Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006466.1 Corchorus capsularis cultivar CVL-1 contig06487, 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: 22077
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:2799 original size:15 final size:15
Alignment explanation
Indices: 2779--2833 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
2769 TAATTTGCCT
2779 TATATATATATATAA
1 TATATATATATATAA
*
2794 TATATATATATCTAA
1 TATATATATATATAA
* *
2809 TACAGATAT-TATAA
1 TATATATATATATAA
2823 TATA-ATATATA
1 TATATATATATA
2834 CTACAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 4 0.12
14 9 0.26
15 21 0.62
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:5970 original size:3 final size:3
Alignment explanation
Indices: 5962--5991 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5952 GAGAGTCTTT
*
5962 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5992 AAAAAACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:6544 original size:2 final size:2
Alignment explanation
Indices: 6533--6567 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6523 ACAAATTAAT
6533 TA TA -A TA 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 TA
6568 ACAATAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10745 original size:25 final size:24
Alignment explanation
Indices: 10711--10757 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
10701 TGTATTCTTC
*
10711 TCATCATCATCATGTAATAAAATGA
1 TCATCATCATCAT-CAATAAAATGA
*
10736 TCATGATCATCATCAATAAAAT
1 TCATCATCATCATCAATAAAAT
10758 CCAATTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (24 bp):
TCATCATCATCATCAATAAAATGA
Found at i:11818 original size:30 final size:30
Alignment explanation
Indices: 11782--11872 Score: 114
Period size: 30 Copynumber: 3.0 Consensus size: 30
11772 ATGGTTAAAA
11782 TTGACCAAAATTAAAGTTGAGTGGCTTATT
1 TTGACCAAAATTAAAGTTGAGTGGCTTATT
* * **
11812 TTGACCAAAATTGAGAGTTCA-TGG-TTGAAA
1 TTGACCAAAATT-AAAGTTGAGTGGCTT-ATT
11842 TTGACCAAAATTAAAGTTGAGTGGCTTATT
1 TTGACCAAAATTAAAGTTGAGTGGCTTATT
11872 T
1 T
11873 AACCGTTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
29 8 0.16
30 33 0.67
31 8 0.16
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (30 bp):
TTGACCAAAATTAAAGTTGAGTGGCTTATT
Found at i:11823 original size:58 final size:60
Alignment explanation
Indices: 11753--11872 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
11743 AAAGGGATTA
11753 TTTGACCAAAATTGAGAG-T-ATGGTTAAAATTGACCAAAATTAAAGTTGAGTGGCTTAT
1 TTTGACCAAAATTGAGAGTTCATGGTTAAAATTGACCAAAATTAAAGTTGAGTGGCTTAT
*
11811 TTTGACCAAAATTGAGAGTTCATGGTTGAAATTGACCAAAATTAAAGTTGAGTGGCTTAT
1 TTTGACCAAAATTGAGAGTTCATGGTTAAAATTGACCAAAATTAAAGTTGAGTGGCTTAT
11871 TT
1 TT
11873 AACCGTTTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 18 0.31
59 1 0.02
60 40 0.68
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (60 bp):
TTTGACCAAAATTGAGAGTTCATGGTTAAAATTGACCAAAATTAAAGTTGAGTGGCTTAT
Found at i:12154 original size:11 final size:11
Alignment explanation
Indices: 12132--12167 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12122 GTTTCCGTTT
12132 TTTTGTTTTTTG
1 TTTTG-TTTTTG
12144 TTTTGTTTTTG
1 TTTTGTTTTTG
*
12155 CTTTGTTTTTG
1 TTTTGTTTTTG
12166 TT
1 TT
12168 GTGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:12390 original size:12 final size:12
Alignment explanation
Indices: 12368--12420 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
