Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009567.1 Corchorus capsularis cultivar CVL-1 contig09588, 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: 26590
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:340 original size:22 final size:22
Alignment explanation
Indices: 307--466 Score: 108
Period size: 22 Copynumber: 7.2 Consensus size: 22
297 TCTCTATGTC
*
307 GTTATCAAAATTTCATAAGATG
1 GTTATTAAAATTTCATAAGATG
* * * *
329 GTTATTATAATTCCATGAGAAG
1 GTTATTAAAATTTCATAAGATG
* * *
351 GTTATCAAAATTCCAT-AGTGTG
1 GTTATTAAAATTTCATAAG-ATG
**
373 GTTACCAAAATTTCAT-AGAGTG
1 GTTATTAAAATTTCATAAGA-TG
** *
395 GTTACCAAAATTTCATAGGATCAG
1 GTTATTAAAATTTCATAAGAT--G
* * *
419 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCATAAGATG
* *
441 GTTATTGAAATTTCATAAGGTG
1 GTTATTAAAATTTCATAAGATG
463 GTTA
1 GTTA
467 ATTATCACAA
Statistics
Matches: 112, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.02
22 90 0.80
23 2 0.02
24 18 0.16
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
GTTATTAAAATTTCATAAGATG
Found at i:428 original size:24 final size:22
Alignment explanation
Indices: 307--484 Score: 96
Period size: 22 Copynumber: 7.8 Consensus size: 22
297 TCTCTATGTC
* *
307 GTTATCAAAATTTCATAAG-ATG
1 GTTATTAAAATTTCATAGGTA-G
* * *
329 GTTATTATAATTCCAT-GAGAAG
1 GTTATTAAAATTTCATAG-GTAG
* *
351 GTTATCAAAATTCCATAGTGT-G
1 GTTATTAAAATTTCATAG-GTAG
**
373 GTTACCAAAATTTCATAGAGT-G
1 GTTATTAAAATTTCATAG-GTAG
**
395 GTTACCAAAATTTCATAGGATCAG
1 GTTATTAAAATTTCATAGG-T-AG
* *
419 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCATAGGTAG
*
441 GTTATTGAAATTTCATAAGGT-G
1 GTTATTAAAATTTCAT-AGGTAG
463 GTTAATTATCACAATTTCATAG
1 GTT-ATTA--A-AATTTCATAG
485 AAAGATTATC
Statistics
Matches: 127, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
21 1 0.01
22 87 0.69
23 11 0.09
24 17 0.13
25 3 0.02
26 8 0.06
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGTAG
Found at i:555 original size:22 final size:22
Alignment explanation
Indices: 505--872 Score: 87
Period size: 22 Copynumber: 16.5 Consensus size: 22
495 AAAAAGATTT
* *
505 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
528 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
549 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
570 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
593 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
615 CAAAATTTCATA-TGAAGGTTATA
1 CAAAATTTCATAGTG-AGGTTA-A
* *
638 AAAGTCTCAATTTCATAAG-GA-G-TAC
1 CAA-----AATTTCAT-AGTGAGGTTAA
* * *
663 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
* * * * *
684 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGTGAGGTTAA
* *
705 CGAAATTTCATAAAGAT-AGGATTAT
1 CAAAATTTCAT--AG-TGAGG-TTAA
* *
730 CAAAATTT-ATA-TGAAGATTAT
1 CAAAATTTCATAGTG-AGGTTAA
** *
751 CAAAATTTCATAGTGTCGTTAT
1 CAAAATTTCATAGTGAGGTTAA
* * *
773 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
* * * * * *
795 CAAAACTACATAATGTGATTAT
1 CAAAATTTCATAGTGAGGTTAA
* *
817 CAAAATTTCATA-TAGGGGTCAA
1 CAAAATTTCATAGT-GAGGTTAA
* * * *
839 CAAAATTTTATAGAGATGTTAT
1 CAAAATTTCATAGTGAGGTTAA
861 CAAAATTTCATA
1 CAAAATTTCATA
873 AATAGGTTAT
Statistics
Matches: 252, Mismatches: 65, Indels: 57
0.67 0.17 0.15
Matches are distributed among these distances:
19 3 0.01
20 18 0.07
21 30 0.12
22 160 0.63
23 9 0.04
24 5 0.02
25 13 0.05
26 2 0.01
27 1 0.00
28 9 0.04
29 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:750 original size:21 final size:23
Alignment explanation
Indices: 699--828 Score: 99
Period size: 22 Copynumber: 5.8 Consensus size: 23
