Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007778.1 Corchorus capsularis cultivar CVL-1 contig07799, 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: 115822
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:671 original size:323 final size:328
Alignment explanation
Indices: 1--1864 Score: 1951
Period size: 323 Copynumber: 5.7 Consensus size: 328
* * * *
1 ATTTTGGTCAAATCGTGTACTAATCATCACGATTTTTGGCTAAAAATGCATTCCGGTGCTCTGGC
1 ATTTTGGCCAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGC
* *
66 TCAGTTTTTCATGATTTTTGGCGCCAAGAATCATTAAAATATATACATTTATCTAACCAAATCTC
66 TCAGTTTTTCATGATTTTTGTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATCTC
*
131 AGCCACTTTGGATTTATA-GATTTGATTTTACGGGCATTAGAATCATGTGTCGATTTTATCAGAA
131 AGCCACTTTGGATTTA-AGGATTTGATTTTACGAGCATTAGAA-CA---GTCGATTTTATCAGAA
* * *
195 ATTAATTCGGAACTATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTTAATCTTATTGGC
191 ATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGC
* *
260 TTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGACGAAAAATATTTCGGGTCAATT
256 TTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCGGGTCAATT
325 TTTGCAAA
321 TTTGCAAA
*
333 ATTTTGGCCAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAATGCGTTCCGGTGCTCCGGC
1 ATTTTGGCCAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGC
* *
398 ACAGTTTTTCATTATTTTTGTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATCTC
66 TCAGTTTTTCATGATTTTTGTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATCTC
*
463 AGTCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAG-A-A-T-G-TTTTATCAGAAATTAA
131 AGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAACAGTCGATTTTATCAGAAATTAA
523 TTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGA
196 TTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGA
* *
588 ATTATATACTTTTTATGAGTATTTTGGCCGAAAATTAAGTAAAAATATTTCGGGTCAATTTTTGT
261 ATTATATACTTTTTATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGC
653 AAA
326 AAA
* *
656 ATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTCCGGTGCTTCGG
1 ATTTTGGCCAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAATGCGTTCCGGTGCTCCGG
* * * * * * *
721 CTCAGTTTTTCATGATTTTTGGT-GTCAAGACTCATTGAAATATATATATTAATCTTACCGAATC
65 CTCAGTTTTTCATGATTTTT-GTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATC
*
785 TCAGCCACTTTGGATTTAAGGAATTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGA
129 TCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAA-CA---GTCGATTTTATCAGA
**
850 TTTTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTG---A-------AA-------GG
190 AATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGG
* *
898 CTTTGAATTATATTCTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAAT
255 CTTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCGGGTCAAT
963 TTTTGCAAA
320 TTTTGCAAA
* * *
972 ATTTTGGCTAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAATGCGTTACGGTGCTCCGGC
1 ATTTTGGCCAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGC
* *
1037 TCAGTTTTTCATTATTTTTGTCGCCAAAAATCATTAAAATATATACATTCATCTAACCAAATCTC
66 TCAGTTTTTCATGATTTTTGTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATCTC
* * * * * * *
1102 GGCCTCATTGGAATTAAGGATTTGATTTTATGAGCATTAGAATCATGTGTCGATTTTTTCATAAA
131 AGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAA-CA---GTCGATTTTATCAGAAA
* * * * * * *
1167 TTAATT-GGAACAATATAAGAAATTCAATATTAGAAACGTGAAAACCCCTTCAACCTTTTTGGAT
192 TTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCT
* * ** * *
1231 ATGAATTATATACTTTTTACGAGTA-TTTCCCCTAAAAATTAAGGAAAAATATTTCGCGTCAATT
257 TTGAATTATATACTTTTTATGAGTATTTTGGCC-GAAAATTAAGGAAAAATATTTCGGGTCAATT
*
1295 TATGCAAA
321 TTTGCAAA
* * * * *
1303 ATTTT-GCCTAAAT-AT-T--T--CGCGTCAGGATTTTTGGCTAAAAATGCATTCTGGTGCTCCG
1 ATTTTGGCC-AAATCGTGTACTAAC-CATCACGATTTTTGGCTAAAAATGCGTTCCGGTGCTCCG
* * * * * * * *
1361 GCTCAGTTTTTTATGATTTTTAG-CTCTAAGACTCTTTGAAATATCTATATTCATCTAACCAAAT
64 GCTCAGTTTTTCATGATTTTT-GTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAAT
* * * *
1425 CTCAGTCACTTTAGATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTGTCGATTTTGTCAG
128 CTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAA-CA---GTCGATTTTATCAG
*** * ** * *
1490 AAATTATTTAGAAATTTAAAATAATATAGGAAAATTTATATTAGAAAC-T-ACAAAACCCTTCAA
189 -AA--A-TT---AATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGA-AAAGCCCTTCAA
* * * **
1553 TCTTTTTGGCGTTT-AATTATGTATTTTTTATGAGTATTTTGGCCCAAAATTGAGAAAAAAAAAA
246 TCTTTTTGGC-TTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATT----AAGGAAAAA
**
1617 TATTTCACGTCAA-TTTTGACAAA
306 TATTTCGGGTCAATTTTTG-CAAA
* * * * * * * **
1640 ATGTTGACCAAATCGTGTAC-AA-CATCAC-AGTTTTTTGTTTAAAATGCTTTTCGGTGCTCCAA
1 ATTTTGGCCAAATCGTGTACTAACCATCACGA-TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGG
* * ** * * * * * * **
1702 CTCAATTTTTCAGGATTTTT-TACATCATGACTTATTGAAAATATCTATATTTATCTAATTAAAT
65 CTCAGTTTTTCATGATTTTTGT-CGCCAAGAATCATT-AAAATATATACATTCATCTAACCAAAT
* * * * *
1766 CTCAGCCACATTGAATTTAAGGATATGATTTTACGAGCATTAAAATCATGT-GTCAATTTATTCA
128 CTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAA-CA-GTCG--ATTTTA-TCA
* * *
1830 GAAATTAATTCGAAATAATATAGGAAATTCGATAT
188 GAAATTAATTCGGAACAATATAGGAAAATCGATAT
1865 ATTCCATGTC
Statistics
Matches: 1303, Mismatches: 165, Indels: 126
0.82 0.10 0.08
Matches are distributed among these distances:
314 32 0.02
315 145 0.11
316 101 0.08
317 1 0.00
323 174 0.13
324 126 0.10
325 5 0.00
326 140 0.11
327 5 0.00
329 3 0.00
330 11 0.01
331 72 0.06
332 159 0.12
333 100 0.08
334 55 0.04
336 4 0.00
337 33 0.03
338 5 0.00
339 5 0.00
340 59 0.05
341 68 0.05
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (328 bp):
ATTTTGGCCAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGC
TCAGTTTTTCATGATTTTTGTCGCCAAGAATCATTAAAATATATACATTCATCTAACCAAATCTC
AGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAACAGTCGATTTTATCAGAAATTAA
TTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGA
ATTATATACTTTTTATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGC
AAA
Found at i:6673 original size:23 final size:25
Alignment explanation
Indices: 6641--6707 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 25
