Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002089.1 Hibiscus syriacus cultivar Beakdansim tig00004262_pilon, 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: 110938
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:530 original size:20 final size:20
Alignment explanation
Indices: 485--530 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
475 TTAACTCATT
*
485 TATATTGAACAATAATGGTA
1 TATATTGAACAATAATGATA
**
505 GCTATTGAACAATAATGATA
1 TATATTGAACAATAATGATA
525 TATATT
1 TATATT
531 ATTATAGATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (20 bp):
TATATTGAACAATAATGATA
Found at i:2328 original size:29 final size:29
Alignment explanation
Indices: 2286--2344 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2276 ATTTTCACCT
2286 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
*
2315 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
2344 A
1 A
2345 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:6951 original size:29 final size:27
Alignment explanation
Indices: 6918--6974 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 27
6908 ATTTTCACCT
*
6918 AACTAAATTGATGTAAGTAATGACATCAA
1 AACTAAATTGATGT-AGCAA-GACATCAA
6947 AACTAAATTGATGTAGCAAGACATCAA
1 AACTAAATTGATGTAGCAAGACATCAA
6974 A
1 A
6975 TTAATTTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.33
28 4 0.15
29 14 0.52
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (27 bp):
AACTAAATTGATGTAGCAAGACATCAA
Found at i:9157 original size:31 final size:31
Alignment explanation
Indices: 9119--9185 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
9109 AGATGTATTT
*
9119 ATTATGAAAGTAACAGCGTACAAGACAACAA
1 ATTATGAAAGTAACAGCGGACAAGACAACAA
9150 ATTATGAAAGTAACAGCGGACAAGACAACAA
1 ATTATGAAAGTAACAGCGGACAAGACAACAA
9181 ATTAT
1 ATTAT
9186 ATAGGCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (31 bp):
ATTATGAAAGTAACAGCGGACAAGACAACAA
Found at i:10943 original size:3 final size:3
Alignment explanation
Indices: 10935--10978 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
10925 TCTCGAAAAA
* * * *
10935 TAT TAT TAT AAT AAT TAT TAT TAT TTT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
10979 CATAATACAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:11061 original size:20 final size:20
Alignment explanation
Indices: 11032--11075 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11022 GCCCACCAAT
11032 CAAC-CCCAATACACCAACC
1 CAACACCCAATACACCAACC
* *
11051 CAACACCCAATACACTAGCC
1 CAACACCCAATACACCAACC
11071 CAACA
1 CAACA
11076 ATTAAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.43, C:0.48, G:0.02, T:0.07
Consensus pattern (20 bp):
CAACACCCAATACACCAACC
Found at i:12398 original size:59 final size:59
Alignment explanation
Indices: 12324--12476 Score: 202
Period size: 59 Copynumber: 2.6 Consensus size: 59
12314 TGTTAATACC
* *
12324 ATTTTAATCCTTAAGTTTTTGTTTTTGCTATTTTAGTCCTTTAAATGTATGTATTTT-CT
1 ATTTTAGTCCTTAAGTTTTTGTTTTTGCTATTTTAGTCCTTTAAATGTATAT-TTTTGCT
* * * *
12383 A-TTTAGTCCTTTAAGTTTCTATTTTTGATATTTTAGTCCTTTAAATGTATATTTTTGTT
1 ATTTTAGTCC-TTAAGTTTTTGTTTTTGCTATTTTAGTCCTTTAAATGTATATTTTTGCT
*
12442 ATTTTAGTCCCTTAAGTTTTAGTTTTTGCTATTTT
1 ATTTTAGT-CCTTAAGTTTTTGTTTTTGCTATTTT
12477 GGTCATCAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
58 11 0.14
59 41 0.51
60 26 0.32
61 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.59
Consensus pattern (59 bp):
ATTTTAGTCCTTAAGTTTTTGTTTTTGCTATTTTAGTCCTTTAAATGTATATTTTTGCT
Found at i:12420 original size:30 final size:30
Alignment explanation
Indices: 12324--12502 Score: 154
Period size: 30 Copynumber: 6.1 Consensus size: 30
12314 TGTTAATACC
* * *
12324 ATTTTAATCC-TTAAGTTTTTGTTTTTGCT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCT
* *
12353 ATTTTAGTCCTTTAAATGTATGTA-TTTT-CT
1 ATTTTAGTCCTTT-AA-GTTTCTATTTTTGCT
*
12383 A-TTTAGTCCTTTAAGTTTCTATTTTTGAT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCT
* * * *
12412 ATTTTAGTCCTTTAAATGTATATTTTTGTT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCT
*
12442 ATTTTAGTCCCTTAAGTTT-TAGTTTTTGCT
1 ATTTTAGTCCTTTAAGTTTCTA-TTTTTGCT
* * * *
12472 ATTTTGGT-CATCAACTTTCTATTTTTGCT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCT
12501 AT
1 AT
12503 GTTGGTCATC
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.04
28 6 0.05
29 41 0.33
30 61 0.50
31 6 0.05
32 4 0.03
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAGTTTCTATTTTTGCT
Found at i:12499 original size:29 final size:29
Alignment explanation
