Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019029.1 Corchorus olitorius cultivar O-4 contig19062, 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: 69769
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6330 original size:21 final size:21
Alignment explanation
Indices: 6306--6348 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6296 CAGAAATTAT
6306 TTTGTTGCCTCTTGAAATGTG
1 TTTGTTGCCTCTTGAAATGTG
6327 TTTGTTGCCTCTTGAAATGTG
1 TTTGTTGCCTCTTGAAATGTG
6348 T
1 T
6349 GGGGATCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (21 bp):
TTTGTTGCCTCTTGAAATGTG
Found at i:25911 original size:103 final size:102
Alignment explanation
Indices: 25766--25990 Score: 258
Period size: 102 Copynumber: 2.2 Consensus size: 102
25756 AAACTTTATA
* * * * * * *
25766 ATAATAATAAATTTTAAATTATAATACTTACCCTATACTTTTTTTATTTCTAAAT-T-TGGTTAA
1 ATAATAATAAATTTTAAATTACAATACTAACCCAATA-ATTTTTT-TTACT-AATGTGGGGCTAA
** * *
25829 TTTTTATGAAATTATAGTTAAATATTCAAACTAAAACCTT
63 AATTTATGAAATTATAGTAAAATATTCAAACTAAAACCCT
*
25869 ATAATAATAAATTTTAAACTT-CAGTACTAACCCAATAATTTTTTTTACTAATGTGGGGCTAAAA
1 ATAATAATAAATTTTAAA-TTACAATACTAACCCAATAATTTTTTTTACTAATGTGGGGCTAAAA
*
25933 TTTATGAAATTATGGTAAAATATTCAAACTAAAACCCT
65 TTTATGAAATTATAGTAAAATATTCAAACTAAAACCCT
* *
25971 ATACTAATAAATCTTAAATT
1 ATAATAATAAATTTTAAATT
25991 TTGAGTTCTA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 3 0.03
101 7 0.07
102 62 0.60
103 30 0.29
104 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (102 bp):
ATAATAATAAATTTTAAATTACAATACTAACCCAATAATTTTTTTTACTAATGTGGGGCTAAAAT
TTATGAAATTATAGTAAAATATTCAAACTAAAACCCT
Found at i:26534 original size:22 final size:22
Alignment explanation
Indices: 26509--26760 Score: 128
Period size: 22 Copynumber: 11.6 Consensus size: 22
26499 TGTTAGTAAA
* *
26509 CACACTCTGAAATTTTGATAAT
1 CACACTATGAAATTTTGATAAC
*
26531 CACACTATGAAATTGTGATAAC
1 CACACTATGAAATTTTGATAAC
* * *
26553 CTCGCTATGAAATTTTGATAAA
1 CACACTATGAAATTTTGATAAC
*
26575 CATTC-CTATAAAATTTTGATAAAC
1 CA--CACTATGAAATTTTGAT-AAC
* * *
26599 CTCCCTATAAAATTTTGATAAC
1 CACACTATGAAATTTTGATAAC
* *
26621 CTC-CTTATGAAATCTTGAT---
1 CACAC-TATGAAATTTTGATAAC
*
26640 -A-ACTA-CAAATTTTGATAAC
1 CACACTATGAAATTTTGATAAC
* * * *
26659 CTCCCTATGATATTTCGATAAC
1 CACACTATGAAATTTTGATAAC
* * * * *
26681 CTCATTACGAAATTTTGTTAAT
1 CACACTATGAAATTTTGATAAC
* * * *
26703 CTCCCTAGGAAATTTTGATCTA-
1 CACACTATGAAATTTTGAT-AAC
*
26725 CATACTATGAAATTTTGATAAC
1 CACACTATGAAATTTTGATAAC
*
26747 C-CTCTTATGAAATT
1 CACAC-TATGAAATT
26761 CTGAAAACTA
Statistics
Matches: 175, Mismatches: 40, Indels: 30
0.71 0.16 0.12
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 1 0.01
21 6 0.03
22 123 0.70
23 30 0.17
24 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (22 bp):
CACACTATGAAATTTTGATAAC
Found at i:26615 original size:46 final size:44
Alignment explanation
Indices: 26518--26619 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 44
26508 ACACACTCTG
* * * *
26518 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAAACACACTATAAAATTGTGATAACCTCCCTATA
*
26562 AAATTTTGATAAACATTC-CTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACA--CACTATAAAATTGTGAT-AACCTCCCTATA
26608 AAATTTTGATAA
1 AAATTTTGATAA
26620 CCTCCTTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 14 0.28
45 13 0.26
46 23 0.46
