Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2162
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: 90937
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:1254 original size:22 final size:22
Alignment explanation
Indices: 1228--1282 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1218 TTTTTCTTTG
1228 TTTCT-ATTTCTTCTCTCTTTTT
1 TTTCTCATTT-TTCTCTCTTTTT
* *
1250 TTTCTCCTTTTTTTCTCTTTTT
1 TTTCTCATTTTTCTCTCTTTTT
*
1272 TTT-TCTTTTTT
1 TTTCTCATTTTT
1283 TTAGTTGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 19 0.66
23 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTCATTTTTCTCTCTTTTT
Found at i:1283 original size:22 final size:24
Alignment explanation
Indices: 1238--1284 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
1228 TTTCTATTTC
1238 TTCTCTCTTTTTTTTCTCCTTTTT
1 TTCTCTCTTTTTTTTCTCCTTTTT
1262 TTCTCT-TTTTTTTTCT--TTTTT
1 TTCTCTCTTTTTTTTCTCCTTTTT
1283 TT
1 TT
1285 AGTTGAACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
23 10 0.43
24 6 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTCTCTCTTTTTTTTCTCCTTTTT
Found at i:1284 original size:10 final size:10
Alignment explanation
Indices: 1243--1284 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1233 ATTTCTTCTC
1243 TCTTTTTTTT
1 TCTTTTTTTT
*
1253 CTCCTTTTTTTC
1 -T-CTTTTTTTT
1265 TCTTTTTTTT
1 TCTTTTTTTT
1275 TCTTTTTTTT
1 TCTTTTTTTT
1285 AGTTGAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1284 original size:11 final size:11
Alignment explanation
Indices: 1245--1284 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1235 TTCTTCTCTC
*
1245 TTTTTTTTCTC
1 TTTTTTTTCTT
*
1256 CTTTTTTTCTCT
1 TTTTTTTTCT-T
1268 TTTTTTTTCTT
1 TTTTTTTTCTT
1279 TTTTTT
1 TTTTTT
1285 AGTTGAACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:3166 original size:20 final size:21
Alignment explanation
Indices: 3141--3189 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3131 GCACTCGTTA
3141 GATGAAAAGACATACTT-TTG
1 GATGAAAAGACATACTTGTTG
**
3161 GATGAAAAGATGTACTTGTTG
1 GATGAAAAGACATACTTGTTG
*
3182 GACGAAAA
1 GATGAAAA
3190 AAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
GATGAAAAGACATACTTGTTG
Found at i:8790 original size:20 final size:20
Alignment explanation
Indices: 8765--8818 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
8755 CTACCACTAT
* *
8765 TTGTATCGATACATGGTCCA
1 TTGTATCGATACATGATCAA
*
8785 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
8805 TTGTATCGATACAT
1 TTGTATCGATACAT
8819 TGCTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:11062 original size:21 final size:20
Alignment explanation
Indices: 11028--11070 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
11018 TATTAAAAAG
*
11028 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
11049 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
11069 TT
1 TT
11071 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:11069 original size:20 final size:21
Alignment explanation
Indices: 11028--11070 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
11018 TATTAAAAAG
*
11028 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
11049 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
11069 TT
1 TT
11071 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:13399 original size:34 final size:33
Alignment explanation
Indices: 13356--13421 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
13346 TATTACAAGC
13356 AATGTATCGATACAATT-TCATCATGTATCGATAT
1 AATGTATCGATAC-ATTGTCAT-ATGTATCGATAT
*
13390 AATGTATCGATACATTGTCCTATGTATCGATA
1 AATGTATCGATACATTGTCATATGTATCGATA
13422 CAAATAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (33 bp):
AATGTATCGATACATTGTCATATGTATCGATAT
Found at i:20599 original size:3 final size:3
Alignment explanation
