Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014882.1 Corchorus capsularis cultivar CVL-1 contig14903, 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: 18569
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:130 original size:2 final size:2
Alignment explanation
Indices: 123--147 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
113 ATGTACATTC
123 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
148 TTTTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1800 original size:11 final size:11
Alignment explanation
Indices: 1757--1794 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1747 CCTATATATA
*
1757 AAATAAATTAT
1 AAATTAATTAT
1768 CAAA-TAATTAT
1 -AAATTAATTAT
1779 AAATTAATTAT
1 AAATTAATTAT
1790 AAATT
1 AAATT
1795 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:3691 original size:16 final size:17
Alignment explanation
Indices: 3659--3691 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3649 CTACACCGTA
3659 AATCTTTTACTTTCTTTG
1 AATCTTTTAC-TTCTTTG
3677 AATCTTTTA-TTCTTT
1 AATCTTTTACTTCTTT
3692 AAGGACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (17 bp):
AATCTTTTACTTCTTTG
Found at i:4030 original size:100 final size:100
Alignment explanation
Indices: 3926--4115 Score: 233
Period size: 100 Copynumber: 1.9 Consensus size: 100
3916 ACTTTACCCT
* * **
3926 TTTTTTACAAATATATTTCTTTAAATT-GC-TATAATTAAAATATATTAATTATGTCATTATTAA
1 TTTTTTACAAATATATTTC--TAAATTGGCATATAA-TAAAACATATTAACTATACCATTATTAA
*
3989 AAGATAA-TTTATGTATTTTTTTTTTCCGATAGTACCA
63 AAGATAATTTTATGTACTTTTTTTTTCCGATAGTACCA
* * *
4026 TTTTTTTCAAATATATTTCTAAATTGGCATTATAATAATACATTTTAACTATACCATTATTAAAA
1 TTTTTTACAAATATATTTCTAAATTGGCA-TATAATAAAACATATTAACTATACCATTATTAAAA
* *
4091 TATAATTTTGTGTACTTTTTTTTTC
65 GATAATTTTATGTACTTTTTTTTTC
4116 AAATATATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
98 6 0.08
99 2 0.03
100 46 0.61
101 22 0.29
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (100 bp):
TTTTTTACAAATATATTTCTAAATTGGCATATAATAAAACATATTAACTATACCATTATTAAAAG
ATAATTTTATGTACTTTTTTTTTCCGATAGTACCA
Found at i:5263 original size:87 final size:88
Alignment explanation
Indices: 5117--5291 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 88
5107 CACATTGGAT
5117 TCAAAAATTTATTTTACGAGCATCTCAATCCGTTTTGATTTAATTAGAGATTAATTCGG-AAAAA
1 TCAAAAATTTATTTTACGAGCATCTCAATCCGTTTTGATTTAATTAGAGATTAATTCGGAAAAAA
5181 AATTAGGAAAGACGATATTAGAA
66 AATTAGGAAAGACGATATTAGAA
5204 TCAAAAATTTATTTTACGAGCATCTCAATCCGTTTTGATTTAATTAGAGATTAATTCGGAAAAAA
1 TCAAAAATTTATTTTACGAGCATCTCAATCCGTTTTGATTTAATTAGAGATTAATTCGGAAAAAA
5269 AATTAGGAAAGACGATATTAGAA
66 AATTAGGAAAGACGATATTAGAA
5292 GCGTGAGAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 59 0.68
88 28 0.32
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (88 bp):
TCAAAAATTTATTTTACGAGCATCTCAATCCGTTTTGATTTAATTAGAGATTAATTCGGAAAAAA
AATTAGGAAAGACGATATTAGAA
Found at i:9066 original size:331 final size:329
Alignment explanation
Indices: 5350--11050 Score: 4908
Period size: 331 Copynumber: 17.3 Consensus size: 329
5340 TGAATAACCT
* * * * * * * *
5350 TTCAATATTTTTGGTGTTGAATTATATATTTTTTATAAGTTTCGTGG-CAAAAATGGA-CAAAAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAAA
