Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 1 of 22
Found at i:5292 original size:10 final size:10
Alignment explanation
Indices: 5277--5301 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5267 AAATTAAAAC
5277 AATTCAATAT
1 AATTCAATAT
5287 AATTCAATAT
1 AATTCAATAT
5297 AATTC
1 AATTC
5302 TGTAATTCTT
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:0.12, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTCAATAT
Found at i:8633 original size:17 final size:17
Alignment explanation
Indices: 8611--8644 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8601 ATATATTTGT
8611 TTTAAAGAAAAAGAACA
1 TTTAAAGAAAAAGAACA
* *
8628 TTTAAATAAAAATAACA
1 TTTAAAGAAAAAGAACA
8645 ACTTTTGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
TTTAAAGAAAAAGAACA
Found at i:10929 original size:2 final size:2
Alignment explanation
Indices: 10916--10949 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
10906 ATCTCTACTT
* *
10916 TA TA TG TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10950 AATCCTCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11087 original size:80 final size:80
Alignment explanation
Indices: 10994--11153 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
10984 TGGCTTAGTA
10994 AGTTTCTAAATGGATAGTAATATTATTTTGTAGTGAAGACTGTTAGGTTAATTGAGTTACAAAGT
1 AGTTTCTAAATGGATAGTAATATTATTTTGTAGTGAAGACTGTTAGGTTAATTGAGTTACAAAGT
11059 TGAAGTAAAACAATT
66 TGAAGTAAAACAATT
11074 AGTTTCTAAATGGATAGTAATATTATTTTGTAGTGAAGACTGTTAGGTTAATTGAGTTACAAAGT
1 AGTTTCTAAATGGATAGTAATATTATTTTGTAGTGAAGACTGTTAGGTTAATTGAGTTACAAAGT
* *
11139 TGAATTAAAATAATT
66 TGAAGTAAAACAATT
11154 CGTACTAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (80 bp):
AGTTTCTAAATGGATAGTAATATTATTTTGTAGTGAAGACTGTTAGGTTAATTGAGTTACAAAGT
TGAAGTAAAACAATT
Found at i:13105 original size:21 final size:21
Alignment explanation
Indices: 13079--13121 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13069 AATAACTATG
*
13079 TAATTTAAACATAAATAAAAT
1 TAATTTAAAAATAAATAAAAT
13100 TAATTTAAAAATAAATAAAAT
1 TAATTTAAAAATAAATAAAAT
13121 T
1 T
13122 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATTTAAAAATAAATAAAAT
Found at i:13129 original size:21 final size:21
Alignment explanation
Indices: 13079--13132 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
13069 AATAACTATG
* *
13079 TAATTTAAACATAAATAAAAT
1 TAATATAAAAATAAATAAAAT
*
13100 TAATTTAAAAATAAATAAAATT
1 TAATATAAAAATAAATAAAA-T
13122 TAA-ATAAAAAT
1 TAATATAAAAAT
13133 TCTAAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATATAAAAATAAATAAAAT
Found at i:16229 original size:154 final size:155
Alignment explanation
Indices: 15974--16281 Score: 361
Period size: 154 Copynumber: 2.0 Consensus size: 155
15964 CATCATCGTT
*
15974 GAAGGAAGCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCC
1 GAAGGAAGCCAAGTGTCCTCTCCACCTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCC
* * * * * * *
16039 CCACCCTTTCCTTGGCCTACCAACTAGGCTTGTTGATAGCTCCCTGTCCTAGTCATCCTTTCTGT
66 CCACCCTTTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGT
*
16104 AACCTTTATTTTCACTCATTTCATC
131 AACCTTTATTTTCACTCACTTCATC
* * * * * *
16129 GAAGGAGGCCAAGTGTCCTCTCCACAC-CCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCC
1 GAAGGAAGCCAAGTGTCCTCTCCAC-CTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCC
** * * * * * *
16192 TTCACTCTTTCATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCT
65 CCCACCCTTTCATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCT
*
16256 GTAACCTTTATTTTCTCTCACTTCAT
129 GTAACCTTTATTTTCACTCACTTCAT
16282 TTCCTTCATT
Statistics
Matches: 127, Mismatches: 24, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
153 2 0.02
154 94 0.74
155 30 0.24
156 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.10, T:0.41
Consensus pattern (155 bp):
GAAGGAAGCCAAGTGTCCTCTCCACCTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCC
CCACCCTTTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGT
AACCTTTATTTTCACTCACTTCATC
Found at i:18247 original size:2 final size:2
Alignment explanation
Indices: 18240--18271 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18230 TAATATGGGC
18240 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
18272 GTTTTCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20230 original size:2 final size:2
Alignment explanation
Indices: 20223--20264 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20213 ATGTCTCACT
20223 TA TA TA TA TA TA TA 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
20265 AAAGTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22723 original size:21 final size:20
Alignment explanation
Indices: 22651--22724 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
22641 GAAAAGCTCT
*
22651 TAAATAATAAAGTAATTTAAACC
1 TAAATAA-AAA-TAATTTAAA-A
*
22674 TAAATAAAAATAA-ATAAAA
1 TAAATAAAAATAATTTAAAA
*
22693 CTAATTTAAAAATAACTTTAAAA
1 -TAA-ATAAAAATAA-TTTAAAA
22716 TAAATAAAA
1 TAAATAAAA
22725 TCTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 6 0.14
23 12 0.29
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAATAAAAATAATTTAAAA
Found at i:25970 original size:154 final size:155
Alignment explanation
Indices: 25689--25985 Score: 373
Period size: 154 Copynumber: 1.9 Consensus size: 155
25679 GAGGGAAGCT
* *
25689 AAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
1 AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
* * * * * *
25754 CTTAGCCTACCAACTAGGCTTGTTGATAGCTCGCTGTCCTAGTCATCCTTTCTGTAACCTTTATT
66 ATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTATT
*
25819 TTCACTCATTTCAGCGAAGGAGGCC
131 TTCACTCACTTCAGCGAAGGAGGCC
* * * * * **
25844 AAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCTTCACTCTTTC
1 AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
* * * * *
25908 ATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCTGTAACCTTTAT
66 ATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTAT
*
25972 TTTCTCTCACTTCA
130 TTTCACTCACTTCA
25986 TTTCCTTCTT
Statistics
Matches: 119, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 2 0.02
154 95 0.80
155 22 0.18
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.43
Consensus pattern (155 bp):
AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
ATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTATT
TTCACTCACTTCAGCGAAGGAGGCC
Found at i:27935 original size:2 final size:2
Alignment explanation
Indices: 27928--27969 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
27918 TAATATGGGC
*
27928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
27970 GTTTTCGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29929 original size:2 final size:2
Alignment explanation
Indices: 29922--29953 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29912 ATGTCTCACT
29922 TA TA 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
29954 AAAGTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32409 original size:21 final size:20
Alignment explanation
Indices: 32337--32410 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
32327 GAAAAGCTCT
*
32337 TAAATAATAAAGTAATTTAAACC
1 TAAATAA-AAA-TAATTTAAA-A
*
32360 TAAATAAAAATAA-ATAAAA
1 TAAATAAAAATAATTTAAAA
*
32379 CTAATTTAAAAATAACTTTAAAA
1 -TAA-ATAAAAATAA-TTTAAAA
32402 TAAATAAAA
1 TAAATAAAA
32411 TCTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 6 0.14
23 12 0.29
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAATAAAAATAATTTAAAA
Found at i:35648 original size:154 final size:155
Alignment explanation
Indices: 35364--35671 Score: 368
Period size: 154 Copynumber: 2.0 Consensus size: 155
35354 CATCATCGTT
* *
35364 GAAGGAAGCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTATTTCTTTTCCACTTCTCTTCC
1 GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTCTTCC
* ** * * * * * *
35429 CCACTCTTTCCTTAGCCTACCAACTAGGCTTGTTGATAGCTCCCTGTCCTAGTCATCCTTTCTGT
66 CCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAGCTCACTATCCTAGTCATCCTTCCTGT
*
35494 AACCTTTATTTTCACTCATTTCATC
131 AACCTTTATTTTCACTCACTTCATC
* * * * *
35519 GAAGGAGGCCAAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCT-TTCC
1 GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTCTTCC
* * * * * *
35582 GTCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATCGTTTACTATCTTGGTCATCCTTCCTG
66 -CCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAGCTCACTATCCTAGTCATCCTTCCTG
* *
35647 TAACCTTTGTTTTCTCTCACTTCAT
130 TAACCTTTATTTTCACTCACTTCAT
35672 TTCCCTTTTT
Statistics
Matches: 127, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
153 4 0.03
154 92 0.72
155 31 0.24
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (155 bp):
GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTCTTCC
CCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAGCTCACTATCCTAGTCATCCTTCCTGT
AACCTTTATTTTCACTCACTTCATC
Found at i:37583 original size:2 final size:2
Alignment explanation
Indices: 37576--37601 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37566 TAATATGGGC
37576 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
37602 GTTTTCGATG
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):
AT
Found at i:39561 original size:2 final size:2
Alignment explanation
Indices: 39554--39591 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39544 GTCTCACTTT
39554 TA TA TA TA TA 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
39592 AAAGTAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42048 original size:21 final size:20
Alignment explanation
Indices: 41976--42049 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
41966 GAAAAGCTCT
*
41976 TAAATAATAAAGTAATTTAAACC
1 TAAATAA-AAA-TAATTTAAA-A
*
41999 TAAATAAAAATAA-ATAAAA
1 TAAATAAAAATAATTTAAAA
*
42018 CTAATTTAAAAATAACTTTAAAA
1 -TAA-ATAAAAATAA-TTTAAAA
42041 TAAATAAAA
1 TAAATAAAA
42050 TCTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 6 0.14
23 12 0.29
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAATAAAAATAATTTAAAA
Found at i:45301 original size:154 final size:155
Alignment explanation
Indices: 45020--45319 Score: 379
Period size: 154 Copynumber: 1.9 Consensus size: 155
45010 GTTGAGGGAA
* *
45020 GCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * * *
45085 TTCCTTAGCCTACCAACTAGGCTTGTTGATAGCTCGCTGTCCTAGTCATCCTTTCTGTAACCTTT
66 TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
*
45150 ATTTTCACTCATTTCAGCGAAGGAG
131 ATTTTCACTCACTTCAGCGAAGGAG
* * * * * **
45175 GCCAAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCTTCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * *
45239 TTCATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCTGTAACCTT
66 TTCATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTT
*
45303 TATTTTCTCTCACTTCA
130 TATTTTCACTCACTTCA
45320 TTTCCTTCTT
Statistics
Matches: 122, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 2 0.02
154 95 0.78
155 25 0.20
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (155 bp):
GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
ATTTTCACTCACTTCAGCGAAGGAG
Found at i:45671 original size:2 final size:2
Alignment explanation
Indices: 45666--45690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45656 TTAAAAAAAA
45666 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
45691 GTTGAATTTT
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:49219 original size:2 final size:2
Alignment explanation
Indices: 49212--49247 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49202 ATGTCTCACT
49212 TA TA TA TA 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
49248 AAAGTAAAGA
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):
TA
Found at i:51700 original size:21 final size:20
Alignment explanation
Indices: 51628--51701 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
51618 GAAAAGCTCT
*
51628 TAAATAATAAAGTAATTTAAACC
1 TAAATAA-AAA-TAATTTAAA-A
*
51651 TAAATAAAAATAA-ATAAAA
1 TAAATAAAAATAATTTAAAA
*
51670 CTAATTTAAAAATAACTTTAAAA
1 -TAA-ATAAAAATAA-TTTAAAA
51693 TAAATAAAA
1 TAAATAAAA
51702 TCTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 6 0.14
23 12 0.29
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAATAAAAATAATTTAAAA
Found at i:54947 original size:154 final size:155
Alignment explanation
Indices: 54666--54965 Score: 379
Period size: 154 Copynumber: 1.9 Consensus size: 155
54656 GTTGAGGGAA
* *
54666 GCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * * *
54731 TTCCTTAGCCTACCAACTAGGCTTGTTGATAGCTCGCTGTCCTAGTCATCCTTTCTGTAACCTTT
66 TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
*
54796 ATTTTCACTCATTTCAGCGAAGGAG
131 ATTTTCACTCACTTCAGCGAAGGAG
* * * * * **
54821 GCCAAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCTTCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * *
54885 TTCATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCTGTAACCTT
66 TTCATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTT
*
54949 TATTTTCTCTCACTTCA
130 TATTTTCACTCACTTCA
54966 TTTCCTTCTT
Statistics
Matches: 122, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 2 0.02
154 95 0.78
155 25 0.20
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (155 bp):
GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
ATTTTCACTCACTTCAGCGAAGGAG
Found at i:58776 original size:2 final size:2
Alignment explanation
Indices: 58769--58802 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58759 TTTCACTTCT
58769 TA TA TA 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
58803 GTATTTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60059 original size:33 final size:34
Alignment explanation
Indices: 60022--60086 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
60012 TTTATTTAAA
* * *
60022 AATATTTAATAAATATATTTAAAAT-TAAAATTT
1 AATATATAAAAAATATATATAAAATATAAAATTT
*
60055 AATATATAAAAAATTTATATAAAATATAAAAT
1 AATATATAAAAAATATATATAAAATATAAAAT
60087 AAATTAAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AATATATAAAAAATATATATAAAATATAAAATTT
Found at i:60386 original size:13 final size:13
Alignment explanation
Indices: 60368--60394 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60358 TTTATTTTTA
60368 AACATAAAAAAAT
1 AACATAAAAAAAT
60381 AACATAAAAAAAT
1 AACATAAAAAAAT
60394 A
1 A
60395 TTTATAAAAA
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AACATAAAAAAAT
Found at i:60401 original size:14 final size:14
Alignment explanation
Indices: 60371--60411 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
60361 ATTTTTAAAC
**
60371 ATAAAAAAATA-AC
1 ATAAAAAAATATTT
60384 ATAAAAAAATATTT
1 ATAAAAAAATATTT
60398 AT-AAAAAATATTT
1 ATAAAAAAATATTT
60411 A
1 A
60412 AAATATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 23 0.92
14 2 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAAAAAATATTT
Found at i:60508 original size:49 final size:49
Alignment explanation