Indices: 20591--20615 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20581 TCCGAGTCAC
20591 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
20616 TTCCTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:21555 original size:13 final size:13
Alignment explanation
Indices: 21537--21593 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
21527 CATAAAGTGT
21537 TGTATCGATACAA
1 TGTATCGATACAA
21550 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
21565 GTGTTGTACCGATACAA
1 ----TGTATCGATACAA
21582 TGTATCGATACA
1 TGTATCGATACA
21594 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:21572 original size:32 final size:32
Alignment explanation
Indices: 21519--21614 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
21509 CAATGATTTA
21519 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
21552 TATCGATACATAAGTGTTGTACCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
21584 TATCGATACATAAGTTTTGTATCGATACAAT
1 TATCGATACATAAGTGTTGTATCGATACAAT
21615 TTAAGCTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:21606 original size:19 final size:18
Alignment explanation
Indices: 21519--21612 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
21509 CAATGATTTA
21519 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
21539 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
21552 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
21571 TACCGATAC--AA---TG
1 TATCGATACATAAGTTTG
21584 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
21603 TATCGATACA
1 TATCGATACA
21613 ATTTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:21673 original size:13 final size:13
Alignment explanation
Indices: 21655--21679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21645 ATTACTCAAA
21655 TGTATCGATACAT
1 TGTATCGATACAT
21668 TGTATCGATACA
1 TGTATCGATACA
21680 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21732 original size:52 final size:51
Alignment explanation
Indices: 21668--21816 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
21658 ATCGATACAT
**
21668 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
21720 TGTATCGATACACTA-CAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
21772 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
21817 TCATATTTCG
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 86 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:25931 original size:13 final size:13
Alignment explanation
Indices: 25890--25938 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
25880 CCGTTACAAG
25890 CAATGTATCGATA
1 CAATGTATCGATA
25903 CAAT-T-TC-AT-
1 CAATGTATCGATA
25912 C-ATGTATCGATA
1 CAATGTATCGATA
25924 CAATGTATCGATA
1 CAATGTATCGATA
25937 CA
1 CA
25939 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:25954 original size:33 final size:34
Alignment explanation
Indices: 25890--25959 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
25880 CCGTTACAAG
*
25890 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
25924 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCACCATGTATCGATA
25957 CAA
1 CAA
25960 ACAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Found at i:30566 original size:22 final size:22
Alignment explanation
Indices: 30541--30582 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30531 TTTTTAAAGA
*
30541 TTTGATAAAGGAGGAGAAATGT
1 TTTGATAAAGGAGGAAAAATGT
*
30563 TTTGATAAAGGTGGAAAAAT
1 TTTGATAAAGGAGGAAAAAT
30583 ATGTTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
TTTGATAAAGGAGGAAAAATGT
Found at i:31194 original size:13 final size:13
Alignment explanation
Indices: 31176--31202 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31166 ACATTATGCT
31176 TTGTATCGATACA
1 TTGTATCGATACA
31189 TTGTATCGATACA
