Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold311
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: 800152
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 7
Found at i:581 original size:24 final size:25
Alignment explanation
Indices: 549--595 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
539 GCAAATAAAT
*
549 TTTGATATG-AATTACTTGATTATG
1 TTTGATATGAAATCACTTGATTATG
573 TTTGATATGAAATCACTTGATTA
1 TTTGATATGAAATCACTTGATTA
596 AGGGGGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (25 bp):
TTTGATATGAAATCACTTGATTATG
Found at i:1246 original size:20 final size:20
Alignment explanation
Indices: 1223--1295 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1213 ACAATTCAAA
1223 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1243 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1264 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1284 GTATCGATACAT
1 GTATCGATACAT
1296 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1267 original size:21 final size:21
Alignment explanation
Indices: 1241--1316 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1231 ACATGTTGCA
1241 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1262 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1282 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1303 TTGTATCGATACAT
1 ATGTATCGATACAT
1317 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1274 original size:41 final size:41
Alignment explanation
Indices: 1223--1316 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1213 ACAATTCAAA
*
1223 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1264 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1305 GTATCGATACAT
1 GTATCGATACAT
1317 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1373 original size:13 final size:13
Alignment explanation
Indices: 1355--1380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1345 TACAGCAAGT
1355 ATGTATCGATACA
1 ATGTATCGATACA
1368 ATGTATCGATACA
1 ATGTATCGATACA
1381 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3301 original size:29 final size:29
Alignment explanation
Indices: 3259--3317 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3249 TTTGTATGCG
*
3259 GTGCGATGTTAACTTTTTGTTAAGACAAA
1 GTGCGATGTTAACTTTGTGTTAAGACAAA
3288 GTGCGATGTTAACTTTGTGTTAAGACAAA
1 GTGCGATGTTAACTTTGTGTTAAGACAAA
3317 G
1 G
3318 ATGCATGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (29 bp):
GTGCGATGTTAACTTTGTGTTAAGACAAA
Found at i:6765 original size:3 final size:3
Alignment explanation
Indices: 6759--6792 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6749 CATCATCCTT
*
6759 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6793 CTTACACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:7356 original size:27 final size:28
Alignment explanation
Indices: 7326--7395 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
7316 AAAAATTTAA
7326 TAAAAAATATATATAATTATT-AAAAAT
1 TAAAAAATATATATAATTATTAAAAAAT
* *
7353 TAAATAAAAAT-TAT-ATTTTTAAAAAAAT
1 TAAA-AAATATATATAATTATT-AAAAAAT
7381 TAAAAAATA-ATATAA
1 TAAAAAATATATATAA
7396 ATAAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
26 5 0.14
27 14 0.40
28 16 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAAATATATATAATTATTAAAAAAT
Found at i:7448 original size:30 final size:29
Alignment explanation
Indices: 7391--7448 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
7381 TAAAAAATAA
*
7391 TATAAATAAAATTAATTTAAATTATTTATT
1 TATAAATAAAATAAATTTAAA-TATTTATT
7421 TATAAATATAAATAAAATTTAAA-ATTTA
1 TATAAATA-AAAT-AAATTTAAATATTTA
7449 AATTTCGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 13 0.52
31 4 0.16
32 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATAAATAAAATAAATTTAAATATTTATT
Found at i:7892 original size:10 final size:10
Alignment explanation
Indices: 7877--7901 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7867 TAAAATATTT
7877 ATTTAATTAA
1 ATTTAATTAA
7887 ATTTAATTAA
1 ATTTAATTAA
7897 ATTTA
1 ATTTA
7902 TTAGACATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTAATTAA
Found at i:8802 original size:2 final size:2
Alignment explanation
Indices: 8795--8834 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8785 CTTATTTGGA
8795 AT AT 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 AT AT
8835 TCAACTGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10436 original size:50 final size:50
Alignment explanation
Indices: 10347--10586 Score: 293
Period size: 50 Copynumber: 4.8 Consensus size: 50
10337 ATTTTTTACT
* * * * * *
10347 AACTTCTGACAATTGAGAGAAGTACCCGTAATTATTGACTATGCTTCACC
1 AACTTTTGACAATCGAGAGAGGTAGCCGTAATTGTTGACTATTCTTCACC
* * *
10397 AACCTTTGACGATCGAGAGAGGTAGCCGTAATTGTTGACTATTCTTCATC
1 AACTTTTGACAATCGAGAGAGGTAGCCGTAATTGTTGACTATTCTTCACC
* *
10447 AACATTTGACAATCGAGAGAGGT-GACCGTAATTGTTGACTATTCTTAACC
1 AACTTTTGACAATCGAGAGAGGTAG-CCGTAATTGTTGACTATTCTTCACC
* * *
10497 AACTTTTGATAATCGAGAGAGGTGGCCATAATTGTTGACTATTCTTCACC
1 AACTTTTGACAATCGAGAGAGGTAGCCGTAATTGTTGACTATTCTTCACC
* * ** *
10547 AACTTTTGACAATAGAGAAATATAACCGTAATTGTTGACT
1 AACTTTTGACAATCGAGAGAGGTAGCCGTAATTGTTGACT
10587 TTAAGCATCT
Statistics
Matches: 163, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 161 0.99
51 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (50 bp):
AACTTTTGACAATCGAGAGAGGTAGCCGTAATTGTTGACTATTCTTCACC
Found at i:15035 original size:50 final size:50
Alignment explanation
Indices: 14957--15162 Score: 281
Period size: 50 Copynumber: 4.1 Consensus size: 50
14947 GCAAAGTGAT
14957 TTGACTATTCTTCACCAA-CTTCTGACAATCGAGAGAGGTAGCCGTAATTG
1 TTGACTATTCTTCACCAACCTT-TGACAATCGAGAGAGGTAGCCGTAATTG
* * * *
15007 TTAACTATCCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTAGCCGTAATTG
* *
15057 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAGGTAACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTAGCCGTAATTG
* * * * *
15107 TTGACTATTCTTCACCAACCTTTGATAATAGAGAAACGT-GATCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTAG-CCGTAATTG
15157 TTGACT
1 TTGACT
15163 CTAAACATCT
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 136 0.98
51 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTAGCCGTAATTG
Found at i:15130 original size:100 final size:100
Alignment explanation
Indices: 14957--15162 Score: 315
Period size: 100 Copynumber: 2.1 Consensus size: 100
14947 GCAAAGTGAT
*
14957 TTGACTATTCTTCACCAACTTCTGACAATCGAGAGAGGTAGCCGTAATTGTTAACTATCCTTCAC
1 TTGACTATTCTTCACCAACTTCTGACAATCGAGAGAGGTAACCGTAATTGTTAACTATCCTTCAC
* * * *
15022 CAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
66 CAACCTTTGACAATAGAGAAACGTGATCGTAATTG
* * *
15057 TTGACTATTCTTCACCAACCTT-TGATAATCGAGAGAGGTAACCGTAATTGTTGACTATTCTTCA
1 TTGACTATTCTTCACCAA-CTTCTGACAATCGAGAGAGGTAACCGTAATTGTTAACTATCCTTCA
*
15121 CCAACCTTTGATAATAGAGAAACGTGATCGTAATTG
65 CCAACCTTTGACAATAGAGAAACGTGATCGTAATTG
15157 TTGACT
1 TTGACT
15163 CTAAACATCT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 93 0.97
101 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACTTCTGACAATCGAGAGAGGTAACCGTAATTGTTAACTATCCTTCAC
CAACCTTTGACAATAGAGAAACGTGATCGTAATTG
Found at i:15905 original size:17 final size:18
Alignment explanation
Indices: 15883--15917 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
15873 ATGTCTAATT
15883 TTTTTAAAAATTT-TTAA
1 TTTTTAAAAATTTATTAA
*
15900 TTTTTAAATATTTATTAA
1 TTTTTAAAAATTTATTAA
15918 CAACATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTAAAAATTTATTAA
Found at i:21166 original size:19 final size:19
Alignment explanation
Indices: 21131--21174 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21121 TATAAATTTT
21131 TTTAATATAAATTAATTTAA
1 TTTAATATAAA-TAATTTAA
