Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019944.1 Corchorus olitorius cultivar O-4 contig19977, 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: 65604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9649 original size:24 final size:24
Alignment explanation
Indices: 9611--9676 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
9601 GAAAATCACA
*
9611 CGGCCACATGATGGTCGTGAGATT
1 CGGCCACATGGTGGTCGTGAGATT
*
9635 CGGTCACATGGTGGTCGTGAGATT
1 CGGCCACATGGTGGTCGTGAGATT
9659 CGGCCACATGGTGGTCGT
1 CGGCCACATGGTGGTCGT
9677 TAGAAAAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.26
Consensus pattern (24 bp):
CGGCCACATGGTGGTCGTGAGATT
Found at i:11338 original size:6 final size:6
Alignment explanation
Indices: 11324--11355 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11314 TTTGTTTCTT
*
11324 CTTTCC CTTTTC CTTTTC CTTTTC CTTTTC CT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CT
11356 CACGAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
CTTTTC
Found at i:21314 original size:11 final size:10
Alignment explanation
Indices: 21293--21345 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
21283 TGCTCGAGTA
*
21293 ATGTTCATTT
1 ATGTTCGTTT
21303 AGTGTTCGTTT
1 A-TGTTCGTTT
21314 ATTGTTCGTTT
1 A-TGTTCGTTT
*
21325 AATAGCTCGTTT
1 -AT-GTTCGTTT
21337 ATGTTCGTT
1 ATGTTCGTT
21346 AATTAAGATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.19
11 21 0.58
12 8 0.22
ACGTcount: A:0.15, C:0.11, G:0.19, T:0.55
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:21431 original size:30 final size:30
Alignment explanation
Indices: 21410--21474 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
21400 ATTTAAATTT
21410 TATTAGAAATATTTA-TTAATATGTAATAAA
1 TATTAG-AATATTTATTTAATATGTAATAAA
**
21440 TATTAGAATATTTATTTAATATACAATAAA
1 TATTAGAATATTTATTTAATATGTAATAAA
21470 TATTA
1 TATTA
21475 TTAGAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (30 bp):
TATTAGAATATTTATTTAATATGTAATAAA
Found at i:21477 original size:33 final size:32
Alignment explanation
Indices: 21403--21480 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
21393 AAATAATATT
* **
21403 TAAATTTTATTAGAAATATTTATTAATATGTAA
1 TAAATATTATTAG-AATATTTATTAATATACAA
21436 T-AA-A-TATTAGAATATTTATTTAATATACAA
1 TAAATATTATTAGAATATTTA-TTAATATACAA
21466 TAAATATTATTAGAA
1 TAAATATTATTAGAA
21481 ATAATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 8 0.21
30 16 0.42
31 2 0.05
32 3 0.08
33 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (32 bp):
TAAATATTATTAGAATATTTATTAATATACAA
Found at i:22469 original size:29 final size:29
Alignment explanation
Indices: 22437--22497 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
22427 TCAATATACA
*
22437 TTTCAAATAACAATTAATATTAGCTTTAT
1 TTTCAAACAACAATTAATATTAGCTTTAT
22466 TTTCAAACAACAATTAATATTAGCTTTAT
1 TTTCAAACAACAATTAATATTAGCTTTAT
22495 TTT
1 TTT
22498 GATGAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.46
Consensus pattern (29 bp):
TTTCAAACAACAATTAATATTAGCTTTAT
Found at i:22735 original size:23 final size:23
Alignment explanation
Indices: 22709--22753 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22699 ACTCAATTAG
* * *
22709 TGTTCATGAACACGTTCGTTTAT
1 TGTTCACGAACAAGTTCATTTAT
22732 TGTTCACGAACAAGTTCATTTA
