Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 42 of 126
Found at i:12456521 original size:58 final size:58
Alignment explanation
Indices: 12456439--12456583 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 58
12456429 ATATTATAAT
* ** * *
12456439 TTTTATT-AATTCATATTTTAATAATAATTATTTTAAGAATGTTATT-AAAT-TATATACTA
1 TTTTATTAAATT-ATA-TTTAATAATAATCAAGTTAA-AATATGATTAAAATGTATAT-CTA
* * * *
12456498 TTTTATTAAATTGTATTTAATAATAATCAAGTTAAAATATGATTAAAATGTTTATTTT
1 TTTTATTAAATTATATTTAATAATAATCAAGTTAAAATATGATTAAAATGTATATCTA
12456556 TTTTATTAAATTATATTTAATAATAATC
1 TTTTATTAAATTATATTTAATAATAATC
12456584 TTATTAAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 7 0.10
58 49 0.67
59 13 0.18
60 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATCAAGTTAAAATATGATTAAAATGTATATCTA
Found at i:12456617 original size:58 final size:58
Alignment explanation
Indices: 12456498--12456617 Score: 129
Period size: 58 Copynumber: 2.1 Consensus size: 58
12456488 TTATATACTA
* * * **
12456498 TTTTATTAAATTGTATTTAATAATAATCAAGTTAAAATATGATTAAAATGTTTATTTT
1 TTTTATTAAATTATATTTAATAATAATCAAGTTAAAATATGAATAAAATATTTATAGT
* *
12456556 TTTTATTAAATTATATTTAATAATAATCTTA-TTAAAAT-TTAATAACAATAATTTA-AGT
1 TTTTATTAAATTATATTTAATAATAATC-AAGTTAAAATATGAATAA-AAT-ATTTATAGT
12456614 TTTT
1 TTTT
12456618 TTCCTTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
57 5 0.10
58 42 0.81
59 5 0.10
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATCAAGTTAAAATATGAATAAAATATTTATAGT
Found at i:12456715 original size:44 final size:44
Alignment explanation
Indices: 12456652--12456764 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
12456642 TTCATTTAAT
* * *
12456652 CAAACACAAGAATATTATTACAGTTCTATTCCATTCCATTCAAC
1 CAAACATAAAAATATTATTACAGTTCTATTACATTCCATTCAAC
* *
12456696 CAAACATAAAAATATTATTACAGTTTTATTACATTCCATTCAAT
1 CAAACATAAAAATATTATTACAGTTCTATTACATTCCATTCAAC
* *
12456740 CAAACAATTAAAATACTGATTACAG
1 CAAAC-ATAAAAATA-TTATTACAG
12456765 CCCTATTCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 44 0.73
45 8 0.13
46 8 0.13
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.33
Consensus pattern (44 bp):
CAAACATAAAAATATTATTACAGTTCTATTACATTCCATTCAAC
Found at i:12456731 original size:39 final size:43
Alignment explanation
Indices: 12456638--12456745 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 43
12456628 TATTATAACA
* * * *
12456638 TCATTTCATTTAATCAAACACAAGAATATTATTACAGTTCTAT
1 TCATTACATTCAACCAAACACAAAAATATTATTACAGTTCTAT
* * *
12456681 TCCATTCCATTCAACCAAACATAAAAATATTATTACAGTTTTAT
1 T-CATTACATTCAACCAAACACAAAAATATTATTACAGTTCTAT
* *
12456725 TACATTCCATTCAATCAAACA
1 T-CATTACATTCAACCAAACA
12456746 ATTAAAATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 1 0.02
44 55 0.98
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (43 bp):
TCATTACATTCAACCAAACACAAAAATATTATTACAGTTCTAT
Found at i:12456786 original size:16 final size:15
Alignment explanation
Indices: 12456758--12456813 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
12456748 TAAAATACTG
*
12456758 ATTACAGCCCTATTC
1 ATTACAGCTCTATTC
* *
12456773 TATTAGAGTTCTATTAC
1 -ATTACAGCTCTATT-C
12456790 ATTACAGCTCTATTCC
1 ATTACAGCTCTATT-C
12456806 ATTACAGC
1 ATTACAGC
12456814 GAACCAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (15 bp):
ATTACAGCTCTATTC
Found at i:12465374 original size:50 final size:50
Alignment explanation
Indices: 12465315--12465417 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
12465305 TCTTTGATCT
12465315 AATATAAATTAATTAATTTATCTATTTTTTTAATAGAGCGAACAAAATAC
1 AATATAAATTAATTAATTTATCTATTTTTTTAATAGAGCGAACAAAATAC
12465365 AATATAAATTAATTAATTTATCTATTTTTTTAATAGAGCGAACAAAATAC
1 AATATAAATTAATTAATTTATCTATTTTTTTAATAGAGCGAACAAAATAC
12465415 AAT
1 AAT
12465418 CTTACTTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (50 bp):
AATATAAATTAATTAATTTATCTATTTTTTTAATAGAGCGAACAAAATAC
Found at i:12468789 original size:33 final size:31
Alignment explanation
Indices: 12468719--12468789 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
12468709 TAAATTTAAA
*
12468719 TTTTAATCTTTTAAAAAATATCGAATTTGAT
1 TTTTAATCTTTTAAAAAAAATCGAATTTGAT
** * *
12468750 CATTAATCTTTTAAAAAAAATTGAAATGTTGTT
1 TTTTAATCTTTTAAAAAAAATCG-AAT-TTGAT
12468783 TTTTAAT
1 TTTTAAT
12468790 AAAAATACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
31 19 0.61
32 3 0.10
33 9 0.29
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (31 bp):
TTTTAATCTTTTAAAAAAAATCGAATTTGAT
Found at i:12471187 original size:18 final size:18
Alignment explanation
Indices: 12471155--12471189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12471145 TAATTGATCG
*
12471155 AATCGATCTAATTCGATT
1 AATCGATCGAATTCGATT
*
12471173 AATCGATCGAGTTCGAT
1 AATCGATCGAATTCGAT
12471190 CGAAAGTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (18 bp):
AATCGATCGAATTCGATT
Found at i:12476920 original size:24 final size:24
Alignment explanation
Indices: 12476892--12476941 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12476882 TTAATTTTTA
* *
12476892 ATGTTTATGTTTTTTGTCAATTTG
1 ATGTTTATATTTTTTATCAATTTG
12476916 ATGTTTATATTTTTTATCAATTTG
1 ATGTTTATATTTTTTATCAATTTG
12476940 AT
1 AT
12476942 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (24 bp):
ATGTTTATATTTTTTATCAATTTG
Found at i:12477136 original size:27 final size:25
Alignment explanation
Indices: 12477106--12477163 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
12477096 TTTTATGCTG
*
12477106 TTTTT-TTTAAATTATGATTTTTTATA
1 TTTTTATTTTAATT-TGATTTTTT-TA
*
12477132 TTTTTAATTTTGATTTGATTTTTTTA
1 TTTTT-ATTTTAATTTGATTTTTTTA
12477158 TTTTTA
1 TTTTTA
12477164 AATTATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 12 0.43
27 9 0.32
28 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.72
Consensus pattern (25 bp):
TTTTTATTTTAATTTGATTTTTTTA
Found at i:12483935 original size:70 final size:70
Alignment explanation
Indices: 12483822--12483972 Score: 266
Period size: 70 Copynumber: 2.2 Consensus size: 70
12483812 CAATTAGGTA
* *
12483822 TAAAATAAAGATATCAAATAGGTAGTTTTAGACAATTTTAGAAGTTAAATTATATATTAACCCTT
1 TAAAATGAATATATCAAATAGGTAGTTTTAGACAATTTTAGAAGTTAAATTATATATTAACCCTT
*
12483887 TTATC
66 CTATC
*
12483892 TAAAATGAATATATCAAATAGGTATTTTTAGACAATTTTAGAAGTTAAATTATATATTAACCCTT
1 TAAAATGAATATATCAAATAGGTAGTTTTAGACAATTTTAGAAGTTAAATTATATATTAACCCTT
12483957 CTATC
66 CTATC
12483962 TAAAATGAATA
1 TAAAATGAATA
12483973 CCGTATTGCT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 77 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (70 bp):
TAAAATGAATATATCAAATAGGTAGTTTTAGACAATTTTAGAAGTTAAATTATATATTAACCCTT
CTATC
Found at i:12485368 original size:29 final size:29
Alignment explanation
Indices: 12485333--12485609 Score: 211
Period size: 30 Copynumber: 9.4 Consensus size: 29
12485323 CAAAGAATTT
* *
12485333 GGGGTCAAAATGTGATTTGGGAAAGTTTA
1 GGGGTCAAAATGTAATTTTGGAAAGTTTA
* * *
12485362 GAGGTCAAAATGTGATTTTGGGAAGGTTTA
1 GGGGTCAAAATGTAATTTT-GGAAAGTTTA
** *
12485392 GGGGTTGAAATGCAATTTTGGAGAAGTTT-
1 GGGGTCAAAATGTAATTTTGGA-AAGTTTA
* * * *
12485421 GGAGTTAAAAAGTTATTTTGGAGAAGTTT-
1 GGGGTCAAAATGTAATTTTGGA-AAGTTTA
* *
12485450 GGGGTCAAAATGTAATTTTAGACAAATTTA
1 GGGGTCAAAATGTAATTTTGGA-AAGTTTA
*
12485480 -GGGTCACAATGTAATTTTGGGAAAGTTTA
1 GGGGTCAAAATGTAATTTT-GGAAAGTTTA
***
12485509 GGGGTCAAAATGTAATTTTGGAAAAAAATA
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTA
* *
12485539 AGGGTTAAAATGTAATTTTGGAAAAGTTT-
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTA
* * * * *
12485568 GGCCGTCAAAATGTTATGTTAGGGAAGCTTA
1 GG-GGTCAAAATGTAAT-TTTGGAAAGTTTA
*
12485599 AGGGTCAAAAT
1 GGGGTCAAAAT
12485610 ATGATTTCTT
Statistics
Matches: 197, Mismatches: 42, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
29 92 0.47
30 100 0.51
31 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGGAAAGTTTA
Found at i:12485403 original size:59 final size:59
Alignment explanation
Indices: 12485333--12485530 Score: 215
Period size: 59 Copynumber: 3.4 Consensus size: 59
12485323 CAAAGAATTT
* * *
12485333 GGGGTCAAAATGTGATTTGGGA-AAGTTTAGAGGTCAAAATGTGATTTTGGGAAGGTTTA
1 GGGGTCAAAATGTAATTTTGGACAAGTTTAGAGGTCAAAATGTAATTTTGGGAA-GTTTA
** * * * * * *
12485392 GGGGTTGAAATGCAATTTTGGAGAAGTTTGGA-GTTAAAAAGTTATTTTGGAGAAGTTT-
1 GGGGTCAAAATGTAATTTTGGACAAGTTTAGAGGTCAAAATGTAATTTTGG-GAAGTTTA
* * *
12485450 GGGGTCAAAATGTAATTTTAGACAAATTTAG-GGTCACAATGTAATTTTGGGAAAGTTTA
1 GGGGTCAAAATGTAATTTTGGACAAGTTTAGAGGTCAAAATGTAATTTTGGG-AAGTTTA
12485509 GGGGTCAAAATGTAATTTTGGA
1 GGGGTCAAAATGTAATTTTGGA
12485531 AAAAAATAAG
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
57 1 0.01
58 44 0.39
59 57 0.50
60 11 0.10
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGGTCAAAATGTAATTTTGGACAAGTTTAGAGGTCAAAATGTAATTTTGGGAAGTTTA
Found at i:12485601 original size:60 final size:57
Alignment explanation
Indices: 12485330--12485609 Score: 195
Period size: 59 Copynumber: 4.7 Consensus size: 57
12485320 TTTCAAAGAA
* * * * * * *
12485330 TTTGGGGTCAAAATGTGATTTGGGAAAGTTTAGAGGTCAAAATGTGATTTTGGGAAGG
