Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021355.1 Corchorus olitorius cultivar O-4 contig21388, 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: 77095
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2150 original size:199 final size:199
Alignment explanation
Indices: 1810--2209 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 199
1800 CTTATCATCC
*
1810 CTAAAAGCAATGGAAATTCAAAAGGATCAAAAGCAAGCTTGTTCATATACCCGGTTCTAAAGATG
1 CTAAAAGCAATGGAAATTCAAAAGGATCAAAAGCAAGCTTGTTCATATACCCGATTCTAAAGATG
1875 CTATGGCAGAGTTGGTGAAGCTTGTAGCGGGAATCGTGGCGGCAAATGGCATTATCCCACAGCAA
66 CTATGGCAGAGTTGGTGAAGCTTGTAGCGGGAATCGTGGCGGCAAATGGCATTATCCCACAGCAA
1940 AGGGCCTATAAATAGTTATGGTCTTCACTTCAACAAGAACAACAATCATCTACAGAATTCTCTTC
131 AGGGCCTATAAATAGTTATGGTCTTCACTTCAACAAGAACAACAATCATCTACAGAATTCTCTTC
2005 TGTT
196 TGTT
2009 CTAAAAGCAATGGAAATTCAAAAGGATCAAAAGCAAGCTTGTTCATATACCCGATTCTAAAGATG
1 CTAAAAGCAATGGAAATTCAAAAGGATCAAAAGCAAGCTTGTTCATATACCCGATTCTAAAGATG
* * *
2074 CTATGGCAGAGTTGGTGAAGCTTGTAGCGGGAATCGTGGCTGCAAATGGCATTATCCCGCAGCAG
66 CTATGGCAGAGTTGGTGAAGCTTGTAGCGGGAATCGTGGCGGCAAATGGCATTATCCCACAGCAA
* *
2139 AGGGCCTATAAATAGTTATGGTCTTCACTTCAACAAGAACAACAGTCATCTACAGATTTCTCTTC
131 AGGGCCTATAAATAGTTATGGTCTTCACTTCAACAAGAACAACAATCATCTACAGAATTCTCTTC
2204 TGTT
196 TGTT
2208 CT
1 CT
2210 CCTCACCACT
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 195 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (199 bp):
CTAAAAGCAATGGAAATTCAAAAGGATCAAAAGCAAGCTTGTTCATATACCCGATTCTAAAGATG
CTATGGCAGAGTTGGTGAAGCTTGTAGCGGGAATCGTGGCGGCAAATGGCATTATCCCACAGCAA
AGGGCCTATAAATAGTTATGGTCTTCACTTCAACAAGAACAACAATCATCTACAGAATTCTCTTC
TGTT
Found at i:6802 original size:23 final size:23
Alignment explanation
Indices: 6776--6846 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
6766 TCTGTTCACG
*
6776 AACAACATTACAATCACTAAACA
1 AACAACATTACAATCAGTAAACA
* * ** *
6799 AACAA-A-CA-AATCTGTTCACG
1 AACAACATTACAATCAGTAAACA
6819 AACAACATTACAATCAGTAAACA
1 AACAACATTACAATCAGTAAACA
6842 AACAA
1 AACAA
6847 ACAAACGATC
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
20 12 0.35
21 2 0.06
22 2 0.06
23 18 0.53
ACGTcount: A:0.55, C:0.24, G:0.04, T:0.17
Consensus pattern (23 bp):
AACAACATTACAATCAGTAAACA
Found at i:6818 original size:43 final size:43
Alignment explanation
Indices: 6766--6851 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
6756 ACTAATTGAG
6766 TCTGTTCACGAACAACATTACAATCACTAAACAAACAAACAAA
1 TCTGTTCACGAACAACATTACAATCACTAAACAAACAAACAAA
*
6809 TCTGTTCACGAACAACATTACAATCAGTAAACAAACAAACAAA
1 TCTGTTCACGAACAACATTACAATCACTAAACAAACAAACAAA
6852 CGATCACCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.19
Consensus pattern (43 bp):
TCTGTTCACGAACAACATTACAATCACTAAACAAACAAACAAA
Found at i:6896 original size:17 final size:17
Alignment explanation
Indices: 6874--6927 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
6864 AAAGAAATAA
6874 ACAGTTCATGAACACCT
1 ACAGTTCATGAACACCT
**
6891 ACAGTTC-T-AA-AATT
1 ACAGTTCATGAACACCT
6905 A-AGTTCATGAACACCT
1 ACAGTTCATGAACACCT
6921 ACAGTTC
1 ACAGTTC
6928 TAAAATTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 4 0.14
16 4 0.14
17 12 0.41
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (17 bp):
ACAGTTCATGAACACCT
Found at i:6910 original size:30 final size:30
Alignment explanation
Indices: 6876--6936 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6866 AGAAATAAAC
