Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008213.1 Corchorus capsularis cultivar CVL-1 contig08234, 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: 62909
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5272 original size:115 final size:115
Alignment explanation
Indices: 5070--5301 Score: 455
Period size: 115 Copynumber: 2.0 Consensus size: 115
5060 GCCATTTAAG
5070 ATTCATAGAGCATTATCTATAGATAAACTTTCATTCTCATGAGAATAATATGTATATGCTCAAAG
1 ATTCATAGAGCATTATCTATAGATAAACTTTCATTCTCATGAGAATAATATGTATATGCTCAAAG
*
5135 CCTCAACAGTGGCATAATAAGTATAGTCATGACCTCTATAATGGCCCATA
66 CCTCAACAGGGGCATAATAAGTATAGTCATGACCTCTATAATGGCCCATA
5185 ATTCATAGAGCATTATCTATAGATAAACTTTCATTCTCATGAGAATAATATGTATATGCTCAAAG
1 ATTCATAGAGCATTATCTATAGATAAACTTTCATTCTCATGAGAATAATATGTATATGCTCAAAG
5250 CCTCAACAGGGGCATAATAAGTATAGTCATGACCTCTATAATGGCCCATA
66 CCTCAACAGGGGCATAATAAGTATAGTCATGACCTCTATAATGGCCCATA
5300 AT
1 AT
5302 AATTTCAAAC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (115 bp):
ATTCATAGAGCATTATCTATAGATAAACTTTCATTCTCATGAGAATAATATGTATATGCTCAAAG
CCTCAACAGGGGCATAATAAGTATAGTCATGACCTCTATAATGGCCCATA
Found at i:6499 original size:30 final size:30
Alignment explanation
Indices: 6437--6701 Score: 316
Period size: 30 Copynumber: 8.7 Consensus size: 30
6427 CATGGTTTAT
*
6437 ATGACAACTTATGGTGTCAATTGAATAA-ATC
1 ATGACAACTTCTGGTGTCAATTG--TAAGATC
* *
6468 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * *
6498 ATGACAACTTCTAGTGTCATTTGTAAGAGC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * *
6528 ATGACAACTTCTAGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* *
6558 ATTAACAACTTCTGGTGTCAATTGTAAAATC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
* *
6589 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * *
6619 ATGACAACTTATGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* *
6649 ATTGACAACTTCTGGTGTCAATTGTAACACC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
6680 ATTGACAACTTCTGGTGTCAAT
1 A-TGACAACTTCTGGTGTCAAT
6702 GGAGATTTAT
Statistics
Matches: 205, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.01
30 110 0.54
31 93 0.45
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATC
Found at i:6566 original size:61 final size:60
Alignment explanation
Indices: 6437--6699 Score: 312
Period size: 61 Copynumber: 4.3 Consensus size: 60
6427 CATGGTTTAT
* * * * *
6437 ATGACAACTTATGGTGTCAATTGAATAA-ATCATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCATTTG--TAAGATCATGACAACTTCTGGTGTCAATTGTAAGACC
* * * * **
6498 ATGACAACTTCTAGTGTCATTTGTAAGAGCATGACAACTTCTAGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCATTTGTAAGATCATGACAACTTCTGGTGTCAATTGTAAGACC
* * * *
6558 ATTAACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCATTTGTAAGACC
1 A-TGACAACTTCTGGTGTCATTTGTAAGATCATGACAACTTCTGGTGTCAATTGTAAGACC
* * *
6619 ATGACAACTTATGGTGTCATTTGTAAGATTATTGACAACTTCTGGTGTCAATTGTAACACC