*
21151 TTTAATAATAAA-AATTTTA
1 TTTAAT-ATAAATAATTTAA
21170 TTTAA
1 TTTAA
21175 ATTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATATAAATAATTTAA
Found at i:21186 original size:25 final size:25
Alignment explanation
Indices: 21123--21190 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
21113 GGTCGAAATA
* *
21123 TAAATTTTTTTAATATAAA-TTAATT
1 TAAATTTTATT-ATAAAAATTTAATT
* * *
21148 T-AATTTAATAATAAAAATTTTATT
1 TAAATTTTATTATAAAAATTTAATT
21172 TAAATTTTATTATAAAAAT
1 TAAATTTTATTATAAAAAT
21191 ATAAATATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 6 0.18
24 12 0.35
25 16 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAATTTTATTATAAAAATTTAATT
Found at i:21205 original size:20 final size:20
Alignment explanation
Indices: 21172--21209 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21162 AAATTTTATT
* *
21172 TAAATTTTATTATAAAAATA
1 TAAATATTAATATAAAAATA
21192 TAAATATTAATATAAAAA
1 TAAATATTAATATAAAAA
21210 AATTTCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:21407 original size:15 final size:15
Alignment explanation
Indices: 21387--21418 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21377 ATTTAAGTTA
21387 TTAAATAAATTAAAT
1 TTAAATAAATTAAAT
*
21402 TTAAATATATTAAAT
1 TTAAATAAATTAAAT
21417 TT
1 TT
21419 TATTCGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATAAATTAAAT
Found at i:21523 original size:12 final size:13
Alignment explanation
Indices: 21499--21537 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
21489 TCAAATGAAT
21499 AATA-AATAATTA
1 AATATAATAATTA
*
21511 AATTTAA-AATTA
1 AATATAATAATTA
21523 AATATAATAATTA
1 AATATAATAATTA
21536 AA
1 AA
21538 CTTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAATAATTA
Found at i:21616 original size:6 final size:6
Alignment explanation
Indices: 21599--21641 Score: 56
Period size: 5 Copynumber: 7.5 Consensus size: 6
21589 CTTAAATCAT
21599 ATTTAA ATTTTAA ATTTAA ATTT-A ATTT-A ATTTAA A-TTAA ATT
1 ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
21642 CGAACTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.44
6 13 0.38
7 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:21632 original size:16 final size:16
Alignment explanation
Indices: 21601--21641 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
21591 TAAATCATAT
21601 TTAAATTTTAAATTTAAA
1 TTAAA-TTT-AATTTAAA
*
21619 TTTAATTTAATTTAAA
1 TTAAATTTAATTTAAA
21635 TTAAATT
1 TTAAATT
21642 CGAACTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 3 0.14
18 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAATTTAATTTAAA
Found at i:21892 original size:21 final size:21
Alignment explanation
Indices: 21868--21909 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21858 AAAAATATTT
*
21868 TTATTTAAAT-TTAATTATAAA
1 TTATATAAATATTAA-TATAAA
21889 TTATATAAATATTAATATAAA
1 TTATATAAATATTAATATAAA
21910 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATAAATATTAATATAAA
Found at i:21913 original size:49 final size:49
Alignment explanation
Indices: 21845--21963 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 49
21835 TTGATTTGAT
*
21845 TAAA-ATTAATGATAAAAATA-TTTTTATTTAA-ATTTAATTATAAATTATA
1 TAAATATTAATAATAAAAATATTTTTTATTTAATA-TTAATTATAAA-TA-A
**
21894 TAAATATTAAT-ATAAAAATAATTTTTTATTTTTTATTAATTATAAATAA
1 TAAATATTAATAATAAAAAT-ATTTTTTATTTAATATTAATTATAAATAA
* *
21943 TAAATATAAATAATATAAATA
1 TAAATATTAATAATAAAAATA
21964 AATTAAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
49 24 0.39
50 16 0.26
51 20 0.33
52 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (49 bp):
TAAATATTAATAATAAAAATATTTTTTATTTAATATTAATTATAAATAA
Found at i:21952 original size:13 final size:14
Alignment explanation
Indices: 21934--21966 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
21924 TTTTATTAAT
21934 TATAAATAATA-AA
1 TATAAATAATATAA
21947 TATAAATAATATAA
1 TATAAATAATATAA
21961 -ATAAAT
1 TATAAAT
21967 TAAATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAATAATATAA
Found at i:21970 original size:9 final size:10
Alignment explanation
Indices: 21941--21985 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
21931 AATTATAAAT
21941 AATAAATATA
1 AATAAATATA
21951 AAT-AATATA
1 AATAAATATA
21960 AATAAAT-TA
1 AATAAATATA
21969 AATTAAACT-TA
1 AA-TAAA-TATA
21980 AATAAA
1 AATAAA
21986 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 14 0.44
11 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAAATATA
Found at i:23216 original size:10 final size:10
Alignment explanation
Indices: 23203--23231 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
23193 TTACCTTTTT
23203 TATATATAAA
1 TATATATAAA
23213 TATATATAAA
1 TATATATAAA
23223 TATATATAA
1 TATATATAA
23232 TAAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATATATAAA
Found at i:23244 original size:20 final size:20
Alignment explanation
Indices: 23203--23267 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
23193 TTACCTTTTT
*
23203 TATATATAAATATATATAAA
1 TATATATAAAAATATATAAA
*
23223 TATATATAATAAAT-TATTAA
1 TATATATAA-AAATATATAAA
* *
23243 TACATA-AAAATTAATATAAA
1 TATATATAAAAAT-ATATAAA
23263 T-TATA
1 TATATA
23268 ATAATTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 3 0.08
19 5 0.14
20 25 0.69
21 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATATAAAAATATATAAA
Found at i:23623 original size:2 final size:2
Alignment explanation
Indices: 23618--23658 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
23608 CACTCTCTTT
*
23618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23659 GTTCTCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24517 original size:23 final size:22
Alignment explanation
Indices: 24462--24519 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
24452 ATAATATTTG
* *
24462 ATAATTCATTATTATAAATATAA
1 ATAATT-ATTTTTAAAAATATAA
*
24485 ATAATTATTTTTAAAAATAATTA
1 ATAATTATTTTTAAAAAT-ATAA
24508 ATAATTATTTTT
1 ATAATTATTTTT
24520 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTATTTTTAAAAATATAA
Found at i:25113 original size:20 final size:18
Alignment explanation
Indices: 25063--25113 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 18
25053 AATTTTTATG
25063 TAATTTATATGTATTTAATT
1 TAATTTATA--TATTTAATT
25083 TAA-TTATTATATTTCATATT
1 TAATTTA-TATATTT-A-ATT
25103 TAATTTATATA
1 TAATTTATATA
25114 ACTTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 15 0.56
21 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATTTATATATTTAATT
Found at i:30748 original size:2 final size:2
Alignment explanation
Indices: 30743--30776 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
30733 AGATCAGTCT
*
30743 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30777 TAGCTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34010 original size:22 final size:22
Alignment explanation
Indices: 33976--34032 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
33966 CTGGACATGT
*
33976 TAAAAAAA-ACATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
33997 TAAAAAAATGCATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
34019 TAAAAAAATGCATG
1 TAAAAAAATGCATG
34033 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 8 0.24
22 26 0.76
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
TAAAAAAATGCATGAAACATAA
Found at i:34987 original size:20 final size:19
Alignment explanation
Indices: 34940--35014 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
34930 AAAAAGATAT
*
34940 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
34959 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
34980 CATGTATCGATATA-TCAAAA
1 AATGTATCGATACATTC--AA
35000 AATGTATCGATACAT
1 AATGTATCGATACAT
