Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012951.1 Corchorus olitorius cultivar O-4 contig12984, 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: 72114
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1020 original size:6 final size:6
Alignment explanation
Indices: 1009--1034 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
999 TTTTATATAG
1009 TAGTAA TAGTAA TAGTAA TAGTAA TA
1 TAGTAA TAGTAA TAGTAA TAGTAA TA
1035 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
TAGTAA
Found at i:5963 original size:21 final size:20
Alignment explanation
Indices: 5939--5977 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5929 TGTGGGATGA
*
5939 GAAATCAGGGCTAGTGTTCAT
1 GAAATCAGGG-TAATGTTCAT
5960 GAAATCAGGGTAATGTTC
1 GAAATCAGGGTAATGTTC
5978 TAAGCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (20 bp):
GAAATCAGGGTAATGTTCAT
Found at i:13193 original size:23 final size:23
Alignment explanation
Indices: 13167--13215 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
13157 CTAAATTTCT
* * *
13167 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
13190 AAGTTTAAACAATCAACTCTATA
1 AAGTTTAAACAATCAACTCTATA
13213 AAG
1 AAG
13216 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Found at i:21218 original size:185 final size:183
Alignment explanation
Indices: 20759--21248 Score: 777
Period size: 184 Copynumber: 2.7 Consensus size: 183
20749 AATTAACACT
* * * * *
20759 AAATCAGGTTCTATACACATGAAATTAGGTTAAATTTCACACGTGCACTTCCCAATTAGATAGAA
1 AAATCAGGTTCTAAACACATGAAATTAGGTTTAATTCCACACGTGCACATCCCGATT-GATAGAA
* *
20824 TTTAAAAACCCTAGAGTGCCGAGCCCTTAATTACATAAATTGCAAGTTGGGCGGCACTCAATTTC
65 TTTAAAAACCCTAGAGTGACGAGCCCTTAATTGCATAAATTGCAAGTTGGGCGGCACTCAATTTC
*
20889 CCCATATTCTTAGGGTTTCGGCTAAAATTGTTATTTTGGCCAATTATTTACATC
130 CCCATATTCTTAGGGTTTCGGCTAAAATTGCTATTTTGGCCAATTATTTACATC
20943 AAATCAGGTTCTAAACACATGAAATTAGGTTTAATTCCACACGTGCACATCCCGATTGAATAGAA
1 AAATCAGGTTCTAAACACATGAAATTAGGTTTAATTCCACACGTGCACATCCCGATTG-ATAGAA
21008 TTTAAAAACCCTAGAGTGACGAGCCCTTAATTGCATAAATTGCAAGTTGGGCGGCACTCAATTTC
65 TTTAAAAACCCTAGAGTGACGAGCCCTTAATTGCATAAATTGCAAGTTGGGCGGCACTCAATTTC
* *
21073 CTCATATTCTTAGGGTTTCGGCTAAAATTGCTATTTTTGGCTAATTATTTACATC
130 CCCATATTCTTAGGGTTTCGGCTAAAATTGCTA-TTTTGGCCAATTATTTACATC
*
21128 AAATCAGGTTCTAAACACATGAAATCAGGTTTAATTCCACACGTGCACATCCCGATTGAT-GAAT
1 AAATCAGGTTCTAAACACATGAAATTAGGTTTAATTCCACACGTGCACATCCCGATTGATAGAA-
** * *
21192 TTTGGCAAACCCTAGCA-TGTCGAGCCCTTAATTGCAAAAATTGCAAGTTGGGCGGCA
65 TTT-AAAAACCCTAG-AGTGACGAGCCCTTAATTGCATAAATTGCAAGTTGGGCGGCA
21249 TGCTCTTTAA
Statistics
Matches: 286, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
183 4 0.01
184 157 0.55
185 124 0.43
186 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (183 bp):
AAATCAGGTTCTAAACACATGAAATTAGGTTTAATTCCACACGTGCACATCCCGATTGATAGAAT
TTAAAAACCCTAGAGTGACGAGCCCTTAATTGCATAAATTGCAAGTTGGGCGGCACTCAATTTCC
CCATATTCTTAGGGTTTCGGCTAAAATTGCTATTTTGGCCAATTATTTACATC
Found at i:21542 original size:22 final size:22
Alignment explanation
Indices: 21493--21543 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21483 AAATATTACC
* **
21493 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
21515 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
21538 A-AATTA
1 ATAATTA
21544 AGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:24264 original size:26 final size:27
Alignment explanation
Indices: 24235--24288 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
24225 AAATTAAAAG
*
24235 TGAACCTA-AAATGACCAAAATGCCCC
1 TGAACATACAAATGACCAAAATGCCCC
*
24261 TGAACATACAAATGACCAGAATGCCCC
1 TGAACATACAAATGACCAAAATGCCCC
24288 T
1 T
24289 AGGTGACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.17
Consensus pattern (27 bp):
TGAACATACAAATGACCAAAATGCCCC
Found at i:24619 original size:53 final size:50
Alignment explanation
Indices: 24562--24675 Score: 122
