Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013627.1 Corchorus capsularis cultivar CVL-1 contig13648, 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: 95513
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2967 original size:15 final size:15
Alignment explanation
Indices: 2947--2976 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2937 ATTTGATAAA
2947 TAAGTTTATAATATT
1 TAAGTTTATAATATT
2962 TAAGTTTATAATATT
1 TAAGTTTATAATATT
2977 AAGATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TAAGTTTATAATATT
Found at i:5590 original size:20 final size:21
Alignment explanation
Indices: 5557--5595 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5547 TAGAAAATAA
* *
5557 GGTAAAAATGTATATAAAAGT
1 GGTAAAAATCTATAGAAAAGT
5578 GGTAAAAA-CTATAGAAAA
1 GGTAAAAATCTATAGAAAA
5596 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.18, T:0.23
Consensus pattern (21 bp):
GGTAAAAATCTATAGAAAAGT
Found at i:9387 original size:18 final size:18
Alignment explanation
Indices: 9364--9401 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9354 TATATTGTAT
* *
9364 TTGGGCTTAATACGTTAG
1 TTGGGCCTAATACATTAG
9382 TTGGGCCTAATACATTAG
1 TTGGGCCTAATACATTAG
9400 TT
1 TT
9402 AGTGGCCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (18 bp):
TTGGGCCTAATACATTAG
Found at i:10299 original size:30 final size:31
Alignment explanation
Indices: 10249--10322 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
10239 GCCGCGATAT
* * * *
10249 TCAATTAAGGATACACCGTTACCA-CTTGTG
1 TCAATTCAGGATACAACGTTACCAGATTATG
* *
10279 TCAATTCAGGATATAACGTTATCAGATTATG
1 TCAATTCAGGATACAACGTTACCAGATTATG
10310 TCAATTCAGGATA
1 TCAATTCAGGATA
10323 AAATCAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
TCAATTCAGGATACAACGTTACCAGATTATG
Found at i:13773 original size:14 final size:14
Alignment explanation
Indices: 13754--13784 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13744 AACAATTGCA
13754 ACTGTAACAAAAAG
1 ACTGTAACAAAAAG
*
13768 ACTGTAACGAAAAG
1 ACTGTAACAAAAAG
13782 ACT
1 ACT
13785 ATATAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (14 bp):
ACTGTAACAAAAAG
Found at i:15717 original size:13 final size:13
Alignment explanation
Indices: 15699--15726 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15689 CGTCCAAAAG
15699 AAAAACAAAAACA
1 AAAAACAAAAACA
15712 AAAAACAAAAACA
1 AAAAACAAAAACA
15725 AA
1 AA
15727 CTTCTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAACA
Found at i:18268 original size:22 final size:22
Alignment explanation
Indices: 18238--18468 Score: 163
Period size: 22 Copynumber: 10.6 Consensus size: 22
18228 TCCAACGTAG
* *
18238 AAATATTGATAACCACATTGTGA
1 AAAT-TTGATAACCACACTATGA
** *
18261 AAATTTGATAACCTTATTATGA
1 AAATTTGATAACCACACTATGA
* * *
18283 AATTTTGATAACCTCCCTATGA
1 AAATTTGATAACCACACTATGA
* *
18305 AAATTTGATAACCAAACTGTGA
1 AAATTTGATAACCACACTATGA
* *
18327 AAATTTTGATAACTACACAATGA
1 AAA-TTTGATAACCACACTATGA
*
18350 AAATTTGATAATCTC-CA-AATGA
1 AAATTTGATAA-C-CACACTATGA
* *
18372 AAATTTGATAATCACATTAT-A
1 AAATTTGATAACCACACTATGA
* **
18393 AAA-TTGGTAACGGCACTATGA
1 AAATTTGATAACCACACTATGA
*
18414 AAATTTTGATAACCTCA-TA--A
1 AAA-TTTGATAACCACACTATGA
* *
18434 AATTTTGATAACCACACCATG-
1 AAATTTGATAACCACACTATGA
18455 AAATTTCGATAACC
1 AAATTT-GATAACC
18469 TCCATATGAG
Statistics
Matches: 165, Mismatches: 31, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.07
