Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014970.1 Corchorus capsularis cultivar CVL-1 contig14991, 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: 88854
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4553 original size:8 final size:8
Alignment explanation
Indices: 4535--4579 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
4525 TCATACATAC
4535 CCAAATA-
1 CCAAATAT
4542 CCAAATAT
1 CCAAATAT
4550 CCAAATA-
1 CCAAATAT
4557 CCAAATAT
1 CCAAATAT
4565 CCAAATAT
1 CCAAATAT
*
4573 TCAAATA
1 CCAAATA
4580 CTCATCAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
7 14 0.40
8 21 0.60
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (8 bp):
CCAAATAT
Found at i:4555 original size:15 final size:15
Alignment explanation
Indices: 4535--4571 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
4525 TCATACATAC
4535 CCAAATACCAAATAT
1 CCAAATACCAAATAT
4550 CCAAATACCAAATAT
1 CCAAATACCAAATAT
4565 CCAAATA
1 CCAAATA
4572 TTCAAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (15 bp):
CCAAATACCAAATAT
Found at i:4558 original size:23 final size:24
Alignment explanation
Indices: 4531--4580 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
4521 ATATTCATAC
4531 ATACCCAAATA-CCAAATATCCAA
1 ATACCCAAATATCCAAATATCCAA
*
4554 ATA-CCAAATATCCAAATATTCAA
1 ATACCCAAATATCCAAATATCCAA
4577 ATAC
1 ATAC
4581 TCATCAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (24 bp):
ATACCCAAATATCCAAATATCCAA
Found at i:9384 original size:26 final size:29
Alignment explanation
Indices: 9355--9488 Score: 90
Period size: 26 Copynumber: 4.7 Consensus size: 29
9345 CAACAATTAA
9355 AAGTCCTCAAACACAAGGGCA-T-T-TAT
1 AAGTCCTCAAACACAAGGGCACTCTATAT
*
9381 AAGTCC-CTAAACAC-AGAGGCAATTCTATAT
1 AAGTCCTC-AAACACAAG-GGC-ACTCTATAT
9411 CGAAGTCCTCAAACACAAGGGCA-T-T-TAT
1 --AAGTCCTCAAACACAAGGGCACTCTATAT
* *
9439 AAGTCC-CTAAACAC-AGAGGCACCTCTCTCAA
1 AAGTCCTC-AAACACAAG-GGCA-CTCTAT-AT
9470 AAGTCCTCAAACACAAGGG
1 AAGTCCTCAAACACAAGGG
9489 TATTCATCCC
Statistics
Matches: 88, Mismatches: 1, Indels: 33
0.72 0.01 0.27
Matches are distributed among these distances:
25 6 0.07
26 31 0.35
27 1 0.01
28 5 0.06
29 3 0.03
30 5 0.06
31 16 0.18
32 18 0.20
33 3 0.03
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (29 bp):
AAGTCCTCAAACACAAGGGCACTCTATAT
Found at i:9445 original size:58 final size:57
Alignment explanation
Indices: 9353--9596 Score: 261
Period size: 58 Copynumber: 4.3 Consensus size: 57
9343 CCCAACAATT
*
9353 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCAATTCTATATC
1 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGC-A-CCTATATC
* * *
9412 -GAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCACCTCTCTC
1 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCACCTATATC
* * * *
9468 AAAAGTCCTCAAACACAAGGG--TAT-TCA-TCCCTAAGCACAGAGGCACCTACATC
1 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCACCTATATC
* *
9521 -AAAGTCCTCAAGCACAAGGGTACCTATATTA-AAGTCCCTAAACACAGAGGCATCTATA-C
1 AAAAGTCCTCAAACACAAGGG---C-AT-TTATAAGTCCCTAAACACAGAGGCACCTATATC
* *
9580 TAAAGTCCCCAAACACA
1 AAAAGTCCTCAAACACA
9597 TATAACACAG
Statistics
Matches: 155, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
52 19 0.12
53 22 0.14
54 2 0.01
55 2 0.01
56 5 0.03
57 20 0.13
58 47 0.30
59 3 0.02
60 35 0.23
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (57 bp):
AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCACCTATATC
Found at i:9578 original size:30 final size:30
Alignment explanation
Indices: 9495--9596 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
9485 AGGGTATTCA
* * *
9495 TCCCTAAGCACAGAGGCACCTACATCAAAG
1 TCCCTAAACACAGAGGCACCTATATTAAAG
* *
9525 T-CCTCAAGCACA-AGGGTACCTATATTAAAG
1 TCCCT-AAACACAGA-GGCACCTATATTAAAG
* *
9555 TCCCTAAACACAGAGGCATCTATACTAAAG
1 TCCCTAAACACAGAGGCACCTATATTAAAG
*
