Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2040
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: 59511
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1510 original size:33 final size:33
Alignment explanation
Indices: 1434--1595 Score: 218
Period size: 34 Copynumber: 4.8 Consensus size: 33
1424 CAACCTTCTA
* * *
1434 AAGTCCACAACTTTGTGGCACCTTTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCA-CTCTTTTCCTTTT
* *
1468 AACGCCCACAACTCTGTGGCACTCTTTTCCTTCT
1 AA-GTCCACAACTCTGTGGCACTCTTTTCCTTTT
1502 AAGTCCACAACTC-GTGGCACTCTTCTTCCTTTT
1 AAGTCCACAACTCTGTGGCACTCTT-TTCCTTTT
*
1535 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCACTC-TTTTCCTTTT
*
1569 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACTCTTTT
1596 AAGCCCATAA
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
32 11 0.10
33 33 0.29
34 52 0.46
35 18 0.16
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCTGTGGCACTCTTTTCCTTTT
Found at i:1550 original size:66 final size:68
Alignment explanation
Indices: 1427--1590 Score: 235
Period size: 67 Copynumber: 2.4 Consensus size: 68
1417 CCAGTGGCAA
* * *
1427 CCTTCTAAAGTCCACAACTTTGTGGCACCTTTTTTTCTTTTAACGCCCACAACTCTGTGGCACTC
1 CCTTCT-AAGTCCACAAC-TCGTGGCACCTTTCTTCCTTTTAACGCCCACAACTCTGTGGCACTC
1492 -TTTT
64 TTTTT
1496 CCTTCTAAGTCCACAACTCGTGGCA-CTCTTCTTCCTTTTAA-GCCCACAACTCTGTGGCACTCT
1 CCTTCTAAGTCCACAACTCGTGGCACCT-TTCTTCCTTTTAACGCCCACAACTCTGTGGCACTCT
1559 TTTT
65 TTTT
*
1563 CCTTTTAAGTCCACAACTCTGTGGCACC
1 CCTTCTAAGTCCACAACTC-GTGGCACC
1591 CTTTTAAGCC
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
66 23 0.26
67 40 0.46
68 17 0.20
69 7 0.08
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (68 bp):
CCTTCTAAGTCCACAACTCGTGGCACCTTTCTTCCTTTTAACGCCCACAACTCTGTGGCACTCTT
TTT
Found at i:1561 original size:27 final size:28
Alignment explanation
Indices: 1529--1644 Score: 101
Period size: 34 Copynumber: 3.9 Consensus size: 28
1519 CACTCTTCTT
1529 CCTTTTAAGCCCACAACTCTGTGGCACTC
1 CCTTTTAAGCCCACAACTCTGTGGCAC-C
*
1558 TTTTTCCTTTTAAGTCCACAACTCTGTGGCA-C
1 -----CCTTTTAAGCCCACAACTCTGTGGCACC
* *
1590 CCTTTTAAGCCCATAAGT-TGGTGGCACC
1 CCTTTTAAGCCCACAACTCT-GTGGCACC
* *
1618 CCTTTTAAAGCCCACAAGTCAGTGGCA
1 CCTTTT-AAGCCCACAACTCTGTGGCA
1645 ACCTTCAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.01
27 21 0.29
28 7 0.10
29 17 0.24
32 1 0.01
34 25 0.35
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.30
Consensus pattern (28 bp):
CCTTTTAAGCCCACAACTCTGTGGCACC
Found at i:1636 original size:29 final size:28
Alignment explanation
Indices: 1583--1690 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 28
1573 CCACAACTCT
* *
1583 GTGGCACCCTTT-TAAGCCCATAAGTTG
1 GTGGCACCCTTTAAAAGCCCACAAGTTG
* **
1610 GTGGCACCCCTTTTAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTAAAAGCCCACAAGTTG
* * *
1639 GTGGCAACCTTCAAAAGCACACAAGTTG
1 GTGGCACCCTTTAAAAGCCCACAAGTTG
*
1667 AT-GCAACCCTTTCAAAAGCCCACA
1 GTGGC-ACCCTTT-AAAAGCCCACA
1691 CAAGTTGATG
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
27 8 0.13
28 28 0.44
29 27 0.43
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (28 bp):
GTGGCACCCTTTAAAAGCCCACAAGTTG
Found at i:1920 original size:49 final size:49
Alignment explanation
Indices: 1807--2042 Score: 260
Period size: 49 Copynumber: 4.7 Consensus size: 49
1797 CACTTGAAGA
* * *
1807 CCAATGTCGCTGGCCTTGAATTAGGACATTGGCACCTTAACCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGT
*
1859 CCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * *
1908 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * *
1957 CCAATAG-CGCTGGCCTTGAATCAGCATATTGGCAACTTTTC-TGTCTTGAGT
1 CCAAT-GTCGCTGGCCTTGAATCAGCACATTGGC-AC-CTTCATCT-TTAAGT
* * *
2008 CTAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
2043 AAGTCCAATA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
49 83 0.53
50 6 0.04
51 34 0.22
52 35 0.22
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:2890 original size:19 final size:19
Alignment explanation
Indices: 2866--2929 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
2856 TTTCAACGAT
2866 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