Period size: 50 Copynumber: 2.2 Consensus size: 50
24552 TCTTTGGGGA
* *
24562 ATCGTCTTCCGAATCAATTTCTTTGAATTGTCTTCCAA-TCTAATAATAAAAGG
1 ATCGTCTTCCGAATC---TCCTTTGAAATGTCTTCCAATTC-AATAATAAAAGG
** **
24615 ATCGTCTTCCGCTTCTCCTTTGAAATGTCTTCCAATTCAATCTTAAAAGG
1 ATCGTCTTCCGAATCTCCTTTGAAATGTCTTCCAATTCAATAATAAAAGG
*
24665 ACCGTCTTCCG
1 ATCGTCTTCCG
24676 CTTATCCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
50 38 0.72
51 2 0.04
53 13 0.25
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (50 bp):
ATCGTCTTCCGAATCTCCTTTGAAATGTCTTCCAATTCAATAATAAAAGG
Found at i:24662 original size:50 final size:50
Alignment explanation
Indices: 24582--24688 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
24572 GAATCAATTT
* * *
24582 CTTTGAATTGTCTTCCAATCTAATAATAAAAGGATCGTCTTCCGCTTCTC
1 CTTTGAAATGTCTTCCAATCTAATAATAAAAGGACCGTCTTCCGCTTATC
**
24632 CTTTGAAATGTCTTCCAAT-TCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAAATGTCTTCCAATCT-AATAATAAAAGGACCGTCTTCCGCTTATC
24682 CTTTGAA
1 CTTTGAA
24689 CAGTCTCCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (50 bp):
CTTTGAAATGTCTTCCAATCTAATAATAAAAGGACCGTCTTCCGCTTATC
Found at i:24694 original size:23 final size:23
Alignment explanation
Indices: 24668--24720 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
24658 TAAAAGGACC
24668 GTCTTCCGCTTATCCTTTGAACA
1 GTCTTCCGCTTATCCTTTGAACA
*
24691 GTCTCCCGCTTATCCTTTGAACA
1 GTCTTCCGCTTATCCTTTGAACA
24714 GTCTTCC
1 GTCTTCC
24721 AATTCGATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.34, G:0.13, T:0.38
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACA
Found at i:24708 original size:73 final size:73
Alignment explanation
Indices: 24618--24767 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 73
24608 TAAAAGGATC
* *
24618 GTCTTCCGCTTCTCCTTTGAA-ATGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 GTCTCCCGCTTATCCTTTGAACA-GTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
24682 CTTTGAACA
65 CTTTGAACA
*
24691 GTCTCCCGCTTATCCTTTGAACAGTCTTCCAATTCGATCTTAAAAGGACCGTCTTCCGCTTATCC
1 GTCTCCCGCTTATCCTTTGAACAGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC
*
24756 TTTGAACT
66 TTTGAACA
24764 GTCT
1 GTCT
24768 TCCAATTCGA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 71 0.99
74 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (73 bp):
GTCTCCCGCTTATCCTTTGAACAGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC
TTTGAACA
Found at i:24837 original size:51 final size:50
Alignment explanation
Indices: 24691--24838 Score: 233
Period size: 50 Copynumber: 2.9 Consensus size: 50
24681 CCTTTGAACA
* *
24691 GTCTCCCGCTTATCCTTTGAACAGTCTTCCAATTCGATCTTAAAAGGACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCGATCTTAAAAGGACC
24741 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCGATCTTAAAAGGACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCGATCTTAAAAGGACC
* * * *
24791 GTCTTCCGCTTATCCTTTTGTACTGTCTCCCAATTCAATCTAAAAAGG
1 GTCTTCCGCTTATCC-TTTGAACTGTCTTCCAATTCGATCTTAAAAGG
24839 TATTGTACCG
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 63 0.69
51 28 0.31
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (50 bp):
GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCGATCTTAAAAGGACC
Found at i:25052 original size:68 final size:68
Alignment explanation
Indices: 24946--25102 Score: 242
Period size: 68 Copynumber: 2.3 Consensus size: 68
24936 AGAAATGAAC
* * * *
24946 TTGGCTTATGAAAAAGCCTCTACTGCTTGGATGTAACCAAGGTTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCC-CTACTGCTCGGATGGAACCAAGGTTTGAACTGACTCGTATGGAAAC
25011 GAGT
65 GAGT
* *
25015 TTGGCTTGTGGAAAAGCCCTGCTGCTCGGATGGAACCAAGGTTTGAACTGACTCGTATGGGAACG
1 TTGGCTTGTGGAAAAGCCCTACTGCTCGGATGGAACCAAGGTTTGAACTGACTCGTATGGAAACG
25080 AGT
66 AGT
*
25083 TTGACTTGTGGAAAAGCCCT
1 TTGGCTTGTGGAAAAGCCCT
25103 TGTTGCTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