6876 AGTTCATGAACACCTACAGTTCTAAAATTA
1 AGTTCATGAACACCTACAGTTCTAAAATTA
6906 AGTTCATGAACACCTACAGTTCTAAAATTA
1 AGTTCATGAACACCTACAGTTCTAAAATTA
6936 A
1 A
6937 CATCTGCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (30 bp):
AGTTCATGAACACCTACAGTTCTAAAATTA
Found at i:11108 original size:55 final size:55
Alignment explanation
Indices: 11026--11133 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
11016 CTTTTTGGCT
*
11026 TTTTTTTTTCCGTTCTCTGGGTTTTGTTTGTAACCCTTGATCATTGTTATGTCGC
1 TTTTTTTTCCCGTTCTCTGGGTTTTGTTTGTAACCCTTGATCATTGTTATGTCGC
*
11081 TTTTTTTTCCCGTTCTTTGGGTTTTGTTTGTAACCCTTGATCATTGTTATGTC
1 TTTTTTTTCCCGTTCTCTGGGTTTTGTTTGTAACCCTTGATCATTGTTATGTC
11134 ACTTCTTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.56
Consensus pattern (55 bp):
TTTTTTTTCCCGTTCTCTGGGTTTTGTTTGTAACCCTTGATCATTGTTATGTCGC
Found at i:11187 original size:28 final size:28
Alignment explanation
Indices: 11147--11202 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11137 TCTTCTTATG
* *
11147 TGCTTCTTTTTTGTTTTCCCAGGTTGAT
1 TGCTTCTTCTTTGCTTTCCCAGGTTGAT
* *
11175 TGCTTCTTCTTTGCTTTGCCGGGTTGAT
1 TGCTTCTTCTTTGCTTTCCCAGGTTGAT
11203 CATGGCAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.05, C:0.20, G:0.21, T:0.54
Consensus pattern (28 bp):
TGCTTCTTCTTTGCTTTCCCAGGTTGAT
Found at i:12563 original size:29 final size:30
Alignment explanation
Indices: 12505--12572 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
12495 ATGCACAAAT
*
12505 CTGCAGAAACTTGAACAAGTTGTAGAAAAA
1 CTGCAGAAACTTGAACAAGTTGCAGAAAAA
*
12535 -TGCAGAAACATT-AACGAAG-TGCAGTAAAA
1 CTGCAGAAAC-TTGAAC-AAGTTGCAGAAAAA
*
12564 CTGTAGAAA
1 CTGCAGAAA
12573 ACATATATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (30 bp):
CTGCAGAAACTTGAACAAGTTGCAGAAAAA
Found at i:15741 original size:25 final size:25
Alignment explanation
Indices: 15713--15761 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
15703 GGTAGAATAG
*
15713 GCATTGGAGGCAAAGGTGCCAATTT
1 GCATTGGAGGAAAAGGTGCCAATTT
*
15738 GCATTGGCGGAAAAGGTGCCAATT
1 GCATTGGAGGAAAAGGTGCCAATT
15762 GTTGATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (25 bp):
GCATTGGAGGAAAAGGTGCCAATTT
Found at i:16558 original size:25 final size:26
Alignment explanation
Indices: 16527--16579 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
16517 GGCTTGCCTG
16527 GCGCGGCCCAAACG-ATAGGCCAGGC
1 GCGCGGCCCAAACGCATAGGCCAGGC
* *
16552 GCGCGGCCCAAGCGCCTAGGCCAGGC
1 GCGCGGCCCAAACGCATAGGCCAGGC
16578 GC
1 GC
16580 ACGGGCCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.19, C:0.40, G:0.38, T:0.04
Consensus pattern (26 bp):
GCGCGGCCCAAACGCATAGGCCAGGC
Found at i:22034 original size:3 final size:3
Alignment explanation
Indices: 22026--22087 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
22016 GGTGTCCGGC
22026 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
22074 AAA AAG AAA AAG AA
1 AAG AAG AAG AAG AA
22088 AGTTTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22158 original size:24 final size:25
Alignment explanation
Indices: 22118--22168 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
22108 AAATGGGCTG
*
22118 GCCAGGCGCAGGCCCAG-GCTGCCA
1 GCCAGGCGCAGGCCCAGCGCGGCCA
*
22142 GCCAGGACGC-GGGCCAGCGCGGCCA
1 GCCAGG-CGCAGGCCCAGCGCGGCCA
22167 GC
1 GC
22169 GTGCTAGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.16, C:0.41, G:0.41, T:0.02
Consensus pattern (25 bp):
GCCAGGCGCAGGCCCAGCGCGGCCA
