Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2382
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: 87864
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2934 original size:35 final size:35
Alignment explanation
Indices: 2879--2949 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
2869 TGTGGTTCAG
* *
2879 AACATTATATATATAAATGGTAAAAAA-ATAATAA
1 AACATTAAATATAAAAATGGTAAAAAATATAATAA
2913 AACATTAAATATTAAAAATGGTAAAAAATTATAATAA
1 AACATTAAATA-TAAAAATGGTAAAAAA-TATAATAA
2950 TTCTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 10 0.31
35 15 0.47
37 7 0.22
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (35 bp):
AACATTAAATATAAAAATGGTAAAAAATATAATAA
Found at i:2966 original size:27 final size:26
Alignment explanation
Indices: 2936--3032 Score: 72
Period size: 28 Copynumber: 3.5 Consensus size: 26
2926 AAAAATGGTA
*
2936 AAAAATTATAATAATTC-TAAAAAAATT
1 AAAAATTATAA-AAATCATAAAAAAA-T
*
2963 AAAATTTATAAAAATCATAAAAAAAT
1 AAAAATTATAAAAATCATAAAAAAAT
* * *
2989 AAAAGAGTTTTAAAAAT-ATTTAAAAATT
1 AAAA-A-TTATAAAAATCA-TAAAAAAAT
3017 AAAAAATTATTAAAAA
1 -AAAAATTA-TAAAAA
3033 ATTGTAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
26 9 0.16
27 21 0.37
28 23 0.40
29 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAATTATAAAAATCATAAAAAAAT
Found at i:2983 original size:18 final size:18
Alignment explanation
Indices: 2934--2984 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 18
2924 TTAAAAATGG
*
2934 TAAAAAATTATAATAATTC
1 TAAAAAAATATAA-AATTC
2953 TAAAAAAAT-TAAAATT-
1 TAAAAAAATATAAAATTC
*
2969 TATAAAAATCATAAAA
1 TAAAAAAAT-ATAAAA
2985 AAATAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 4 0.14
18 8 0.29
19 8 0.29
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAAATATAAAATTC
Found at i:3029 original size:28 final size:28
Alignment explanation
Indices: 2956--3042 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
2946 ATAATTCTAA
* *
2956 AAAAATT-AAAATTTA-TAAAAATCA-TA
1 AAAAATTAAAAAATTATTAAAAAT-ATTT
* *
2982 AAAAAATAAAAGAGTT-TTAAAAATATTT
1 AAAAATTAAAA-AATTATTAAAAATATTT
3010 AAAAATTAAAAAATTATTAAAAA-ATTGT
1 AAAAATTAAAAAATTATTAAAAATATT-T
3038 AAAAA
1 AAAAA
3043 GATGAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.12
27 10 0.20
28 34 0.68
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAATTAAAAAATTATTAAAAATATTT
Found at i:3041 original size:19 final size:19
Alignment explanation
Indices: 2934--3042 Score: 68
Period size: 19 Copynumber: 5.8 Consensus size: 19
2924 TTAAAAATGG
*
2934 TAAAAAATTATAATAAT-T
1 TAAAAAATTATAAAAATAT
*
2952 CTAAAAAA--ATTAAAAT-T
1 -TAAAAAATTATAAAAATAT
* *
2969 TATAAAAATCATAAAAA-AA
1 TA-AAAAATTATAAAAATAT
* *
2988 TAAAAGAGTTTTAAAAATAT
1 TAAAA-AATTATAAAAATAT
*
3008 TTAAAAATTA-AAAAATTAT
1 TAAAAAATTATAAAAA-TAT
*
3027 TAAAAAATTGTAAAAA
1 TAAAAAATTATAAAAA
3043 GATGAAAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
16 2 0.03
17 12 0.17
18 8 0.12
19 37 0.54
20 10 0.14
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAAATTATAAAAATAT
Found at i:3408 original size:10 final size:10
Alignment explanation
Indices: 3395--3477 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 10
3385 TTTTGACAAT
3395 TTTTTAATAA
1 TTTTTAATAA
3405 -TTTT--TAA
1 TTTTTAATAA
3412 TTTTTAAT-A
1 TTTTTAATAA
*
3421 TTTTTACCT--
1 TTTTTA-ATAA
*
3430 TTTTAAATAA
1 TTTTTAATAA
3440 -TTTT-ATAA
1 TTTTTAATAA
*
3448 TTATTT-ACAA
1 TT-TTTAATAA
3458 TTTTTAATAA
1 TTTTTAATAA
3468 TTTTT-ATAA
1 TTTTTAATAA
3477 T
1 T
3478 ATTCTAAACC
