Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2019
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: 56899
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1499 original size:15 final size:15
Alignment explanation
Indices: 1475--1645 Score: 55
Period size: 15 Copynumber: 10.7 Consensus size: 15
1465 GTTTAAATAG
*
1475 ATAAAAAAATATAAA
1 ATAAATAAATATAAA
*
1490 ATAAATAAATAAAAA
1 ATAAATAAATATAAA
*
1505 AAAAATAAA-A-AAA
1 ATAAATAAATATAAA
*
1518 AGTAAAAAACATATATAA
1 A-TAAATAA-ATATA-AA
*
1536 GAAAAAT-AATAATGAAA
1 -ATAAATAAAT-AT-AAA
*
1553 ATAATATTAGTATATAAA
1 ATAA-A-TA-AATATAAA
* * *
1571 TAGAAATAAAAATATA
1 -ATAAATAAATATAAA
1587 ATAAATAGAAATATAATA
1 ATAAAT--AAATATAA-A
* *
1605 ATAGTAGAAATAT-AA
1 ATA-AATAAATATAAA
*
1620 ATAGATAAATA-AAA
1 ATAAATAAATATAAA
*
1634 ATTAGATAAATA
1 A-TAAATAAATA
1646 ATAATAGTAT
Statistics
Matches: 117, Mismatches: 20, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
13 4 0.03
14 15 0.13
15 41 0.35
16 12 0.10
17 21 0.18
18 15 0.13
19 7 0.06
20 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (15 bp):
ATAAATAAATATAAA
Found at i:1509 original size:19 final size:19
Alignment explanation
Indices: 1469--1518 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1459 TAAAAAGTTT
* *
1469 AAATAGATAAAAAAATATA
1 AAATAAATAAAAAAATAAA
1488 AAATAAATAAATAAAA-AAA
1 AAATAAATAAA-AAAATAAA
1507 AAATAAA-AAAAA
1 AAATAAATAAAAA
1519 GTAAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 3 0.11
19 19 0.68
20 4 0.14
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (19 bp):
AAATAAATAAAAAAATAAA
Found at i:1513 original size:34 final size:35
Alignment explanation
Indices: 1475--1547 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
1465 GTTTAAATAG
1475 ATAAAAAAATA-TAAAATAA-ATAAATAA-AAAAAAA
1 ATAAAAAAA-AGTAAAA-AACATAAATAAGAAAAAAA
* *
1509 ATAAAAAAAAGTAAAAAACATATATAAGAAAAATA
1 ATAAAAAAAAGTAAAAAACATAAATAAGAAAAAAA
1544 ATAA
1 ATAA
1548 TGAAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 3 0.09
34 21 0.62
35 10 0.29
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (35 bp):
ATAAAAAAAAGTAAAAAACATAAATAAGAAAAAAA
Found at i:1526 original size:11 final size:11
Alignment explanation
Indices: 1477--1518 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1467 TTAAATAGAT
*
1477 AAAAAAATATA
1 AAAAAAAAATA
1488 AAATAAATAAATA
1 AAA-AAA-AAATA
1501 AAAAAAAAATA
1 AAAAAAAAATA
1512 AAAAAAA
1 AAAAAAA
1519 GTAAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:1620 original size:29 final size:29
Alignment explanation
Indices: 1587--1703 Score: 85
Period size: 29 Copynumber: 4.0 Consensus size: 29
1577 TAAAAATATA
*
1587 ATAAATAGAAATATAATAATAGTAGAAAT
1 ATAAATAGAAATATAATAATAATAGAAAT
* * * *
1616 ATAAATAGATAA-ATAAAAATTAGATAAAT
1 ATAAATAGA-AATATAATAATAATAGAAAT
* * * * * *
1645 A-ATAATAGTATTAGAATAACAAAATAAAT
1 ATA-AATAGAAATATAATAATAATAGAAAT
* *
1674 ATAAATAGAAACATAATAATAATAGCAAT
1 ATAAATAGAAATATAATAATAATAGAAAT
1703 A
1 A
1704 ATATATTAAA
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
28 2 0.03
29 59 0.92
30 3 0.05
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (29 bp):
ATAAATAGAAATATAATAATAATAGAAAT
Found at i:1622 original size:44 final size:44
Alignment explanation
Indices: 1568--1654 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