1 TGTTCACGAACAAGTTCATTTA
22754 AACGAGCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (23 bp):
TGTTCACGAACAAGTTCATTTAT
Found at i:34931 original size:22 final size:22
Alignment explanation
Indices: 34899--34940 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34889 GAGTAAACGC
*
34899 AATGTTATTCTTATATAGTCGT
1 AATGTTATTCTCATATAGTCGT
*
34921 AATGTTTTTCTCATATAGTC
1 AATGTTATTCTCATATAGTC
34941 TCTTGCACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (22 bp):
AATGTTATTCTCATATAGTCGT
Found at i:40519 original size:24 final size:24
Alignment explanation
Indices: 40492--40539 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40482 AAATGAGAAA
40492 ATAGAAGTAAACAATAGTATTAAG
1 ATAGAAGTAAACAATAGTATTAAG
** * *
40516 ATAGTTGTAAAGATTAGTATTAAG
1 ATAGAAGTAAACAATAGTATTAAG
40540 TGTTTTCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (24 bp):
ATAGAAGTAAACAATAGTATTAAG
Found at i:40983 original size:6 final size:6
Alignment explanation
Indices: 40972--40996 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40962 CAGTGGATTC
40972 GGTTTT GGTTTT GGTTTT GGTTTT G
1 GGTTTT GGTTTT GGTTTT GGTTTT G
40997 TGGAGCATAA
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:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GGTTTT
Found at i:42200 original size:36 final size:37
Alignment explanation
Indices: 42133--42205 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
42123 TGTTTGATTA
*
42133 ATTGGGCCCGGGAAGGAAATAATGAAGCCAACTGGGT
1 ATTGGGCCCGGGAAGGAAATAATGAAGCCAACAGGGT
* *
42170 ATTGGGCCTGGGAA-GAAATAATGAATCCAACAGGGT
1 ATTGGGCCCGGGAAGGAAATAATGAAGCCAACAGGGT
42206 TCAATAACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 20 0.61
37 13 0.39
ACGTcount: A:0.34, C:0.15, G:0.33, T:0.18
Consensus pattern (37 bp):
ATTGGGCCCGGGAAGGAAATAATGAAGCCAACAGGGT
Found at i:45506 original size:63 final size:63
Alignment explanation
Indices: 45407--45532 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
45397 CTTTCCTGAA
* *
45407 CAAATGCAGATATATTATACCATCCTGAATTCTGTACCGACAAATCATCAAACTAAACACGAC
1 CAAATGCAGATATATTACACCATCCTGAATTCTGTACCGACAAATCATAAAACTAAACACGAC
* *
45470 CAAATGCAGATATATTACACCATGCTGAATTCTGTACCGACAAATCATAAAACTAAGCACGAC
1 CAAATGCAGATATATTACACCATCCTGAATTCTGTACCGACAAATCATAAAACTAAACACGAC
45533 TGAAGACACC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (63 bp):
CAAATGCAGATATATTACACCATCCTGAATTCTGTACCGACAAATCATAAAACTAAACACGAC
Found at i:52934 original size:30 final size:30
Alignment explanation
Indices: 52898--52957 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
52888 TAGTTACCCA
*
52898 AACAGAGCGAAGCGTATAGTGGCGAAAGCG
1 AACAGAGCGAAGCGTACAGTGGCGAAAGCG
52928 AACAGAGCGAAGCGTACAGTGGCGAAAGCG
1 AACAGAGCGAAGCGTACAGTGGCGAAAGCG
52958 GAAAGCAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.37, T:0.08
Consensus pattern (30 bp):
AACAGAGCGAAGCGTACAGTGGCGAAAGCG
Found at i:60442 original size:19 final size:17
Alignment explanation
Indices: 60405--60455 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
60395 TGAAATTTAT
60405 TAATTATTAAATAAATAA
1 TAATTATT-AATAAATAA
60423 TAATTATTAATCAGAATAA
1 TAATTATTAAT-A-AATAA
*
60442 TTATTATTAA-AAAT
1 TAATTATTAATAAAT
60456 TCCATCTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 9 0.30