689 CTCATAGAGT
* **
699 GATTATCGAAATTTCATAAAGATA
1 GATTATCAAAATTTCATAGTGA-A
723 GGATTATCAAAATTT-ATA-TGAA
1 -GATTATCAAAATTTCATAGTGAA
**
745 GATTATCAAAATTTCATAGTGTC
1 GATTATCAAAATTTCATAGTGAA
* *
768 G-TTATCAAAATTTCAAAGCG-A
1 GATTATCAAAATTTCATAGTGAA
* * * * *
789 GGTTATCAAAACTACATAATG-T
1 GATTATCAAAATTTCATAGTGAA
811 GATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
829 TAGGGGTCAA
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
21 15 0.17
22 50 0.58
23 5 0.06
24 3 0.03
25 13 0.15
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGAA
Found at i:844 original size:88 final size:88
Alignment explanation
Indices: 751--915 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
741 TGAAGATTAT
* * *
751 CAAAATTTCATAGTG-TCGTTATCAAAATTTCA-AAGCGAGGTTATCAAAACTACATAATGTGAT
1 CAAAATTTCATAGAGAT-GTTATCAAAATTTCATAA-AGAGGTTATCAAAACTACAAAATGTGAT
814 TATC-AAAATTTCATATAGGGGTCAA
64 TA-CAAAAATTTCATATAGGGGTCAA
* * ** *
839 CAAAATTTTATAGAGATGTTATCAAAATTTCATAAATAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAGAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAACTACAAAATGTGATTA
904 CAAAAATTTCAT
66 CAAAAATTTCAT
916 TGTGGTATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
87 1 0.02
88 62 0.94
89 3 0.05
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (88 bp):
CAAAATTTCATAGAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAACTACAAAATGTGATTA
CAAAAATTTCATATAGGGGTCAA
Found at i:873 original size:66 final size:67
Alignment explanation
Indices: 707--873 Score: 162
Period size: 66 Copynumber: 2.5 Consensus size: 67
697 GTGATTATCG
* *
707 AAATTTCATAAAGATAGGATTATCAAAATTT-AT-ATGAAGATTATCAAAATTTCATAGTGTCGT
1 AAATTTC--AAAGAGAGG-TTATCAAAATTTCATAATGAAGATTATCAAAATTTCATAGTGGCGT
* *
770 TATCA
63 CAACA
* * * * *
775 AAATTTCAAAGCGAGGTTATCAAAACTACATAATG-TGATTATCAAAATTTCATA-TAGGGGTCA
1 AAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAAGATTATCAAAATTTCATAGT-GGCGTCA
838 ACA
65 ACA
* * *
841 AAATTTTATAGAGATGTTATCAAAATTTCATAA
1 AAATTTCAAAGAGAGGTTATCAAAATTTCATAA
874 ATAGGTTATC
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
65 11 0.14
66 60 0.74
67 3 0.04
68 7 0.09
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (67 bp):
AAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAAGATTATCAAAATTTCATAGTGGCGTCAA
CA
Found at i:896 original size:21 final size:22
Alignment explanation
Indices: 663--896 Score: 94
Period size: 22 Copynumber: 10.7 Consensus size: 22
653 TAAGGAGTAC
* *
663 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAAATAGGTTAT
* * *
684 C-AAATCTCATAGAGT-GATTAT
1 CAAAATTTCATA-AATAGGTTAT
*
705 CGAAATTTCATAAAGATAGGATTAT
1 CAAAATTTCAT-AA-ATAGG-TTAT
* *
730 CAAAATTT-ATATGA-AGATTAT
1 CAAAATTTCATA-AATAGGTTAT
*
751 CAAAATTTCAT-AGT-GTCGTTAT
1 CAAAATTTCATAAATAG--GTTAT
**
773 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-ATAGGTTAT
* *
795 CAAAACTACAT-AAT-GTGATTAT
1 CAAAATTTCATAAATAG-G-TTAT
* ** * *
817 CAAAATTTCATATAGGGGTCAA
1 CAAAATTTCATAAATAGGTTAT
* * * *
839 CAAAATTTTATAGAGATGTTAT
1 CAAAATTTCATAAATAGGTTAT
861 CAAAATTTCATAAATAGGTTAT
1 CAAAATTTCATAAATAGGTTAT
*
883 CAAATTTTCA-AAAT
1 CAAAATTTCATAAAT
897 GTGATTACAA
Statistics
Matches: 156, Mismatches: 37, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
20 10 0.06
21 24 0.15
22 100 0.64
23 6 0.04
24 5 0.03
25 11 0.07
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAATAGGTTAT
Found at i:1028 original size:19 final size:19
Alignment explanation
Indices: 998--1064 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
988 TGACGGAGTA