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAAACACACTATAAAATTGTGATAACCTCCCTATA
Found at i:26947 original size:22 final size:22
Alignment explanation
Indices: 26922--27088 Score: 99
Period size: 22 Copynumber: 7.6 Consensus size: 22
26912 AATCACATTT
* *
26922 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTCTA
*
26944 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
26966 T-AAAATTTCATTGACCCCTCTA
1 TGAAAATTTGA-TAACCTCTCTA
* * *
26988 TGAAATTTTGATAATCACATC-A
1 TGAAAATTTGATAACCTC-TCTA
* * * *
27010 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* ** *
27032 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* *
27054 TGAAATTTTGATAATCT-TCCTA
1 TGAAAATTTGATAACCTCT-CTA
*
27076 T-AAATTTTGATAA
1 TGAAAATTTGATAA
27089 TCCGGTCTCT
Statistics
Matches: 114, Mismatches: 26, Indels: 11
0.75 0.17 0.07
Matches are distributed among these distances:
21 20 0.18
22 85 0.75
23 9 0.08
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:27036 original size:44 final size:45
Alignment explanation
Indices: 26985--27090 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 45
26975 ATTGACCCCT
*
26985 CTATGAAATTTTGATAATC-ACA-TCATGTAATTTTGATAA-CCTC
1 CTATGAAATTTTGATAATCAACACT-ATGAAATTTTGATAATCCTC
* *
27028 GCTTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCCTC
27073 CTAT-AAATTTTGATAATC
1 CTATGAAATTTTGATAATC
27091 CGGTCTCTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
43 13 0.24
44 37 0.69
45 4 0.07
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (45 bp):
CTATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCCTC
Found at i:27060 original size:88 final size:88
Alignment explanation
Indices: 26897--27061 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 88
26887 AGAAATACCA
* ** ** **
26897 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTTTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAACCTGCTTATGAAATTTTGATAACAAC
*
26962 TCTATAAAATTTCATTGACCCCT
66 ACTATAAAATTTCATTGACCCCT
* *
26985 CTATGAAATTTTGATAATCACATCATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAACCT-GCTTATGAAATTTTGATAACAA
*
27049 CACTATGAAATTT
65 CACTATAAAATTT
27062 TGATAATCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
88 63 0.97
89 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATCATGAAAATTTGATAACCTGCTTATGAAATTTTGATAACAAC
ACTATAAAATTTCATTGACCCCT
Found at i:27203 original size:22 final size:22
Alignment explanation
Indices: 27174--27265 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
27164 AAATTGAGAC
27174 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTCATATGAAA
*
27195 TTTTGATAACC-ACACCT-TGAAA
1 TTTTGATAACCTTCA--TATGAAA
* **
27217 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTTCATATGAAA
* * *
27239 -TATCAGTAACCTTCTTATGAAA
1 TTTTGA-TAACCTTCATATGAAA
27261 TTTTG
1 TTTTG
27266 TTGACCACAC
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
21 9 0.17
22 40 0.75
23 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTTCATATGAAA
Found at i:27448 original size:22 final size:22
Alignment explanation
Indices: 27318--27549 Score: 152
Period size: 22 Copynumber: 10.5 Consensus size: 22
27308 TGATAATCTC
* * *
27318 TTTGATAACATTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* * * *
27340 TGTGATAACCATACTATGAAAC
1 TTTGATAACCTTCCTATGAAAT
