Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold503
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 149721
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.23
Warning! 42174 characters in sequence are not A, C, G, or T
Found at i:1286 original size:44 final size:44
Alignment explanation
Indices: 1229--1405 Score: 302
Period size: 44 Copynumber: 4.0 Consensus size: 44
1219 GTATGGGAAC
*
1229 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
*
1273 ATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1317 ACAAGATCTGCTAT-TATTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCT-TTGATCTACTTCACGCCAATACATGAAG
* *
1361 ACAAAATCTGCTATCATTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1405 A
1 A
1406 AAAAATACTA
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.01
44 125 0.99
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (44 bp):
ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
Found at i:1295 original size:117 final size:118
Alignment explanation
Indices: 1089--1325 Score: 350
Period size: 117 Copynumber: 2.0 Consensus size: 118
1079 TACAATTTTA
* * * * * *
1089 TACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGATACATGA
1 TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
* * *
1154 AGACAATATTTGCTTTCTTCGATCTACTT-CGCCAATACATGAAGACAAGATC
66 AGACAAGATCTGCTATCTTCGATCTACTTACGCCAATACATGAAGACAAGATC
*
1206 TACTTCACCACCAGTATGGGAACACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGA
1 TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
* *
1271 AGATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
66 AGACAAGATCTGCTATCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATC
1325 T
1 T
1326 GCTATTATTG
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 82 0.77
119 24 0.23
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (118 bp):
TACTTCACCACCAGTATGGGAACACAAGATCTGCTACCTTCGATCTACTTCACGCCAATACATGA
AGACAAGATCTGCTATCTTCGATCTACTTACGCCAATACATGAAGACAAGATC
Found at i:1633 original size:87 final size:89
Alignment explanation
Indices: 1513--1673 Score: 240
Period size: 87 Copynumber: 1.8 Consensus size: 89
1503 TATTAAGCCC
*
1513 TAAACCTTATTTAATATATAAATTAAAAAACACTAATCAATCTAAATCC-TAAACTCTAACCCTA
1 TAAACCTTATTTAATATATAAATTAAAAAACACTAATCAATCTAAA-CCTTAAACCCTAA-CCTA
1577 AC-CCGAATCCCTAACCCCTAACACT
64 ACACCGAATCCCTAACCCCTAACACT
* * *
1602 TAAACCTTATTT-A-ATATAAATTAAAACACACTAATTAATCTAAACCTTAAACCCTAACCTGAC
1 TAAACCTTATTTAATATATAAATTAAAAAACACTAATCAATCTAAACCTTAAACCCTAACCTAAC
1665 ACCGAATCC
66 ACCGAATCC
1674 ATAAGCCTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
86 7 0.11
87 46 0.70
88 1 0.02
89 12 0.18
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (89 bp):
TAAACCTTATTTAATATATAAATTAAAAAACACTAATCAATCTAAACCTTAAACCCTAACCTAAC
ACCGAATCCCTAACCCCTAACACT
Found at i:1727 original size:21 final size:21
Alignment explanation
Indices: 1687--1727 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1677 AGCCTTAAAT
* * *
1687 CCCTAACTCTTAATCTCTAAC
1 CCCTAACCCTTAACCCCTAAC
1708 CCCTAACCCTTAACCCCTAA
1 CCCTAACCCTTAACCCCTAA
1728 ATCACAACCC
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:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACCCTTAACCCCTAAC
Found at i:1766 original size:14 final size:15
Alignment explanation
Indices: 1747--1779 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1737 CTTAAACCAA
1747 AATCCCTAATT-CAT
1 AATCCCTAATTCCAT
1761 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1776 AATC
1 AATC
1780 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:2286 original size:41 final size:41
Alignment explanation
Indices: 2222--2505 Score: 415
Period size: 41 Copynumber: 6.9 Consensus size: 41
2212 TCAAAAACGG
* *
2222 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * * * **
2263 GCATTAGTGGCACTTCTTCAAAAACACCGCTAAAGGTCTAA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * * *
2304 GCATTAGCGGAGCTTCTTCAAAAACGCCACTAAAGGTCTGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
*
2345 GCATTAGTGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
*
2386 GCATTAGCGGCGCTTCGTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
2427 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * *
2468 GCGTTAGCGGCGCTTCTTCAAAAACTCCACTAAAGGCC
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
2506 TCAAAAACTC
Statistics
Matches: 218, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 218 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:2601 original size:39 final size:39
Alignment explanation
Indices: 2547--2675 Score: 161
Period size: 40 Copynumber: 3.3 Consensus size: 39
2537 TAGGCTTGTT
* * *
2547 GCGGCGCTTTTCAAAAAACACCGCTAATGCTT-ATTTTTT
1 GCGGCG-TTTTCAAAAAGCGCCGCTAATGCTTGATTTTTA
**
2586 GCGGCGTTTTCCAAAAAGCGCCGCTAATGCTTGACCTTTA
1 GCGGCGTTTT-CAAAAAGCGCCGCTAATGCTTGATTTTTA
*
2626 GCGGCGTTTTTAGAAAAGCGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTTCA-AAAAGCGCCGCTAATGCTTGATTTTTA
*
2666 GTGGCGTTTT
1 GCGGCGTTTT
2676 TTGTCCAAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 4 0.05
39 26 0.33
40 48 0.62
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (39 bp):
GCGGCGTTTTCAAAAAGCGCCGCTAATGCTTGATTTTTA
Found at i:3429 original size:20 final size:20
Alignment explanation
Indices: 3392--3434 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3382 AAAATAAACA
* **
3392 TATAATTATTTATTTAATAT
1 TATAATTATTCAAATAATAT
3412 TATAATTATTCAAATAATAT
1 TATAATTATTCAAATAATAT
3432 TAT
1 TAT
3435 TGAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTATTCAAATAATAT
Found at i:32581 original size:27 final size:28
Alignment explanation
Indices: 32529--32581 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
32519 GGCTTGTCTC
* **
32529 TAATTTGGTCACCCCAATTTTATTTTTT
1 TAATTTGGTCACCCAAAAATTATTTTTT
32557 TAATTTGGTCACCCAAAAATT-TTTT
1 TAATTTGGTCACCCAAAAATTATTTT
32582 ATCAAATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (28 bp):
TAATTTGGTCACCCAAAAATTATTTTTT
Found at i:33241 original size:22 final size:22
Alignment explanation
Indices: 33216--33292 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
33206 CCAAAATATT
33216 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
33238 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
33262 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
33284 ATCTCCTAA
1 ATCTCCTAA
33293 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:33270 original size:46 final size:46
Alignment explanation
Indices: 33203--33297 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
33193 ACAAAGATAG
33203 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
33249 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
33295 AAA
1 AAA
33298 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:37855 original size:49 final size:49
Alignment explanation
Indices: 37779--37877 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
37769 GATAGAAACC
37779 AAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAAGAAA
1 AAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAAGAAA
37828 AAAATATTATCTCCCTAAACTTT-GCATCTAATCTCCTAATTAAAAGAAA
1 AAAATATTATCT-CCTAAACTTTAGCATCTAATCTCCTAATTAAAAGAAA
37877 A
1 A
37878 TAGATATACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 39 0.80
50 10 0.20
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.32
Consensus pattern (49 bp):
AAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAAGAAA
Found at i:42007 original size:43 final size:42
Alignment explanation
Indices: 41899--42009 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 42
41889 ACCGTTACTC
* *
41899 GGTGGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATAT
1 GGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAGTGATAT
* *
41941 GG-GGAATCAGCACATAACAACCCCTTTCACAATCAAG-GATAT
1 GGTGGAATCAGCACTTAGCAACCCCTTT-ACAATC-AGTGATAT
*
41983 GGTGGAATCAGCACTTAGCTACCCCTT
1 GGTGGAATCAGCACTTAGCAACCCCTT
42010 GGGGAATTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
40 2 0.03
41 20 0.34
42 13 0.22
43 23 0.40
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
GGTGGAATCAGCACTTAGCAACCCCTTTACAATCAGTGATAT
Found at i:42069 original size:41 final size:41
Alignment explanation
Indices: 42012--42199 Score: 243
Period size: 41 Copynumber: 4.6 Consensus size: 41
42002 TACCCCTTGG
* * *
42012 GGAATTTGCACTTAGCAACCCCTTTTTTATCAGAGTTTCGA
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCGA
* * *
42053 GGAATCTGCACTTAGCAACCTCTTTTTGATTAGAGTTTCGA
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCGA
* *
42094 GGAATCTGTACTTAGCAACCCCTTTTTGATCAGTGATTCGA
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCGA
* * *
42135 GGAATCTGCACTTAACAACCCCTTTTTAATCAGTGATTCTG-
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTC-GA
* *
42176 GGAATCTACACTTAGAAACCCCTT
1 GGAATCTGCACTTAGCAACCCCTT
42200 ACATTCAATG
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 130 0.99
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (41 bp):
GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCGA
Found at i:44014 original size:6 final size:6
Alignment explanation
Indices: 43977--44002 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43967 TTTCGTCCTT
43977 TACAGA TACAGA TACAGA TACAGA TA
1 TACAGA TACAGA TACAGA TACAGA TA
44003 TAAATACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
TACAGA
Found at i:44399 original size:19 final size:18
Alignment explanation
Indices: 44361--44396 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44351 TCACATAAAT
44361 TTTAGGGTTAAATTAGCC
1 TTTAGGGTTAAATTAGCC
*
44379 TTTAGGGTTTAATTAGCC
1 TTTAGGGTTAAATTAGCC
44397 CTTACCGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (18 bp):
TTTAGGGTTAAATTAGCC
Found at i:47956 original size:23 final size:24
Alignment explanation
Indices: 47930--47982 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
47920 GTGCCGCATT
47930 TTGGTAC-AGCATGGTGTGTAG-GG
1 TTGGTACGAG-ATGGTGTGTAGAGG
47953 TTGG-ACGGAGATGGTGTGTAGAGG
1 TTGGTAC-GAGATGGTGTGTAGAGG
47977 TTGGTA
1 TTGGTA
47983 GGTAGGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.08
23 15 0.58
24 8 0.31
25 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.45, T:0.30
Consensus pattern (24 bp):
TTGGTACGAGATGGTGTGTAGAGG
Found at i:50196 original size:14 final size:15
Alignment explanation
Indices: 50177--50205 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50167 GCAAAACCTC
50177 TTTATTTTT-TATTT
1 TTTATTTTTATATTT
50191 TTTATTTTTATATTT
1 TTTATTTTTATATTT
50206 CAATCCACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTTTATATTT
Found at i:64029 original size:71 final size:72
Alignment explanation
Indices: 63943--64085 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
63933 TAAAAATTAA
63943 TGTTTTTTCATATTTTAAATAAAAAACATAAAAATCTATAATATTTTTAAAAATAAAGAATTTTG
1 TGTTTTTTCATATTTTAAATAAAAAACATAAAAATCTATAATATTTTTAAAAATAAAGAATTTTG
64008 AAATAAT
66 AAATAAT
64015 TGTTTTTTCA-ATTTTAAATAAAAAACATAAAAATCTATAATATTTTTAAAAATAAAGAATTTTG
1 TGTTTTTTCATATTTTAAATAAAAAACATAAAAATCTATAATATTTTTAAAAATAAAGAATTTTG
64079 AAATAAT
66 AAATAAT
64086 AAAAACTCTT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 61 0.86
72 10 0.14
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (72 bp):
TGTTTTTTCATATTTTAAATAAAAAACATAAAAATCTATAATATTTTTAAAAATAAAGAATTTTG
AAATAAT
Found at i:65008 original size:18 final size:17
Alignment explanation
Indices: 64982--65029 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
64972 TAACAATGAA
*
64982 TTTTGAAATTTTTTATAT
1 TTTTAAAATTTTTT-TAT
65000 TTTTAAAATTATTTTTAT
1 TTTTAAAATT-TTTTTAT
*
65018 TTTTTAAATTTT
1 TTTTAAAATTTT
65030 AATGAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 21 0.78
19 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTAAAATTTTTTTAT
Found at i:66736 original size:66 final size:66
Alignment explanation
Indices: 66650--66830 Score: 188
Period size: 66 Copynumber: 2.7 Consensus size: 66
66640 GAGAAAGATC
* * * * *
66650 AAATATCG-GATCTTCTCAAGCTCTTGAACGAGATATCATGTCTTCTCAATCCCAAGCTCTTGAA
1 AAATATCGAG-TCTTCCCAAGCTCTTGAACGAGATATCATGTCTTCTCAATCCAAAGATCCTAAA
66714 C-
65 CT
* * * *
66715 ACAATATCGAGTCTTCCCAAGCTCCTAAACGATATATCAAT-TCTTCTTAATCCAAAGATCCTAA
1 A-AATATCGAGTCTTCCCAAGCTCTTGAACGAGATATC-ATGTCTTCTCAATCCAAAGATCCTAA
66779 ACT
64 ACT
* * * * *
66782 AAATATCAAGTCTTCCAAAACTCTTGAACGAGATATCAAGCCTTCTCAA
1 AAATATCGAGTCTTCCCAAGCTCTTGAACGAGATATCATGTCTTCTCAA
66831 GTTCCTGAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
65 2 0.02
66 87 0.94
67 4 0.04
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.29
Consensus pattern (66 bp):
AAATATCGAGTCTTCCCAAGCTCTTGAACGAGATATCATGTCTTCTCAATCCAAAGATCCTAAAC
T
Found at i:67672 original size:25 final size:25
Alignment explanation
Indices: 67642--67732 Score: 173
