Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012125.1 Corchorus capsularis cultivar CVL-1 contig12146, 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: 40645
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:303 original size:24 final size:25
Alignment explanation
Indices: 271--319 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
261 TTGAATGATT
*
271 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
* *
295 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
320 AGGAAATGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:374 original size:21 final size:22
Alignment explanation
Indices: 340--382 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
330 AAAATTGTCC
340 AAAGGAGGACGGTATCTAGTAA
1 AAAGGAGGACGGTATCTAGTAA
* *
362 AAAGG-GGGCGGTATTTAGTAA
1 AAAGGAGGACGGTATCTAGTAA
383 TCCTCAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (22 bp):
AAAGGAGGACGGTATCTAGTAA
Found at i:22243 original size:21 final size:20
Alignment explanation
Indices: 22193--22243 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
22183 TCCAGCATCA
*
22193 CCAAATGGTATTCCTGTCACT
1 CCAAATGG-ATTCCTGGCACT
*
22214 CAAAATGGATTCCTGGCAACT
1 CCAAATGGATTCCTGGC-ACT
*
22235 CCAATTGGA
1 CCAAATGGA
22244 ACATTAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
CCAAATGGATTCCTGGCACT
Found at i:29193 original size:35 final size:36
Alignment explanation
Indices: 29147--29220 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 36
29137 GGTAACGGTA
29147 TAAAGTCGTTGCTT-TCAAGCTAGTATATGACTATG
1 TAAAGTCGTTGCTTATCAAGCTAGTATATGACTATG
29182 TAAAGTCGTTGCTTACAATCAAGCTAGTATATGACTATG
1 TAAAGTCGTTGCTT---ATCAAGCTAGTATATGACTATG
29221 CTTTGCTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 14 0.40
39 21 0.60
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (36 bp):
TAAAGTCGTTGCTTATCAAGCTAGTATATGACTATG
Found at i:33582 original size:31 final size:31
Alignment explanation
Indices: 33547--33612 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
33537 AACTTTATGT
* * *
33547 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTATACCCTT-TTCTTTAAAACATA
33578 TTTCCAATTATACCCTTTTCTTTAAAACATA
1 TTTCCAATTATACCCTTTTCTTTAAAACATA
33609 TTTC
1 TTTC
33613 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTTTCTTTAAAACATA
Found at i:34111 original size:22 final size:22
Alignment explanation
Indices: 34086--34226 Score: 115
Period size: 22 Copynumber: 6.3 Consensus size: 22
34076 TTGTCTCTAT
*
34086 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCATAGG
* *
34108 ATGGTTATTATAATTTCATGAGG
1 ATGGTTATCAAAATTTCAT-AGG
* *
34131 A-GGTTATCAAAATTCCAAAGCG
1 ATGGTTATCAAAATTTCATAG-G
*
34153 -TGGTTACCAAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGG
* * *
34174 ATCAGGTTATTAAAATCTCTTAGG
1 AT--GGTTATCAAAATTTCATAGG
* **
34198 TTGGTTATTGAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGG
*
34220 GTGGTTA
1 ATGGTTA
34227 ATTATCACAA
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.03
22 71 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAGG
Found at i:34385 original size:22 final size:21
Alignment explanation
Indices: 34337--34619 Score: 96
Period size: 22 Copynumber: 12.8 Consensus size: 21
34327 TTTCATGGGG
* *
34337 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
34359 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
34381 AGGTTAT-AAAAGTCTCAATTTCACA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* *
34406 AGGATTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
34428 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
34447 AGTGATTAACGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
34470 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
34495 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
34515 TGTTGTTATC--AATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
* *
34537 ATGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
34557 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
34580 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
