Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007404.1 Corchorus capsularis cultivar CVL-1 contig07425, 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: 52318
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1443 original size:22 final size:22
Alignment explanation
Indices: 1418--1585 Score: 71
Period size: 22 Copynumber: 7.7 Consensus size: 22
1408 ATGATCCCAT
1418 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
* ** *
1440 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTTC
* * * *
1462 TAT-AGAATTTCGAGAATCTTTT
1 TATGA-AATTTTGATAACCTTTC
* **
1484 TAT-AATTTTTTTTAACC-TTC
1 TATGAAATTTTGATAACCTTTC
*
1504 TTATGAAATTTT-ATTAACCTCTC
1 -TATGAAATTTTGA-TAACCTTTC
* * ***
1527 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTTTC
*
1549 TATGAAA-TTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-TC
*
1570 AATGAAATTTTGATAA
1 TATGAAATTTTGATAA
1586 TCAACACTAT
Statistics
Matches: 104, Mismatches: 32, Indels: 20
0.67 0.21 0.13
Matches are distributed among these distances:
20 4 0.04
21 24 0.23
22 73 0.70
23 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:3064 original size:22 final size:22
Alignment explanation
Indices: 3036--3263 Score: 161
Period size: 22 Copynumber: 10.6 Consensus size: 22
3026 TTTTAAAACC
*
3036 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAATCTCACTA
* * *
3058 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCTCACTA
3080 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AATC-TCACTA
* * *
3103 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCACTA
*
3126 TAAAATTTTGATAA-CT-AC--
1 TGAAATTTTGATAATCTCACTA
* *
3144 ---AATTTTGATAAGCTCCCTA
1 TGAAATTTTGATAATCTCACTA
** * *
3163 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCACTA
* *
3185 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCACTA
* **
3207 TGAAATTTTGAT-CTACAAACTA
1 TGAAATTTTGATAAT-CTCACTA
*
3229 TGAAATTTTGATAACCTTCA-TA
1 TGAAATTTTGATAATC-TCACTA
3251 TGAAATTTTGATA
1 TGAAATTTTGATA
3264 TCCTCCCTGA
Statistics
Matches: 163, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.07
16 2 0.01
17 1 0.01
20 1 0.01
21 3 0.02
22 106 0.65
23 37 0.23
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCACTA
Found at i:3085 original size:44 final size:44
Alignment explanation
Indices: 3036--3263 Score: 195
Period size: 44 Copynumber: 5.3 Consensus size: 44
3026 TTTTAAAACC
* *
3036 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCCTA
* *
3080 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATC-ACACTATGAAATTTTGAT-AACCTCCCTA
* * *
3126 TAAAATTTTG---AT-A-ACTA--CAATTTTGATAAGCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCCTA
** * * * * *
3163 TGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCCTA
* * * *
3207 TGAAATTTTGAT-CTACAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAAT-CACACTATGAAATTTTGATAACCTCCCTA
3251 TGAAATTTTGATA
1 TGAAATTTTGATA
3264 TCCTCCCTGA
Statistics
Matches: 143, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
37 16 0.11
38 9 0.06
40 4 0.03
42 5 0.03
44 73 0.51
45 17 0.12
46 19 0.13
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (44 bp):
TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCCTA
Found at i:3108 original size:23 final size:23
Alignment explanation
Indices: 3038--3139 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
3028 TTAAAACCTG
* * * *
3038 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
3060 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
3082 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
3105 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
3128 AAATTTTGATAA
1 AAATTTTGATAA
3140 CTACAATTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 27 0.40
23 41 0.60
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:3172 original size:37 final size:38
Alignment explanation
Indices: 3106--3177 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
3096 CTTCCTATAA
3106 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
* * **
3144 AATTTTGAT-AAGCTCCCTATGATTTTTTGATAAC
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAC
3178 CTCATTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 21 0.70
38 9 0.30
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (38 bp):
AATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