20 16 0.10
21 15 0.09
22 88 0.53
23 34 0.21
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:18306 original size:44 final size:44
Alignment explanation
Indices: 18258--18832 Score: 195
Period size: 44 Copynumber: 13.0 Consensus size: 44
18248 AACCACATTG
*
18258 TGAAAATTTGATAACCTTATTATGAAATTTTGATAACCTCCCTA
1 TGAAAATTTGATAACCTTACTATGAAATTTTGATAACCTCCCTA
** * * *
18302 TGAAAATTTGATAACCAAACTGTGAAAATTTTGATAA-CTACACAA
1 TGAAAATTTGATAACCTTACTATG-AAATTTTGATAACCT-CCCTA
* * * * * * **
18347 TGAAAATTTGATAATC-TCCAAATGAAAATTTGATAATCACATTA
1 TGAAAATTTGATAACCTTAC-TATGAAATTTTGATAACCTCCCTA
* ***
18391 T-AAAA-TTGGTAACGGCACTATGAAAATTTTGATAACCT--C-A
1 TGAAAATTTGATAACCTTACTATG-AAATTTTGATAACCTCCCTA
** * * *
18431 T-AAAATTTTGATAACCACACCATGAAATTTCGATAACCTCCATA
1 TGAAAA-TTTGATAACCTTACTATGAAATTTTGATAACCTCCCTA
* * * *
18475 TGAGAATGAAACTGTAATATCCTCT-CTATGTAATTTTGATAACCTCTCC-A
1 T--G-A--AAA-TTTGATAACCT-TACTATGAAATTTTGATAACCTC-CCTA
* * *
18525 T-AAAATTTTCATAACCTCT-CTATGAAATTTTGTTAACCTCCTTA
1 TGAAAA-TTTGATAACCT-TACTATGAAATTTTGATAACCTCCCTA
* * * * * *
18569 GGAGATTTTGATAA---GA--A-CAAATTTTGGTAACCTCCCTCTCTA
1 TGAAAATTTGATAACCTTACTATGAAATTTTGATAACCT--C-C-CTA
* ** * * ** *
18611 TG-AAATTTTATTAACCTTTTTATTAAATTTTAATAACAACACTA
1 TGAAAATTTGA-TAACCTTACTATGAAATTTTGATAACCTCCCTA
* *
18655 T-AAAATTTCGATAACCTT-CATATGAAATTTTGTTAACCTCCATA
1 TGAAAATTT-GATAACCTTAC-TATGAAATTTTGATAACCTCCCTA
* * * ** * **
18699 AGAAATTTTGATAAGCTTTTTATGAAATTTTGGTAACCTCTGTA
1 TGAAAATTTGATAACCTTACTATGAAATTTTGATAACCTCCCTA
** * * * *
18743 TGAAGTTTTGATAA-CTACACTATGAAGTTTTGATAACATCCATA
1 TGAAAATTTGATAACCT-TACTATGAAATTTTGATAACCTCCCTA
* * ** * *
18787 TGAAATTTTGGTAACCACATTATGAAATTTTGATAACCTTCCTA
1 TGAAAATTTGATAACCTTACTATGAAATTTTGATAACCTCCCTA
18831 TG
1 TG
18833 TAATGTTGTT
Statistics
Matches: 389, Mismatches: 102, Indels: 80
0.68 0.18 0.14
Matches are distributed among these distances:
38 14 0.04
39 1 0.00
40 7 0.02
41 20 0.05
42 28 0.07
43 20 0.05
44 210 0.54
45 43 0.11
46 2 0.01
47 1 0.00
48 12 0.03
50 30 0.08
51 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
TGAAAATTTGATAACCTTACTATGAAATTTTGATAACCTCCCTA
Found at i:18358 original size:67 final size:66
Alignment explanation
Indices: 18238--18470 Score: 176
Period size: 67 Copynumber: 3.6 Consensus size: 66
18228 TCCAACGTAG
* * * ** * **
18238 AAATATTGATAACCACATTGTGAAAATTTGATAACCTTATTATGAAATTTTGATAACCTCCCTAT
1 AAAT-TTGATAACCAAACTGTGAAAATTTGATAACCTCACAATGAAAATTTGATAACCTCCAAAT
18303 GA
65 GA
*
18305 AAATTTGATAACCAAACTGTGAAAATTTTGATAA-CTACACAATGAAAATTTGATAATCTCCAAA
1 AAATTTGATAACCAAACTGTGAAAA-TTTGATAACCT-CACAATGAAAATTTGATAACCTCCAAA
18369 TGA
64 TGA
* * * * * ** *
18372 AAATTTGATAATCACATTAT-AAAA-TTGGTAACGGCACTATGAAAATTTTGATAACCT-C--AT
1 AAATTTGATAACCAAACTGTGAAAATTTGATAACCTCACAATGAAAA-TTTGATAACCTCCAAAT
18432 -A
65 GA
* **
18433 AAATTTTGATAACCACACCATG-AAATTTCGATAACCTC
1 AAA-TTTGATAACCAAACTGTGAAAATTT-GATAACCTC
18471 CATATGAGAA
Statistics
Matches: 134, Mismatches: 24, Indels: 19
0.76 0.14 0.11
Matches are distributed among these distances:
61 4 0.03
62 19 0.14
63 2 0.01
64 23 0.17
65 10 0.07
66 25 0.19
67 51 0.38
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (66 bp):
AAATTTGATAACCAAACTGTGAAAATTTGATAACCTCACAATGAAAATTTGATAACCTCCAAATG
A
Found at i:18531 original size:22 final size:22