Indices: 12464--12520 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
12454 TAAGTTTTAG
*
12464 TTTTTGCTATTTTGGTCATCAACTTTCTA
1 TTTTTGCTATGTTGGTCATCAACTTTCTA
*
12493 TTTTTGCTATGTTGGTCATCAAGTTTCT
1 TTTTTGCTATGTTGGTCATCAACTTTCT
12521 GTTAATCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (29 bp):
TTTTTGCTATGTTGGTCATCAACTTTCTA
Found at i:12531 original size:29 final size:29
Alignment explanation
Indices: 12470--12531 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
12460 TTAGTTTTTG
* ** *
12470 CTATTTTGGTCATCAACTTTCTATTTTTG
1 CTATGTTGGTCATCAACTTTCTATTAATC
* *
12499 CTATGTTGGTCATCAAGTTTCTGTTAATC
1 CTATGTTGGTCATCAACTTTCTATTAATC
12528 CTAT
1 CTAT
12532 TTCGGTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.50
Consensus pattern (29 bp):
CTATGTTGGTCATCAACTTTCTATTAATC
Found at i:12538 original size:29 final size:28
Alignment explanation
Indices: 12474--12538 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
12464 TTTTTGCTAT
** *
12474 TTTGGTCATCAACTTTCTATTTTTGCTA
1 TTTGGTCATCAACTTTCTATTAATCCTA
* *
12502 TGTTGGTCATCAAGTTTCTGTTAATCCTA
1 T-TTGGTCATCAACTTTCTATTAATCCTA
12531 TTTCGGTC
1 TTT-GGTC
12539 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.49
Consensus pattern (28 bp):
TTTGGTCATCAACTTTCTATTAATCCTA
Found at i:17434 original size:60 final size:59
Alignment explanation
Indices: 17265--17438 Score: 156
Period size: 60 Copynumber: 2.9 Consensus size: 59
17255 TATATGTCCC
* * * * * * *
17265 CAAATTATGACCCTTATTTTAAATTAGTCCTTAAACTTTTAAATATTTCAATTCCATCCAT
1 CAAA-TATGACTCTCATTCTAAATTAGTCC-TAAACTTTTGAATCTTCCAATTTCATCCAT
* * * *
17326 -AAGATATGATTCTCATTCTAAATTACTCGTTAAACTTTTG-AGCATTCCAATTTCATCC-T
1 CAA-ATATGACTCTCATTCTAAATTAGTC-CTAAACTTTTGAATC-TTCCAATTTCATCCAT
*
17385 CAAACTATGACTCTCATTCTAAATTAGTTCCTAAAATTTTGAATCTTCCAATTT
1 CAAA-TATGACTCTCATTCTAAATTAG-TCCTAAACTTTTGAATCTTCCAATTT
17439 GACCCACATA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
59 3 0.03
60 82 0.91
61 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (59 bp):
CAAATATGACTCTCATTCTAAATTAGTCCTAAACTTTTGAATCTTCCAATTTCATCCAT
Found at i:19077 original size:23 final size:22
Alignment explanation
Indices: 19049--19092 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19039 ACGCCTAATA
*
19049 AAATTTTAAATATTAATATTTTT
1 AAATTTCAAATATTAA-ATTTTT
*
19072 AAATTTCAATTATTAAATTTT
1 AAATTTCAAATATTAAATTTT
19093 ATGTGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTCAAATATTAAATTTTT
Found at i:25286 original size:20 final size:20
Alignment explanation
Indices: 25261--25301 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25251 GCTTGGTACA
*
25261 ACAAAATCAGATTACAAATT
1 ACAAAATCAGAGTACAAATT
*
25281 ACAAAATCAGAGTACCAATT
1 ACAAAATCAGAGTACAAATT
25301 A
1 A
25302 TCACATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (20 bp):
ACAAAATCAGAGTACAAATT
Found at i:30503 original size:43 final size:43
Alignment explanation
Indices: 30391--30718 Score: 287
Period size: 42 Copynumber: 7.7 Consensus size: 43
30381 ATGGTAATTA
* *
30391 GCGGCGTTTGTTTCCAAAAACGCCGCTATA-ATTCTGACGTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGA-TCTGACCTTTT
* * * * *
30434 ACGGTGTTTGT-TCTAAAAACGCTGCTACAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
30476 GCGGCGTTTGTATCCAAAAACACTGCTATAGATCTGACATTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
30519 ACGGCGTTTGT-TCCAAAAACGCCGTTATAGATCTCGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTT
** * * *
30562 GCGGCGTTTGTA-CTGAAAACACCGCTACATATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
30604 GCGGCGTTTGTAT-AAAAAACGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
** * ** * * *
30646 GCGGTAATTT-TA--AAAAAACGCCATTATATATCTCAACCTTTG
1 GCGG-CGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTT
* *
30688 GCGGCGTTTGTTTCC-AAAACGCCGCTGTAGA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGA
30719 CACCCGTTTT
Statistics
Matches: 227, Mismatches: 48, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
41 21 0.09
42 112 0.49
43 94 0.41
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:30537 original size:85 final size:84
Alignment explanation
Indices: 30391--30649 Score: 306
Period size: 85 Copynumber: 3.0 Consensus size: 84
30381 ATGGTAATTA
* * * * *
30391 GCGGCGTTTGTTTCCAAAAACGCCGCTATAATTCTGACGTTTTACGGTGTTTGTTCTAAAAACGC
1 GCGGCGTTTGTATCCAAAAACACCGCTATAA-TCTGACATTTTACGGCGTTTGTTCAAAAAACGC
* *
30456 TGCTACAGATCTGACCTTTT
65 CGCTATAGATCTGACCTTTT
* *