*
2885 TTGTATCCATAC---A--A
1 TTGTATCGATACATAAGTA
*
2899 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
2917 TTGTATCGATACA
1 TTGTATCGATACA
2930 ATGTACAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
19 23 0.64
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:2908 original size:32 final size:32
Alignment explanation
Indices: 2867--2934 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
2857 TTCAACGATT
2867 TGTATCGATACATAAGTATTGTATCCATACAA
1 TGTATCGATACATAAGTATTGTATCCATACAA
* *
2899 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCCATACAA
2931 TGTA
1 TGTA
2935 CAGTTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCCATACAA
Found at i:3114 original size:53 final size:53
Alignment explanation
Indices: 3015--3145 Score: 228
Period size: 53 Copynumber: 2.5 Consensus size: 53
3005 TACTAATCTT
*
3015 TGTATCGATACATGCAGGCAAA-TTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTTGCCCAAATGTATCGATACACTATGAAA
*
3067 TGTATCGATACTTGCAGGCAAATTTTGCCCAAATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTTGCCCAAATGTATCGATACACTATGAAA
*
3120 TGTATTGATACATGCAGGCAAATTTT
1 TGTATCGATACATGCAGGCAAATTTT
3146 CATATTTCGG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 21 0.28
53 53 0.72
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (53 bp):
TGTATCGATACATGCAGGCAAATTTTGCCCAAATGTATCGATACACTATGAAA
Found at i:6580 original size:20 final size:20
Alignment explanation
Indices: 6555--6595 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6545 CATCTCCTTT
6555 TTTTTTGCT-TTTGCTTCTGC
1 TTTTTT-CTCTTTGCTTCTGC
*
6575 TTTTTTTTCTTTGCTTCTGC
1 TTTTTTCTCTTTGCTTCTGC
6595 T
1 T
6596 ATGTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.00, C:0.20, G:0.12, T:0.68
Consensus pattern (20 bp):
TTTTTTCTCTTTGCTTCTGC
Found at i:6606 original size:26 final size:26
Alignment explanation
Indices: 6551--6617 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
6541 TATCCATCTC
* *
6551 CTTTTTTTTTGCTTTTGCTTCTGCTT
1 CTTTTTTTTTGCTTCTGCTTATGCTT
*
6577 -TTTTTTCTTTGCTTCTGC-TATGTTT
1 CTTTTTT-TTTGCTTCTGCTTATGCTT
6602 CTTTTTTGTTTTGCTT
1 C-TTTTT-TTTTGCTT
6618 TGTTTTGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 11 0.32
26 10 0.29
27 12 0.35
28 1 0.03
ACGTcount: A:0.01, C:0.16, G:0.12, T:0.70
Consensus pattern (26 bp):
CTTTTTTTTTGCTTCTGCTTATGCTT
Found at i:6621 original size:21 final size:22
Alignment explanation
Indices: 6555--6622 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
6545 CATCTCCTTT
*
6555 TTTTTTGCTTTTGCTTCTGCTTTTT
1 TTTTTTGCTTTTGCTT-TG--TTTC
* *
6580 TTTCTTTGCTTCTGCTATGTTTC
1 TTT-TTTGCTTTTGCTTTGTTTC
6603 TTTTTTG-TTTTGCTTTGTTT
1 TTTTTTGCTTTTGCTTTGTTT
6623 TGGTTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 11 0.30
22 4 0.11
23 6 0.16
25 5 0.14
26 11 0.30
ACGTcount: A:0.01, C:0.15, G:0.13, T:0.71
Consensus pattern (22 bp):
TTTTTTGCTTTTGCTTTGTTTC
Found at i:6704 original size:27 final size:26
Alignment explanation
Indices: 6652--6712 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
6642 TCTACTTCTA
* *
6652 TTTTTGCTATTCTTTTCTTTTGTTGT
1 TTTTTTCTATTCTTTTCTTCTGTTGT
*
6678 GTTTTTTCTCTTCTTTATCTTCT-TTGT
1 -TTTTTTCTATTCTTT-TCTTCTGTTGT
6705 TTCTTTTC
1 TT-TTTTC
6713 CACTTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 22 0.76
28 5 0.17
ACGTcount: A:0.03, C:0.16, G:0.08, T:0.72
Consensus pattern (26 bp):
TTTTTTCTATTCTTTTCTTCTGTTGT
Found at i:10995 original size:14 final size:14
Alignment explanation
Indices: 10976--11004 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10966 GAAATGTGTG
10976 ACCACGTTTATGGC
1 ACCACGTTTATGGC
10990 ACCACGTTTATGGC
1 ACCACGTTTATGGC
11004 A
1 A
11005 TAATGAACAT
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:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (14 bp):
ACCACGTTTATGGC
Found at i:13479 original size:13 final size:13
Alignment explanation
Indices: 13461--13485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13451 TTAGAAGCAA
13461 TGTATCGATACAT
1 TGTATCGATACAT
13474 TGTATCGATACA
1 TGTATCGATACA
13486 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13579 original size:19 final size:19
