATTGG
*
1241764 GGTAACATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
*
1241785 GGAATCATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
1241806 GGTATCATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
1241827 GGTATCATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
1241848 GGTATCATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
1241869 GGTATCATTGGGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
1241890 GGT-TCATTGGGGT
1 GGTATCATTGGGGT
1241903 AAAAAGACGC
Statistics
Matches: 148, Mismatches: 7, Indels: 9
0.90 0.04 0.05
Matches are distributed among these distances:
19 5 0.03
20 20 0.14
21 115 0.78
22 4 0.03
23 4 0.03
ACGTcount: A:0.17, C:0.09, G:0.38, T:0.37
Consensus pattern (21 bp):
GGTATCATTGGGGTTCATTGG
Found at i:1241749 original size:12 final size:11
Alignment explanation
Indices: 1241722--1241903 Score: 123
Period size: 11 Copynumber: 17.4 Consensus size: 11
1241712 GATATCATTT
1241722 GGTATCATAGG
1 GGTATCATAGG
1241733 GGTATCATTAGG
1 GGTATCA-TAGG
* *
1241745 TGTAT--T-TG
1 GGTATCATAGG
*
1241753 GGTATCATTGG
1 GGTATCATAGG
* *
1241764 GGTAACATTGG
1 GGTATCATAGG
*
1241775 GGT-TCATTGG
1 GGTATCATAGG
* *
1241785 GGAATCATTGG
1 GGTATCATAGG
*
1241796 GGT-TCATTGG
1 GGTATCATAGG
*
1241806 GGTATCATTGG
1 GGTATCATAGG
*
1241817 GGT-TCATTGG
1 GGTATCATAGG
*
1241827 GGTATCATTGG
1 GGTATCATAGG
*
1241838 GGT-TCATTGG
1 GGTATCATAGG
*
1241848 GGTATCATTGG
1 GGTATCATAGG
*
1241859 GGT-TCATTGG
1 GGTATCATAGG
*
1241869 GGTATCATTGG
1 GGTATCATAGG
*
1241880 GGT-TCATTGG
1 GGTATCATAGG
*
1241890 GGT-TCATTGG
1 GGTATCATAGG
1241900 GGTA
1 GGTA
1241904 AAAAGACGCA
Statistics
Matches: 153, Mismatches: 8, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
8 5 0.03
9 1 0.01
10 69 0.45
11 70 0.46
12 8 0.05
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (11 bp):
GGTATCATAGG
Found at i:1241777 original size:42 final size:39
Alignment explanation
Indices: 1241690--1241902 Score: 214
Period size: 42 Copynumber: 5.1 Consensus size: 39
1241680 AAGTTCATAA
* * *
1241690 GGGTATCATTGGGGTTTTTTGGGATATCATT-TGGTATCATAG
1 GGGT-TCATTGGGG-TATTTGGG-T-TCATTGGGGTATCATTG
* *
1241732 GGGTATCATTAGGTGTATTTGGGTATCATTGGGGTAACATTG
1 GGGT-TCATT-GGGGTATTTGGGT-TCATTGGGGTATCATTG
*
1241774 GGGTTCATTGGGGAATCATTGGGGTTCATTGGGGTATCATTG
1 GGGTTCATTGGGG--T-ATTTGGGTTCATTGGGGTATCATTG
1241816 GGGTTCATTGGGGTATCATTGGGGTTCATTGGGGTATCATTG
1 GGGTTCATTGGGGTAT--TT-GGGTTCATTGGGGTATCATTG
1241858 GGGTTCATTGGGGTATCATTGGGGTTCATTGGGGT-TCATTG
1 GGGTTCATTGGGGTAT--TT-GGGTTCATTGGGGTATCATTG
1241899 GGGT
1 GGGT
1241903 AAAAAGACGC
Statistics
Matches: 154, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
39 2 0.01
40 4 0.03
41 23 0.15
42 115 0.75
43 10 0.06
ACGTcount: A:0.16, C:0.08, G:0.37, T:0.38
Consensus pattern (39 bp):
GGGTTCATTGGGGTATTTGGGTTCATTGGGGTATCATTG
Found at i:1246956 original size:101 final size:101
Alignment explanation
Indices: 1246781--1247079 Score: 517
Period size: 101 Copynumber: 3.0 Consensus size: 101
1246771 GCTGGTCCAG
* *
1246781 GCGGGCAACCTAATTAACCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAG
1 GCGGGCAACCTAATTAATCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAA
*
1246846 TTATAGTTTACCAAAACTGAGTGATTAACGGAATTT
