Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021142.1 Corchorus olitorius cultivar O-4 contig21175, 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: 43356
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8363 original size:2 final size:2
Alignment explanation
Indices: 8356--8387 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8346 CGGAATTAAT
*
8356 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8388 CACACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8426 original size:2 final size:2
Alignment explanation
Indices: 8421--8448 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8411 ACATACATAC
8421 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
8449 GAACAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15772 original size:25 final size:25
Alignment explanation
Indices: 15738--15785 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
15728 TTTAGCCCTT
15738 ATATATAGCCTTGTTTCATTCATGA
1 ATATATAGCCTTGTTTCATTCATGA
15763 ATATATAGCCTTGTTTCATTCAT
1 ATATATAGCCTTGTTTCATTCAT
15786 TAACCAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (25 bp):
ATATATAGCCTTGTTTCATTCATGA
Found at i:23604 original size:28 final size:29
Alignment explanation
Indices: 23531--23604 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
23521 TAGCGTAAGG
* *
23531 GGACAAAACATCCCAAAATTGGAGTTTAGA
1 GGACAAAACAT-CCAAAATTGGAATTCAGA
* ** *
23561 GGGCAAAATGTCCAAAGTTGGAATTCAGA
1 GGACAAAACATCCAAAATTGGAATTCAGA
23590 -GACAAAACATCCAAA
1 GGACAAAACATCCAAA
23605 CCCTACAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 12 0.34
29 15 0.43
30 8 0.23
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (29 bp):
GGACAAAACATCCAAAATTGGAATTCAGA
Found at i:26613 original size:44 final size:43
Alignment explanation
Indices: 26563--26666 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
26553 GTCTCTGTGT
*
26563 GGTTATCAAAATTTCATAAG-ATGATTACTATAATTTCATGAT-GA
1 GGTTATCAAAATTTCAT-AGTATGATTACCA-AATTTCAT-ATGGA
* * * *
26607 GGTTATCAAAATTCCATAGTGTGGTTACCAAGTTTCATATGGA
1 GGTTATCAAAATTTCATAGTATGATTACCAAATTTCATATGGA
*
26650 AGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
26667 GGGCAGGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.04
43 26 0.51
44 23 0.45
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTATGATTACCAAATTTCATATGGA
Found at i:26752 original size:68 final size:65
Alignment explanation
Indices: 26559--26793 Score: 215
Period size: 65 Copynumber: 3.5 Consensus size: 65
26549 TCTTGTCTCT
* * * * * *
26559 GTGTGGTTATCAAAATTTCATAAGATGATTA-CTATAATTTCATGATG-AGGTTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATAGGAAG-TTATC-AAAATTTCAT-AGGAAGGTTATCAAAATTTC
26622 ATA
63 ATA
* * *
26625 GTGTGGTTACC-AAGTTTCATATGGAAGTTATCAAAATTTCATGGGCAGGTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
26689 A
65 A
* * * **
26690 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAATGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGA--A-GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTC
26755 ATA
63 ATA
* * * *
26758 GTGTGGTTATCACAATTTTATAGAAAGGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATCAAA
26794 GAGATTATCA
Statistics
Matches: 141, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
64 1 0.01
65 53 0.38
66 33 0.23
67 1 0.01
68 53 0.38
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:26774 original size:22 final size:22
Alignment explanation
Indices: 26559--26780 Score: 131
Period size: 22 Copynumber: 10.0 Consensus size: 22
26549 TCTTGTCTCT
