Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 304 of 335
Found at i:90349238 original size:26 final size:26
Alignment explanation
Indices: 90349202--90349285 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
90349192 CATGAAATTC
90349202 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
90349228 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
90349254 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
90349280 TTATCA
1 TTATCA
90349286 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:90352139 original size:5 final size:5
Alignment explanation
Indices: 90352129--90352172 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
90352119 CAATTTGTTA
90352129 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
90352173 ACACACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:90354379 original size:87 final size:85
Alignment explanation
Indices: 90354277--90354572 Score: 340
Period size: 86 Copynumber: 3.4 Consensus size: 85
90354267 GTTTTGCTTT
* * * **
90354277 TGTTTTAATTTCCACTTCACCTTTAAAATGTGTTTTTCTGTTTTCCACACCAATGAACCTTTAAA
1 TGTTTTAAATTCCACTTCAGCTTTAAAATGTATTTTTCAATTTTCCACACCAAT-AACCTTTAAA
** *
90354342 CACTTCTAGACTTATTTTTTTG
65 CACGACTAGACTTA-CTTTTTG
* * * * *
90354364 TGTTTTAAATTCCACTTGAGCTATAAAATGTATTTTTCAATTTTTCACACCAATATATCTTTAAG
1 TGTTTTAAATTCCACTTCAGCTTTAAAATGTATTTTTCAATTTTCCACACCAATA-ACCTTTAAA
* *
90354429 CACGACTAGACTTGCTTTTTA
65 CACGACTAGACTTACTTTTTG
* * * * * *
90354450 TGTTTTAAATTTCACTTCAGCTCTAAATTGTACTTTTCAATTTACTACACCAATAATCCTTTAAA
1 TGTTTTAAATTCCACTTCAGCTTTAAAATGTATTTTTCAATTTTCCACACCAATAA-CCTTTAAA
*
90354515 CACGACTACACTTACTTTTTG
65 CACGACTAGACTTACTTTTTG
* *
90354536 TGTTTTAAATTCCACTTTAGCTTTAAAATGTTTTTTT
1 TGTTTTAAATTCCACTTCAGCTTTAAAATGTATTTTT
90354573 TTTAATCTCC
Statistics
Matches: 173, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
85 1 0.01
86 108 0.62
87 64 0.37
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.46
Consensus pattern (85 bp):
TGTTTTAAATTCCACTTCAGCTTTAAAATGTATTTTTCAATTTTCCACACCAATAACCTTTAAAC
ACGACTAGACTTACTTTTTG
Found at i:90355282 original size:15 final size:16
Alignment explanation
Indices: 90355262--90355302 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
90355252 TCATCGTTCG
90355262 GTAAAAAAA-AAATTA
1 GTAAAAAAAGAAATTA
90355277 GTAAAATAAAAGAAATTA
1 GT-AAA-AAAAGAAATTA
90355295 GTAAAAAA
1 GTAAAAAA
90355303 TTAATCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 6 0.26
17 7 0.30
18 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (16 bp):
GTAAAAAAAGAAATTA
Found at i:90355292 original size:18 final size:18
Alignment explanation
Indices: 90355266--90355300 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
90355256 CGTTCGGTAA
90355266 AAAAAAAATTAGTAAAAT
1 AAAAAAAATTAGTAAAAT
*
90355284 AAAAGAAATTAGTAAAA
1 AAAAAAAATTAGTAAAA
90355301 AATTAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAAAAAAATTAGTAAAAT
Found at i:90357443 original size:10 final size:10
Alignment explanation
Indices: 90357428--90357453 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
90357418 TGCTCCTTGT
90357428 ACTATGTACA
1 ACTATGTACA
90357438 ACTATGTACA
1 ACTATGTACA
90357448 ACTATG
1 ACTATG
90357454 CTAAACCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (10 bp):
ACTATGTACA
Found at i:90359531 original size:182 final size:181
Alignment explanation
Indices: 90359222--90359549 Score: 500
Period size: 182 Copynumber: 1.8 Consensus size: 181
90359212 TGCAACATGA
*
90359222 CCGTGTGGACCACACGCCCTGGACACACAGCGTGTCCTAGGCCGTGTGAAAACTAGGGCTAAATT
1 CCGTGTGAACCACACGCCCTGGACACACAGCGTGTCCTAGGCCGTGTGAAAACTAGGGCTAAATT
* *
90359287 TTCAAATTTTAAACAAGTCAGAGAACTCCAAGGGTGAGGCATACGACCGTGTGTTCGGACACACG
66 TTCAAATTTTAAACAAGACAGAGAACTCCAAGGGTGAGGCATACAACCGTGTGTTCGGACACACG
90359352 AGCGTGTGGGAGACCATATGGGTGTGAGAGAAATGAACGACGTAGCACAGG
131 AGCGTGTGGGAGACCATATGGGTGTGAGAGAAATGAACGACGTAGCACAGG
* * * *
90359403 CCGTGTGAACCACACGGCTTGGACACAC-GGGTATGTCCTAGGCCGTGTGAAAA-TTGGAGCTAA
1 CCGTGTGAACCACACGCCCTGGACACACAGCG--TGTCCTAGGCCGTGTGAAAACTAGG-GCTAA
* *
90359466 ATTTTCAAATTTTAAACAAGACAGAGAGCTCCACA-GGTGAGGCATACAACCGTGTGTTTGGACA
63 ATTTTCAAATTTTAAACAAGACAGAGAACTCCA-AGGGTGAGGCATACAACCGTGTGTTCGGACA
* *
90359530 CATGGGCGTGTGGGAGACCA
127 CACGAGCGTGTGGGAGACCA
90359550 CACGAGCGTA
Statistics
Matches: 132, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
180 2 0.02
181 28 0.21
182 101 0.77
183 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (181 bp):
CCGTGTGAACCACACGCCCTGGACACACAGCGTGTCCTAGGCCGTGTGAAAACTAGGGCTAAATT
TTCAAATTTTAAACAAGACAGAGAACTCCAAGGGTGAGGCATACAACCGTGTGTTCGGACACACG
AGCGTGTGGGAGACCATATGGGTGTGAGAGAAATGAACGACGTAGCACAGG
Found at i:90359938 original size:10 final size:10
Alignment explanation
Indices: 90359923--90359952 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
90359913 CCTTCCCCCA
90359923 CCCTTTTTTT
1 CCCTTTTTTT
*
90359933 CCCTTTCTTT
1 CCCTTTTTTT
90359943 CCCTTTTTTT
1 CCCTTTTTTT
90359953 TCCTCTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
CCCTTTTTTT
Found at i:90359946 original size:20 final size:21
Alignment explanation
Indices: 90359923--90359962 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
90359913 CCTTCCCCCA
90359923 CCCTTTTTTTCCCT-TTCTTT
1 CCCTTTTTTTCCCTCTTCTTT
*
90359943 CCCTTTTTTTTCCTCTTCTT
1 CCCTTTTTTTCCCTCTTCTT
90359963 CCTCAACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
CCCTTTTTTTCCCTCTTCTTT
Found at i:90360150 original size:18 final size:18
Alignment explanation
Indices: 90360129--90360174 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
90360119 TTTCTATTAT
90360129 TTATTTATTTTCCCCTTA
1 TTATTTATTTTCCCCTTA
**
90360147 TTA-TTATTGTTTTCCTTA
1 TTATTTATT-TTCCCCTTA
90360165 TTATTTATTT
1 TTATTTATTT
90360175 AATCATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTATTTTCCCCTTA
Found at i:90360460 original size:3 final size:3
Alignment explanation
Indices: 90360452--90360476 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
90360442 TCTCCGTTCA
90360452 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
90360477 CTACTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:90362447 original size:5 final size:5
Alignment explanation
Indices: 90362437--90362465 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
90362427 AGTTGTCTGT
90362437 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
90362466 GAACACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:90368352 original size:20 final size:19
Alignment explanation
Indices: 90368306--90368352 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
90368296 GTAATTCATG
90368306 TTTAATTGCTGAATGGAGT
1 TTTAATTGCTGAATGGAGT
* *
90368325 TTTGAATTGGTAGAATTGAGT
1 TTT-AATTGCT-GAATGGAGT
90368346 TTTAATT
1 TTTAATT
90368353 TTAAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTAATTGCTGAATGGAGT
Found at i:90372277 original size:39 final size:40
Alignment explanation
Indices: 90372173--90372326 Score: 238
Period size: 40 Copynumber: 3.9 Consensus size: 40
90372163 AGAATTGAGA
*
90372173 GTTATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
*
90372213 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
*
90372253 GTTATATTC-GGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* * * *
90372292 GTTACATTCGGGCTAAGTCCTGAAGGGCATTCGTG
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
90372327 TCGGTGATGT
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
39 37 0.35
40 69 0.65
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (40 bp):
GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
Found at i:90372278 original size:79 final size:80
Alignment explanation
Indices: 90372173--90372326 Score: 247
Period size: 79 Copynumber: 1.9 Consensus size: 80
90372163 AGAATTGAGA
*
90372173 GTTATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAG
1 GTTATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGTTACATCCGGGCTAAGTCCCGAAG
90372238 AGCATTCGTGCTAGT
66 AGCATTCGTGCTAGT
* * * *
90372253 GTTATATTC-GGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTACATTCGGGCTAAGTCCTGAAG
1 GTTATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGTTACATCCGGGCTAAGTCCCGAAG
*
90372317 GGCATTCGTG
66 AGCATTCGTG
90372327 TCGGTGATGT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 60 0.88
80 8 0.12
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (80 bp):
GTTATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGTTACATCCGGGCTAAGTCCCGAAG
AGCATTCGTGCTAGT
Found at i:90372393 original size:44 final size:44
Alignment explanation
Indices: 90372321--90372452 Score: 158
Period size: 43 Copynumber: 3.0 Consensus size: 44
90372311 CTGAAGGGCA
* * * * *
90372321 TTCGTGTCGGTGATGTGTAATCAGGCCTTCATGCCTAGCAGGCT
1 TTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
* * * *
90372365 TTTGTGCTAGTGATGTGTATTCGGGCCTTCGTTCCTAGCAAGC-