1 TTGTATCGATACA
31202 T
1 T
31203 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:31288 original size:13 final size:13
Alignment explanation
Indices: 31267--31297 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31257 CGATACATGG
*
31267 TACAATGTATCGA
1 TACATTGTATCGA
31280 TACATTGTATCGA
1 TACATTGTATCGA
31293 TACAT
1 TACAT
31298 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:31309 original size:33 final size:33
Alignment explanation
Indices: 31251--31319 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
31241 CTACCACTGT
* *
31251 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGATACAATGTATCAATACA
*
31284 TTGTATCGATACATGATGA-ATTGTATCAATACA
1 TTGTATCGATACATGAT-ACAATGTATCAATACA
31317 TTG
1 TTG
31320 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCAATACA
Found at i:32425 original size:21 final size:21
Alignment explanation
Indices: 32380--32431 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
32370 TGGATTAATG
* *
32380 GATGCACTTGTTAGATGTAAG
1 GATGAACTTGTTAGATGTAAA
32401 GATGAACTTGTTAGATAG-AAA
1 GATGAACTTGTTAGAT-GTAAA
32422 GATGCAACTT
1 GATG-AACTT
32432 TTATAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (21 bp):
GATGAACTTGTTAGATGTAAA
Found at i:35123 original size:4 final size:4
Alignment explanation
Indices: 35114--35139 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35104 AATAAAAGGA
35114 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
35140 CCAAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:36546 original size:26 final size:25
Alignment explanation
Indices: 36517--36597 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
36507 TTACAATGAA
36517 AAATATAAAATAATTATAAAAATATT
1 AAATATAAAATAATTAT-AAAATATT
**
36543 AAAT-TAAAAT--TTATAGCATATTT
1 AAATATAAAATAATTATAAAATA-TT
36566 AAATATAATAA-AATTATAAAATATT
1 AAATATAA-AATAATTATAAAATATT
36591 GAAATAT
1 -AAATAT
36598 TTTATATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
22 4 0.09
23 10 0.22
24 3 0.07
25 10 0.22
26 18 0.40
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATATAAAATAATTATAAAATATT
Found at i:36664 original size:13 final size:14
Alignment explanation
Indices: 36646--36674 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36636 TATGATTTAG
36646 AAAAATAAAAT-TA
1 AAAAATAAAATATA
36659 AAAAATAAAATATA
1 AAAAATAAAATATA
36673 AA
1 AA
36675 GCAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAAAATATA
Found at i:38285 original size:219 final size:219
Alignment explanation
Indices: 37836--38391 Score: 909
Period size: 219 Copynumber: 2.5 Consensus size: 219
37826 AAGACTTTTT
* * *
37836 TTTATATTCACTTGTCATATATTAATAATTTTATTTTTGAAATATATGTACCTTATAAATAATCA
1 TTTAAATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCA
* * * *
37901 AACCCAAATTGAGAAAAGAAAACTTTATTTACTAGGATTATCTAATGTTTAATATAACTGAAATC
66 AACCCAAATTGAGAAAAGAAAACCTTATTTACTAGGATTATCTAGTGTATGATATAACTGAAATC
*
37966 TTATAAAAAAATATACATTTAAGATTATTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCT
131 TTATAAAAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCT
*
38031 CATATGATTTTATGAAGATGTTTC
196 CATATAATTTTATGAAGATGTTTC
* *
38055 CTTAAATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAAAAATCA
1 TTTAAATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCA
*
38120 AACCCAAATTGAGAAAAGAAAACCTTATTTACTAGGATTATCTAGTGTATGATATAACTTAAATC
66 AACCCAAATTGAGAAAAGAAAACCTTATTTACTAGGATTATCTAGTGTATGATATAACTGAAATC
** *
38185 TTAT-AAAAAATATATGTTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTTT
131 TTATAAAAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCT
38249 CATATAATTTTATGAAGATAGTTTC
196 CATATAATTTTATGAAGAT-GTTTC
*
38274 TTTACATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCA
1 TTTAAATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCA
* * *
38339 AACTCAAATTGAGAAAAGAAAA-CTCTATTTACTAGGATTATTTAGTGTCTGAT
66 AACCCAAATTGAGAAAAGAAAACCT-TATTTACTAGGATTATCTAGTGTATGAT
38392 TTTATTTGAA
Statistics
Matches: 314, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
218 76 0.24
219 238 0.76
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (219 bp):
TTTAAATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCA
AACCCAAATTGAGAAAAGAAAACCTTATTTACTAGGATTATCTAGTGTATGATATAACTGAAATC
TTATAAAAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCT
CATATAATTTTATGAAGATGTTTC
Found at i:38514 original size:170 final size:166
Alignment explanation
Indices: 38218--38553 Score: 469
Period size: 170 Copynumber: 2.0 Consensus size: 166
38208 TTACTTTTTA
* * * * *
38218 GATTTTGTTTGAATAACTTAAATCTTTTTTTCATATAATTTTATGAAGATAGTTTCTTTACATTC
1 GATTTTATTTGAATAACTTAAATCTTTTTTTCAAATAATTTTATGAAGACAGTCTCCTTACATTC
* * *
38283 ACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACTCAAAT
66 ACTTATCATATATTAATAATTTTATTTTTAAAATATATATACCTTATAAAAAATAAAACTCAAAT
* *
38348 TGAGAAAAGAAAACTCTATTTACTAGGATTATTTAGTGTCT
131 T---AAAA-AAAA-TCTATTTACTAAGATTATCTAGTGTCT
* *
38389 GATTTTATTTGAATAATTTAAAT-TTTTTTCTTAAATAATTTTATGAAGACA-TCTCCTTACATT
1 GATTTTATTTGAATAACTTAAATCTTTTTT-TCAAATAATTTTATGAAGACAGTCTCCTTACATT
* * *
38452 TATTTATTATATATTAATAATTTTATTTTTAAAATATATATACCTTATAAAAAATAAAACTCAAA
65 CACTTATCATATATTAATAATTTTATTTTTAAAATATATATACCTTATAAAAAATAAAACTCAAA
38517 TTAAAAAAAATCTATTTACTAAGATTATCTAGTGTCT
130 TTAAAAAAAATCTATTTACTAAGATTATCTAGTGTCT
38554 AATATAAAAA
Statistics
Matches: 149, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
165 25 0.17
166 4 0.03
167 4 0.03
170 77 0.52
171 39 0.26
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (166 bp):
GATTTTATTTGAATAACTTAAATCTTTTTTTCAAATAATTTTATGAAGACAGTCTCCTTACATTC
ACTTATCATATATTAATAATTTTATTTTTAAAATATATATACCTTATAAAAAATAAAACTCAAAT
TAAAAAAAATCTATTTACTAAGATTATCTAGTGTCT
Found at i:40909 original size:43 final size:43
Alignment explanation
Indices: 40827--40909 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
40817 AATAATTATT
* * *
40827 ATATTAATAAAATAATATTTTAATAATTATTGTAATATTTAAA
1 ATATTAATAAAATAATATTTTAATAATAATAGCAATATTTAAA
* * *
40870 ATATTAATATAATTAT-TTTTAATAATAAATAGCATTATTT
1 ATATTAATAAAATAATATTTTAATAAT-AATAGCAATATTT
40910 TAAGTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 10 0.30
43 23 0.70
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (43 bp):
ATATTAATAAAATAATATTTTAATAATAATAGCAATATTTAAA
Found at i:44408 original size:2 final size:2
Alignment explanation
Indices: 44403--44427 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44393 GTCATATATA
44403 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
44428 ACATGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45815 original size:2 final size:2
Alignment explanation
Indices: 45808--45849 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
45798 TAAGAGCGAG
* * *
45808 TA TA TA TA TA TA TA TA TA TA AA CA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45850 ACAACTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:46443 original size:15 final size:16
Alignment explanation
Indices: 46415--46444 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46405 AAGAATAAAG
46415 ATTTAATATTTTTTCT
1 ATTTAATATTTTTTCT
46431 ATTTAAT-TTTTTTC
1 ATTTAATATTTTTTC
46445 AAGTGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTAATATTTTTTCT
Found at i:47830 original size:48 final size:48
Alignment explanation
Indices: 47759--47856 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
47749 TTTGGATTGA
47759 CTTGGATATTTGGATAGAGAGGAAGATGGATGATTTGATGATAAGTGT
1 CTTGGATATTTGGATAGAGAGGAAGATGGATGATTTGATGATAAGTGT
