Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010845.1 Corchorus capsularis cultivar CVL-1 contig10866, 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: 68056
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1988 original size:30 final size:31
Alignment explanation
Indices: 1920--1991 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
1910 GAAGGATGCT
* * *
1920 CGGAAACAGGAGGCTTAGGCTCGGAAATTGGCC
1 CGGAAATAGGAGGCTTACGCTCGGAAA-T-GAC
*
1953 CGGAAATAGGAGGCTTACGCTCGGGAA-GAC
1 CGGAAATAGGAGGCTTACGCTCGGAAATGAC
1983 CGGAAATAG
1 CGGAAATAG
1992 AAGCAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.31
33 24 0.69
ACGTcount: A:0.31, C:0.19, G:0.36, T:0.14
Consensus pattern (31 bp):
CGGAAATAGGAGGCTTACGCTCGGAAATGAC
Found at i:2571 original size:8 final size:8
Alignment explanation
Indices: 2560--2591 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2550 CTCAGATCCT
2560 AAAAGAAA
1 AAAAGAAA
2568 AAAAGAAA
1 AAAAGAAA
2576 GAAAAGAAA
1 -AAAAGAAA
2585 AAAAGAA
1 AAAAGAA
2592 CGGATCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:3114 original size:2 final size:2
Alignment explanation
Indices: 3107--3133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3097 TTTCTTCACC
3107 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
3134 GATTATAACA
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:5390 original size:14 final size:15
Alignment explanation
Indices: 5364--5392 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5354 TTCTAGTACA
5364 TTTGAACGTTTGAAC
1 TTTGAACGTTTGAAC
5379 TTTGAA-GTTTGAAC
1 TTTGAACGTTTGAAC
5393 CCTTGAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
TTTGAACGTTTGAAC
Found at i:6981 original size:30 final size:30
Alignment explanation
Indices: 6940--7000 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
6930 CCCAATTGCC
* * *
6940 TTGCGCTTTGGTTGTTTGTTTTGCTTTGTT
1 TTGCCCTTTGGTGGTTTGTTTTGCCTTGTT
6970 TTGCCCTTTGGTGGTTTGTTTTGCCTTGTT
1 TTGCCCTTTGGTGGTTTGTTTTGCCTTGTT
7000 T
1 T
7001 CAGATGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.00, C:0.13, G:0.26, T:0.61
Consensus pattern (30 bp):
TTGCCCTTTGGTGGTTTGTTTTGCCTTGTT
Found at i:9505 original size:332 final size:333
Alignment explanation
Indices: 8621--10028 Score: 2075
Period size: 333 Copynumber: 4.2 Consensus size: 333
8611 GTCTGAGCGG
* * *
8621 AACGCATTTTTAGCCAAAAACCGCG--A--T-GTACATGATTTAGG-TAAAAATTTTACAAAAAT
1 AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCT-AAAATTTTGCAAAAAT
*
8680 TGACCCGAGAAATTTTT-TCACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACAC
65 TGACCCGAGAAATTTTTCT-ACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGC
* * *
8744 CAAAAAGATTGATGGTCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTACGAATTAATTT
129 CAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTT
8809 CTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAG
194 CTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAG
* *
8874 ATTTGGTTAGATGAATATATATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACC
259 ATTTGGTTAGATGAATATATATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAACC
* *
8939 GGAGCACTGG
324 GGAGCACCGA
* * *
8949 AACACATTTTTAGCCAAAAACCGTGACAGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAATT
1 AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
*
9014 GACCCGAGAAATTTGTCCT-CAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCC
66 GACCCGAGAAATTT-TTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCC
* * *
9078 AAAAAGATTGATGGCCTTTTCACGCTTCTAATATCGATTTTCCTAAATTTTTCCGAATTAATTTC
130 AAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTC
* *
9143 TCATTAAATCGACACATGATTTTGATGCTCGTAAAATCAAATCCTTAAATCCATTGTGGCTGAGA
195 TCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAGA
* * * *
9208 TTTGGTTGGATGAATATAGATATTT-AAAGAGTCTTGGCGCAAAAAAATCATGCCAAACTAAACC
260 TTTGGTTAGATGAATATATATATTTCAATGAGTCTTGGCGC-AAAAAATCATGCAAAACTAAACC
*
9272 GGAGCACAGA
324 GGAGCACCGA
* *
9282 AACGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
