Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013927.1 Corchorus olitorius cultivar O-4 contig13960, 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: 55580
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:237 original size:16 final size:16
Alignment explanation
Indices: 212--248 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
202 ACTGAAGGGT
*
212 TTTTTTTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
228 TTTTTCTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
244 TTTTT
1 TTTTT
249 TGACCTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTC
Found at i:248 original size:11 final size:11
Alignment explanation
Indices: 212--247 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
202 ACTGAAGGGT
*
212 TTTTTTTTTTC
1 TTTTCTTTTTC
223 TTTTCTTTTTC
1 TTTTCTTTTTC
234 TTTTC-TTTTC
1 TTTTCTTTTTC
244 TTTT
1 TTTT
248 TTGACCTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:3705 original size:15 final size:15
Alignment explanation
Indices: 3685--3714 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3675 ATTCTTCTAC
*
3685 TTTTCTTTAGTTTTA
1 TTTTCTCTAGTTTTA
3700 TTTTCTCTAGTTTTA
1 TTTTCTCTAGTTTTA
3715 GGTCTAGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTCTCTAGTTTTA
Found at i:7445 original size:52 final size:53
Alignment explanation
Indices: 7388--7534 Score: 161
Period size: 52 Copynumber: 2.9 Consensus size: 53
7378 GATTGAAAAC
*
7388 CTTTGAAAA-AACTTGAATTGAATACTTCGA-AAACTTGATGGGAACTTTCCC-A
1 CTTTGAAAAGAACTT-AATTGAACACTT-GAGAAACTTGATGGGAACTTTCCCGA
* *
7440 CTTTGAAAAGAGCTTAATTGAACACTTTAGAAACTTGATGGGAACTTTCCCGA
1 CTTTGAAAAGAACTTAATTGAACACTTGAGAAACTTGATGGGAACTTTCCCGA
* *
7493 -TTTGAAAAGAGCTAAATTGAA-A----A-AAACTTGATGGGAACTTTC
1 CTTTGAAAAGAACTTAATTGAACACTTGAGAAACTTGATGGGAACTTTC
7535 TCAATTTAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 12
0.85 0.04 0.12
Matches are distributed among these distances:
46 19 0.22
47 1 0.01
51 2 0.02
52 61 0.69
53 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (53 bp):
CTTTGAAAAGAACTTAATTGAACACTTGAGAAACTTGATGGGAACTTTCCCGA
Found at i:7555 original size:36 final size:36
Alignment explanation
Indices: 7515--7590 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
7505 TAAATTGAAA
* *
7515 AAAACTT-GATGGGAACTTTCTCAATTTAAAAACTTT
1 AAAACTTAG-TGGGAACTTTCCCAATTTAAAAACTAT
*
7551 AAAACTTAGTGGGAACTTTCCCAATTTGAAAACTAT
1 AAAACTTAGTGGGAACTTTCCCAATTTAAAAACTAT
7587 AAAA
1 AAAA
7591 AAAGCCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 35 0.97
37 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (36 bp):
AAAACTTAGTGGGAACTTTCCCAATTTAAAAACTAT
Found at i:16336 original size:465 final size:467
Alignment explanation
Indices: 15459--16395 Score: 1713
Period size: 465 Copynumber: 2.0 Consensus size: 467
15449 CATTGTTCAA