6631 CTCAGCCGCG
*
6641 TGGCCTGTTCTCCCAAATCGGCGCT
1 TGGCCTGTTCTCTCAAATCGGCGCT
6666 TGG-C-GTTCTCTC-AA-C--CGCT
1 TGGCCTGTTCTCTCAAATCGGCGCT
6685 TGGCCTGTTCTCTCAAATCGGCG
1 TGGCCTGTTCTCTCAAATCGGCG
6708 GCCTGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
19 7 0.20
20 1 0.03
21 9 0.26
22 4 0.11
23 8 0.23
24 1 0.03
25 5 0.14
ACGTcount: A:0.12, C:0.34, G:0.24, T:0.30
Consensus pattern (25 bp):
TGGCCTGTTCTCTCAAATCGGCGCT
Found at i:6696 original size:21 final size:21
Alignment explanation
Indices: 6625--6700 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 21
6615 GCCGATGACT
* *
6625 TGTTCTCTCAGCCGCGTGGCC
1 TGTTCTCTCAACCGCTTGGCC
*
6646 TGTTCTCCCAAATCGGCGCTTGG-C
1 TGTTCTCTC-AA-C--CGCTTGGCC
6670 -GTTCTCTCAACCGCTTGGCC
1 TGTTCTCTCAACCGCTTGGCC
6690 TGTTCTCTCAA
1 TGTTCTCTCAA
6701 ATCGGCGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 7 0.16
20 1 0.02
21 19 0.42
22 3 0.07
23 8 0.18
24 1 0.02
25 6 0.13
ACGTcount: A:0.11, C:0.36, G:0.22, T:0.32
Consensus pattern (21 bp):
TGTTCTCTCAACCGCTTGGCC
Found at i:6840 original size:78 final size:78
Alignment explanation
Indices: 6711--6858 Score: 287
Period size: 78 Copynumber: 1.9 Consensus size: 78
6701 ATCGGCGGCC
6711 TGAAAAACAAACAGAAGTTAAAATCGAAGAAACAAAATCAAGAAAGAAGACGAAACGAAAAACAA
1 TGAAAAACAAACAGAAGTTAAAATCGAAGAAACAAAATCAAGAAAGAAGACGAAACGAAAAACAA
6776 GAAATTCGACTAT
66 GAAATTCGACTAT
*
6789 TGAAAAACAAACAGACGTTAAAATCGAAGAAACAAAATCAAGAAAGAAGACGAAACGAAAAACAA
1 TGAAAAACAAACAGAAGTTAAAATCGAAGAAACAAAATCAAGAAAGAAGACGAAACGAAAAACAA
6854 GAAAT
66 GAAAT
6859 CGGATATGGA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.10
Consensus pattern (78 bp):
TGAAAAACAAACAGAAGTTAAAATCGAAGAAACAAAATCAAGAAAGAAGACGAAACGAAAAACAA
GAAATTCGACTAT
Found at i:7313 original size:19 final size:19
Alignment explanation
Indices: 7289--7327 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
7279 CAGTCCATTT
7289 ATTTATTATCCATTATAAC
1 ATTTATTATCCATTATAAC
7308 ATTTATTATCCATTATAAC
1 ATTTATTATCCATTATAAC
7327 A
1 A
7328 ATTCCTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTATTATCCATTATAAC
Found at i:13614 original size:1 final size:1
Alignment explanation
Indices: 13608--13633 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13598 TATTACCCAG
13608 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13634 CTGTGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23017 original size:2 final size:2
Alignment explanation
Indices: 23007--23035 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22997 ACACACAAGA
23007 AT AT A- 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
23036 TGTTAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23412 original size:5 final size:5
Alignment explanation
Indices: 23394--23432 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
23384 GTGGCTGCAT
*
23394 AAAGAA AAAAA AAAGAA AAAGA AAAGA AAAGA AAAGA AA
1 AAAG-A AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AA
23433 CAATCCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 22 0.73
6 8 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:23423 original size:10 final size:11