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
7 3 0.05
8 9 0.16
9 28 0.48
10 18 0.31
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:3415 original size:18 final size:18
Alignment explanation
Indices: 3392--3465 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
3382 CTATTTTGAC
3392 AATTTTTTAATAATTTTT
1 AATTTTTTAATAATTTTT
3410 AA-TTTTTAAT-ATTTTT
1 AATTTTTTAATAATTTTT
* *
3426 ACCTTTTTAAATAATTTTAT
1 A-ATTTTTTAATAATTTT-T
* *
3446 AATTATTT-ACAATTTTT
1 AATTTTTTAATAATTTTT
3463 AAT
1 AAT
3466 AATTTTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.15
17 12 0.26
18 16 0.35
19 9 0.20
20 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTTAATAATTTTT
Found at i:3417 original size:17 final size:17
Alignment explanation
Indices: 3395--3465 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
3385 TTTTGACAAT
3395 TTTTTAATAATTTTTAA
1 TTTTTAATAATTTTTAA
*
3412 TTTTTAAT-ATTTTTACC
1 TTTTTAATAATTTTTA-A
3429 TTTTTAAATAATTTTATAA
1 TTTTT-AATAATTTT-TAA
*
3448 TTATTT-ACAATTTTTAA
1 TT-TTTAATAATTTTTAA
3465 T
1 T
3466 AATTTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.15
17 17 0.37
18 10 0.22
19 7 0.15
20 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATAATTTTTAA
Found at i:3440 original size:28 final size:27
Alignment explanation
Indices: 3409--3473 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
3399 TAATAATTTT
* *
3409 TAATTTTTAATATTTTTAC-CTTTTTAAA
1 TAATTTTTAAT-TATTTACAATTTTT-AA
3437 TAATTTTATAATTATTTACAATTTTTAA
1 TAATTTT-TAATTATTTACAATTTTTAA
3465 TAATTTTTA
1 TAATTTTTA
3474 TAATATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 22 0.67
29 9 0.27
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
TAATTTTTAATTATTTACAATTTTTAA
Found at i:6131 original size:13 final size:13
Alignment explanation
Indices: 6115--6143 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6105 ATAAATGAAG
6115 TTCATAATTAGTA
1 TTCATAATTAGTA
6128 TTCATAATTAGTA
1 TTCATAATTAGTA
6141 TTC
1 TTC
6144 TAAGTTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCATAATTAGTA
Found at i:9593 original size:10 final size:10
Alignment explanation
Indices: 9578--9605 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9568 GTTCTTTCTA
9578 TTGTTCTTTG
1 TTGTTCTTTG
9588 TTGTTCTTTG
1 TTGTTCTTTG
9598 TTGTTCTT
1 TTGTTCTT
9606 CTTTTGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.18, T:0.71
Consensus pattern (10 bp):
TTGTTCTTTG
Found at i:28903 original size:11 final size:11
Alignment explanation
Indices: 28887--28912 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28877 TGTTGTTACT
28887 TAAAATAAAAA
1 TAAAATAAAAA
28898 TAAAATAAAAA
1 TAAAATAAAAA
28909 TAAA
1 TAAA
28913 TTATAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:30615 original size:41 final size:41
Alignment explanation
Indices: 30570--30718 Score: 244
Period size: 41 Copynumber: 3.6 Consensus size: 41
30560 CATTGAATGT
*
30570 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAA
* *
30611 AAGGGGTTGCTAATTGCAAATTCCCCGAATCACTTATCGAA
1 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAA
*
30652 AAGGGGTTGCTAAGTGCAAATTCTCCGAATCACTGATCGAA
1 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAA
**
30693 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCAAATTCCCC
30719 AAATTATTTA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCGAA
Found at i:30716 original size:82 final size:82
Alignment explanation
Indices: 30570--30811 Score: 254
Period size: 82 Copynumber: 2.9 Consensus size: 82
30560 CATTGAATGT
* * * **