1 AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
* *
9347 GACCC-A-AATATTTTTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAACTCAACGTC
66 GACCCGAGAA-ATTTTTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCC
* *
9410 AAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTTTATTTTTCTGAATTAATTTC
130 AAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTC
*
9475 TCATTAAATCGAGACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAGA
195 TCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAGA
*
9540 TTTGGTTAGATGAATATATATACTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAACCG
260 TTTGGTTAGATGAATATATATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAACCG
9605 GAGCACCGA
325 GAGCACCGA
* * * *
9614 AACGCATTTTAAGCCAAAAACCGTGATACTTAGTACACGATATGGGCTAAAATTTTGCAAAAATT
1 AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
** * * * * **
9679 GAAGCGAAAAATTTTTCTTCAATTTCTGGCCAGACTACTCATAAAAAATATATAATTCAACGTGA
66 GACCCGAGAAATTTTTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCA
* * ** * *
9744 AAAAGATTGATGGGCTTTTAACACTTCTAATATTGATTTTAATATTTTTTTCCGAATTAATTTAT
131 AAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCT
* * *
9809 CATTAAATCGACATATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCCATTGCGGCTGAGAA
196 CATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAG-A
* ** * *
9874 TTT-GTTAGTTTTATATAAATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCG
260 TTTGGTTAGATGAATATATATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAACCG
*
9938 GAGCACCGG
325 GAGCACCGA
* * * *
9947 AATGCATTTTTAGCCAAAAACCGTGATGGTTAGAACACGATTTTGGCTAAAATTTTGCAAAAATT
1 AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
* * *
10012 GACGCGAAAAAATTTTC
66 GACCCGAGAAATTTTTC
10029 ATTAATTTTT
Statistics
Matches: 983, Mismatches: 82, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
328 23 0.02
330 1 0.00
331 5 0.01
332 300 0.31
333 645 0.66
334 8 0.01
335 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (333 bp):
AACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAATTTTGCAAAAATT
GACCCGAGAAATTTTTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAACGCCA
AAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGAATTAATTTCT
CATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGAGAT
TTGGTTAGATGAATATATATATTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTAAACCGG
AGCACCGA
Found at i:9969 original size:665 final size:666
Alignment explanation
Indices: 8618--10040 Score: 2143
Period size: 665 Copynumber: 2.1 Consensus size: 666
8608 TGAGTCTGAG
* * *
8618 CGGAACGCATTTTTAGCCAAAAACCGCGA----T-GTACATGATTTAGG-TAAAAATTTTACAAA
1 CGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTAGGCT-AAAATTTTGCAAA
*
8677 AATTGACCCGAGAAATTTTTTCACAATTTTTGGCCAGAATACTCATAAAAAATATATAATTCAAC
65 AATTGACCCGAGAAATTTTTTCACAATTTTTGGCCAGAATACTCATAAAAAATATATAACTCAAC
* *
8742 ACCAAAAAGATTGATGGTCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTACGAATTAAT
130 ACCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTACGAATTAAT
8807 TTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTG
195 TTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTG
* *
8872 AGATTTGGTTAGATGAATATATATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAA
260 AGATTTGGTTAGATGAATATATATACTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTAAA
* * * * *
8937 CCGGAGCACTGGAACACATTTTTAGCCAAAAACCGTGACAGTTAGTACACGATTTGGGCTAAAAT
325 CCGGAGCACCGAAACACATTTTAAGCCAAAAACCGTGACACTTAGTACACGATATGGGCTAAAAT
* * *
9002 TTTGCAAAAATTGACCCGAGAAATTTGTCCTCAATTTTTGGCCAGAATACTCATAAAAAATATAT
390 TTTGCAAAAATTGAACCGAAAAATTTGTCCTCAATTTCTGGCCAGAATACTCATAAAAAATATAT
* * **
9067 AATTCAACGCCAAAAAGATTGATGGCCTTTTCACGCTTCTAATATCGATTTTCCTAAATTTTTCC
455 AATTCAACGCCAAAAAGATTGATGGCCTTTTAACACTTCTAATATCGATTTTAATAAATTTTTCC
* * *
9132 GAATTAATTTCTCATTAAATCGACACATGATTTTGATGCTCGTAAAATCAAATCCTTAAATCCAT
520 GAATTAATTTATCATTAAATCGACACATGATTCTCATGCTCGTAAAATCAAATCCTTAAATCCAT
* * * *