35015 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:35615 original size:32 final size:33
Alignment explanation
Indices: 35570--35638 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
35560 TTTTTTTTTA
**
35570 AAAAAAATGTGCCACTAACTTATGTAGGCTTTG
1 AAAAAAATGTGCCACTAACACATGTAGGCTTTG
* * *
35603 AAAAAAGT-TGCCACTGACACATGTGGGCTTTG
1 AAAAAAATGTGCCACTAACACATGTAGGCTTTG
35635 AAAA
1 AAAA
35639 GAGTGTTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (33 bp):
AAAAAAATGTGCCACTAACACATGTAGGCTTTG
Found at i:36336 original size:255 final size:256
Alignment explanation
Indices: 35625--37120 Score: 2110
Period size: 257 Copynumber: 5.8 Consensus size: 256
35615 ACTGACACAT
* ** * * *
35625 GTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAAGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT-CGTGG
35690 GCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
65 GCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * *
35755 GGTGCCACTGACTCATGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAATGGTGCCACTG
130 GGTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTG
*
35820 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGAGCTTTGAAAAGGTGCCACTGACTTGC
195 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
*
35882 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT-CGTGG
35947 GCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
65 GCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
*
36012 GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTG
130 GGTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTG
*
36077 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTTGC
195 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
*
36139 GTAGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT-GTGGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTCGTGGG
36203 CTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
66 CTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* *
36268 GTGCCACTGACTCGTGGGCTTTGAAAAAGTACCTCTGACTCGTGGGCTTGAAAGGGTGCCATTGA
131 GTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGA
* * * *
36333 CTTGTAGGCTTTGAAAGAGTGCCACTAACTCGTGGGCTTTGAAAATGTGCCACTAACTTGC
196 CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
* * *
36394 GT-GGCCTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTT-GTGGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTCGTGGG
* * * * *
36457 CTTTGAAA-GAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGCAA
66 CTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AA
* * * ** * * *
36521 GGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
129 AGGTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGC-TTG-AAAGGGTGCCA
* * *
36586 CTGACTTGTGGGCTTTGAAAAAAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
192 CTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGACTT
36651 --
255 GC
* * *
36651 ATGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGGTGCCACTGATTTACGTGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT-CGTGG
* *
36713 GCTTTGAAAGGAGTGCCACTGACTTATGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
65 GCTTTGAAAGGA-TGCCACTGAC-T-CGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
36778 AAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGC
127 AAAGG-TGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGC-TTGAAAGGGTGC
* *
36843 CACTGACTTGTGGGCTTTGAAAG-GTACCACTGACTCGTGGGCTTTGAAAAGGTACCACTGAC-T
190 CACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTT
36906 -C
255 GC
* * * *
36907 GTGGGCTTTGAAAAG-GTACCACTGAC-T-CGTGGGC-TTGAAGGGGTGCCACTGAC-TCGTGGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTCGTGGG
* *
36967 CTTTGAAAAGG-TGCCACTAACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTT
66 CTTTG-AAAGGATGCCACTGAC-T-CGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTT
* * * * * * *
37031 TGAAAGGGAGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTCGCAAGGGC
125 TGAAA-GGTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGCTT-GAAAGGGT
37096 GCCACTGACTTGTGGGCTTTGAAAG
188 GCCACTGACTTGTGGGCTTTGAAAG
37121 GGATGAACAT
Statistics
Matches: 1140, Mismatches: 78, Indels: 44
0.90 0.06 0.03
Matches are distributed among these distances:
252 23 0.02
253 25 0.02
254 120 0.11
255 365 0.32
256 45 0.04
257 383 0.34
258 52 0.05
259 45 0.04
260 82 0.07
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (256 bp):
GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTCGTGGG
CTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
GTGCCACTGACTCGTGGGCTTTGAAAAAGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGA
CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
Found at i:37122 original size:28 final size:28
Alignment explanation
Indices: 35624--37122 Score: 1826
Period size: 28 Copynumber: 52.6 Consensus size: 28
35614 CACTGACACA
* **
35624 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
35653 TGCGTGGGCTTTAAAAAGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
*
35683 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
35713 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35741 TGTGGGCTTTGAAA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
35768 CATGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35796 CGTGGGC-TTGAAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
35823 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
35851 CGTGAGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35879 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
35911 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
35940 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
35970 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35998 TGTGGGCTTTGAAA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36025 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36053 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36080 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
36108 CGTGGGCTTTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36136 TGCGTAGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
36168 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36197 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36225 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
36253 TGTGGGCTTTGAAA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * *
36280 CGTGGGCTTTGAAAAAGTACCTCTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36308 CGTGGGC-TTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36335 TGTAGGCTTTGAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** *
36363 CGTGGGCTTTGAAAATGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36391 TGCGTGGCCTTAAAAGGAGTGCCACTGACTT
1 TGTG-GGCTTTGAAAGG-GTGCCACTGAC-T
*
36422 GTGTGGGCTTTGAAAGGGAGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36451 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36479 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36507 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36535 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36563 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
** *
36592 TGTGGGCTTTGAAAAAAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
36621 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
36650 TATGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36678 TGTGGGCTTTGAAAAGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
36706 TACGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
