Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024203.1 Corchorus olitorius cultivar O-4 contig24236, 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: 118707
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6579 original size:2 final size:2
Alignment explanation
Indices: 6572--6650 Score: 88
Period size: 2 Copynumber: 40.0 Consensus size: 2
6562 AACCTTTTTG
* * *
6572 AT AT AT AT AT AT AT AT GT AT GT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
6614 AT AT AT CT AT AT AT AT AT AA AT AA AT A- AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6651 CAAGTAAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:10127 original size:18 final size:18
Alignment explanation
Indices: 10104--10140 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10094 ACCGCTAAAA
10104 CACAATGCATCATAATCG
1 CACAATGCATCATAATCG
10122 CACAATGCATCATAATCG
1 CACAATGCATCATAATCG
10140 C
1 C
10141 TCCCCCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.22
Consensus pattern (18 bp):
CACAATGCATCATAATCG
Found at i:14894 original size:48 final size:48
Alignment explanation
Indices: 14840--14986 Score: 276
Period size: 48 Copynumber: 3.1 Consensus size: 48
14830 AATTGAAGCA
*
14840 CAATGACAACTCCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
1 CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
14888 CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
1 CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
*
14936 CAATGACAACTTCAGGTGTCAAACATACTATGTGACAACTTCTGGTGT
1 CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
14984 CAA
1 CAA
14987 AATGAAAATG
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (48 bp):
CAATGACAACTTCAGGCGTCAAACATACTATGTGACAACTTCTGGTGT
Found at i:14908 original size:19 final size:19
Alignment explanation
Indices: 14872--14909 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14862 ACATACTATG
* *
14872 TGACAACTTCTGGTGTCAA
1 TGACAACTTCAGGCGTCAA
14891 TGACAACTTCAGGCGTCAA
1 TGACAACTTCAGGCGTCAA
14910 ACATACTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (19 bp):
TGACAACTTCAGGCGTCAA
Found at i:14944 original size:19 final size:19
Alignment explanation
Indices: 14920--14957 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
14910 ACATACTATG
*
14920 TGACAACTTCTGGTGTCAA
1 TGACAACTTCAGGTGTCAA
14939 TGACAACTTCAGGTGTCAA
1 TGACAACTTCAGGTGTCAA
14958 ACATACTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (19 bp):
TGACAACTTCAGGTGTCAA
Found at i:15102 original size:34 final size:36
Alignment explanation
Indices: 15013--15109 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 36
15003 ATAATTCCAA
* ***
15013 CCTCAGCATGACAACTTCTACTGTCAACTTTAATTT
1 CCTCAGCATGACAACTTCTAGTGTCAAAAATAATTT
* *
15049 CCTCAGCGTAACAACTTCTAGTGTCAAAAATAATTT
1 CCTCAGCATGACAACTTCTAGTGTCAAAAATAATTT
15085 -CTCA-CATGACAACTTCTAGTGTCAA
1 CCTCAGCATGACAACTTCTAGTGTCAA
15110 TTAAATTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 19 0.36
35 4 0.08
36 30 0.57
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (36 bp):
CCTCAGCATGACAACTTCTAGTGTCAAAAATAATTT
Found at i:19352 original size:26 final size:26
Alignment explanation
Indices: 19323--19374 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
19313 TAAATAAGTC
*
19323 TTAGTTCTGAGACCTTATC-TACCATT
1 TTAGTTCTGAGAACTTA-CGTACCATT
19349 TTAGTTCTGAGAACTTACGTACCATT
1 TTAGTTCTGAGAACTTACGTACCATT
19375 CTAGCTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (26 bp):
TTAGTTCTGAGAACTTACGTACCATT
Found at i:19493 original size:15 final size:15
Alignment explanation
