Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016222.1 Corchorus olitorius cultivar O-4 contig16255, 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: 44691
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1638 original size:42 final size:44
Alignment explanation
Indices: 1587--1680 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
1577 AGTGCGTTAC
*
1587 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
1628 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCC-TCATCTCTAGATAATTCATCAAAATAAAA
*
1673 TTAATATT
1 CTAATATT
1681 AATTGTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
45 34 0.72
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:7288 original size:1 final size:1
Alignment explanation
Indices: 7282--7313 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
7272 ACACAAATGC
7282 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7314 CGATGGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15504 original size:32 final size:32
Alignment explanation
Indices: 15463--15537 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
15453 TTACACTTGA
15463 TGACACATGTTGATGACAAGCCTTTCTCCATT
1 TGACACATGTTGATGACAAGCCTTTCTCCATT
15495 TGACACATGTTGATGACAAGCCTTTCTCCATT
1 TGACACATGTTGATGACAAGCCTTTCTCCATT
15527 TGACACATGTT
1 TGACACATGTT
15538 AGTCAACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (32 bp):
TGACACATGTTGATGACAAGCCTTTCTCCATT
Found at i:16661 original size:19 final size:20
Alignment explanation
Indices: 16616--16673 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
16606 GCTGCTCTAA
*
16616 TAATCTCATCTGTACAGTACC
1 TAATCTAATCTGTACAGTA-C
*
16637 TAATCTAATCTGTACAGT-G
1 TAATCTAATCTGTACAGTAC
* *
16656 TAATCTTATATGTACAGT
1 TAATCTAATCTGTACAGT
16674 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTAATCTGTACAGTAC
Found at i:19942 original size:145 final size:146
Alignment explanation
Indices: 19761--20070 Score: 550
Period size: 146 Copynumber: 2.1 Consensus size: 146
19751 ATTGTACATA
* *
19761 AATTTTGTAACCTTACATCTTTAAAACTTCTAGTAATCTTGTATAGAAA-TTTAGTAACATCTTA
1 AATTTAGTAACCTCACATCTTTAAAACTTCTAGTAATCTTGTATAGAAATTTTAGTAACATCTTA
*
19825 TCAATTGGAGGTTACCAAAATGATTGCATAATTTAACAAAAATAGGTAATGTGTTACCAAAAACT
66 TCAATTGAAGGTTACCAAAATGATTGCATAATTTAACAAAAATAGGTAATGTGTTACCAAAAACT
19890 CTACATGTTTTCTATT
131 CTACATGTTTTCTATT
*
19906 AATTTAGTAACCTCACATCTTTAAAACTTTTAGTAATCTTGTATAGAAATTTTAGTAACATCTTA
1 AATTTAGTAACCTCACATCTTTAAAACTTCTAGTAATCTTGTATAGAAATTTTAGTAACATCTTA
*
19971 TCAATTGAAGGTTACCAAACTGATTGCATAATTTAACAAAAATAGGTAATGTGTTACCAAAAACT
66 TCAATTGAAGGTTACCAAAATGATTGCATAATTTAACAAAAATAGGTAATGTGTTACCAAAAACT
*
20036 CTAGATGTTTTCTATT
131 CTACATGTTTTCTATT
*
20052 AATATAGTAACCTCACATC
1 AATTTAGTAACCTCACATC
20071 ATAAGAAATT
Statistics
Matches: 157, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
145 46 0.29
146 111 0.71
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (146 bp):
AATTTAGTAACCTCACATCTTTAAAACTTCTAGTAATCTTGTATAGAAATTTTAGTAACATCTTA
TCAATTGAAGGTTACCAAAATGATTGCATAATTTAACAAAAATAGGTAATGTGTTACCAAAAACT
CTACATGTTTTCTATT
Found at i:20281 original size:19 final size:20
Alignment explanation
Indices: 20232--20271 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20222 ATCGAGATTC
20232 AGTAACCTTATTAACATTTT
1 AGTAACCTTATTAACATTTT
*
20252 AGTAACTTTATTAA-ATTTT
1 AGTAACCTTATTAACATTTT
20271 A
1 A
20272 TATCCCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (20 bp):
AGTAACCTTATTAACATTTT
Found at i:20654 original size:24 final size:22
Alignment explanation
Indices: 20622--20665 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