Found at i:22282 original size:19 final size:18
Alignment explanation
Indices: 22249--22292 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
22239 AATACAATAG
22249 AAAGAAAAAAAAAGAAAGA
1 AAAGAAAAAAAAAGAAA-A
** *
22268 AAAGAAAAAGGAAGAGAA
1 AAAGAAAAAAAAAGAAAA
22286 AAAGAAA
1 AAAGAAA
22293 GGGAAACAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAAAA
Found at i:25928 original size:27 final size:29
Alignment explanation
Indices: 25877--25947 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 29
25867 TTTCCTAATT
*
25877 TGTTTATGGGTTTT-TCAATTTGATGATG
1 TGTTTATAGGTTTTCTCAATTTGATGATG
25905 T-TTT-TAGGTTTTCTCAATTTGATGATG
1 TGTTTATAGGTTTTCTCAATTTGATGATG
*
25932 TGTTTATGGGTTTTCT
1 TGTTTATAGGTTTTCT
25948 TTCTTCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 7 0.18
27 18 0.47
28 4 0.11
29 9 0.24
ACGTcount: A:0.15, C:0.06, G:0.23, T:0.56
Consensus pattern (29 bp):
TGTTTATAGGTTTTCTCAATTTGATGATG
Found at i:26342 original size:14 final size:15
Alignment explanation
Indices: 26311--26343 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26301 TAAAGGCTAG
*
26311 AGAATTCAAAGGTCA
1 AGAATTCAAAGATCA
26326 AGAATTCAAA-ATCA
1 AGAATTCAAAGATCA
26340 AGAA
1 AGAA
26344 GGTGAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (15 bp):
AGAATTCAAAGATCA
Found at i:30356 original size:21 final size:22
Alignment explanation
Indices: 30331--30378 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
30321 ATGATATACC
30331 TTTTTGA-ATAATCACTGTAAT
1 TTTTTGATATAATCACTGTAAT
* * *
30352 TTTTTTATGTAATCACTGTATT
1 TTTTTGATATAATCACTGTAAT
30374 TTTTT
1 TTTTT
30379 TTATAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTTTGATATAATCACTGTAAT
Found at i:30357 original size:22 final size:22
Alignment explanation
Indices: 30338--30384 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
30328 ACCTTTTTGA
30338 ATAATCACTGTAATTTTTTTAT
1 ATAATCACTGTAATTTTTTTAT
* *
30360 GTAATCACTGT-ATTTTTTTTT
1 ATAATCACTGTAATTTTTTTAT
30381 ATAA
1 ATAA
30385 CTTTAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (22 bp):
ATAATCACTGTAATTTTTTTAT
Found at i:32886 original size:32 final size:32
Alignment explanation
Indices: 32850--32915 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
32840 ATTTTAATTC
* *
32850 ATCTTAGCCAAATTACCAAAACTAACAAAACA
1 ATCTTAACCAAATTAACAAAACTAACAAAACA
** *
32882 ATCTTAACTTAATTAACAAAATTAACAAAACA
1 ATCTTAACCAAATTAACAAAACTAACAAAACA
32914 AT
1 AT
32916 AAAAAAGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.55, C:0.20, G:0.02, T:0.24
Consensus pattern (32 bp):
ATCTTAACCAAATTAACAAAACTAACAAAACA
Found at i:33492 original size:18 final size:18
Alignment explanation
Indices: 33469--33507 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
33459 TTATGTTGGC
*
33469 CTTCATCTTCGTCTTCAT
1 CTTCATCTTCGACTTCAT
*
33487 CTTCATCTTGGACTTCAT
1 CTTCATCTTCGACTTCAT
33505 CTT
1 CTT
33508 TCAAGATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.31, G:0.08, T:0.49
Consensus pattern (18 bp):
CTTCATCTTCGACTTCAT
Found at i:36134 original size:22 final size:23
Alignment explanation
Indices: 36108--36160 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
36098 AAAATGATAT
36108 ACCTTTTTGA-ATAATCACTGTA
1 ACCTTTTTGATATAATCACTGTA
* * *
36130 ACCTTTTTTATGTAATCAGTGTA
1 ACCTTTTTGATATAATCACTGTA
*
36153 ACTTTTTT
1 ACCTTTTT
36161 TATAACTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (23 bp):
ACCTTTTTGATATAATCACTGTA