1 TTTGGGGTCAAAATGTAATTTAGGAAAATTAAG-GGTCAAAATGTAATTTTGGAAAAG
** * * * * * * * *
12485388 TTTAGGGGTTGAAATGCAATTTTGGAGAAGTT-TGGAGTTAAAAAGTTATTTTGGAGAAG
1 TTT-GGGGTCAAAATGTAATTTAGGA-AAATTAAGG-GTCAAAATGTAATTTTGGAAAAG
* * *
12485447 TTTGGGGTCAAAATGTAATTTTA-GACAAATTTAGGGTCACAATGTAATTTTGGGAAAG
1 TTTGGGGTCAAAATGTAA-TTTAGGA-AAATTAAGGGTCAAAATGTAATTTTGGAAAAG
* * *
12485505 TTTAGGGGTCAAAATGTAATTTTGGAAAAAAATAAGGGTTAAAATGTAATTTTGGAAAAG
1 TTT-GGGGTCAAAATGTAATTTAGG--AAAATTAAGGGTCAAAATGTAATTTTGGAAAAG
* * **
12485565 TTTGGCCGTCAAAATGTTATGTTAGGGAAGCTTAAGGGTCAAAAT
1 TTTGG-GGTCAAAATGTAAT-TTA-GGAAAATTAAGGGTCAAAAT
12485610 ATGATTTCTT
Statistics
Matches: 172, Mismatches: 38, Indels: 22
0.74 0.16 0.09
Matches are distributed among these distances:
58 45 0.26
59 61 0.35
60 61 0.35
61 3 0.02
62 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (57 bp):
TTTGGGGTCAAAATGTAATTTAGGAAAATTAAGGGTCAAAATGTAATTTTGGAAAAG
Found at i:12487945 original size:39 final size:38
Alignment explanation
Indices: 12487902--12488498 Score: 353
Period size: 39 Copynumber: 15.3 Consensus size: 38
12487892 GCCCCTGTCG
* * * *
12487902 CGGGGTAAGAGATTACTTGATGGTGATCTGCCTCAGGCT
1 CGGGGTAAAAGATTGC-TGATGGTGATCTGCCCCAAGCT
* ** *
12487941 CGGGGTAAAAGATTGAATGACT-GCAATTTGCCCCAAGCT
1 CGGGGTAAAAGATTG-CTGA-TGGTGATCTGCCCCAAGCT
* *
12487980 CGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCT
1 CGGGGTAAAAGATT-GCTGATGGTGATCTGCCCCAAGCT
* * * * *
12488019 CGGGGTAAAAGA-T-CGGATGGCTGCAATCTGTCCTAGGGT
1 CGGGGTAAAAGATTGCTGATGG-TG--ATCTGCCCCAAGCT
* * * * *
12488058 CGGGGTAAGAGATTGGCTGATAGTTATCTGCTCTAAGCT
1 CGGGGTAAAAGATT-GCTGATGGTGATCTGCCCCAAGCT
* * *
12488097 CGGGGTAAAAGA-T-CGGATGGCTGCAATTTGCCCCAGGCT
1 CGGGGTAAAAGATTGCTGATGG-TG--ATCTGCCCCAAGCT
* * *
12488136 CAGGGTAAGAGATTGGCTAATGGTGA-CTTG-CCCAAGCT
1 CGGGGTAAAAGATT-GCTGATGGTGATC-TGCCCCAAGCT
* * *
12488174 TGGGGTAAAAGA-T-CGGATGGCTGCAATTTGCCCCAAGCT
1 CGGGGTAAAAGATTGCTGATGG-TG--ATCTGCCCCAAGCT
* * * *
12488213 CAGGGTAAGAGATTGGCTAATAGTGATCTGCCCCAAGCT
1 CGGGGTAAAAGATT-GCTGATGGTGATCTGCCCCAAGCT
* * **
12488252 CGGGGTAAAAGA-T-CAGATGACTGCAATCTGCTTCAAGCT
1 CGGGGTAAAAGATTGCTGATG-GTG--ATCTGCCCCAAGCT
* *
12488291 CGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAACT
1 CGGGGTAAAAGATTG-CTGATGGTGATCTGCCCCAAGCT
* *
12488330 CGGGGTAAAAGA-T-CGGATGGCTGCAATCTACCCCAAGCT
1 CGGGGTAAAAGATTGCTGATGG-TG--ATCTGCCCCAAGCT
* * *
12488369 CAGGGTAAAAGATTGGCTGATAGTGATCTGCCTCAAGCT
1 CGGGGTAAAAGATT-GCTGATGGTGATCTGCCCCAAGCT
** * *
12488408 CGGGGTAAAAGA-T-AAGATGGCTATAATCTGCCCCAGGCT
1 CGGGGTAAAAGATTGCTGATGG---TGATCTGCCCCAAGCT
* * *
12488447 CGAGGTAAGAGATTGGTTGATGGTGATCTGCCCC-AGCCT
1 CGGGGTAAAAGATT-GCTGATGGTGATCTGCCCCAAG-CT
12488486 CGGGGTAAAAGAT
1 CGGGGTAAAAGAT
12488499 CGAATGGCTG
Statistics
Matches: 420, Mismatches: 94, Indels: 88
0.70 0.16 0.15
Matches are distributed among these distances:
35 5 0.01
36 25 0.06
37 8 0.02
38 26 0.06
39 310 0.74
40 8 0.02
41 9 0.02
42 29 0.07
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (38 bp):
CGGGGTAAAAGATTGCTGATGGTGATCTGCCCCAAGCT
Found at i:12488003 original size:78 final size:78
Alignment explanation
Indices: 12487867--12488615 Score: 815
Period size: 78 Copynumber: 9.6 Consensus size: 78
12487857 GAATTTTTTT
* ** * * *
12487867 GTAAAAGATTGGATGATTGCAATCTGCCCC-TGTCGCGGGGTAAGAGATT-ACTTGATGGTGATC
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAG-CTCGGGGTAAGAGATTGGC-TGATGGTGATC
* *
12487930 TGCCTCAGGCTCGGG
64 TGCCCCAAGCTCGGG
* * * * *
12487945 GTAAAAGATTGAATGACTGCAATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
12488010 CCCCAAGCTCGGG
66 CCCCAAGCTCGGG
* * * * * *
12488023 GTAAAAGATCGGATGGCTGCAATCTGTCCTAGGGTCGGGGTAAGAGATTGGCTGATAGTTATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
* *
12488088 CTCTAAGCTCGGG
66 CCCCAAGCTCGGG
* * * *
12488101 GTAAAAGATCGGATGGCTGCAATTTGCCCCAGGCTCAGGGTAAGAGATTGGCTAATGGTGA-CTT
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATC-T
*
12488165 G-CCCAAGCTTGGG
65 GCCCCAAGCTCGGG
* * * *
12488178 GTAAAAGATCGGATGGCTGCAATTTGCCCCAAGCTCAGGGTAAGAGATTGGCTAATAGTGATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
12488243 CCCCAAGCTCGGG
66 CCCCAAGCTCGGG
* * ** *
12488256 GTAAAAGATCAGATGACTGCAATCTGCTTCAAGCTCGGGGTAAGAGATTGACTGATGGTGATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
*
12488321 CCCCAAACTCGGG
66 CCCCAAGCTCGGG
* * * *
12488334 GTAAAAGATCGGATGGCTGCAATCTACCCCAAGCTCAGGGTAAAAGATTGGCTGATAGTGATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
*
12488399 CCTCAAGCTCGGG
66 CCCCAAGCTCGGG
** ** * * *
12488412 GTAAAAGATAAGATGGCTATAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTG
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
12488477 CCCC-AGCCTCGGG
66 CCCCAAG-CTCGGG
* * * * * * * * * *
12488490 GTAAAAGATCGAATGGCTGCAATCTGTCCTAGGTTCGGAGTAAGAGATTGGTTGATAGTGATTTA
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
* *
12488555 CCTCAAGCTTGGG
66 CCCCAAGCTCGGG
* ** ** * * *
12488568 GTAAACGATCGGATGAATGTGATCTACCCCATGATCGGGGTAAGAGAT
1 GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGAT
12488616 CAAAATCTTC
Statistics
Matches: 568, Mismatches: 96, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
77 73 0.13
78 491 0.86
79 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (78 bp):
GTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG
CCCCAAGCTCGGG
Found at i:12488855 original size:50 final size:49
Alignment explanation
Indices: 12488761--12488905 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 49
12488751 AGACTCGTCG
* * ** * * ***
12488761 TTGCGACCTCAATCTTTCCCGTCATGTTTTTAAGGTACCAGGTTCGTTG
1 TTGCGACCTCAACCTTTCCCATCAAATCTTTAAGGTACCGGGTTCGCCA
* *
12488810 TTGTTG-CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCA
1 TTG-CGACCTCAACCTTTCCCATCAAATCTT-TAAGGTACCGGGTTCGCCA
* *
12488860 TTGCGACCTCAACCTTTCCCTTCAAATCTTTACGGTACCGCGGTTC
1 TTGCGACCTCAACCTTTCCCATCAAATCTTTAAGGTACCG-GGTTC
12488906 ATTTCATCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
49 32 0.41
50 46 0.59
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (49 bp):
TTGCGACCTCAACCTTTCCCATCAAATCTTTAAGGTACCGGGTTCGCCA
Found at i:12497754 original size:51 final size:51
Alignment explanation
Indices: 12497697--12497984 Score: 443
Period size: 51 Copynumber: 5.6 Consensus size: 51
12497687 TTTCATTTGA
* * * * *
12497697 TACTCACAATGACATATTA-TCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
12497748 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
12497799 TACTCACGATAACACTTAGTCATCAGACCTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
12497850 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
12497901 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
12497952 TACTCACGATGACACTTAGTCACCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
12497985 CGTTTATAGC
Statistics
Matches: 219, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
50 3 0.01
51 212 0.97
52 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:12502414 original size:57 final size:58
Alignment explanation
Indices: 12502344--12502738 Score: 421
Period size: 57 Copynumber: 6.8 Consensus size: 58
12502334 AAAAATGTAC
* * *
12502344 TTTTGGATGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTTAGGGATAAAATGGT-AT
1 TTTTGG-TGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTAGGGGTAAAATGGTAAT
* * * *
12502402 TTTTGGTGAAATCGAGGTT-GAAATGGGATTTTGTAAAGTTT-GGGGACAAAATGGTAA-
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTG-AAAGTTTAGGGG-TAAAATGGTAAT
* * * *
12502459 TTTTGGTG-AATTGGGGTTAAAAATGGGATTTTGAAAG-TTCGAGGGCAAAATGGTAAT
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTAG-GGGTAAAATGGTAAT
** * *
12502516 TTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAAAGAGTTTTGGGGGTAAAATGGTAAT
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAA-AG-TTTAGGGGTAAAATGGTAAT
* * *
12502576 TTTTGGTGGAATC-GGGTTAAAAATGGGATTTTGAAAAG-TTCGGGGTAAAATGGTAAT
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTG-AAAGTTTAGGGGTAAAATGGTAAT
* * * * * *
12502633 TTTTGGTAAAATCAGGGATAAAAATGGAATTTTGGAGAGTTTTGGGGTAAAACGGTAAT
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGTTTAGGGGTAAAATGGTAAT
*
12502692 TTTTGGTGAAA-CTGGGGTCAAAAATGGAATTTTGAAAGTTTAGGGGT
1 TTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGAAAGTTTAGGGGT
12502739 CAAAGTATAA
Statistics
Matches: 288, Mismatches: 33, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
55 2 0.01
56 38 0.13
57 87 0.30
58 64 0.22
59 67 0.23
60 27 0.09
61 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTAGGGGTAAAATGGTAAT
Found at i:12502461 original size:29 final size:29
Alignment explanation
Indices: 12502429--12502518 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 29
12502419 TTGAAATGGG
12502429 ATTTTGTAAAGTTTGGGGACAAAATGGTA
1 ATTTTGTAAAGTTTGGGGACAAAATGGTA
* *
12502458 ATTTTGGTGAA--TTGGGGTTA-AAAATGG-G
1 ATTTT-GTAAAGTTTGGGG--ACAAAATGGTA
*
12502486 ATTTTG-AAAGTTCGAGGG-CAAAATGGTA
