Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 132 of 313
Found at i:42622220 original size:37 final size:37
Alignment explanation
Indices: 42622176--42622321 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
42622166 GATAGCTTTA
*
42622176 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
42622213 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
42622250 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
42622287 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
42622322 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:42624853 original size:16 final size:16
Alignment explanation
Indices: 42624829--42624882 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
42624819 TTTGGTTCGC
*
42624829 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
42624845 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
* * *
42624861 TGTATTAGAATAGAGG
1 TGTAATGGATTAGAGG
42624877 TGTAAT
1 TGTAAT
42624883 AGCATAATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:42625053 original size:18 final size:17
Alignment explanation
Indices: 42625032--42625066 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42625022 TTATTATTAA
*
42625032 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42625050 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42625067 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:42625241 original size:47 final size:46
Alignment explanation
Indices: 42625169--42625337 Score: 145
Period size: 47 Copynumber: 3.7 Consensus size: 46
42625159 TCAATTAAAA
*
42625169 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * * *
42625216 TATATGAATTTGTATAATTTTAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
42625261 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
42625307 TATATGAATTTATATAATTTAAAATAATTAT
1 TATATGAATTTATATAATTTAAAATAATTAT
42625338 TATTAAATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 8 0.08
46 9 0.09
47 46 0.48
48 7 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:42625241 original size:101 final size:93
Alignment explanation
Indices: 42625126--42625346 Score: 243
Period size: 91 Copynumber: 2.3 Consensus size: 93
42625116 ATACTATCAA
* *
42625126 ATATAATTTGAAATAATTAATATTAAATATATTTCAATTAAAATATATGATTTAATAAAATTT-A
1 ATATAATTTAAAATAATTATTATTAAATATA--T-AATT-AAATA-ATGA--T-ATAAAATTTCA
42625190 AAATAATT-ATAACTAATAAATTTTCTTATATGAATTT
58 AAA-AATTCATAA-TAATAAATTTTCTTATATGAATTT
* * * * *
42625227 GTATAATTTTAAATAATTATTATT-AA-ATATAATTTAATAATGATATATAATTTCATAAAATTC
1 ATATAATTTAAAATAATTATTATTAAATATATAATTAAATAATGATATAAAATTTCAAAAAATTC
* *
42625290 TTGATAATAAATTTTCTTATATGAATTT
66 ATAATAATAAATTTTCTTATATGAATTT
42625318 ATATAATTTAAAATAATTATTATTAAATA
1 ATATAATTTAAAATAATTATTATTAAATA
42625347 ACATTCAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
91 58 0.55
92 8 0.08
93 1 0.01
94 4 0.04
95 4 0.04
96 4 0.04
97 1 0.01
99 3 0.03
100 2 0.02
101 21 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (93 bp):
ATATAATTTAAAATAATTATTATTAAATATATAATTAAATAATGATATAAAATTTCAAAAAATTC
ATAATAATAAATTTTCTTATATGAATTT
Found at i:42635220 original size:20 final size:20
Alignment explanation
Indices: 42635195--42635237 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
42635185 TGTAATGATT
42635195 AACTAAACTGCTTTAAAAGA
1 AACTAAACTGCTTTAAAAGA
42635215 AACTAAACTGCTTTAAAAGA
1 AACTAAACTGCTTTAAAAGA
42635235 AAC
1 AAC
42635238 CAAAGCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (20 bp):
AACTAAACTGCTTTAAAAGA
Found at i:42639475 original size:3 final size:3
Alignment explanation
Indices: 42639462--42639492 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
42639452 TTATTTTTAA
42639462 TTG TT- TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
42639493 AGGAGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:42639681 original size:21 final size:23
Alignment explanation
Indices: 42639627--42639681 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 23
42639617 TTCGTGCCGT
*
42639627 TTGAAGAATA-AAAATATCAATA
1 TTGAAGAATACAAAACATCAATA
* *
42639649 TT-AATAAAACAAAACA-CAA-A
1 TTGAAGAATACAAAACATCAATA
42639669 TTGAAGAATACAA
1 TTGAAGAATACAA
42639682 GGATGATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 7 0.27
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
TTGAAGAATACAAAACATCAATA
Found at i:42643314 original size:23 final size:24
Alignment explanation
Indices: 42643288--42643332 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
42643278 TTATTACTTT
42643288 ATCAATAATT-AATATTTAAAAAA
1 ATCAATAATTAAATATTTAAAAAA
* **
42643311 ATCATTGCTTAAATATTTAAAA
1 ATCAATAATTAAATATTTAAAA
42643333 TTTTAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
ATCAATAATTAAATATTTAAAAAA
Found at i:42648145 original size:4 final size:4
Alignment explanation
Indices: 42648136--42648160 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42648126 CATTGGACAT
42648136 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
42648161 TGTAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:42648755 original size:15 final size:16
Alignment explanation
Indices: 42648725--42648757 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42648715 AAGTGTATAT
42648725 ATATATATTATAGTTA
1 ATATATATTATAGTTA
*
42648741 ATATAT-TTGTAGTTA
1 ATATATATTATAGTTA
42648756 AT
1 AT
42648758 TTTAACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (16 bp):
ATATATATTATAGTTA
Found at i:42648869 original size:19 final size:20
Alignment explanation
Indices: 42648829--42648870 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
42648819 AATTAGATTT
**
42648829 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATAGAAA
42648849 ATTT-AAATAAAAATAGAAA
1 ATTTAAAATAAAAATAGAAA
42648868 ATT
1 ATT
42648871 GTAACATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTAAAATAAAAATAGAAA
Found at i:42649354 original size:16 final size:15
Alignment explanation
Indices: 42649312--42649354 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
42649302 CTTTTCAATT
*
42649312 ATTATATTTTTTGTAA
1 ATTATA-TTTTTATAA
*
42649328 ATTTTATTTTTATAA
1 ATTATATTTTTATAA
42649343 ATTATATGTTTT
1 ATTATAT-TTTT
42649355 TTTTCTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
ATTATATTTTTATAA
Found at i:42655198 original size:13 final size:13
Alignment explanation
Indices: 42655180--42655204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42655170 AATTTCCATT
42655180 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
42655193 AGAAAAAAAGAA
1 AGAAAAAAAGAA
42655205 GTGAGAGAGG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:42662511 original size:45 final size:45
Alignment explanation
Indices: 42662438--42662643 Score: 344
Period size: 45 Copynumber: 4.6 Consensus size: 45
42662428 TACGTATGAT
* * *
42662438 CACTTATCAC-TTATC-CCTGATCAGATAAGTGTAGTTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
42662481 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
42662526 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
* *
42662571 CATTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
42662617 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
42662644 AGCACTCAAA
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 10 0.06
44 4 0.03
45 108 0.70
46 32 0.21
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:42667911 original size:48 final size:48
Alignment explanation
Indices: 42667829--42667922 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
42667819 TTTCTTGGCT
* * *
42667829 TAAAAATGCCTAAGTCAGCCTAATTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
*
42667877 TAAAAACGCCTAAGTTAG-CTCAA-TTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AATTTC-CAACAATAAAGGATTCAAC
42667923 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
Found at i:42670531 original size:3 final size:3
Alignment explanation
Indices: 42670523--42670550 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42670513 TCTTTGTTCC