Found at i:36145 original size:23 final size:23
Alignment explanation
Indices: 36119--36163 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
36109 CCTTTTTGAA
36119 TAATCACTGTAACCTTTTTTATG
1 TAATCACTGTAACCTTTTTTATG
* *
36142 TAATCAGTGTAACTTTTTTTAT
1 TAATCACTGTAACCTTTTTTAT
36164 AACTTTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
TAATCACTGTAACCTTTTTTATG
Found at i:37050 original size:3 final size:3
Alignment explanation
Indices: 37042--37087 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
37032 ATATCGGTGG
*
37042 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC TTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
37088 GGTGGCTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:37245 original size:32 final size:32
Alignment explanation
Indices: 37209--37274 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
37199 ATTTTAATTC
* *
37209 ATCTTAGCCCAATTACCAAAACTAACAAAACA
1 ATCTTAACCCAATTAACAAAACTAACAAAACA
* *
37241 ATCTTAACTCAATTAACAAAATTAACAAAACA
1 ATCTTAACCCAATTAACAAAACTAACAAAACA
37273 AT
1 AT
37275 AAAAAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.23
Consensus pattern (32 bp):
ATCTTAACCCAATTAACAAAACTAACAAAACA
Found at i:38570 original size:6 final size:6
Alignment explanation
Indices: 38559--38583 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38549 GCTACAAAAC
38559 CGTCCT CGTCCT CGTCCT CGTCCT C
1 CGTCCT CGTCCT CGTCCT CGTCCT C
38584 CTCAACCTCA
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:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CGTCCT
Found at i:40472 original size:22 final size:23
Alignment explanation
Indices: 40447--40499 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40437 AAAATGATAT
40447 ACCTTTTTGA-ATAATCAATGTA
1 ACCTTTTTGATATAATCAATGTA
* * *
40469 ACCTTTTTTATGTAATCAGTGTA
1 ACCTTTTTGATATAATCAATGTA
*
40492 ACTTTTTT
1 ACCTTTTT
40500 TATAACTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (23 bp):
ACCTTTTTGATATAATCAATGTA
Found at i:40484 original size:23 final size:23
Alignment explanation
Indices: 40458--40502 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40448 CCTTTTTGAA
40458 TAATCAATGTAACCTTTTTTATG
1 TAATCAATGTAACCTTTTTTATG
* *
40481 TAATCAGTGTAACTTTTTTTAT
1 TAATCAATGTAACCTTTTTTAT
40503 AACTTTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (23 bp):
TAATCAATGTAACCTTTTTTATG
Found at i:41390 original size:3 final size:3
Alignment explanation
Indices: 41382--41417 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
41372 ATATCGGTGG
*
41382 CTC CTC CTC CTC CTC TTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
41418 TGGCTTGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
CTC
Found at i:41573 original size:32 final size:32
Alignment explanation
Indices: 41537--41602 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
41527 ATTTTAATTC
* *
41537 ATCTTAGCCCAATTACCAAAACTAACAAAACA
1 ATCTTAACCCAATTAACAAAACTAACAAAACA
*
41569 ATCTTAACTCAATTAACAAAACTAACAAAACA
1 ATCTTAACCCAATTAACAAAACTAACAAAACA
41601 AT
1 AT
41603 AAAAAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.53, C:0.24, G:0.02, T:0.21
Consensus pattern (32 bp):
ATCTTAACCCAATTAACAAAACTAACAAAACA
Found at i:43145 original size:88 final size:88
Alignment explanation
Indices: 42913--43267 Score: 556
Period size: 88 Copynumber: 4.0 Consensus size: 88
42903 CTATGCTGTA
* * * **
42913 GGCATGAGG-TTTTTAAATCGGGTGATGGAGAATTAGTGTGCAGGTATTGAAGTTTAGGTCCAAA