1 TTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
* *
90372408 TTCGTGCCAGTGATGTGTATTTGGGTCTTCGTGCCTAGCAGGCT
1 TTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
90372452 T
1 T
90372453 AATGCTGGTG
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 37 0.51
44 35 0.49
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.36
Consensus pattern (44 bp):
TTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
Found at i:90372630 original size:25 final size:25
Alignment explanation
Indices: 90372583--90372637 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
90372573 TGTGTAATAA
*
90372583 CGAATGAATATAGGTACTATGTGTG
1 CGAATGAATATAGGCACTATGTGTG
*
90372608 CGAATGAAT-TGAGGCACTGTGTGTG
1 CGAATGAATAT-AGGCACTATGTGTG
90372633 CGAAT
1 CGAAT
90372638 TCTTTAACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (25 bp):
CGAATGAATATAGGCACTATGTGTG
Found at i:90372680 original size:28 final size:28
Alignment explanation
Indices: 90372649--90372802 Score: 123
Period size: 28 Copynumber: 5.5 Consensus size: 28
90372639 CTTTAACCGA
*
90372649 GCACTATGTGTACGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
** ** * ** *
90372677 GCACTGCGTGTGCGA-ATTCTTTGACCGA
1 GCACTATGTGTGCGAGA-TCGGTCAGTGG
90372705 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
* * ** * * *
90372733 GCATTGTGTGTGCGA-ATTCTTTAACTGA
1 GCACTATGTGTGCGAGA-TCGGTCAGTGG
90372761 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
*
90372789 GCACTGTGTGTGCG
1 GCACTATGTGTGCG
90372803 GATTTCATTT
Statistics
Matches: 90, Mismatches: 32, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
27 2 0.02
28 86 0.96
29 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCAGTGG
Found at i:90372688 original size:56 final size:56
Alignment explanation
Indices: 90372620--90372802 Score: 321
Period size: 56 Copynumber: 3.3 Consensus size: 56
90372610 AATGAATTGA
*
90372620 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTACGAGATCGGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
* *
90372676 GGCACTGCGTGTGCGAATTCTTTGACCGAGCACTATGTGTGCGAGATCGGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
* *
90372732 GGCATTGTGTGTGCGAATTCTTTAACTGAGCACTATGTGTGCGAGATCGGTCAGTG
1 GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
90372788 GGCACTGTGTGTGCG
1 GGCACTGTGTGTGCG
90372803 GATTTCATTT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (56 bp):
GGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
Found at i:90374980 original size:75 final size:75
Alignment explanation
Indices: 90374861--90375031 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
90374851 CATGGCAAAG
** *
90374861 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
90374920 CCATACTGAGC
65 CCATACCGAGC
90374931 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
90374996 CATACCGAGT
66 CATACCGAGC
***
90375006 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
90375032 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:90374999 original size:35 final size:35
Alignment explanation
Indices: 90374864--90375029 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
90374854 GGCAAAGTGT
* **
90374864 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
90374899 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
90374934 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
90374974 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
90375009 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
90375030 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:90376604 original size:20 final size:19
Alignment explanation
Indices: 90376558--90376604 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
90376548 GTAATTCATG
90376558 TTTAATTGCTGAATGGAGT
1 TTTAATTGCTGAATGGAGT
* *
90376577 TTTGAATTGGTAGAATTGAGT
1 TTT-AATTGCT-GAATGGAGT
90376598 TTTAATT
1 TTTAATT
90376605 TTAAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTAATTGCTGAATGGAGT
Found at i:90379854 original size:21 final size:22
Alignment explanation
Indices: 90379830--90379870 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
90379820 AAAGTTCATG
*
90379830 AAATTTTAAAAAA-TAAAATAA
1 AAATATTAAAAAATTAAAATAA
90379851 AAATATTAAAAAATTAAAAT
1 AAATATTAAAAAATTAAAAT
90379871 TTATTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATTAAAAAATTAAAATAA
Found at i:90379981 original size:25 final size:24
Alignment explanation
Indices: 90379948--90380027 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
90379938 TTATCAAATT
90379948 AAAATTAAAATAAAAATATAGAATC
1 AAAA-TAAAATAAAAATATAGAATC
*
90379973 AAAACTAAAATAAATAATA-AAAAT-
1 AAAA-TAAAATAAA-AATATAGAATC
* * * *
90379997 TAGATTAAATATAAATATAGAATC
1 AAAATAAAATAAAAATATAGAATC
90380021 AAAATAA
1 AAAATAA
90380028 TAAAGCACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
22 4 0.10
23 11 0.26
24 6 0.14
25 17 0.40
26 4 0.10
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAATAAAATAAAAATATAGAATC
Found at i:90389366 original size:25 final size:25
Alignment explanation
Indices: 90389321--90389370 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
90389311 ATGAGAATTC
* *
90389321 TTATTTAAACATAATAGTATATAAA
1 TTATTTAAACATAAAAATATATAAA
90389346 TTATTTAAA-ATAAAAAATATATAAA
1 TTATTTAAACAT-AAAAATATATAAA
90389371 ACATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATTTAAACATAAAAATATATAAA
Found at i:90390739 original size:14 final size:15
Alignment explanation
Indices: 90390720--90390755 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
90390710 AAAGAAAGAA
90390720 AAAATAATA-AAAAG
1 AAAATAATATAAAAG
90390734 AAAAT-ATATAAAAG
1 AAAATAATATAAAAG
90390748 AAAATAAT
1 AAAATAAT
90390756 GCTTTTTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 15 0.75
15 2 0.10
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAATAATATAAAAG
Found at i:90390744 original size:15 final size:15
Alignment explanation
Indices: 90390714--90390753 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
90390704 GATTCTAAAG
*
90390714 AAAGAAAAAATAATAA
1 AAAGAAAATATAAT-A
90390730 AAAGAAAATAT-ATA
1 AAAGAAAATATAATA
90390744 AAAGAAAATA
1 AAAGAAAATA
90390754 ATGCTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAGAAAATATAATA
Found at i:90399140 original size:33 final size:33
Alignment explanation
Indices: 90399098--90399164 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
90399088 GGAAAGCCCT
90399098 CTTTATAAAGACCCAACTTGAATGGAATATGAG
1 CTTTATAAAGACCCAACTTGAATGGAATATGAG
90399131 CTTTATAAAGACCCAACTTGAATGGAATATGAG
1 CTTTATAAAGACCCAACTTGAATGGAATATGAG
90399164 C
1 C
90399165 ATTCATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (33 bp):
CTTTATAAAGACCCAACTTGAATGGAATATGAG
Found at i:90400889 original size:28 final size:27
Alignment explanation
Indices: 90400837--90400889 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
90400827 CTATTCAGAA
* *
90400837 ATCAGTGTTAACTAGGCCTTAGCCCAT
1 ATCAGTATTAACTAGGCCATAGCCCAT
*
90400864 ATCAGTATTAATCTGGGCCATAGCCC
1 ATCAGTATTAA-CTAGGCCATAGCCC
90400890 CTTACAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTAGGCCATAGCCCAT
Found at i:90400949 original size:28 final size:28
Alignment explanation
Indices: 90400851--90400949 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
90400841 GTGTTAACTA
*
90400851 GGCCTTAGCCCATATCAGTATTAATCTG
1 GGCCTTAGCCCATATCAGTATCAATCTG
* * *
90400879 GGCCATAGCCCCT-TACAGTAACAGAGTATACTG
1 GGCCTTAGCCCATAT-CAGTATC--A--AT-CTG
90400912 GG-CTTAGCCCATATCAGTATCAATCTG
1 GGCCTTAGCCCATATCAGTATCAATCTG
*
90400939 GGCCGTAGCCC
1 GGCCTTAGCCC
90400950 TATTACAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
27 6 0.11
28 25 0.45
30 2 0.04
32 16 0.29
33 6 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (28 bp):
GGCCTTAGCCCATATCAGTATCAATCTG
Found at i:90400974 original size:60 final size:60
Alignment explanation
Indices: 90400851--90400985 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 60
90400841 GTGTTAACTA
* *
90400851 GGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTATACTG
1 GGCCTTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGT-ACAGAGTATACTG
* *
90400912 GG-CTTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTACAGAG-TATACTG
90400972 GGCCTT-GCCCATAT
1 GGCCTTAGCCCATAT
90400986 TAACATAGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
59 3 0.05
60 51 0.77
61 9 0.14
62 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (60 bp):
GGCCTTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTACAGAGTATACTG
Found at i:90403140 original size:19 final size:18
Alignment explanation
Indices: 90403103--90403145 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
90403093 ATACATACAG
90403103 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
90403120 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
90403139 TACTAAT
1 TAATAAT
90403146 CAAAATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 13 0.59