*
15459 ACTAGACCATAGGAATGATAATTTCAAATACTTTAGAGACTGTTTGGTTCATGAAAGAAATGAGG
1 ACTAGACCATAGGAATGATAATTTCAAATACTTTAGAGACTCTTTGGTTCATGAAAGAAATGAGG
*
15524 TTACCGTCTCATCTTATTCCTTTGTCAAGTAAGATTGGCTGAAATTAGTGATTTTTTTATAAAAA
66 TTACCGCCTCATCTTATTCCTTTGTCAAGTAAGATTGGCTGAAATTAGTGATTTTTTTAT----A
*
15589 AAAAAAAATAATGCACAATAAAATTATTATTAGAGATGGATAGACCTATACCGTACCGAATCCAA
127 AAAAAAAATAATGCACAATAAAATTATTATTAGAGATGGAGAGACCTATACCGTACCGAATCCAA
15654 GCGACCAAAATGAAAAAACAAAGCATCAAGCCAAAAAACAAAAAACCTTTGCTTATCCTTAATTA
192 GCGACCAAAATGAAAAAACAAAGCATCAAGCCAAAAAACAAAAAACCTTTGCTTATCCTTAATTA
15719 ATCAATAAACATTCTATCTTGCCTTTCAAAAAATAAAAAAGCCAAAAGAAAAAACCAACAACACA
257 ATCAATAAACATTCTATCTTGCCTTTCAAAAAATAAAAAAGCCAAAAGAAAAAACCAACAACACA
15784 CATGAAAATCAAAGTCACAGTCACATACTAATTAAAGGCCGTTTATCATGAGAATTGAAAGGCAC
322 CATGAAAATCAAAGTCACAGTCACATACTAATTAAAGGCCGTTTATCATGAGAATTGAAAGGCAC
*
15849 GCACAGCCACAAAGGACATTAGATATTATCAAGCCATGTCAAGTGGTCCTATTTATACCCTAATT
387 GCACAGCCACAAAGGACATTAGATATTATCAAGCCATGTCAAGTGCTCCTATTTATACCCTAATT
15914 TACAAGTTGAGTAATT
452 TACAAGTTGAGTAATT
*
15930 ACTAGACCATAGGAATGATAATTTCAAATACTTTAGAGACTCTTTGGTTTATGAAAGAAATGAGG
1 ACTAGACCATAGGAATGATAATTTCAAATACTTTAGAGACTCTTTGGTTCATGAAAGAAATGAGG
15995 TTACCGCCTCATCTTATTCCTTTGTCAAGTAAGATTGGCTGAAATTAGTGATTTTTTTAT-AAAA
66 TTACCGCCTCATCTTATTCCTTTGTCAAGTAAGATTGGCTGAAATTAGTGATTTTTTTATAAAAA
16059 AAAA-AATGCACAATAAAATTATTATTAGAGATGGAGATGACCCTATACCGTACCGAATCCAAGC
131 AAAATAATGCACAATAAAATTATTATTAGAGATGGAGA-GA-CCTATACCGTACCGAATCCAAGC
*
16123 GACCAAAATGGAAAAACAAAGCATCAAGCC-AAAAA-AAAAAA-CTTTGCTTATCCTTAATTAAT
194 GACCAAAATGAAAAAACAAAGCATCAAGCCAAAAAACAAAAAACCTTTGCTTATCCTTAATTAAT
*
16185 CAATAAACTTTCTATCTTGCCTTTCAAAAAAATAAAAAAGCCAAAAGAAAAAACCAACAACACAC
259 CAATAAACATTCTATCTTGCCTTTC-AAAAAATAAAAAAGCCAAAAGAAAAAACCAACAACACAC
16250 ATGAAAATCAAAGTCACAGTCACATACTAATTAAAGGCCGTTTATCATGAGAATTGAAAGGCACG
323 ATGAAAATCAAAGTCACAGTCACATACTAATTAAAGGCCGTTTATCATGAGAATTGAAAGGCACG
16315 CACAGCCACAAAGGACATTAGATATTATCAAGCCATGTCAAGTGCTCCTATTTATACCCTAATTT
388 CACAGCCACAAAGGACATTAGATATTATCAAGCCATGTCAAGTGCTCCTATTTATACCCTAATTT
16380 ACAAGTTGAGTAATT
453 ACAAGTTGAGTAATT
16395 A
1 A
16396 AGTAATTGTG
Statistics
Matches: 456, Mismatches: 7, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
464 45 0.10
465 222 0.49
466 15 0.03
467 52 0.11
471 122 0.27
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (467 bp):
ACTAGACCATAGGAATGATAATTTCAAATACTTTAGAGACTCTTTGGTTCATGAAAGAAATGAGG
TTACCGCCTCATCTTATTCCTTTGTCAAGTAAGATTGGCTGAAATTAGTGATTTTTTTATAAAAA
AAAATAATGCACAATAAAATTATTATTAGAGATGGAGAGACCTATACCGTACCGAATCCAAGCGA
CCAAAATGAAAAAACAAAGCATCAAGCCAAAAAACAAAAAACCTTTGCTTATCCTTAATTAATCA
ATAAACATTCTATCTTGCCTTTCAAAAAATAAAAAAGCCAAAAGAAAAAACCAACAACACACATG
AAAATCAAAGTCACAGTCACATACTAATTAAAGGCCGTTTATCATGAGAATTGAAAGGCACGCAC
