Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012774.1 Corchorus capsularis cultivar CVL-1 contig12795, 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: 55848
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:89 original size:41 final size:41
Alignment explanation
Indices: 10--1201 Score: 666
Period size: 41 Copynumber: 28.9 Consensus size: 41
1 CTTCCGGCA
*** * *
10 GGGAAGGGCAAACTGGGACTTC-AAACAACGCCTTCCGATT
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
*
50 GGGAAGGGCAAAATGGGAAAACTAAACAACACCTTCCGATTG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
* * * *
92 AGGAAGGGCAGACT-AGAAAACTAATCAACACCTTCCGATG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* **
132 GGGAAGGGCAAACT-GGAAAAC-AATAAAACACCTTCCGACC
1 GGGAAGGGCAAACTGGGAAAACTAA-ACAACACCTTCCGATG
* * * * *
172 AGGAAGGGCAAAATGGTAAAACTAATCAACACCTTCTGATG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
**
213 GGGAAGGGCAAACTGGGAAAACTTAAA-AACACCTTCCGACC
1 GGGAAGGGCAAACTGGGAAAAC-TAAACAACACCTTCCGATG
* * * *
254 GGGAAGAGCAAAATGGGAAAACTAAACAACACTTTCCGACG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * * * *
295 AGGAAGGGCAGACT-AGAAAACTAATCAACACCTTCTGACG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
*
335 GGGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGACT-
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
* * * *
376 GCGAAGGGCAAGCTGGGAATTGGCAATTAGACAACACCTTCC-AGTG
1 GGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGA-TG
* **
422 GGGAACGGCAAACTGGG-AATTTAAACAACACCTTCCGAT-
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * *
461 GGGAAGGGCAAAATGGGAAAACAAAACAACACCTTCCGATA
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * *
502 AGGAAGGGCAGACT-GGAAAACTAATCAACACCTTCCGACG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * *
542 GGGAAGGGCAAACTAGGAAAACTAAATAACACCTTCCGACAG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
* * ** ** * * * * *
584 TGGAAAGGCAAGTTGGGAGTAGGCAAATAGAATTTA-CGTCCTGGTG
1 GGGAAGGGCAAACTGGGA--AAACTAA-ACAA--CACCTTCC-GATG
* * * * * *
630 GGGAAGGGCAAACTAGCAGAACTAAACAACACTTTCTGGTG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * *
671 GGGAAGGGCAAACT------AGTGAACAACATCTTCCGACG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * *
706 GGGAAGGGCACACTAGGAAAACGAAACAACACCTCCCGACT-
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
* ** *
747 GGAAAGGGCAAGTTGGGAATTGGCAACTAGACAACACC-T----TG
1 GGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGATG
* * *
788 GGGAAGGGCAAACTAGGAGAACTAGACAACACCTTCC-AGTG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
*
829 GGGAAGGGCAAACT-GG-----TAAACAACACCTTCCGACG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * * *
864 GGGAAGGGCACACTAGGAAAACAAAACGACAACTTCCGACT-
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TG
* * *
905 GGGAAGAGCAAGCTGGGAATTGGCAACTAGACAACACCTTCC-AGTG
1 GGGAAGGGCAAACTGGGAA-----AACTAAACAACACCTTCCGA-TG
* * * * * * *
951 GGAAAGAGCAAACTAGGAGAACTAGACAACACCTTCTGGTG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
*
992 GGGAAGGGCAAACT-GG-----TAAACAACACCTTCCGA-C
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * *
1026 GGGAAGGGCAGACTGAG-AAACTAGACAACACCTTCCGATG
1 GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
* * * * *
1066 GGGAAGGGCATACTAGTAATTTGACAACTAGACAACACCTTCCGGTG
1 GGGAAGGGCAAACT-G-----GGAAAACTAAACAACACCTTCCGATG
* * * * *
1113 GGGAAGGGCAGACTGAGAAACTGGCAACTAGAGAACACCTTCCGTTG
1 GGGAAGGGCAAACTG-GGAA-----AACTAAACAACACCTTCCGATG
*
1160 AGGAAGGGCAAACTGGGAATAAGCAACTAAACAACACCTTCC
1 GGGAAGGGCAAACTGGG---AA--AACTAAACAACACCTTCC
1202 TACCAAGAAG
Statistics