Period size: 25 Copynumber: 3.6 Consensus size: 25
67632 ATTATTATTT
67642 TATATTTACGAGTCAAATATAGTAG
1 TATATTTACGAGTCAAATATAGTAG
67667 TATATTTACGAGTCAAATATAGTAG
1 TATATTTACGAGTCAAATATAGTAG
67692 TATATTTACGAGTCAAATATAGTAG
1 TATATTTACGAGTCAAATATAGTAG
*
67717 TATATTTACAAGTCAA
1 TATATTTACGAGTCAA
67733 GTGGTTTTGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (25 bp):
TATATTTACGAGTCAAATATAGTAG
Found at i:71750 original size:21 final size:22
Alignment explanation
Indices: 71724--71765 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
71714 GATACTGCTG
71724 TCACATCGCATCCTCA-AGCTC
1 TCACATCGCATCCTCAGAGCTC
* *
71745 TCACATGGCCTCCTCAGAGCT
1 TCACATCGCATCCTCAGAGCT
71766 ATGATTACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.24
Consensus pattern (22 bp):
TCACATCGCATCCTCAGAGCTC
Found at i:75799 original size:16 final size:16
Alignment explanation
Indices: 75778--75834 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
75768 TTTGGTTCGC
*
75778 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
75794 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
75810 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
75826 TGTAATGGA
1 TGTAATGGA
75835 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:76101 original size:18 final size:17
Alignment explanation
Indices: 76080--76114 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
76070 TTATTATTAA
*
76080 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
76098 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
76115 TCTTAANNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:83371 original size:12 final size:12
Alignment explanation
Indices: 83354--83384 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
83344 GCCAATTTAT
83354 TTCACTTCAATA
1 TTCACTTCAATA
83366 TTCACTTCAATA
1 TTCACTTCAATA
83378 TTCACTT
1 TTCACTT
83385 AAGGCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCACTTCAATA
Found at i:87707 original size:58 final size:58
Alignment explanation
Indices: 87636--87757 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 58
87626 GTATTCTGAT
* * *
87636 AAAACGTTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGATATAAACAG
1 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
* *
87694 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCTACTTCTAGCAGAAATAAATAA
1 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
87752 AAAACA
1 AAAACA
87758 GTATAAAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (58 bp):
AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
Found at i:90304 original size:6 final size:6
Alignment explanation
Indices: 90295--90330 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
90285 ACTTGGGACC
90295 TCCGAG TCCGAG TCCGAG TCC--G TCCGAG TCCGAG TC
1 TCCGAG TCCGAG TCCGAG TCCGAG TCCGAG TCCGAG TC
90331 GTGTTAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 24 0.86
ACGTcount: A:0.14, C:0.36, G:0.31, T:0.19
Consensus pattern (6 bp):
TCCGAG
Found at i:90321 original size:16 final size:16
Alignment explanation
Indices: 90300--90330 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
90290 GGACCTCCGA
90300 GTCCGAGTCCGAGTCC
1 GTCCGAGTCCGAGTCC
90316 GTCCGAGTCCGAGTC
1 GTCCGAGTCCGAGTC
90331 GTGTTAATAG
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:0.13, C:0.35, G:0.32, T:0.19
Consensus pattern (16 bp):
GTCCGAGTCCGAGTCC
Found at i:90973 original size:8 final size:8
Alignment explanation
Indices: 90960--90984 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
90950 TTTTAAATGA
90960 TATTTTAT
1 TATTTTAT
90968 TATTTTAT
1 TATTTTAT
90976 TATTTTAT
1 TATTTTAT
90984 T
1 T
90985 TAGTGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:99879 original size:5 final size:5
Alignment explanation
Indices: 99869--99905 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
99859 ATTTAAAGAT
99869 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
99906 GATGAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:121633 original size:25 final size:26
Alignment explanation
Indices: 121587--121638 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
121577 TAAACATATG
121587 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
121612 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