AGCCACAAAGGACATTAGATATTATCAAGCCATGTCAAGTGCTCCTATTTATACCCTAATTTACA
AGTTGAGTAATT
Found at i:20313 original size:21 final size:21
Alignment explanation
Indices: 20287--20351 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 21
20277 TTGGTTTCAC
20287 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
* *
20308 TTGTTTGACGAAATTATGTATTACAA
1 TTGTTTGATG-GA--A--TATTACAA
20334 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
20352 TATTGATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 1 0.03
24 1 0.03
25 1 0.03
26 17 0.49
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:20355 original size:26 final size:24
Alignment explanation
Indices: 20299--20355 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
20289 GTTTGATGGA
20299 ATATTACAATTGTTTGACGAAATT
1 ATATTACAATTGTTTGACGAAATT
*
20323 ATGTATTACAATTGTTTGATGGAATATT
1 A--TATTACAATTGTTTGA-CGAA-ATT
20351 ATATT
1 ATATT
20356 GATTGAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 1 0.04
26 20 0.71
27 3 0.11
28 4 0.14
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (24 bp):
ATATTACAATTGTTTGACGAAATT
Found at i:22048 original size:15 final size:16
Alignment explanation
Indices: 22012--22050 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
22002 TGCTTTGTTT
*
22012 TGTTTTCTAGTATAAT
1 TGTTTTCTAGTATAAG
*
22028 TGTTTTCT-GTTTAAG
1 TGTTTTCTAGTATAAG
22043 TGTTTTCT
1 TGTTTTCT
22051 TTCAACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (16 bp):
TGTTTTCTAGTATAAG
Found at i:22439 original size:34 final size:32
Alignment explanation
Indices: 22377--22442 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
22367 TTTTCTGAAA
*
22377 AAAAAAAATATTTTTCTTTGCGTCTTTAATTT
1 AAAAAAAATATTTTTCTTTACGTCTTTAATTT
*
22409 AAAAAAAATATTCTGATT-TTTACGTTTTTAATTT
1 AAAAAAAATATT-T--TTCTTTACGTCTTTAATTT
22443 TTGTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 12 0.41
33 1 0.03
34 14 0.48
35 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (32 bp):
AAAAAAAATATTTTTCTTTACGTCTTTAATTT
Found at i:25531 original size:21 final size:21
Alignment explanation
Indices: 25487--25532 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
25477 GGTTATCCGT
* *
25487 GCCTTCCTCCACGTCATCCTC
1 GCCTTCCTCCACGTCAGCCGC
* *
25508 GCCTTCCTCCGCTTCAGCCGC
1 GCCTTCCTCCACGTCAGCCGC
25529 GCCT
1 GCCT
25533 CATGCCCGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.52, G:0.15, T:0.26
Consensus pattern (21 bp):
GCCTTCCTCCACGTCAGCCGC
Found at i:25755 original size:21 final size:21
Alignment explanation
Indices: 25729--25799 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
25719 CGACCATTCA
** *
25729 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCATGC
25750 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCATGC
25771 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCATGC
25792 CCGTGCCA
1 CCGTGCCA
25800 TCGCCATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.15, C:0.49, G:0.24, T:0.11
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCATGC
Found at i:29097 original size:15 final size:16
Alignment explanation
Indices: 29061--29099 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
29051 TGCTTTGTTT
*
29061 TGTTTTCTAGTATAAT
1 TGTTTTCTAGTATAAG
*
29077 TGTTTTCT-GTTTAAG
1 TGTTTTCTAGTATAAG
29092 TGTTTTCT
1 TGTTTTCT
29100 TTCAACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (16 bp):
TGTTTTCTAGTATAAG
Found at i:30487 original size:529 final size:527
Alignment explanation
Indices: 29428--30616 Score: 1966
Period size: 529 Copynumber: 2.3 Consensus size: 527
29418 GACAATTTTG
*
29428 ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTGAAAACCGTGGGAA
1 ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAAACCGTGGGAA
* * * * * * *
29493 AATTTGTGGCTATTTGGTACGGCCTTTGCCACGACTTTTCAATTTTCCACGGGTTTTGCAGCGGG
66 AATTCGTTGCTATTTGGCACGACCTTTACCACGACTTTTTAATTTTCAACGGGTTTTGCAGCGGG
29558 TTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGAAGATTGACCTCAAACCCTACACTT
131 -TTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGAAGATTGACCTCAAACCCTACACTT
*
29623 ATATGAGCTAATAATTGGATAATGATCACATAATTGCATTTATATCATCTCAAAATTCTATATTG
195 ATATGAGCTAATAATTGGATAATGATCACATAATTGCATTTATAACATCTCAAAATTCTATATTG
* * * *
29688 TTCCCAAAAATTGTGTAATTTCTAATTACTTAAAAAAATTAATTGAATCTTTACACAATGTCATA
260 TCCCCAAAAATTCTATAATTTCTAAATACTTAAAAAAATTAATTGAATCTTTACACAATGTCATA
*
29753 ATATACAAATGTGTTAGTAGTGTGTTCATGATAGTATTACAAATACATTTAGACAATTAAGTCTA
325 ATATACAAATGTGTTACTAGTGTGTTCATGATAGTATTACAAATACATTTAGACAATTAAGTCTA
* *
29818 GTTACAATTTTGAATTTTTTACACTCCCCAAACTATTTTACCTTAAATTCCACATCAAATACTCA
390 GTTACAATTTTGAATTTTTTACACTCCCCAAAATATTTTACATTAAATTCCACATCAAATACTCA
*
29883 AGCTTAACACAGTAGGGTACCATAAAAACCTTTAATTTTATGGGAACTTCAAATTATCTTCGTTT
455 AGCTTAACACAGTAGGGTACCATAAAAACCATTAATTTTATGGGAACTTCAAATTATCTTCGTTT
29948 AAGGTAAA
520 AAGGTAAA
* *
29956 ATTCTTAGACATGAATTCTATATTTGCCATGGTTTTTGAAACGGTTTTCTTAAAAACCGTTGGAA
1 ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAAACCGTGGGAA
* * *
30021 AATTCGTTGCTATTAGGCACGACCTTTACCACGATTTTTTAATTTTCAATGGGTTTTGCAGCGGG
66 AATTCGTTGCTATTTGGCACGACCTTTACCACGACTTTTTAATTTTCAACGGGTTTTGCAGCGGG
* * * *
30086 TTACAGATTCCCGTGGCAAAAGTTGTGGCAAATTGCGAGATGATTGACCTCAAACCCTACAGTTA
131 TTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGAAGATTGACCTCAAACCCTACACTTA
* * * *
30151 TATGAGTTAGTAACTT-GCTAATGATTACATAATTGCATTTATAACATCTCAAAATTCTATATTG
196 TATGAGCTAATAA-TTGGATAATGATCACATAATTGCATTTATAACATCTCAAAATTCTATATTG
*
30215 TCCCCAAAAATTCTATAATTTCTAAATGCTTAAAAAAATTTAATTGAATCTTTACACAATGTCAT
260 TCCCCAAAAATTCTATAATTTCTAAATACTTAAAAAAA-TTAATTGAATCTTTACACAATGTCAT