Matches: 889, Mismatches: 182, Indels: 156
0.72 0.15 0.13
Matches are distributed among these distances:
34 13 0.01
35 70 0.08
36 17 0.02
37 1 0.00
39 33 0.04
40 188 0.21
41 335 0.38
42 34 0.04
43 3 0.00
44 7 0.01
45 8 0.01
46 109 0.12
47 69 0.08
49 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.14
Consensus pattern (41 bp):
GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATG
Found at i:193 original size:81 final size:81
Alignment explanation
Indices: 11--581 Score: 502
Period size: 81 Copynumber: 7.0 Consensus size: 81
1 CTTCCGGCAG
* * * *
11 GGAAGGGCAAACTGG--GACTTCAAACAACGCCTTCCGATTGGGAAGGGCAAAATGGGAAAACTA
1 GGAAGGGCAAACTGGAAAAC-T-AAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC-A
* *
74 A-ACAACACCTTCCGATTGA
63 ATAAAACACCTTCCGA-CGA
* * *
93 GGAAGGGCAGACTAGAAAACTAATCAACACCTTCCGATGGGGAAGGGCAAACT-GGAAAACAATA
1 GGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACAATA
*
157 AAACACCTTCCGACCA
66 AAACACCTTCCGACGA
* * * *
173 GGAAGGGCAAAATGGTAAAACTAATCAACACCTTCTGATGGGGAAGGGCAAACTGGGAAAAC-TT
1 GGAAGGGCAAACTGG-AAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACAAT
237 AAAAACACCTTCCGACCG-
65 -AAAACACCTTCCGA-CGA
* * * * * * *
255 GGAAGAGCAAAATGGGAAAACTAAACAACACTTTCCGACGAGGAAGGGCAGACT-AGAAAACTAA
1 GGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC-AA
* * *
319 T-CAACACCTTCTGACGG
64 TAAAACACCTTCCGACGA
* * **
336 GGAAGGGCAAACTAGGAAAACTAAACAACACCTTCCGACT-GCGAAGGGCAAGCTGGGAATTGGC
1 GGAAGGGCAAACT-GGAAAACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA--AAC
* *
400 AATTAGACAACACCTTCC-AGTGG
62 AA-TA-A-AACACCTTCCGA-CGA
* * ** *
423 GGAACGGCAAACTGGGAATTTAAACAACACCTTCCGAT-GGGAAGGGCAAAATGGGAAAACAA-A
1 GGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACAATA
**
486 ACAACACCTTCCGATAA
66 A-AACACCTTCCGACGA
* * * *
503 GGAAGGGCAGACTGGAAAACTAATCAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAACTAA-
1 GGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAC-AAT
*
567 ATAACACCTTCCGAC
65 AAAACACCTTCCGAC
582 AGTGGAAAGG
Statistics
Matches: 402, Mismatches: 64, Indels: 47
0.78 0.12 0.09
Matches are distributed among these distances:
80 61 0.15
81 153 0.38
82 112 0.28
83 10 0.02
84 4 0.01
85 17 0.04
86 22 0.05
87 23 0.06
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (81 bp):
GGAAGGGCAAACTGGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACAATA
AAACACCTTCCGACGA
Found at i:755 original size:76 final size:76
Alignment explanation
Indices: 629--915 Score: 204
Period size: 76 Copynumber: 3.7 Consensus size: 76
619 ACGTCCTGGT
* * * * * * *
629 GGGGAAGGGCAAACTAGCAGAACTAAACAACACTTTCTG-GTGGGGAAGGGCAAACTAGTGAACA
1 GGGGAAGGGCACACTAGGAAAACAAAACAACACCTTCCGACT-GGGAAGGGCAAACTAGTGAACA
*
693 ACATCTTCCGAC
65 ACAACTTCCGAC
* * * ** *
705 GGGGAAGGGCACACTAGGAAAACGAAACAACACCTCCCGACTGGAAAGGGCAAGTTGGGAATTGG
1 GGGGAAGGGCACACTAGGAAAACAAAACAACACCTTCCGACTGGGAAGGGCAAACT----AGT-G
* **
770 CAACTAGACAAC-ACC-TT
61 -AAC-A-ACAACTTCCGAC
* * * * * * *
787 GGGGAAGGGCAAACTAGGAGAACTAGACAACACCTTCC-AGTGGGGAAGGGCAAACTGGTAAACA
1 GGGGAAGGGCACACTAGGAAAACAAAACAACACCTTCCGACT-GGGAAGGGCAAACTAGTGAACA
*
851 ACACCTTCCGAC
65 ACAACTTCCGAC
* * *
863 GGGGAAGGGCACACTAGGAAAACAAAACGACAACTTCCGACTGGGAAGAGCAA
1 GGGGAAGGGCACACTAGGAAAACAAAACAACACCTTCCGACTGGGAAGGGCAA
916 GCTGGGAATT
Statistics
Matches: 158, Mismatches: 40, Indels: 26
0.71 0.18 0.12
Matches are distributed among these distances:
74 4 0.03
75 3 0.02
76 88 0.56
77 3 0.02
78 1 0.01
80 2 0.01
81 3 0.02
82 47 0.30
83 3 0.02
84 4 0.03
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.12
Consensus pattern (76 bp):
GGGGAAGGGCACACTAGGAAAACAAAACAACACCTTCCGACTGGGAAGGGCAAACTAGTGAACAA
