Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020751.1 Corchorus olitorius cultivar O-4 contig20784, 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: 130596
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:791 original size:323 final size:321
Alignment explanation
Indices: 173--994 Score: 958
Period size: 323 Copynumber: 2.5 Consensus size: 321
163 TTTTTTGTTA
* * * **
173 TTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCTTCAAACAAAATCCCAGCCAC
1 TTGCATGATTTTTGACG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCAC
* * * * * * * * *
238 GTTCGATTTAGGTATTTGTTTTTACGACCATCTTAATCTTTTTTCAATTTAATTAAAAATTATTT
65 ATTAGATTAAGG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * *
303 CGGAAAATAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCGTTGAAT
129 CGGAAAA-AAATAGAAAAATGATATTAAAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAAT
* ***
368 TATATATTTTTTCTGAGTATTGTGGCAAAAAAATTCAGAAAAACTTTTCCGATCAGTTTTTAGCC
193 TATATATTTTTTCTGAGTATTGTGGCAAAAAAATTAAGAAAAACAAATCCGATCAGTTTTTAGCC
* *
433 GAAATCATGTACTAACCATCACAGTATTTGGCTAAAAACGCG-TTCCCGAGCCCCGATTCAATT
258 GAAAACATGTACTAACCATCACAGTATTTGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAATT
*
496 TTGCATGATTTTTGACGCAGAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCAC
1 TTGCATGATTTTTGACG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCAC
* *
561 ATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
65 ATTAGAT-TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* *
626 CGGAAAAAAATTAGAAAAATAATATTAAAAGCGTGAAAAGA-CCATCAATCTTTTTGGTGTTGAA
129 CGGAAAAAAA-TAGAAAAATGATATTAAAAGCGTGAAAA-ACCCATCAATCTTTTTGGCGTTGAA
* *
690 TTATATA-TTTTTCTGAGTATTGTGGC-AAAAAATTAAGGAAAAA-AAATCGGGTCAGTTTTTAG
192 TTATATATTTTTTCTGAGTATTGTGGCAAAAAAATTAA-GAAAAACAAATCCGATCAGTTTTTAG
* * ** * * *
752 CCGAAAAACGTGTACTAACCATCAC-G-ATTTTGGGGCTAAAAATGCGTTTCGGGGGTCCCGGCT
256 CCG-AAAACATGTACTAACCATCACAGTA-TTT--GGCTAAAAACGCGTTTCCCGAGCCCCGACT
*
815 CAGTT
317 CAATT
* * * ** *
820 TTGCATGATTTTCGTCAGAAAGACTCCTTGTAATATCTATATTCATTTAACCAATCTCAGGCTCT
1 TTGCATGATTTTTGAC-GAAAGACTCCTTGAAATATCTATATTCATCAAACCAA----ATG-TC-
*
885 GAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
59 -AGCCACATTAGA-TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* *
950 A-TAGATTCGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAA
122 ATTA-ATTCGGAAAAAAATAGAAAAATGATATTAAAAGCGTGAAAA
995 TATTTCAAAT
Statistics
Matches: 428, Mismatches: 52, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
320 1 0.00
321 30 0.07
322 47 0.11
323 179 0.42
324 65 0.15
325 1 0.00
328 2 0.00
329 2 0.00
330 27 0.06
331 73 0.17
332 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (321 bp):
TTGCATGATTTTTGACGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACA
TTAGATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
GAAAAAAATAGAAAAATGATATTAAAAGCGTGAAAAACCCATCAATCTTTTTGGCGTTGAATTAT
ATATTTTTTCTGAGTATTGTGGCAAAAAAATTAAGAAAAACAAATCCGATCAGTTTTTAGCCGAA
AACATGTACTAACCATCACAGTATTTGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAATT
Found at i:1655 original size:554 final size:551
Alignment explanation
Indices: 494--2099 Score: 2162
Period size: 553 Copynumber: 2.9 Consensus size: 551
484 CCCGATTCAA
* * * * * **