Alignment explanation
Indices: 18506--18564 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
18496 CTCTCTATGT
18506 AATTTTGATAACCTCTCCATAA
1 AATTTTGATAACCTCTCCATAA
* * *
18528 AATTTTCATAACCTCTCTATGA
1 AATTTTGATAACCTCTCCATAA
*
18550 AATTTTGTTAACCTC
1 AATTTTGATAACCTC
18565 CTTAGGAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (22 bp):
AATTTTGATAACCTCTCCATAA
Found at i:18682 original size:22 final size:22
Alignment explanation
Indices: 18609--18832 Score: 152
Period size: 22 Copynumber: 10.2 Consensus size: 22
18599 CCTCCCTCTC
**
18609 TATGAAATTTT-ATTAACCTTTT
1 TATGAAATTTTGA-TAACCTTCA
* * **
18631 TATTAAATTTTAATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
* *
18652 CTATAAAATTTCGATAACCTTCA
1 -TATGAAATTTTGATAACCTTCA
* *
18675 TATGAAATTTTGTTAACCTCCA
1 TATGAAATTTTGATAACCTTCA
* * **
18697 TAAGAAATTTTGATAAGCTTTT
1 TATGAAATTTTGATAACCTTCA
* *
18719 TATGAAATTTTGGTAACC-TCTG
1 TATGAAATTTTGATAACCTTC-A
* *
18741 TATGAAGTTTTGATAA-CTACA
1 TATGAAATTTTGATAACCTTCA
* * *
18762 CTATGAAGTTTTGATAACATCCA
1 -TATGAAATTTTGATAACCTTCA
* *
18785 TATGAAATTTTGGTAACC-ACA
1 TATGAAATTTTGATAACCTTCA
*
18806 TTATGAAATTTTGATAACCTTCC
1 -TATGAAATTTTGATAACCTTCA
18829 TATG
1 TATG
18833 TAATGTTGTT
Statistics
Matches: 155, Mismatches: 38, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
21 5 0.03
22 142 0.92
23 8 0.05
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:18745 original size:66 final size:67
Alignment explanation
Indices: 18675--18825 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 67
18665 ATAACCTTCA
* * *** *
18675 TATGAAATTTTGTTAACCTCCA-TAAGAAATTTTGATAAGC-TTTTTATGAAATTTTGGTAACCT
1 TATGAAATTTTGATAACCTACACTAAGAAATTTTGATAA-CATCCATATGAAATTTTGGTAACCA
18738 C-T
65 CAT
* * *
18740 GTATGAAGTTTTGATAA-CTACACTATGAAGTTTTGATAACATCCATATGAAATTTTGGTAACCA
1 -TATGAAATTTTGATAACCTACACTAAGAAATTTTGATAACATCCATATGAAATTTTGGTAACCA
18804 CAT
65 CAT
18807 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
18826 TCCTATGTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
65 5 0.07
66 63 0.89
67 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (67 bp):
TATGAAATTTTGATAACCTACACTAAGAAATTTTGATAACATCCATATGAAATTTTGGTAACCAC
AT
Found at i:21544 original size:25 final size:25
Alignment explanation
Indices: 21516--21601 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
21506 TCTAGAATTG
21516 TTTTCTTAATGCTAATTGCTTAAGC
1 TTTTCTTAATGCTAATTGCTTAAGC
* * ** **
21541 TTTTCTTCATTCATGTTTGTCACTTCTG-
1 TTTTCTTAATGC-TAATTG---CTTAAGC
*
21569 TTTTTTTAATGCTAATTGCTTAAGC
1 TTTTCTTAATGCTAATTGCTTAAGC
21594 TTTTCTTA
1 TTTTCTTA
21602 TTGTTTTTCA
Statistics
Matches: 42, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
24 4 0.10
25 17 0.40
26 4 0.10
27 4 0.10
28 9 0.21
29 4 0.10
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (25 bp):
TTTTCTTAATGCTAATTGCTTAAGC
Found at i:22188 original size:21 final size:22
Alignment explanation
Indices: 22164--22213 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
22154 TTTTCCTATA
*
22164 TGCTACGAGC-TTATTTGCATT
1 TGCTACGAGCTTTATTTACATT
22185 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGCTTTATTTACATT
22207 TGCTACG
1 TGCTACG
22214 GACATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (22 bp):
TGCTACGAGCTTTATTTACATT
Found at i:22221 original size:22 final size:22
Alignment explanation