1 ATTTTGTAAAGTTTG-GGGACAAAATGGTA
12502514 ATTTT
1 ATTTT
12502519 TGGTGAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
26 2 0.04
27 8 0.17
28 18 0.38
29 15 0.31
30 5 0.10
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
ATTTTGTAAAGTTTGGGGACAAAATGGTA
Found at i:12502548 original size:29 final size:29
Alignment explanation
Indices: 12502329--12502725 Score: 98
Period size: 29 Copynumber: 13.7 Consensus size: 29
12502319 TTGACTTTCG
* * *
12502329 AGGG-TAAAAATGTACTTTTGGATGAAATC
1 AGGGTTAAAAATGGAATTTTGG-TGAAATT
* * *
12502358 GGGGTTAAAAATAGAATTTT-G-GAAGTTT
1 AGGGTTAAAAATGGAATTTTGGTGAA-ATT
* *
12502386 AGGGAT-AAAATGGTATTTTTGGTGAAA-T
1 AGGGTTAAAAATGG-AATTTTGGTGAAATT
* * *
12502414 CGAGGTT-GAAATGGGATTTT-GT-AAAGTT
1 AG-GGTTAAAAATGGAATTTTGGTGAAA-TT
* *
12502442 TGGG-GACAAAATGGTAATTTTGGTG-AATT
1 AGGGTTA-AAAATGG-AATTTTGGTGAAATT
* *
12502471 GGGGTTAAAAATGGGA-TTT--TGAAAGTT
1 AGGGTTAAAAATGGAATTTTGGTGAAA-TT
*
12502498 CGAGGG--CAAAATGGTAATTTTTGGTGAAATT
1 --AGGGTTAAAAATGG-AA-TTTTGGTGAAATT
*** **
12502529 AGGGTTAAAAATGGAATTTTAAAGAGTTTT
1 AGGGTTAAAAATGGAATTTTGGTGA-AATT
* * *
12502559 GGGGGT-AAAATGGTAATTTTTGGTGGAA-T
1 AGGGTTAAAAATGG-AA-TTTTGGTGAAATT
* * *
12502588 CGGGTTAAAAATGGGATTTT-G-AAAAGTT
1 AGGGTTAAAAATGGAATTTTGGTGAAA-TT
* * * *
12502616 CGGGGT-AAAATGGTAATTTTTGGTAAAATC
1 AGGGTTAAAAATGG-AA-TTTTGGTGAAATT
* * **
12502646 AGGGATAAAAATGGAATTTTGGAGAGTTT
1 AGGGTTAAAAATGGAATTTTGGTGAAATT
* * * *
12502675 TGGGGT-AAAACGGTAATTTTTGGTGAAACT
1 AGGGTTAAAAATGG-AA-TTTTGGTGAAATT
* *
12502705 GGGGTCAAAAATGGAATTTTG
1 AGGGTTAAAAATGGAATTTTG
12502726 AAAGTTTAGG
Statistics
Matches: 263, Mismatches: 66, Indels: 78
0.65 0.16 0.19
Matches are distributed among these distances:
25 2 0.01
26 7 0.03
27 33 0.13
28 43 0.16
29 80 0.30
30 62 0.24
31 31 0.12
32 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AGGGTTAAAAATGGAATTTTGGTGAAATT
Found at i:12502751 original size:117 final size:114
Alignment explanation
Indices: 12502344--12502738 Score: 449
Period size: 117 Copynumber: 3.4 Consensus size: 114
12502334 AAAAATGTAC
* * *
12502344 TTTTGGATGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTTAGGGATAAAATGGT-ATTTTTGG
1 TTTTGG-TGAAAT-GGGGTTAAAAATGGAATTTTGAAAG-TTAGGGGTAAAATGGTAATTTTTGG
** * *
12502408 TGAAATC-GAGGTTGAAATGGGATTTTGTAA-AG-TTTGGGGACAAAATGGTAA-
63 TGAAATCAG-GGTAAAAATGGAATTTTG-AAGAGTTTTGGGG-TAAAATGGTAAT
* * * *
12502459 TTTTGGTGAATTGGGGTTAAAAATGGGATTTTGAAAGTTCGAGGGCAAAATGGTAATTTTTGGTG
1 TTTTGGTGAAATGGGGTTAAAAATGGAATTTTGAAAGTTAG-GGGTAAAATGGTAATTTTTGGTG
* *
12502524 AAATTAGGGTTAAAAATGGAATTTTAAAGAGTTTTGGGGGTAAAATGGTAAT
65 AAATCAGGG-TAAAAATGGAATTTTGAAGAGTTTT-GGGGTAAAATGGTAAT
* * * * *
12502576 TTTTGGTGGAATCGGGTTAAAAATGGGATTTTGAAAAGTTCGGGGTAAAATGGTAATTTTTGGTA
1 TTTTGGTGAAATGGGGTTAAAAATGGAATTTTG-AAAGTTAGGGGTAAAATGGTAATTTTTGGTG
* *
12502641 AAATCAGGGATAAAAATGGAATTTTGGAGAGTTTTGGGGTAAAACGGTAAT
65 AAATCAGGG-TAAAAATGGAATTTTGAAGAGTTTTGGGGTAAAATGGTAAT
*
12502692 TTTTGGTGAAACTGGGGTCAAAAATGGAATTTTGAAAGTTTAGGGGT
1 TTTTGGTGAAA-TGGGGTTAAAAATGGAATTTTGAAAG-TTAGGGGT
12502739 CAAAGTATAA
Statistics
Matches: 241, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
112 3 0.01
113 32 0.13
114 23 0.10
115 21 0.09
116 42 0.17
117 112 0.46
118 8 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (114 bp):
TTTTGGTGAAATGGGGTTAAAAATGGAATTTTGAAAGTTAGGGGTAAAATGGTAATTTTTGGTGA
AATCAGGGTAAAAATGGAATTTTGAAGAGTTTTGGGGTAAAATGGTAAT
Found at i:12503543 original size:35 final size:33
Alignment explanation
Indices: 12503476--12503544 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 33
12503466 TTTATTCCAT
*
12503476 CTTTTCATTTTCTTTCTTTTTTAAAACTAAACC
1 CTTTTCATTTTCTTTCTTTTTTAAAACCAAACC
*
12503509 CTTTTCATTTTCTCTT-TTTAGTTTTAAACCAAACC
1 CTTTTCATTTTCT-TTCTTT--TTTAAAACCAAACC
12503544 C
1 C
12503545 AGATCTGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.52
34 2 0.06
35 13 0.42
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.52
Consensus pattern (33 bp):
CTTTTCATTTTCTTTCTTTTTTAAAACCAAACC
Found at i:12503572 original size:15 final size:16
Alignment explanation
Indices: 12503543--12503574 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12503533 TAAACCAAAC
12503543 CCAGATCTGGGAAAAT
1 CCAGATCTGGGAAAAT
*
12503559 CCAGATCTGGAAAAAT
1 CCAGATCTGGGAAAAT
12503575 TCAAAACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (16 bp):
CCAGATCTGGGAAAAT
Found at i:12503862 original size:19 final size:20
Alignment explanation
Indices: 12503840--12503877 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12503830 TGATACTATT
*
12503840 TAATACCCTTAT-TTAATAA
1 TAATACCATTATATTAATAA
*
12503859 TAATATCATTATATTAATA
1 TAATACCATTATATTAATA
12503878 TTATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATACCATTATATTAATAA
Found at i:12504559 original size:14 final size:15
Alignment explanation
Indices: 12504534--12504565 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
12504524 CAATTGGGCC
12504534 TTTGTAATTTGGACA
1 TTTGTAATTTGGACA
12504549 TTTGTAA-TTGGACA
1 TTTGTAATTTGGACA
12504563 TTT
1 TTT
12504566 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTGTAATTTGGACA
Found at i:12504596 original size:17 final size:17
Alignment explanation
Indices: 12504562--12504637 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
12504552 GTAATTGGAC
12504562 ATTTAAATTT-T-A-AA
1 ATTTAAATTTATAATAA
12504576 ATTTAAATTTATAATAA
1 ATTTAAATTTATAATAA
* *
12504593 ATTTAAATTTTTATACAA
1 ATTTAAATTTATA-ATAA
* *
12504611 ATTTAAATTCAAAATAA
1 ATTTAAATTTATAATAA
*
12504628 ATCTAAATTT
1 ATTTAAATTT
12504638 TAAACTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 1 0.02
17 25 0.50
18 13 0.26
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTATAATAA
Found at i:12504648 original size:35 final size:35
Alignment explanation
Indices: 12504574--12504648 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
12504564 TTAAATTTTA
* * * *
12504574 AAATTTAAATTTATAATAAATTTAAATTTTTATAC
1 AAATTTAAATTCAAAATAAATCTAAATTTTTAAAC
12504609 AAATTTAAATTCAAAATAAATCTAAA-TTTTAAAC
1 AAATTTAAATTCAAAATAAATCTAAATTTTTAAAC
12504643 TAAATT
1 -AAATT
12504649 CATTGGCCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (35 bp):
AAATTTAAATTCAAAATAAATCTAAATTTTTAAAC
Found at i:12505289 original size:198 final size:201
Alignment explanation
Indices: 12504866--12505381 Score: 871
Period size: 198 Copynumber: 2.6 Consensus size: 201
12504856 CCGTCCTGCT
* * *
12504866 TTTTATTGCTTCGACCAGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCT-
1 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTAGCTCG-TG
* * * * *
12504930 TTGAGCGTTGAGTTGGTATTCTTCTCTGTATATTATCAGGAAGATAATCGCCTCGCTTGTTTCGA
65 TTGAGCGTTGAATTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGA
*
12504995 TTCGCTTCTCTCTGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAG
130 TTCGCTTCTCTCGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAG
12505060 CTAACCA
195 CTAACCA
12505067 -TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTAGCTCGTGT
1 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTAGCTCGTGT
* *
12505131 TGAGCGTTGAATTGGTATTC-T-TCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGAT
66 TGAGCGTTGAATTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGAT
12505194 TCGCTTCTCT-GGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGC
131 TCGCTTCTCTCGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGC
12505258 TAACCA
196 TAACCA
* *
12505264 TTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGT
1 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTAGCTCGTGT
12505329 TGAGCGTTGAATTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
66 TGAGCGTTGAATTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
12505382 AATCAATGTT
Statistics
Matches: 297, Mismatches: 14, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
197 59 0.20
198 128 0.43
199 3 0.01
200 107 0.36
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (201 bp):
TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTAGCTCGTGT
TGAGCGTTGAATTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGAT
TCGCTTCTCTCGGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGC
TAACCA
Found at i:12517474 original size:29 final size:29
Alignment explanation
Indices: 12517437--12517523 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
12517427 TGATGGAATT
12517437 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGG-TAAAAATGGAATTTTGGAAAGTTTA
*
12517467 GGGGT-AAAATGGTAATTTTGGTGAAA--CTA
1 GGGGTAAAAATGG-AATTTT-G-GAAAGTTTA
*
12517496 GGGTTAAAAATAGG-ATTTTGGAAAGTTT
1 GGGGTAAAAAT-GGAATTTTGGAAAGTTT
12517524 GAGATAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.09
28 8 0.17
29 19 0.40
30 10 0.21
31 6 0.13
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:12517544 original size:58 final size:59
Alignment explanation
Indices: 12517420--12517546 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 59
12517410 GTTAAAAATG
* * * * * * * *
