Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 21 of 292
Found at i:5572168 original size:21 final size:22
Alignment explanation
Indices: 5572130--5572185 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
5572120 TTTATTACTG
5572130 GTGGTTT-ATCCAC-A--ATGA
1 GTGGTTTCATCCACAACTATGA
5572148 GTGG-TTCATCCACAACTATGA
1 GTGGTTTCATCCACAACTATGA
*
5572169 GTGGTTTTATCCACAAC
1 GTGGTTTCATCCACAAC
5572186 GATGTGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.06
18 10 0.31
19 1 0.03
21 8 0.25
22 11 0.34
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (22 bp):
GTGGTTTCATCCACAACTATGA
Found at i:5574347 original size:19 final size:20
Alignment explanation
Indices: 5574307--5574348 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5574297 TTGGTTCATG
5574307 TTTTCAATCTCATATCTCAA
1 TTTTCAATCTCATATCTCAA
5574327 TTTTCAATTCTCA-AT-TCAA
1 TTTTCAA-TCTCATATCTCAA
5574346 TTT
1 TTT
5574349 CTCGTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAATCTCATATCTCAA
Found at i:5575592 original size:26 final size:26
Alignment explanation
Indices: 5575555--5575638 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5575545 TGATACAAAT
* *
5575555 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5575581 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5575607 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5575633 TGATAA
1 TGATAA
5575639 GAATTTCATG
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:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5585126 original size:23 final size:23
Alignment explanation
Indices: 5585112--5585236 Score: 74
Period size: 26 Copynumber: 4.9 Consensus size: 23
5585102 AAATGACATA
5585112 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
*
5585135 ATAATATAAAAGTATATATGTGAA-A-
1 ATAATATAAAA-TA-A-ATAT-AATAT
*
5585160 ATAATATATAATATATATAAATAATAT
1 ATAATATA-AA-ATA-A-ATATAATAT
5585187 GAGTAATATATAAAATAATTATATAATAT
1 -A-TAATAT--AAAATAA--ATATAATAT
*
5585216 ATAATATAAAAATAAAAATAA
1 ATAATAT-AAAATAAATATAA
5585237 AGCAAATAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
23 11 0.13
24 7 0.08
25 11 0.13
26 21 0.25
27 9 0.11
28 3 0.04
29 18 0.22
30 2 0.02
31 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:5585136 original size:7 final size:7
Alignment explanation
Indices: 5585109--5585223 Score: 81
Period size: 7 Copynumber: 17.1 Consensus size: 7
5585099 ATAAAATGAC
5585109 ATAATAAT
1 ATAAT-AT
5585117 ATAA-A-
1 ATAATAT
5585122 ATAA-AT
1 ATAATAT
5585128 ATAATAT
1 ATAATAT
5585135 ATAATAT
1 ATAATAT
5585142 A-AA-AGT
1 ATAATA-T
5585148 AT-ATAT
1 ATAATAT
*
5585154 GTGAA-A-
1 AT-AATAT
5585160 ATAATAT
1 ATAATAT
5585167 ATAATAT
1 ATAATAT
*
5585174 AT-ATAA
1 ATAATAT
5585180 ATAATAT
1 ATAATAT
5585187 GAGTAATAT
1 -A-TAATAT
5585196 ATAA-A-
1 ATAATAT
5585201 ATAATTAT
1 ATAA-TAT
5585209 ATAATAT
1 ATAATAT
5585216 ATAATAT
1 ATAATAT
5585223 A
1 A
5585224 AAAATAAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
5 12 0.14
6 20 0.23
7 39 0.44
8 11 0.12
9 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:5585173 original size:20 final size:19
Alignment explanation
Indices: 5585109--5585224 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 19
5585099 ATAAAATGAC
5585109 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
* *
5585128 ATAATATATAATATAAAAGT
1 ATAATATATAAAATAATA-T
*
5585148 AT-ATATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
5585167 ATAATATATATAAATAATAT
1 ATAATATATA-AAATAATAT
5585187 GAGTAATATATAAAATAATTAT
1 -A-TAATATATAAAATAA-TAT
*
5585209 ATAATATATAATATAA
1 ATAATATATAAAATAA
5585225 AAATAAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.12
19 15 0.18
20 38 0.46
21 8 0.10
22 12 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:5586035 original size:43 final size:43
Alignment explanation
Indices: 5585974--5586161 Score: 331
Period size: 43 Copynumber: 4.4 Consensus size: 43
5585964 TTATTTAAAA
*
5585974 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
*
5586017 AAACGCCCCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
5586060 AAACGTCGCTAAAGGTCATGACCTATAGCGGCGCTTTTCGCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
5586103 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
5586146 AAACGCCGCTAAAGGT
1 AAACGCCGCTAAAGGT
5586162 AATAAAATTT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 136 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5586291 original size:19 final size:21
Alignment explanation
Indices: 5586250--5586297 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
5586240 TTAAAATTTT
5586250 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
5586271 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
5586290 AACTAAAA
1 AACTAAAA
5586298 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:5590594 original size:7 final size:7
Alignment explanation
Indices: 5590584--5590673 Score: 99
Period size: 7 Copynumber: 12.3 Consensus size: 7
5590574 GACTAAAATA
*
5590584 TTAAATT
1 TTAATTT
*
5590591 TTAAATT
1 TTAATTT
*
5590598 TTACGTTT
1 TTA-ATTT
*
5590606 TTTATTTT
1 TTAAT-TT
5590614 TTAATTT
1 TTAATTT
5590621 TTAATTT
1 TTAATTT
5590628 TTAATTT
1 TTAATTT
*
5590635 TTAAATT
1 TTAATTT
5590642 TTAATTTT
1 TTAA-TTT
5590650 TTAATTTT
1 TTAA-TTT
5590658 TTAATTT
1 TTAATTT
5590665 TTAATTT
1 TTAATTT
5590672 TT
1 TT
5590674 GAGTTTATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
7 49 0.67
8 24 0.33
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (7 bp):
TTAATTT
Found at i:5590619 original size:22 final size:21
Alignment explanation
Indices: 5590589--5590673 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 21
5590579 AAATATTAAA
*
5590589 TTTTAAATTTTACGTTTTTTATT
1 TTTTAAATTTTA-ATTTTTTA-T
* *
5590612 TTTTAATTTTTAATTTTTAAT
1 TTTTAAATTTTAATTTTTTAT
5590633 TTTTAAATTTTAATTTTTTAATT
1 TTTTAAATTTTAATTTTTT-A-T
*
5590656 TTTTAATTTTTAATTTTT
1 TTTTAAATTTTAATTTTT
5590674 GAGTTTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
21 18 0.33
22 7 0.13
23 29 0.54
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTAAATTTTAATTTTTTAT
Found at i:5590639 original size:44 final size:44
Alignment explanation
Indices: 5590584--5590673 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 44
5590574 GACTAAAATA
*
5590584 TTAAATTTTAAATTTTACGTTTTTT-ATTTTTTAATTTTTAATTT
1 TTAAATTTTAAATTTTA-ATTTTTTAATTTTTTAATTTTTAATTT
*
5590628 TTAATTTTTAAATTTTAATTTTTTAATTTTTTAATTTTTAATTT
1 TTAAATTTTAAATTTTAATTTTTTAATTTTTTAATTTTTAATTT
5590672 TT
1 TT
5590674 GAGTTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 6 0.14
44 37 0.86
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (44 bp):
TTAAATTTTAAATTTTAATTTTTTAATTTTTTAATTTTTAATTT
Found at i:5590687 original size:7 final size:7
Alignment explanation
Indices: 5590603--5590690 Score: 63
Period size: 7 Copynumber: 12.4 Consensus size: 7
5590593 AAATTTTACG
5590603 TTTTTTA
1 TTTTTTA
5590610 TTTTTTAA
1 TTTTTT-A
*
5590618 TTTTTAA
1 TTTTTTA
*
5590625 TTTTTAA
1 TTTTTTA
*
5590632 TTTTTAA
1 TTTTTTA
* *
5590639 ATTTTAA
1 TTTTTTA
5590646 TTTTTTAA
1 TTTTTT-A
5590654 TTTTTTAA
1 TTTTTT-A
*
5590662 TTTTTAA
1 TTTTTTA
*
5590669 TTTTTGA
1 TTTTTTA
*
5590676 --GTTTA
1 TTTTTTA
5590681 TTTTTTA
1 TTTTTTA
5590688 TTT
1 TTT
5590691 CGGTTTAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
5 3 0.04
7 45 0.66
8 20 0.29
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TTTTTTA
Found at i:5590699 original size:37 final size:37
Alignment explanation
Indices: 5590609--5590687 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
5590599 TACGTTTTTT
*
5590609 ATTTTTTAA-TTTTTAATTTTTAATTTTTAAATTTTA
1 ATTTTTTAATTTTTTAATTTTTAATTTTTAAAGTTTA
*
5590645 ATTTTTTAATTTTTTAATTTTTAATTTTT-GAGTTT-
1 ATTTTTTAATTTTTTAATTTTTAATTTTTAAAGTTTA
5590680 ATTTTTTA
1 ATTTTTTA
5590688 TTTCGGTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
35 8 0.20
36 13 0.32
37 19 0.47
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.71
Consensus pattern (37 bp):
ATTTTTTAATTTTTTAATTTTTAATTTTTAAAGTTTA
Found at i:5591430 original size:26 final size:26
Alignment explanation
Indices: 5591394--5591499 Score: 167
Period size: 26 Copynumber: 4.1 Consensus size: 26
5591384 TGATACAAAT
5591394 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5591420 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5591446 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
5591472 TGATAATGGGTTAGGTGAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5591498 TG
1 TG
5591500 TAAGAATTTC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5593159 original size:27 final size:27
Alignment explanation
Indices: 5593118--5593238 Score: 170
Period size: 27 Copynumber: 4.4 Consensus size: 27
5593108 GAGGAAGCGT
*
5593118 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