1 ATGACAACTTCTGGTGTCATTTGTAAGATCA-TGACAACTTCTGGTGTCAATTGTAAGACC
6680 ATTGACAACTTCTGGTGTCA
1 A-TGACAACTTCTGGTGTCA
6700 ATGGAGATTT
Statistics
Matches: 173, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
59 3 0.02
60 53 0.31
61 100 0.58
62 17 0.10
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (60 bp):
ATGACAACTTCTGGTGTCATTTGTAAGATCATGACAACTTCTGGTGTCAATTGTAAGACC
Found at i:6592 original size:91 final size:91
Alignment explanation
Indices: 6437--6699 Score: 377
Period size: 91 Copynumber: 2.9 Consensus size: 91
6427 CATGGTTTAT
* * * * *
6437 ATGACAACTTATGGTGTCAATTGAATAA-ATCA-TGACAACTTCTGGTGTCAATTGCAAAATCAT
1 ATGACAACTTATAGTGTCATTTG--TAAGATTATTAACAACTTCTGGTGTCAATTGTAAAATCAT
* *
6500 GACAACTTCTAGTGTCATTTGTAAGAGC
64 GACAACTTCTGGTGTCATTTGTAAGACC
*
6528 ATGACAACTTCTAGTGTCATTTGTAAGATTATTAACAACTTCTGGTGTCAATTGTAAAATCATGA
1 ATGACAACTTATAGTGTCATTTGTAAGATTATTAACAACTTCTGGTGTCAATTGTAAAATCATGA
6593 CAACTTCTGGTGTCATTTGTAAGACC
66 CAACTTCTGGTGTCATTTGTAAGACC
* * * *
6619 ATGACAACTTATGGTGTCATTTGTAAGATTATTGACAACTTCTGGTGTCAATTGTAACACCATTG
1 ATGACAACTTATAGTGTCATTTGTAAGATTATTAACAACTTCTGGTGTCAATTGTAAAATCA-TG
6684 ACAACTTCTGGTGTCA
65 ACAACTTCTGGTGTCA
6700 ATGGAGATTT
Statistics
Matches: 156, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
89 3 0.02
90 3 0.02
91 132 0.85
92 18 0.12
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (91 bp):
ATGACAACTTATAGTGTCATTTGTAAGATTATTAACAACTTCTGGTGTCAATTGTAAAATCATGA
CAACTTCTGGTGTCATTTGTAAGACC
Found at i:14235 original size:21 final size:20
Alignment explanation
Indices: 14206--14253 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
14196 TAGATTTAGA
* *
14206 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
14227 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
14247 TTTAATT
1 TTTAATT
14254 AATCTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:19076 original size:19 final size:19
Alignment explanation
Indices: 19045--19097 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
19035 GAAATTCTTG
19045 ATGATGAAG-AAAGAATATA
1 ATGA-GAAGAAAAGAATATA
* *
19064 ATGAGAAGAAAAGATTCTA
1 ATGAGAAGAAAAGAATATA
*
19083 AAGAAGAAGAAAAGA
1 ATG-AGAAGAAAAGA
19098 GACGATGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 14 0.48
20 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (19 bp):
ATGAGAAGAAAAGAATATA
Found at i:24934 original size:16 final size:16
Alignment explanation
Indices: 24898--24972 Score: 109
Period size: 16 Copynumber: 4.8 Consensus size: 16
24888 ATTGGGCGGG
*
24898 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
24913 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
24929 TTCGGGTTCAGG-ATTT
1 TTCGGGTTCGGGTA-TT
24945 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
24961 TTCGGGTTCGGG
1 TTCGGGTTCGGG
24973 CTCGGTTCGG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
15 15 0.28
16 38 0.70
17 1 0.02
ACGTcount: A:0.07, C:0.15, G:0.39, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:24970 original size:6 final size:6