20612 TAAGTATTCA
20622 ATAACCTTAATAAACTTTTTTTTT
1 ATAACCTT-ATAAA-TTTTTTTTT
*
20646 ATAATCTTATAAATTTTTTT
1 ATAACCTTATAAATTTTTTT
20666 AGTAATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAACCTTATAAATTTTTTTTT
Found at i:23350 original size:134 final size:133
Alignment explanation
Indices: 23086--23332 Score: 343
Period size: 134 Copynumber: 1.8 Consensus size: 133
23076 TGATTCAAAG
* *
23086 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAGTCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATAACTA
* * **
23151 TTTTATTTTTACCAGTTTACTATTTTATTTTAATTAAAAACCTTAAATATTAGAAATTTTAAAAT
66 TTTTACTTTTACCAGTTTACTATTTAATTTTAATTAAAAAAATTAAATA-TAGAAATTTTAAAAT
23216 ATAC
130 ATAC
* * ** *
23220 TTTTATAGTTTTACTCAAGTAAAAACTCTATTTTAATTTTATTAAATCTAATATTTTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATAACTA
* *
23285 TTTTACTTTTACCATTTTACTAATTTAATTTT-TTTAAAAAAAATTAAA
66 TTTTACTTTTACCAGTTTACT-ATTTAATTTTAATT-AAAAAAATTAAA
23333 AAGCTTTTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
134 79 0.81
135 19 0.19
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (133 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATAACTA
TTTTACTTTTACCAGTTTACTATTTAATTTTAATTAAAAAAATTAAATATAGAAATTTTAAAATA
TAC
Found at i:28354 original size:2 final size:2
Alignment explanation
Indices: 28347--28373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28337 ACATACATAC
28347 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 A
28374 AGTTAGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28501 original size:41 final size:42
Alignment explanation
Indices: 28439--28557 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 42
28429 TAAAGAGAAT
* * * *
28439 TGCCTTTGTGTTATAATTGTGTTTGGGGACTTTGATATAG-G
1 TGCCTCTGTGTTATAAATGTGTTTGGGGACTTTGAGAGAGAG
* * *
28480 TGCCTCTGCGTTATAAATGTGTTTGAGGACTTTAGAGAGAGAAT
1 TGCCTCTGTGTTATAAATGTGTTTGGGGACTTT-GAGAGAG-AG
* *
28524 TGCCCCTGTGTTATAGATGTGTTTGGGGACTTTG
1 TGCCTCTGTGTTATAAATGTGTTTGGGGACTTTG
28558 GGGAGGGAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 29 0.45
42 5 0.08
43 1 0.02
44 29 0.45
ACGTcount: A:0.19, C:0.11, G:0.29, T:0.40
Consensus pattern (42 bp):
TGCCTCTGTGTTATAAATGTGTTTGGGGACTTTGAGAGAGAG
Found at i:28545 original size:44 final size:42
Alignment explanation
Indices: 28432--28557 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 42
28422 TTTGTCATAA
* *
28432 AGAGAATTGCCTTTGTGTTATAATTGTGTTTGGGGACTTTGAT
1 AGAGAATTGCCTCTGTGTTATAA-TGTGTTTGGGGACTTTGAG
* * * *
28475 ATAG--GTGCCTCTGCGTTATAAATGTGTTTGAGGACTTTAGAG
1 AGAGAATTGCCTCTGTGTTAT-AATGTGTTTGGGGACTTT-GAG
*
28517 AGAGAATTGCCCCTGTGTTATAGATGTGTTTGGGGACTTTG
1 AGAGAATTGCCTCTGTGTTATA-ATGTGTTTGGGGACTTTG
28558 GGGAGGGAGA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
41 27 0.40
42 7 0.10
43 5 0.07
44 28 0.42
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.39
Consensus pattern (42 bp):
AGAGAATTGCCTCTGTGTTATAATGTGTTTGGGGACTTTGAG
Found at i:28920 original size:2 final size:2
Alignment explanation
Indices: 28913--28943 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28903 TGGAAGAAAA
28913 AT 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 AT A
28944 CTTAGAGGCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33683 original size:2 final size:2
Alignment explanation
Indices: 33670--33708 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
33660 ACTAAAAATA
33670 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33709 TTCCCAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34131 original size:39 final size:39
Alignment explanation