30476 GCGGCGTTTGTATCCAAAAACACTGCTATAGATCTGACATTTTACGGCGTTTGTTCCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACACCGCTATA-ATCTGACATTTTACGGCGTTTGTTCAAAAAACGC
* *
30541 CGTTATAGATCTCGATCTTTT
65 CGCTATAGATCT-GACCTTTT
** * * *
30562 GCGGCGTTTGTA-CTGAAAACACCGCTACATATCTGACCTTTTGCGGCGTTTGTAT-AAAAAACG
1 GCGGCGTTTGTATCCAAAAACACCGCTATA-ATCTGACATTTTACGGCGTTTGT-TCAAAAAACG
*
30625 CCGCTATAGATCTGACTTTTT
64 CCGCTATAGATCTGACCTTTT
30646 GCGG
1 GCGG
30650 TAATTTTAAA
Statistics
Matches: 150, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
84 10 0.07
85 119 0.79
86 21 0.14
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (84 bp):
GCGGCGTTTGTATCCAAAAACACCGCTATAATCTGACATTTTACGGCGTTTGTTCAAAAAACGCC
GCTATAGATCTGACCTTTT
Found at i:30662 original size:41 final size:42
Alignment explanation
Indices: 30448--30667 Score: 151
Period size: 43 Copynumber: 5.2 Consensus size: 42
30438 TGTTTGTTCT
* ** *
30448 AAAAACGCTGCTACAGATCTGACCTTTTGCGGCGTTTGTATCC
1 AAAAACGCCGCTACAGATCTGACCTTTTGCGGAATTTGTAT-A
* * * * * ** *
30491 AAAAACACTGCTATAGATCTGACATTTTACGGCGTTTGT-TCC
1 AAAAACGCCGCTACAGATCTGACCTTTTGCGGAATTTGTAT-A
* * * **
30533 AAAAACGCCGTTATAGATCTCGATCTTTTGCGGCGTTTGTACT-
1 AAAAACGCCGCTACAGATCT-GACCTTTTGCGGAATTTGTA-TA
* * * **
30576 GAAAACACCGCTACATATCTGACCTTTTGCGGCGTTTGTATA
1 AAAAACGCCGCTACAGATCTGACCTTTTGCGGAATTTGTATA
* *
30618 AAAAACGCCGCTATAGATCTGACTTTTTGCGGTAATTT-TA-A
1 AAAAACGCCGCTACAGATCTGACCTTTTGCGG-AATTTGTATA
30659 AAAAACGCC
1 AAAAACGCC
30668 ATTATATATC
Statistics
Matches: 149, Mismatches: 23, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
41 11 0.07
42 68 0.46
43 69 0.46
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (42 bp):
AAAAACGCCGCTACAGATCTGACCTTTTGCGGAATTTGTATA
Found at i:33240 original size:15 final size:16
Alignment explanation
Indices: 33197--33240 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
33187 GCAGATCAGC
33197 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
*
33214 TTTTTCTT-AAAATTA
1 TTTTTCTTAAAAATGA
33229 TTTTT-TTAAAAA
1 TTTTTCTTAAAAA
33241 GATAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 15 0.60
16 4 0.16
17 4 0.16
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:44282 original size:10 final size:10
Alignment explanation
Indices: 44267--44332 Score: 62
Period size: 10 Copynumber: 6.4 Consensus size: 10
44257 TGCTTGAAGA
44267 AAAAAAAAAG
1 AAAAAAAAAG
44277 AAAAAAAAAG
1 AAAAAAAAAG
* **
44287 GAAAAAATGG
1 AAAAAAAAAG
44297 AAAAGAAAAA-
1 AAAA-AAAAAG
44307 AAATGAAAAAAG
1 AAA--AAAAAAG
*
44319 AAAAAAAATG
1 AAAAAAAAAG
44329 AAAA
1 AAAA
44333 GAGAAAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 33 0.73
11 8 0.18
12 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:44300 original size:15 final size:15
Alignment explanation
Indices: 44281--44324 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
44271 AAAAAGAAAA
44281 AAAAAGGAAAAAATG
1 AAAAAGGAAAAAATG
* *
44296 GAAAAGAAAAAAAATG
1 AAAAAG-GAAAAAATG
*
44312 AAAAAAGAAAAAA
1 AAAAAGGAAAAAA
44325 AATGAAAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAAGGAAAAAATG
Found at i:44316 original size:32 final size:32
Alignment explanation
Indices: 44267--44340 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 32
44257 TGCTTGAAGA
* *
44267 AAAAAAAAAGAAAAAAAAAGGAAAAAATGGAAAAG
1 AAAAAAAATGAAAAAAGAA--AAAAAAT-GAAAAG
44302 AAAAAAAATGAAAAAAGAAAAAAAATGAAAAG
1 AAAAAAAATGAAAAAAGAAAAAAAATGAAAAG
*
44334 AGAAAAA
1 AAAAAAA
44341 TGAGGGTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 12 0.33
33 7 0.19
35 17 0.47
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (32 bp):
AAAAAAAATGAAAAAAGAAAAAAAATGAAAAG
Found at i:44325 original size:17 final size:17
Alignment explanation
Indices: 44267--44340 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
44257 TGCTTGAAGA
* *
44267 AAAAAAAAAGAAAAAAA
1 AAAAAAAATGAAAAAAG
*
44284 AAGGAAAAAATG-GAAAAG
1 AA--AAAAAATGAAAAAAG
44302 AAAAAAAATGAAAAAAG
1 AAAAAAAATGAAAAAAG
*
44319 AAAAAAAATGAAAAGAG
1 AAAAAAAATGAAAAAAG
44336 AAAAA
1 AAAAA
44341 TGAGGGTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.16
17 28 0.57
18 6 0.12
19 7 0.14
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
AAAAAAAATGAAAAAAG
Found at i:44325 original size:25 final size:26
Alignment explanation
Indices: 44261--44325 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 26
44251 GTACTATGCT
*
44261 TGAAGAAA-AAAAAAAGAAAAAAAAA
1 TGAAAAAAGAAAAAAAGAAAAAAAAA
* *
44286 GGAAAAAATG--GAAAAG-AAAAAAAA
1 TGAAAAAA-GAAAAAAAGAAAAAAAAA
44310 TGAAAAAAGAAAAAAA
1 TGAAAAAAGAAAAAAA
