Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015751.1 Corchorus olitorius cultivar O-4 contig15784, 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: 70315
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3168 original size:50 final size:50
Alignment explanation
Indices: 3049--3315 Score: 475
Period size: 50 Copynumber: 5.4 Consensus size: 50
3039 AGATATACAG
*
3049 AAGAGTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGT-CTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
3098 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
3148 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC-TTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
*
3197 AAGATTGAATTGGAAGACAGTTCCAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
* * *
3247 AAGATTGAATTGGAAGACAGCTCGAAGGATAAGCAGAAGACAGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
3297 AAGATTGAATTGGAAGACA
1 AAGATTGAATTGGAAGACA
3316 ATTTGAAGAA
Statistics
Matches: 210, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
49 91 0.43
50 119 0.57
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:3225 original size:99 final size:99
Alignment explanation
Indices: 3049--3315 Score: 471
Period size: 99 Copynumber: 2.7 Consensus size: 99
3039 AGATATACAG
* *
3049 AAGAGTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCTTTTAAGATTGAATTGGAAG
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTAAGATTGAATTGGAAG
*
3114 ACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
66 ACAGTTCCAAGGATAAGCGGAAGACGGTCCTTTT
3148 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTAAGATTGAATTGGAAG
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTAAGATTGAATTGGAAG
3213 ACAGTTCCAAGGATAAGCGGAAGACGGTCCTTTT
66 ACAGTTCCAAGGATAAGCGGAAGACGGTCCTTTT
* * *
3247 AAGATTGAATTGGAAGACAGCTCGAAGGATAAGCAGAAGACAGTCCTTTTAAGATTGAATTGGAA
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC-TTTAAGATTGAATTGGAA
3312 GACA
65 GACA
3316 ATTTGAAGAA
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
99 139 0.86
100 22 0.14
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (99 bp):
AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTAAGATTGAATTGGAAG
ACAGTTCCAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:3623 original size:29 final size:28
Alignment explanation
Indices: 3534--3633 Score: 128
Period size: 29 Copynumber: 3.5 Consensus size: 28
3524 CTTTGCTTCT
*
3534 CATTTTGGTCATTTTACATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * *
3562 CATTTTGGTCATTTTGTCAGGACCAGGGT
1 CATTTTGGTCATTTT-TCATGTCCAGGGG
*
3591 CATTTTGGTCATTTTTCATGTTCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
3619 ACATTTTAGTCATTT
1 -CATTTTGGTCATTT
3634 CAAGTGTACT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 24 0.39
29 37 0.61
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:9891 original size:14 final size:15
Alignment explanation
Indices: 9869--9901 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
9859 AACGAAAATT
*
9869 AAAACTAAAAAC-AG
1 AAAAATAAAAACGAG
9883 AAAAATAAAAACGAG
1 AAAAATAAAAACGAG
9898 AAAA
1 AAAA
9902 TTCTTAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.09, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAAATAAAAACGAG
Found at i:10677 original size:28 final size:27
Alignment explanation
Indices: 10633--10690 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
10623 ATTAGTGGCC
* *
10633 AAATAAATCAATAATTATCAAAATCATA
1 AAATAAAACAATAATTAGCAAAAT-ATA
*
10661 AAATAAAACAA-AGATTAGCAAACTATA
1 AAATAAAACAATA-ATTAGCAAAATATA
10688 AAA
1 AAA
10691 CCAAGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.22
Consensus pattern (27 bp):
AAATAAAACAATAATTAGCAAAATATA
Found at i:15038 original size:1 final size:1
Alignment explanation
Indices: 15032--15067 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
