Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024497.1 Corchorus olitorius cultivar O-4 contig24530, whole genome shotgun sequence
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: 130598
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1699 original size:11 final size:11
Alignment explanation
Indices: 1685--1718 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1675 TAAAGGAAAA
1685 AGCTAGGAAGG
1 AGCTAGGAAGG
1696 AGCTAGGAAGG
1 AGCTAGGAAGG
1707 AGCTAGGAAGG
1 AGCTAGGAAGG
1718 A
1 A
1719 TCCTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:2112 original size:21 final size:21
Alignment explanation
Indices: 2088--2263 Score: 259
Period size: 21 Copynumber: 8.4 Consensus size: 21
2078 CTTAGGCAAT
*
2088 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2109 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2130 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2151 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2172 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
2193 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2214 TCCAATGAGCTTGGAA-CTTAC
1 TCCAATGAGCTTGGAACCTT-C
2235 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2256 TCCAATGA
1 TCCAATGA
2264 ACTTCTAGCA
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
20 3 0.02
21 144 0.98
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:5901 original size:21 final size:21
Alignment explanation
Indices: 5877--5916 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5867 TGATTTGGGC
* * *
5877 AATTTATAAGGGAATTTTAGA
1 AATTAATAAAGGAAATTTAGA
5898 AATTAATAAAGGAAATTTA
1 AATTAATAAAGGAAATTTA
5917 AAGAGTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
AATTAATAAAGGAAATTTAGA
Found at i:7280 original size:17 final size:18
Alignment explanation
Indices: 7250--7284 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7240 TAAGAAGGTT
7250 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
7268 TTCAAAACT-CAAAAAAA
1 TTCAAAAATCCAAAAAAA
7285 AAAAAAGAAT
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:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:7285 original size:18 final size:18
Alignment explanation
Indices: 7250--7285 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7240 TAAGAAGGTT
*
7250 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCAAAAAAAA
*
7268 TTCAAAACTCAAAAAAAA
1 TTCAAAAATCAAAAAAAA
7286 AAAAAGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCAAAAAAAA
Found at i:7447 original size:62 final size:61
Alignment explanation
Indices: 7331--7451 Score: 172
Period size: 62 Copynumber: 2.0 Consensus size: 61
7321 ATTTAAATTC
* * * *
7331 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAATCATTCAATTCATGTTTTTCAAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAACATTCAATACATATTTTTCAAAAG
*
7392 TTTTCAATTTAGGGAAAGTTCCCATCAAGTTTTCAAAACATTCAA-ACATCATTTTTCAAA
1 TTTTCAAATT-GGGAAAGTTCCCATCAAGTTTTCAAAACATTCAATACAT-ATTTTTCAAA
7452 TAGATTCGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 12 0.23
62 41 0.77
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (61 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAACATTCAATACATATTTTTCAAAAG
Found at i:11764 original size:21 final size:21
Alignment explanation
Indices: 11738--11779 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11728 GCATCTTAGG
11738 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
11759 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
11780 TTCTTCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:13617 original size:33 final size:32
Alignment explanation
Indices: 13579--13726 Score: 145