Indices: 60384--60516 Score: 140
Period size: 49 Copynumber: 2.8 Consensus size: 49
60374 AAAAAATAAC
60384 ATAAAA-AAATATT-TATA-AAAAATAT-T-T-AAAATATAACATAAAA
1 ATAAAATAAATATTATATATAAAAATATATATAAAAATATAACATAAAA
* *
60427 ATAATATACATATTATAT-TAATACACATATATATAAAAATAT-ACAT-AAA
1 ATAAAATAAATATTATATATAA-A-A-ATATATATAAAAATATAACATAAAA
60476 ATAAAATAAATTATTAATATATAAAAATATATATAAAAATA
1 ATAAAATAAA-TATT-ATATATAAAAATATATATAAAAATA
60517 ATATTTTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
43 5 0.07
44 6 0.08
45 5 0.07
46 1 0.01
47 1 0.01
48 4 0.05
49 27 0.36
50 10 0.14
51 12 0.16
52 3 0.04
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (49 bp):
ATAAAATAAATATTATATATAAAAATATATATAAAAATATAACATAAAA
Found at i:60950 original size:24 final size:23
Alignment explanation
Indices: 60907--60968 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 23
60897 ACAACATGAA
*
60907 AAAT-AATAAA-AA-TAAGATAT
1 AAATAAATAAATAATTAAAATAT
* *
60927 AAATACATGAATATATTAAAATAT
1 AAATAAATAAATA-ATTAAAATAT
*
60951 AGATAAATAAATAATTAA
1 AAATAAATAAATAATTAA
60969 CGTGTAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 1 0.03
23 6 0.19
24 17 0.53
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATAAATAAATAATTAAAATAT
Found at i:61119 original size:37 final size:36
Alignment explanation
Indices: 61059--61146 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
61049 ACATTACTTG
*
61059 AAAATA-ATATACACATAATATAAATATACGTACATATA-
1 AAAATATATATA-AAATAATATAAAT-TA-GTA-ATATAT
*
61097 AAAATATATATAAAATAA-ATAAATTATTAATATAT
1 AAAATATATATAAAATAATATAAATTAGTAATATAT
*
61132 AAAAAATATATAAAA
1 AAAATATATATAAAA
61147 ATATAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 5 0.11
35 16 0.36
36 2 0.04
37 6 0.13
38 11 0.24
39 5 0.11
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.31
Consensus pattern (36 bp):
AAAATATATATAAAATAATATAAATTAGTAATATAT
Found at i:61133 original size:19 final size:19
Alignment explanation
Indices: 61092--61152 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
61082 ATATACGTAC
61092 ATAT-AAAAATATATATAAA
1 ATATAAAAAATATATA-AAA
* * *
61111 ATA-AATAAAT-TATTAAT
1 ATATAAAAAATATATAAAA
61128 ATATAAAAAATATATAAAA
1 ATATAAAAAATATATAAAA
61147 ATATAA
1 ATATAA
61153 TATTTTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 5 0.15
18 9 0.27
19 19 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAAAAATATATAAAA
Found at i:61141 original size:33 final size:31
Alignment explanation
Indices: 61104--61172 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
61094 ATAAAAATAT
61104 ATATAAAATAAATA-AATTATTAATATATAAAAA
1 ATATAAAA-AAATATAA-TATT-ATATATAAAAA
* *
61137 ATATATAAAAATATAATATTTTATATAAAAA
1 ATATAAAAAAATATAATATTATATATAAAAA
61168 A-ATAA
1 ATATAA
61173 TACAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.09
31 11 0.34
32 9 0.28
33 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
ATATAAAAAAATATAATATTATATATAAAAA
Found at i:61152 original size:8 final size:9
Alignment explanation
Indices: 61092--61152 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
61082 ATATACGTAC
*
61092 ATATAAAAA
1 ATATATAAA
61101 TATATATAAA
1 -ATATATAAA
*
61111 ATAAATAAA
1 ATATATAAA
* *
61120 TTAT-TAAT
1 ATATATAAA
*
61128 ATATAAAAA
1 ATATATAAA
61137 ATATATAAA
1 ATATATAAA
61146 A-ATATAA
1 ATATATAA
61153 TATTTTATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 12 0.29
9 21 0.51
10 8 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATATAAA
Found at i:61153 original size:26 final size:26
Alignment explanation
Indices: 61099--61155 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
61089 TACATATAAA
* *
61099 AATATATATAAAATAAATAAATTATT
1 AATATATAAAAAATAAATAAAATATT
*
61125 AATATATAAAAAATATATAAAA-ATAT
1 AATATATAAAAAATAAATAAAATAT-T
61151 AATAT
1 AATAT
61156 TTTATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATATATAAAAAATAAATAAAATATT
Found at i:70116 original size:26 final size:26
Alignment explanation
Indices: 70063--70145 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 26
70053 ACCAATTTTG
* * *
70063 ACAAACAATAAGCTACCATTTTTTACAA
1 ACAAA-AATAATC-ACCATATTTGACAA
70091 ACAAAAATAATCACCATATTTGACAAA
1 ACAAAAATAATCACCATATTTGAC-AA
* * **
70118 TATAAAAAAAATCATTATATTTGACAA
1 -ACAAAAATAATCACCATATTTGACAA
70145 A
1 A
70146 TACAAAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 25 0.54
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (26 bp):
ACAAAAATAATCACCATATTTGACAA
Found at i:70125 original size:28 final size:28
Alignment explanation
Indices: 70091--70152 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
70081 TTTTTTACAA
*
70091 ACAAAAATAATCACCATATTTGACAAAT
1 ACAAAAAAAATCACCATATTTGACAAAT
* **
70119 ATAAAAAAAATCATTATATTTGACAAAT
1 ACAAAAAAAATCACCATATTTGACAAAT
70147 ACAAAA
1 ACAAAA
70153 TGTGACATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (28 bp):
ACAAAAAAAATCACCATATTTGACAAAT
Found at i:70237 original size:32 final size:32
Alignment explanation
Indices: 70196--70259 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
70186 CACTACACCA
70196 AGTTTCCATTGTTTGGGCAAAGCAAAGAGGAT
1 AGTTTCCATTGTTTGGGCAAAGCAAAGAGGAT
70228 AGTTTCCATTGTTTGGGCAAAGCAAAGAGGAT
1 AGTTTCCATTGTTTGGGCAAAGCAAAGAGGAT
70260 GATGTGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (32 bp):
AGTTTCCATTGTTTGGGCAAAGCAAAGAGGAT
Found at i:71308 original size:12 final size:12
Alignment explanation
Indices: 71293--71334 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
71283 AATAATTATG
71293 TATTAAATTTTA
1 TATTAAATTTTA
*
71305 TATTAAAAATTTA
1 TATT-AAATTTTA
71318 TA-TAAATTTTA
1 TATTAAATTTTA
*
71329 AATTAA
1 TATTAA
71335 TTTATAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 8 0.32
12 8 0.32
13 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTAAATTTTA
Found at i:72980 original size:61 final size:59
Alignment explanation
Indices: 72855--72970 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
72845 TGATGGATGA
* * * *
72855 ATAAATGTAATTTTTTTTAAGATTGTGAATAAAAATGAAATATTAATAAAAATTGTAAATG
1 ATAAATGTAA-TTTTTTAAAAATTATGAATAAAAAT-AAATATTAATAAAAATTATAAATG
72916 ATAAATGTAA-TTTTTAAAAATTATGAATAAAAAT-AATA-TAATAAAAAGTTATAAA
1 ATAAATGTAATTTTTTAAAAATTATGAATAAAAATAAATATTAATAAAAA-TTATAAA
72971 CCGTTGATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 9 0.18
57 10 0.20
59 21 0.42
61 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (59 bp):
ATAAATGTAATTTTTTAAAAATTATGAATAAAAATAAATATTAATAAAAATTATAAATG
Found at i:73328 original size:7 final size:7
Alignment explanation
Indices: 73316--73349 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
73306 ATTAAAATTA
73316 AATAAAT
1 AATAAAT
73323 AATAAAT
1 AATAAAT
73330 AATAAAT
1 AATAAAT
73337 AATAAAT
1 AATAAAT
73344 AATAAA
1 AATAAA
73350 CTAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:73506 original size:2 final size:2
Alignment explanation
Indices: 73499--73532 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
73489 GACTTTTACA
73499 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
73533 GCCACTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78781 original size:23 final size:23
Alignment explanation
Indices: 78731--78783 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
78721 ATTTGTTTCT
*
78731 TCAACATTTGGTGTAATATTATG
1 TCAATATTTGGTGTAATATTATG
*
78754 TCAATATTTGGTGTAATTTTATG
1 TCAATATTTGGTGTAATATTATG
78777 TCAATAT
1 TCAATAT