26559 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * *
26582 G-ATGATTA-CTATAATTTCAT-
1 GTGTGGTTATC-AAAATTTCATA
* *
26602 GATGAGGTTATCAAAATTCCATA
1 G-TGTGGTTATCAAAATTTCATA
* *
26625 GTGTGGTTA-CCAAGTTTCATA
1 GTGTGGTTATCAAAATTTCATA
26646 -TG-GAAGTTATCAAAATTTCAT-
1 GTGTG--GTTATCAAAATTTCATA
* *
26667 GGGCAGGTTATCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
26690 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* *
26712 G-GATCAGGTTATTAAAATTTCTTA
1 GTG-T--GGTTATCAAAATTTCATA
**
26736 G-GAAT-GTTATTGAAATTTCATA
1 GTG--TGGTTATCAAAATTTCATA
* *
26758 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
26780 G
1 G
26781 AAAGGTTATC
Statistics
Matches: 154, Mismatches: 27, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 16 0.10
22 108 0.70
23 6 0.04
24 18 0.12
25 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:26898 original size:22 final size:21
Alignment explanation
Indices: 26840--26915 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
26830 TCCATAGTGT
*
26840 GGTTAACAAAATTTCATAAGGA
1 GGTT-ACAAAATTTTATAAGGA
* **
26862 GGTTACTAATATTTTATGGGGA
1 GGTTAC-AAAATTTTATAAGGA
* *
26884 GGTTATCAAAATTTTATATGAA
1 GGTTA-CAAAATTTTATAAGGA
*
26906 GGTTATAAAA
1 GGTTACAAAA
26916 CTCTCAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 6 0.14
22 36 0.84
23 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (21 bp):
GGTTACAAAATTTTATAAGGA
Found at i:27091 original size:88 final size:89
Alignment explanation
Indices: 26938--27193 Score: 231
Period size: 88 Copynumber: 2.9 Consensus size: 89
26928 TAAGGAGTCC
* * * * *
26938 CAAAATTTGATAGA-AGGTTATC-AAATCTCATAGAGTGATTATCGAAAATT-CATAGAGATCG-
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATC-AAAATTACA-A-A-AT-GT
* *
26999 GATTATCAAAATTT-ATAGGA-AGATTAT
61 GATTATCAAAATTTCATAGGAGAGATCAA
* ** * *
27026 CAAAATTTCATAGTGTTGTTATCAAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGAT
1 CAAAATTTCATAGAGAGGTTATC-AAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGAT
* *
27090 TATCAAAATTTCATA-GAGGGGTCAA
64 TATCAAAATTTCATAGGAGAGATCAA
* * *
27115 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
*
27180 CCAAAATTTCATAG
66 TCAAAATTTCATAG
27194 TGGTATTTCT
Statistics
Matches: 135, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
87 1 0.01
88 77 0.57
89 34 0.25
90 7 0.05
91 16 0.12
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (89 bp):
CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
TCAAAATTTCATAGGAGAGATCAA
Found at i:27156 original size:22 final size:22
Alignment explanation
Indices: 26938--27823 Score: 202
Period size: 22 Copynumber: 40.2 Consensus size: 22
26928 TAAGGAGTCC
*
26938 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
26959 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
26980 CGAAAA-TTCATAGAGATCGGATTAT
1 C-AAAATTTCATAGAGA--GG-TTAT
*
27005 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAG-AGGTTAT
* **
27026 CAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
27048 CAAAAATTTCAAAGCGAGGTTAT
1 C-AAAATTTCATAGAGAGGTTAT
* * *
27071 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * *
27093 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGAGGTTAT
*
27115 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
27137 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * * * *
27159 CAAATTTTCA-AAATGTGATTAC
1 CAAAATTTCATAGA-GAGGTTAT
* *
27181 CAAAATTTCAT--AGTGGTATTT
1 CAAAATTTCATAGAGAGGT-TAT
* **
27202 CTGGGGAGGTTATCA-A-A-A--TT-T
1 C----AAAATT-TCATAGAGAGGTTAT
* * *
27223 CACAGTATGGTTACCAAATTATGAAGGTTAT
1 CA-A-AAT--TT--CATA-GA-G-AGGTTAT
