Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008860.1 Corchorus capsularis cultivar CVL-1 contig08881, 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: 94780
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10208 original size:59 final size:59
Alignment explanation
Indices: 10116--10239 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 59
10106 TGGACTGAGT
*
10116 TTTATGAGTATGTGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCTAAG
1 TTTATGAGTATGTGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAG
10175 TTTATGAGTATGTGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAG
1 TTTATGAGTATGTGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAG
10234 TTTATG
1 TTTATG
10240 GATGATATGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (59 bp):
TTTATGAGTATGTGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAG
Found at i:10248 original size:51 final size:51
Alignment explanation
Indices: 10187--10291 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
10177 TATGAGTATG
10187 TGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAGTTTA
1 TGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAGTTTA
* *
10238 TGGATGATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCTAAGTTTA
1 TGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAGTTTA
10289 TGG
1 TGG
10292 CTTGTGACAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (51 bp):
TGGATAATATGGGTGGATGTATATGGAAATTGCTATTGGAAGCCAAGTTTA
Found at i:24329 original size:14 final size:14
Alignment explanation
Indices: 24302--24347 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
24292 TAATGAAAAA
24302 TATC-CCTTTTCTC
1 TATCTCCTTTTCTC
24315 TATCT-CTTGTTCTC
1 TATCTCCTT-TTCTC
*
24329 TCTCTCCTTTTCTC
1 TATCTCCTTTTCTC
24343 TATCT
1 TATCT
24348 TTTCCCTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 18 0.64
15 3 0.11
ACGTcount: A:0.07, C:0.35, G:0.02, T:0.57
Consensus pattern (14 bp):
TATCTCCTTTTCTC
Found at i:29143 original size:14 final size:14
Alignment explanation
Indices: 29116--29161 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
29106 TAATGAAAAA
29116 TATC-CCTTTTCTC
1 TATCTCCTTTTCTC
29129 TATCT-CTTGTTCTC
1 TATCTCCTT-TTCTC
*
29143 TCTCTCCTTTTCTC
1 TATCTCCTTTTCTC
29157 TATCT
1 TATCT
29162 GTTCCCTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 18 0.64
15 3 0.11
ACGTcount: A:0.07, C:0.35, G:0.02, T:0.57
Consensus pattern (14 bp):
TATCTCCTTTTCTC
Found at i:29685 original size:166 final size:166
Alignment explanation
Indices: 29402--29714 Score: 468
Period size: 166 Copynumber: 1.9 Consensus size: 166
29392 AACATATGAA
* * *
29402 AATTACTAAAAAATCCCTATCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTC
1 AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATCTTTTTCGTCTTTAC
* *
29467 ACACTTGACCGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGTGATTAAATAACTAAACTTT
66 ACACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTAAACTTT
*
29532 TTGGTCATTTCTCAATTAACTTTAATAAAGTAGTGG
131 TTGATCATTTCTCAATTAACTTTAATAAAGTAGTGG
* * * *
29568 AATTACTAAAAGATTCCTACCCCGGATTAATGATGAGCTG-GAGAAGTAATCTTTTTCGTCTTTA
1 AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGC-GAGAGAACTAATCTTTTTCGTCTTTA
* * * *
29632 C-CTACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATATCTAAACT
65 CAC-ACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTAAACT
29696 TTTTGATCATTTCTCAATT
129 TTTTGATCATTTCTCAATT
29715 GACAAATGAC
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
165 1 0.01
166 129 0.98
167 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (166 bp):
AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATCTTTTTCGTCTTTAC
ACACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTAAACTTT
TTGATCATTTCTCAATTAACTTTAATAAAGTAGTGG
Found at i:30036 original size:29 final size:29
Alignment explanation
Indices: 30004--30062 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
29994 AATATATATA
*
30004 TATATATATATATAAATGAA-GAATTAGTT
1 TATATATATAT-TAAATAAATGAATTAGTT
*
30033 TATATATATATTATATAAATGAATTAGTT