68 65 0.80
69 16 0.20
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCTACTGCTCGGATGGAACCAAGGTTTGAACTGACTCGTATGGAAACG
AGT
Found at i:25890 original size:50 final size:50
Alignment explanation
Indices: 25740--25890 Score: 189
Period size: 50 Copynumber: 3.0 Consensus size: 50
25730 TTAAATGCCC
* * *
25740 TTTGAAAAGCGAATTTTGATCTTG-GACTCACAACTGGAATGCAATCTTAC
1 TTTGAAAAGCGAATTTTGATCTTGAG-CTCACAAATGGAAAGCAATCTTAT
* * * *
25790 TTTGAAAAGCGAGTTTTAAT-TTGGAACTCACAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTT-GAGCTCACAAATGGAAAGCAATCTTAT
* *
25840 TTTGAAAAGCGAATTTTGATCTTGAGCTCATAAATGGAAAGAAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAAAGCAATCTTAT
25890 T
1 T
25891 ATAAAACTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
49 2 0.02
50 81 0.95
51 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAAAGCAATCTTAT
Found at i:34059 original size:78 final size:78
Alignment explanation
Indices: 33892--34052 Score: 268
Period size: 78 Copynumber: 2.1 Consensus size: 78
33882 AAAATCTAGT
* * * * *
33892 TAAAGTAGTTAAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAA
33957 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
33970 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAAA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAA
34035 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
34048 TAAAA
1 TAAAA
34053 CTGTAAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.35
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAA
GTTTTTAGTTGAG
Found at i:34160 original size:6 final size:6
Alignment explanation
Indices: 34143--34192 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
34133 GTACTTTTTA
34143 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
34190 ATA
1 ATA
34193 ATATATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:36904 original size:12 final size:11
Alignment explanation
Indices: 36875--36902 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
36865 TTTTGGTTGA
36875 TTTTTTAAATT
1 TTTTTTAAATT
36886 TTTTTTAAATT
1 TTTTTTAAATT
36897 TTTTTT
1 TTTTTT
36903 TACAGGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:37008 original size:15 final size:15
Alignment explanation
Indices: 36977--37056 Score: 70
Period size: 18 Copynumber: 4.9 Consensus size: 15
36967 TGGAGGAGGA
36977 GGTTATGGTGGTGGT
1 GGTTATGGTGGTGGT
** *
36992 GGTGGTGGCTATGGTGGA
1 GGTTATGG---TGGTGGT
*
37010 GGTTATGGCGGTGGT
1 GGTTATGGTGGTGGT
37025 GGTTACAGTGGTGGTGGT
1 GGTT--A-TGGTGGTGGT
37043 GGTTATGGTGGTGG
1 GGTTATGGTGGTGG
37057 CGGTGGCGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
15 24 0.47
16 1 0.02
17 1 0.02
18 25 0.49
ACGTcount: A:0.09, C:0.04, G:0.54, T:0.34
Consensus pattern (15 bp):
GGTTATGGTGGTGGT
Found at i:37040 original size:18 final size:18
Alignment explanation
Indices: 37019--37062 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
37009 AGGTTATGGC
37019 GGTGGTGGTTACAGTGGT
1 GGTGGTGGTTACAGTGGT
**
37037 GGTGGTGGTTATGGTGGT
1 GGTGGTGGTTACAGTGGT
*
37055 GGCGGTGG
1 GGTGGTGG
37063 CGGCAGCGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.05, G:0.57, T:0.32
Consensus pattern (18 bp):
GGTGGTGGTTACAGTGGT
Found at i:38402 original size:29 final size:29
Alignment explanation
Indices: 38370--38429 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
38360 GGAGAGTTAG
*
38370 GAGAGTTCCTCCATATGGAGCTGGATGTA
1 GAGAGTTCCCCCATATGGAGCTGGATGTA
*
38399 GAGAGTTCCCCCGTATGGAGCTGGATGTA
1 GAGAGTTCCCCCATATGGAGCTGGATGTA
38428 GA
1 GA
38430 CCAATGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.25
Consensus pattern (29 bp):
GAGAGTTCCCCCATATGGAGCTGGATGTA
Found at i:44166 original size:27 final size:28
Alignment explanation
Indices: 44133--44185 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
44123 TTCAAAAATT
44133 TACTACTGCCAAAT-TATAATTTAAAAA
1 TACTACTGCCAAATATATAATTTAAAAA