CAACTTCCGAC
Found at i:996 original size:163 final size:162
Alignment explanation
Indices: 198--1122 Score: 729
Period size: 158 Copynumber: 5.7 Consensus size: 162
188 TAAAACTAAT
* * * * *
198 CAACACCTTCTGATGGGGAAGGGCAAACTGGGAAAACTTAAA-AACACCTTCCGACCGGGAAGAG
1 CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAAC-TAAACAACACCTTCCGACTGGGAAGAG
** * * ** * *
262 CAAAATGGGAA-----AACTAAACAACACTTTCCGACGAGGAAGGGCAGACTA-GAAAACTA-AT
65 CAAGCTGGGAATTGGCAACTAGACAACACCTTCCGGTG-GGAAGGGCAAACTAGGAGAACTAGA-
**
320 CAACACCTTCTGACGGGGAAGGGCAAACTAGGAAAACTAAA
128 CAACACCTTCTGGTGGGGAAGGGCAAACT-GG-----TAAA
* * * * * *
361 CAACACCTTCCGACTGCGAAGGGCA-AGCTGGGAATTGGCAATTAGACAACACCTTCC-AGTGGG
1 CAACACCTTCCGACGGGGAAGGGCACA-CTAGGAA-----AACTAAACAACACCTTCCGACT-GG
* * * * * *
424 GAACG-GCAAACTGGGAATT------TAAACAACACCTTCCGATGGGAAGGGCAAAATGGGAAAA
59 GAA-GAGCAAGCTGGGAATTGGCAACTAGACAACACCTTCCGGTGGGAAGGGCAAACTAGGAGAA
* * * * ** * *
482 CAAAACAACACCTTCCGATAAGGAAGGGCAGACTGGAAAACTAAT
123 CTAGACAACACCTTCTGGTGGGGAAGGGCAAACTGG-----TAAA
* * *
527 CAACACCTTCCGACGGGGAAGGGCAAACTAGGAAAACTAAATAACACCTTCCGACAGTGGAA-AG
1 CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAACTAAACAACACCTTCCGACTG-GGAAGA-
* * * * ** * *
591 GCAAGTTGGGAGTAGGCAAATAGA-ATTTA-CGTCCTGGTGGGGAAGGGCAAACTAGCAGAACTA
64 GCAAGCTGGGAATTGGCAACTAGACA-ACACCTTCC-GGT-GGGAAGGGCAAACTAGGAGAACTA
* * * *
654 AACAACACTTTCTGGTGGGGAAGGGCAAACTAGTGAA
126 GACAACACCTTCTGGTGGGGAAGGGCAAACTGGTAAA
* * * * *
691 CAACATCTTCCGACGGGGAAGGGCACACTAGGAAAACGAAACAACACCTCCCGACTGGAAAGGGC
1 CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAACTAAACAACACCTTCCGACTGGGAAGAGC
*
756 AAGTTGGGAATTGGCAACTAGACAACACCTT---G-GGGAAGGGCAAACTAGGAGAACTAGACAA
66 AAGCTGGGAATTGGCAACTAGACAACACCTTCCGGTGGGAAGGGCAAACTAGGAGAACTAGACAA
**
817 CACCTTCCAGTGGGGAAGGGCAAACTGGTAAA
131 CACCTTCTGGTGGGGAAGGGCAAACTGGTAAA
* * *
849 CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAACAAAACGACAACTTCCGACTGGGAAGAGC
1 CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAACTAAACAACACCTTCCGACTGGGAAGAGC
* *
914 AAGCTGGGAATTGGCAACTAGACAACACCTTCCAGTGGGAAAGAGCAAACTAGGAGAACTAGACA
66 AAGCTGGGAATTGGCAACTAGACAACACCTTCCGGTGGG-AAGGGCAAACTAGGAGAACTAGACA
979 ACACCTTCTGGTGGGGAAGGGCAAACTGGTAAA
130 ACACCTTCTGGTGGGGAAGGGCAAACTGGTAAA
* * *
1012 CAACACCTTCCGAC-GGGAAGGGCAGACT--GAGAAACTAGACAACACCTTCCGA-TGGGGAAGG
1 CAACACCTTCCGACGGGGAAGGGCACACTAGGA-AAACTAAACAACACCTTCCGACT-GGGAAGA
* * *
1073 GCATA-CTAGTAATTTGACAACTAGACAACACCTTCCGGTGGGGAAGGGCA
64 GCA-AGCTGGGAA-TTGGCAACTAGACAACACCTTCCGGT-GGGAAGGGCA
1123 GACTGAGAAA
Statistics
Matches: 627, Mismatches: 95, Indels: 81
0.78 0.12 0.10
Matches are distributed among these distances:
158 142 0.23
160 4 0.01
161 48 0.08
162 63 0.10
163 125 0.20
164 56 0.09
166 50 0.08
167 58 0.09
168 35 0.06
169 46 0.07
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (162 bp):
CAACACCTTCCGACGGGGAAGGGCACACTAGGAAAACTAAACAACACCTTCCGACTGGGAAGAGC
AAGCTGGGAATTGGCAACTAGACAACACCTTCCGGTGGGAAGGGCAAACTAGGAGAACTAGACAA
CACCTTCTGGTGGGGAAGGGCAAACTGGTAAA
Found at i:1058 original size:39 final size:39
Alignment explanation
Indices: 1011--1134 Score: 140
Period size: 47 Copynumber: 2.9 Consensus size: 39
1001 AAACTGGTAA
*
1011 ACAACACCTTCCGACGGGAAGGGCAGACTGAGAAACTAG
1 ACAACACCTTCCGAGGGGAAGGGCAGACTGAGAAACTAG
*
1050 ACAACACCTTCCGATGGGGAAGGGCATACTAGTAATTTGACAACTAG
1 ACAACACCTTCCGA-GGGGAAGGGCAGACT-G--A---GA-AACTAG
*
1097 ACAACACCTTCCGGTGGGGAAGGGCAGACTGAGAAACT
1 ACAACACCTTCC-GAGGGGAAGGGCAGACTGAGAAACT
1135 GGCAACTAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
39 14 0.19
40 17 0.24
41 3 0.04
43 1 0.01