Found at i:3291 original size:18 final size:20
Alignment explanation
Indices: 3251--3300 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
3241 AACCTTCATA
3251 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
3271 TG-AATTTTGATATCC-CCC
1 TGAAATTTTGATATCCTCCC
3289 TGAAATTTTGAT
1 TGAAATTTTGAT
3301 TAGTACTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.17
19 22 0.76
20 2 0.07
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:3434 original size:22 final size:22
Alignment explanation
Indices: 3409--3638 Score: 132
Period size: 22 Copynumber: 10.5 Consensus size: 22
3399 AATCAAATTT
*
3409 TGAAAGTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
3431 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
** * * *
3453 CAAAATTTTGTTGACCCCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
3475 TGAAATTCTGAGAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
3497 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
3519 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
3541 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
*
3563 T-AAATTTTGATAATCCGGTCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * *
3587 TGAAATTTCGATAA-TTACTCTA
1 TGAAATTTTGATAACCT-CTTTA
* *
3609 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
*
3629 TCAAATTTTG
1 TGAAATTTTG
3639 GCACTCCTTA
Statistics
Matches: 158, Mismatches: 37, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
20 8 0.05
21 25 0.16
22 106 0.67
23 2 0.01
24 3 0.02
25 11 0.07
26 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:3690 original size:22 final size:21
Alignment explanation
Indices: 3661--3800 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
3651 ACATTGAGAC
3661 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
3682 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
3704 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
3726 TATT-AGTAACCTCCTGATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
3748 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
3770 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
3792 TTTTGATAA
1 TTTTGATAA
3801 TCTCTTTGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.12
22 78 0.84
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:3724 original size:44 final size:42
Alignment explanation
Indices: 3676--3800 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 42
3666 TAACCTTCAT
* * * *
3676 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTTT-ATAACCTC-CTATGAAATTTTGATAACCACACC
* * *
3720 ATGAAATATTAGTAACCTCCTGATGAAATTTTGTTAACCACACT
1 ATGAAATTTTA-TAACCTCCT-ATGAAATTTTGATAACCACACC
*
3764 ATGAAATTCTTATAACCTCGCTATGACATTTTGATAA
1 ATGAAATT-TTATAACCTC-CTATGAAATTTTGATAA
3801 TCTCTTTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.04
44 59 0.88
45 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (42 bp):
ATGAAATTTTATAACCTCCTATGAAATTTTGATAACCACACC
Found at i:3943 original size:22 final size:21
Alignment explanation
Indices: 3889--3974 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
3879 ATAACCCGAC
* * *
3889 CCTATGAAATTTTGGTAATCA
1 CCTATGAAATTTTGATAACCT
*
3910 CACTATGGAATTTTGATAACCT
1 C-CTATGAAATTTTGATAACCT
* *
3932 CCTCATGAAATTATAATAACCAT
1 CCT-ATGAAATTTTGATAACC-T
*
3955 CTTATGAAATTTTGATAACC
1 CCTATGAAATTTTGATAACC
3975 ACATAGAGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.06
22 46 0.88
23 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCT
Found at i:4172 original size:19 final size:19
Alignment explanation
Indices: 4141--4190 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
4131 TATTAACATT
4141 TAAAA-ATTGAAATT-AAAA
1 TAAAATATT-AAATTCAAAA
4159 GTAAAATATTAAATTCAAAA
1 -TAAAATATTAAATTCAAAA
4179 -AATAATATTAAA
1 TAA-AATATTAAA
4191 GGAAAGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 19 0.68
20 7 0.25
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAATATTAAATTCAAAA
Found at i:5839 original size:97 final size:97
Alignment explanation
Indices: 5650--5839 Score: 346
Period size: 96 Copynumber: 2.0 Consensus size: 97
5640 TATATAATCT
5650 AATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTA
1 AATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTA
*
5715 ATGGGAATTTAGAAATATGTTTTAAAAAAAGG
