Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014357.1 Corchorus capsularis cultivar CVL-1 contig14378, 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: 110403
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3242 original size:75 final size:75
Alignment explanation
Indices: 3150--3291 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 75
3140 AAATCTTAAG
** * *
3150 TAATTTGGAGGTTACATGAATGTCATTATATTTGGACGGTTACAAGTACTTGTAACGTCTATTCA
1 TAATTTGGAGGTTACATGAATAACATCATATTTGGACGGTTACAAATACTTGTAACGTCTATTCA
3215 AGGTATTTAC
66 AGGTATTTAC
** *
3225 TAATTTGGAGGTTACATGCGTAACATCATATTTGGACGGTTACAAATACTTGTAACGTCTCTTCA
1 TAATTTGGAGGTTACATGAATAACATCATATTTGGACGGTTACAAATACTTGTAACGTCTATTCA
3290 AG
66 AG
3292 ATATATAGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (75 bp):
TAATTTGGAGGTTACATGAATAACATCATATTTGGACGGTTACAAATACTTGTAACGTCTATTCA
AGGTATTTAC
Found at i:4302 original size:75 final size:75
Alignment explanation
Indices: 4173--4326 Score: 245
Period size: 75 Copynumber: 2.1 Consensus size: 75
4163 ACAAGTCTAC
* * *
4173 TCAAGGTATTTATTAATTTGGAGGTTACATGCACAACATCATATTTGGATAGTTACAAAAACTTA
1 TCAAGGTATTTAGTAATTTGGAGGTTACATGCACAACATCATATTTCGAAAGTTACAAAAACTTA
**
4238 TAATGTCTCT
66 TAACCTCTCT
* *
4248 TCAAGGTATTTAGTAATTTGGAGGTTACATGCACAACATCATATTTCGAAAGTTACAAATACTTG
1 TCAAGGTATTTAGTAATTTGGAGGTTACATGCACAACATCATATTTCGAAAGTTACAAAAACTTA
4313 TAACCTCTCT
66 TAACCTCTCT
4323 TCAA
1 TCAA
4327 TGCACAACAT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (75 bp):
TCAAGGTATTTAGTAATTTGGAGGTTACATGCACAACATCATATTTCGAAAGTTACAAAAACTTA
TAACCTCTCT
Found at i:5280 original size:76 final size:74
Alignment explanation
Indices: 5136--5450 Score: 368
Period size: 75 Copynumber: 4.2 Consensus size: 74
5126 AATATGTAAC
* * * *
5136 TGTAACTGCCTGAATATGATGTTGTGCATGTAACCTTCAAATTAGTAAATATCTTAAAGAGACGT
1 TGTAACTGCC-AAATATGATGTTGTGCATGTAACCTTCAAATTATTAAATACCTTGAAGAGACGT
*
5201 TACAAATATT
65 TACAAGTATT
* * *
5211 TGTAACTGACCAAAATATGATGTTGTGCATGTAA-TTTCCAAATTACTAGATACCTTGAAGAGA-
1 TGTAACTG-CC-AAATATGATGTTGTGCATGTAACCTT-CAAATTATTAAATACCTTGAAGAGAC
*
5274 GATTACAAGCATT
63 G-TTACAAGTATT
* * *
5287 TGTAACTGTCCAAATATGATGTTGTGCATGTAACC-TCCAATTATTACATA-CTTTAAGAGACGT
1 TGTAACTG-CCAAATATGATGTTGTGCATGTAACCTTCAAATTATTAAATACCTTGAAGAGACGT
5350 TACAAGTATT
65 TACAAGTATT
* * * *
5360 TGTAACTGCCCGAATATGATGTTGTGCATATAACCTTCAAATTATTAAATACCTTGAATAGATGT
1 TGTAACTG-CCAAATATGATGTTGTGCATGTAACCTTCAAATTATTAAATACCTTGAAGAGACGT
*
5425 TACAAGTACT
65 TACAAGTATT
*
5435 TGTAACCGTCCAAATA
1 TGTAACTG-CCAAATA
5451 AATGCCATGC
Statistics
Matches: 205, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
73 51 0.25
74 25 0.12
75 66 0.32
76 63 0.31
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (74 bp):
TGTAACTGCCAAATATGATGTTGTGCATGTAACCTTCAAATTATTAAATACCTTGAAGAGACGTT
ACAAGTATT
Found at i:5415 original size:148 final size:151
Alignment explanation
Indices: 5148--5450 Score: 418
Period size: 148 Copynumber: 2.0 Consensus size: 151
5138 TAACTGCCTG
5148 AATATGATGTTGTGCATGTAACCTTCAAATTAGTAAATATCTTAAAGAGACGTTACAAATATTTG
1 AATATGATGTTGTGCATGTAACCTTCAAATTAGTAAATATCTTAAAGAGACGTTACAAATATTTG
* * *
5213 TAACTGACCAAAATATGATGTTGTGCATGTAATTTCCAAATTACTAGATACCTTGAAGAGA-GAT
66 TAACTGACCAAAATATGATGTTGTGCATATAACTTCCAAATTACTAAATACCTTGAAGAGATG-T
* *
5277 TACAAGCATTTGTAACTGTCCA
130 TACAAGCACTTGTAACCGTCCA
* * * * *
5299 AATATGATGTTGTGCATGTAACC-TCCAATTATTACATA-CTTTAAGAGACGTTACAAGTATTTG
1 AATATGATGTTGTGCATGTAACCTTCAAATTAGTAAATATCTTAAAGAGACGTTACAAATATTTG