12358 ATGTTGGCAA
12368 CAACATTTTGTGT
1 CAAC-TTTTGTGT
12381 CAACTTTTGT-T
1 CAACTTTTGTGT
*
12392 -AA-TGTTG-G-
1 CAACTTTTGTGT
12400 CAACTTTTGTGT
1 CAACTTTTGTGT
12412 CAACTTTTG
1 CAACTTTTG
12421 ATAATGTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
9 6 0.18
10 6 0.18
11 2 0.06
12 15 0.45
13 4 0.12
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (12 bp):
CAACTTTTGTGT
Found at i:12411 original size:31 final size:32
Alignment explanation
Indices: 12368--12433 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
12358 ATGTTGGCAA
*
12368 CAACATTTTGTGTCAACTTTTGTTAATGTTGG
1 CAACATTTTGTGTCAACTTTTGATAATGTTGG
12400 CAAC-TTTTGTGTCAACTTTTGATAATGTTGG
1 CAACATTTTGTGTCAACTTTTGATAATGTTGG
12431 CAA
1 CAA
12434 AATGCATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (32 bp):
CAACATTTTGTGTCAACTTTTGATAATGTTGG
Found at i:14342 original size:441 final size:438
Alignment explanation
Indices: 13469--14394 Score: 1051
Period size: 441 Copynumber: 2.1 Consensus size: 438
13459 AGCAAAAGAT
* * * *
13469 ATAAAATAGAAAAAGTATGAGGGTCATTTGGTAACTAATTCAAATAAGAAAATATTTCTTAATAG
1 ATAAAGTAGAAAAA-TATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATAG
* * * *
13534 ATATCTTGAAATATAAAAATTCCCTTTTGAACACTTCATGAAACTCGTAGATCAAATTAACTTTC
65 AGATCTTGAAACATAAAAATTCCCTTTTAAACACTTCATGAAACTAGTAGATCAAATTAACTTTC
* * * * * * *
13599 GGGTTCTTCATGAAAGTCGTATATCATTCAGTAACCTTTTAACTGACACTTGAATAACTTTAATC
130 GGATTCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATC
** * * * * *
13664 GGACATGTGAATTGAAAATTATATTGTATTAAGACCAACAATCGAAACGACCAAATTTAGGAAGT
195 GGACATGTGAATAAAAAATTATATTGTATTAAAACCAACAATCAAAACCACAAAATTTAGGAAGC
* * * *
13729 ATTTTTGTGAATTATAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
260 ATTTTTGTGAATTAAAACATAAAAATTTGCTTTTGAGTCATGCATGAAAATTGTAGATCATGAAA
*
13794 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAAAAAAGAATAAAAAAATAAA
325 TTACCTTTTAATAGACACATAAATCAACTTAATCGGACAAATAGAAAAAAGAATAAAAAAATAAA
* ** * * * ** *
13859 TCTTAAACGTTAGATGTTAGATTAAGATAGAATTTGTAAAGGACTACGTAGT
390 ACGCAAACGTTAAATGTCAGACT-A-ATA-AATTTGTAAAGGACTAAATAGC
* * * * *
13911 GTAAAGTAGAAAAATATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGA
1 ATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGA
* * * *
13976 GATCTTGAAGCATAAAAATTCCCTTTTAAACCCTTCATGAAACTAGTAGATTAAATTTAGCTTTC
66 GATCTTGAAACATAAAAATTCCCTTTTAAACACTTCATGAAACTAGTAGATCAAA-TTAACTTTC
14041 GGA-TCTTTCATGAAAGTTC-TAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAA
130 GGATTC-TTCATGAAAG-TCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAA
* * ** *
14104 TCGGATATGTGTATAAAAAATTATA-TGATATTAAATTAACCGGCAATCAAAACCACAAAATTTC
193 TCGGACATGTGAATAAAAAATTATATTG-TATT-AA--AACCAACAATCAAAACCACAAAATTTA
* *
14168 GGAAGCATTTTT-TAGAATTAAAACATTAAAA-TTGACTTTTGAGTTATGCATGAAAATTGTAGA
254 GGAAGCATTTTTGT-GAATTAAAACATAAAAATTTG-CTTTTGAGTCATGCATGAAAATTGTAGA
* * * * * * *
14231 TTATGAAATTATCTTTTAATAGATACTTAAATCACCTTAATCGGACATATAGAAAAAA-AATACA
317 TCATGAAATTACCTTTTAATAGACACATAAATCAACTTAATCGGACAAATAGAAAAAAGAATAAA
* * *
14295 AAAATAAAAGGCAACGCGTTAAATCGTCCAGCCT-AT-AA-TTGTAAAGGACTAAATAGC
382 AAAATAAAACGCAA-ACGTTAAAT-GT-CAGACTAATAAATTTGTAAAGGACTAAATAGC
* * * *
14352 ATAAAGTATAAAAGTATGAGGATCATTAGATAAATAATCCAAA
1 ATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAA
14395 AAAATATTAG
Statistics
