Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 82 of 211
Found at i:25386872 original size:18 final size:17
Alignment explanation
Indices: 25386851--25386927 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
25386841 TTTTCTCTCA
25386851 CTTTTTCGATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
25386869 CTTTTGCAATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
25386887 CTTCTTCATTTTCTTTTT
1 CTTTTTCA-TTTCTTTTT
* **
25386905 -GTTTTC-TTTCAATTT
1 CTTTTTCATTTCTTTTT
25386920 CTTTTTCA
1 CTTTTTCA
25386928 ATCTCTTTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
15 7 0.15
16 5 0.11
17 5 0.11
18 30 0.64
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.69
Consensus pattern (17 bp):
CTTTTTCATTTCTTTTT
Found at i:25386926 original size:6 final size:6
Alignment explanation
Indices: 25386821--25386913 Score: 53
Period size: 6 Copynumber: 15.3 Consensus size: 6
25386811 TTTTTTTCAA
* * ** * *
25386821 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * * *
25386871 TTTGCA ATTTCT TTTTCT TCTTCA TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
25386914 CAATTTCTTT
Statistics
Matches: 60, Mismatches: 24, Indels: 5
0.67 0.27 0.06
Matches are distributed among these distances:
5 4 0.07
6 49 0.82
7 4 0.07
8 3 0.05
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTTCT
Found at i:25388007 original size:12 final size:12
Alignment explanation
Indices: 25387992--25388026 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
25387982 TTTTGCTCGA
*
25387992 TTTTTTTCACTT
1 TTTTTTTCAATT
*
25388004 TTTTTTTGAATT
1 TTTTTTTCAATT
25388016 TTTTTTTCAAT
1 TTTTTTTCAAT
25388027 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:25388019 original size:14 final size:14
Alignment explanation
Indices: 25388002--25388052 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
25387992 TTTTTTTCAC
25388002 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
*
25388015 TTTTTTTTCAATCAAAT
1 TTTTTTTT---TCGAAT
25388032 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
25388046 TTTTTTT
1 TTTTTTT
25388053 GATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 8 0.25
14 12 0.38
16 1 0.03
17 11 0.34
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:25389429 original size:11 final size:10
Alignment explanation
Indices: 25389404--25389464 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25389394 ACCAATAAAA
25389404 TAAA-TGAGC
1 TAAATTGAGC
*
25389413 TGAATTGTAGC
1 TAAATTG-AGC
25389424 TAAATTGAGC
1 TAAATTGAGC
**
25389434 TCGATTGAGC
1 TAAATTGAGC
25389444 TGAAA-TGAGC
1 T-AAATTGAGC
*
25389454 TCAATTGAGC
1 TAAATTGAGC
25389464 T
1 T
25389465 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25389465 original size:20 final size:20
Alignment explanation
Indices: 25389405--25389465 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25389395 CCAATAAAAT
*
25389405 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25389425 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25389446 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25389466 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25390609 original size:132 final size:132
Alignment explanation
Indices: 25390372--25390621 Score: 401
Period size: 132 Copynumber: 1.9 Consensus size: 132
25390362 TCAAACTACC
* *
25390372 AAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCTAATAACGAGATC
1 AAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACAAGATC
* * * *
25390437 AAAGGCCTGACAAATGCATTCCAAACTAAATGGGACCATTCAGGAGTTTGTTAGTGATACGAGTC
66 AAAGGCCCGACAAATGCAGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTAGTGATACGAGTC
25390502 AT
131 AT
* ** *
25390504 AAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCCCAATAACAAGATC
1 AAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACAAGATC
*
25390569 AAAGGCCCGACAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTA
66 AAAGGCCCGACAAATGCAGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTA
25390622 ACAAGGCCTT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (132 bp):
AAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACAAGATC
AAAGGCCCGACAAATGCAGTCCAAACTAAATGGGACCATTCAAGAGCTTGTTAGTGATACGAGTC
AT
Found at i:25401494 original size:50 final size:50
Alignment explanation
Indices: 25401436--25401537 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
25401426 TGTGGCAATT
25401436 TGAGCCCATCACTTTCTTGAACTTGGGTTGGGCCTTTATGACTCGTATCA
1 TGAGCCCATCACTTTCTTGAACTTGGGTTGGGCCTTTATGACTCGTATCA
*
25401486 TGAGCCCATCACTTTCTTGAATTTGGGTTGGGCCTTTATGACTCGTATCA
1 TGAGCCCATCACTTTCTTGAACTTGGGTTGGGCCTTTATGACTCGTATCA
25401536 TG
1 TG
25401538 TTCTTAAGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (50 bp):
TGAGCCCATCACTTTCTTGAACTTGGGTTGGGCCTTTATGACTCGTATCA
Found at i:25405099 original size:19 final size:19
Alignment explanation
Indices: 25405075--25405112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
25405065 TAAGTAGGGG
25405075 TGGACT-TCTTGATTGGGCT
1 TGGACTATCTT-ATTGGGCT
25405094 TGGACTCATCTTATTGGGC
1 TGGACT-ATCTTATTGGGC
25405113 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.39
Consensus pattern (19 bp):
TGGACTATCTTATTGGGCT
Found at i:25410103 original size:30 final size:30
Alignment explanation
Indices: 25410069--25410165 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25410059 TAAACTAAAA
25410069 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25410099 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
25410129 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25410158 ATGAGCTA
1 -TGAGCTA
25410166 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25412356 original size:12 final size:12
Alignment explanation
Indices: 25412341--25412371 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25412331 TTCTTTTTGC
25412341 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25412353 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25412365 TTTTCAA
1 TTTTCAA
25412372 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25412448 original size:6 final size:6
Alignment explanation
Indices: 25412432--25412481 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25412422 TTTCTTTTTA
*
25412432 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25412481 T
1 T
25412482 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:25412464 original size:37 final size:37
Alignment explanation
Indices: 25412421--25412491 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25412411 CTTGCCTCTC
25412421 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25412458 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
25412492 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25412492 original size:16 final size:16
Alignment explanation
Indices: 25412417--25412477 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
25412407 GCCTCTTGCC
*
25412417 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
25412433 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
25412449 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
25412465 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
25412478 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:25413365 original size:11 final size:12