Indices: 19473--19504 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19463 TGATACAGGT
19473 CAAATCCAGACCAAG
1 CAAATCCAGACCAAG
19488 CAAATCCAGACCAAG
1 CAAATCCAGACCAAG
19503 CA
1 CA
19505 CAAGTGCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.34, G:0.12, T:0.06
Consensus pattern (15 bp):
CAAATCCAGACCAAG
Found at i:22721 original size:2 final size:2
Alignment explanation
Indices: 22716--22748 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22706 ACATATATAA
22716 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22749 TATAACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22909 original size:17 final size:17
Alignment explanation
Indices: 22887--22921 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22877 AACATAGAAC
22887 AACTTAGATTTCATCCA
1 AACTTAGATTTCATCCA
22904 AACTTAGATTTCATCCA
1 AACTTAGATTTCATCCA
22921 A
1 A
22922 GAAGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (17 bp):
AACTTAGATTTCATCCA
Found at i:25983 original size:12 final size:12
Alignment explanation
Indices: 25966--25994 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
25956 CCGGATCAGG
25966 TTGGGTTCGGGT
1 TTGGGTTCGGGT
25978 TTGGGTTCGGGT
1 TTGGGTTCGGGT
25990 TTGGG
1 TTGGG
25995 GCATCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.52, T:0.41
Consensus pattern (12 bp):
TTGGGTTCGGGT
Found at i:26763 original size:22 final size:22
Alignment explanation
Indices: 26715--26763 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
26705 TTGCCATTTT
*
26715 TCTCT-CTCCCCCCACTAACTC
1 TCTCTCCTCCCCCCACTAACTA
* * *
26736 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCCCCCCACTAACTA
26758 TCTCTC
1 TCTCTC
26764 TTTATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCTCCTCCCCCCACTAACTA
Found at i:27295 original size:16 final size:15
Alignment explanation
Indices: 27275--27331 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
27265 TTTTTTCAGG
*
27275 TTCGGGTTTTGGTTT
1 TTCGGGTTTTGATTT
*
27290 TATCGGGTTTTAAATTT
1 T-TCGGGTTTT-GATTT
*
27307 TTCGGGTTCTGATTTT
1 TTCGGGTTTTGA-TTT
27323 TTCGGGTTT
1 TTCGGGTTT
27332 AAGTTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.06
16 28 0.82
17 4 0.12
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.56
Consensus pattern (15 bp):
TTCGGGTTTTGATTT
Found at i:27338 original size:16 final size:15
Alignment explanation
Indices: 27287--27343 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
27277 CGGGTTTTGG
*
27287 TTTTATCGGGTTTTAA
1 TTTTTTCGGG-TTTAA
* *
27303 ATTTTTCGGGTTCTGA
1 TTTTTTCGGGTT-TAA
27319 TTTTTTCGGGTTTAA
1 TTTTTTCGGGTTTAA
27334 GTTTTTTCGG
1 -TTTTTTCGG
27344 CTTGGGTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.12
16 30 0.88
ACGTcount: A:0.12, C:0.09, G:0.23, T:0.56
Consensus pattern (15 bp):
TTTTTTCGGGTTTAA
Found at i:27343 original size:32 final size:32
Alignment explanation
Indices: 27275--27339 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
27265 TTTTTTCAGG
* *
27275 TTCGGGTTTTGGTTTTATCGGGTTTTAAATTT
1 TTCGGGTTCTGATTTTATCGGGTTTTAAATTT
* *
27307 TTCGGGTTCTGATTTTTTCGGG-TTTAAGTTT
1 TTCGGGTTCTGATTTTATCGGGTTTTAAATTT
27338 TT
1 TT
27340 TCGGCTTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.11, C:0.08, G:0.25, T:0.57
Consensus pattern (32 bp):
TTCGGGTTCTGATTTTATCGGGTTTTAAATTT
Found at i:28129 original size:16 final size:16
Alignment explanation
Indices: 28110--28141 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28100 GCTCTACAAG
*
28110 GCAGAAAAGCTCTGAA
1 GCAGAAAAGCCCTGAA
28126 GCAGAAAAGCCCTGAA
1 GCAGAAAAGCCCTGAA
28142 AAATCAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (16 bp):
