Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009596.1 Corchorus capsularis cultivar CVL-1 contig09617, 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: 107416
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:113 original size:34 final size:37
Alignment explanation
Indices: 65--133 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 37
55 TTATTTTAAT
65 ATGTAAAATATTTTA-TTAAATA-AGAATATATATAC
1 ATGTAAAATATTTTATTTAAATATAGAATATATATAC
* * *
100 ATGTAAGA-ATTTTATTTTAATATATAATATATAT
1 ATGTAAAATATTTTATTTAAATATAGAATATATAT
134 TATTAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 13 0.45
36 10 0.34
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (37 bp):
ATGTAAAATATTTTATTTAAATATAGAATATATATAC
Found at i:137 original size:22 final size:20
Alignment explanation
Indices: 112--151 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
102 GTAAGAATTT
112 TATT-TTAATATATAATATA
1 TATTATTAATATATAATATA
*
131 TATTATTAATATGTAATATA
1 TATTATTAATATATAATATA
151 T
1 T
152 GTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTATTAATATATAATATA
Found at i:746 original size:2 final size:2
Alignment explanation
Indices: 741--766 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
731 TTTTTTTTTA
741 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
767 TCTCCTCCGT
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:967 original size:21 final size:21
Alignment explanation
Indices: 943--990 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
933 TGAGATTATG
943 AGATTAAACACTGTACAAATC
1 AGATTAAACACTGTACAAATC
*** *
964 AGATTAGTTACTGTACAAATG
1 AGATTAAACACTGTACAAATC
985 AGATTA
1 AGATTA
991 TAATCAGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (21 bp):
AGATTAAACACTGTACAAATC
Found at i:2426 original size:24 final size:24
Alignment explanation
Indices: 2394--2439 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2384 AGTGGAGAAT
2394 GAGAAAAAA-AAAAGTAAGGAAAAC
1 GAGAAAAAACAAAA-TAAGGAAAAC
* *
2418 GAGATAAAACAAAATTAGGAAA
1 GAGAAAAAACAAAATAAGGAAA
2440 TGCTACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.67, C:0.04, G:0.20, T:0.09
Consensus pattern (24 bp):
GAGAAAAAACAAAATAAGGAAAAC
Found at i:2761 original size:12 final size:12
Alignment explanation
Indices: 2744--2774 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2734 TGAACCTTAA
2744 TTTCTTCATCTT
1 TTTCTTCATCTT
*
2756 TTTCTTCATTTT
1 TTTCTTCATCTT
2768 TTTCTTC
1 TTTCTTC
2775 TGTCGGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCTTCATCTT
Found at i:4054 original size:26 final size:26
Alignment explanation
Indices: 4023--4072 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4013 GGTTTTGTTG
*
4023 TTTCTCTTTATTTACGTCTTTGTTAA
1 TTTCTCTTTATATACGTCTTTGTTAA
*
4049 TTTCTCTTTCTATACGTCTTTGTT
1 TTTCTCTTTATATACGTCTTTGTT
4073 GATTCGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.18, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTCTCTTTATATACGTCTTTGTTAA
Found at i:4765 original size:18 final size:18
Alignment explanation
Indices: 4742--4784 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4732 TTTCATAACA
*
4742 AATTTATAATTAATT-TAT
1 AATTTATAATT-ATTAGAT
4760 AATTTATAATTATTAGAT
1 AATTTATAATTATTAGAT
4778 AATTTAT
1 AATTTAT
4785 TTTATATAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATTTATAATTATTAGAT
Found at i:9335 original size:13 final size:14