Alignment explanation
Indices: 25413349--25413398 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
25413339 ATATACTTCG
25413349 ATTTTTTTTT-A
1 ATTTTTTTTTCA
*
25413360 ATTTTTTTTTTCG
1 A-TTTTTTTTTCA
*
25413373 A-TTTTTTTTAA
1 ATTTTTTTTTCA
25413384 ATTTTTTTTTCA
1 ATTTTTTTTTCA
25413396 ATT
1 ATT
25413399 ACAATATGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.31
12 21 0.66
13 1 0.03
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:25413372 original size:24 final size:24
Alignment explanation
Indices: 25413345--25413393 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25413335 TTTTATATAC
*
25413345 TTCGATTTTTTTTTAATTTTTTTT
1 TTCGATTTTTTTTAAATTTTTTTT
25413369 TTCGATTTTTTTTAAATTTTTTTT
1 TTCGATTTTTTTTAAATTTTTTTT
25413393 T
1 T
25413394 CAATTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (24 bp):
TTCGATTTTTTTTAAATTTTTTTT
Found at i:25413377 original size:23 final size:24
Alignment explanation
Indices: 25413345--25413394 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
25413335 TTTTATATAC
*
25413345 TTCGATTTTTTTTTAATTTTTTTT
1 TTCGATTTTTTTTTAAATTTTTTT
25413369 TTCGA-TTTTTTTTAAATTTTTTT
1 TTCGATTTTTTTTTAAATTTTTTT
25413392 TTC
1 TTC
25413395 AATTACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (24 bp):
TTCGATTTTTTTTTAAATTTTTTT
Found at i:25415088 original size:30 final size:30
Alignment explanation
Indices: 25415054--25415150 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25415044 TAAACTAAAA
*
25415054 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
25415084 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25415114 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25415143 ATGAGCTA
1 -TGAGCTA
25415151 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:25415514 original size:30 final size:30
Alignment explanation
Indices: 25415478--25415543 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
25415468 TGAATGGTCC
25415478 CTCCTTAGTTACCGATTTAGGAGTCGGCCA
1 CTCCTTAGTTACCGATTTAGGAGTCGGCCA
* *
25415508 CTCCTTAGTTACTGATTTAGGAGTTGGCCA
1 CTCCTTAGTTACCGATTTAGGAGTCGGCCA
25415538 CTCCTT
1 CTCCTT
25415544 GATTGCCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (30 bp):
CTCCTTAGTTACCGATTTAGGAGTCGGCCA
Found at i:25420237 original size:23 final size:22
Alignment explanation
Indices: 25420185--25420237 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25420175 TCCACGTCTT
*
25420185 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25420207 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25420230 TTTCTTTT
1 TTTCTTTT
25420238 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25425853 original size:30 final size:30
Alignment explanation
Indices: 25425813--25425885 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
25425803 CGAGTTTAAA
*
25425813 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
25425842 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
25425872 CTAAATATGAGCTA
1 CTAAATATGAGCTA
25425886 GGAGTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:25425896 original size:30 final size:30
Alignment explanation
Indices: 25425832--25425897 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
25425822 GCTAAGTTTT
* *
25425832 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
25425862 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
25425892 AGCTCG
1 AGCTCG
25425898 GTTTAGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:25429169 original size:30 final size:30
Alignment explanation
Indices: 25429135--25429231 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25429125 TAAACTAAAA
25429135 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25429165 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
25429195 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25429224 ATGAGCTA
1 -TGAGCTA
25429232 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25431424 original size:12 final size:12
Alignment explanation
Indices: 25431409--25431439 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25431399 TTCTTTTTGC
25431409 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25431421 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
25431433 ATTTCAA
1 TTTTCAA
25431440 GTTCTCTCAA
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:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25431509 original size:6 final size:6
Alignment explanation
Indices: 25431500--25431549 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
25431490 TTTCTTTTTA
25431500 TTTCTT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25431549 T
1 T
25431550 GTTTTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.25
6 21 0.52
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:25431511 original size:21 final size:20
Alignment explanation
Indices: 25431487--25431549 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
25431477 CTCTTGCCTC
25431487 TCTTTTCTTTTTATTTCTTTT
1 TCTTTTCTTTTT-TTTCTTTT
* * *
25431508 TCTTTTTCTTCTCTTGCTTTT
1 TC-TTTTCTTTTTTTTCTTTT
25431529 TCTTTTTCTTTTCTTTTCTTT
1 TC-TTTTCTTTT-TTTTCTTT
25431550 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTCTTTTTTTTCTTTT
Found at i:25431532 original size:37 final size:37
Alignment explanation
Indices: 25431489--25431559 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25431479 CTTGCCTCTC
25431489 TTTTCTTTTTA-TTTCTTTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25431526 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTTCTTTTCTTTGTTTTCTCTT
25431560 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.77
Consensus pattern (37 bp):
TTTTCTTTTTATTTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25431559 original size:27 final size:26
Alignment explanation
Indices: 25431487--25431560 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
25431477 CTCTTGCCTC
25431487 TCTTTTCTTT-TTATTTCTTTTTCTTT
1 TCTTTTCTTTGTT-TTTCTTTTTCTTT
*
25431513 T-TCTTCTCTTGCTTTTTCTTTTTCTTT
1 TCTTTTCT-TTG-TTTTTCTTTTTCTTT
25431540 TCTTTTCTTTGTTTTCTCTTT
1 TCTTTTCTTTGTTTT-TCTTT
25431561 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 5 0.12
26 7 0.17
27 22 0.54
28 7 0.17
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (26 bp):
TCTTTTCTTTGTTTTTCTTTTTCTTT
Found at i:25431965 original size:98 final size:98
Alignment explanation
Indices: 25431791--25431997 Score: 389
Period size: 98 Copynumber: 2.1 Consensus size: 98
25431781 CAAAGTTGGA
25431791 TGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAG
1 TGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAG
25431856 AAATGGTATTTGGTTTTGGTACGTTTTGGTATT
66 AAATGGTATTTGGTTTTGGTACGTTTTGGTATT
*
25431889 TGTGTATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAG
1 TGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAG
25431954 AAATGGTATTTGGTTTTGGTACGTTTTGGTATT
66 AAATGGTATTTGGTTTTGGTACGTTTTGGTATT
*
25431987 TG-GGAATTGGT
1 TGTGGATTTGGT
25431998 ACGAAAGGGT
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
97 7 0.07
98 99 0.93
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.40
Consensus pattern (98 bp):
TGTGGATTTGGTTTAAGTCGAAATGGTATGAATAGAATGGAAGAGTTCGGTTTAGGATAATTAAG