*
44160 TACTACTGGCAAATATATAATTTAAA
1 TACTACTGCCAAATATATAATTTAAA
44186 TTTTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (28 bp):
TACTACTGCCAAATATATAATTTAAAAA
Found at i:50794 original size:158 final size:159
Alignment explanation
Indices: 50505--50823 Score: 577
Period size: 158 Copynumber: 2.0 Consensus size: 159
50495 AATATAAAAG
50505 TTATATGAATCATTTGATAAATAAACCAAAAAAATGATTTATTTATTGATAGCGGGATCCACCAA
1 TTATATGAATCATTTGATAAATAAACCAAAAAAATGATTTATTTATTGATAGCGGGATCCACCAA
*
50570 TAGTTACTTTATTCCAAACTTCCCAAAACGCCCTCAATTATCAATCGAAATAACAAAAAAATCAA
66 TAGTTACTTTATTCCAAACTTCCCAAAACGCCCTCAATTATCAACCGAAATAACAAAAAAATCAA
*
50635 GCATGAAAGTACCAAAATACCCCTGACAA
131 GCATAAAAGTACCAAAATACCCCTGACAA
*
50664 TTATATGAATCATTTGATAAATAAA-CAAAAAATTGATTTATTTATTGATAGCGGGATCCACCAA
1 TTATATGAATCATTTGATAAATAAACCAAAAAAATGATTTATTTATTGATAGCGGGATCCACCAA
*
50728 TAGTTACTTTATTCCAAACTTCCCAAAACGCCCTCAATTATCAACCTAAATAACAAAAAAATCAA
66 TAGTTACTTTATTCCAAACTTCCCAAAACGCCCTCAATTATCAACCGAAATAACAAAAAAATCAA
**
50793 GCATAAAAGTATTAAAATACCCCTGACAA
131 GCATAAAAGTACCAAAATACCCCTGACAA
50822 TT
1 TT
50824 TATTCTTGGA
Statistics
Matches: 154, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
158 129 0.84
159 25 0.16
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (159 bp):
TTATATGAATCATTTGATAAATAAACCAAAAAAATGATTTATTTATTGATAGCGGGATCCACCAA
TAGTTACTTTATTCCAAACTTCCCAAAACGCCCTCAATTATCAACCGAAATAACAAAAAAATCAA
GCATAAAAGTACCAAAATACCCCTGACAA
Found at i:60129 original size:3 final size:3
Alignment explanation
Indices: 60121--60159 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
60111 CTTTATTTCT
60121 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60160 ATAATTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61855 original size:54 final size:54
Alignment explanation
Indices: 61797--62542 Score: 1056
Period size: 54 Copynumber: 13.8 Consensus size: 54
61787 TAGCCTAATT
* *
61797 ACTAATTACTGCTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
61851 ACTAACTT-CTATTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAA-TTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
61905 ACTGACTT-CTATTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACT-AATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * *
61959 ACTAACTT-CTATTTACTCTTTCTTTTACTCTTTAGCTTAATTACCTAGAATTAA
1 ACTAA-TTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
62013 ACTAATTACCGTTTACTCCTTCTTTTACTCTTTAGTTTGATTACCCATAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
62067 ACTAATTA-TAGTTTACTCCTTCTTTTACTCCTTAGTTTAATTATCCAAAATTAA
1 ACTAATTACT-GTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
62121 ACTAATTACAGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACGCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
**
62175 ACTAATTACTGTTTACTATTTCTTTTACTCTTTTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTC---TTTAGTTTAATTACCCAGAATTAA
*
62232 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGCTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
62286 ACTAATTACTGTTTACTCATTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
62340 ACTAATTACAGTTTACTCCTTCTTTAACTCTTTAGTTTAATTACCCAAAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
62394 ACTAATTACAGTTTACT-C--CTTTTACTCTTTAGTTTAATTACCTAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
62445 ACTAATTACTGTTTACTCCTTCTTTTAATCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* ** * *
62499 ACCAATTACTGTTTACTATTTCTTTTGCTTTTTTTAGTTTAATT
1 ACTAATTACTGTTTACTCCTTCTTTTAC--TCTTTAGTTTAATT
62543 GCTCTGATTT
Statistics
Matches: 630, Mismatches: 48, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
51 46 0.07
52 1 0.00
53 4 0.01
54 512 0.81
55 3 0.00
56 13 0.02
57 51 0.08
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (54 bp):
ACTAATTACTGTTTACTCCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
Done.