9585 TCCCCAAACACA
1 TCCCTAAACACA
9597 TATAACACAG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 52 0.87
31 4 0.07
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCACCTATATTAAAG
Found at i:9714 original size:2 final size:2
Alignment explanation
Indices: 9677--9705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9667 TTCCATTATG
9677 TA TA 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 TA TA T
9706 GCATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11244 original size:16 final size:16
Alignment explanation
Indices: 11219--11249 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11209 ATGAATAGGC
11219 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
11235 AATCACTCAAAGCAA
1 AATCAATCAAAGCAA
11250 AGCAATGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.06, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:15867 original size:13 final size:13
Alignment explanation
Indices: 15845--15884 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
15835 CAGAGAATAT
15845 TATCAACAGAAGA
1 TATCAACAGAAGA
*
15858 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
15871 TTTCAACTGAAGA
1 TATCAACAGAAGA
15884 T
1 T
15885 TATCTAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:18467 original size:2 final size:2
Alignment explanation
Indices: 18419--18447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18409 TAACTAAAGA
18419 AT 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 AT A
18448 ACTTTACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30722 original size:20 final size:18
Alignment explanation
Indices: 30697--30759 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
30687 TTATGACAGT
30697 TTTTTTTTAAAAATAGGTAG
1 TTTTTTTT-AAAAT-GGTAG
*
30717 TTTTTTTTTTAAATGAGTAG
1 -TTTTTTTTAAAATG-GTAG
* *
30737 TTTTATTTAAGATGGTAG
1 TTTTTTTTAAAATGGTAG
30755 TTTTT
1 TTTTT
30760 ATTTTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.22
19 12 0.33
20 8 0.22
21 8 0.22
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (18 bp):
TTTTTTTTAAAATGGTAG
Found at i:30740 original size:18 final size:18
Alignment explanation
Indices: 30719--30759 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
30709 ATAGGTAGTT
30719 TTTTTTTTAA-ATGAGTAG
1 TTTTTTTTAAGATG-GTAG
*
30737 TTTTATTTAAGATGGTAG
1 TTTTTTTTAAGATGGTAG
30755 TTTTT
1 TTTTT
30760 ATTTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (18 bp):
TTTTTTTTAAGATGGTAG
Found at i:35234 original size:27 final size:28
Alignment explanation
Indices: 35204--35267 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 28
35194 ACGAAGATCC
*
35204 TTTTGTTT-GTGAAGGAGAACAATTTGA
1 TTTTGTTTGGTGAAGGAGAACAATCTGA
35231 TTTTGTTCTTGGTGAAGGAGAACAATCTGA
1 TTTTG-T-TTGGTGAAGGAGAACAATCTGA
35261 TTTTGTT
1 TTTTGTT
35268 CTTGATGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 3 0.09
30 23 0.70
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (28 bp):
TTTTGTTTGGTGAAGGAGAACAATCTGA
Found at i:35248 original size:30 final size:30
Alignment explanation
Indices: 35212--35279 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
35202 CCTTTTGTTT
*
35212 GTGAAGGAGAACAATTTGATTTTGTTCTTG
1 GTGAAGGAGAACAATCTGATTTTGTTCTTG
35242 GTGAAGGAGAACAATCTGATTTTGTTCTTG
1 GTGAAGGAGAACAATCTGATTTTGTTCTTG
*
35272 ATGAAGGA
1 GTGAAGGA
35280 TTTGTTTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.07, G:0.28, T:0.35
Consensus pattern (30 bp):
GTGAAGGAGAACAATCTGATTTTGTTCTTG
Found at i:46379 original size:16 final size:16
Alignment explanation
Indices: 46358--46392 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
46348 ACAATTCAGA
46358 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
46374 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
46390 AAG
1 AAG
46393 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:46590 original size:89 final size:89