Matches: 404, Mismatches: 68, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
441 149 0.37
442 97 0.24
443 4 0.01
444 21 0.05
445 128 0.32
446 2 0.00
447 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (438 bp):
ATAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGA
GATCTTGAAACATAAAAATTCCCTTTTAAACACTTCATGAAACTAGTAGATCAAATTAACTTTCG
GATTCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
GACATGTGAATAAAAAATTATATTGTATTAAAACCAACAATCAAAACCACAAAATTTAGGAAGCA
TTTTTGTGAATTAAAACATAAAAATTTGCTTTTGAGTCATGCATGAAAATTGTAGATCATGAAAT
TACCTTTTAATAGACACATAAATCAACTTAATCGGACAAATAGAAAAAAGAATAAAAAAATAAAA
CGCAAACGTTAAATGTCAGACTAATAAATTTGTAAAGGACTAAATAGC
Found at i:16192 original size:42 final size:42
Alignment explanation
Indices: 16144--16372 Score: 224
Period size: 42 Copynumber: 5.5 Consensus size: 42
16134 AGAGTCAACA
* * * *
16144 CCTGCATTAAGTGCATCCTTAGCAGCCTCTTTAGACCCAATG
1 CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
* * * * **
16186 CCTGCATCAACTACATCCTGAACAGCCTCCTCAGATCCAACA
1 CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
* * *
16228 ACTGCGTCAAGTGCATCCTTAACAGCCTCCGCAGACCCAATG
1 CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
* * * *
16270 CCTGCATCAAGTGCATTCTTAGCAGCTTCCCCAGACCCAATG
1 CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
* * * * * * *
16312 CCTGCATTAAGTACATTCTTAACAGCCTCCCCACAGCCAACG
1 CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
* *
16354 CCTACATCAAGTACATCCT
1 CCTGCATCAAGTGCATCCT
16373 GAGCACCCTC
Statistics
Matches: 152, Mismatches: 35, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 152 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (42 bp):
CCTGCATCAAGTGCATCCTTAACAGCCTCCTCAGACCCAATG
Found at i:16371 original size:126 final size:126
Alignment explanation
Indices: 16144--16372 Score: 296
Period size: 126 Copynumber: 1.8 Consensus size: 126
16134 AGAGTCAACA
* ***
16144 CCTGCATTAAGTGCATCCTTAGCAGCCTCTTTAGACCCAATGCCTGCATCAACTACATCCTGAAC
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATGCCTGCATCAACTACATCCTGAAC
* * * * * *
16209 AGCCTCCTCAGATCCAACAACTGCGTCAAGTGCATCCTTAACAGCCTCCGCAGACCCAATG
66 AGCCTCCCCACAGCCAACAACTACATCAAGTACATCCTTAACAGCCTCCGCAGACCCAATG
* * * * * *
16270 CCTGCATCAAGTGCATTCTTAGCAGCTTCCCCAGACCCAATGCCTGCATTAAGTACATTCTTAAC
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATGCCTGCATCAACTACATCCTGAAC
**
16335 AGCCTCCCCACAGCCAACGCCTACATCAAGTACATCCT
66 AGCCTCCCCACAGCCAACAACTACATCAAGTACATCCT
16373 GAGCACCCTC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
126 85 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (126 bp):
CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATGCCTGCATCAACTACATCCTGAAC
AGCCTCCCCACAGCCAACAACTACATCAAGTACATCCTTAACAGCCTCCGCAGACCCAATG
Found at i:19482 original size:42 final size:42
Alignment explanation
Indices: 19430--19643 Score: 175
Period size: 42 Copynumber: 5.1 Consensus size: 42
19420 TCCATAGAGT
* * *
19430 CAACACCTGCATTAAGTGCATCCTTAGTAGCCTCCCTAGACC
1 CAACGCCTGCATCAAGTGCATCCTTAGCAGCCTCCCTAGACC
* * * * * **
19472 CAATGCCTGCATCAACTACATCCTGAACAGCCT-CCTCAGGTC
1 CAACGCCTGCATCAAGTGCATCCTTAGCAGCCTCCCT-AGACC
* * *
19514 CAACGGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACC
1 CAACGCCTGCATCAAGTGCATCCTTAGCAGCCTCCCTAGACC
* * * **
19556 CAACACCTGCATCAAGTACATCCTGAATAGCCTCTCC-AGACC
1 CAACGCCTGCATCAAGTGCATCCTTAGCAGCCTC-CCTAGACC
* * *