Alignment explanation
Indices: 24961--25027 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
24951 TTCGGGTATT
* * *
24961 TTCGGG TTCGGG CTC-GG TTCGGG TTCGGG CTC-GG ATCGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
*
25007 TTCGGG TCCGGG -TCGGG TTCG
1 TTCGGG TTCGGG TTCGGG TTCG
25028 TGTTTACTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 12 0.24
6 39 0.76
ACGTcount: A:0.01, C:0.22, G:0.48, T:0.28
Consensus pattern (6 bp):
TTCGGG
Found at i:24981 original size:17 final size:17
Alignment explanation
Indices: 24961--25011 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
24951 TTCGGGTATT
24961 TTCGGGTTCGGGCTCGG
1 TTCGGGTTCGGGCTCGG
24978 TTCGGGTTCGGGCTCGG
1 TTCGGGTTCGGGCTCGG
* *
24995 ATCGGGTTCGGGTTCGG
1 TTCGGGTTCGGGCTCGG
25012 GTCCGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.29
Consensus pattern (17 bp):
TTCGGGTTCGGGCTCGG
Found at i:24994 original size:23 final size:23
Alignment explanation
Indices: 24976--25027 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
24966 GTTCGGGCTC
24976 GGTTCGGGTTCGGGCTCGGATCG
1 GGTTCGGGTTCGGGCTCGGATCG
*
24999 GGTTCGGGTTCGGG-TCCGGGTCG
1 GGTTCGGGTTCGGGCT-CGGATCG
25022 GGTTCG
1 GGTTCG
25028 TGTTTACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.02, C:0.21, G:0.50, T:0.27
Consensus pattern (23 bp):
GGTTCGGGTTCGGGCTCGGATCG
Found at i:25819 original size:22 final size:23
Alignment explanation
Indices: 25776--25826 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
25766 TATTTTGATC
* *
25776 TCGGGCTCGGGTCGGGTTCGGGT
1 TCGGGTTCGGGTCGAGTTCGGGT
25799 TCGGGTTCGGG-CGAGTTCGGGT
1 TCGGGTTCGGGTCGAGTTCGGGT
25821 TCGGGT
1 TCGGGT
25827 AATTTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (23 bp):
TCGGGTTCGGGTCGAGTTCGGGT
Found at i:25822 original size:6 final size:6
Alignment explanation
Indices: 25776--25826 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
25766 TATTTTGATC
* *
25776 TCGGGC TCGGG- TCGGGT TCGGGT TCGGGT TCGGG- -CGAGT TCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
25821 TCGGGT
1 TCGGGT
25827 AATTTCGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 3 0.08
5 5 0.12
6 32 0.80
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (6 bp):
TCGGGT
Found at i:25833 original size:16 final size:16
Alignment explanation
Indices: 25797--25838 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
25787 TCGGGTTCGG
*
25797 GTTCGGGTTCGGGCGA
1 GTTCGGGTTCGGGCAA
*
25813 GTTCGGGTTCGGGTAA
1 GTTCGGGTTCGGGCAA
*
25829 TTTCGGGTTC
1 GTTCGGGTTC
25839 TGAGTTCGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.17, G:0.43, T:0.33
Consensus pattern (16 bp):
GTTCGGGTTCGGGCAA
Found at i:26773 original size:31 final size:29
Alignment explanation
Indices: 26709--26773 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
26699 TGTGGGGCTT
*
26709 ATTTGTCCCAAAATATAGGTAAGGGGCCG