Indices: 34073--34150 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
34063 CTGTGCCCGT
*
34073 TAACCTAGCTTAAATCTCTTCTGAAAAAGTG-TTTCTGGA
1 TAACCTAGCTTAAACCTCTTCTGAAAAAGTGCTTT-TGGA
*
34112 TAACCTAGTTTAAACCTCTTCTGAAAAAGTGCTTTTGGA
1 TAACCTAGCTTAAACCTCTTCTGAAAAAGTGCTTTTGGA
34151 AAAAACTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.92
40 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (39 bp):
TAACCTAGCTTAAACCTCTTCTGAAAAAGTGCTTTTGGA
Found at i:34223 original size:13 final size:13
Alignment explanation
Indices: 34205--34244 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
34195 AAACAACTGA
34205 AAAGCACTTCTGG
1 AAAGCACTTCTGG
34218 AAAGCACTTCTGG
1 AAAGCACTTCTGG
34231 AAAGCACTTCTGG
1 AAAGCACTTCTGG
34244 A
1 A
34245 TTTTCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:35596 original size:13 final size:13
Alignment explanation
Indices: 35574--35608 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35564 TCACATCTGG
35574 CAAAATTAATATA
1 CAAAATTAATATA
* *
35587 CAAGATTAATATG
1 CAAAATTAATATA
35600 CAAAATTAA
1 CAAAATTAA
35609 AGTAAATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (13 bp):
CAAAATTAATATA
Found at i:37790 original size:175 final size:173
Alignment explanation
Indices: 37464--37790 Score: 476
Period size: 175 Copynumber: 1.9 Consensus size: 173
37454 TTTATTTAGC
* *
37464 TAGCATGTTCGATCAATTTAGTTTTTTGCTAACATAATTACTAATTGATTAATTTATTTATGGGA
1 TAGCATGTTCAATCAATTAAGTTTTTTGCTAACATAATTACTAATTGATTAATTTATTTATGGGA
* * *
37529 AAATTAAATAATTATGAATCAATTATAACTTTGAGTGACAAAGTTAACTAACGACTAACTTGATT
66 AAATTAAATAATCATAAATCAATTATAACTTTGAGTGACAAAGTTAACTAACGACTAACTTGAAT
* * *
37594 GATTTATTTATTTAGCATGTTCTTTTTTTTGCATCAATTTATT
131 CATTTATCTATTTACCATGTTCTTTTTTTTGCATCAATTTATT
* *
37637 TAGCATGTTCAATCAATTGAATTTTTTTTGCTAACATAATTACTAATTGATTAATTTATTTATGT
1 TAGCATGTTCAATCAATT-AA-GTTTTTTGCTAACATAATTACTAATTGATTAATTTATTTATGG
* * * * * *
37702 TAAAATTAAATAATCATAAATTAGTTATAACTTTGATTGGCAAAGTTAACTAATGACTAACTTGA
64 GAAAATTAAATAATCATAAATCAATTATAACTTTGAGTGACAAAGTTAACTAACGACTAACTTGA
37767 ATCATTTGA-CTATTTACCATGTTC
129 ATCATTT-ATCTATTTACCATGTTC
37791 AATAATTAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
173 17 0.13
174 1 0.01
175 116 0.86
176 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (173 bp):
TAGCATGTTCAATCAATTAAGTTTTTTGCTAACATAATTACTAATTGATTAATTTATTTATGGGA
AAATTAAATAATCATAAATCAATTATAACTTTGAGTGACAAAGTTAACTAACGACTAACTTGAAT
CATTTATCTATTTACCATGTTCTTTTTTTTGCATCAATTTATT
Found at i:37966 original size:135 final size:134
Alignment explanation
Indices: 37809--38079 Score: 472
Period size: 135 Copynumber: 2.0 Consensus size: 134
37799 ATTTTTTTGG
37809 TAACATAATCACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTATGGTAAAAT
1 TAACATAATCACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTATGGTAAAAT
*
37874 TAAATAATTATCAATCAATTTA-AACTTTGATTGACAAAAATAACTAACGACTAACATGGATTCA
66 TAAATAATCATCAATCAA-TTACAACTTTGATTGACAAAAATAACTAACGACTAAC-TGGATTCA
37938 TTTATT
129 TTTATT
* *
37944 TAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGTGATTTATGGTAAAAT
1 TAACATAATCACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTATGGTAAAAT
* *
38009 TAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACTAACTTGATTCATT
66 TAAATAATCATCAATCAATTACAACTTTGATTGACAAAAATAACTAACGACTAACTGGATTCATT
38074 TATT
131 TATT
38078 TA
1 TA
38080 TTTAGCATGT
Statistics
Matches: 130, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
134 18 0.14
135 112 0.86
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (134 bp):
TAACATAATCACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCGATTTATGGTAAAAT
TAAATAATCATCAATCAATTACAACTTTGATTGACAAAAATAACTAACGACTAACTGGATTCATT
TATT
Found at i:38191 original size:130 final size:132
Alignment explanation
Indices: 38031--38523 Score: 469
Period size: 145 Copynumber: 3.6 Consensus size: 132
38021 AATCAATTAC
* *
38031 AACTTTGATTGACAAAATTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC
1 AACTTTGATTGACAAAGTT-ACTTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC
38096 AATTTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAAT-T-AT-AGG
65 AA-TTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAATATCATAAGG
38158 AG-T
129 AGTT
* * * * *
38161 AACTTTGATTGGCAAAGTTGACTTAGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAATC
1 AACTTTGATTGACAAAGTT-ACTTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC
* * *
38226 -AGTT-TCTTTTTGCTAACATAATTACTAATTGATTTATTTATTTATGGCAAAATTTAATAATCA
65 AATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGC--AA---AAT-ATCA
**
38289 TCAATTAGTTAT
124 T-AAGGAG-T-T
* * * * *
38301 AACTTTGATTGCCAAAGTTAATTAACGACTAATTTGATTCATTTATTTATTCAGTATGTTCAATC
1 AACTTTGATTGACAAAGTTACTT-ACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC
* *
38366 AATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATGATCAAATCA
65 AATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGC-AAA--AT---AT--
** *
38431 CCATCAATCAATTAT
122 -CAT-AA-GGAGT-T
* *
38446 AACTTTGATTGACAAAGTTGA-TTAAGGACTAACTTGATTCATTTATTTATTTAGCATTTTCAAT
1 AACTTTGATTGACAAAGTT-ACTT-ACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
*
38510 CAAGTTATTTTTTT
64 CAATTTATTTTTTT
38524 TAGTGGCCAA
Statistics
Matches: 301, Mismatches: 37, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
127 42 0.14
128 2 0.01
129 3 0.01
130 57 0.19
132 3 0.01
134 1 0.00
135 2 0.01
137 3 0.01
138 1 0.00
139 3 0.01
140 55 0.18
141 6 0.02
142 43 0.14
145 78 0.26
146 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (132 bp):
AACTTTGATTGACAAAGTTACTTACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCA
ATTTATTTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAATATCATAAGGAG
TT
Found at i:38487 original size:145 final size:142
Alignment explanation
Indices: 38160--38523 Score: 484
Period size: 145 Copynumber: 2.6 Consensus size: 142
38150 ATTATAGGAG
* * * *
38160 TAACTTTGATTGGCAAAGTTGACTT-AGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAA
1 TAACTTTGATTGACAAAGTTGA-TTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* * * *
38224 TC-AGTT-TCTTTTTGCTAACATAATTACTAATTGATTTATTTATTTATGGCAAAATTTAATAAT
65 TCAAGTTATTTTTTTGCTAACATAATTACTAATTGATTTATTTATTTATAGCAAAATTAAATAAC
* *
38287 CATCAATTAGTTA
130 CATCAATCAATTA
* * * * * *
38300 TAACTTTGATTGCCAAAGTTAATTAACGACTAATTTGATTCATTTATTTATTCAGTATGTTCAAT
1 TAACTTTGATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
*
38365 CAATTTATTTTTTTGCTAACATAATTACTAATTGATTCT-TTTATTTATAGCAAAATGATCAAAT
66 CAAGTTATTTTTTTGCTAACATAATTACTAATTGATT-TATTTATTTATAGCAAAAT--T-AAAT
*
38429 CACCATCAATCAATTA
127 AACCATCAATCAATTA
*
38445 TAACTTTGATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTATTTAGCATTTTCAAT
1 TAACTTTGATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
38510 CAAGTTATTTTTTT
66 CAAGTTATTTTTTT
38524 TAGTGGCCAA
Statistics
Matches: 192, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
139 2 0.01
140 54 0.28
141 3 0.02
142 45 0.23
143 1 0.01
144 1 0.01
145 86 0.45
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (142 bp):
TAACTTTGATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
CAAGTTATTTTTTTGCTAACATAATTACTAATTGATTTATTTATTTATAGCAAAATTAAATAACC
ATCAATCAATTA
Found at i:38662 original size:173 final size:175
Alignment explanation