5593145 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5593172 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
5593199 TCTGGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
*
5593227 TCTGGTGACTCT
1 TCTGGTGGCTCT
5593239 ATCACATTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 73 0.87
28 11 0.13
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5593203 original size:54 final size:55
Alignment explanation
Indices: 5593118--5593257 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
5593108 GAGGAAGCGT
* * * *
5593118 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
* *
5593172 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
* **
5593227 TCTGGTGACTCTATCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
5593258 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
Found at i:5593247 original size:27 final size:28
Alignment explanation
Indices: 5593118--5593257 Score: 148
Period size: 27 Copynumber: 5.2 Consensus size: 28
5593108 GAGGAAGCGT
* * *
5593118 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTACCACAATTATCTGTA
* *
5593145 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTACCACAATTATCTGTA
*
5593172 TCTGGTGGCTCTGCCAC-ATATATCTGT-
1 TCTGGTGGCTCTACCACAAT-TATCTGTA
*
5593199 TCTGGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTACCACAATTATCTGTA
* *
5593227 TCTGGTGACTCTATCAC-ATTATCTGT-
1 TCTGGTGGCTCTACCACAATTATCTGTA
5593253 TCTGG
1 TCTGG
5593258 CAGCCATGCT
Statistics
Matches: 104, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.06
27 81 0.78
28 17 0.16
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTACCACAATTATCTGTA
Found at i:5593343 original size:19 final size:22
Alignment explanation
Indices: 5593319--5593358 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
5593309 CTCCCCACAC
5593319 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
5593338 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
5593359 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:5594457 original size:12 final size:10
Alignment explanation
Indices: 5594412--5594436 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5594402 TAACGAGTAT
5594412 AAATTTAAAA
1 AAATTTAAAA
5594422 AAATTTAAAA
1 AAATTTAAAA
5594432 AAATT
1 AAATT
5594437 CTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:5595171 original size:15 final size:16
Alignment explanation
Indices: 5595153--5595186 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5595143 AGAAGCTATA
5595153 GTTTAGT-GTTTAGGG
1 GTTTAGTAGTTTAGGG
*
5595168 GTTTAGTATTTTAGGG
1 GTTTAGTAGTTTAGGG
5595184 GTT
1 GTT
5595187 ATAGATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (16 bp):
GTTTAGTAGTTTAGGG
Found at i:5595436 original size:41 final size:41
Alignment explanation
Indices: 5595239--5595438 Score: 283
Period size: 41 Copynumber: 4.9 Consensus size: 41
5595229 GAGTTATATG
* * *
5595239 ACTTTTAGTGGCGTTTTACCGAAAGCGCCGCTAATGCTCCG
1 ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCCA
* * *
5595280 ACTTTTAGCGGTGTTTTACCGAAAGCGCCGCTAATGCTCCG
1 ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCCA
* *
5595321 ACTTTTAGCGGCATTTTATCGAAAGCGCCGCTATTGCTCCA
1 ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCCA
* *
5595362 ACTTTTAGCGGCGTTTTACCTAAAGCGCCGCTATTGCTCTA
1 ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCCA
* * *
5595403 ACTTTTAGTGGCGTTTTACCTAAAACGCCGCTATTG
1 ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTG
5595439 TTCTATGTTT
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 146 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (41 bp):
ACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCCA
Found at i:5599064 original size:25 final size:25
Alignment explanation
Indices: 5599007--5599114 Score: 180
Period size: 25 Copynumber: 4.2 Consensus size: 25
5598997 CATGAAATTC
5599007 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
*
5599033 TTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
5599058 TTATCATGAAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
*
5599083 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACC-A
5599109 TTATCA
1 TTATCA
5599115 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 50 0.64
26 28 0.36
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:5599112 original size:51 final size:51
Alignment explanation
Indices: 5599007--5599114 Score: 200
Period size: 51 Copynumber: 2.1 Consensus size: 51
5598997 CATGAAATTC
5599007 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCA
5599058 TTATCATGAAACATTTACCTAA-CCATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACC-A
5599109 TTATCA
1 TTATCA
5599115 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 27 0.48
51 29 0.52
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (51 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCA
Found at i:5601639 original size:22 final size:23
Alignment explanation
Indices: 5601605--5601653 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5601595 TACTAACATG
*
5601605 TATATATACTATATATTTTTAT-
1 TATATATACTATACATTTTTATA
*
5601627 TATAT-TACGTATACGTTTTTATA
1 TATATATAC-TATACATTTTTATA
5601650 TATA
1 TATA
5601654 CGCTATGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TATATATACTATACATTTTTATA
Found at i:5603334 original size:31 final size:32
Alignment explanation
Indices: 5603276--5603339 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
5603266 CATACATTTG
5603276 TCATAAATTAATATATTTATTACATAAAAATC
1 TCATAAATTAATATATTTATTACATAAAAATC
*
5603308 TCAT-AATATAAT-TATTTAATTA-ATAAATATC
1 TCATAAAT-TAATATATTT-ATTACATAAAAATC
5603339 T
1 T
5603340 TTTACTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (32 bp):
TCATAAATTAATATATTTATTACATAAAAATC
Found at i:5603622 original size:3 final size:3
Alignment explanation
Indices: 5603614--5603675 Score: 63
Period size: 3 Copynumber: 19.3 Consensus size: 3
5603604 TTTATTTAAC
5603614 AAT AAT AAT AAT AAT AAT AAT AATT AAT AACT AAT ATAT AA- ACCAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA-T AAT A-AT AAT A--AT
*
5603660 AAT AAT AAT TAT AAT A
1 AAT AAT AAT AAT AAT A
5603676 TATTTATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 1 0.02
3 39 0.76
4 10 0.20
5 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5605310 original size:25 final size:27
Alignment explanation
Indices: 5605273--5605325 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5605263 TCAAACATGC
5605273 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5605299 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5605325 A
1 A
5605326 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5605681 original size:13 final size:13
Alignment explanation
Indices: 5605663--5605728 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
5605653 AGTTCTTCAT
5605663 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
5605676 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
5605689 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
5605702 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
5605715 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
5605728 T
1 T
5605729 TTGGTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5606301 original size:18 final size:18
Alignment explanation
Indices: 5606278--5606312 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5606268 AGCTTTTCTT
5606278 CCAGAAGTGCTTTTGAAG
1 CCAGAAGTGCTTTTGAAG
5606296 CCAGAAGTGCTTTTGAA
1 CCAGAAGTGCTTTTGAA
5606313 AAGCAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
CCAGAAGTGCTTTTGAAG
Found at i:5607493 original size:32 final size:32
Alignment explanation
Indices: 5607456--5607520 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5607446 AATGCTTACC
5607456 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
5607488 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
5607520 A
1 A
5607521 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:5608773 original size:137 final size:136
Alignment explanation
Indices: 5608534--5608808 Score: 487
Period size: 137 Copynumber: 2.0 Consensus size: 136
5608524 AGTCCATTCA
*
5608534 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATT
* *
5608599 CAGATAACAGTATGGCCCATACGCCCATTTAAAAATACATGCAACATCAGTAAACATATGCAAGC
66 CAGATAACAGTATGGCCCATACGCCCATCTAAAAATACATGCAACATCAAT-AACATATGCAAGC
5608664 CCATTTG
130 CCATTTG
*
5608671 GGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATT
* *
5608736 CAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAATAACATATGCAAGCC
66 CAGATAACAGTATGGCCCATACGCCCATCTAAAAATACATGCAACATCAATAACATATGCAAGCC
5608801 CATTTG
131 CATTTG
5608807 GG
1 GG
5608809 GAGACTACTC
Statistics
Matches: 132, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 22 0.17
137 110 0.83
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (136 bp):
GGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATT
CAGATAACAGTATGGCCCATACGCCCATCTAAAAATACATGCAACATCAATAACATATGCAAGCC
CATTTG
Found at i:5610616 original size:26 final size:26
Alignment explanation
Indices: 5610586--5610667 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
5610576 TGAAATTCCC
*
5610586 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5610612 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5610638 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
5610664 ATCA
1 ATCA
5610668 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5613654 original size:16 final size:16
Alignment explanation
Indices: 5613633--5613663 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5613623 CCATGTTATT
5613633 AGGATTGATCTTACCA
1 AGGATTGATCTTACCA
5613649 AGGATTGATCTTACC
1 AGGATTGATCTTACC
5613664 TAAACCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (16 bp):
AGGATTGATCTTACCA
Found at i:5617896 original size:7 final size:7
Alignment explanation
Indices: 5617894--5617941 Score: 78
Period size: 7 Copynumber: 6.7 Consensus size: 7
5617884 ATTTTTTAGT
*
5617894 TTTTTAG
1 TTTTTAA
5617901 TTTTTTAA
1 TT-TTTAA
5617909 TTTTTAA
1 TTTTTAA
5617916 TTTTTAA
1 TTTTTAA
5617923 TTTTTAA
1 TTTTTAA
5617930 TTTTTAA
1 TTTTTAA
5617937 TTTTT
1 TTTTT
5617942 TTGAGCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTTTAA
Found at i:5617942 original size:8 final size:7
Alignment explanation
Indices: 5617902--5617941 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
5617892 GTTTTTTAGT
5617902 TTTTTAA
1 TTTTTAA
5617909 TTTTTAA
1 TTTTTAA
5617916 TTTTTAA
1 TTTTTAA
5617923 TTTTTAA
1 TTTTTAA
5617930 TTTTTAA
1 TTTTTAA
5617937 TTTTT
1 TTTTT
5617942 TTGAGCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTAA
Found at i:5618520 original size:7 final size:7
Alignment explanation
Indices: 5618507--5618548 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
5618497 AACCCCAAAC
5618507 CCATAAA
1 CCATAAA
*
5618514 CCTTAAA
1 CCATAAA
5618521 CCATAAA
1 CCATAAA
*
5618528 CCATAAT
1 CCATAAA
5618535 CCATAAA
1 CCATAAA
*
5618542 CCTTAAA
1 CCATAAA
5618549 ATAGTAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
CCATAAA
Found at i:5618526 original size:14 final size:14
Alignment explanation
Indices: 5618507--5618548 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
5618497 AACCCCAAAC
5618507 CCATAAACCTTAAA
1 CCATAAACCTTAAA
* *
5618521 CCATAAACCATAAT
1 CCATAAACCTTAAA
5618535 CCATAAACCTTAAA
1 CCATAAACCTTAAA
5618549 ATAGTAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
CCATAAACCTTAAA
Found at i:5618589 original size:14 final size:14
Alignment explanation
Indices: 5618567--5618611 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
5618557 TCATACACTT
5618567 TAAACCCTAAA-TAA
1 TAAACCCTAAACT-A
*
5618581 TATACCCTAAACTA
1 TAAACCCTAAACTA
5618595 TAAACCCTAAACTA
1 TAAACCCTAAACTA
5618609 TAA
1 TAA
5618612 TGATAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 27 0.96
15 1 0.04
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:5618746 original size:14 final size:14
Alignment explanation
Indices: 5618705--5618752 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5618695 ACTAATTAAT
*
5618705 CTAAACCCTAAACTT
1 CTAAACCCTAAA-TC
*
5618720 CT-AATCCTCAAATC
1 CTAAACCCT-AAATC
5618734 CTAAACCCTAAATC
1 CTAAACCCTAAATC
5618748 CTAAA
1 CTAAA
5618753 TATGAACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAACCCTAAATC
Found at i:5618824 original size:11 final size:11
Alignment explanation
Indices: 5618808--5618839 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5618798 TAAACCCCAA
*
5618808 CCTTAAACTAC
1 CCTTAAACCAC
5618819 CCTTAAACCAC
1 CCTTAAACCAC
5618830 CCTTAAACCA
1 CCTTAAACCA
5618840 TGATCCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (11 bp):
CCTTAAACCAC
Found at i:5619101 original size:30 final size:31
Alignment explanation
Indices: 5619044--5619101 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5619034 TTTAAAATTA
*
5619044 TTTTAAAAAATAGTATTTTCATTTTTTTCAT
1 TTTTAAAAAATAGTATTTTCATGTTTTTCAT
*
5619075 TTTTAACAAATA-T-TTTTCTATGTTTTT
1 TTTTAAAAAATAGTATTTTC-ATGTTTTT
5619102 ACTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 8 0.33
31 11 0.46
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTAAAAAATAGTATTTTCATGTTTTTCAT
Found at i:5619473 original size:115 final size:116
Alignment explanation
Indices: 5619267--5619565 Score: 431
Period size: 115 Copynumber: 2.6 Consensus size: 116
5619257 TCGAGCATTA
* * * * *
5619267 GCGGCGTTTTTTATAAAGCGCCGCTAAAGGTGTACCTATAGTGGCGTTTTT-AAAAGTGCCGCTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCGCTA
* *
5619331 CAGCAACTAAAAGGTCAATAAATAAACGACGTCGTTTTGCAAAACTCTTTT
66 AAGCAACTAAAAGGTCAATAAATAAACGACATCGTTTTGCAAAACTCTTTT
*
5619382 GCGGCGCTTTTTAAAAAATGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCGCTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCGCTA
* * * *
5619447 AAGCCACTAAAAGGTCAATACA-AAACGACATTGTTTTGTAAAACTCTTTT
66 AAGCAACTAAAAGGTCAATAAATAAACGACATCGTTTTGCAAAACTCTTTT
* * * *
5619497 GCGGCGCTTTTTGAAAAACGCCGCTATAGGTGTACCTATAGCGGCGCTTCTTAAAAAACGCCGCT
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCG-TTTTTAAAAAGCGCCGCT
5619562 AAAG
65 AAAG
5619566 ATGTACCTAT
Statistics
Matches: 165, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 114 0.69
116 51 0.31
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (116 bp):
GCGGCGCTTTTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCGCTA
AAGCAACTAAAAGGTCAATAAATAAACGACATCGTTTTGCAAAACTCTTTT
Found at i:5619541 original size:155 final size:155
Alignment explanation
Indices: 5619382--5619758 Score: 628
Period size: 155 Copynumber: 2.4 Consensus size: 155
5619372 AAACTCTTTT
* * *
5619382 GCGGCGCTTTTTAAAAAATGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCGCTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCACTA
5619447 AAGCCACTAAAAGGTCAATACAAAACGACATTGTTTTGTAAAACTCTTTTGCGGCGCTTTTTGAA
66 AAGCCACTAAAAGGTCAATACAAAACGACATTGTTTTGTAAAACTCTTTTGCGGCGCTTTTTGAA
*
5619512 AAACGCCGCTATAGGTGTACCTATA
131 AAACGCCGCTAAAGGTGTACCTATA
* * *
5619537 GCGGCGCTTCTTAAAAAACGCCGCTAAAGATGTACCTATAGCAGCGTTTTTAAGAAGCGCCACTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCACTA
* * *
5619602 AAGCCACTAAAAGGTCAATACAAAGCGACGTTGTTTTGTAAAACTCTTTTGCGGTGCTTTTTGAA
66 AAGCCACTAAAAGGTCAATACAAAACGACATTGTTTTGTAAAACTCTTTTGCGGCGCTTTTTGAA
5619667 AAACGCCGCTAAAGGTGTACCTATA
131 AAACGCCGCTAAAGGTGTACCTATA
* * *
5619692 GCGGCGCTTGTTGAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGCTTTTTAAAAAACGCCACT
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCG-TTTTTAAAAAGCGCCACT
5619757 AA
65 AA
5619759 TGTTCGTTCT
Statistics
Matches: 205, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
155 187 0.91
156 18 0.09
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (155 bp):
GCGGCGCTTCTTAAAAAACGCCGCTAAAGGTGTACCTATAGCGGCGTTTTTAAAAAGCGCCACTA
AAGCCACTAAAAGGTCAATACAAAACGACATTGTTTTGTAAAACTCTTTTGCGGCGCTTTTTGAA
AAACGCCGCTAAAGGTGTACCTATA
Found at i:5619542 original size:40 final size:40
Alignment explanation
Indices: 5619497--5619604 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
5619487 AAACTCTTTT
* * *
5619497 GCGGCGCTTTTTGAAAAACGCCGCTATAGGTGTACCTATA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGATGTACCTATA
*
5619537 GCGGCGCTTCTTAAAAAACGCCGCTAAAGATGTACCTATA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGATGTACCTATA
* * * *
5619577 GCAGCG-TTTTTAAGAAGCGCCACTAAAG
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAG
5619605 CCACTAAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 18 0.31
40 41 0.69
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (40 bp):
GCGGCGCTTTTTAAAAAACGCCGCTAAAGATGTACCTATA
Found at i:5619717 original size:40 final size:40
Alignment explanation
Indices: 5619652--5619758 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
5619642 AAACTCTTTT
*
5619652 GCGGTGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
*
5619692 GCGGCGCTTGTTGAAAAACGCCGCTAAAGGTGTACCTATA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
* *
5619732 GCGGCGCTTTTTAAAAAACGCCACTAA
1 GCGGCGCTTTTTGAAAAACGCCGCTAA
5619759 TGTTCGTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (40 bp):
GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
Found at i:5621666 original size:26 final size:26
Alignment explanation
Indices: 5621636--5621743 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
5621626 TGAAATTCCC
5621636 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5621662 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5621688 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5621714 ATCGTGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5621740 ATCA
1 ATCA
5621744 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5622079 original size:24 final size:24
Alignment explanation