36738 ATGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36767 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36795 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36823 CGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36851 TGTGGGCTTTGAAA-GGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36878 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36906 CGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36934 CGTGGGC-TTGAAGGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
36961 CGTGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
36989 TGCGTGGGCTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGG-GTGCCACTGAC-T
*
37021 GTGTGGGCTTTGAAAGGGAGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
37050 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
37078 TGTGGGCTTCGCAAGGGCGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
37106 TGTGGGCTTTGAAAGGG
1 TGTGGGCTTTGAAAGGG
37123 ATGAACATTC
Statistics
Matches: 1300, Mismatches: 133, Indels: 75
0.86 0.09 0.05
Matches are distributed among these distances:
27 190 0.15
28 706 0.54
29 94 0.07
30 180 0.14
31 119 0.09
32 7 0.01
33 4 0.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:38362 original size:13 final size:11
Alignment explanation
Indices: 38341--38416 Score: 68
Period size: 12 Copynumber: 6.7 Consensus size: 11
38331 GACCCTTCTA
38341 TTTTTTTGCTAT
1 TTTTTTTGCT-T
38353 TTTTTCTTGCTTT
1 TTTTT-TTGC-TT
*
38366 TTTTTTTGTTTT
1 TTTTTTTG-CTT
*
38378 TTTGTTTTGTTT
1 TTT-TTTTGCTT
38390 TTTTTTTGC--
1 TTTTTTTGCTT
38399 TTTTTTTG-TT
1 TTTTTTTGCTT
38409 TTTTTTTG
1 TTTTTTTG
38417 GGTGTAAAGG
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 5 0.09
12 19 0.34
13 15 0.27
14 1 0.02
ACGTcount: A:0.01, C:0.05, G:0.11, T:0.83
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:38367 original size:1 final size:1
Alignment explanation
Indices: 38363--38415 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
38353 TTTTTCTTGC
* * * ** *
38363 TTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTTGCTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38416 GGGTGTAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:38372 original size:25 final size:23
Alignment explanation
Indices: 38341--38415 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 23
38331 GACCCTTCTA
38341 TTTTTTTGCTATTTTTTCTTGCTTT
1 TTTTTTTGCT-TTTTTTCTTG-TTT
* *
38366 TTTTTTTGTTTTTTTGTTTTGTTT
1 TTTTTTTGCTTTTTT-TCTTGTTT
*
38390 TTTTTTTGCTTTTTTTGTT-TTT
1 TTTTTTTGCTTTTTTTCTTGTTT
38412 TTTT
1 TTTT
38416 GGGTGTAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
22 7 0.16
23 3 0.07
24 22 0.49
25 13 0.29
ACGTcount: A:0.01, C:0.05, G:0.09, T:0.84
Consensus pattern (23 bp):
TTTTTTTGCTTTTTTTCTTGTTT
Found at i:38379 original size:8 final size:8
Alignment explanation
Indices: 38366--38413 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
38356 TTCTTGCTTT
38366 TTTTTTTG
1 TTTTTTTG
38374 TTTTTTTG
1 TTTTTTTG
38382 TTTTGTTT-
1 TTTT-TTTG
38390 TTTTTTTG
1 TTTTTTTG
38398 CTTTTTTTG
1 -TTTTTTTG
38407 TTTTTTT
1 TTTTTTT
38414 TTGGGTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.08
8 23 0.62
9 11 0.30
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:51464 original size:20 final size:22
Alignment explanation
Indices: 51437--51494 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
51427 CTGGACATGT
51437 TAAAAAAAA-CATGAAACATAA
1 TAAAAAAAAGCATGAAACATAA
51458 TAAAAAAAATGCATGAAACATAA
1 TAAAAAAAA-GCATGAAACATAA
*
51481 TAAAAAAATGCATG
1 TAAAAAAAAGCATG
51495 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 9 0.26
22 5 0.15
23 20 0.59
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (22 bp):
TAAAAAAAAGCATGAAACATAA
Found at i:51472 original size:23 final size:23
Alignment explanation
Indices: 51437--51494 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 23
51427 CTGGACATGT
51437 TAAAAAAAA--CATGAAACATAA
1 TAAAAAAAATGCATGAAACATAA
51458 TAAAAAAAATGCATGAAACATAA
1 TAAAAAAAATGCATGAAACATAA
51481 T-AAAAAAATGCATG
1 TAAAAAAAATGCATG
51495 GTCAAAGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.26
22 13 0.37
23 13 0.37
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (23 bp):
TAAAAAAAATGCATGAAACATAA
Found at i:52450 original size:20 final size:19
Alignment explanation
Indices: 52403--52476 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
52393 AAAAAGATAT
*
52403 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
52422 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
52443 CATGTATCGATATA-TCGAA
1 AATGTATCGATACATTC-AA
52462 AATGTATCGATACAT
1 AATGTATCGATACAT
52477 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 15 0.34
20 28 0.64
21 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:52811 original size:16 final size:16
Alignment explanation
Indices: 52770--52817 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
52760 TATAATACTT
52770 TAAAT-AATAATAAAAA
1 TAAATAAATAA-AAAAA
* *
52786 TAACACAAATAAAAACA
1 TAA-ATAAATAAAAAAA
52803 TAAATAAATAAAAAA
1 TAAATAAATAAAAAA
52818 TTTTCTCTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.50
17 8 0.31
18 5 0.19
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAATAAATAAAAAAA
Found at i:53256 original size:31 final size:32
Alignment explanation
Indices: 53212--53274 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
53202 TAAATGATTT
*
53212 TATAAACATTAAAT-TAAATATATAATT-TTAA
1 TATAAACATTAAATAT-AATAAATAATTATTAA
53243 TATAAA-ATATAAATATAATAAATAATTATTAA
1 TATAAACAT-TAAATATAATAAATAATTATTAA
53275 AAATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 2 0.07
31 21 0.75
32 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TATAAACATTAAATATAATAAATAATTATTAA
Found at i:53326 original size:39 final size:40
Alignment explanation
Indices: 53270--53350 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
53260 ATAAATAATT
* *
53270 ATTAAAAATATATATTTT-A-TCTTAATAATTTAATAAAAA
1 ATTAAAAATATATATTTTAACACTTAA-AAATTAATAAAAA
*
53309 ATTAAAAAT-TTTAATTTTAACACTTAAAAATTAATAAAAA
1 ATTAAAAATATAT-ATTTTAACACTTAAAAATTAATAAAAA
53349 AT
1 AT
53351 AATAAAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.06
39 14 0.39
40 15 0.42
41 5 0.14
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (40 bp):
ATTAAAAATATATATTTTAACACTTAAAAATTAATAAAAA
Found at i:53752 original size:65 final size:66
Alignment explanation
Indices: 53675--53809 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 66
53665 AGATTCGTGT
* ** ** * *
53675 ATTTTTTAAATTTGAATG-TTCAGTTATAAGAAATTTTTATTGGATTGAAATTTCAAATTATATT
1 ATTTTTTAAATTTGAATGCTT-AGTTACAAGAAATTTTTATTAAATCAAAATTTAAAATGATATT
53739 AA
65 AA
* *
53741 ATTTTTT-AATTTGAATGCTTGGTTACAAGAGATTTTTATTAAATCAAAATTTAAAATGATATTA
1 ATTTTTTAAATTTGAATGCTTAGTTACAAGAAATTTTTATTAAATCAAAATTTAAAATGATATTA
53805 A
66 A
53806 ATTT
1 ATTT
53810 ATATGACATA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
65 50 0.85
66 9 0.15
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (66 bp):
ATTTTTTAAATTTGAATGCTTAGTTACAAGAAATTTTTATTAAATCAAAATTTAAAATGATATTA
A
Found at i:53861 original size:14 final size:14
Alignment explanation
Indices: 53825--53857 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53815 ACATAAAAAA
53825 AATTAATTTAGATT
1 AATTAATTTAGATT
*
53839 AATCAATTT-GATT
1 AATTAATTTAGATT
53852 AATTAA
1 AATTAA
53858 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (14 bp):
AATTAATTTAGATT
Found at i:59548 original size:2 final size:2
Alignment explanation
Indices: 59541--59576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
59531 TTAGCTATGC
59541 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
59577 TGGTATAAAA
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:59606 original size:22 final size:23
Alignment explanation
Indices: 59581--59625 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