* * * *
27254 TAAACTTTTATTATG-GA-GTAAT
1 CAAAATTTCA-TA-GAGAGGTTAT
*
27276 CAAAATTTC--AGAGAGGATAT
1 CAAAATTTCATAGAGAGGTTAT
27296 CAAAATTTCATATGA-AGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
* * *
27318 CAAAATTTCATAG-TATGTAGAT
1 CAAAATTTCATAGAGAGGT-TAT
* * *
27340 CAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAGAGAGGTTAT
*
27362 CAAAATTTCATA-ATGAGGTTAC
1 CAAAATTTCATAGA-GAGGTTAT
** * *
27384 CAAAAAATCATAGGGAGGTAAT
1 CAAAATTTCATAGAGAGGTTAT
* *
27406 CGAAA-TT--T-G-TA-GTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
27422 CAAGACTTCATA-AGGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* *
27444 CAAAAGTTT-AGAGGGAGGTTTAT
1 CAAAA-TTTCATAGAGAGG-TTAT
*
27467 CAAAATTTTATAG-GAAGGTTTAT
1 CAAAATTTCATAGAG-AGG-TTAT
*
27490 CAAAATTTCATAGTGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * * * *
27512 TACAATTTCATAGTGTGATT-T
1 CAAAATTTCATAGAGAGGTTAT
* * * *
27533 CAAAATTTCAGAGTGTGATTA-
1 CAAAATTTCATAGAGAGGTTAT
*
27554 CTAACAA-TTCATATGA-AGGTTTT
1 C-AA-AATTTCATA-GAGAGGTTAT
* * *
27577 TAAATTTTCATA-ACGTGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* *
27599 CAATATATCATATG-GAGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
* * * *
27621 CAACATCTCATAGTGTTGGTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * *
27644 CAAAATTTCATTGGGAAGTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
27666 CAAAATTTCATAGTGAGGTCT-T
1 CAAAATTTCATAGAGAGGT-TAT
* * * * * *
27688 CAAAATTCCTTCGGGAGGCTAA
1 CAAAATTTCATAGAGAGGTTAT
*
27710 CAAAATTTCATA-AGAAGGTTAA
1 CAAAATTTCATAGAG-AGGTTAT
* * * * *
27732 AAAAATTTTATAAAAAGGTTCT
1 CAAAATTTCATAGAGAGGTTAT
* **
27754 C-AAATTCCATAGTA-TCGTTAT
1 CAAAATTTCATAG-AGAGGTTAT
* * *
27775 TAAAAATTCATAG-GAATGTTAT
1 CAAAATTTCATAGAG-AGGTTAT
27797 CAAAATTTCATA-AGGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
*
27819 AAAAA
1 CAAAA
27824 ATAGTGTAAT
Statistics
Matches: 630, Mismatches: 152, Indels: 165
0.67 0.16 0.17
Matches are distributed among these distances:
16 7 0.01
17 3 0.00
18 3 0.00
19 6 0.01
20 28 0.04
21 69 0.11
22 384 0.61
23 91 0.14
24 12 0.02
25 12 0.02
26 6 0.01
27 2 0.00
28 1 0.00
29 1 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:27317 original size:64 final size:66
Alignment explanation
Indices: 27242--27397 Score: 160
Period size: 64 Copynumber: 2.4 Consensus size: 66
27232 GTTACCAAAT
* * * *
27242 TATGAAGGTTATTAAACTTTTATTATGGA-GTA-ATCAAAATTTCAGAGAG-GA-TATCAAAATT
1 TATGAAGGTTATCAAAATTTCA-TA-GGATGTAGATCAAAATTTCAGAGAGAGATTAACAAAATT
27303 TCA
64 TCA
* * *
27306 TATGAAGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTC
1 TATGAAGGTTATCAAAATTTCATAGGATGTAGATCAAAATTTCAGAGAGAGATTAACAAAATTTC
27371 A
66 A
* **
27372 TAATG-AGGTTACCAAAAAATCATAGG
1 T-ATGAAGGTTATCAAAATTTCATAGG
27398 GAGGTAATCG
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 2 0.03
63 5 0.07
64 34 0.45
65 2 0.03
66 30 0.39
67 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (66 bp):
TATGAAGGTTATCAAAATTTCATAGGATGTAGATCAAAATTTCAGAGAGAGATTAACAAAATTTC
A
Found at i:27495 original size:23 final size:23
Alignment explanation
Indices: 27440--27502 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27430 CATAAGGAGG
* * *
27440 TTATCAAAAGTTTAGAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
27463 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
*
27486 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
27503 TGAGGTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:27508 original size:23 final size:22
Alignment explanation
Indices: 27274--27823 Score: 239