GCAGAAAAGCCCTGAA
Found at i:29208 original size:33 final size:33
Alignment explanation
Indices: 29159--29229 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
29149 AAGCATCTGA
* * *
29159 TCAGCAAAAGGTCAGTGAGCTGATGAATCCAAG
1 TCAGCAAAAGGCCAGTGAGATGATCAATCCAAG
*
29192 TCAGTAAAAGGCCAGTGAGATGATCAATCCAAG
1 TCAGCAAAAGGCCAGTGAGATGATCAATCCAAG
*
29225 CCAGC
1 TCAGC
29230 TGAAGGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (33 bp):
TCAGCAAAAGGCCAGTGAGATGATCAATCCAAG
Found at i:32594 original size:38 final size:38
Alignment explanation
Indices: 32543--32768 Score: 353
Period size: 38 Copynumber: 5.9 Consensus size: 38
32533 AAATTTATTA
*
32543 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
*
32581 GTCTTGGTCCCAAGCGAATGATGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
32619 GTCTTGGTCCCAAGCCAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
32657 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
32695 GTCTTGATCCCAAGCGAATAATAAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* ** * *
32733 GTCTTGATCAAAAGCGAATAATGAATTTGGTCGCTT
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTT
32769 TCTTGCAAGT
Statistics
Matches: 174, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 174 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (38 bp):
GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
Found at i:37542 original size:25 final size:26
Alignment explanation
Indices: 37514--37563 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
37504 TAAGAAAGGT
37514 TGAAGCAAAACACCAATA-AAAAAAG
1 TGAAGCAAAACACCAATATAAAAAAG
*
37539 TGAAGGAAAACACCAATATAAAAAA
1 TGAAGCAAAACACCAATATAAAAAA
37564 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (26 bp):
TGAAGCAAAACACCAATATAAAAAAG
Found at i:37677 original size:33 final size:33
Alignment explanation
Indices: 37639--37789 Score: 162
Period size: 33 Copynumber: 4.6 Consensus size: 33
37629 CGATCAACTC
* *
37639 AGATCGATGCTAAAATTATTGGTTTATCAGCTT
1 AGATCGACGCTAAAATTATTGGGTTATCAGCTT
* *
37672 AGATCGACGCTAAAGTTATTGGGTTCTCAGC-T
1 AGATCGACGCTAAAATTATTGGGTTATCAGCTT
* * *
37704 -CATCGATGCTAAAATTATTGGGTTATTAGCTT
1 AGATCGACGCTAAAATTATTGGGTTATCAGCTT
* * * ** * *
37736 AGATCGACGCTGAAATAACTGGACTCTTAGCTT
1 AGATCGACGCTAAAATTATTGGGTTATCAGCTT
37769 AGATCGACGCTAAAATTATTG
1 AGATCGACGCTAAAATTATTG
37790 AGTTGCCAAA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
31 25 0.26
32 2 0.02
33 69 0.72
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (33 bp):
AGATCGACGCTAAAATTATTGGGTTATCAGCTT
Found at i:41523 original size:22 final size:22
Alignment explanation
Indices: 41495--41545 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
41485 TCCTATTATG
*
41495 AAATTTTTACAACATTCCTATA
1 AAATTTTGACAACATTCCTATA
* * *
41517 AAATTTTGATAACGTTCCTATG
1 AAATTTTGACAACATTCCTATA
41539 AAATTTT
1 AAATTTT
41546 AGTAAGCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATTTTGACAACATTCCTATA
Found at i:41602 original size:22 final size:22
Alignment explanation
Indices: 41558--41685 Score: 130
Period size: 22 Copynumber: 5.8 Consensus size: 22
41548 TAAGCTCTAA
* * * *
41558 ATGAAATTTTGGTGATCATATT
1 ATGAAATTTTGATAACCACATT
*
41580 ATGAAATTGTGATAACCACATT
1 ATGAAATTTTGATAACCACATT
* * *
41602 ATGAAATTGTGATAACCTCAGT
1 ATGAAATTTTGATAACCACATT
*
41624 ATGAAATTTTGATAACCAAATT
1 ATGAAATTTTGATAACCACATT
* ** *
41646 ATGAAATTTTAATAACTTCAAT
1 ATGAAATTTTGATAACCACATT
*
41668 ATGAAATTTTGACAACCA
1 ATGAAATTTTGATAACCA
41686 TACAGAGACA
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 86 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACATT
Found at i:41661 original size:66 final size:66
Alignment explanation
Indices: 41558--41684 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
41548 TAAGCTCTAA
* * * * * * *
41558 ATGAAATTTTGGTGATCATATTATGAAATTGTGATAACCACATTATGAAATTGTGATAACCTCAG
1 ATGAAATTTTGATAACCAAATTATGAAATTGTAATAACCACAATATGAAATTGTGACAACCTCAG
41623 T
66 T
* ** *
41624 ATGAAATTTTGATAACCAAATTATGAAATTTTAATAACTTCAATATGAAATTTTGACAACC
1 ATGAAATTTTGATAACCAAATTATGAAATTGTAATAACCACAATATGAAATTGTGACAACC
41685 ATACAGAGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (66 bp):
ATGAAATTTTGATAACCAAATTATGAAATTGTAATAACCACAATATGAAATTGTGACAACCTCAG
T
Found at i:43365 original size:7 final size:7
Alignment explanation
Indices: 43353--43392 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
43343 CCTATTACTA
43353 TATATAT
1 TATATAT
43360 TATATAT
1 TATATAT
* *
43367 AATATAA
1 TATATAT
43374 TATATAT
1 TATATAT
43381 TA-ATAT
1 TATATAT
43387 TATATA
1 TATATA
43393 GTCTAAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TATATAT
Found at i:47735 original size:4 final size:4
Alignment explanation
Indices: 47726--47751 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
47716 AAAATATTCA
47726 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
47752 ATAGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:50897 original size:23 final size:23
Alignment explanation
Indices: 50852--50898 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
50842 GCTAGTGGTC
*
50852 TTTAGCCTCTTTGATGCTCTGTT
1 TTTAGCCTCTATGATGCTCTGTT
*
50875 TTTAGCCT-TATGATGTCTTTGTT
1 TTTAGCCTCTATGATG-CTCTGTT
50898 T
1 T
50899 ATCTGCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.55
Consensus pattern (23 bp):
TTTAGCCTCTATGATGCTCTGTT
Found at i:55743 original size:30 final size:30
Alignment explanation
Indices: 55707--55855 Score: 208
Period size: 30 Copynumber: 5.0 Consensus size: 30
55697 TTTACTATTT
* * *
55707 CAATTGACACCAGAAGTTGTCATGGTCTTA
1 CAATTGACACCAGAAGTTGTCATGATTTTG
*
55737 CAATTGACACCAAAAGTTGTCATGATTTTG
1 CAATTGACACCAGAAGTTGTCATGATTTTG
*
55767 CAATTGACACCAGAAATTGTCATGATTTTG
1 CAATTGACACCAGAAGTTGTCATGATTTTG
*
55797 CAATTGACACCAGAAATTGTCATGATTTTG
1 CAATTGACACCAGAAGTTGTCATGATTTTG
* * * *
55827 CAATTAACAGCTGAAGTTGTCATAATTTT
1 CAATTGACACCAGAAGTTGTCATGATTTT
55856 ATATCTTAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 108 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (30 bp):
CAATTGACACCAGAAGTTGTCATGATTTTG
Found at i:59163 original size:4 final size:4
Alignment explanation
Indices: 59156--59196 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
59146 AGGAATATAT
* *
59156 ATAG ATAG ATAG ATAG ATAT ATAG AT-C ATAG ATA- ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
59197 AATCCATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
3 5 0.16
4 26 0.84
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (4 bp):
ATAG
Found at i:59209 original size:26 final size:27
Alignment explanation
Indices: 59156--59210 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
59146 AGGAATATAT
* * *
59156 ATAGATAGATAGATAGATATATAGATC
1 ATAGATAGATAGATAAATACATACATC
*
59183 ATAGATA-ATAGATAAATCCATACATC
1 ATAGATAGATAGATAAATACATACATC
59209 AT
1 AT
59211 GTTAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (27 bp):
ATAGATAGATAGATAAATACATACATC
Found at i:60088 original size:42 final size:45
Alignment explanation
Indices: 60035--60131 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 45
60025 AAAGTGCATT
* *
60035 ACCTAA-ATTCTACT-CT-GTCTCTAGAT-GATTCATCAAAATAA
1 ACCTAATATTCTACTCCTCATCTCTAGATAAATTCATCAAAATAA