121638 A
1 A
121639 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:121648 original size:40 final size:41
Alignment explanation
Indices: 121561--121650 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 41
121551 TGATATGTAC
121561 ATAT-TATAAAAATGTATAAACATATGAATTATAAAACATG
1 ATATATATAAAAATGTATAAACATATGAATTATAAAACATG
* * *
121601 A-AAATATAAATAAT-TATAAA-ATATGAATGTATATAATAT-
1 ATATATATAAA-AATGTATAAACATATGAAT-TATAAAACATG
121640 ATATATATAAA
1 ATATATATAAA
121651 CTATATACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
39 10 0.24
40 29 0.69
41 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (41 bp):
ATATATATAAAAATGTATAAACATATGAATTATAAAACATG
Found at i:124349 original size:18 final size:18
Alignment explanation
Indices: 124326--124370 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
124316 CAAATCCAAT
*
124326 TCTCTCAATTCTTTCTAG
1 TCTCTCAATTCTTTCAAG
*
124344 TCTCTCTAA-TCTTTCAAT
1 TCTCTC-AATTCTTTCAAG
124362 TCTCTCAAT
1 TCTCTCAAT
124371 ATTTTAGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (18 bp):
TCTCTCAATTCTTTCAAG
Found at i:124868 original size:6 final size:6
Alignment explanation
Indices: 124857--124881 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
124847 ATTTTTACAG
124857 CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC C
124882 CATCGAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:125042 original size:3 final size:3
Alignment explanation
Indices: 125034--125085 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
125024 CTTGGCAATT
*
125034 TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
125082 TTA T
1 TTA T
125086 CTACTTATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:130157 original size:54 final size:50
Alignment explanation
Indices: 130041--130157 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 50
130031 TCGAAAAAAG
*
130041 GAAAAGGAAAAG-AGAGAAAAAATCAAAATCAAAATCAAAATAAAAAAACA
1 GAAAA-GAAAAGAAGAGAAAAAATCAAAATCAAAATAAAAATAAAAAAACA
* *
130091 -AAAAG-AAA-AAGAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAA-A
1 GAAAAGAAAAGAAGAGAAA-AAATCAAAATCAAAATAAAAATA--AAAA--AACA
130142 GAAAAGAAAAGAAGAG
1 GAAAAGAAAAGAAGAG
130158 GCCAATGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
47 10 0.18
48 21 0.38
49 4 0.07
50 4 0.07
51 1 0.02
52 7 0.13
53 3 0.05
54 5 0.09
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.09
Consensus pattern (50 bp):
GAAAAGAAAAGAAGAGAAAAAATCAAAATCAAAATAAAAATAAAAAAACA
Found at i:130552 original size:6 final size:6
Alignment explanation
Indices: 130517--130544 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
130507 AGAGAGATGA
130517 AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
130545 AATGAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:133417 original size:86 final size:87
Alignment explanation
Indices: 133234--133951 Score: 1027
Period size: 86 Copynumber: 8.3 Consensus size: 87
133224 GATCAGTAAG
* * *
133234 GATC-AAAGACAAAGCCTTGCCTCCATCGGTCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGC
1 GATCGAAA-ACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
133298 TTTCCTGCGTTAACAGCGAAGTA
65 CTTCCTGCGTTAACAGCGAAGCA
133321 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
*
133385 TTCTTGCGTTAACAGCGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* * *
133407 GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
133472 TTCCTGCGTTAACAGCGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* * *
133494 AATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
*
133558 TTCCTTCGTTAACAGCGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
133580 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
* *
133644 TTCCTGCATTAACAGCGAAGTA
66 TTCCTGCGTTAACAGCGAAGCA
* * *
133666 GATCGAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAG-GAGCAAATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
*
133730 TTTCTGCGTTAACAGCGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* * * * * *
133752 GATCAAAAACAAAACCTTGCCTCCATCGATTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
* * *
133817 TTCCTGCATTGACAACGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* *
133839 GATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAGTAGAGCTGGTTAAAGATAGCAGATCTT