59571 ATATATTGGT
59581 ATAAAAAAATCAT-AATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
*
59603 ATAAAAAAATTATAAATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
59626 TTTAAAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAAAAAATCATAAATTTAAAA
Found at i:60064 original size:2 final size:2
Alignment explanation
Indices: 60057--60091 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60047 TATGAAATGC
60057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60092 AAGACTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61911 original size:4 final size:4
Alignment explanation
Indices: 61902--61932 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
61892 GTTTGGTGAA
61902 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
61933 AAAATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:61992 original size:10 final size:10
Alignment explanation
Indices: 61977--62038 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
61967 TTTAAAATAT
61977 TATATTTTTA
1 TATATTTTTA
61987 TATATTTTT-
1 TATATTTTTA
* *
61996 TATATATTAA
1 TATATTTTTA
62006 TA-ATTTATT-
1 TATATTT-TTA
62015 T-TATTTTTA
1 TATATTTTTA
62024 TATATTTTTA
1 TATATTTTTA
62034 TATAT
1 TATAT
62039 ACGTGTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 2 0.05
9 16 0.37
10 25 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTTTTA
Found at i:62251 original size:4 final size:4
Alignment explanation
Indices: 62242--62272 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
62232 TAATTTTTTA
62242 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
62273 ACATACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:62365 original size:4 final size:4
Alignment explanation
Indices: 62350--62411 Score: 72
Period size: 4 Copynumber: 15.5 Consensus size: 4
62340 TCAAGAGGGA
* * *
62350 AAAG AGAG AAAG AAAG AAAG AAAG AGAAA AAAA AAAG AAA- AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
*
62398 AAAG AAAA AAAG AA
1 AAAG AAAG AAAG AA
62412 TAAATTTACG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 3 0.06
4 44 0.88
5 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:62732 original size:2 final size:2
Alignment explanation
Indices: 62725--62760 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
62715 TGTATTAATT
* *
62725 TA TA TA TA TA TA TA TA TT TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62761 AAATTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63037 original size:23 final size:22
Alignment explanation
Indices: 63006--63055 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
62996 GTCATATTCA
*
63006 TTTTTTTATATTATATTTTAAT
1 TTTTTTTATATCATATTTTAAT
* *
63028 TATTTTTTATGTCATATTTTTAT
1 T-TTTTTTATATCATATTTTAAT
63051 TTTTT
1 TTTTT
63056 GTACATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTATATCATATTTTAAT
Found at i:63984 original size:15 final size:16
Alignment explanation
Indices: 63964--63993 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63954 TTTTTAAATA
63964 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
63979 AATTTTATTTAATTA
1 AATTTTATTTAATTA
63994 AAAAATTTAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:64720 original size:15 final size:15
Alignment explanation
Indices: 64695--64740 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
64685 TAATTGAAGC
64695 TATTATTTATTTATAT
1 TATT-TTTATTTATAT
*
64711 TATTTTTA-TTACTCT
1 TATTTTTATTTA-TAT
64726 TATTTTTATTT-TAT
1 TATTTTTATTTATAT
64740 T
1 T
64741 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTTATTTATAT
Found at i:64817 original size:2 final size:2
Alignment explanation
Indices: 64810--64873 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
64800 CGTAGGCATC
*
64810 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA 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
64852 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
64874 CACAGACGAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66446 original size:15 final size:16
Alignment explanation
Indices: 66414--66466 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
66404 ATCAACTTTC
*
66414 AAAATTAAATAATTTA
1 AAAATTAAATAATATA
*
66430 AAAATTGAAT-ATAT-
1 AAAATTAAATAATATA
66444 AAAATTAAATTAAT-T-
1 AAAATTAAA-TAATATA
66459 AAAATTAA
1 AAAATTAA
66467 TCGATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.25
15 13 0.41
16 11 0.34
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATTAAATAATATA
Found at i:66673 original size:33 final size:30
Alignment explanation
Indices: 66622--66713 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 30
66612 TATGGTATCA
* *
66622 ATATAATTATATTTTAAAAATTTATATAATAT
1 ATATAATTATATATT-AAAATTAATATAA-AT
*
66654 ATATTATTAATATATTAAAATTAATATAAAT
1 ATATAATT-ATATATTAAAATTAATATAAAT
* * *
66685 ATA-AAATATA-ATTATAATATAATAAAAAT
1 ATATAATTATATATTAAAAT-TAATATAAAT
66714 TTTATGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.14
29 12 0.24
30 2 0.04
31 5 0.10
32 19 0.37
33 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATTATATATTAAAATTAATATAAAT
Found at i:66686 original size:18 final size:20
Alignment explanation
Indices: 66644--66711 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
66634 TTTAAAAATT
*
66644 TATATAATATAT-ATTATTAA
1 TATATAAAATATAATTA-TAA
66664 TATATTAAAAT-TAA-TATAA
1 TATA-TAAAATATAATTATAA
66683 -ATATAAAATATAATTATAA
1 TATATAAAATATAATTATAA
66702 TATAATAAAA
1 TAT-ATAAAA
66712 ATTTTATGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 8 0.20
20 9 0.22
21 12 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAAAATATAATTATAA
Found at i:69234 original size:70 final size:70
Alignment explanation
Indices: 69121--69262 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
69111 ACAAATTGGT
*
69121 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATGG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
69186 GAGTC
66 GAGTC
69191 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
69256 GAGTC
66 GAGTC
69261 AC
1 AC
69263 CTTTAGAATC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (70 bp):
ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
GAGTC
Found at i:72478 original size:37 final size:37
Alignment explanation
Indices: 72437--72526 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
72427 TTTTTTTCAA
* ** *
72437 TGGCACAGTTCGAAACAAAAATTACTATTCTTACTGG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
* * *
72474 TGGCACGGGTCGGAACAAAAAGCACTATTTTTACTAG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
72511 TGGCACAGGTCGAAAC
1 TGGCACAGGTCGAAAC
72527 CAGTTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (37 bp):
TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
Found at i:72680 original size:16 final size:16
Alignment explanation
Indices: 72659--72693 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
72649 ACAAAAGCAA
72659 AAATCACA-TATTTCAC
1 AAATCACATTATTT-AC
72675 AAATCACATTATTTAC
1 AAATCACATTATTTAC
72691 AAA
1 AAA
72694 GCAATTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATCACATTATTTAC
Found at i:76105 original size:13 final size:13
Alignment explanation
Indices: 76087--76143 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
76077 CATAAAGTGT
76087 TGTATCGATACAA
1 TGTATCGATACAA
76100 TGTATCGATACATAA
1 TGTATCGATAC--AA
76115 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
76132 TGTATCGATACA
1 TGTATCGATACA
76144 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:76122 original size:32 final size:32
Alignment explanation
Indices: 76067--76164 Score: 187
Period size: 32 Copynumber: 3.0 Consensus size: 32
76057 TTCAACGATT
76067 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