1 GGCATG-GGATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAA
42977 TGGAGAAAGGAAT-AAA-ATGTAGCGCG
65 TGGAGAAAGGAATAAAACAT-TA---CG
*
43003 GGCATGGGGTTTTTAAATT-AGGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAA
1 GGCATGGGATTTTTAAATTGA-GTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAA
43067 TGGAGAAAGGAATAAAACATTACG
65 TGGAGAAAGGAATAAAACATTACG
43091 GGCATGGGATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAAT
1 GGCATGGGATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAAT
43156 GGAGAAAGGAATAAAACATTACG
66 GGAGAAAGGAATAAAACATTACG
*
43179 GGCATGGAATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAAT
1 GGCATGGGATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAAT
*
43244 GGAGAAAGGAATAAAGCATTACG
66 GGAGAAAGGAATAAAACATTACG
43267 G
1 G
43268 AATGGAATAT
Statistics
Matches: 252, Mismatches: 8, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
88 174 0.69
89 3 0.01
90 68 0.27
91 5 0.02
92 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.31, T:0.26
Consensus pattern (88 bp):
GGCATGGGATTTTTAAATTGAGTAATGGAGAATTAGTGTGCAGGTATTGAAGTAGAGGTCCAAAT
GGAGAAAGGAATAAAACATTACG
Found at i:56645 original size:43 final size:43
Alignment explanation
Indices: 56584--56670 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
56574 AGTATTGCAC
56584 GCGCTTCGCCGCGTGTGTTGTTTGATTAAGGATTTGAATTTGA
1 GCGCTTCGCCGCGTGTGTTGTTTGATTAAGGATTTGAATTTGA
56627 GCGCTTCGCCGCGTGTGTTGTTTGATTAAGGATTTGAATTTGA
1 GCGCTTCGCCGCGTGTGTTGTTTGATTAAGGATTTGAATTTGA
56670 G
1 G
56671 ATATCTTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.39
Consensus pattern (43 bp):
GCGCTTCGCCGCGTGTGTTGTTTGATTAAGGATTTGAATTTGA
Found at i:57074 original size:33 final size:33
Alignment explanation
Indices: 57027--57110 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
57017 TAGGCGCGGA
* * *
57027 GCTGT-CCTGGAGGACGGCCCACCATGGTGGGT
1 GCTGTCCCAGGAGGACGGCACACCACGGTGGGT
*
57059 GCTGTCCCAGGAGGACGGCACACCACGGTGTGT
1 GCTGTCCCAGGAGGACGGCACACCACGGTGGGT
*
57092 GAC-GTCCCCGGAGGACGGC
1 G-CTGTCCCAGGAGGACGGC
57111 TCCGTGCCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.11
33 39 0.87
34 1 0.02
ACGTcount: A:0.15, C:0.31, G:0.39, T:0.14
Consensus pattern (33 bp):
GCTGTCCCAGGAGGACGGCACACCACGGTGGGT
Found at i:57832 original size:2 final size:2
Alignment explanation
Indices: 57825--57849 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57815 AAATGTGTAT
57825 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 T
57850 GTCTTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58137 original size:7 final size:7
Alignment explanation
Indices: 58095--58128 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
58085 ATATATATTT
58095 ATAATAGA
1 ATAA-AGA
*
58103 AAAAAGA
1 ATAAAGA
58110 ATAAAGA
1 ATAAAGA
58117 ATAAAGA
1 ATAAAGA
58124 ATAAA
1 ATAAA
58129 TAAATAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.88
8 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
ATAAAGA
Found at i:64197 original size:25 final size:24
Alignment explanation
Indices: 64169--64230 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
64159 GTGGATTGTA
*
64169 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
64194 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
64218 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
64231 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:65467 original size:46 final size:46