1 TATATATATATTAAATAAATGAATTAGTT
30062 T
1 T
30063 CAAATTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (29 bp):
TATATATATATTAAATAAATGAATTAGTT
Found at i:30071 original size:29 final size:31
Alignment explanation
Indices: 30003--30071 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 31
29993 GAATATATAT
*
30003 ATATATATATATATAAATGAAGAATTAGTTTAT
1 ATATATATATATATAAAT--AGAATTAGTTTAA
30036 ATATATAT-TATATAAAT-GAATTAGTTTCAA
1 ATATATATATATATAAATAGAATTAGTTT-AA
30066 AT-TATA
1 ATATATA
30072 CCAACTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 14 0.41
30 3 0.09
32 9 0.26
33 8 0.24
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (31 bp):
ATATATATATATATAAATAGAATTAGTTTAA
Found at i:39385 original size:17 final size:16
Alignment explanation
Indices: 39331--39381 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
39321 ATCACCCCCC
*
39331 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
39348 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
39365 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
39381 A
1 A
39382 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:42813 original size:2 final size:2
Alignment explanation
Indices: 42806--42834 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42796 ATTCATTGTA
42806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42835 ATCCTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49004 original size:47 final size:48
Alignment explanation
Indices: 48933--49027 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 48
48923 TCTAACCAAC
*
48933 ACAAGTAGGGATATATATGGAAACAAAGTACCAATTACATT-TTTTTT
1 ACAAGTAGGGATATATATGAAAACAAAGTACCAATTACATTATTTTTT
*
48980 ACAAGTAGGGATATATATGAAAACAAAGTATCAATTACATTATTTTTT
1 ACAAGTAGGGATATATATGAAAACAAAGTACCAATTACATTATTTTTT
49028 GAGTGAGTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (48 bp):
ACAAGTAGGGATATATATGAAAACAAAGTACCAATTACATTATTTTTT
Found at i:53768 original size:26 final size:26
Alignment explanation
Indices: 53739--53810 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
53729 GTTTGTTTAT
53739 TTAATTGGTAGGTAGGTATTTAGATG
1 TTAATTGGTAGGTAGGTATTTAGATG
*
53765 TTAATTGGTAGATAGGTATTTAGATG
1 TTAATTGGTAGGTAGGTATTTAGATG
* *
53791 TT--TTGGTATGTAGATATTTA
1 TTAATTGGTAGGTAGGTATTTA
53811 TTCTCTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.36
26 27 0.64
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (26 bp):
TTAATTGGTAGGTAGGTATTTAGATG
Found at i:65825 original size:1 final size:1
Alignment explanation
Indices: 65819--65848 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
65809 GCTTCTTCCC
65819 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
65849 GTCTCTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66892 original size:24 final size:24
Alignment explanation
Indices: 66833--66904 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
66823 CGGGCCTTAA
*
66833 TCTATCTT-TTCTTTTTTTCCTTCC
1 TCTATCTTCTT-TTTTTTTCTTTCC
* *
66857 TCT-TCTTCTTTTTATTTCTTTTC
1 TCTATCTTCTTTTTTTTTCTTTCC
66880 TCTATCTTCTTTTTTTTTCTCTTCC
1 TCTATCTTCTTTTTTTTTCT-TTCC
66905 AGCCATACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 17 0.43
24 20 0.50
25 3 0.08
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.69
Consensus pattern (24 bp):
TCTATCTTCTTTTTTTTTCTTTCC
Found at i:66953 original size:12 final size:12
Alignment explanation
Indices: 66924--66953 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
66914 TGCCGCCATG
*
66924 ACCGCCGGAGCC
1 ACCGCTGGAGCC
66936 ACCGCTGGAGCC
1 ACCGCTGGAGCC
66948 ACCGCT
1 ACCGCT
66954 AGCCGCCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.30, T:0.07
Consensus pattern (12 bp):
ACCGCTGGAGCC
Found at i:71734 original size:31 final size:31
Alignment explanation
Indices: 71699--71757 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
71689 ATGTTTTCCG
* *
71699 ATTGTACC-TTTATTTTTAAAATATATTTTCA
1 ATTGTACCATTT-TCTTTAAAACATATTTTCA
71730 ATTGTACCATTTTCTTTAAAACATATTT
1 ATTGTACCATTTTCTTTAAAACATATTT
