Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 137 of 141
Found at i:44481735 original size:41 final size:40
Alignment explanation
Indices: 44481524--44481755 Score: 190
Period size: 41 Copynumber: 5.7 Consensus size: 40
44481514 AATTAAAACA
* *
44481524 GATTCAAC-GGCACTTAGCCTGCTAAGCTTAAAGCCTGATT
1 GATTC-ACTGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
*
44481564 CAGA-TCACCGGCACTTAGCCTGCTAGGC-TTATAGCCTGATT
1 --GATTCACTGGCACTTAGCCTGCTAGGCTTTA-AGCCTGATT
* ** * * *
44481605 CAGTTCACCAGCATTTAGCCTGCTAGGCTTAAAGCTTGATT
1 GA-TTCACTGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
* *
44481646 CAGA-TC-GTCGGCACTTAGTCTGCTAGGC-TTATAGCCTGATT
1 --GATTCACT-GGCACTTAGCCTGCTAGGCTTTA-AGCCTGATT
*
44481687 CAGTTCACTGGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT
1 GA-TTCACTGGCACTTAGCCTGCTAGGCTTTAAGCCTG-ATT
*
44481729 GATTCACTGGCAATATA-CCTGCTAGGC
1 GATTCACTGGCACT-TAGCCTGCTAGGC
44481756 GCTGAGCCTG
Statistics
Matches: 155, Mismatches: 20, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.01
40 6 0.04
41 132 0.85
42 14 0.09
43 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GATTCACTGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
Found at i:44481750 original size:123 final size:123
Alignment explanation
Indices: 44481531--44481755 Score: 321
Period size: 123 Copynumber: 1.8 Consensus size: 123
44481521 ACAGATTCAA
44481531 CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTAT
1 CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTAT
*
44481596 AGCCTGATTCAGTTCACCAGCATTTAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
66 AGCCTGATTCAGTTCACCAGCATATAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
* * * * *
44481654 CGGCACTTAGTCTGCTAGGCTTATAGCCTGATTCAGTTCACTGGCACTTAGCCTGCTAGGCTT-T
1 CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTAT
* **
44481718 AAGCCTGAATTGA-TTCACTGGCAATATA-CCTGCTAGGC
66 -AGCCTG-ATTCAGTTCACCAGC-ATATAGCCTGCTAGGC
44481756 GCTGAGCCTG
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
122 1 0.01
123 81 0.90
124 8 0.09
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (123 bp):
CGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTAT
AGCCTGATTCAGTTCACCAGCATATAGCCTGCTAGGCTTAAAGCTTGATTCAGATCGT
Found at i:44481764 original size:41 final size:41
Alignment explanation
Indices: 44481655--44481768 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
44481645 TCAGATCGTC
* * * *
44481655 GGCACTTAGTCTGCTAGGC-TTATAGCCTG-ATTCAGTTCACT
1 GGCAATTAGCCTGCTAGGCGCTA-AGCCTGAATTGA-TTCACT
* **
44481696 GGCACTTAGCCTGCTAGGCTTTAAGCCTGAATTGATTCACT
1 GGCAATTAGCCTGCTAGGCGCTAAGCCTGAATTGATTCACT
*
44481737 GGCAATATA-CCTGCTAGGCGCTGAGCCTGAAT
1 GGCAAT-TAGCCTGCTAGGCGCTAAGCCTGAAT
44481769 ACGCAATTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 55 0.86
42 9 0.14
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.30
Consensus pattern (41 bp):
GGCAATTAGCCTGCTAGGCGCTAAGCCTGAATTGATTCACT
Found at i:44481766 original size:82 final size:81
Alignment explanation
Indices: 44481526--44481755 Score: 286
Period size: 82 Copynumber: 2.8 Consensus size: 81
44481516 TTAAAACAGA
* * *
44481526 TTCAACGGCACTTAGCCTGCTAAGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACTGGCACTTAGCCTGCTAGG
44481591 CTTATAGCCTGATTCAG
65 CTTATAGCCTGATTCAG
* * * * *
44481608 TTCACCAGCATTTAGCCTGCTAGGCTTAAAGCTTGATTCAGATC-GTCGGCACTTAGTCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACT-GGCACTTAGCCTGCTAG
44481672 GCTTATAGCCTGATTCAG
64 GCTTATAGCCTGATTCAG
* * *
44481690 TTCACTGGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT-GATTCACTGGCAATATA-CCTGCTA
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCACTGGCACT-TAGCCTGCTA
44481753 GGC
63 GGC
44481756 GCTGAGCCTG
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
81 2 0.02
82 119 0.94
83 6 0.05
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (81 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCACTGGCACTTAGCCTGCTAGGC
TTATAGCCTGATTCAG
Found at i:44483372 original size:433 final size:433
Alignment explanation
Indices: 44482566--44483436 Score: 1724
Period size: 433 Copynumber: 2.0 Consensus size: 433
44482556 AAATATATAT
44482566 ATGCTTATATACCTTTCTTACTTTAACCGTTTGCAAAAAATTATATAAGTATAAACTTCTATGTT
1 ATGCTTATATACCTTTCTTACTTTAACCGTTTGCAAAAAATTATATAAGTATAAACTTCTATGTT
44482631 CGAACATTAGAAATACATATATATGTATATATATATATAAATCATTCAAATTTTAAATATATTAA
66 CGAACATTAGAAATACATATATATGTATATATATATATAAATCATTCAAATTTTAAATATATTAA
44482696 ATAGATATATATTAATTTAATAACATTTAATAGCTAATAGACTTACCTCGGATGGTGACAAGTCG
131 ATAGATATATATTAATTTAATAACATTTAATAGCTAATAGACTTACCTCGGATGGTGACAAGTCG
44482761 AAACCGGACTATTAATCGATAACTTTAGCTTTTCCCCGATCCAACTTTGATTTCTTCGGTTCTTG
196 AAACCGGACTATTAATCGATAACTTTAGCTTTTCCCCGATCCAACTTTGATTTCTTCGGTTCTTG
44482826 ATCTAAATATATTCAAATGAGCTAGTTTAAATATAATTACATTCAATTTAGTCCAAAAGCACATA
261 ATCTAAATATATTCAAATGAGCTAGTTTAAATATAATTACATTCAATTTAGTCCAAAAGCACATA
*
44482891 AATGGGCAAATTACTATTTTGCCCCTAACATTTACACTTTTTGCAATTTTATCCCTATTGCATAA
326 AATGGGCAAATTACTATTTTGCCCCTAACATTAACACTTTTTGCAATTTTATCCCTATTGCATAA
44482956 AACACAAAATTTCCCCACATTATACAAGGGCCGAATATCCCTA
391 AACACAAAATTTCCCCACATTATACAAGGGCCGAATATCCCTA
44482999 ATGCTTATATACCTTTCTTACTTTAACCGTTTGCAAAAAATTATATAAGTATAAACTTCTATGTT
1 ATGCTTATATACCTTTCTTACTTTAACCGTTTGCAAAAAATTATATAAGTATAAACTTCTATGTT
44483064 CGAACATTAGAAATACATATATATGTATATATATATATAAATCATTCAAATTTTAAATATATTAA
66 CGAACATTAGAAATACATATATATGTATATATATATATAAATCATTCAAATTTTAAATATATTAA
*
44483129 ATAGATATATATTAATTTAATAACATTTAATAGCTAATAGACTTACGTCGGATGGTGACAAGTCG
131 ATAGATATATATTAATTTAATAACATTTAATAGCTAATAGACTTACCTCGGATGGTGACAAGTCG
44483194 AAACCGGACTATTAATCGATAACTTTAGCTTTTCCCCGATCCAACTTTGATTTCTTCGGTTCTTG
196 AAACCGGACTATTAATCGATAACTTTAGCTTTTCCCCGATCCAACTTTGATTTCTTCGGTTCTTG
44483259 ATCTAAATATATTCAAATGAGCTAGTTTAAATATAATTACATTCAATTTAGTCCAAAAGCACATA
261 ATCTAAATATATTCAAATGAGCTAGTTTAAATATAATTACATTCAATTTAGTCCAAAAGCACATA
44483324 AATGGGCAAATTACTATTTTGCCCCTAACATTAACACTTTTTGCAATTTTATCCCTATTGCATAA
326 AATGGGCAAATTACTATTTTGCCCCTAACATTAACACTTTTTGCAATTTTATCCCTATTGCATAA
44483389 AACACAAAATTTCCCCACATTATACAAGGGCCGAATATCCCTA
391 AACACAAAATTTCCCCACATTATACAAGGGCCGAATATCCCTA
44483432 ATGCT
1 ATGCT
44483437 CATACAAGTC
Statistics
Matches: 436, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
433 436 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (433 bp):
ATGCTTATATACCTTTCTTACTTTAACCGTTTGCAAAAAATTATATAAGTATAAACTTCTATGTT
CGAACATTAGAAATACATATATATGTATATATATATATAAATCATTCAAATTTTAAATATATTAA
ATAGATATATATTAATTTAATAACATTTAATAGCTAATAGACTTACCTCGGATGGTGACAAGTCG
AAACCGGACTATTAATCGATAACTTTAGCTTTTCCCCGATCCAACTTTGATTTCTTCGGTTCTTG
ATCTAAATATATTCAAATGAGCTAGTTTAAATATAATTACATTCAATTTAGTCCAAAAGCACATA
AATGGGCAAATTACTATTTTGCCCCTAACATTAACACTTTTTGCAATTTTATCCCTATTGCATAA
AACACAAAATTTCCCCACATTATACAAGGGCCGAATATCCCTA
Found at i:44484584 original size:19 final size:19
Alignment explanation
Indices: 44484562--44484643 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 19
44484552 GTGTGGGTTT
*
44484562 ATGCACCTCGTGTGCCAAG
1 ATGCACCTCATGTGCCAAG
* * *
44484581 ATGCTCTTCATGTGCCAGG
1 ATGCACCTCATGTGCCAAG
* * * *
44484600 ATGCGCTTCAAGTGCCAGG
1 ATGCACCTCATGTGCCAAG
*** *
44484619 ATGCGTTTCATGTGCCAAT
1 ATGCACCTCATGTGCCAAG
44484638 ATGCAC
1 ATGCAC
44484644 TATGTGTGTC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.27
Consensus pattern (19 bp):
ATGCACCTCATGTGCCAAG
Found at i:44485117 original size:24 final size:24
Alignment explanation
Indices: 44485085--44485134 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
44485075 ACTATTTAAT
44485085 AATATCAAATAATCAAAGATTCTC
1 AATATCAAATAATCAAAGATTCTC
*
44485109 AATATCAAATAATCGAAGATTCTC
1 AATATCAAATAATCAAAGATTCTC
44485133 AA
1 AA
44485135 CACTCCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (24 bp):
AATATCAAATAATCAAAGATTCTC
Found at i:44496865 original size:21 final size:21
Alignment explanation
Indices: 44496832--44496885 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
44496822 TTAATAAATG
44496832 TTTTTATA-A-TTCTCT-AATT
1 TTTTTATATATTTCT-TGAATT
44496851 TTTTTATATATTTCTTGAATT
1 TTTTTATATATTTCTTGAATT
*
44496872 TTATTTATTTATTT
1 TT-TTTATATATTT
44496886 ATAAATCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 10 0.33
22 10 0.33
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTATATATTTCTTGAATT
Found at i:44497350 original size:3 final size:3
Alignment explanation
Indices: 44497342--44497397 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
44497332 GTTTTTAAGC
44497342 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44497389 TTAA TTA TT
1 TT-A TTA TT
44497398 GTGAGTATGG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44497746 original size:13 final size:13
Alignment explanation
Indices: 44497728--44497752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44497718 TAATATATTT
44497728 ATTAATTAAAAAC
1 ATTAATTAAAAAC
44497741 ATTAATTAAAAA
1 ATTAATTAAAAA
44497753 TAAAAAACTT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:44501359 original size:27 final size:27
Alignment explanation
Indices: 44501329--44501380 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
44501319 AATTAAAAGA
*
44501329 TAAAGA-ACAAATTAAAAAAGTAAATAT
1 TAAAGACAAAAATTAAAAAA-TAAATAT
*
44501356 TAAAGACAAAAATTAAAGAATAAAT
1 TAAAGACAAAAATTAAAAAATAAAT
44501381 TAACTTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (27 bp):
TAAAGACAAAAATTAAAAAATAAATAT
Found at i:44502090 original size:12 final size:13
Alignment explanation
Indices: 44502059--44502096 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
44502049 GATCCGTTCG
44502059 TATTAATTTTTTA
1 TATTAATTTTTTA
44502072 TATTAATTTTTTA
1 TATTAATTTTTTA
44502085 TA-TAATTTTTTA
1 TATTAATTTTTTA
44502097 AAAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:44502363 original size:19 final size:19
Alignment explanation
Indices: 44502336--44502384 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
44502326 TGAAAAAAAC
* *
44502336 AACAATAAAATAGCAACAA
1 AACAGTAAAACAGCAACAA
*
44502355 AACAGTAAAAACAGCAAGAA
1 AACAGT-AAAACAGCAACAA
*
44502375 AATAGTAAAA
1 AACAGTAAAA
44502385 AAATAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.10
Consensus pattern (19 bp):
AACAGTAAAACAGCAACAA
Found at i:44502370 original size:20 final size:20
Alignment explanation
Indices: 44502342--44502385 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
44502332 AAACAACAAT
*
44502342 AAAATAGCAACAAAACAGTA
1 AAAACAGCAACAAAACAGTA
* *