44326 ATGAAAAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
23 1 0.03
24 15 0.48
25 15 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (26 bp):
TGAAAAAAGAAAAAAAGAAAAAAAAA
Found at i:45565 original size:91 final size:91
Alignment explanation
Indices: 45448--45619 Score: 274
Period size: 91 Copynumber: 1.9 Consensus size: 91
45438 AAAGAGATGG
* *
45448 ATCAACATTTCCAATGGAAAGTTCATAATAAGAAGAACTCATCCAATGA-GAGAGAATAAGTTCA
1 ATCAACATTTCCAATGGAAAGCTCATAATAAGAAGAACTCATCCAATGAGGA-AGAAGAAGTTCA
45512 TAATGAGAAGAACTTGTCCAACTTTGC
65 TAATGAGAAGAACTTGTCCAACTTTGC
* * *
45539 ATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAAAGCTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCAT
*
45604 AATGAGAAGAGCTTGT
66 AATGAGAAGAACTTGT
45620 TCGACCTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 72 0.97
92 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (91 bp):
ATCAACATTTCCAATGGAAAGCTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTCCAACTTTGC
Found at i:45770 original size:331 final size:331
Alignment explanation
Indices: 45209--45952 Score: 1059
Period size: 331 Copynumber: 2.2 Consensus size: 331
45199 GGAGGTGAAC
* *
45209 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGTAGAAGAAGTTCATA
1 CAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCATA
* * * *
45274 ATGAGAAGAGCCTATTCGACCTATCACTAGATTTACAGCATTTCGAATTAGTGACACCTCGCTTG
65 ATGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAGCATTTCGAATCAGTGACACCTCGCTTG
* *
45339 AGGAATTGACATTTTCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAA
130 AGGAATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAA
* *
45404 TGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGA-TCAACATTTCCAATGGAAA
195 TGAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGAT-GACTCAACATTTCCAATGGAAA
* * *
45468 GTTCATAATAAGAAGAACTCATCCAATGA-GAGAGAATAAGTTCATAATGAGAAGAACTTGTCCA
259 GTTCATAATAAGAAGAACTCATCCAACGAGGA-AGAAGAAGTTCATAATGAGAAGAACATGTCCA
*
45532 ACTTTGCAT
323 ACCTTGCAT
* *
45541 CAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAA
1 CAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAA
* *
45606 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCAC-GACATTTCGAATCAGTGACGCCTCG-TTA
66 TGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAG-CATTTCGAATCAGTGACACCTCGCTT-
*
45669 GAAGG-ATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCAT
129 G-AGGAATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCAT
* * ** * * *
45733 AATGAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAATAGGTGACTCAACATTTTTAGTTGAG
193 AATGAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGACTCAACATTTCCAATGGAA
* *
45798 AGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTTCA
258 AGTTCATAATAAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTCCA
45863 ACCTTGCAT
323 ACCTTGCAT
* ** * * * *
45872 TAGTA-TTTCCAGGGAAGAGTTCATAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 CAACATTTTCAATGG-AGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATA
*
45936 ATGAGAAGAACTTGTTC
65 ATGAGAAGAGCTTGTTC
45953 AATCCAATGC
Statistics
Matches: 368, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
330 12 0.03
331 311 0.85
332 45 0.12
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (331 bp):
CAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAGCATTTCGAATCAGTGACACCTCGCTTGA
GGAATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAAT
GAAAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGACTCAACATTTCCAATGGAAAGT
TCATAATAAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTCCAACC
TTGCAT
Found at i:45861 original size:20 final size:20
Alignment explanation
Indices: 45799--45862 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
45789 TTAGTTGAGA
45799 GTTCATAATGAGAAGAAC-T
1 GTTCATAATGAGAAGAACAT
** * * * *
45818 CATC-CAACGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACAT
45838 GTTCATAATGAGAAGAACAT
1 GTTCATAATGAGAAGAACAT
45858 GTTCA
1 GTTCA
45863 ACCTTGCATT
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 14 0.47
21 4 0.13
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACAT
Found at i:46122 original size:3 final size:3
Alignment explanation
Indices: 46116--46161 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
46106 GTCAAAAAAA
*
46116 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46162 ATACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:46751 original size:14 final size:15
Alignment explanation