1 ATTTGTCCCAAAATATAGGTAAGGGGCCA
*
26738 ATTTGTCCCAAAATCAATA-GTTAGAGGGCCA
1 ATTTGTCCCAAAAT--ATAGGTAAG-GGGCCA
26769 ATTTG
1 ATTTG
26774 GGCATTAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 14 0.45
30 4 0.13
31 13 0.42
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (29 bp):
ATTTGTCCCAAAATATAGGTAAGGGGCCA
Found at i:32873 original size:91 final size:91
Alignment explanation
Indices: 32688--32864 Score: 345
Period size: 91 Copynumber: 1.9 Consensus size: 91
32678 TCAATTGTAA
32688 TATAGCTGTAGCACTTGTATAAGCAAATGTCTAAATCATAAATTATGTAAATATTTCCTTATTAT
1 TATAGCTGTAGCACTTGTATAAGCAAATGTCTAAATCATAAATTATGTAAATATTTCCTTATTAT
32753 AAGCATGCATCTGAAAATTTCCTTAT
66 AAGCATGCATCTGAAAATTTCCTTAT
32779 TATAGCTGTAGCACTTGTATAAGCAAATGTCTAAATCATAAATTATGTAAATATTTCCTTATTAT
1 TATAGCTGTAGCACTTGTATAAGCAAATGTCTAAATCATAAATTATGTAAATATTTCCTTATTAT
*
32844 AATCATGCATCTGAAAATTTC
66 AAGCATGCATCTGAAAATTTC
32865 ACTCTTATAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (91 bp):
TATAGCTGTAGCACTTGTATAAGCAAATGTCTAAATCATAAATTATGTAAATATTTCCTTATTAT
AAGCATGCATCTGAAAATTTCCTTAT
Found at i:37943 original size:21 final size:21
Alignment explanation
Indices: 37902--37943 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37892 ATTGTCAAAC
*
37902 ACCGCCCCCTTTTTGCTACTT
1 ACCGCCCCCTTTTTACTACTT
37923 ACCGCCCCACTTTTTAC-ACTT
1 ACCGCCCC-CTTTTTACTACTT
37944 TTTCCCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (21 bp):
ACCGCCCCCTTTTTACTACTT
Found at i:39212 original size:13 final size:13
Alignment explanation
Indices: 39194--39218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39184 AACCGGTTTC
39194 ATCCTTTATGTGT
1 ATCCTTTATGTGT
39207 ATCCTTTATGTG
1 ATCCTTTATGTG
39219 CAAATATCTA
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
ATCCTTTATGTGT
Found at i:40509 original size:18 final size:18
Alignment explanation
Indices: 40486--40525 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40476 GCTTCCACAC
*
40486 ATCATCAGCTCCGACAAA
1 ATCATCAGATCCGACAAA
40504 ATCATCAGATCCGACAAA
1 ATCATCAGATCCGACAAA
40522 ATCA
1 ATCA
40526 GGCTGCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.17
Consensus pattern (18 bp):
ATCATCAGATCCGACAAA
Found at i:47890 original size:16 final size:17
Alignment explanation
Indices: 47869--47900 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47859 GTCTAACGTG
47869 TCGTGTAA-CGTGTTAT
1 TCGTGTAACCGTGTTAT
47885 TCGTGTAACCGTGTTA
1 TCGTGTAACCGTGTTA
47901 ACCCGAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (17 bp):
TCGTGTAACCGTGTTAT
Found at i:49938 original size:15 final size:15
Alignment explanation
Indices: 49918--49966 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
49908 AGTTATAACA
49918 ATAAAAATAAAATAT
1 ATAAAAATAAAATAT
*
49933 ATAAAAGATAAAAAAT
1 ATAAAA-ATAAAATAT
* *
49949 ATAAGATTAAAATAT
1 ATAAAAATAAAATAT
49964 ATA
1 ATA
49967 TACCTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
ATAAAAATAAAATAT