66 TTATAGTTTACCAAAACTGAGTGATTAACGCAATTT
1246882 GCGGGCAACCTAATTAATCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAA
1 GCGGGCAACCTAATTAATCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAA
1246947 TTATAGTTTACCAAAACTGAGTGATTAACGCAATTT
66 TTATAGTTTACCAAAACTGAGTGATTAACGCAATTT
* * * *
1246983 GCGGGCAACCTAATTAATAGTTTATAAATATATTGCGTGTGAATATAAAATGAACGTAAGTGCAA
1 GCGGGCAACCTAATTAATCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAA
* *
1247048 TTACAGTTTACCAAAACTGAGTGAATAACGCA
66 TTATAGTTTACCAAAACTGAGTGATTAACGCA
1247080 TCTTGTATGT
Statistics
Matches: 189, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 189 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (101 bp):
GCGGGCAACCTAATTAATCGTTTATAAATATATTGCGTGTGAACATAAAATGAAAGTAAGCGCAA
TTATAGTTTACCAAAACTGAGTGATTAACGCAATTT
Found at i:1247003 original size:50 final size:50
Alignment explanation
Indices: 1246848--1247006 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 50
1246838 AAGCGCAGTT
*
1246848 ATAGTTTACCAAAACTGAGTGATTAACGGAATTTGCGGGCAACCTAATTA
1 ATAGTTTACCAAAACTGAGTGATTAACGCAATTTGCGGGCAACCTAATTA
* ** * * * ** ** *** *
1246898 ATCGTTTATAAATATATTGCGTG-TGAACATAAAATGAAAGTAAGCGC-AATT-
1 ATAGTTTACCAA-A-ACTGAGTGATTAACGCAATTTGCGGGCAA-C-CTAATTA
1246949 ATAGTTTACCAAAACTGAGTGATTAACGCAATTTGCGGGCAACCTAATTA
1 ATAGTTTACCAAAACTGAGTGATTAACGCAATTTGCGGGCAACCTAATTA
1246999 ATAGTTTA
1 ATAGTTTA
1247007 TAAATATATT
Statistics
Matches: 74, Mismatches: 28, Indels: 14
0.64 0.24 0.12
Matches are distributed among these distances:
48 1 0.01
49 11 0.15
50 29 0.39
51 21 0.28
52 11 0.15
53 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (50 bp):
ATAGTTTACCAAAACTGAGTGATTAACGCAATTTGCGGGCAACCTAATTA
Found at i:1247407 original size:33 final size:33
Alignment explanation
Indices: 1247361--1247512 Score: 121
Period size: 33 Copynumber: 4.6 Consensus size: 33
1247351 ATCTAAAACA
*
1247361 AAATAA-AAACCGACTAGCATCAATGCCAT-TT
1 AAATAACAAACCGACCAGCATCAATGCCATCTT
* * *
1247392 AAAGTATCAAACCGACCAGTATCAATGTCATCTT
1 AAA-TAACAAACCGACCAGCATCAATGCCATCTT
* * *
1247426 AAATAACAAACCGACCA-CTATCAGTGCCAACTA
1 AAATAACAAACCGACCAGC-ATCAATGCCATCTT
* * * * * *
1247459 AAAAAACAAACCAACCAGTACCAGTGCCATCTG
1 AAATAACAAACCGACCAGCATCAATGCCATCTT
* * *
1247492 AGATAGCAAACCGAACAGCAT
1 AAATAACAAACCGACCAGCAT
1247513 ATTAAGTGTA
Statistics
Matches: 93, Mismatches: 23, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
31 3 0.03
32 2 0.02
33 83 0.89
34 5 0.05
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (33 bp):
AAATAACAAACCGACCAGCATCAATGCCATCTT
Found at i:1247833 original size:9 final size:9
Alignment explanation
Indices: 1247821--1247888 Score: 109
Period size: 9 Copynumber: 7.6 Consensus size: 9
1247811 AAATGCGGGA
1247821 AATTGATAT
1 AATTGATAT
*
1247830 AATTGGTAT
1 AATTGATAT
1247839 AATTGATAT
1 AATTGATAT
* *
1247848 TATGGATAT
1 AATTGATAT
1247857 AATTGATAT
1 AATTGATAT
1247866 AATTGATAT
1 AATTGATAT
1247875 AATTGATAT
1 AATTGATAT
1247884 AATTG
1 AATTG
1247889 GTCTAAGGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (9 bp):
AATTGATAT
Found at i:1253699 original size:16 final size:17
Alignment explanation
Indices: 1253678--1253717 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1253668 ATTTACTTCC