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:90405113 original size:28 final size:28
Alignment explanation
Indices: 90405077--90405175 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
90405067 GTGTTAACTA
* *
90405077 GGCCTTAGCCCATATCAGTATTAATTTG
1 GGCCATAGCCCATATCAGTATCAATTTG
* *
90405105 GGCCATAGCCCCT-TACAGTAACAGAGTATACTG
1 GGCCATAGCCCATAT-CAGTATCA-A-T-T--TG
*
90405138 GGCC-TAGCCCATATCAGTATCAATCTG
1 GGCCATAGCCCATATCAGTATCAATTTG
90405165 GGCCATAGCCC
1 GGCCATAGCCC
90405176 TATTACAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 23 0.41
29 1 0.02
30 2 0.04
31 2 0.04
32 14 0.25
33 7 0.12
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (28 bp):
GGCCATAGCCCATATCAGTATCAATTTG
Found at i:90405200 original size:60 final size:59
Alignment explanation
Indices: 90405077--90405211 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 59
90405067 GTGTTAACTA
* * *
90405077 GGCCTTAGCCCATATCAGTATTAATTTGGGCCATAGCCCCTTACAGTAACAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGT-ACAGAGTATACTG
*
90405138 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTACAGAG-TATACTG
*
90405198 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
90405212 TAACATATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 3 0.05
60 52 0.79
61 8 0.12
62 3 0.05
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (59 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTACAGAGTATACTG
Found at i:90407363 original size:19 final size:18
Alignment explanation
Indices: 90407326--90407369 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
90407316 ATACATACAG
90407326 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
90407343 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
90407362 TACTAATT
1 TAATAATT
90407370 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:90409413 original size:18 final size:18
Alignment explanation
Indices: 90409390--90409427 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
90409380 TTACATTAAG
90409390 TTAATT-AACTTTAACTTA
1 TTAATTCAACTTTAA-TTA
*
90409408 TTAATTCAATTTTAATTA
1 TTAATTCAACTTTAATTA
90409426 TT
1 TT
90409428 TATATACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTCAACTTTAATTA
Found at i:90413610 original size:14 final size:15
Alignment explanation
Indices: 90413591--90413619 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
90413581 GAGACTACTC
90413591 AATATGT-ATGTCAA
1 AATATGTCATGTCAA
90413605 AATATGTCATGTCAA
1 AATATGTCATGTCAA
90413620 CCCTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (15 bp):
AATATGTCATGTCAA
Found at i:90422872 original size:2 final size:2
Alignment explanation
Indices: 90422865--90422890 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90422855 TATCAATTCC
90422865 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
90422891 CTACAGTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90428580 original size:24 final size:24
Alignment explanation
Indices: 90428548--90428595 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
90428538 CAAAAGTACT
90428548 AGCAATACCTATCTCTTTATTATC
1 AGCAATACCTATCTCTTTATTATC
90428572 AGCAATACCTATCTCTTTATTATC
1 AGCAATACCTATCTCTTTATTATC
90428596 TAGCCTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (24 bp):
AGCAATACCTATCTCTTTATTATC
Found at i:90428642 original size:13 final size:13
Alignment explanation
Indices: 90428620--90428652 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
90428610 AAGGGTTTGT
90428620 TTAT-TAAACTAA
1 TTATCTAAACTAA
90428632 TTATCTAAACTAA
1 TTATCTAAACTAA
*
90428645 TTAACTAA
1 TTATCTAA
90428653 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:90443360 original size:47 final size:45
Alignment explanation
Indices: 90443209--90443382 Score: 138
Period size: 46 Copynumber: 3.8 Consensus size: 45
90443199 ACATCTTGTA
* * * * *
90443209 GTCGATGCATGTCCTAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GTCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CAT-TCAAT
* *
90443255 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATTTCAAT
1 GTCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCA-TTCAAT
* * *
90443301 GTCGATACCATGTCCCAAATATGGTCTTACACTGGCTCTCA-T-AAT
1 GTCGAT-GCATGTCCCAAACAT-GTCTTACACTAGCTCTCATTCAAT
** *
90443346 GTGGCTGATGCATGTCTGAGACATGTCTTACACTAGC
1 GT--C-GATGCATGTCCCAAACATGTCTTACACTAGC
90443383 ACACAAATGA
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
45 5 0.05
46 55 0.52
47 25 0.24
48 20 0.19
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (45 bp):
GTCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATTCAAT
Found at i:90447558 original size:20 final size:20
Alignment explanation
Indices: 90447529--90447571 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
90447519 CAAAACGTTG
*
90447529 AAAGAGAAGAAGGA-AAAGA
1 AAAGAGAAGAAGCACAAAGA
90447548 AAAGAAGAAGAAGCACAAAGA
1 AAAG-AGAAGAAGCACAAAGA
90447569 AAA
1 AAA
90447572 TGACGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAGAAGAAGCACAAAGA
Found at i:90456038 original size:13 final size:13
Alignment explanation
Indices: 90456022--90456047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
90456012 AAATTTAAAC
90456022 TAAAAATAAAATA
1 TAAAAATAAAATA
90456035 TAAAAATAAAATA
1 TAAAAATAAAATA
90456048 AATATATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:90456050 original size:17 final size:17
Alignment explanation
Indices: 90456024--90456067 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
90456014 ATTTAAACTA
90456024 AAAATAAAATATAAAAAT
1 AAAAT-AAATATAAAAAT
*
90456042 AAAATAAATATATAAAT
1 AAAATAAATATAAAAAT
90456059 -AAATAAATA
1 AAAATAAATA
90456068 AACTGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.36
17 11 0.44
18 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAATATAAAAAT
Found at i:90456060 original size:4 final size:4
Alignment explanation
Indices: 90456025--90456084 Score: 50
Period size: 4 Copynumber: 13.8 Consensus size: 4
90456015 TTTAAACTAA
*
90456025 AAAT AAAAT ATAA- AAAT AAAAT AAAT ATAT AAAT AAAT AAAT AAACT
1 AAAT -AAAT A-AAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
90456072 GAAAT AGAAT AAA
1 -AAAT A-AAT AAA
90456085 GGGGGTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
3 2 0.04
4 26 0.55
5 16 0.34
6 3 0.06
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:90456268 original size:15 final size:13
Alignment explanation
Indices: 90456230--90456282 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
90456220 GGTAGAGGAA
90456230 GAAGAA-AAAAGG
1 GAAGAAGAAAAGG
*
90456242 GAAAAAGAAAAGG
1 GAAGAAGAAAAGG
90456255 GAAGAAGATGAAAGG
1 GAAGAAGA--AAAGG
90456270 AGAAG-AGAAAAGG
1 -GAAGAAGAAAAGG
90456283 AGGCAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 8 0.23
16 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (13 bp):
GAAGAAGAAAAGG
Found at i:90456268 original size:28 final size:28
Alignment explanation
Indices: 90456226--90456282 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
90456216 TTGGGGTAGA
90456226 GGAAGAAGAAAAAAGG-GAAAAAGAAAAG
1 GGAAGAAGAAAAAAGGAG-AAAAGAAAAG
** *
90456254 GGAAGAAGATGAAAGGAGAAGAGAAAAG
1 GGAAGAAGAAAAAAGGAGAAAAGAAAAG
90456282 G
1 G
90456283 AGGCAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (28 bp):
GGAAGAAGAAAAAAGGAGAAAAGAAAAG
Found at i:90459226 original size:18 final size:18
Alignment explanation
Indices: 90459203--90459247 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
90459193 CAATTGTCAT
*
90459203 TTTATTCAAGCATTACAA
1 TTTATTCAAACATTACAA
*
90459221 TTTATTCAAACATTATAA
1 TTTATTCAAACATTACAA
90459239 TTTATTCAA
1 TTTATTCAA
90459248 TTTAGTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTATTCAAACATTACAA
Found at i:90460446 original size:29 final size:29
Alignment explanation
Indices: 90460410--90460467 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
90460400 TTTATTTTTA
90460410 ATGTTATAAAATTATATTTAAAGTAATTT
1 ATGTTATAAAATTATATTTAAAGTAATTT
*
90460439 ATGTTATAAAATTATATTTAAAGTTATTT
1 ATGTTATAAAATTATATTTAAAGTAATTT
90460468 TTCTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
ATGTTATAAAATTATATTTAAAGTAATTT
Found at i:90460733 original size:9 final size:9
Alignment explanation
Indices: 90460719--90460758 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
90460709 TCTTTAATTT
90460719 TTTAATATA
1 TTTAATATA
90460728 TTTAATA-A
1 TTTAATATA
*
90460736 TTTTATATA
1 TTTAATATA
90460745 TTTAA-AT-
1 TTTAATATA
90460752 TTTAATA
1 TTTAATA
90460759 ATTATTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
7 5 0.19
8 10 0.37
9 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAATATA
Found at i:90460733 original size:17 final size:17
Alignment explanation
Indices: 90460711--90460758 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
90460701 TACTTTTATC
*
90460711 TTTAATTTTTTAATATA
1 TTTAATATTTTAATATA