Indices: 22164--22223 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
22154 TTTTCCTATA
*
22164 TGCTACGAGC-TTATTTGCATT
1 TGCTACGAGCATTATTTACATT
*
22185 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGCATTATTTACATT
22207 TGCTACG-GACATTATTT
1 TGCTACGAG-CATTATTT
22224 TAGGGTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (22 bp):
TGCTACGAGCATTATTTACATT
Found at i:26024 original size:91 final size:91
Alignment explanation
Indices: 25922--26091 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 91
25912 AACGGGTAGA
* * *
25922 TTCTTTTTTAGGAAAGATGAGAGATTTGACCGAGGGAGAGAAAAATATAGTTTTTTGGAGAGATA
1 TTCTTTTTTAGGAAAGATGAGAGATTTGACCGAGAGAGAGAAAAATATAGTTTTTTAGAAAGATA
**
25987 TATTGTTGGAGTTAACTAGTAGGTTT
66 TATTGACGGAGTTAACTAGTAGGTTT
26013 TTCTTTTTTAGGAAAGATGAGAGATTTGACCGAGAGAGAGAAAAATATAGTTTTTTAGAAAGATA
1 TTCTTTTTTAGGAAAGATGAGAGATTTGACCGAGAGAGAGAAAAATATAGTTTTTTAGAAAGATA
26078 TATTGACGGAGTTA
66 TATTGACGGAGTTA
26092 CCGGTCAATG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (91 bp):
TTCTTTTTTAGGAAAGATGAGAGATTTGACCGAGAGAGAGAAAAATATAGTTTTTTAGAAAGATA
TATTGACGGAGTTAACTAGTAGGTTT
Found at i:26254 original size:29 final size:29
Alignment explanation
Indices: 26192--26264 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
26182 GTCTGAGGGG
*
26192 GCAAAACGTCCCAAAATTGAAGTTCATGGT
1 GCAAAACGT-CCAAAATTGAAGTTCATGGA
* *
26222 GCAAAATGTCCAAAATTGAAGTT-TTAGGA
1 GCAAAACGTCCAAAATTGAAGTTCAT-GGA
26251 GCAAAACGTCCAAA
1 GCAAAACGTCCAAA
26265 CAGTACAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.76
30 8 0.21
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (29 bp):
GCAAAACGTCCAAAATTGAAGTTCATGGA
Found at i:27979 original size:29 final size:30
Alignment explanation
Indices: 27947--28004 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
27937 TTTCCCCATC
27947 AACT-TCAATTTTGGACATTTTGCCCCCTG
1 AACTCTCAATTTTGGACATTTTGCCCCCTG
*
27976 AACTCTCAATTTTGGACGTTTTGCCCCCT
1 AACTCTCAATTTTGGACATTTTGCCCCCT
28005 TTCAAGCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (30 bp):
AACTCTCAATTTTGGACATTTTGCCCCCTG
Found at i:28117 original size:32 final size:32
Alignment explanation
Indices: 28076--28151 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
28066 AAATCCCACG
**
28076 TGGCAATGCCACGTCATCGGTTTGGTCCGACA
1 TGGCAATGCCACGTCATCAATTTGGTCCGACA
* * *
28108 TGGCAATGCCATGTCATCAATTTGGTCTGACG
1 TGGCAATGCCACGTCATCAATTTGGTCCGACA
28140 TGGCAATGCCAC
1 TGGCAATGCCAC
28152 ATCAGCTGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (32 bp):
TGGCAATGCCACGTCATCAATTTGGTCCGACA
Found at i:28239 original size:30 final size:28
Alignment explanation
Indices: 28197--28267 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 28
28187 TAAGAGGGGG
28197 CAAAACGTCCAAAATTGAGAGTTTAAGGGA
1 CAAAACGTCCAAAATTGA-AGTTT-AGGGA
* * *
28227 CGAAATGTCCAAAATTGAAGTTTAGGGG
1 CAAAACGTCCAAAATTGAAGTTTAGGGA
28255 CAAAACGTCCAAA
1 CAAAACGTCCAAA
28268 CGCCACAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 15 0.42
29 5 0.14
30 16 0.44
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (28 bp):
CAAAACGTCCAAAATTGAAGTTTAGGGA
Found at i:29146 original size:50 final size:51
Alignment explanation
Indices: 29058--29155 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
29048 AAGCCCTTAT
* * *
29058 TTGAGCATTTTCGTATATGTTACGGTCTTATCTAACCAAATTAAAAGCTAAA
1 TTGAGCATTTTCG-ATACGTTACGGCCTTATCTAACCAAATCAAAAGCTAAA