19 14 0.47
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATTATTAATAAATAA
Found at i:63750 original size:22 final size:22
Alignment explanation
Indices: 63598--63821 Score: 113
Period size: 22 Copynumber: 10.0 Consensus size: 22
63588 TCTTATCTCT
63598 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * * *
63621 G-ATGGTTATTATAATTTCACGA
1 GTGTGGTTATCAAAATTTCA-TA
* *
63643 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
* * *
63664 ATGTGGTTACCAAAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
*
63686 -TG-GAAGTTATCAAAATTTCCT-
1 GTGTG--GTTATCAAAATTTCATA
*
63707 GTGAAGGTTATC--AATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
63728 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* * *
63750 G-GATCAAGTTATTAAAATTTCTTA
1 GTG-T--GGTTATCAAAATTTCATA
* * *
63774 GGAAGCTGGTTATTAAGATTTCATA
1 -G-TG-TGGTTATCAAAATTTCATA
* *
63799 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
63821 G
1 G
63822 AAAGGTTATC
Statistics
Matches: 151, Mismatches: 34, Indels: 33
0.69 0.16 0.15
Matches are distributed among these distances:
20 14 0.09
21 7 0.05
22 94 0.62
23 2 0.01
24 16 0.11
25 16 0.11
27 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:63759 original size:66 final size:66
Alignment explanation
Indices: 63598--63770 Score: 185
Period size: 66 Copynumber: 2.6 Consensus size: 66
63588 TCTTATCTCT
* * * * *
63598 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCACGAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAGGATAAGTTATTAAAATTTCACGAGAAGGTTATC-AAATTCCA
63662 TA
65 TA
* * * * *
63664 ATGTGGTTACCAAAATTTTATATGG--AAGTTATCAAAATTTC-CTGTGAAGGTTATC-AATTTC
1 GTGTGGTTACCAAAATTTCATA-GGATAAGTTATTAAAATTTCAC-GAGAAGGTTATCAAATTCC
63725 ATA
64 ATA
63728 GTGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGAT-AAGTTATTAAAATTTC
63771 TTAGGAAGCT
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
63 2 0.02
64 28 0.32
65 1 0.01
66 56 0.64
67 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAGGATAAGTTATTAAAATTTCACGAGAAGGTTATCAAATTCCAT
A
Found at i:63766 original size:24 final size:25
Alignment explanation
Indices: 63739--63799 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
63729 TGTGGTTACC
*
63739 AAAATTTCATAGG-ATCAAGTTATT
1 AAAATTTCATAGGAAGCAAGTTATT
* **
63763 AAAATTTCTTAGGAAGCTGGTTATT
1 AAAATTTCATAGGAAGCAAGTTATT
*
63788 AAGATTTCATAG
1 AAAATTTCATAG
63800 TGTGGTTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
AAAATTTCATAGGAAGCAAGTTATT
Found at i:63906 original size:44 final size:44
Alignment explanation
Indices: 63858--63942 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
63848 TGGCATAGCA
* *
63858 AGGTTA-TAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGG
1 AGGTTACTAA-AATTTCATAGGGAGGTTAACAAAATTTCATAAGG
* * * *
63902 AGGTTACTAACATTTCATGGGGAGTTTATCAAAATTTCATA
1 AGGTTACTAAAATTTCATAGGGAGGTTAACAAAATTTCATA
63943 TTGTGGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 31 0.91
45 3 0.09
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (44 bp):
AGGTTACTAAAATTTCATAGGGAGGTTAACAAAATTTCATAAGG
Found at i:63952 original size:22 final size:22
Alignment explanation
Indices: 63839--63956 Score: 78
Period size: 22 Copynumber: 5.4 Consensus size: 22