* * * * *
5413 T-TCTATCAGGTCAATTTTTGCAAATTTTTAGCCGAAATCGTGTAATAACCATCATAGTTTTTGG
65 TGT-T-TCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * *
5477 CTAAAAACACGTTTCGGAGCCCATGCTCATTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAGA
128 CTAAAAACACGTTTCGGGGCCCA-GCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAA
* * *
5542 TATCTATATAAATCTAACCAAATCTCATCCACATTGGATATAAGGATTTGATTTTACGAGCATCT
192 TATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * **
5607 CAATCAGGTTTCGATTTAAATAGAAATTAA-TCGGAAAAATACGAAAAAAAAATATTAGAAGCGT
257 CAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATA-GGAAAAACGATATTAGAAGCGT
**
5671 GAGAAATCC
321 GAGAAGCCC
*
5680 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAAGAAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATTGAGGAGAAA
* * * * * * * *
5745 TGTTTTGGGTAAAGTTGTGCAAAATTTTAACCGACATTGTGTACTAACCATCACGGTTTTT-GAT
65 TGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * * * * *
5809 AAAAACGCG-TTCAGGGGCCACAACTCAGTTTTGCATGAATTTTGGCGCCATGACTTATTGAAAT
130 AAAAACACGTTTC-GGGGCC-CAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAAT
** * * * * *
5873 ATCTATATTTATCTAACAAAATCTCAGT-CAAATTGGATTTAAGAATTTCTTTTTACGAGCGTCT
193 ATCTATATACATCTAACCAAATCTCA-TCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * * *
5937 CAATCCGGTTTCAATTTAATTAGAAATTAATTTGAAAAAAAAGGAAAAAATGATATTAGAAGCGT
257 CAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGG-AAAAACGATATTAGAAGCGT
*
6002 GAGAAGGCC
321 GAGAAGCCC
* * * *
6011 TTCAATTTTTTTGGCGTTGAGTTATATATTTTTTTATGAGTATTGTGGCAAAAAACTGAGGAGAT
1 TTCAATCTTTTTGGCGTTGAGTTATATA-TTTTTTATGAGTA-TGTGGCCAAAAATTGAGGAGAA
* * * *
6076 ATGTTTCGGGTAAATTTTTACAAAATTTTAGCTGAAATTGTGTACTAACCATCAC-GATTTTTGA
64 ATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGG
* * * * ** * * *
6140 C-CAAAACGCGTTCCGGAGCCCAGGCTGTGTTTTGCATGAGTTTTGGTGACAAGACTCATTGAAA
128 CTAAAAACACGTTTCGGGGCCCA-GCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAA
* * * * *
6204 TATCTATATCCATCTAACGAAATCTCAGCCACATTGGATTTTAGGATTT-TTTTTAGGAGCATCT
192 TATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * * **
6268 AAATCAT-GTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGTAAACCAATATTAGAAGTTT
257 CAATC-TGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCGT
* * *
6332 CA-ATATCCT
321 GAGA-AGCCC
* * *
6341 TTTAATCTTTTT-GCTGTTGAGTTATATATTTTTTATGAGTATCGTGGCCAAAAATTTACGA-AA
1 TTCAATCTTTTTGGC-GTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAA
* * * * * *
6404 ATTATTTTGAGTAAATTTTTTCAAACTTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGG
64 A-TGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * * *
6469 CTAAAAACACGTTCCGGGGCCCAGAC-CTAATTTTGCAAT-ATTTTTTGCGCCAAGATTCCTTGA
128 CTAAAAACACGTTTCGGGGCCCAG-CTC-AGTTTTGC-ATGATTTTTGGCGTCAAGACTCATTGA
* * * * * *
6532 AATATCTTTATACATTTAACCAAATCTCATCCACATTGCATTCAAGGATTTGTTTTAACAAGCAT
190 AATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
** * * * ** *
6597 CAAAATCCGGTTTCAATTTAATTTGAAATTAATTTTGAAAAATAGGAAAAATGATATTAGAAGCG
255 CTCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCG
*
6662 TGAGAAGCAC
320 TGAGAAGCCC
* ** * *
6672 TTCAATCTTTTTGGCGTTGAATTTATATATAATTTATGAGTATTATGGCTAAAAATTGAGGGAGA