** * *
5362 TAACTG-CCCGAATATGATGTTGTGCATATAACCTT-CAAATTATTAAATACCTTGAATAGATGT
66 TAACTGACCAAAATATGATGTTGTGCATATAA-CTTCCAAATTACTAAATACCTTGAAGAGATGT
*
5425 TACAAGTACTTGTAACCGTCCA
130 TACAAGCACTTGTAACCGTCCA
5447 AATA
1 AATA
5451 AATGCCATGC
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
148 68 0.50
149 32 0.24
150 12 0.09
151 23 0.17
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (151 bp):
AATATGATGTTGTGCATGTAACCTTCAAATTAGTAAATATCTTAAAGAGACGTTACAAATATTTG
TAACTGACCAAAATATGATGTTGTGCATATAACTTCCAAATTACTAAATACCTTGAAGAGATGTT
ACAAGCACTTGTAACCGTCCA
Found at i:7577 original size:16 final size:16
Alignment explanation
Indices: 7534--7584 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
7524 ATTAAAATAT
* *
7534 ATAGTCAATTTCCTAA
1 ATAGTCAATTACCAAA
* *
7550 AGATTC-ATTACCAAA
1 ATAGTCAATTACCAAA
*
7565 ATAGTCAATTACCGAA
1 ATAGTCAATTACCAAA
7581 ATAG
1 ATAG
7585 GGCAAGGGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (16 bp):
ATAGTCAATTACCAAA
Found at i:8241 original size:40 final size:40
Alignment explanation
Indices: 8192--8269 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
8182 ATTTGATTTT
* * *
8192 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGGTA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGGTA
8232 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTG
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTG
8270 AAGACTTGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 15 0.45
41 17 0.52
42 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGGTA
Found at i:8655 original size:16 final size:16
Alignment explanation
Indices: 8634--8668 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
8624 ATTTGAAAAA
8634 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
8650 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
8666 CTT
1 CTT
8669 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:9380 original size:11 final size:11
Alignment explanation
Indices: 9364--9406 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
9354 TATACTATAT
9364 CTAATTAATAG
1 CTAATTAATAG
*
9375 CTAATTAATAT
1 CTAATTAATAG
9386 CTAATTAATAG
1 CTAATTAATAG
*
9397 TTAATTAATA
1 CTAATTAATA
9407 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:9388 original size:22 final size:22
Alignment explanation
Indices: 9360--9406 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9350 TCATTATACT
9360 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
9382 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
9404 ATA
1 ATA
9407 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:10318 original size:31 final size:31
Alignment explanation
Indices: 10274--10366 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
10264 ACCCATCTCG
** * *
10274 TTTATTATTAAAATAGTCAATAACCAAAATT
1 TTTATTACCAAAATAGTCAATTACCAAAATA
* *
10305 TTTATTACGAAAATAGTCAATTACCAAAACA
1 TTTATTACCAAAATAGTCAATTACCAAAATA
10336 TTTATTACCAAAATAGTCAATTACCAAAATA
1 TTTATTACCAAAATAGTCAATTACCAAAATA
10367 GGGCAGGGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (31 bp):
TTTATTACCAAAATAGTCAATTACCAAAATA
Found at i:10333 original size:16 final size:16
Alignment explanation
Indices: 10283--10367 Score: 84
Period size: 16 Copynumber: 5.4 Consensus size: 16
10273 GTTTATTATT
*
10283 AAAATAGTCAATAACC
1 AAAATAGTCAATTACC
* ** *
10299 AAAAT-TTTTATTACG
1 AAAATAGTCAATTACC
10314 AAAATAGTCAATTACC
1 AAAATAGTCAATTACC
* **
10330 AAAACA-TTTATTACC
1 AAAATAGTCAATTACC
10345 AAAATAGTCAATTACC
1 AAAATAGTCAATTACC