12517420 TAATTTTTGATGGAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGG
1 TAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGAGATAAAACGA
12517479 TAA-TTTTGGTGAAACTAGGGTTAAAAATAGG-ATTTTGGAAAGTTT-GAGATAAAACGA
1 TAATTTTTGGTGAAACTAGGGTTAAAAAT-GGAATTTTGGAAAGTTTAGAGATAAAACGA
12517536 TAATTTTTGGT
1 TAATTTTTGGT
12517547 TAAATCTCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
57 11 0.19
58 42 0.72
59 5 0.09
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
TAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGAGATAAAACGA
Found at i:12519192 original size:14 final size:15
Alignment explanation
Indices: 12519167--12519198 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
12519157 CAATTGGGCC
12519167 TTTGTAATTTGGACA
1 TTTGTAATTTGGACA
12519182 TTTGTAA-TTGGACA
1 TTTGTAATTTGGACA
12519196 TTT
1 TTT
12519199 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTGTAATTTGGACA
Found at i:12519227 original size:17 final size:17
Alignment explanation
Indices: 12519205--12519254 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
12519195 ATTTAATTTA
*
12519205 AAATTTAAATTTTATAC
1 AAATTTAAATTTTAAAC
* *
12519222 AAATTTAAATTTAAAAT
1 AAATTTAAATTTTAAAC
*
12519239 AAATCTAAATTTTAAA
1 AAATTTAAATTTTAAA
12519255 ACTAAATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATTTTAAAC
Found at i:12519353 original size:14 final size:15
Alignment explanation
Indices: 12519334--12519379 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
12519324 AACCTAGCTA
12519334 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
12519349 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
12519363 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
12519379 A
1 A
12519380 ATATCCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:12519377 original size:16 final size:16
Alignment explanation
Indices: 12519332--12519381 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
12519322 TAAACCTAGC
12519332 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
12519348 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
12519362 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
12519378 TAAT
1 TAAT
12519382 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:12520024 original size:96 final size:96
Alignment explanation
Indices: 12519840--12520031 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
12519830 AATTTTGAAG
** ** * *
12519840 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAAATTTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAAATTTTCA
*
12519905 TAATCGAAGATAAGGAAACATTGCCTCGATT
66 TAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
12519936 AAGGATATTCAATTATTTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGTGCAAAATTTTG
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGC-AAATTTTC
*
12520001 A-AATTCGAA-ATAAA-AGAATATTGCCTCGATT
65 ATAA-TCGAAGATAAAGA-AACATTGCCTCGATT
12520032 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 68 0.83
97 13 0.16
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAAATTTTCA
TAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:12520280 original size:29 final size:30
Alignment explanation
Indices: 12520248--12520309 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
12520238 AAAACGAGAC
12520248 TTTTTGGA-TACCCGGGGGTAAAATGGTAA
1 TTTTTGGACTACCCGGGGGTAAAATGGTAA
****
12520277 -TTTTGGACTTTTGGGGGGTAAAATGGTAA
1 TTTTTGGACTACCCGGGGGTAAAATGGTAA
12520306 TTTT
1 TTTT
12520310 AGGGAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.06, G:0.31, T:0.39
Consensus pattern (30 bp):
TTTTTGGACTACCCGGGGGTAAAATGGTAA
Found at i:12520503 original size:29 final size:27
Alignment explanation
Indices: 12520448--12520584 Score: 98
Period size: 28 Copynumber: 4.8 Consensus size: 27
12520438 TTTTAAGGTC
* *
12520448 AAAAAT-GAAATTTTTGGAACTTCGGGGTT
1 AAAAATAG-AATTTTT-GAAGTTTGGGG-T
* *
12520477 AAATATAGAATTTTTAGAAGTTTGGGGG
1 AAAAATAGAATTTTT-GAAGTTTGGGGT
* *
12520505 AAAAAT-GTAATTTTTGGAAGTTTAAGGCT
1 AAAAATAG-AATTTTT-GAAGTTT-GGGGT
* *
12520534 CAAAATGGAATTTTTGAAAGTTTGGGGT
1 AAAAATAGAATTTTTG-AAGTTTGGGGT
*
12520562 AAAAATATAATTTTTGTAAGTTT
1 AAAAATAGAATTTTTG-AAGTTT
12520585 TTGAGGTCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 42 0.49
29 41 0.48
30 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (27 bp):
AAAAATAGAATTTTTGAAGTTTGGGGT
Found at i:12520518 original size:57 final size:57
Alignment explanation
Indices: 12520448--12520639 Score: 147
Period size: 57 Copynumber: 3.3 Consensus size: 57
12520438 TTTTAAGGTC
* ** * *
12520448 AAAAATGAAATTTTTGGAA-CTTCGGGGTTAAATATAGAATTTTT-AGAAGTTTGGGGG
1 AAAAATGTAATTTTTGGAAGCTTAAGGCTCAAA-ATAGAATTTTTGA-AAGTTTGGGGG
* * *
12520505 AAAAATGTAATTTTTGGAAGTTTAAGGCTCAAAATGGAATTTTTGAAAGTTTGGGGT
1 AAAAATGTAATTTTTGGAAGCTTAAGGCTCAAAATAGAATTTTTGAAAGTTTGGGGG
* * * * * * *
12520562 AAAAATATAATTTTTGTAAGTTTTTGAGG-TCAAAATATAATTTTGGAGAAGTTCGGGGG
1 AAAAATGTAATTTTTGGAAG--CTTAAGGCTCAAAATAGAATTTTTGA-AAGTTTGGGGG
* **
12520621 TCAAAATACAATTTTTGGA
1 -AAAAATGTAATTTTTGGA
12520640 TAATTTAGGG
Statistics
Matches: 110, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
57 56 0.51
58 24 0.22
59 15 0.14
60 15 0.14
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (57 bp):
AAAAATGTAATTTTTGGAAGCTTAAGGCTCAAAATAGAATTTTTGAAAGTTTGGGGG
Found at i:12520599 original size:30 final size:28
Alignment explanation
Indices: 12520429--12520637 Score: 116
Period size: 29 Copynumber: 7.2 Consensus size: 28
12520419 AAAATGGTAA
*
12520429 TTTTGAAAGTTTTAAGGTCAAAA-ATGAAAT
1 TTTTGAAAG-TTTGAGGTCAAAATAT--AAT
* * * * * *
12520459 TTTTGGAACTTCGGGGTTAAATATAGAAT
1 TTTTGAAAGTTTGAGGTCAAA-ATATAAT
* ** *
12520488 TTTT-AGAAGTTTGGGGGAAAAATGTAAT
1 TTTTGA-AAGTTTGAGGTCAAAATATAAT
* * **
12520516 TTTTGGAAGTTTAAGGCTCAAAATGGAAT
1 TTTTGAAAGTTTGAGG-TCAAAATATAAT
* *
12520545 TTTTGAAAGTTTGGGGTAAAAATATAAT
1 TTTTGAAAGTTTGAGGTCAAAATATAAT
*
12520573 TTTTGTAAGTTTTTGAGGTCAAAATATAAT
1 TTTTGAAAG--TTTGAGGTCAAAATATAAT
* * * *
12520603 TTTGGAGAAGTTCGGGGGTCAAAATACAAT
1 TTTTGA-AAGTT-TGAGGTCAAAATATAAT
12520633 TTTTG
1 TTTTG
12520638 GATAATTTAG
Statistics
Matches: 135, Mismatches: 35, Indels: 18
0.72 0.19 0.10
Matches are distributed among these distances:
28 34 0.25
29 50 0.37
30 47 0.35
31 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (28 bp):
TTTTGAAAGTTTGAGGTCAAAATATAAT
Found at i:12522619 original size:31 final size:30
Alignment explanation
Indices: 12522579--12522637 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
12522569 ACATATCTTA
* *
12522579 AATTCAAATTTATAATAAATTTAAATTTTTC
1 AATTCAAATTTAAAATAAACTT-AATTTTTC
*
12522610 AATTTAAATTTAAAATAAACTTAATTTT
1 AATTCAAATTTAAAATAAACTTAATTTT
12522638 AAAATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTCAAATTTAAAATAAACTTAATTTTTC
Found at i:12522638 original size:17 final size:17
Alignment explanation
Indices: 12522613--12522651 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12522603 ATTTTTCAAT
12522613 TTAAATTTAAAATAAAC
1 TTAAATTTAAAATAAAC
* *
12522630 TTAATTTTAAAATAAAT
1 TTAAATTTAAAATAAAC
12522647 TTAAA
1 TTAAA
12522652 CTTTGTTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:12522846 original size:47 final size:47
Alignment explanation
Indices: 12522757--12522849 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
12522747 TGTGTGGATA
*
12522757 CCATTTTGGTATATAAATATATATTTTGTACCATTTTAGTAAATAAC
1 CCATTTTGGTATATAAATATATATTTTGTACCATATTAGTAAATAAC
* * ** *
12522804 CCATTTTGGTATTTAATTAT-TACTTTTGTATTATATTGGTAAATAA
1 CCATTTTGGTATATAAATATATA-TTTTGTACCATATTAGTAAATAA
12522850 TAATAATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 2 0.05
47 37 0.95
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (47 bp):
CCATTTTGGTATATAAATATATATTTTGTACCATATTAGTAAATAAC
Found at i:12524074 original size:43 final size:43
Alignment explanation
Indices: 12523993--12524077 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
12523983 ATTAACATGT
* *
12523993 TAAATTATATTACTTGACTTGTGTTAATATGGTTACATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
* *
12524036 TAAATTATATTACTTTACTTTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTTGTATTAATATGCTT-ACATGTTA
12524078 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
Found at i:12524774 original size:45 final size:45
Alignment explanation
Indices: 12524643--12524776 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 45
12524633 CCCTAGCTCA
12524643 TCAAGCCAAGGATATCA-ACCTCAGTTTAACGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAGA-CTCAGTTTAACGAGCCACCGTAATAC
* *
12524688 TCAAGCCAAGGATAT--G-CTCAGTTTGACGAGCTACCGTAATAC
1 TCAAGCCAAGGATATCAGACTCAGTTTAACGAGCCACCGTAATAC
* *
12524730 TCAAGCCAAGGATATCAGACTCAGTTTTACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGACTCAGTTTAACGAGCCACCGTAATAC
12524775 TC
1 TC
12524777 TACTCCTCCC
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
42 39 0.49
44 1 0.01
45 40 0.50
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGACTCAGTTTAACGAGCCACCGTAATAC