78784 CTTAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (23 bp):
TCAATATTTGGTGTAATATTATG
Found at i:79700 original size:266 final size:266
Alignment explanation
Indices: 79214--79728 Score: 897
Period size: 266 Copynumber: 1.9 Consensus size: 266
79204 GGATTATGGA
* * *
79214 AAATGATTAAGGTGAAACATCCGCATGTCCAAGAGAAGCTATTCATGGATAATTAAAGGGTTATG
1 AAATAATTAAGGTGAAACATCCACATGTCCAAGAGAAGCTATTCACGGATAATTAAAGGGTTATG
79279 GGAGATGGAAAGGAAGATCAGGTCAAGCAAGATGATTTGCCCAAGATGCCTAATTATTTGAAGGC
66 GGAGATGGAAAGGAAGATCAGGTCAAGCAAGATGATTTGCCCAAGATGCCTAATTATTTGAAGGC
79344 AATGATCTTGGGAAGGGTAAGAAGTCACCGTCCTGAGAGTATTTTTGGTGCCCAAGAATGATACC
131 AATGATCTTGGGAAGGGTAAGAAGTCACCGTCCTGAGAGTATTTTTGGTGCCCAAGAATGATACC
79409 ACTAATTTTCTGGTAGCAAAAATA-GGGTGAGATAAGAAGACTGGGAAAGTGATTCGCAATGCAT
196 ACTAATTTTCTGGTAGCAAAAATAGGGGTGAGATAAGAAGACTGGGAAAGTGATTCGCAATGCAT
79473 TACAGT
261 TACAGT
* * *
79479 AAATAATTATGGTGAAACATCCACATGTTCAAGAGAAGCTGTTCACGGATAATTAAAGGGGTTAT
1 AAATAATTAAGGTGAAACATCCACATGTCCAAGAGAAGCTATTCACGGATAATTAAA-GGGTTAT
* *
79544 GGGAGATGGAGAGGAAGATCAGGTCAAGGAAGATGATTTGCCCAAGATGCCTAATTATTTGAAGG
65 GGGAGATGGAAAGGAAGATCAGGTCAAGCAAGATGATTTGCCCAAGATGCCTAATTATTTGAAGG
* *
79609 CAATGATCTTGGGAAGGGTAAGAAGTCACCGTCCTGGGGGTATTTTTGGTGCCCAAGAATGATAC
130 CAATGATCTTGGGAAGGGTAAGAAGTCACCGTCCTGAGAGTATTTTTGGTGCCCAAGAATGATAC
* * *
79674 CATTAATTTTCTGGTAGCAGAAATAGGGGTGGGATAAGAAGACTGGGAAAGTGAT
195 CACTAATTTTCTGGTAGCAAAAATAGGGGTGAGATAAGAAGACTGGGAAAGTGAT
79729 GCACAATGGG
Statistics
Matches: 235, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
265 51 0.22
266 156 0.66
267 28 0.12
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (266 bp):
AAATAATTAAGGTGAAACATCCACATGTCCAAGAGAAGCTATTCACGGATAATTAAAGGGTTATG
GGAGATGGAAAGGAAGATCAGGTCAAGCAAGATGATTTGCCCAAGATGCCTAATTATTTGAAGGC
AATGATCTTGGGAAGGGTAAGAAGTCACCGTCCTGAGAGTATTTTTGGTGCCCAAGAATGATACC
ACTAATTTTCTGGTAGCAAAAATAGGGGTGAGATAAGAAGACTGGGAAAGTGATTCGCAATGCAT
TACAGT
Found at i:81122 original size:13 final size:13
Alignment explanation
Indices: 81104--81135 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
81094 TTCAAAAGTG
*
81104 ATAAAATTATGTA
1 ATAAAATTATATA
81117 ATAAAATTATATA
1 ATAAAATTATATA
81130 ATAAAA
1 ATAAAA
81136 CACATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
ATAAAATTATATA
Found at i:86499 original size:27 final size:25
Alignment explanation
Indices: 86449--86504 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
86439 TTTAAATAAT
86449 ATTAAAAATAAAAAATTAATTTTATA
1 ATTAAAAATAAAAAATTAATTTTA-A
* **
86475 ATTAAATATAAATAAATTCTTTTTAA
1 ATTAAAAATAAA-AAATTAATTTTAA
86501 ATTA
1 ATTA
86505 TTAAAAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTAAAAATAAAAAATTAATTTTAA
Found at i:93192 original size:20 final size:22
Alignment explanation
Indices: 93167--93222 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
93157 TATAATCGTA
93167 TTTAAAATATTT-AT-ATTA-AT
1 TTTAAAAT-TTTAATAATTATAT
93187 TTTAAAATTTTAATAATTATAT
1 TTTAAAATTTTAATAATTATAT
*
93209 TTTATAGATTTTAA
1 TTTA-AAATTTTAA
93223 AATATTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 4 0.13
22 6 0.19
23 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAAAATTTTAATAATTATAT
Found at i:93209 original size:32 final size:35
Alignment explanation
Indices: 93173--93250 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 35
93163 CGTATTTAAA
93173 ATATTTATATTA-ATTTTAAAAT-TTTAATAATT-
1 ATATTTATATTAGATTTTAAAATATTTAATAATTC
* *
93205 ATATTT-TA-TAGATTTTAAAATATTTATTTATTC
1 ATATTTATATTAGATTTTAAAATATTTAATAATTC
93238 ATATTTATTATTA
1 ATATTTA-TATTA
93251 TTATTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 2 0.05
31 12 0.32
32 14 0.37
33 6 0.16
35 2 0.05
36 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (35 bp):
ATATTTATATTAGATTTTAAAATATTTAATAATTC
Found at i:93232 original size:23 final size:23
Alignment explanation
Indices: 93179--93233 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
93169 TAAAATATTT
*
93179 ATATTAATTTTAAAATTTTAATA
1 ATATTTATTTTAAAATTTTAATA
* *
93202 AT-TATATTTTATAGATTTTAA-A
1 ATATTTATTTTA-AAATTTTAATA
93224 ATATTTATTT
1 ATATTTATTT
93234 ATTCATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTTATTTTAAAATTTTAATA
Found at i:93263 original size:14 final size:15
Alignment explanation
Indices: 93224--93265 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
93214 AGATTTTAAA
93224 ATATTTAT-TTATTC
1 ATATTTATATTATTC
93238 ATATTTATTATTATT-
1 ATATTTA-TATTATTC
*
93253 ATTTTTATATTAT
1 ATATTTATATTAT
93266 GTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 7 0.28
16 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTATATTATTC
Found at i:93557 original size:11 final size:11
Alignment explanation
Indices: 93543--93578 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
93533 TTCACAAGCA
93543 AATAATAATAT
1 AATAATAATAT
*
93554 AATAATAATAA
1 AATAATAATAT
93565 AATAATAATTAT
1 AATAATAA-TAT
93577 AA
1 AA
93579 AATTAGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATAATAT
Found at i:93562 original size:14 final size:14
Alignment explanation
Indices: 93543--93581 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
93533 TTCACAAGCA
*
93543 AATAATAATATAAT
1 AATAATAAAATAAT
93557 AATAATAAAATAAT
1 AATAATAAAATAAT
*
93571 AATTATAAAAT
1 AATAATAAAAT
93582 TAGCAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:94041 original size:18 final size:18
Alignment explanation
Indices: 94014--94048 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
94004 CAGGATTTGA
94014 TTTTTCCTTTTCTTTTTT
1 TTTTTCCTTTTCTTTTTT
*
94032 TTTTTTCTTTTCTTTTT
1 TTTTTCCTTTTCTTTTT
94049 CAACATTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCCTTTTCTTTTTT
Found at i:94513 original size:14 final size:15
Alignment explanation
Indices: 94488--94517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
94478 TCCATTAATA
94488 TAATACATAAAAAAT
1 TAATACATAAAAAAT
94503 TAATA-ATAAAAAAT
1 TAATACATAAAAAAT
94517 T
1 T
94518 CAGTCCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATACATAAAAAAT
Found at i:99313 original size:6 final size:6
Alignment explanation
Indices: 99304--99329 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
99294 AGGAAAAAAA
99304 AACATG AACATG AACATG AACATG AA
1 AACATG AACATG AACATG AACATG AA
99330 AATGTTATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AACATG
Found at i:100398 original size:13 final size:12
Alignment explanation
Indices: 100366--100399 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
100356 AAAACATACA
100366 AAAAATTTATAT
1 AAAAATTTATAT
*
100378 TAAAATTTATAT
1 AAAAATTTATAT
100390 AAAATATTTA
1 AAAA-ATTTA
100400 ATACTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAAATTTATAT
Found at i:101129 original size:11 final size:12
Alignment explanation
Indices: 101110--101144 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
101100 AATATTATCA
101110 TATATTTTTAAT
1 TATATTTTTAAT
*
101122 TA-ATTTTTTAT
1 TATATTTTTAAT
101133 TATATTTTTAAT
1 TATATTTTTAAT
101145 ATACTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTTTTAAT
Found at i:108863 original size:18 final size:19
Alignment explanation
Indices: 108826--108864 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
108816 TATATAGGTT
108826 GCAAAATGCTAAAGAAAACA
1 GCAAAATGC-AAAGAAAACA
*
108846 GCAAAATG-AAATAAAACA
1 GCAAAATGCAAAGAAAACA
108864 G
1 G
108865 AATCTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (19 bp):