* *
29110 TTGAGCATTTTC-ATACGTTAGGGCCTTATTTAACCAAATCAAAAGC
1 TTGAGCATTTTCGATACGTTACGGCCTTATCTAACCAAATCAAAAGC
29156 ATGACCCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 29 0.71
52 12 0.29
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (51 bp):
TTGAGCATTTTCGATACGTTACGGCCTTATCTAACCAAATCAAAAGCTAAA
Found at i:35293 original size:16 final size:16
Alignment explanation
Indices: 35272--35304 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35262 TGAGACCAAC
35272 CACTAAGATTGTGCCA
1 CACTAAGATTGTGCCA
35288 CACTAAGATTGTGCCA
1 CACTAAGATTGTGCCA
35304 C
1 C
35305 GTCAAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (16 bp):
CACTAAGATTGTGCCA
Found at i:36795 original size:83 final size:83
Alignment explanation
Indices: 36691--36855 Score: 253
Period size: 83 Copynumber: 2.0 Consensus size: 83
36681 AACCTCAAGC
36691 CTGCCCCTGAGTTTCTAATTGTTGCAATCATGATAATTATACACATTCATGGTTGTCACAACAT-
1 CTGCCCCTGAGTTTCTAATTGTTGCAATCATGATAATTATACACATTCATGGTTGTCACAACATG
36755 A-AGTATGCTAATGAAGTTG
66 AGAGTA--CTAATGAAGTTG
* * * * *
36774 CTGCCCCTGAGTTTCTTATTGTTGTATTCATGATAATTATACACATTCATGGTTGTCGCAGCATG
1 CTGCCCCTGAGTTTCTAATTGTTGCAATCATGATAATTATACACATTCATGGTTGTCACAACATG
36839 AGAGTACTAATGAAGTT
66 AGAGTACTAATGAAGTT
36856 ATATCATTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
83 70 0.93
84 1 0.01
85 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (83 bp):
CTGCCCCTGAGTTTCTAATTGTTGCAATCATGATAATTATACACATTCATGGTTGTCACAACATG
AGAGTACTAATGAAGTTG
Found at i:41472 original size:6 final size:6
Alignment explanation
Indices: 41453--41495 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
41443 CAAAGCAAAA
*
41453 TAAAT- TAAACC TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
41496 TAGCAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:42859 original size:22 final size:21
Alignment explanation
Indices: 42829--42887 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
42819 AATTCTTGTT
* *
42829 TCTTAAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
42851 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
42870 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
42888 ACACAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:42874 original size:11 final size:11
Alignment explanation
Indices: 42857--42888 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42847 ATTGTCTTCA
42857 AATCTTCAAAT
1 AATCTTCAAAT
*
42868 TATCTTCAAAT
1 AATCTTCAAAT
42879 AATCTTCAAA
1 AATCTTCAAA
42889 CACAAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:42888 original size:22 final size:22
Alignment explanation
Indices: 42829--42888 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
42819 AATTCTTGTT
* *
42829 TCTTAAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
42851 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
42870 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
42889 CACAAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:43066 original size:20 final size:20
Alignment explanation
Indices: 43043--43081 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43033 AAAATAGGGT
43043 AAAAACACATAAAAATAGCA
1 AAAAACACATAAAAATAGCA
** *
43063 AAAAGTATATAAAAATAGC
1 AAAAACACATAAAAATAGC
43082 TATAAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAACACATAAAAATAGCA
Found at i:46613 original size:36 final size:37