AAATGGTATTTGGTTTTGGTACGTTTTGGTATT
Found at i:25432015 original size:21 final size:21
Alignment explanation
Indices: 25431989--25432045 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
25431979 TTGGTATTTG
*
25431989 GGAATTGGTACGAAAGGGTAT
1 GGAATTGGTACGAAAGAGTAT
* *
25432010 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAAGAGTAT
*
25432031 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
25432046 TTGGTTATGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAAGAGTAT
Found at i:25436321 original size:17 final size:17
Alignment explanation
Indices: 25436296--25436350 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
25436286 TCTCTTTTCA
*
25436296 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
25436313 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTT-TGAATT
* *
25436331 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
25436348 TTC
1 TTC
25436351 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:25436348 original size:18 final size:19
Alignment explanation
Indices: 25436311--25436362 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
25436301 TTTTTTTGAA
25436311 TTTTCTTTT-TTTTATCAT
1 TTTTCTTTTCTTTTATCAT
*
25436329 TTTTCTTTTCTTTTGT-AT
1 TTTTCTTTTCTTTTATCAT
25436347 TTTCGTCTTTTCTTTT
1 TTT--TCTTTTCTTTT
25436363 TCTCTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 11 0.37
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCTTTTATCAT
Found at i:25438590 original size:13 final size:13
Alignment explanation
Indices: 25438572--25438623 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
25438562 AAACCGTATG
25438572 CAATTTTTTTTTT
1 CAATTTTTTTTTT
25438585 CAATTTTTTTTTT
1 CAATTTTTTTTTT
25438598 CAA-TTTTTTTTT
1 CAATTTTTTTTTT
*
25438610 GAACTTTTTTTTTT
1 CAA-TTTTTTTTTT
25438624 ACGCACCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 11 0.31
13 16 0.44
14 9 0.25
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:25438940 original size:24 final size:23
Alignment explanation
Indices: 25438886--25438963 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
25438876 GGATAATTAA
**
25438886 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
25438909 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
25438933 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
25438954 GAAATAGTAT
1 GAAATGGTAT
25438964 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:25438948 original size:21 final size:21
Alignment explanation
Indices: 25438922--25438988 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
25438912 TTGGTATTTG
25438922 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25438943 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25438964 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
25438987 GG
1 GG
25438989 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:25443003 original size:30 final size:30
Alignment explanation
Indices: 25442969--25443065 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25442959 TAAACTAAAA
25442969 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25442999 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
25443029 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25443058 ATGAGCTA
1 -TGAGCTA
25443066 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25445269 original size:12 final size:11
Alignment explanation
Indices: 25445238--25445265 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25445228 TTTTCTTTTT
25445238 GCTTTTCAAAG
1 GCTTTTCAAAG
25445249 GCTTTTCAAAG
1 GCTTTTCAAAG
25445260 GCTTTT
1 GCTTTT
25445266 TCAAGTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (11 bp):
GCTTTTCAAAG
Found at i:25446297 original size:11 final size:10
Alignment explanation
Indices: 25446281--25446338 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
25446271 TCTTAACGAT
25446281 TTTTTTTTTGA
1 TTTTTTTTT-A
25446292 -TTTTTTTTA
1 TTTTTTTTTA
25446301 TTTTTTTTTCA
1 TTTTTTTTT-A
** *
25446312 AATTTTTTTC
1 TTTTTTTTTA
25446322 TTTTTTTTT-
1 TTTTTTTTTA
25446331 TTTTTTTT
1 TTTTTTTT
25446339 CCAATACAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 9 0.22
10 23 0.57
11 8 0.20
ACGTcount: A:0.09, C:0.03, G:0.02, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:25446303 original size:21 final size:20
Alignment explanation
Indices: 25446279--25446338 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
25446269 TTTCTTAACG
25446279 ATTTTTTTTTTGATTTTTTTT
1 ATTTTTTTTTT-ATTTTTTTT
* *
25446300 ATTTTTTTTTCAAATTTTTTT
1 ATTTTTTTTT-TATTTTTTTT
*
25446321 CTTTTTTTTTT-TTTTTTT
1 ATTTTTTTTTTATTTTTTT
25446339 CCAATACAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 6 0.18
21 27 0.82
ACGTcount: A:0.10, C:0.03, G:0.02, T:0.85
Consensus pattern (20 bp):
ATTTTTTTTTTATTTTTTTT
Found at i:25446305 original size:22 final size:23
Alignment explanation
Indices: 25446280--25446334 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
25446270 TTCTTAACGA
*
25446280 TTTTTTTTTTGATTTTTTT-TAT
1 TTTTTTTTTTAATTTTTTTCTAT
** *
25446302 TTTTTTTTCAAATTTTTTTCTTT
1 TTTTTTTTTTAATTTTTTTCTAT
25446325 TTTTTTTTTT
1 TTTTTTTTTT
25446335 TTTTCCAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.09, C:0.04, G:0.02, T:0.85
Consensus pattern (23 bp):
TTTTTTTTTTAATTTTTTTCTAT
Found at i:25448026 original size:30 final size:30
Alignment explanation
Indices: 25447992--25448088 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25447982 TAAACTAAAA
25447992 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25448022 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
25448052 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25448081 ATGAGCTA
1 -TGAGCTA
25448089 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25454803 original size:67 final size:71
Alignment explanation
Indices: 25454659--25454805 Score: 230
Period size: 67 Copynumber: 2.1 Consensus size: 71
25454649 GGGGAATCAT
*
25454659 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATACAATGG
25454724 ATATCG
66 ATATCG
***
25454730 CACTTAGCAA-CCC-C-GGGGAATCAGCACATAGCAACCCCC-TTTCATTTCAAAGATATGGTGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATACAATGG
25454791 ATATCG
66 ATATCG
25454797 CACTTAGCA
1 CACTTAGCA
25454806 CCACCAATGA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
67 33 0.46
68 25 0.35
69 1 0.01
70 3 0.04
71 10 0.14
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATACAATGG
ATATCG
Found at i:25454847 original size:26 final size:26
Alignment explanation
Indices: 25454817--25454867 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
25454807 CACCAATGAA
*
25454817 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
25454843 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
25454868 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:25454857 original size:100 final size:102
Alignment explanation
Indices: 25454729--25454945 Score: 336
Period size: 102 Copynumber: 2.2 Consensus size: 102
25454719 AATGGATATC
25454729 GCACTTAGCAA-CCC-CGGGGAATCAGCACATAGCAACCCCCTTT-CATTTCAAAGATATGGTGG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATATGGTGG
* *
25454791 AT-ATCGCACTTAGCACCACCAATGAA-CGGGGAATCA