494 TTTTGCATGATTTTTGACGCAGAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
* * * * * *
559 ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* * * * * *
624 TTCGGAAAAAAATTAGAAAAATAATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGA
131 TTCGGAAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
* * *
689 ATTATATATTTTTCTGAGTATTGTGGCAAAAAATTAAGGAAAAAAA--ATCGGGTCAGTTTTTAG
196 ATTATATTTTTTTCTGAGTATTGTGGCAAAAAATTAA-GAAAAAAACTATCCGATCAGTTTTTAG
* * * * ** * *
752 CCGAAAAACGTGTACTAACCATCACGATTTTGGGGCTAAAAATGCGTTTCGGGGGTCCCGGCTCA
260 CCG-AAATCGTGTACTAACCATCACGATTTT-TGGCTCAAAACGCG-TTCCCGAGTCCCGACTCA
* * * * ** *
817 GTTTTGCATGATTTTCGTCAG-AAAGACTCCTTGTAATATCTATATTCATTTAACCAATCTCAGG
322 ATTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCAAACC-A--T-ATG
*
881 CTCTGAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATT
382 -TC--AGCCACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATT
946 AGAAATAGATTCGG-AAAAAAA-TAGAAAAATGATATTTAAAGCGAGAAAATATTTCAAATTTTT
444 AGAAATAGATTCGGAAAAAAAATTAGAAAAATGATATTTAAAGCGAGAAAATATTTCAAATTTTT
* *
1009 TTGTTGCGTTGAATTGTGTATTTTTTGCCGAATTTTTTTTTGT
509 TTGTTGCATTGAATTGTGTATTTTTTGCCGAATATTTTTTTGT
1052 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
* * * *
1117 ACGTTCGATTTAAGTATTTCTTTTTACGAGCATCTGAATCTTATTTCAATTTAATTAAAAATTCA
66 ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* *
1182 TTCGGAAAAAAGAAATGGAAAAATGATATCAAAAGCGTGAAAAGCCCGTCAATCTTTTTGACGTT
131 TTCGG-AAAAA-AAATGGAAAAATGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
1247 GAATTAT-TTTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAAAAACTTTTCCGATCAGTTTTT
194 GAATTATATTTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAAC-TATCCGATCAGTTTTT
*
1310 AGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTCAAAACGCGTTCCCGAGTCCCGACTCAT
258 AGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTCAAAACGCGTTCCCGAGTCCCGACTCAA
* *
1375 TTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTATATTCATCAAACCATATGTCAGCG
323 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCATATGTCAGCC
* *
1440 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAGTAGA
388 ACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
*
1505 TTCGGAAAAAAAATTAAAAAAAAATGATATTTAAAGCGAGAAAATATTTC-AATTTTTTCT-TTG
453 TTCGGAAAAAAAATT--AGAAAAATGATATTTAAAGCGAGAAAATATTTCAAATTTTTT-TGTTG
1568 CATTGAATTGTGTATTTTTTGCCGAAAATATTTTTTTG-
515 CATTGAATTGTGTATTTTTTGCCG--AATATTTTTTTGT
* *
1606 TTTTGCATGATTTTTTACGTAAATACTCCTTCAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
* *
1671 ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATTTTGTTTCAATTTAATTAAACATTAA
66 ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* * * * * *
1736 TTCGGAAAAAAAATGG-AGAACGATATTAGAAGCGTGAAAAGCCTGCCAATCTTTTTGGCTTTGA
131 TTCGGAAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
*
1800 ATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTAAG-AAAAAACATATCCGATCAGTTTTTA
196 ATTATAT-TTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAAC-TATCCGATCAGTTTTT-
** * * * *
1864 AG-CGAAATCGTGTA-TGTTCCATCACGGTTTTTGGCTCATAACGCGTTCCCAAGCCCCGACTCA
258 AGCCGAAATCGTGTACT-AACCATCACGATTTTTGGCTCAAAACGCGTTCCCGAGTCCCGACTCA
* *
1927 ATTTTGCATGATTTTTGGCGCAAAGACACCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