*
1253678 TTATATCCT-TAGTTCG
1 TTATATCCTGTAATTCG
1253694 TTATAT-CTGTAATTCG
1 TTATATCCTGTAATTCG
1253710 TTATATCC
1 TTATATCC
1253718 GTATTACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (17 bp):
TTATATCCTGTAATTCG
Found at i:1259262 original size:13 final size:12
Alignment explanation
Indices: 1259244--1259278 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1259234 TAACTTAACC
1259244 CTGGGTTTACTTT
1 CTGGGTTTAC-TT
1259257 CTGGGTTTAC-T
1 CTGGGTTTACTT
1259268 CTGGGTTTACT
1 CTGGGTTTACT
1259279 AGAGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (12 bp):
CTGGGTTTACTT
Found at i:1259499 original size:11 final size:11
Alignment explanation
Indices: 1259483--1259525 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1259473 AAAATTCTCG
1259483 AGTAAACCCAA
1 AGTAAACCCAA
**
1259494 AGTAAACCCCCG
1 AGTAAA-CCCAA
1259506 AGTAAACCCAA
1 AGTAAACCCAA
1259517 AGTAAACCC
1 AGTAAACCC
1259526 CGAGTGGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.47, C:0.33, G:0.12, T:0.09
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:1259536 original size:22 final size:23
Alignment explanation
Indices: 1259481--1259530 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1259471 AAAAAATTCT
1259481 CGAGTAAACCCAAAGTAAACCCC
1 CGAGTAAACCCAAAGTAAACCCC
1259504 CGAGTAAACCCAAAGTAAA-CCC
1 CGAGTAAACCCAAAGTAAACCCC
1259526 CGAGT
1 CGAGT
1259531 GGACCCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.42, C:0.32, G:0.16, T:0.10
Consensus pattern (23 bp):
CGAGTAAACCCAAAGTAAACCCC
Found at i:1262761 original size:3 final size:3
Alignment explanation
Indices: 1262753--1262788 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1262743 TCATTATCCC
*
1262753 CAT CAT CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1262789 TATATACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:1262771 original size:12 final size:12
Alignment explanation
Indices: 1262729--1262787 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
1262719 ATATTGAATA
* *
1262729 CATCATTATCCC
1 CATCATCATCAC
* *
1262741 CATCATTATCCC
1 CATCATCATCAC
1262753 CATCATCATCAC
1 CATCATCATCAC
*
1262765 CATCATCATCAT
1 CATCATCATCAC
1262777 CATCATCATCA
1 CATCATCATCA
1262788 TTATATACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.31
Consensus pattern (12 bp):
CATCATCATCAC
Found at i:1268513 original size:89 final size:89
Alignment explanation
Indices: 1268357--1268530 Score: 287
Period size: 89 Copynumber: 2.0 Consensus size: 89
1268347 TAACCCCGTA
* *
1268357 TATTAGATTTCCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGATCTGTGA
1 TATTAGATTTCCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGAACCGTGA
1268422 ATGTGTGACTGGGGCATTAACGAT
66 ATGTGTGACTGGGGCATTAACGAT
* * *
1268446 TATTTGATTTTCCGGTGTTAACCGTGGAAAATATTCCGTAGTAGAACCGT-GGAGTTGAACCGTG
1 TATTAGATTTCCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACC-TAGGAGTTGAACCGTG
1268510 AATGTGTGACTGGGGCATTAA
65 AATGTGTGACTGGGGCATTAA
1268531 GCAGAGAAGT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 78 0.99
90 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (89 bp):
TATTAGATTTCCCGGTGTCAACCGTGGAAAATATTCCGTAGTAGAACCTAGGAGTTGAACCGTGA