Indices: 38362--38696 Score: 480
Period size: 173 Copynumber: 1.9 Consensus size: 175
38352 CAGTATGTTC
*
38362 AATCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATGATCAA
1 AATCAAGTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAAT-ATCAA
* *
38427 ATCACCATCAATCAATTATAACTTTGATTGACAAAGTTGATTAAGGACTAACTTGATTCATTTAT
65 ATAACCATCAATCAATTATAACTTTGATTGACAAAGTTGATTAACGACTAACTTGATTCATTTAT
* *
38492 TTATTTAGCATTTTCAATCAAGTTATTTTTTTTAGTGGCCAAAAAA
130 ATATTTAGCATGTTCAATCAAGTTATTTTTTTTAGTGGCCAAAAAA
* *
38538 AATCAAGTTATTTTTTTGAC-AACATAATTACTAATTGATT-TATTTATTTATGGTAAAAT-T-A
1 AATCAAGTTATTTTTTTG-CTAACATAATTACTAATTGATTCT-TTTATTTATAGCAAAATATCA
* * * * **
38599 AATAATCATCCATCATTTATAACTTTGATTGGCAAAGTTTTTTAACGACTAACTTGATTCATTTA
64 AATAACCATCAATCAATTATAACTTTGATTGACAAAGTTGATTAACGACTAACTTGATTCATTTA
* *
38664 TATATTTTGCATGTTCAATCAATTTATTTTTTT
129 TATATTTAGCATGTTCAATCAAGTTATTTTTTT
38697 CAACATAATT
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
173 87 0.61
174 1 0.01
175 1 0.01
176 52 0.37
177 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (175 bp):
AATCAAGTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATATCAAA
TAACCATCAATCAATTATAACTTTGATTGACAAAGTTGATTAACGACTAACTTGATTCATTTATA
TATTTAGCATGTTCAATCAAGTTATTTTTTTTAGTGGCCAAAAAA
Found at i:39323 original size:23 final size:22
Alignment explanation
Indices: 39293--39337 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
39283 AAAAACTTTT
* *
39293 TTTAAAAATTAAACAAAATAAA
1 TTTAAAAAATAAAAAAAATAAA
39315 TTTAGAAAAATAAAAAAAATAAA
1 TTTA-AAAAATAAAAAAAATAAA
39338 GGAACTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TTTAAAAAATAAAAAAAATAAA
Found at i:43163 original size:29 final size:30
Alignment explanation
Indices: 43105--43177 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
43095 GGAGCAAGAG
*
43105 AACCAGATCTAAATCAAAAGAGATGTGGGA
1 AACCAGATCTGAATCAAAAGAGATGTGGGA
43135 AACCAGATCTGAATC-AAAGAGATGTGGGA
1 AACCAGATCTGAATCAAAAGAGATGTGGGA
*
43164 AACCAGATCAGAAT
1 AACCAGATCTGAAT
43178 AGAAGAGCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.16
Consensus pattern (30 bp):
AACCAGATCTGAATCAAAAGAGATGTGGGA
Found at i:43191 original size:29 final size:29
Alignment explanation
Indices: 43105--43191 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
43095 GGAGCAAGAG
*
43105 AACCAGATCTA-AATCAAAAGAGATGTGGGA
1 AACCAGATC-AGAATC-AAAGAGATATGGGA
* *
43135 AACCAGATCTGAATCAAAGAGATGTGGGA
1 AACCAGATCAGAATCAAAGAGATATGGGA
*
43164 AACCAGATCAGAAT-AGAAGAGCTATGGG
1 AACCAGATCAGAATCA-AAGAGATATGGG
43192 GTTAGGAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 1 0.02
29 37 0.73
30 13 0.25
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (29 bp):
AACCAGATCAGAATCAAAGAGATATGGGA
Found at i:44632 original size:21 final size:22
Alignment explanation
Indices: 44608--44667 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
44598 AGTAGTTTAT
* *
44608 TTTAGTTGCTGGAATTTG-CAA
1 TTTAGTTGCTGGAAATTGTAAA
* *
44629 TTTACTTGCTGCAAATTGTAAA
1 TTTAGTTGCTGGAAATTGTAAA
44651 TTTAGTTGCTGGAAATT
1 TTTAGTTGCTGGAAATT
44668 CAAATTTGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTAGTTGCTGGAAATTGTAAA
Found at i:44674 original size:21 final size:22
Alignment explanation
Indices: 44608--44674 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 22
44598 AGTAGTTTAT
*
44608 TTTAGTTGCTGGAATTTGC-AA
1 TTTAGTTGCTGGAAATTGCAAA
* * *
44629 TTTACTTGCTGCAAATTGTAAA
1 TTTAGTTGCTGGAAATTGCAAA
44651 TTTAGTTGCTGGAAATT-CAAA
1 TTTAGTTGCTGGAAATTGCAAA
44672 TTT
1 TTT
44675 GCTTTATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (22 bp):
TTTAGTTGCTGGAAATTGCAAA
Done.