44 1 0.01
46 3 0.04
47 32 0.44
48 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.15
Consensus pattern (39 bp):
ACAACACCTTCCGAGGGGAAGGGCAGACTGAGAAACTAG
Found at i:1115 original size:47 final size:45
Alignment explanation
Indices: 1044--1201 Score: 165
Period size: 47 Copynumber: 3.4 Consensus size: 45
1034 CAGACTGAGA
* *
1044 AACTAGACAACACCTTCCGATGGGGAAGGGCATACTAGTAATTTGAC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAACTAG-AATATG-C
* *
1091 AACTAGACAACACCTTCCGGTGGGGAAGGGCAGACTGAGAA-ACTGGC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAACT-AGAATA-T-GC
* * * * *
1138 AACTAGAGAACACCTTCCGTTGAGGAAGGGCAAACTGGGAATAAGC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAACT-AGAATATGC
*
1184 AACTAAACAACACCTTCC
1 AACTAGACAACACCTTCC
1202 TACCAAGAAG
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
46 18 0.19
47 74 0.77
48 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.16
Consensus pattern (45 bp):
AACTAGACAACACCTTCCGATGGGGAAGGGCAAACTAGAATATGC
Found at i:3403 original size:17 final size:16
Alignment explanation
Indices: 3381--3422 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
3371 TAATTTTTCC
3381 TCATTTTTCTTCTTTTT
1 TCATTTTT-TTCTTTTT
*
3398 TCATTTTTAT-TTTTT
1 TCATTTTTTTCTTTTT
3413 TCATTTTTTT
1 TCATTTTTTT
3423 TCTAACCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 8 0.35
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TCATTTTTTTCTTTTT
Found at i:5173 original size:26 final size:25
Alignment explanation
Indices: 5129--5179 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
5119 CTGAATGTAC
* **
5129 AAATGACCAGAATGTCCCTAGTGCAA
1 AAATGACCAAAATACCCCTAG-GCAA
5155 AAATGACCAAAATACCCCTAGGCAA
1 AAATGACCAAAATACCCCTAGGCAA
5180 CCCTAATGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (25 bp):
AAATGACCAAAATACCCCTAGGCAA
Found at i:15992 original size:33 final size:32
Alignment explanation
Indices: 15955--16059 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 32
15945 ATTAGCATCC
* *
15955 AAAACAGGTTTTGTTTCATCACAAACAACACCT
1 AAAACAGGTTTAGTTTCATCGCAAACAACA-CT
* * *
15988 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGGTTTAGTTTCATCGCAAACAACACT
** * *
16020 CAAATTAGGTTTAGTTTTATCGCAAATAACATCT
1 -AAAACAGGTTTAGTTTCATCGCAAACAACA-CT
16054 AAAACA
1 AAAACA
16060 CTCTTTGCAA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
32 2 0.04
33 52 0.93
34 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (32 bp):
AAAACAGGTTTAGTTTCATCGCAAACAACACT
Found at i:26637 original size:30 final size:30
Alignment explanation
Indices: 26601--26661 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
26591 CAAAGGATCA
* *
26601 AATGGCATCTTTGGTGTGATTCCTCTATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
26631 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
26661 A
1 A
26662 TTGATGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:28908 original size:30 final size:30
Alignment explanation
Indices: 28874--28939 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
28864 CAAACAATCT
* *
28874 ATCAATCAACTAACAA-ATAATTGCAATTC-A
1 ATCAACCAA-TAACAAGAT-ATGGCAATTCAA
*
28904 ATCAACCAATAGCAAGATATGGCAATTCAA
1 ATCAACCAATAACAAGATATGGCAATTCAA
28934 ATCAAC
1 ATCAAC
28940 AATTGAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (30 bp):
ATCAACCAATAACAAGATATGGCAATTCAA
Found at i:28942 original size:29 final size:29
Alignment explanation
Indices: 28896--28951 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28886 ACAAATAATT
*
28896 GCAATTCAATCAACCAATAGCAAGATATG
1 GCAATTCAATCAACCAATAGAAAGATATG
*
28925 GCAATTCAAATCAA-CAATTGAAAGATA
1 GCAATTC-AATCAACCAATAGAAAGATA