Indices: 46732--46764 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46722 ATTAGCAAGC
46732 AAAAAAC-CCAAAGG
1 AAAAAACACCAAAGG
*
46746 AAAAAACACGAAAGG
1 AAAAAACACCAAAGG
46761 AAAA
1 AAAA
46765 CATGGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAACACCAAAGG
Found at i:48630 original size:15 final size:16
Alignment explanation
Indices: 48595--48639 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
48585 GCAAACCAGC
48595 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
* *
48612 TTTTTCTTAAAATTGT
1 TTTTTCTTAAAAATGA
*
48628 TTTTTTTTAAAA
1 TTTTTCTTAAAA
48640 GACGATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:49788 original size:41 final size:41
Alignment explanation
Indices: 49743--49877 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
49733 TGTTTATTGA
*
49743 AAAAACACCACTATAGGTTAACCCTATTGCGACATTTGTAT
1 AAAAACGCCACTATAGGTTAACCCTATTGCGACATTTGTAT
* * * ** * * *
49784 AAAAACGCCGCTAAAGTTCTAA-TTTATTGCGGCGTTTAT-T
1 AAAAACGCCACTATAGGT-TAACCCTATTGCGACATTTGTAT
* * * *
49824 GAAAAATGCCACTATAGGTGAACCCTATTACGTCATTTGTAT
1 -AAAAACGCCACTATAGGTTAACCCTATTGCGACATTTGTAT
49866 AAAAAC-CCACTA
1 AAAAACGCCACTA
49878 AAGTACTAAT
Statistics
Matches: 69, Mismatches: 21, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
40 9 0.13
41 56 0.81
42 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (41 bp):
AAAAACGCCACTATAGGTTAACCCTATTGCGACATTTGTAT
Found at i:49797 original size:83 final size:83
Alignment explanation
Indices: 49644--50047 Score: 401
Period size: 82 Copynumber: 4.9 Consensus size: 83
49634 ATTCCAACAA
* * * * * * *
49644 TTGCGACGTTTATTTAAAAAACACCACTATAGGTAAACACTATTGCGATGTTTGTATAAAAATGC
1 TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAAAAACGC
*
49709 AGCTAAAGTTATAATCTG
66 CGCTAAAGTTATAATCTG
* * * * *
49727 TTGTGGTGTTTATTGAAAAAACACCACTATAGGTTAACCCTATTGCGACATTTGTATAAAAACGC
1 TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAAAAACGC
* * *
49792 CGCTAAAGTTCTAATTTA
66 CGCTAAAGTTATAATCTG
* * * *
49810 TTGCGGCGTTTATTG-AAAAATGCCACTATAGGTGAACCCTATTACGTCATTTGTATAAAAAC-C
1 TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAAAAACGC
*
49873 CACTAAAG-TACTAATCTG
66 CGCTAAAGTTA-TAATCTG
* * * * * * *
49891 TTACGACGTTTATTGAAAAAACGCCACTATAGATGGA-CCTATTACGGCGTTTGTATAAAAATGC
1 TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAAAAACGC
*
49955 CGCTAAAG-TA-AGTCTTTG
66 CGCTAAAGTTATAATC--TG
* * * * *
49973 ATGCGGTGTTTATCG-AAAAACGCCACTATAGATGAACCCTATTGCGGCGTTTGTA-AAGAAACG
1 TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAA-AAACG
*
50036 CCGTTAAAGTTA
65 CCGCTAAAGTTA
50048 CCATTTTGTG
Statistics
Matches: 270, Mismatches: 43, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
80 4 0.01
81 70 0.26
82 111 0.41
83 85 0.31
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (83 bp):
TTGCGGCGTTTATTGAAAAAACGCCACTATAGGTGAACCCTATTGCGACGTTTGTATAAAAACGC
CGCTAAAGTTATAATCTG
Found at i:50011 original size:163 final size:164
Alignment explanation
Indices: 49694--50015 Score: 393
Period size: 163 Copynumber: 2.0 Consensus size: 164
49684 TATTGCGATG
** ** **
49694 TTTGTATAAAAATGCAGCTAAAGTTATAATCTGTTGTGGTGTTTATTGAAAAAACACCACTATAG
1 TTTGTATAAAAACCCAGCTAAAGTTATAATCTGTTACGACGTTTATTGAAAAAACACCACTATAG
* * * * *
49759 GTTAACCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTTCTAATTTATTGCGGCGTTTATT
66 ATGAACCCTATTACGACATTTGTATAAAAACGCCGCTAAAGTTCT-ATTGATTGCGGCGTTTATC
* *
49824 GAAAAATGCCACTATAGGTGAACCCTATTACGTCA
130 GAAAAACGCCACTATAGATGAACCCTATTACGTCA
*
49859 TTTGTATAAAAACCCA-CTAAAG-TACTAATCTGTTACGACGTTTATTGAAAAAACGCCACTATA
1 TTTGTATAAAAACCCAGCTAAAGTTA-TAATCTGTTACGACGTTTATTGAAAAAACACCACTATA
* * * * *
49922 GATGGA-CCTATTACGGCGTTTGTATAAAAATGCCGCTAAAGTAAGTCT-TTGA-TGCGGTGTTT
65 GATGAACCCTATTACGACATTTGTATAAAAACGCCGCTAAAGT---TCTATTGATTGCGGCGTTT
49984 ATCGAAAAACGCCACTATAGATGAACCCTATT
127 ATCGAAAAACGCCACTATAGATGAACCCTATT
50016 GCGGCGTTTG
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
163 72 0.54
164 45 0.34
165 14 0.10
166 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (164 bp):
TTTGTATAAAAACCCAGCTAAAGTTATAATCTGTTACGACGTTTATTGAAAAAACACCACTATAG
ATGAACCCTATTACGACATTTGTATAAAAACGCCGCTAAAGTTCTATTGATTGCGGCGTTTATCG
AAAAACGCCACTATAGATGAACCCTATTACGTCA
Found at i:50242 original size:20 final size:20
Alignment explanation
Indices: 50219--50316 Score: 65
Period size: 20 Copynumber: 4.7 Consensus size: 20
50209 AGATAAAGAA
*
50219 AATTTAGATAAATTAAAAAT
1 AATTTAAATAAATTAAAAAT
*
50239 AATTTAAAT-AATTTAAAAT
1 AATTTAAATAAATTAAAAAT
* * *