1558 ATTAGTATAT
1568 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGTAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGTAG
* *
1612 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATAGTA
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTA
1655 TTAGAATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 28 0.74
45 5 0.13
46 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
Found at i:1646 original size:15 final size:14
Alignment explanation
Indices: 1566--1682 Score: 62
Period size: 15 Copynumber: 8.1 Consensus size: 14
1556 ATATTAGTAT
*
1566 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
1579 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
1595 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
1609 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
1624 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
1639 ATAAATAATAATAG
1 ATAAATAAAAATAG
*
1653 TATTAGAATAACAA-A-
1 -A-TA-AATAAAAATAG
*
1668 ATAAATATAAATAG
1 ATAAATAAAAATAG
1682 A
1 A
1683 AACATAATAA
Statistics
Matches: 82, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 22 0.27
15 35 0.43
16 6 0.07
17 7 0.09
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:2902 original size:16 final size:18
Alignment explanation
Indices: 2888--2924 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2878 ATAATTTAAA
2888 ATATAAATTTATTAATATAT
1 ATATAAATTTATT-A-ATAT
2908 ATATAAATTTATTAATA
1 ATATAAATTTATTAATA
2925 CATGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 1 0.06
20 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:27626 original size:17 final size:17
Alignment explanation
Indices: 27604--27647 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
27594 TCCGTACCTA
*
27604 TATCTTCGTGGGATTTT
1 TATCTTCGTGAGATTTT
27621 TATCTTCGTGAGATTTT
1 TATCTTCGTGAGATTTT
27638 TATCTTCGTG
1 TATCTTCGTG
27648 CGGCCATAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (17 bp):
TATCTTCGTGAGATTTT
Found at i:31973 original size:13 final size:13
Alignment explanation
Indices: 31955--31980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31945 GCTCGGCAGG
31955 GACACGTCCGTGT
1 GACACGTCCGTGT
31968 GACACGTCCGTGT
1 GACACGTCCGTGT
31981 TCGATTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACACGTCCGTGT
Found at i:32263 original size:56 final size:57
Alignment explanation
Indices: 32193--32305 Score: 133
Period size: 56 Copynumber: 2.0 Consensus size: 57
32183 TCTAATGGGA
*
32193 AATCATCCAAAAAATGCAT-TAAACATGGGGTA-AAA-ATGTATAAATTACGGTTTATT
1 AATCATCCAAAAAAT--ATCTAAACATGGGATAGAAATATGTATAAATTACGGTTTATT
* * * *
32249 AATCATCTATAAAATATGCTAAGCATGGGATAGAAATATGTATAAATTATGGTTTAT
1 AATCATCCAAAAAATAT-CTAAACATGGGATAGAAATATGTATAAATTACGGTTTAT
32306 CAGAAAGCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
54 2 0.04
56 24 0.50
57 3 0.06
58 19 0.40
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (57 bp):
AATCATCCAAAAAATATCTAAACATGGGATAGAAATATGTATAAATTACGGTTTATT
Found at i:37976 original size:23 final size:23
Alignment explanation
Indices: 37950--38025 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
37940 ATAAGTGCCA
37950 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
37973 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