30570 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAATTGCAAATTCC
1 AAGGGGTTGCTAAGTGCAAATTCACCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
30635 CCGAATCACTTA-TCGAA
66 CCGAATCACTTATTC-AA
*
30652 AAGGGGTTGCTAAGTGCAAATTCTCCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCAAATTCACCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
* * * *
30717 CCAAATTATTTATTCTA
66 CCGAATCACTTATTCAA
* ** ** * * *
30734 AAGGTAGTTGCTAAGTGCTGATTCCACCGTTTC-CTTGATTGTGAAAGGGGTTGCTATGTGCTGA
1 AAGG-GGTTGCTAAGTGCAAATT-CACCGAATCAC-TGATCG-AAAAGGGGTTGCTAAGTGCTGA
*
30798 TTCCCCGTATCACT
62 TTCCCCGAATCACT
30812 GAATATAAGG
Statistics
Matches: 133, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
82 74 0.56
83 18 0.14
84 11 0.08
85 30 0.23
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (82 bp):
AAGGGGTTGCTAAGTGCAAATTCACCGAATCACTGATCGAAAAGGGGTTGCTAAGTGCTGATTCC
CCGAATCACTTATTCAA
Found at i:30836 original size:41 final size:43
Alignment explanation
Indices: 30692--30846 Score: 124
Period size: 42 Copynumber: 3.7 Consensus size: 43
30682 CACTGATCGA
** ** * * *
30692 AAAGG-GGTTGCTAAGTGCTGATTCC-CCAAATTATTTATTCT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATAT
* * * *
30733 AAAGGTAGTTGCTAAGTGCTGATTCCACCGTTTCCTTGATTGT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATAT
*
30776 GAAAGG-GGTTGCTATGTGCTGATTCC-CCGTATCAC-TGAATAT
1 -AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGAATAT
* *
30818 -AAGGTGGTTGCTAGGTGCTGATTTCACCG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCG
30847 AGTAACGGTT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
40 4 0.04
41 23 0.25
42 33 0.35
43 28 0.30
44 5 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (43 bp):
AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATAT
Found at i:30846 original size:84 final size:85
Alignment explanation
Indices: 30692--30846 Score: 204
Period size: 85 Copynumber: 1.8 Consensus size: 85
30682 CACTGATCGA
* * * * *
30692 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATTATTTATTCTAAAGGTAGTTGCTAAGTGCTGATT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCACTGAATATAAAGGTAGTTGCTAAGTGCTGATT
30757 CCACCGTTTCCTTGATTGTG
66 CCACCGTTTCCTTGATTGTG
* ** * *
30777 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATAT-AAGGTGGTTGCTAGGTGCTGATT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCACTGAATATAAAGGTAGTTGCTAAGTGCTGATT
*
30841 TCACCG
66 CCACCG
30847 AGTAACGGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
84 26 0.44
85 33 0.56
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (85 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCACTGAATATAAAGGTAGTTGCTAAGTGCTGATT
CCACCGTTTCCTTGATTGTG
Found at i:33109 original size:10 final size:11
Alignment explanation
Indices: 33083--33107 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33073 CATAGATAGG
33083 TTTTAATGAAT
1 TTTTAATGAAT
33094 TTTTAATGAAT
1 TTTTAATGAAT
33105 TTT
1 TTT
33108 AAAGGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTTAATGAAT
Found at i:37325 original size:26 final size:26
Alignment explanation
Indices: 37296--37345 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
37286 AAAAATTGTT
*
37296 AAAACTCTTCTAAAAG-AAACTCAAGA
1 AAAACTCTT-AAAAAGAAAACTCAAGA
*
37322 AAAATTCTTAAAAAGAAAACTCAA
1 AAAACTCTTAAAAAGAAAACTCAA
37346 AGAGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAACTCTTAAAAAGAAAACTCAAGA
Found at i:41277 original size:101 final size:100
Alignment explanation
Indices: 41161--41380 Score: 266