76100 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
76132 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
76164 T
1 T
76165 TTAAGCTACT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:76124 original size:19 final size:19
Alignment explanation
Indices: 76066--76162 Score: 101
Period size: 19 Copynumber: 5.7 Consensus size: 19
76056 TTTCAACGAT
76066 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
76086 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
76100 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
76118 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
76132 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
76150 TTGTATCGATACA
1 TTGTATCGATACA
76163 ATTTAAGCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:76225 original size:13 final size:13
Alignment explanation
Indices: 76207--76231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76197 TACTCAACTG
76207 TATCGATACATTA
1 TATCGATACATTA
76220 TATCGATACATT
1 TATCGATACATT
76232 GATCTTTGTA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:80447 original size:19 final size:18
Alignment explanation
Indices: 80405--80448 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
80395 ATGACGTGTT
*
80405 TGATGACGTTGCTAATGT
1 TGATGACGTTGCTAATGA
* *
80423 TGATGACGTTGTTTATTGA
1 TGATGACGTTG-CTAATGA
80442 TGATGAC
1 TGATGAC
80449 ATGGCATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TGATGACGTTGCTAATGA
Found at i:80901 original size:24 final size:24
Alignment explanation
Indices: 80869--80922 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
80859 AAAGAATCCT
** *
80869 TAATAAGAATCTTTAATATTATGC
1 TAATAAGAATCACTAATATGATGC
*
80893 TAATTAGAATCACTAATATGATGC
1 TAATAAGAATCACTAATATGATGC
*
80917 TGATAA
1 TAATAA
80923 AGTCAACTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (24 bp):
TAATAAGAATCACTAATATGATGC
Found at i:81142 original size:16 final size:15
Alignment explanation
Indices: 81112--81159 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
81102 ATTTATTGAA
81112 AAAAATATTAAATTT
1 AAAAATATTAAATTT
*
81127 AAAAATATATATATTT
1 AAAAATAT-TAAATTT
81143 AAAAA-A-TAAA-TT
1 AAAAATATTAAATTT
81155 AAAAA
1 AAAAA
81160 AATAAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
15 9 0.30
16 11 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATATTAAATTT
Found at i:81511 original size:30 final size:28
Alignment explanation
Indices: 81476--81568 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 28
81466 AAGTCAAAGG
81476 ATTTATTTATAAGTATATTAAAAATTAAA
1 ATTTATTTA-AAGTATATTAAAAATTAAA
* *
81505 ATTT-TATTCAAGTATAAATTAAAAATTATA
1 ATTTAT-TTAAAGTAT--ATTAAAAATTAAA
*
81535 ATTTATTTAAA-TATAATAAAAATATAAAA
1 ATTTATTTAAAGTATATTAAAAAT-T-AAA
81564 ATTTA
1 ATTTA
81569 AGTAATATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.15
28 8 0.15
29 16 0.30
30 20 0.38
31 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTTATTTAAAGTATATTAAAAATTAAA
Found at i:81566 original size:29 final size:28
Alignment explanation
Indices: 81476--81582 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 28
81466 AAGTCAAAGG
*
81476 ATTTATTTATAAGTATATTAAAAATTAAAA
1 ATTTATTTA-AA-TATAATAAAAATTAAAA
* * * *
81506 TTTTATTCAAGTATAAATTAAAAATT-ATA
1 ATTTATTTAAATAT-AA-TAAAAATTAAAA
81535 ATTTATTTAAATATAATAAAAATATAAAA
1 ATTTATTTAAATATAATAAAAAT-TAAAA
**
81564 ATTTAAGT-AATATAATAAA
1 ATTTATTTAAATATAATAAA
81583 TTTAACTTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.11
28 17 0.27
29 23 0.37
30 15 0.24
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATTTATTTAAATATAATAAAAATTAAAA
Found at i:83315 original size:2 final size:2
Alignment explanation
Indices: 83308--83333 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83298 AAATTGAATT
83308 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
83334 ATTCATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84012 original size:20 final size:20
Alignment explanation
Indices: 83989--84073 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
83979 AAGTACCCAG
83989 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
84009 ATGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
84039 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
84060 ATGTATCGATACAT
1 ATGTATCGATACAT
84074 CTAGTTAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
20 27 0.50
21 2 0.04
24 5 0.09
27 5 0.09
30 2 0.04
31 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:84518 original size:13 final size:14
Alignment explanation
Indices: 84496--84524 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
84486 ATATCTTAGC
84496 AAAACATCAACACA
1 AAAACATCAACACA
84510 AAAAC-TCAACACA
1 AAAACATCAACACA
84523 AA
1 AA
84525 TCTATTCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACATCAACACA
Found at i:88156 original size:16 final size:16
Alignment explanation
Indices: 88135--88165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88125 TAATCAAAAA
88135 ATTAATTTAGATTTGG
1 ATTAATTTAGATTTGG
*
88151 ATTAATTTAGCTTTG
1 ATTAATTTAGATTTG
88166 ACATTATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (16 bp):
ATTAATTTAGATTTGG
Found at i:88972 original size:21 final size:20
Alignment explanation
Indices: 88940--88980 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
88930 TTATCACTTA
*
88940 AAAAATTAATAAAAAATAAT
1 AAAAATAAATAAAAAATAAT
*
88960 AAAAATAACATAAAAACTAAT
1 AAAAATAA-ATAAAAAATAAT
88981 TTTATGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAAATAAT
Found at i:89601 original size:5 final size:5
Alignment explanation
Indices: 89591--89616 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
89581 ATGGATGCAT
89591 GCGAG GCGAG GCGAG GCGAG GCGAG G
1 GCGAG GCGAG GCGAG GCGAG GCGAG G
89617 GGCTAGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.62, T:0.00
Consensus pattern (5 bp):
GCGAG
Found at i:91954 original size:2 final size:2
Alignment explanation
Indices: 91947--92010 Score: 71
Period size: 2 Copynumber: 33.0 Consensus size: 2
91937 AATTTAAACC
* * *
91947 AT AT AT AT AT AT AT A- AT AT TT AT AT -T TT GT AT -T AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
91987 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
92011 TGCACAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.06
2 49 0.91
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:94518 original size:22 final size:24
Alignment explanation
Indices: 94473--94519 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
94463 TCTGTGCTCG
94473 TAATTAATATTAATATATAGTAAAA
1 TAATTAATATTAATATATA-TAAAA
*
94498 TAATTATTATTAAT-TAT-TAAAA
1 TAATTAATATTAATATATATAAAA
94520 ATGCATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
24 3 0.14
25 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAATTAATATTAATATATATAAAA
Found at i:94678 original size:2 final size:2
Alignment explanation
Indices: 94667--94711 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
94657 TTATTCTCTC
*
94667 AT AT AG 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 AT AT AT
94709 AT A
1 AT A
94712 AATGAACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:95407 original size:16 final size:15
Alignment explanation
Indices: 95382--95415 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
95372 CTTTGCATAC
*
95382 ATACATACATAAATAT
1 ATACACACAT-AATAT
95398 ATACACACATAATAT
1 ATACACACATAATAT
95413 ATA
1 ATA
95416 TTAATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (15 bp):
ATACACACATAATAT
Found at i:96588 original size:2 final size:2
Alignment explanation
Indices: 96583--96619 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
96573 TTTTATTATC
* *