ATGTGTGACTGGGGCATTAACGAT
Found at i:1269739 original size:26 final size:25
Alignment explanation
Indices: 1269710--1269760 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1269700 TTATTTTTTA
*
1269710 CAATCCTAACCTATCGTATCGTGTAT
1 CAATCCTAACCTATCGT-GCGTGTAT
* *
1269736 CAATCCTATCGTATCGTGCGTGTAT
1 CAATCCTAACCTATCGTGCGTGTAT
1269761 ACTGTTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (25 bp):
CAATCCTAACCTATCGTGCGTGTAT
Found at i:1269801 original size:42 final size:42
Alignment explanation
Indices: 1269737--1269840 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
1269727 ATCGTGTATC
*
1269737 AATCCTATCGTATCGTGCGTGTATACTGTTCTAACGTGCGTT
1 AATCCTATCCTATCGTGCGTGTATACTGTTCTAACGTGCGTT
* *
1269779 AATCCTATCCTATCGTGGGTGTATACTGTTCTATCGTGCGTT
1 AATCCTATCCTATCGTGCGTGTATACTGTTCTAACGTGCGTT
* * *
1269821 AATGCTATTCTATCTTGCGT
1 AATCCTATCCTATCGTGCGT
1269841 TAATCCCATC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.40
Consensus pattern (42 bp):
AATCCTATCCTATCGTGCGTGTATACTGTTCTAACGTGCGTT
Found at i:1269831 original size:21 final size:21
Alignment explanation
Indices: 1269747--1269844 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1269737 AATCCTATCG
*
1269747 TATCGTGCGTGT-ATACTGTTC
1 TATCGTGCGT-TAATACTATTC
* * *
1269768 TAACGTGCGTTAATCCTATCC
1 TATCGTGCGTTAATACTATTC
* *
1269789 TATCGTGGGTGT-ATACTGTTC
1 TATCGTGCGT-TAATACTATTC
*
1269810 TATCGTGCGTTAATGCTATTC
1 TATCGTGCGTTAATACTATTC
*
1269831 TATCTTGCGTTAAT
1 TATCGTGCGTTAAT
1269845 CCCATCAGGT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.03
21 58 0.95
22 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
TATCGTGCGTTAATACTATTC
Found at i:1270546 original size:21 final size:21
Alignment explanation
Indices: 1270522--1270574 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1270512 CAATCCTATC
1270522 CTATCGTGCGTGTATACTGTT
1 CTATCGTGCGTGTATACTGTT
*
1270543 CTATCGTGCGTGTATATTGTT
1 CTATCGTGCGTGTATACTGTT
*
1270564 CTTTCGTGCGT
1 CTATCGTGCGT
1270575 TAATGCTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (21 bp):
CTATCGTGCGTGTATACTGTT
Found at i:1271029 original size:14 final size:14
Alignment explanation
Indices: 1271010--1271038 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1271000 TGAAACATTT
1271010 CAGACCAGATACTA
1 CAGACCAGATACTA
1271024 CAGACCAGATACTA
1 CAGACCAGATACTA
1271038 C
1 C
1271039 TGTAGTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (14 bp):
CAGACCAGATACTA
Found at i:1277403 original size:23 final size:23
Alignment explanation
Indices: 1277377--1277425 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1277367 AATATTTGTC
*
1277377 AATCTGTGTCATTATAACTGCAT
1 AATCTGTATCATTATAACTGCAT
*
1277400 AATCTGTATCATTATAAGTGCAT
1 AATCTGTATCATTATAACTGCAT
1277423 AAT
1 AAT
1277426 TACAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (23 bp):
AATCTGTATCATTATAACTGCAT
Found at i:1278355 original size:14 final size:14
Alignment explanation
Indices: 1278336--1278384 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1278326 TTTCTGCTAC
*
1278336 AAAAACCCAAAAAA
1 AAAAACCAAAAAAA
1278350 AAAAA-CAAAAAAA
1 AAAAACCAAAAAAA
*
1278363 AAAAAACAAAAAAA
1 AAAAACCAAAAAAA
1278377 AAACAACC
1 AAA-AACC