28952 GAATAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (29 bp):
GCAATTCAATCAACCAATAGAAAGATATG
Found at i:29805 original size:30 final size:30
Alignment explanation
Indices: 29771--29838 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
29761 GGGATCGTAT
*
29771 ATGACCGGCCATTGCATGGAGCAATCGCAC
1 ATGACCGGCCATTACATGGAGCAATCGCAC
*
29801 ATGACCGGCCATTACATGGGGCAATCGCAC
1 ATGACCGGCCATTACATGGAGCAATCGCAC
*
29831 AAGACCGG
1 ATGACCGG
29839 GCTCAAGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.15
Consensus pattern (30 bp):
ATGACCGGCCATTACATGGAGCAATCGCAC
Found at i:30481 original size:11 final size:11
Alignment explanation
Indices: 30465--30497 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
30455 AAGTTCGTGT
30465 TTGAAGATTTC
1 TTGAAGATTTC
30476 TTGAAGATATT-
1 TTGAAGAT-TTC
30487 TTGAAGATTTC
1 TTGAAGATTTC
30498 AAGTCAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (11 bp):
TTGAAGATTTC
Found at i:36383 original size:17 final size:17
Alignment explanation
Indices: 36361--36394 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36351 GTAGTTTAAA
36361 AAAAAAATCTTTTTCAT
1 AAAAAAATCTTTTTCAT
* *
36378 AAAAAAGTGTTTTTCAT
1 AAAAAAATCTTTTTCAT
36395 GCAAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (17 bp):
AAAAAAATCTTTTTCAT
Found at i:39498 original size:22 final size:22
Alignment explanation
Indices: 39439--39829 Score: 260
Period size: 22 Copynumber: 17.8 Consensus size: 22
39429 TTTTACTGAA
*
39439 TTACTGATTACCA--TTACTATT
1 TTACTGATTACTATTTTACT-TT
*
39460 TCACTGATTA-T-TCTTTACTTT
1 TTACTGATTACTAT-TTTACTTT
*
39481 GTACTGATTACTATTTTACTCTT
1 TTACTGATTACTATTTTACT-TT
* *
39504 GT--TGATTACCT-TCTTACTTT
1 TTACTGATTA-CTATTTTACTTT
*
39524 TTACTGATTACCATTTTACTCTT
1 TTACTGATTACTATTTTACT-TT
*
39547 TTACTGATTACTATTTTCTGCTCCTTTT
1 TTACTGATTACTA--TT-T--TAC-TTT
* *
39575 TTACTGATTACTCTTTTAGTTT
1 TTACTGATTACTATTTTACTTT
* * *
39597 TTACTGATTAC-CTTTTGCGTT
1 TTACTGATTACTATTTTACTTT
*
39618 TTACTGATTACCT-TTTTACTTC
1 TTACTGATTA-CTATTTTACTTT
*
39640 TTACTGATTAGCT-TTTTACTCT
1 TTACTGATTA-CTATTTTACTTT
*
39662 TTACTGATCACCT-TTTTAC-TT
1 TTACTGATTA-CTATTTTACTTT
* * *
39683 TTACTGATTTC-CTTTTACTTC
1 TTACTGATTACTATTTTACTTT
* * *
39704 TTACTTATTACTTTTTTTAC-TC
1 TTACTGATTAC-TATTTTACTTT
39726 TTACTGATTACTA-TTTACTTT
1 TTACTGATTACTATTTTACTTT
*
39747 TTACTGACTACTATTTTACTCTT
1 TTACTGATTACTATTTTACT-TT
* * *
39770 GT--TGATTACCT-TCTTGCTTT
1 TTACTGATTA-CTATTTTACTTT
39790 TTACTGATTACTATTTTACTCTT
1 TTACTGATTACTATTTTACT-TT
*
39813 TTACTGATTACTCTTTT
1 TTACTGATTACTATTTT
39830 TACCCTTTCA
Statistics
Matches: 296, Mismatches: 43, Indels: 60
0.74 0.11 0.15
Matches are distributed among these distances:
20 18 0.06
21 94 0.32
22 114 0.39
23 47 0.16
25 3 0.01
26 3 0.01
28 16 0.05
29 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (22 bp):
TTACTGATTACTATTTTACTTT
Found at i:39533 original size:43 final size:42
Alignment explanation
Indices: 39473--39812 Score: 263
Period size: 43 Copynumber: 7.7 Consensus size: 42
39463 CTGATTATTC
* *
39473 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* * *
39515 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTATTGATTAC---CT
* * * * *
39563 TCTGCTCCTTTTTTACTGATTACTCTTTTAGTTTTTACTGATTACCT
1 T-T--TAC-TTTTTACTGATTACTATTTTA-CTCTTATTGATTACCT
* * * *
39610 TTTGCGTTTTACTGATTACCT-TTTTACTTCTTACTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTATTGATTA-CCT
* * * * *
39654 TTTACTCTTTACTGATCACCT-TTTTACTTTTACTGATTTCCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTATTGATTACCT
* * * *
39696 TTTACTTCTTACTTATTACTTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTAC-TATTTTACTCTTATTGATTACCT