1 GATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTT
* * *
133902 GCCTTCCTGCATTGACAACGAAGCA
63 GCCTTCCTGCGTTAACAGCGAAGCA
* *
133927 GATCGAAGACACTAGCCTTGCCTCC
1 GATCGAAAACA-AAGCCTTGCCTCC
133952 CTAAGCAGTA
Statistics
Matches: 573, Mismatches: 49, Indels: 18
0.90 0.08 0.03
Matches are distributed among these distances:
86 321 0.56
87 161 0.28
88 85 0.15
89 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (87 bp):
GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGCA
Found at i:133537 original size:173 final size:173
Alignment explanation
Indices: 133234--133951 Score: 1025
Period size: 173 Copynumber: 4.1 Consensus size: 173
133224 GATCAGTAAG
* *
133234 GATC-AAAGACAAAGCCTTGCCTCCATCGGTCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGC
1 GATCGAAA-ACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * * * *
133298 TTTCCTGCGTTAACAGCGAAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
65 CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCT
133363 GGTTAAAGAAGCAGATCTTGCCTTCTTGCGTTAACAGCGAAGCA
130 GGTTAAAGAAGCAGATCTTGCCTTCTTGCGTTAACAGCGAAGCA
133407 GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
* *
133472 TTCCTGCGTTAACAGCGAAGCAAATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
66 TTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
133537 GTTAAAGAAGCAGATCTTGCCTTCCTT-CGTTAACAGCGAAGCA
131 GTTAAAGAAGCAGATCTTGCCTT-CTTGCGTTAACAGCGAAGCA
* * *
133580 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
* * * *
133644 TTCCTGCATTAACAGCGAAGTAGATCGAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTG
66 TTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
* *
133709 GTTAAAGGAGCAAATCTTGCCTT-TCTGCGTTAACAGCGAAGCA
131 GTTAAAGAAGCAGATCTTGCCTTCT-TGCGTTAACAGCGAAGCA
* * * * *
133752 GATCAAAAACAAAACCTTGCCTCCATCGATTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
* * * *
133817 TTCCTGCATTGACAACGAAGCAGATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAGTAGAG
66 TTCCTGCATTAACAGCGAAGCAGATC-AA-AAACAAAGCCTTGCCTC-CATCGGTTGCAGTAGAG
* * * *
133880 CTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAACGAAGCA
128 CTGGTTAAAGA-AGCAGATCTTGCCTTCTTGCGTTAACAGCGAAGCA
* *
133927 GATCGAAGACACTAGCCTTGCCTCC
1 GATCGAAAACA-AAGCCTTGCCTCC
133952 CTAAGCAGTA
Statistics
Matches: 493, Mismatches: 41, Indels: 19
0.89 0.07 0.03
Matches are distributed among these distances:
170 1 0.00
171 1 0.00
172 156 0.32
173 241 0.49
174 39 0.08
175 44 0.09
176 11 0.02
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (173 bp):
GATCGAAAACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
TTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTG
GTTAAAGAAGCAGATCTTGCCTTCTTGCGTTAACAGCGAAGCA
Found at i:133703 original size:259 final size:259
Alignment explanation
Indices: 133235--133951 Score: 1071
Period size: 259 Copynumber: 2.8 Consensus size: 259
133225 ATCAGTAAGG
* * * * *
133235 ATCAAAGACAAAGCCTTGCCTCCATCGGTCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGCTT
1 ATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCT
*
133300 TCCTGCGTTAACAGCGAAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
66 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* *
133365 TTAAAGAAGCAGATCTTGCCTTCTTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
131 TTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
* * *
133430 CATCGATCGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAA
196 CATCGATCGCAGTGGAGCTGGTTAAAG-GAGCAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAA
* *
133495 ATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGA-AGCAGATCTTGCCT
1 ATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCT
*
133559 TCCTTCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
66 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
*
133624 TTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAACAAAGCCTTGCCTC
131 TTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
* * * * *
133689 TATCGGTTGCAGTGGAGCTGGTTAAAGGAGCAAATCTTGCCTTTCTGCGTTAACAGCGAAGCAG
196 CATCGATCGCAGTGGAGCTGGTTAAAGGAGCAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAA
* * *
133753 ATCAAAAACAAAACCTTGCCTCCATCGATTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCT
1 ATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCT
* * * * *
133818 TCCTGCATTGACAACGAAGCAGATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAGTAGAGC
66 TCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGC
* * * *
133881 TGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACTAGCCTT
128 TGGTTAAAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACA-AAGCCTT
133946 GCCTCC
191 GCCTCC
133952 CTAAGCAGTA
Statistics
Matches: 415, Mismatches: 36, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
258 79 0.19
259 197 0.47
260 80 0.19
261 48 0.12
262 11 0.03
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (259 bp):
ATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCT
TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
TTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
CATCGATCGCAGTGGAGCTGGTTAAAGGAGCAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAA
Found at i:133859 original size:44 final size:44
Alignment explanation
Indices: 133811--133949 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
133801 GACAACAGAT
133811 CTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACAAAC
* ** * * ** * * *
133855 CTTGCC-TCTCT-CGGTTGTAGTA-G-AGCTGGTTAAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTG-ACAACGAAGCAGATCGAAGACA-CAAAC
* *
133899 CTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACAAAC
133943 CTTGCCT
1 CTTGCCT
133950 CCCTAAGCAG
Statistics
Matches: 65, Mismatches: 22, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
43 15 0.23
44 35 0.54
45 15 0.23
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAGACACAAAC
Found at i:135899 original size:3 final size:3
Alignment explanation
Indices: 135882--135938 Score: 87
Period size: 3 Copynumber: 18.3 Consensus size: 3
135872 CTTGGCAATT
135882 TTA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
135929 TCA TTA TTA T
1 TTA TTA TTA T
135939 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:136239 original size:3 final size:3
Alignment explanation
Indices: 136222--136275 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
136212 CTTGGCAATT
* *
136222 TTA TTA TTTA GTTA TTA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
136269 TTA TTA T
1 TTA TTA T
136276 CTACTTATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:138414 original size:44 final size:44
Alignment explanation
Indices: 138349--138458 Score: 186
Period size: 44 Copynumber: 2.5 Consensus size: 44
138339 CAGATTACAT
*
138349 TTATCACTTGTCACTGGTCAGATAAGTGTAGCTAAAGCTA-CAAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATC-AC
138393 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCAC
*
138437 TTATCACTTGTCACTAATCAGA
1 TTATCACTTGTCACTGATCAGA
138459 AGTACTCAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 62 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCAC
Found at i:139682 original size:12 final size:12
Alignment explanation
Indices: 139664--139698 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
139654 CCCCGATGGA
139664 AACACCAATGTT
1 AACACCAATGTT
* *
139676 GACACCAATGCT
1 AACACCAATGTT
139688 AACACCAATGT
1 AACACCAATGT
139699 CGATATCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (12 bp):
AACACCAATGTT
Found at i:139708 original size:24 final size:24
Alignment explanation
Indices: 139664--139710 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
139654 CCCCGATGGA
*
139664 AACACCAATGTTGACACCAATGCT
1 AACACCAATGTCGACACCAATGCT
* *
139688 AACACCAATGTCGATATCAATGC
1 AACACCAATGTCGACACCAATGC
139711 CAATATTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (24 bp):
AACACCAATGTCGACACCAATGCT
Found at i:143419 original size:32 final size:32
Alignment explanation
Indices: 143376--143441 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
143366 CCCATCATGT
*
143376 CTGGGTCTGTCCAAATCTTGAACCCGTGATCG
1 CTGGGTATGTCCAAATCTTGAACCCGTGATCG
143408 CTGGGTATGTCCAAATCTTGAACCCGTGATCG
1 CTGGGTATGTCCAAATCTTGAACCCGTGATCG
143440 CT
1 CT
143442 AACCATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (32 bp):
CTGGGTATGTCCAAATCTTGAACCCGTGATCG
Found at i:147339 original size:43 final size:42
Alignment explanation
Indices: 147267--147536 Score: 264
Period size: 42 Copynumber: 6.4 Consensus size: 42