96583 AT AT AT AC AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96620 ATTGCACGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:101764 original size:21 final size:21
Alignment explanation
Indices: 101724--101766 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
101714 GCGTTTATAA
*
101724 ATTTATTTATAATTACAATAT
1 ATTTATTTATAATTAAAATAT
101745 ATTTA-TTATAATTATAAATAT
1 ATTTATTTATAATTA-AAATAT
101766 A
1 A
101767 AATAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATTTATAATTAAAATAT
Found at i:101781 original size:30 final size:30
Alignment explanation
Indices: 101747--101810 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
101737 TACAATATAT
101747 TTATTATAATTATAAATATAAATAATATTA
1 TTATTATAATTATAAATATAAATAATATTA
* *
101777 TTATTTTAATTATAAATATAATTAATATTA
1 TTATTATAATTATAAATATAAATAATATTA
101807 TTAT
1 TTAT
101811 AATCATCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATTATAATTATAAATATAAATAATATTA
Found at i:101800 original size:24 final size:25
Alignment explanation
Indices: 101726--101805 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 25
101716 GTTTATAAAT
* *
101726 TTATTTATAATTA-CAATATATTTA
1 TTATTTATAATTATAAATATAATTA
*
101750 TTATAATTATAAATATAAATA-ATATTA
1 TTAT--TTATAATTATAAATATA-ATTA
101777 TTATTT-TAATTATAAATATAATTA
1 TTATTTATAATTATAAATATAATTA
*
101801 ATATT
1 TTATT
101806 ATTATAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
24 23 0.50
25 3 0.07
26 9 0.20
27 11 0.24
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
TTATTTATAATTATAAATATAATTA
Found at i:101967 original size:21 final size:21
Alignment explanation
Indices: 101942--101981 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
101932 TAAAAAAATT
101942 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
101963 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
101982 AAAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:101989 original size:22 final size:21
Alignment explanation
Indices: 101943--101991 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
101933 AAAAAAATTT
* *
101943 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTAAAA
101964 ATTTTATAATTAA-ATTTAAAA
1 ATTTTAT-ATTAATATTTAAAA
*
101985 AATTTAT
1 ATTTTAT
101992 TGATTAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTATATTAATATTTAAAA
Found at i:106328 original size:27 final size:26
Alignment explanation
Indices: 106280--106332 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
106270 TTAATGGTTA
106280 AAATTTTTTTATATTAAATAAATATTT
1 AAATTTTTTTATATTAAATAAA-ATTT
**
106307 AAATATTTTTTAT-TTATTTAAAATTT
1 AAAT-TTTTTTATATTAAATAAAATTT
106333 GATATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.48
28 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
AAATTTTTTTATATTAAATAAAATTT
Found at i:106715 original size:29 final size:26
Alignment explanation
Indices: 106663--106715 Score: 61
Period size: 29 Copynumber: 1.9 Consensus size: 26
106653 TAATGTTTAA
* *
106663 TAATTAAAAATAATTTTATTTAAATT
1 TAATTAAAAATAATTTAATATAAATT
106689 TAATTATAAAATATATATTAATATAAA
1 TAATTA-AAAATA-AT-TTAATATAAA
106716 ATAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 6 0.27
27 6 0.27
28 2 0.09
29 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTAAAAATAATTTAATATAAATT
Found at i:106726 original size:17 final size:17
Alignment explanation
Indices: 106683--106726 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
106673 TAATTTTATT
106683 TAAATTTAATTATAAAA
1 TAAATTTAATTATAAAA
*
106700 TATATATTAA-TATAAAA
1 TAAAT-TTAATTATAAAA
106717 TAAAATTTAA
1 T-AAATTTAA
106727 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAATTATAAAA
Found at i:107505 original size:23 final size:23
Alignment explanation
Indices: 107462--107506 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
107452 TTTAAAGTTA
* *
107462 TTTTATTTTAAGATATGATTTAT
1 TTTTATTTTAAAATATAATTTAT
107485 TTTTATTTATAAAAT-TAATTTA
1 TTTTATTT-TAAAATATAATTTA
107507 ATTTAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTATTTTAAAATATAATTTAT
Found at i:108536 original size:28 final size:28
Alignment explanation
Indices: 108480--108541 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
108470 ATTAAGAAAC
* *
108480 TTTATTTTCTCTTTTTTAATTTTAATTA
1 TTTATTTTCTCTTTTTTAAGTTAAATTA
108508 TTTATTTAT-TCTTTTTT-AGTTAAATTTA
1 TTTATTT-TCTCTTTTTTAAGTTAAA-TTA
108536 TTTATT
1 TTTATT
108542 AATTTTATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 24 0.80
29 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTATTTTCTCTTTTTTAAGTTAAATTA
Found at i:110974 original size:44 final size:44
Alignment explanation
Indices: 110879--110976 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 44
110869 ATAATCAAAA
* **
110879 ATTAATTTTTTAATTTTTTAAAATAATTTTTTTAAACTTAATTT
1 ATTAATTTTTTAATTTTTTAAAATAATATTAATAAACTTAATTT
*
110923 AAT-ATTTTTT-ATTTTATTAAAAATAATAATTAATAAA-TT-ATTT
1 ATTAATTTTTTAATTTT-TT-AAAATAAT-ATTAATAAACTTAATTT
110966 ATTAATTTTTT
1 ATTAATTTTTT
110977 GAAATTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
42 5 0.11
43 15 0.33
44 19 0.42
45 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (44 bp):
ATTAATTTTTTAATTTTTTAAAATAATATTAATAAACTTAATTT
Found at i:111981 original size:10 final size:10
Alignment explanation
Indices: 111966--111995 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
111956 TAAATATATT
111966 TTAAAAATTA
1 TTAAAAATTA
*
111976 TTAAAAATGA
1 TTAAAAATTA
111986 TTAAAAATTA
1 TTAAAAATTA
111996 ATTTTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:116068 original size:2 final size:2
Alignment explanation
Indices: 116061--116085 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116051 AATTTAATTG
116061 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
116086 ATTGTTAAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116854 original size:20 final size:20
Alignment explanation
Indices: 116831--116872 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
116821 TATTTATATT
*
116831 TTATTTTA-ATTTTATTTAAA
1 TTATTTTATA-TTTATGTAAA
116851 TTATTTTATATTTATGTAAA
1 TTATTTTATATTTATGTAAA
116871 TT
1 TT
116873 TTAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTTATATTTATGTAAA
Found at i:124198 original size:7 final size:7
Alignment explanation
Indices: 124186--124254 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
124176 CTATACATAT
124186 TTTAAAA
1 TTTAAAA
124193 TTT-AAA
1 TTTAAAA
*
124199 TTTAAAT
1 TTTAAAA
124206 TTTGAAAA
1 TTT-AAAA
*
124214 TCT-AAA
1 TTTAAAA
*
124220 --TAGAA
1 TTTAAAA
124225 TTT-AAA
1 TTTAAAA
124231 TTT-AAA
1 TTTAAAA
124237 TTTAAAA
1 TTTAAAA
*
124244 TTTAAAT
1 TTTAAAA
124251 TTTA
1 TTTA
124255 GATGATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 2 0.04
6 20 0.40
7 22 0.44
8 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:124201 original size:6 final size:6
Alignment explanation
Indices: 124190--124252 Score: 58
Period size: 6 Copynumber: 10.0 Consensus size: 6
124180 ACATATTTTA
*
124190 AAATTT AAATTT AAATTTT GAAAATCT AAA--T AGAATTT AAATTT AAATTT
1 AAATTT AAATTT AAA-TTT --AAATTT AAATTT A-AATTT AAATTT AAATTT
124240 AAAATTT AAATTT
1 -AAATTT AAATTT
124253 TAGATGATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 29 0.59
7 11 0.22
8 2 0.04
9 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:124204 original size:13 final size:13
Alignment explanation
Indices: 124186--124252 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
124176 CTATACATAT
124186 TTTAAAATTTAAA
1 TTTAAAATTTAAA
*
124199 TTTAAATTTTGAAAA
1 TTTAAAATTT--AAA
*
124214 TCT-AAA--TAGAA
1 TTTAAAATTTA-AA
124225 TTT-AAATTTAAA
1 TTTAAAATTTAAA
124237 TTTAAAATTTAAA
1 TTTAAAATTTAAA
124250 TTT
1 TTT
124253 TAGATGATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 1 0.02