Period size: 101 Copynumber: 2.2 Consensus size: 100
41151 GCACGGAATG
* * *
41161 TGTGTAGGCCACTATGTAAAAGTGAAAGTCAT-GATCACATGTGTAGTACTATGTGCAGGCTACT
1 TGTGCAGGCTACTATGT-AAAG-GAAAGT-ATCGATCACATGTGTAGTACTATGTGCAGACTACT
*
41225 ACGTGTACCAGAATGAT-A-GGTCGCATGTGTAGTACTA
63 ACGTGTACCAG-ATGATAATGGTCACATGTGTAGTACTA
** * *
41262 TGTGCAGGCTACTATGCGTACCGGATAGTTTCGATCACATGTGTAGTACTATGTGCAGACTACTA
1 TGTGCAGGCTACTAT--GTAAAGGAAAGTATCGATCACATGTGTAGTACTATGTGCAGACTACTA
* * *
41327 TGTGTATCAGATGGTAATGGTCACATGTGTAGTACTA
64 CGTGTACCAGATGATAATGGTCACATGTGTAGTACTA
41364 TGTGCAGGCTACTATGT
1 TGTGCAGGCTACTATGT
41381 GAACTGAACA
Statistics
Matches: 103, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
100 7 0.07
101 59 0.57
102 35 0.34
103 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (100 bp):
TGTGCAGGCTACTATGTAAAGGAAAGTATCGATCACATGTGTAGTACTATGTGCAGACTACTACG
TGTACCAGATGATAATGGTCACATGTGTAGTACTA
Found at i:41325 original size:51 final size:51
Alignment explanation
Indices: 41191--41381 Score: 244
Period size: 51 Copynumber: 3.8 Consensus size: 51
41181 AGTGAAAGTC
* *
41191 ATGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TG
1 ATGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTA
* * * *
41240 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTA
* * * *
41291 TTCGATCACATGTGTAGTACTATGTGCAGACTACTATGTGTATCAGATGGTA
1 AT-GATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTA
*
41343 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 ATGATCACATGTGTAGTACTATGTGCAGGCTACTATGTG
41382 AACTGAACAT
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.32
51 78 0.64
52 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (51 bp):
ATGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTA
Found at i:41550 original size:23 final size:22
Alignment explanation
Indices: 41524--41567 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
41514 AATTGACTAA
41524 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
41547 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
41568 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:44236 original size:127 final size:127
Alignment explanation
Indices: 44010--44259 Score: 437
Period size: 127 Copynumber: 2.0 Consensus size: 127
44000 ATTTCTGTCA
44010 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTATTTTAAAAGTCACTATTTGTGAATTTGTTAATT
1 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTATTTTAAAAGTCACTATTTGTGAATTTGTTAATT
* *
44075 TTTCATTTTGTTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTTGTTG
66 TTGCATTTTGGTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTTGTTG
* * *
44137 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTGTTTTAAAAGTCATTATTTGTGAATTTTTTAATT
1 TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTATTTTAAAAGTCACTATTTGTGAATTTGTTAATT
* *
44202 TTGCATTTTGGTTAAATTTTTTTTGTTCAATTTTAACTTAGCTAATTTTTCTATGTTT
66 TTGCATTTTGGTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTT
44260 TTTTCAAGTG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 116 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (127 bp):
TTCCAAGTTTTTGGCGCCGTTGTCGGGGACTATTTTAAAAGTCACTATTTGTGAATTTGTTAATT
TTGCATTTTGGTTAAATTTTTTCTGTTCAATTTTAACTTAGCTAATTTTTCAATGTTTGTTG
Found at i:47634 original size:320 final size:320
Alignment explanation
Indices: 47052--47692 Score: 1282
Period size: 320 Copynumber: 2.0 Consensus size: 320
47042 ATGTTGATTG
47052 TTTGGTACCATTTGGAAATAGTTGGTCTGTGTCACTTGGGTGATTTTGATGCATGTGAGTAATGG