42670523 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42670551 AAAAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42676991 original size:20 final size:20
Alignment explanation
Indices: 42676961--42677020 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
42676951 ATATTCTTTT
42676961 TAATATAATATAAAAATT-AA
1 TAAT-TAATATAAAAATTAAA
**
42676981 TAAATTAATATAAATTTTAAA
1 T-AATTAATATAAAAATTAAA
42677002 TAATTAA-ATAAAATATTAA
1 TAATTAATATAAAA-ATTAA
42677021 GTATTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.15
20 22 0.67
21 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTAATATAAAAATTAAA
Found at i:42679457 original size:14 final size:14
Alignment explanation
Indices: 42679438--42679477 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42679428 TTGATTGGTA
42679438 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42679452 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42679466 GGAAAATGTTTT
1 GTAAAATGTTTT
42679478 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42679486 original size:20 final size:20
Alignment explanation
Indices: 42679461--42679500 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42679451 CGTAAAATGA
*
42679461 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
42679481 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
42679501 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:42679490 original size:34 final size:35
Alignment explanation
Indices: 42679446--42679512 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42679436 TAGTAAAATG
*
42679446 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
42679480 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
42679513 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:42679516 original size:14 final size:15
Alignment explanation
Indices: 42679440--42679516 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42679430 GATTGGTAGT
* *
42679440 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
42679454 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
42679468 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
42679488 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
42679503 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
42679517 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:42682333 original size:25 final size:26
Alignment explanation
Indices: 42682305--42682365 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
42682295 GAATATGCTG
42682305 AGAAGAGAAG-ATGAAGAACAGAAGA
1 AGAAGAGAAGAATGAAGAACAGAAGA
**
42682330 AGAA-A-AAGGAATGAAGAATGGAAGA
1 AGAAGAGAA-GAATGAAGAACAGAAGA
42682355 AGAAGAAGAAG
1 AGAAG-AGAAG
42682366 GAGCCTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 21 0.72
27 2 0.07
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.33, T:0.05
Consensus pattern (26 bp):
AGAAGAGAAGAATGAAGAACAGAAGA
Found at i:42682450 original size:18 final size:17
Alignment explanation
Indices: 42682427--42682460 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42682417 TTTGCAACAC
42682427 AAGGGGAAGGGAGAAGGG
1 AAGGGGAAGGGA-AAGGG
42682445 AAGGGGAAGGGAAAGG
1 AAGGGGAAGGGAAAGG
42682461 TTAAAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGAAAGGG
Found at i:42682539 original size:41 final size:41
Alignment explanation
Indices: 42682482--42682571 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
42682472 AAGAAGGCGT
42682482 CATTTTCCGGAAAATGTCTTACCGAGTTTAAAAGCGTAAGA
1 CATTTTCCGGAAAATGTCTTACCGAGTTTAAAAGCGTAAGA
42682523 CATTTTCCGGAAAATGTCTTACCGAGTTTAAAAGCGTAAGA
1 CATTTTCCGGAAAATGTCTTACCGAGTTTAAAAGCGTAAGA
42682564 CATTTTCC
1 CATTTTCC
42682572 TCAAATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (41 bp):
CATTTTCCGGAAAATGTCTTACCGAGTTTAAAAGCGTAAGA
Found at i:42688552 original size:15 final size:16
Alignment explanation
Indices: 42688527--42688559 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42688517 TTGATAAACT
*
42688527 AAAAATCTAAGTGCTG
1 AAAAATCTAAGTACTG
42688543 AAAAAT-TAAGTACTG
1 AAAAATCTAAGTACTG
42688558 AA
1 AA
42688560 TTTTTATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (16 bp):
AAAAATCTAAGTACTG
Found at i:42689100 original size:29 final size:30
Alignment explanation
Indices: 42689042--42689114 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 30
42689032 TTATATTAAA
* *
42689042 TAAAAAATAAAATGATTATTAAACACA-TT
1 TAAAAAATAAAATGATTATAAAACAAATTT
42689071 TAAAAAATAAAAT-ATTA-AAAACATTAATTTT
1 TAAAAAATAAAATGATTATAAAACA--AA-TTT
42689102 TAATAAAATAAAA
1 TAA-AAAATAAAA
42689115 AAAATCCAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 5 0.14
28 4 0.11
29 14 0.38
31 5 0.14
32 9 0.24
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (30 bp):
TAAAAAATAAAATGATTATAAAACAAATTT
Found at i:42695658 original size:18 final size:18
Alignment explanation
Indices: 42695622--42695662 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
42695612 ATCCAATACT
42695622 TAAACTAAATACTATAAAA
1 TAAACTAAATAC-ATAAAA
42695641 TAAACTGAAATA-ATAAAA
1 TAAACT-AAATACATAAAA
42695659 TAAA
1 TAAA
42695663 ATATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (18 bp):
TAAACTAAATACATAAAA
Found at i:42707085 original size:15 final size:17
Alignment explanation
Indices: 42707065--42707103 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42707055 ACATCATTTG
42707065 TTGGATT-TG-TAACTT
1 TTGGATTCTGATAACTT
*
42707080 TTGGATTCTGATAATTT
1 TTGGATTCTGATAACTT
42707097 TTGGATT
1 TTGGATT
42707104 AGGATATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 12 0.57
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (17 bp):
TTGGATTCTGATAACTT
Found at i:42707100 original size:17 final size:15
Alignment explanation
Indices: 42707060--42707103 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
42707050 TATGAACATC
42707060 ATTTGTTGGATTTGTA
1 ATTT-TTGGATTTGTA
*
42707076 ACTTTTGGATTCTGATA
1 ATTTTTGGATT-TG-TA
42707093 ATTTTTGGATT
1 ATTTTTGGATT
42707104 AGGATATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (15 bp):
ATTTTTGGATTTGTA
Found at i:42710476 original size:40 final size:40
Alignment explanation
Indices: 42710421--42710503 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
42710411 CATTTATTCA
42710421 TAATTAATATCTATTTTCCTTTAGATAGAAATTACATGTG
1 TAATTAATATCTATTTTCCTTTAGATAGAAATTACATGTG
42710461 TAATTAATATCTATTTTCCTTTAGATAGAAATTACATGTG
1 TAATTAATATCTATTTTCCTTTAGATAGAAATTACATGTG
42710501 TAA
1 TAA
42710504 CTCTATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (40 bp):
TAATTAATATCTATTTTCCTTTAGATAGAAATTACATGTG
Found at i:42729431 original size:22 final size:22
Alignment explanation
Indices: 42729403--42729446 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42729393 CTGGAGAAAA
42729403 AGGAGTGAGACATGGGACCCTT
1 AGGAGTGAGACATGGGACCCTT
42729425 AGGAGTGAGACATGGGACCCTT
1 AGGAGTGAGACATGGGACCCTT
42729447 TGTCCCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (22 bp):
AGGAGTGAGACATGGGACCCTT
Found at i:42732807 original size:24 final size:24
Alignment explanation
Indices: 42732760--42732844 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
42732750 CGAAAAAAAA
* ** *
42732760 AATATAGAACAATTTGGAGTAAAT
1 AATATAAAACAATTTAAAGCAAAT
*
42732784 AGTATAAAACAATTTAAAGCAAAT
1 AATATAAAACAATTTAAAGCAAAT
* **
42732808 AATATGTAAAACAAATTAAAATAAAT
1 AATA--TAAAACAATTTAAAGCAAAT
42732834 AATATACAAAC
1 AATATA-AAAC
42732845 TACAAAGCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 24 0.49
25 4 0.08
26 21 0.43
ACGTcount: A:0.59, C:0.07, G:0.08, T:0.26
Consensus pattern (24 bp):
AATATAAAACAATTTAAAGCAAAT
Found at i:42732826 original size:26 final size:26
Alignment explanation
Indices: 42732788--42732838 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
42732778 GTAAATAGTA
* *
42732788 TAAAACAATTTAAAGCAAATAATATG
1 TAAAACAAATTAAAACAAATAATATG
*
42732814 TAAAACAAATTAAAATAAATAATAT
1 TAAAACAAATTAAAACAAATAATAT
42732839 ACAAACTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (26 bp):
TAAAACAAATTAAAACAAATAATATG