*
60076 AGCTAATATTCTACTCCTCCATCTCTAGATAAATTCATCAAAATAA
1 ACCTAATATTCTACTCCT-CATCTCTAGATAAATTCATCAAAATAA
60122 ACCTAATATT
1 ACCTAATATT
60132 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 5 0.11
42 8 0.17
43 2 0.04
45 9 0.19
46 23 0.49
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (45 bp):
ACCTAATATTCTACTCCTCATCTCTAGATAAATTCATCAAAATAA
Found at i:62407 original size:11 final size:11
Alignment explanation
Indices: 62364--62401 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
62354 TTCTTATATA
*
62364 AAATAAATTAT
1 AAATTAATTAT
62375 CAAA-TAATTAT
1 -AAATTAATTAT
62386 AAATTAATTAT
1 AAATTAATTAT
62397 AAATT
1 AAATT
62402 GGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:64624 original size:41 final size:41
Alignment explanation
Indices: 64556--64871 Score: 183
Period size: 41 Copynumber: 7.5 Consensus size: 41
64546 TTTTTTTTTT
* * *
64556 GAAGGCCAACTGATGCCATCTTTGAAAACTCAAAACTTTAA
1 GAAGGCCAACCGATGCCAACTTCGAAAACTCAAAACTTTAA
* * **
64597 GAGGGTCAACCGATGCCAACTTCGAAAACTTTAAACTTTAA
1 GAAGGCCAACCGATGCCAACTTCGAAAACTCAAAACTTTAA
* * **
64638 GAAGGCCAACCGATACCAACTTTTTAGAAGGCAACCGATGCCAACTTTGAAAACTAGATA
1 GAAGGCCAACCGATGCCAAC---TTCGAA---AA-C--T--CAA-------AACTTTA-A
*
64698 GAAGGCCAACCGATGCCAAC-TCTGAAAACT--AGA---T-A
1 GAAGGCCAACCGATGCCAACTTC-GAAAACTCAAAACTTTAA
*
64733 GAAGGCCAACCGATGCCAAC-TCTGAAAACTCAAAACCTTAA
1 GAAGGCCAACCGATGCCAACTTC-GAAAACTCAAAACTTTAA
* * *
64774 GAAGGCCAACTGATACCAACTTTGAAAACTCAAAACTTTAA
1 GAAGGCCAACCGATGCCAACTTCGAAAACTCAAAACTTTAA
* *
64815 GAAGGCCAACCGATACCAACTTTGAAAACT-----CTTT-A
1 GAAGGCCAACCGATGCCAACTTCGAAAACTCAAAACTTTAA
64850 GAAGGCCAACCGATGCCAACTT
1 GAAGGCCAACCGATGCCAACTT
64872 TTGAAAAAAA
Statistics
Matches: 222, Mismatches: 26, Indels: 60
0.72 0.08 0.19
Matches are distributed among these distances:
35 53 0.24
36 4 0.02
37 2 0.01
40 2 0.01
41 116 0.52
42 1 0.00
44 5 0.02
47 3 0.01
48 1 0.00
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
54 2 0.01
56 1 0.00
57 3 0.01
59 5 0.02
60 20 0.09
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (41 bp):
GAAGGCCAACCGATGCCAACTTCGAAAACTCAAAACTTTAA
Found at i:64672 original size:25 final size:26
Alignment explanation
Indices: 64637--64685 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
64627 TTAAACTTTA
64637 AGAAGGCCAACCGATACCAACTTTTT
1 AGAAGGCCAACCGATACCAACTTTTT
*
64663 AGAAGG-CAACCGATGCCAACTTT
1 AGAAGGCCAACCGATACCAACTTT
64686 GAAAACTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (26 bp):
AGAAGGCCAACCGATACCAACTTTTT
Found at i:64708 original size:35 final size:35
Alignment explanation
Indices: 64662--64988 Score: 255
Period size: 35 Copynumber: 8.7 Consensus size: 35
64652 ACCAACTTTT
64662 TAGAAGG-CAACCGATGCCAACTTTGAAAACTAGA
1 TAGAAGGCCAACCGATGCCAACTTTGAAAACTAGA
*
64696 TAGAAGGCCAACCGATGCCAACTCTGAAAACTAGA
1 TAGAAGGCCAACCGATGCCAACTTTGAAAACTAGA
* *
64731 TAGAAGGCCAACCGATGCCAACTCTGAAAACTCAAAA
1 TAGAAGGCCAACCGATGCCAACTTTGAAAACT--AGA
* * *
64768 CCTTAAGAAGGCCAACTGATACCAACTTTGAAAACTCAAAA
1 ---T-AGAAGGCCAACCGATGCCAACTTTGAAAACT--AGA
* ***
64809 CTTTAAGAAGGCCAACCGATACCAACTTTGAAAACTCTT
1 ---T-AGAAGGCCAACCGATGCCAACTTTGAAAACTAGA
*
64848 TAGAAGGCCAACCGATGCCAACTTTTGAAAAAAAAACTCGA
1 TAGAAGGCCAACCGATGCCAAC-TTTG-----AAAACTAGA
* * *
64889 TTTTAAAGAAGGCAAACCGATGCCAACATTGAAAACTAGT
1 ---T--AGAAGGCCAACCGATGCCAACTTTGAAAACTAGA
**
64929 TAGAAGGCCAACCGATGCCAACTTTTGAAGATTTA-A
1 TAGAAGGCCAACCGATGCCAAC-TTTGAA-AACTAGA
*
64965 -AGAAGGCCAACCGATGCCGACTTT
1 TAGAAGGCCAACCGATGCCAACTTT
64989 TATAAAACTC
Statistics
Matches: 250, Mismatches: 23, Indels: 40