1 TTTGGTACCATTTGGAAATAGTTGGTCTGTGTCACTTGGGTGATTTTGATGCATGTGAGTAATGG
47117 TCCAAATTGTAGGATTATATTAACATGGTATAGGTCAACTATGGTATGTTTTAAAATGGTAGCAA
66 TCCAAATTGTAGGATTATATTAACATGGTATAGGTCAACTATGGTATGTTTTAAAATGGTAGCAA
47182 TGTGTTCAAATATGCATAAGTTTAGGTATGTTAGTTTGATTTTGATTCAGGTGCCTATATGAAAT
131 TGTGTTCAAATATGCATAAGTTTAGGTATGTTAGTTTGATTTTGATTCAGGTGCCTATATGAAAT
47247 ATTGGTTGAATGGAATTTGTCATTTGAGTTGGTCATTTTGTGCATGTTTTGGTATGTTTTGATGC
196 ATTGGTTGAATGGAATTTGTCATTTGAGTTGGTCATTTTGTGCATGTTTTGGTATGTTTTGATGC
47312 CTTGGACAAGGGTCCTAACGGCTTGTAGGTACATGCTTGAAAAGGGTGAAGGAAATGGCT
261 CTTGGACAAGGGTCCTAACGGCTTGTAGGTACATGCTTGAAAAGGGTGAAGGAAATGGCT
47372 TTTGGTACCATTTGGAAATAGTTGGTCTGTGTCACTTGGGTGATTTTGATGCATGTGAGTAATGG
1 TTTGGTACCATTTGGAAATAGTTGGTCTGTGTCACTTGGGTGATTTTGATGCATGTGAGTAATGG
47437 TCCAAATTGTAGGATTATATTAACATGGTATAGGTCAACTATGGTATGTTTTAAAATGGTAGCAA
66 TCCAAATTGTAGGATTATATTAACATGGTATAGGTCAACTATGGTATGTTTTAAAATGGTAGCAA
47502 TGTGTTCAAATATGCATAAGTTTAGGTATGTTAGTTTGATTTTGATTCAGGTGCCTATATGAAAT
131 TGTGTTCAAATATGCATAAGTTTAGGTATGTTAGTTTGATTTTGATTCAGGTGCCTATATGAAAT
47567 ATTGGTTGAATGGAATTTGTCATTTGAGTTGGTCATTTTGTGCATGTTTTGGTATGTTTTGATGC
196 ATTGGTTGAATGGAATTTGTCATTTGAGTTGGTCATTTTGTGCATGTTTTGGTATGTTTTGATGC
47632 CTTGGACAAGGGTCCTAACGGCTTGTAGGTACATGCTTGAAAAGGGTGAAGGAAATGGCT
261 CTTGGACAAGGGTCCTAACGGCTTGTAGGTACATGCTTGAAAAGGGTGAAGGAAATGGCT
47692 T
1 T
47693 GATTTTGGCC
Statistics
Matches: 321, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 321 1.00
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.39
Consensus pattern (320 bp):
TTTGGTACCATTTGGAAATAGTTGGTCTGTGTCACTTGGGTGATTTTGATGCATGTGAGTAATGG
TCCAAATTGTAGGATTATATTAACATGGTATAGGTCAACTATGGTATGTTTTAAAATGGTAGCAA
TGTGTTCAAATATGCATAAGTTTAGGTATGTTAGTTTGATTTTGATTCAGGTGCCTATATGAAAT
ATTGGTTGAATGGAATTTGTCATTTGAGTTGGTCATTTTGTGCATGTTTTGGTATGTTTTGATGC
CTTGGACAAGGGTCCTAACGGCTTGTAGGTACATGCTTGAAAAGGGTGAAGGAAATGGCT
Found at i:47909 original size:55 final size:55
Alignment explanation
Indices: 47850--48015 Score: 128
Period size: 55 Copynumber: 3.0 Consensus size: 55
47840 GGCACACAGG
*
47850 TGTGTAAGGCCATTTCGAGCGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
1 TGTGTAAGGCCATTTCGAGAGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
* * ** * * * * **
47905 TGTGTGA-CCCAACTCAGAGAGTAACAAAGGCATGAGTCACA---GCTTG-GCACACAGG-
1 TGTGTAAGGCCATTTC-GAGAGTTAC-ACGGCTTG-G-CACACGGGCTTGTG-GC-TTGGC
*
47960 TGTGTAAGGCCATTTCGAGTGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
1 TGTGTAAGGCCATTTCGAGAGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
48015 T
1 T
48016 TGGAACACTA
Statistics
Matches: 77, Mismatches: 22, Indels: 24
0.63 0.18 0.20
Matches are distributed among these distances:
52 4 0.05
53 1 0.01
54 14 0.18
55 39 0.51
56 14 0.18
57 1 0.01
58 4 0.05
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (55 bp):
TGTGTAAGGCCATTTCGAGAGTTACACGGCTTGGCACACGGGCTTGTGGCTTGGC
Found at i:49580 original size:40 final size:40
Alignment explanation
Indices: 49530--49737 Score: 317
Period size: 40 Copynumber: 5.2 Consensus size: 40
49520 ACCGAAATGT
* *
49530 AAACAGGGGCACGCAAGTGCAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
* * * *
49570 AAGCAAGGGCACTTAAGTGCAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
49610 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
* **
49650 AAACAGGGGCACGTAAGTGTAATTAGGGGTTGCGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
* *
49690 AAATAGGGGCACGTAAGTGTAATCAGGGGTACTGAAGTAC
1 AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