Found at i:42732889 original size:22 final size:21
Alignment explanation
Indices: 42732863--42732911 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
42732853 AATTTAAAAT
*
42732863 AAATAACATATAAGACAATTTA
1 AAATAACATATAA-AAAATTTA
** *
42732885 AAATATGATGTAAAAAATTTA
1 AAATAACATATAAAAAATTTA
42732906 AAATAA
1 AAATAA
42732912 ATAATATGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATAACATATAAAAAATTTA
Found at i:42732952 original size:28 final size:26
Alignment explanation
Indices: 42732896--42732969 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
42732886 AATATGATGT
42732896 AAAAAA-TTTAAAATAAATAATATGTA-
1 AAAAAAGTTTAAAATAAATAATA--TAC
*
42732922 AAAAGAAGTTTCAAATAAATAATATAC
1 AAAA-AAGTTTAAAATAAATAATATAC
*
42732949 AAAATAGTTTAAAATAAATAA
1 AAAAAAGTTTAAAATAAATAA
42732970 ATGATGTGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.50
27 6 0.14
28 15 0.36
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (26 bp):
AAAAAAGTTTAAAATAAATAATATAC
Found at i:42733121 original size:28 final size:29
Alignment explanation
Indices: 42733089--42733158 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
42733079 GGAAAACTTG
*
42733089 AAATAAATAATAATAAAACAATTTAAAAT
1 AAATAAATAATAAGAAAACAATTTAAAAT
* **
42733118 -AAT-AATATATGAGAAAAGGATTTAAAAT
1 AAATAAATA-ATAAGAAAACAATTTAAAAT
42733146 AAATAAATGAATA
1 AAATAAAT-AATA
42733159 GCATATTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
27 4 0.12
28 19 0.59
29 3 0.09
30 5 0.16
31 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATAAATAATAAGAAAACAATTTAAAAT
Found at i:42734396 original size:6 final size:6
Alignment explanation
Indices: 42734387--42734454 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
42734377 TAGGTTTAGG
* * *
42734387 TTGGGT TTGGGT TTGGGT TGGTGGT TTTGG- TT-GGT TTGAGT TTGGG-
1 TTGGGT TTGGGT TTGGGT TTG-GGT TTGGGT TTGGGT TTGGGT TTGGGT
*
42734433 TTGGGT CTTGTTGT TTGGGT TT
1 TTGGGT -TTG-GGT TTGGGT TT
42734455 TGGGCCTCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 9 0.18
6 26 0.53
7 10 0.20
8 2 0.04
ACGTcount: A:0.01, C:0.01, G:0.44, T:0.53
Consensus pattern (6 bp):
TTGGGT
Found at i:42734430 original size:29 final size:30
Alignment explanation
Indices: 42734379--42734436 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
42734369 ATTAGGGTTA
*
42734379 GGTTTAGGTTGGGTTTGGGTTTGGGTTGGT
1 GGTTTAGGTTGGGTTTGAGTTTGGGTTGGT
*
42734409 GGTTTTGGTT-GGTTTGAGTTTGGGTTGG
1 GGTTTAGGTTGGGTTTGAGTTTGGGTTGG
42734437 GTCTTGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (30 bp):
GGTTTAGGTTGGGTTTGAGTTTGGGTTGGT
Found at i:42734931 original size:25 final size:25
Alignment explanation
Indices: 42734887--42734999 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
42734877 ACGAGCATGT
* * *
42734887 TAACGGGAAGCTCTTCCGAGCCATA
1 TAACGGGAAGCTCATACGAGCCAAA
42734912 TAACGGGAAGCTCATACGAGCCAAA
1 TAACGGGAAGCTCATACGAGCCAAA
* *
42734937 TATCGGGAAACTCATGA-GAGCCAAA
1 TAACGGGAAGCTCAT-ACGAGCCAAA
* * * *
42734962 TATCAGGGTA-CTCATATGAGCTAAA
1 TAAC-GGGAAGCTCATACGAGCCAAA
42734987 TAACGGGAAGCTC
1 TAACGGGAAGCTC
42735000 GTGAGAGCCA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
24 5 0.07
25 65 0.87
26 5 0.07
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (25 bp):
TAACGGGAAGCTCATACGAGCCAAA
Found at i:42734958 original size:50 final size:50
Alignment explanation
Indices: 42734904--42735010 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
42734894 AAGCTCTTCC
*
42734904 GAGCCATATAAC-GGGAAGCTCATACGAGCCAAATATCGGGAAACTCATGA
1 GAGCCATATAACAGGGAA-CTCATACGAGCCAAATAACGGGAAACTCATGA
* * * * * * *
42734954 GAGCCAAATATCAGGGTACTCATATGAGCTAAATAACGGGAAGCTCGTGA
1 GAGCCATATAACAGGGAACTCATACGAGCCAAATAACGGGAAACTCATGA
42735004 GAGCCAT
1 GAGCCAT
42735011 GGTGTGTCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 43 0.91
51 4 0.09
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (50 bp):
GAGCCATATAACAGGGAACTCATACGAGCCAAATAACGGGAAACTCATGA
Found at i:42736706 original size:28 final size:28
Alignment explanation
Indices: 42736674--42736734 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
42736664 AATTGAAGAA
*
42736674 TAAAGATGAAAACATGTTAGAGTATGTT
1 TAAAGATGAAAACATATTAGAGTATGTT
**
42736702 TAAAGATGAAAATGTATTAGAGTATGTT
1 TAAAGATGAAAACATATTAGAGTATGTT
42736730 TAAAG
1 TAAAG
42736735 CTCTAAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (28 bp):
TAAAGATGAAAACATATTAGAGTATGTT
Found at i:42740161 original size:21 final size:21
Alignment explanation
Indices: 42740140--42740180 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42740130 AAGTTATAAT
42740140 TTAATTTAATAA-TAATTAAA
1 TTAATTTAATAACTAATTAAA
* *
42740160 TTATTTTTATAACTAATTAAA
1 TTAATTTAATAACTAATTAAA
42740181 CCATTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTAATAACTAATTAAA
Found at i:42743536 original size:11 final size:9
Alignment explanation
Indices: 42743510--42743535 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42743500 TGAGGCAGCG
42743510 GGGAGAGAT
1 GGGAGAGAT
42743519 GGGAGAGAT
1 GGGAGAGAT
42743528 GGGAGAGA
1 GGGAGAGA
42743536 GGAGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.58, T:0.08
Consensus pattern (9 bp):
GGGAGAGAT
Found at i:42762791 original size:20 final size:19
Alignment explanation
Indices: 42762768--42762810 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
42762758 TATTTTTTTA
42762768 ATTTAAAAATT-TAGAAAATT
1 ATTTAAAAATTATA-AAAA-T
42762788 ATTTAAAAATTATAAAAAT
1 ATTTAAAAATTATAAAAAT
42762807 ATTT
1 ATTT
42762811 TTTTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 15 0.68
21 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTAAAAATTATAAAAAT
Found at i:42762804 original size:19 final size:20
Alignment explanation
Indices: 42762768--42762810 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
42762758 TATTTTTTTA
*
42762768 ATTTAAAAATTTAGAAAATT
1 ATTTAAAAATTTAGAAAAAT
*
42762788 ATTTAAAAA-TTATAAAAAT
1 ATTTAAAAATTTAGAAAAAT
42762807 ATTT
1 ATTT
42762811 TTTTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTAAAAATTTAGAAAAAT
Found at i:42763321 original size:59 final size:60
Alignment explanation
Indices: 42763249--42763399 Score: 191
Period size: 59 Copynumber: 2.5 Consensus size: 60
42763239 CTAGTTGGTT
* *
42763249 ACCCAACTTTTAGGGCG-TTTTATTTTGGTCACTCAAAATTAAAT-TTTTGCAATTTAATC
1 ACCCAACTTTTAGGGCGCTTTTATTTTAGTCACTCAAAATTAAATCCTTT-CAATTTAATC
* * *
42763308 ACCCAACTTTTAGGACGCTTTTATTTTTGTCA-TCAAAATTAAATCCTTTCAATTTAGTC
1 ACCCAACTTTTAGGGCGCTTTTATTTTAGTCACTCAAAATTAAATCCTTTCAATTTAATC
** * *
42763367 ACCCAAAGTTTAGGGTGCTTTCATTTTAGTCAC
1 ACCCAACTTTTAGGGCGCTTTTATTTTAGTCAC
42763400 CCAAGCCTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 63 0.80
60 16 0.20
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (60 bp):
ACCCAACTTTTAGGGCGCTTTTATTTTAGTCACTCAAAATTAAATCCTTTCAATTTAATC
Found at i:42764824 original size:14 final size:14
Alignment explanation
Indices: 42764791--42764832 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
42764781 TTAATTATGT
* *
42764791 TATTATTAAAATTA
1 TATTATTTATATTA
*
42764805 -ATTATTTTTATTA
1 TATTATTTATATTA
42764818 TATTATTTATATTA
1 TATTATTTATATTA
42764832 T
1 T
42764833 TAATTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTTATATTA
Found at i:42764988 original size:15 final size:16
Alignment explanation
Indices: 42764970--42765001 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
42764960 TTTATATGTA
42764970 TGTTTTTTTTA-TTTT
1 TGTTTTTTTTACTTTT
42764985 TGTTTTTTTTACTTTT
1 TGTTTTTTTTACTTTT
42765001 T
1 T
42765002 TATATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (16 bp):
TGTTTTTTTTACTTTT
Found at i:42765038 original size:18 final size:18
Alignment explanation
Indices: 42764992--42765039 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
42764982 TTTTGTTTTT
42764992 TTTACTTTTTTATATATAC
1 TTTA-TTTTTTATATATAC
42765011 TTTATATTTTATATATATAC
1 TTTAT-TTTT-TATATATAC
42765031 TTT-TTTTTT
1 TTTATTTTTT
42765040 GTAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 9 0.33