15022 AAATGGATGT
15032 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15068 CACCATTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15438 original size:49 final size:50
Alignment explanation
Indices: 15346--15445 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 50
15336 TTTCAAGACC
*
15346 AAAGAGATACTTATGCAGGTTTTGTAGCAGATAAATGGAAATTAGAATAT
1 AAAGAGATACTTATGCAGGTTTTGTAGCAGACAAATGGAAATTAGAATAT
*
15396 AAAGAGATACTTATGCAGG-TTTGTAGCAGACAAATGGCAATTAGAATAT
1 AAAGAGATACTTATGCAGGTTTTGTAGCAGACAAATGGAAATTAGAATAT
15445 A
1 A
15446 TATATATCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 29 0.60
50 19 0.40
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (50 bp):
AAAGAGATACTTATGCAGGTTTTGTAGCAGACAAATGGAAATTAGAATAT
Found at i:15448 original size:2 final size:2
Alignment explanation
Indices: 15441--15482 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
15431 GGCAATTAGA
*
15441 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15483 TGGCAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16864 original size:685 final size:688
Alignment explanation
Indices: 15496--17570 Score: 3628
Period size: 685 Copynumber: 3.0 Consensus size: 688
15486 CAAAATAACT
*
15496 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAACACCCCCTCTTCCCATTTCACCATTTTA
1 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCA-CCCCTCTTCCCATTTCACCATTTTA
15561 ATCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTT
65 ATCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTT
15626 GGAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCT
130 GGAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCT
15691 AGCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACC-AGCATATATAGG
195 AGCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACCAAGCATATATAGG
* *
15755 AAAATGAAGTAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTATACAGGGTATTTAT
260 AAAATGAAGCAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTAT
* *
15820 ACATAGGTTGTATGTATGATAAGATTACAAAATCGTGACATTCTCTAATAGATAGAGATTACATA
325 ACATAGGTTGTATATATGATAAGATTACAAAATCGTGACAGTCTCTAATAGATAGAGATTACATA
15885 TTTAAATTCAAAGTTATATTTGAATATGTCAAGGGT-GAATAAAACGTTATCCTTCTATACGCGC
390 TTTAAATTCAAAG------TTGAATATGTCAAGGGTGGAATAAAACGTTATCCTTCTATACGCGC
* * *
15949 CCTCAAGATAGAGTCTCTAGGTAAGACTCCTATCTTGGAAGCTAGGTGTTAAAACTTCGATCTCA
449 CCTCAAGATAGAGTCTCAAGGTAAGACTCCTATCTTGGAAGCTAGGTGCTGAAACTTCGATCTCA
* *
16014 TAAGAGGCTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAG-TTGC
514 AAAAAGGCTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTT-C
* *
16078 CCGACATTTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAGGAG
578 CCGGCATTTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAGGAT
*
16143 TCATGGAGACATATGTTGCTCCAACATTGCCACAAAGGATGATGGG
643 TCATGGAGACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
*
16189 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCACTCCCTC-ACCCATTTCACCATTTTA
1 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCAC-CCCTCTTCCCATTTCACCATTTTA
16253 ATCAACAAAGAAAACATAGT-AATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTT
65 ATCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTT
* * *
16317 GGAGAGTAAAGCATCAAACTAAACTAAGACTTATTGAAGGACTACAATAGAATTCATAAAAATCT
130 GGAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCT
*
16382 AGCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAGCCAAGCATATATAGG
195 AGCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACCAAGCATATATAGG
*
16447 AAAATGAAGCAGAGTGTTTGAAAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTAT
260 AAAATGAAGCAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTAT
*
16512 ACATAGGTTGTATATATGATAAGATTACAAAATAGTGACAGTCTCTAATAGATAGAGATTACATA