998 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
* *
1018 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
*
1037 ATCGAAATTC-AGTGAGGAT
1 ATCAAAATTCAAG-GAGGAT
1056 ATCAAAATT
1 ATCAAAATT
1065 TCATATGAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.03
19 33 0.82
20 6 0.15
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:1126 original size:22 final size:22
Alignment explanation
Indices: 1101--1191 Score: 62
Period size: 22 Copynumber: 4.1 Consensus size: 22
1091 AGTTTAGTTT
*
1101 TTTTGATTACCTCATTATAAAA
1 TTTTGATTACCTCACTATAAAA
* * *
1123 TTTTG-TTAATCTCCCTATGAAA
1 TTTTGATT-ACCTCACTATAAAA
* *
1145 TTTTGATCTACAT-ACTATGAAA
1 TTTTGAT-TACCTCACTATAAAA
* *
1167 TTTTGATAACCCTC-TTATAAAA
1 TTTTGATTA-CCTCACTATAAAA
1189 TTT
1 TTT
1192 CCCAACCATT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
21 3 0.06
22 46 0.87
23 3 0.06
24 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTGATTACCTCACTATAAAA
Found at i:4495 original size:3 final size:3
Alignment explanation
Indices: 4487--4514 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4477 ACATATATAT
4487 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4515 TTATTATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11338 original size:70 final size:73
Alignment explanation
Indices: 11221--11372 Score: 229
Period size: 70 Copynumber: 2.1 Consensus size: 73
11211 GGTCTTTTCT
11221 CACTTTTCAGATGACTAAAAAACCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTTT
1 CACTTTTCAGATGACTAAAAAA-CCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTTT
*
11286 TTGTAATTA
65 TCGTAATTA
* * *
11295 CACTTTTCGGATGACT-AAAAA-GC-CTATGAGTTTCCCCTATTCCTTTTCCTTTTACCCTTTTT
1 CACTTTTCAGATGACTAAAAAACCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTTTT
11357 CGTAATTA
66 CGTAATTA
*
11365 CACATTTC
1 CACTTTTC
11373 CCTTCCTTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
70 52 0.71
71 1 0.01
73 5 0.07
74 15 0.21
ACGTcount: A:0.22, C:0.28, G:0.08, T:0.42
Consensus pattern (73 bp):
CACTTTTCAGATGACTAAAAAACCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTTTT
CGTAATTA
Found at i:14021 original size:13 final size:13
Alignment explanation
Indices: 14003--14027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13993 TACATGACCC
14003 TCCAATTTGTCCT
1 TCCAATTTGTCCT
14016 TCCAATTTGTCC
1 TCCAATTTGTCC
14028 CTCCTGATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.44
Consensus pattern (13 bp):
TCCAATTTGTCCT
Found at i:16363 original size:96 final size:97
Alignment explanation
Indices: 16185--16367 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 97
16175 CCTTTAGCAT
* * * *
16185 CAGGTCATTTTTGGCCCCCTGATGGCTGTGACGGATAACCTTTGCCTTATGGGCCGTTTCTAGCT
1 CAGGCCATTTTTGGCCCCCGGATGGCTGTGACGGATAACCTTTGCCTTACGAGCCGTTTCTAGCT
**
16250 GGTAATGGACGCAATGGATAGTTTTTGCAACC
66 GCCAATGGACGCAATGGATAGTTTTTGCAACC
* * * *
16282 CAGGCCATTTTTGG-CCCCGGATGGCTGTGATGGATAACCTTTGCCTTCCGAGCTGTTTCTGGCT
1 CAGGCCATTTTTGGCCCCCGGATGGCTGTGACGGATAACCTTTGCCTTACGAGCCGTTTCTAGCT
* * **
16346 GCCGATGGCCGTGATGGATAGT
66 GCCAATGGACGCAATGGATAGT
16368 GCTTGGCTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 59 0.82
97 13 0.18
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.31
Consensus pattern (97 bp):
CAGGCCATTTTTGGCCCCCGGATGGCTGTGACGGATAACCTTTGCCTTACGAGCCGTTTCTAGCT
GCCAATGGACGCAATGGATAGTTTTTGCAACC
Found at i:16699 original size:28 final size:28
Alignment explanation
Indices: 16667--16739 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
16657 GGGTCATCCA
16667 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