90460728 TTTAATAATTTT-ATATA
1 TTTAAT-ATTTTAATATA
90460745 TTTAA-ATTTTAATA
1 TTTAATATTTTAATA
90460759 ATTATTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 3 0.11
17 16 0.57
18 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATATTTTAATATA
Found at i:90471757 original size:29 final size:29
Alignment explanation
Indices: 90471715--90471774 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
90471705 TCATGTCTCC
90471715 AATTACTTTTTGACTATAAGCACTAATTA
1 AATTACTTTTTGACTATAAGCACTAATTA
90471744 AATTACTTTTTGACTATAAGCACTAATTA
1 AATTACTTTTTGACTATAAGCACTAATTA
90471773 AA
1 AA
90471775 GAGTAGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (29 bp):
AATTACTTTTTGACTATAAGCACTAATTA
Found at i:90485208 original size:23 final size:24
Alignment explanation
Indices: 90485159--90485209 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
90485149 ATCGTATTGG
*
90485159 TTTTTCATATATTTAATTTTGCGAT
1 TTTTTCATATATTTAATTTT-CAAT
90485184 TTTTTCATAGT-TTTAATTTT-AAT
1 TTTTTCATA-TATTTAATTTTCAAT
90485207 TTT
1 TTT
90485210 AAACCCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTTTCATATATTTAATTTTCAAT
Found at i:90489095 original size:2 final size:2
Alignment explanation
Indices: 90489083--90489127 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
90489073 ATTATTGTTT
90489083 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90489124 TA TA
1 TA TA
90489128 AAGTAAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90491151 original size:54 final size:54
Alignment explanation
Indices: 90491069--90491200 Score: 255
Period size: 54 Copynumber: 2.4 Consensus size: 54
90491059 CGTGTAAAAT
*
90491069 GGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAGG
1 GGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAAG
90491123 GGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAAG
1 GGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAAG
90491177 GGATTTAGCCTGGACTGGTAATCC
1 GGATTTAGCCTGGACTGGTAATCC
90491201 TACTGTAAGG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (54 bp):
GGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAAG
Found at i:90491287 original size:46 final size:46
Alignment explanation
Indices: 90491235--90491418 Score: 296
Period size: 46 Copynumber: 4.0 Consensus size: 46
90491225 AGTGTGCTCT
*
90491235 CTGATATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
90491281 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCACGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
90491327 CTGCTATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
90491373 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
90491419 ATGACAGAAA
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:90491424 original size:46 final size:46
Alignment explanation
Indices: 90491250--90491466 Score: 240
Period size: 46 Copynumber: 4.6 Consensus size: 46
90491240 ATGAAATGTG
* * * **
90491250 TAAGACCATGATTGAAAGATACCATGGCAACCTGATATGAAATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
* * **
90491296 TAAGACCATGGTTGAAAGATACCACGGCAACCTG-CTATGAAATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGAC-ATGAAAAGAA
*
90491342 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
*
90491388 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAA-G-A--A
* * *
90491437 GTAAGACCATAGTTGAAAGACACTATGGCA
1 -TAAGACCATGGTTGAAAGATACCATGGCA
90491467 TTATATCAAA
Statistics
Matches: 152, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
45 5 0.03
46 118 0.78
47 2 0.01
49 1 0.01
50 26 0.17
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAA
Found at i:90507820 original size:21 final size:21
Alignment explanation
Indices: 90507794--90507834 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90507784 AGACGAGCGA
* *
90507794 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
90507815 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
90507835 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:90523071 original size:14 final size:15
Alignment explanation
Indices: 90523052--90523080 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
90523042 GAGACTACTC
90523052 AATATGT-ATGTCAA
1 AATATGTCATGTCAA
90523066 AATATGTCATGTCAA
1 AATATGTCATGTCAA
90523081 CCTTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (15 bp):
AATATGTCATGTCAA
Found at i:90538350 original size:6 final size:6
Alignment explanation
Indices: 90538339--90538435 Score: 114
Period size: 6 Copynumber: 16.3 Consensus size: 6
90538329 CAACCCAATC
90538339 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TATTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T-TTATT
*
90538388 TTCT-TT TCTT-TT ATTATT TATTA-T TTTATT TTTA-T TTTA-T TTTATT
1 TT-TATT T-TTATT TTTATT T-TTATT TTTATT TTTATT TTTATT TTTATT
90538434 TT
1 TT
90538436 AGTTAAATAT
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
5 15 0.18
6 56 0.68
7 11 0.13
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:90538447 original size:37 final size:37
Alignment explanation
Indices: 90538374--90538447 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
90538364 TTATTTTTAT
* * **
90538374 TTTTATTTATTATTTTCTTTTCTTTTATTATTTATTA
1 TTTTATTTATTATTTTATTTTATTTTATTAAATATTA
90538411 TTTTATTT-TTATTTTATTTTATTTTAGTTAAATATTA
1 TTTTATTTATTATTTTATTTTATTTTA-TTAAATATTA
90538448 ATAAATTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 16 0.50
37 16 0.50
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (37 bp):
TTTTATTTATTATTTTATTTTATTTTATTAAATATTA
Found at i:90539554 original size:116 final size:117
Alignment explanation
Indices: 90539349--90539576 Score: 395
Period size: 116 Copynumber: 2.0 Consensus size: 117
90539339 AGTTTTCCAT
* * *
90539349 GGTTATGAGTATAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTATAGCTCAAATCGTGACTAACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
90539414 CTACTTCACGTCAAAAGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCACGTCAAAAGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
*
90539466 GGTTATGAGTATGGCTCAAATCGTGAC-AACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTATAGCTCAAATCGTGACTAACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
**
90539530 CTACTTCGTGTCAAAAGTTGTGTGACGTGACAAGTAAAACTCCGCTA
66 CTACTTCACGTCAAAAGTTGTGTGACGTGACAAGTAAAACTCCGCTA
90539577 ACTGGAAATA
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 81 0.77
117 24 0.23
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (117 bp):
GGTTATGAGTATAGCTCAAATCGTGACTAACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCACGTCAAAAGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:90539657 original size:114 final size:113
Alignment explanation
Indices: 90539378--90539660 Score: 331
Period size: 116 Copynumber: 2.5 Consensus size: 113
90539368 ATCGTGACTG
*
90539378 ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCACGTCAAAAGTTGTGTGACGTG
1 ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGTTGTGTGACGTG
* ** * *
90539443 ACAAGTAAAACTCCGCTAGCCGAGGTTATGAGTATGGCTCAAATCGTGACA
66 ACAAGTAAAACTCCGCTAACCGAAATAATAAGTATGG--CAAATCGTGA-A
*
90539494 ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGTGTCAAAAGTTGTGTGACGTG
1 ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGTTGTGTGACGTG
* * * ** *
90539559 ACAAGTAAAACTCCGCTAACTGGAAATAAATAA-TTTAGG-AGTATTTTG-G
66 ACAAGTAAAACTCCGCTAAC-CGAAAT-AATAAGTAT-GGCA-AATCGTGAA
* *
90539608 GCTGAGTAACCGGGGTGGGGTGCTTGGGTTGTCATCTCT-CTTCGCGTCAAAAG
1 ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCAT-TCTACTTCGCGTCAAAAG
90539661 GTTTAATATA
Statistics
Matches: 146, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
114 46 0.32
115 4 0.03
116 86 0.59
117 5 0.03
118 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (113 bp):
ACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGTTGTGTGACGTG
ACAAGTAAAACTCCGCTAACCGAAATAATAAGTATGGCAAATCGTGAA
Found at i:90539733 original size:19 final size:20
Alignment explanation
Indices: 90539703--90539753 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
90539693 TAAATTTTTT
90539703 AAAAAA-AAAAAAAAGAG-A
1 AAAAAAGAAAAAAAAGAGAA
*
90539721 AAAAGAGAAAAAAAAGAGAA
1 AAAAAAGAAAAAAAAGAGAA
90539741 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
90539754 TAAGTACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 13 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAGAA
Found at i:90539734 original size:11 final size:11
Alignment explanation
Indices: 90539707--90539753 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
90539697 TTTTTTAAAA
*
90539707 AAAAAAAAAAG
1 AAAAAAAAGAG
*
90539718 -AGAAAAAGAG
1 AAAAAAAAGAG
90539728 AAAAAAAAGAG
1 AAAAAAAAGAG
90539739 AAAAAAAAGA-
1 AAAAAAAAGAG
90539749 AAAAA
1 AAAAA
90539754 TAAGTACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 13 0.41
11 19 0.59
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:90540406 original size:20 final size:20