44502362 AAAACAGCAAGAAAATAGTA
1 AAAACAGCAACAAAACAGTA
44502382 AAAA
1 AAAA
44502386 AATAATAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAACAGCAACAAAACAGTA
Found at i:44503242 original size:19 final size:19
Alignment explanation
Indices: 44503214--44503250 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44503204 CAATTAAGTT
* *
44503214 AAATTTAAATTGTTTTTTA
1 AAATTAAAATAGTTTTTTA
44503233 AAATTAAAATAGTTTTTT
1 AAATTAAAATAGTTTTTT
44503251 CATTCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
AAATTAAAATAGTTTTTTA
Found at i:44507656 original size:18 final size:18
Alignment explanation
Indices: 44507631--44507712 Score: 128
Period size: 18 Copynumber: 4.6 Consensus size: 18
44507621 ATGGTCTGAC
*
44507631 TCTTCTTCCTCAACTGCA
1 TCTTCTTCCTCACCTGCA
*
44507649 TTTTCTTCCTCACCTGCA
1 TCTTCTTCCTCACCTGCA
44507667 TCTTCTTCCTCACCTGCA
1 TCTTCTTCCTCACCTGCA
*
44507685 TCTTCTTCCTCACCTACA
1 TCTTCTTCCTCACCTGCA
*
44507703 ACTTCTTCCT
1 TCTTCTTCCT
44507713 TGGTCACATC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.13, C:0.41, G:0.04, T:0.41
Consensus pattern (18 bp):
TCTTCTTCCTCACCTGCA
Found at i:44514652 original size:22 final size:22
Alignment explanation
Indices: 44514624--44514668 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
44514614 TTTGTACTTA
44514624 TGGATCGAAGAAATAAGTGAAG
1 TGGATCGAAGAAATAAGTGAAG
*
44514646 TGGATCGAAGAAATGAGTGAAG
1 TGGATCGAAGAAATAAGTGAAG
44514668 T
1 T
44514669 AGTAACTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.33, T:0.20
Consensus pattern (22 bp):
TGGATCGAAGAAATAAGTGAAG
Found at i:44517039 original size:25 final size:26
Alignment explanation
Indices: 44517018--44517067 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
44517008 CAAAAAAACT
* *
44517018 AAAATCTAACCTAAAAA-GAAAAGAG
1 AAAACCTAAACTAAAAATGAAAAGAG
44517043 AAAACCTAAACTAAAAATGAAAAGA
1 AAAACCTAAACTAAAAATGAAAAGA
44517068 ATAGAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.66, C:0.12, G:0.10, T:0.12
Consensus pattern (26 bp):
AAAACCTAAACTAAAAATGAAAAGAG
Found at i:44533507 original size:50 final size:50
Alignment explanation
Indices: 44533448--44534119 Score: 435
Period size: 50 Copynumber: 13.5 Consensus size: 50
44533438 GCAGCGGAAC
* * * *
44533448 AGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTACAATTTGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * * ***
44533498 AGATCGAAGCCACAACGGCGAATCTTA-TTTCCAGGCGA-TGC-AGCAGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGAC-ATTGCAATTTGAA
* * *
44533546 CAGATTC-AAGCTACAACAGCGAATCTCACTTCCCCGACATTGTAATTTGAA
1 -AGA-TCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * * ***
44533597 AGATCGAAGCCACAATGGCGAATCTTACTT-TCCTAGCGA-TGC-AGCGGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGA-C-ATTGCAATTTGAA
* * *
44533646 TAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTTGAA
1 -AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * * **** *
44533697 AGATTGAAGCCACAACGGCGAATCTTACTT-TCCTAGCGA-TGCAGCGGGAC
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGA-C-ATTGCAATTTGAA
* * *
44533747 AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCAATTTGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * * ***
44533797 AGATCGAAGCCACAACGGTGAATCTTACTT-TCCTAGCGA-TGC-AGCGGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGA-C-ATTGCAATTTGAA
* * *
44533846 CAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTTGAA
1 -AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * * ***
44533897 AGATCGAAGCCACAACGGCGAATCTTA-TTTCCAGGCGA-TGC-AGCGGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGAC-ATTGCAATTTGAA
* * * *
44533945 CAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTACAATTTGAA
1 -AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* * * ***
44533996 AGATCGAAGCCACAACGGTGAATCTTACTT-CCAGACGA-TGC-AGCAGAA
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGAC-ATTGCAATTTGAA
*** * * * *
44534044 CAGATCGAAGCTTTATCAGCAAATCTCACTTCCCCGACATTGCAATTTAAA
1 -AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
* *
44534095 AGATTGAAGCCACAACGGTGAATCT
1 AGATCGAAGCCACAACGGCGAATCT
44534120 TATTTCCAGG
Statistics
Matches: 458, Mismatches: 131, Indels: 66
0.70 0.20 0.10
Matches are distributed among these distances:
48 12 0.03
49 115 0.25
50 300 0.66
51 31 0.07
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (50 bp):
AGATCGAAGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTTGAA
Found at i:44533685 original size:100 final size:99
Alignment explanation
Indices: 44533397--44534223 Score: 1207
Period size: 99 Copynumber: 8.3 Consensus size: 99
44533387 TTGCAACTCA
* * * *
44533397 AAAGATTGAAGCCACGACGGTGAATCTTATTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
*
44533462 ACAGCGAATCTCACTTCCCCGACATTACAATTTG
66 ACAGCGAATCTCACTTCCCCGACATTGCAATTTG
* *
44533496 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCAGAACAGATTCAAGCTACA
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
*
44533561 ACAGCGAATCTCACTTCCCCGACATTGTAATTTG
66 ACAGCGAATCTCACTTCCCCGACATTGCAATTTG
* *
44533595 AAAGATCGAAGCCACAATGGCGAATCTTACTTTCCTA-GCGATGCAGCGGAATAGATTGAAGCTA
1 AAAGATCGAAGCCACAACGGCGAATCTTA-TTTCC-AGGCGATGCAGCGGAACAGATTGAAGCTA
44533659 CAACAGCGAATCTCACTTCCCCGACATTGCAATTTG
64 CAACAGCGAATCTCACTTCCCCGACATTGCAATTTG
* *
44533695 AAAGATTGAAGCCACAACGGCGAATCTTACTTTCCTA-GCGATGCAGCGGGACAGATTGAAGCTA
1 AAAGATCGAAGCCACAACGGCGAATCTTA-TTTCC-AGGCGATGCAGCGGAACAGATTGAAGCTA
* *
44533759 CAACGGCGAATCTCACTTCCCCAACATTGCAATTTG
64 CAACAGCGAATCTCACTTCCCCGACATTGCAATTTG
*
44533795 AAAGATCGAAGCCACAACGGTGAATCTTACTTTCCTA-GCGATGCAGCGGAACAGATTGAAGCTA
1 AAAGATCGAAGCCACAACGGCGAATCTTA-TTTCC-AGGCGATGCAGCGGAACAGATTGAAGCTA
44533859 CAACAGCGAATCTCACTTCCCCGACATTGCAATTTG
64 CAACAGCGAATCTCACTTCCCCGACATTGCAATTTG
44533895 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
*
44533960 ACAGCGAATCTCACTTCCCCGACATTACAATTTG
66 ACAGCGAATCTCACTTCCCCGACATTGCAATTTG
* * * * * **
44533994 AAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGACGATGCAGCAGAACAGATCGAAGCTTTA
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
* * *
44534059 TCAGCAAATCTCACTTCCCCGACATTGCAATTTA
66 ACAGCGAATCTCACTTCCCCGACATTGCAATTTG
* * * *
44534093 AAAGATTGAAGCCACAACGGTGAATCTTATTTCCAGGCGATGCAGCGGCACAGATTGAAGCTACG
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
** * * * *
44534158 AC-GACGAATCTTGCTTTCCCGATATTACAA-CT-
66 ACAG-CGAATCTCACTTCCCCGACATTGCAATTTG
* *
44534190 AAAGATTGAAGCCGCAACGGCGAATCTTATTTCC
1 AAAGATCGAAGCCACAACGGCGAATCTTATTTCC
44534224 TCGGCGAGAC
Statistics
Matches: 668, Mismatches: 56, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
97 32 0.05
98 3 0.00
99 351 0.53
100 281 0.42
101 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (99 bp):
AAAGATCGAAGCCACAACGGCGAATCTTATTTCCAGGCGATGCAGCGGAACAGATTGAAGCTACA
ACAGCGAATCTCACTTCCCCGACATTGCAATTTG
Found at i:44535850 original size:4 final size:4
Alignment explanation
Indices: 44535841--44535878 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
44535831 CATTTGCTTG
* *
44535841 ATTT ATTT ATTC ATTT ATTT ATTT ACTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
44535879 CCATTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:44537182 original size:21 final size:21
Alignment explanation
Indices: 44537158--44537210 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
44537148 AAATATAATG
*
44537158 TATTATATATTTTTTAAAATT
1 TATTATATATTTTTTAAAATA
*
44537179 TATTA-A-ATTTATTAAAATA
1 TATTATATATTTTTTAAAATA
*
44537198 T-TTATGTATTTTT
1 TATTATATATTTTT
44537211 AGTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 6 0.23
21 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATATATTTTTTAAAATA
Found at i:44540356 original size:34 final size:35
Alignment explanation
Indices: 44540300--44540366 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
44540290 CAAACACCAG
*
44540300 AAAATATTTTCCAGCAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGCAAATCATTTTACAGAAAAGT
* *
44540335 AAAACATTTTCCA-TAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGCAAATCATTTTACAGAAAA
44540367 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGCAAATCATTTTACAGAAAAGT
Found at i:44549087 original size:41 final size:41
Alignment explanation
Indices: 44549059--44549201 Score: 209
Period size: 41 Copynumber: 3.5 Consensus size: 41
44549049 TGATTCAGAA
*
44549059 CACCTGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCTGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
* *
44549100 CACCAGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
1 CACCTGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
*
44549141 CA-CTGGCATTAAGCTTGCTAGACGTAAAGTCTGAATTATTT
1 CACCT-GCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
*
44549182 CA-CTGGCATTAAGTCTGCTA
1 CACCT-GCATTAAGCCTGCTA
44549202 TGCACAGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 92 0.99
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (41 bp):
CACCTGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
Found at i:44549216 original size:82 final size:81
Alignment explanation
Indices: 44549064--44549217 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 81
44549054 CAGAACACCT
*
44549064 GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAGCATTAAGCCTGCTAGATGTAAAG
1 GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAGCATTAAGCCTGCTA-ATGCAAAG
*
44549129 TCTGAATTATTTCACTG
65 CCTGAATTATTTCACTG
* * ** *
44549146 GCATTAAGCTTGCTAGACGTAAAGTCTGAATTATTTCACTGGCATTAAGTCTGCT-ATGCACAGA
1 GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAGCATTAAGCCTGCTAATGCA-A-A
44549210 GCCTGAAT
64 GCCTGAAT
44549218 AACTCAGATA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 4 0.06
81 1 0.02
82 58 0.92
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (81 bp):
GCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAGCATTAAGCCTGCTAATGCAAAGC
CTGAATTATTTCACTG
Found at i:44549429 original size:61 final size:61
Alignment explanation
Indices: 44549324--44549439 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
44549314 GTATATATAA
* * * * *
44549324 TTCATAACATTAAGTTTAGCTCAAAGAACTTGTATATTACATTCGAACCTCATATGTTTAG
1 TTCAAAACATTAAATTCAGCTCAAAGAACTTGTATACTACATTCGAACCACATATGTTTAG
* * *
44549385 TTCAAAACATTAAATTCAGCTCAATGAATTTGTA-ACCTATATTCGAACCACATAT
1 TTCAAAACATTAAATTCAGCTCAAAGAACTTGTATA-CTACATTCGAACCACATAT
44549440 ATATATATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 1 0.02
61 45 0.98
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.35