Indices: 5622052--5622100 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5622042 ACATTCACAG
5622052 AATTCCCGAAAATTGGGGCGTTAC
1 AATTCCCGAAAATTGGGGCGTTAC
** *
5622076 AATTTGCGAAAATTGGGGTGTTAC
1 AATTCCCGAAAATTGGGGCGTTAC
5622100 A
1 A
5622101 CTATAAACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (24 bp):
AATTCCCGAAAATTGGGGCGTTAC
Found at i:5623714 original size:5 final size:6
Alignment explanation
Indices: 5623701--5623747 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
5623691 ATAATTTAAT
5623701 AAATAA AAATAA AAATCTAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
5623748 ACATATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:5623748 original size:20 final size:20
Alignment explanation
Indices: 5623701--5623741 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5623691 ATAATTTAAT
**
5623701 AAATAAAAATAAAAATCTAA
1 AAATAAAAATAAAAATAAAA
5623721 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
5623741 A
1 A
5623742 TAAAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:5623781 original size:9 final size:9
Alignment explanation
Indices: 5623767--5623861 Score: 145
Period size: 9 Copynumber: 10.6 Consensus size: 9
5623757 TTTATACAAA
5623767 TAATTCGGT
1 TAATTCGGT
5623776 TAATTCGGT
1 TAATTCGGT
* *
5623785 TAATTTGGA
1 TAATTCGGT
5623794 TAATTCGGT
1 TAATTCGGT
5623803 TAATTCGGT
1 TAATTCGGT
5623812 TAATTCGGT
1 TAATTCGGT
*
5623821 TAATTCTGT
1 TAATTCGGT
*
5623830 TAATTCGAT
1 TAATTCGGT
*
5623839 TAATTCGAT
1 TAATTCGGT
5623848 TAATTCGGT
1 TAATTCGGT
5623857 TAATT
1 TAATT
5623862 TTATACTTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 78 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:5624944 original size:127 final size:126
Alignment explanation
Indices: 5624458--5625010 Score: 556
Period size: 128 Copynumber: 4.4 Consensus size: 126
5624448 GGTAAATCAC
* * * * * * * * * *
5624458 AACCCAGCATGATTAGGCACGATTTATCGAATTTCCAAATACGAAATATTGCCTTATTTTAA-TC
1 AACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATTCTAAGTT
* * * * * * *
5624522 TAAG-AAACATGGATGAAATTTCCAAGGGATATTCCATGTTTTAGTCGAACGAAAGATTGC
66 TAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAACGAAAAATCGA
* * * *
5624582 AACCCAGCACAATTGGGCACGATCCCTCAAACTTCCAAACACGAAACATTGCCTTATTCT-AGTT
1 AACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATTCTAAGTT
* * ** * *
5624646 TGAGAAAACACGGATGAAATTTCAAAAGGATATTCCGTATCATAGTCGAATGAAAGAAAATCAA
66 TAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAACG--A-AAAATCGA
* * * * * *
5624710 AACCCAACACGATTGGGCACGATCTTTCAAACTTCCAAACATGAAATATTGCCTC-GTCTCAGCT
1 AACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATTCTAAGTT
* * * *
5624774 TAAGAAAACATGGATGAAATTTTAAAGAGGATAATCCGCATTTTAGTCGAATGAAAAATCGA
66 TAAGAAAACATGGATGAAATTTCAAA-AGGATATTCCGTATTTTAGTCGAACGAAAAATCGA
* * * * * * * *
5624836 AACCTAGCACGATTGGGCACGATCTCTCGAAGTCCCCAAATACGAAATATTGCCTCGTTTTAATT
1 AACCCAGCACGATTGGGCACGATCTCTCAAACT-TCCAAACACGAAATATTGCCTCATTCTAAGT
* * *
5624901 TTAACAAAACATGGATGAAATTTCCAAAGGATATTCCGTATTTTAGTTGAACGAAAAATCGA
65 TTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAACGAAAAATCGA
* * * * *
5624963 AACCCAGCACGATTGGGCACAATTTCTCGAACCTCCAAACACAAAATA
1 AACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATA
5625011 ATTCCTTAAG
Statistics
Matches: 350, Mismatches: 70, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
123 1 0.00
124 53 0.15
125 39 0.11
126 47 0.13
127 83 0.24
128 105 0.30
129 22 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (126 bp):
AACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAATATTGCCTCATTCTAAGTT
TAAGAAAACATGGATGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAACGAAAAATCGA
Found at i:5626649 original size:3 final size:3
Alignment explanation
Indices: 5626574--5626637 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
5626564 TTATACTTTC
* **
5626574 TAT TATT TAT TGT TAT TGG TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5626620 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
5626638 ATGTTTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5627000 original size:23 final size:26
Alignment explanation
Indices: 5626970--5627024 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
5626960 ACATGTGCTA
*
5626970 TATGTATAT-TTTTTCT-T-CTATAT
1 TATGTATATGTATTTCTATGCTATAT
5626993 TATGTATATGTATTTCTAATGCTATAT
1 TATGTATATGTATTTCT-ATGCTATAT
5627020 TATGT
1 TATGT
5627025 TTTCATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 9 0.33
24 6 0.22
26 1 0.04
27 11 0.41
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.58
Consensus pattern (26 bp):
TATGTATATGTATTTCTATGCTATAT
Found at i:5627023 original size:21 final size:18
Alignment explanation
Indices: 5626999--5627043 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
5626989 ATATTATGTA
5626999 TATGTATTTCTAATGCTATAT
1 TATGTATTTC--ATG-TATAT
5627020 TATGT-TTTCATGTATAT
1 TATGTATTTCATGTATAT
5627037 TATGTAT
1 TATGTAT
5627044 ATACCTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
20 4 0.17
21 5 0.22
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.56
Consensus pattern (18 bp):
TATGTATTTCATGTATAT
Found at i:5627188 original size:24 final size:24
Alignment explanation
Indices: 5627142--5627188 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5627132 CATATATATA
**
5627142 CTATTATTTTATTTATTTTTATTC
1 CTATTATTTTATTTATTAATATTC
5627166 CTATTATATTTA-TTATTAATATT
1 CTATTAT-TTTATTTATTAATATT
5627189 AGTATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (24 bp):
CTATTATTTTATTTATTAATATTC
Found at i:5628627 original size:25 final size:27
Alignment explanation
Indices: 5628590--5628642 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5628580 TCACACATGC
5628590 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5628616 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5628642 A
1 A
5628643 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5630161 original size:26 final size:26
Alignment explanation
Indices: 5630125--5630284 Score: 261
Period size: 26 Copynumber: 6.2 Consensus size: 26
5630115 CATGAAATTC
*
5630125 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
5630151 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGGAACATTTACCTAACCCA
*
5630176 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
5630202 TTATCATGGAACATTTACCTAA-CCA
1 TTATCATGGAACATTTACCTAACCCA
*
5630227 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
5630253 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
5630279 TTATCA
1 TTATCA
5630285 ATTTGTATCA
Statistics
Matches: 128, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
25 48 0.38
26 80 0.62
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:5630205 original size:51 final size:51
Alignment explanation
Indices: 5630125--5630284 Score: 284
Period size: 51 Copynumber: 3.1 Consensus size: 51
5630115 CATGAAATTC
* * *
5630125 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCA
5630176 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCA
5630227 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACC-A
5630279 TTATCA
1 TTATCA
5630285 ATTTGTATCA
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 98 0.93
52 7 0.07
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (51 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCA
Found at i:5630256 original size:77 final size:77
Alignment explanation
Indices: 5630125--5630284 Score: 286
Period size: 77 Copynumber: 2.1 Consensus size: 77
5630115 CATGAAATTC
5630125 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCATTATCATGGAACAT
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCATTATCATGGAACAT
5630190 TTACCTAACCTA
66 TTACCTAACCTA
* *
5630202 TTATCATGGAACATTTACCTAA-CCATTATCATGGAACATTTACCTAACCTATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACC-ATTATCATGGAACA
5630266 TTTACCTAACCTA
65 TTTACCTAACCTA
5630279 TTATCA
1 TTATCA
5630285 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
76 26 0.32
77 54 0.68
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (77 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCATTATCATGGAACAT
TTACCTAACCTA
Found at i:5634451 original size:24 final size:27
Alignment explanation
Indices: 5634415--5634466 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
5634405 TCAAACATGC
5634415 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
*
5634441 ATTT-GGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5634466 A
1 A
5634467 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5635976 original size:26 final size:26
Alignment explanation
Indices: 5635940--5636101 Score: 270
Period size: 26 Copynumber: 6.2 Consensus size: 26
5635930 CATGAAATTC