20 12 0.44
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTTTATATATAC
Found at i:42765047 original size:19 final size:20
Alignment explanation
Indices: 42765005--42765048 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42764995 ACTTTTTTAT
*
42765005 ATATACTTTATATTTTATAT
1 ATATACTTTATATTTTATAA
* *
42765025 ATATACTTT-TTTTTTGTAA
1 ATATACTTTATATTTTATAA
42765044 ATATA
1 ATATA
42765049 ATATACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATACTTTATATTTTATAA
Found at i:42765080 original size:162 final size:162
Alignment explanation
Indices: 42764898--42765210 Score: 626
Period size: 162 Copynumber: 1.9 Consensus size: 162
42764888 TATACATATG
42764898 GGCATTTTTTATATATATAGGTATATATATATTTTTAAGCTTTTATAAATACATGCATATATTTT
1 GGCATTTTTTATATATATAGGTATATATATATTTTTAAGCTTTTATAAATACATGCATATATTTT
42764963 ATATGTATGTTTTTTTTATTTTTGTTTTTTTTACTTTTTTATATATACTTTATATTTTATATATA
66 ATATGTATGTTTTTTTTATTTTTGTTTTTTTTACTTTTTTATATATACTTTATATTTTATATATA
42765028 TACTTTTTTTTTGTAAATATAATATACATATG
131 TACTTTTTTTTTGTAAATATAATATACATATG
42765060 GGCATTTTTTATATATATAGGTATATATATATTTTTAAGCTTTTATAAATACATGCATATATTTT
1 GGCATTTTTTATATATATAGGTATATATATATTTTTAAGCTTTTATAAATACATGCATATATTTT
42765125 ATATGTATGTTTTTTTTATTTTTGTTTTTTTTACTTTTTTATATATACTTTATATTTTATATATA
66 ATATGTATGTTTTTTTTATTTTTGTTTTTTTTACTTTTTTATATATACTTTATATTTTATATATA
42765190 TACTTTTTTTTTGTAAATATA
131 TACTTTTTTTTTGTAAATATA
42765211 TACACATGTA
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 151 1.00
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (162 bp):
GGCATTTTTTATATATATAGGTATATATATATTTTTAAGCTTTTATAAATACATGCATATATTTT
ATATGTATGTTTTTTTTATTTTTGTTTTTTTTACTTTTTTATATATACTTTATATTTTATATATA
TACTTTTTTTTTGTAAATATAATATACATATG
Found at i:42765150 original size:15 final size:16
Alignment explanation
Indices: 42765132--42765163 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
42765122 TTTATATGTA
42765132 TGTTTTTTTTA-TTTT
1 TGTTTTTTTTACTTTT
42765147 TGTTTTTTTTACTTTT
1 TGTTTTTTTTACTTTT
42765163 T
1 T
42765164 TATATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (16 bp):
TGTTTTTTTTACTTTT
Found at i:42765200 original size:18 final size:18
Alignment explanation
Indices: 42765154--42765201 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
42765144 TTTTGTTTTT
42765154 TTTACTTTTTTATATATAC
1 TTTA-TTTTTTATATATAC
42765173 TTTATATTTTATATATATAC
1 TTTAT-TTTT-TATATATAC
42765193 TTT-TTTTTT
1 TTTATTTTTT
42765202 GTAAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 9 0.33
20 12 0.44
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTTTATATATAC
Found at i:42765209 original size:19 final size:20
Alignment explanation
Indices: 42765167--42765210 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
42765157 ACTTTTTTAT
*
42765167 ATATACTTTATATTTTATAT
1 ATATACTTTATATTTTATAA
* *
42765187 ATATACTTT-TTTTTTGTAA
1 ATATACTTTATATTTTATAA
42765206 ATATA
1 ATATA
42765211 TACACATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATACTTTATATTTTATAA
Found at i:42772386 original size:10 final size:10
Alignment explanation
Indices: 42772371--42772401 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42772361 ATATCATTAT
42772371 ATTTCTAAAA
1 ATTTCTAAAA
42772381 ATTTCTAAAA
1 ATTTCTAAAA
*
42772391 ATTTATAAAA
1 ATTTCTAAAA
42772401 A
1 A
42772402 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTTCTAAAA
Found at i:42797155 original size:10 final size:11
Alignment explanation
Indices: 42797123--42797152 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
42797113 ATTTACATAT
42797123 GTTTTATTTTC
1 GTTTTATTTTC
42797134 -TTTTATTTTC
1 GTTTTATTTTC
42797144 GTTTTATTT
1 GTTTTATTT
42797153 CGTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (11 bp):
GTTTTATTTTC
Found at i:42803816 original size:44 final size:44
Alignment explanation
Indices: 42803506--42804082 Score: 182
Period size: 44 Copynumber: 13.1 Consensus size: 44
42803496 TAGATCTTAT
* * *
42803506 CTCCCTAAGCAGTAGTAGAGCAGATCGAAGAT-GACGGATTTTAC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAG-CGGATTTTAC
** * * **
42803550 CTCCCT--GTGGTTACAGTGGAGTACATTGAAG-CAG-TAATTTTAC
1 CTCCCTAAGCAG-T--AGTGGAGTAGATTGAAGATAGCGGATTTTAC
* * * * * ** ** * **
42803593 TTCCCTGAGCAGTAGCGAAATAGATTGAAGATTTCAAATCTTGT
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* * *
42803637 CTCCCTAAGTAGTAGTGGAGCAGATCGAAGAT-GACGGATTTTAC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAG-CGGATTTTAC
** * ** ** *
42803681 CTCCCTAAAGTTGTAGTGGAGTACATTGAAGCCAG-TAATTCTAC
1 CTCCCT-AAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* * ** * * * ** * * *
42803725 TTCCTTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* *
42803769 CTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGGATTTTAC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
** * * ** ** *
42803813 CTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAG-TAATTCTAC
1 CTCCCT-AAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* * * * * ** * * *
42803857 TTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* * * *
42803901 CTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTAC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* ** * ** ** *
42803945 CTCCTTGAAGTTGTAGTGGAGTACATTGAAGCCAG-TAATTCTAC
1 CTCCCT-AAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* ** * * * ** * * *
42803989 TTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
* ** *
42804033 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTAC
1 CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
42804077 CTCCCT
1 CTCCCT
42804083 GAGATTACAG
Statistics
Matches: 354, Mismatches: 163, Indels: 32
0.64 0.30 0.06
Matches are distributed among these distances:
42 15 0.04
43 63 0.18
44 199 0.56
45 76 0.21
46 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
CTCCCTAAGCAGTAGTGGAGTAGATTGAAGATAGCGGATTTTAC
Found at i:42804290 original size:132 final size:131
Alignment explanation
Indices: 42803354--42804298 Score: 1275
Period size: 132 Copynumber: 7.2 Consensus size: 131
42803344 GTGGAGCAGG
** * * * *
42803354 TTGAAGATAGCAGATCTTGTC-CCCTTGAGCAGTAGTGGGGCAGATCGAAGATGACAGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTCCC-TAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTAC
* * *
42803418 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTTGGCAGCAGTGGAAT
65 CTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCC-TGGCAGCAGCGGAAT
42803483 AGA
129 AGA
* * * * *
42803486 CTGAAGATTTTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGATGACGGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * * * *
42803551 TCCCTGTGGTTACAGTGGAGTACATTGAAG-CAGTAATTTTACTTCCCTGAGCAGTAGCGAAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG-GCAGCAGCGGAATA
42803615 GA
130 GA
* * *
42803617 TTGAAGATTTCAAATCTTGTCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGACGGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * * *
42803682 TCCCTAAAGTTGTAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCTTGGGCAGCAGCGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAGCAGCGGAATA
42803747 GA
130 GA
* *
42803749 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCGGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
*
42803814 TCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGCGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAGCAGCGGAATA
42803879 GA
130 GA
* *
42803881 TTGAAGATTTCAGATCTTGCCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * *
42803946 TCCTTGAAGTTGTAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAGCAGCGGAATA
42804011 GA
130 GA
* *
42804013 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * * * * *
42804078 TCCCTGAGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATTTTCCTGGGCAACAGTGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAGCAGCGGAATA
42804143 GA
130 GA
* * * * *
42804145 TTGAAGATTACAGATCTTATCTCCCTAAGCAGTATTGGAGCAGATCAAAGATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * * * *
42804210 TCCCTGAGGTTGTAGCGGAGTATATTGAAGCCAGTAATTCTA-TTCCCCCGGTCAGCAGTGGAAT
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTT-CCCTGG-CAGCAGCGGAAT
*
42804274 CGA
129 AGA
* ***
42804277 TCGAAGAAAACAGATCTTGTCT
1 TTGAAGATTTCAGATCTTGTCT
42804299 TCATGTATTG
Statistics
Matches: 736, Mismatches: 71, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
130 2 0.00
131 117 0.16
132 613 0.83
133 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGCAGCAGCGGAATAG
A
Found at i:42811591 original size:20 final size:20
Alignment explanation
Indices: 42811568--42811607 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42811558 TTAATTTCAC
42811568 ATTTCACTATTATATTTTTT
1 ATTTCACTATTATATTTTTT
42811588 ATTTCACTATTATATTTTTT
1 ATTTCACTATTATATTTTTT
42811608 GTGTTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTCACTATTATATTTTTT
Found at i:42813570 original size:41 final size:42
Alignment explanation
Indices: 42813515--42813747 Score: 314
Period size: 41 Copynumber: 5.7 Consensus size: 42
42813505 TTAATTTAAA
* * * *
42813515 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
42813557 TAGATT-ACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATC
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * *
42813598 CAG-CTCACCGACACTTAGCCTGCTAGGCTTATAGTCTGATC
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
42813639 CAG-TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
42813680 CAG-TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
42813721 TAGA-TCACCGGCACTTAGCCTGCTAGG
1 CAGATTCACCGGCACTTAGCCTGCTAGG
42813748 TTTTAAAACC
Statistics
Matches: 171, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 165 0.96
42 5 0.03
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (42 bp):
CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:42816287 original size:20 final size:21
Alignment explanation
Indices: 42816251--42816292 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42816241 TTTGATCAAG
42816251 TAAAATTAAATTAATT-GAAA
1 TAAAATTAAATTAATTGGAAA
*
42816271 TAAATATTATATT-ATTGGAAA
1 TAAA-ATTAAATTAATTGGAAA
42816292 T
1 T
42816293 TAGTTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAAATTAAATTAATTGGAAA
Found at i:42819153 original size:9 final size:9
Alignment explanation
Indices: 42819133--42819169 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
42819123 GTTTTTTGGA
42819133 TTTTAGGG-
1 TTTTAGGGT
42819141 -TTTAGGGT
1 TTTTAGGGT
*
42819149 TTTTAGGAT
1 TTTTAGGGT
42819158 TTTTAGGGT
1 TTTTAGGGT
42819167 TTT
1 TTT
42819170 GGAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:42821018 original size:37 final size:37
Alignment explanation
Indices: 42820903--42821021 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 37
42820893 TATTTTTAGT
* * * *
42820903 TTAATTTGATAAATTAATATAAAGTGGTATCCAAATA
1 TTAATTTGATAAAATAATATAAAGTAGTATCTAAGTA
* * ** ** * *
42820940 TTAATTTGGTAAAAAAATATTTAGTAACATTTTTAGT-
1 TTAATTTGATAAAATAATATAAAGTAGTA-TCTAAGTA
*
42820977 TTAATTTGATAAACTAATATAAAGTAGTATCTAAGTA
1 TTAATTTGATAAAATAATATAAAGTAGTATCTAAGTA
42821014 TTAATTTG
1 TTAATTTG
42821022 GTCAGCAAAT
Statistics
Matches: 59, Mismatches: 21, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 5 0.08
37 51 0.86
38 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (37 bp):
TTAATTTGATAAAATAATATAAAGTAGTATCTAAGTA
Found at i:42824637 original size:60 final size:61
Alignment explanation
Indices: 42824544--42824671 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 61
42824534 ATGTTGAAAG
**
42824544 TCGTAACGATTTTTATTTTCAATAACATTCATAACAATATTAATGATGTTGTCAGAATAAA
1 TCGTAACGATTTTTATTTTCAATAACAGCCATAACAATATTAATGATGTTGTCAGAATAAA
* * * *
42824605 TCGTAACGA-TTTTATTTTCAATAACAGCCATAATAATATTGATGATGTTGTCTGAATAAG
1 TCGTAACGATTTTTATTTTCAATAACAGCCATAACAATATTAATGATGTTGTCAGAATAAA
42824665 T-GTAACG
1 TCGTAACG
42824672 TGAAGTCCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 46 0.75
61 9 0.15
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (61 bp):
TCGTAACGATTTTTATTTTCAATAACAGCCATAACAATATTAATGATGTTGTCAGAATAAA
Found at i:42828095 original size:27 final size:26
Alignment explanation
Indices: 42828057--42828139 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 26
42828047 GGCCAATCAC
*
42828057 ATTGGAGGCACCAAAGGTGCAAATGAG
1 ATTGGAGGCACCAATGGTGCAAA-GAG
*
42828084 ATTGGCGGCACCAATGGTGCCAAAGAG
1 ATTGGAGGCACCAATGGTG-CAAAGAG
*
42828111 ATTGGTGGCACCAATGGTGCCAAAG-G
1 ATTGGAGGCACCAATGGTG-CAAAGAG
42828137 ATT
1 ATT
42828140 AAAATGTAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 4 0.08
27 44 0.85
28 4 0.08
ACGTcount: A:0.31, C:0.18, G:0.33, T:0.18
Consensus pattern (26 bp):
ATTGGAGGCACCAATGGTGCAAAGAG
Found at i:42828711 original size:19 final size:19
Alignment explanation
Indices: 42828687--42828745 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
42828677 TCTAATTAAG
42828687 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
42828706 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
42828724 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
42828743 TAA
1 TAA
42828746 AAAATTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:42828816 original size:18 final size:18
Alignment explanation
Indices: 42828793--42828856 Score: 92
Period size: 18 Copynumber: 3.5 Consensus size: 18
42828783 TAAAATAGAG
42828793 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
42828811 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
42828830 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
42828848 TTATTAAAT
1 TTATTAAAT
42828857 TAAAATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 24 0.62
19 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:42828825 original size:37 final size:37
Alignment explanation
Indices: 42828779--42828872 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
42828769 TTAATTTTTA
42828779 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
42828816 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
*
42828853 AAATTAAAATAAAGTTATTA
1 AAATTAAAATAGAGTTATTA
42828873 TTTAATTAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (37 bp):
AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
Found at i:42828863 original size:18 final size:19
Alignment explanation
Indices: 42828779--42828872 Score: 111
Period size: 19 Copynumber: 5.1 Consensus size: 19
42828769 TTAATTTTTA
42828779 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * *
42828798 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
42828816 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * *
42828835 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
*
42828853 AAATTAAAATAAAGTTATT
1 AAATTAAAATAGAGTTATT
42828872 A
1 A
42828873 TTTAATTAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
18 29 0.48
19 31 0.52
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (19 bp):
AAATTAAAATAGAGTTATT
Found at i:42829081 original size:27 final size:27
Alignment explanation
Indices: 42829025--42829083 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
42829015 TTTTAATCGT
*
42829025 TTGGCACCATTGGTGCCGCGAATCTCA
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
42829052 TTGGCACCTTTGGTGCCTCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
42829079 TTGGC
1 TTGGC
42829084 CTGATCAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:42829147 original size:29 final size:29
Alignment explanation
Indices: 42829123--42829185 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
42829113 TTTTTTTTGT
*
42829123 ATATTTTGGTAAATAAAAAAATTTTTATA
1 ATATTTTGATAAATAAAAAAATTTTTATA
*
42829152 ATATTTTGATAAATAAAAAAA--GTTATA
1 ATATTTTGATAAATAAAAAAATTTTTATA
42829179 ATATTTT
1 ATATTTT
42829186 AATTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 12 0.38
29 20 0.62
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (29 bp):
ATATTTTGATAAATAAAAAAATTTTTATA
Found at i:42830942 original size:25 final size:25
Alignment explanation
Indices: 42830914--42830987 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