1278385 CCCCCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 12 0.39
14 16 0.52
15 3 0.10
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACCAAAAAAA
Found at i:1278360 original size:13 final size:14
Alignment explanation
Indices: 1278344--1278379 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1278334 ACAAAAACCC
1278344 AAAAAAAAAAACAA
1 AAAAAAAAAAACAA
1278358 AAAAAAAAAAACAA
1 AAAAAAAAAAACAA
1278372 AAAAAAAA
1 AAAAAAAA
1278380 CAACCCCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAACAA
Found at i:1278397 original size:1 final size:1
Alignment explanation
Indices: 1278344--1278379 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
1278334 ACAAAAACCC
* *
1278344 AAAAAAAAAAACAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1278380 CAACCCCCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1278411 original size:18 final size:18
Alignment explanation
Indices: 1278369--1278411 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1278359 AAAAAAAAAA
1278369 CAAAAAAAAAACAACCCC
1 CAAAAAAAAAACAACCCC
** *
1278387 CCCAAAAAAAATAACCCC
1 CAAAAAAAAAACAACCCC
1278405 CAAAAAA
1 CAAAAAA
1278412 CCAAAAAACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.33, G:0.00, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAACAACCCC
Found at i:1278428 original size:16 final size:16
Alignment explanation
Indices: 1278405--1278442 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1278395 AAATAACCCC
1278405 CAAA-AAACCAAAAAA
1 CAAACAAACCAAAAAA
1278420 CAAACAAACCAAAAAA
1 CAAACAAACCAAAAAA
1278436 -AAACAAA
1 CAAACAAA
1278443 AAAAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAACAAACCAAAAAA
Found at i:1278436 original size:19 final size:19
Alignment explanation
Indices: 1278414--1278452 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1278404 CCAAAAAACC
* *
1278414 AAAAAACAAACAAACCAAA
1 AAAAAACAAAAAAAACAAA
1278433 AAAAAACAAAAAAAACAAA
1 AAAAAACAAAAAAAACAAA
1278452 A
1 A
1278453 GCCAACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAACAAA
Found at i:1278443 original size:9 final size:9
Alignment explanation
Indices: 1278414--1278452 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1278404 CCAAAAAACC
1278414 AAAAAACAA
1 AAAAAACAA
* *
1278423 ACAAACCAAA
1 AAAAAAC-AA
1278433 AAAAAACAA
1 AAAAAACAA
1278442 AAAAAACAA
1 AAAAAACAA
1278451 AA
1 AA
1278453 GCCAACCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:1278675 original size:21 final size:21
Alignment explanation
Indices: 1278651--1278722 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1278641 ATAATTATTT
1278651 TCTGACAAGTTGACATAAAAA
1 TCTGACAAGTTGACATAAAAA
**
1278672 TCTGACAAGTTGACATAACTA
1 TCTGACAAGTTGACATAAAAA
* *
1278693 TCT-AAAAGTCT-ACATAAAGA
1 TCTGACAAGT-TGACATAAAAA
1278713 TCTGACAAGT
1 TCTGACAAGT
1278723 CAACATAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (21 bp):
TCTGACAAGTTGACATAAAAA
Found at i:1281700 original size:12 final size:13
Alignment explanation
Indices: 1281685--1281714 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1281675 AGAAAAGGAA
1281685 CAAAAAAAAAA-C
1 CAAAAAAAAAACC
1281697 CAAAAAAAAAACC
1 CAAAAAAAAAACC
1281710 CAAAA
1 CAAAA
1281715 CAAACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAACC
Done.