GCAAAATGCAAAGAAAACA
Found at i:115176 original size:22 final size:22
Alignment explanation
Indices: 115151--115214 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
115141 TATTTTATAA
*
115151 ATATCA-ATCTTTTATTATATTT
1 ATATCATAT-TTTAATTATATTT
*
115173 ATATTATATTTTAATTAT-TTT
1 ATATCATATTTTAATTATATTT
115194 -TAT-ATATTATATAATTATATT
1 ATATCATATT-T-TAATTATATT
115215 ATACATTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 10 0.28
22 15 0.42
23 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATCATATTTTAATTATATTT
Found at i:115179 original size:11 final size:10
Alignment explanation
Indices: 115160--115201 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
115150 AATATCAATC
115160 TTTTATTATA
1 TTTTATTATA
115170 TTTATATTATA
1 TTT-TATTATA
115181 TTTTAATTAT-
1 TTTT-ATTATA
115191 TTTTA-TATA
1 TTTTATTATA
115200 TT
1 TT
115202 ATATAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.10
9 3 0.10
10 8 0.28
11 15 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATTATA
Found at i:115210 original size:21 final size:20
Alignment explanation
Indices: 115168--115217 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
115158 TCTTTTATTA
115168 TATTTATATTATATTTTAAT
1 TATTTATATTATATTTTAAT
*
115188 TATTTTTA-TATATTATATAAT
1 TATTTATATTATATT-T-TAAT
115209 TATATTATA
1 TAT-TTATA
115218 CATTAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 7 0.28
22 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATATTATATTTTAAT
Found at i:116767 original size:18 final size:16
Alignment explanation
Indices: 116746--116781 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
116736 ATTTATCTTA
116746 TTAATTATTTTTAAGTTT
1 TTAATT-TTTTT-AGTTT
116764 TTAATTTTTTTAGTTT
1 TTAATTTTTTTAGTTT
116780 TT
1 TT
116782 TTTAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (16 bp):
TTAATTTTTTTAGTTT
Found at i:118162 original size:32 final size:33
Alignment explanation
Indices: 118100--118168 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
118090 ATTTAATTTA
* * *
118100 ATAATATAAAAATAAAAATATACCTTTTAAA-T
1 ATAATATAAAAACAAAAATAGACCTATTAAAGT
*
118132 ATAATATAAAGACAACAAATAGA-CTATTAAAGT
1 ATAATATAAAAACAA-AAATAGACCTATTAAAGT
118165 ATAA
1 ATAA
118169 AAACACACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 20 0.65
33 11 0.35
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.29
Consensus pattern (33 bp):
ATAATATAAAAACAAAAATAGACCTATTAAAGT
Found at i:119100 original size:12 final size:12
Alignment explanation
Indices: 119043--119109 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
119033 TTATTATTTA
119043 ATAATAAA-AAT
1 ATAATAAATAAT
*
119054 AT-ATAAATGAT
1 ATAATAAATAAT
119065 A-ATATAAA-AAT
1 ATA-ATAAATAAT
* *
119076 ATATTTTAATAAT
1 ATA-ATAAATAAT
119089 ATAATAAATAAT
1 ATAATAAATAAT
*
119101 AAAATAAAT
1 ATAATAAAT
119110 TTTTAAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
10 5 0.11
11 8 0.18
12 25 0.57
13 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:119881 original size:6 final size:7
Alignment explanation
Indices: 119864--119888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
119854 AAACATGATA
119864 AAAAAAT
1 AAAAAAT
119871 AAAAAAT
1 AAAAAAT
119878 AAAAAAT
1 AAAAAAT
119885 AAAA
1 AAAA
119889 TATTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:119906 original size:9 final size:9
Alignment explanation
Indices: 119892--119916 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
119882 AATAAAATAT
119892 TTAATATAA
1 TTAATATAA
119901 TTAATATAA
1 TTAATATAA
119910 TTAATAT
1 TTAATAT
119917 GATATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAATATAA
Found at i:120670 original size:2 final size:2
Alignment explanation
Indices: 120663--120700 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
120653 TTAATTATCC
*
120663 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120701 GATTATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:124919 original size:2 final size:2
Alignment explanation
Indices: 124912--124946 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
124902 CAACTGAATA
124912 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
124947 AAACTCGTTC
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:130748 original size:14 final size:15
Alignment explanation
Indices: 130729--130761 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
130719 ATTATAATTT
130729 AAATAAAAA-ATAAA
1 AAATAAAAAGATAAA
*
130743 AAATAAAAAGATATA
1 AAATAAAAAGATAAA
130758 AAAT
1 AAAT
130762 TTAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAAAGATAAA
Found at i:131218 original size:18 final size:18
Alignment explanation
Indices: 131179--131236 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
131169 ATTTTTATTT
131179 TTAT-AAATT-ATTTAATA
1 TTATAAAATTAATTTAA-A
131196 TTTATAAAATTAATTTAAA
1 -TTATAAAATTAATTTAAA
* * *
131215 TTATAATATAAATTTTAA
1 TTATAAAATTAATTTAAA
131233 TTAT
1 TTAT
131237 CTTTTAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 23 0.66
19 6 0.17
20 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATAAAATTAATTTAAA
Found at i:131292 original size:141 final size:140
Alignment explanation
Indices: 131033--131292 Score: 298
Period size: 141 Copynumber: 1.8 Consensus size: 140
131023 ATGCAAAAAA
* *
131033 TATTCTTATAAATTATTTAATTTTTATAAAATTAATTGAAGTTATAATATTATAATATTTTTATT
1 TATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAATATTTTTATT
* * * * * *
131098 TTTTGCAATTATTTATAAGAAGAAAAAAATCATATAGGGAGAAATATAAATAAAAATTAAATTAA
66 TTTAG-AATTATTTATAAGAAGAAAAAAATAAAAAAGGAAGAAATAGAAATAAAAATTAAATTAA
131163 ATGAATATTTT
130 ATGAATATTTT
* *
131174 TATTTTTATAAATTATTTAATATTTATAAAATTAATTTAAATTATAATA-TA-AAT-TTTAATTA
1 TATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAATATTT--TTA
* *
131236 TCTTTTAG-TTTATTTATCAAGAAGATAAAATGAA-AAAAAAGGAAGAAA-GGAAATAAA
64 T-TTTTAGAATTATTTAT-AAGAAGA-AAAA--AATAAAAAAGGAAGAAATAGAAATAAA
131293 CAAAAAAATT
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
138 3 0.03
139 11 0.11
140 13 0.13
141 61 0.61
142 10 0.10
143 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (140 bp):
TATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAATATTTTTATT
TTTAGAATTATTTATAAGAAGAAAAAAATAAAAAAGGAAGAAATAGAAATAAAAATTAAATTAAA
TGAATATTTT
Found at i:133635 original size:15 final size:15
Alignment explanation
Indices: 133615--133675 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
133605 ATAATTGTGT
*
133615 TTATAATATTTTATA
1 TTATAAAATTTTATA
133630 TTATAAAAATTTTAATA
1 TTAT-AAAATTTT-ATA
*
133647 TGT-TAAAAATTTATA
1 T-TATAAAATTTTATA
133662 TTATATAAATTTTA
1 TTATA-AAATTTTA
133676 AAACATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.03
15 10 0.26
16 21 0.55
17 5 0.13
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TTATAAAATTTTATA
Found at i:133643 original size:16 final size:16
Alignment explanation
Indices: 133622--133675 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
133612 TGTTTATAAT
133622 ATTTTATATTATAAAA
1 ATTTTATATTATAAAA
133638 ATTTTAATATGT-TAAAA
1 ATTTT-ATAT-TATAAAA
*
133655 A-TTTATATTATATAA
1 ATTTTATATTATAAAA
133670 ATTTTA
1 ATTTTA
133676 AAACATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 1 0.03
15 9 0.27
16 12 0.36
17 10 0.30
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTTTATATTATAAAA
Found at i:136296 original size:2 final size:2
Alignment explanation
Indices: 136289--136325 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