66 ATCA-CGCACATAGCACCACCAATAAATCGGGGAATCA
25454827 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATATGGTG
*
25454892 GATCACGCACATAGCACCACCCATAAATCGGGGAATCA
65 GATCACGCACATAGCACCACCAATAAATCGGGGAATCA
**
25454930 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
25454946 TTTATATACA
Statistics
Matches: 108, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
98 11 0.10
99 3 0.03
100 29 0.27
102 40 0.37
103 25 0.23
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (102 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATATGGTGG
ATCACGCACATAGCACCACCAATAAATCGGGGAATCA
Found at i:25455307 original size:29 final size:29
Alignment explanation
Indices: 25455274--25455337 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
25455264 TAATCCACCA
25455274 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
25455303 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
25455333 CCCAA
1 CCCAA
25455338 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:25455311 original size:30 final size:30
Alignment explanation
Indices: 25455281--25455337 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
25455271 CCACCCAACT
25455281 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
25455310 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
25455338 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:25458602 original size:11 final size:10
Alignment explanation
Indices: 25458577--25458637 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25458567 AACCAATAAA
25458577 TAAA-TGAGC
1 TAAATTGAGC
*
25458586 TGAATTGTAGC
1 TAAATTG-AGC
25458597 TAAATTGAGC
1 TAAATTGAGC
**
25458607 TCGATTGAGC
1 TAAATTGAGC
25458617 TGAAA-TGAGC
1 T-AAATTGAGC
*
25458627 TCAATTGAGC
1 TAAATTGAGC
25458637 T
1 T
25458638 GGGAGTTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25458638 original size:20 final size:20
Alignment explanation
Indices: 25458578--25458638 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25458568 ACCAATAAAT
*
25458578 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25458598 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25458619 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25458639 GGAGTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25460315 original size:11 final size:12
Alignment explanation
Indices: 25460285--25460316 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25460275 TTTCACTCTT
25460285 CTCTTTTTCAAA
1 CTCTTTTTCAAA
25460297 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
25460309 TTCTTTTT
1 CTCTTTTT
25460317 TCGCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:25460341 original size:14 final size:13
Alignment explanation
Indices: 25460309--25460356 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
25460299 CTTTTTCAAA
**
25460309 TTCTTTTTTCGCT
1 TTCTTTTTTCATT
25460322 TT-TTTTTTCAATT
1 TTCTTTTTTC-ATT
25460335 TTCTTTTCTTCATT
1 TTCTTTT-TTCATT
25460349 TTCTTTTT
1 TTCTTTTT
25460357 CTCTCACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 7 0.23
13 6 0.20
14 14 0.47
15 3 0.10
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (13 bp):
TTCTTTTTTCATT
Found at i:25460356 original size:15 final size:16
Alignment explanation
Indices: 25460322--25460358 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
25460312 TTTTTTCGCT
*
25460322 TTTTTTTTCAATTTTC
1 TTTTTCTTCAATTTTC
25460338 -TTTTCTTC-ATTTTC
1 TTTTTCTTCAATTTTC
25460352 TTTTTCT
1 TTTTTCT
25460359 CTCACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCAATTTTC
Found at i:25460384 original size:18 final size:18
Alignment explanation
Indices: 25460363--25460421 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
25460353 TTTTCTCTCA
25460363 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
25460381 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
25460399 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
25460417 GTTTT
1 CTTTT
25460422 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:25460438 original size:6 final size:6
Alignment explanation
Indices: 25460333--25460425 Score: 53
Period size: 6 Copynumber: 15.3 Consensus size: 6
25460323 TTTTTTTCAA
* * ** * *
25460333 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * * *
25460383 TTTGCA ATTTCT TTTTCT TCTTCG TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
25460426 CAATTTCTTT
Statistics
Matches: 60, Mismatches: 24, Indels: 5
0.67 0.27 0.06
Matches are distributed among these distances:
5 4 0.07
6 49 0.82
7 4 0.07
8 3 0.05
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTTCT
Found at i:25462613 original size:20 final size:20
Alignment explanation
Indices: 25462590--25462636 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25462580 GGGTTAAGAT
*
25462590 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
25462610 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
25462630 TGAGCTG
1 TGAGCTG
25462637 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:25469096 original size:48 final size:48
Alignment explanation
Indices: 25469044--25469149 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
25469034 TTGTCTTTTC
*
25469044 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
25469092 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
25469140 TTTCTTTTTC
1 TTTCTTTTTC
25469150 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:25470243 original size:11 final size:11
Alignment explanation
Indices: 25470229--25470253 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25470219 CTTTTTTTCC
25470229 TTTTTTTTGAA
1 TTTTTTTTGAA
25470240 TTTTTTTTGAA
1 TTTTTTTTGAA
25470251 TTT
1 TTT
25470254 CTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:25471776 original size:20 final size:20
Alignment explanation
Indices: 25471753--25471799 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
25471743 GGGTTAAGAT
* *
25471753 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAACTCGAG
* *
25471773 TGAGTTGACTTGAACTCGAG
1 TGAGCTGAATTGAACTCGAG
25471793 TGAGCTG
1 TGAGCTG
25471800 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAG
Found at i:25472184 original size:12 final size:12
Alignment explanation
Indices: 25472151--25472187 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25472141 CTTTTTTCCC
25472151 TTTTTTTC--AA
1 TTTTTTTCTGAA
*
25472161 TTTTTTTTTGAA
1 TTTTTTTCTGAA
25472173 TTTTTTTCTGAA
1 TTTTTTTCTGAA
25472185 TTT
1 TTT
25472188 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 7 0.30
12 16 0.70
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTCTGAA
Found at i:25473569 original size:11 final size:10
Alignment explanation
Indices: 25473544--25473604 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25473534 ACCAATAAAA
25473544 TAAA-TGAGC
1 TAAATTGAGC
*
25473553 TGAATTGTAGC
1 TAAATTG-AGC
25473564 TAAATTGAGC
1 TAAATTGAGC
**
25473574 TCGATTGAGC
1 TAAATTGAGC
25473584 TGAAA-TGAGC
1 T-AAATTGAGC
*
25473594 TCAATTGAGC
1 TAAATTGAGC
25473604 T
1 T
25473605 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25473605 original size:20 final size:20
Alignment explanation
Indices: 25473545--25473605 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25473535 CCAATAAAAT