63829 ATCAAAGAGA
** **
63839 TTATCAAAATGGCATAGCAAGG
1 TTATCAAAATTTCATAGGGAGG
* *
63861 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGGGAGG
* *
63883 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
63905 TTA-CTAACATTTCATGGGGAGT
1 TTATC-AAAATTTCATAGGGAGG
** *
63927 TTATCAAAATTTCATATTGTGG
1 TTATCAAAATTTCATAGGGAGG
63949 TTATCAAA
1 TTATCAAA
63957 TTTTTTTAGT
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
21 3 0.04
22 67 0.92
23 3 0.04
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:64074 original size:22 final size:23
Alignment explanation
Indices: 64022--64280 Score: 113
Period size: 22 Copynumber: 11.6 Consensus size: 23
64012 TAATGAATAC
* *
64022 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
64043 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
64064 CGAAATTTCATAAAGATCGATCGAATTAT
1 CAAAATTTCAT--AGA--GAT-G-ATTAT
* *
64093 CAAAAATT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
64114 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
64136 CAAAATTTCAAAGCGA-GATTAT
1 CAAAATTTCATAGAGATGATTAT
64158 C-AAATTTACATA-ATG-TGATTAT
1 CAAAATTT-CATAGA-GATGATTAT
* * *
64180 TAAAATTTCATAGAG--GAGTCAA
1 CAAAATTTCATAGAGATGA-TTAT
* * *
64202 CAAAATTTTATAGAGA-GGTCAT
1 CAAAATTTCATAGAGATGATTAT
* *
64224 CAAAATTTCATAAAGA-GCTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
64246 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
64267 CAAAAATTTCATAG
1 C-AAAATTTCATAG
64281 TGGTATTTCT
Statistics
Matches: 184, Mismatches: 30, Indels: 46
0.71 0.12 0.18
Matches are distributed among these distances:
20 10 0.05
21 32 0.17
22 108 0.59
23 13 0.07
24 3 0.02
26 3 0.02
27 1 0.01
28 3 0.02
29 11 0.06
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:64555 original size:23 final size:22
Alignment explanation
Indices: 64505--64600 Score: 106
Period size: 23 Copynumber: 4.3 Consensus size: 22
64495 AAATTTGTAG
* * *
64505 TTATCAAGATTTCATAAGGA-GA
1 TTATCAAAATTTTAT-AGGAGGT
64527 TTATCAAAATTTTATAGAGAGGT
1 TTATCAAAATTTTATAG-GAGGT
64550 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGG-AGGT
*
64573 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAG-GAGGT
64595 TTATCA
1 TTATCA
64601 CAACTTCATA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.03
22 22 0.33
23 41 0.62
24 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:64582 original size:104 final size:105
Alignment explanation
Indices: 64398--64600 Score: 241
Period size: 104 Copynumber: 1.9 Consensus size: 105
64388 TTTCATAGTT
* * *
64398 TAGTTTTCAAAATTTCATACGAGGATTATCAAAATTTCATAGGGAGATTAACAAAATTTTATAAT
1 TAGTTATCAAAATTTCATACGAGGATTATCAAAATTTCATAGAGAGATTAACAAAATTTTATAAG
*
64463 AAAGTTATAAAAAAA-TCATAGGGAGGTTATCAAAATTTG
66 AAAGTTATAAAAAAATTCATAGCGAGGTTATCAAAATTTG
* * * * *
64502 TAGTTATCAAGATTTCATAAG-GAGATTATCAAAATTTTATAGAGAGGTTTATCAAAATTTTATA
1 TAGTTATCAAAATTTCATACGAG-GATTATCAAAATTTCATAGAGA-GATTAACAAAATTTTATA
* * * *
64566 GGAAGGTT-TATCAAAATTTCATAGCGAGGTTATCA
64 AGAAAGTTATA-AAAAAATTCATAGCGAGGTTATCA
64601 CAACTTCATA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
103 1 0.01
104 40 0.49
105 25 0.30
106 16 0.20
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (105 bp):
TAGTTATCAAAATTTCATACGAGGATTATCAAAATTTCATAGAGAGATTAACAAAATTTTATAAG