Period size: 22 Copynumber: 25.3 Consensus size: 22
27264 TTATGGAGTA
* *
27274 ATCAAAATTTC--AGAGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
27294 ATCAAAATTTCATA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* *
27316 ATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* *
27338 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
27360 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* ** * *
27382 ACCAAAAAATCATAGGGAGGTA
1 ATCAAAATTTCATAGTGAGGTT
*
27404 ATCGAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
* *
27420 ATCAAGACTTCATAAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
27442 ATCAAAAGTTT-AGAGGGAGGTTT
1 ATCAAAA-TTTCATAGTGAGG-TT
*
27465 ATCAAAATTTTATAG-GAAGGTTT
1 ATCAAAATTTCATAGTG-AGG-TT
27488 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * * *
27510 ATTACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
27532 -TCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
27553 A-CTAACAA-TTCATA-TGAAGGTT
1 ATC-AA-AATTTCATAGTG-AGGTT
* * * ** *
27575 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* *
27597 ATCAATATATCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
27619 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* * *
27642 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
27664 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGTGAGGT-T
* * * * *
27687 -TCAAAATTCCTTCGGGAGGCT
1 ATCAAAATTTCATAGTGAGGTT
* *
27708 AACAAAATTTCATAAG-AAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
** * ***
27730 AAAAAAATTTTATAAAAAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
27752 CTC-AAATTCCATAGT-ATCGTT
1 ATCAAAATTTCATAGTGA-GGTT
* * *
27773 ATTAAAAATTCATAG-GAATGTT
1 ATCAAAATTTCATAGTG-AGGTT
27795 ATCAAAATTTCATAAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
*
27817 ATAAAAA
1 ATCAAAA
27824 ATAGTGTAAT
Statistics
Matches: 397, Mismatches: 95, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
16 7 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 12 0.03
21 45 0.11
22 259 0.65
23 67 0.17
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:27665 original size:45 final size:45
Alignment explanation
Indices: 27592--27680 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
27582 TTTCATAACG
* * *
27592 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
27637 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
27681 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:27875 original size:22 final size:22
Alignment explanation
Indices: 27833--27875 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27823 AATAGTGTAA
27833 TTATCATAATTTAATAGGAATG
1 TTATCATAATTTAATAGGAATG
* *
27855 TTATCATAATTTCATATGAAT
1 TTATCATAATTTAATAGGAAT
27876 ATTTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATCATAATTTAATAGGAATG
Found at i:34906 original size:10 final size:10
Alignment explanation
Indices: 34893--34918 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34883 AACCAAATAT
34893 AACCGACCGA
1 AACCGACCGA
34903 AACCGACCGA
1 AACCGACCGA
34913 AACCGA
1 AACCGA
34919 AATTGGCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.38, G:0.19, T:0.00
Consensus pattern (10 bp):
AACCGACCGA
Found at i:37770 original size:13 final size:13
Alignment explanation
Indices: 37752--37782 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
37742 TATCGTCATC
37752 TTGATAACCCCTA
1 TTGATAACCCCTA
37765 TTGATAACCCCTA
1 TTGATAACCCCTA
37778 -TGATA
1 TTGATA
37783 TATATTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (13 bp):
TTGATAACCCCTA
Done.