Consensus pattern (61 bp):
TTCAAAACATTAAATTCAGCTCAAAGAACTTGTATACTACATTCGAACCACATATGTTTAG
Found at i:44552145 original size:75 final size:75
Alignment explanation
Indices: 44552016--44552210 Score: 257
Period size: 75 Copynumber: 2.6 Consensus size: 75
44552006 ATTAATGGCA
* * * * * * *
44552016 TTGCCTTCGATAGAATATCCGTTGAATTGGCAGATCGAGGTACATGAAATATGACTCTATACTGA
1 TTGCCTTCGATGGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGACTCTATAATGA
* **
44552081 ATTTATGGTG
66 ATTCATGACG
*
44552091 TTGCCTTCGATGGAATATCCATTGAACTGGTAGATCGTGGTACATAAAACATGACTCTATAATGA
1 TTGCCTTCGATGGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGACTCTATAATGA
44552156 ATTCATGACG
66 ATTCATGACG
* *
44552166 TTGCCTTCGATGCAA-AGTGCATTGAACTGGCAGATCGTGGTACAT
1 TTGCCTTCGATGGAATA-TCCATTGAACTGGCAGATCGTGGTACAT
44552211 GAATAATGGT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 104 0.99
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (75 bp):
TTGCCTTCGATGGAATATCCATTGAACTGGCAGATCGTGGTACATAAAACATGACTCTATAATGA
ATTCATGACG
Found at i:44573109 original size:76 final size:75
Alignment explanation
Indices: 44572967--44573110 Score: 162
Period size: 76 Copynumber: 1.9 Consensus size: 75
44572957 AGCATTAATT
* * * * * **
44572967 TTTTGGATGAATAATTTAAGCTCATGCTTAGGAGCGATACAATATTTTAAGCTCGTGTTTGGGAG
1 TTTTGGATGAATAATTTAAGATCATGCTTAGGAACAATACAATAATTTAAGCTCGTGCTTAAGAG
44573032 CATCATTTTG
66 CATCATTTTG
* * *** *
44573042 TTTTGGATGAATAATTTTATGATCATGTTTAGGAACAATGTGATAATTTAAGCTTGTGCTTAAGA
1 TTTTGGATGAATAA-TTTAAGATCATGCTTAGGAACAATACAATAATTTAAGCTCGTGCTTAAGA
44573107 GCAT
65 GCAT
44573111 TAATTTTTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
75 14 0.25
76 41 0.75
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.40
Consensus pattern (75 bp):
TTTTGGATGAATAATTTAAGATCATGCTTAGGAACAATACAATAATTTAAGCTCGTGCTTAAGAG
CATCATTTTG
Found at i:44581762 original size:120 final size:120
Alignment explanation
Indices: 44581544--44581773 Score: 388
Period size: 120 Copynumber: 1.9 Consensus size: 120
44581534 GCTTTGGAAT
44581544 TTTTCAATGCTTTCTAAAAAATTCTATGAGTTCCTGATTTAGTCTCGACTTGTTTCTAACATGTA
1 TTTTCAATGCTTTCTAAAAAATTCTATGAGTTCCTGATTTAGTCTCGACTTGTTTCTAACATGTA
* *
44581609 TTTAGGGCCTCGAGGTCTCATATAAGGGTCAATATGTATGATTTTGATTTGAAAA
66 TTTAGGGCCTCGAGGGCTCATATAAGGGACAATATGTATGATTTTGATTTGAAAA
* * *
44581664 TTTTCAATGCTTTCTGAAAAATTCTCTGAGTTCCTGATTTAGTCTCGACTTGTTTCTAACCTGTA
1 TTTTCAATGCTTTCTAAAAAATTCTATGAGTTCCTGATTTAGTCTCGACTTGTTTCTAACATGTA
* **
44581729 TTTAGGGCCTTGAGGGCTTGTATAAGGGACAATATGTATGATTTT
66 TTTAGGGCCTCGAGGGCTCATATAAGGGACAATATGTATGATTTT
44581774 AATTGGTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 102 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (120 bp):
TTTTCAATGCTTTCTAAAAAATTCTATGAGTTCCTGATTTAGTCTCGACTTGTTTCTAACATGTA
TTTAGGGCCTCGAGGGCTCATATAAGGGACAATATGTATGATTTTGATTTGAAAA
Found at i:44594837 original size:24 final size:25
Alignment explanation
Indices: 44594809--44594864 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
44594799 TTAATATTGT
44594809 TTTCTCTCATCCCATAATCTT-TCTA
1 TTTCTCTCA-CCCATAATCTTCTCTA
*
44594834 -TTCTCTCACCCTTAATCTTCTCTA
1 TTTCTCTCACCCATAATCTTCTCTA
44594858 TTTCTCT
1 TTTCTCT
44594865 TATTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
24 12 0.43
25 6 0.21
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTCTCTCACCCATAATCTTCTCTA
Found at i:44596134 original size:13 final size:13
Alignment explanation
Indices: 44596116--44596140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44596106 GCTACTGTTT
44596116 GTTGATCACTATC
1 GTTGATCACTATC
44596129 GTTGATCACTAT
1 GTTGATCACTAT
44596141 AGTCGTGCCA
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:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
GTTGATCACTATC
Found at i:44599646 original size:35 final size:35
Alignment explanation
Indices: 44599600--44599671 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
44599590 GTTATGGTCG
*
44599600 AATCCGGAAGTGTTACAAAGAAGGGTTTCGAAACT
1 AATCCGAAAGTGTTACAAAGAAGGGTTTCGAAACT
*
44599635 AATCCGAAAGTGTTACAAAGAAGGGTTTTGAAACT
1 AATCCGAAAGTGTTACAAAGAAGGGTTTCGAAACT
44599670 AA
1 AA
44599672 CTTTACTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (35 bp):
AATCCGAAAGTGTTACAAAGAAGGGTTTCGAAACT
Found at i:44605753 original size:15 final size:14
Alignment explanation
Indices: 44605720--44605753 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44605710 AAAATATTTA
*
44605720 ATTTATCAAAAATC
1 ATTTTTCAAAAATC
*
44605734 ATTTTTCAAAAATT
1 ATTTTTCAAAAATC
44605748 ATTTTT
1 ATTTTT
44605754 ATCCAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTTCAAAAATC
Found at i:44615682 original size:16 final size:16
Alignment explanation
Indices: 44615661--44615711 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
44615651 AATTAATTTG
44615661 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
44615677 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
* * *
44615693 CAATTACGCATTTATT
1 CTATTACGCCTCTATT
44615709 CTA
1 CTA
44615712 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.43
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:44624060 original size:2 final size:2
Alignment explanation
Indices: 44624053--44624103 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
44624043 TCCATCTACT
44624053 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
44624095 TT TC TC TC T
1 TC TC TC TC T
44624104 TCCACTTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:44630688 original size:16 final size:16
Alignment explanation
Indices: 44630667--44630697 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44630657 TCTTCAAGAA
*
44630667 AAGAAAGATTACGCCC
1 AAGAAAGAGTACGCCC
44630683 AAGAAAGAGTACGCC
1 AAGAAAGAGTACGCC
44630698 TACGCCCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (16 bp):
AAGAAAGAGTACGCCC
Found at i:44634280 original size:15 final size:15
Alignment explanation
Indices: 44634260--44634289 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44634250 TGAAATGTTA
44634260 GTGAACTACCTGTAC
1 GTGAACTACCTGTAC
44634275 GTGAACTACCTGTAC
1 GTGAACTACCTGTAC
44634290 ATGGGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (15 bp):
GTGAACTACCTGTAC
Found at i:44635028 original size:25 final size:25
Alignment explanation
Indices: 44635000--44635056 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
44634990 ACTTGTGAAG
44635000 CCTTTGTGGTGAGTCACCTATAAAA
1 CCTTTGTGGTGAGTCACCTATAAAA
* * *
44635025 CCTTTGTGGTGAGTCACTTGTAAAG
1 CCTTTGTGGTGAGTCACCTATAAAA
44635050 CCTTTGT
1 CCTTTGT
44635057 TGTAATAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (25 bp):
CCTTTGTGGTGAGTCACCTATAAAA
Found at i:44636388 original size:21 final size:21
Alignment explanation
Indices: 44636362--44636404 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
44636352 TTTGGGTGGA
*
44636362 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
44636383 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
44636404 T
1 T
44636405 GGCGTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:44641944 original size:8 final size:8
Alignment explanation
Indices: 44641931--44641959 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
44641921 NNNNNNNNNN
44641931 CAGTGTTA
1 CAGTGTTA
44641939 CAGTGTTA
1 CAGTGTTA
44641947 CAGTGTTA
1 CAGTGTTA
44641955 CAGTG
1 CAGTG
44641960 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:44642073 original size:23 final size:23
Alignment explanation
Indices: 44642047--44642121 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
44642037 GTGTTATTGA
*
44642047 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
*
44642070 TCAGTGTTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
44642093 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
44642116 TCAGTG
1 TCAGTG
44642122 TTGCACTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:44645771 original size:16 final size:16
Alignment explanation
Indices: 44645721--44645772 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
44645711 GGGTGAGAAG
44645721 TAAAAGTTTAAGGAGAAAA
1 TAAAAGTTTAAGG-G--AA
**
44645740 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTAAGGGAA
44645757 TAAAAGTTTAAGGGAA
1 TAAAAGTTTAAGGGAA
44645773 CGTAAATAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
19 2 0.07
20 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTAAGGGAA
Found at i:44645911 original size:21 final size:22
Alignment explanation
Indices: 44645885--44645927 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
44645875 TTTTAGGGAA
44645885 AAAGTGGGA-GGAGTATAAATT
1 AAAGTGGGAGGGAGTATAAATT
44645906 AAAGTGGGAGGGAGTATAAATT
1 AAAGTGGGAGGGAGTATAAATT
44645928 TTGGGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (22 bp):
AAAGTGGGAGGGAGTATAAATT
Found at i:44646169 original size:9 final size:9
Alignment explanation
Indices: 44646151--44646187 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
44646141 TATAGTTTGA
44646151 TATTCGAAT
1 TATTCGAAT
*
44646160 TATTCAAAT
1 TATTCGAAT
*
44646169 TATTCGAGT
1 TATTCGAAT
44646178 TATTCGAAT
1 TATTCGAAT
44646187 T
1 T
44646188 CGAAAACCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44649567 original size:21 final size:21
Alignment explanation
Indices: 44649541--44649604 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
44649531 ATTTGGTGGA
*
44649541 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
*
44649562 TCAGCTCTCACGAGCTTCTAT
1 TCAGCTCTCACGAGCTTCTGT
*
44649583 TTAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
44649604 T
1 T
44649605 GGCGTGTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.16, C:0.30, G:0.17, T:0.38
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:44650896 original size:50 final size:50
Alignment explanation
Indices: 44650833--44651241 Score: 423
Period size: 50 Copynumber: 8.2 Consensus size: 50
44650823 GGGTGTTACA
*
44650833 TTTGTGGTGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAG-C
1 TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * * * *
44650882 TCTTGTGACAATTTACTTGGGAAGCCTTTGTGGCGAGTTACTTGTAAAGCC
1 T-TTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * * *
44650933 TTTGTGACAATTTACTTGGGAAGCCTTCGTGGTGAGTCACCTGTAAGGCC
1 TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * * *
44650983 TTTGTGGTGATTTACTTGGGAAGCTTTTATGGCGAGTCACCTGTAAAGCC
1 TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * *
44651033 TTTTTGGTGATTTACTT-GGAAGGCCTTT-TGGGTGAGTCACCTATAAAGCC