** *
27362 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
27384 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* *
27408 TTT-ATTATCC-ACACTATGAAAT
1 TTTGA-TAACCTTC-CTATGAAAT
*
27430 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
27452 TTTGATAA-CTTCCATATGAAATT
1 TTTGATAACCTTCC-TATGAAA-T
* * *
27475 TTTG-TAACC-ACACTACGGAAT
1 TTTGATAACCTTC-CTATGAAAT
27496 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * *
27518 TATAATAACCATCTTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
27540 TTTTATAACC
1 TTTGATAACC
27550 ACACAGAGAC
Statistics
Matches: 165, Mismatches: 32, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
21 13 0.08
22 122 0.74
23 13 0.08
24 17 0.10
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:27497 original size:66 final size:65
Alignment explanation
Indices: 27366--27553 Score: 218
Period size: 66 Copynumber: 2.8 Consensus size: 65
27356 TGAAACTTCA
* * * *
27366 ATAACCTTCCTAAGAAATTTTAATAACCTGATCCTATGAAATTTTATTATCCACACTATGAAATT
1 ATAACCTTCCCATGAAATTTTAATAACCT--TCCTATGAAATTTT-TTAACCACACTACGAAATT
27431 TTG
63 TTG
* *
27434 ATAACCTTCCCATGAAATTTTGATAA-CTTCCATATGAAATTTTTGTAACCACACTACGGAATTT
1 ATAACCTTCCCATGAAATTTTAATAACCTTCC-TATGAAATTTTT-TAACCACACTACGAAATTT
27498 TG
64 TG
* * *
27500 ATAACC-TCCTCATGAAATTATAATAACCATCTTATGAAATTTTTATAACCACAC
1 ATAACCTTCC-CATGAAATTTTAATAACCTTCCTATGAAATTTTT-TAACCACAC
27554 AGAGACAAGA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
65 7 0.07
66 70 0.67
67 5 0.05
68 23 0.22
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (65 bp):
ATAACCTTCCCATGAAATTTTAATAACCTTCCTATGAAATTTTTTAACCACACTACGAAATTTTG
Found at i:27747 original size:19 final size:20
Alignment explanation
Indices: 27716--27753 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27706 TATTGACATT
27716 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
27735 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
27754 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:28030 original size:14 final size:15
Alignment explanation
Indices: 27999--28036 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
27989 CGGTCAAAAT
27999 TTAAATTTT--ATAA
1 TTAAATTTTAAATAA
28012 TTAAATTTTAAATAA
1 TTAAATTTTAAATAA
28027 -TAAATTTTAA
1 TTAAATTTTAA
28037 TCTTGTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATTTTAAATAA
Found at i:31340 original size:2 final size:2
Alignment explanation
Indices: 31335--31362 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31325 AAAAAAAACA
31335 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
31363 TAAACATGCA
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:31799 original size:65 final size:65
Alignment explanation
Indices: 31716--31846 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
31706 TTTAACACCT
*
31716 CACTGGTGTTAAAGCACTTTCTCACTTTGAAGAGAAAGTATTTGGGTTAGTTAAACTTTCTTATC
1 CACTGGTGTTAAAACACTTTCTCACTTTGAAGAGAAAGTATTTGGGTTAGTTAAACTTTCTTATC
*
31781 CACTGGTGTTAAAACACTTTCTCACTTTGGAGAGAAAGTATTTGGGTTAGTTAAACTTTCTTATC
1 CACTGGTGTTAAAACACTTTCTCACTTTGAAGAGAAAGTATTTGGGTTAGTTAAACTTTCTTATC
31846 C
1 C
31847 TAAACTTTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (65 bp):
CACTGGTGTTAAAACACTTTCTCACTTTGAAGAGAAAGTATTTGGGTTAGTTAAACTTTCTTATC
Found at i:38115 original size:2 final size:2
Alignment explanation
Indices: 38108--38147 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