Period size: 33 Copynumber: 4.5 Consensus size: 32
13569 GCTATGATCA
* ** *
13579 ACCAAAACAGATTTATTTTCATCACAATTAGC
1 ACCAAAACAGATTTAGTTTCATCACAAACAAC
13611 ATCCAAAACAGAATTT-GTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTAGTTTCATCACAAACAAC
*
13644 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTTAGTTTCATCACAAACAAC
** * * *
13677 ACTCAAATTAGGTTTAGTATCATCGCAAACAAC
1 AC-CAAAACAGATTTAGTTTCATCACAAACAAC
*
13710 ATCTAAAACAGATTTAG
1 A-CCAAAACAGATTTAG
13727 AATTACTCTT
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
32 7 0.07
33 83 0.86
34 6 0.06
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (32 bp):
ACCAAAACAGATTTAGTTTCATCACAAACAAC
Found at i:14959 original size:10 final size:10
Alignment explanation
Indices: 14937--14970 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
14927 ACCTCCTGTA
14937 ACATACC-TC
1 ACATACCTTC
14946 ACATACCTTC
1 ACATACCTTC
14956 ACATACCTTC
1 ACATACCTTC
14966 ACATA
1 ACATA
14971 ATTCTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (10 bp):
ACATACCTTC
Found at i:15787 original size:15 final size:16
Alignment explanation
Indices: 15757--15796 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
15747 TTGCTTTGTT
15757 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
15773 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
15788 TTGCTTTCT
1 TTGTTTTCT
15797 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:19207 original size:21 final size:21
Alignment explanation
Indices: 19182--19230 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
19172 ACATTCACCA
*
19182 TGCCATCACCGGTTAAGCCCG
1 TGCCATCACCGGCTAAGCCCG
* * *
19203 TGCCACCACCGGCTATGCCTG
1 TGCCATCACCGGCTAAGCCCG
19224 TGCCATC
1 TGCCATC
19231 GCCATTCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.20
Consensus pattern (21 bp):
TGCCATCACCGGCTAAGCCCG
Found at i:23418 original size:15 final size:16
Alignment explanation
Indices: 23388--23427 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
23378 TTGCTTTGTT
23388 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
23404 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
23419 TTGCTTTCT
1 TTGTTTTCT
23428 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:28828 original size:20 final size:19
Alignment explanation
Indices: 28805--28847 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28795 AAACAATTAC
28805 AAAAACAAAAACAG-GAAAA
1 AAAAACAAAAA-AGCGAAAA
**
28824 AAAAACGCAAAAGCGAAAA
1 AAAAACAAAAAAGCGAAAA
28843 AAAAA
1 AAAAA
28848 ACTTGTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAGCGAAAA
Found at i:35672 original size:18 final size:18
Alignment explanation
Indices: 35635--35677 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35625 TACAAAGTTG
*
35635 AATAAAAAACAAGGGTAA
1 AATAAAAAAAAAGGGTAA
35653 AATAAAAATAAAAGGG-AA
1 AATAAAAA-AAAAGGGTAA
*
35671 AAGAAAA
1 AATAAAA
35678 GATACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.09
Consensus pattern (18 bp):
AATAAAAAAAAAGGGTAA
Found at i:36832 original size:10 final size:11
Alignment explanation
Indices: 36801--36833 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
36791 TTACATAGTT
36801 TTATTTATGTA
1 TTATTTATGTA
36812 TTATTTTATGTA
1 TTA-TTTATGTA
36824 TTA-TTATGTA
1 TTATTTATGTA
36834 ATTTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (11 bp):
TTATTTATGTA
Found at i:37042 original size:3 final size:3
Alignment explanation
Indices: 37034--37059 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
37024 CAAAGAAAGA
37034 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
37060 ATGGATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42552 original size:20 final size:21
