Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014802.1 Corchorus olitorius cultivar O-4 contig14835, 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: 66053
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:2085 original size:34 final size:34
Alignment explanation
Indices: 2022--2088 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2012 AAATGCTTTT
**
2022 GATGGGAACTTTCCCATTTTAAAAGACTAAAACC
1 GATGGGAACTTTCCCAAATTAAAAGACTAAAACC
*
2056 GATGGGAACTTTCCCTAAATTGAAA-ACTAAAAC
1 GATGGGAACTTTCCC-AAATTAAAAGACTAAAAC
2089 TTGGTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (34 bp):
GATGGGAACTTTCCCAAATTAAAAGACTAAAACC
Found at i:2175 original size:33 final size:33
Alignment explanation
Indices: 2115--2207 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
2105 AAAATTGAAT
* *
2115 GGGAACTTTCCCAATTTGAAAACTTAAAACCGGC
1 GGGAACTTTCCCAA-TTAAAAACTTAAAACCAGC
* * *
2149 GGGAACTTTCCCGATTAAAAACTTAAAACTAGT
1 GGGAACTTTCCCAATTAAAAACTTAAAACCAGC
*
2182 GGGAACTTTCCCAATAAAAAACTTAA
1 GGGAACTTTCCCAATTAAAAACTTAA
2208 TGAAATTCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 39 0.75
34 13 0.25
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (33 bp):
GGGAACTTTCCCAATTAAAAACTTAAAACCAGC
Found at i:9835 original size:2 final size:2
Alignment explanation
Indices: 9828--9864 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9818 GACTTATAAT
*
9828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9865 GTATTCTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10207 original size:19 final size:18
Alignment explanation
Indices: 10170--10217 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
10160 GAATTAATTC
*
10170 TTATTAAATTTTCTTTTG
1 TTATTAAATTTTCTATTG
*
10188 TTATTACAATTTTGTATTG
1 TTATTA-AATTTTCTATTG
10207 TGTATATAAAT
1 T-TAT-TAAAT
10218 AATACTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 6 0.24
21 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.58
Consensus pattern (18 bp):
TTATTAAATTTTCTATTG
Found at i:14845 original size:2 final size:2
Alignment explanation
Indices: 14833--14892 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
14823 AGTTTAGACT
* * *
14833 TA TA TA GTA TA TA GA TA TA TA GA TA TA GA TA TA TA TA TA -A TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14875 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
14893 AAAGATAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:14907 original size:21 final size:21
Alignment explanation
Indices: 14861--14908 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14851 ATAGATATAG
* * *
14861 ATATATATATAATATATATAT
1 ATATATATATAAAAGATAAAT
14882 ATATATATATAAAAGATAAAT
1 ATATATATATAAAAGATAAAT
*
14903 TTATAT
1 ATATAT
14909 GTTTAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATATATATAAAAGATAAAT
Found at i:23471 original size:13 final size:13
Alignment explanation
Indices: 23454--23492 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
23444 TCTATTTTTC
23454 AAAAAAAAAA-AA
1 AAAAAAAAAACAA
* *
23466 CAAAAAAAAGCAA
1 AAAAAAAAAACAA
23479 AAAAAAAAAACAA
1 AAAAAAAAAACAA
23492 A
1 A
23493 GCAATATGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.90, C:0.08, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:23482 original size:18 final size:18
Alignment explanation
Indices: 23458--23496 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
23448 TTTTTCAAAA
*
23458 AAAAAAAACAAAAAAAAGC
1 AAAAAAAA-AAAACAAAGC
23477 AAAAAAAAAAAACAAAGC
1 AAAAAAAAAAAACAAAGC
23495 AA
1 AA
23497 TATGGGCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAACAAAGC
Found at i:24052 original size:2 final size:2
Alignment explanation
Indices: 24041--24079 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
24031 TACTATACAC
*
24041 TA TA TA -A TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24080 CCATAATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:26444 original size:17 final size:17
Alignment explanation
Indices: 26422--26455 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26412 TCTTATTCAC
26422 CTTCATAATTTTGTTTT
1 CTTCATAATTTTGTTTT
26439 CTTCATAATTTTGTTTT
1 CTTCATAATTTTGTTTT
26456 GACCAAGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
CTTCATAATTTTGTTTT
Found at i:31444 original size:47 final size:48
Alignment explanation
Indices: 31370--31465 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
31360 ACGGCAGGGG
31370 ACAAAATGTCCTTTTTTCATAGTTCAAGGGGCAAAATCATATATATAT
1 ACAAAATGTCCTTTTTTCATAGTTCAAGGGGCAAAATCATATATATAT
31418 ACAAAATGTCC-TTTTTCATAGTTCAAGGGGCAAAATCATATATATAT
1 ACAAAATGTCCTTTTTTCATAGTTCAAGGGGCAAAATCATATATATAT