Alignment explanation
Indices: 23394--23432 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
23384 GTGGCTGCAT
*
23394 AAAGAAAAAAA
1 AAAGAAAAAGA
23405 AAAGAAAAAGA
1 AAAGAAAAAGA
23416 AAAG-AAAAGA
1 AAAGAAAAAGA
23426 AAAGAAA
1 AAAGAAA
23433 CAATCCATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:26420 original size:3 final size:3
Alignment explanation
Indices: 26412--26444 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
26402 TATGGTATAC
26412 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26445 TATATAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29487 original size:14 final size:13
Alignment explanation
Indices: 29461--29497 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
29451 ACAGGGCACT
29461 ATAATTAAATTAA
1 ATAATTAAATTAA
29474 ATAATTATAATTAA
1 ATAATTA-AATTAA
*
29488 AGAATTAAAT
1 ATAATTAAAT
29498 CTTGGAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
ATAATTAAATTAA
Found at i:36119 original size:2 final size:2
Alignment explanation
Indices: 36112--36153 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
36102 CTGGTTTTGG
36112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36154 TTCATTATTA
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):
AT
Found at i:48271 original size:30 final size:30
Alignment explanation
Indices: 48233--48313 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
48223 AAGAAGCACC
* *
48233 AAAAGAGATAAAAACAACAGTAGCACCACC
1 AAAAGAGATAAAAAGAACAGTAGCACCACA
* *
48263 ATAGGAGATAAAAAGAACAGTAGCACCACA
1 AAAAGAGATAAAAAGAACAGTAGCACCACA
48293 AAAAGAGATAAAAAGAACAGT
1 AAAAGAGATAAAAAGAACAGT
48314 GAGTTAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.58, C:0.16, G:0.17, T:0.09
Consensus pattern (30 bp):
AAAAGAGATAAAAAGAACAGTAGCACCACA
Found at i:69165 original size:20 final size:22
Alignment explanation
Indices: 69129--69174 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
69119 TTACTTATCA
69129 AAAAAGATTACCAAAAAAATC-
1 AAAAAGATTACCAAAAAAATCT
69150 AAAAAGATTACC-AAAAAATCT
1 AAAAAGATTACCAAAAAAATCT
69171 AAAA
1 AAAA
69175 TACATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.67, C:0.13, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAAAGATTACCAAAAAAATCT
Found at i:69429 original size:23 final size:25
Alignment explanation
Indices: 69384--69429 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
69374 CTCTTCATCT
69384 CTTTCTTCTTCCCTCATCTCCAAGC
1 CTTTCTTCTTCCCTCATCTCCAAGC
*
69409 CTTTCTT-TTCTCTC-TCTCCAA
1 CTTTCTTCTTCCCTCATCTCCAA
69430 AACTCCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.11, C:0.41, G:0.02, T:0.46
Consensus pattern (25 bp):
CTTTCTTCTTCCCTCATCTCCAAGC
Found at i:74065 original size:6 final size:6
Alignment explanation
Indices: 74056--74080 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
74046 TTTGTAAGTG
74056 TATGAT TATGAT TATGAT TATGAT T
1 TATGAT TATGAT TATGAT TATGAT T
74081 GGCTATAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATGAT
Found at i:78065 original size:157 final size:157
Alignment explanation