0.80 0.07 0.13
Matches are distributed among these distances:
34 10 0.04
35 118 0.47
36 10 0.04
37 6 0.02
40 8 0.03
41 74 0.30
44 1 0.00
45 3 0.01
46 20 0.08
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (35 bp):
TAGAAGGCCAACCGATGCCAACTTTGAAAACTAGA
Found at i:66928 original size:2 final size:2
Alignment explanation
Indices: 66921--66951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66911 TCTATACCTT
66921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66952 TTTACCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67096 original size:13 final size:13
Alignment explanation
Indices: 67078--67102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67068 TAGAAATTCC
67078 AAATAATATTTAT
1 AAATAATATTTAT
67091 AAATAATATTTA
1 AAATAATATTTA
67103 GAACATTGAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:69422 original size:19 final size:19
Alignment explanation
Indices: 69398--69436 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
69388 ACAATGTACC
*
69398 TTTGAAGTATTGAGCTTTT
1 TTTGAAGTATTAAGCTTTT
69417 TTTGAAGTATTAAGCTTTT
1 TTTGAAGTATTAAGCTTTT
69436 T
1 T
69437 GCAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (19 bp):
TTTGAAGTATTAAGCTTTT
Found at i:79255 original size:33 final size:33
Alignment explanation
Indices: 79212--79301 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
79202 TATTATTTTC
*
79212 TCTCCCAGTGCCTTTACGATTTTCATTTT-AATT
1 TCTCCTAGTGCCTTTA-GATTTTCATTTTAAATT
*
79245 TCTCCTAGTGCCTTTAGTATTTACATTTTAAATT
1 TCTCCTAGTGCCTTTAG-ATTTTCATTTTAAATT
*
79279 TCTCCTAGTTCCTTTAGGATTTT
1 TCTCCTAGTGCCTTTA-GATTTT
79302 GATTAGTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 1 0.02
33 25 0.50
34 23 0.46
35 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (33 bp):
TCTCCTAGTGCCTTTAGATTTTCATTTTAAATT
Found at i:86750 original size:3 final size:3
Alignment explanation
Indices: 86742--86776 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
86732 GATGTATCTT
86742 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86777 GATGTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:87381 original size:26 final size:26
Alignment explanation
Indices: 87352--87406 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
87342 ATAAATGGTT
87352 CAATTTAATACTTTTTCTGATAAGTG
1 CAATTTAATACTTTTTCTGATAAGTG
*
87378 CAATTTAGTACTTTTTCTGATAAGTG
1 CAATTTAATACTTTTTCTGATAAGTG
87404 CAA
1 CAA
87407 CTCATGTGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (26 bp):
CAATTTAATACTTTTTCTGATAAGTG
Found at i:89583 original size:19 final size:19
Alignment explanation
Indices: 89549--89597 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
89539 GGAGAAAAAA
*
89549 AAGAAAA-AAAAAGGAGAG
1 AAGAAAAGAAAATGGAGAG
89567 AAGAAAAGAAAATGGAGAG
1 AAGAAAAGAAAATGGAGAG
*
89586 GA-AAAAGAAAAT
1 AAGAAAAGAAAAT
89598 ATAATTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (19 bp):
AAGAAAAGAAAATGGAGAG
Found at i:91380 original size:94 final size:94
Alignment explanation
Indices: 91259--91449 Score: 364
Period size: 94 Copynumber: 2.0 Consensus size: 94
91249 GACGTTTCAA
*
91259 ACATATTTACAAACATGCAAGGAAGCATGTTGTTATTAGAGAGTGGAGTAGCATGTTGTAATTTG
1 ACATATTTACAAACATGCAAGGAAGCATGTTGTTATTAGAGAGTGGAGTAGAATGTTGTAATTTG
*
91324 AAGACATTTTTAATTATTATGTAACATAT
66 AAGACATTTTCAATTATTATGTAACATAT
91353 ACATATTTACAAACATGCAAGGAAGCATGTTGTTATTAGAGAGTGGAGTAGAATGTTGTAATTTG
1 ACATATTTACAAACATGCAAGGAAGCATGTTGTTATTAGAGAGTGGAGTAGAATGTTGTAATTTG
91418 AAGACATTTTCAATTATTATGTAACATAT
66 AAGACATTTTCAATTATTATGTAACATAT
91447 ACA
1 ACA
91450 AAGCAGGAGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (94 bp):