1 TTTGTGGCGATTTACTTGGGAA-GCCTTTGT-GGTGAGTCACCTGTAAAGCC
* * * *
44651083 TTTTTGGTGATTTACTTGGGAAACCTTTGTGGCGAGTCACCTGTAAAGCC
1 TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * * * * * * *
44651133 TTTGTGACGATTTTCTTGGAAAACCTTTATGGTAACTCACTTGTAAAGCC
1 TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
* * ** *
44651183 TTTGTGGCAATTTATTTGGGAAGTCC-TTGT-GACAGGTTACCTGTAAAGCC
1 TTTGTGGCGATTTACTTGGGAAG-CCTTTGTGGTGA-GTCACCTGTAAAGCC
*
44651233 TATGTGGCG
1 TTTGTGGCG
44651242 TAATGCTTGG
Statistics
Matches: 302, Mismatches: 50, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
49 8 0.03
50 285 0.94
51 9 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (50 bp):
TTTGTGGCGATTTACTTGGGAAGCCTTTGTGGTGAGTCACCTGTAAAGCC
Found at i:44653626 original size:40 final size:38
Alignment explanation
Indices: 44653562--44653750 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 38
44653552 ATCTAATGTT
* * *
44653562 CCATTTCATATATCTATTTCCATATAACCTATTCATATAA
1 CCATTTCATATAT-T-TTTTCATATAACCGATTCGTATAA
*
44653602 GCATTTCATATATCATTTTTCATATAACCGATTCGTATAA
1 CCATTTCATATAT--TTTTTCATATAACCGATTCGTATAA
* *
44653642 CCATTTCATATATTTATTTCCATATAACCAATACGTATAA
1 CCATTTCATATATTT-TTT-CATATAACCGATTCGTATAA
* *
44653682 CCATTTCATATATAATTTTTTATATAATCGATTCGTATAA
1 CCATTTCATATAT--TTTTTCATATAACCGATTCGTATAA
*
44653722 ACATTTCATATATTTATTTCCATATAACC
1 CCATTTCATATATTT-TTT-CATATAACC
44653751 AATCATATAG
Statistics
Matches: 127, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 4 0.03
39 6 0.05
40 111 0.87
41 4 0.03
42 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (38 bp):
CCATTTCATATATTTTTTCATATAACCGATTCGTATAA
Found at i:44653660 original size:80 final size:79
Alignment explanation
Indices: 44653562--44653759 Score: 297
Period size: 80 Copynumber: 2.5 Consensus size: 79
44653552 ATCTAATGTT
* * *
44653562 CCATTTCATATATCTATTTCCATATAACCTATTCATATAAGCATTTCATATATCATTTTTCATAT
1 CCATTTCATATATTTATTTCCATATAACC-ATTCATATAACCATTTCATATATAATTTTTCATAT
44653627 AACCGATTCGTATAA
65 AACCGATTCGTATAA
* * *
44653642 CCATTTCATATATTTATTTCCATATAACCAATACGTATAACCATTTCATATATAATTTTTTATAT
1 CCATTTCATATATTTATTTCCATATAACC-ATTCATATAACCATTTCATATATAATTTTTCATAT
*
44653707 AATCGATTCGTATAA
65 AACCGATTCGTATAA
* *
44653722 ACATTTCATATATTTATTTCCATATAACCAATCATATA
1 CCATTTCATATATTTATTTCCATATAACCATTCATATA
44653760 GAATTTTTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 6 0.06
80 100 0.94
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (79 bp):
CCATTTCATATATTTATTTCCATATAACCATTCATATAACCATTTCATATATAATTTTTCATATA
ACCGATTCGTATAA
Found at i:44653693 original size:13 final size:13
Alignment explanation
Indices: 44653562--44653693 Score: 90
Period size: 13 Copynumber: 9.9 Consensus size: 13
44653552 ATCTAATGTT
*
44653562 CCATTTCATATAT
1 CCATTTCATATAA
*
44653575 CTATTTCCATATAA
1 CCATTT-CATATAA
44653589 CC-TATTCATATAA
1 CCAT-TTCATATAA
*
44653602 GCATTTCATAT-A
1 CCATTTCATATAA
*
44653614 TCATTTTTCATATAA
1 CCA--TTTCATATAA
*
44653629 CCGA-TTCGTATAA
1 CC-ATTTCATATAA
*
44653642 CCATTTCATATAT
1 CCATTTCATATAA
**
44653655 TTATTTCCATATAA
1 CCATTT-CATATAA
* * *
44653669 CCAATACGTATAA
1 CCATTTCATATAA
44653682 CCATTTCATATA
1 CCATTTCATATA
44653694 TAATTTTTTA
Statistics
Matches: 90, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
12 4 0.04
13 57 0.63
14 26 0.29
15 2 0.02
16 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (13 bp):
CCATTTCATATAA
Found at i:44658327 original size:19 final size:20
Alignment explanation
Indices: 44658303--44658341 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
44658293 GATATTCCTT
44658303 TAGTGTA-TTTGATTATCTC
1 TAGTGTATTTTGATTATCTC
44658322 TAGTGTATTTTTGATTATCT
1 TAGTGTA-TTTTGATTATCT
44658342 TGTGGGTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (20 bp):
TAGTGTATTTTGATTATCTC
Found at i:44658938 original size:19 final size:20
Alignment explanation
Indices: 44658914--44658959 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
44658904 CATCCAAACA
44658914 CCAGAAAA-T-AGTAACTTTT
1 CCAGAAAAGTAAGTAA-TTTT
*
44658933 CCAGAAAAGTAAGTCATTTT
1 CCAGAAAAGTAAGTAATTTT
44658953 CCAGAAA
1 CCAGAAA
44658960 TAATTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAGTAATTTT
Found at i:44660112 original size:25 final size:25
Alignment explanation
Indices: 44660083--44660132 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
44660073 CATTCTCTTA
44660083 CCATTTC-ATCATAT-ACATATATCAT
1 CCATTTCAAT-ATATCA-ATATATCAT
44660108 CCATTTCAATATATCAATATATCAT
1 CCATTTCAATATATCAATATATCAT
44660133 GTACCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (25 bp):
CCATTTCAATATATCAATATATCAT
Found at i:44660577 original size:2 final size:2
Alignment explanation
Indices: 44660570--44660601 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44660560 GTATAATAAC
44660570 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
44660602 CGATTCATTT
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:44661306 original size:25 final size:25
Alignment explanation
Indices: 44661277--44661326 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
44661267 CATTCTCTTA
44661277 CCATTTC-ATCATAT-ACATATATCAT
1 CCATTTCAAT-ATATCA-ATATATCAT
44661302 CCATTTCAATATATCAATATATCAT
1 CCATTTCAATATATCAATATATCAT
44661327 TTACCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (25 bp):
CCATTTCAATATATCAATATATCAT
Found at i:44661771 original size:2 final size:2
Alignment explanation
Indices: 44661764--44661795 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44661754 GTATAATAAC
44661764 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
44661796 CGATTCATTT
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:44662540 original size:16 final size:16
Alignment explanation
Indices: 44662518--44662567 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
44662508 TAAGTATAAA
*
44662518 ATGTTTTTCTTTCTTT
1 ATGTTTTTCTTACTTT
* *
44662534 TTGTTTTACTTACTTT
1 ATGTTTTTCTTACTTT
**
44662550 ATGTTTTTAATACTTT
1 ATGTTTTTCTTACTTT
44662566 AT
1 AT
44662568 TATTAATTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (16 bp):
ATGTTTTTCTTACTTT
Found at i:44667715 original size:22 final size:22
Alignment explanation
Indices: 44667690--44667731 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
44667680 TAAGATATAC
44667690 ATTGAATTTTATTGCCTCGATA
1 ATTGAATTTTATTGCCTCGATA
44667712 ATTGAATTTTATTGCCTCGA
1 ATTGAATTTTATTGCCTCGA
44667732 CAATCACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTGAATTTTATTGCCTCGATA
Found at i:44690690 original size:5 final size:5
Alignment explanation
Indices: 44690680--44690711 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
44690670 TAAGTTCCCT
44690680 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
44690712 CATGCCTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:44697642 original size:68 final size:68
Alignment explanation
Indices: 44697533--44697668 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
44697523 GAACAAATTT
*
44697533 TAACGTTAGTGCCTAAATTAAAAAAATTCAAAGTAGGTGACCAAAACATGAACGCGGGCATAGTT
1 TAACGTTAGTGCCTAAATTAAAAAAATTCAAAGTAGGTGACCAAAACATGAACGCGAGCATAGTT
44697598 GAG
66 GAG
*
44697601 TAACGTTAGTGCCTAAATTAAAAAAATTTAAAGTAGGTGACCAAAACATGAACGCGAGCATAGTT
1 TAACGTTAGTGCCTAAATTAAAAAAATTCAAAGTAGGTGACCAAAACATGAACGCGAGCATAGTT
44697666 GAG
66 GAG
44697669 AGACCATTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (68 bp):
TAACGTTAGTGCCTAAATTAAAAAAATTCAAAGTAGGTGACCAAAACATGAACGCGAGCATAGTT
GAG
Found at i:44699471 original size:16 final size:17
Alignment explanation
Indices: 44699439--44699471 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44699429 TCTCTTAGGG
*
44699439 TTAGGGTTTTTATTTTA
1 TTAGGGTTTTTAGTTTA
44699456 TTAGGGTTTTT-GTTTA
1 TTAGGGTTTTTAGTTTA
44699472 GGGTTTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (17 bp):
TTAGGGTTTTTAGTTTA
Found at i:44701965 original size:39 final size:39
Alignment explanation
Indices: 44701922--44702000 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
44701912 ATCAATGGCT
44701922 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
*
44701961 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
44702000 A
1 A
44702001 TAATCATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (39 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
Found at i:44701983 original size:17 final size:17
Alignment explanation
Indices: 44701921--44701987 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
44701911 CATCAATGGC
*
44701921 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
44701938 TACAATTAGAACTCTAAGATTA
1 TACAATTAGAA-GCT--G--TA
*
44701960 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
44701977 TACAATTAGAA
1 TACAATTAGAA
44701988 CTCTAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 22 0.55
18 2 0.05
19 1 0.03
20 1 0.03
21 2 0.05
22 12 0.30
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:44703545 original size:20 final size:20
Alignment explanation
Indices: 44703499--44703545 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
44703489 AGCTCGTTTC
*
44703499 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
* *
44703519 CAACTCA-TTCGAGATCAATT
1 CAGCTCACTT-GAGATCAAGT
44703539 CAGCTCA
1 CAGCTCA
44703546 ATTTTAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:44712628 original size:39 final size:39
Alignment explanation
Indices: 44712585--44712663 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
44712575 ATCATTGGCT
* * *
44712585 ACAATTAAAAGTTGTATACAATTAGTACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAAATCTAAGATTAC
*
44712624 ACAATTAGAAGCTGTATACAATTAGAAATCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAAATCTAAGATTAC
44712663 A
1 A
44712664 TAATCATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (39 bp):
ACAATTAAAAGCTGTATACAATTAGAAATCTAAGATTAC
Found at i:44717450 original size:13 final size:13
Alignment explanation
Indices: 44717432--44717457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44717422 CAATCGTGAC
44717432 ACACGACCATGTG
1 ACACGACCATGTG
44717445 ACACGACCATGTG
1 ACACGACCATGTG
44717458 TCTCCTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
ACACGACCATGTG
Found at i:44726679 original size:114 final size:114
Alignment explanation
Indices: 44726474--44727575 Score: 1849
Period size: 114 Copynumber: 9.7 Consensus size: 114
44726464 NNNNNNNNNT
* * ** * *
44726474 CCGCTAAATCCCCGAAACCTCAGAAAACGGCGTCGTTGGACTTAGGTTTTTTTGTGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