Indices: 77869--78185 Score: 634
Period size: 157 Copynumber: 2.0 Consensus size: 157
77859 TAATGATACC
77869 TTTTGGGACCAACTTATTGATGTACACATTTTATTAATATTGTAAATAAATTACTCTCGCTAAGA
1 TTTTGGGACCAACTTATTGATGTACACATTTTATTAATATTGTAAATAAATTACTCTCGCTAAGA
77934 GTCACGTTACTGGACTTTTAATTTTAATGATCATGATCAAAATATTCACAACAATTCAAACAGTA
66 GTCACGTTACTGGACTTTTAATTTTAATGATCATGATCAAAATATTCACAACAATTCAAACAGTA
77999 CTAAAATATTCAATATTTTGATTTCCT
131 CTAAAATATTCAATATTTTGATTTCCT
78026 TTTTGGGACCAACTTATTGATGTACACATTTTATTAATATTGTAAATAAATTACTCTCGCTAAGA
1 TTTTGGGACCAACTTATTGATGTACACATTTTATTAATATTGTAAATAAATTACTCTCGCTAAGA
78091 GTCACGTTACTGGACTTTTAATTTTAATGATCATGATCAAAATATTCACAACAATTCAAACAGTA
66 GTCACGTTACTGGACTTTTAATTTTAATGATCATGATCAAAATATTCACAACAATTCAAACAGTA
78156 CTAAAATATTCAATATTTTGATTTCCT
131 CTAAAATATTCAATATTTTGATTTCCT
78183 TTT
1 TTT
78186 ATGATTGGTA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (157 bp):
TTTTGGGACCAACTTATTGATGTACACATTTTATTAATATTGTAAATAAATTACTCTCGCTAAGA
GTCACGTTACTGGACTTTTAATTTTAATGATCATGATCAAAATATTCACAACAATTCAAACAGTA
CTAAAATATTCAATATTTTGATTTCCT
Found at i:81875 original size:17 final size:17
Alignment explanation
Indices: 81853--81889 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
81843 GAATGGATTT
81853 TGGGGTTTGATTGCTTA
1 TGGGGTTTGATTGCTTA
*
81870 TGGGGTTTGATTTCTTA
1 TGGGGTTTGATTGCTTA
81887 TGG
1 TGG
81890 AGAAAAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.35, T:0.49
Consensus pattern (17 bp):
TGGGGTTTGATTGCTTA
Found at i:81899 original size:25 final size:25
Alignment explanation
Indices: 81871--81921 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
81861 GATTGCTTAT
81871 GGGGTTTGATT-TCTTATGGAGAAAA
1 GGGGTTTGATTCT-TTATGGAGAAAA
81896 GGGGTTTGATTCTTTATGGAGAAAA
1 GGGGTTTGATTCTTTATGGAGAAAA
81921 G
1 G
81922 ATGTCTGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (25 bp):
GGGGTTTGATTCTTTATGGAGAAAA
Found at i:83832 original size:66 final size:66
Alignment explanation
Indices: 83719--83909 Score: 287
Period size: 66 Copynumber: 2.9 Consensus size: 66
83709 AAATATCATG
* * * * * *
83719 TTTCTCAAGTTAAAGAGAGGATACCTATTCGTGTGGTGAATTTGTTGGATGATGAGAGGACTGAT
1 TTTCTCAAGGTGAGGAGAAGATACCTATTCGTGTGGTGAATTCGTTGGATGATGAGAGGAATGAT
83784 -
66 A
83784 TTATCTCAAGGTGAGGAGAACG-TACCTATTCGTGTGGTGAATTCGTTGGATGATGAGAGGAATG
1 TT-TCTCAAGGTGAGGAGAA-GATACCTATTCGTGTGGTGAATTCGTTGGATGATGAGAGGAATG
83848 ATA
64 ATA
*
83851 TTTCTCAAGGTGAGGAGAAGATACCTATTCGTGTGGTGAATTCTTTGGATGATGAGAGG
1 TTTCTCAAGGTGAGGAGAAGATACCTATTCGTGTGGTGAATTCGTTGGATGATGAGAGG
83910 CCCCCATCTT
Statistics
Matches: 115, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
65 3 0.03
66 109 0.95
67 3 0.03
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (66 bp):
TTTCTCAAGGTGAGGAGAAGATACCTATTCGTGTGGTGAATTCGTTGGATGATGAGAGGAATGAT
A
Found at i:85887 original size:10 final size:10
Alignment explanation
Indices: 85868--85899 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
85858 GTTGAGGAGG
*
85868 AAAAAGAAGA
1 AAAAAAAAGA
85878 AAAAAAAAGA
1 AAAAAAAAGA
85888 AAAAAAAAGA
1 AAAAAAAAGA
85898 AA
1 AA