* *
39738 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
*
39781 TCTTGCTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
39813 TTACTGATTA
Statistics
Matches: 243, Mismatches: 37, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.00
42 38 0.16
43 126 0.52
44 29 0.12
45 9 0.04
46 1 0.00
47 2 0.01
48 4 0.02
50 13 0.05
51 19 0.08
52 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
Found at i:39550 original size:116 final size:116
Alignment explanation
Indices: 39427--39769 Score: 263
Period size: 116 Copynumber: 3.0 Consensus size: 116
39417 TTTTTACTCA
*
39427 TCTTTTACTGAATTACTGATTACCAT-TACTATTTCACTGATTATTC-TTTACTTTGTACTGATT
1 TCTTTTACTGAATTACT-ATTACC-TCTACTATTTCACTGATTACTCTTTTACTTTGTACTGATT
** *
39490 ACTATTTTAC-TCTTGTTGATTACCTTCTTACTTTTTACTGATTACCATTTTAC
64 AC-ATTTTACGTCTTACTGATTACCTTCTTACTTCTTACTGATTACCATTTTAC
** * * * * *
39543 TCTTTTACTG-ATTACTATTTTCTGCTCCTTTTTTACTGATTACTCTTTTAGTTTTTACTGATTA
1 TCTTTTACTGAATTACTATTACCT-CTACTATTTCACTGATTACTCTTTTACTTTGTACTGATTA
* * * * * *
39607 CCTTTTGCGTTTTACTGATTACCTTTTTACTTCTTACTGATTAGCTTTTTAC
65 CATTTTACGTCTTACTGATTACCTTCTTACTTCTTACTGATTACCATTTTAC
* * *
39659 TC-TTTACTG-ATCACCT-TT---T-TACT-TTT-ACTGATTTC-CTTTTACTTCT-TACTTATT
1 TCTTTTACTGAATTA-CTATTACCTCTACTATTTCACTGATTACTCTTTTACTT-TGTACTGATT
* * * *
39713 ACTTTTTTTAC-TCTTACTGATTA-CTAT-TTACTTTTTACTGACTACTATTTTAC
64 AC--ATTTTACGTCTTACTGATTACCT-TCTTACTTCTTACTGATTACCATTTTAC
39766 TCTT
1 TCTT
39770 GTTGATTACC
Statistics
Matches: 187, Mismatches: 30, Indels: 28
0.76 0.12 0.11
Matches are distributed among these distances:
107 42 0.22
108 22 0.12
109 8 0.04
110 3 0.02
112 1 0.01
113 1 0.01
114 4 0.02
115 39 0.21
116 67 0.36
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (116 bp):
TCTTTTACTGAATTACTATTACCTCTACTATTTCACTGATTACTCTTTTACTTTGTACTGATTAC
ATTTTACGTCTTACTGATTACCTTCTTACTTCTTACTGATTACCATTTTAC
Found at i:39557 original size:15 final size:15
Alignment explanation
Indices: 39539--39592 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
39529 GATTACCATT
39539 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
39554 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
39567 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
39582 TTACTCTTTTA
1 TTACTCTTTTA
39593 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:39683 original size:7 final size:7
Alignment explanation
Indices: 39572--39751 Score: 51
Period size: 7 Copynumber: 25.1 Consensus size: 7
39562 TTCTGCTCCT
39572 TTTTTAC
1 TTTTTAC
**
39579 TGATTAC
1 TTTTTAC
*
39586 TCTTTTAG
1 T-TTTTAC
39594 TTTTTAC
1 TTTTTAC
**
39601 TGATTAC
1 TTTTTAC
* *
39608 CTTTTGC
1 TTTTTAC
*
39615 GTTTTAC
1 TTTTTAC
**
39622 TGATTACC
1 TTTTTA-C
39630 TTTTTAC
1 TTTTTAC
*
39637 TTCTTAC
1 TTTTTAC
**
39644 TGATTAGC
1 TTTTTA-C
39652 TTTTTAC
1 TTTTTAC
*
39659 TCTTTAC
1 TTTTTAC
** *
39666 TGATCACC
1 TTTTTA-C
39674 TTTTTAC
1 TTTTTAC
39681 -TTTTAC
1 TTTTTAC
*
39687 TGATTT-C
1 T-TTTTAC
*
39694 CTTTTAC
1 TTTTTAC
*
39701 TTCTTAC
1 TTTTTAC
*
39708 TTATTAC
1 TTTTTAC
39715 TTTTTTTAC
1 --TTTTTAC
*
39724 -TCTTAC
1 TTTTTAC
**
39730 TGATTAC
1 TTTTTAC
*
39737 TATTTAC
1 TTTTTAC
39744 TTTTTAC
1 TTTTTAC
39751 T
1 T
39752 GACTACTATT
Statistics
Matches: 119, Mismatches: 44, Indels: 20
0.65 0.24 0.11
Matches are distributed among these distances:
6 14 0.12
7 78 0.66
8 21 0.18
9 6 0.05
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (7 bp):
TTTTTAC
Found at i:39750 original size:14 final size:13
Alignment explanation
Indices: 39673--39751 Score: 59
Period size: 14 Copynumber: 5.7 Consensus size: 13
39663 TACTGATCAC