Alignment explanation
Indices: 13535--13587 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
13525 CTACCAATTT
* **
13535 CATGTATCGATACCATTGTG
1 CATGTATCGATA-CAGTGAA
13555 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
13574 CATGTATCGATACA
1 CATGTATCGATACA
13588 ATGTATCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAGTGAA
Found at i:14777 original size:33 final size:32
Alignment explanation
Indices: 14735--14801 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
14725 GTTACAAGCT
* *
14735 AATGTATCGATACATTTTAGGATGTATTGATAC
1 AATGTATCGATACATATT-GGATGTATCGATAC
*
14768 AATGTATCGATACATATTGGGTGTATCGATAC
1 AATGTATCGATACATATTGGATGTATCGATAC
14800 AA
1 AA
14802 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATATTGGATGTATCGATAC
Found at i:16910 original size:20 final size:21
Alignment explanation
Indices: 16887--16926 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16877 GTGGGCTGCC
* *
16887 CGGTTGCGACTTGG-GGGTGT
1 CGGTCGCGACCTGGTGGGTGT
16907 CGGTCGCGACCTGGTGGGTG
1 CGGTCGCGACCTGGTGGGTG
16927 CTGCTTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.05, C:0.20, G:0.50, T:0.25
Consensus pattern (21 bp):
CGGTCGCGACCTGGTGGGTGT
Found at i:23563 original size:13 final size:13
Alignment explanation
Indices: 23545--23570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23535 ACATTTTGGG
23545 ATGTATCGATACA
1 ATGTATCGATACA
23558 ATGTATCGATACA
1 ATGTATCGATACA
23571 TATTGGGTGT
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:23587 original size:32 final size:33
Alignment explanation
Indices: 23523--23590 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
23513 CGTTACAAGC
*
23523 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
23556 CAATGTATCGATACATATTGGG-TGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
23588 CAA
1 CAA
23591 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (33 bp):
CAATGTATCGATACATATTGGGATGTATCGATA
Found at i:29408 original size:20 final size:20
Alignment explanation
Indices: 29383--29507 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
29373 TTTTAACTAG
29383 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
29403 ATGTATCGATACATCTGGGAAAAAAGATAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
29434 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
29454 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
29474 ATTTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
29494 ATGTATCGATACAT
1 ATGTATCGATACAT
29508 CTGGGTAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 59 0.72
21 1 0.01
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 14 0.17
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:29446 original size:51 final size:51
Alignment explanation
Indices: 29383--29569 Score: 225
Period size: 51 Copynumber: 3.9 Consensus size: 51
29373 TTTTAACTAG
* *
29383 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGATAGA
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
* * *
29434 ATGTATCAATACATTGAAGAATGTATCGATACA--T---T-----CATA-C
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
* *
29474 ATTTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
*
29525 ATGTATCAGTACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
29570 TGTGACTTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
40 30 0.27
41 3 0.03
42 1 0.01
45 1 0.01
49 1 0.01
50 3 0.03
51 73 0.65
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (51 bp):
ATGTATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
Found at i:29541 original size:91 final size:91
Alignment explanation
Indices: 29386--29558 Score: 319
Period size: 91 Copynumber: 1.9 Consensus size: 91
29376 TAACTAGATG
29386 TATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGATAGAATGTATCAATACATTGA
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGATAGAATGTATCAATACATTGA
*
29451 AGAATGTATCGATACATTCATACATT
66 AAAATGTATCGATACATTCATACATT
* *
29477 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAGTACATTGA
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGATAGAATGTATCAATACATTGA
29542 AAAATGTATCGATACAT