Found at i:50751 original size:882 final size:858
Alignment explanation
Indices: 48933--51542 Score: 2818
Period size: 882 Copynumber: 3.0 Consensus size: 858
48923 CCATAACAAA
* * * ** *** * **
48933 AAGGATTTGGAACAGATAATAAGGCAGTCACCTGGATTGTGGCCTCACTCGGATTAGGTCCACAC
1 AAGGATCTGGACCAGATAATAAGGCAGACGTCTGGATTGAAACCTCACTCGGGTCGGGTCCACAC
* * * *
48998 TTCACATCAAATACCTGAATTGAAAATGTGAAATTATTAAAATAAAAATATATAGTTATAAGAAT
66 TTCACA-CAAATACCTGGATTGAAATTGTAAAATTATTAAAATGAAAATATATAGTTATAAGAAT
* * * *
49063 AAGAATGAAAATTAAAAAT-TATAAGATTAGAATATATATACCTTTATTAGGCATGGGCGATAGG
130 AAAAATAAAAATTAAAAATATATAAGATTAAAATATATATACCTTTATTAGGCATGGG-GATAGC
* *
49127 AAATAACTGCAACAAAGCACCTTGACGAGTGATATTGTCGAGGACACGTAAACG-ATATCCATGT
194 AAATAACTGCAACAAAGCACCTTGAC-AATGATATTGCCGAGGACACG-AAACGAATATCCATGT
* * **
49191 TTGCATAATATATTATGTCTCCATTAACATGAAAG-CA--CG-----T--GTGTT----CTTCAA
257 TTGGATAATATATTATCTCTCCATTAACCCGAAAGACATGCGTTCAATCCGTGTTAAAACTTCAA
* * * * *
49242 GGATGATCTCACCGTCATGTAAAATGTCCCACACATCATAAACGTGAGTCCTCGATATAAACTTT
322 CGATGGTCTCACCGTCACGTACAATGTCCCACACATCATAAACGTAAGTCCTC-ATATAAACTTT
* * * *
49307 ATGCACTCCAACATGTCTTGATACATTAATT-TATATGCTAAGCTCAACATGTCGTCGAATGTTG
386 ATACAGTCCAACGTGTCTTGATACATT-ATTGTATATGCTAAGCTAAACATGTCGTCGAATGTTG
* * * * *
49371 TTACAATCGCATATACAATATCGAACACAACAACTCTAGC-TATGAACAGAACGAATGTGATCGT
450 TTACAATCGCATATACTATATCGAACACAAGAACTCTA-CATATGAATAGAACCACTGTGATCGT
* * * *
49435 GAATATGCTCATGTAAATATTAACCATATGATTTAATTG-CTGATTCGTGGTTCCTTTTTTACCG
514 GAATATACTCATATAAATATTCACCATATGATTTAATTGTC-GATTCG-GGTTCCTTTTTCA-CG
* * * *
49499 TTGTTCAGTCTGAATATACCTTTTAGGAGTGCCATCCAGCTCATGAAATGGATGAAGGCGACCAA
576 TTGTTC-GTCTGAATATATCTTTCAGGAGTGTCATCCAGCTCATGAAATGGATGAAGGCGACCGA
*
49564 ATAACCCA-AGGGAACATACAAAGAGTTTGATATTTCTATGTAAGATACAAGATAAAATATATCT
640 AT--CACAGAGGGAACATAC-AAGAGTTTG--A-TTCTATGT-AGATACAAGATAAAATATATCT
* * *
49628 CCAAGCTACATACAAAATTTAAATTATAGATACAAAGTCAAATATTAGTTTCCACACGATATCAA
698 ACAAGCTAGATACAAAATTTAAATTATAGATACAAAGTCAAATATTAGTTT-CACACGATATCAG
*
49693 AGCAACTGGCTTGAATAACTGAAGGTCTGAAGGAAGTTGGTACGCATCATCAACATTCCCCCTAC
762 AGCAACTGGCTTGAATAACTGAAGGTCTGAAGGAAGTTGGTACACATCATCAACATTCCCCCTAC
*
49758 CAACTGTTCCGTGTCTGCTTCAGTTCCTTC-C
827 CAACTGTTCCGTGTCTGCTTCAGTTCCTTCTG
* * * * *
49789 AAGGTATCTGGACCAGATAATAATGTAGTCGTCTGGATTGTACCCTCACTCGGGTCGGGTCCACA
1 AAGG-ATCTGGACCAGATAATAAGGCAGACGTCTGGATTGAAACCTCACTCGGGTCGGGTCCACA
* * * *
49854 CTTCATACCAAATACCTGGATTGAAATTATAAAATTATTAGAATGAAAATATATAGTTATAACAA
65 CTTCACA-CAAATACCTGGATTGAAATTGTAAAATTATTAAAATGAAAATATATAGTTATAAGAA
49919 TAAAAATAAAATATATAAAAGATAAAAAATATAAGATTAAAATATATATACCTTTATTAGGCATG
129 TAAAAATAAAA-AT-TAAAA-AT-----ATATAAGATTAAAATATATATACCTTTATTAGGCATG
* *
49984 GAGGATA-CAAAGTAACTGCAACAAAGCACCTTGACAATAGATATTGGCGAGGACACAGAGACGA
186 G-GGATAGCAAA-TAACTGCAACAAAGCACCTTGACAAT-GATATTGCCGAGGACAC-GAAACGA
*
50048 ATATCCATGTTTGGATAATATATTATTTCTCCATTAACCCGAAAGTACATGCGTTCAATCCGTAT