71758 CTAAATTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (31 bp):
ATTGTACCATTTTCTTTAAAACATATTTTCA
Found at i:72100 original size:19 final size:21
Alignment explanation
Indices: 72068--72110 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
72058 TTCTTTACTA
72068 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
72089 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
72108 TTA
1 TTA
72111 AATTTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:72532 original size:22 final size:22
Alignment explanation
Indices: 72503--72668 Score: 108
Period size: 22 Copynumber: 7.5 Consensus size: 22
72493 TTCTTGTCTC
72503 TAAG-TGGTTATCAAAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
72524 TAAGATGGTTATTATAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
72546 TGAGGA-GGTTATCAAAATTCCA
1 T-AAGATGGTTATCAAAATTTCA
*
72568 T-AG-TGCGGTTACCAAAATTTCA
1 TAAGAT--GGTTATCAAAATTTCA
*
72590 T-AGTATGGTTACCAAAATTTCA
1 TAAG-ATGGTTATCAAAATTTCA
* * * *
72612 TAGGATCAGGTTATTAAAATCTCT
1 TAAGAT--GGTTATCAAAATTTCA
* **
72636 TAAGTTGGTTATTGAAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
72658 TAGGGTGGTTA
1 TAAGATGGTTA
72669 ATTATCACAA
Statistics
Matches: 114, Mismatches: 21, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 88 0.77
23 4 0.04
24 17 0.15
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (22 bp):
TAAGATGGTTATCAAAATTTCA
Found at i:72763 original size:22 final size:23
Alignment explanation
Indices: 72704--72764 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
72694 ATCAAAGAGA
*
72704 TTAT-CAAAATGTCATAGCGAGG
1 TTATACAAAATTTCATAGCGAGG
* * *
72726 TTATATAAGAATTTCATAGTGTGG
1 TTATACAA-AATTTCATAGCGAGG
72750 TTA-ACAAAATTTCAT
1 TTATACAAAATTTCAT
72765 TAAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (23 bp):
TTATACAAAATTTCATAGCGAGG
Found at i:72829 original size:22 final size:22
Alignment explanation
Indices: 72780--73087 Score: 115
Period size: 22 Copynumber: 13.8 Consensus size: 22
72770 ATTTAATGGG
* *
72780 GAGGTCATCAAAATTTTATAGT
1 GAGGTTATCAAAATTTCATAGT
*
72802 GTGGTTATCAAAATTTCATA-T
1 GAGGTTATCAAAATTTCATAGT
* *
72823 GAAGGTTATAAAAGTCTCAATTTCATAGG
1 G-AGGTTAT-CAA-----AATTTCATAGT
* *
72852 GA-G-TACCAAAATTTGATAG-
1 GAGGTTATCAAAATTTCATAGT
* * * *
72871 AAGGTTAT-GAAATCTCATAGA
1 GAGGTTATCAAAATTTCATAGT
* * * *
72892 GTGATTATCGAAATTTCATAGA
1 GAGGTTATCAAAATTTCATAGT
* *
72914 GATCGAATTATCAAAATTT-ATAGA
1 GA--G-GTTATCAAAATTTCATAGT
* *
72938 AAGATTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
** * *
72960 GTTGTTATCAAAATTTCAAAGC
1 GAGGTTATCAAAATTTCATAGT
* * *
72982 GAGGTTATCAAGATTACATAAT
1 GAGGTTATCAAAATTTCATAGT
* * * * *
73004 GTGATTATCAGAATTTAATAGA
1 GAGGTTATCAAAATTTCATAGT
* * * * * **
73026 GGGGTCAACACAATTTTATAAA
1 GAGGTTATCAAAATTTCATAGT
**
73048 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGT
*
73070 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
73088 AAATGTGATT
Statistics
Matches: 214, Mismatches: 56, Indels: 32
0.71 0.19 0.11
Matches are distributed among these distances:
19 1 0.00
20 19 0.09
21 22 0.10
22 135 0.63
23 2 0.01
24 7 0.03
25 14 0.07
26 2 0.01
27 1 0.00
28 10 0.05
29 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:73215 original size:19 final size:19
Alignment explanation
Indices: 73185--73232 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
73175 TTATGGAGTA
73185 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
73205 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
73224 ATCAAAATT
1 ATCAAAATT
73233 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:73251 original size:22 final size:22
Alignment explanation
Indices: 73223--73760 Score: 138
Period size: 22 Copynumber: 24.7 Consensus size: 22
73213 TCAGGGAGGA
73223 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
73245 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
73267 TTTCAAAATTTCACAAG-AGGAT
1 TATCAAAATTTCATATGAAGG-T
*
73289 TATCAAAATTTCATA-GTACTATGT
1 TATCAAAATTTCATATG-A--AGGT
* * * *
73313 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