Alignment explanation
Indices: 42516--42555 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42506 GGGTTTAGAT
42516 TTGGTCCTTGTAACCTTTCTA
1 TTGGTCCTTGTAACCTTTCTA
42537 TTGG-CCTT-TAATCCTTTCT
1 TTGGTCCTTGTAA-CCTTTCT
42556 TTCTAATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 11 0.61
21 4 0.22
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (21 bp):
TTGGTCCTTGTAACCTTTCTA
Found at i:43897 original size:21 final size:21
Alignment explanation
Indices: 43873--43923 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
43863 TCTCATTCAT
43873 ATCATGATTCATTGGATTGAG
1 ATCATGATTCATTGGATTGAG
43894 ATCATGATTCATTGGATTGAG
1 ATCATGATTCATTGGATTGAG
43915 ATCATGATT
1 ATCATGATT
43924 TATAGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (21 bp):
ATCATGATTCATTGGATTGAG
Found at i:54573 original size:10 final size:11
Alignment explanation
Indices: 54550--54578 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54540 TCACTTGATC
54550 TTGTTTTACTT
1 TTGTTTTACTT
54561 TTGTTTT-CTT
1 TTGTTTTACTT
54571 TTGTTTTA
1 TTGTTTTA
54579 AAGGACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.07, C:0.07, G:0.10, T:0.76
Consensus pattern (11 bp):
TTGTTTTACTT
Found at i:61216 original size:24 final size:24
Alignment explanation
Indices: 61179--61237 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
61169 CAATATGTTT
* * *
61179 ATCTATTCTAGGAGGGCTATGAACA
1 ATCTATT-TGGGAGGACTATAAACA
61204 ATCTATTTGGGAGGACTATAAACA
1 ATCTATTTGGGAGGACTATAAACA
*
61228 ATCTGTTTGG
1 ATCTATTTGG
61238 AGATCTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (24 bp):
ATCTATTTGGGAGGACTATAAACA
Found at i:63092 original size:20 final size:20
Alignment explanation
Indices: 63067--63106 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
63057 AATTACAAAC
*
63067 AAACTCACATTCTGTGAGAG
1 AAACTCACATTCCGTGAGAG
63087 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
63107 TTGAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:64171 original size:293 final size:293
Alignment explanation
Indices: 63644--64229 Score: 1163
Period size: 293 Copynumber: 2.0 Consensus size: 293
63634 CATATAATAG
63644 CATGGGCAATAGCATTGTGGCTAATGGCTATGTTTCAGCAATAACGAGTCTAGATCAATGGTGGT
1 CATGGGCAATAGCATTGTGGCTAATGGCTATGTTTCAGCAATAACGAGTCTAGATCAATGGTGGT
*
63709 TGGTGATTGGCGCCTAGAAGCGTCGATCCTATATTTCAGCAATTTACTGAAGATTCAGTGAAGTA
66 TGGTGATTGGCGCCTAGAAGCGTCGATCCTATATTTCAGCAATTTACTGAAGATTCAGTGAAGCA
63774 GTGTGGGAGATCAGTTCTTCACATCAAGTTCGATTCTTGAGGAAGTGTAGAAGGCCCATCAAGAC
131 GTGTGGGAGATCAGTTCTTCACATCAAGTTCGATTCTTGAGGAAGTGTAGAAGGCCCATCAAGAC
63839 TTCAAGGCCCATGCCGTCCCCTATAAGTAGAGACCCCTGCTTCAGTTTTCAGTCTACCTCAACAC
196 TTCAAGGCCCATGCCGTCCCCTATAAGTAGAGACCCCTGCTTCAGTTTTCAGTCTACCTCAACAC
63904 ACACAAACTTGCCCTGAGCTTTTTCTCTCAAAT
261 ACACAAACTTGCCCTGAGCTTTTTCTCTCAAAT
63937 CATGGGCAATAGCATTGTGGCTAATGGCTATGTTTCAGCAATAACGAGTCTAGATCAATGGTGGT
1 CATGGGCAATAGCATTGTGGCTAATGGCTATGTTTCAGCAATAACGAGTCTAGATCAATGGTGGT
64002 TGGTGATTGGCGCCTAGAAGCGTCGATCCTATATTTCAGCAATTTACTGAAGATTCAGTGAAGCA
66 TGGTGATTGGCGCCTAGAAGCGTCGATCCTATATTTCAGCAATTTACTGAAGATTCAGTGAAGCA
64067 GTGTGGGAGATCAGTTCTTCACATCAAGTTCGATTCTTGAGGAAGTGTAGAAGGCCCATCAAGAC
131 GTGTGGGAGATCAGTTCTTCACATCAAGTTCGATTCTTGAGGAAGTGTAGAAGGCCCATCAAGAC
64132 TTCAAGGCCCATGCCGTCCCCTATAAGTAGAGACCCCTGCTTCAGTTTTCAGTCTACCTCAACAC
196 TTCAAGGCCCATGCCGTCCCCTATAAGTAGAGACCCCTGCTTCAGTTTTCAGTCTACCTCAACAC
64197 ACACAAACTTGCCCTGAGCTTTTTCTCTCAAAT
261 ACACAAACTTGCCCTGAGCTTTTTCTCTCAAAT
64230 TTCTCTGCAA
Statistics
Matches: 292, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
293 292 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (293 bp):