247 ATATCCATGTTTGGATAATATATTATCTCTCCATTAACCCGAAAG-ACATGCGTTCAATCCG--T
* *
50113 GTTTAAAACTTCAACGATGGTCTCACCGTCACGTACAATGTCCC-CTTACATCATTAACGTTAGT
309 G-TTAAAACTTCAACGATGGTCTCACCGTCACGTACAATGTCCCAC--ACATCATAAACGTAAGT
* * * * *
50177 CTCTCATAAAAACTTTATTCAGTTCAACGTGTCTTGATACAGTATTGTATATACTAAGCTAAACA
371 C-CTCATATAAACTTTATACAGTCCAACGTGTCTTGATACATTATTGTATATGCTAAGCTAAACA
* * *
50242 TGTCGTCAAATGTTGTTACTATCGCATATACTATATTGAACACAAGAACTCTACATATGAATAGA
435 TGTCGTCGAATGTTGTTACAATCGCATATACTATATCGAACACAAGAACTCTACATATGAATAGA
* * *
50307 ACCACTGTGATCGTGAATATACTCATATAAATA-TCACTAGATGATTTAATCGTCGATTCGCGGT
500 ACCACTGTGATCGTGAATATACTCATATAAATATTCACCATATGATTTAATTGTCGATTCG-GGT
* * *
50371 TCCTTTTTCAGCGTTGTTCGGTCTGAATATATCTTTCAGGAGTGTCATTCAACTCATGAAATCGA
564 TCCTTTTTCA-CGTTGTTC-GTCTGAATATATCTTTCAGGAGTGTCATCCAGCTCATGAAATGGA
* * * * *
50436 TGAAGGTGACCGAATCACATGAGGGAACAAATAAGGAGTTTGATTCAATATAGGATACAAGATAA
627 TGAAGGCGACCGAATCACA-GAGGGAACATACAA-GAGTTTGATTCTATGTA-GATACAAGATAA
* * * *
50501 AATATATCTACAAGGTAGATACATAATTTAAATTATGGATACAAAATCAAATATTAGTTTCTACA
689 AATATATCTACAAGCTAGATACAAAATTTAAATTATAGATACAAAGTCAAATATTAGTTTC-ACA
* * * * * * *
50566 CGATACCAGAG-AACTGGTTTGAGTAACTAAAGGACTGAAGGAAGTTGATACACATTATCAACAT
753 CGATATCAGAGCAACTGGCTTGAATAACTGAAGGTCTGAAGGAAGTTGGTACACATCATCAACAT
* * *
50630 TGCCCCGTACCAACCGTTCCGTCTCTGCTTCAGTTCCTTCTG
818 T-CCCCCTACCAACTGTTCCGTGTCTGCTTCAGTTCCTTCTG
* * * *
50672 AAGGATCTGGACCAGATAATAAGGCAGACGTTTGGATTGAAACCTCACTTGGGTCGTGTCCACAT
1 AAGGATCTGGACCAGATAATAAGGCAGACGTCTGGATTGAAACCTCACTCGGGTCGGGTCCACAC
* * *
50737 TTCACACAAAATACCTGGATTGAAATTGTAAAATTATTAAAATGAGATTATATAATTATAAGAAT
66 TTCACAC-AAATACCTGGATTGAAATTGTAAAATTATTAAAATGAAAATATATAGTTATAAGAAT
* * * *
50802 AAAATTAAAAATT-AAAATA-ATAAGATTATAGAATATAAATCCCTTTATTGGGCATGGGGGATA
130 AAAAATAAAAATTAAAAATATATAAGATTA-A-AATATATATACCTTTATTAGGCAT-GGGGATA
* * * * *
50865 GCAAATAACTGCAACAGAGCATCTTGACGATTGATATTGCCGAGTACATGGAAACGAATATCCAT
192 GCAAATAACTGCAACAAAGCACCTTGAC-AATGATATTGCCGAGGACA-CGAAACGAATATCCAT
* * * *
50930 GTTTGG---ATATATTATCTCTTCATTAAACCAAAAG-CATGTGCGTTCAATCC---CTAAAACT
255 GTTTGGATAATATATTATCTCTCCATTAACCCGAAAGACA--TGCGTTCAATCCGTGTTAAAACT
* * * * * * * *
50988 TGAATGATGGTCTAACCGTCGCGTCACGTACAATGTCCCACAAATTATAAACGAAAGTCCCCCTA
318 TCAACGATGGTCT---C-AC-CGTCACGTACAATGTCCCACACATCATAAACGTAAGTCCTCATA
*
51053 TAAACTTTATACAGTCCGACGTGTCTTGATACATTATTGTATATGCTAAGCTAAACATGTCGTCG
378 TAAACTTTATACAGTCCAACGTGTCTTGATACATTATTGTATATGCTAAGCTAAACATGTCGTCG
** * * * * * *
51118 AATAATGTTTCAATCGAATATATTGTATCGAACACAAGAACTCTAGATATGAATAAAACCACTGT
443 AATGTTGTTACAATCGCATATACTATATCGAACACAAGAACTCTACATATGAATAGAACCACTGT
* * * * * **
51183 GATTGTGAATATGA-TTATATAAATATTCACCATATGAATTATTTGTCGA-T----TTGC-AATT
508 GATCGTGAATAT-ACTCATATAAATATTCACCATATGATTTAATTGTCGATTCGGGTTCCTTTTT
* * * * * *
51241 C-C--T-TT-GACT--ATA-CT-TTTGAAGAGTGTCATCCAGCTCATGAAATGGATGAAGACAAC