37996 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38019 CACTGAT
1 CACTGAT
38026 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38125 original size:8 final size:8
Alignment explanation
Indices: 38112--38140 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38102 ACCCGGGACT
38112 CACTGTAA
1 CACTGTAA
38120 CACTGTAA
1 CACTGTAA
38128 CACTGTAA
1 CACTGTAA
38136 CACTG
1 CACTG
38141 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:38271 original size:18 final size:17
Alignment explanation
Indices: 38245--38283 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38235 ATTTTCCTTC
38245 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
38262 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
38280 CACA
1 CACA
38284 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:45305 original size:23 final size:23
Alignment explanation
Indices: 45279--45354 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
45269 ATAAGTGCCA
45279 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
45302 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
45325 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
45348 CACTGAT
1 CACTGAT
45355 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:45454 original size:8 final size:8
Alignment explanation
Indices: 45441--45469 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
45431 ACCCGGGACT
45441 CACTGTAA
1 CACTGTAA
45449 CACTGTAA
1 CACTGTAA
45457 CACTGTAA
1 CACTGTAA
45465 CACTG
1 CACTG
45470 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:45600 original size:18 final size:17
Alignment explanation
Indices: 45574--45612 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
45564 ATTTTCCTTC
45574 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
45591 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
45609 CACA
1 CACA
45613 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:50854 original size:44 final size:43
Alignment explanation
Indices: 50806--51531 Score: 212
Period size: 44 Copynumber: 16.4 Consensus size: 43
50796 AATTCACAAC
* * *
50806 CTTATCTCTCTGAGGTAGTAAGAGAACAGGTTGAAGATTGAAGT
1 CTTATCTCTCTGAGGTAGCAAG-GAGCAGATTGAAGATTGAAGT
* * * * * *
50850 CTTATCTTTCTGGGGTAGTAAGGAAGCAGACTGAGGGTTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGG-AGCAGATTGAAGATTGAAG-T
* *
50895 CTTATCTC-CATGAGGGAGCAATGGAGCAGATCGAAGATGGTGAA-T
1 CTTATCTCTC-TGAGGTAGCAA-GGAGCAGATTGAAGAT--TGAAGT
* * * ** * *
50940 CTTATCT-TCCCGAGGTAGCAGGGGAGTAGATTTTAG--TCATAGC
1 CTTATCTCT-CTGAGGTAGCA-AGGAGCAGATTGAAGATTGA-AGT
*
50983 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGT
1 CTTATCTCTCTGAGGTAGCAAG-GAGCAGATTGAAGATTGAAGT
** *
51027 CTTATCT-TCCTGAGGTAGCAAAAAAGCAGACT-AAGGATTGAAGAT
1 CTTATCTCT-CTGAGGTAGC-AAGGAGCAGATTGAA-GATTGAAG-T
* * * ** *
51072 CTTATCTCCCTAAGCAGTAG-TA-GAGCAGATCAAAGATGGCGAA-T
1 CTTATCTCTCTGAG--GTAGCAAGGAGCAGATTGAAGAT--TGAAGT
** ***** *
51116 CTTATCT-TCTCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGC
1 CTTATCTCTCT-GAGGTAGCA-AGGAGCAGATTGAAGATTGAAGT
* * *
51160 CTTATCTCTCTGAGGTAGCGAGAGAGCAGGTTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAG-GAGCAGATTGAAGATTGAAGT
* * * *
51204 CTTATCT-TCCTGAGATAGTAAGGAAGCAGACTGAATATT-ATAGAT