47807 CTTGGATATTTGGATAGAGAGGAAGATGGATGATTTGATGATAAGTGT
1 CTTGGATATTTGGATAGAGAGGAAGATGGATGATTTGATGATAAGTGT
47855 CT
1 CT
47857 AATACAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.34
Consensus pattern (48 bp):
CTTGGATATTTGGATAGAGAGGAAGATGGATGATTTGATGATAAGTGT
Found at i:47836 original size:24 final size:25
Alignment explanation
Indices: 47761--47843 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 25
47751 TGGATTGACT
47761 TGGAT-ATTTGGATAGAGAGGAAGA
1 TGGATGATTTGGATAGAGAGGAAGA
* ***
47785 TGGATGATTTGATGATA-AG-TG-TCT
1 TGGATGATTTG--GATAGAGAGGAAGA
47809 TGGAT-ATTTGGATAGAGAGGAAGA
1 TGGATGATTTGGATAGAGAGGAAGA
47833 TGGATGATTTG
1 TGGATGATTTG
47844 ATGATAAGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
21 4 0.09
22 2 0.05
23 6 0.14
24 15 0.34
25 11 0.25
26 2 0.05
27 4 0.09
ACGTcount: A:0.31, C:0.01, G:0.35, T:0.33
Consensus pattern (25 bp):
TGGATGATTTGGATAGAGAGGAAGA
Found at i:49685 original size:50 final size:50
Alignment explanation
Indices: 49614--49769 Score: 213
Period size: 50 Copynumber: 3.1 Consensus size: 50
49604 GCTTAGAGTT
* * * * * *
49614 AACAATTATGGCCACTTCTCTCTACTATCAAAGGTTAGTGAAGAATAGTT
1 AACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTC
*
49664 AACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTC
* * * *
49714 AACAATTAGGGTCATCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTC
49764 AACAAT
1 AACAAT
49770 GGCAACACCT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (50 bp):
AACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTC
Found at i:54202 original size:50 final size:51
Alignment explanation
Indices: 54147--54381 Score: 334
Period size: 50 Copynumber: 4.7 Consensus size: 51
54137 CTATTATGGC
* *
54147 CACCTCTCTCTATTGTCAAAGGTTGATGAAAAATAGTCAACAATTACGACT
1 CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGACT
* *
54198 -ACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTTAACAATTATGA-T
1 CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGACT
* * * *
54247 CACCTCTCTCTATTGTTAAAGGTTGGTAAAGAATAATCAACAATTACGGCT
1 CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGACT
* *
54298 -ACCTCTCTCTATTGTCAAAAGTTGGTGAAGAATAGTCAACAATTACG-GT
1 CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGACT
* *
54347 CATCTCTCTCGATTGTCAAAGGTTGGTGAAGAATA
1 CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATA
54382 ATTAATAATG
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
49 2 0.01
50 160 0.98
51 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (51 bp):
CACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGACT
Found at i:55356 original size:22 final size:24
Alignment explanation
Indices: 55331--55380 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
55321 TGAGAATCGA
*
55331 TAAAATTTTA-ACGAAAAA-AATT
1 TAAAATTTTATACAAAAAATAATT
*
55353 TAAAATTTTATATAAAAAATAATT
1 TAAAATTTTATACAAAAAATAATT
55377 TAAA
1 TAAA
55381 CTCAACCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 6 0.25
24 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAATTTTATACAAAAAATAATT
Found at i:58698 original size:15 final size:15
Alignment explanation
Indices: 58678--58727 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
58668 TTATTTTTAT
58678 TTAAAAATTTAAAAA
1 TTAAAAATTTAAAAA
*
58693 TT-AAAATATT-AAAT
1 TTAAAAAT-TTAAAAA
* *
58707 TTAATAATATAAAAA
1 TTAAAAATTTAAAAA
58722 TTAAAA
1 TTAAAA
58728 TATATATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATTTAAAAA
Found at i:58707 original size:21 final size:21
Alignment explanation
Indices: 58682--58726 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
58672 TTTTATTTAA
58682 AAATTTAAAAAT-TAAAATATT
1 AAATTTAAAAATATAAAA-ATT
*
58703 AAATTTAATAATATAAAAATT
1 AAATTTAAAAATATAAAAATT
58724 AAA
1 AAA