34602 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
34620 AAATGTGATT
Statistics
Matches: 193, Mismatches: 41, Indels: 54
0.67 0.14 0.19
Matches are distributed among these distances:
19 2 0.01
20 26 0.13
21 25 0.13
22 98 0.51
23 5 0.03
24 7 0.04
25 19 0.10
26 7 0.04
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:34750 original size:20 final size:20
Alignment explanation
Indices: 34725--34775 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
34715 TTATGGAGTA
34725 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
34745 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
34764 ATCAAAATTTCA
1 ATCAAAATTTCA
34776 TATTTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:34857 original size:22 final size:22
Alignment explanation
Indices: 34725--35281 Score: 172
Period size: 22 Copynumber: 25.7 Consensus size: 22
34715 TTATGGAGTA
*
34725 ATCAAAATTTC--AAGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
34745 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
***
34764 ATCAAAATTTCATATTTTA-GTT
1 ATCAAAATTTCATA-AGGAGGTT
* * *
34786 TTTAAAATTTCACAA-GAGAGTT
1 ATCAAAATTTCATAAGGAG-GTT
* * * *
34808 ATCAAATTTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
*
34830 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
34852 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** *
34874 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
34896 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
* ** *
34912 ATCAAGATTTCATAAAAAAGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
34934 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
* *
34957 ATCAAAAATTT--TTAGGAAGATTT
1 ATC-AAAATTTCATAAGG-AG-GTT
* *
34980 ATCAAAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* *
35002 ATCAAAATTTCA-AAGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
*
35024 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
35046 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
35068 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
35090 ATCAATATCTCAT-AGTGTTGGTT
1 ATCAAAATTTCATAAG-G-AGGTT
** *
35113 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
* **
35135 ATCAAAATTTCGTATTGAGGTCT
1 ATCAAAATTTCATAAGGAGGT-T
* * *
35158 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
35179 AACCAAATTTCATAAGAAAGTT
1 ATCAAAATTTCATAAGGAGGTT
** * ** *
35201 GAAAAAAAATT-ATAAAAAAGTT
1 -ATCAAAATTTCATAAGGAGGTT
* * * *
35223 CTCGAAATTTCAT-AGTATTGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
35245 ATTAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
35267 ATCAAAATTTCATAA
1 ATCAAAATTTCATAA
35282 TGGGATCATA
Statistics
Matches: 393, Mismatches: 107, Indels: 72
0.69 0.19 0.13
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 20 0.05
20 11 0.03
21 16 0.04
22 273 0.69
23 50 0.13
24 10 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:34960 original size:23 final size:23
Alignment explanation
Indices: 34932--35011 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
34922 CATAAAAAAG
34932 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
34955 TTATCAAAAATTTT-TAGGAAGAT
1 TTATC-AAAATTTTATAGGGAGGT
* * * *
34978 TTATCAAAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
35000 TTATCAAAATTT
1 TTATCAAAATTT
35012 CAAAGTGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
22 19 0.40
23 20 0.43
24 8 0.17
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:35505 original size:22 final size:22
Alignment explanation
Indices: 35436--35685 Score: 137
Period size: 22 Copynumber: 11.5 Consensus size: 22
35426 TAAAAGTCTC
* *
35436 AATTTCATAG-G-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
35456 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* **
35476 AATCTCATAGAGTGATTATTGA
1 AATTTCATAGAGTGATTATCAA
35498 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
35523 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
35544 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* *
35566 AATTTAAAAACGAG-G-TTATCAA
1 AATTT-CATA-GAGTGATTATCAA
* *