10361 AAAATAG
1 AAAATAG
10368 GGCAGGGGGT
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
15 22 0.42
16 30 0.58
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAATAGTCAATTACC
Found at i:10879 original size:83 final size:83
Alignment explanation
Indices: 10735--10945 Score: 350
Period size: 83 Copynumber: 2.5 Consensus size: 83
10725 TTGAATTATA
* ** *
10735 TATTAATGACACTATTTATTACAAAAATAGTCAATTACCAAAATAGGGCAGGGGGAGAAAGTGTA
1 TATTAATGACACTATTTACTATTAAAATAGTCAATTACCAAAATAGGACAGGGGGAGAAAGTGTA
10800 AGAAACTAATTAAAGGAC
66 AGAAACTAATTAAAGGAC
* *
10818 TATTACTGACACTATTTACTATTAAAATAGTCAATTACCAAAATAGGACAGGGGGATAAAGTGTA
1 TATTAATGACACTATTTACTATTAAAATAGTCAATTACCAAAATAGGACAGGGGGAGAAAGTGTA
*
10883 AGAAACTAATTGAAGGAC
66 AGAAACTAATTAAAGGAC
*
10901 TATTATTGACACTATTTACTATTAAAATAGTCAATTACCAAAATA
1 TATTAATGACACTATTTACTATTAAAATAGTCAATTACCAAAATA
10946 TTTATTACCA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 120 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (83 bp):
TATTAATGACACTATTTACTATTAAAATAGTCAATTACCAAAATAGGACAGGGGGAGAAAGTGTA
AGAAACTAATTAAAGGAC
Found at i:10945 original size:16 final size:16
Alignment explanation
Indices: 10924--11008 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
10914 ATTTACTATT
10924 AAAATAGTCAATTACC
1 AAAATAGTCAATTACC
**
10940 AAAATA-TTTATTACC
1 AAAATAGTCAATTACC
10955 AAAATAGTCAATTACC
1 AAAATAGTCAATTACC
**
10971 AAAATA-TTTATTACC
1 AAAATAGTCAATTACC
*
10986 AAAGTAGTCAATTACC
1 AAAATAGTCAATTACC
*
11002 GAAATAG
1 AAAATAG
11009 GACAGGGGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
15 25 0.45
16 31 0.55
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.29
Consensus pattern (16 bp):
AAAATAGTCAATTACC
Found at i:10954 original size:15 final size:15
Alignment explanation
Indices: 10934--10988 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
10924 AAAATAGTCA
10934 ATTACCAAAATATTT
1 ATTACCAAAATATTT
**
10949 ATTACCAAAATAGTCA
1 ATTACCAAAATA-TTT
10965 ATTACCAAAATATTT
1 ATTACCAAAATATTT
10980 ATTACCAAA
1 ATTACCAAA
10989 GTAGTCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (15 bp):
ATTACCAAAATATTT
Found at i:10959 original size:31 final size:31
Alignment explanation
Indices: 10924--11007 Score: 150
Period size: 31 Copynumber: 2.7 Consensus size: 31
10914 ATTTACTATT
10924 AAAATAGTCAATTACCAAAATATTTATTACC
1 AAAATAGTCAATTACCAAAATATTTATTACC
10955 AAAATAGTCAATTACCAAAATATTTATTACC
1 AAAATAGTCAATTACCAAAATATTTATTACC
* *
10986 AAAGTAGTCAATTACCGAAATA
1 AAAATAGTCAATTACCAAAATA
11008 GGACAGGGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (31 bp):
AAAATAGTCAATTACCAAAATATTTATTACC
Found at i:12090 original size:235 final size:236
Alignment explanation
Indices: 11678--12127 Score: 742
Period size: 235 Copynumber: 1.9 Consensus size: 236
11668 TCATCTCAAT
* * *
11678 ATTAACCAAAGTGTAGGGCCTTAAAGTAATTTGATCGGTGGAAAAAGACTAAAATGTTTAATTAT
1 ATTAACCAAAGTGTAGGGCCTTAAAGTAATATGATCGGTGGAAAAAAACTAAAATGTTGAATTAT
* * *
11743 TTAGCCCCTGCATTAACCCAAACATGGGACTAAATAGGAAATTCATTCGAGTAATAATGTTAATA
66 CTAGCCCCTGCATTAACCCAAACATGGGACTAAATAAGAAATTCATTCAAGTAATAATGTTAATA
* *
11808 AGATGAATAATACTTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAGGAGAAAAAAATTTCA
131 AGATGAATAATACTTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAGGACAAAAAAAGTTCA
*
11873 AACCGAACCTCCTTATCGATTCTTAGGACTCCTCAAGGGTC
196 AACCGAACCTCCTCATCGATTCTTAGGACTCCTCAAGGGTC
*
11914 ATTAACCAAAGTTTAGGGCCTTAAAGTAATATGATCGGTGGAAAAAAACTAAAATGTTGAATTAT
1 ATTAACCAAAGTGTAGGGCCTTAAAGTAATATGATCGGTGGAAAAAAACTAAAATGTTGAATTAT