Alignment explanation
Indices: 9312--9340 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9302 CCATTCTTTC
9312 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
9326 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
9340 T
1 T
9341 ATTTAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:10142 original size:15 final size:15
Alignment explanation
Indices: 10124--10156 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10114 TGCCAAGTAA
10124 AAAAAGACGACTAAC
1 AAAAAGACGACTAAC
10139 AAAAAGACGACTAAC
1 AAAAAGACGACTAAC
10154 AAA
1 AAA
10157 GTATAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.18, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAGACGACTAAC
Found at i:11961 original size:24 final size:24
Alignment explanation
Indices: 11934--11981 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11924 ATTAGAATGG
11934 TCATGATTGAATTTTTGAAAGAAC
1 TCATGATTGAATTTTTGAAAGAAC
*
11958 TCATGATTGAGTTTTTGAAAGAAC
1 TCATGATTGAATTTTTGAAAGAAC
11982 ATATCACGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (24 bp):
TCATGATTGAATTTTTGAAAGAAC
Found at i:25898 original size:20 final size:21
Alignment explanation
Indices: 25856--25899 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
25846 AAGTGAAGCG
*
25856 TTTTTATTTTTCCTTTTGATT
1 TTTTTATTTTTCCTTTTCATT
25877 TTTTTA-TTTTCCTTTTC-TT
1 TTTTTATTTTTCCTTTTCATT
25896 TTTT
1 TTTT
25900 GGGTTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTATTTTTCCTTTTCATT
Found at i:29930 original size:17 final size:18
Alignment explanation
Indices: 29888--29932 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
29878 AAAATGCCAC
29888 GTGCCACGTGTCATTTTT
1 GTGCCACGTGTCATTTTT
*
29906 GTGGCACGTGTCATTTTT
1 GTGCCACGTGTCATTTTT
29924 GT-CCACGTG
1 GTGCCACGTG
29933 GCATGCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (18 bp):
GTGCCACGTGTCATTTTT
Found at i:30881 original size:2 final size:2
Alignment explanation
Indices: 30874--30910 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
30864 AAAATGACCC
30874 TA TA TA TA T- 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 TA
30911 GCTTTCAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33192 original size:1 final size:1
Alignment explanation
Indices: 33186--33215 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
33176 TAATCTTTTG
33186 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33216 GCTCTAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37398 original size:15 final size:15
Alignment explanation
Indices: 37378--37409 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
37368 TTAATTACCT
*
37378 TCACTGTTATGATCA
1 TCACTGTTATCATCA
37393 TCACTGTTATCATCA
1 TCACTGTTATCATCA
37408 TC
1 TC
37410 CGAATGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (15 bp):
TCACTGTTATCATCA
Found at i:46321 original size:15 final size:16
Alignment explanation
Indices: 46291--46323 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
46281 ACCTTTAAAG
*
46291 AAGAAGAAGAACAAAA
1 AAGAAGAAGAAAAAAA
46307 AAGAA-AAGAAAAAAA
1 AAGAAGAAGAAAAAAA
46322 AA
1 AA
46324 CGAACGCGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAAAAAA
Found at i:48387 original size:45 final size:45
Alignment explanation
Indices: 48323--48413 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
48313 ATTACTCTTT
48323 CCCTTTCTCTTTTCTGTTTTTCTATTTTTCTATCAGAACTTAATG