*
30280 AATATACAAATGTGTTACTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAGTC
324 AATATACAAATGTGTTACTAGTGTGTTCAT-GATAGTATTACAAATACATTTAGACAATTAAGTC
* *
30345 TAGTTACAATTTTGATTTTTTTCCACTCCCCAAAATATTTTACATTAAATTCCACATCAAATACT
388 TAGTTACAATTTTGAATTTTTTACACTCCCCAAAATATTTTACATTAAATTCCACATCAAATACT
* * *
30410 CGAGCTTAACACAGTAGGGTACCATAAAAACCATTAATTTTATGGGAACTTCAAATTGTCTTTGT
453 CAAGCTTAACACAGTAGGGTACCATAAAAACCATTAATTTTATGGGAACTTCAAATTATCTTCGT
*
30475 TTAGGGTAAA
518 TTAAGGTAAA
30485 ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAAACCGTGGGAA
1 ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAAACCGTGGGAA
* * *
30550 AATTCGTTGCTATTTGGCACGACCTTTACCACGAGTTTTTAATTTTCAACGGATTTTGCAGCAGG
66 AATTCGTTGCTATTTGGCACGACCTTTACCACGACTTTTTAATTTTCAACGGGTTTTGCAGCGGG
30615 TT
131 TT
30617 CGTGGCTTTG
Statistics
Matches: 613, Mismatches: 45, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
527 150 0.24
528 174 0.28
529 289 0.47
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (527 bp):
ATTCTTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAAACCGTGGGAA
AATTCGTTGCTATTTGGCACGACCTTTACCACGACTTTTTAATTTTCAACGGGTTTTGCAGCGGG
TTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGAAGATTGACCTCAAACCCTACACTTA
TATGAGCTAATAATTGGATAATGATCACATAATTGCATTTATAACATCTCAAAATTCTATATTGT
CCCCAAAAATTCTATAATTTCTAAATACTTAAAAAAATTAATTGAATCTTTACACAATGTCATAA
TATACAAATGTGTTACTAGTGTGTTCATGATAGTATTACAAATACATTTAGACAATTAAGTCTAG
TTACAATTTTGAATTTTTTACACTCCCCAAAATATTTTACATTAAATTCCACATCAAATACTCAA
GCTTAACACAGTAGGGTACCATAAAAACCATTAATTTTATGGGAACTTCAAATTATCTTCGTTTA
AGGTAAA
Found at i:30832 original size:18 final size:18
Alignment explanation
Indices: 30809--30848 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
30799 TAAAGTCTCT
*
30809 ACCCTCCTGAAACCTCAA
1 ACCCTCCTGAAACCCCAA
*
30827 ACCCTCTTGAAACCCCAA
1 ACCCTCCTGAAACCCCAA
30845 ACCC
1 ACCC
30849 AGGTATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.47, G:0.05, T:0.15
Consensus pattern (18 bp):
ACCCTCCTGAAACCCCAA
Found at i:31433 original size:24 final size:24
Alignment explanation
Indices: 31404--31454 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
31394 TATTTTAATT
31404 ATATCTCTTTTTCTTTTAAATAGG
1 ATATCTCTTTTTCTTTTAAATAGG
*
31428 ATATCTCTTTTTCTTTTAAATGGG
1 ATATCTCTTTTTCTTTTAAATAGG
31452 ATA
1 ATA
31455 CAATTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
ATATCTCTTTTTCTTTTAAATAGG
Found at i:41098 original size:19 final size:18
Alignment explanation
Indices: 41065--41100 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41055 TTGAGATAAT
41065 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
41083 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
41101 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.