66 ATGGCAATTTAGAAATATGTTTTAAAAAAAGG
**
5747 AATAATTAATAATGGAATAATTTATGATT-AAAAAATAATGGAATAATTACCATATTATTTAGTA
1 AATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTA
5811 ATGGCAATTTAGAAATATGTTTTAAAAAA
66 ATGGCAATTTAGAAATATGTTTTAAAAAA
5840 GGGTACAATT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 61 0.68
97 29 0.32
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.36
Consensus pattern (97 bp):
AATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTA
ATGGCAATTTAGAAATATGTTTTAAAAAAAGG
Found at i:5855 original size:29 final size:31
Alignment explanation
Indices: 5822--5885 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
5812 TGGCAATTTA
*
5822 GAAATATGTTTTAAAAA-A-GGGTACAATTG
1 GAAATATGTTTTAAAAATAGGGGTACAATCG
5851 GAAATATGTTTTAAAAATAGGGGTACAATCG
1 GAAATATGTTTTAAAAATAGGGGTACAATCG
5882 GAAA
1 GAAA
5886 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAGGGGTACAATCG
Found at i:5937 original size:2 final size:2
Alignment explanation
Indices: 5932--5967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5922 AGGGTACTTT
5932 TA TA TA 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
5968 AGTAAGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6195 original size:29 final size:29
Alignment explanation
Indices: 6130--6196 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
6120 GAAAATGGTC
*
6130 TATTTGACCAAAATTAAGAGTTCAGGGGT
1 TATTTGACCAAAATTAAAAGTTCAGGGGT
* *
6159 GACATTGACCAAAA-TAAAAGTTCAGGGGCT
1 TA-TTTGACCAAAATTAAAAGTTCAGGGG-T
6189 TATTTGAC
1 TATTTGAC
6197 TGTTAGGGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (29 bp):
TATTTGACCAAAATTAAAAGTTCAGGGGT
Found at i:7514 original size:6 final size:7
Alignment explanation
Indices: 7492--7516 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7482 CCATTGGGAC
7492 TTTCCTT
1 TTTCCTT
7499 TTTCCTT
1 TTTCCTT
7506 TTTCCTT
1 TTTCCTT
7513 TTTC
1 TTTC
7517 TTGGGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:12494 original size:12 final size:12
Alignment explanation
Indices: 12479--12532 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
12469 GGTGGTTTCC
12479 GTGGGGGCTATG
1 GTGGGGGCTATG
*
12491 GTGGGGGCTCTG
1 GTGGGGGCTATG
*
12503 GCGGGGGCTATG
1 GTGGGGGCTATG
* *
12515 GTGGAGGCTTTG
1 GTGGGGGCTATG
12527 GTGGGG
1 GTGGGG
12533 ATTCTGATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.06, C:0.11, G:0.59, T:0.24
Consensus pattern (12 bp):
GTGGGGGCTATG
Found at i:24788 original size:112 final size:112
Alignment explanation
Indices: 24591--24815 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
24581 CATTGTCCAG
24591 AAATTTGGTTCTCCACGTGTTATTATATGATTGGTTTGGTCCCATCATTTTTTTTATTTTGAAAA
1 AAATTTGGTTCTCCACGTGTTATTATATGATTGGTTTGGTCCCATCATTTTTTTTATTTTGAAAA
24656 ATAGATAACTTTCATTATGTAACTGATTTTATAATAATTTTAGAAAT
66 ATAGATAACTTTCATTATGTAACTGATTTTATAATAATTTTAGAAAT
24703 AAATTTGGTTCTCCACGTGTTATTATATGATTGGTTTGGTCCCATCATTTTTTTTATTTTGAAAA
1 AAATTTGGTTCTCCACGTGTTATTATATGATTGGTTTGGTCCCATCATTTTTTTTATTTTGAAAA
24768 ATAGATAACTTTCATTATGTAACTGATTTTATAATAATTTTAGAAAT
66 ATAGATAACTTTCATTATGTAACTGATTTTATAATAATTTTAGAAAT
24815 A
1 A
24816 TCATTTTTCA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (112 bp):
AAATTTGGTTCTCCACGTGTTATTATATGATTGGTTTGGTCCCATCATTTTTTTTATTTTGAAAA
ATAGATAACTTTCATTATGTAACTGATTTTATAATAATTTTAGAAAT
Found at i:29616 original size:107 final size:106
Alignment explanation
Indices: 29435--29698 Score: 406
Period size: 107 Copynumber: 2.5 Consensus size: 106
29425 AATTTTTCTA
** *
29435 ACCCTTAAAATAAAATTTTAATTTTGATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
29498 TTTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* *
29540 ACCCTTAAAATAAATATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAA-ATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
29605 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* *
29647 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTTAAATTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
29699 AGGCTAAACT
Statistics
Matches: 146, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
105 25 0.17
106 16 0.11
107 102 0.70
108 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:30226 original size:220 final size:220
Alignment explanation
Indices: 29881--30280 Score: 773
Period size: 220 Copynumber: 1.8 Consensus size: 220