1 CTTATCTCT-CTGAGGTAGCAAGG-AGCAGATTGAAGATTGA-AG-T
* * * * *
51249 CTTATCTC-CATTAGGTAGCAATAGAGCAAATCGAAGATGGCGAA-T
1 CTTATCTCTC-TGAGGTAGCAA-GGAGCAGATTGAAGAT--TGAAGT
* * *
51294 CTTATCTC-CTTGAGGTAGCAAGGGAGCAGATTTAAGCCACT--AGC
1 CTTATCTCTC-TGAGGTAGCAA-GGAGCAGATTGAAG--ATTGAAGT
* * * * *
51338 CTTGTCT-TCTGA-GCAGCAATAGAGCA-AGCTGAAGATTGTAGAT
1 CTTATCTCTCTGAGGTAGCAA-GGAGCAGA-TTGAAGATTGAAG-T
* * * *
51381 ATTATCTC-CATGAGGTAGCAATGTAGCAGATCGAAGACGGTGAA-T
1 CTTATCTCTC-TGAGGTAGCAA-GGAGCAGATTGAAGA--TTGAAGT
* * *
51426 CTTATCT-TCCTGAAGTAGCAAGGGAGCAGATCT-AAGCCA-T-CAGC
1 CTTATCTCT-CTGAGGTAGCAA-GGAGCAGAT-TGAAG--ATTGAAGT
* ** *
51470 CTCATCTCTCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGC-AAGGAGCAGATTGAAGATTGAAGT
*
51514 TTTATCT-TCCTGAGGTAG
1 CTTATCTCT-CTGAGGTAG
51532 TAAAGGGGCA
Statistics
Matches: 491, Mismatches: 123, Indels: 136
0.65 0.16 0.18
Matches are distributed among these distances:
40 2 0.00
41 3 0.01
42 24 0.05
43 51 0.10
44 200 0.41
45 187 0.38
46 9 0.02
47 14 0.03
48 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (43 bp):
CTTATCTCTCTGAGGTAGCAAGGAGCAGATTGAAGATTGAAGT
Found at i:51163 original size:177 final size:177
Alignment explanation
Indices: 50805--51410 Score: 731
Period size: 177 Copynumber: 3.4 Consensus size: 177
50795 GAATTCACAA
* * * * *
50805 CCTTATCTCTCTGAGGTAGTAAGAGAACAGGTTGAAGATTGAAGTCTTATCTTTCTGGGGTAGTA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCA
* * * *
50870 AGGAAGCAGACTGAGGGTTGAAGATCTTATCTCCATGAGGGAGCAATGGAGCAGATCGAAGATGG
66 AGGAAGCAGACTAAGGATTGAAGATCTTATCTCCAT-AGGCAGCAATAGAGCAGATCGAAGATGG
* * * * *
50935 TGAATCTTATCTTCCCGAGGTAGCAGGGGAGTAGATTTTAGTCA-TAG
130 CGAATCTTATCTTCTCGAGGTAGCAGAGGAGCAGATTTTAGCCACTAG
50982 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCA
** * * * * *
51047 AAAAAGCAGACTAAGGATTGAAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGC
66 AGGAAGCAGACTAAGGATTGAAGATCTTATCTCCATAGGCAGCAATAGAGCAGATCGAAGATGGC
*
51112 GAATCTTATCTTCTCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAG
131 GAATCTTATCTTCTCGAGGTAGCAGAGGAGCAGATTTTAGCCACTAG
* * * *
51159 CCTTATCTCTCTGAGGTAGCGAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGATAGTA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCA
* * *
51224 AGGAAGCAGACTGAA-TATT-ATAGATCTTATCTCCATTAGGTAGCAATAGAGCAAATCGAAGAT
66 AGGAAGCAGACT-AAGGATTGA-AGATCTTATCTCCA-TAGGCAGCAATAGAGCAGATCGAAGAT
* * *
51287 GGCGAATCTTATCTCCTTGAGGTAGCA-AGGGAGCAGATTTAAGCCACTAG
128 GGCGAATCTTATCTTCTCGAGGTAGCAGA-GGAGCAGATTTTAGCCACTAG
* * * * * * *
51337 CCTTGTCT-TCTGA-GCAGCAATAGAGCAAGCTGAAGATTGTAGATATTATC-TCCATGAGGTAG
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAG-TCTTATCTTCC-TGAGGTAG
* *
51399 CAATGTAGCAGA
64 CAAGGAAGCAGA
51411 TCGAAGACGG
Statistics
Matches: 371, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
176 89 0.24
177 208 0.56
178 74 0.20
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (177 bp):
CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCA
AGGAAGCAGACTAAGGATTGAAGATCTTATCTCCATAGGCAGCAATAGAGCAGATCGAAGATGGC
GAATCTTATCTTCTCGAGGTAGCAGAGGAGCAGATTTTAGCCACTAG
Found at i:51400 original size:132 final size:134
Alignment explanation
Indices: 51234--51531 Score: 369
Period size: 132 Copynumber: 2.2 Consensus size: 134
51224 AGGAAGCAGA