1 TTCAATCTTTTTGGCGTTG-AGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATTGA-GGAGA
* * * * * * *
6737 AA-CTATCGGTTAAATTTTTGCAAAAATTTAGCCGAAACCGTATA-TCAATCCGTATATCACGGT
63 AATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AA-CC----ATCACAGT
* ** * * * * *
6800 TTTTGGCCAAAAATGCG-TTCTGGAGCCTCGGTTCTGTTTTGCATGATTTTTGGCATCAAGACTC
122 TTTTGGCTAAAAACACGTTTC-GGGGCC-CAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTC
* * * * * * * *
6864 ATTGTAATATCTATATCCATCTAACGAAATCTCAGCCACATTGGATTTTAGAATTTGCTTTTAGG
185 ATTGAAATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACG
* *
6929 AGCATCTCAATCCGGTTTCGATTTAATTAGAAATAAATTCGGAAAAATAGG-AAAACTGATATTA
250 AGCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAAC-GATATTA
* *
6993 GAAGCTTGA-ATAGCCT
314 GAAGCGTGAGA-AGCCC
* * *
7009 TTCAATCTTTTTGGTGTTGATTTATATATTTTTTATGAGTATCGTGGCCAAAAATTGATGA-AAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAAA
* * *
7073 -GTCTATCGGGTAAATTTTTGCAAATTTTTAGCCGAAATCGTGTATTAACCCATCACAATTTTTG
65 TGT-T-TCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CCATCACAGTTTTTG
* *
7137 GCTAAAAACACGTTTCAGGGCCCAGACTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAA
127 GCTAAAAACACGTTTCGGGGCCCAG-CTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAA
* * *
7202 ATATCTATATAAATCTAACCAAATCTCATCCACATTGGATTTATGGATTTGTTTTTATGAGCATC
191 ATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
7267 TCAATCAGGTTTCGATTTAATTAGAAATTAATTCAGAAAAATACGAAAAATGATATTAGAAGCGT
256 TCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCGT
*
7332 GAGAAACCC
321 GAGAAGCCC
* * *
7341 TTCAATCCTTTTGGCTTTGAGTTCTATATTTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAA
1 TTCAATCTTTTTGGCGTTGAGTTATATA-TTTTTTATGAGTA-TGTGGCCAAAAATTGAGGAGAA
* * * * *
7406 ATGCTTCGGGTAAAATTTTGCAAAATTTTAGCCGACATCGTG---T-A-CGTCAC-GTTTTTTTT
64 ATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG--TTTTTG
** * * * * * *
7465 GCTAAAAACGTGTTCCGGGGTCTC-GACTCAGTTTTGCATGAATTTT-GCCTCCATGACTCCTTG
127 GCTAAAAACACGTTTCGGGG-CCCAG-CTCAGTTTTGCATGATTTTTGGCGT-CAAGACTCATTG
** *** * *
7528 AAATATCTATATTTATCTAGGGAAATCTCAGCCACATTGGATTTAAGGATTTCTTTTTACGAGCA
189 AAATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
*
7593 TCTCAATCTGGTTTCGATTTAATTAGAAATTAATTC--AATACAAAAGGAAAAACGATATTAGAA
254 TCTCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAA-A-AATAGGAAAAACGATATTAGAA
* *
7656 GCATGAGATGCCC
317 GCGTGAGAAGCCC
* * * *
7669 TTCAATTTTTTTGGCGTTGAGTTATATATTTTTTATGAGGATTGTGGCAAAAAATT-ATGGAGAT
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATTGA-GGAGAA
* * ** *
7733 ACGTTTCGGGTAAATTTTTGCAAAACTTTAGCCGAAATCGTGTACTAACCATCACAAATTTTGAC
64 ATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGC
* * * * * ***
7798 CAAAAACGCGTTCCGGAGCCCCAGCTCTGTTTTGCATGATTTTTGGTAACAAGACTCATTGAAAT
129 TAAAAACACGTTTCGG-GGCCCAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAAT
** * * * * *
7863 ATCTATAT-CTATCTAAAGATATCTCAGCCACATTGGATTTTAGGA--T-TTTTTAGGAGCATCA
193 ATCTATATAC-ATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * * *
7924 AAATCAT-GTTTCGATTTAATTAGAAATTAATTTGGAAAAGATATGAAAACCAATATTAGAAGCT
257 CAATC-TGGTTTCGATTTAATTAGAAATTAATTCGGAAAA-ATAGGAAAAACGATATTAGAAGCG