572 CACGTTGTTCGTCTGAATATATCTTTCAGGAGTGTCATCCAGCTCATGAAATGGATGAAGGCGAC
** * *
51297 CGAATCAACAGAGGGAACATACAAGAGTTTTTTTCTATGTCAGATATAAGATAAAATATATCTTC
637 CGAATC-ACAGAGGGAACATACAAGAGTTTGATTCTATGT-AGATACAAGATAAAATATATCTAC
*
51362 AAGCTAGATACAAAATTTAAATTATATATACAAAGTCAAATATTAGTTTACACACGATATCAGAG
700 AAGCTAGATACAAAATTTAAATTATAGATACAAAGTCAAATATTAGTTT-CACACGATATCAGAG
** *
51427 CAACCAGCTTAAATAACTGAAGGTCTGAAGGAAGTTGGTACACATCATCAACATTCCCCCTACCA
764 CAACTGGCTTGAATAACTGAAGGTCTGAAGGAAGTTGGTACACATCATCAACATTCCCCCTACCA
* *
51492 ACTATTGCGTGTCTGCTTCAGTTCCTTCTG
829 ACTGTTCCGTGTCTGCTTCAGTTCCTTCTG
* * *
51522 AAGTATCTTGACCATATAATA
1 AAGGATCTGGACCAGATAATA
51543 TATAGTTATA
Statistics
Matches: 1482, Mismatches: 205, Indels: 140
0.81 0.11 0.08
Matches are distributed among these distances:
850 143 0.10
851 99 0.07
852 4 0.00
853 3 0.00
855 3 0.00
856 4 0.00
857 116 0.08
858 3 0.00
859 5 0.00
860 3 0.00
862 3 0.00
863 3 0.00
865 23 0.02
866 83 0.06
867 43 0.03
868 140 0.09
869 37 0.02
870 18 0.01
871 39 0.03
872 9 0.01
873 2 0.00
874 81 0.05
875 8 0.01
876 1 0.00
878 3 0.00
879 3 0.00
880 3 0.00
881 54 0.04
882 236 0.16
883 8 0.01
884 3 0.00
885 145 0.10
886 151 0.10
887 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (858 bp):
AAGGATCTGGACCAGATAATAAGGCAGACGTCTGGATTGAAACCTCACTCGGGTCGGGTCCACAC
TTCACACAAATACCTGGATTGAAATTGTAAAATTATTAAAATGAAAATATATAGTTATAAGAATA
AAAATAAAAATTAAAAATATATAAGATTAAAATATATATACCTTTATTAGGCATGGGGATAGCAA
ATAACTGCAACAAAGCACCTTGACAATGATATTGCCGAGGACACGAAACGAATATCCATGTTTGG
ATAATATATTATCTCTCCATTAACCCGAAAGACATGCGTTCAATCCGTGTTAAAACTTCAACGAT
GGTCTCACCGTCACGTACAATGTCCCACACATCATAAACGTAAGTCCTCATATAAACTTTATACA
GTCCAACGTGTCTTGATACATTATTGTATATGCTAAGCTAAACATGTCGTCGAATGTTGTTACAA
TCGCATATACTATATCGAACACAAGAACTCTACATATGAATAGAACCACTGTGATCGTGAATATA
CTCATATAAATATTCACCATATGATTTAATTGTCGATTCGGGTTCCTTTTTCACGTTGTTCGTCT
GAATATATCTTTCAGGAGTGTCATCCAGCTCATGAAATGGATGAAGGCGACCGAATCACAGAGGG
AACATACAAGAGTTTGATTCTATGTAGATACAAGATAAAATATATCTACAAGCTAGATACAAAAT
TTAAATTATAGATACAAAGTCAAATATTAGTTTCACACGATATCAGAGCAACTGGCTTGAATAAC
TGAAGGTCTGAAGGAAGTTGGTACACATCATCAACATTCCCCCTACCAACTGTTCCGTGTCTGCT
TCAGTTCCTTCTG
Found at i:50823 original size:21 final size:21
Alignment explanation
Indices: 50790--50829 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
50780 GAGATTATAT
*
50790 AATTATAAGAATAAAATTAAA
1 AATTAAAAGAATAAAATTAAA
* *
50811 AATTAAAATAATAAGATTA
1 AATTAAAAGAATAAAATTA
50830 TAGAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AATTAAAAGAATAAAATTAAA
Found at i:51602 original size:15 final size:15
Alignment explanation
Indices: 51556--51602 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
51546 AGTTATACCA
*
51556 ATAAAAGTAAAATAT
1 ATAAAATTAAAATAT
51571 A-AAAATTAAAA-ATT
1 ATAAAATTAAAATA-T
*
51585 ATAAGATTAAAATAT
1 ATAAAATTAAAATAT
51600 ATA
1 ATA
51603 TACCTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 14 0.52