19598 CAGCAG-CTACATCAAGTGTATCCTTAGCAGCCT-CCTCAGACC
1 CAAC-GCCTGCATCAAGTGCATCCTTAGCAGCCTCCCT-AGACC
19640 CAAC
1 CAAC
19644 CTCCTCAGGT
Statistics
Matches: 129, Mismatches: 37, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
40 2 0.02
41 3 0.02
42 121 0.94
43 3 0.02
ACGTcount: A:0.28, C:0.37, G:0.14, T:0.21
Consensus pattern (42 bp):
CAACGCCTGCATCAAGTGCATCCTTAGCAGCCTCCCTAGACC
Found at i:19577 original size:84 final size:84
Alignment explanation
Indices: 19430--19632 Score: 255
Period size: 84 Copynumber: 2.4 Consensus size: 84
19420 TCCATAGAGT
* * * * * **
19430 CAACACCTGCATTAAGTGCATCCTTAGTAGCCTCCCTAGACCCAATGCCTGCATCAACTACATCC
1 CAACAGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCATCAACTACATCC
**
19495 TGAACAGCCTC-CTCAGGTC
66 TGAACAGCCTCTC-CAGACC
* *
19514 CAACGGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCATCAAGTACATCC
1 CAACAGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCATCAACTACATCC
*
19579 TGAATAGCCTCTCCAGACC
66 TGAACAGCCTCTCCAGACC
* * *
19598 CAGCAGCTACATCAAGTGTATCCTTAGCAGCCTCC
1 CAACAGCTGCATCAAGTGCATCCTTAGCAGCCTCC
19633 TCAGACCCAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 101 0.99
85 1 0.01
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (84 bp):
CAACAGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCATCAACTACATCC
TGAACAGCCTCTCCAGACC
Found at i:19762 original size:141 final size:141
Alignment explanation
Indices: 19502--19768 Score: 383
Period size: 141 Copynumber: 1.9 Consensus size: 141
19492 TCCTGAACAG
* * * *
19502 CCTCCTCAGGTCCAACGGCTGCATCAAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCA
1 CCTCCTCAGGTCCAAAGGCTACATCAAGTGCACCCTTAGCAGACTCCATAAACCCAACACCTGCA
* * * * **
19567 TCAAGTACATCCTGAATAGCCTCTCCAGACCCAGCAGCTACATCAAGTGTATCCTTAGCAGCCTC
66 TCAAGTACATCCTGAACAGCCTCCCCACACCCAACAGCTACATCAAGTACATCCTTAGCAGCCTC
19632 CTCAGACCCAA
131 CTCAGACCCAA
* *
19643 CCTCCTCAGGTCCAAAGGCTACATCAAGTGCACCCTTAGCAGACTCCATAGACCCAACGCCTGCA
1 CCTCCTCAGGTCCAAAGGCTACATCAAGTGCACCCTTAGCAGACTCCATAAACCCAACACCTGCA
* * *
19708 TCAAGTACATCCTTAACAGCCTCCCCACAGCCAAC-GCCTGCATCAAGTACATCCTTAGCAG
66 TCAAGTACATCCTGAACAGCCTCCCCACACCCAACAG-CTACATCAAGTACATCCTTAGCAG
19769 TCTCTATAGA
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
140 1 0.01
141 109 0.99
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.19
Consensus pattern (141 bp):
CCTCCTCAGGTCCAAAGGCTACATCAAGTGCACCCTTAGCAGACTCCATAAACCCAACACCTGCA
TCAAGTACATCCTGAACAGCCTCCCCACACCCAACAGCTACATCAAGTACATCCTTAGCAGCCTC
CTCAGACCCAA
Found at i:20531 original size:16 final size:16
Alignment explanation
Indices: 20495--20566 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
20485 TGACCTCATT
* *
20495 AGGTGAGTATTGTACT
1 AGGTGAGTATTGCACC
*
20511 GGGTGAGTATCT-CACC
1 AGGTGAGTAT-TGCACC
20527 AGGTGAGTATTGCACC
1 AGGTGAGTATTGCACC
*
20543 AGGTGAGCATTGCACC
1 AGGTGAGTATTGCACC
20559 AGGTGAGT
1 AGGTGAGT
20567 GTTTATACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.02
16 46 0.96
17 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (16 bp):
AGGTGAGTATTGCACC
Found at i:20581 original size:17 final size:17
Alignment explanation
Indices: 20556--20600 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
20546 TGAGCATTGC
20556 ACCAGGTGAGTGTTTAT
1 ACCAGGTGAGTGTTTAT
* * *
20573 ACTAGGTGAATGTTTGT
1 ACCAGGTGAGTGTTTAT
20590 ACCAGGTGAGT
1 ACCAGGTGAGT