Found at i:12524794 original size:21 final size:21
Alignment explanation
Indices: 12524768--12524812 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12524758 ACGAGCCACC
12524768 GCAATACTCTACTCCTCCCAG
1 GCAATACTCTACTCCTCCCAG
*
12524789 GCAATACTCTACTCCTCCGAG
1 GCAATACTCTACTCCTCCCAG
12524810 GCA
1 GCA
12524813 GATGAACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.40, G:0.13, T:0.22
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCAG
Found at i:12528356 original size:12 final size:12
Alignment explanation
Indices: 12528339--12528363 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12528329 CAATATGTGT
12528339 AACTGGATTTTC
1 AACTGGATTTTC
12528351 AACTGGATTTTC
1 AACTGGATTTTC
12528363 A
1 A
12528364 TCGTCATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AACTGGATTTTC
Found at i:12529087 original size:4 final size:4
Alignment explanation
Indices: 12529078--12529138 Score: 79
Period size: 4 Copynumber: 15.0 Consensus size: 4
12529068 TCTCTCCTTC
* *
12529078 TTCT TTCT TTCCT CTCA TTC- TTCT TTCT TTCT TTCT TTCT TTCTT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT
12529127 TTCT TTCT TTCT
1 TTCT TTCT TTCT
12529139 CGTTTATTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:12529098 original size:20 final size:20
Alignment explanation
Indices: 12529069--12529108 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12529059 CATTACATTT
*
12529069 CTCTCCTTCTTCTTTCTTTC
1 CTCTCATTCTTCTTTCTTTC
12529089 CTCTCATTCTTCTTTCTTTC
1 CTCTCATTCTTCTTTCTTTC
12529109 TTTCTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.60
Consensus pattern (20 bp):
CTCTCATTCTTCTTTCTTTC
Found at i:12529127 original size:17 final size:17
Alignment explanation
Indices: 12529078--12529138 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
12529068 TCTCTCCTTC
* * *
12529078 TTCTTTCTTTCCTCTCA
1 TTCTTTCTTTCTTTTCT
12529095 TTC-TTCTTTC-TTTCT
1 TTCTTTCTTTCTTTTCT
12529110 TTCTTTCTTTCTTTTCT
1 TTCTTTCTTTCTTTTCT
12529127 TTCTTTCTTTCT
1 TTCTTTCTTTCT
12529139 CGTTTATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.15
16 14 0.35
17 20 0.50
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTTCTTTCTTTTCT
Found at i:12529250 original size:19 final size:19
Alignment explanation
Indices: 12529226--12529264 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12529216 TTTACAATCA
12529226 AAATAAAATTAACACACAC
1 AAATAAAATTAACACACAC
12529245 AAATAAAATTAACACACAC
1 AAATAAAATTAACACACAC
12529264 A
1 A
12529265 CATGGCACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAATTAACACACAC
Found at i:12530550 original size:16 final size:14
Alignment explanation
Indices: 12530513--12530544 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12530503 TGTTTCACTG
*
12530513 AAAATAATTTTCGA
1 AAAATAATTTTTGA
12530527 AAAATAATTTTTGA
1 AAAATAATTTTTGA
12530541 AAAA
1 AAAA
12530545 ACTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (14 bp):
AAAATAATTTTTGA
Found at i:12542198 original size:24 final size:24
Alignment explanation
Indices: 12542171--12542228 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
12542161 ATTTAAAAAG
* * *
12542171 AAATAATAAAGATTTTATATTAAT
1 AAATATTAAAGATATTATACTAAT
* *
12542195 AAATATTAAATATATTATGCTAAT
1 AAATATTAAAGATATTATACTAAT
12542219 AAATATTAAA
1 AAATATTAAA
12542229 TCTTTTAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (24 bp):
AAATATTAAAGATATTATACTAAT
Found at i:12548577 original size:23 final size:23
Alignment explanation
Indices: 12548549--12548592 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
12548539 AATTTAAAAT
12548549 TAAAAAATAAGT-AATAATTTTTA
1 TAAAAAATAAGTGAA-AATTTTTA
12548572 TAAAAAATAAGTGAAAATTTT
1 TAAAAAATAAGTGAAAATTTT
12548593 CTTCTCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
TAAAAAATAAGTGAAAATTTTTA
Found at i:12551462 original size:30 final size:29
Alignment explanation
Indices: 12551406--12551462 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
12551396 CTACTAAAAA
* *
12551406 AAAGATAAATTAGTCTTTTATGTTAAAGT
1 AAAGATAAATTAATCTTTTATATTAAAGT
12551435 AAAGAGTAAATTAATCTTTT-TAATTAAA
1 AAAGA-TAAATTAATCTTTTAT-ATTAAA
12551463 AAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (29 bp):
AAAGATAAATTAATCTTTTATATTAAAGT
Found at i:12553675 original size:120 final size:120
Alignment explanation
Indices: 12553452--12553686 Score: 364
Period size: 120 Copynumber: 2.0 Consensus size: 120
12553442 TTTTTCCATG
* *
12553452 TGTTCCACGAACGGGTCAATTCAAGTGAGTTGAATGAGCCACATCTAATTGATTGACCTCCATGA
1 TGTTCCACGAACGAGTCAATTAAAGTGAGTTGAATGAGCCACATCTAATTGATTGACCTCCATGA
* **
12553517 GATACTCTTTGCGTGTCAAGGATTTTGATCTGCCACCCGTTACACTTACACTTTA
66 GATACTCTTTGCGTGTCAAGAATTTTGATCCACCACCCGTTACACTTACACTTTA
* * *
12553572 TGTTCCACGAACGAGTCAGTTAAAGTGAGTTGAATGAGCCCCAAT-TAATTGATTGACTTCCATG
1 TGTTCCACGAACGAGTCAATTAAAGTGAGTTGAATGAGCCAC-ATCTAATTGATTGACCTCCATG
* *
12553636 AGATACTCTTTGCGTGTCAAGAATTTTGTTCCACGACCCGTTACACTTACA
65 AGATACTCTTTGCGTGTCAAGAATTTTGATCCACCACCCGTTACACTTACA
12553687 TCTTGTGGTA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
120 102 0.98
121 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (120 bp):
TGTTCCACGAACGAGTCAATTAAAGTGAGTTGAATGAGCCACATCTAATTGATTGACCTCCATGA
GATACTCTTTGCGTGTCAAGAATTTTGATCCACCACCCGTTACACTTACACTTTA
Found at i:12556456 original size:22 final size:21
Alignment explanation
Indices: 12556413--12556460 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
12556403 CAATATGAGG
12556413 AAAAATAAAAGAAACATAATT
1 AAAAATAAAAGAAACATAATT
* *
12556434 AAAATTAAAAGAAAATATAATT
1 AAAAATAAAAG-AAACATAATT
12556456 AAAAA
1 AAAAA
12556461 ATAGAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAATAAAAGAAACATAATT
Found at i:12556468 original size:20 final size:21
Alignment explanation
Indices: 12556414--12556470 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
12556404 AATATGAGGA
*
12556414 AAAATAAAAG-AAACATAATT
1 AAAATAAAAGAAAATATAATT
12556434 AAAATTAAAAGAAAATATAATT
1 AAAA-TAAAAGAAAATATAATT
*
12556456 AAAA-AATAGAAAATA
1 AAAATAAAAGAAAATA
12556471 GGGAAGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.42
21 6 0.18
22 13 0.39
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAATAAAAGAAAATATAATT
Found at i:12557299 original size:29 final size:30
Alignment explanation
Indices: 12557257--12557330 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
12557247 ATAGACATAA
*
12557257 ATTAAATACAAATAAACA-ATATCTTAAAT
1 ATTAAATACAAATAAAAATATATCTTAAAT
* *
12557286 ATTAAATCCTAATAAAAATATATCTTAAA-
1 ATTAAATACAAATAAAAATATATCTTAAAT
*
12557315 ATAAAATA-AAATAAAA
1 ATTAAATACAAATAAAA
12557331 CCCAGTCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.18
29 21 0.55
30 10 0.26
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (30 bp):
ATTAAATACAAATAAAAATATATCTTAAAT
Found at i:12559381 original size:21 final size:24
Alignment explanation
Indices: 12559357--12559411 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 24
12559347 CCTGCAACTT
*
12559357 CTACCGATACAAGCAT-C-C-TAA
1 CTACCGATACAAGCATACACAGAA
*
12559378 CTACCAATACAAGCATACACAGAA
1 CTACCGATACAAGCATACACAGAA
12559402 CTACCGATAC
1 CTACCGATAC
12559412 CTACTATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.54
22 1 0.04
23 1 0.04
24 11 0.39
ACGTcount: A:0.42, C:0.33, G:0.09, T:0.16
Consensus pattern (24 bp):
CTACCGATACAAGCATACACAGAA
Found at i:12566432 original size:6 final size:6
Alignment explanation
Indices: 12566423--12566499 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
12566413 TATCTTAAGA
* * * *
12566423 TTAATT TTAAAT TT-TAT TTAAAT TTAAAT TT-ATT TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
12566469 TT--AT TTAAAT TT-ATT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
12566500 TCAAATTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 42 0.72
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
TTAAAT
Found at i:12566443 original size:17 final size:16
Alignment explanation
Indices: 12566423--12566510 Score: 87
Period size: 17 Copynumber: 5.7 Consensus size: 16
12566413 TATCTTAAGA
*
12566423 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
12566440 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
12566457 TTAAGTTTAAATTTAT
1 TTAAATTTAAATTTAT
12566473 TTAAATTT--A--T-T
1 TTAAATTTAAATTTAT
*
12566484 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
*
12566500 TCAAATTTAAA
1 TTAAATTTAAA
12566511 AATAATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 22 0.37
17 25 0.42
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:12566474 original size:27 final size:27
Alignment explanation
Indices: 12566411--12566508 Score: 108
Period size: 27 Copynumber: 3.5 Consensus size: 27
12566401 TTGGATTTCG
* *
12566411 TTTATCTTAAGATTAATTTTAAATTT-TA
1 TTTAT-TTAA-ATTTATTTTAAATTTAAA
*
12566439 TTTAAATTTAAATTTATTTTAAGTTTAAA
1 TTT--ATTTAAATTTATTTTAAATTTAAA
12566468 TTTATTTAAATTTATTTTAAATTTAAA
1 TTTATTTAAATTTATTTTAAATTTAAA
* *
12566495 TTTAATCAAATTTA
1 TTTATTTAAATTTA