16 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (15 bp):
ATAAAATTAAAATAT
Found at i:53142 original size:2 final size:2
Alignment explanation
Indices: 53135--53160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53125 GAAGATTAAA
53135 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
53161 TTGTACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57347 original size:156 final size:158
Alignment explanation
Indices: 57048--57407 Score: 392
Period size: 156 Copynumber: 2.3 Consensus size: 158
57038 TCATCTCAAA
* * ** *
57048 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGAGGAGTCAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAGGAGACAAACCAAC
* * * *
57113 TTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGGATAATCTAA
66 TTCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGGATAATCTAA
*
57178 GTCTACTGGTGG-AAAA-GT-AGC-CTTGT
131 GTCTACT-GTGGAAAAATGTCAGCTCAT-T
** * * * *
57204 TGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGGGGAGAGAAACCTAG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAGGAGACAAACCAAC
* * * ** *
57269 TTCACTA-CCAAGGGAAGCTCGGTTTTACTTTTAGAATTTTTTTCCTTAGCCTTATGTTGATATT
66 TTCACTATCCAAGAG-AGCTCGGTTTTAC--TTAGAA-TTTTTCCCATAGCCTTATGGGGATAAT
* *
57333 CTAAGTC-CCT-TGGAAAAATTTCAGCTCATT
127 CTAAGTCTACTGTGGAAAAATGTCAGCTCATT
*
57363 CAGACTTAGAATGAAAAACTTATGCTAATTTTTCATTTAAGGACA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
57408 GTTTGAGGTG
Statistics
Matches: 169, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
155 4 0.02
156 75 0.44
157 4 0.02
158 9 0.05
159 75 0.44
160 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (158 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAGGAGACAAACCAAC
TTCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGGATAATCTAA
GTCTACTGTGGAAAAATGTCAGCTCATT
Found at i:57787 original size:17 final size:17
Alignment explanation
Indices: 57767--57799 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
57757 GCAGCCTATC
57767 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
57784 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
57800 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:57972 original size:21 final size:21
Alignment explanation
Indices: 57948--57987 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
57938 AGAAGAGTTC
57948 GCCTTCCTCAGCAAGTAAAAT
1 GCCTTCCTCAGCAAGTAAAAT
57969 GCCTTCCTCAGCAAGTAAA
1 GCCTTCCTCAGCAAGTAAA
57988 GCCCGCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
GCCTTCCTCAGCAAGTAAAAT
Found at i:60324 original size:30 final size:29
Alignment explanation
Indices: 60268--60324 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
60258 ATTGCAAATA
* * *
60268 TTTTAAGTACATGGTAAAAGTGTAAATCT
1 TTTTAAGGACATGGCAAAAGTATAAATCT
*
60297 TTTTAGAGGACATGGCAAAATTATAAAT
1 TTTTA-AGGACATGGCAAAAGTATAAAT
60325 TTTCACCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (29 bp):
TTTTAAGGACATGGCAAAAGTATAAATCT
Done.