Alignment explanation
Indices: 46555--46624 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
46545 CAAAGGATCA
* * *
46555 TTTTTTTTTTGGGGCCAGAACAAAGGGTCATTTCTTT
1 TTTTTTTTTTGGCGCAAAAACAAAGGGTCATTTCTTT
*
46592 TTTTTTTTTTGGCG-AAAAACAACGGGTCATTTC
1 TTTTTTTTTTGGCGCAAAAACAAAGGGTCATTTC
46625 AATAGTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 16 0.55
37 13 0.45
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.44
Consensus pattern (37 bp):
TTTTTTTTTTGGCGCAAAAACAAAGGGTCATTTCTTT
Found at i:53077 original size:21 final size:21
Alignment explanation
Indices: 53051--53112 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
53041 GCATAGCTTG
53051 GAATCGATTGGAATATTCTTA
1 GAATCGATTGGAATATTCTTA
** *
53072 GAATCGATT-GAATGAAGCTTT
1 GAATCGATTGGAAT-ATTCTTA
*
53093 GGATCGATTGGAATATTCTT
1 GAATCGATTGGAATATTCTT
53113 GCTTAAAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.37
Consensus pattern (21 bp):
GAATCGATTGGAATATTCTTA
Found at i:60720 original size:15 final size:16
Alignment explanation
Indices: 60688--60721 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
60678 AAAGAAGAAT
*
60688 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
60704 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
60719 TAA
1 TAA
60722 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:61995 original size:19 final size:18
Alignment explanation
Indices: 61962--61997 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
61952 TTGAAATAAT
61962 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
61980 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
61998 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:64493 original size:115 final size:115
Alignment explanation
Indices: 64291--64525 Score: 470
Period size: 115 Copynumber: 2.0 Consensus size: 115
64281 CATCCTAGCT
64291 TTGAAACCGGGCTTAGCCTCAATTTCATCCTTAGGTAGCAACGAAATCATACTTGAAACTTTGGA
1 TTGAAACCGGGCTTAGCCTCAATTTCATCCTTAGGTAGCAACGAAATCATACTTGAAACTTTGGA
64356 CCGAATTGAGAAGCTCCAATTCGATAAAATTGATATTTAAACTTCTTGAA
66 CCGAATTGAGAAGCTCCAATTCGATAAAATTGATATTTAAACTTCTTGAA
64406 TTGAAACCGGGCTTAGCCTCAATTTCATCCTTAGGTAGCAACGAAATCATACTTGAAACTTTGGA
1 TTGAAACCGGGCTTAGCCTCAATTTCATCCTTAGGTAGCAACGAAATCATACTTGAAACTTTGGA
64471 CCGAATTGAGAAGCTCCAATTCGATAAAATTGATATTTAAACTTCTTGAA
66 CCGAATTGAGAAGCTCCAATTCGATAAAATTGATATTTAAACTTCTTGAA
64521 TTGAA
1 TTGAA
64526 CTTCAAAATC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 120 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (115 bp):
TTGAAACCGGGCTTAGCCTCAATTTCATCCTTAGGTAGCAACGAAATCATACTTGAAACTTTGGA
CCGAATTGAGAAGCTCCAATTCGATAAAATTGATATTTAAACTTCTTGAA
Found at i:70675 original size:15 final size:16
Alignment explanation
Indices: 70643--70676 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
70633 AAAGAAGAAT
*
70643 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
70659 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
70674 TAA
1 TAA
70677 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:71833 original size:18 final size:18
Alignment explanation
Indices: 71812--71847 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
71802 AAATTGGGAT
71812 TTTAACTTCAATTATAGG
1 TTTAACTTCAATTATAGG
71830 TTTAACTTCAATTATAGG
1 TTTAACTTCAATTATAGG
71848 ATTTCTTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTAACTTCAATTATAGG
Found at i:73338 original size:2 final size:2
Alignment explanation
Indices: 73331--73357 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73321 TTTGGAATTA
73331 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 A
73358 AGGAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78306 original size:11 final size:11
Alignment explanation
Indices: 78290--78321 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
78280 GAAGTTCGTG
78290 TTTGAAGATTA
1 TTTGAAGATTA
*
78301 TTTGAAGATAA
1 TTTGAAGATTA
78312 TTTGAAGATT
1 TTTGAAGATT
78322 TGAACACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:79739 original size:15 final size:15
Alignment explanation
Indices: 79719--79754 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
79709 TAGTATTTAG
*
79719 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
79734 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
79749 TTTAAT
1 TTTAAT
79755 CCTCTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:81124 original size:15 final size:15
Alignment explanation
Indices: 81101--81143 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
81091 CCTTGCTAAG
*
81101 CCAGTAGATGAGCCA
1 CCAGAAGATGAGCCA
81116 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
81131 CAAGAAGATGAGC
1 CCAGAAGATGAGC
81144 AACCTGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.09
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:83088 original size:18 final size:19
Alignment explanation
Indices: 83065--83102 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
83055 AAAGGGTAGT
83065 TAAAAA-AAATCTTTTTCA
1 TAAAAAGAAATCTTTTTCA
* *
83083 TAAAAAGAAGTGTTTTTCA
1 TAAAAAGAAATCTTTTTCA
83102 T
1 T
83103 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
TAAAAAGAAATCTTTTTCA
Found at i:85358 original size:6 final size:6
Alignment explanation
Indices: 85347--85377 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
85337 ATAATTGCCA
85347 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
85378 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:85413 original size:15 final size:15
Alignment explanation
Indices: 85395--85430 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
85385 TAGTTTTTAG
85395 TTTAATTGTTTTCTT
1 TTTAATTGTTTTCTT
85410 TTTAATTGTTTTCTT
1 TTTAATTGTTTTCTT
85425 TTTAAT
1 TTTAAT
85431 CCCCTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTAATTGTTTTCTT
Found at i:85972 original size:21 final size:21
Alignment explanation
Indices: 85948--85987 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
85938 GTTGAACTTC
85948 TTCATTTCTGAATCTGTCTTT
1 TTCATTTCTGAATCTGTCTTT
*
85969 TTCATTTCTGTATCTGTCT
1 TTCATTTCTGAATCTGTCT
85988 CGTCCATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.57
Consensus pattern (21 bp):
TTCATTTCTGAATCTGTCTTT
Found at i:91258 original size:24 final size:24
Alignment explanation
Indices: 91193--91262 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
91183 GCTAGTATTT
*
91193 TGACAAAAAATTTCAATAG-G-CTCA
1 TGAC-AAAAATTTCAA-AGAGCCTAA
91217 TGAC--AAATTT-AAAGAGCCTAA
1 TGACAAAAATTTCAAAGAGCCTAA
91238 TGACAAAAATTTCAAAGAGCCTAA
1 TGACAAAAATTTCAAAGAGCCTAA
91262 T
1 T
91263 ATTTTTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 13 0.32
23 6 0.15
24 16 0.40
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
TGACAAAAATTTCAAAGAGCCTAA
Done.