85900 TGGGTAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:105817 original size:13 final size:13
Alignment explanation
Indices: 105799--105831 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
105789 TAGGTTATAT
105799 CATAAGAAGAGAA
1 CATAAGAAGAGAA
105812 CATAAGAAGAGAA
1 CATAAGAAGAGAA
105825 CA-AAGAA
1 CATAAGAA
105832 AGTAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.64, C:0.09, G:0.21, T:0.06
Consensus pattern (13 bp):
CATAAGAAGAGAA
Found at i:109218 original size:2 final size:2
Alignment explanation
Indices: 109211--109245 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
109201 ATATACAATT
109211 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 T
109246 GTGTTGCTAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112152 original size:15 final size:15
Alignment explanation
Indices: 112132--112160 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
112122 AAATATATTC
112132 AACATTGCATTCATG
1 AACATTGCATTCATG
112147 AACATTGCATTCAT
1 AACATTGCATTCAT
112161 ATATTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
AACATTGCATTCATG
Found at i:113732 original size:331 final size:330
Alignment explanation
Indices: 113123--115820 Score: 3468
Period size: 333 Copynumber: 8.1 Consensus size: 330
113113 GTGTATTAAC
* * * * *
113123 CGGTTTTTTGCTAAAACCGTGTTCCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGAGGCC-AA
1 CGGTTTTTTGCTAAAAACGCGTTCCGGGGC-CCCACTCAGTTTTGCATGATTTTT-G-CGCCGAG
* * * * * *
113187 ACTCCTTGAAA----TATATTCATCGTACCAAATCTCAGCCATATTGGATTTAAGGATACGTTCT
63 ACTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTTT
* * * * * *
113248 TACAATGATTTGAAAATTGTTTCAATTTAATCAGAAATTATTTTTGAAAAAAATAGGAAAAACGA
128 TACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTT--AAAAAATAGGAAAAACGG
* * * * *
113313 TATTAGAACCGTAAAAAACCATTCAATCTTTTTTTTATTGAATTATATATTTC-TTATGAGTATT
191 TATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATA-TTCGTTATGAGTATT
*
113377 GGGGCAAAGAATTGAGGAAAAAAATTT-TGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGT
255 GGGGCAAAGAATTGAGGAAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGT
*
113441 ACAAACCATCA
320 ACTAACCATCA
* * * * *
113452 TGGTTTTTTGCTAAAAACACGTTCCGAGGTCCCATCTCAGTTTTGCATGATTTTTGGCGCTGAGA
1 CGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCA-CTCAGTTTTGCATGATTTTT-GCGCCGAGA
* * * * *
113517 CTCCTTGAAATATCTATATTCATCTTAT-TAAATATCAGCCACATTGGATTTAAGGATGAC-TTT
64 CTCCTTGAAATTTCTATATTCATCTT-TCCAAATCTCATCCACAATGGATTTAAGGAT-ACGTTT
* * * * **
113580 TTACGAGGATCTGAAAATTGTTTTGATTTAATCAGAACTTAATTTGAAAAAATAGGAGAAACAAT
127 TTACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTAAAAAATAGGAAAAACGGT
*
113645 ATTTGAAGCGTGAAAATCCCTTCAATCTTTTTTGTATTGAATTATATATTTC-TTATGAGTTATT
192 ATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATA-TTCGTTATGAG-TATT
* * *
113709 GGGGCAAAGAATTGAGGAAAAAATTTTCCAGGTCA-TTTTTCCAAAATTTTAACCGAAATCGTGT
255 GGGGCAAAGAATTGAGGAAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGT
*
113773 ACCAACCATCA
320 ACTAACCATCA
* * * ** * *
113784 TGGTTTTTTTGCCAAAAACGCGTTCCGGGGCTTCGGCTCAGTTTTCCATGATTTTTGGCGCCAAG