35588 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* *
35610 AATTTCATAGAGGGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
35632 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
35654 ATTTTCA-AAATGTAATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
35676 AATTTCATAG
1 AATTTCATAG
35686 TGGTATTTCT
Statistics
Matches: 178, Mismatches: 33, Indels: 35
0.72 0.13 0.14
Matches are distributed among these distances:
19 3 0.02
20 20 0.11
21 28 0.16
22 102 0.57
23 6 0.03
24 7 0.04
25 12 0.07
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:35614 original size:66 final size:66
Alignment explanation
Indices: 35535--35688 Score: 195
Period size: 66 Copynumber: 2.3 Consensus size: 66
35525 TTTATAGAAA
** *
35535 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTT-AAAAACGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGTGGGGTTATCAAAATTTCAAAAA-GAGGTTATCAAAATTACAAAAT
35599 GT
65 GT
* * * * *
35601 GATTATCAGAATTTCATAGAGGGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGTGGGGTTATCAAAATTTCAAAAAGAGGTTATCAAAATTACAAAATG
35666 T
66 T
*
35667 AATTA-CAAAAATTTCATAGTGG
1 GATTATC-AAAATTTCATAGTGG
35689 TATTTCTGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 70 0.93
67 4 0.05
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGTGGGGTTATCAAAATTTCAAAAAGAGGTTATCAAAATTACAAAATG
T
Found at i:35651 original size:44 final size:43
Alignment explanation
Indices: 35436--36233 Score: 187
Period size: 44 Copynumber: 18.7 Consensus size: 43
35426 TAAAAGTCTC
* * *
35436 AATTTCATAGGGA-G-TACCAAAATTTGATAGA-AGGTTATCA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATCA
* * * **
35476 AATCTCATAGAGTGATTATTGAAATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGAGA--GG-TTATC-A
* * * **
35523 AATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTGTTATCAA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATC-A
* * * * *
35566 AATTT-AAAAACGAGGTTATCAAAATTACATA-ATGTGATTATCA
1 AATTTCATAGA-GAGGTTATCAAAATTTCATAGA-GAGGTTATCA
* *
35609 GAATTTCATAGAGGGGTTATCAAAATTTCATAAAGAGGTTATCA
1 -AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATCA
* * *
35653 AATTTTCA-A-A-ATGTAATTACAAAAATTTCAT--AGTGG---T--
1 AA-TTTCATAGAGAGGTTA-T-C-AAAATTTCATAGAGAGGTTATCA
* * * * *
35690 -ATTTC-TGGGGAGATTATCAAAATTTCATAGTA-TGGTTACCA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAG-AGAGGTTATCA
* * * * *
35731 AA-TT-A-GGA-AGGTTATTAAACTTTTATTATG-GA-GTAATCAA
1 AATTTCATAGAGAGGTTATCAAAATTTCA-TA-GAGAGGTTATC-A
* * * *
35771 AATTTGA-AGA-AGGATATCAAAA-TTC--AGGGAGGATATCAA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATC-A
* ** *
35810 AATTTCTTATGA-AGGTTATCAAAATTTCATAGTTTA-GTTTTCAA
1 AATTTCATA-GAGAGGTTATCAAAATTTCATAG-AGAGGTTATC-A
* * * *
35854 AATTTCACA-AGAGGATTATCAAAATTTCATAG-TATGTAGATCAA
1 AATTTCATAGAGAGG-TTATCAAAATTTCATAGAGAGGT-TATC-A
* * * *
35898 AATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGATTATCAA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGA-GAGGTTATC-A
** * *
35942 AAAATCATAGGGAGGTTATCAAAA-TT--T-G-TA-GTTATCA
1 AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATCA
* * *
35979 AGATTTCATA-AGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAA
1 A-ATTTCATAGAG-AGGTTATCAAAATTTCATAGAGAGG-TTATC-A
* * *
36025 AATTTTATAG-GAAGATTTATCAAAATTTCATAGTGAGGTTATCA
1 AATTTCATAGAG-AG-GTTATCAAAATTTCATAGAGAGGTTATCA
* * * * * * *
36069 CAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGATTA-CTA
1 -AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATC-A
* * * * *
36113 ACAATTCATATG-GAGGTTTTTAAATTTTCATA-ACGTGGTTATCA
1 A-ATTTCATA-GAGAGGTTATCAAAATTTCATAGA-GAGGTTATCA
* * * * * *
36157 ATATATCATATG-GAGGTTATCAACATCTCATAGTGTTGGTCATCAA
1 A-ATTTCATA-GAGAGGTTATCAAAATTTCATAGAG-AGGTTATC-A
* * *
36203 AATTTCATTGGGAAGTTATCAAAATTTCATA
1 AATTTCATAGAGAGGTTATCAAAATTTCATA
36234 TTGAGGTCTT
Statistics
Matches: 564, Mismatches: 120, Indels: 143
0.68 0.15 0.17
Matches are distributed among these distances:
34 10 0.02
35 5 0.01
36 5 0.01
37 8 0.01
38 25 0.04
39 32 0.06
40 18 0.03
41 25 0.04
42 39 0.07
43 31 0.05