73336 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
73358 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
73380 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
73396 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
73418 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
* *
73441 TATCAAAATTTCATA-GCGAGTT
1 TATCAAAATTTCATATG-AAGGT
* *
73463 TATCACAATTT-AGTGTG-A--T
1 TATCAAAATTTCA-TATGAAGGT
* * *
73482 TATCAAAATTTCAGA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
*
73504 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
73526 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
73548 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
73570 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
73593 CATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
73615 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
73637 CT-TCAAAATTCCTTAGGGAA-GT
1 -TATCAAAATTTCATA-TGAAGGT
* * *
73659 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
73681 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
73702 TCTCGAAATTCCATA-GAATCGT
1 TATCAAAATTTCATATGAA-GGT
* * * * *
73724 TGTTAAAATTTTATAGGAATGT
1 TATCAAAATTTCATATGAAGGT
73746 TATCAAAATTTCATA
1 TATCAAAATTTCATA
73761 ATGGGATCAT
Statistics
Matches: 377, Mismatches: 93, Indels: 92
0.67 0.17 0.16
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 3 0.01
19 11 0.03
20 4 0.01
21 35 0.09
22 243 0.64
23 51 0.14
24 2 0.01
25 16 0.04
26 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:73278 original size:44 final size:43
Alignment explanation
Indices: 73223--73455 Score: 172
Period size: 44 Copynumber: 5.3 Consensus size: 43
73213 TCAGGGAGGA
*
73223 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAG-TTAGT
* *
73267 TTTCAAAATTTCACAAG-AGGATTATCAAAATTTCATAGTACTATGT
1 TATCAAAATTTCATAAGAAGG-TTATCAAAATTTCATAGT--TA-GT
* * * * * * *
73313 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGAT
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAG-T
** * *
73358 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGT
* * * **
73396 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAG--T
73441 TATCAAAATTTCATA
1 TATCAAAATTTCATA
73456 GCGAGTTTAT
Statistics
Matches: 149, Mismatches: 26, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
38 25 0.17
39 4 0.03
41 2 0.01
42 1 0.01
43 8 0.05
44 57 0.38
45 19 0.13
46 2 0.01
47 29 0.19
48 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGT
Found at i:74747 original size:19 final size:20
Alignment explanation
Indices: 74725--74768 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
74715 GAAAATCCCA
74725 TTCAACCCTTA-AAAATACC
1 TTCAACCCTTATAAAATACC
*
74744 TTCAACCCTTATAGAATACC
1 TTCAACCCTTATAAAATACC
74764 TTCAA
1 TTCAA
74769 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.30
Consensus pattern (20 bp):
TTCAACCCTTATAAAATACC
Found at i:75516 original size:17 final size:17
Alignment explanation
Indices: 75468--75510 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
75458 TTTGATCACC
75468 GGTGATCTTGCATCATT
1 GGTGATCTTGCATCATT
75485 GGTGATCTTGCATCATT
1 GGTGATCTTGCATCATT
75502 GGTGATCTT
1 GGTGATCTT
75511 AGATCACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (17 bp):
GGTGATCTTGCATCATT
Found at i:87144 original size:18 final size:18
Alignment explanation
Indices: 87130--87165 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
87120 GACAAAGTAC
87130 CCAGATATCACAAAGCAA
1 CCAGATATCACAAAGCAA
*
87148 CCAGATATGACAAAGCAA
1 CCAGATATCACAAAGCAA
87166 TTAACAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (18 bp):
CCAGATATCACAAAGCAA
Found at i:89496 original size:12 final size:12
Alignment explanation
Indices: 89481--89512 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
89471 TCGCATGCGA
89481 TGGCCGGTCATG
1 TGGCCGGTCATG
*
89493 TGGCTGGTCATG
1 TGGCCGGTCATG
89505 TGGCCGGT
1 TGGCCGGT
89513 GTTGCGCGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.44, T:0.28
Consensus pattern (12 bp):
TGGCCGGTCATG
Done.