325 ACATAGGTTGTATATATGATAAGATTACAAAATCGTGACAGTCTCTAATAGATAGAGATTACATA
*
16577 TTTAAATTCAAAG-T-AATATGTCAAGGGTGGGATAAAACGTTATCCTTCTATACGCGCCCTCAA
390 TTTAAATTCAAAGTTGAATATGTCAAGGGTGGAATAAAACGTTATCCTTCTATACGCGCCCTCAA
* * *
16640 GATAGAGTCTCCAGGTAAGACTCCTATCTTGGAAGCTAGGTGCTGAAACTTCGATCTCAGAATAG
455 GATAGAGTCTCAAGGTAAGACTCCTATCTTGGAAGCTAGGTGCTGAAACTTCGATCTCAAAAAAG
* *
16705 GCTTGTTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTTACCGGCAT
520 GCTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTTCCCGGCAT
16770 TTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGC-GAGATTCATGG
585 TTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAG-GATTCATGG
16834 AGACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
649 AGACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
*
16874 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCA-CCCTCTTCTCATTTCACCATTTTAA
1 TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCACCCCTCTTCCCATTTCACCATTTTAA
16938 TCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTTG
66 TCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTTG
17003 GAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCTA
131 GAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCTA
17068 GCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACCAAGCATATATAGGA
196 GCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACCAAGCATATATAGGA
17133 AAATGAAGCAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTATA
261 AAATGAAGCAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTATA
17198 CATAGGTTGTATATATGATAAGATTACAAAATCGTGACAGTCTCTAATAGATAGAGATTACATAT
326 CATAGGTTGTATATATGATAAGATTACAAAATCGTGACAGTCTCTAATAGATAGAGATTACATAT
*
17263 TTAAATTCAAAGTTATATAATTTGAATATGTCAAGGGTGGAATAAATCGTTATCCTTCTATACGC
391 TTAAATTCAAAG---------TTGAATATGTCAAGGGTGGAATAAAACGTTATCCTTCTATACGC
* *
17328 GCCCTCAAGATAGAGTCTCAAGGTAAGACTCATATCTTGGAAGTTAGGTGCTGAAACTTCGATCT
447 GCCCTCAAGATAGAGTCTCAAGGTAAGACTCCTATCTTGGAAGCTAGGTGCTGAAACTTCGATCT
*
17393 CAAAAAAGGCTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTG
512 CAAAAAAGGCTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTT
17458 CCCGGCATTTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAGGA
577 CCCGGCATTTACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAGGA
*
17523 TTCATAGAGACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
642 TTCATGGAGACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
17570 T
1 T
17571 GCCTGTGTAG
Statistics
Matches: 1321, Mismatches: 42, Indels: 35
0.94 0.03 0.03
Matches are distributed among these distances:
683 5 0.00
684 51 0.04
685 603 0.46
686 2 0.00
691 157 0.12
692 187 0.14
693 43 0.03
695 1 0.00
696 271 0.21
697 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (688 bp):
TACCTATCATCAATCAATGACAGAAGATCTTCCTAAGCACCCCTCTTCCCATTTCACCATTTTAA
TCAACAAAGAAAACATAGTAAATAATCATGTCAACAAATGTATATCAAGTGGCACAATTATGTTG
GAGAGTAAAGCATCAAACTAAACTAAGACTTATTGGAGTACTACAATAGAATTCACAAAAATCTA
GCAAGTGAAAATTGATTTTAAAAATCAAAGAATCAAAGAATGAATTCAACCAAGCATATATAGGA
AAATGAAGCAGAGTGTTTGAGAGGTAAAAGGTATATTTCATTGATGTTTCTACAGGGTATTTATA
CATAGGTTGTATATATGATAAGATTACAAAATCGTGACAGTCTCTAATAGATAGAGATTACATAT
TTAAATTCAAAGTTGAATATGTCAAGGGTGGAATAAAACGTTATCCTTCTATACGCGCCCTCAAG
ATAGAGTCTCAAGGTAAGACTCCTATCTTGGAAGCTAGGTGCTGAAACTTCGATCTCAAAAAAGG
CTTGGTAGTAAATCTGCCAATTGATCATGAGTGGAAACCTGTCGAACTGCGAGCTTCCCGGCATT
TACTTTATCTCGAACAAAAAGGAGACATATGTTTCATCTTAGAGTGTAAAGCAGGATTCATGGAG
ACATATGTTGCTCCAACATTGTCACAAAGGATGATGGG
Found at i:24846 original size:57 final size:57
Alignment explanation
Indices: 24784--24898 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
24774 ACCTGTATTC
*
24784 CTAACTAACACATGTCACACCTATAAGGATGTAACCCTAACTAACACATGGCTTTTA
1 CTAACTAACACATGTCACACCTATAAGGATATAACCCTAACTAACACATGGCTTTTA