50258 AGTTATTAA-AAATAAAGAATATT
1 AATT-TAAATAAATTAA-AA-A-T
*
50281 CAATATAAATAATTATTAAAAAT
1 -AATTTAAATAA--ATTAAAAAT
50304 AATTTAAATAAAT
1 AATTTAAATAAAT
50317 ATATTTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 18
0.67 0.13 0.21
Matches are distributed among these distances:
19 12 0.21
20 17 0.29
21 2 0.03
22 11 0.19
23 5 0.09
24 5 0.09
25 2 0.03
26 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATTAAAAAT
Found at i:50377 original size:22 final size:21
Alignment explanation
Indices: 50352--50422 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
50342 AAAATGTCTG
*
50352 TTAACATATATTAAATAATTTT
1 TTAA-ATATATTAAAGAATTTT
*
50374 TTAATATATTTTAAAGAATTGTT
1 TTAA-ATATATTAAAGAATT-TT
50397 TTAGAATGAATATTAAAGAATTTT
1 TTA-AAT--ATATTAAAGAATTTT
50421 TT
1 TT
50423 TATTATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 17 0.41
23 7 0.17
24 5 0.12
25 12 0.29
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (21 bp):
TTAAATATATTAAAGAATTTT
Found at i:50561 original size:25 final size:26
Alignment explanation
Indices: 50512--50561 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
50502 ACTTCAAATA
50512 TGACAATAATTAAATTGTCACTTTTG
1 TGACAATAATTAAATTGTCACTTTTG
50538 TGACAATAA-TAAGA-TGTCACTTTT
1 TGACAATAATTAA-ATTGTCACTTTT
50562 AGTGTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (26 bp):
TGACAATAATTAAATTGTCACTTTTG
Found at i:52016 original size:18 final size:19
Alignment explanation
Indices: 51973--52024 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
51963 GGGTTAGAAA
*
51973 TAAGTTG-TAATTAGTTGT
1 TAAGTTGTTAATTTGTTGT
51991 T-AGTTTGTTAATTTGTT-T
1 TAAG-TTGTTAATTTGTTGT
52009 TAAGTTGTTATATTTG
1 TAAGTTGTTA-ATTTG
52025 AGCTATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 12 0.41
19 15 0.52
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (19 bp):
TAAGTTGTTAATTTGTTGT
Found at i:52468 original size:23 final size:23
Alignment explanation
Indices: 52422--52494 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
52412 AGAATAATTA
*
52422 TGTCTTTGTGACATG--T-TCTC
1 TGTCTTTATGACATGTTTATCTC
52442 TGTCTTTAT-AGCATGTTTATCTC
1 TGTCTTTATGA-CATGTTTATCTC
* *
52465 TGTCTTTGTGACATGTTTTTCTC
1 TGTCTTTATGACATGTTTATCTC
52488 TGTCTTT
1 TGTCTTT
52495 TGGTAGCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.02
20 12 0.27
22 1 0.02
23 30 0.67
24 1 0.02
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (23 bp):
TGTCTTTATGACATGTTTATCTC
Found at i:53618 original size:3 final size:3
Alignment explanation
Indices: 53612--53660 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
53602 TCTCATCATA
53612 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53659 AA
1 AA
53661 AAGATAACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56668 original size:26 final size:26
Alignment explanation
Indices: 56639--56708 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
56629 CAAAAACCAA
*
56639 TCCCAGGCCACCGCCGTTTCGTCCAC
1 TCCCAGGCCACCACCGTTTCGTCCAC
56665 TCCCAGGCCACCACCGTTTCGTCCAC
1 TCCCAGGCCACCACCGTTTCGTCCAC
56691 TCCCAGGCCACCACCGTT
1 TCCCAGGCCACCACCGTT
56709 GATACCAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.14, C:0.50, G:0.17, T:0.19
Consensus pattern (26 bp):
TCCCAGGCCACCACCGTTTCGTCCAC
Found at i:57032 original size:14 final size:13
Alignment explanation
Indices: 57005--57029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56995 AAAAGATTGA
57005 AAAAATAAAAAAT
1 AAAAATAAAAAAT
57018 AAAAATAAAAAA
1 AAAAATAAAAAA
57030 ATATTTGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:68439 original size:23 final size:24
Alignment explanation
Indices: 68392--68441 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
68382 GCCATTTTTG
* *
68392 TGTCAATTTAAAACCTGCAAGTGTT
1 TGTCAATTTAAAA-CGGCAAATGTT
68417 TGTCAATTTAAAA-GGCAAATGTT
1 TGTCAATTTAAAACGGCAAATGTT
68440 TG
1 TG
68442 ATCTTGTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
25 13 0.57
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (24 bp):
TGTCAATTTAAAACGGCAAATGTT
Found at i:69492 original size:15 final size:16
Alignment explanation
Indices: 69474--69504 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
69464 GGATAATTTT
69474 TTTAAAAA-TAAATTA
1 TTTAAAAAGTAAATTA
69489 TTTAAAAAGTAAATTA
1 TTTAAAAAGTAAATTA
69505 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTAAAAAGTAAATTA
Found at i:74174 original size:2 final size:2
Alignment explanation
Indices: 74167--74193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