1 CCCTTTCTCTTTTCTGTTTTTCTATTTTTCTATCAGAACTTAATG
48368 CCCTTTCTCTTTTCTGTTTTTCTATTTTTCTATCAGAACTTAATG
1 CCCTTTCTCTTTTCTGTTTTTCTATTTTTCTATCAGAACTTAATG
48413 C
1 C
48414 GGAGGATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (45 bp):
CCCTTTCTCTTTTCTGTTTTTCTATTTTTCTATCAGAACTTAATG
Found at i:50735 original size:53 final size:54
Alignment explanation
Indices: 50672--50775 Score: 156
Period size: 53 Copynumber: 1.9 Consensus size: 54
50662 GATATTACAG
50672 ATTAAATTATCTAGTCCAACAAAT-CAACCCCTGGCCATTAGCAGAAGATGAAA
1 ATTAAATTATCTAGTCCAACAAATACAACCCCTGGCCATTAGCAGAAGATGAAA
* * **
50725 ATTAAATTATCTAGTCCAACAGATCACAATCTTTGGCCATTAGCAGAAGAT
1 ATTAAATTATCTAGTCCAACAAAT-ACAACCCCTGGCCATTAGCAGAAGAT
50776 ATTAAGGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 23 0.51
55 22 0.49
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (54 bp):
ATTAAATTATCTAGTCCAACAAATACAACCCCTGGCCATTAGCAGAAGATGAAA
Found at i:59510 original size:57 final size:57
Alignment explanation
Indices: 59441--59555 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
59431 TCAAAAAAAT
* *
59441 ATATTTTCTATTTTATTATTATTTAAATATTAGTATTCGATAAAAATGGTCATATTA
1 ATATTTTATATTTTATTATTATTTAAATATTAGTATTAGATAAAAATGGTCATATTA
*
59498 ATATTTTATATTTTATTATTATTTAAATATTAGTATTAGATAAAAATGGTCATGTTA
1 ATATTTTATATTTTATTATTATTTAAATATTAGTATTAGATAAAAATGGTCATATTA
59555 A
1 A
59556 GAAATCTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (57 bp):
ATATTTTATATTTTATTATTATTTAAATATTAGTATTAGATAAAAATGGTCATATTA
Found at i:61195 original size:30 final size:29
Alignment explanation
Indices: 61153--61211 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
61143 TAATAAACTA
*
61153 GTTTTTTTATTTT-ATTTGTATCAATTTAT
1 GTTTTTTTATTTTAATTTCT-TCAATTTAT
61182 GTTTTTTTAATTTTAATTTCTTCAATTTAT
1 GTTTTTTT-ATTTTAATTTCTTCAATTTAT
61212 ATATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (29 bp):
GTTTTTTTATTTTAATTTCTTCAATTTAT
Found at i:62589 original size:20 final size:20
Alignment explanation
Indices: 62564--62608 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
62554 TAAAGCTTGC
*
62564 AAATTTTGAC-CATGTCAAAA
1 AAATTTTAACACA-GTCAAAA
62584 AAATTTTAACAACAGTCAAAA
1 AAATTTTAAC-ACAGTCAAAA
62605 AAAT
1 AAAT
62609 CAAACAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (20 bp):
AAATTTTAACACAGTCAAAA
Found at i:62614 original size:20 final size:21
Alignment explanation
Indices: 62577--62615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62567 TTTTGACCAT
**
62577 GTCAAAAAAATTTTAACAACA
1 GTCAAAAAAATTCAAACAACA
62598 GTCAAAAAAA-TCAAACAA
1 GTCAAAAAAATTCAAACAA
62616 GAACTTACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.18
Consensus pattern (21 bp):
GTCAAAAAAATTCAAACAACA
Found at i:63625 original size:15 final size:14
Alignment explanation
Indices: 63607--63640 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
63597 TTTGTTATTT
*
63607 AAAAAAATCCCAGGA
1 AAAAAAACCCCA-GA
63622 AAAAAAACCCCAGA
1 AAAAAAACCCCAGA
63636 AAAAA
1 AAAAA
63641 TAAACTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.68, C:0.21, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAAAACCCCAGA
Found at i:68336 original size:35 final size:36
Alignment explanation
Indices: 68285--68358 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
68275 ATCCAAACCT
*
68285 TTACCATTTTTATCAACCCAATTGACTTGTA-AATG
1 TTACCATTTTGATCAACCCAATTGACTTGTACAATG