12566509 AAAATAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
27 35 0.57
28 16 0.26
29 8 0.13
30 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTATTTAAATTTATTTTAAATTTAAA
Found at i:12566492 original size:11 final size:11
Alignment explanation
Indices: 12566411--12566492 Score: 62
Period size: 11 Copynumber: 7.4 Consensus size: 11
12566401 TTGGATTTCG
*
12566411 TTTATCTTAAGA
1 TTTATTTTAA-A
*
12566423 TTAATTTTAAA
1 TTTATTTTAAA
12566434 TTT-TATTTAAA
1 TTTAT-TTTAAA
* *
12566445 TTTAAATTT-AT
1 TTT-ATTTTAAA
*
12566456 TTTAAGTTTAAA
1 TTT-ATTTTAAA
12566468 TTTA-TTTAAA
1 TTTATTTTAAA
12566478 TTTATTTTAAA
1 TTTATTTTAAA
12566489 TTTA
1 TTTA
12566493 AATTTAATCA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
10 11 0.19
11 32 0.55
12 15 0.26
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:12568274 original size:30 final size:30
Alignment explanation
Indices: 12568235--12568384 Score: 196
Period size: 30 Copynumber: 5.0 Consensus size: 30
12568225 CCCCAAACAA
*
12568235 TCCAGAAATTGCATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCTAAAACTTT
* *
12568266 TCCAAAATTATATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
*
12568296 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
*
12568326 TCTAAAATTACATTTTGA-CCTCAAAAC-TT
1 TCCAAAATTACATTTTGACCCT-AAAACTTT
* * *
12568355 TCCTAAATTACATTTTAACCCAAAAACTTT
1 TCCAAAATTACATTTTGACCCTAAAACTTT
12568385 CCTAAATCCC
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
29 24 0.23
30 76 0.73
31 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCTAAAACTTT
Found at i:12568403 original size:30 final size:28
Alignment explanation
Indices: 12568240--12568405 Score: 161
Period size: 30 Copynumber: 5.6 Consensus size: 28
12568230 AACAATCCAG
* * *
12568240 AAATTGCATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCC-AAAAC-TTTCCT
* *
12568270 AAATTATATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCC-AAAAC-TTTCCT
* *
12568300 AAATTACATTTTGACCCCAAAACTTTTCT
1 AAATTACATTTT-AACCCAAAACTTTCCT
*
12568329 AAAATTACATTTTGACCTCAAAACTTTCCT
1 -AAATTACATTTTAACC-CAAAACTTTCCT
12568359 AAATTACATTTTAACCCAAAAACTTTCCT
1 AAATTACATTTTAACCC-AAAACTTTCCT
**
12568388 AAATCCCATTTTTAACCC
1 AAATTACA-TTTTAACCC
12568406 CGATTTCACC
Statistics
Matches: 118, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.01
29 38 0.32
30 75 0.64
31 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATTACATTTTAACCCAAAACTTTCCT
Found at i:12568420 original size:29 final size:30
Alignment explanation
Indices: 12568393--12568487 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 30
12568383 TTCCTAAATC
12568393 CCATTTTTAACCCCGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATTTCACCAAAA-TTA
* *
12568424 CCA-TTTTACCCCCGAAGCTTCTA--AAAA-T-
1 CCATTTTTAACCCCG-A-TTTC-ACCAAAATTA
12568452 CCATTTTTAA-CCCGATTTCACCAAAATTA
1 CCATTTTTAACCCCGATTTCACCAAAATTA
12568481 CCATTTT
1 CCATTTT
12568488 GGCCCCGGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 5 0.10
28 8 0.15
29 13 0.25
30 10 0.19
31 8 0.15
32 3 0.06
33 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (30 bp):
CCATTTTTAACCCCGATTTCACCAAAATTA
Found at i:12568421 original size:58 final size:56
Alignment explanation
Indices: 12568359--12568487 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 56
12568349 AAACTTTCCT
12568359 AAATTA-CATTTTAACCCAAAAACTTTCCT-AAATCCCATTTTTAACCCCGATTTCACCA
1 AAATTACCATTTTAACCCAAAAAC-TT-CTAAAAT-CCATTTTTAA-CCCGATTTCACCA
* ** *
12568417 AAATTTACCATTTTACCCCCGAAGCTTCTAAAAATCCATTTTTAACCCGATTTCACCA
1 AAA-TTACCATTTTAACCCAAAAACTTCT-AAAATCCATTTTTAACCCGATTTCACCA
12568475 AAATTACCATTTT
1 AAATTACCATTTT
12568488 GGCCCCGGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
57 10 0.16
58 21 0.33
59 15 0.24
60 17 0.27
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (56 bp):
AAATTACCATTTTAACCCAAAAACTTCTAAAATCCATTTTTAACCCGATTTCACCA
Found at i:12568494 original size:29 final size:29
Alignment explanation
Indices: 12568397--12568487 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 29
12568387 TAAATCCCAT
12568397 TTTTAACCCCGATTTCACCAAAATTTACCA
1 TTTTAACCCCGATTTCACCAAAA-TTACCA
* *
12568427 TTTTACCCCCGAAGCTTCTA--AAAA-T-CCA
1 TTTTAACCCCG-A-TTTC-ACCAAAATTACCA
12568455 TTTTTAA-CCCGATTTCACCAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAATTACCA
12568484 TTTT
1 TTTT
12568488 GGCCCCGGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 5 0.10
28 12 0.24
29 9 0.18
30 10 0.20
31 5 0.10
32 3 0.06
33 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCAAAATTACCA
Found at i:12568524 original size:58 final size:58
Alignment explanation
Indices: 12568388--12568529 Score: 155
Period size: 58 Copynumber: 2.4 Consensus size: 58
12568378 AAACTTTCCT
*
12568388 AAATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAAGCTTCTAA
1 AAATCCCATTTTT-ACCCCGATTTCACCAAAATTTACCATTTTACCCCCG-AGCTTCCAA
* ** * *
12568448 AAAT-CCATTTTTAACCCGATTTCACCAAAA-TTACCATTTTGGCCCCG-GGTATCCAT
1 AAATCCCATTTTTACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAGCT-TCCAA
* *
12568504 AAGTCCCGTTTTTCACCCCGATTTCA
1 AAATCCCATTTTT-ACCCCGATTTCA
12568530 TCATTTATCA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
55 2 0.03
56 6 0.09
57 22 0.31
58 28 0.40
59 8 0.11
60 4 0.06
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.32
Consensus pattern (58 bp):
AAATCCCATTTTTACCCCGATTTCACCAAAATTTACCATTTTACCCCCGAGCTTCCAA
Found at i:12579742 original size:30 final size:30
Alignment explanation
Indices: 12579480--12579720 Score: 383
Period size: 30 Copynumber: 8.0 Consensus size: 30
12579470 CCCCAAACAA
*
12579480 TCCAGAAATTGCATTTTGACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
12579511 TCCAAAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
12579541 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
12579571 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
12579601 TCCAAAATTATATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
12579631 TCCAAAATTACATTTTGACCCCAAAGCTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
12579661 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
12579691 TCCAAAATTGCATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
12579721 CCTAAATCCC
Statistics
Matches: 196, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
30 192 0.98
31 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:12579756 original size:29 final size:29
Alignment explanation
Indices: 12579729--12579823 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 29
12579719 TTCCTAAATC
12579729 CCATTTTTAACCCCGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATTT-ACCAAAA-TTA
* * *
12579760 CCA-TTTT-ACCCCGAAGCTTA-TAAAAAT-
1 CCATTTTTAACCCCG-A-TTTACCAAAATTA
12579787 CCATTTTTAACCCCGATTTTACCAAAATTA
1 CCATTTTTAACCCCGA-TTTACCAAAATTA
12579817 CCATTTT
1 CCATTTT
12579824 GGCCTCCGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
27 3 0.06
28 9 0.18
29 21 0.41
30 13 0.25
31 5 0.10
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
CCATTTTTAACCCCGATTTACCAAAATTA
Found at i:12579765 original size:90 final size:87
Alignment explanation
Indices: 12579480--12579771 Score: 345
Period size: 90 Copynumber: 3.3 Consensus size: 87
12579470 CCCCAAACAA
*
12579480 TCCAGAAATTGCATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCA
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCA
**
12579545 AAATTACATTTTGACCCTAAAACTTT
65 AAATTACATTTTGACCC--CGA-TTT
* *
12579571 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTTCCAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAA
*
12579636 AATTACATTTTGACCCCAAAGCTTT
66 AATTACATTTTGACCCC---GATTT
** * *
12579661 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTGCATTTTGACCCCAAAAC-TTTCCTA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAA
** *
12579725 AATCCCATTTTTAACCCCGATTT
66 AATTACA-TTTTGACCCCGATTT
*
12579748 CACCAAAATTTACCATTTT-ACCCC
1 -TCCAAAA-TTA-CATTTTGACCCC
12579772 GAAGCTTATA
Statistics
Matches: 177, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
87 4 0.02
88 6 0.03
89 19 0.11
90 144 0.81
91 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (87 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAA
AATTACATTTTGACCCCGATTT
Found at i:12583738 original size:29 final size:31
Alignment explanation
Indices: 12583685--12583743 Score: 86
Period size: 29 Copynumber: 1.9 Consensus size: 31
12583675 TTGAATCGAA
*
12583685 ACATTTTAATAATTTTTAATAATTTTATTTTT
1 ACATTTTAATAATTTTT-AGAATTTTATTTTT
12583717 ACATTTTAAT-ATTTTT-GAATTTTATTT
1 ACATTTTAATAATTTTTAGAATTTTATTT
12583744 AACAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
31 6 0.23
32 10 0.38
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (31 bp):
ACATTTTAATAATTTTTAGAATTTTATTTTT
Found at i:12583751 original size:29 final size:31
Alignment explanation
Indices: 12583684--12583761 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
12583674 TTTGAATCGA
*
12583684 AACATTTTAATAATTTTTAATAATTTTATTTT