74157 TGATTTCTTT
74167 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
74194 GAAAATTCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75173 original size:23 final size:23
Alignment explanation
Indices: 75118--75202 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 23
75108 AACAATTATG
* *
75118 GGAATTATCTTTTGCAATTTATTG
1 GGAATTATCTTTAGCAATTT-TTA
* **
75142 GGAACTATCTTTAGTGATTTTTA
1 GGAATTATCTTTAGCAATTTTTA
75165 GGAATTATCTTT-GCAATTTTTTA
1 GGAATTATCTTTAGCAA-TTTTTA
75188 GGAATTATCTCTTAG
1 GGAATTATCT-TTAG
75203 GACTTTTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.04
23 29 0.58
24 18 0.36
25 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.48
Consensus pattern (23 bp):
GGAATTATCTTTAGCAATTTTTA
Found at i:75197 original size:46 final size:47
Alignment explanation
Indices: 75118--75212 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 47
75108 AACAATTATG
* *
75118 GGAATTATCTTTTGCAATTTATTGGGAACTATCT-TTAGTGATTTTTA
1 GGAATTATCTTTTGCAATTTATTAGGAACTATCTCTTAG-GACTTTTA
* *
75165 GGAATTATC-TTTGCAATTTTTTAGGAATTATCTCTTAGGACTTTTA
1 GGAATTATCTTTTGCAATTTATTAGGAACTATCTCTTAGGACTTTTA
75211 GG
1 GG
75213 GTTTTTGAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
46 30 0.70
47 13 0.30
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.47
Consensus pattern (47 bp):
GGAATTATCTTTTGCAATTTATTAGGAACTATCTCTTAGGACTTTTA
Found at i:78753 original size:40 final size:38
Alignment explanation
Indices: 78680--78760 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 38
78670 TTTGAGGGAT
*
78680 CAAAGATGAAATTTCCATGTGCAGAGTTGGCCACCTAC
1 CAAAGATGAAATTTCCATGTGCAGAGTTGGCCACCAAC
*
78718 CAAAGATGAATTTTCTCATGTGTACA-AGTTGGCCACCAAC
1 CAAAGATGAAATTTC-CATGTG--CAGAGTTGGCCACCAAC
78758 CAA
1 CAA
78761 CTTGTCAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 14 0.37
39 6 0.16
40 16 0.42
41 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (38 bp):
CAAAGATGAAATTTCCATGTGCAGAGTTGGCCACCAAC
Found at i:78790 original size:17 final size:17
Alignment explanation
Indices: 78757--78790 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
78747 TGGCCACCAA
* *
78757 CCAACTTGTCAACTTTG
1 CCAACTTGCCAAATTTG
78774 CCAACTTGCCAAATTTG
1 CCAACTTGCCAAATTTG
78791 ACAATTTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (17 bp):
CCAACTTGCCAAATTTG
Found at i:83334 original size:32 final size:32
Alignment explanation
Indices: 83293--83366 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
83283 TATAGTTGAG
83293 TTTTAGGGACTAAACTTATAAATAACCTAATA
1 TTTTAGGGACTAAACTTATAAATAACCTAATA
*
83325 TTTTAGGGACTAAACTTATAAATAATCTAATA
1 TTTTAGGGACTAAACTTATAAATAACCTAATA
83357 TTTTAGGGAC
1 TTTTAGGGAC
83367 CAAAGATGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (32 bp):
TTTTAGGGACTAAACTTATAAATAACCTAATA
Found at i:89859 original size:22 final size:21
Alignment explanation
Indices: 89834--89889 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
89824 GTAATTTGAT
*
89834 ATATTTTTATTATATATTTAAA
1 ATATTTTTATTATA-AATTAAA
* *
89856 ATATTTTATATT-TAAATTGAT
1 ATATTTT-TATTATAAATTAAA
89877 ATATTTTTATTAT
1 ATATTTTTATTAT
89890 TCTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 9 0.31
23 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATTTTTATTATAAATTAAA
Found at i:89865 original size:16 final size:16
Alignment explanation
Indices: 89841--89871 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89831 GATATATTTT
89841 TATTATATATTTAAAA
1 TATTATATATTTAAAA
*
89857 TATTTTATATTTAAA
1 TATTATATATTTAAA
89872 TTGATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATATATTTAAAA
Found at i:96705 original size:36 final size:35
Alignment explanation
Indices: 96665--96740 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 35
96655 AAAATACTTT
96665 AATTTAGGGTTTAGAATATAATTAAAGTATTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTA-TTTTGG
96701 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
96736 AATTT
1 AATTT
96741 TGAACATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 11 0.28
36 29 0.73
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:104181 original size:2 final size:2
Alignment explanation
Indices: 104174--104202 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
104164 AATTTTCTTT
104174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104203 TCTTTAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105212 original size:185 final size:183
Alignment explanation
Indices: 104925--105587 Score: 661
Period size: 185 Copynumber: 3.5 Consensus size: 183