Alignment explanation
Indices: 90540376--90540423 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
90540366 AATTTAGGAT
* * *
90540376 TTTAT-TTTAATTATATTTG
1 TTTATCTTTAATTAAATGTA
90540395 TTTATCTTTAATTAAATGTA
1 TTTATCTTTAATTAAATGTA
90540415 TTTATCTTT
1 TTTATCTTT
90540424 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTATCTTTAATTAAATGTA
Found at i:90544935 original size:29 final size:29
Alignment explanation
Indices: 90544899--90544956 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
90544889 TTTATTTTTA
90544899 ATGTTATAAAATTATATTTAAAGTAATTT
1 ATGTTATAAAATTATATTTAAAGTAATTT
*
90544928 ATGTTATAAAATTATATTTAAAGTTATTT
1 ATGTTATAAAATTATATTTAAAGTAATTT
90544957 TTCTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
ATGTTATAAAATTATATTTAAAGTAATTT
Found at i:90545220 original size:17 final size:17
Alignment explanation
Indices: 90545200--90545247 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
90545190 TCCTTTTATC
*
90545200 TTTAATTTTTTAATATA
1 TTTAATATTTTAATATA
90545217 TTTAATGATTTT-ATATA
1 TTTAAT-ATTTTAATATA
90545234 TTTAA-ATTTTAATA
1 TTTAATATTTTAATA
90545248 ATTATTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 3 0.11
17 16 0.57
18 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAATATTTTAATATA
Found at i:90545368 original size:20 final size:21
Alignment explanation
Indices: 90545345--90545396 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
90545335 TGATAAGTAC
90545345 AATTTAAATATTATAA-TAAA
1 AATTTAAATATTATAATTAAA
*
90545365 AA-TTCAA-ATTATAATTAAA
1 AATTTAAATATTATAATTAAA
90545384 ATATTTTAAATAT
1 A-A-TTTAAATAT
90545397 ATCCAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 3 0.12
22 4 0.16
23 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAAATATTATAATTAAA
Found at i:90558743 original size:18 final size:20
Alignment explanation
Indices: 90558700--90558743 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
90558690 ACAATGGAAC
*
90558700 AAAATATATTAAATTTTCTT
1 AAAATATATTAAATTATCTT
*
90558720 ATAATATATT-AATTATC-T
1 AAAATATATTAAATTATCTT
90558738 AAAATA
1 AAAATA
90558744 AATATAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATATATTAAATTATCTT
Found at i:90558790 original size:21 final size:20
Alignment explanation
Indices: 90558766--90558806 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
90558756 TCAAAAATGG
*
90558766 AAAAATTATAAAAATCTAAAT
1 AAAAACTATAAAAA-CTAAAT
*
90558787 AAAAACTCTAAAAACTAAAT
1 AAAAACTATAAAAACTAAAT
90558807 TATAAATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAACTATAAAAACTAAAT
Found at i:90560448 original size:26 final size:26
Alignment explanation
Indices: 90560419--90560471 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
90560409 TCAAACATGC
90560419 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
90560445 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
90560471 A
1 A
90560472 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:90561989 original size:26 final size:26
Alignment explanation
Indices: 90561957--90562064 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
90561947 TGAAATGCCC
90561957 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
90561983 ATTATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* * *
90562009 ATCATAGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
90562035 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
90562061 ATCA
1 ATCA
90562065 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
25 4 0.06
26 65 0.90
27 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:90562035 original size:52 final size:52
Alignment explanation
Indices: 90561957--90562064 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
90561947 TGAAATGCCC
* * *
90561957 ATCATGGAACATTTACCTAAACCATTATTATGGAACATTTACCTAACCTATT
1 ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
* *
90562009 ATCATAGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
90562061 ATCA
1 ATCA
90562065 ATTTGTACCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (52 bp):
ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:90568275 original size:134 final size:134
Alignment explanation
Indices: 90568007--90568276 Score: 292
Period size: 134 Copynumber: 2.0 Consensus size: 134
90567997 TTGCCTTGCC
* * * * *
90568007 TTAGAAAACACGAGTGAAATTCCAAAGGGATATTCGATTATTTTGAACAAACGGGAGATTTGCAA
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
* * * * * * *
90568072 CCCAGCACGATAGGCCACTATTCCTTGAACTGCTAAATACCGAACATTTTCTTTGTTTTTATAAG
66 ACCAGCACGATAGGCCACAATTCCATGAACTGCCAAATACCAAACATTCTCTTTGTTTTAATAAG
90568137 TTTT
131 TTTT
* * * *
90568141 TTAGAAAATATGAATGAAATTCTAAAGAGACATTCGATTATTTTGAGCAAACGAGA-AATTGCAA
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
* * * * * * *
90568205 ACCAGCATGTTAGGGCACAATTCCATGGATTGCCGAATATCAAACA-TCTCTTTCGTTTTAATGA
66 ACCAGCACGATAGGCCACAATTCCATGAACTGCCAAATACCAAACATTCTCTTT-GTTTTAAT-A
*
90568269 ATTTTT
129 AGTTTT
90568275 TT
1 TT
90568277 TAAGAGTCTA
Statistics
Matches: 110, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
132 6 0.05
133 48 0.44
134 56 0.51
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (134 bp):
TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
ACCAGCACGATAGGCCACAATTCCATGAACTGCCAAATACCAAACATTCTCTTTGTTTTAATAAG
TTTT
Found at i:90568498 original size:3 final size:3
Alignment explanation
Indices: 90568490--90568556 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
90568480 ATATTATGTC
90568490 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
90568538 TAA TAA TAG CAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
90568557 GTAAATATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:90568905 original size:3 final size:3
Alignment explanation
Indices: 90568731--90568875 Score: 52
Period size: 3 Copynumber: 48.7 Consensus size: 3
90568721 ATAATGACGA
* * * * *
90568731 AAT AGT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AAT ACT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT
* * * *
90568776 AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC AAT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * **
90568821 AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AAT AGC AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
90568867 AATT AAT AA
1 AA-T AAT AA
90568876 ATAAATATAA
Statistics
Matches: 105, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
2 10 0.10
3 87 0.83
4 7 0.07
5 1 0.01
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:90570546 original size:44 final size:44
Alignment explanation
Indices: 90570306--90570548 Score: 196
Period size: 44 Copynumber: 5.5 Consensus size: 44
90570296 TGAGTTCTTG
* * *
90570306 ATCTGCT-TCTTCGA-TCTGTTCCCCATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAACT-TGTTCCCTATAAGCACAGGGATGCCAA
* *
90570349 ATCTGCTGTCTTCAACTTGTTCCCTAT-AGACACAGGGATGTCAA
1 ATCTGCTATCTTCAACTTGTTCCCTATAAG-CACAGGGATGCCAA
* *
90570393 ATCTGCTATGTTCAACTTGTTCCCTATAAGCACAGGGATTCC--
1 ATCTGCTATCTTCAACTTGTTCCCTATAAGCACAGGGATGCCAA
** * * * * *
90570435 ATGCTGAAATCTTCGA-TCTGCTTCACC-GTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCAACT-TG-TTC-CCTATAAGCACAGGGATGCCAA
* *
90570481 ATCTGCTATCTTCGA-TCTGTTCTCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTCAACT-TGTTCCCTATAAGCACAGGGATGCCAA
* * *
90570525 ATCTGTTGTTTTCAACTTGTTCCC
1 ATCTGCTATCTTCAACTTGTTCCC
90570549 CGACAATACG
Statistics
Matches: 160, Mismatches: 28, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
42 3 0.02
43 20 0.12
44 114 0.71
45 21 0.13
46 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (44 bp):
ATCTGCTATCTTCAACTTGTTCCCTATAAGCACAGGGATGCCAA
Found at i:90571056 original size:206 final size:206
Alignment explanation
Indices: 90570689--90571597 Score: 1364
Period size: 205 Copynumber: 4.4 Consensus size: 206
90570679 GGGAACATCC
* * *
90570689 GAAAGTCAAAT-ATGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTG
1 GAAAGCCAAATCA-GCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTG
* * * ** *
90570753 GATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTATTGAAGTGG
65 GATCTTGCTTCAGTAAAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGA
* * * * *
90570818 AGATACCAGACTTCGATTTGTTCTCTGACAATACAGAGACCACAAATCATCTTAGATTTGTTTCA
130 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
90570883 TCGTAATCACGT
195 TCGTAATCACGT
* * *
90570895 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
* **
90570960 ATCTTGCTTCAGTAAAAACATCTGAAGGTCAGATCTGCTATGTATCTACTCTCCATTGAAGT-AG
66 ATCTTGCTTCAGTAAAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGA-
* *
90571024 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
130 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
90571089 TCGTAATCACGT
195 TCGTAATCACGT
*