1 AACATTTTAATAATTTTT-AGAATTTTATTTT
*
12583716 TACATTTTAAT-ATTTTT-GAATTTTA-TTT
1 AACATTTTAATAATTTTTAGAATTTTATTTT
*
12583744 AACAATTTT-ATAAATTTT
1 AAC-ATTTTAATAATTTTT
12583762 GATAATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.17
29 17 0.43
31 6 0.15
32 10 0.25
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (31 bp):
AACATTTTAATAATTTTTAGAATTTTATTTT
Found at i:12588362 original size:18 final size:18
Alignment explanation
Indices: 12588339--12588374 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12588329 ATTTTACAAT
12588339 TCGAATAATTCAAATAAC
1 TCGAATAATTCAAATAAC
12588357 TCGAATAATTCAAATAAC
1 TCGAATAATTCAAATAAC
12588375 ATATTGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
TCGAATAATTCAAATAAC
Found at i:12598380 original size:20 final size:20
Alignment explanation
Indices: 12598338--12598379 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
12598328 TAATTATTAG
12598338 AAATTTATTAAAAAACCATA
1 AAATTTATTAAAAAACCATA
*
12598358 AAATTTATT-AAAAGCCATA
1 AAATTTATTAAAAAACCATA
12598377 AAA
1 AAA
12598380 AAATTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AAATTTATTAAAAAACCATA
Found at i:12604357 original size:30 final size:30
Alignment explanation
Indices: 12604292--12604357 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
12604282 TATAAAATAT
* * *
12604292 TTAATTTATTTTTAATAAAATTTTATGATTT
1 TTAATTTATTTCTAAT-AAATTTTATGAATG
*
12604323 TTAATTTATTTCTAAT-CATTATTATGAATG
1 TTAATTTATTTCTAATAAATT-TTATGAATG
12604353 TTAAT
1 TTAAT
12604358 GATCTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 12 0.40
31 15 0.50
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (30 bp):
TTAATTTATTTCTAATAAATTTTATGAATG
Found at i:12606076 original size:21 final size:20
Alignment explanation
Indices: 12606038--12606077 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12606028 TATTCATAAA
**
12606038 TTTTAAATTTAATCTTTATT
1 TTTTAAATTTAAAATTTATT
12606058 TTTTAAATTTTAAAATTTAT
1 TTTTAAA-TTTAAAATTTAT
12606078 GTTTACTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTTAAAATTTATT
Found at i:12606854 original size:31 final size:29
Alignment explanation
Indices: 12606801--12606874 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 29
12606791 AAAATTATTA
* *
12606801 TTTTAGAATTTTTTAA--TTTTTAACTTT
1 TTTTATAATTTTTTAATCTTTTTAAATTT
12606828 TTTTATATATTCTTTTAATCTTTTTAAATTT
1 TTTTATA-ATT-TTTTAATCTTTTTAAATTT
12606859 TTTTATAATTTTTTAA
1 TTTTATAATTTTTTAA
12606875 AATAATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 6 0.15
28 3 0.07
29 12 0.29
30 3 0.07
31 17 0.41
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTTATAATTTTTTAATCTTTTTAAATTT
Found at i:12606916 original size:18 final size:19
Alignment explanation
Indices: 12606885--12606935 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
12606875 AATAATATAA
*
12606885 ATTTTAGAACTTTTATAAA-T
1 ATTTTA-AA-TTTTAAAAATT
12606905 ATTTTAAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
12606924 ATTTTAAATTTT
1 ATTTTAAATTTT
12606936 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.28
19 15 0.52
20 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:12606937 original size:9 final size:9
Alignment explanation
Indices: 12606801--12606937 Score: 64
Period size: 9 Copynumber: 14.4 Consensus size: 9
12606791 AAAATTATTA
12606801 TTTTAGAATT
1 TTTTA-AATT
12606811 TTTT-AA-T
1 TTTTAAATT
*
12606818 TTTTAACTTT
1 TTTTAA-ATT
12606828 TTTTATATATT
1 TTTTA-A-ATT
12606839 CTTTT-AATCT
1 -TTTTAAAT-T
12606849 TTTTAAATTT
1 TTTTAAA-TT
12606859 TTTTATAATT
1 TTTTA-AATT
*
12606869 TTTTAAAATA
1 TTTT-AAATT
* *
12606879 ATATAAATT
1 TTTTAAATT
** *
12606888 TTAGAACTT
1 TTTTAAATT
* *
12606897 TTATAAATA
1 TTTTAAATT
12606906 TTTTAAATT
1 TTTTAAATT
**
12606915 TTAAAAATT
1 TTTTAAATT
12606924 ATTTTAAATT
1 -TTTTAAATT
12606934 TTTT
1 TTTT
12606938 TGTAATTTTT
Statistics
Matches: 97, Mismatches: 19, Indels: 23
0.70 0.14 0.17
Matches are distributed among these distances:
7 5 0.05
8 3 0.03
9 40 0.41
10 38 0.39
11 7 0.07
12 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTAAATT
Found at i:12611338 original size:31 final size:29
Alignment explanation
Indices: 12611264--12611368 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
12611254 TTAATATAAT
*
12611264 ATTTGATATTTAAATTT--T-TTTTTGTCTA
1 ATTTGGTATTTAAATTTAATATTTTT-T-TA
* *
12611292 ATTTGATATTCAAATTTGATATATTTTTTTA
1 ATTTGGTATTTAAATTT-A-ATATTTTTTTA
*
12611323 ATTTGGTATTTAAATTTAATATTTTTTTG
1 ATTTGGTATTTAAATTTAATATTTTTTTA
*
12611352 AGTTGGTATTTAAATTT
1 ATTTGGTATTTAAATTT
12611369 TTTGGGGTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
28 16 0.24
29 26 0.39
30 1 0.01
31 17 0.25
32 2 0.03
33 5 0.07
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (29 bp):
ATTTGGTATTTAAATTTAATATTTTTTTA
Found at i:12611642 original size:29 final size:27
Alignment explanation
Indices: 12611598--12611673 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
12611588 AAAAAATATC
12611598 AAGTTTAGGTACCAAATTAGGTCAAAAAA
1 AAGTTTA-GTACCAAATTAGGT-AAAAAA
* *
12611627 AAGTTTAGATATCAAATTAGATAAAAAA
1 AAGTTTAG-TACCAAATTAGGTAAAAAA
*
12611655 AA-TTAAGTACCAAATTAGG
1 AAGTTTAGTACCAAATTAGG
12611674 AAACAGTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 10 0.24
27 4 0.10
28 9 0.22
29 18 0.44
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.26
Consensus pattern (27 bp):
AAGTTTAGTACCAAATTAGGTAAAAAA
Found at i:12616468 original size:12 final size:12
Alignment explanation
Indices: 12616440--12616477 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12616430 ATTTGGGATG
12616440 GTCATGGTCAT-
1 GTCATGGTCATA
12616451 GATCATGGTCATA
1 G-TCATGGTCATA
*
12616464 GTCATAGTCATA
1 GTCATGGTCATA
12616476 GT
1 GT
12616478 GCTTGTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (12 bp):
GTCATGGTCATA
Found at i:12620755 original size:103 final size:102
Alignment explanation
Indices: 12620577--12620789 Score: 327
Period size: 103 Copynumber: 2.1 Consensus size: 102
12620567 ATCAAGCTTA
* * * *
12620577 TTCTTTTTTAATCACTGGTCTGATGTGGTAACTTTGAGTACTCCTATAATCAGTGCATGATGCAG
1 TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAGTACTCCTATAATCAGTGCATGATGCAG
*
12620642 ATCAAGATTATGAAGTTGCAAGGAGATGAATGCACTG
66 ATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
* * * *
12620679 TTCTTTTTTAATCACTAGTTTGTTGCGGCAAATTTGAGTTGCTCCTATAATCATTGCATGATGCA
1 TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAG-TACTCCTATAATCAGTGCATGATGCA
12620744 GATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
65 GATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
*
12620782 CTCTTTTT
1 TTCTTTTT
12620790 GAAGTCATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
102 32 0.32
103 68 0.68
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (102 bp):
TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAGTACTCCTATAATCAGTGCATGATGCAG
ATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
Found at i:12621067 original size:88 final size:88
Alignment explanation
Indices: 12620918--12621090 Score: 256
Period size: 88 Copynumber: 2.0 Consensus size: 88
12620908 TATTCGATGC
* * * * *
12620918 TAAGTCGATATGTCCGTTGCTTTCGTCATTCTGAGCTCAAACAAACCAGGGCGTAACTATAGATG
1 TAAGTCGATATGTCCATTGCTTTCGTCATTCCGAGCTCAAACAAACAAGGACATAACTATAGATG
* *
12620983 GAAACGTGGTGGATATAATTTGT
66 GAAACATGGCGGATATAATTTGT
* * *
12621006 TAAGTCGTTATGTCCATTGCTTTCGTCATTCCGAGCTCAAAGAAACAAGGACATAACTATAGTTG
1 TAAGTCGATATGTCCATTGCTTTCGTCATTCCGAGCTCAAACAAACAAGGACATAACTATAGATG
12621071 GAAACATGGCGGATATAATT
66 GAAACATGGCGGATATAATT
12621091 CTTGTTAGTA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (88 bp):
TAAGTCGATATGTCCATTGCTTTCGTCATTCCGAGCTCAAACAAACAAGGACATAACTATAGATG
GAAACATGGCGGATATAATTTGT
Found at i:12625122 original size:12 final size:12
Alignment explanation
Indices: 12625094--12625131 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12625084 ATTTGGGATG
12625094 GTCATGGTCAT-
1 GTCATGGTCATA
12625105 GATCATGGTCATA
1 G-TCATGGTCATA
*
12625118 GTCATAGTCATA
1 GTCATGGTCATA
12625130 GT
1 GT
12625132 GCTTGTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (12 bp):
GTCATGGTCATA
Found at i:12629415 original size:103 final size:102
Alignment explanation
Indices: 12629237--12629449 Score: 327
Period size: 103 Copynumber: 2.1 Consensus size: 102
12629227 ATCAAGCTTA
* * * *
12629237 TTCTTTTTTAATCACTGGTCTGATGTGGTAACTTTGAGTACTCCTATAATCAGTGCATGATGCAG
1 TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAGTACTCCTATAATCAGTGCATGATGCAG
*
12629302 ATCAAGATTATGAAGTTGCAAGGAGATGAATGCACTG
66 ATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
* * * *
12629339 TTCTTTTTTAATCACTAGTTTGTTGCGGCAAATTTGAGTTGCTCCTATAATCATTGCATGATGCA
1 TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAG-TACTCCTATAATCAGTGCATGATGCA
12629404 GATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
65 GATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
*
12629442 CTCTTTTT
1 TTCTTTTT