5635940 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5635966 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5635992 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5636018 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5636044 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5636070 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5636096 TTATCA
1 TTATCA
5636102 ATTTGTATCA
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 130 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5636073 original size:78 final size:78
Alignment explanation
Indices: 5635940--5636101 Score: 306
Period size: 78 Copynumber: 2.1 Consensus size: 78
5635930 CATGAAATTC
5635940 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
5636005 TTTACCTAACCTA
66 TTTACCTAACCTA
* *
5636018 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTATCATGGAACA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
5636083 TTTACCTAACCTA
66 TTTACCTAACCTA
5636096 TTATCA
1 TTATCA
5636102 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (78 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCATTATCATGGAACA
TTTACCTAACCTA
Found at i:5636909 original size:24 final size:23
Alignment explanation
Indices: 5636884--5636971 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 23
5636874 TATGTTTTAT
5636884 ATATAT-T-ATGTATATATTTTC
1 ATATATATTATGTATATATTTTC
5636905 A-ATATTATTA-GT-TATATTTT-
1 ATATA-TATTATGTATATATTTTC
* *
5636925 ATATACTATTCCATGTAAATATTTCC
1 ATATA-TATT--ATGTATATATTTTC
*
5636951 ATATCATCTTATGTATATATT
1 ATAT-ATATTATGTATATATT
5636972 CTTAAACATT
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
20 4 0.08
21 17 0.33
22 3 0.06
23 2 0.04
24 12 0.23
25 6 0.12
26 7 0.13
27 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATATATTATGTATATATTTTC
Found at i:5637149 original size:32 final size:30
Alignment explanation
Indices: 5637076--5637150 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
5637066 ATATTAGTAC
5637076 ATATAT-TTATTATTCTTGTATACATATTT
1 ATATATATTATTATTCTTGTATACATATTT
* *
5637105 ATATATAGTATTATT-TTCGTATATATATCATT
1 ATATATATTATTATTCTT-GTATACATAT--TT
*
5637137 ATATTTATTATTAT
1 ATATATATTATTAT
5637151 ACCTATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 8 0.21
30 16 0.42
32 14 0.37
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (30 bp):
ATATATATTATTATTCTTGTATACATATTT
Found at i:5637273 original size:11 final size:11
Alignment explanation
Indices: 5637251--5637281 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5637241 ATATTTATTT
5637251 TATATATATATG
1 TATATAT-TATG
5637263 TATATATTATG
1 TATATATTATG
5637274 TATATATT
1 TATATATT
5637282 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:5639076 original size:29 final size:27
Alignment explanation
Indices: 5639044--5639097 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
5639034 CATTTTTTAT
*
5639044 CATTTAAACCATTTTTTTATTTTAAAATA
1 CATTTAAACC-TTTTGTT-TTTTAAAATA
*
5639073 CATTTTAACCTTTTGTTTTTTAAAA
1 CATTTAAACCTTTTGTTTTTTAAAA
5639098 GAAAAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 6 0.26
29 9 0.39
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (27 bp):
CATTTAAACCTTTTGTTTTTTAAAATA
Found at i:5641072 original size:21 final size:21
Alignment explanation
Indices: 5641048--5641089 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5641038 GTAAATAATT
5641048 ATATATATATATATATCTTTA
1 ATATATATATATATATCTTTA
* *
5641069 ATATATATATGTATATGTTTA
1 ATATATATATATATATCTTTA
5641090 TGCAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (21 bp):
ATATATATATATATATCTTTA
Found at i:5642521 original size:20 final size:21
Alignment explanation
Indices: 5642498--5642538 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5642488 CAATTTTCTA
*
5642498 TATTTTTTTATTAA-ATTTTG
1 TATTTTTTTATAAACATTTTG
5642518 TATTTTTTTATAAACATTTTG
1 TATTTTTTTATAAACATTTTG
5642539 AGTACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TATTTTTTTATAAACATTTTG
Found at i:5643901 original size:22 final size:21
Alignment explanation
Indices: 5643860--5643901 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5643850 TTTAGATAAA
*
5643860 ATTATTAAAAATACAGAAAAT
1 ATTATTAAAAATACAAAAAAT
*
5643881 ATTATTATAAAATATAAAAAA
1 ATTATTA-AAAATACAAAAAA
5643902 AGCTGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTATTAAAAATACAAAAAAT
Found at i:5644020 original size:16 final size:17
Alignment explanation
Indices: 5643977--5644032 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
5643967 CATGGTAAAA
*
5643977 AAATAATAAAGAATTATT
1 AAATATTAAA-AATTATT
5643995 AGAATCATTAAAAATTA-T
1 A-AAT-ATTAAAAATTATT
5644013 AAATATT-AAAATATATT
1 AAATATTAAAAAT-TATT
5644030 AAA
1 AAA
5644033 ATTTTAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 7 0.21
18 3 0.09
19 8 0.24
20 5 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
AAATATTAAAAATTATT
Found at i:5644057 original size:29 final size:28
Alignment explanation
Indices: 5644019--5644123 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
5644009 TTATAAATAT
5644019 TAAAATATATTAAAATTTTAGAAAAATGTA
1 TAAAA-ATATTAAAATTTTAGAAAAAT-TA
* * *
5644049 TAAAAATATAAATAATTCTA-AATAATTA
1 TAAAAATATTAA-AATTTTAGAAAAATTA
* * *
5644077 TTTAAAATATTAAAAATTAAGATAAAA-TA
1 -TAAAAATATTAAAATTTTAGA-AAAATTA
*
5644106 TAAAAATATAGAAAATTT
1 TAAAAATAT-TAAAATTT
5644124 ATAAAAAGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
28 14 0.24
29 30 0.52
30 14 0.24
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAAATATTAAAATTTTAGAAAAATTA
Found at i:5644499 original size:18 final size:18
Alignment explanation
Indices: 5644479--5644512 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5644469 TTTTTATTAT
5644479 TTTTA-AATATTTCTATC
1 TTTTATAATATTTCTATC
*
5644496 TTTTATAATTTTTCTAT
1 TTTTATAATATTTCTAT
5644513 ATGTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATAATATTTCTATC
Found at i:5644514 original size:26 final size:27
Alignment explanation
Indices: 5644470--5644528 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
5644460 TTTTATGATT
* *
5644470 TTTTATTATTTTTAAATAT-TTCTATC
1 TTTTATAATTTTTAAATATGTTATATC
** *
5644496 TTTTATAATTTTTCTATATGTTATATT
1 TTTTATAATTTTTAAATATGTTATATC
5644523 TTTTAT
1 TTTTAT
5644529 TTTTCATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATAATTTTTAAATATGTTATATC
Found at i:5644526 original size:18 final size:18
Alignment explanation
Indices: 5644488--5644525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5644478 TTTTTAAATA
* *
5644488 TTTCTATCTTTTATAATT
1 TTTCTATATGTTATAATT
5644506 TTTCTATATGTTAT-ATT
1 TTTCTATATGTTATAATT
5644523 TTT
1 TTT
5644526 TATTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTCTATATGTTATAATT
Found at i:5644786 original size:13 final size:13
Alignment explanation
Indices: 5644770--5644794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5644760 AAAAAAATTC
5644770 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
5644783 AAAAAAAAAGAA
1 AAAAAAAAAGAA
5644795 ATTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:5644929 original size:25 final size:25
Alignment explanation
Indices: 5644891--5644938 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5644881 ATATAATCTT
*
5644891 TAAATTTATAATTTTTTAGAAAATA
1 TAAATTTATAATTTCTTAGAAAATA
*
5644916 TAAATTT-TAGATTTCTTATAAAA
1 TAAATTTATA-ATTTCTTAGAAAA
5644939 AATTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAATTTATAATTTCTTAGAAAATA
Found at i:5644965 original size:19 final size:20
Alignment explanation
Indices: 5644941--5644983 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5644931 TTATAAAAAA
5644941 TTTTAA-TTTTAAAAATTAT
1 TTTTAATTTTTAAAAATTAT
*
5644960 TTTTAATTTTTGAAAATTAT
1 TTTTAATTTTTAAAAATTAT
5644980 TTTT
1 TTTT
5644984 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATTTTTAAAAATTAT
Found at i:5646685 original size:19 final size:20
Alignment explanation
Indices: 5646663--5646708 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
5646653 GTGACTAGGT
5646663 CGTGTGGAAGGGT-CTA-GAC
1 CGTGTGGAAGGGTAC-ACGAC
*
5646682 CGTGTGGCAGGGTACACGAC
1 CGTGTGGAAGGGTACACGAC
5646702 CGTGTGG
1 CGTGTGG
5646709 CTGAGGGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (20 bp):
CGTGTGGAAGGGTACACGAC
Found at i:5647498 original size:7 final size:7
Alignment explanation
Indices: 5647450--5647483 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
5647440 TTTTTTTTTT
5647450 TCAAAAA
1 TCAAAAA
5647457 TCAAAAA
1 TCAAAAA
5647464 TCAAAAA
1 TCAAAAA
5647471 TCAAAAA
1 TCAAAAA
5647478 TCAAAA
1 TCAAAA
5647484 CAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
TCAAAAA
Found at i:5647914 original size:9 final size:10
Alignment explanation
Indices: 5647865--5647923 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
5647855 TCACTCCTAC
*
5647865 TTTTAATAGT
1 TTTTAATATT
5647875 TTTT-ATA-T
1 TTTTAATATT
* *
5647883 TTGTGATATT
1 TTTTAATATT
*
5647893 TTTATAATTTT
1 TTT-TAATATT
5647904 TTTTAA-ATT
1 TTTTAATATT