31465 A
1 A
31466 TATATATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 37 0.77
48 11 0.23
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (48 bp):
ACAAAATGTCCTTTTTTCATAGTTCAAGGGGCAAAATCATATATATAT
Found at i:31462 original size:2 final size:2
Alignment explanation
Indices: 31455--31483 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31445 GGGCAAAATC
31455 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
31484 AAAGATTAAG
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:31761 original size:17 final size:16
Alignment explanation
Indices: 31721--31763 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
31711 CATGTAATCT
* *
31721 TTGATCACCGGTGATC
1 TTGATCACTGATGATC
31737 TTGCATCACTGATGATC
1 TTG-ATCACTGATGATC
31754 TTAGATCACT
1 TT-GATCACT
31764 AGTGATCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (16 bp):
TTGATCACTGATGATC
Found at i:32850 original size:21 final size:21
Alignment explanation
Indices: 32826--32908 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
32816 TATCTTAGAT
32826 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
32847 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
32868 ATAAATAATA-AGTTCAAAATAA
1 AT-AATAATATA-TTTTAAATAA
32890 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
32909 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 18 0.35
22 21 0.41
23 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:38532 original size:3 final size:3
Alignment explanation
Indices: 38500--38597 Score: 134
Period size: 3 Copynumber: 33.3 Consensus size: 3
38490 CTATATATAT
38500 ATA A-A ATA A-A AT- ATA AT- ATA ATA TATA ATA ATA AT- ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT-A
38542 ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
38588 ATA ATA ATA A
1 ATA ATA ATA A
38598 ACTATATAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 16
0.84 0.00 0.16
Matches are distributed among these distances:
2 10 0.11
3 68 0.78
4 9 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40244 original size:20 final size:19
Alignment explanation
Indices: 40216--40253 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40206 TAGTTTACCC
*
40216 TTTTTAAATTATAATTAATG
1 TTTTAAAATTA-AATTAATG
40236 TTTTAAAATTAAATTAAT
1 TTTTAAAATTAAATTAAT
40254 AAGAGACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTAAATTAATG
Found at i:40431 original size:60 final size:60
Alignment explanation
Indices: 40367--40495 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
40357 GCAAAAATGT
* * * * * *
40367 TCAAATAAGA-ACCCGTTCTTTTAATTTGGTCAAATAGGACCATAAC-TTATGCGAAGATGC
1 TCAAATAAGAGA-CCATGCTTTTAATTTGGCCAAATAGGACCATAACGTT-GGCGAAAAAGC
* * *
40427 TCAAATAAGAGATCATGCTTTTAATTTGGCCAAATAGGTCCCTAACGTTGGCGAAAAAGC
1 TCAAATAAGAGACCATGCTTTTAATTTGGCCAAATAGGACCATAACGTTGGCGAAAAAGC
40487 TCAAATAAG
1 TCAAATAAG
40496 GCTCTGATGT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
60 55 0.95
61 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (60 bp):
TCAAATAAGAGACCATGCTTTTAATTTGGCCAAATAGGACCATAACGTTGGCGAAAAAGC
Found at i:40834 original size:22 final size:22
Alignment explanation
Indices: 40782--40993 Score: 88
Period size: 22 Copynumber: 9.5 Consensus size: 22
40772 TGACAATCAA
* ** *
40782 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGTGAGGTT
* * *
40804 ATCACAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
40826 ACCAAAATTTCATA-TAGAGGTT
1 ACCAAAATTTCATAGT-GAGGTT
**** *
40848 ATTGGAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGTG-AGGTT
* **
40870 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
* *** *
40892 ACCAAAATTTCCTAAAAAAGTT
1 ACCAAAATTTCATAGTGAGGTT
* * *
40914 ACCAAAATTTCTTAGGGATGTT
1 ACCAAAATTTCATAGTGAGGTT
** *
40936 AATAAAATTTCATA-TGTAAGTT
1 ACCAAAATTTCATAGTG-AGGTT
* *
40958 AACAAAATTTCATGGGGAGGGAGGTT
1 ACCAAAATTTCAT----AGTGAGGTT
40984 ACCAAAATTT
1 ACCAAAATTT
40994 GTGCTTATCA
Statistics
Matches: 140, Mismatches: 40, Indels: 16
0.71 0.20 0.08
Matches are distributed among these distances:
21 3 0.02
22 120 0.86
23 2 0.01
26 14 0.10
27 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGAGGTT
Found at i:41050 original size:22 final size:23
Alignment explanation
Indices: 41025--41073 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
41015 GGAGATTAAC
41025 AAAAGTTTATAGG-GAGGTTAT-G
1 AAAAGTTTAT-GGAGAGGTTATCG
*
41047 AAAATTTTATGGAGAGGTTATCG
1 AAAAGTTTATGGAGAGGTTATCG
41070 AAAA
1 AAAA
41074 TACACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.31
Consensus pattern (23 bp):
AAAAGTTTATGGAGAGGTTATCG