*
25473545 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25473565 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25473586 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25473606 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25475174 original size:21 final size:22
Alignment explanation
Indices: 25475129--25475177 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
25475119 TCTTTTTTTA
25475129 TTTCTTTTTCTTTTCAATCTCTT
1 TTTC-TTTTCTTTTCAATCTCTT
* *
25475152 TTTCTTTTCTTTT-GATTTCTT
1 TTTCTTTTCTTTTCAATCTCTT
25475173 TTTCT
1 TTTCT
25475178 CGCTCGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 9 0.38
23 4 0.17
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTCTTTTCTTTTCAATCTCTT
Found at i:25486354 original size:18 final size:18
Alignment explanation
Indices: 25486331--25486366 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
25486321 AGATTAAAAG
25486331 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
25486349 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
25486367 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:25493344 original size:16 final size:16
Alignment explanation
Indices: 25493323--25493355 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25493313 TTCGCTGTAT
25493323 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
*
25493339 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCATAA
25493355 T
1 T
25493356 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCATAA
Found at i:25493609 original size:18 final size:17
Alignment explanation
Indices: 25493588--25493622 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25493578 TTATTATTAA
*
25493588 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25493606 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25493623 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25493786 original size:120 final size:120
Alignment explanation
Indices: 25493568--25494179 Score: 967
Period size: 120 Copynumber: 5.1 Consensus size: 120
25493558 TTAATCATAT
* *
25493568 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* * *
25493633 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * * *
25493688 TTTAACATAATTATTATTAAATACATTTTAATTAAAATATATGATTTAATAAAATTTTTAATAAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* * * *
25493753 CAATATTCTTATATGAATTTACTAAAATTATAATATATGATGCTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
25493808 TTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATTATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* *
25493873 AAATATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
25493928 TTTAAAATAATAATTATTAAATATAATTTAA-TAAAAAATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
*
25493992 AAAATATTCTTATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 -AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
25494048 TCTAAAATAATTATTATTAAATATAATTTAA-TATAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTA-AAATATATAATTTAATAAAATTCTTAATAT
25494112 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
25494168 TCTAAAATAATT
1 TTTAAAATAATT
25494180 GATTTTGTGG
Statistics
Matches: 462, Mismatches: 28, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
119 31 0.07
120 401 0.87
121 30 0.06
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:25493849 original size:18 final size:17
Alignment explanation
Indices: 25493826--25493862 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
25493816 AATTATTATT
25493826 AAATATA-T-TTTAATTA
1 AAATATATTATTTAA-TA
25493842 AAATATATTATTTAATA
1 AAATATATTATTTAATA
25493859 AAAT
1 AAAT
25493863 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 7 0.37
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATATATTATTTAATA
Found at i:25493942 original size:13 final size:12
Alignment explanation
Indices: 25493918--25493958 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
25493908 TATAATAGTA
25493918 TAAAATATAATT
1 TAAAATATAATT
25493930 TAAAATAATAATT
1 TAAAAT-ATAATT
*
25493943 ATTAAATATAATT
1 -TAAAATATAATT
25493956 TAA
1 TAA
25493959 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:25493968 original size:17 final size:17
Alignment explanation
Indices: 25493946--25493980 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
25493936 AATAATTATT
25493946 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
25493963 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
25493980 A
1 A
25493981 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:25494091 original size:18 final size:17
Alignment explanation
Indices: 25494068--25494102 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
25494058 TTATTATTAA
25494068 ATATAATTTAATATAAAT
1 ATATAATTTAATA-AAAT
25494086 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25494103 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25497487 original size:23 final size:23
Alignment explanation
Indices: 25497453--25497514 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
25497443 CGGTTTTGGG
* **
25497453 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATACGA
**
25497476 TTTGGTTTGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATACGA
25497499 TTTGGTACGAAATGGT
1 TTTGGTACGAAATGGT
25497515 TATGGTTCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATACGA
Found at i:25506840 original size:20 final size:20
Alignment explanation
Indices: 25506817--25506873 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
25506807 GGGTTAAGAT
*
25506817 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
25506837 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
*
25506857 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
25506874 AAACGGAGCT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:25509702 original size:10 final size:9
Alignment explanation
Indices: 25509689--25509724 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
25509679 CTTTTCACTT
25509689 TTTTTTGTTC
1 TTTTTT-TTC
25509699 TTTTTTTTAC
1 TTTTTTTT-C
25509709 TTTTTTTTC
1 TTTTTTTTC
25509718 TTTTTTT
1 TTTTTTT
25509725 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:25509710 original size:22 final size:21
Alignment explanation
Indices: 25509680--25509745 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
25509670 CTCGCAAGAC
*
25509680 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
25509702 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
* *
25509723 TTGCTCACTTCTTTTT-TTTTT
1 TT-TTCACTTTTTTTTCTTTTT
25509744 TT
1 TT
25509746 GAATTTCGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 12 0.32
22 26 0.68
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:25517585 original size:23 final size:23
Alignment explanation
Indices: 25517545--25517589 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25517535 GGGTTTGTTA
* **
25517545 CGAAATGGTAATGTGATTTGGTT
1 CGAAATCGTAATACGATTTGGTT
25517568 CGAAATCGTAATACGATTTGGT
1 CGAAATCGTAATACGATTTGGT
25517590 ATAAAATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (23 bp):
CGAAATCGTAATACGATTTGGTT
Found at i:25520640 original size:19 final size:20
Alignment explanation