90571101 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACATAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
* * * *
90571166 ATC-TGCTTCAGTGAAATCATCTGAAGG-CGAGATCTGCTATGTGTCTGCTTTCCATCAAAGTGA
66 ATCTTGCTTCAGTAAAAACATCTGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATCAAAGTGA
* * *
90571229 AGATGCCAAACTTCAATTCGTTCACTGACAATACAGAGACGACAAATTATCTTAGATTTGCTTCA
130 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
90571294 TCGTAATCACGT
195 TCGTAATCACGT
* *
90571306 GAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAACATAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
* * * * * *
90571371 A-CCTGCTTCAGTGAAATCATCTGAAGATGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
66 ATCTTGCTTCAGTAAAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGAA
*
90571435 GATGCCAAACTTCGATTCATTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAT
131 GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAT
90571500 CGTAATCACGT
196 CGTAATCACGT
* *
90571511 GAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAACACAAGAATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
*
90571576 AT-TTGCTTCAGT-ATAACATCTG
66 ATCTTGCTTCAGTAAAAACATCTG
90571598 TAGGCCAAAT
Statistics
Matches: 655, Mismatches: 41, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
204 10 0.02
205 386 0.59
206 258 0.39
207 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (206 bp):
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
ATCTTGCTTCAGTAAAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGAA
GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAT
CGTAATCACGT
Found at i:90579802 original size:134 final size:134
Alignment explanation
Indices: 90579534--90579803 Score: 301
Period size: 134 Copynumber: 2.0 Consensus size: 134
90579524 TTGCCTTGCC
* * * * *
90579534 TTAGAAAACACGAGTGAAATTCCAAAGGGATATTCGATTATTTTGAACAAACGGGAGATTTGCAA
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
* * * * * * *
90579599 CCCAGCACGATAGGGCACTATTCCCTGAACTGCTAAATACCGAACATTTCCTTTGTTTTTATAAG
66 ACCAGCACGATAGGGCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTTGTTTTAATAAG
90579664 TTTT
131 TTTT
* * * *
90579668 TTAGAAAATATGAATGAAATTCTAAAGAGACATTCGATTATTTTGAGCAAACGAGA-AATTGCAA
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
* * * * * *
90579732 ACCAGCATGTTAGGGCACAATTCCATGGATTGCCGAATATCAAACATCT-CTTTCGTTTTAATGA
66 ACCAGCACGATAGGGCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTT-GTTTTAAT-A
*
90579796 ATTTTT
129 AGTTTT
90579802 TT
1 TT
90579804 TAAGAGTCTA
Statistics
Matches: 111, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
132 4 0.04
133 51 0.46
134 56 0.50
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (134 bp):
TTAGAAAACACGAATGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAA
ACCAGCACGATAGGGCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTTGTTTTAATAAG
TTTT
Found at i:90579820 original size:134 final size:134
Alignment explanation
Indices: 90579548--90579803 Score: 291
Period size: 133 Copynumber: 1.9 Consensus size: 134
90579538 AAAACACGAG
* * * * *
90579548 TGAAATTCCAAAGGGATATTCGATTATTTTGAACAAACGGGAGATTTGCAACCCAGCACGATAGG
1 TGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAAACCAGCACGATAGG
* * * * * *
90579613 GCACTATTCCCTGAACTGCTAAATACCGAACATTTCCTTTGTTTTTATAAGTTTTTTAGAAAATA
66 GCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTTGTTTTAATAAGTTTTTTAGAAAATA
*
90579678 TGAA
131 TAAA
* * * *
90579682 TGAAATTCTAAAGAGACATTCGATTATTTTGAGCAAACGAGA-AATTGCAAACCAGCATGTTAGG
1 TGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAAACCAGCACGATAGG
* * * * *
90579746 GCACAATTCCATGGATTGCCGAATATCAAACATCT-CTTTCGTTTTAATGAATTTTTTT
66 GCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTT-GTTTTAAT-AAGTTTTTT
90579804 TAAGAGTCTA
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
132 4 0.04
133 51 0.51
134 45 0.45
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (134 bp):
TGAAATTCCAAAGAGACATTCGATTATTTTGAACAAACGAGAGAATTGCAAACCAGCACGATAGG
GCACAATTCCATGAACTGCCAAATACCAAACATCTCCTTTGTTTTAATAAGTTTTTTAGAAAATA
TAAA
Found at i:90580025 original size:3 final size:3
Alignment explanation
Indices: 90580017--90580071 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
90580007 ATATTATGTC
* *
90580017 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
90580065 TAA TAA T
1 TAA TAA T
90580072 GTAAATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:90580419 original size:3 final size:3
Alignment explanation
Indices: 90580245--90580389 Score: 52
Period size: 3 Copynumber: 48.7 Consensus size: 3
90580235 ATAATGACGA
* * * * *
90580245 AAT AGT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AAT ACT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT
* * * *
90580290 AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC AAT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * **
90580335 AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AAT AGC AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
90580381 AATT AAT AA
1 AA-T AAT AA
90580390 ATAAATATAA
Statistics
Matches: 105, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
2 10 0.10
3 87 0.83
4 7 0.07
5 1 0.01
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:90592299 original size:26 final size:25
Alignment explanation
Indices: 90592236--90592309 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 25
90592226 CAACCCAGTC
90592236 TTTCTTTT-TATTTTTATTTATTTAT
1 TTTCTTTTAT-TTTTTATTTATTTAT
*
90592261 TTT-TTTTCCTTTTATTATTTA-TTAT
1 TTTCTTTT-ATTTT-TTATTTATTTAT
90592286 TTTC-TTTATATTTTTATTTTATTT
1 TTTCTTTTAT-TTTTTA-TTTATTT
90592310 TAGTTAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
24 8 0.20
25 23 0.56
26 10 0.24
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTCTTTTATTTTTTATTTATTTAT
Found at i:90592301 original size:20 final size:21
Alignment explanation
Indices: 90592247--90592303 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
90592237 TTCTTTTTAT
*
90592247 TTTTATTTATTTATTTTTTTTCC
1 TTTTA-TTATTTA-TTATTTTCC
90592270 TTTTATTATTTATTATTTT-C
1 TTTTATTATTTATTATTTTCC
90592290 TTTATATT-TTTATT
1 TTT-TATTATTTATT
90592304 TTATTTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 10 0.31
21 10 0.31
22 7 0.22
23 5 0.16
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTATTATTTATTATTTTCC
Found at i:90592307 original size:22 final size:24
Alignment explanation
Indices: 90592248--90592310 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 24
90592238 TCTTTTTATT
90592248 TTTAT-TTATTTATTTT-TTTTCC
1 TTTATATTATTTATTTTATTTTCC
90592270 TTT-TATTATTTA--TTATTTT-C
1 TTTATATTATTTATTTTATTTTCC
90592290 TTTATATT-TTTATTTTATTTT
1 TTTATATTATTTATTTTATTTT
90592311 AGTTAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 17 0.47
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATATTATTTATTTTATTTTCC
Found at i:90592307 original size:29 final size:28
Alignment explanation
Indices: 90592240--90592309 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
90592230 CCAGTCTTTC
*
90592240 TTTTTATTTTTATTTATTTATTTTTTTTC
1 TTTTTA-TTTTATTTATTTATTTTTTTTA
*
90592269 CTTTTA--TTATTTA-TTATTTTCTTTATA
1 TTTTTATTTTATTTATTTATTTT-TTT-TA
90592296 TTTTTATTTTATTT
1 TTTTTATTTTATTT
90592310 TAGTTAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 7 0.21
26 10 0.29
27 6 0.18
29 11 0.32
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTTATTTTATTTATTTATTTTTTTTA
Found at i:90593398 original size:118 final size:118
Alignment explanation
Indices: 90593172--90593384 Score: 390
Period size: 118 Copynumber: 1.8 Consensus size: 118
90593162 TGTTTTCCAT
* *
90593172 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
90593237 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
**
90593290 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
90593355 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
90593385 TTGGGTAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
Found at i:90593553 original size:12 final size:12
Alignment explanation
Indices: 90593538--90593568 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
90593528 AAAAAATCAA
90593538 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
90593550 AAAAAAAAGAAG
1 AAAAAAAAAAAG
90593562 AAAAAAA
1 AAAAAAA
90593569 TAAGTACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:90596180 original size:24 final size:23
Alignment explanation
Indices: 90596132--90596185 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
90596122 AACAAAATTA
90596132 TTAA-TTTTTAATTTAAATAAAT
1 TTAATTTTTTAATTTAAATAAAT
**
90596154 TTATATTTTTTATATTT-AATATTT
1 TTA-ATTTTTTA-ATTTAAATAAAT
90596178 TTAATTTT
1 TTAATTTT
90596186 CAATATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.11
23 6 0.22
24 14 0.52
25 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAATTTTTTAATTTAAATAAAT
Found at i:90596190 original size:16 final size:16