Alignment explanation
Indices: 46437--46658 Score: 331
Period size: 89 Copynumber: 2.4 Consensus size: 89
46427 GCTTAAGAAG
*
46437 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGACTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGG--AATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
* *
46502 ACTGAAGACCCAGTTATTTGGG-AGTT
64 ACTGAAGACCCAATTA-TTGGGAAATT
* *
46528 ATTGAAAGAAGATCCATGTATGTGGTATTCTTCTTTCAAAGAAGA-TCCAATTATTGCAGAATTA
1 ATTGAAAGAAGATCCACGTATGTGGAATTCTTCTTTCAAAGAAGACT-CAATTATTGCAGAATTA
46592 CTGAAGACCCAATTATTGGGAAATT
65 CTGAAGACCCAATTATTGGGAAATT
46617 ATTGAAAGAAGATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGA--ATTCTTCTTTCAAA
46659 TTATCAAAGA
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
88 6 0.05
89 76 0.63
91 38 0.32
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (89 bp):
ATTGAAAGAAGATCCACGTATGTGGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATTAC
TGAAGACCCAATTATTGGGAAATT
Found at i:46923 original size:99 final size:101
Alignment explanation
Indices: 46743--46927 Score: 232
Period size: 104 Copynumber: 1.8 Consensus size: 101
46733 AATTTGTTTG
* * * * *
46743 TTCAAGGTTAAGTCGCCAAGACCCTTGAGTCAAATTATCATCAATTCGAGATCAAGTCATCAAAG
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTA-CATCAATTCAAGACCAAGTCATC--AG
*
46808 ACCCTCGAATCGAATCAAATCCAATTCCCAAGTCTTCAA
63 ACCCTCGAATCAAATCAAATCCAATTCCCAAGTCTTCAA
* *
46847 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAA-TA-ATCAATTCAAGACCAAGTCATTC-GAC
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTACATCAATTCAAGACCAAGTCA-TCAGAC
*
46909 CCTTGAATCAAATCAAATC
65 CCTCGAATCAAATCAAATC
46928 AAGTTCTCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
99 20 0.28
101 18 0.25
102 2 0.03
103 2 0.03
104 29 0.41
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (101 bp):
TTCAAGATCAAGTCGCCAAGACCCTTGAATCAAATTACATCAATTCAAGACCAAGTCATCAGACC
CTCGAATCAAATCAAATCCAATTCCCAAGTCTTCAA
Found at i:49056 original size:90 final size:90
Alignment explanation
Indices: 48899--49083 Score: 338
Period size: 90 Copynumber: 2.1 Consensus size: 90
48889 GTTTGGAATA
48899 TTCC-TTGGTGTGTGGTCTTCAAATCGGCCCAATGAGTTTCCAATGGTCTTCAATTCTTCAAGAT
1 TTCCTTTGGTGTGTGGTCTTCAAATCGGCCCAATGAGTTTCCAATGGTCTTCAATTCTTCAAGAT
48963 GAGATCTTATAAAGCCCACTAAAGC
66 GAGATCTTATAAAGCCCACTAAAGC
48988 TTCCTTTGGTGTGTGGTCTTCAAATCGGCCCAATGAGTCTT-CAATGGTCTTCAATTCTTCAAGA
1 TTCCTTTGGTGTGTGGTCTTCAAATCGGCCCAATGAGT-TTCCAATGGTCTTCAATTCTTCAAGA
*
49052 TGAGATCTTATAAAGCCCAGTAAAGC
65 TGAGATCTTATAAAGCCCACTAAAGC
49078 TTCCTT
1 TTCCTT
49084 AAACCTTTTT
Statistics
Matches: 93, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
89 4 0.04
90 87 0.94
91 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (90 bp):
TTCCTTTGGTGTGTGGTCTTCAAATCGGCCCAATGAGTTTCCAATGGTCTTCAATTCTTCAAGAT
GAGATCTTATAAAGCCCACTAAAGC
Found at i:49188 original size:33 final size:33
Alignment explanation
Indices: 49145--49242 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
49135 GATCATGTGG
* *
49145 CCGGGTATGGCCGAGTCATGTGTCCGGTGGTGT
1 CCGGGCATGGCCGAGTCATGTGACCGGTGGTGT
* *
49178 CCGGGCATGGCCAAGTCATGTGGCCGGTGGTGT
1 CCGGGCATGGCCGAGTCATGTGACCGGTGGTGT
*
49211 CCGGGCATGGCCGAGTCACGTGACCGGTGGTG
1 CCGGGCATGGCCGAGTCATGTGACCGGTGGTG
49243 CGCGGCTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.21
Consensus pattern (33 bp):
CCGGGCATGGCCGAGTCATGTGACCGGTGGTGT
Found at i:55731 original size:33 final size:32
Alignment explanation
Indices: 55676--55791 Score: 142
Period size: 33 Copynumber: 3.5 Consensus size: 32
55666 AGTTAAAGGA
* * *
55676 TCATGTGGCCGGTTGTGGCCGGGTATGGCCGAG
1 TCATGTGG-CGGTGGTGTCCGGGCATGGCCGAG
* *
55709 TCAAGTGTGCGGTGGTGTCCGGGCATGGCCAAG
1 TCATGTG-GCGGTGGTGTCCGGGCATGGCCGAG
55742 TCATGTGGCCGGTGGTGTCCGGGCATGGCCGAG
1 TCATGTGG-CGGTGGTGTCCGGGCATGGCCGAG