136279 ACTCTATACC
136289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
136326 TTATTCGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:136384 original size:13 final size:13
Alignment explanation
Indices: 136350--136384 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
136340 ATTTGATCGA
136350 TTTAACTTTATTT
1 TTTAACTTTATTT
*
136363 TTTTA-TTTATTT
1 TTTAACTTTATTT
136375 TTTAACTTTA
1 TTTAACTTTA
136385 CTTGGCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTAACTTTATTT
Found at i:136692 original size:126 final size:125
Alignment explanation
Indices: 136467--136723 Score: 311
Period size: 125 Copynumber: 2.0 Consensus size: 125
136457 ATCCATGCAA
* * * *
136467 TTTGTGGTCGAGGCCAGCCAATGAGACTATACGGATTTGACTTGACGAAGTGGGTACCGCATTGG
1 TTTGTGATCGAGCCCAGCCAATGAGACTAGACGGATTTGACTTGACGAAGTGGATACCGCATTGG
* * *** * * *
136532 TAGGGCGATGGGATCTGTCCACCCTGGAACTGATCTAAAGCGATAAGGAATGTTCAGCTGT
66 CAGGCCGAAACGATCTGTCCACCCTGGAACTGATCT-AAGCAAAAAGGAATGTTCAGCTGC
* *
136593 TTTGTGATCGAGCCCAGCCAATGA-A-TAGACGGCTTTGACTTGACGAAGTTGGATACGGCATTG
1 TTTGTGATCGAGCCCAGCCAATGAGACTAGACGGATTTGACTTGACGAAG-TGGATACCGCATTG
* * * *
136656 GCAGGCCGAAAACGATCTGTCCTCGCTGGAATTGATCTAATCAAAAAGGAATGTTCAGCTGC
65 GCAGGCCG-AAACGATCTGTCCACCCTGGAACTGATCTAAGCAAAAAGGAATGTTCAGCTGC
136718 TTTGTG
1 TTTGTG
136724 GGATATAAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
124 21 0.19
125 45 0.41
126 45 0.41
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (125 bp):
TTTGTGATCGAGCCCAGCCAATGAGACTAGACGGATTTGACTTGACGAAGTGGATACCGCATTGG
CAGGCCGAAACGATCTGTCCACCCTGGAACTGATCTAAGCAAAAAGGAATGTTCAGCTGC
Found at i:136898 original size:13 final size:13
Alignment explanation
Indices: 136880--136909 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
136870 TAACTAAACT
*
136880 AATAAATTATTTA
1 AATAAAATATTTA
136893 AATAAAATATTTA
1 AATAAAATATTTA
136906 AATA
1 AATA
136910 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAAAATATTTA
Found at i:138013 original size:22 final size:19
Alignment explanation
Indices: 137972--138015 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
137962 TTAGTTAATT
137972 TTTAAATATTATTAAAATA
1 TTTAAATATTATTAAAATA
137991 TTTAAATAATTATATAAAAATA
1 TTTAAAT-ATTAT-T-AAAATA
138013 TTT
1 TTT
138016 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 1 0.05
22 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAATATTATTAAAATA
Found at i:138210 original size:2 final size:2
Alignment explanation
Indices: 138203--138236 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
138193 ATTGATAGTT
138203 TA TA TA 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
138237 CTAGTAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:140922 original size:18 final size:16
Alignment explanation
Indices: 140885--140919 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
140875 TTCGTTTATG
140885 TTTCTCTACAAGTGTT
1 TTTCTCTACAAGTGTT
*
140901 TTTCTCTACTAGTGTT
1 TTTCTCTACAAGTGTT
140917 TTT
1 TTT
140920 TTCCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTCTCTACAAGTGTT
Found at i:142511 original size:20 final size:20
Alignment explanation
Indices: 142486--142523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
142476 TAAATAGTAA
*
142486 TAAATAAAATTGTAATTTTC
1 TAAATAAAATTATAATTTTC
*
142506 TAAATAGAATTATAATTT
1 TAAATAAAATTATAATTT
142524 ACTTAGTAAT
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:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAATAAAATTATAATTTTC
Found at i:148146 original size:8 final size:8
Alignment explanation
Indices: 148135--148169 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
148125 ATTAATTATA
148135 TATAAAAT
1 TATAAAAT
148143 TATAAAAT
1 TATAAAAT
*
148151 TAAAAAAT
1 TATAAAAT
148159 ATATAAAAT
1 -TATAAAAT
148168 TA
1 TA
148170 ACTAATTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TATAAAAT
Found at i:148165 original size:17 final size:16
Alignment explanation
Indices: 148138--148170 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
148128 AATTATATAT
148138 AAAATTATAAAATTAA
1 AAAATTATAAAATTAA
148154 AAAATATATAAAATTAA
1 AAAAT-TATAAAATTAA
148171 CTAATTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTATAAAATTAA
Found at i:150330 original size:21 final size:21
Alignment explanation
Indices: 150304--150344 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
150294 CAAGATTGAT
*
150304 TGAAAAGATAAA-TTTGATTTC
1 TGAAAA-ATAAAGTTGGATTTC
150325 TGAAAAATAAAGTTGGATTT
1 TGAAAAATAAAGTTGGATTT
150345 GGGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (21 bp):
TGAAAAATAAAGTTGGATTTC
Found at i:150642 original size:9 final size:10
Alignment explanation
Indices: 150606--150640 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
150596 TATTATTATC
150606 TTTTAATAAT
1 TTTTAATAAT
*
150616 TTTAAATAAT
1 TTTTAATAAT
150626 TTTTAA-AAT
1 TTTTAATAAT
150635 TTTTAA
1 TTTTAA
150641 AAAATCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:152500 original size:3 final size:3
Alignment explanation
Indices: 152492--152535 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
152482 GCATCTTTCG
152492 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
152536 GTAGGTGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:153029 original size:9 final size:8
Alignment explanation
Indices: 153015--153057 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
153005 CTGATTTGAG
153015 TTAAATTAT
1 TTAAATT-T
153024 TTAAATTT
1 TTAAATTT
*
153032 TTAAAATT
1 TTAAATTT
153040 TTAAATTATT
1 TTAAA-T-TT
153050 TTAAATTT
1 TTAAATTT
153058 GAATTATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.50
9 8 0.27
10 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTAAATTT
Found at i:153044 original size:16 final size:17
Alignment explanation
Indices: 153023--153057 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
153013 AGTTAAATTA
153023 TTTAAATT-TTTAAAAT
1 TTTAAATTATTTAAAAT
*
153039 TTTAAATTATTTTAAAT
1 TTTAAATTATTTAAAAT
153056 TT
1 TT
153058 GAATTATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAAATTATTTAAAAT
Found at i:153159 original size:31 final size:31
Alignment explanation
Indices: 153124--153220 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 31
153114 ACTAATAAGA
*
153124 TTTAATTAGATCATTTATTAAATTTAATTAT
1 TTTAATTAGATCATTTATTAAGTTTAATTAT
*
153155 TTTAAATTTATATCA-TT-TTAAGTTTAATTCAT
1 TTT-AA-TTAGATCATTTATTAAGTTTAATT-AT
* * *
153187 TTGAATTTGA--ATTATATTAAGTTTAAATAT
1 TTTAATTAGATCATT-TATTAAGTTTAATTAT
153217 TTTA
1 TTTA
153221 TACATGAATC
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 9 0.17
31 27 0.51
32 8 0.15
33 7 0.13
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTAATTAGATCATTTATTAAGTTTAATTAT
Found at i:153161 original size:15 final size:15
Alignment explanation
Indices: 153141--153220 Score: 72
Period size: 15 Copynumber: 5.2 Consensus size: 15
153131 AGATCATTTA
153141 TTAAATTTAATTATT
1 TTAAATTTAATTATT
*
153156 TTAAATTTATATCATT
1 TTAAATTTA-ATTATT
*
153172 TTAAGTTTAATTCA-T
1 TTAAATTTAATT-ATT
* *
153187 TTGAATTTGAATTATA
1 TTAAATTT-AATTATT
* *
153203 TTAAGTTTAAATATT
1 TTAAATTTAATTATT
153218 TTA
1 TTA
153221 TACATGAATC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
15 27 0.53
16 24 0.47
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (15 bp):
TTAAATTTAATTATT
Found at i:153174 original size:16 final size:15
Alignment explanation