Found at i:41244 original size:22 final size:22
Alignment explanation
Indices: 41219--41363 Score: 121
Period size: 22 Copynumber: 6.6 Consensus size: 22
41209 TATAGGCAGA
* *
41219 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAATGAGG
* * * *
41241 TTATCGAAACTTT-GTAGTAAGG
1 TTATC-AAAATTTCATAATGAGG
* *
41263 TTACCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAATGAGG
* **
41285 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAATGAGG
* *
41307 TTATCGAAATTCCATAATGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
41329 TTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCATAATGAGG
*
41351 TTATCAATATTTC
1 TTATCAAAATTTC
41364 TACATTGGAG
Statistics
Matches: 93, Mismatches: 28, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
21 6 0.06
22 81 0.87
23 6 0.06
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:41289 original size:66 final size:66
Alignment explanation
Indices: 41219--41363 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 66
41209 TATAGGCAGA
* ** * *
41219 TTATCAAAATTTCACACTGAGGTTATCGAAACTT-TGTAGTAAGGTTACCAAAATTTCATAATGT
1 TTATCAAAATTTCACACGGAGGTTATCGAAA-TTCCATAATAAGGTTACCAAAATTTCAAAATGT
41283 GG
65 GG
* * * * * *
41285 TTATCAAATTTTCATAGGGAGGTTATCGAAATTCCATAATGAGGTTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCACACGGAGGTTATCGAAATTCCATAATAAGGTTACCAAAATTTCAAAATGTG
41350 G
66 G
*
41351 TTATCAATATTTC
1 TTATCAAAATTTC
41364 TACATTGGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 2 0.03
66 63 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (66 bp):
TTATCAAAATTTCACACGGAGGTTATCGAAATTCCATAATAAGGTTACCAAAATTTCAAAATGTG
G
Found at i:42104 original size:78 final size:78
Alignment explanation
Indices: 41944--42093 Score: 255
Period size: 78 Copynumber: 1.9 Consensus size: 78
41934 AGATTTATAG
* * *
41944 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATATTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATATTTATAACTATTTCAGTT
42009 TACCATTAGACTA
66 TACCATTAGACTA
* *
42022 TTTTACTCAACTAAAAACTCTATTTTCATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATATTTATAACTATTTCAGTT
42087 TACCATT
66 TACCATT
42094 TTATTATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATATTTATAACTATTTCAGTT
TACCATTAGACTA
Found at i:43725 original size:16 final size:16
Alignment explanation
Indices: 43704--43741 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
43694 TAAAATCAAT
43704 TTTCACCAAATTTAAA
1 TTTCACCAAATTTAAA
*
43720 TTTCACCAAATTTTAA
1 TTTCACCAAATTTAAA
43736 TTTCAC
1 TTTCAC
43742 GTGTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTCACCAAATTTAAA
Found at i:47435 original size:19 final size:20
Alignment explanation
Indices: 47411--47464 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
47401 GTGGTCTATG
47411 TTTGGTGTAATG-ATCATTA
1 TTTGGTGTAATGTATCATTA
47430 TTTGGTGTAATGGTATCATTA
1 TTTGGTGTAAT-GTATCATTA
47451 -TTGAGTGTAATGTA
1 TTTG-GTGTAATGTA
47465 AAATCTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.34
20 7 0.22
21 14 0.44
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTGGTGTAATGTATCATTA
Found at i:48540 original size:3 final size:3
Alignment explanation
Indices: 48532--48566 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
48522 TTTCACAAAA
48532 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48567 AGGAGCAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:51615 original size:31 final size:31
Alignment explanation
Indices: 51580--51641 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
51570 TCACTTTTAG
* *
51580 TGAATCAAACTCAACTTTGAAATCATGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
51611 TGAATCAAACTCAACTTTGAAACCAAGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
51642 AGTTTCTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (31 bp):
TGAATCAAACTCAACTTTGAAACCAAGATCA
Found at i:52891 original size:2 final size:2
Alignment explanation
Indices: 52884--52921 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52874 GTAAGTCGGT
52884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52922 GGTGGTGCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65870 original size:38 final size:38
Alignment explanation
Indices: 65814--65889 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
65804 TGAAATGAAC
65814 TTAATCACATGTTACAATTATAAGGAACATCTATATAT
1 TTAATCACATGTTACAATTATAAGGAACATCTATATAT
* * *
65852 TTAATCGCATGTTGCAATTATAAGGAACATTTATATAT
1 TTAATCACATGTTACAATTATAAGGAACATCTATATAT
65890 GGGATTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (38 bp):
TTAATCACATGTTACAATTATAAGGAACATCTATATAT
Done.