Indices: 25520608--25520646 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25520598 ATATTTCCTG
*
25520608 CAAAAAAATCATTGGAAAATT
1 CAAAAAAA-CATTGAAAAATT
25520629 CAAAAAAA-ATTGAAAAAT
1 CAAAAAAACATTGAAAAAT
25520647 ATGAAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.21
Consensus pattern (20 bp):
CAAAAAAACATTGAAAAATT
Found at i:25530361 original size:6 final size:6
Alignment explanation
Indices: 25530350--25530383 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
25530340 AATTTTTTTC
* *
25530350 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
25530384 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:25530435 original size:21 final size:20
Alignment explanation
Indices: 25530391--25530435 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25530381 CAAATTCTTT
*
25530391 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
25530411 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
25530432 TTTC
1 TTTC
25530436 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:25531445 original size:15 final size:15
Alignment explanation
Indices: 25531425--25531461 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
25531415 GAATACAAAC
25531425 TTTTTTTTTTTCGGA
1 TTTTTTTTTTTCGGA
25531440 TTTTTTTTTTTCGGA
1 TTTTTTTTTTTCGGA
25531455 TTTTTTT
1 TTTTTTT
25531462 AAATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTTTCGGA
Found at i:25536794 original size:10 final size:9
Alignment explanation
Indices: 25536781--25536816 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
25536771 CTTTTCACTT
25536781 TTTTTTGTTC
1 TTTTTT-TTC
25536791 TTTTTTTTAC
1 TTTTTTTT-C
25536801 TTTTTTTTC
1 TTTTTTTTC
25536810 TTTTTTT
1 TTTTTTT
25536817 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:25536802 original size:22 final size:21
Alignment explanation
Indices: 25536772--25536831 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
25536762 CTCGCAAGAC
*
25536772 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
25536794 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
*
25536815 TTGCTCACTTCTTTTTT
1 TT-TTCACTT-TTTTTT
25536832 TTTGATGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 5 0.16
22 21 0.66
23 6 0.19
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:25544591 original size:22 final size:22
Alignment explanation
Indices: 25544563--25544606 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25544553 TTTTGAACCA
25544563 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
25544585 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
25544607 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:25549912 original size:10 final size:10
Alignment explanation
Indices: 25549896--25549953 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
25549886 CAACTCCGAC
25549896 CAGCTCAATT
1 CAGCTCAATT
* *
25549906 GAGCTCATTT
1 CAGCTCAATT
25549916 CAGCTCAA-T
1 CAGCTCAATT
25549925 CAAGCTCAATT
1 C-AGCTCAATT
*
25549936 TAGCTACAATT
1 CAGCT-CAATT
25549947 CAGCTCA
1 CAGCTCA
25549954 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25552449 original size:6 final size:6
Alignment explanation
Indices: 25552416--25552523 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
25552406 AAAGAAATTG
* * * ** *
25552416 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
25552463 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
25552514 AAAGAA AAAG
1 AAAGAA AAAG
25552524 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:25552467 original size:27 final size:27
Alignment explanation
Indices: 25552437--25552545 Score: 87
Period size: 27 Copynumber: 3.9 Consensus size: 27
25552427 AAAGAAAACG
*
25552437 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAGAAATTGAAAAAGAAA
** **
25552464 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAGAAATTGAAAAAGAAA
*
25552494 ATGAAG-AAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAG-AAATTGAAAAAGAAA
* *
25552521 AAG-CGAAAAAAGAATTTGAAAAAGA
1 AAGAAG-AAAAAGAAATTGAAAAAGA
25552546 GTTTGAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
26 6 0.10
27 29 0.46
28 7 0.11
29 2 0.03
30 19 0.30
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAGAAATTGAAAAAGAAA
Found at i:25552477 original size:18 final size:18
Alignment explanation
Indices: 25552420--25552478 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
25552410 AAATTGAAAG
* *
25552420 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
25552438 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
25552456 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
25552474 AAAAG
1 AAAAG
25552479 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:25552505 original size:14 final size:13
Alignment explanation
Indices: 25552484--25552521 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25552474 AAAAGTGAGA
25552484 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25552496 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
25552511 GAAAAAGAAAA
1 GAAAAAGAAAA
25552522 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:25552518 original size:13 final size:12
Alignment explanation
Indices: 25552402--25552521 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
25552392 AGAAAGAGAT
*
25552402 TGAAAAAGAAAT
1 TGAAAAAGAAAA
25552414 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
25552424 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
25552435 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* **
25552447 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
25552460 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
25552470 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
25552484 -GAAAAAGAAAA
1 TGAAAAAGAAAA
25552495 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
25552509 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
25552522 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 35 0.42
13 14 0.17
14 12 0.14
15 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:25552558 original size:12 final size:12
Alignment explanation
Indices: 25552527--25552558 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25552517 GAAAAAGCGA
*
25552527 AAAAAGAATTTG
1 AAAAAGAGTTTG
25552539 AAAAAGAGTTTG
1 AAAAAGAGTTTG
25552551 AAAAAGAG
1 AAAAAGAG
25552559 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:25554224 original size:10 final size:10
Alignment explanation
Indices: 25554208--25554265 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
25554198 CAACTCCGAC
25554208 CAGCTCAATT
1 CAGCTCAATT
* *
25554218 GAGCTCATTT
1 CAGCTCAATT
25554228 CAGCTCAA-T
1 CAGCTCAATT
25554237 CGAGCTCAATT
1 C-AGCTCAATT
*
25554248 TAGCTACAATT
1 CAGCT-CAATT
25554259 CAGCTCA
1 CAGCTCA
25554266 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25554231 original size:20 final size:20
Alignment explanation
Indices: 25554208--25554268 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25554198 CAACTCCGAC
25554208 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
25554228 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
25554249 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
25554269 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:25572840 original size:42 final size:42