1 CGG-TTTTTTGCTAAAAACGCGTTCCGGGGC-CCCACTCAGTTTTGCATGATTTTT-GCGCCGAG
* * * *
113849 AATCCTTGAAATTTCTGTATTCATCTTTCCAAATCTCATCCACAATGAATTTAAGGATACATTTT
63 ACTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTTT
113914 TACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAA-TTTAAAAAATAGGAAAAA-GGTA
128 TACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTAAAAAATAGGAAAAACGGTA
* * *
113977 TTTGAAGCGTGAAAAACCCTTCATTTTTTGAATTATGTATTGAATTATGTATTCGTTATGAGTAT
193 TTTGAAGCGTGAAAAACCCTTCAATCTTT---TT-TGTATTGAATTATATATTCGTTATGAGTAT
* * * * *
114042 TGGGCCAAAGAATTGAAGAAAAATAAATTTCCAGGTCATTTTTTGCTAAATTTTAACCGTAATCG
254 TGGGGCAAAGAATTG-AGGAAAA-AAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCG
114107 TGTACTAACCATCA
317 TGTACTAACCATCA
* * * * **
114121 CGGTTTTTTTTGGCCAAAAAAGCGTTTCGGGGCCCCGACTCAGTTTTCCATGATAGATTGCGCCG
1 CGG--TTTTTT-GCTAAAAACGCGTTCCGGGGCCCC-ACTCAGTTTTGCATGAT-TTTTGCGCCG
*
114186 AGACTCCTTGAAATTTCTGTATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACG-T
61 AGACTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTT
* * *
114250 TTTACGAGGATCTGAAAATTGTTTTGATTTAATCAAAAATTAATTTTTTAAAAAATAGAAAAAAC
126 TTTACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAA--TTTTAAAAAATAGGAAAAAC
* *
114315 GGTATTTGAAGCGTGAAAAACCATTCAATCTTTTTTGTATTGACTTATATATTCGTTATGAGTAT
189 GGTATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTAT
* *
114380 TGGGGCAAAGAATTGTGGAAAAAAAATTTCCGGATCATTTTTTGCAAAATTTTAACCGAAATCGT
254 TGGGGCAAAGAATTGAGG-AAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGT
114445 GTACT---CATCA
318 GTACTAACCATCA
* * *
114455 TGGTTTTTTGCTAAAAACACGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTTGCACCGAGA
1 CGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCC-ACTCAGTTTTGCATGA-TTTTTGCGCCGAGA
* * **
114520 CTCCTTTAAATTTCTATATTCATCTTACCAAATCTCATCTGCAATGGATTTAAGGATACGTTTTT
64 CTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTTTT
*
114585 ACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAAATTTTAAAAAAATAGAAAAAACGGT
129 ACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATT-AATTTT-AAAAAATAGGAAAAACGGT
* * *
114650 ATTTGAAGCTTGAAAAACCCTTCAAT-TTTTTTGTATCGAATTATATATTAGTTATGAGTATTGG
192 ATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTGG
* * * *
114714 GACAAAGAATTGTGGAAAAAAATTTCCGGATCATTTTTTTGCAAAATTTTAACCGAAATCATGTA
257 GGCAAAGAATTGAGGAAAAAAATTTCCGGGTCA-TTTTTTGCAAAATTTTAACCGAAATCGTGTA
*
114779 CTAACCATAA
321 CTAACCATCA
* * * * *
114789 CGGTTTTTTTGCTAAAAATGTGTTCCGGGACGACGACTCAGTTTTGCATGATTCTTTGCGCC-AT
1 CGG-TTTTTTGCTAAAAACGCGTTCCGGGGC-CCCACTCAGTTTTGCATGATT-TTTGCGCCGA-
* * * *
114853 GACTCCTTTAAATTTCTATATTCATCTTACCAAATCTCATCCGCAATGGATTTAAGGATACATTT
62 GACTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTT
* *
114918 TTACGAAGATCTGAAAATTGTTTCGATTTAATCAGAAATTAA-TTTAGAAAAATAGGAAAAACTG
127 TTACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTA-AAAAATAGGAAAAACGG
114982 TATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTG
191 TATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTG
* * * *