Alignment explanation
Indices: 90596152--90596201 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
90596142 ATTTAAATAA
*
90596152 ATTT-ATATTTTTTAT
1 ATTTAATATTTTTAAT
90596167 ATTTAATATTTTTAAT
1 ATTTAATATTTTTAAT
*
90596183 -TTTCAATATATGTTAAT
1 ATTT-AATAT-TTTTAAT
90596200 AT
1 AT
90596202 CATGTGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 7 0.24
16 15 0.52
17 6 0.21
18 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
ATTTAATATTTTTAAT
Found at i:90597588 original size:20 final size:20
Alignment explanation
Indices: 90597563--90597600 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
90597553 TGGTTTTAGC
*
90597563 CTTCTGGTAAGCTACTCTTT
1 CTTCTGCTAAGCTACTCTTT
*
90597583 CTTCTGCTAAGCTGCTCT
1 CTTCTGCTAAGCTACTCT
90597601 ATTGATGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (20 bp):
CTTCTGCTAAGCTACTCTTT
Found at i:90601922 original size:21 final size:21
Alignment explanation
Indices: 90601898--90601947 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
90601888 GGTATCAACA
*
90601898 ATACTTTTGTGAAAGGTACTG
1 ATACTTTTGTGAAAGGTACCG
* *
90601919 ATAC-TTTGTTAAGGGTACCG
1 ATACTTTTGTGAAAGGTACCG
90601939 ATACTTTTG
1 ATACTTTTG
90601948 GGACAGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (21 bp):
ATACTTTTGTGAAAGGTACCG
Found at i:90609381 original size:16 final size:17
Alignment explanation
Indices: 90609360--90609414 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
90609350 TTAGAATCTT
90609360 TTTTAAATTATTAT-AA
1 TTTTAAATTATTATAAA
*
90609376 TTTTAAA-AATATATAAA
1 TTTTAAATTAT-TATAAA
*
90609393 TTTTGAAATTTTTATAAA
1 TTTT-AAATTATTATAAA
90609411 TTTT
1 TTTT
90609415 TGAATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
17 6 0.19
18 13 0.41
19 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAAATTATTATAAA
Found at i:90609385 original size:18 final size:18
Alignment explanation
Indices: 90609359--90609414 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
90609349 TTTAGAATCT
*
90609359 TTTTTAAATTATTAT-AA
1 TTTTAAAATTATTATAAA
*
90609376 TTTTAAAAATA-TATAAA
1 TTTTAAAATTATTATAAA
* *
90609393 TTTTGAAATTTTTATAAA
1 TTTTAAAATTATTATAAA
90609411 TTTT
1 TTTT
90609415 TGAATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 3 0.09
17 19 0.59
18 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTAAAATTATTATAAA
Found at i:90609417 original size:19 final size:17
Alignment explanation
Indices: 90609387--90609422 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
90609377 TTTAAAAATA
90609387 TATAAATTTTGAAATTTT
1 TATAAATTTTG-AATTTT
90609405 TATAAATTTTTGAATTTT
1 TATAAA-TTTTGAATTTT
90609423 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TATAAATTTTGAATTTT
Found at i:90615477 original size:27 final size:26
Alignment explanation
Indices: 90615447--90615506 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
90615437 AGGGAGAGAG
*
90615447 AAGAAAGGGAAAGGAAAAGGAGGAA-GA
1 AAGAAA-GGAAAAGAAAAGGA-GAAGGA
90615474 AAGAGAAGGAAAAGAAAAGGAGAAGGA
1 AAGA-AAGGAAAAGAAAAGGAGAAGGA
90615501 AAGAAA
1 AAGAAA
90615507 AGAGAGAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 23 0.77
28 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (26 bp):
AAGAAAGGAAAAGAAAAGGAGAAGGA
Found at i:90615498 original size:17 final size:17
Alignment explanation
Indices: 90615475--90615513 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
90615465 GGAGGAAGAA
90615475 AGAGAAGGAAAAGAAAAG
1 AGAGAAGG-AAAGAAAAG
90615493 -GAGAAGGAAAGAAAAG
1 AGAGAAGGAAAGAAAAG
90615509 AGAGA
1 AGAGA
90615514 GACGAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGAGAAGGAAAGAAAAG
Found at i:90615507 original size:43 final size:43
Alignment explanation
Indices: 90615419--90615533 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 43
90615409 GAGGGGGAGG
* * *
90615419 AGGAGGAAGAGGAAGAGAAGGGAGAGAGAAGAAAGGGAAAGGAAA
1 AGGAGGAAGA--AAGAGAAGGAAAAGAAAAGAAAGGGAAAGGAAA
90615464 AGGAGGAAGAAAGAGAAGGAAAAGAAAAGGAGAA-GGAAA-GAAA
1 AGGAGGAAGAAAGAGAAGGAAAAGAAAA-GA-AAGGGAAAGGAAA
*
90615507 AGAGAGAGACG-AAGAG-AGGAAAAGAAA
1 AG-GAG-GAAGAAAGAGAAGGAAAAGAAA
90615534 GAAGAGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 32 0.52
44 15 0.24
45 15 0.24
ACGTcount: A:0.58, C:0.01, G:0.41, T:0.00
Consensus pattern (43 bp):
AGGAGGAAGAAAGAGAAGGAAAAGAAAAGAAAGGGAAAGGAAA
Found at i:90615546 original size:22 final size:21
Alignment explanation
Indices: 90615502--90615554 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
90615492 GGAGAAGGAA
* *
90615502 AGAAAAGAGAGAGACGAAGAG
1 AGAAAAGAAAGAGACGAAAAG
90615523 AGGAAAAGAAAGAAGA-GAAAAG
1 A-GAAAAGAAAG-AGACGAAAAG
90615545 AG-AAAGAAAG
1 AGAAAAGAAAG
90615555 GAAAGCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 15 0.54
23 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (21 bp):
AGAAAAGAAAGAGACGAAAAG
Found at i:90615552 original size:20 final size:20
Alignment explanation
Indices: 90615526--90615572 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
90615516 CGAAGAGAGG
90615526 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
90615546 GAAAGAAAGGAAAGCAAAGA
1 AAAAGAAAGGAAAGAAAAGA
90615566 AAAAGAA
1 AAAAGAA
90615573 GGATAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGAAAGAAAAGA
Found at i:90615565 original size:27 final size:26
Alignment explanation
Indices: 90615455--90615571 Score: 82
Period size: 27 Copynumber: 4.5 Consensus size: 26
90615445 AGAAGAAAGG
* *
90615455 GAAAG-GAAAAGGAGGAAGAAAGAGAAG
1 GAAAGAGAAAA-GAGAAAGAAAG-GAAA
* *
90615482 GAAA-AGAAAAGGAGAAGGAAAGAAAA
1 GAAAGAGAAAA-GAGAAAGAAAGGAAA
* * * *
90615508 GAGAGAGACGAAGAG-AGGAAAAGAAA
1 GAAAGAGA-AAAGAGAAAGAAAGGAAA
90615534 G-AAGAGAAAAGAGAAAGAAAGGAAA
1 GAAAGAGAAAAGAGAAAGAAAGGAAA
90615559 GCAAAGA-AAAAGA
1 G-AAAGAGAAAAGA
90615572 AGGATAAGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
24 5 0.07
25 15 0.21
26 21 0.29
27 29 0.40
28 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (26 bp):
GAAAGAGAAAAGAGAAAGAAAGGAAA
Found at i:90619389 original size:16 final size:17
Alignment explanation
Indices: 90619363--90619407 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
90619353 TTTTTTTCAT
90619363 TTAAA-AATAAAAT-AA
1 TTAAATAATAAAATAAA
90619378 TTAAATAAT-AAATAAA
1 TTAAATAATAAAATAAA
* *
90619394 TTTAATAAAAAAAT
1 TTAAATAATAAAAT
90619408 GGTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.36
16 12 0.48
17 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAATAATAAAATAAA
Found at i:90619450 original size:18 final size:20
Alignment explanation
Indices: 90619426--90619475 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
90619416 TTAAAATTTT
90619426 GAAATAATTTTT-TTAAAAA
1 GAAATAATTTTTATTAAAAA
90619445 -AAATAATATTTTAATTAAAAA
1 GAAATAAT-TTTT-ATTAAAAA
*
90619466 GATATAATTT
1 GAAATAATTT
90619476 AAGGATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
21 9 0.35
22 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
GAAATAATTTTTATTAAAAA
Found at i:90619755 original size:22 final size:22
Alignment explanation
Indices: 90619727--90619768 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
90619717 GCCTTCGGAT
90619727 GGCCTCTTAATGGCTGATTTCA
1 GGCCTCTTAATGGCTGATTTCA
90619749 GGCCTCTTAATGGCTGATTT
1 GGCCTCTTAATGGCTGATTT
90619769 TAATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (22 bp):
GGCCTCTTAATGGCTGATTTCA
Found at i:90621484 original size:21 final size:22
Alignment explanation
Indices: 90621460--90621603 Score: 84
Period size: 21 Copynumber: 6.3 Consensus size: 22
90621450 CAATGAGAGA
*
90621460 AAATTAATAT-GAAAAAAATAT
1 AAATTAACATGGAAAAAAATAT
*
90621481 AAATTTACATGGAAAAAAATAATT
1 AAATTAACATGGAAAAAAAT-A-T
*
90621505 AAATTTACATGGAAAAAAAGATAATTT
1 AAATTAACATGG-AAAAAA-AT-A--T
* *
90621532 AAATGAA-ATAAGAAAAAAAT-T
1 AAATTAACAT-GGAAAAAAATAT
*
90621553 AAATTTACATGGAAAAAAATAATTT
1 AAATTAACATGGAAAAAAAT-A--T
*
90621578 AAATGAA-AT-GAAAAAAAT-T
1 AAATTAACATGGAAAAAAATAT
90621597 AAATTAA
1 AAATTAA
90621604 AATGAGAAGA
Statistics
Matches: 100, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.07
21 23 0.23
22 11 0.11
23 10 0.10
24 15 0.15
25 14 0.14
26 12 0.12
27 8 0.08
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (22 bp):
AAATTAACATGGAAAAAAATAT
Found at i:90621507 original size:24 final size:24
Alignment explanation
Indices: 90621470--90621581 Score: 119
Period size: 24 Copynumber: 4.7 Consensus size: 24
90621460 AAATTAATAT
90621470 GAAAAAAAT-A-TAAATTTACATG
1 GAAAAAAATAATTAAATTTACATG
90621492 GAAAAAAATAATTAAATTTACATG
1 GAAAAAAATAATTAAATTTACATG
* *
90621516 GAAAAAAAGATAATTTAAA-TGAAAT-
1 G-AAAAAA-ATAA-TTAAATTTACATG
90621541 -AAGAAAAA-AATTAAATTTACATG
1 GAA-AAAAATAATTAAATTTACATG
90621564 GAAAAAAATAATTTAAAT
1 GAAAAAAATAA-TTAAAT
90621582 GAAATGAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
21 5 0.07
22 15 0.20
23 9 0.12
24 21 0.28
25 12 0.16