Indices: 153141--153188 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
153131 AGATCATTTA
*
153141 TTAAATTTAATTATT
1 TTAAATTTAATCATT
153156 TTAAATTTATATCATT
1 TTAAATTTA-ATCATT
*
153172 TTAAGTTTAATTCATT
1 TTAAATTTAA-TCATT
153188 T
1 T
153189 GAATTTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (15 bp):
TTAAATTTAATCATT
Found at i:155855 original size:3 final size:3
Alignment explanation
Indices: 155849--155873 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
155839 TCTGTAGTAG
155849 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
155874 GGTTATTCAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:157095 original size:21 final size:23
Alignment explanation
Indices: 157045--157088 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
157035 ATTAATAAGT
*
157045 ATATTTTATAA-ATAAAATATAA
1 ATATTTTATAATATATAATATAA
157067 ATATTTTATAATATATAATATA
1 ATATTTTATAATATATAATATA
157089 TTATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTTTATAATATATAATATAA
Found at i:157097 original size:19 final size:19
Alignment explanation
Indices: 157056--157106 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
157046 TATTTTATAA
*
157056 ATAAAATATAA-ATATTTT
1 ATAATATATAATATATTTT
157074 ATAATATATAATATATTATT
1 ATAATATATAATATATT-TT
157094 -TAATATATAATAT
1 ATAATATATAATAT
157107 TTGATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 10 0.33
19 18 0.60
20 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATATAATATATTTT
Found at i:157995 original size:17 final size:18
Alignment explanation
Indices: 157964--157998 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
157954 GTCTCTCCGA
157964 AAAAAAACACAAACAATT
1 AAAAAAACACAAACAATT
*
157982 AAAAAAAC-CTAACAATT
1 AAAAAAACACAAACAATT
157999 GCTAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAACACAAACAATT
Found at i:158046 original size:23 final size:23
Alignment explanation
Indices: 158003--158047 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
157993 ACAATTGCTA
* *
158003 ATAAACAATATAACAAATAAATC
1 ATAAAAAATATAAAAAATAAATC
158026 ATAAAAAATA-AAAAAATTAAAT
1 ATAAAAAATATAAAAAA-TAAAT
158048 AAAAAACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAAATATAAAAAATAAATC
Found at i:158424 original size:3 final size:3
Alignment explanation
Indices: 158418--158472 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
158408 ACATAATAAC
158418 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
158466 ATA ATA A
1 ATA ATA A
158473 GAAGAAGAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:161556 original size:29 final size:29
Alignment explanation
Indices: 161499--161557 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
161489 TAATTTGATT
* ** *
161499 ATTATATATTTTATATTTTATTTATATAA
1 ATTATATATGTTATATTTTACGTAAATAA
*
161528 ATTATGTATGTTATATTTTACGTAAATAA
1 ATTATATATGTTATATTTTACGTAAATAA
161557 A
1 A
161558 AATATTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (29 bp):
ATTATATATGTTATATTTTACGTAAATAA
Found at i:163084 original size:20 final size:20
Alignment explanation
Indices: 163059--163108 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
163049 TCATAAATTT
163059 AAATTAATTTAATTTTATTC
1 AAATTAATTTAATTTTATTC
* *
163079 AAATT-ATAATAATTTTATTT
1 AAATTAAT-TTAATTTTATTC
163099 AAATTTAATT
1 AAA-TTAATT
163109 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 2 0.08
22 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTAATTTAATTTTATTC
Found at i:163780 original size:5 final size:5
Alignment explanation
Indices: 163766--163798 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
163756 TTTTTTTATT
163766 TTAAA TTTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA -TTAAA TTAAA TTAAA TTAAA TTAAA TT
163799 TAAAAACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:163792 original size:15 final size:16
Alignment explanation
Indices: 163765--163802 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
163755 TTTTTTTTAT
163765 TTTAAATTTAAATTAAA
1 TTTAAA-TTAAATTAAA
163782 -TTAAATTAAATTAAA
1 TTTAAATTAAATTAAA
163797 TTTAAA
1 TTTAAA
163803 AACTTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:164839 original size:3 final size:3
Alignment explanation
Indices: 164831--164862 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
164821 TTGATAAAGT
164831 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
164863 GGATGTGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:165262 original size:23 final size:23
Alignment explanation
Indices: 165236--165281 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
165226 CGAGGGAAAA
165236 GGATAAGTTCAAAAAGAGTGGAT
1 GGATAAGTTCAAAAAGAGTGGAT
*
165259 GGATAAGTTCAAAAAGATTGGAT
1 GGATAAGTTCAAAAAGAGTGGAT
165282 TAGATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.24
Consensus pattern (23 bp):
GGATAAGTTCAAAAAGAGTGGAT
Found at i:165287 original size:24 final size:23
Alignment explanation
Indices: 165237--165287 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
165227 GAGGGAAAAG
*
165237 GATAAGTTCAAAAAGAGTGGATG
1 GATAAGTTCAAAAAGAGTGGATA
*
165260 GATAAGTTCAAAAAGATTGGATTA
1 GATAAGTTCAAAAAGAGTGGA-TA
165284 GATA
1 GATA
165288 TATAAGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (23 bp):
GATAAGTTCAAAAAGAGTGGATA
Found at i:165367 original size:18 final size:19
Alignment explanation
Indices: 165344--165386 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
165334 TTTTAAATTT
*
165344 TTAAAT-TTTAATATTTAA-
1 TTAAATATTTAA-ATTAAAG
165362 TTAAATATTTAAATTAAAG
1 TTAAATATTTAAATTAAAG
165381 TTAAAT
1 TTAAAT
165387 GAGTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAATATTTAAATTAAAG
Found at i:165370 original size:12 final size:13
Alignment explanation
Indices: 165320--165379 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 13
165310 TATTAAATTA
165320 ATTTAAATTAAAT
1 ATTTAAATTAAAT
165333 -TTT---TTAAAT
1 ATTTAAATTAAAT
* *
165342 TTTTAAATTTTAAT
1 ATTTAAA-TTAAAT
165356 ATTT-AATTAAAT
1 ATTTAAATTAAAT
165368 ATTTAAATTAAA
1 ATTTAAATTAAA
165380 GTTAAATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
9 6 0.16
10 3 0.08
12 12 0.32
13 9 0.24
14 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTAAATTAAAT
Found at i:165472 original size:16 final size:16
Alignment explanation
Indices: 165451--165483 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
165441 TATTAGATAT
*
165451 AATTATTTTAATTTTA
1 AATTATTTTAAATTTA
165467 AATTATTTTAAATTTA
1 AATTATTTTAAATTTA
165483 A
1 A
165484 GTTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:165488 original size:22 final size:22
Alignment explanation
Indices: 165457--165498 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
165447 ATATAATTAT
* *
165457 TTTAATTTTAAATTATTTTAAA
1 TTTAAGTTTAAATAATTTTAAA
165479 TTTAAGTTTAAATAATTTTA
1 TTTAAGTTTAAATAATTTTA
165499 TATACGAGTA
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:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAAGTTTAAATAATTTTAAA
Found at i:166835 original size:34 final size:34
Alignment explanation
Indices: 166768--166983 Score: 283
Period size: 34 Copynumber: 6.4 Consensus size: 34
166758 AAGCCAAGAG
* * *
166768 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
166801 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
166835 TGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
166868 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