CATGGGCAATAGCATTGTGGCTAATGGCTATGTTTCAGCAATAACGAGTCTAGATCAATGGTGGT
TGGTGATTGGCGCCTAGAAGCGTCGATCCTATATTTCAGCAATTTACTGAAGATTCAGTGAAGCA
GTGTGGGAGATCAGTTCTTCACATCAAGTTCGATTCTTGAGGAAGTGTAGAAGGCCCATCAAGAC
TTCAAGGCCCATGCCGTCCCCTATAAGTAGAGACCCCTGCTTCAGTTTTCAGTCTACCTCAACAC
ACACAAACTTGCCCTGAGCTTTTTCTCTCAAAT
Found at i:68353 original size:11 final size:11
Alignment explanation
Indices: 68339--68376 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
68329 ATTCATAACA
68339 AATTTATAATT
1 AATTTATAATT
68350 AATTTATAATT
1 AATTTATAATT
68361 -ATTTGATAATT
1 AATTT-ATAATT
*
68372 TATTT
1 AATTT
68377 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:82505 original size:22 final size:22
Alignment explanation
Indices: 82480--82581 Score: 66
Period size: 22 Copynumber: 4.6 Consensus size: 22
82470 AATATTTTTA
82480 TAAAATTTGATAAATATCCTAT
1 TAAAATTTGATAAATATCCTAT
* *
82502 TAAATTTTGATAAA-AACGCTAT
1 TAAAATTTGATAAATATC-CTAT
* *
82524 AAAAATTTTTGATAATTAT-CTA-
1 TAAAA--TTTGATAAATATCCTAT
* * *
82546 TGAAATTGTGATAAATTTCATAT
1 TAAAATT-TGATAAATATCCTAT
* *
82569 GAAACTTTGATAA
1 TAAAATTTGATAA
82582 CCTAACTATG
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
20 2 0.03
21 10 0.17
22 31 0.53
23 7 0.12
24 8 0.14
25 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TAAAATTTGATAAATATCCTAT
Found at i:83956 original size:32 final size:32
Alignment explanation
Indices: 83914--83988 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
83904 TAGATTCGTA
*
83914 TCAATTGGTAATCAGAGCATAGGTTGTCATCT
1 TCAATCGGTAATCAGAGCATAGGTTGTCATCT
83946 TCAATCGGTAATCAGAGCATAGGTTGTCATCT
1 TCAATCGGTAATCAGAGCATAGGTTGTCATCT
83978 TCAATCGGTAA
1 TCAATCGGTAA
83989 ATCTATCCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (32 bp):
TCAATCGGTAATCAGAGCATAGGTTGTCATCT
Found at i:85005 original size:15 final size:15
Alignment explanation
Indices: 84985--85016 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
84975 CCTTGGGGGT
84985 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
*
85000 TCAAAATCGACAAGC
1 TCAAAATCAACAAGC
85015 TC
1 TC
85017 CACTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:85704 original size:66 final size:66
Alignment explanation
Indices: 85597--85723 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
85587 AGTAATTCTG
* *
85597 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
85662 A
66 A
* * * *
85663 AACCTAATTTAAGTGTTGTTTGCGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA
85724 AACAAATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 53 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (66 bp):
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A
Found at i:85712 original size:33 final size:33
Alignment explanation
Indices: 85609--85738 Score: 120
Period size: 33 Copynumber: 3.9 Consensus size: 33
85599 CCTGATTTGA
*
85609 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
1 GTGTTGTTTGCGATGACACT-AAATCTGTTTTAG
* * * * * ** *
85642 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
1 GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
*
85675 GTGTTGTTTGCGATGACACTAAATTTGTTTTAG
1 GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
* *
85708 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
1 GTGTTGTTTGCGATGACACTAAA-TCTGTTTT
85739 GGATGCTAAT
Statistics
Matches: 74, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
32 3 0.04
33 70 0.95
34 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (33 bp):
GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
Found at i:109385 original size:24 final size:24
Alignment explanation
Indices: 109350--109406 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
109340 AGAAATTAAA