104915 TACATATTAT
* * * *
104925 ATTGCGCCTAAAATGTTACCAAAGTTTAAGGTGATGAAGATTTTGAATTTCCCACGATAACAAAA
1 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
* * * * *
104990 TAAGTTTAAAATAAAAAATGTAATGAATATCTATAAGAAACCAGGTTGCACCGAAGAATGTTATA
66 TAAG-TTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTAT-
* * * *
105055 GGTCATTTAAAAAGTAAGTTACGATTTGAAATGCTAATTTTATG-TCAATAAAATCA
129 GGTC--TAAAAAAGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATCA
* * * * *
105111 ATTGCACCTAAAATGTTACCAAATTTTAAGTTGACGAGGCTTTTGAATTTCTCACTACAACAAAA
1 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
*
105176 TAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAAAATGTTATGA
66 TAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTATG-
* * ** * * * *
105241 GTCGCAAATAAGGTATTTTGTGATCTGAAATGTTAATTTTATGTTTAATAATATCG
130 GTC-TAAA-AAAGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATCA
* * *
105297 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGGCGTGGC-TTTGAACTTCCCACGATAACAAAA
1 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
* * * *
105361 TAAGTTAAAATATAAAAAATGTTATGAATATCTATAATAAATCATA-TTGCGTCTAAGAATATTA
66 TAAGTT-AAA-ATAAAAAATGTTATGAATATCTATAAGAAATCA-AGTTGCGCCCAAGAATGTTA
* *
105425 GGGGTCGCTAAAAATCTTAGTAGGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATCA
128 -TGGT--CTAAAAA----AGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATCA
* * * * * * * * *
105488 GTTGTGCCTAAAATGTTACTAGATTTTAAGTTGAC-AGGGCCTTCGACA-ATCTCACGATAACAA
1 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGA-GGCTTTTGA-ATTTCCCACGATAACAA
* * * * *
105551 AATACGTTAAAATCTAAAATTGTTAGGAATATGTATA
64 AATAAGTTAAAAT-AAAAAATGTTATGAATATCTATA
105588 GTAAATTTGG
Statistics
Matches: 395, Mismatches: 65, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
184 3 0.01
185 109 0.28
186 108 0.27
187 50 0.13
188 5 0.01
189 1 0.00
190 2 0.01
191 92 0.23
192 24 0.06
193 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
TAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTATGG
TCTAAAAAAGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATCA
Found at i:105313 original size:186 final size:183
Alignment explanation
Indices: 104925--105587 Score: 663
Period size: 186 Copynumber: 3.5 Consensus size: 183
104915 TACATATTAT
* * * *
104925 ATTGCGCCTAAAATGTTACCAAAGTTTAAGGTGATGAAGATTTTGAATTTCCCACGATAACAAAA
1 ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
* * * * *
104990 TAAGTTTAAAATAAAAAATGTAATGAATATCTATAAGAAACCAGGTTGCACCGAAGAATGTTAT-
66 TAAG-TTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTATG
** * * *
105054 AGGTCATTTAAAAAGTAAGTTACGATTTGAAATGCTAATTTTATG-TCAATAAAATC
130 A-GTC--GCAAAAAGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATC
* * * * *
105110 AATTGCACCTAAAATGTTACCAAATTTTAAGTTGACGAGGCTTTTGAATTTCTCACTACAACAAA
1 -ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAA
*
105175 ATAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAAAATGTTATG
65 ATAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTATG
** * * *
105240 AGTCGCAAATAAGGTATTTTGTGATCTGAAATGTTAATTTTATGTTTAATAATATC
130 AGTCGCAAA-AA-GTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATC
* * *
105296 GATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGGCGTGGC-TTTGAACTTCCCACGATAACAAA
1 -ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAA
* * * *
105360 ATAAGTTAAAATATAAAAAATGTTATGAATATCTATAATAAATCATA-TTGCGTCTAAGAATATT
65 ATAAGTT-AAA-ATAAAAAATGTTATGAATATCTATAAGAAATCA-AGTTGCGCCCAAGAATGTT
* * *
105424 AGGGGTCGCTAAAAATCTTAGTAGGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATC
127 ATGAGTCGC--AAAA----AGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATC
* * * * * * * *
105487 AGTTGTGCCTAAAATGTTACTAGATTTTAAGTTGAC-AGGGCCTTCGACA-ATCTCACGATAACA
1 A-TTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGA-GGCTTTTGA-ATTTCCCACGATAACA
* * * * *
105550 AAATACGTTAAAATCTAAAATTGTTAGGAATATGTATA
63 AAATAAGTTAAAAT-AAAAAATGTTATGAATATCTATA
105588 GTAAATTTGG
Statistics
Matches: 399, Mismatches: 60, Indels: 31
0.81 0.12 0.06
Matches are distributed among these distances:
183 3 0.01
184 2 0.01
185 107 0.27
186 109 0.27
187 52 0.13
188 2 0.01
189 3 0.01
190 3 0.01
191 92 0.23
192 25 0.06
193 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTGCGCCTAAAATGTTACCAAAGTTTAAGTTGACGAGGCTTTTGAATTTCCCACGATAACAAAA
TAAGTTAAAATAAAAAATGTTATGAATATCTATAAGAAATCAAGTTGCGCCCAAGAATGTTATGA
GTCGCAAAAAGTAAGTTGCGATTTGAAATGTTAATTTTATGTTTAATAAAATC
Done.