42830904 GAAATAAATT
42830914 TGTAATAAATATCTTAAATGCTTAA
1 TGTAATAAATATCTTAAATGCTTAA
* *
42830939 TGT-AT---GAT-TTAACT-CTTAAA
1 TGTAATAAATATCTTAAATGCTT-AA
*
42830959 AGTAATAAATATCTTAAATGCTTAA
1 TGTAATAAATATCTTAAATGCTTAA
42830984 TGTA
1 TGTA
42830988 TGATTTAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 9 0.25
21 4 0.11
24 4 0.11
25 13 0.36
26 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (25 bp):
TGTAATAAATATCTTAAATGCTTAA
Found at i:42830950 original size:20 final size:20
Alignment explanation
Indices: 42830927--42830995 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
42830917 AATAAATATC
42830927 TTAAATGCTTAATGTATGAT
1 TTAAATGCTTAATGTATGAT
* * *
42830947 TTAACT-CTTAAAAGTAATAAATAT
1 TTAAATGCTT-AATGT-AT---GAT
42830971 CTTAAATGCTTAATGTATGAT
1 -TTAAATGCTTAATGTATGAT
42830992 TTAA
1 TTAA
42830996 CTCTTAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 13 0.36
21 4 0.11
24 4 0.11
25 9 0.25
26 3 0.08
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (20 bp):
TTAAATGCTTAATGTATGAT
Found at i:42830979 original size:45 final size:45
Alignment explanation
Indices: 42830915--42831009 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
42830905 AAATAAATTT
42830915 GTAATAAATATCTTAAATGCTTAATGTATGATTTAACTCTTAAAA
1 GTAATAAATATCTTAAATGCTTAATGTATGATTTAACTCTTAAAA
42830960 GTAATAAATATCTTAAATGCTTAATGTATGATTTAACTCTTAAAA
1 GTAATAAATATCTTAAATGCTTAATGTATGATTTAACTCTTAAAA
42831005 GTAAT
1 GTAAT
42831010 CACTTTTCTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (45 bp):
GTAATAAATATCTTAAATGCTTAATGTATGATTTAACTCTTAAAA
Found at i:42837510 original size:19 final size:18
Alignment explanation
Indices: 42837488--42837531 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
42837478 TCTGAATTTA
42837488 TAAAAAATCATCAAAATTC
1 TAAAAAAT-ATCAAAATTC
* *
42837507 TAAAAAAATATTAAAATTT
1 T-AAAAAATATCAAAATTC
42837526 TAAAAA
1 TAAAAA
42837532 GAAACCATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATATCAAAATTC
Found at i:42837755 original size:25 final size:24
Alignment explanation
Indices: 42837721--42837771 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
42837711 TGAAAGGGTT
42837721 TTTTTATTTAATATTAATATAATTA
1 TTTTTATTTAATATTAAT-TAATTA
*
42837746 TTTTTATTTAATATTAATTTATTA
1 TTTTTATTTAATATTAATTAATTA
42837770 TT
1 TT
42837772 ATATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTATTTAATATTAATTAATTA
Found at i:42837777 original size:18 final size:17
Alignment explanation
Indices: 42837724--42837778 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
42837714 AAGGGTTTTT
*
42837724 TTATTTAATATTAATATAA
1 TTATTTATTATT-ATAT-A
42837743 TTATTT-TTATT-TAATA
1 TTATTTATTATTAT-ATA
42837759 TTAATTTATTATTATATA
1 TT-ATTTATTATTATATA
42837777 TT
1 TT
42837779 TTTGAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 14 0.45
19 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTATTATTATATA
Found at i:42837778 original size:25 final size:25
Alignment explanation
Indices: 42837725--42837779 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
42837715 AGGGTTTTTT
*
42837725 TATTTAATATTAATATAATTATTTT
1 TATTTAATATTAATATAATTATTTA
*
42837750 TATTTAATATTAAT-TTATTATTATA
1 TATTTAATATTAATATAATTATT-TA
42837775 TATTT
1 TATTT
42837780 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTAATATTAATATAATTATTTA
Found at i:42837804 original size:30 final size:29
Alignment explanation
Indices: 42837755--42837813 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
42837745 ATTTTTATTT
*
42837755 AATATTAATTTATTATTATATATTTTTGAA
1 AATATTAATGTATTATTATAT-TTTTTGAA
* *
42837785 AATATTTATGTATTTTTATATTTTTTGAA
1 AATATTAATGTATTATTATATTTTTTGAA
42837814 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (29 bp):
AATATTAATGTATTATTATATTTTTTGAA
Found at i:42845359 original size:2 final size:2
Alignment explanation
Indices: 42845352--42845377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42845342 CCCTTGGTAA
42845352 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
42845378 GTGTTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42855758 original size:16 final size:16
Alignment explanation
Indices: 42855729--42855762 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42855719 AATCCTCTTT
*
42855729 TTAACTTCCAACCCTA
1 TTAACGTCCAACCCTA
*
42855745 TTAACGTCCTACCCTA
1 TTAACGTCCAACCCTA
42855761 TT
1 TT
42855763 TTTCTTATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.03, T:0.35
Consensus pattern (16 bp):
TTAACGTCCAACCCTA
Found at i:42860943 original size:22 final size:20
Alignment explanation
Indices: 42860918--42860962 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
42860908 AATGTTTTTT
*
42860918 TTTTTAATTTGAACTTTTAAAA
1 TTTTTAATTTAAAC--TTAAAA
42860940 TTTTTAATTTAAACTTAAAA
1 TTTTTAATTTAAACTTAAAA
42860960 TTT
1 TTT
42860963 AGGGATAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTAAACTTAAAA
Found at i:42869707 original size:21 final size:21
Alignment explanation
Indices: 42869677--42869738 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
42869667 CTTCCCCCTT
*
42869677 TTTTTTATTTTTATTTTAAAA
1 TTTTTAATTTTTATTTTAAAA
*
42869698 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTAT-TTTAAAA
* * *
42869720 TTTTAAAATTTAATTTTAA
1 TTTTTAATTTTTATTTTAA
42869739 TTATTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAATTTTTATTTTAAAA
Found at i:42893189 original size:21 final size:21
Alignment explanation
Indices: 42893163--42893218 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
42893153 AATAGCGGTG
*
42893163 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* * *
42893184 GCGGTGAGTTTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
*
42893205 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
42893219 AACAATGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.36, T:0.32
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:42895840 original size:30 final size:30
Alignment explanation
Indices: 42895765--42895847 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
42895755 TAAAAAATTT
* *
42895765 AGGGTCTAATT-AAATTTTTAAAATTTTATA
1 AGGGT-TAATTAAAATTTTCAAAATTTTAAA
* * *
42895795 A-GATTAATGAGAATTTTCAAAATTTTAAA
1 AGGGTTAATTAAAATTTTCAAAATTTTAAA
42895824 AGGGTTAATTAAAATTTTTCAAAA
1 AGGGTTAATTAAAA-TTTTCAAAA
42895848 ATTTCAAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 4 0.10
29 19 0.45
30 10 0.24
31 9 0.21
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.41
Consensus pattern (30 bp):
AGGGTTAATTAAAATTTTCAAAATTTTAAA
Found at i:42897046 original size:17 final size:18
Alignment explanation
Indices: 42897024--42897057 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42897014 CTTAAAAAAA
*
42897024 TATAAAT-TTTTGAATTT
1 TATAAATATTTTAAATTT
42897041 TATAAATATTTTAAATT
1 TATAAATATTTTAAATT
42897058 CTTGAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATAAATATTTTAAATTT
Found at i:42902736 original size:16 final size:17
Alignment explanation
Indices: 42902704--42902736 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42902694 AAATAAAATC
*
42902704 TAAATTTCATTTCGATA
1 TAAATTTCATATCGATA
42902721 TAAATTTC-TATCGATA
1 TAAATTTCATATCGATA
42902737 CTGGTCACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (17 bp):
TAAATTTCATATCGATA
Found at i:42904688 original size:18 final size:18
Alignment explanation
Indices: 42904652--42904723 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
42904642 AAAATTTCAG
42904652 AAAAAATTCAAAATAATTTT
1 AAAAAA-TCAAAAT-ATTTT
42904672 AAAAAATCAAAATATTTT
1 AAAAAATCAAAATATTTT
* *
42904690 AAAAAATTAAATATATATT
1 AAAAAATCAAA-ATATTTT
*
42904709 AAAAATTCTAAAATA
1 AAAAAATC-AAAATA
42904724 AAAATTCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 15 0.33
19 22 0.48
20 9 0.20
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATCAAAATATTTT
Found at i:42904727 original size:14 final size:14
Alignment explanation
Indices: 42904708--42904735 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42904698 AAATATATAT