ACATATTTACAAACATGCAAGGAAGCATGTTGTTATTAGAGAGTGGAGTAGAATGTTGTAATTTG
AAGACATTTTCAATTATTATGTAACATAT
Found at i:92278 original size:6 final size:6
Alignment explanation
Indices: 92267--92291 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
92257 TACGTTGAAC
92267 GGGAAT GGGAAT GGGAAT GGGAAT G
1 GGGAAT GGGAAT GGGAAT GGGAAT G
92292 TGAAACGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGGAAT
Found at i:103383 original size:28 final size:29
Alignment explanation
Indices: 103343--103399 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
103333 GGAATCTGAG
103343 GTAATCCTTTAGAAAATTTT-GGGGTTTT
1 GTAATCCTTTAGAAAATTTTGGGGGTTTT
103371 GTAATCCTTTAGAAAATTTTGGGGGTTTT
1 GTAATCCTTTAGAAAATTTTGGGGGTTTT
103400 TATTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.46
Consensus pattern (29 bp):
GTAATCCTTTAGAAAATTTTGGGGGTTTT
Found at i:104877 original size:2 final size:2
Alignment explanation
Indices: 104870--104903 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
104860 GTGAGGATGG
104870 AT AT AT 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 AT AT AT
104904 TACATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106329 original size:36 final size:37
Alignment explanation
Indices: 106259--106329 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
106249 ACAATCTATT
*
106259 AATTGCTGATATTGTATAGAGTACCTAACCCATGAATG
1 AATTGCTGATAATG-ATAGAGTACCTAACCCATGAATG
* *
106297 AATTGCTGATAATG-TAGGGTATCTAACCCATGA
1 AATTGCTGATAATGATAGAGTACCTAACCCATGA
106330 CTTATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 17 0.57
38 13 0.43
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (37 bp):
AATTGCTGATAATGATAGAGTACCTAACCCATGAATG
Found at i:106685 original size:89 final size:89
Alignment explanation
Indices: 106534--106700 Score: 271
Period size: 89 Copynumber: 1.9 Consensus size: 89
106524 TAGCTAGTCA
* * *
106534 AATCATAATAATGGTCGCATTAGATTGGTCTATTTAAACAAAAAATTGCAACCAATATTTAGAAA
1 AATCACAATAATGGTCACATTAGATTGGTCAATTTAAACAAAAAATTGCAACCAATATTTAGAAA
*
106599 GCAATATTGGTCGTAAAGTTGGCT
66 GCAACATTGGTCGTAAAGTTGGCT
* * *
106623 AATCACAATATTGGTCACATTAGATTGGTCAATTTGAACAAAAAATTGCAACCAATGTTTAGAAA
1 AATCACAATAATGGTCACATTAGATTGGTCAATTTAAACAAAAAATTGCAACCAATATTTAGAAA
106688 GCAACATTGGTCG
66 GCAACATTGGTCG
106701 CAAACTTTGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (89 bp):
AATCACAATAATGGTCACATTAGATTGGTCAATTTAAACAAAAAATTGCAACCAATATTTAGAAA
GCAACATTGGTCGTAAAGTTGGCT
Found at i:112795 original size:19 final size:18
Alignment explanation
Indices: 112762--112797 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
112752 TTGAAATTAT
112762 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
112780 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
112798 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:117539 original size:10 final size:10
Alignment explanation
Indices: 117517--117550 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
117507 ACCTCTTGTA
117517 ACATACC-TC
1 ACATACCTTC
117526 ACATACCTTC
1 ACATACCTTC
117536 ACATACCTTC
1 ACATACCTTC
117546 ACATA
1 ACATA
117551 ATTCTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (10 bp):
ACATACCTTC
Found at i:118372 original size:15 final size:16
Alignment explanation
Indices: 118339--118372 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
118329 TTACTTTGCT
118339 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
118355 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
118370 TTG
1 TTG
118373 CCTTCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.