* * *
44726539 CAAAAATGTCGCTAAATCCCTGAGCATTAGC-GACGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAG-CGCTTTCTTATAAATG
44726588 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44726653 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44726702 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44726767 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44726816 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44726881 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44726930 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44726995 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44727044 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44727109 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44727158 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44727223 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
44727272 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
*
44727337 CAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCGCTTTCTTATAAATG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
* ** * *
44727386 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG-TTTTTTGCGGCGCTTTAC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
* * * * * *
44727450 GAAAAACGCCGCTAAAGCCCTGAG-ATTAGCGGCG-TTTACTTAAAAACG
66 CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTT-CTTATAAATG
* * * * *** * **
44727498 CCGCTAAATTCCCGAAAGCTCGGGAAACGACGTCGCTGGGATTAGG--TTTTTGCGGCGC-TTTC
1 CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
44727560 TCAAAAACGCCGCTAA
66 -CAAAAACGCCGCTAA
44727576 TGCTTATTTG
Statistics
Matches: 956, Mismatches: 29, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
110 3 0.00
111 29 0.03
112 57 0.06
113 38 0.04
114 828 0.87
115 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (114 bp):
CCGCTAAATCCCCGAAAGCTCAGAAAATGGTTTCGTTGGTCTTAGGTTTTTTTGCGGCGCTTTTC
CAAAAACGCCGCTAAATCCCTAAGCATTAGCAGCGCTTTCTTATAAATG
Found at i:44727949 original size:18 final size:20
Alignment explanation
Indices: 44727912--44727950 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44727902 CTATTTACAC
44727912 AAAAAAATTATAATTATAAT
1 AAAAAAATTATAATTATAAT
44727932 AAAAAAATTA-AATT-TAAT
1 AAAAAAATTATAATTATAAT
44727950 A
1 A
44727951 TTATTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATTATAATTATAAT
Found at i:44728145 original size:9 final size:9
Alignment explanation
Indices: 44728133--44728204 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
44728123 TTATTAAAAA
44728133 TGAGAGAGT
1 TGAGAGAGT
44728142 TGAGAG-GCT
1 TGAGAGAG-T
*
44728151 TGAGAGACT
1 TGAGAGAGT
*
44728160 TGAGAGGGTT
1 TGAGAGAG-T
*
44728170 TGAGAGAATT
1 TGAGAG-AGT
* *
44728180 TAAGAGAAT
1 TGAGAGAGT
44728189 TGAGAGAGT
1 TGAGAGAGT
44728198 TGAGAGA
1 TGAGAGA
44728205 AGGATGTGAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
8 1 0.02
9 36 0.72
10 13 0.26
ACGTcount: A:0.35, C:0.03, G:0.39, T:0.24
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:44728777 original size:19 final size:19
Alignment explanation
Indices: 44728734--44728794 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
44728724 TTTGAAATTT
**
44728734 AAAATATAAAAAATTAAAAA
1 AAAATAT-AAAAATTAACTA
44728754 TAAAATATAAAAATTAACTA
1 -AAAATATAAAAATTAACTA
*
44728774 AAAATATAGAAACTT-ACTA
1 AAAATATA-AAAATTAACTA
44728793 AA
1 AA
44728795 TATTTTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 14 0.39
20 15 0.42
21 7 0.19
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATATAAAAATTAACTA
Found at i:44729529 original size:2 final size:2
Alignment explanation
Indices: 44729522--44729550 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44729512 GTACAAGCAA
44729522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44729551 AATNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44734906 original size:2 final size:2
Alignment explanation
Indices: 44734899--44734927 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44734889 GTACAAGCAA
44734899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44734928 AATTTCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44744780 original size:27 final size:27
Alignment explanation
Indices: 44744749--44744807 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
44744739 AATACGCCAG
*
44744749 AAAATGAAAGCCTTTATGGTAGTCTAT
1 AAAATGAAAGCCTTTATGGCAGTCTAT
* * *
44744776 GAAATGGAAGCCTTTGTGGCAGTCTAT
1 AAAATGAAAGCCTTTATGGCAGTCTAT
44744803 AAAAT
1 AAAAT
44744808 AGAAGTCTTT
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:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (27 bp):
AAAATGAAAGCCTTTATGGCAGTCTAT
Found at i:44744812 original size:27 final size:26
Alignment explanation
Indices: 44744756--44744829 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
44744746 CAGAAAATGA
* * *
44744756 AAGCCTTTATGGTAGTCTATGAAATGG
1 AAGCCTTTGTGG-AGTCTATAAAATAG
44744783 AAGCCTTTGTGGCAGTCTATAAAATAG
1 AAGCCTTTGTGG-AGTCTATAAAATAG
*
44744810 AAGTCTTTGTGGAGATCTAT
1 AAGCCTTTGTGGAG-TCTAT
44744830 GGAAAGTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 2 0.05
27 39 0.95
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (26 bp):
AAGCCTTTGTGGAGTCTATAAAATAG
Found at i:44744978 original size:26 final size:26
Alignment explanation
Indices: 44744946--44744996 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
44744936 CAAACCCTGG
*
44744946 AAGAATGATATGTATGGCT-AACTTTA
1 AAGAATGATAGGTATGG-TAAACTTTA
*
44744972 AAGAATGGTAGGTATGGTAAACTTT
1 AAGAATGATAGGTATGGTAAACTTT
44744997 GAGAGAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (26 bp):
AAGAATGATAGGTATGGTAAACTTTA
Found at i:44756511 original size:29 final size:29
Alignment explanation
Indices: 44756478--44756775 Score: 253
Period size: 29 Copynumber: 10.4 Consensus size: 29
44756468 TTAGAGTCTC
* * * *
44756478 GCCATAAAGGCGTCCTTTTAACAGAGTTT
1 GCCACAAAGGCATCCTTTTAACAGAGATA
** * * * *
44756507 GCCA-TGAGGCATTCATTTATCTGAGATA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
*
44756535 GCAACAAAGGCATCCTTTTAACAGAGATA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
* * *
44756564 GCCACAAATGCATCCTTTTAACAAAGATT
1 GCCACAAAGGCATCCTTTTAACAGAGATA
* * * ** * *
44756593 GACACAAAGACTTTTTTTTTAACAAAGATT
1 GCCACAAAGGC-ATCCTTTTAACAGAGATA
** * *
44756623 GCCACAAAGGTTTCCTTTTAATAGAGACA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
* * *
44756652 GCAACAAAGACATCCTTTTAACAAAGATA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
* * *
44756681 GTCACAAAGGCATCCTTTTAATAGAGATC
1 GCCACAAAGGCATCCTTTTAACAGAGATA
*
44756710 GCCACAAAGGCTTCCTTTTAACAGAGATA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
*
44756739 GCCACAAAGGCATCC-ATT--CAGAGATA
1 GCCACAAAGGCATCCTTTTAACAGAGATA
*
44756765 ACCACAAAGGC
1 GCCACAAAGGC
44756776 TCACTTATGC
Statistics
Matches: 212, Mismatches: 55, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
26 18 0.08
28 20 0.09
29 151 0.71
30 23 0.11
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (29 bp):
GCCACAAAGGCATCCTTTTAACAGAGATA
Found at i:44756659 original size:88 final size:86
Alignment explanation
Indices: 44756538--44756753 Score: 270
Period size: 88 Copynumber: 2.5 Consensus size: 86
44756528 TGAGATAGCA
* *
44756538 ACAAAGGCATCCTTTTAACAGAGATAGCCACAAATGCATCCTTTTAACAAAGATTGACACAAAGA
1 ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAA-GCATCCTTTTAACAAAGATAGACACAAAGA
* ** *
44756603 CTTTTTTTTTAACAAAGATTGCC
65 C-ATCCTTTTAACAAAGATCGCC
* * * * * *
44756626 ACAAAGGTTTCCTTTTAATAGAGACAGCAACAAAGACATCCTTTTAACAAAGATAGTCACAAAGG
1 ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAG-CATCCTTTTAACAAAGATAGACACAAAGA
* *
44756691 CATCCTTTTAATAGAGATCGCC
65 CATCCTTTTAACAAAGATCGCC
44756713 ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGGCATCC
1 ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAA-GCATCC
44756754 ATTCAGAGAT
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
87 51 0.47
88 57 0.53
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (86 bp):
ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGCATCCTTTTAACAAAGATAGACACAAAGAC
ATCCTTTTAACAAAGATCGCC
Found at i:44756668 original size:117 final size:116
Alignment explanation
Indices: 44756529--44756748 Score: 305
Period size: 117 Copynumber: 1.9 Consensus size: 116
44756519 TCATTTATCT
* * * * *
44756529 GAGATAGCAACAAAGGCATCCTTTTAACAGAGATAGCCACAAATGCATCCTTTTAACAAAGATTG
1 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
** *
44756594 ACACAAAGACTTTTTTTTTAACAAAGATTGCCACAAAGGTTTCCTTTTAATA
66 ACACAAAGAC-TTCCTTTTAACAAAGATAGCCACAAAGGTTTCCTTTTAATA
* * *
44756646 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGTCACAAAGGCATCCTTTTAATAGAGATCG
1 GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
* * *
44756711 CCACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGG
66 ACACAAAGACTTCCTTTTAACAAAGATAGCCACAAAGG
44756749 CATCCATTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
116 24 0.27
117 65 0.73
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (116 bp):
GAGACAGCAACAAAGACATCCTTTTAACAAAGATAGCCACAAAGGCATCCTTTTAACAAAGATCG
ACACAAAGACTTCCTTTTAACAAAGATAGCCACAAAGGTTTCCTTTTAATA
Found at i:44779850 original size:15 final size:14
Alignment explanation
Indices: 44779825--44779856 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
44779815 AACGAATAAT
44779825 AATTTTAAAAATTA
1 AATTTTAAAAATTA
44779839 AATTTGTAAAAATTA
1 AATTT-TAAAAATTA
44779854 AAT
1 AAT
44779857 CGAATATCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTTTAAAAATTA
Found at i:44780961 original size:21 final size:22
Alignment explanation
Indices: 44780935--44780981 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
44780925 ATCAATAGAC
44780935 CATAATTTAAAATTTTCACTA-
1 CATAATTTAAAATTTTCACTAT
44780956 CATAATTTAAAATTTTCACTAT
1 CATAATTTAAAATTTTCACTAT
44780978 CATA
1 CATA
44780982 TTTCCTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
CATAATTTAAAATTTTCACTAT
Found at i:44787045 original size:29 final size:29
Alignment explanation
Indices: 44786953--44787047 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
44786943 GGTGTTAGGC
* * * *
44786953 ACTGGTGATTACAATTTTAGGTACTTTGT
1 ACTGGTGATTATAGTTTCAGGTACTATGT
* * *
44786982 AACT-GTG-TTATAGTTCCAGGCACTCTGT
1 -ACTGGTGATTATAGTTTCAGGTACTATGT
* *
44787010 GCCGGTGATTATAGTTTCAGGTACTATGT
1 ACTGGTGATTATAGTTTCAGGTACTATGT
44787039 ACTGGTGAT
1 ACTGGTGAT
44787048 AGATACCATA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