* *
11979 CTAGCCCCT-CATTAACCCAAACATGGGAGC-ATATAATAAATTCATTCAAGTAATAATGTTAAT
66 CTAGCCCCTGCATTAACCCAAACATGGGA-CTAAATAAGAAATTCATTCAAGTAATAATGTTAAT
*
12042 AAGATGAATAATACTTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTTC
130 AAGATGAATAATACTTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAGGACAAAAAAAGTTC
**
12107 AAACCGAGTCTCCTCATCGAT
195 AAACCGAACCTCCTCATCGAT
12128 CAGGATTCCT
Statistics
Matches: 198, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
235 128 0.65
236 70 0.35
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (236 bp):
ATTAACCAAAGTGTAGGGCCTTAAAGTAATATGATCGGTGGAAAAAAACTAAAATGTTGAATTAT
CTAGCCCCTGCATTAACCCAAACATGGGACTAAATAAGAAATTCATTCAAGTAATAATGTTAATA
AGATGAATAATACTTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAGGACAAAAAAAGTTCA
AACCGAACCTCCTCATCGATTCTTAGGACTCCTCAAGGGTC
Found at i:32985 original size:19 final size:20
Alignment explanation
Indices: 32949--32992 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
32939 ATCTTACCTT
*
32949 TTTAAAACAAAAACCTAAAC
1 TTTAAAACAAAAAACTAAAC
*
32969 TTTAAAA-AAAAAACTAATC
1 TTTAAAACAAAAAACTAAAC
32988 TTTAA
1 TTTAA
32993 TCTTAATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (20 bp):
TTTAAAACAAAAAACTAAAC
Found at i:33379 original size:8 final size:9
Alignment explanation
Indices: 33352--33397 Score: 51
Period size: 8 Copynumber: 5.1 Consensus size: 9
33342 AATCGAATCC
33352 TCTTCTCTTCT
1 TCTTCT-TT-T
33363 TCTTCTTTT
1 TCTTCTTTT
33372 TCTT-TTTT
1 TCTTCTTTT
*
33380 TC-TATTTT
1 TCTTCTTTT
33388 TCTTCTTTT
1 TCTTCTTTT
33397 T
1 T
33398 GAGCCTGAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 1 0.03
8 12 0.38
9 11 0.34
10 2 0.06
11 6 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (9 bp):
TCTTCTTTT
Found at i:36189 original size:27 final size:28
Alignment explanation
Indices: 36136--36196 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
36126 AAAATGGACT
* *
36136 AAAAATGACCAAAATGCCCCTTTAATGC
1 AAAAATGACCAAAATACCCCTTGAATGC
*
36164 AAAAATGACCAAAATACCCC-TGAATGT
1 AAAAATGACCAAAATACCCCTTGAATGC
36191 AAAAAT
1 AAAAAT
36197 TGATTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (28 bp):
AAAAATGACCAAAATACCCCTTGAATGC
Found at i:47558 original size:12 final size:13
Alignment explanation
Indices: 47541--47569 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
47531 ACTACCTACC
47541 AAACAAATAAA-T
1 AAACAAATAAATT
47553 AAACAAATAAATT
1 AAACAAATAAATT
47566 AAAC
1 AAAC
47570 TCACATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
AAACAAATAAATT
Found at i:49105 original size:54 final size:54
Alignment explanation
Indices: 49041--49151 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
49031 AAAGAGATAA
* *
49041 AGGTCACTCAGAGGAAAGATGAATCC-ATGA-CATGTGATACAGTTGCCAAGGATG
1 AGGTCACTCAGAGGAAAGATGAATCCGA-GATAAT-TGATAAAGTTGCCAAGGATG
*
49095 AGGTCACTCAGAGGAAAGATGACTCCGAGATAATTGATAAAGTTGCCAAGGATG
1 AGGTCACTCAGAGGAAAGATGAATCCGAGATAATTGATAAAGTTGCCAAGGATG
49149 AGG
1 AGG
49152 AGAGTGTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
54 49 0.94
55 3 0.06
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (54 bp):
AGGTCACTCAGAGGAAAGATGAATCCGAGATAATTGATAAAGTTGCCAAGGATG
Found at i:53655 original size:31 final size:31
Alignment explanation
Indices: 53617--53698 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
53607 AAATAACTGA
*
53617 TCAATTGAGTCCCTCTACTTAATAACA-CTTG
1 TCAATTGAGTCTCTCTACTTAATAACATC-TG
* *
53648 TCAATTGAATCTCTCTACTTGATAACATCTG