*
55775 TCATGTGACCGGTGGTG
1 TCATGTG-GCGGTGGTG
55792 CGCGGCTTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.01
33 70 0.97
34 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.44, T:0.23
Consensus pattern (32 bp):
TCATGTGGCGGTGGTGTCCGGGCATGGCCGAG
Found at i:57272 original size:29 final size:32
Alignment explanation
Indices: 57226--57328 Score: 151
Period size: 32 Copynumber: 3.3 Consensus size: 32
57216 CCTGCACATC
* *
57226 ATAATGATATTCTTGTGCATCTCCCGCACA-T
1 ATAATGATATCCGTGTGCATCTCCCGCACACT
57257 AGT-A-G-TATCCGTGTGCATCTCCCGCACACT
1 A-TAATGATATCCGTGTGCATCTCCCGCACACT
57287 ATAATGATATCCGTGTGCATCTCCCGCACACT
1 ATAATGATATCCGTGTGCATCTCCCGCACACT
57319 ATAATGATAT
1 ATAATGATAT
57329 TTATGTGATT
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
29 22 0.34
30 4 0.06
31 3 0.05
32 36 0.55
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (32 bp):
ATAATGATATCCGTGTGCATCTCCCGCACACT
Found at i:59575 original size:2 final size:2
Alignment explanation
Indices: 59568--59592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59558 ATAGTATGTT
59568 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
59593 GATGATAGAA
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:63699 original size:16 final size:16
Alignment explanation
Indices: 63678--63711 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
63668 ATTATTGTAC
63678 ATATGATGTTGAGAAA
1 ATATGATGTTGAGAAA
63694 ATATGATGTTGAGAAA
1 ATATGATGTTGAGAAA
63710 AT
1 AT
63712 CAGACTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (16 bp):
ATATGATGTTGAGAAA
Found at i:65654 original size:103 final size:103
Alignment explanation
Indices: 65475--65682 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
65465 AGCGACTAAT
65475 CAATCAACAAAGTTCAAACTTGAAGCAACTTGATCAACTGCTTCTTCCAAGTACCCCTTGACTAA
1 CAATCAACAAAGTTCAAACTTGAAGCAACTTGATCAACTGCTTCTTCCAAGTACCCCTTGACTAA
65540 TATGTTTGGCTAATGTATTGAAGTTTGCACTTCTATAC
66 TATGTTTGGCTAATGTATTGAAGTTTGCACTTCTATAC
65578 CAATCAACAAAGTTCAAACTTGAAGCAACTTGATCAACTGCTTCTTCCAAGTACCCCTTGACTAA
1 CAATCAACAAAGTTCAAACTTGAAGCAACTTGATCAACTGCTTCTTCCAAGTACCCCTTGACTAA
65643 TATGTTTGGCTAATGTATTGAAGTTTGCACTTCTATAC
66 TATGTTTGGCTAATGTATTGAAGTTTGCACTTCTATAC
65681 CA
1 CA
65683 GATTCCTCTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (103 bp):
CAATCAACAAAGTTCAAACTTGAAGCAACTTGATCAACTGCTTCTTCCAAGTACCCCTTGACTAA
TATGTTTGGCTAATGTATTGAAGTTTGCACTTCTATAC
Found at i:79715 original size:86 final size:83
Alignment explanation
Indices: 79596--79759 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 83
79586 TAAAATTACA
* * * * * *
79596 TATTAATGACACTATTTATTATCGAAATAGTCAATTATCAAAATAGGATAGGGG-GAAGAAAGTG
1 TATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAAATAGG-CAGGGGAAAAG-AAGTA
*
79660 TAAGAAACTAATTGAAGGAC
64 TAAGAAACAAATTGAAGGAC
*
79680 TATTAATGACACTATTTTTATTACCAAAATAGTCAATTACCAAATTAGGCAGGGGAAAAGAAGTA
1 TATTAATGACACTA--TTTATTACCAAAATAGTCAATTACCAAAATAGGCAGGGGAAAAGAAGTA
79745 TAAGAAACAAATTGA
64 TAAGAAACAAATTGA
79760 GGAGTTTCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 14 0.20
85 23 0.33
86 32 0.46
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (83 bp):
TATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAAATAGGCAGGGGAAAAGAAGTATA
AGAAACAAATTGAAGGAC
Found at i:80519 original size:28 final size:30
Alignment explanation
Indices: 80452--80519 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
80442 GTGGCATCCG
* *
80452 ACGTGACATACCACGTGTACAAAAAATGTC
1 ACGTGACATGCCACGTGTACAAAAAATGCC
* *
80482 ACGTGGCATGCCACGTGT-C-AGAAATGCC
1 ACGTGACATGCCACGTGTACAAAAAATGCC
*
80510 ACGTGCCATG
1 ACGTGACATG
80520 TGTCATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 16 0.48
29 1 0.03
30 16 0.48
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (30 bp):
ACGTGACATGCCACGTGTACAAAAAATGCC
Done.