39673 CTTTTTACTTTTA
1 CTTTTTACTTTTA
* *
39686 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
39700 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
39714 CTTTTTTTACTCTTA
1 C--TTTTTACTTTTA
**
39729 CTGATTACTATTTA
1 CTTTTTACT-TTTA
39743 CTTTTTACT
1 CTTTTTACT
39752 GACTACTATT
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
13 13 0.27
14 25 0.51
15 4 0.08
16 7 0.14
ACGTcount: A:0.18, C:0.19, G:0.03, T:0.61
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:39856 original size:66 final size:64
Alignment explanation
Indices: 39717--39864 Score: 167
Period size: 66 Copynumber: 2.3 Consensus size: 64
39707 CTTATTACTT
* * * *
39717 TTTTTAC-TCTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACC
1 TTTTTACTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACC
* * * *
39780 TTCTTGCTTTTTACTGATTACTATTTTACTCTTTTACTGATTACTCTTTTTACCCTT-TCAG-GT
1 TTTTTACTTTTTACTGATTACTA-TTTACT-TTTTACTGACTACT-ATTTTACCCTTGT-AGAGT
39843 ACC
62 ACC
39846 TTTTTACTTTTTACTGATT
1 TTTTTACTTTTTACTGATT
39865 GCCTGCTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
63 5 0.07
64 14 0.20
65 6 0.09
66 35 0.50
67 10 0.14
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (64 bp):
TTTTTACTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACCCTTGTAGAGTACC
Found at i:40110 original size:55 final size:55
Alignment explanation
Indices: 40049--40299 Score: 421
Period size: 55 Copynumber: 4.6 Consensus size: 55
40039 CATTTTAACT
*
40049 CTTAATTATCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
** *
40104 CTTAATTATTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
40159 CTTAATTACCGGTTTATTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
40214 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCCCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
40269 CTTAATTACTGATTTACTGATTTCTATTACT
1 CTTAATTACCGATTTACTGATTACTATTACT
40300 CTTTACTGAT
Statistics
Matches: 184, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 184 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (55 bp):
CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:40355 original size:22 final size:22
Alignment explanation
Indices: 40295--40356 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
40285 CTGATTTCTA
**
40295 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTGCCACT
*
40317 TTACTCTTTACTGATTGCCATT
1 TTACTCTTTACTGATTGCCACT
40339 TTAC-CTTTTACTGATTGC
1 TTACTC-TTTACTGATTGC
40357 ATCTTTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (22 bp):
TTACTCTTTACTGATTGCCACT
Found at i:43593 original size:27 final size:25
Alignment explanation
Indices: 43554--43627 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
43544 AATGGACTCG
* *
43554 AAATGACCGAAATGCCCCTGGTGCCGA
1 AAATGACCAAAATGCCCCTGGT-AC-A
* * *
43581 AAATGACCAAAATACCCTTAGTACA
1 AAATGACCAAAATGCCCCTGGTACA
*
43606 AGAATGACCAAAATGTCCCTGG
1 A-AATGACCAAAATGCCCCTGG
43628 GCGACCCTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.05
26 17 0.46
27 18 0.49
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.18
Consensus pattern (25 bp):
AAATGACCAAAATGCCCCTGGTACA
Found at i:44955 original size:2 final size:2
Alignment explanation
Indices: 44948--44976 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44938 GCATTGACGA
44948 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
44977 GTTAAGTTCA
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:46725 original size:41 final size:41
Alignment explanation
Indices: 46668--46749 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
46658 ATGCTTACAA
*
46668 TAAAATGTTGGGAGTGATGGAGCTTGCGTTCTATAAAATTT