24841 CTAACTAACACATGTCACACCTATAAGGATATAACCCTAACTAACACATGGCTTTTA
1 CTAACTAACACATGTCACACCTATAAGGATATAACCCTAACTAACACATGGCTTTTA
24898 C
1 C
24899 CCACTAAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.26
Consensus pattern (57 bp):
CTAACTAACACATGTCACACCTATAAGGATATAACCCTAACTAACACATGGCTTTTA
Found at i:27482 original size:273 final size:272
Alignment explanation
Indices: 26984--27526 Score: 824
Period size: 273 Copynumber: 2.0 Consensus size: 272
26974 ACGCGTTAAA
* *
26984 TCGTTCAACCCATAATTGTAAAGAATTAAATAGCATAAAGCAAAAAAAGTGTGAGGATCATTAGA
1 TCGTCCAACCCATAATTGTAAAGAATTAAATAACATAAAGCAAAAAAAGTGTGAGGATCATTAGA
* *
27049 TAAATAATCAAACAAAAAATTATTAGTTTATGGAGAGTAGATCCACGAATAGTAACTTATACATA
66 TAAATAATCAAACAAAAAATTATTAGTTTATGGAGAATAGATCCACGAATAGTAACTTATACACA
* * *
27114 AAGTTCCCCAAACGCCCTCGATCATCAACCTAAACTCCGAAAAAACCTAGCATGAAAGTACCGAA
131 AAGTTCCCAAAACACCCTCGATCATCAACCTAAACTACGAAAAAACCTAGCATGAAAGTACCGAA
* **
27179 TTACCCTTCATCATTTGTTCTTGGGTGAATGTGGTGAGATTTTTGAACC-GGTTTTCTGGTACTT
196 TTACCCTTCA-CATTTGTTCTTAGGTGAATGTGGTGAGATTTTTGAACCAACTTTTCTGGTACTT
27243 TAACATTCAAAAT
260 TAACATTCAAAAT
* * *
27256 TCGTCCAACTCATAATTGTAAAGGATTAAATAACATAAAGCAAAAAAAGTTTGAGGATCATTAGA
1 TCGTCCAACCCATAATTGTAAAGAATTAAATAACATAAAGCAAAAAAAGTGTGAGGATCATTAGA
*
27321 TAAATAATCAAACAAAAAAATTATTAGTTTATGGAGAATGAGATCCACGAATAGTAACTTATTCA
66 TAAATAATCAAAC-AAAAAATTATTAGTTTATGGAGAAT-AGATCCACGAATAGTAACTTATACA
* * * * *
27386 CAAGGTTCCCAAAACACCCTCGGTCATCAACTTAAAAC-AC-AAAAAACCTAGCGTGAAAGTACT
129 CAAAGTTCCCAAAACACCCTCGATCATCAACCT-AAACTACGAAAAAACCTAGCATGAAAGTACC
*
27449 GAATTACCCCTT-ACAATTTGTTCTTAGGTGAATGTGGTGAGATTTTTGAACCAACTTTTTTGGT
193 GAATTA-CCCTTCAC-ATTTGTTCTTAGGTGAATGTGGTGAGATTTTTGAACCAACTTTTCTGGT
27513 ACTTTAACATTCAA
256 ACTTTAACATTCAA
27527 CTTTTAGTTA
Statistics
Matches: 245, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
272 74 0.30
273 88 0.36
274 79 0.32
275 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (272 bp):
TCGTCCAACCCATAATTGTAAAGAATTAAATAACATAAAGCAAAAAAAGTGTGAGGATCATTAGA
TAAATAATCAAACAAAAAATTATTAGTTTATGGAGAATAGATCCACGAATAGTAACTTATACACA
AAGTTCCCAAAACACCCTCGATCATCAACCTAAACTACGAAAAAACCTAGCATGAAAGTACCGAA
TTACCCTTCACATTTGTTCTTAGGTGAATGTGGTGAGATTTTTGAACCAACTTTTCTGGTACTTT
AACATTCAAAAT
Found at i:30848 original size:1 final size:1
Alignment explanation
Indices: 30844--30902 Score: 91
Period size: 1 Copynumber: 59.0 Consensus size: 1
30834 GCAAAAGAAG
* * *
30844 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30903 GACTAACAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.95, C:0.00, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:33976 original size:32 final size:32
Alignment explanation
Indices: 33925--33985 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
33915 AATCTTCAAG
*
33925 CTACTCAAGAATATGGAATAATCC-GAGAAATC
1 CTACTCAAGAACATGGAATAA-CCTGAGAAATC
* *
33957 CTACTCAAGAACGTTGAATAACCTGAGAA
1 CTACTCAAGAACATGGAATAACCTGAGAA
33986 CTCCGGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (32 bp):
CTACTCAAGAACATGGAATAACCTGAGAAATC
Found at i:39816 original size:45 final size:45
Alignment explanation
Indices: 39729--39816 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 45
39719 TCTCTCCATT
** * *
39729 TCCCTCTGAATCTGAGCAGCAGCAGCAGCCTCTGACTTCCTCTGC
1 TCCCTCTGAATCTGAGCAGCAGCAGCAGCAACAGACTCCCTCTGC
* * * *
39774 TCCCTCTGACTTTGAGCAGCAGCAGCAGTAACAGCCTCCCTCT
1 TCCCTCTGAATCTGAGCAGCAGCAGCAGCAACAGACTCCCTCT
39817 CCCTATAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (45 bp):
TCCCTCTGAATCTGAGCAGCAGCAGCAGCAACAGACTCCCTCTGC
Found at i:40012 original size:15 final size:17
Alignment explanation
Indices: 39993--40036 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 17
39983 ATTAATCGTA
39993 AATAAACTAATCAAA-T
1 AATAAACTAATCAAACT
40009 -ATAAACTAAGTCAAACT