38098 ACATCCCTTT
38108 TA 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 TA
38148 CTTAAGGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41099 original size:2 final size:2
Alignment explanation
Indices: 41094--41137 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
41084 TATGTAGATG
41094 TA TA 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 TA TA
41136 TA
1 TA
41138 CCAATATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42231 original size:12 final size:12
Alignment explanation
Indices: 42214--42238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42204 TCGCCTTCTG
42214 ATCTTGTTTAAT
1 ATCTTGTTTAAT
42226 ATCTTGTTTAAT
1 ATCTTGTTTAAT
42238 A
1 A
42239 CTCCTTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATCTTGTTTAAT
Found at i:45107 original size:11 final size:9
Alignment explanation
Indices: 45082--45106 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
45072 ACTAAAAATA
45082 ATATATAGT
1 ATATATAGT
45091 ATATATAGT
1 ATATATAGT
45100 ATATATA
1 ATATATA
45107 TGGTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:52329 original size:130 final size:131
Alignment explanation
Indices: 52194--52456 Score: 411
Period size: 130 Copynumber: 2.0 Consensus size: 131
52184 GCCATTAGAC
52194 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * * *
52259 TTTAATTTTTACCATTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
52323 T
131 T
* * * * *
52324 TTTTATAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
52389 TTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
52454 T
131 T
52455 TT
1 TT
52457 CTTAAATGAC
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
130 86 0.72
131 34 0.28
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
T
Found at i:60238 original size:32 final size:32
Alignment explanation
Indices: 60178--60239 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
60168 ACCCCCATTG
* * * **
60178 GCCGGTCGCGATTCGGTCGCGATTGGCCATGA
1 GCCGGTCGCGATCCGCTCGCAACCGGCCATGA
60210 GCCGGTCGCGATCCGCTCGCAACCGGCCAT
1 GCCGGTCGCGATCCGCTCGCAACCGGCCAT
60240 ATTTTCGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.13, C:0.35, G:0.34, T:0.18
Consensus pattern (32 bp):
GCCGGTCGCGATCCGCTCGCAACCGGCCATGA
Found at i:60321 original size:21 final size:21
Alignment explanation
Indices: 60291--60333 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
60281 ATTTACCCCG
*
60291 TCTGGCGTCGATGGCTCGTTA
1 TCTGGCGTCGATGGATCGTTA
*
60312 TCTGGGGTCGATGGATCGTTA
1 TCTGGCGTCGATGGATCGTTA
60333 T
1 T
60334 TGTCCATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.35, T:0.35
Consensus pattern (21 bp):
TCTGGCGTCGATGGATCGTTA
Found at i:62810 original size:105 final size:106
Alignment explanation
Indices: 62626--62829 Score: 365
Period size: 105 Copynumber: 1.9 Consensus size: 106
62616 AACACATATT
*
62626 TACATAGAGCGATATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGTGATCT
1 TACATAGAGCGA-ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCT
*
62691 CTAAACCGCAAAAAAGAAATTACATACCATCACCATTTGACA
65 CTAAACCGCAAAAAAGAAAATACATACCATCACCATTTGACA
62733 TACATAGAGCG-ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTC
1 TACATAGAGCGAATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTC
*
62797 TAAACCGTAAAAAAGAAAATACATACCATCACC