44 234 0.41
45 74 0.13
46 53 0.09
47 5 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (43 bp):
AATTTCATAGAGAGGTTATCAAAATTTCATAGAGAGGTTATCA
Found at i:35791 original size:20 final size:20
Alignment explanation
Indices: 35766--35838 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 20
35756 TTATGGAGTA
*
35766 ATCAAAATTTGAAGAAGGAT
1 ATCAAAATTTCAAGAAGGAT
* *
35786 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGAAGGAT
* *
35805 ATCAAAATTTCTTATGAAGGTT
1 ATCAAAATTTC--AAGAAGGAT
35827 ATCAAAATTTCA
1 ATCAAAATTTCA
35839 TAGTTTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 16 0.36
20 11 0.25
22 17 0.39
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAAGAAGGAT
Found at i:35920 original size:22 final size:22
Alignment explanation
Indices: 35785--36233 Score: 187
Period size: 22 Copynumber: 20.7 Consensus size: 22
35775 TGAAGAAGGA
35785 TATCAAAA-TTC--AGGGAGGA-
1 TATCAAAATTTCATAGGGA-GAT
* * * *
35804 TATCAAAATTTCTTATGAAGGT
1 TATCAAAATTTCATAGGGAGAT
**
35826 TATCAAAATTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-GGAGAT
* * *
35848 TTTCAAAATTTCACA-AGAGGAT
1 TATCAAAATTTCATAGGGA-GAT
*
35870 TATCAAAATTTCATA-GTATG-T
1 TATCAAAATTTCATAGGGA-GAT
*
35891 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGGAGAT
* **
35914 TAACAAAATTTCATAATGAGAT
1 TATCAAAATTTCATAGGGAGAT
** *
35936 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGGAGAT
*
35958 TATCAAAA-TT--T--GTAG-T
1 TATCAAAATTTCATAGGGAGAT
* * *
35974 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGGGAGA-T
* *
35996 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGA-GAT
* *
36019 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGGAGA-T
* *
36042 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGGGAGAT
* * *
36064 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGGGAGAT
* * *
36086 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGAGAT
* *
36108 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATAGGGAGAT
* * * ** * *
36130 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGGGAGAT
* * * *
36152 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAGGGAGAT
* * ** *
36174 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GGAGAT
* *
36197 CATCAAAATTTCATTGGGA-AGT
1 TATCAAAATTTCATAGGGAGA-T
36219 TATCAAAATTTCATA
1 TATCAAAATTTCATA
36234 TTGAGGTCTT
Statistics
Matches: 322, Mismatches: 83, Indels: 47
0.71 0.18 0.10
Matches are distributed among these distances:
16 8 0.02
17 5 0.02
19 10 0.03
20 5 0.02
21 6 0.02
22 226 0.70
23 62 0.19
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGGAGAT
Found at i:36293 original size:22 final size:21
Alignment explanation
Indices: 36259--36299 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
36249 TTCCTTGGGG
**
36259 ATGTTAACCAAATTTCATAAGA
1 ATGTTAAAAAAATTT-ATAAGA
36281 ATGTTAAAAAAATTTATAA
1 ATGTTAAAAAAATTTATAA
36300 AAAGGTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (21 bp):
ATGTTAAAAAAATTTATAAGA
Found at i:36342 original size:22 final size:22
Alignment explanation
Indices: 36311--36364 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
36301 AAGGTTCTCG
* * * *
36311 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
36333 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
36355 AAATTTCATA
1 AAATTTCATA
36365 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:39424 original size:8 final size:8
Alignment explanation
Indices: 39411--39439 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39401 AACCATCTTG
39411 CCTTTGCA
1 CCTTTGCA
39419 CCTTTGCA
1 CCTTTGCA
39427 CCTTTGCA
1 CCTTTGCA
39435 CCTTT
1 CCTTT
39440 CATCGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.38, G:0.10, T:0.41
Consensus pattern (8 bp):
CCTTTGCA
Found at i:39540 original size:2 final size:2
Alignment explanation
Indices: 39533--39560 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39523 ATTTTTAGTA
39533 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
39561 TACTAAAAAT
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
Done.