* *
7988 TCA-ATAGCCT
320 TGAGA-AGCCC
* * * * * * *
7998 TTCAATCTTTTTGGTGTTGAGTTATATGTTTTTTATGAGTATCGCGACAAAAAATTTACGA-AAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAAA
** * * * *
8062 T-TATATCTAGT-AATTTTTTCAAATTTTTAGCCGAAATCGTGTACTAACCATCATAATTTTTGG
65 TGT-T-TCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
* * * *
8125 CTAAAAACACGTTTCAGGGCCCAGACTCAGTTTTGCAAT-ATTTTTTGCGCCAAGACTCCTTGAA
128 CTAAAAACACGTTTCGGGGCCCAG-CTCAGTTTTGC-ATGATTTTTGGCGTCAAGACTCATTGAA
* * * * *
8189 ATA-CTTTATAAATTTAACCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTACGAGAATC
191 ATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
** * *
8253 AAAATCCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCGT
256 TCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCGT
*
8318 GAGAAGCAC
321 GAGAAGCCC
* * ** *
8327 TTCAATCTTTTTGGCGTTAAATTTATATATAATTTATGAGTATTGTGGCTAAAAATTGA-GAGAA
1 TTCAATCTTTTTGGCGTT-GAGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATTGAGGAGAA
** * * *
8391 AACTTTCGGTTAAATTTTTGCAAAAATTTAGCCGAAATC---T--T----A--ACGGTTTTTGGC
64 ATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGC
* * * * *
8445 CAAAAA-AGCG-TTCTGGAGCCTCAGTTCTGTTTTGCATGATTTTTGGCATCAAGACTCATTGAA
129 TAAAAACA-CGTTTC-GGGGCC-CAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAA
* * * * *
8508 ATATCTATATCCATCTAATCAAATCTCAGCGAC-----A-TT--GGA-----TTTTAGGAGCATC
191 ATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * *
8560 TCAATCCGGTTTCGATTTAATTAGAAATAAATTAGGAAAAATAGG-AAAACTGATATTAGAAGCT
256 TCAATCTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAAC-GATATTAGAAGCG
*
8624 TGA-ATAGCCT
320 TGAGA-AGCCC
* * * * *
8634 TTCAATCTTTTTGGTGCTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGATGA-AAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAAA
* * * * * * *
8698 TTTTATCGGGTGAATTTTTGCAAATTTTTAACCGAAATCGTGTATTAAACATTACAGTTTTTGGC
65 TGTT-TCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGC
* * ** *
8763 TAAAAACACGTTTCGGGGCCCAGGTTCAGTTTTTCATGATTTTTGGTATCAAGACTCCTTGAAAT
129 TAAAAACACGTTTCGGGGCCCA-GCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAAT
* *
8828 ATCTATATAAATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGATTTTACGAGCATCTC
193 ATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTC
* *
8893 AATCTGGTTTCGATTTAATTAGAAATTAATTCAGATAAAATAGGAAAAACGATATTAGATGCGTG
258 AATCTGGTTTCGATTTAATTAGAAATTAATTCGGA-AAAATAGGAAAAACGATATTAGAAGCGTG
*
8958 AGAATCCC
322 AGAAGCCC
* * * * *
8966 TTGAATCTTTTTGGCGTTTAGTTATATA-TTTTTATGAGTACTGTGGCAAAAAATTTAGCAGAAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATTGAGGAGAAA
* * * * * *
9030 TGTTTCGGGAAAATCTTTACAAAGTTTTAGCCGAAATCATGTACTAACCATCAC-GATTTTTGAC
65 TGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGGC
* * * * ** *
9094 TAAAAACGCATTCCGGGGCTCCAGCTCTA-TTTTGCATGATTTTTGACACCAAGTCTCATTGAAA
129 TAAAAACACGTTTCGGGGC-CCAGCTC-AGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAA
* * * *
9158 TATCTATATCCATCTAACCAAATCTCAACCAAATTAGATTTAAGGATTTGTTTTTACGAGCATCT
192 TATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* *
9223 GAATCAT-GTTTCGATTTAATTAGAAATTAATTCGGACAAAATAGGAAAACCGATATTAGAAGCG