66 TAAACCGCAAAAAAGAAAATACATACCATCACC
62830 TCCTGAAAGT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
105 83 0.88
107 11 0.12
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (106 bp):
TACATAGAGCGAATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTC
TAAACCGCAAAAAAGAAAATACATACCATCACCATTTGACA
Found at i:62917 original size:80 final size:75
Alignment explanation
Indices: 62744--63046 Score: 301
Period size: 75 Copynumber: 3.8 Consensus size: 75
62734 ACATAGAGCG
*
62744 ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTCTAAACCGTAAAA
1 ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTCTAAACCGCAAAA
62809 AAGAAAATAC
66 AAGAAAATAC
*
62819 ATACCATCACCTCCTGAAAGTGAACACATATTTGACATACATACATAGAGCGATCTCTAAACCGC
1 ATACCATCACCTTCTGAAAGTGAACACATATTTG----ACATACATAGAGCGATCTCTAAACCGC
62884 AAAAAAAGAAAATAC
62 -AAAAAAGAAAATAC
* * *
62899 ATACCATCACCTTCTGAAAGCG-A-ACATATTTCACATACATATTTGA-C-ATAC-ATAAAGCGA
1 ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATA---GAGCGAT-CTCTAAA-C--
*
62959 TCTCTAAACCGCAAAAAAGAAAATAC
59 -CGC---A----AAAA-AGAAAATAC
* *
62985 ATACCATCGCCTTCTAAAAGTGAACACATATATTGACATACATAGAGCGATCTCTAAACCGC
1 ATACCATCACCTTCTGAAAGTGAACACATAT-TTGACATACATAGAGCGATCTCTAAACCGC
63047 TCTAGATCTT
Statistics
Matches: 189, Mismatches: 13, Indels: 43
0.77 0.05 0.18
Matches are distributed among these distances:
74 9 0.05
75 39 0.21
76 3 0.02
77 2 0.01
78 8 0.04
79 29 0.15
80 34 0.18
81 2 0.01
84 2 0.01
85 4 0.02
86 30 0.16
87 4 0.02
88 12 0.06
89 11 0.06
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.22
Consensus pattern (75 bp):
ATACCATCACCTTCTGAAAGTGAACACATATTTGACATACATAGAGCGATCTCTAAACCGCAAAA
AAGAAAATAC
Found at i:62940 original size:13 final size:13
Alignment explanation
Indices: 62922--62952 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62912 CTGAAAGCGA
62922 ACATATTTCACAT
1 ACATATTTCACAT
*
62935 ACATATTTGACAT
1 ACATATTTCACAT
62948 ACATA
1 ACATA
62953 AAGCGATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.35
Consensus pattern (13 bp):
ACATATTTCACAT
Found at i:63050 original size:86 final size:84
Alignment explanation
Indices: 62857--63028 Score: 211
Period size: 86 Copynumber: 2.0 Consensus size: 84
62847 TATTTGACAT
* * *
62857 ACATACATAGAGCGATCTCTAAACCGCAAAAAAAGAAAATACATACCATCACCTTCTGAAAGCGA
1 ACATACATAAACCGA-CTCTAAACCGCAAAAAAAGAAAATACATACCATCACCTTCTAAAAGCGA
62922 ACATATTTCACATACATATTTG
65 ACATATTTCACATACATA--TG
* * *
62944 ACATACATAAAGCGATCTCTAAACCGC-AAAAAAGAAAATACATACCATCGCCTTCTAAAAGTGA
1 ACATACATAAACCGA-CTCTAAACCGCAAAAAAAGAAAATACATACCATCACCTTCTAAAAGCG-
*
63008 ACACATATATTGACATACATA
64 A-ACATAT-TTCACATACATA
63029 GAGCGATCTC
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
86 33 0.43
87 27 0.35
88 6 0.08
89 11 0.14
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (84 bp):
ACATACATAAACCGACTCTAAACCGCAAAAAAAGAAAATACATACCATCACCTTCTAAAAGCGAA
CATATTTCACATACATATG
Found at i:69709 original size:26 final size:27
Alignment explanation
Indices: 69662--69714 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
69652 TTTTTTTTTC
* *
69662 GAAAAAATAGAAAAAAGGAAAACAAAA
1 GAAAAAATAGAAAAAAGCAAAAAAAAA
* *
69689 GAAAAGAT-GAAAAAATCAAAAAAAAA
1 GAAAAAATAGAAAAAAGCAAAAAAAAA
69715 TTTCTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (27 bp):
GAAAAAATAGAAAAAAGCAAAAAAAAA
Done.