27 1 0.02
28 18 0.36
29 28 0.56
30 3 0.06
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (29 bp):
ACTGGTGATTATAGTTTCAGGTACTATGT
Found at i:44792041 original size:19 final size:19
Alignment explanation
Indices: 44792019--44792056 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
44792009 CGATTTGGGT
44792019 TCTCAAG-CACAATTTTCAA
1 TCTCAAGTC-CAATTTTCAA
44792038 TCTCAAGTCCAATTTTCAA
1 TCTCAAGTCCAATTTTCAA
44792057 GTTCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (19 bp):
TCTCAAGTCCAATTTTCAA
Found at i:44794364 original size:121 final size:121
Alignment explanation
Indices: 44794209--44794462 Score: 472
Period size: 121 Copynumber: 2.1 Consensus size: 121
44794199 AATTACATCA
* *
44794209 AATTGTAAAGAATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTACTAAAATCTCCATTTA
1 AATTGAAAAG-ATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTA
44794274 AAATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
65 AAATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
*
44794331 AATTTAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
1 AATTGAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
44794396 AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
66 AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
44794452 AATTGAAAAGA
1 AATTGAAAAGA
44794463 CCTTAATACA
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 120 0.94
122 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (121 bp):
AATTGAAAAGATTTTGAAAAAGTGGAATTTGAAAATGAAATTCAACTAATAAAATCTCCATTTAA
AATTACTCGCAAAATTTGAAATTATTTAATTTTTTTACAAATAAATTTATTTTTAG
Found at i:44797576 original size:3 final size:3
Alignment explanation
Indices: 44797568--44797603 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
44797558 TTCATCTGCA
44797568 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44797604 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44798908 original size:12 final size:11
Alignment explanation
Indices: 44798891--44798925 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
44798881 AACAAATCCT
44798891 CTCTCATATTTC
1 CTCTCA-ATTTC
44798903 CTCTCAA-TTC
1 CTCTCAATTTC
44798913 CTCTCAATTTC
1 CTCTCAATTTC
44798924 CT
1 CT
44798926 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:44798967 original size:29 final size:29
Alignment explanation
Indices: 44798935--44799021 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
44798925 TTCCAAAATT
44798935 CTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAAATCTATATTTAATTTCAATTTC
* * *
44798964 CTCTC-AAT-T-TCCTTCAA----AAATT-
1 CTCTCAAATCTAT-ATTTAATTTCAATTTC
*
44798986 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCTATATTTAATTTCAATTTC
44799015 CTCTCAA
1 CTCTCAA
44799022 TTTCCTTNNN
Statistics
Matches: 42, Mismatches: 7, Indels: 18
0.63 0.10 0.27
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 4 0.10
25 1 0.02
26 1 0.02
27 5 0.12
28 7 0.17
29 12 0.29
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (29 bp):
CTCTCAAATCTATATTTAATTTCAATTTC
Found at i:44798972 original size:51 final size:51
Alignment explanation
Indices: 44798906--44799028 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 51
44798896 ATATTTCCTC
* *
44798906 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
44798956 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
44799007 TCAATTTCCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
44799029 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 4 0.06
51 66 0.94
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
Found at i:44800014 original size:7 final size:7
Alignment explanation
Indices: 44800002--44800026 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44799992 ATTTGATTGA
44800002 TATTTAG
1 TATTTAG
44800009 TATTTAG
1 TATTTAG
44800016 TATTTAG
1 TATTTAG
44800023 TATT
1 TATT
44800027 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:44800568 original size:18 final size:18
Alignment explanation
Indices: 44800542--44800576 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44800532 AGGTGCGTTT
*
44800542 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
44800560 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
44800577 TCCTTTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:44801039 original size:43 final size:43
Alignment explanation
Indices: 44800987--44801085 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 43
44800977 TTATTTGTAC
* *
44800987 AAATATTTTGA-ATATTTTGATATTATTTTATGTAAAAAAATA
1 AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
* *
44801029 GAAATTTTTTGAGTTATTTTGATATTATTTAATGTAATAAAATA
1 -AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
44801073 AAAGTTTATTTGA
1 AAA-TTT-TTTGA
44801086 TGTAATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 13 0.27
44 31 0.63
45 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (43 bp):
AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
Found at i:44801048 original size:44 final size:45
Alignment explanation
Indices: 44800999--44801085 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
44800989 ATATTTTGAA
*
44800999 TATTTTGATATTATTTTATGTAAAAAAATAGAAA-TTT-TTTGAGT
1 TATTTTGATATTATTTAATGTAAAAAAATA-AAAGTTTATTTGAGT
*
44801043 TATTTTGATATTATTTAATGTAATAAAATAAAAGTTTATTTGA
1 TATTTTGATATTATTTAATGTAAAAAAATAAAAGTTTATTTGA
44801086 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 31 0.79
45 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTAATGTAAAAAAATAAAAGTTTATTTGAGT
Found at i:44801088 original size:25 final size:25
Alignment explanation
Indices: 44801053--44801145 Score: 168
Period size: 25 Copynumber: 3.7 Consensus size: 25
44801043 TATTTTGATA
* *
44801053 TTATTTAATGTAATAAAATAAAAGT
1 TTATTTGATGTAATAAAATAGAAGT
44801078 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
44801103 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
44801128 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
44801146 ACCCNNNNNN
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:44801325 original size:23 final size:23
Alignment explanation
Indices: 44801295--44802273 Score: 725
Period size: 23 Copynumber: 40.8 Consensus size: 23
44801285 NNNNNNNNNN
44801295 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
44801318 ATTTAATTAAAAACCCTAAACCCTTA
1 ATTTAATTAAAAACCCT-AA-CC-TA
44801344 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
*
44801368 ATTCAATTAAAAACCCTAAACC--
1 ATTTAATTAAAAACCCT-AACCTA
44801390 -TTTAACTTAAAAACCCTAACCTA
1 ATTTAA-TTAAAAACCCTAACCTA
44801413 ATTTAATTAAAAACCCTAGCCTAACCTA
1 ATTTAATTAAAAA--C---CCTAACCTA
*
44801441 AATTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801464 AATTAATTAAAAACCCTAAACCCTTA
1 ATTTAATTAAAAACCCT-AA-CC-TA
44801490 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
* *
44801514 ATTCAATTAAAAAACCTAAACC--
1 ATTTAATTAAAAACCCT-AACCTA
* *
44801536 -CTTATCTTAAAAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAACCTA
44801559 ATTTAATTAAAAACCCTAATTCTAACCTA
1 ATTTAATTAAAAA-CC-----CTAACCTA
*
44801588 ATTCAATTAAAAACCCTAACC--
1 ATTTAATTAAAAACCCTAACCTA
*
44801609 -CTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801631 ATTTAATTAAAAACCCTAGCCTAATCTA
1 ATTTAATTAAAAA--C---CCTAACCTA
44801659 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801682 ATTTAATTAAAAACTCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
44801705 ATTTAATTAAAAACCCTAAACC--
1 ATTTAATTAAAAACCCT-AACCTA
*
44801727 -CTTAATTAAAAACCCTAACCCTA
1 ATTTAATTAAAAACCCTAA-CCTA
*** * *****
44801750 ACCCAAACCTAATTCAATTAAAAACCCTAA
1 A-TTTAA-TTAA---AAACCCTAA-CCT-A
*
44801780 ACCCTTAACTTAAAAACCCTAACCTA
1 A--TTTAA-TTAAAAACCCTAACCTA
44801806 ATTTAATTAAAAACCCTAAACCCTTA
1 ATTTAATTAAAAACCCT-AA-CC-TA
44801832 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
*
44801856 ATTCAATTAAAAACCCTAACCCTTA
1 ATTTAATTAAAAACCCTAA-CC-TA
44801881 A-TTAA--AAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801901 ATTTAATTAAAAACCCTAGCCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801924 ATTTAATT-AAAACCCTAGCCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44801946 ATTTAATTAAAAACCCAAAACCCTTA
1 ATTTAATTAAAAACCC-TAA-CC-TA
44801972 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
* *
44801996 ATTTAATTAAAAACCCTAGCTTA
1 ATTTAATTAAAAACCCTAACCTA
44802019 ATTTAATT-AAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44802041 ATTTAATTAAAAATCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
44802064 ATTTAATTAAAAACCCTAAACCCTTA
1 ATTTAATTAAAAACCCT-AA-CC-TA
44802090 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
*
44802114 ATTTAATTAAAAACCCTAGCCTA
1 ATTTAATTAAAAACCCTAACCTA
44802137 ATTTAATT-AAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44802159 ATTTAATTAAAAATCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
44802182 ATTTAATTAAAAACCCTAAACCCTTA
1 ATTTAATTAAAAACCCT-AA-CC-TA
44802208 A-TTAA--AAACCCTAACCCTAACCTA
1 ATTTAATTAAA----AACCCTAACCTA
*
44802232 ATTTAATTAAAAACCCTAGCCTA
1 ATTTAATTAAAAACCCTAACCTA
*
44802255 ATTTATTTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAA
44802274 ACCCTTAACT
Statistics
Matches: 791, Mismatches: 56, Indels: 218
0.74 0.05 0.20
Matches are distributed among these distances:
20 23 0.03
21 37 0.05
22 95 0.12
23 320 0.40
24 60 0.08
25 77 0.10
26 37 0.05
27 56 0.07
28 48 0.06
29 28 0.04
30 2 0.00
31 8 0.01
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:44802008 original size:118 final size:119
Alignment explanation
Indices: 44801295--44802273 Score: 1078
Period size: 118 Copynumber: 8.2 Consensus size: 119
44801285 NNNNNNNNNN
*
44801295 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCT-
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCTA
44801356 AACCCTAACCTAATTCAATTAAA----AACCCTAAACC---TTTAACTTAAAAACCCTAACCTA
65 AACCCT----TAATT-AA--AAACCCTAACCCT-AACCTAATTTAA-TTAAAAACCCTAACCTA
* *
44801413 ATTTAATTAAAAACCCTAGCCTAACCTAAATTAATTAAAAACCCTAACCTAAATTAATTAAAAAC
1 ATTTAATTAAAAA--C---CCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAAC
* *
44801478 CCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAAACCTAAACC--
61 CCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCTA
* * *
44801536 -CTTATCTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAATTCTAACCTAATTCAATTAAAA
1 ATTTA-ATTAAAAACCCTAACCTAATTTAATTAAAAA-CC-----CTAACCTAATTTAATTAAAA
*
44801600 ACCCT-AACCCTTAATT--AAA----AACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATCT
59 ACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAA--C---CCTAACCT
44801658 A
119 A
*
44801659 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*
44801724 ACCCTTAATTAAAAACCCTAACCCTAACCCAAACCTAATTCAATTAAAAACCCTAAACC--
66 ACCCTTAATTAAAAACCCTAACCCT------AACCTAATTTAATTAAAAACCCT-AACCTA
* *
44801783 -CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCT
1 ATTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCT
*
44801844 AACCCTAACCTAATTCAATTAAAAACCCTAACCCT----TAA-TTAA--AAAAACCCTAACCTA
64 -A----AACC--CTT-AATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
* * *
44801901 ATTTAATTAAAAACCCTAGCCTAATTTAATT-AAAACCCTAGCCTAATTTAATTAAAAACCCAAA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
* *
44801965 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAGCTTA
66 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802019 ATTTAATT-AAAACCCTAACCTAATTTAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*
44802083 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAGCCTA
66 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802137 ATTTAATT-AAAACCCTAACCTAATTTAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
*
44802201 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAGCCTA
66 ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802255 ATTTATTTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAA
44802274 ACCCTTAACT
Statistics
Matches: 753, Mismatches: 37, Indels: 141
0.81 0.04 0.15
Matches are distributed among these distances:
111 19 0.03
112 2 0.00
114 4 0.01
115 3 0.00
116 11 0.01
117 86 0.11
118 299 0.40
119 36 0.05
120 7 0.01
121 9 0.01
122 35 0.05
123 84 0.11
124 75 0.10
125 30 0.04
126 9 0.01
127 4 0.01
128 1 0.00
129 2 0.00
130 37 0.05
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (119 bp):
ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
ACCCTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
Found at i:44802224 original size:95 final size:96
Alignment explanation
Indices: 44801295--44802273 Score: 851
Period size: 95 Copynumber: 10.2 Consensus size: 96
44801285 NNNNNNNNNN
44801295 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
*
44801360 CTAACCTAATTCAATTAAAAACCCTAAACC--
66 CTAACCTAATTTAATTAAAAACCCT-AACCTA
*
44801390 -TTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAA-CCTAAATTAATTAAA-
1 ATTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCTA----AACCCTTAATTAA--AAAC
*
44801452 ---AACCCTAACCTAAATTAATTAAAAACCCTAAACCCTTA
59 CCTAACCCTAACCTAATTTAATTAAAAACCCT-AA-CC-TA
* * *
44801490 A-TTAA--AAACCCTAACCCTAACCTAATTCAATTAAAAAACCTAAACCCTT-ATCT-TAAA---
1 ATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAAT-TAAAAACCC
44801547 -AACCCTAACCTAATTTAATTAAAAACCCTAATTCTAACCTA
61 TAACCCTAACCTAATTTAATTAAAAA-CC-----CTAACCTA
* * *
44801588 ATTCAATTAAAAACCCTAACC---CTTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCT-
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTA
* *
44801648 AGCCTAATCTAATTTAATTAAAAACCCTAACCTA
63 ACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44801682 ATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
*
44801747 CTAACCCAAACCTAATTCAATTAAAAACCCTAAACC--
66 CT------AACCTAATTTAATTAAAAACCCT-AACCTA
*
44801783 -CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAAC
1 ATTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAAC
*
44801847 CCTAACCTAATTCAATTAAAAACCCTAACCCTTA
65 CCTAACCTAATTTAATTAAAAACCCTAA-CC-TA
* *
44801881 A-TTAA--AAAAACCCTAACCTAATTTAATTAAAAACCCT--AGCC-TAATTTAATTAA----AA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAA-AAACCCTAA
* *
44801936 CCCTAGCCTAATTTAATTAAAAACCCAAAACCCTTA
64 CCCTAACCTAATTTAATTAAAAACCC-TAA-CC-TA
* *
44801972 A-TTAA--AAACCCTAACCCTAACCTAATTTAATTAAAAACCCT--A-GCTTAATTTAATTAA--
1 ATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAA-AAACC
*
44802029 --AACCCTAACCTAATTTAATTAAAAATCCTAACCTA
60 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802064 ATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAA
1 ATTTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCTAAACCCT----TAA-TTAA--AAA
*
44802125 ----AACCCTAGCCTAATTTAATT-AAAACCCTAACCTA
58 CCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802159 ATTTAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
*
44802224 CTAACCTAATTTAATTAAAAACCCTAGCCTA
66 CTAACCTAATTTAATTAAAAACCCTAACCTA
*
44802255 ATTTATTTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAA
44802274 ACCCTTAACT
Statistics
Matches: 757, Mismatches: 45, Indels: 163
0.78 0.05 0.17
Matches are distributed among these distances:
89 15 0.02
90 27 0.04
91 27 0.04
92 10 0.01
93 21 0.03
94 59 0.08
95 261 0.34
96 91 0.12
97 54 0.07
98 30 0.04
99 9 0.01
100 35 0.05
101 93 0.12
102 21 0.03
103 4 0.01
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (96 bp):
ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
CTAACCTAATTTAATTAAAAACCCTAACCTA
Found at i:44802227 original size:45 final size:43
Alignment explanation
Indices: 44801661--44802223 Score: 442
Period size: 45 Copynumber: 12.4 Consensus size: 43
44801651 CTAATCTAAT
* *
44801661 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---C
*
44801707 TTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTAACCC
1 TTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCTAACCC
* *
44801748 -----T---AACCCAAACCTAATTCAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AACCC
44801784 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AACCC
44801829 TTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAACCC
1 TTAATTAAAAACCCTAA-CCTAA--T--TT-AATTAAAAACCCTAACCC
* *
44801878 TTAATTAAAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAAT
1 TTAATT--AAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---C
* *
44801926 TTAATT-AAAACCCTAGCCTAATTTAATTAAAAACCCAAAACCC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCC-TAACCC
*
44801969 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-A-GC
1 TTAATT--AAA----AACCCTAACCTAATTTAATTAAAAACCCTAACCC
* *
44802016 TTAATTTAATTAAAACCCTAACCTAATTTAATTAAAAATCCTAACCTAAT
1 TTAA-TT-A--AAAACCCTAACCTAATTTAATTAAAAACCCTAACC---C
*
44802066 TTAATTAAAAACCCTAAACCCTTAA-TTAA--AAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCT-AA-CC-TAATTTAATTAAA----AACCCTAACC---C
* *
44802116 TTAATTAAAAACCCTAGCCTAATTTAATT-AAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---C
*
44802161 TTAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AACCC
44802205 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
44802224 CTAACCTAAT
Statistics
Matches: 438, Mismatches: 26, Indels: 108
0.77 0.05 0.19
Matches are distributed among these distances:
32 4 0.01
33 5 0.01
35 14 0.03
36 6 0.01
42 1 0.00
43 6 0.01
44 49 0.11
45 156 0.36
46 42 0.10
47 21 0.05
48 23 0.05
49 23 0.05
50 77 0.18
51 11 0.03
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (43 bp):
TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCC
Found at i:44802286 original size:23 final size:21
Alignment explanation
Indices: 44802260--44802303 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
44802250 GCCTAATTTA
44802260 TTTAAAAACCCTAAACCCTTAAC
1 TTTAAAAACCCT-AA-CCTTAAC
44802283 TTTAAAAACCCTAACCTTAAC
1 TTTAAAAACCCTAACCTTAAC
44802304 GTAATGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (21 bp):
TTTAAAAACCCTAACCTTAAC
Found at i:44802434 original size:111 final size:111
Alignment explanation
Indices: 44802305--44802516 Score: 370
Period size: 111 Copynumber: 1.9 Consensus size: 111
44802295 AACCTTAACG
*
44802305 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
44802370 ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
* * * *
44802416 TAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAATTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
*
44802481 ATTTTACTAACCATTAATACAATTTTTTGACTTAAT
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAAT
44802517 ACAATTTATT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 95 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (111 bp):
TAATGTTAGATTTCGAAAAATATTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTAACTTAATTACATTCACA
Found at i:44805286 original size:124 final size:127
Alignment explanation
Indices: 44805114--44805465 Score: 488
Period size: 124 Copynumber: 2.8 Consensus size: 127
44805104 CCCAAACATG
*
44805114 CTACTGTAGCAAAAGCGCG-TCCACGAGGACT-CGATTTCACAAATTCTTCTCAAATAGCATCCT
1 CTACTGTAGCAAAAACGCGCTCCACGAGG-CTGCGATTTCACAAATTCTTCTCAAATAGCATCCT
* *
44805177 GCTAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AA-TATTTCTTAC-ATGAT
65 GCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTT-CTATGAC
* *
44805238 CTACTGTAGCAAAAACGCGCT-GACGAGGCTGCAATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAACGCGCTCCACGAGGCTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
44805302 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTATGAC
* * *
44805364 CTACTGTAGC-AAAAGGC-CGTCCACGAGGGC-GCGATTTTACAAATTCTTCTCAAATACCATCC
1 CTACTGTAGCAAAAACGCGC-TCCACGA-GGCTGCGATTTCACAAATTCTTCTCAAATAGCATCC
* **
44805426 TGCTAGAAGTGATTTTATATTATTTTATCAGAAACGTCAA
64 TGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
44805466 CTCGAAATTA
Statistics
Matches: 204, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
123 2 0.01
124 98 0.48
125 11 0.05
126 90 0.44
127 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (127 bp):
CTACTGTAGCAAAAACGCGCTCCACGAGGCTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTATGAC
Found at i:44805433 original size:126 final size:124
Alignment explanation
Indices: 44805114--44805465 Score: 496
Period size: 126 Copynumber: 2.8 Consensus size: 124
44805104 CCCAAACATG
* *
44805114 CTACTGTAGCAAAAGCGCGTCCACGAGGACTCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
44805179 TAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGAT
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGAC
* * *
44805238 CTACTGTAGCAAAAACGCG-CTGACGA-GGCTGCAATTTCACAAATTCTTCTCAAATAGCATCCT
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGC-GCGATTTCACAAATTCTTCTCAAATAGCATCCT
* *
44805301 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTT-CTGTGAC
64 GCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AA-TATTTCTTAC-ATGAC
* *
44805364 CTACTGTAGCAAAAG-GCCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATACCATCCTG
1 CTACTGTAGCAAAAGCG-CGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* **
44805428 CTAGAAGTGATTTTATATTATTTTATCAGAAACGTCAA