58727 ATATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTAAAAATATAAAAATT
Found at i:59544 original size:4 final size:4
Alignment explanation
Indices: 59535--59569 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
59525 AGGAAATTGT
59535 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
59570 TTGTGTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:60512 original size:15 final size:15
Alignment explanation
Indices: 60474--60512 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
60464 TCAAGAATAC
60474 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
60489 AATACAAAAAGAGAG
1 AAAAAAAAAAGAAAG
60504 AAAAAAAAA
1 AAAAAAAAA
60513 CCAGTATTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:61281 original size:12 final size:11
Alignment explanation
Indices: 61259--61334 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
61249 AGAGAAAGAA
*
61259 GAGAGAGGAGG
1 GAGATAGGAGG
61270 GATGATAGGAGG
1 GA-GATAGGAGG
*
61282 AGAGACAGGA--
1 -GAGATAGGAGG
*
61292 GAGATAGTA--
1 GAGATAGGAGG
61301 GAGATAGGAGG
1 GAGATAGGAGG
61312 GATGATAGGAGG
1 GA-GATAGGAGG
*
61324 AGAGACAGGAG
1 -GAGATAGGAG
61335 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:61310 original size:42 final size:42
Alignment explanation
Indices: 61249--61367 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
61239 TAGCCCTCAA
* *
61249 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
61291 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
61333 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
61368 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:61351 original size:18 final size:18
Alignment explanation
Indices: 61324--61373 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
61314 TGATAGGAGG
*
61324 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
61342 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
61360 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
61374 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:66359 original size:15 final size:15
Alignment explanation
Indices: 66339--66374 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
66329 TTCATGGTTG
*
66339 TCATCACTTTATTTC
1 TCATCACTCTATTTC
*
66354 TCATCACTCTATTTT
1 TCATCACTCTATTTC
66369 TCATCA
1 TCATCA
66375 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (15 bp):
TCATCACTCTATTTC
Found at i:66432 original size:25 final size:25
Alignment explanation
Indices: 66377--66432 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
66367 TTTCATCAAT
*
66377 TTTTTTAATTTAATTTTATAAAATA
1 TTTTATAATTTAATTTTATAAAATA
*
66402 TGTTATAATTT-A-TTTATAAATTATA
1 TTTTATAATTTAATTTTATAAA--ATA
66427 TTTTAT
1 TTTTAT
66433 TGTACATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 1 0.04
25 17 0.65
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTATAATTTAATTTTATAAAATA
Found at i:68554 original size:13 final size:13
Alignment explanation
Indices: 68536--68583 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
68526 AAAATTTTAT
68536 TTTCTTTTAAGAA
1 TTTCTTTTAAGAA
* *
68549 TTTCTTTTGATAA
1 TTTCTTTTAAGAA
*
68562 TTTTATTTTAAGAA
1 -TTTCTTTTAAGAA
68576 -TTCTTTTA
1 TTTCTTTTA
68584 TACCTTTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 7 0.25
13 11 0.39
14 10 0.36
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (13 bp):
TTTCTTTTAAGAA
Found at i:68577 original size:14 final size:14
Alignment explanation
Indices: 68534--68577 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
68524 TAAAAATTTT
68534 ATTTTCTTTTAAGA
1 ATTTTCTTTTAAGA
* *
68548 A-TTTCTTTTGATA
1 ATTTTCTTTTAAGA
*
68561 ATTTTATTTTAAGA
1 ATTTTCTTTTAAGA
68575 ATT
1 ATT
68578 CTTTTATACC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTTCTTTTAAGA
Found at i:70691 original size:35 final size:35