1 AATAAACTAA-TCAAACT
40026 AATAAACTAAT
1 AATAAACTAAT
40037 TAAGAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 2 0.08
18 9 0.36
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAAACTAATCAAACT
Found at i:56131 original size:13 final size:13
Alignment explanation
Indices: 56113--56137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56103 CGAAGAAACA
56113 AACAAAACAAAAT
1 AACAAAACAAAAT
56126 AACAAAACAAAA
1 AACAAAACAAAA
56138 GTCGCATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.16, G:0.00, T:0.04
Consensus pattern (13 bp):
AACAAAACAAAAT
Found at i:56286 original size:56 final size:56
Alignment explanation
Indices: 56200--56312 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
56190 TTAGCATATT
56200 ACACATACGGGGTTGACATACATTTAGGGTATAATTTTTATTATTAATTAATAAAA
1 ACACATACGGGGTTGACATACATTTAGGGTATAATTTTTATTATTAATTAATAAAA
56256 ACACATACGGGGTTGACATACATTTAGGGTATAATTTTTATTATTAATTAATAAAA
1 ACACATACGGGGTTGACATACATTTAGGGTATAATTTTTATTATTAATTAATAAAA
56312 A
1 A
56313 TTTAATTAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (56 bp):
ACACATACGGGGTTGACATACATTTAGGGTATAATTTTTATTATTAATTAATAAAA
Found at i:57650 original size:2 final size:2
Alignment explanation
Indices: 57645--57686 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
57635 CACACTAATC
57645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57687 TCTATAAGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57976 original size:128 final size:128
Alignment explanation
Indices: 57748--57990 Score: 396
Period size: 128 Copynumber: 1.9 Consensus size: 128
57738 GTGGATAGGC
*
57748 TATCTACATGATATGTAGGATTTTCCCTTGATTTTAGATACTTCAAAAAATGTATAATTTTATCC
1 TATCTACATGACATGTAGGATTTTCCCTTGATTTTAGATACTTCAAAAAATGTATAATTTTATCC
* * *
57813 AACTACTTATTCAAATTAGGTATAAAATTTGAATTCAAAATTTACCAAATTAATATTTATTTT
66 AACTAATTATTCAAATTAAGTATAAAATTTGAATTCAAAATGTACCAAATTAATATTTATTTT
* * * * *
57876 TATCTATATGACATGTAGGATTTTTCCTTGGTTTTAGATACTTCAAAATATGTATAATTTTATTC
1 TATCTACATGACATGTAGGATTTTCCCTTGATTTTAGATACTTCAAAAAATGTATAATTTTATCC
*
57941 AAGTAATTATTCAAATTAAGTATAAAATTTGAATTCAAAATGTACCAAAT
66 AACTAATTATTCAAATTAAGTATAAAATTTGAATTCAAAATGTACCAAAT
57991 ATATATATAT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 105 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (128 bp):
TATCTACATGACATGTAGGATTTTCCCTTGATTTTAGATACTTCAAAAAATGTATAATTTTATCC
AACTAATTATTCAAATTAAGTATAAAATTTGAATTCAAAATGTACCAAATTAATATTTATTTT
Found at i:57996 original size:2 final size:2
Alignment explanation
Indices: 57989--58019 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
57979 AATGTACCAA
57989 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
58020 TTTACTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62290 original size:42 final size:42
Alignment explanation
Indices: 62233--62351 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
62223 ATATCCATTG
* * *
62233 ATATATG-TCATACATCCTTCATGCATTGTCCATGT-CTTTGT
1 ATATATGTTCATACATCCATCAGGCATTATCCAT-TCCTTTGT
62274 ATATATGTTCATACATCCATCAGGCATTATCCATTCCTTTGT
1 ATATATGTTCATACATCCATCAGGCATTATCCATTCCTTTGT
* **
62316 ATATATGTTCATGCATAGATC-GTGCATTATCCATTC
1 ATATATGTTCATACATCCATCAG-GCATTATCCATTC
62352 ATTACTACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
41 9 0.13
42 60 0.87
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (42 bp):
ATATATGTTCATACATCCATCAGGCATTATCCATTCCTTTGT
Found at i:63577 original size:12 final size:12
Alignment explanation
Indices: 63530--63578 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
63520 TGCTTCCCCC
* *
63530 TCTTAGAGTTGC
1 TCTTAGAATTGT
63542 TCTTAGAATTGT
1 TCTTAGAATTGT
63554 TCTTAGAATTGT
1 TCTTAGAATTGT
*
63566 TCTTAAAATTGT
1 TCTTAGAATTGT
63578 T
1 T
63579 GTCATTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (12 bp):
TCTTAGAATTGT
Done.