Alignment explanation
Indices: 65400--65493 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
65390 CTAGTGTCCA
65400 GGGCAAATACTAATCCAGATCCGACCCGCGTCGCGCACCTGGTTAT
1 GGGCAAATACTAATCCAGATCCGACCCGCGTCGCGCACCTGGTTAT
* *
65446 GGGCAAATACTAATCCGGATCCGACCCGCGTCGTGCACCTGGTTAT
1 GGGCAAATACTAATCCAGATCCGACCCGCGTCGCGCACCTGGTTAT
65492 GG
1 GG
65494 TGGGTGAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (46 bp):
GGGCAAATACTAATCCAGATCCGACCCGCGTCGCGCACCTGGTTAT
Found at i:75231 original size:22 final size:20
Alignment explanation
Indices: 75203--75350 Score: 100
Period size: 22 Copynumber: 7.0 Consensus size: 20
75193 GTCTCTATGT
75203 GGTTATCAAAATTTCATAACGA
1 GGTTATCAAAATTTCAT-A-GA
*
75225 GGTTATCACACAATATCATAGTA
1 GGTTATCA-A-AATTTCATAG-A
* *
75248 TGGTTGTCAAAATTTCATAGTGT
1 -GGTTATCAAAATTTCATA--GA
* *
75271 GGTTACCATAATTTCATAGGAA
1 GGTTATCAAAATTTCATA-G-A
* * *
75293 AGTTATCAAAATTTTATAGT
1 GGTTATCAAAATTTCATAGA
* *
75313 TGTTACCAAAATTTCATAG-
1 GGTTATCAAAATTTCATAGA
*
75332 GGGTATCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
75351 GGAGATTTAG
Statistics
Matches: 99, Mismatches: 20, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
19 16 0.16
20 16 0.16
21 2 0.02
22 46 0.46
23 4 0.04
24 15 0.15
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (20 bp):
GGTTATCAAAATTTCATAGA
Found at i:75303 original size:44 final size:42
Alignment explanation
Indices: 75204--75350 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 42
75194 TCTCTATGTG
** * * * *
75204 GTTATCAAAATTTCATAACGAGGTTATCACACAATATCATAGTA
1 GTTATCAAAATTTCATAGTGTGGTTA-C-CAAAATTTCATAGGA
* *
75248 TGGTTGTCAAAATTTCATAGTGTGGTTACCATAATTTCATAGGAAA
1 --GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGG--A
*
75294 GTTATCAAAATTTTATAGT-T-GTTACCAAAATTTCATAGG-
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
*
75333 GGTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
75351 GGAGATTTAG
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
39 16 0.18
42 18 0.21
43 1 0.01
44 28 0.32
45 1 0.01
46 23 0.26
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (42 bp):
GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
Found at i:75470 original size:28 final size:28
Alignment explanation
Indices: 75438--75510 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
75428 TGAGATATAA
75438 GAAACCGATCACCGACCGAGACATAGAT
1 GAAACCGATCACCGACCGAGACATAGAT
75466 GAAACCGATCACCGACCGAGACATAGAT
1 GAAACCGATCACCGACCGAGACATAGAT
75494 GAAACCGAT-ACC-ACCGA
1 GAAACCGATCACCGACCGA
75511 TGGCGTCCGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.11
27 3 0.07
28 37 0.82
ACGTcount: A:0.40, C:0.30, G:0.21, T:0.10
Consensus pattern (28 bp):
GAAACCGATCACCGACCGAGACATAGAT
Found at i:76742 original size:22 final size:22
Alignment explanation
Indices: 76561--76819 Score: 114
Period size: 22 Copynumber: 11.7 Consensus size: 22
76551 GTCGGTGAGA
* *
76561 TATCAAAATTTCATAGTGCGGT
1 TATCAAAATTTCATAGTGTGAT
* * * *
76583 TACCAAAATTTTATAG-GAAGGT
1 TATCAAAATTTCATAGTG-TGAT
* * * *
76605 TATCAAAATTTTAAAGAGTGGT
1 TATCAAAATTTCATAGTGTGAT
* * * *
76627 TATTAAAATTTCATCGGGATCGGGT
1 TATCAAAATTTCATAGTG-T--GAT
* * *** *
76652 TATTAAAATTTTATAGAAAGGT
1 TATCAAAATTTCATAGTGTGAT
***
76674 TATCAAAATTTCATAAG-AACAT
1 TATCAAAATTTCAT-AGTGTGAT
* *
76696 TATCAAAATTTCATA-TCGAGGT
1 TATCAAAATTTCATAGT-GTGAT
*
76718 TATCAGAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