9197 TGTGGCTGAGATTTGGTTGGATGAATATAGATATTTAAAGAGTCTTGGCGCAAAAAAATCATGCC
585 TGCGGCTGAGATTTGGTTAGATGAATATAAATATTTAAAGAGTCTTGGCGCAAAAAAATCATGCA
9262 AAACTAAACCGGAGCAC
650 AAACTAAACCGGAGCAC
* * *
9279 AGAAACGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAA
1 CGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAA
9344 ATTGACCC---AAATATTTTTCTACAATTTTTGGCCAGAATACTCATAAAAAATATATAACTCAA
66 ATTGACCCGAGAAAT-TTTTTC-ACAATTTTTGGCCAGAATACTCATAAAAAATATATAACTCAA
** *
9406 CGTCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTTTATTTTT-CTGAATTA
129 CACCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTAC-GAATTA
*
9470 ATTTCTCATTAAATCGAGACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGC
193 ATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGC
*
9535 TGAGATTTGGTTAGATGAATATATATACTTCAATGAGTCTTGGCGCAAAAAATCATGCAAAACTA
258 TGAGATTTGGTTAGATGAATATATATACTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTA
* *
9600 AACCGGAGCACCGAAACGCATTTTAAGCCAAAAACCGTGATACTTAGTACACGATATGGGCTAAA
323 AACCGGAGCACCGAAACACATTTTAAGCCAAAAACCGTGACACTTAGTACACGATATGGGCTAAA
* * * *
9665 ATTTTGCAAAAATTGAAGCGAAAAATTTTTCTTCAATTTCTGGCCAGACTACTCATAAAAAATAT
388 ATTTTGCAAAAATTGAACCGAAAAATTTGTCCTCAATTTCTGGCCAGAATACTCATAAAAAATAT
** * * **
9730 ATAATTCAACGTGAAAAAGATTGATGGGCTTTTAACACTTCTAATATTGATTTTAATATTTTTTT
453 ATAATTCAACGCCAAAAAGATTGATGGCCTTTTAACACTTCTAATATCGATTTTAATAAATTTTT
* *
9795 CCGAATTAATTTATCATTAAATCGACATATGATTCTCATGCTCGTCAAATCAAATCCTTAAATCC
518 CCGAATTAATTTATCATTAAATCGACACATGATTCTCATGCTCGTAAAATCAAATCCTTAAATCC
* ** *
9860 ATTGCGGCTGAGAATTT-GTTAGTTTTATATAAATATTTCAATGAGTCTTGGCGC-AAAAAATCA
583 ATTGCGGCTGAG-ATTTGGTTAGATGAATATAAATATTT-AAAGAGTCTTGGCGCAAAAAAATCA
*
9923 TGCAAAACTGAACCGGAGCAC
646 TGCAAAACTAAACCGGAGCAC
* * *
9944 CGGAATGCATTTTTAGCCAAAAACCGTGATGGTTAGAACACGATTTTGGCTAAAATTTTGCAAAA
1 CGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAA
* ** *
10009 ATTGACGCGA-AAAAATTTTCATTAATTTTTGG
66 ATTGACCCGAGAAATTTTTTCA-CAATTTTTGG
10041 TCATAATCAA
Statistics
Matches: 684, Mismatches: 64, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
661 25 0.04
663 4 0.01
664 7 0.01
665 578 0.85
666 66 0.10
667 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (666 bp):
CGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAATTTTGCAAAA
ATTGACCCGAGAAATTTTTTCACAATTTTTGGCCAGAATACTCATAAAAAATATATAACTCAACA
CCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTACGAATTAATT
TCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGCTGA
GATTTGGTTAGATGAATATATATACTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTAAAC
CGGAGCACCGAAACACATTTTAAGCCAAAAACCGTGACACTTAGTACACGATATGGGCTAAAATT
TTGCAAAAATTGAACCGAAAAATTTGTCCTCAATTTCTGGCCAGAATACTCATAAAAAATATATA
ATTCAACGCCAAAAAGATTGATGGCCTTTTAACACTTCTAATATCGATTTTAATAAATTTTTCCG
AATTAATTTATCATTAAATCGACACATGATTCTCATGCTCGTAAAATCAAATCCTTAAATCCATT
GCGGCTGAGATTTGGTTAGATGAATATAAATATTTAAAGAGTCTTGGCGCAAAAAAATCATGCAA
AACTAAACCGGAGCAC
Found at i:14067 original size:20 final size:20
Alignment explanation
Indices: 14044--14105 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
14034 AATATTACCA
14044 AAATCAAATTAGTATTAACC
1 AAATCAAATTAGTATTAACC
* *
14064 AAAT-AAACT-GAATT-ACC
1 AAATCAAATTAGTATTAACC
14081 AAAATCAAATTAGTATTAACC
1 -AAATCAAATTAGTATTAACC
14102 AAAT
1 AAAT
14106 AAACTGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.09
18 8 0.24
19 8 0.24
20 12 0.35
21 3 0.09
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (20 bp):
AAATCAAATTAGTATTAACC
Found at i:14088 original size:38 final size:38
Alignment explanation
Indices: 14037--14115 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
14027 ATAGAAAAAT
14037 ATTACCAAAATCAAATTAGTATTAACCAAATAAACTGA
1 ATTACCAAAATCAAATTAGTATTAACCAAATAAACTGA
14075 ATTACCAAAATCAAATTAGTATTAACCAAATAAACTGA
1 ATTACCAAAATCAAATTAGTATTAACCAAATAAACTGA
14113 ATT
1 ATT
14116 GTCGTCTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (38 bp):
ATTACCAAAATCAAATTAGTATTAACCAAATAAACTGA
Found at i:21390 original size:16 final size:16
Alignment explanation