1 TCAATTGAGTCTCTCTACTTAATAACATCTG
*
53679 TCAATTAAGTCTCTCTACTT
1 TCAATTGAGTCTCTCTACTT
53699 GCAGGATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (31 bp):
TCAATTGAGTCTCTCTACTTAATAACATCTG
Found at i:63581 original size:32 final size:30
Alignment explanation
Indices: 63529--63620 Score: 166
Period size: 30 Copynumber: 3.0 Consensus size: 30
63519 ACATAAAAGT
63529 TAGGACCGATTCCCCATTTCGGGGCTTCCC
1 TAGGACCGATTCCCCATTTCGGGGCTTCCC
63559 TAGGACCGATTCCCCCCATTTCGGGGCTTCCC
1 TAGGACCGATT--CCCCATTTCGGGGCTTCCC
63591 TAGGACCGATTCCCCATTTCGGGGCTTCCC
1 TAGGACCGATTCCCCATTTCGGGGCTTCCC
63621 ATTTCAAGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.50
32 30 0.50
ACGTcount: A:0.13, C:0.38, G:0.23, T:0.26
Consensus pattern (30 bp):
TAGGACCGATTCCCCATTTCGGGGCTTCCC
Found at i:64524 original size:33 final size:33
Alignment explanation
Indices: 64482--64548 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
64472 AAATTTCAAA
64482 CTAGAAATTGTAAGGGCATTCACAAAGGAATAC
1 CTAGAAATTGTAAGGGCATTCACAAAGGAATAC
64515 CTAGAAATTGTAAGGGCATTCACAAAGGAATAC
1 CTAGAAATTGTAAGGGCATTCACAAAGGAATAC
64548 C
1 C
64549 CTCCCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (33 bp):
CTAGAAATTGTAAGGGCATTCACAAAGGAATAC
Found at i:73241 original size:3 final size:3
Alignment explanation
Indices: 73233--73289 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
73223 GAATTGGAAC
73233 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
73281 AAG AAG AAG
1 AAG AAG AAG
73290 CATAAGAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:74860 original size:86 final size:85
Alignment explanation
Indices: 74684--74861 Score: 196
Period size: 86 Copynumber: 2.1 Consensus size: 85
74674 TCGAAAAACC
* ** * *
74684 CATAAACAATTCAACCCAAAAAATCATAAAACAGCATTTTTTTTTCTAGAAACCCATAACCCAGA
1 CATAAACAATTCAACCCAAAAAATCATAAAACAACA-TAATTTTTCCAGAAACCCATAACCCAAA
* ** **
74749 ATCAATTATTATCGGAAAACC
65 ATCAATTATTACCAAAAAAAA
* * *
74770 CATAAACAATTCAACTCAAAAAATCATAAAACAACA-AATTTTTCCGGAAACCCATGACCCAAAA
1 CATAAACAATTCAACCCAAAAAATCATAAAACAACATAATTTTTCCAGAAACCCATAACCCAAAA
*
74834 TCGATTATTACCCAAAAAATAA
66 TCAATTATTA-CCAAAAAA-AA
74856 CATAAA
1 CATAAA
74862 AACACAAACA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
84 31 0.41
85 5 0.07
86 40 0.53
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (85 bp):
CATAAACAATTCAACCCAAAAAATCATAAAACAACATAATTTTTCCAGAAACCCATAACCCAAAA
TCAATTATTACCAAAAAAAA
Found at i:75673 original size:29 final size:30
Alignment explanation
Indices: 75629--75700 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
75619 GCCAATTTGT
* * *
75629 AACGTTTTGCCTCAAA-TCGACCCAAT-TGA
1 AACGTTCTGCCCCAAATTAGACCC-ATCTGA
*
75658 AAGGTTCTGCCCCAAATTAGACCCATCCTGA
1 AACGTTCTGCCCCAAATTAGACCCAT-CTGA
75689 AACGTTCTGCCC
1 AACGTTCTGCCC
75701 TTAATTGAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 15 0.43
30 6 0.17
31 14 0.40
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (30 bp):
AACGTTCTGCCCCAAATTAGACCCATCTGA
Found at i:78315 original size:16 final size:15
Alignment explanation
Indices: 78278--78327 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
78268 ATTAGTTAAA
*
78278 ATTAATTTTGATTTA
1 ATTAATTTTGATTTC
*
78293 ATAAATTTGTGATTTC
1 ATTAATTT-TGATTTC
*
78309 ATTAATTTTTGTTTTC
1 ATTAA-TTTTGATTTC
78325 ATT
1 ATT
78328 TAGCAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 7 0.24
16 19 0.66
17 3 0.10
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTAATTTTGATTTC
Found at i:78951 original size:16 final size:16