Alignment explanation
Indices: 25572793--25572875 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
25572783 AATATGTGTG
25572793 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
25572835 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
25572876 CTTTGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.39
Consensus pattern (42 bp):
AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
Found at i:25574788 original size:10 final size:10
Alignment explanation
Indices: 25574773--25574834 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25574763 TTTGAACCAT
*
25574773 TACCAATTCG
1 TACCAATTCA
*
25574783 TACCAAATACCA
1 TACC-AAT-TCA
*
25574795 TACCATTTCA
1 TACCAATTCA
25574805 TACCAATTCCA
1 TACCAATT-CA
* *
25574816 TACCATTTCG
1 TACCAATTCA
25574826 TACCAATTC
1 TACCAATTC
25574835 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:25574818 original size:21 final size:21
Alignment explanation
Indices: 25574773--25574835 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25574763 TTTGAACCAT
* *
25574773 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
25574795 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
25574816 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
25574836 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25579154 original size:15 final size:16
Alignment explanation
Indices: 25579129--25579160 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
25579119 TATCTCACAC
25579129 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
25579145 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
25579160 T
1 T
25579161 TTCACATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:25580158 original size:12 final size:12
Alignment explanation
Indices: 25580141--25580184 Score: 63
Period size: 13 Copynumber: 3.7 Consensus size: 12
25580131 TACAAACTCT
25580141 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
25580153 TTTTTTTTTCAAA
1 TTTTTTTTT-GAA
25580166 TTTTTTTTTG-A
1 TTTTTTTTTGAA
25580177 TTTTTTTT
1 TTTTTTTT
25580185 ACAATATCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.31
12 9 0.31
13 11 0.38
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25580158 original size:13 final size:13
Alignment explanation
Indices: 25580140--25580184 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
25580130 ATACAAACTC
25580140 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
*
25580153 -TTTTTTTTTCAA
1 TTTTTTTTTTGAA
*
25580165 ATTTTTTTTTG-A
1 TTTTTTTTTTGAA
25580177 TTTTTTTT
1 TTTTTTTT
25580185 ACAATATCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:25586376 original size:74 final size:72
Alignment explanation
Indices: 25586239--25586390 Score: 236
Period size: 74 Copynumber: 2.1 Consensus size: 72
25586229 TAGCCAACAT
*
25586239 AGTTG-AGTTGCAACACTACGTAGAGATCATCGGTATGGTTACATGGCGATCAAGCTCGAAAAAG
1 AGTTGAAGTTGCAACACTACGTAGAGATCATCGATATGGTTACATGGCGATCAAGCTCGAAAAAG
25586303 CAACTCA
66 CAACTCA
*
25586310 AGTTGAAGTTGCCATACACTACGTAGAGATCATCGATATGGTTCACATGGCGATCAAGGTCG-AA
1 AGTTGAAGTTG-CA-ACACTACGTAGAGATCATCGATATGGTT-ACATGGCGATCAAGCTCGAAA
25586374 AAGCAACTCA
63 AAGCAACTCA
*
25586384 AGATGAA
1 AGTTGAA
25586391 AGGAGCCATA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
71 5 0.07
72 5 0.07
73 2 0.03
74 45 0.61
75 17 0.23
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (72 bp):
AGTTGAAGTTGCAACACTACGTAGAGATCATCGATATGGTTACATGGCGATCAAGCTCGAAAAAG
CAACTCA
Found at i:25589973 original size:23 final size:22
Alignment explanation
Indices: 25589921--25589973 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25589911 TCCACGTCTT
*
25589921 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25589943 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25589966 TTTCTTTT
1 TTTCTTTT
25589974 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25594162 original size:10 final size:10
Alignment explanation
Indices: 25594146--25594203 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
25594136 CAACTCCGAC
25594146 CAGCTCAATT
1 CAGCTCAATT
* *
25594156 GAGCTCATTT
1 CAGCTCAATT
25594166 CAGCTCAA-T
1 CAGCTCAATT
25594175 CGAGCTCAATT
1 C-AGCTCAATT
*
25594186 TAGCTACAATT
1 CAGCT-CAATT
25594197 CAGCTCA
1 CAGCTCA
25594204 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25594169 original size:20 final size:20
Alignment explanation
Indices: 25594146--25594206 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25594136 CAACTCCGAC
25594146 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
25594166 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
25594187 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
25594207 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:25596676 original size:15 final size:15
Alignment explanation
Indices: 25596658--25596691 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25596648 AAAAGAAATT
*
25596658 GAAAGAAAACAAAAA
1 GAAAAAAAACAAAAA
*
25596673 GAAAAAAAAGAAAAA
1 GAAAAAAAACAAAAA
25596688 GAAA
1 GAAA
25596692 TTGCAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
GAAAAAAAACAAAAA
Found at i:25596686 original size:6 final size:6
Alignment explanation
Indices: 25596677--25596763 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
25596667 CAAAAAGAAA
** * ** ** *
25596677 AAAAAG AAAAAG AAATTG CAAAAG AAAAAG AAATCG AAAAAG TGAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
25596725 AAAAAG AAAATG AAGAAAAG AAAATTG AAAAAG AAAAAG
1 AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAAAAG
25596764 CGAAAAAAGA
Statistics
Matches: 58, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
6 47 0.81
7 7 0.12
8 4 0.07
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (6 bp):
AAAAAG
Found at i:25596717 original size:18 final size:18
Alignment explanation
Indices: 25596677--25596718 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25596667 CAAAAAGAAA
*
25596677 AAAAAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATCG
*
25596695 CAAAAGAAAAAGAAATCG
1 AAAAAGAAAAAGAAATCG
25596713 AAAAAG
1 AAAAAG
25596719 TGAGAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAAGAAATCG
Found at i:25596745 original size:14 final size:13
Alignment explanation
Indices: 25596724--25596761 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25596714 AAAAGTGAGA
25596724 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25596736 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
25596751 GAAAAAGAAAA
1 GAAAAAGAAAA
25596762 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:25596758 original size:13 final size:12
Alignment explanation
Indices: 25596645--25596761 Score: 54
Period size: 12 Copynumber: 10.0 Consensus size: 12
25596635 AGAAAGAGAT
*
25596645 TGAAAAAGAAAT
1 TGAAAAAGAAAA
25596657 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
25596667 -CAAAAAG-AAA
1 TGAAAAAGAAAA
25596677 --AAAAAGAAAA
1 TGAAAAAGAAAA
* **
25596687 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
25596700 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
25596710 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
25596724 -GAAAAAGAAAA
1 TGAAAAAGAAAA