26 8 0.11
27 5 0.07
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.27
Consensus pattern (24 bp):
GAAAAAAATAATTAAATTTACATG
Found at i:90621586 original size:46 final size:44
Alignment explanation
Indices: 90621495--90621650 Score: 195
Period size: 46 Copynumber: 3.4 Consensus size: 44
90621485 TTACATGGAA
90621495 AAAAATAATTAAATTTACATGGAAAAAAAGATAATTTAAATGAAATAAG
1 AAAAA-AATTAAATTTACATGG-AAAAAA-ATAATTTAAATGAAAT--G
90621544 AAAAAAATTAAATTTACATGGAAAAAAATAATTTAAATGAAATG
1 AAAAAAATTAAATTTACATGGAAAAAAATAATTTAAATGAAATG
* * * *
90621588 AAAAAAATTAAATTAAAATGAGAAGATAGATAATTTAAATGAAATG
1 AAAAAAATTAAATTTACATG-GAA-AAAAATAATTTAAATGAAATG
*
90621634 ATAAAAAATTATATTTA
1 A-AAAAAATTAAATTTA
90621651 AATAAAATAA
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
44 19 0.19
45 3 0.03
46 36 0.37
47 19 0.19
48 16 0.16
49 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.10, T:0.28
Consensus pattern (44 bp):
AAAAAAATTAAATTTACATGGAAAAAAATAATTTAAATGAAATG
Found at i:90621621 original size:118 final size:117
Alignment explanation
Indices: 90621468--90621691 Score: 258
Period size: 118 Copynumber: 1.9 Consensus size: 117
90621458 GAAAATTAAT
* * * *
90621468 ATGAAAAAAATATAAATTTACATGGAAAAAAATAA-TTAAATTTACATGGA-AAAAAAGATA-AT
1 ATGAAAAAAATATAAATTAAAATGGAAAAAAATAATTTAAA-TGAAAT-GATAAAAAA-ATATAT
* * * *
90621530 TTAAATGAAATAAGAAAAAAATTAAATTTACATGGAAAAAAATAATTTAAATGAA
63 TTAAATAAAATAAGAAAAAAATTAAAATAAAATGGAAAAAAATAATTTAAATGAA
* * *
90621585 ATGAAAAAAAT-TAAATTAAAATGAGAAGATAGATAATTTAAATGAAATGATAAAAAATTATATT
1 ATGAAAAAAATATAAATTAAAATG-GAA-AAAAATAATTTAAATGAAATGATAAAAAAATATATT
* *
90621649 TAAATAAAATAAGGAAAAAATTAAAATAAAATGGAAAGAAATA
64 TAAATAAAATAAGAAAAAAATTAAAATAAAATGGAAAAAAATA
90621692 TAACTTGAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
116 10 0.11
117 18 0.20
118 56 0.63
119 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.26
Consensus pattern (117 bp):
ATGAAAAAAATATAAATTAAAATGGAAAAAAATAATTTAAATGAAATGATAAAAAAATATATTTA
AATAAAATAAGAAAAAAATTAAAATAAAATGGAAAAAAATAATTTAAATGAA
Found at i:90621649 original size:26 final size:25
Alignment explanation
Indices: 90621526--90621672 Score: 86
Period size: 21 Copynumber: 6.1 Consensus size: 25
90621516 GAAAAAAAGA
90621526 TAATTTAAATGAAATAAGA-AAAAAAT
1 TAATTTAAATGAAAT--GATAAAAAAT
*
90621552 TAAATTTACATG----GA-AAAAAA-
1 T-AATTTAAATGAAATGATAAAAAAT
90621572 TAATTTAAATGAAATGA-AAAAAAT
1 TAATTTAAATGAAATGATAAAAAAT
* *
90621596 TAAATTAAAATGAGAA-GAT---AGA-
1 T-AATTTAAATGA-AATGATAAAAAAT
90621618 TAATTTAAATGAAATGATAAAAAAT
1 TAATTTAAATGAAATGATAAAAAAT
* * *
90621643 TATATTTAAATAAAATAAGGAAAAAAT
1 TA-ATTTAAATGAAATGA-TAAAAAAT
90621670 TAA
1 TAA
90621673 AATAAAATGG
Statistics
Matches: 96, Mismatches: 9, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
19 9 0.09
20 3 0.03
21 21 0.22
22 1 0.01
23 10 0.10
24 3 0.03
25 14 0.15
26 17 0.18
27 18 0.19
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.28
Consensus pattern (25 bp):
TAATTTAAATGAAATGATAAAAAAT
Found at i:90622082 original size:15 final size:15
Alignment explanation
Indices: 90622052--90622093 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
90622042 CCAACTGCTC
* *
90622052 CTTGTCCCATCACCA
1 CTTGTCCCACCGCCA
90622067 CTTGTCCCACCGCCA
1 CTTGTCCCACCGCCA
*
90622082 C-TGTGCCACCGC
1 CTTGTCCCACCGC
90622094 TCCATTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.14, C:0.50, G:0.14, T:0.21
Consensus pattern (15 bp):
CTTGTCCCACCGCCA
Found at i:90623291 original size:3 final size:3
Alignment explanation
Indices: 90623047--90623275 Score: 80
Period size: 3 Copynumber: 76.0 Consensus size: 3
90623037 AATTAAATTA
* * *
90623047 ATT ATT ATT ATCT CTT ATT ATT ATT ATT GTT ATT ATT ATC ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
90623093 ATT -TT GTT AAT ACT ACT ATT ATG ACT A-T ATT -TT ATT -TT TTGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * * * *
90623135 GTT GATTT ACTT ACT GTT -TT GTT ATT AATT CATT AAT -TT ATT ATT
1 ATT -A-TT A-TT ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT ATT
* * * * *
90623180 AAT A-T ATT ATT ATT CTT AATGT ATT ATC ATT ACT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
90623226 TTT ATT ACT ATT ATC ATT -TT -TT AATT ATT GTT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
90623270 ATT ATT
1 ATT ATT
90623276 TTAAAATATT
Statistics
Matches: 168, Mismatches: 42, Indels: 32
0.69 0.17 0.13
Matches are distributed among these distances:
2 17 0.10
3 129 0.77
4 19 0.11
5 3 0.02
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:90623330 original size:2 final size:2
Alignment explanation
Indices: 90623323--90623352 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
90623313 TGATATTAAA
90623323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90623353 TATCAGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90623560 original size:8 final size:7
Alignment explanation
Indices: 90623521--90623562 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
90623511 TTTTCATCAC
90623521 TATTATT
1 TATTATT
90623528 TA-TACTT
1 TATTA-TT
90623535 TATTA-T
1 TATTATT
90623541 TATTATT
1 TATTATT
90623548 TATTATCT
1 TATTAT-T
90623556 TATTATT
1 TATTATT
90623563 GTTATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.26
7 14 0.45
8 9 0.29
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTATT
Found at i:90623697 original size:3 final size:3
Alignment explanation
Indices: 90623534--90623678 Score: 102
Period size: 3 Copynumber: 48.0 Consensus size: 3
90623524 TATTTATACT
* * *
90623534 TTA TTA TTA TTA TTTA TTA -TC TTA TTA TTG TTA TT- TAA TATA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * * * * * * *
90623579 TGA TTA TCA CTA TTA TTA TT- TTA CTAA TTG TAA CTTA ATA CTT- TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA -TTA TTA
90623625 TT- TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90623670 TTA TTA TTA
1 TTA TTA TTA
90623679 CCTCCTTATT
Statistics
Matches: 111, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
2 8 0.07
3 91 0.82
4 12 0.11
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:90625105 original size:5 final size:6
Alignment explanation
Indices: 90625080--90625209 Score: 62
Period size: 6 Copynumber: 22.5 Consensus size: 6
90625070 TTATAAATTT
* * *
90625080 AAATGA AAATGA AAATAA AAATAA AAATTG- AAATGA AAAT-A AATTG-
1 AAATGA AAATGA AAATGA AAATGA AAA-TGA AAATGA AAATGA AAATGA
* ** * * *
90625126 AAATGA TAAATAAA TAAATTT AAATG- AAACG- AAGTTA AAATG- AAATG-
1 AAATGA -AAAT-GA -AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA
* *
90625173 AAATG- AAATG- AAATGA AAATTA AAATTA AAATGA AAA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAA
90625210 AAAAAAAAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
5 36 0.36
6 53 0.53
7 5 0.05
8 6 0.06
ACGTcount: A:0.65, C:0.01, G:0.12, T:0.23
Consensus pattern (6 bp):
AAATGA
Found at i:90625125 original size:16 final size:17
Alignment explanation
Indices: 90625104--90625140 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
90625094 ATAAAAATAA
90625104 AAATTGAAATGA-AAAT
1 AAATTGAAATGATAAAT
90625120 AAATTGAAATGATAAAT
1 AAATTGAAATGATAAAT
90625137 AAAT
1 AAAT
90625141 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (17 bp):
AAATTGAAATGATAAAT
Found at i:90625178 original size:10 final size:10
Alignment explanation
Indices: 90625163--90625190 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
90625153 AACGAAGTTA
90625163 AAATGAAATG
1 AAATGAAATG
90625173 AAATGAAATG
1 AAATGAAATG
90625183 AAATGAAA
1 AAATGAAA
90625191 ATTAAAATTA
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:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (10 bp):
AAATGAAATG
Found at i:90625500 original size:49 final size:48
Alignment explanation
Indices: 90625427--90625556 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 48
90625417 GAAAAAAAAA
* * * *
90625427 TTTACATCTCTAGTGCCGACTATTACATGGCTAGCA-AAAAATTATTTTT
1 TTTACATCTCTGGTACCGACTATTACATGACCAGCACAAAAA-T-TTTTT
** *
90625476 TTTACATCTCTGGTACCGGTTATTACATGACCAGCACCTAAAATTTTTT
1 TTTACATCTCTGGTACCGACTATTACATGACCAGCA-CAAAAATTTTTT
* *
90625525 TTTACATCTCTGGTGCCGACCATTACATGACC
1 TTTACATCTCTGGTACCGACTATTACATGACC
90625557 TGTACCCAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 63 0.93
50 1 0.01
51 4 0.06
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (48 bp):
TTTACATCTCTGGTACCGACTATTACATGACCAGCACAAAAATTTTTT
Found at i:90627721 original size:19 final size:18
Alignment explanation
Indices: 90627668--90627722 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
90627658 TGAACTAATG
90627668 AATGAATAGGATTTAAAT
1 AATGAATAGGATTTAAAT
** *
90627686 AAAAAAGTGGGATTTAAAGT
1 AATGAA-TAGGATTTAAA-T
*
90627706 AATGAATAGGAATTAAA
1 AATGAATAGGATTTAAA
90627723 AAAAAGGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (18 bp):
AATGAATAGGATTTAAAT
Done.