16695 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
16723 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
16740 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:16879 original size:19 final size:19
Alignment explanation
Indices: 16828--16880 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
16818 ATGCACCTTG
16828 GCATTTTAG-CATAT--TT
1 GCATTTTAGTCATATAGTT
* * *
16844 TCA-TTTAGTAATTTAGTT
1 GCATTTTAGTCATATAGTT
16862 GCATTTTAGTCATATAGTT
1 GCATTTTAGTCATATAGTT
16881 AAAGCTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
18 4 0.15
19 13 0.48
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (19 bp):
GCATTTTAGTCATATAGTT
Found at i:20270 original size:55 final size:55
Alignment explanation
Indices: 20211--20575 Score: 536
Period size: 55 Copynumber: 6.6 Consensus size: 55
20201 GAAAAGGGCA
20211 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
*
20266 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTC
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
* * * *
20321 ATCAGTAAATCAGTAATTAGGTAAAAAGAGATTAATCATAGTCAAGGTAATAATA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
* * * *
20376 ATCAGCAAATCAGTAATTAAGTAAAAAGGGATTAATCAAAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
* * * * * *
20431 ACCGGTAAATCAGTAATTATGTAAAAAGGGATTAATCAGAGTTAAGGAAATAG-C
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
* * *
20485 AATCAGTAAATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTTAAGGAAATAG-C
1 -ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
20540 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAA
1 -ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAA
20576 CCAGTAATTA
Statistics
Matches: 286, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
55 286 1.00
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (55 bp):
ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTC
Found at i:20277 original size:29 final size:29
Alignment explanation
Indices: 20244--20333 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
20234 AAAAGAGATT
20244 AATCAGAGTCAAGGTAATAGTCATCAGTA
1 AATCAGAGTCAAGGTAATAGTCATCAGTA
* * ** *
20273 AATCAGTAATTAA-GTAA-A---AAGAGATT
1 AATCAG-AGTCAAGGTAATAGTCATCAG-TA
*
20299 AATCAGAGTCAAGGTAATGGTCATCAGTA
1 AATCAGAGTCAAGGTAATAGTCATCAGTA
20328 AATCAG
1 AATCAG
20334 TAATTAGGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
25 7 0.16
26 11 0.26
28 1 0.02
29 17 0.40
30 7 0.16
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (29 bp):
AATCAGAGTCAAGGTAATAGTCATCAGTA
Found at i:20315 original size:26 final size:26
Alignment explanation
Indices: 20231--20315 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
20221 CAGTAATTAA
20231 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
* * * * *
20257 GT-AATAGTCATCAGTAAATCAGTAATTAA-
1 GTAAAAAG--A-GA-TTAATCAG-AGTCAAG
20286 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
20312 GTAA
1 GTAA
20316 TGGTCATCAG
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 8 0.19
26 13 0.31
27 2 0.05
28 2 0.05
29 9 0.21
30 8 0.19
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (26 bp):
GTAAAAAGAGATTAATCAGAGTCAAG
Found at i:20789 original size:24 final size:24
Alignment explanation
Indices: 20761--20807 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20751 GAGATTGGTA
*
20761 ATTAAAGTAGTAATTTAGATTCAT
1 ATTAAAGTAGTAATTGAGATTCAT
*
20785 ATTAAAGTGGTAATTGAGATTCA
1 ATTAAAGTAGTAATTGAGATTCA
20808 AAGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (24 bp):
ATTAAAGTAGTAATTGAGATTCAT
Found at i:21084 original size:27 final size:26