49730 AAACAGGG
1 AAACAGGG
49738 TATAATTTAC
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 151 1.00
ACGTcount: A:0.35, C:0.17, G:0.33, T:0.15
Consensus pattern (40 bp):
AAACAGGGGCACGTAAGTGTAATCAGGGGTACCGAAGTAC
Found at i:49727 original size:20 final size:19
Alignment explanation
Indices: 49533--49737 Score: 115
Period size: 20 Copynumber: 10.3 Consensus size: 19
49523 GAAATGTAAA
*
49533 CAGGGGCACGCAAGTGCAAT
1 CAGGGGTACG-AAGTGCAAT
* *
49553 CAGGGGTACCGAAGTACAAG
1 CAGGGGTA-CGAAGTGCAAT
* * *
49573 CAAGGGCACTTAAGTGCAAT
1 CAGGGGTAC-GAAGTGCAAT
* *
49593 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTGCAAT
* *
49613 CAGGGGCACGTAAGTGTAAT
1 CAGGGGTACG-AAGTGCAAT
* *
49633 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTGCAAT
* *
49653 CAGGGGCACGTAAGTGTAAT
1 CAGGGGTACG-AAGTGCAAT
* * *
49673 TAGGGGTTGCGAAGTACAAAT
1 CAGGGG-TACGAAGTGC-AAT
* *
49694 -AGGGGCACGTAAGTGTAAT
1 CAGGGGTACG-AAGTGCAAT
* *
49713 CAGGGGTACTGAAGTACAAA
1 CAGGGGTAC-GAAGTGCAAT
49733 CAGGG
1 CAGGG
49738 TATAATTTAC
Statistics
Matches: 136, Mismatches: 38, Indels: 22
0.69 0.19 0.11
Matches are distributed among these distances:
19 10 0.07
20 115 0.85
21 11 0.08
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (19 bp):
CAGGGGTACGAAGTGCAAT
Found at i:52554 original size:27 final size:27
Alignment explanation
Indices: 52524--52586 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
52514 TAGGTCTGAC
* *
52524 TTAAAACATGCATTGATGCTGTCCGAA
1 TTAAAACATGCATTGATGCTATCCAAA
*
52551 TTAAAACCTGCATTGATGCTATCCAAA
1 TTAAAACATGCATTGATGCTATCCAAA
*
52578 TTATAACAT
1 TTAAAACAT
52587 ACTTAATAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (27 bp):
TTAAAACATGCATTGATGCTATCCAAA
Found at i:58323 original size:25 final size:25
Alignment explanation
Indices: 58268--58324 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
58258 ATTTTCCTCC
58268 TAAA-TTTCAATTTTATTTAATTAT
1 TAAATTTTCAATTTTATTTAATTAT
*
58292 TTAATTTTCAA-TTTATTTAATTAT
1 TAAATTTTCAATTTTATTTAATTAT
58316 TAATATTTT
1 TAA-ATTTT
58325 ATACTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TAAATTTTCAATTTTATTTAATTAT
Found at i:60599 original size:24 final size:25
Alignment explanation
Indices: 60542--60613 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
60532 AATTTTCCTC
*
60542 TTAA-ATTTTAATTTTATTTAATTAT
1 TTAATATTTTAA-TTTATTGAATTAT
*
60567 TTGAT-TTTTAATTTATTGAATTA-
1 TTAATATTTTAATTTATTGAATTAT
60590 TTAATATTTT-ATTCTAATTGAATT
1 TTAATATTTTAATT-T-ATTGAATT
60614 TTTCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.17
24 16 0.40
25 17 0.43
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (25 bp):
TTAATATTTTAATTTATTGAATTAT
Found at i:63497 original size:18 final size:18
Alignment explanation
Indices: 63474--63560 Score: 86
Period size: 18 Copynumber: 4.7 Consensus size: 18
63464 CAAATACCAA
63474 ATACCAAAATATCTAATG
1 ATACCAAAATATCTAATG
* *
63492 ATACCAAAATTTCTAATAA
1 ATACCAAAATATCTAAT-G
*
63511 ATAACCAAAATATGTAAATG
1 AT-ACCAAAATATCT-AATG
*
63531 ATACC-AAATCTCTAATG
1 ATACCAAAATATCTAATG
*
63548 TATAACAAAATAT
1 -ATACCAAAATAT
63561 TTAACAGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.07
18 26 0.47
19 10 0.18
20 12 0.22
21 3 0.05
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (18 bp):
ATACCAAAATATCTAATG
Found at i:63518 original size:38 final size:38
Alignment explanation
Indices: 63472--63577 Score: 112
Period size: 38 Copynumber: 2.8 Consensus size: 38
63462 ACCAAATACC
*
63472 AAAT-ACCAAAATATCT-AATGATACCAAAATTTCTAAT