*
68320 TTACGATTTTGATCAACCCAATTGACTTGTACAATG
1 TTACCATTTTGATCAACCCAATTGACTTGTACAATG
68356 TTA
1 TTA
68359 TGGTAATAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 29 0.81
36 7 0.19
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
TTACCATTTTGATCAACCCAATTGACTTGTACAATG
Found at i:76637 original size:1 final size:1
Alignment explanation
Indices: 76633--76663 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
76623 AAATATCTGC
76633 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
76664 GAGCATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:78591 original size:33 final size:33
Alignment explanation
Indices: 78530--78594 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
78520 CTTTTACACT
* *
78530 GAGCCTCCCCATTAGGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTAGGACAGCTCAGCCACGGCG
*
78563 GAGCCTCCCCACTGGGACAGCTTC-GCCACGGC
1 GAGCCTCCCCACTAGGACAGC-TCAGCCACGGC
78595 AGGCCGCCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.17, C:0.42, G:0.29, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACAGCTCAGCCACGGCG
Found at i:91479 original size:33 final size:33
Alignment explanation
Indices: 91432--91518 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
91422 GCCACGGCAA
**
91432 GCCGCCCTCA-TGGGGCGGCTTCACCATGAGCAG
1 GCCGCCC-CACTGGGGCGGCTTCACCATGAAAAG
*
91465 GCCGCCCCACTGGGGCGGCTTCCCCATGAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
*
91498 GCCGCCCCACTTGGGCGGCTT
1 GCCGCCCCACTGGGGCGGCTT
91519 AGCCAGGGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.14, C:0.39, G:0.32, T:0.15
Consensus pattern (33 bp):
GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
Found at i:91634 original size:33 final size:33
Alignment explanation
Indices: 91572--91664 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
91562 GCCACTAGGT
*
91572 CGTCCTAGTGGGGTGGCT--AGCCGTGGCAGAGC
1 CGTCCTAGTGGGGAGGCTCCA-CCGTGGCAGAGC
91604 CGTCCTAGTGGGGAGGCTCCACCGTGGCAGAGC
1 CGTCCTAGTGGGGAGGCTCCACCGTGGCAGAGC
*
91637 CGTCCTAGTGGGGAGGCTCCGCCGTGGC
1 CGTCCTAGTGGGGAGGCTCCACCGTGGC
91665 TAAGGGCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 17 0.30
33 39 0.68
34 1 0.02
ACGTcount: A:0.12, C:0.29, G:0.42, T:0.17
Consensus pattern (33 bp):
CGTCCTAGTGGGGAGGCTCCACCGTGGCAGAGC
Found at i:98604 original size:12 final size:13
Alignment explanation
Indices: 98572--98604 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
98562 TCTACATCCG
98572 TAATTAAATGCTA
1 TAATTAAATGCTA
*
98585 TTATTAAATGCT-
1 TAATTAAATGCTA
98597 TAATTAAA
1 TAATTAAA
98605 GTATTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (13 bp):
TAATTAAATGCTA
Found at i:103174 original size:27 final size:24
Alignment explanation
Indices: 103118--103172 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
103108 AATTAGATAC
*
103118 AGTATAAGTTAATACTAGTGTGTG
1 AGTATAAGTTAATAATAGTGTGTG
103142 AGTATAAGTTAATAATAGTGTGTG
1 AGTATAAGTTAATAATAGTGTGTG
103166 AGATATA
1 AG-TATA
103173 TATAAATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (24 bp):
AGTATAAGTTAATAATAGTGTGTG
Found at i:103616 original size:33 final size:33
Alignment explanation
Indices: 103570--103701 Score: 129
Period size: 33 Copynumber: 3.9 Consensus size: 33
103560 AAGCCGATTT
*
103570 ATTATGGGTTAAAACTCTCCGAGAGGTGAACCC
1 ATTATGGGTTAAAACTCTCCAAGAGGTGAACCC
* * ***
103603 ATTGTGGGTTAAAACTCTTCAAGAGGTGATTTTTTAC