257 CAATC-TGGTTTCGATTTAATTAGAAATTAATTCGGA-AAAATAGGAAAAACGATATTAGAAGCG
* *
9287 TGAAAAGCCT
320 TGAGAAGCCC
* *
9297 TTCAATCTTTTTGGCGTTGAATTATATATTTTTCTATGAGTATCGTGACCAAAAATTGAGGA-AT
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTT-TATGAGTAT-GTGGCCAAAAATTGAGGAGA-
* * * * * * *
9361 ACTCTTTTGGGTAAATTTTTGCAAAATTTTAGCTGAAATAGTGTACTAACTATCAC-GATTTCTG
63 AATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTG
* * * * * *
9425 GCTAAAAATACG-TTCTGAGGCCCAGTCTCAGTTTTGCATAATTTTTTGGTGTCAAGATTCCTTG
127 GCTAAAAACACGTTTC-GGGGCCCAG-CTCAGTTTTGCATGA-TTTTTGGCGTCAAGACTCATTG
* * * * * *
9489 AAATATCTATATTCATCTAATCAAATCTCATACACATTGGATTTATGTATTTG-TTTTACAAGCA
189 AAATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
** *
9553 TCAAAATTCT-GTTTCGATTTCATTAGAAATTAATTCGGTAAAATATAGGAAAAACGATATTAGA
254 TCTCAA-TCTGGTTTCGATTTAATTAGAAATTAATTCGG-AAAA-ATAGGAAAAACGATATTAGA
* *
9617 AGCGTGAAAATCCC
316 AGCGTGAGAAGCCC
* *** * * *
9631 TTCAATATTTTTGTTATTATATTATATTATATATATATATATATATATTATGAGTATTGTGGCTA
1 TTCAATCTTTTTG--------GCGT-TGA-GT-TATATAT-T-T-T-TTATGAGTA-TGTGGCCA
* * * *
9696 AAAATTGAAGGAGAAACT-TTT-TGTTAAATTTTTGCAAAATTGTAGCCGAAATCGTGGACTAAC
50 AAAATTG-AGGAGAAA-TGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * * ** * * * **
9759 CATCA-TGGTTTTGGGTAAAAATGCGTTTCGGGTTTCCTA-CTCAGTTTTGCATAATTTTTAACG
113 CATCACAGTTTTTGGCTAAAAACACGTTTCGGG--GCCCAGCTCAGTTTTGCATGATTTTTGGCG
* * * **
9822 TCAATACTCATTGAAATATCTATATGA-ATCTAACGAAATCTTAGACACATTGGATTTAAGGATT
176 TCAAGACTCATTGAAATATCTATAT-ACATCTAACCAAATCTCATCCACATTGGATTTAAGGATT
**
9886 TGTTTTTACGAGCATCTCAATCCAGTTTCGATTTAATTAGAAATTAATTCGGGAGAAAATAGGAA
240 TGTTTTTACGAGCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTC-GGA-AAAATAGGAA
*
9951 AAACGATA-TAGAAACGTGAGAAGCCC
303 AAACGATATTAGAAGCGTGAGAAGCCC
* * ** * *
9977 TTGAAACTTTTTGGCGTT-AAAT-TGT-TTTTTTATTAGTAT-T---C------T---G-G--AT
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATGTGGCCAAAAATTGAGGAGAAAT
* ** * * * ** * **
10023 TTTTCGGGTCTATTTTTGTAAAATTTTAGCTGAAATTGTGTACTAATTATTACAGTTTTTATCTA
66 GTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTA
* * * ** * * *
10088 AAAACTCATTCCGGGGCCCCTTCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATAT
131 AAAACACGTTTCGGGG-CCCAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAATAT
** * * * *
10153 CTATATTTATTTAACCAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCCTCTGAA
195 CTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAA
* * * * * * *
10218 TCAT-ATTTTGATTTAATTGGAAATTAATTCGGACAAAATAGGAAAACCGATATTATAAGTGTTA
260 TC-TGGTTTCGATTTAATTAGAAATTAATTCGGA-AAAATAGGAAAAACGATATTAGAAGCGTGA
* * *
10282 AAAGTCT
323 GAAGCCC
** * * * * * *
10289 TTCAATAGTTCTGGTGTTGAATTATATATTTTTTATAAGTATCGTGGCAAAAAATTGGGGA-AAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAGGAGAAA
* * * * * * * *
10353 T-TTTCTGGTAAATTTTT-TATAAATTTTAGACGAAATTGTATGCTAACTATCA-TGATTTTTGG
65 TGTTTCGGGTAAATTTTTGCA-AAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGG
* * * * * *
10415 CTAAAAACACGTTAT-GAGACGCATGCTCAGTTTTGCATAATTTTTGGTGTCAAGACTCCTTGAA
128 CTAAAAACACGTT-TCGGGGCCCA-GCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAA
* * * *
10479 ATATCTAT-T--TTCTTACCAAATCTCATCAACATTGGATTTAAGAATTTGTTTTTACGAGCATC