115047 GGGGAAA-AATTGAGGAAAAAAAATTT-CAGGTCATTTTTTGCGAAATTTTAACAGAAATCGTGT
256 GGGCAAAGAATTGAGG-AAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGT
*
115110 ACTAACCATAA
320 ACTAACCATCA
* * * ** *
115121 CAGTTTTTAG-TCAAAAAGGCGTTCCGGGGCCCCGGTTCAGTTTTGCATGATTTTTTGAGCCGAG
1 CGGTTTTTTGCT-AAAAACGCGTTCCGGGGCCCC-ACTCAGTTTTGCATGA-TTTTTGCGCCGAG
* * *
115185 ACTCCTCT-AATTTTCTTTATTCATCTTTCCAAATCTCATCCACAATGGATTTAATGATACGTTT
63 ACTCCT-TGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTT
115249 TTACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTAAAATAAATAGGAAAAACG
127 TTACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTT-AAA-AAATAGGAAAAACG
*
115314 GTATTTGAAGCGTGAAAAACCCTTCAATCTTTTTGGTATTGAATTATATATTCGTTATGAGTATT
190 GTATTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATT
* * * *
115379 GGGGGAAACAATTGAGGTAAAAAAATTT-CGGGTCATTTTTTGCGAAATTTTAACCGAAATCTTG
255 GGGGCAAAGAATTGAGG-AAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTG
*
115443 CACTAACCATCA
319 TACTAACCATCA
* * *
115455 CAGTTTTTTGCCAAAAAGGCGTTCCGGGGCCCCAGCTCAGTTTTGCATGAGTTTTTGCGCCGAGA
1 CGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCA-CTCAGTTTTGCATGA-TTTTTGCGCCGAGA
* * *
115520 CTTCTTGAAATTTCTGTATTCATCTTTACAAATCTCATCCACAATGGATTTAAGGATACGTTTTT
64 CTCCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTTTT
* *
115585 ACGAGAATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTTAAAAAATAGAAAAAACGGTA
129 ACGAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAA-TTTTAAAAAATAGGAAAAACGGTA
* * * *
115650 TTTGAAACGTGAAAAACCCGTCAACCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTGGA
193 TTTGAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTGGG
* * *
115715 ACAAAGAATTGAGG-AAAAAATTTCTGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGTATT
258 GCAAAGAATTGAGGAAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGTACT
115779 AACCATCA
323 AACCATCA
* * *
115787 CGATTTTTTTGCCAAAAACGCGTTCCGAGGCCCC
1 CG-GTTTTTTGCTAAAAACGCGTTCCGGGGCCCC
115821 GG
Statistics
Matches: 2106, Mismatches: 202, Indels: 118
0.87 0.08 0.05
Matches are distributed among these distances:
328 5 0.00
329 58 0.03
330 20 0.01
331 433 0.21
332 274 0.13
333 482 0.23
334 311 0.15
335 180 0.09
336 14 0.01
337 82 0.04
338 96 0.05
339 102 0.05
340 2 0.00
341 17 0.01
342 30 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (330 bp):
CGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCACTCAGTTTTGCATGATTTTTGCGCCGAGACT
CCTTGAAATTTCTATATTCATCTTTCCAAATCTCATCCACAATGGATTTAAGGATACGTTTTTAC
GAGGATCTGAAAATTGTTTCGATTTAATCAGAAATTAATTTTAAAAAATAGGAAAAACGGTATTT
GAAGCGTGAAAAACCCTTCAATCTTTTTTGTATTGAATTATATATTCGTTATGAGTATTGGGGCA
AAGAATTGAGGAAAAAAATTTCCGGGTCATTTTTTGCAAAATTTTAACCGAAATCGTGTACTAAC
CATCA
Found at i:114021 original size:12 final size:12
Alignment explanation
Indices: 114004--114029 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
113994 CCTTCATTTT
114004 TTGAATTATGTA
1 TTGAATTATGTA
114016 TTGAATTATGTA
1 TTGAATTATGTA
114028 TT
1 TT
114030 CGTTATGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGAATTATGTA
Done.