Alignment explanation
Indices: 78930--78961 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
78920 CACAATTCAG
78930 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
78946 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
78962 GAAGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
AAAGCAGAAAAGCTCT
Found at i:79392 original size:104 final size:98
Alignment explanation
Indices: 79255--79441 Score: 232
Period size: 99 Copynumber: 1.8 Consensus size: 98
79245 TTGTGTTCGC
* * *
79255 TCAAGATCAAGTCATTCGACCCTTGAATCAAATTATCATCAATTCGAGATCAAGTCA-TCAAAGA
1 TCAAGATCAAGTCATCCGACCCTTGAATCAAA-T-T-ATCAATTCAAGACCAAGTCATTC---GA
*
79319 CCCTCGAATCGAATCAAATCAAATTCCCAAGTCATCAAT
60 CCCTCGAATCAAATCAAATCAAATTCCCAAGTCATCAAT
* * * *
79358 TCAAGATCACGTCGTCCAGACCCTTGAATTAAATTATCAATTCAAGACCAAGTCATTCGACCCTT
1 TCAAGATCAAGTCATCC-GACCCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCTC
79423 GAATCAAATCAAATCAAAT
65 GAATCAAATCAAATCAAAT
79442 CAAATCAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
99 24 0.32
101 18 0.24
102 3 0.04
103 15 0.20
104 14 0.19
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (98 bp):
TCAAGATCAAGTCATCCGACCCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCTCG
AATCAAATCAAATCAAATTCCCAAGTCATCAAT
Found at i:79434 original size:5 final size:5
Alignment explanation
Indices: 79424--79449 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
79414 TCGACCCTTG
79424 AATCA AATCA AATCA AATCA AATCA A
1 AATCA AATCA AATCA AATCA AATCA A
79450 GTTCTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AATCA
Found at i:81015 original size:6 final size:6
Alignment explanation
Indices: 81006--81040 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
80996 AAAAAAAGGA
81006 AAAAAG AAAAAG AAAAAG AAGAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAA
81041 GAGTTTCTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:81020 original size:13 final size:13
Alignment explanation
Indices: 80997--81040 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
80987 AATATTACAA
80997 AAAAAAGGAAAAA-
1 AAAAAA-GAAAAAG
81010 AGAAAAAGAAAAAG
1 A-AAAAAGAAAAAG
*
81024 AAGAAAGAAAAAG
1 AAAAAAGAAAAAG
81037 AAAA
1 AAAA
81041 GAGTTTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:81030 original size:19 final size:20
Alignment explanation
Indices: 80998--81040 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
80988 ATATTACAAA
80998 AAAAAGGAAAAAAGAAAAAG
1 AAAAAGGAAAAAAGAAAAAG
*
81018 AAAAA-GAAGAAAGAAAAAG
1 AAAAAGGAAAAAAGAAAAAG
81037 AAAA
1 AAAA
81041 GAGTTTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGGAAAAAAGAAAAAG
Found at i:85857 original size:16 final size:16
Alignment explanation
Indices: 85836--85869 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
85826 ACAATTCAGA
85836 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
85852 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
85868 AA
1 AA
85870 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:86287 original size:104 final size:98
Alignment explanation
Indices: 86150--86336 Score: 234
Period size: 99 Copynumber: 1.8 Consensus size: 98
86140 TTGTGTTCGC
* * *
86150 TCAAGATCAAGTCATTCGACCCTTGAATCAAATTATCATCAATTCGAGATCAAGTCA-TCAAAGA
1 TCAAGATCAAGTCAGTCGACCCTTGAATCAAA-T-T-ATCAATTCAAGACCAAGTCATTC---GA
*
86214 CCCTCGAATCGAATCAAATCAAATTCCCAAGTCATCAAT
60 CCCTCGAATCAAATCAAATCAAATTCCCAAGTCATCAAT
*
86253 TCAAGATCAAGTC-GTCAAGACCCTTGAATTAAATTATCAATTCAAGACCAAGTCATTCGACCCT