29871 ACATTATAAT
29881 TAGTATAGATATTAAATAAATTAATATTAAGAAAAACATAAAATTGAAATAAATACAATAAAAAT
1 TAGTATAGATATTAAATAAATTAATATTAAGAAAAACATAAAATTGAAATAAATACAATAAAAAT
29946 AAGTTTATTAATTTACTTTTTTTTTTATCAAATTTGACTTTAAATGCAAATATTTAATTACATTA
66 AAGTTTATTAATTTACTTTTTTTTTTATCAAATTTGACTTTAAATGCAAATATTTAATTACATTA
*
30011 TTCTAAAAATGAGCATTTTGTCAGTTTCTATCTTAATCTATATGTAAGTAGTGACACAAACTCAG
131 TTCTAAAAATGAGCATTTTATCAGTTTCTATCTTAATCTATATGTAAGTAGTGACACAAACTCAG
30076 GACTTCACATTATAATTAGTATAGA
196 GACTTCACATTATAATTAGTATAGA
30101 TAGTATAGATATTAAATAAATTAATATTAAGAAAAACATAAAATTGAAATAAATACAATAAAAAT
1 TAGTATAGATATTAAATAAATTAATATTAAGAAAAACATAAAATTGAAATAAATACAATAAAAAT
30166 AAGTTTATTAATTTACTTTTTTTTTTATCAAATTTGACTTTAAATGCAAATATTTAATTACATTA
66 AAGTTTATTAATTTACTTTTTTTTTTATCAAATTTGACTTTAAATGCAAATATTTAATTACATTA
* *
30231 TTCTAAAAATGAGCATTTTATCGGTTTCTGTCTTAATCTATATGTAAGTA
131 TTCTAAAAATGAGCATTTTATCAGTTTCTATCTTAATCTATATGTAAGTA
30281 AACAAACTCA
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 177 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (220 bp):
TAGTATAGATATTAAATAAATTAATATTAAGAAAAACATAAAATTGAAATAAATACAATAAAAAT
AAGTTTATTAATTTACTTTTTTTTTTATCAAATTTGACTTTAAATGCAAATATTTAATTACATTA
TTCTAAAAATGAGCATTTTATCAGTTTCTATCTTAATCTATATGTAAGTAGTGACACAAACTCAG
GACTTCACATTATAATTAGTATAGA
Found at i:38435 original size:11 final size:11
Alignment explanation
Indices: 38411--38445 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
38401 TTGACAGCGC
38411 AACAAAAACAA
1 AACAAAAACAA
* *
38422 AACGAAAACGA
1 AACAAAAACAA
38433 AACAAAAACAA
1 AACAAAAACAA
38444 AA
1 AA
38446 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:39887 original size:58 final size:59
Alignment explanation
Indices: 39818--39947 Score: 174
Period size: 60 Copynumber: 2.2 Consensus size: 59
39808 GGCTAATCGC
**** *
39818 TCAAATAGGACCTTAA-TATTCCGAAATGCTCAAATAAGGG-TCCATGCTTTTAATTTGA
1 TCAAATAGGACCTTAACTATAAAAAAATACTCAAATAAGGGCT-CATGCTTTTAATTTGA
*
39876 TCAAATAGGACCTTAACTTATAAAAAAATACTCAAATAAGGGCTCATGCTTTTAATTTGG
1 TCAAATAGGACCTTAAC-TATAAAAAAATACTCAAATAAGGGCTCATGCTTTTAATTTGA
39936 TCAAATAGGACC
1 TCAAATAGGACC
39948 CTAGCGTTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
58 16 0.25
60 46 0.73
61 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (59 bp):
TCAAATAGGACCTTAACTATAAAAAAATACTCAAATAAGGGCTCATGCTTTTAATTTGA
Found at i:39963 original size:60 final size:61
Alignment explanation
Indices: 39841--39976 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 61
39831 TAATATTCCG
*
39841 AAATGCTCAAATAAGGGTCCATGCTTTTAATTTGATCAAATAGGACCTTAACTTAT-AAAA
1 AAATGCTCAAATAAGGGTCCATGCTTTTAATTTGATCAAATAGGACCCTAACTTATAAAAA
* * * **
39901 AAATACTCAAATAAGGG-CTCATGCTTTTAATTTGGTCAAATAGGACCCTAGCGTT-TGCAAA
1 AAATGCTCAAATAAGGGTC-CATGCTTTTAATTTGATCAAATAGGACCCTAAC-TTATAAAAA
39962 AAATGCTCAAATAAG
1 AAATGCTCAAATAAG
39977 ATATTGGTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 47 0.70
61 19 0.28
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (61 bp):
AAATGCTCAAATAAGGGTCCATGCTTTTAATTTGATCAAATAGGACCCTAACTTATAAAAA
Found at i:40078 original size:32 final size:31
Alignment explanation
Indices: 40025--40096 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
40015 TATCGGGACA
*
40025 CTATTTGAGCATTTTCACATACATTATG-GTC
1 CTATTTGATCATTTTCACATACATTA-GAGTC
* *
40056 CTATTTGATCATTTTTCGCATACTTTAGAGTC
1 CTATTTGATCA-TTTTCACATACATTAGAGTC
40088 CTATTTGAT
1 CTATTTGAT
40097 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
32 25 0.69
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (31 bp):
CTATTTGATCATTTTCACATACATTAGAGTC
Found at i:46388 original size:21 final size:23
Alignment explanation
Indices: 46345--46392 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
46335 AAAAGTGAAA
**
46345 ACATAAGTTAGAACTCTTGAAAC
1 ACATAAGTTAGAACTCTCCAAAC
46368 ACATAAGTTAG-A-TCTCCAAAC
1 ACATAAGTTAGAACTCTCCAAAC
46389 ACAT
1 ACAT
46393 TTGTTGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (23 bp):
ACATAAGTTAGAACTCTCCAAAC
Found at i:48745 original size:1 final size:1
Alignment explanation
Indices: 48739--48772 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
48729 TTCTGTTTAG
48739 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48773 GTTGAGAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.