66 AAAATGTATCGATACAT
29559 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (91 bp):
TATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGATAGAATGTATCAATACATTGA
AAAATGTATCGATACATTCATACATT
Found at i:32900 original size:63 final size:63
Alignment explanation
Indices: 32822--32949 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
32812 GATACATGTA
32822 GGCAAAAATGTGATTTTTTTATACTTTTTGCCTCCCGAACAGGTCACCTTAGTTAGGAATAGT
1 GGCAAAAATGTGATTTTTTTATACTTTTTGCCTCCCGAACAGGTCACCTTAGTTAGGAATAGT
* *
32885 GGCAAAAATGTGATTTTTTTATACTTTTTGCCTCCCGGATAGGTCACCTTAGTTAGGAATAGT
1 GGCAAAAATGTGATTTTTTTATACTTTTTGCCTCCCGAACAGGTCACCTTAGTTAGGAATAGT
32948 GG
1 GG
32950 GAAATGGGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (63 bp):
GGCAAAAATGTGATTTTTTTATACTTTTTGCCTCCCGAACAGGTCACCTTAGTTAGGAATAGT
Found at i:34083 original size:41 final size:41
Alignment explanation
Indices: 33975--34214 Score: 209
Period size: 41 Copynumber: 5.9 Consensus size: 41
33965 CTAAACGTCG
* * * ***
33975 CTAAAGTTTTCCTATTAGCAACGTTTATATTAAAAACAACA
1 CTAAATTTTTCATATTAGCGACGTTTATATTAAAAATGCCA
** ** * * * *
34016 CTAAATATTTTCA-ATTAATGGTGTTTAGT-GTAAAAACGTCG
1 CTAAAT-TTTTCATATTAGCGACGTTTA-TATTAAAAATGCCA
* *
34057 CTAAATTTTTCATATTGGCGACGTTTATATTAAAAATGACA
1 CTAAATTTTTCATATTAGCGACGTTTATATTAAAAATGCCA
* * *
34098 TTAAA-TTTTCCTATTAGCGACGTTTATGTTAAAAATGCCA
1 CTAAATTTTTCATATTAGCGACGTTTATATTAAAAATGCCA
* *
34138 CTAAATTTTTCCTATTAGCGACATTTATATTAAAAATGCCA
1 CTAAATTTTTCATATTAGCGACGTTTATATTAAAAATGCCA
* * *
34179 CTAAATTTTTTCA-ATTGGCAACATTTATATTAAAAA
1 CTAAA-TTTTTCATATTAGCGACGTTTATATTAAAAA
34215 CATCGCTAAA
Statistics
Matches: 162, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
40 42 0.26
41 108 0.67
42 12 0.07
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (41 bp):
CTAAATTTTTCATATTAGCGACGTTTATATTAAAAATGCCA
Found at i:34159 original size:81 final size:81
Alignment explanation
Indices: 33975--34187 Score: 239
Period size: 81 Copynumber: 2.6 Consensus size: 81
33965 CTAAACGTCG
* * ** * * **
33975 CTAAAGTTTTCCTATTAGCAACGTTTATATTAAAAACAACACTAAATATTTTCAATTAATGGTGT
1 CTAAATTTTTCCTATTAGCGACGTTTATATTAAAAATGACACTAAAT-TTTCCAATTAACGACGT
* *
34040 TTAGTGTAAAAACGTCG
65 TTAGTGTAAAAACGCCA
* * * * *
34057 CTAAATTTTTCATATTGGCGACGTTTATATTAAAAATGACATTAAATTTTCCTATTAGCGACGTT
1 CTAAATTTTTCCTATTAGCGACGTTTATATTAAAAATGACACTAAATTTTCCAATTAACGACGTT
*
34122 TA-TGTTAAAAATGCCA
66 TAGTG-TAAAAACGCCA
* *
34138 CTAAATTTTTCCTATTAGCGACATTTATATTAAAAATGCCACTAAATTTT
1 CTAAATTTTTCCTATTAGCGACGTTTATATTAAAAATGACACTAAATTTT
34188 TTCAATTGGC
Statistics
Matches: 109, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
80 2 0.02
81 67 0.61
82 40 0.37
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (81 bp):
CTAAATTTTTCCTATTAGCGACGTTTATATTAAAAATGACACTAAATTTTCCAATTAACGACGTT
TAGTGTAAAAACGCCA
Found at i:35581 original size:58 final size:57
Alignment explanation
Indices: 35491--35606 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 57
35481 AGGATTAATT
* * * * *
35491 AAATGATAACGATCGTGTTACGGAGAACAATTTTCTAGCGACTCTACTTCAGCTTTGC
1 AAATGATAACGATCATATTACAGAGAACAATTTTC-AACGACTCTACTTCAGCATTGC
* *
35549 AAATGATAACGATCATATTATAGAGAACAATTTTCAACGACTTTACTTCAGCATTGC
1 AAATGATAACGATCATATTACAGAGAACAATTTTCAACGACTCTACTTCAGCATTGC
35606 A
1 A
35607 GTAGTAGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 20 0.39
58 31 0.61
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (57 bp):
AAATGATAACGATCATATTACAGAGAACAATTTTCAACGACTCTACTTCAGCATTGC
Found at i:40460 original size:20 final size:19
Alignment explanation
Indices: 40435--40487 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
40425 CTACTAGTTT
**
40435 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
40455 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
40474 CATGTATCGATACA
1 CATGTATCGATACA
40488 TTTGGATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:40479 original size:19 final size:20
Alignment explanation
Indices: 40435--40507 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
40425 CTACTAGTTT
**
40435 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