11 7 0.16
12 6 0.14
13 23 0.52
14 2 0.05
15 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:127770 original size:21 final size:21
Alignment explanation
Indices: 127741--127780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
127731 TGTTTTGAAT
*
127741 TTTTTTTTTAAATTATTAAGA
1 TTTTATTTTAAATTATTAAGA
*
127762 TTTTATTTTTAATTATTAA
1 TTTTATTTTAAATTATTAA
127781 AATTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTATTTTAAATTATTAAGA
Found at i:127770 original size:22 final size:21
Alignment explanation
Indices: 127739--127780 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
127729 GTTGTTTTGA
*
127739 ATTTTTTTTTTAAATTATTAAG
1 ATTTTATTTTT-AATTATTAAG
127761 ATTTTATTTTTAATTATTAA
1 ATTTTATTTTTAATTATTAA
127781 AATTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTATTTTTAATTATTAAG
Found at i:127840 original size:26 final size:26
Alignment explanation
Indices: 127811--127899 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 26
127801 ATAAAATATA
127811 TGATTATTAACAAAATATATGATTAT
1 TGATTATTAACAAAATATATGATTAT
* *
127837 TGATTATTTTAA-ATATAAGATTTGATCT-T
1 TGATTA--TTAACA-A-AATATATGAT-TAT
127866 TGATTATTAACAAAATATATGATTAT
1 TGATTATTAACAAAATATATGATTAT
127892 TGATTATT
1 TGATTATT
127900 CCAAATTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
25 1 0.02
26 23 0.44
27 6 0.12
28 6 0.12
29 15 0.29
30 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (26 bp):
TGATTATTAACAAAATATATGATTAT
Found at i:128280 original size:11 final size:11
Alignment explanation
Indices: 128254--128307 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
128244 GTATCTGTAC
128254 TTTATTTTTAT
1 TTTATTTTTAT
128265 ATTTATTTTTAT
1 -TTTATTTTTAT
* *
128277 TTTAATTATAT
1 TTTATTTTTAT
*
128288 TTTA--ATTAT
1 TTTATTTTTAT
128297 TTTATTTTTAT
1 TTTATTTTTAT
128308 ATAAATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.20
11 17 0.49
12 11 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:128298 original size:26 final size:27
Alignment explanation
Indices: 128267--128324 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
128257 ATTTTTATAT
*
128267 TTATTTTTATTTTAAT-TATATTTTAA
1 TTATTTTTATTTTAATATAAATTTTAA
*
128293 TTA-TTTTATTTTTATATAAATTTTAA
1 TTATTTTTATTTTAATATAAATTTTAA
128319 TATATT
1 T-TATT
128325 AATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.41
26 13 0.48
27 2 0.07
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTATTTTTATTTTAATATAAATTTTAA
Found at i:128300 original size:37 final size:37
Alignment explanation
Indices: 128259--128340 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
128249 TGTACTTTAT
* ** *
128259 TTTTATATTTATTTTTATTTTAATTATATT-TTAATTA
1 TTTTATATTTATATAAATTTTAA-TATATTAATAATTA
*
128296 TTTTATTTTTATATAAATTTTAATATATTAATAATTA
1 TTTTATATTTATATAAATTTTAATATATTAATAATTA
*
128333 TATTATAT
1 TTTTATAT
128341 AAATTTTGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 6 0.16
37 31 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (37 bp):
TTTTATATTTATATAAATTTTAATATATTAATAATTA
Found at i:136649 original size:7 final size:7
Alignment explanation
Indices: 136590--136648 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
136580 AAATCTATTC
136590 AAAATTT
1 AAAATTT
136597 AAAATTT
1 AAAATTT
136604 AAAATTT
1 AAAATTT
136611 -AAATTT
1 AAAATTT
* *
136617 AGATTTT
1 AAAATTT
136624 AAAAAATTT
1 --AAAATTT
136633 -AAATTT
1 AAAATTT
*
136639 AAATTTT
1 AAAATTT
136646 AAA
1 AAA
136649 TGACATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
6 12 0.28
7 26 0.60
9 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (7 bp):
AAAATTT
Found at i:136664 original size:35 final size:36
Alignment explanation
Indices: 136590--136663 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
136580 AAATCTATTC
* *
136590 AAAATTTAAAATTTAAAATTTAAATTTAGATTTTAA
1 AAAATTTAAAATTTAAAATTTAAATTGACATTTTAA
*
136626 AAAATTT-AAATTTAAATTTTAAA-TGACATTTTAA
1 AAAATTTAAAATTTAAAATTTAAATTGACATTTTAA
136660 AAAA
1 AAAA
136664 AAATTCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 13 0.37
35 15 0.43
36 7 0.20
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (36 bp):
AAAATTTAAAATTTAAAATTTAAATTGACATTTTAA
Found at i:140622 original size:53 final size:52
Alignment explanation
Indices: 140525--140624 Score: 119
Period size: 53 Copynumber: 1.9 Consensus size: 52
140515 ATTTGTACAA
* * * * * *
140525 TTTTAATTTTTTTCTTTTATATTTTCCCATATTTTCTTAATTTAAACAATTT
1 TTTTAAATTTTTTCTTTCATATTCTCACATACTTTATTAATTTAAACAATTT
* *
140577 TTTTAAATTTTTTCTTCTCATATTCTCATATACTTTATTATTTTAAAC
1 TTTTAAATTTTTTCTT-TCATATTCTCACATACTTTATTAATTTAAAC
140625 GTATTTTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
52 15 0.38
53 24 0.62
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (52 bp):
TTTTAAATTTTTTCTTTCATATTCTCACATACTTTATTAATTTAAACAATTT
Found at i:144498 original size:13 final size:13
Alignment explanation
Indices: 144480--144507 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
144470 TTGGACTTAC
144480 ATCATTACTCACT
1 ATCATTACTCACT
144493 ATCATTACTCACT
1 ATCATTACTCACT
144506 AT
1 AT
144508 GTTACAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (13 bp):
ATCATTACTCACT
Found at i:144531 original size:2 final size:2
Alignment explanation
Indices: 144524--144548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
144514 AATTTAATTG
144524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
144549 ATTGTTAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:155831 original size:32 final size:32
Alignment explanation
Indices: 155771--155840 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
155761 TTAACACATG
* *
155771 TATTAAAATTTATATAATATGAATTATTAATA
1 TATTAAAATTTATATAATATCAATTATTAAAA
155803 TATTAAAATTTATATAA-A-CACATGTATTAAAA
1 TATTAAAATTTATATAATATCA-AT-TATTAAAA
155835 T-TTAAA
1 TATTAAA
155841 TATGATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 8 0.24
32 25 0.74
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (32 bp):
TATTAAAATTTATATAATATCAATTATTAAAA
Found at i:156588 original size:17 final size:17
Alignment explanation
Indices: 156566--156606 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
156556 GGATTGTAGG
156566 AAAGTAATTTCC-AAAGT
1 AAAGTAA-TTCCTAAAGT
*
156583 AAAGTAATTCCTAAGGT
1 AAAGTAATTCCTAAAGT
156600 AAAGTAA
1 AAAGTAA
156607 CATTTTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (17 bp):
AAAGTAATTCCTAAAGT
Found at i:157350 original size:19 final size:18
Alignment explanation
Indices: 157326--157375 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
157316 TTTTATTTTA
*
157326 TATATTTTTTAATATATTT
1 TATATTTTTTAATAT-TTG
*
157345 TATATTTGTTTGATATTTG
1 TATATTT-TTTAATATTTG
157364 TATTATTTTTTA
1 TA-TATTTTTTA
157376 TTTATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (18 bp):
TATATTTTTTAATATTTG
Found at i:158618 original size:19 final size:21
Alignment explanation
Indices: 158574--158620 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
158564 ATAATATTTT
158574 TAATTTTTTAATTAAATTTAAA
1 TAATTTTTTAATTAAA-TTAAA
158596 TAATTTTTTAATTAAA-T-AA
1 TAATTTTTTAATTAAATTAAA
158615 TAATTT
1 TAATTT
158621 AAATCGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.32
20 1 0.04
22 16 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTTTTTAATTAAATTAAA
Found at i:162302 original size:25 final size:24
Alignment explanation
Indices: 162274--162320 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
162264 TTAAATATAG
162274 TTATATAAG-TATGATATGTATAAAA
1 TTAT-TAAGATATGATATG-ATAAAA
162299 TTATTAAGATATGATATGATAA
1 TTATTAAGATATGATATGATAA
162321 GATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (24 bp):
TTATTAAGATATGATATGATAAAA
Done.