* * * * *
51234 CTGAATATTATAGATCTTATCTCCATTAGGTAGCAATAG-AGCAAATCGAAGATGGCGAATCTTA
1 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAAT-GTAGCAAATCGAAGACGGCGAATCTTA
* * **
51298 TC-TCCTTGAGGTAGCAAGGGAGCAGATTTAAGCCA-CTAGCCTTGTCT-TCTGA-GCAGCAATA
65 TCTTCC-TGAAGTAGCAAGGGAGCAGATCTAAGCCATC-AGCCTCATCTCTCTGAGGCAGCAA-A
51359 -GAGCAAG
127 GGAGCAAG
* *
51366 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAATGTAGCAGATCGAAGACGGTGAATCTTAT
1 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAATGTAGCAAATCGAAGACGGCGAATCTTAT
*
51431 CTTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCATCAGCCTCATCTCTCTGAGGTAGCAAAGGAG
66 CTTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCATCAGCCTCATCTCTCTGAGGCAGCAAAGGAG
*
51496 CAGG
131 CAAG
*
51500 CTGAAGATTGTAG-TTTTATCTTCC-TGAGGTAG
1 CTGAAGATTGTAGATATTATC-TCCATGAGGTAG
51532 TAAAGGGGCA
Statistics
Matches: 145, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
131 1 0.01
132 92 0.63
133 24 0.17
134 28 0.19
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (134 bp):
CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAATGTAGCAAATCGAAGACGGCGAATCTTAT
CTTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCATCAGCCTCATCTCTCTGAGGCAGCAAAGGAG
CAAG
Found at i:51487 original size:354 final size:353
Alignment explanation
Indices: 50805--51498 Score: 809
Period size: 354 Copynumber: 2.0 Consensus size: 353
50795 GAATTCACAA
* * * *
50805 CCTTATCTCTCTGAGGTAGTAAGAGAACAGGTTGAAGATTGAAGTCTTATCTTTCTGGGGTAGTA
1 CCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATTGAAGTCTTATCTTCCTGAGATAGTA
* * * *
50870 AGGAAGCAGACTGAGGGTTGAAGATCTTATCTCCATGAGGGAGCAATGGAGCAGATCGAAGATGG
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCATGAGGGAGCAATAGAGCAAATCGAAGATGG
* * * * * *
50935 TGAATCTTATCTTCCCGAGGTAGCAGGGGAGTAGATTTTAGTCATAGCCTTATCTCTCTGAGGTA
131 CGAATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTAAGCCATAGCCTTATCTCTCTGAGGCA
* * * * *
51000 GCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCAAAAAAGCAGACTAAGGAT
196 GCAAGAGAGCAAGCTGAAGATTGAAGTATTATCTTCCTGAGGTAGCAAAAAAGCAGACGAAGGAG
* * *
51065 TGAAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGCGAATCTTATCTTCTCGAG
261 TGAAGATCTTATCTCCCTAAGCAGAAGTAGAGCAGATCAAAGAT-GCGAACCTCATCTTCTCGAG
*
51130 GTAGCAGAGGAGCAGATTTTAGCCACCAG
325 GTAGCAAAGGAGCAGATTTTAGCCACCAG
* * *
51159 CCTTATCTCTCTGAGGTAGCGAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGATAGTA
1 CCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATTGAAGTCTTATCTTCCTGAGATAGTA
* * *
51224 AGGAAGCAGACTGAATATT-ATAGATCTTATCTCCATTAGGTAGCAATAGAGCAAATCGAAGATG
66 AGGAAGCAGACTGAAGATTGA-AGATCTTATCTCCATGAGGGAGCAATAGAGCAAATCGAAGATG
* *
51288 GCGAATCTTATC-TCCTTGAGGTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCT-TCTGA-
130 GCGAATCTTATCTTCC-CGAGGTAGCAAGGGAGCAGATTTAAGCCA-TAGCCTTATCTCTCTGAG
* * ***
51350 GCAGCAATAGAGCAAGCTGAAGATTGTAGATATTATC-TCCATGAGGTAGCAATGTAGCAGATCG
193 GCAGCAAGAGAGCAAGCTGAAGATTGAAG-TATTATCTTCC-TGAGGTAGCAAAAAAGCAGA-CG
* * * * *
51414 AA-GACGGTG-A-ATCTTATCTTCCTGAAGTAGCAAG-GGAGCAGATCTAAGCCAT-C-AGCCTC
255 AAGGA--GTGAAGATCTTATCTCCCT-AAGCAG-AAGTAGAGCAGATCAAAG--ATGCGAACCTC
51473 ATC-TCTCTGAGGTAGCAAAGGAGCAG
314 ATCTTCTC-GAGGTAGCAAAGGAGCAG
51499 GCTGAAGATT
Statistics