1 TCAAGATCAAGTCAGTC--GACCCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCT
*
86317 TGAATCAAATCAAATCAAAT
64 CGAATCAAATCAAATCAAAT
86337 CAAATCAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
99 24 0.32
101 18 0.24
102 5 0.07
103 14 0.19
104 14 0.19
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.26
Consensus pattern (98 bp):
TCAAGATCAAGTCAGTCGACCCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCTCG
AATCAAATCAAATCAAATTCCCAAGTCATCAAT
Found at i:86329 original size:5 final size:5
Alignment explanation
Indices: 86319--86344 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
86309 TCGACCCTTG
86319 AATCA AATCA AATCA AATCA AATCA A
1 AATCA AATCA AATCA AATCA AATCA A
86345 GTTCTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AATCA
Found at i:88160 original size:12 final size:12
Alignment explanation
Indices: 88139--88172 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88129 GTATAGTACA
88139 ATATAGTATATT
1 ATATAGTATATT
*
88151 ATATATTATATT
1 ATATAGTATATT
*
88163 TTATAGTATA
1 ATATAGTATA
88173 ATAGTAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
ATATAGTATATT
Found at i:88274 original size:7 final size:7
Alignment explanation
Indices: 88246--88297 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
88236 CAAAAAAATT
*
88246 TAATAGA
1 TAATAAA
88253 TAATAAA
1 TAATAAA
88260 TAGA-AAA
1 TA-ATAAA
88267 TAATAAA
1 TAATAAA
88274 T-ATAGAA
1 TAATA-AA
88281 TAATAAA
1 TAATAAA
*
88288 TAATTAA
1 TAATAAA
88295 TAA
1 TAA
88298 ATTGGGGGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 4 0.10
7 31 0.79
8 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (7 bp):
TAATAAA
Found at i:88756 original size:85 final size:85
Alignment explanation
Indices: 88606--88784 Score: 331
Period size: 85 Copynumber: 2.1 Consensus size: 85
88596 TATCAGGTTA
*
88606 GCTTTCTTGACGTTTGATTTCTCTGCTAGGGTTAGGGTTTATTTGTTTGGGTTTTCTAATGATTA
1 GCTTTCTTGACGTTTGATTTCTCTGCTAGGGTTAGGGTTTATTTGTTTGGGTTTTCTAATAATTA
88671 AACAAATGTGTGTTTTTAAG
66 AACAAATGTGTGTTTTTAAG
* *
88691 GCTTTCTTGACGTTTGATTTCTCTGCTAGGGTTAGGGTTTATTTGTTTGGTTTTTGTAATAATTA
1 GCTTTCTTGACGTTTGATTTCTCTGCTAGGGTTAGGGTTTATTTGTTTGGGTTTTCTAATAATTA
88756 AACAAATGTGTGTTTTTAAG
66 AACAAATGTGTGTTTTTAAG
88776 GCTTTCTTG
1 GCTTTCTTG
88785 TTTGAATTTG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.18, C:0.09, G:0.23, T:0.49
Consensus pattern (85 bp):
GCTTTCTTGACGTTTGATTTCTCTGCTAGGGTTAGGGTTTATTTGTTTGGGTTTTCTAATAATTA
AACAAATGTGTGTTTTTAAG
Found at i:88840 original size:53 final size:52
Alignment explanation
Indices: 88778--88907 Score: 208
Period size: 53 Copynumber: 2.5 Consensus size: 52
88768 TTTTTAAGGC
**
88778 TTTCTTGTTTGAATTTGTTGTCTGATCATCAAACCCACTTTTTTATATTTGTA
1 TTTCTTGTTTGAATTTGTTGTCTGATCATCAAACCCAC-TTTCGATATTTGTA
*
88831 TTTCTTGTTTGAATTTGTTGTCTGATCATCAAACCCACTTTCGATTTTTGTA
1 TTTCTTGTTTGAATTTGTTGTCTGATCATCAAACCCACTTTCGATATTTGTA
*
88883 -TTCTGGTTTGAATTTGTTGTCTGAT
1 TTTCTTGTTTGAATTTGTTGTCTGAT
88908 TTGGGATATG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 24 0.33
52 11 0.15
53 38 0.52
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (52 bp):
TTTCTTGTTTGAATTTGTTGTCTGATCATCAAACCCACTTTCGATATTTGTA
Found at i:91187 original size:30 final size:30
Alignment explanation
Indices: 91151--91208 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
91141 TTACCCATCT
91151 AAACCACCTACTACTG-TTGTGCCAAAAAAA
1 AAACCACCTACTACTGTTTG-GCCAAAAAAA
91181 AAACCACCTACTACTGTTTGGCCAAAAA
1 AAACCACCTACTACTGTTTGGCCAAAAA
91209 TGTATTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (30 bp):