20601 ATTTGTATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (17 bp):
ACCAGGTGAGTGTTTAT
Found at i:20605 original size:17 final size:17
Alignment explanation
Indices: 20495--20607 Score: 90
Period size: 16 Copynumber: 6.9 Consensus size: 17
20485 TGACCTCATT
*
20495 AGGTGAGTA-TTGTACT
1 AGGTGAGTATTTGTACC
* * *
20511 GGGTGAGTATCT-CACC
1 AGGTGAGTATTTGTACC
*
20527 AGGTGAGTA-TTGCACC
1 AGGTGAGTATTTGTACC
* *
20543 AGGTGAGCA-TTGCACC
1 AGGTGAGTATTTGTACC
* * *
20559 AGGTGAGTGTTTATACT
1 AGGTGAGTATTTGTACC
* *
20576 AGGTGAATGTTTGTACC
1 AGGTGAGTATTTGTACC
20593 AGGTGAGTATTTGTA
1 AGGTGAGTATTTGTA
20608 TTGGGTGAGT
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
15 1 0.01
16 44 0.57
17 32 0.42
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (17 bp):
AGGTGAGTATTTGTACC
Found at i:21650 original size:15 final size:15
Alignment explanation
Indices: 21632--21734 Score: 73
Period size: 15 Copynumber: 6.5 Consensus size: 15
21622 GACTCCCTCA
*
21632 AGGGAGTCTCCCCTG
1 AGGGAGTCTCCCATG
*
21647 AGGGAGTCTCGCATAG
1 AGGGAGTCTCCCAT-G
*
21663 CAAGGGAGTCTCCCTTG
1 --AGGGAGTCTCCCATG
* * *
21680 AGGGAGTATCGCATAACA
1 AGGGAGTCTCCCAT---G
*
21698 AGGGAGTCTCCCTTG
1 AGGGAGTCTCCCATG
21713 AGGGAGTCT-CCACTG
1 AGGGAGTCTCCCA-TG
21728 AGGGAGT
1 AGGGAGT
21735 ATCTTCTGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
14 2 0.03
15 41 0.60
16 1 0.01
17 1 0.01
18 23 0.34
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.20
Consensus pattern (15 bp):
AGGGAGTCTCCCATG
Found at i:21667 original size:33 final size:33
Alignment explanation
Indices: 21630--21777 Score: 189
Period size: 33 Copynumber: 4.6 Consensus size: 33
21620 GAGACTCCCT
*
21630 CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAG
1 CAAGGGAGTCTCCCTTGAGGGAGTCTCGCATAG
* *
21663 CAAGGGAGTCTCCCTTGAGGGAGTATCGCATAA
1 CAAGGGAGTCTCCCTTGAGGGAGTCTCGCATAG
21696 CAAGGGAGTCTCCCTTGAGGGAGTCTC-CACT-G
1 CAAGGGAGTCTCCCTTGAGGGAGTCTCGCA-TAG
* * *
21728 --AGGGAGTAT-CTTCTGAAGGAGTCTCGCATAG
1 CAAGGGAGTCTCCCT-TGAGGGAGTCTCGCATAG
21759 CAAGGGAGTCTCCCTTGAG
1 CAAGGGAGTCTCCCTTGAG
21778 AGAATCTTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
29 2 0.02
30 20 0.21
31 3 0.03
32 2 0.02
33 68 0.70
34 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.32, T:0.22
Consensus pattern (33 bp):
CAAGGGAGTCTCCCTTGAGGGAGTCTCGCATAG
Found at i:21668 original size:48 final size:48
Alignment explanation
Indices: 21589--21686 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
21579 TAGCAAGAAC
* * *
21589 GTCTCCCCTGAGGGAGTCTTGCGTAATAAGGGAGACTCCCTCAAGGGA
1 GTCTCCCCTGAGGGAGTCTCGCATAACAAGGGAGACTCCCTCAAGGGA
* * **
21637 GTCTCCCCTGAGGGAGTCTCGCATAGCAAGGGAGTCTCCCTTGAGGGA
1 GTCTCCCCTGAGGGAGTCTCGCATAACAAGGGAGACTCCCTCAAGGGA
21685 GT
1 GT
21687 ATCGCATAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (48 bp):
GTCTCCCCTGAGGGAGTCTCGCATAACAAGGGAGACTCCCTCAAGGGA
Found at i:21670 original size:18 final size:18
Alignment explanation
Indices: 21647--21707 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
21637 GTCTCCCCTG
21647 AGGGAGTCTCGCATAGCA
1 AGGGAGTCTCGCATAGCA
* *
21665 AGGGAGTCTC-CCTTG--
1 AGGGAGTCTCGCATAGCA
* *
21680 AGGGAGTATCGCATAACA
1 AGGGAGTCTCGCATAGCA
21698 AGGGAGTCTC
1 AGGGAGTCTC
21708 CCTTGAGGGA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.27
16 2 0.06
17 3 0.09
18 19 0.58
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (18 bp):
AGGGAGTCTCGCATAGCA
Done.