* *
76740 TATCAAAATTTTACAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
76762 TATCAAAATTTCATAGAG-G-T
1 TATCAAAATTTCATAGTGTGAT
* ** * *
76782 TGTTGAAATTTCACAGTGTGGT
1 TATCAAAATTTCATAGTGTGAT
*
76804 TATCATAATTTCATAG
1 TATCAAAATTTCATAG
76820 AGAGAATAAC
Statistics
Matches: 184, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
20 14 0.08
21 4 0.02
22 144 0.78
23 5 0.03
25 17 0.09
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:76833 original size:64 final size:65
Alignment explanation
Indices: 76671--76840 Score: 168
Period size: 64 Copynumber: 2.6 Consensus size: 65
76661 TTTATAGAAA
*
76671 GGTTATCAAAATTTCATA-AGA-ACATTATCAAAATTTCATATCGAGGTTATCAGAATTTCATAG
1 GGTTATCAAAATTTCATAGAGAGA-A-TATCAAAATTTCATA-CGAGGTTATCAGAATTTCACAG
76734 TGT
63 TGT
* * * * * * * *
76737 GATTATCAAAATTTTACAGTGTGATTATCAAAATTTCATA-GAGGTTGT-TGAAATTTCACAGTG
1 GGTTATCAAAATTTCATAGAGAGAATATCAAAATTTCATACGAGGTTATCAG-AATTTCACAGTG
76800 T
65 T
* * *
76801 GGTTATCATAATTTCATAGAGAGAATAACAAAATATCATA
1 GGTTATCAAAATTTCATAGAGAGAATATCAAAATTTCATA
76841 ATATCATAGG
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
63 1 0.01
64 50 0.60
66 30 0.36
67 1 0.01
68 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (65 bp):
GGTTATCAAAATTTCATAGAGAGAATATCAAAATTTCATACGAGGTTATCAGAATTTCACAGTGT
Found at i:76907 original size:22 final size:21
Alignment explanation
Indices: 76855--76910 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
76845 CATAGGAAGG
*
76855 TTATCAAAATTTCATAAGGAG
1 TTATCAAAATTTCATAAGGAA
* *
76876 TTATCGAAATTTCAT-AGTATAA
1 TTATCAAAATTTCATAAG--GAA
76898 TTATCAAAATTTC
1 TTATCAAAATTTC
76911 TTATTGTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 14 0.48
22 13 0.45
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAAGGAA
Found at i:76985 original size:22 final size:22
Alignment explanation
Indices: 76935--77082 Score: 154
Period size: 22 Copynumber: 6.7 Consensus size: 22
76925 CAAAGAGATG
* *
76935 TATCAAAATTTCATAGTGTA-AT
1 TATCAAAATTTCATAG-GGAGGT
* *
76957 TACCAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGGAGGT
* * *
76979 TATCAAAATTTTATTGTGAGGT
1 TATCAAAATTTCATAGGGAGGT
* *
77001 AATCTAAATTTCATAGGGAGGT
1 TATCAAAATTTCATAGGGAGGT
* *
77023 TTTCAAAATTTTATAGGGAGGT
1 TATCAAAATTTCATAGGGAGGT
* *
77045 TATCGAAATTTCATAGGGACGT
1 TATCAAAATTTCATAGGGAGGT
*
77067 TATCGAAATTTCATAG
1 TATCAAAATTTCATAG
77083 TGCAGTTTTC
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
21 2 0.02
22 102 0.98
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGGAGGT
Found at i:77046 original size:66 final size:66
Alignment explanation
Indices: 76940--77095 Score: 170
Period size: 66 Copynumber: 2.4 Consensus size: 66
76930 AGATGTATCA
* * ** * * * *
76940 AAATTTCATAGTGTAATTACCAAAATTTCATAGGAAGGTTATCAAAATTTTATTGTGAGGTAATC
1 AAATTTCATAGTGCAGTTTTCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGGACGTAATC
*
77005 T
66 G
* * * * *
77006 AAATTTCATAG-GGAGGTTTTCAAAATTTTATAGGGAGGTTATCGAAATTTCATAGGGACGTTAT
1 AAATTTCATAGTGCA-GTTTTCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGGACGTAAT
77070 CG
65 CG
77072 AAATTTCATAGTGCAGTTTTCAAA
1 AAATTTCATAGTGCAGTTTTCAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
65 2 0.03
66 70 0.95
67 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (66 bp):
AAATTTCATAGTGCAGTTTTCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGGACGTAATC
G
Done.