40455 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
* *
40474 CATGTATCGATACATTTGGA
1 CATGTATCGATACAATTGAA
* *
40494 TATGCATCGATACA
1 CATGTATCGATACA
40508 TACAAGGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:43414 original size:91 final size:90
Alignment explanation
Indices: 43299--43511 Score: 347
Period size: 91 Copynumber: 2.3 Consensus size: 90
43289 ATACTTTAAA
43299 GTATCGATACATAAGTA-TTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACC
1 GTATCGATACAT-A-TACTTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACC
43363 CTTGTATATATCAATACACTTTCAGAT
64 CTTGTATATATCAATACACTTTCAGAT
*
43390 GTATCGATACACTATACTTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCT
1 GTATCGATACA-TATACTTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCC
*
43455 TTGTATATATCGATACACTTTCAGAT
65 TTGTATATATCAATACACTTTCAGAT
* *
43481 ATATCGATACATTATGCTTTGTATCGATACA
1 GTATCGATACA-TATACTTTGTATCGATACA
43512 ATGTATCAAT
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
90 2 0.02
91 112 0.97
92 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (90 bp):
GTATCGATACATATACTTTGTATCGATACATTATGGTTGACTTAAGCTACAAAGGTCAAAACCCT
TGTATATATCAATACACTTTCAGAT
Found at i:51347 original size:33 final size:33
Alignment explanation
Indices: 51281--51347 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
51271 TGAGAGTTGA
* *
51281 TCACTTCACTTTCGCAACACATGAATGAGCACT
1 TCACTTCACTCTCACAACACATGAATGAGCACT
* * * *
51314 TCACTTCACTCTCACAGCGCATGGATGATCACT
1 TCACTTCACTCTCACAACACATGAATGAGCACT
51347 T
1 T
51348 TAGTTCTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.28
Consensus pattern (33 bp):
TCACTTCACTCTCACAACACATGAATGAGCACT
Found at i:52305 original size:19 final size:20
Alignment explanation
Indices: 52279--52333 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
52269 GTATCGATAT
*
52279 AATGTATCGATACATGTTC-
1 AATGTATCGATACATGTACA
*
52298 ATTGTATCGATACATGTACA
1 AATGTATCGATACATGTACA
52318 AATGTATCGATACATG
1 AATGTATCGATACATG
52334 AAACTAGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATGTACA
Found at i:52891 original size:13 final size:13
Alignment explanation
Indices: 52873--52898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52863 TACAGCAAGT
52873 ATGTATCGATACA
1 ATGTATCGATACA
52886 ATGTATCGATACA
1 ATGTATCGATACA
52899 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:55162 original size:21 final size:21
Alignment explanation
Indices: 55129--55173 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55119 TTGCAAGTTG
*
55129 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
55151 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
55171 AAA
1 AAA
55174 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:56995 original size:15 final size:15
Alignment explanation
Indices: 56975--57005 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56965 TAAAAATGTC
*
56975 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
56990 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
57005 C
1 C
57006 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:59366 original size:28 final size:28
Alignment explanation
Indices: 59285--59366 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
59275 TTTTGGAGAT
*
59285 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
59313 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
59341 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
59367 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:59508 original size:50 final size:50
Alignment explanation
Indices: 59349--59511 Score: 173
Period size: 52 Copynumber: 3.2 Consensus size: 50
59339 GAAATAACGA
* * *
59349 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCG
* * * * * *
59400 GAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCG
*** *
59453 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAGTCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCG
59503 GGTTGGAGT
1 GGTTGGAGT
Statistics
Matches: 90, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
50 31 0.34
51 1 0.01
52 33 0.37
53 15 0.17
54 10 0.11
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCG
Done.