5647913 TTTTAATATT
1 TTTTAATATT
5647923 T
1 T
5647924 ATCCATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 4 0.10
9 14 0.35
10 14 0.35
11 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTAATATT
Found at i:5648070 original size:20 final size:18
Alignment explanation
Indices: 5648014--5648071 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 18
5648004 ATAATAACTT
*
5648014 TAAATTTTCTAATTTTTT
1 TAAATTTTCTAATTTTTA
5648032 TACAATTATTCTTACATTTTTAA
1 TA-AATT-TTC-TA-ATTTTT-A
5648055 TAAATTTTCTATATTTT
1 TAAATTTTCTA-ATTTT
5648072 GCATATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 10 0.30
21 5 0.15
22 10 0.30
23 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTTCTAATTTTTA
Found at i:5648826 original size:29 final size:30
Alignment explanation
Indices: 5648770--5648848 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
5648760 ATCTCAAAAT
* *
5648770 TATACATAAATTTTGATTTAATGTATAATTG
1 TATACATAAATTTTAATTTAA-GTATAATTA
*
5648801 TATACATAAACTTTAATTTAA-TATAATTA
1 TATACATAAATTTTAATTTAAGTATAATTA
*
5648830 TATACGTGAAATTTTAATT
1 TATACAT-AAATTTTAATT
5648849 GTTATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.31
30 10 0.24
31 19 0.45
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (30 bp):
TATACATAAATTTTAATTTAAGTATAATTA
Found at i:5654443 original size:2 final size:2
Alignment explanation
Indices: 5654436--5654467 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5654426 GCTATTATTA
5654436 AT 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 AT
5654468 TTGGTGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5665889 original size:26 final size:26
Alignment explanation
Indices: 5665859--5665915 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
5665849 TCGTCGGTCG
*
5665859 CCGCCGTCGTCGACCACCGCCGGCCA
1 CCGCCGTCGTCGACCACAGCCGGCCA
5665885 CCGCCGTCGTCGACCACAGCCGGCCA
1 CCGCCGTCGTCGACCACAGCCGGCCA
5665911 CCGCC
1 CCGCC
5665916 TACGGTGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.12, C:0.54, G:0.26, T:0.07
Consensus pattern (26 bp):
CCGCCGTCGTCGACCACAGCCGGCCA
Found at i:5666307 original size:27 final size:28
Alignment explanation
Indices: 5666277--5666352 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 28
5666267 GGTTTCTTGG
*
5666277 TTTTTTTGGGGGGTTAGG-TTTTTCTT-
1 TTTTTTTTGGGGGTTAGGTTTTTTCTTC
**
5666303 TTTTTTTTTTGGGTTAGGTTTTTTCTTC
1 TTTTTTTTGGGGGTTAGGTTTTTTCTTC
*
5666331 TTTTTTTT--TGGTTAGGTTTTTT
1 TTTTTTTTGGGGGTTAGGTTTTTT
5666353 TCGGGGGGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 28 0.64
27 8 0.18
28 8 0.18
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.70
Consensus pattern (28 bp):
TTTTTTTTGGGGGTTAGGTTTTTTCTTC
Found at i:5666338 original size:26 final size:27
Alignment explanation
Indices: 5666287--5666352 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
5666277 TTTTTTTGGG
*
5666287 GGGTTAGG-TTTTTCTTTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTCTTTTTTTT
5666313 GGGTTAGGTTTTTTC-TTCTTTTTTTT
1 GGGTTAGGTTTTTTCTTTCTTTTTTTT
*
5666339 TGGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
5666353 TCGGGGGGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 31 0.84
27 6 0.16
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.70
Consensus pattern (27 bp):
GGGTTAGGTTTTTTCTTTCTTTTTTTT
Found at i:5667216 original size:30 final size:30
Alignment explanation
Indices: 5667180--5667241 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5667170 TTTTGAAAAA
5667180 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
5667210 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
5667240 CA
1 CA
5667242 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:5667556 original size:77 final size:78
Alignment explanation
Indices: 5667390--5667584 Score: 293
Period size: 77 Copynumber: 2.5 Consensus size: 78
5667380 ATGTGACACG
* * *
5667390 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTG-AAAAATACCT
* * *
5667455 CAGTGTGTGATCTA
65 CAGTGCGTGAGCCA
* * *
5667469 AAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTG-AAAATAGCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTC
5667533 AGTGCGTGAGCCA
66 AGTGCGTGAGCCA
5667546 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
5667585 TTTGAAAGGC
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 57 0.54
79 49 0.46
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTC
AGTGCGTGAGCCA
Found at i:5667671 original size:171 final size:168
Alignment explanation
Indices: 5667446--5667752 Score: 445
Period size: 171 Copynumber: 1.8 Consensus size: 168
5667436 ATAAATTGAA
* * * *
5667446 AAAATACCTCAGTGTGTGATCTAAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTAAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
* *
5667511 AGATAGAAATTGAAAATAGCTCAGTGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
5667575 TGATTTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
127 TGATTTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* * * * *
5667617 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTAAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
* * *
5667682 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
5667747 TTTTTT
131 TTTTTT
5667753 GAAAAACAGA
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
167 2 0.02
168 44 0.36
170 18 0.15
171 57 0.47
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (168 bp):
AAAATACCTCAGCGTGTGACCTAAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
Found at i:5667857 original size:77 final size:75
Alignment explanation
Indices: 5667600--5667952 Score: 453
Period size: 77 Copynumber: 4.7 Consensus size: 75
5667590 AAGGCAGAAA
* * * *** *
5667600 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATAT
5667665 GAGTTGATTTTT
64 GAGTTGATTTTT
* * * ** *
5667677 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATATGA
5667741 GTTGATTTTT
66 GTTGATTTTT
*
5667751 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATATGA
5667816 GTTGATTTTTTT
66 GTTGA--TTTTT
* * * * *
5667828 TTGAAAAACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTTCTCGCAAAATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATATGA
*
5667893 GTTGA--ATT
66 GTTGATTTTT
*
5667901 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
5667953 TGAACAGAAA
Statistics
Matches: 250, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
72 45 0.18
73 5 0.02
74 41 0.16
75 59 0.24
76 26 0.10
77 74 0.30
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATATGA
GTTGATTTTT
Found at i:5667919 original size:149 final size:148
Alignment explanation
Indices: 5667600--5667952 Score: 467
Period size: 149 Copynumber: 2.4 Consensus size: 148
5667590 AAGGCAGAAA
* * * ***
5667600 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATAC
* * * * *
5667665 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
64 GAGTTGATTTTTTTGAAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTC
* *
5667730 TCGCAATATGAGTTGATTTTT
129 TCGCAAAATGAGTTGA-TATT
* *
5667751 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
* **
5667816 GTTGATTTTTTTTTGAAAAACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTT
66 GTTGA--TTTTTTTG-AAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCT
5667881 CTCGCAAAATGAGTTGA-ATT
128 CTCGCAAAATGAGTTGATATT
*
5667901 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
5667953 TGAACAGAAA
Statistics
Matches: 179, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
149 78 0.44
150 5 0.03
151 39 0.22
152 57 0.32
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (148 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGA
GTTGATTTTTTTGAAAACAAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTAACCTCTC
GCAAAATGAGTTGATATT
Found at i:5667972 original size:49 final size:49
Alignment explanation
Indices: 5667906--5668001 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
5667896 GAATTTTGAA
*
5667906 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
5667955 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5668002 CTCGCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5667990 original size:121 final size:121
Alignment explanation
Indices: 5667834--5668073 Score: 417
Period size: 121 Copynumber: 2.0 Consensus size: 121
5667824 TTTTTTGAAA
*
5667834 AACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTAATTTCTCGCAAAATGAGTTGAA
1 AACAAAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAAAATGAGTTGAA
*
5667899 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* * * * *
5667955 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAAAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAAAATGAGTTGAA
5668020 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5668074 CTCGCAATAT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (121 bp):
AACAAAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTAATTTCTCGCAAAATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5668035 original size:72 final size:72
Alignment explanation
Indices: 5667955--5668181 Score: 285
Period size: 72 Copynumber: 3.0 Consensus size: 72
5667945 ACTCATTTTG
5667955 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5668020 TTTTGAA
66 TTTTGAA
5668027 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5668092 TTTTTTTTTTGAA
66 ------TTTTGAA
* * * * ** *
5668105 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
*
5668169 TGATTTTTGAA
62 TGAATTTTGAA
5668180 AA
1 AA
5668182 AGTAGAAATT
Statistics
Matches: 137, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
72 65 0.47
74 1 0.01
75 8 0.06
78 8 0.06
79 20 0.15
81 34 0.25
82 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:5668257 original size:13 final size:13
Alignment explanation
Indices: 5668230--5668263 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5668220 GAGTTGATTC
*
5668230 TTGAACAACATAAA
1 TTGAA-AACAGAAA
5668244 TTGAAAACAGAAA
1 TTGAAAACAGAAA
5668257 TTGAAAA
1 TTGAAAA
5668264 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:5668353 original size:140 final size:142
Alignment explanation
Indices: 5668100--5668674 Score: 566
Period size: 142 Copynumber: 3.9 Consensus size: 142
5668090 AATTTTTTTT
5668100 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
5668164 TGAGCTGATTTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATT
62 TGAGCTGA-TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATT
* *
5668229 C-TTGAACAACATAA-A
126 CTTTCAAAAACATAATA
5668244 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
5668309 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTTC
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTTC
5668374 AAAAACATAATA
131 AAAAACATAATA
* * * * * *
5668386 ATGAAAAAAGAAATGGAAAATACCTCGGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * * * *** * * **
5668451 TTGATTTTTTGAAAGA-CAGAAATTGAAAGTCTTAATTAAAAATACCTCGGCGTGCGACCTGAGG
66 CTGA--TTTTGAAAAAGTAGAAATTAAAAG-----GTTCAACCCACCTC-TC--GCAATATGA-G
** * * ** * *
5668515 CTCAACTCACCTCTC-GCAATATGAGTTGAA
120 -TTGA-T--TCTTTCAAAAACAT-A-AT--A
* * * * *
5668545 ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
1 T-TGAAA-ACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
5668610 AGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTT
64 AGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTT
5668675 GACAAACAGA
Statistics
Matches: 349, Mismatches: 57, Indels: 47
0.77 0.13 0.10
Matches are distributed among these distances:
140 59 0.17
141 47 0.13
142 63 0.18
143 34 0.10
144 15 0.04
147 2 0.01
148 8 0.02
149 2 0.01
150 2 0.01
151 7 0.02
152 7 0.02
153 2 0.01
154 2 0.01
155 13 0.04
156 5 0.01
157 1 0.00
159 11 0.03
160 15 0.04
161 54 0.15
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (142 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTTC
AAAAACATAATA
Found at i:5668720 original size:127 final size:126
Alignment explanation
Indices: 5668516--5668743 Score: 341
Period size: 127 Copynumber: 1.8 Consensus size: 126
5668506 GACCTGAGGC
*
5668516 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
1 TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
5668581 CCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGT
66 CCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGT
** * * * *
5668642 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAATTACCTCATCGTG
1 TCAACCCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAAATTGAAAATACCTCAGCGTG
* * *
5668706 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
64 CCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
5668744 ATTAGAACAC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
126 27 0.30
127 60 0.67
128 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (126 bp):
TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
CCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGT
Found at i:5668734 original size:73 final size:71
Alignment explanation
Indices: 5668642--5668836 Score: 248
Period size: 72 Copynumber: 2.7 Consensus size: 71
5668632 ATTAAAAGGT
* * * * *
5668642 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGA-AAACAAAAATTGAAAATACCTCAGCGTGC
*
5668707 CCTGAGGC
64 CCCGAGGC
* *
5668715 TCAACTCACCTCTCGCAATATGAGTTGATATTAGAACACAAAAATTGAAAATACCTCAGCGTGCC
1 TCAACTCACCTCTCGCAATATGAGTTGAT-TTTGAAAACAAAAATTGAAAATACCTCAGCGTGCC
5668780 CCGAGGC
65 CCGAGGC
* * *
5668787 TCAACTCACCTTTCGCAATATGGGCTGATTTTGAAAAACAAAAATT-AAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTGAAAA
5668837 GGCTTAACTC
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 7 0.07
72 68 0.64
73 31 0.29
74 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTGAAAATACCTCAGCGTGCCC
CGAGGC
Found at i:5668939 original size:122 final size:124
Alignment explanation
Indices: 5668711--5668957 Score: 333
Period size: 122 Copynumber: 2.0 Consensus size: 124
5668701 TCGTGTCCTG
* * ** * * *
5668711 AGGCTCAACTCACCTCTCGCAATATGAGTTGATATTAGAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATAAATCAATATTAGAACACAAAAACTAAAAATACCTCAGCA
5668776 TGCCCCGAGGCTCAACTCACCTTTCGCAATATGGGCTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTTTCGCAATATGGGCTGATTTTG-AAAACAAAAATTAAA
* * *
5668836 AGGCTTAACTCACCTCTCGCAATATAAATCAAT-TTA-AA-ACATAAACTAAAAATACCTCGGCA
1 AGGCTCAACTCACCTCTCGCAATATAAATCAATATTAGAACACAAAAACTAAAAATACCTCAGCA
*
5668898 TGCCCCGAGGCTCAACTCA-CTTCTCGCAATATGAG-TCGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTT-TCGCAATATGGGCT-GATTTTGAAAACAAAAATTAAA
5668957 A
1 A
5668958 ATACCTCATC
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
121 20 0.18
122 56 0.51
123 2 0.02
124 3 0.03
125 28 0.26
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATAAATCAATATTAGAACACAAAAACTAAAAATACCTCAGCA
TGCCCCGAGGCTCAACTCACCTTTCGCAATATGGGCTGATTTTGAAAACAAAAATTAAA
Found at i:5668979 original size:71 final size:70
Alignment explanation
Indices: 5668836--5669011 Score: 194
Period size: 71 Copynumber: 2.5 Consensus size: 70
5668826 AAAAATTAAA
* * * * * * *
5668836 AGGCTTAACTCACCTCTCGCAATATAAATC-AATTTAAAACATAAACTAAAAATACCTCGGCATG
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCATG
5668900 CCCCG
66 CCCCG
* * *
5668905 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTGAAAACAAAAATTAAAAATACCTCATCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTT-AAAACAAAAACTAAAAATACCTCAGCAT
* **
5668970 GTCTTG
65 GCCCCG
*
5668976 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTCGATTTT
5669012 CCTTGAAAAG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
69 26 0.29
70 5 0.06
71 59 0.66
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCATG
CCCCG
Found at i:5669893 original size:7 final size:7
Alignment explanation
Indices: 5669881--5669913 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5669871 GATCCCTCTC
5669881 TTTTTCT
1 TTTTTCT
5669888 TTTTTCT
1 TTTTTCT
5669895 TTTTTCT
1 TTTTTCT
5669902 TTTCTT-T
1 TTT-TTCT
5669909 TTTTT
1 TTTTT
5669914 AAGATGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 21 0.84
8 2 0.08
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:5681349 original size:2 final size:2
Alignment explanation
Indices: 5681300--5681330 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5681290 GGTATTTAAA
*
5681300 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5681331 GTAGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5687889 original size:72 final size:72
Alignment explanation
Indices: 5687750--5687892 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
5687740 AAGTATCATA
** * ** * *
5687750 GATTGATTGCCTCTTTTGTGGCATTTAAAAACGTCACGGAAAATGCTATCCAAAATGTGACACAT
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
5687815 TGTTTGT
66 TGTTTGT
* * *
5687822 GATTGATTGCCTCTTTTTTAACATTTAAAAACATCACAAAAAATTCTATTCAAAACGTCACGA-A
1 GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCAC-ACA
5687886 TTGTTTG
65 TTGTTTG
5687893 ACTATTTTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (72 bp):
GATTGATTGCCTCTTTTGTAACATTTAAAAACATCACAAAAAATGCTATCCAAAACGTCACACAT
TGTTTGT
Found at i:5691610 original size:22 final size:21
Alignment explanation
Indices: 5691584--5691631 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
5691574 AATTTTTGAT
*
5691584 TTATTGTTCTATTTTATTTATC
1 TTATTGTT-TATTTTAATTATC
*
5691606 TTATTTGTTTATTTTAATTATT
1 TTA-TTGTTTATTTTAATTATC
5691628 TTAT
1 TTAT
5691632 CTAACTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 17 0.74
23 5 0.22
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTATTGTTTATTTTAATTATC
Found at i:5692121 original size:20 final size:20
Alignment explanation
Indices: 5692096--5692136 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5692086 TTTTCAACAG
5692096 ATTATAGTGGTCAAATGGTT
1 ATTATAGTGGTCAAATGGTT