322 ATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCATATGTCAGC
* * * *
1992 CACATTTGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAATTTA
387 CACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA-ATA
* * *
2057 -ATTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAA
451 GATTCGGAAAAAAAATTAGAAAAATGATATTTAAAGCGAGAAAA
2100 GACCATCTTT
Statistics
Matches: 937, Mismatches: 92, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
550 70 0.07
551 75 0.08
552 11 0.01
553 269 0.29
554 174 0.19
555 11 0.01
556 2 0.00
557 68 0.07
558 137 0.15
559 51 0.05
560 69 0.07
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (551 bp):
TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
TTCGGAAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
ATTATATTTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAACTATCCGATCAGTTTTTAGC
CGAAATCGTGTACTAACCATCACGATTTTTGGCTCAAAACGCGTTCCCGAGTCCCGACTCAATTT
TGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCATATGTCAGCCACA
TTAGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTC
GGAAAAAAAATTAGAAAAATGATATTTAAAGCGAGAAAATATTTCAAATTTTTTTGTTGCATTGA
ATTGTGTATTTTTTGCCGAATATTTTTTTGT
Found at i:7128 original size:32 final size:32
Alignment explanation
Indices: 7082--7167 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
7072 GCACAAAAAC
*
7082 CCGATATGGCAATGCCACGTCATCAGTTTGGT
1 CCGACATGGCAATGCCACGTCATCAGTTTGGT
* *
7114 CCGACATGGCAATGCCACATCATCATTTTGGT
1 CCGACATGGCAATGCCACGTCATCAGTTTGGT
* *
7146 CTGACATGGCATTGCCACGTCA
1 CCGACATGGCAATGCCACGTCA
7168 GCGGCATGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (32 bp):
CCGACATGGCAATGCCACGTCATCAGTTTGGT
Found at i:25371 original size:31 final size:29
Alignment explanation
Indices: 25329--25393 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 29
25319 GCTTATTACC
25329 CAAATTAGCCCCTTAACTATTCATTTTGGGA
1 CAAATTAGCCCCTTAACT-TT-ATTTTGGGA
* *
25360 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTAGCCCCTTAACTTTATTTTGGGA
25389 CAAAT
1 CAAAT
25394 AAATTCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 13 0.41
30 2 0.06
31 17 0.53
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (29 bp):
CAAATTAGCCCCTTAACTTTATTTTGGGA
Found at i:39021 original size:39 final size:39
Alignment explanation
Indices: 38967--39048 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
38957 GTAGCAACAG
38967 TAGCATCTGTTGCTTCATTTACTGTCCTCATAACTGCAC
1 TAGCATCTGTTGCTTCATTTACTGTCCTCATAACTGCAC
39006 TAGCATCTGTTGCTTCATTTACTGTCCTCATAACTGCAC
1 TAGCATCTGTTGCTTCATTTACTGTCCTCATAACTGCAC
39045 TAGC
1 TAGC
39049 TCTCTTATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (39 bp):
TAGCATCTGTTGCTTCATTTACTGTCCTCATAACTGCAC
Found at i:41800 original size:19 final size:20
Alignment explanation
Indices: 41776--41820 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
41766 AGAAGTTTAC
41776 GATATAATAGAC-ATTGTAA
1 GATATAATAGACAATTGTAA
* *
41795 GATATAATTGCCAATTGTAA
1 GATATAATAGACAATTGTAA
41815 -ATATAA
1 GATATAA
41821 ATATTTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (20 bp):
GATATAATAGACAATTGTAA
Found at i:42518 original size:14 final size:13
Alignment explanation
Indices: 42499--42537 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
42489 ACTCAACACT