1 TAAAATGTTGGGAGTGATGGAGCTTGAGTTCTATAAAATTT
46709 TAAAATGTTGGGAGTGATGGAGCTTGAGTTCTATAAAATTT
1 TAAAATGTTGGGAGTGATGGAGCTTGAGTTCTATAAAATTT
46750 GTACTCTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (41 bp):
TAAAATGTTGGGAGTGATGGAGCTTGAGTTCTATAAAATTT
Found at i:49110 original size:25 final size:27
Alignment explanation
Indices: 49058--49110 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
49048 TTACTCAACT
**
49058 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
49085 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
49110 A
1 A
49111 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:49730 original size:138 final size:139
Alignment explanation
Indices: 49573--49826 Score: 406
Period size: 138 Copynumber: 1.8 Consensus size: 139
49563 CATTGTTTAA
* *
49573 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTT-TATTTTAATTAAATTTAATATCCTTATA
1 ACTTTTATAACTTTACTCAACTAAAAACTCTATTTTATA-TTTAATTAAATCTAATATCCTTAT-
* * *
49637 AC-TATTTAATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATATATATTAGAAT
64 ACTTATTTAATATTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATATATATTAGAAT
49700 TTTCTAAATAT
129 TTTCTAAATAT
*
49711 ACTTTTATAGCTTTACTCAACTAAAAACTCTATTTTATATTTAATTAAATCTAATATCCTTATAC
1 ACTTTTATAACTTTACTCAACTAAAAACTCTATTTTATATTTAATTAAATCTAATATCCTTATAC
*
49776 TTATTTTATATTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATAT
66 TTATTTAATATTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATAT
49827 TAAAATTTTA
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
137 2 0.02
138 86 0.81
139 18 0.17
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (139 bp):
ACTTTTATAACTTTACTCAACTAAAAACTCTATTTTATATTTAATTAAATCTAATATCCTTATAC
TTATTTAATATTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATATATATTAGAATTT
TCTAAATAT
Found at i:51076 original size:22 final size:22
Alignment explanation
Indices: 51048--51089 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
51038 GTTTATAATA
51048 TTCTTGGGTCATCCGGGTTAAC
1 TTCTTGGGTCATCCGGGTTAAC
*
51070 TTCTTGGGTCATTCGGGTTA
1 TTCTTGGGTCATCCGGGTTA
51090 TGGGTTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (22 bp):
TTCTTGGGTCATCCGGGTTAAC
Found at i:51602 original size:77 final size:77
Alignment explanation
Indices: 51475--51624 Score: 273
Period size: 77 Copynumber: 1.9 Consensus size: 77
51465 GAATGACAAA
51475 TATTTATGCCAATTTCTTGTGGTTCGAACTTCCAAAATAGTTTCGTATAACAAATGCTTTTGAAA
1 TATTTATGCCAATTTCTTGTGGTTCGAACTTCCAAAATAGTTTCGTATAACAAATGCTTTTGAAA
*
51540 CGGTACTGGTAC
66 CAGTACTGGTAC
* *
51552 TATTTTTGCCAATTTCTTGTGGTTCGAACTTCCAAAATGGTTTCGTATAACAAATGCTTTTGAAA
1 TATTTATGCCAATTTCTTGTGGTTCGAACTTCCAAAATAGTTTCGTATAACAAATGCTTTTGAAA
51617 CAGTACTG
66 CAGTACTG
51625 CAACCGGGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (77 bp):
TATTTATGCCAATTTCTTGTGGTTCGAACTTCCAAAATAGTTTCGTATAACAAATGCTTTTGAAA
CAGTACTGGTAC
Found at i:53353 original size:16 final size:16
Alignment explanation
Indices: 53334--53364 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53324 CCCGAAACCG
53334 AACCCGAAAAAACTCA
1 AACCCGAAAAAACTCA
53350 AACCCGAAAAAACTC
1 AACCCGAAAAAACTC
53365 GAGTCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.32, G:0.06, T:0.06
Consensus pattern (16 bp):
AACCCGAAAAAACTCA
Found at i:53415 original size:20 final size:20
Alignment explanation
Indices: 53387--53425 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53377 ACCCGAATTC
*
53387 AATACTAATATTTGAAAATA
1 AATAATAATATTTGAAAATA
*
53407 AATAATAATTTTTGAAAAT
1 AATAATAATATTTGAAAAT
53426 TTCATCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AATAATAATATTTGAAAATA
Done.