42904708 TAAAAATTCTAAAA
1 TAAAAATTCTAAAA
42904722 TAAAAATTCTAAAA
1 TAAAAATTCTAAAA
42904736 AAGTTCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAATTCTAAAA
Found at i:42905407 original size:26 final size:26
Alignment explanation
Indices: 42905378--42905448 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
42905368 ATACGTATTT
42905378 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
42905404 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
42905433 AATTATTTAATATTTA
1 AATTATTT-ATATTTA
42905449 AATTTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 7 0.18
27 6 0.16
28 7 0.18
29 18 0.47
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:42905417 original size:16 final size:16
Alignment explanation
Indices: 42905396--42905445 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
42905386 ATATTTAGTC
42905396 ATATAATAAATTATTA
1 ATATAATAAATTATTA
42905412 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
42905425 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
42905442 ATAT
1 ATAT
42905446 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:42905421 original size:29 final size:30
Alignment explanation
Indices: 42905388--42905445 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
42905378 AATTATTTAT
42905388 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
42905417 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
42905446 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:42907973 original size:15 final size:16
Alignment explanation
Indices: 42907953--42907982 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42907943 GCCGTTGTTC
42907953 GAAGAGAAA-AAGAGA
1 GAAGAGAAACAAGAGA
42907968 GAAGAGAAACAAGAG
1 GAAGAGAAACAAGAG
42907983 CTGAGATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAGAAACAAGAGA
Found at i:42913283 original size:35 final size:35
Alignment explanation
Indices: 42913236--42913311 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
42913226 GATTTCTAGT
* *
42913236 AAAAA-CAACAAAAATATATTCACTCAAATAGTTC
1 AAAAAGCAACAAAAATATATTCACACAAAAAGTTC
*
42913270 AAAAAGCAACAAAAGTATATTCACACAAAAAGTTC
1 AAAAAGCAACAAAAATATATTCACACAAAAAGTTC
42913305 AAAAAGC
1 AAAAAGC
42913312 TTTGCAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.58, C:0.17, G:0.07, T:0.18
Consensus pattern (35 bp):
AAAAAGCAACAAAAATATATTCACACAAAAAGTTC
Found at i:42925687 original size:8 final size:8
Alignment explanation
Indices: 42925674--42925698 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42925664 ACACACACAT
42925674 ATATACAC
1 ATATACAC
42925682 ATATACAC
1 ATATACAC
42925690 ATATACAC
1 ATATACAC
42925698 A
1 A
42925699 CACTAAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (8 bp):
ATATACAC
Found at i:42927658 original size:17 final size:17
Alignment explanation
Indices: 42927590--42927670 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 17
42927580 AATTTTAAAT
42927590 TAAATTATAATTATTT-
1 TAAATTATAATTATTTA
*
42927606 TAAATGTGTAATT-TTTA
1 TAAAT-TATAATTATTTA
* *
42927623 CAAGTT-TAATT-TTTAA
1 TAAATTATAATTATTT-A
42927639 TAAATTATAATTATTTA
1 TAAATTATAATTATTTA
42927656 TAAATGTATAATTAT
1 TAAAT-TATAATTAT
42927671 CACAATTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 8 0.15
16 14 0.26
17 20 0.37
18 12 0.22
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TAAATTATAATTATTTA
Found at i:42927685 original size:50 final size:50
Alignment explanation
Indices: 42927579--42927675 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
42927569 TTTTAATTAA
* * *
42927579 TAATTTTAAATTAAATTATAATTATTTTAAATGTGTAATTTTTACAAGTT
1 TAATTTTAAATTAAATTATAATTATTTTAAATGTATAATTATCACAAGTT
*
42927629 TAATTTTTAA-TAAATTATAATTATTTATAAATGTATAATTATCACAA
1 TAATTTTAAATTAAATTATAATTATTT-TAAATGTATAATTATCACAA
42927676 TTTCTATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 16 0.38
50 26 0.62
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (50 bp):
TAATTTTAAATTAAATTATAATTATTTTAAATGTATAATTATCACAAGTT
Found at i:42927686 original size:49 final size:49
Alignment explanation
Indices: 42927579--42927711 Score: 137
Period size: 49 Copynumber: 2.7 Consensus size: 49
42927569 TTTTAATTAA
* * *
42927579 TAATTTTAAATTAAATTATAATTATTTTAAATGTGTAATTTTTACAAGTT
1 TAATTTT-AATTAAATTATAATTATTTTAAATGTATAATTATCACAAGTT
42927629 TAATTTTTAA-TAAATTATAATTATTTATAAATGTATAATTATCACAA-TT
1 TAA-TTTTAATTAAATTATAATTATTT-TAAATGTATAATTATCACAAGTT
* * * *
42927678 TCTATTTTATTTCAATTAT-TTTATTTTTAAATGT
1 T-AATTTTAATTAAATTATAATTA-TTTTAAATGT
42927712 GAAACTTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
49 34 0.48
50 33 0.46
51 4 0.06
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (49 bp):
TAATTTTAATTAAATTATAATTATTTTAAATGTATAATTATCACAAGTT
Found at i:42932243 original size:6 final size:6
Alignment explanation
Indices: 42932234--42932259 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42932224 ATTTCAATTC
42932234 AATATA AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AA
42932260 AGAAAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:42934377 original size:29 final size:29
Alignment explanation
Indices: 42934323--42934379 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
42934313 CTCTGTATTG
* * * *
42934323 AAAAGTTACAAAATAATTATTTAATTATA
1 AAAAATTACAAAATAATCACTCAATTATA
42934352 AAAAATTACAAAATAATCACTCAATTAT
1 AAAAATTACAAAATAATCACTCAATTAT
42934380 TCAATTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTACAAAATAATCACTCAATTATA
Found at i:42938892 original size:17 final size:17
Alignment explanation
Indices: 42938870--42938904 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42938860 ATATAACAAA
42938870 AATAAAT-ATAAAATAAT
1 AATAAATAAT-AAATAAT
42938887 AATAAATAATAAATAAT
1 AATAAATAATAAATAAT
42938904 A
1 A
42938905 TCCATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAATAATAAATAAT
Found at i:42940554 original size:93 final size:93
Alignment explanation
Indices: 42940367--42940558 Score: 264
Period size: 93 Copynumber: 2.1 Consensus size: 93
42940357 CATGAAACTG
* * *
42940367 AAAGAAAATTTCTTTAGTGGTTCGGCCGAGAAATATGCTGGTGTGTTATATGGTCTTGGTGTTGA
1 AAAGAAAACTTCTTTAGTGGTTCGACCGAGAAATATGCTGGTGTGTTATATGGTCTTGGTGTTCA
*
42940432 GAATGGATAGAATACTCTCTAATAAATC
66 GAATGGACAGAATACTCTCTAATAAATC
* *
42940460 AAAGAAAACTTCTTTAGTTGG-TCGACTGAGAAATATGCTGGTTTGTTATATGGTCTTGGTTGTT
1 AAAGAAAACTTCTTTAG-TGGTTCGACCGAGAAATATGCTGGTGTGTTATATGGTCTTGG-TGTT
* *
42940524 CAGAATTGACAGAATACT-TCTTAA-ATATC
64 CAGAATGGACAGAATACTCTC-TAATAAATC
42940553 AAAGAA
1 AAAGAA
42940559 TTATGAAATA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 63 0.72
94 25 0.28
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (93 bp):
AAAGAAAACTTCTTTAGTGGTTCGACCGAGAAATATGCTGGTGTGTTATATGGTCTTGGTGTTCA
GAATGGACAGAATACTCTCTAATAAATC
Found at i:42945435 original size:16 final size:16
Alignment explanation
Indices: 42945410--42945440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42945400 GGTACAAGAT
*
42945410 TTTAATTTTTTTTATC
1 TTTAACTTTTTTTATC
42945426 TTTAACTTTTTTTAT
1 TTTAACTTTTTTTAT
42945441 ATAATTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAACTTTTTTTATC
Found at i:42969263 original size:24 final size:24
Alignment explanation
Indices: 42969236--42969287 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42969226 TTAGTAAGTC
*
42969236 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
42969260 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
42969284 AAAT
1 AAAT
42969288 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:42971233 original size:24 final size:24
Alignment explanation
Indices: 42971206--42971257 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42971196 TTAGTAAGTC
*
42971206 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
42971230 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
42971254 AAAT
1 AAAT
42971258 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:42979428 original size:21 final size:21