* *
109350 AAAAAAAAAAAAGATCA-TCAAATCT
1 AAAAAATAAAAA-TTCATTCAAAT-T
*
109375 AAAAAATAAAAATTTATTCAAATT
1 AAAAAATAAAAATTCATTCAAATT
109399 AAAAAATA
1 AAAAAATA
109407 TCAAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAAAATAAAAATTCATTCAAATT
Found at i:117325 original size:15 final size:15
Alignment explanation
Indices: 117301--117330 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
117291 CCAATTTCCA
117301 TTTTTGTATATATAT
1 TTTTTGTATATATAT
*
117316 TTTTTTTATATATAT
1 TTTTTGTATATATAT
117331 AAAATGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTGTATATATAT
Found at i:119179 original size:15 final size:16
Alignment explanation
Indices: 119147--119185 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
119137 TCATTTGTTC
119147 TGTTTTCTAGTATAAT
1 TGTTTTCTAGTATAAT
*
119163 TGTTTTCTA-TTTAAT
1 TGTTTTCTAGTATAAT
*
119178 TGCTTTCT
1 TGTTTTCT
119186 TTCAACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
TGTTTTCTAGTATAAT
Found at i:119571 original size:24 final size:25
Alignment explanation
Indices: 119529--119590 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
119519 GCGTTTTTGA
* *
119529 AAAAAAAAAGTTTTGTGTTTGGCGTCAT
1 AAAAAAAAA--TTTGT-TTCGGCATCAT
*
119557 AAAAAAAAATTTGTTTCTGCATCAT
1 AAAAAAAAATTTGTTTCGGCATCAT
*
119582 AAAAGAAAA
1 AAAAAAAAA
119591 GAAAATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 16 0.53
26 5 0.17
28 9 0.30
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.31
Consensus pattern (25 bp):
AAAAAAAAATTTGTTTCGGCATCAT
Found at i:121762 original size:21 final size:21
Alignment explanation
Indices: 121710--121768 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
121700 CCCGGCCACG
* * **
121710 GCCCGGCCACCCGAGCCATCT
1 GCCCGGCCATCCGCGCCGCCT
121731 GCCCGGCCATCCGCGCCGCCT
1 GCCCGGCCATCCGCGCCGCCT
* *
121752 GCCCGGTCATCTGCGCC
1 GCCCGGCCATCCGCGCC
121769 TTCCTCCGCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.08, C:0.53, G:0.27, T:0.12
Consensus pattern (21 bp):
GCCCGGCCATCCGCGCCGCCT
Found at i:121959 original size:23 final size:21
Alignment explanation
Indices: 121911--121953 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
121901 TGCAGCATCC
*
121911 TCCGCGCACCATGCCTGGCCA
1 TCCGCGCACCATGCCAGGCCA
121932 TCCGCGCGACC-TGCCAGGCCA
1 TCCGCGC-ACCATGCCAGGCCA
121953 T
1 T
121954 ATCCGCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.14, C:0.47, G:0.26, T:0.14
Consensus pattern (21 bp):
TCCGCGCACCATGCCAGGCCA
Found at i:125322 original size:15 final size:16
Alignment explanation
Indices: 125290--125328 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
125280 TGCTTTGTTC
*
125290 TGTTTTCTAGTATAAT
1 TGTTTTCTAATATAAT
125306 TGTTTTCTAAT-TAAT
1 TGTTTTCTAATATAAT
*
125321 TGCTTTCT
1 TGTTTTCT
125329 TTCAATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (16 bp):
TGTTTTCTAATATAAT
Found at i:127942 original size:21 final size:21
Alignment explanation
Indices: 127916--128070 Score: 242
Period size: 21 Copynumber: 7.4 Consensus size: 21
127906 TGCTAGAAGT
127916 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
127937 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
127958 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
127979 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
128000 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
128021 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
128042 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
128063 TCATTGGA
1 TCATTGGA
128071 ATTGCCTAAG
Statistics
Matches: 129, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
20 2 0.02
21 127 0.98
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.