Alignment explanation
Indices: 70645--70715 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
70635 ATATATACTT
*
70645 AAATAAAGTGACTAAGAATATCCATGCATAATAAA
1 AAATAAAGTGACTAAGAATATCCATACATAATAAA
70680 AAATAAAGTGACTAAGAATATCCATACATAATAAA
1 AAATAAAGTGACTAAGAATATCCATACATAATAAA
70715 A
1 A
70716 GATATGATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.23
Consensus pattern (35 bp):
AAATAAAGTGACTAAGAATATCCATACATAATAAA
Found at i:75743 original size:21 final size:21
Alignment explanation
Indices: 75719--75766 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
75709 CACTCGTTAA
75719 ATGAAAAGATGCACTTATTGG
1 ATGAAAAGATGCACTTATTGG
* *
75740 ATGAAAAGATGTACTTGTTGG
1 ATGAAAAGATGCACTTATTGG
75761 ATGAAA
1 ATGAAA
75767 CAATGCAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (21 bp):
ATGAAAAGATGCACTTATTGG
Found at i:79981 original size:16 final size:16
Alignment explanation
Indices: 79964--80027 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
79954 TTTTATTCAG
*
79964 ATCATTTTGAGTTTAG
1 ATCATTTTGAGTTTAA
* *
79980 ATCATTTCGTA-TTCAA
1 ATCATTTTG-AGTTTAA
* * *
79996 ATCATTCTAAATTTAA
1 ATCATTTTGAGTTTAA
80012 ATCATTTTGAGTTTAA
1 ATCATTTTGAGTTTAA
80028 GTTAATTAGT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (16 bp):
ATCATTTTGAGTTTAA
Found at i:79984 original size:32 final size:32
Alignment explanation
Indices: 79939--80020 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
79929 AGAGCGATTT
* * * *
79939 TAAATTTGAATCATTTTTTATTCAGATCATTT
1 TAAATTTAAATCATTTTGTATTCAAATCATTC
* * * *
79971 TGAGTTTAGATCATTTCGTATTCAAATCATTC
1 TAAATTTAAATCATTTTGTATTCAAATCATTC
80003 TAAATTTAAATCATTTTG
1 TAAATTTAAATCATTTTG
80021 AGTTTAAGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (32 bp):
TAAATTTAAATCATTTTGTATTCAAATCATTC
Found at i:82824 original size:3 final size:3
Alignment explanation
Indices: 82816--82841 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
82806 GAAACTTTTC
82816 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
82842 TTACCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:84474 original size:21 final size:21
Alignment explanation
Indices: 84448--84488 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84438 CTATTTAAAT
84448 TATTATT-TTAATAATAAAAAA
1 TATTATTATTAA-AATAAAAAA
*
84469 TATTATTATTTAAATAAAAA
1 TATTATTATTAAAATAAAAA
84489 TATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTATTATTAAAATAAAAAA
Found at i:84502 original size:20 final size:20
Alignment explanation
Indices: 84464--84504 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
84454 TTTAATAATA
* * *
84464 AAAAATATTATTATTTAAAT
1 AAAAATATAAATATATAAAT
84484 AAAAATATAAATATATAAAT
1 AAAAATATAAATATATAAAT
84504 A
1 A
84505 TAATATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATATAAATATATAAAT
Found at i:85229 original size:23 final size:23
Alignment explanation
Indices: 85192--85236 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
85182 ATTTATCTTA
85192 TTTTCTTTTCATTTAACTGTTTATT
1 TTTTCTTTT-ATTTAACT-TTTATT
85217 TTTTCTTTT-TTTAACTTTTA
1 TTTTCTTTTATTTAACTTTTA
85237 GCAATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
25 9 0.45
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTCTTTTATTTAACTTTTATT
Found at i:85259 original size:18 final size:18
Alignment explanation
Indices: 85232--85293 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
85222 TTTTTTTAAC
*
85232 TTTTAGCAATTGTATTTT
1 TTTTACCAATTGTATTTT
*
85250 TTTTACCAATAATAATATTTTT
1 TTTTACCAAT--T-GTA-TTTT
85272 TCTTTACC-ATTGTATTTT
1 T-TTTACCAATTGTATTTT
85290 TTTT
1 TTTT
85294 TATAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
17 3 0.08
18 14 0.39
19 2 0.06
20 2 0.06
21 2 0.06
22 7 0.19
23 6 0.17