Alignment explanation
Indices: 42979404--42979446 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
42979394 CAAACATAAC
42979404 AAATT-ATCAACTTTTCCAAAA
1 AAATTAATCAA-TTTTCCAAAA
*
42979425 AAATTAATCAATTTTTCAAAA
1 AAATTAATCAATTTTCCAAAA
42979446 A
1 A
42979447 TCATTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTAATCAATTTTCCAAAA
Found at i:42979985 original size:22 final size:22
Alignment explanation
Indices: 42979935--42979985 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
42979925 TCATATAATT
42979935 ATATT-TT-TTTTAAAATTAAA
1 ATATTATTGTTTTAAAATTAAA
*
42979955 ATA-TA-TGTTTTAAATTTAAA
1 ATATTATTGTTTTAAAATTAAA
42979975 ATATTATTGTT
1 ATATTATTGTT
42979986 ATTATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 2 0.08
22 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
ATATTATTGTTTTAAAATTAAA
Found at i:42982068 original size:46 final size:46
Alignment explanation
Indices: 42982015--42982245 Score: 347
Period size: 46 Copynumber: 5.0 Consensus size: 46
42982005 ACAATGCTAT
* * * *
42982015 AACTCAGTATCGTTTTCCTCATTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTCTCAC
* * *
42982061 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTCTCAC
* *
42982107 AACTCAGCATGGTTTTCGTTACTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTCTCAC
*
42982153 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTCTCAC
*
42982199 AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACGTTC-CAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC-TTCTCAC
42982245 A
1 A
42982246 CTTTGCCATG
Statistics
Matches: 171, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 169 0.99
47 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTCTCAC
Found at i:42998327 original size:11 final size:11
Alignment explanation
Indices: 42998311--42998336 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42998301 AAAAATTAAA
42998311 AAAAGTATTTT
1 AAAAGTATTTT
42998322 AAAAGTATTTT
1 AAAAGTATTTT
42998333 AAAA
1 AAAA
42998337 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:43002924 original size:28 final size:30
Alignment explanation
Indices: 43002857--43002927 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 30
43002847 TTTTTTCCAA
* *
43002857 TTTTTCATTTTTGATGATTTTTTTAAGTTTT
1 TTTTTTATTTTTGA-GAATTTTTTAAGTTTT
* **
43002888 TCTGATATTTTTGA-AATTTTTT-AGTTTT
1 TTTTTTATTTTTGAGAATTTTTTAAGTTTT
43002916 TTTTTTATTTTT
1 TTTTTTATTTTT
43002928 TCTTGGCACA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
28 15 0.47
29 7 0.22
31 10 0.31
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (30 bp):
TTTTTTATTTTTGAGAATTTTTTAAGTTTT
Found at i:43008105 original size:31 final size:28
Alignment explanation
Indices: 43008020--43008115 Score: 95
Period size: 31 Copynumber: 3.2 Consensus size: 28
43008010 AGTATCAAAT
**
43008020 TTATACATGAACTTTGA-TTTGGCTCAA
1 TTATACATGAACTTTGATTTTGATTCAA
*
43008047 TTATACACATGAAATTTGATTTGTGATTCATA
1 TTAT--ACATGAACTTTGATTT-TGATTCA-A
43008079 TGTATACATGAAGCTTTGATTTTGATTCAA
1 T-TATACATGAA-CTTTGATTTTGATTCAA
*
43008109 TTGTACA
1 TTATACA
43008116 CATTTAAAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 4 0.07
29 17 0.30
30 4 0.07
31 19 0.33
32 10 0.18
33 3 0.05
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (28 bp):
TTATACATGAACTTTGATTTTGATTCAA
Found at i:43009335 original size:18 final size:18
Alignment explanation
Indices: 43009275--43009348 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 18
43009265 AAATAAAAAC
*
43009275 AAAAATATTAAAAAA-TT
1 AAAAATATAAAAAAATTT
* * * *
43009292 AAAAATA-ATAATAACTC
1 AAAAATATAAAAAAATTT
*
43009309 ATAAA-ATAAAAAAATTT
1 AAAAATATAAAAAAATTT
43009326 AAAAATAT-AAAAAATATT
1 AAAAATATAAAAAAAT-TT
43009344 AAAAA
1 AAAAA
43009349 AATCTAAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
16 5 0.12
17 29 0.67
18 9 0.21
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAAATTT
Found at i:43009357 original size:43 final size:43
Alignment explanation
Indices: 43009267--43009358 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 43
43009257 CATATTTTAA
* * * *
43009267 ATAAAA-ACAAAAATATTAAAAAATTAAAAATAATAATAACTC
1 ATAAAATAAAAAAATATTAAAAAATAAAAAATAATAAAAAATC
*
43009309 ATAAAATAAAAAAAT-TTAAAAATATAAAAAATATTAAAAAAATC
1 ATAAAATAAAAAAATATTAAAAA-ATAAAAAATAAT-AAAAAATC
43009353 -TAAAAT
1 ATAAAAT
43009359 TCAATGCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 13 0.31
43 23 0.55
44 6 0.14
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (43 bp):
ATAAAATAAAAAAATATTAAAAAATAAAAAATAATAAAAAATC
Found at i:43011327 original size:8 final size:8
Alignment explanation
Indices: 43011316--43011343 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
43011306 TAAAATTACA
43011316 AAAAAATC
1 AAAAAATC
43011324 AAAAAATC
1 AAAAAATC
43011332 AAAAAATC
1 AAAAAATC
43011340 AAAA
1 AAAA
43011344 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATC
Found at i:43020351 original size:20 final size:20
Alignment explanation
Indices: 43020328--43020393 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
43020318 AAATTTTGTC
43020328 ATAAAAATAGATATTTGATT
1 ATAAAAATAGATATTTGATT
*
43020348 ATAATAGTAATTAAAT-TTTG-TT
1 ATAA-A--AA-TAGATATTTGATT
*
43020370 ATAAAAACAGATATTTGATT
1 ATAAAAATAGATATTTGATT
43020390 ATAA
1 ATAA
43020394 TAGTAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 10 0.27
21 2 0.05
22 6 0.16
23 6 0.16
24 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (20 bp):
ATAAAAATAGATATTTGATT
Found at i:43020374 original size:42 final size:42
Alignment explanation
Indices: 43020315--43020399 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
43020305 AGTTCTGGGC
*
43020315 ATTAAATTTTGTCATAAAAATAGATATTTGATTATAATAGTA
1 ATTAAATTTTGTCATAAAAACAGATATTTGATTATAATAGTA
*
43020357 ATTAAATTTTGTTATAAAAACAGATATTTGATTATAATAGTA
1 ATTAAATTTTGTCATAAAAACAGATATTTGATTATAATAGTA
43020399 A
1 A
43020400 AAAAATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.42
Consensus pattern (42 bp):
ATTAAATTTTGTCATAAAAACAGATATTTGATTATAATAGTA
Found at i:43025374 original size:51 final size:54
Alignment explanation
Indices: 43025312--43025418 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
43025302 TTGATAGCTT
* * *
43025312 AAAGAATCACATTCTC-A-A-AAGGGTGAATGTCGTGAAGGACAAGTGGATGAG
1 AAAGAACCACATTCTCAACAGAAGGGTGAATGTCGTGAAGGACAAATGGACGAG
43025363 AAAGAACCACATTCTCAACAGAAGGGTGAATGTCGTGAAGGACAAATGGACGAG
1 AAAGAACCACATTCTCAACAGAAGGGTGAATGTCGTGAAGGACAAATGGACGAG
43025417 AA
1 AA
43025419 CCTTTCGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 15 0.30
52 1 0.02
53 1 0.02
54 33 0.66
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Consensus pattern (54 bp):
AAAGAACCACATTCTCAACAGAAGGGTGAATGTCGTGAAGGACAAATGGACGAG
Found at i:43032745 original size:23 final size:22
Alignment explanation
Indices: 43032701--43032744 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43032691 TGTGACTTTT
43032701 TTTAAAAAAAAATTGTTGAAAA
1 TTTAAAAAAAAATTGTTGAAAA
43032723 TTTAAAAAAAAATT-TATGAAAA
1 TTTAAAAAAAAATTGT-TGAAAA
43032745 AATGGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
TTTAAAAAAAAATTGTTGAAAA
Found at i:43044233 original size:73 final size:72
Alignment explanation
Indices: 43044098--43044269 Score: 254
Period size: 73 Copynumber: 2.4 Consensus size: 72
43044088 AAAATAAGCA
* * * *
43044098 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACGTCGTTTCCCGAGCTTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTCACGAGCTTT
43044163 CGGGGAT
66 CGGGGAT
* * * *
43044170 TTAGCGACGTTTCTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTATGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTCACGAGCTT
*
43044235 TTGGGGAT
65 TCGGGGAT
43044243 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
43044270 TAATGCTCAG
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 23 0.26
73 65 0.74
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (72 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTCACGAGCTTT
CGGGGAT
Done.