Alignment explanation
Indices: 21054--21118 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
21044 GAGAGAGTAA
21054 AAAAAATGGTAATTAAAGTA-AAAGAGT
1 AAAAAATGGTAA-T-AAGTACAAAGAGT
* *
21081 AAAATATGGTAATCAGTACAAAGAGT
1 AAAAAATGGTAATAAGTACAAAGAGT
21107 AAAAAATGGTAA
1 AAAAAATGGTAA
21119 CAAGCAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 19 0.56
27 11 0.32
ACGTcount: A:0.57, C:0.03, G:0.18, T:0.22
Consensus pattern (26 bp):
AAAAAATGGTAATAAGTACAAAGAGT
Found at i:22862 original size:14 final size:14
Alignment explanation
Indices: 22843--22894 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
22833 CAAGAGATAT
*
22843 TTTTCAAAAAATTG
1 TTTTCAAAAAATAG
*
22857 TTTTCAAGAAAA-GG
1 TTTTCAA-AAAATAG
22871 TTTTC-AAAAATGAG
1 TTTTCAAAAAAT-AG
22885 TTTTCAAAAA
1 TTTTCAAAAA
22895 GGTTTAGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.12
13 1 0.03
14 19 0.59
15 8 0.25
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAAATAG
Found at i:22887 original size:28 final size:26
Alignment explanation
Indices: 22843--22899 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
22833 CAAGAGATAT
*
22843 TTTTCAAAAAATTGTTTTCAAGAAAAGG
1 TTTTCAAAAAATAGTTTTC-A-AAAAGG
22871 TTTTC-AAAAATGAGTTTTCAAAAAGG
1 TTTTCAAAAAAT-AGTTTTCAAAAAGG
22897 TTT
1 TTT
22900 AGAGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 9 0.33
27 7 0.26
28 11 0.41
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAAATAGTTTTCAAAAAGG
Found at i:25646 original size:45 final size:45
Alignment explanation
Indices: 25595--25735 Score: 203
Period size: 45 Copynumber: 3.2 Consensus size: 45
25585 TCCAATAATA
* * *
25595 TTATCAAAGTCGACCCCAAAACAGGTCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCGCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* *
25640 TTATCAAAGTTGACCGCAGAATAGGTCTTTCTCAATTTTCAGCAG
1 TTATCAAAGTTGACCGCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* *
25685 TTATCAAAGTTGACCGCAGAACAGGTCTTTTTCAG-TTCCAGCAG
1 TTATCAAAGTTGACCGCAGAACAGGTCTTTCTCAGTTTTCAGCAG
*
25729 TTTTCAA
1 TTATCAA
25736 GGCCGACCAC
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 14 0.16
45 72 0.84
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
TTATCAAAGTTGACCGCAGAACAGGTCTTTCTCAGTTTTCAGCAG
Found at i:26009 original size:27 final size:28
Alignment explanation
Indices: 25979--26031 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
25969 GCATTAGGGT
25979 CATCCA-GGGGCATTTTGGTCATTTTCA
1 CATCCAGGGGGCATTTTGGTCATTTTCA
*
26006 CATCTAGGGGGCATTTTGGTCATTTT
1 CATCCAGGGGGCATTTTGGTCATTTT
26032 TGCATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (28 bp):
CATCCAGGGGGCATTTTGGTCATTTTCA
Found at i:26017 original size:28 final size:28
Alignment explanation
Indices: 25985--26057 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
25975 GGGTCATCCA
25985 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
26013 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
**
26041 GGGATATTTTGGTCATT
1 GGGGCATTTTGGTCATT
26058 CTTAATCTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:26197 original size:19 final size:19
Alignment explanation
Indices: 26146--26198 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
26136 ATGCACCTTG
26146 GCATTTTAG-CATAT--TT
1 GCATTTTAGTCATATAGTT
* * *
26162 TCA-TTTAGTAATTTAGTT
1 GCATTTTAGTCATATAGTT
26180 GCATTTTAGTCATATAGTT
1 GCATTTTAGTCATATAGTT
26199 AAAGCTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
18 4 0.15
19 13 0.48
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (19 bp):
GCATTTTAGTCATATAGTT
Done.