166902 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
166936 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
166970 TGTTGATTAAATGG
1 TGTTGATTAAATGG
166984 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.24
34 121 0.76
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:166949 original size:68 final size:67
Alignment explanation
Indices: 166768--166985 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
166758 AAGCCAAGAG
* * * * *
166768 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
166833 AT
66 AT
* ** * *
166835 TGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
166900 AT
66 AT
* * *
166902 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
166967 CAT
65 CAT
166970 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
166986 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:171449 original size:34 final size:34
Alignment explanation
Indices: 171380--171597 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
171370 AAGTGGGAGA
* * *
171380 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
171413 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
171447 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
171480 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
171514 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
171548 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
171582 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
171598 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:171563 original size:68 final size:67
Alignment explanation
Indices: 171380--171599 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
171370 AAGTGGGAGA
* * * * *
171380 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
171445 CC
66 CC
* ** * *
171447 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
171512 CC
66 CC
* * *
171514 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
171579 GCC
65 GCC
171582 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
171600 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:173444 original size:14 final size:14
Alignment explanation
Indices: 173427--173455 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
173417 TATGTACTTA
173427 TATATATATATATT
1 TATATATATATATT
173441 TATATATATATATT
1 TATATATATATATT
173455 T
1 T
173456 GGGTGCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATATATATATT
Found at i:174146 original size:20 final size:21
Alignment explanation
Indices: 174110--174148 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
174100 TTTAAAAATA
174110 AATATAAATAATTTTATTTTT
1 AATATAAATAATTTTATTTTT
174131 AATA-AAAT-ATTATTATTT
1 AATATAAATAATT-TTATTT
174149 AATTCAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATAAATAATTTTATTTTT
Found at i:174440 original size:18 final size:18
Alignment explanation
Indices: 174419--174471 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
174409 TATTTTTATA
174419 TATAAAATATAAATATTT
1 TATAAAATATAAATATTT
* *
174437 TATAATATA-AAATA-AT
1 TATAAAATATAAATATTT
*
174453 TATTAAATATATAATATTT
1 TATAAAATATA-AATATTT
174472 AATTATTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 12 0.44
19 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATATAAATATTT
Found at i:174445 original size:16 final size:15
Alignment explanation
Indices: 174423--174560 Score: 67
Period size: 15 Copynumber: 9.1 Consensus size: 15
174413 TTTATATATA
174423 AAATATAAATATTTT
1 AAATATAAATATTTT
174438 ATAATATAAAATAATTATT
1 A-AATAT-AAAT-ATT-TT
174457 AAATATATAATA-TTT
1 AAATATA-AATATTTT
*
174472 AATTATTACAATA--TT
1 AAATA-TA-AATATTTT
* *
174487 AATTTTAAATA-TTT
1 AAATATAAATATTTT
*
174501 AAATAT-AATATATT
1 AAATATAAATATTTT
** *
174515 AAA-AT-TTTATTTA
1 AAATATAAATATTTT
174528 AAAGTA-AAATATTTT
1 AAA-TATAAATATTTT
174543 AAATAATTAAATATTTT
1 AAAT-A-TAAATATTTT
174560 A
1 A
174561 TATTTATAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
13 17 0.18
14 14 0.15
15 23 0.24
16 12 0.12
17 16 0.17
18 11 0.11
19 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (15 bp):
AAATATAAATATTTT
Found at i:174456 original size:21 final size:22
Alignment explanation
Indices: 174412--174563 Score: 69
Period size: 21 Copynumber: 7.4 Consensus size: 22
174402 ATAAGTATAT
174412 TTTTATATATAAAATATAAATA
1 TTTTATATATAAAATATAAATA
*
174434 TTTTATA-ATATAAA-ATAATTA
1 TTTTATATATA-AAATATAAATA
** * * *
174455 TTAAATATATAATATTTAATTA
1 TTTTATATATAAAATATAAATA
** * * *
174477 TTACA-ATATTAATTTTAAATA
1 TTTTATATATAAAATATAAATA
* *
174498 -TTTAAATATAATATATTAAA-A
1 TTTTATATATAAAATA-TAAATA
174519 TTTTAT-T-TAAAAGTA-AAATA
1 TTTTATATATAAAA-TATAAATA
174539 TTTTA-A-AT--AAT-TAAATA
1 TTTTATATATAAAATATAAATA
174556 TTTTATAT
1 TTTTATAT
174564 TTATAATTAT
Statistics
Matches: 99, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
17 11 0.11
18 3 0.03
19 3 0.03
20 13 0.13
21 38 0.38
22 31 0.31
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TTTTATATATAAAATATAAATA
Found at i:176287 original size:97 final size:97
Alignment explanation
Indices: 176180--176363 Score: 271
Period size: 97 Copynumber: 1.9 Consensus size: 97
176170 GTCAATAATA
* * * *
176180 ATGTAATTTATTGATAGAGTGTTCAATTTCTAATTTTAATAATAAAAAATTAAACATCGACAA-T
1 ATGTAATTTATCGATAAAATATTCAATTTCTAATTTTAATAATAAAAAATTAAACATCGACAACT
*
176244 CTAAATTATGAAAAGAAAAAAAAGCCAAAAGTC
66 -TAAATTATGAAAAAAAAAAAAAGCCAAAAGTC
* * *
176277 ATGTAATTTATCGCTAAAATATTGAATTTTTAATTTTAATAATAAAAAATTAAACATCGACAACT
1 ATGTAATTTATCGATAAAATATTCAATTTCTAATTTTAATAATAAAAAATTAAACATCGACAACT
*
176342 TCAATTATGAAAAAAAAAAAAA
66 TAAATTATGAAAAAAAAAAAAA
176364 AAACAGACTT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 76 0.99
98 1 0.01
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (97 bp):
ATGTAATTTATCGATAAAATATTCAATTTCTAATTTTAATAATAAAAAATTAAACATCGACAACT
TAAATTATGAAAAAAAAAAAAAGCCAAAAGTC
Found at i:178597 original size:21 final size:21
Alignment explanation
Indices: 178564--178631 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
178554 CATAATAAAT
178564 ATAATT-ATATTATTAAATTTA
1 ATAATTAAT-TTATTAAATTTA
*
178585 ATAATTAATTTATAAAAATTATA
1 ATAATTAATTTAT-TAAATT-TA
* *
178608 A-AA-AAATTAATTAAATTTA
1 ATAATTAATTTATTAAATTTA
178627 CATAA
1 -ATAA
178632 ATTTCAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 18 0.47
22 9 0.24
23 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAATTTATTAAATTTA
Found at i:179409 original size:28 final size:26
Alignment explanation
Indices: 179338--179412 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
179328 TTAAATCTAA
*
179338 TATTGAATA-AATAAAAAATATTTAAT
1 TATT-AATATAATAAAAAATTTTTAAT
* * *
179364 TATTTATTTAACATAAAAATTTTTAAT
1 TATTAATATAATA-AAAAATTTTTAAT
179391 TATTAAATATATATAAAAAATT
1 TATT-AATATA-ATAAAAAATT
179413 AATATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
25 2 0.05
26 7 0.18
27 16 0.42
28 11 0.29
29 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TATTAATATAATAAAAAATTTTTAAT
Found at i:179534 original size:16 final size:18
Alignment explanation
Indices: 179509--179556 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
179499 TCAATTTATT
*
179509 AAAATATTTAT-TATATA
1 AAAATATTTATAAATATA
179526 AAAAT-TTTATAAATATAA
1 AAAATATTTATAAATAT-A
*
179544 AAAATATATATAA
1 AAAATATTTATAA
179557 TTTAAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 6 0.23
19 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATTTATAAATATA
Done.