1 AAATAACCAAAATATCTAAATGATACC-AAATCTCTAAT
*
63509 AAATAACCAAAATATGTAAATGATACCAAATCTCTAAT
1 AAATAACCAAAATATCTAAATGATACCAAATCTCTAAT
** *
63547 GTATAA-CAAAATATTTAACA-GAATACCAAAT
1 AAATAACCAAAATATCTAA-ATG-ATACCAAAT
63578 TTTTTTACTC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
37 16 0.27
38 35 0.58
39 9 0.15
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (38 bp):
AAATAACCAAAATATCTAAATGATACCAAATCTCTAAT
Found at i:78526 original size:39 final size:41
Alignment explanation
Indices: 78425--78608 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
78415 TTGAATGATG
* *
78425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
78465 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
78505 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
78544 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
78583 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
78609 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:78561 original size:79 final size:80
Alignment explanation
Indices: 78425--78608 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
78415 TTGAATGATG
*
78425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
78489 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
78504 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
78566 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
78583 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
78609 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:78631 original size:78 final size:79
Alignment explanation
Indices: 78478--78641 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
78468 GGACTAAGAT
* **
78478 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
78543 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
78557 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
78619 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
78635 CCGAAGG
1 CCGAAGG
78642 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:86545 original size:41 final size:41
Alignment explanation
Indices: 86357--86538 Score: 188
Period size: 40 Copynumber: 4.6 Consensus size: 41
86347 TTGAATGATG
* * *
86357 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
* *
86397 TCCGGACTAAGAT-CCGAAGGCA-----GCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
86432 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
86471 TCCGGGTTAAGTCCCGAAGGCAATTTGTGCGAGTTACTAATA
1 TCCGGGCTAAGTCCCGAAGGC-ATTTGTGCGAGTTACTAATA
* *
86513 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
86539 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
34 9 0.08
35 14 0.12
36 4 0.03
39 21 0.18
40 27 0.23
41 24 0.20
42 19 0.16
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:86556 original size:82 final size:79
Alignment explanation
Indices: 86419--86571 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 79
86409 TCCGAAGGCA
* ** *
86419 GCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 GCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATCC-GGTTAAATC
86484 CCGAAGGCAATTTGT
65 CCGAAGGCAATTTGT
* * *
86499 GCGAGTTACTAATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAA
1 GCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAATCCGGTTAAA
*
86563 TTCCGAAGG
63 TCCCGAAGG
86572 TACGTGATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
80 12 0.19
81 25 0.40
82 25 0.40
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
GCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATCCGGTTAAATCC
CGAAGGCAATTTGT
Done.