42499 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
42513 AACTGACTCAACA
1 AACTGACTCAAAA
42526 AACTGACT-AAAA
1 AACTGACTCAAAA
42538 CCCAATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:42530 original size:13 final size:13
Alignment explanation
Indices: 42488--42533 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
42478 GCCAGACTCA
42488 GACTCAACACTAACT
1 GACTCAACA--AACT
*
42503 GACTCGAAAAAACT
1 GACTC-AACAAACT
42517 GACTCAACAAACT
1 GACTCAACAAACT
42530 GACT
1 GACT
42534 AAAACCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:61730 original size:28 final size:27
Alignment explanation
Indices: 61698--61763 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
61688 ACATATTAAA
*
61698 TTTATTCTTCTTTTTTTAAGGACTTTAT
1 TTTATTCTTC-TATTTTAAGGACTTTAT
* *
61726 TTTATTGCTACTATTTTAAGGATTTTAT
1 TTTATT-CTTCTATTTTAAGGACTTTAT
*
61754 TCTTCTTCTT
1 T-TTATTCTT
61764 GATGTATAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (27 bp):
TTTATTCTTCTATTTTAAGGACTTTAT
Found at i:71942 original size:139 final size:141
Alignment explanation
Indices: 71690--71958 Score: 418
Period size: 139 Copynumber: 1.9 Consensus size: 141
71680 ATATAGAAGT
* * * * *
71690 ATATATAATTTTTGGCTTAAATGTCATTTTGCACCCTGAAATTTATATGGACTGCCACTTTGCAC
1 ATATATAATTTTTGGCTTAAACGTCAATTTGCACCCTGAAATTTATACGAACTACCACTTTGCAC
* *
71755 CCTGTTTTTTTATTTTGATCACTTTGCACCCTAATATTTTATTTTTGTTCCACGTTACACCTTCC
66 CCTATTATTTTATTTTGATCACTTTGCACCCTAATATTTTATTTTTGTTCCACGTTACACCTTCC
71820 AGAATTCGATA
131 AGAATTCGATA
*
71831 ATATA-AATTTTTGGCTTAAACG-CAAATTTGCA-CCTGAAGTTTATACGAACTACCACTTTGCA
1 ATATATAATTTTTGGCTTAAACGTC-AATTTGCACCCTGAAATTTATACGAACTACCACTTTGCA
* *
71893 TCCTATTATTTTATTTTGATCACTTTGCACCCTAATATTTTATTTTTGTTCCACGTTGCACCTTC
65 CCCTATTATTTTATTTTGATCACTTTGCACCCTAATATTTTATTTTTGTTCCACGTTACACCTTC
71958 C
130 C
71959 GTTATCGAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
139 89 0.76
140 23 0.20
141 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (141 bp):
ATATATAATTTTTGGCTTAAACGTCAATTTGCACCCTGAAATTTATACGAACTACCACTTTGCAC
CCTATTATTTTATTTTGATCACTTTGCACCCTAATATTTTATTTTTGTTCCACGTTACACCTTCC
AGAATTCGATA
Found at i:86140 original size:10 final size:10
Alignment explanation
Indices: 86125--86160 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
86115 TCGTCTCTCT
86125 TTTTCTTTTA
1 TTTTCTTTTA
86135 TTTTCTTTTCA
1 TTTTCTTTT-A
*
86146 TTTTTTTTTA
1 TTTTCTTTTA
86156 TTTTC
1 TTTTC
86161 AGATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:105291 original size:11 final size:11
Alignment explanation
Indices: 105275--105309 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
105265 TTTTTCTGTT
105275 TTTTGTTTTTG
1 TTTTGTTTTTG
*
105286 TTTTGTTTTCG
1 TTTTGTTTTTG
105297 TTTTGTTTTTG
1 TTTTGTTTTTG
105308 TT
1 TT
105310 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:106236 original size:25 final size:25
Alignment explanation
Indices: 106191--106242 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
106181 TTTTGAACTC
* *
106191 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATAATT
*
106216 ATTATTTATT-TAATAATATATAATT
1 ATTATTTATTAT-ATAAAATATAATT
106241 AT
1 AT
106243 ATCTAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATAATT
Found at i:106241 original size:22 final size:22