25596735 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
25596749 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
25596762 AGCGAAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
9 6 0.07
10 16 0.20
11 6 0.07
12 26 0.32
13 14 0.17
14 12 0.15
15 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:25596798 original size:12 final size:12
Alignment explanation
Indices: 25596767--25596798 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25596757 GAAAAAGCGA
*
25596767 AAAAAGAATTTG
1 AAAAAGAGTTTG
25596779 AAAAAGAGTTTG
1 AAAAAGAGTTTG
25596791 AAAAAGAG
1 AAAAAGAG
25596799 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:25598463 original size:10 final size:10
Alignment explanation
Indices: 25598447--25598504 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
25598437 CAACTCCGAC
25598447 CAGCTCAATT
1 CAGCTCAATT
* *
25598457 GAGCTCATTT
1 CAGCTCAATT
25598467 CAGCTCAA-T
1 CAGCTCAATT
25598476 CGAGCTCAATT
1 C-AGCTCAATT
*
25598487 TAGCTACAATT
1 CAGCT-CAATT
25598498 CAGCTCA
1 CAGCTCA
25598505 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25598470 original size:20 final size:20
Alignment explanation
Indices: 25598447--25598507 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25598437 CAACTCCGAC
25598447 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
25598467 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
25598488 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
25598508 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:25602288 original size:13 final size:12
Alignment explanation
Indices: 25602258--25602317 Score: 70
Period size: 13 Copynumber: 5.0 Consensus size: 12
25602248 GTATTACGGT
*
25602258 ATTGTAAAAAAA
1 ATTGAAAAAAAA
25602270 A-T-AAAAAAAA
1 ATTGAAAAAAAA
25602280 ACTTGAAAAAAAA
1 A-TTGAAAAAAAA
25602293 ATTCGAAAAAAAA
1 ATT-GAAAAAAAA
*
25602306 ATTCAAAAAAAA
1 ATTGAAAAAAAA
25602318 GTTTGTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 1 0.02
12 12 0.29
13 21 0.50
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:25602406 original size:26 final size:29
Alignment explanation
Indices: 25602363--25602424 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 29
25602353 GTATTGAAGG
* *
25602363 AAAAAAAGAAGAAAAAAATTCGGAATT-A
1 AAAAAAAGAAGAAAAAAAATCGAAATTGA
25602391 AAAAAAAG-A-AAAAAAAATCGAAATTGA
1 AAAAAAAGAAGAAAAAAAATCGAAATTGA
25602418 AAAAAAA
1 AAAAAAA
25602425 AGAGTGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 14 0.45
27 9 0.29
28 8 0.26
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.11
Consensus pattern (29 bp):
AAAAAAAGAAGAAAAAAAATCGAAATTGA
Found at i:25602427 original size:28 final size:28
Alignment explanation
Indices: 25602363--25602424 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 28
25602353 GTATTGAAGG
*
25602363 AAAAAAAGAAGAAAAAAATTCGGAATTA
1 AAAAAAAGAAGAAAAAAATTCGAAATTA
25602391 AAAAAAAGAA-AAAAAAA-TCGAAATTGA
1 AAAAAAAGAAGAAAAAAATTCGAAATT-A
25602418 AAAAAAA
1 AAAAAAA
25602425 AGAGTGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 7 0.22
27 15 0.47
28 10 0.31
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.11
Consensus pattern (28 bp):
AAAAAAAGAAGAAAAAAATTCGAAATTA
Found at i:25603298 original size:17 final size:15
Alignment explanation
Indices: 25603278--25603316 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
25603268 GCGAGCGAGA
25603278 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
25603295 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
25603310 AAGATGA
1 AA-ATGA
25603317 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:25615914 original size:12 final size:12
Alignment explanation
Indices: 25615897--25615954 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
25615887 AGACCGTATG
25615897 CAATTTTTTTTT
1 CAATTTTTTTTT
25615909 CAA-TTTTTTTT
1 CAATTTTTTTTT
25615920 CAATTTTTTTTT
1 CAATTTTTTTTT
25615932 CTTAA-TTTTTTTT
1 C--AATTTTTTTTT
*
25615945 CGATTTTTTT
1 CAATTTTTTT
25615955 GAATCTACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 12 0.29
12 18 0.44
13 9 0.22
14 2 0.05
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:25615917 original size:11 final size:11
Alignment explanation
Indices: 25615901--25615954 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
25615891 CGTATGCAAT
25615901 TTTTTTTTCAA
1 TTTTTTTTCAA
25615912 TTTTTTTTCAA
1 TTTTTTTTCAA
25615923 TTTTTTTTTCTTAA
1 -TTTTTTTTC--AA
*
25615937 TTTTTTTTCGA
1 TTTTTTTTCAA
25615948 TTTTTTT
1 TTTTTTT
25615955 GAATCTACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 19 0.49
12 9 0.23
13 9 0.23
14 2 0.05
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:25615938 original size:25 final size:23
Alignment explanation
Indices: 25615897--25615954 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 23
25615887 AGACCGTATG
25615897 CAATTTTTTTTTCAATTTTTTTT
1 CAATTTTTTTTTCAATTTTTTTT
25615920 CAATTTTTTTTTCTTAATTTTTTTT
1 CAATTTTTTTTTC--AATTTTTTTT
*
25615945 CGATTTTTTT
1 CAATTTTTTT
25615955 GAATCTACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 13 0.41
25 19 0.59
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
CAATTTTTTTTTCAATTTTTTTT
Found at i:25618665 original size:18 final size:18
Alignment explanation
Indices: 25618630--25618676 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25618620 AGACCGTATG
**
25618630 CAATTTTTTTTTTCTTTT
1 CAATTTTTTTTTGATTTT
25618648 CAATTTTTTTTTGATTTT
1 CAATTTTTTTTTGATTTT
* *
25618666 GACTTTTTTTT
1 CAATTTTTTTT
25618677 ATGTACCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (18 bp):
CAATTTTTTTTTGATTTT
Found at i:25619027 original size:22 final size:22
Alignment explanation
Indices: 25618976--25619041 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
25618966 GGTATTTGGG
* *
25618976 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
25618997 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
25619019 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
25619042 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:25624084 original size:10 final size:10
Alignment explanation
Indices: 25624064--25624095 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
25624054 AAATCGAGTT
25624064 AAAAG-AAAA
1 AAAAGAAAAA
25624073 AAAAGAAAAA
1 AAAAGAAAAA
25624083 AAAAGAAAAA
1 AAAAGAAAAA
25624093 AAA
1 AAA
25624096 GTGAAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:25624102 original size:10 final size:9
Alignment explanation
Indices: 25624064--25624096 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
25624054 AAATCGAGTT
25624064 AAAAGAAAA
1 AAAAGAAAA
25624073 AAAAGAAAAA
1 AAAAG-AAAA
25624083 AAAAGAAAA
1 AAAAGAAAA
25624092 AAAAG
1 AAAAG
25624097 TGAAAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:25625144 original size:18 final size:18
Alignment explanation
Indices: 25625118--25625167 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
25625108 AAATTGAAAG
*
25625118 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
25625136 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
25625154 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
25625168 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Done.