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTACCAATTGTATTTT
Found at i:85990 original size:2 final size:2
Alignment explanation
Indices: 85983--86018 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
85973 GAGATTTCTC
85983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86019 CAATTTATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86226 original size:166 final size:169
Alignment explanation
Indices: 86050--86359 Score: 448
Period size: 174 Copynumber: 1.8 Consensus size: 169
86040 GTTATTTTTT
*
86050 AAAAAAAATAATGATCACAATTTCGTATTATAAAATTTATGTATTAAACTTGAAAAAGATTTC-T
1 AAAAAAAATAATGATCACAATTTCGTATCATAAAATTTATGTATTAAACTTGAAAAAGATTTCTT
* * * * **
86114 -T-GA-CTGAGTTCATTTATCATATTAAACTCTTGAAACTATTAAAAATTGTTGATTTGATTTTT
66 CTACAGCTGAGGTCATTTATCATATTAAAATCTTGAAACTATAAAAAATTGTTGATTTGACATTT
86176 TCATCCAATTTGTCTCTAGTGAAAGAATTTTTTTTTAAA
131 TCATCCAATTTGTCTCTAGTGAAAGAATTTTTTTTTAAA
* *
86215 AAAATAAAATAATGATCACAATTTTGTATCATAAAATTTATTTATTAAACTTGAAAAAGATTTCT
1 AAAA-AAAATAATGATCACAATTTCGTATCATAAAATTTATGTATTAAACTTGAAAAAGATTTCT
*
86280 TCCACCTACAGCTGAGGTCGTTTATCATATTAAAATCTTGAAACTATAAAAAATTGTTGATTTGA
65 T----CTACAGCTGAGGTCATTTATCATATTAAAATCTTGAAACTATAAAAAATTGTTGATTTGA
*
86345 CATTTTCATCTAATT
126 CATTTTCATCCAATT
86360 AAATTATGAT
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
165 4 0.03
166 56 0.45
167 1 0.01
172 1 0.01
173 1 0.01
174 62 0.50
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (169 bp):
AAAAAAAATAATGATCACAATTTCGTATCATAAAATTTATGTATTAAACTTGAAAAAGATTTCTT
CTACAGCTGAGGTCATTTATCATATTAAAATCTTGAAACTATAAAAAATTGTTGATTTGACATTT
TCATCCAATTTGTCTCTAGTGAAAGAATTTTTTTTTAAA
Found at i:86727 original size:64 final size:64
Alignment explanation
Indices: 86626--86754 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
86616 TTTTTGTTTT
86626 TTTTCTTTTTAAAACATCATACGGTATGGACTTTATGTATCAAACTTTTATTGATTAATGGTTA
1 TTTTCTTTTTAAAACATCATACGGTATGGACTTTATGTATCAAACTTTTATTGATTAATGGTTA
86690 TTTTCTTTTTAAAACATCATACGGTATGGACTTTATGTATCAAACTTTTATTGATTAATGGTTA
1 TTTTCTTTTTAAAACATCATACGGTATGGACTTTATGTATCAAACTTTTATTGATTAATGGTTA
86754 T
1 T
86755 ATCAGCATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (64 bp):
TTTTCTTTTTAAAACATCATACGGTATGGACTTTATGTATCAAACTTTTATTGATTAATGGTTA
Found at i:88170 original size:3 final size:3
Alignment explanation
Indices: 88162--88187 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
88152 ACATTTGGTA
88162 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
88188 CCACGCCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:90251 original size:13 final size:14
Alignment explanation
Indices: 90215--90252 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
90205 AAACAATTTA
90215 ATTTCATTAAAAAT
1 ATTTCATTAAAAAT
*
90229 ACTTTCATTAAATAT
1 A-TTTCATTAAAAAT
90244 ATTT-ATTAA
1 ATTTCATTAA
90253 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 4 0.18
15 13 0.59
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTCATTAAAAAT
Found at i:90264 original size:70 final size:71
Alignment explanation
Indices: 90175--90321 Score: 165
Period size: 71 Copynumber: 2.1 Consensus size: 71
90165 ATATATATTT
* * * * * *
90175 TTTATTCATAAGATTTATCTCATTTAT-ATTAAACAA-TTTAATTTCA-TTAAAAATACTTTCAT
1 TTTATTAATAAAATTTATCTAATTTATAAGTAAA-AATTTTAATTTAATTTAAAAA-AATTTCAT
*
90237 TAAATATA
64 TAAATAAA
* **
90245 TTTATTAATAAAATTTATCTAATTTGTAAGTAAAAATTTTAATTTAATTTAAAAAAATTTTGTTA
1 TTTATTAATAAAATTTATCTAATTTATAAGTAAAAATTTTAATTTAATTTAAAAAAATTTCATTA
90310 AATAAA
66 AATAAA
90316 TTTATT
1 TTTATT
90322 TGATAATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
70 25 0.39
71 32 0.50
72 7 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (71 bp):
TTTATTAATAAAATTTATCTAATTTATAAGTAAAAATTTTAATTTAATTTAAAAAAATTTCATTA
AATAAA
Done.