Matches: 286, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
353 35 0.12
354 213 0.74
355 32 0.11
356 4 0.01
357 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (353 bp):
CCTTATCTCTCTGAGGTAGCAAGAGAACAGGTTGAAGATTGAAGTCTTATCTTCCTGAGATAGTA
AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCATGAGGGAGCAATAGAGCAAATCGAAGATGG
CGAATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTAAGCCATAGCCTTATCTCTCTGAGGCA
GCAAGAGAGCAAGCTGAAGATTGAAGTATTATCTTCCTGAGGTAGCAAAAAAGCAGACGAAGGAG
TGAAGATCTTATCTCCCTAAGCAGAAGTAGAGCAGATCAAAGATGCGAACCTCATCTTCTCGAGG
TAGCAAAGGAGCAGATTTTAGCCACCAG
Found at i:51537 original size:44 final size:44
Alignment explanation
Indices: 51479--51588 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
51469 CCTCATCTCT
* * * *
51479 CTGAGGTAGCAAAGGAGCAGGCTGAAGATTGTAG-TTTTATCTTC
1 CTGAGGTAGTAAAGGAGCAGACTAAAGATTGTAGATCTTAT-TTC
* *
51523 CTGAGGTAGTAAAGGGGCAGACTAAAGGTTGTAGATCTTATTTC
1 CTGAGGTAGTAAAGGAGCAGACTAAAGATTGTAGATCTTATTTC
* *
51567 CATGACGTAGTAATGGAGCAGA
1 C-TGAGGTAGTAAAGGAGCAGA
51589 TCGAAGATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 33 0.60
45 22 0.40
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (44 bp):
CTGAGGTAGTAAAGGAGCAGACTAAAGATTGTAGATCTTATTTC
Found at i:51585 original size:133 final size:131
Alignment explanation
Indices: 51234--51590 Score: 343
Period size: 132 Copynumber: 2.7 Consensus size: 131
51224 AGGAAGCAGA
* * * * * * *
51234 CTGAATATTATAGATCTTATCTCCATTAGGTAGCAATA-GAGCAAATCGAAGATGGCGAATCTTA
1 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAA-AGGAGCAGATCGAAGACGGTGAATCTTA
* * * **
51298 TCTCCTTGAGGTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTTCTGAGCAGCAATAGAGC
65 TTTCC-TGAAGTAGCAAGGGAGCAGATCTAAGCCACTAGCCTCATCTTCTGAGCAGCAATAGAGC
51363 AAG
129 AAG
* *
51366 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAATGTAGCAGATCGAAGACGGTGAATCTTAT
1 CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAAAGGAGCAGATCGAAGACGGTGAATCTTAT
*
51431 CTTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCA-TCAGCCTCATCTCTCTGAGGTAGCAA-AGG
66 -TTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCACT-AGCCTCATCT-TCTGA-GCAGCAATA-G
*
51494 AGCAGG
126 AGCAAG
* * * *
51500 CTGAAGATTGTAG-TTTTATCTTCC-TGAGGTAGTAAAGGGGCAGA-CTAA-A-GGTTGTAGATC
1 CTGAAGATTGTAGATATTATC-TCCATGAGGTAGCAAAGGAGCAGATCGAAGACGG-TG-A-ATC
* * *
51560 TTATTTCCATGACGTAGTAATGGAGCAGATC
62 TTATTTCC-TGAAGTAGCAAGGGAGCAGATC
51591 GAAGATGAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
130 2 0.01
131 4 0.02
132 98 0.52
133 57 0.30
134 28 0.15
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (131 bp):
CTGAAGATTGTAGATATTATCTCCATGAGGTAGCAAAGGAGCAGATCGAAGACGGTGAATCTTAT
TTCCTGAAGTAGCAAGGGAGCAGATCTAAGCCACTAGCCTCATCTTCTGAGCAGCAATAGAGCAA
G
Found at i:53790 original size:23 final size:20
Alignment explanation
Indices: 53741--53809 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
53731 CATTTTCCAT
*
53741 CTCCTTCTTTATCAGTCCTC
1 CTCCTTCTTCATCAGTCCTC
53761 CTCCTTCTTCATCAGTCCAT-
1 CTCCTTCTTCATCAGTCC-TC
* * * *
53781 CTCATTCTTCTTCATTCCTT
1 CTCCTTCTTCATCAGTCCTC
53801 CTCCTTCTT
1 CTCCTTCTT
53810 TTGTTCTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.10, C:0.39, G:0.03, T:0.48
Consensus pattern (20 bp):
CTCCTTCTTCATCAGTCCTC
Done.