AAACCACCTACTACTGTTTGGCCAAAAAAA
Found at i:94289 original size:45 final size:45
Alignment explanation
Indices: 94233--94319 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
94223 GAGCGAGTCA
94233 AAGCGGAGAGTGAGGGCTGCTTGGCAATTGAGTTGAAACCATGAC
1 AAGCGGAGAGTGAGGGCTGCTTGGCAATTGAGTTGAAACCATGAC
*
94278 AAGCGGCGAGTGAGGGCTGCTTGGCAATTGAGTTGAAACCAT
1 AAGCGGAGAGTGAGGGCTGCTTGGCAATTGAGTTGAAACCAT
94320 TAGATTTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.21
Consensus pattern (45 bp):
AAGCGGAGAGTGAGGGCTGCTTGGCAATTGAGTTGAAACCATGAC
Found at i:105265 original size:11 final size:13
Alignment explanation
Indices: 105238--105264 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
105228 CAGGTGATAG
105238 GAGGGTGAGGAGA
1 GAGGGTGAGGAGA
105251 GAGGGTGAGGAGA
1 GAGGGTGAGGAGA
105264 G
1 G
105265 GATGATGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.63, T:0.07
Consensus pattern (13 bp):
GAGGGTGAGGAGA
Found at i:105336 original size:17 final size:17
Alignment explanation
Indices: 105309--105351 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
105299 TCCCCCTCAT
105309 GGTACCTAGGTAGCATGA
1 GGTA-CTAGGTAGCATGA
105327 GGTACTAGGTAGCATGA
1 GGTACTAGGTAGCATGA
*
105344 GGTGCTAG
1 GGTACTAG
105352 ATAACATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (17 bp):
GGTACTAGGTAGCATGA
Found at i:106003 original size:156 final size:155
Alignment explanation
Indices: 105705--106005 Score: 326
Period size: 156 Copynumber: 1.9 Consensus size: 155
105695 TCACCTCAAA
* * * * *
105705 TTGTCCTTAAATGAAAGACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAACTTTGTC
1 TTGTCCTTAAATGAAAAACTAGAATAAGTTTTTCACTCTAAGTCTCAACGAGCTG-AACTTTGTC
* * * ** * *
105770 AAGGGACTTAGATTCTTCCCACAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCCCTTGA
65 AAGAGACTTAGATTATCCCCACAAGACTATGGAAAAAATTCTAAGTAAAACAAACCTCCCCTAGA
* *
105835 TGGTGAACTAGGTTTCTCTCCCTGAG
130 TAGAGAACTAGGTTTCTCTCCCTGAG
105861 TTGTCCTTAAATGAAAAACTAGAATAAGTTTTTCACTCTAAGTC-CAACGAAGCTG-A-TTT-TC
1 TTGTCCTTAAATGAAAAACTAGAATAAGTTTTTCACTCTAAGTCTCAACG-AGCTGAACTTTGT-
* * *
105922 CACCAGTAGACTTAGATTATCCCCATGAAG-CTATGGGAAAAATTCTAAGTAAAACAAACCT-CT
64 CA--AG-AGACTTAGATTATCCCCA-CAAGACTATGGAAAAAATTCTAAGTAAAACAAACCTCCC
*
105985 CTAGCATAGAGAAGTAGGTTT
125 CTAG-ATAGAGAACTAGGTTT
106006 GATACCCCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
152 1 0.01
153 5 0.04
154 1 0.01
155 9 0.08
156 101 0.84
157 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (155 bp):
TTGTCCTTAAATGAAAAACTAGAATAAGTTTTTCACTCTAAGTCTCAACGAGCTGAACTTTGTCA
AGAGACTTAGATTATCCCCACAAGACTATGGAAAAAATTCTAAGTAAAACAAACCTCCCCTAGAT
AGAGAACTAGGTTTCTCTCCCTGAG
Found at i:107416 original size:11 final size:11
Alignment explanation
Indices: 107373--107410 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
107363 TTTCTATATA
*
107373 AAATAAATTAT
1 AAATTAATTAT
107384 CAAA-TAATTAT
1 -AAATTAATTAT
107395 AAATTAATTAT
1 AAATTAATTAT
107406 AAATT
1 AAATT
107411 TGTTATGAAT
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:109613 original size:20 final size:20
Alignment explanation
Indices: 109588--109639 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
109578 TAATATATTA
**
109588 ATATATATATTAATCTGAAAT
1 ATATATATATTAAAAT-AAAT
*
109609 A-ATATATAATAAAATAAAT
1 ATATATATATTAAAATAAAT
109628 ATATATATATTA
1 ATATATATATTA
109640 TAGTATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 20 0.77
21 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATATATATTAAAATAAAT
Done.