191 ATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
** *
10541 AAAATCAT-GTTTTGATTTAATTAGAAATTAA----G---AAT------AACGATATTAGAAGCG
256 TCAATC-TGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCG
*
10592 TGAAAAGCCC
320 TGAGAAGCCC
* * * * *
10602 TTCAATCTTTTTGGCGTTGAATTGTATATATATTATGAGTATTGTGGCTAAAAATTGGAGGAGAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTA-TGTGGCCAAAAATT-GAGGAGAA
* *
10667 A-CTTTC-GGTAAAATTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACCATCACAGTTTTTTT
64 ATGTTTCGGGT-AAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG--TTTTT
* * * * * *
10730 GGCTAAAAACACGTTCCGGGGTCCCGGCTCTGTTTT-CTATGATTTTTGGCGTCAATATTCAATG
126 GGCTAAAAACACGTTTCGGGG-CCCAGCTCAGTTTTGC-ATGATTTTTGGCGTCAAGACTCATTG
* * * * * * * *
10794 AAATATCTATATTCATCTAACAAAATTTTATCCACATTGTATTTTAGGATTTCTTTTCACGAGCA
189 AAATATCTATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * *
10859 TCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATACG-AAAACGATATTAGAAG
254 TCTCAATCTGGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATAGGAAAAACGATATTAGAAG
* *
10923 TGTGAGAAGCAC
318 CGTGAGAAGCCC
* * * * *
10935 TTTAAACTTTTTGACATTGAGTTATTTATTTTTTATGAGTATAGTGGCCAAAAATTG-GAGAGAA
1 TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTAT-GTGGCCAAAAATTGAG-GAGAA
* * *
10999 ATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
64 ATGTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
11051 TACGGTACTT
Statistics
Matches: 4341, Mismatches: 785, Indels: 487
0.77 0.14 0.09
Matches are distributed among these distances:
305 1 0.00
306 43 0.01
307 116 0.03
309 1 0.00
310 5 0.00
311 57 0.01
312 163 0.04
313 69 0.02
314 12 0.00
315 57 0.01
316 4 0.00
317 65 0.01
318 96 0.02
319 60 0.01
320 93 0.02
321 1 0.00
323 2 0.00
324 3 0.00
325 1 0.00
326 8 0.00
327 192 0.04
328 351 0.08
329 229 0.05
330 507 0.12
331 669 0.15
332 532 0.12
333 341 0.08
334 122 0.03
335 5 0.00
336 81 0.02
337 178 0.04
338 4 0.00
342 1 0.00
343 2 0.00
344 2 0.00
345 7 0.00
346 89 0.02
347 87 0.02
348 70 0.02
349 13 0.00
350 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (329 bp):
TTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATGTGGCCAAAAATTGAGGAGAAAT
GTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTA
AAAACACGTTTCGGGGCCCAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAATATC
TATATACATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAAT
CTGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCGTGAGAA
GCCC
Found at i:12716 original size:39 final size:36
Alignment explanation
Indices: 12672--12780 Score: 150
Period size: 34 Copynumber: 3.0 Consensus size: 36
12662 AATCAAATTA
*
12672 AATTTTTTTAGTCCAATTCCAATTATATATTACGAGTTG
1 AATTTTATTAGTCCAATTCCAATTATATATTACG-G--G
*
12711 AATTTTATTAGTCCAATTCAAATTATATATTACGGG
1 AATTTTATTAGTCCAATTCCAATTATATATTACGGG
*
12747 --TTTTCTTAGTCCAATTCCAATTATATATTACGGG
1 AATTTTATTAGTCCAATTCCAATTATATATTACGGG
12781 TTAAGTGGAT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
34 32 0.48
36 1 0.02
38 1 0.02
39 32 0.48
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (36 bp):
AATTTTATTAGTCCAATTCCAATTATATATTACGGG
Found at i:12875 original size:28 final size:26