Indices: 21338--21397 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
21328 TTCTTTTCCC
21338 AAATTAAAAGTAATTA
1 AAATTAAAAGTAATTA
* *
21354 ATATTACAAG-ACGATT-
1 AAATTAAAAGTA--ATTA
*
21370 TAATTAAAAGTAATTA
1 AAATTAAAAGTAATTA
21386 AAATTAAAAGTA
1 AAATTAAAAGTA
21398 TTTTTTTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
15 4 0.12
16 26 0.76
17 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATTAAAAGTAATTA
Found at i:21601 original size:5 final size:5
Alignment explanation
Indices: 21591--21617 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21581 AATAAAAAAG
21591 ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT
21618 GGAGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:22392 original size:2 final size:2
Alignment explanation
Indices: 22383--22415 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
22373 ACATTGTGTG
22383 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22416 AGTTCTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37694 original size:54 final size:57
Alignment explanation
Indices: 37623--37733 Score: 183
Period size: 54 Copynumber: 2.0 Consensus size: 57
37613 GCAAGATTAA
*
37623 GTCCTAAATTCCTAATCCTCCTAAGATATGGAGTAAT-T-TAAAATAAATATCCTTT
1 GTCCTAAATTCCTAATCCTCCTAAGATATGGAGTAATATATAAAATAAAAATCCTTT
*
37678 GTCCTAAA-TCCTAATCCTCTTAAGATATGGAGTAATATATAAAATAAAAATCCTTT
1 GTCCTAAATTCCTAATCCTCCTAAGATATGGAGTAATATATAAAATAAAAATCCTTT
37734 ACTAGTTAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 27 0.52
55 9 0.17
56 16 0.31
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (57 bp):
GTCCTAAATTCCTAATCCTCCTAAGATATGGAGTAATATATAAAATAAAAATCCTTT
Found at i:58424 original size:23 final size:23
Alignment explanation
Indices: 58398--58446 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
58388 TAATGTATAG
*
58398 ATAACAAGAATAAACAACTAAAT
1 ATAACAAGAATAAAAAACTAAAT
**
58421 ATAACAAGCTTAAAAAACTAAAT
1 ATAACAAGAATAAAAAACTAAAT
58444 ATA
1 ATA
58447 GCTAGCAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.20
Consensus pattern (23 bp):
ATAACAAGAATAAAAAACTAAAT
Found at i:59326 original size:20 final size:22
Alignment explanation
Indices: 59292--59332 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
59282 CGGGCTATAG
59292 TTTTTTCTTACTACTCCCTACC
1 TTTTTTCTTACTACTCCCTACC
59314 TTTTTT-TTA-TACTCCCTAC
1 TTTTTTCTTACTACTCCCTAC
59333 TTATCAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTTCTTACTACTCCCTACC
Found at i:62835 original size:32 final size:32
Alignment explanation
Indices: 62774--62835 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
62764 CAAATTGATA
* * *
62774 GACAAAATAACCCTCAAACTTTTATAAAATAT
1 GACAAAATAACCCTCAAAATTTGACAAAATAT
*
62806 GACAAAATAATCCTCAAAATTTGACAAAAT
1 GACAAAATAACCCTCAAAATTTGACAAAAT
62836 GACCCCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.26
Consensus pattern (32 bp):
GACAAAATAACCCTCAAAATTTGACAAAATAT
Found at i:62846 original size:22 final size:21
Alignment explanation
Indices: 62798--62846 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
62788 CAAACTTTTA
*
62798 TAAAATATGACAAAATAATCC
1 TAAAATATGACAAAATAACCC
* *
62819 TCAAAATTTGACAAAATGACCCC
1 T-AAAATATGACAAAAT-AACCC
62842 TAAAA
1 TAAAA
62847 AGATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.22
Consensus pattern (21 bp):
TAAAATATGACAAAATAACCC
Found at i:62983 original size:11 final size:11
Alignment explanation
Indices: 62967--62998 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
62957 AAATAAAAAA
62967 ATTAACAATTT
1 ATTAACAATTT
62978 ATTAACAATTT
1 ATTAACAATTT
*
62989 ATTGACAATT
1 ATTAACAATT
62999 ATAAATTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (11 bp):
ATTAACAATTT
Found at i:65219 original size:3 final size:3
Alignment explanation
Indices: 65211--65244 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
65201 ATCTTTAAGC
65211 TGA TGA TGA TGA TGA TGA TGA TGA TGA TTGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA
65245 ATGTCCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Done.