5692116 ATTATAGTGGTCAAATGGTT
1 ATTATAGTGGTCAAATGGTT
5692136 A
1 A
5692137 AGGGAGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTATAGTGGTCAAATGGTT
Found at i:5693780 original size:2 final size:2
Alignment explanation
Indices: 5693773--5693800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5693763 TACTTGAAGC
5693773 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
5693801 TTAGTGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5694176 original size:24 final size:26
Alignment explanation
Indices: 5694126--5694178 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5694116 AAAATCTTCG
5694126 CTTTCATTGCTTCTGCTGCCACTTGAT
1 CTTTCATTGCTTCT-CTGCCACTTGAT
*
5694153 CTTTCGTTGCTTCT-T-CCACTTGAT
1 CTTTCATTGCTTCTCTGCCACTTGAT
5694177 CT
1 CT
5694179 CTTGCTAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
27 13 0.52
ACGTcount: A:0.09, C:0.30, G:0.13, T:0.47
Consensus pattern (26 bp):
CTTTCATTGCTTCTCTGCCACTTGAT
Found at i:5696332 original size:24 final size:25
Alignment explanation
Indices: 5696294--5696341 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5696284 CACGGACCAA
5696294 TTTTTAATAGTAAAAATAGATTATT
1 TTTTTAATAGTAAAAATAGATTATT
* *
5696319 TTTTTAATAG-AAAACTAGTTTAT
1 TTTTTAATAGTAAAAATAGATTAT
5696342 GTTATTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (25 bp):
TTTTTAATAGTAAAAATAGATTATT
Found at i:5701902 original size:18 final size:19
Alignment explanation
Indices: 5701846--5701902 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
5701836 AACTTACAAA
*
5701846 AAAAATACAAAAAATTATTT
1 AAAAATAAAAAAAATTA-TT
*
5701866 AAAAGTAAAAAAGAATTATT
1 AAAAATAAAAAA-AATTATT
*
5701886 AAAAAT-AGAAAAATTAT
1 AAAAATAAAAAAAATTAT
5701903 AACTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 17 0.53
21 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAATAAAAAAAATTATT
Found at i:5702251 original size:21 final size:21
Alignment explanation
Indices: 5702168--5702312 Score: 79
Period size: 21 Copynumber: 7.0 Consensus size: 21
5702158 AGAAATGATC
*
5702168 AAATATATAAAAGTTATAAAAA
1 AAATATA-AAAAATTATAAAAA
* *
5702190 ATAT-TAAAAACATTAT--AGA
1 AAATATAAAAA-ATTATAAAAA
** * **
5702209 AAATAT-TTAAATTTTATTAA
1 AAATATAAAAAATTATAAAAA
5702229 AAATATAAAAAATTATAAAAA
1 AAATATAAAAAATTATAAAAA
* *
5702250 AAATCA-CAAAATTTATAAAAA
1 AAAT-ATAAAAAATTATAAAAA
*
5702271 AAATCATAAAGAACTTAT-AAAA
1 AAAT-ATAAA-AAATTATAAAAA
* *
5702293 AATTGT-AAAAATTATAAAAA
1 AAATATAAAAAATTATAAAAA
5702313 TATATAGTAA
Statistics
Matches: 93, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
18 4 0.04
19 13 0.14
20 18 0.19
21 39 0.42
22 13 0.14
23 6 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATATAAAAAATTATAAAAA
Found at i:5702381 original size:10 final size:11
Alignment explanation
Indices: 5702181--5702382 Score: 52
Period size: 10 Copynumber: 19.7 Consensus size: 11
5702171 TATATAAAAG
5702181 TTATAAAAA-A
1 TTATAAAAATA
*
5702191 -TATTAAAAACA
1 TTA-TAAAAATA
5702202 TTATAGAAAATA
1 TTATA-AAAATA
*
5702214 TT-T--AAATT
1 TTATAAAAATA
*
5702222 TTATTAAAA-A
1 TTATAAAAATA
5702232 -TATAAAAA-A
1 TTATAAAAATA
5702241 TTATAAAAA-A
1 TTATAAAAATA
*
5702251 -AATCACAAAAT-
1 TTAT-A-AAAATA
*
5702262 TTATAAAAAAAA
1 TTAT-AAAAATA
* *
5702274 TCATAAAGAA-C
1 TTATAAA-AATA
5702285 TTATAAAAA-A
1 TTATAAAAATA
*
5702295 TTGT-AAAA-A
1 TTATAAAAATA
5702304 TTATAAAAATA
1 TTATAAAAATA
**
5702315 -TATAGTAATA
1 TTATAAAAATA
5702325 -TATAAAAAT-
1 TTATAAAAATA
** *
5702334 TTAT-AATTTT
1 TTATAAAAATA
5702344 TTA-ATAAAATA
1 TTATA-AAAATA
*
5702355 GTA-AAAAATA
1 TTATAAAAATA
*
5702365 TTGTAAAAA-A
1 TTATAAAAATA
5702375 TTATAAAA
1 TTATAAAA
5702383 TCAAGCAGAG
Statistics
Matches: 144, Mismatches: 27, Indels: 42
0.68 0.13 0.20
Matches are distributed among these distances:
8 6 0.04
9 24 0.17
10 61 0.42
11 36 0.25
12 17 0.12
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (11 bp):
TTATAAAAATA
Found at i:5702778 original size:9 final size:9
Alignment explanation
Indices: 5702764--5702819 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
5702754 ATAGGATACG
5702764 ATAATTTTT
1 ATAATTTTT
5702773 ATAATTTTTTT
1 ATAA--TTTTT
*
5702784 ATAAATTTT
1 ATAATTTTT
5702793 AT-ATTTCTT
1 ATAATTT-TT
5702802 -TACATTTTT
1 ATA-ATTTTT
5702811 ATAATTTTT
1 ATAATTTTT
5702820 TTAAGACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 4 0.10
9 20 0.51
10 6 0.15
11 9 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5703643 original size:15 final size:15
Alignment explanation
Indices: 5703623--5703657 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
5703613 CAACCCTAGT
5703623 CAATTTTTTTTTTTA
1 CAATTTTTTTTTTTA
5703638 CAA--TTTTTTTTTA
1 CAATTTTTTTTTTTA
5703651 CAATTTT
1 CAATTTT
5703658 AAACTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.72
15 5 0.28
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (15 bp):
CAATTTTTTTTTTTA
Found at i:5703646 original size:13 final size:13
Alignment explanation
Indices: 5703628--5703657 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5703618 CTAGTCAATT
5703628 TTTTTTTTTACAA
1 TTTTTTTTTACAA
5703641 TTTTTTTTTACAA
1 TTTTTTTTTACAA
5703654 TTTT
1 TTTT
5703658 AAACTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTACAA
Found at i:5705241 original size:34 final size:35
Alignment explanation
Indices: 5705203--5705272 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
5705193 AATATTCCAC
* * *
5705203 ATATGAAATTCCGTATCGTCCTATT-ATTTTTTTA
1 ATATGAAATTCCGCATCATCCCATTAATTTTTTTA
*
5705237 ATATGAAATTTCGCATCATCCCATTAATTTTTTTA
1 ATATGAAATTCCGCATCATCCCATTAATTTTTTTA
5705272 A
1 A
5705273 CTTTACTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (35 bp):
ATATGAAATTCCGCATCATCCCATTAATTTTTTTA
Found at i:5718896 original size:31 final size:31
Alignment explanation
Indices: 5718858--5718926 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
5718848 AAAAACCCTA
* *
5718858 AAGTTCAGGCTTCAATATA-AGAATAATTGTC
1 AAGTTCAGGCTTCAATATAGA-AACAATTGCC
5718889 AAGTTCAGGCTTCAATATAGAAACAATTGCC
1 AAGTTCAGGCTTCAATATAGAAACAATTGCC
5718920 AAGTTCA
1 AAGTTCA
5718927 AGGACTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
AAGTTCAGGCTTCAATATAGAAACAATTGCC
Found at i:5720754 original size:148 final size:149
Alignment explanation
Indices: 5720578--5720869 Score: 550
Period size: 149 Copynumber: 2.0 Consensus size: 149
5720568 ATTATAATTT
* *
5720578 TATAATGATTTTATCCTTCAGTCTTTATAA-TTTTTTTATCAATTTGATTATTATTAATTTTTTT
1 TATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTTTTT
5720642 AATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAGACT
66 AATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAGACT
5720707 CGAATTGTTATTTTTTTAG
131 CGAATTGTTATTTTTTTAG
5720726 TATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTTTTT
1 TATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTTTTT
5720791 AATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAGACT
66 AATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAGACT
*
5720856 CGAATTGTTGTTTT
131 CGAATTGTTATTTT
5720870 CTTACAGAAA
Statistics
Matches: 140, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
148 29 0.21
149 111 0.79
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (149 bp):
TATAATGATTTTAGCCTTCAGTCTTTATAATTTTTTTTATCAATTTAATTATTATTAATTTTTTT
AATTAAATTTAATCCTAAACTTTTCAGAAATAGTCGTATTTGATCATCAATCTTTTAAAAAGACT
CGAATTGTTATTTTTTTAG
Found at i:5721094 original size:62 final size:61
Alignment explanation
Indices: 5721000--5721121 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 61
5720990 ATTTGAAATT
* *
5721000 ATTATTGTTGGTGTGACACATAAAACAAATAGTGTCATGTTAGCATGAAGTATTCGTAAAA
1 ATTATTGTTGGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAAAA
*
5721061 ATTATTTGTTGGTGTGACACAAAAAACAAATAGTGTCATGTTAGGATGAAGTATTCATAAA
1 ATTA-TTGTTGGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAAA
5721122 CTAACACATG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 4 0.07
62 53 0.93
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (61 bp):
ATTATTGTTGGTGTGACACAAAAAACAAATAGTGTCATGTTAGCATGAAGTATTCATAAAA
Found at i:5721658 original size:16 final size:17
Alignment explanation
Indices: 5721627--5721658 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5721617 TGTTTAAATG
5721627 TAATTTTTCTCTAATTA
1 TAATTTTTCTCTAATTA
5721644 TAATTTTTCTC-AATT
1 TAATTTTTCTCTAATT
5721659 CAACCAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTTCTCTAATTA
Found at i:5722535 original size:21 final size:21
Alignment explanation
Indices: 5722503--5722542 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5722493 ACTCTAAACT
*
5722503 CGAATCTCAAACATTAAACCC
1 CGAATCTCAAACACTAAACCC
5722524 CGAA-CTCAAAACACTAAAC
1 CGAATCTC-AAACACTAAAC
5722543 TCAAACCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.33, G:0.05, T:0.15
Consensus pattern (21 bp):
CGAATCTCAAACACTAAACCC
Done.