Alignment explanation
Indices: 12818--12878 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
12808 AGTAATCTTG
* *
12818 AAGAGGTTGGTTGAGATTAAAATTGT
1 AAGAGTTTGGTTGAAATTAAAATTGT
12844 --GAGTTTGGTTGAAATTAAAATTGGTT
1 AAGAGTTTGGTTGAAATTAAAATT-G-T
12870 AAGAGTTTG
1 AAGAGTTTG
12879 TCTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 20 0.69
25 1 0.03
26 1 0.03
28 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (26 bp):
AAGAGTTTGGTTGAAATTAAAATTGT
Found at i:13037 original size:10 final size:10
Alignment explanation
Indices: 13015--13046 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
13005 GTACTTTTTA
13015 ATATAGTATAT
1 ATATAG-ATAT
13026 ATATAGATAT
1 ATATAGATAT
13036 ATATAGATAT
1 ATATAGATAT
13046 A
1 A
13047 GATATTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
ATATAGATAT
Found at i:16520 original size:37 final size:37
Alignment explanation
Indices: 16479--16552 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
16469 CACAAATAAT
* *
16479 TCTTTTTTTTTTCCATCCCTACAAATAACACTAAAGA
1 TCTTTTTTTTTTCCACCCCCACAAATAACACTAAAGA
16516 TCTTTTTTTTTTCCACCCCCACAAATAACACTAAAGA
1 TCTTTTTTTTTTCCACCCCCACAAATAACACTAAAGA
16553 GTATAAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (37 bp):
TCTTTTTTTTTTCCACCCCCACAAATAACACTAAAGA
Found at i:18224 original size:139 final size:139
Alignment explanation
Indices: 17974--18254 Score: 553
Period size: 139 Copynumber: 2.0 Consensus size: 139
17964 AACAACTCAA
17974 ATAAATATCTATACCCAAACATCTAAATGAAAATTCAACCTAAACTAGAAATTATACCATAAATA
1 ATAAATATCTATACCCAAACATCTAAATGAAAATTCAACCTAAACTAGAAATTATACCATAAATA
18039 AACTACGTACCTACCTACCAAATAAACAAACCAATTACAAACTCACATGCTATGAGAATTGAACC
66 AACTACGTACCTACCTACCAAATAAACAAACCAATTACAAACTCACATGCTATGAGAATTGAACC
18104 CAAGACCTC
131 CAAGACCTC
18113 ATAAATATCTATACCCAAACATCTAAATGAAAATTCAACCTAAACTAGAAATTATACCATAAATA
1 ATAAATATCTATACCCAAACATCTAAATGAAAATTCAACCTAAACTAGAAATTATACCATAAATA
*
18178 AACTACGTACCTACCTACCAAATAAACAAACCAATTACAAACTCACATGCTATGAGAATTGAATC
66 AACTACGTACCTACCTACCAAATAAACAAACCAATTACAAACTCACATGCTATGAGAATTGAACC
18243 CAAGACCTC
131 CAAGACCTC
18252 ATA
1 ATA
18255 GTCTAGGTAG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 141 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (139 bp):
ATAAATATCTATACCCAAACATCTAAATGAAAATTCAACCTAAACTAGAAATTATACCATAAATA
AACTACGTACCTACCTACCAAATAAACAAACCAATTACAAACTCACATGCTATGAGAATTGAACC
CAAGACCTC
Found at i:18386 original size:9 final size:9
Alignment explanation
Indices: 18368--18412 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
18358 ATCTGAATCG
*
18368 GTAAACTTA
1 GTAAAATTA
18377 GTAAAATTA
1 GTAAAATTA
*
18386 GTGAAATTA
1 GTAAAATTA
*
18395 GTAAACTTA
1 GTAAAATTA
*
18404 GTGAAATTA
1 GTAAAATTA
18413 TCTGAATCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (9 bp):
GTAAAATTA
Found at i:18397 original size:18 final size:18
Alignment explanation
Indices: 18374--18412 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18364 ATCGGTAAAC
18374 TTAGTAAAATTAGTGAAA
1 TTAGTAAAATTAGTGAAA
*
18392 TTAGTAAACTTAGTGAAA
1 TTAGTAAAATTAGTGAAA
18410 TTA
1 TTA
18413 TCTGAATCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (18 bp):
TTAGTAAAATTAGTGAAA
Done.