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
44805466 CTCGAAATTA
Statistics
Matches: 202, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
123 3 0.01
124 95 0.47
125 4 0.02
126 96 0.48
127 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGAC
Found at i:44805991 original size:12 final size:12
Alignment explanation
Indices: 44805970--44806005 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
44805960 ATATTTTTTT
44805970 AGCCATAGCCAA
1 AGCCATAGCCAA
*
44805982 AGCCAAAGCCAA
1 AGCCATAGCCAA
44805994 AGCCATAGCCAA
1 AGCCATAGCCAA
44806006 TAGCACAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.33, G:0.17, T:0.06
Consensus pattern (12 bp):
AGCCATAGCCAA
Found at i:44805997 original size:18 final size:18
Alignment explanation
Indices: 44805970--44806005 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44805960 ATATTTTTTT
*
44805970 AGCCATAGCCAAAGCCAA
1 AGCCAAAGCCAAAGCCAA
*
44805988 AGCCAAAGCCATAGCCAA
1 AGCCAAAGCCAAAGCCAA
44806006 TAGCACAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.33, G:0.17, T:0.06
Consensus pattern (18 bp):
AGCCAAAGCCAAAGCCAA
Found at i:44813160 original size:32 final size:32
Alignment explanation
Indices: 44813118--44813193 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
44813108 TGCATGTGTG
* * *
44813118 TAACTTTTCATCTTCAAGTCTCTTCGCATTAT
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
* **
44813150 TAACTCTTCATATTCAAGTCTTTTCACATTCG
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
*
44813182 TAACTTTTCATA
1 TAACTCTTCATA
44813194 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATATTCAAGTCTCTTCACATTAT
Found at i:44817655 original size:32 final size:32
Alignment explanation
Indices: 44817613--44817688 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
44817603 TGCATGTGTG
* * *
44817613 TAACTTTTCATCTTCAAGTCTCTTCGCATTAT
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
* **
44817645 TAACTCTTCATATTCAAGTCTTTTCACATTCG
1 TAACTCTTCATATTCAAGTCTCTTCACATTAT
*
44817677 TAACTTTTCATA
1 TAACTCTTCATA
44817689 ATTTCTTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (32 bp):
TAACTCTTCATATTCAAGTCTCTTCACATTAT
Found at i:44824872 original size:33 final size:33
Alignment explanation
Indices: 44824830--44824896 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
44824820 CACACACTCA
44824830 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
1 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
44824863 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
1 TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
44824896 T
1 T
44824897 AACGCTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (33 bp):
TGCAACGATAGCCTTTGGCCAAATTGATTTTTC
Found at i:44828305 original size:6 final size:6
Alignment explanation
Indices: 44828294--44828359 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
44828284 GTGCGAGCGA
* *
44828294 GAAAAT GAAAAT GAAAAA GAAATT G-AAA- GAAAA- GAAAAT GAAAA-
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
* * * *
44828338 GAGATT GAAAAA GAAATT GAAA
1 GAAAAT GAAAAT GAAAAT GAAA
44828360 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
4 1 0.02
5 13 0.28
6 32 0.70
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
GAAAAT
Found at i:44828324 original size:10 final size:11
Alignment explanation
Indices: 44828322--44828363 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
44828312 GAAATTGAAA
*
44828322 GAAAAGAAAAT
1 GAAAAGAAATT
*
44828333 GAAAAGAGATT
1 GAAAAGAAATT
44828344 GAAAAAGAAATT
1 G-AAAAGAAATT
44828356 G-AAAGAAA
1 GAAAAGAAA
44828364 AGAAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
12 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (11 bp):
GAAAAGAAATT
Found at i:44828353 original size:28 final size:28
Alignment explanation
Indices: 44828293--44828347 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
44828283 AGTGCGAGCG
44828293 AGAAAATGAAAATGAAAAAGAAATTGAA
1 AGAAAATGAAAATGAAAAAGAAATTGAA
*
44828321 AGAAAA-GAAAATG-AAAAGAGATTGAA
1 AGAAAATGAAAATGAAAAAGAAATTGAA
44828347 A
1 A
44828348 AAGAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 13 0.50
27 7 0.27
28 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (28 bp):
AGAAAATGAAAATGAAAAAGAAATTGAA
Found at i:44832209 original size:39 final size:39
Alignment explanation
Indices: 44832131--44832209 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
44832121 CCTCATTTTT
* *
44832131 AGCAACTTCTTCTTTAGCAACAACTTCCTCTTCTGCAGC
1 AGCAACTTCTTCTTTAACAACAACTTCCTCTTATGCAGC
44832170 AGCAACTTCCTTC-TTAACAACAA-TGTCCTCTTGAT-CAGC
1 AGCAACTT-CTTCTTTAACAACAACT-TCCTCTT-ATGCAGC
44832209 A
1 A
44832210 AAAAGACCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 1 0.03
39 29 0.83
40 5 0.14
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (39 bp):
AGCAACTTCTTCTTTAACAACAACTTCCTCTTATGCAGC
Found at i:44842961 original size:41 final size:41
Alignment explanation
Indices: 44842913--44843004 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
44842903 GGCAGATGAG
***
44842913 ACGGGCGTGTGTCAGGTTGTGGGAGCCACACAGGCAAGCAC
1 ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
* * * *
44842954 ATGGGCGTATGTCAGGCCATTGGAGCCACACGGGCAAGCAC
1 ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
*
44842995 ACGGGTGTGT
1 ACGGGCGTGT
44843005 ACAAGGCCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (41 bp):
ACGGGCGTGTGTCAGGCCATGGGAGCCACACAGGCAAGCAC
Found at i:44849216 original size:20 final size:20
Alignment explanation
Indices: 44849193--44849235 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
44849183 TTTTTCATTA
44849193 TTTTCTTCTTTCT-TTTCCTC
1 TTTTCTT-TTTCTGTTTCCTC
44849213 TTTTCTTTTTCTGTTTCCTC
1 TTTTCTTTTTCTGTTTCCTC
44849233 TTT
1 TTT
44849236 CAATTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTTCTGTTTCCTC
Found at i:44858180 original size:48 final size:48
Alignment explanation
Indices: 44858109--44858200 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
44858099 TTGTTTTCTT
*
44858109 AAAAATGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
* *
44858157 AAAAACGCCTAAGTCGGCCTAACTTGTAATGATAAAGGATTCAA
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAA
44858201 CAAAATTCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTTGCAATGATAAAGGATTCAAACGC
Found at i:44858449 original size:19 final size:19
Alignment explanation
Indices: 44858425--44858478 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
44858415 AAAGCTGTAT
44858425 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
44858444 ACAATTAGAAGT-T--GTAT
1 ACAATTAGAACTCTAAG-AC
44858461 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
44858479 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 2 0.07
19 12 0.43
20 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:44858460 original size:36 final size:36
Alignment explanation
Indices: 44858408--44858478 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
44858398 ATCAAAGGCT
44858408 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
* *
44858444 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
44858479 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:44858466 original size:17 final size:17
Alignment explanation
Indices: 44858407--44858470 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
44858397 CATCAAAGGC
* *
44858407 TACAATTAAAAGCTGTA
1 TACAATTAGAAGTTGTA
*
44858424 TACAATTAGAACTCTAAG-A
1 TACAATTAGAAGT-T--GTA
*
44858443 CACAATTAGAAGTTGTA
1 TACAATTAGAAGTTGTA
44858460 TACAATTAGAA
1 TACAATTAGAA
44858471 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 2 0.05
19 12 0.32
20 1 0.03
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGTTGTA
Found at i:44863389 original size:17 final size:17
Alignment explanation
Indices: 44863367--44863430 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
44863357 CATCAAAGGC
*
44863367 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
44863384 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
44863403 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
44863420 TACAATTAGAA
1 TACAATTAGAA
44863431 CTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:44863409 original size:19 final size:19
Alignment explanation
Indices: 44863385--44863438 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
44863375 AAAGCTGTAT
44863385 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
44863404 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
44863421 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
44863439 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:44863416 original size:36 final size:36
Alignment explanation
Indices: 44863368--44863438 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
44863358 ATCAAAGGCT
44863368 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
44863404 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
44863439 TTACATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:44875668 original size:35 final size:35
Alignment explanation
Indices: 44875617--44875684 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
44875607 GTGAATGAAC
44875617 AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
1 AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
*
44875652 AACTTAAAGACAAGTCGAGATGGACCTTGGAAA
1 AACTCAAAGACAAGTCGAGATGGACCTTGGAAA
44875685 TTTGAATCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (35 bp):
AACTCAAAGACAAGTCGAGATGGACCTTGGAAAAA
Found at i:44887572 original size:13 final size:13
Alignment explanation
Indices: 44887554--44887578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44887544 ATAATGACTC
44887554 TAAAAATATTTAA
1 TAAAAATATTTAA
44887567 TAAAAATATTTA
1 TAAAAATATTTA
44887579 CGACTTTATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:44891440 original size:37 final size:37
Alignment explanation
Indices: 44891394--44891511 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
44891384 AGCTTTTCGG
44891394 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
* * *
44891431 AGCACCTGGCTTGTTATCAGGTGGATTAGCTCTTATA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
* * *
44891468 AGCATTTGGTGTGTTATTAGGTGGATTAGATCTTATGA
1 AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTAT-A
44891506 A-CATCT
1 AGCATCT
44891512 AGCATGTTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
37 68 0.97
38 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (37 bp):
AGCATCTGGCGTGTTATTAGGTGGATTAGCTCTTATA
Done.