Alignment explanation
Indices: 106159--106242 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
106149 CGTTTAGTAA
*
106159 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTAATTATTTA-T
* * * *
106183 TTGAACT-CATTATTTA-TTAT
1 TTAAAATATATTAATTATTTAT
*
106203 TTAAAATATATTTATTATTTAT
1 TTAAAATATATTAATTATTTAT
106225 TTAATAATATA-TAATTAT
1 TTAA-AATATATTAATTAT
106243 ATCTAAGATA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 6 0.12
21 9 0.19
22 22 0.46
23 7 0.15
24 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (22 bp):
TTAAAATATATTAATTATTTAT
Found at i:110703 original size:31 final size:31
Alignment explanation
Indices: 110665--110830 Score: 332
Period size: 31 Copynumber: 5.4 Consensus size: 31
110655 AAAATGCCAA
110665 ACCAAGGCGCCGACATGGCATGCCACGTCAG
1 ACCAAGGCGCCGACATGGCATGCCACGTCAG
110696 ACCAAGGCGCCGACATGGCATGCCACGTCAG
1 ACCAAGGCGCCGACATGGCATGCCACGTCAG
110727 ACCAAGGCGCCGACATGGCATGCCACGTCAG
1 ACCAAGGCGCCGACATGGCATGCCACGTCAG
110758 ACCAAGGCGCCGACATGGCATGCCACGTCAG
1 ACCAAGGCGCCGACATGGCATGCCACGTCAG
110789 ACCAAGGCGCCGACATGGCATGCCACGTCAG
1 ACCAAGGCGCCGACATGGCATGCCACGTCAG
110820 ACCAAGGCGCC
1 ACCAAGGCGCC
110831 ATTAGACTAA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 135 1.00
ACGTcount: A:0.26, C:0.36, G:0.29, T:0.09
Consensus pattern (31 bp):
ACCAAGGCGCCGACATGGCATGCCACGTCAG
Found at i:110861 original size:47 final size:47
Alignment explanation
Indices: 110800--110913 Score: 219
Period size: 47 Copynumber: 2.4 Consensus size: 47
110790 CCAAGGCGCC
110800 GACATGGCATGCCACGTCAGACCAAGGCGCCATTAGACTAAGGCACT
1 GACATGGCATGCCACGTCAGACCAAGGCGCCATTAGACTAAGGCACT
*
110847 GACATGGCATGCCACGTCAGACCAAGGCGCCGTTAGACTAAGGCACT
1 GACATGGCATGCCACGTCAGACCAAGGCGCCATTAGACTAAGGCACT
110894 GACATGGCATGCCACGTCAG
1 GACATGGCATGCCACGTCAG
110914 CAATATTGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (47 bp):
GACATGGCATGCCACGTCAGACCAAGGCGCCATTAGACTAAGGCACT
Found at i:124428 original size:21 final size:22
Alignment explanation
Indices: 124386--124428 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
124376 GTCCATCCAA
*
124386 CTTGTTATTTATTCCTTTGAGG
1 CTTGTTATCTATTCCTTTGAGG
124408 CTTGTTATCTATTCC-TTGAGG
1 CTTGTTATCTATTCCTTTGAGG
124429 TCGTCGACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (22 bp):
CTTGTTATCTATTCCTTTGAGG
Found at i:124472 original size:27 final size:27
Alignment explanation
Indices: 124434--124487 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
124424 TGAGGTCGTC
124434 GACCAAGCGAAGAAAATAATCTTAAGA
1 GACCAAGCGAAGAAAATAATCTTAAGA
124461 GACCAAGCGAAGAAAATAATCTTAAGA
1 GACCAAGCGAAGAAAATAATCTTAAGA
124488 TATTGCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (27 bp):
GACCAAGCGAAGAAAATAATCTTAAGA
Found at i:125043 original size:42 final size:42
Alignment explanation
Indices: 124980--125064 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
124970 TTGCTTCCTA
*
124980 TATGTTATTTATTTCTTTATGTTAAGTTGTTAATTAACTTCT
1 TATGTTATTTATTTCTCTATGTTAAGTTGTTAATTAACTTCT
125022 TATGTTATTTATTTCTCTATGTTAAGTTGTTAATTAACTTCT
1 TATGTTATTTATTTCTCTATGTTAAGTTGTTAATTAACTTCT
125064 T
1 T
125065 TTTTACTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.59
Consensus pattern (42 bp):
TATGTTATTTATTTCTCTATGTTAAGTTGTTAATTAACTTCT
Done.