1 ATTATGGGTTAAAACTCTCCAAGAGGTGA----ACCC
* *
103640 ATTATGAGTTAAAACTCTCCGAGAGGTGAACCC
1 ATTATGGGTTAAAACTCTCCAAGAGGTGAACCC
* * *
103673 ATTATGGATTAAAGCTCTTCAAGAGGTGA
1 ATTATGGGTTAAAACTCTCCAAGAGGTGA
103702 TTTATTGCAT
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
33 51 0.66
37 26 0.34
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (33 bp):
ATTATGGGTTAAAACTCTCCAAGAGGTGAACCC
Found at i:103685 original size:70 final size:70
Alignment explanation
Indices: 103570--103704 Score: 234
Period size: 70 Copynumber: 1.9 Consensus size: 70
103560 AAGCCGATTT
* * *
103570 ATTATGGGTTAAAACTCTCCGAGAGGTGAACCCATTGTGGGTTAAAACTCTTCAAGAGGTGATTT
1 ATTATGAGTTAAAACTCTCCGAGAGGTGAACCCATTATGGATTAAAACTCTTCAAGAGGTGATTT
103635 TTTAC
66 TTTAC
*
103640 ATTATGAGTTAAAACTCTCCGAGAGGTGAACCCATTATGGATTAAAGCTCTTCAAGAGGTGATTT
1 ATTATGAGTTAAAACTCTCCGAGAGGTGAACCCATTATGGATTAAAACTCTTCAAGAGGTGATTT
103705 ATTGCATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (70 bp):
ATTATGAGTTAAAACTCTCCGAGAGGTGAACCCATTATGGATTAAAACTCTTCAAGAGGTGATTT
TTTAC
Found at i:105935 original size:31 final size:31
Alignment explanation
Indices: 105877--105935 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
105867 AGTTTTGAGA
* * *
105877 AATTTTTGAAATGCCTATTGTACCCTTATTT
1 AATTTTTAAAATACCTATTATACCCTTATTT
* *
105908 AATTTTTAAAATACTTATTATATCCTTA
1 AATTTTTAAAATACCTATTATACCCTTA
105936 CTTATCTAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (31 bp):
AATTTTTAAAATACCTATTATACCCTTATTT
Found at i:106137 original size:21 final size:21
Alignment explanation
Indices: 106113--106153 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
106103 CTGCACTTTA
106113 ATTTCTCTCTTGCAAACTTCC
1 ATTTCTCTCTTGCAAACTTCC
* * *
106134 ATTTTTTTTTTGCAAACTTC
1 ATTTCTCTCTTGCAAACTTC
106154 TCAACTCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.24, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTCTCTCTTGCAAACTTCC
Found at i:106827 original size:107 final size:108
Alignment explanation
Indices: 106660--106875 Score: 348
Period size: 107 Copynumber: 2.0 Consensus size: 108
106650 TAATGTAAAA
* * * *
106660 AATTAATTAACAATATCCTTATCAATTTTTTTTTTGTTTTTTTTTCCGAATATCTCAGCCTTATA
1 AATTAATTAACAATATCCTTATCAATTTTTTTGTTGTTCTTTTTTCCGAATATCCCAGCCTTAAA
106725 ATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
66 ATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
106768 AATTAATT-A-AATATCCTTAAATCAATTTTTTTGTT-TTCTTTTTTCCGAATATCCCAGCCTTA
1 AATTAATTAACAATATCCTT--ATCAATTTTTTTGTTGTTCTTTTTTCCGAATATCCCAGCCTTA
*
106830 AAATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
64 AAATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
106875 A
1 A
106876 TCCAATTAAT
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
106 9 0.09
107 70 0.69
108 22 0.22
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (108 bp):
AATTAATTAACAATATCCTTATCAATTTTTTTGTTGTTCTTTTTTCCGAATATCCCAGCCTTAAA
ATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
Found at i:106955 original size:17 final size:17
Alignment explanation
Indices: 106933--106965 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
106923 TACTATACAT
*
106933 TAATATGGATGAAATTC
1 TAATATAGATGAAATTC
106950 TAATATAGATGAAATT
1 TAATATAGATGAAATT
106966 TTATATTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.36
Consensus pattern (17 bp):
TAATATAGATGAAATTC
Done.