147257 ACGTCGCTAA
* *
147267 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
* * *
147311 ATTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
* * *
147354 CTTTAGCGGCGCTTAGGAAGAAACACCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGA-TCATGTT
* *
147396 CTATAGCGGCGCTTGGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * * *
147438 ATTTAGCGGCGCTTTGGAAGAAAACACCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* * *
147481 CTATAGCGGCGCTT-GGTCAAAAACG-TGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGA-TCA-TGTT
147522 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
147537 TTTCACAGAC
Statistics
Matches: 191, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.01
41 26 0.14
42 82 0.43
43 71 0.37
44 11 0.06
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:147463 original size:85 final size:85
Alignment explanation
Indices: 147267--147536 Score: 325
Period size: 85 Copynumber: 3.2 Consensus size: 85
147257 ACGTCGCTAA
* * * * * * * **
147267 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCT-AAAGATCATGTTATTTAGCGGCGCTAAGGAAA
1 CTTTAGCGGCGCTTA-GGAAGAAAACACCGCTAAAAG-TAATGTTCTATAGCGGCGCTTGGGAAA
*
147331 TAAACGCCGCTAAAGGTCATGTT
64 -AAACGCCGCTAAAGATCATGTT
147354 CTTTAGCGGCGCTTAGGAAG-AAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGGAAAAA
1 CTTTAGCGGCGCTTAGGAAGAAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGGAAAAA
147418 ACGCCGCTAAAGATCATGTT
66 ACGCCGCTAAAGATCATGTT
* * **
147438 ATTTAGCGGCGCTTTGGAAGAAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGTCAAAA
1 CTTTAGCGGCGCTTAGGAAGAAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGGAAAAA
*
147503 ACG-TGCTAAA-AGT-AGTGTT
66 ACGCCGCTAAAGA-TCA-TGTT
147522 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
147537 TTTCACAGAC
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
83 2 0.01
84 63 0.39
85 76 0.47
86 7 0.04
87 14 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAGGAAGAAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGGAAAAA
ACGCCGCTAAAGATCATGTT
Found at i:147549 original size:127 final size:127
Alignment explanation
Indices: 147286--147535 Score: 355
Period size: 127 Copynumber: 2.0 Consensus size: 127
147276 CGCTTACAGA
* * *
147286 AAAAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGGTCAT
1 AAAAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTAAGGAAATAAACACCGCTAAAAGTAAT
*
147351 GTTCTTTAGCGGCGCTTAGGAAGAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGG
66 GTTCTATAGCGGCGCTTAGGAAGAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGG
**
147413 AAAAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTTTGGAAGA-AAACACCGCTAAAAGTAA
1 AAAAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTAAGGAA-ATAAACACCGCTAAAAGTAA
** * *
147477 TGTTCTATAGCGGCGCTT-GGTCAA-AAAC-GTGCTAAAAGTAGTGTTCTTTAGCGGCGCTT
65 TGTTCTATAGCGGCGCTTAGG--AAGAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTT
147536 ATTTCACAGA
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
126 29 0.26
127 78 0.71
128 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (127 bp):
AAAAAACGCCGCTAAAGATCATGTTATTTAGCGGCGCTAAGGAAATAAACACCGCTAAAAGTAAT
GTTCTATAGCGGCGCTTAGGAAGAAACACCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGG
Found at i:147591 original size:35 final size:36
Alignment explanation
Indices: 147536--147606 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
147526 AGCGGCGCTT
147536 ATTTCACAGACGCCACTATTTGATATGACTTTTAGC
1 ATTTCACAGACGCCACTATTTGATATGACTTTTAGC
147572 ATTTCACAGA-GCCACTATTTGATATGACTTTTAGC
1 ATTTCACAGACGCCACTATTTGATATGACTTTTAGC
147607 GGCGCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
ATTTCACAGACGCCACTATTTGATATGACTTTTAGC
Found at i:149669 original size:21 final size:21
Alignment explanation
Indices: 149645--149716 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
149635 TTCTTTTGAC
* * *
149645 CCTCTGTTTCTTTCGCTGCGG
1 CCTCTGCTTCTCTCGCTGCAG
* *
149666 CCTCTGCTTCTCTCCCTGTAG
1 CCTCTGCTTCTCTCGCTGCAG
* *
149687 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
149708 CCTCTGCTT
1 CCTCTGCTT
149717 TAAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.01, C:0.43, G:0.18, T:0.38
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Done.