AAAGTTATAAAAAAATTCATAGCGAGGTTATCAAAATTTG
Found at i:64742 original size:23 final size:22
Alignment explanation
Indices: 64375--64809 Score: 225
Period size: 22 Copynumber: 19.9 Consensus size: 22
64365 AAACTTCAGG
*
64375 GAGGATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAG-T
* * *
64398 TA-GTTTTCAAAATTTCATA-C
1 GAGGTTATCAAAATTTCATAGT
*
64418 GAGGATTATCAAAATTTCATAGG
1 GAGG-TTATCAAAATTTCATAGT
* * * *
64441 GAGATTAACAAAATTTTATAAT
1 GAGGTTATCAAAATTTCATAGT
* * * ** *
64463 AAAGTTATAAAAAAATCATAGG
1 GAGGTTATCAAAATTTCATAGT
64485 GAGGTTATCAAAA-TT--T-GT
1 GAGGTTATCAAAATTTCATAGT
*
64503 -A-GTTATCAAGATTTCATAAG-
1 GAGGTTATCAAAATTTCAT-AGT
* * *
64523 GAGATTATCAAAATTTTATAGA
1 GAGGTTATCAAAATTTCATAGT
*
64545 GAGGTTTATCAAAATTTTATAG-
1 GAGG-TTATCAAAATTTCATAGT
*
64567 GAAGGTTTATCAAAATTTCATAGC
1 G-AGG-TTATCAAAATTTCATAGT
* *
64591 GAGGTTATCACAACTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * *
64613 GTGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTCATAGT
* *
64635 GTGATTA-CTAACAA-TTCATA-T
1 GAGGTTATC-AA-AATTTCATAGT
* * * **
64656 GGAGGTTTTTAAATTTTCATAAC
1 -GAGGTTATCAAAATTTCATAGT
* * *
64679 GTGGTTATCAATATATCATA-T
1 GAGGTTATCAAAATTTCATAGT
* *
64700 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAGT
* * *
64723 GTTGGTTATCAAAATTTCATTGG
1 G-AGGTTATCAAAATTTCATAGT
* * *
64746 GAAGTTATCAAGATTTGATAGT
1 GAGGTTATCAAAATTTCATAGT
* * *
64768 GAGGTCT-TCAAAATTCCTTAGG
1 GAGGT-TATCAAAATTTCATAGT
*
64790 GAGGTTAACAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
64810 AGAAGGTTAA
Statistics
Matches: 309, Mismatches: 78, Indels: 51
0.71 0.18 0.12
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
19 2 0.01
20 1 0.00
21 10 0.03
22 217 0.70
23 65 0.21
24 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:64816 original size:22 final size:22
Alignment explanation
Indices: 64681--64898 Score: 72
Period size: 22 Copynumber: 9.9 Consensus size: 22
64671 TTCATAACGT
* * * *
64681 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCATAAGAA
* * * **
64703 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATTTCATA-AGAA
**
64726 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
* * *
64749 -GTTATCAAGATTTGAT-AGTGA
1 GGTTATCAAAATTTCATAAG-AA
* * * *
64770 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
64792 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
*
64814 GGTTA-AAAAACTTT-ATTAA-AA
1 GGTTATCAAAA-TTTCA-TAAGAA
* * * *
64835 GGTTCTCGAAATTCCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
* * *
64857 CGCTATTAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
*
64879 GATTATCAAAATTTCATAAG
1 GGTTATCAAAATTTCATAAG
64899 GAGATCATCA
Statistics
Matches: 141, Mismatches: 41, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
20 2 0.01
21 17 0.12
22 100 0.71
23 21 0.15
24 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:64903 original size:22 final size:22
Alignment explanation
Indices: 64864--64911 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
64854 TATCGCTATT
*
64864 AAAATTTCATAAGAAGATTATC
1 AAAATTTCATAAGAAGATCATC
*
64886 AAAATTTCATAAGGAGATCATC
1 AAAATTTCATAAGAAGATCATC
64908 AAAA
1 AAAA
64912 ATAGTGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAAGAAGATCATC
Done.