12629450 GAAGTCATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
102 32 0.32
103 68 0.68
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (102 bp):
TTCTTTTTTAATCACTAGTCTGATGCGGCAAATTTGAGTACTCCTATAATCAGTGCATGATGCAG
ATCAAGATTATGAAGTTGCAAGGAGATGAATGAACTG
Found at i:12634890 original size:31 final size:32
Alignment explanation
Indices: 12634832--12634899 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
12634822 TGTTATTCAA
* *
12634832 ATATTTAAAATTATATAAAATTACTAAA-AAT
1 ATATTGAAAATAATATAAAATTACTAAATAAT
* *
12634863 ATATTGAAAATAATATAACAA-TGCTAAATTAT
1 ATATTGAAAATAATATAA-AATTACTAAATAAT
12634895 ATATT
1 ATATT
12634900 TTTTAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (32 bp):
ATATTGAAAATAATATAAAATTACTAAATAAT
Found at i:12638852 original size:30 final size:30
Alignment explanation
Indices: 12638837--12639011 Score: 203
Period size: 30 Copynumber: 5.9 Consensus size: 30
12638827 AAATTTAGGA
* *
12638837 GTTAAAATGCAATTTTAGAGAAGTTT-A-G
1 GTTAAAATGTAATTTTAGAAAAGTTTAAGG
* *
12638865 GTTCAAAAATGTGATTTTGGAAAAGTTTAAGG
1 GTT--AAAATGTAATTTTAGAAAAGTTTAAGG
* *
12638897 GTTAAAATGTAATTTTAAAAAAGTTTAGGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAAGG
* *
12638927 GTTGAAATGTAATTGTAGAAAAGTTTAAGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAAGG
* *
12638957 GTTAAAATGCACTTTTAGAAAAGTTTAAGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAAGG
* *
12638987 GTT-AAATGAAATTTTAAAAAAGTTT
1 GTTAAAATGTAATTTTAGAAAAGTTT
12639012 GGGGTCAAAA
Statistics
Matches: 124, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
28 3 0.02
29 19 0.15
30 97 0.78
31 1 0.01
32 4 0.03
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (30 bp):
GTTAAAATGTAATTTTAGAAAAGTTTAAGG
Found at i:12638861 original size:60 final size:61
Alignment explanation
Indices: 12638795--12638982 Score: 183
Period size: 60 Copynumber: 3.1 Consensus size: 61
12638785 TAATTTTTGG
*
12638795 AAAAGTTTGGGGCTCAAAATAT-T-ATTTTGGAGAAA-TTT-AGGAGTTAAAATGCAATTTTAG
1 AAAAGTTTGGGGCTCAAAA-ATGTGATTTTGGA-AAAGTTTAAGG-GTTAAAATGCAATTTTAA
* * * *
12638855 AGAAGTTT-AGGTTCAAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAA
1 AAAAGTTTGGGGCTCAAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATGCAATTTTAA
** * * * * *
12638915 AAAAGTTTAGGGG-T-TGAAATGTAATTGTAGAAAAGTTTAAGGGTTAAAATGCACTTTTAG
1 AAAAGTTT-GGGGCTCAAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATGCAATTTTAA
12638975 AAAAGTTT
1 AAAAGTTT
12638983 AAGGGTTAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.02
59 12 0.11
60 87 0.81
61 4 0.04
62 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.35
Consensus pattern (61 bp):
AAAAGTTTGGGGCTCAAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATGCAATTTTAA
Found at i:12638904 original size:90 final size:90
Alignment explanation
Indices: 12638789--12639011 Score: 226
Period size: 90 Copynumber: 2.5 Consensus size: 90
12638779 AAAACATAAT
* * * * * *
12638789 TTTTGGAAAAGTTT-GGGGCTCAAAATATTATTTTGGAGAAA-TTTAGGAGTTAAAATGCAATTT
1 TTTTGGAAAAGTTTAAGGG-TTAAAATATAATTTT-AAAAAAGTTTAGGAGTTAAAATGCAATTG
* *
12638852 TAGAGAAGTTT-A-GGTTCAAAAATGTGA-
64 TAGAAAAGTTTAAGGGTT--AAAATG-CAC
* * * *
12638879 TTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAAAAAAGTTTAGGGGTTGAAATGTAATTGTA
1 TTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAAAAAAGTTTAGGAGTTAAAATGCAATTGTA
12638944 GAAAAGTTTAAGGGTTAAAATGCAC
66 GAAAAGTTTAAGGGTTAAAATGCAC
*
12638969 TTTTAGAAAAGTTTAAGGGTT-AAATGA-AATTTTAAAAAAGTTT
1 TTTTGGAAAAGTTTAAGGGTTAAAAT-ATAATTTTAAAAAAGTTT
12639012 GGGGTCAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
89 25 0.22
90 80 0.71
91 4 0.04
92 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (90 bp):
TTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAAAAAAGTTTAGGAGTTAAAATGCAATTGTA
GAAAAGTTTAAGGGTTAAAATGCAC
Found at i:12639007 original size:29 final size:30
Alignment explanation
Indices: 12638837--12639033 Score: 177
Period size: 30 Copynumber: 6.6 Consensus size: 30
12638827 AAATTTAGGA
* * *
12638837 GTTAAAATGCAATTTTAGAGAAGTTT-A-G
1 GTTAAAATGAAATTTTAAAAAAGTTTAAGG
** **
12638865 GTTCAAAAATGTGATTTTGGAAAAGTTTAAGG
1 GTT--AAAATGAAATTTTAAAAAAGTTTAAGG
* *
12638897 GTTAAAATGTAATTTTAAAAAAGTTTAGGG
1 GTTAAAATGAAATTTTAAAAAAGTTTAAGG
* * * *
12638927 GTTGAAATGTAATTGTAGAAAAGTTTAAGG
1 GTTAAAATGAAATTTTAAAAAAGTTTAAGG
* * *
12638957 GTTAAAATGCACTTTTAGAAAAGTTTAAGG
1 GTTAAAATGAAATTTTAAAAAAGTTTAAGG
*
12638987 GTT-AAATGAAATTTTAAAAAAGTTT-GGG
1 GTTAAAATGAAATTTTAAAAAAGTTTAAGG
* *
12639015 GTCAAAATAAAATTTTAAA
1 GTTAAAATGAAATTTTAAA
12639034 GATAACAAGG
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
28 7 0.05
29 33 0.23
30 97 0.68
31 1 0.01
32 4 0.03
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
GTTAAAATGAAATTTTAAAAAAGTTTAAGG
Found at i:12640494 original size:41 final size:41
Alignment explanation
Indices: 12640428--12640545 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 41
12640418 TTGCAACTTC
* *
12640428 ATCTTCCCCTCTTGGTTAGGGGTAAAGGATTGGAATATTCA
1 ATCTGCCCCTCTTGGTTAGGGGTAAAAGATTGGAATATTCA
* *
12640469 ATCTGCCCTTCTTGGTTAGGGGTAAAAGATTGGAATCTTCA
1 ATCTGCCCCTCTTGGTTAGGGGTAAAAGATTGGAATATTCA
** *
12640510 ATCTGCCCCTCTTAATTAGGGGTAAAAAATTGGAAT
1 ATCTGCCCCTCTTGGTTAGGGGTAAAAGATTGGAAT
12640546 GATGTAGCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (41 bp):
ATCTGCCCCTCTTGGTTAGGGGTAAAAGATTGGAATATTCA
Found at i:12640991 original size:48 final size:48
Alignment explanation
Indices: 12640832--12641006 Score: 151
Period size: 48 Copynumber: 3.6 Consensus size: 48
12640822 ACCATCATAG
* * *
12640832 CCTCAACCTTTCCCTTCAAATCTTCACGGTACCGAG-TTCACTGTTGTGG
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCG-GTTTCAC-GTTGCGA
* * * * *
12640881 CCTCAACCTTTCCCATCATATCTT-TTGAGGTACCAGGTTTGC-CATTGCAA
1 CCTCAACCTTTCCCTTCAAATCTTCAT--GGTACC-GGTTT-CACGTTGCGA
**
12640931 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTTTCGTTGCGA
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTCACGTTGCGA
* *
12640979 CCTCAACATTT-CCTATCACATCTTCATG
1 CCTCAACCTTTCCCT-TCAAATCTTCATG
12641007 TTTCCTTGAT
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
47 3 0.03
48 33 0.32
49 28 0.27
50 32 0.31
51 5 0.05
52 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (48 bp):
CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTCACGTTGCGA
Found at i:12642411 original size:19 final size:18
Alignment explanation
Indices: 12642387--12642422 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12642377 ATACATAGGT
12642387 TTTCAAAATGCCATTTGGG
1 TTTCAAAATGCC-TTTGGG
*
12642406 TTTCAAGATGCCTTTGG
1 TTTCAAAATGCCTTTGG
12642423 CGGGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (18 bp):
TTTCAAAATGCCTTTGGG
Found at i:12646568 original size:57 final size:58
Alignment explanation
Indices: 12646472--12646716 Score: 264
Period size: 57 Copynumber: 4.2 Consensus size: 58
12646462 GGTCAAAACA
* * *
12646472 TAATTTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATG
1 TAATTTTT-GAAAAGTTTA-AGGTTAAAATGTAATTTTAGAAAAGTTT-AGGGTTAAAATG
* * * * *
12646533 CAATTTTTGAAAAGTTT-A-GTCAAAATGCAATTTTGGAAAAGTTTAGGGTCAAAATG
1 TAATTTTTGAAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATG
* * * * *
12646589 TGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAAAATTTTAGGGTTAAAATA
1 TAATTTTTGAAAAGTTTAA-GGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATG
* *
12646648 TAA-TTTT-AAAAGTTTAAGGGTTAAAATGTAAATTTAGAAAAATTTGAGGGTTAAAATG
1 TAATTTTTGAAAAGTTTAA-GGTTAAAATGTAATTTTAGAAAAGTTT-AGGGTTAAAATG
*
12646706 AAATTTTTGAA
1 TAATTTTTGAA
12646717 GAAAATAGGG
Statistics
Matches: 155, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
56 25 0.16
57 59 0.38
58 16 0.10
59 37 0.24
60 11 0.07
61 7 0.05
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.37
Consensus pattern (58 bp):
TAATTTTTGAAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATG
Found at i:12646594 original size:29 final size:30
Alignment explanation
Indices: 12646476--12646712 Score: 272
Period size: 30 Copynumber: 8.1 Consensus size: 30
12646466 AAAACATAAT
* *
12646476 TTTTGGAAAAGTTTAGGGGTTAAAATATAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
*
12646506 TTTTGGAAAAGTTTAAGGGTTAAAATGCAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
* * *
12646536 TTTTTGAAAAGTTT-A--GTCAAAATGCAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
* *
12646563 TTTTGGAAAAGTTT-AGGGTCAAAATGTGA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
*
12646592 TTTTGGAAAAGTTTAAGGGTTAAAATATAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
* * *
12646622 TTTTAGAAAA-TTTTAGGGTTAAAATATAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
12646651 TTTT--AAAAGTTTAAGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
* * * * *
12646679 ATTTAGAAAAATTTGAGGGTTAAAATGAAA
1 TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
12646709 TTTT
1 TTTT
12646713 TGAAGAAAAT
Statistics
Matches: 181, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
27 29 0.16
28 20 0.11
29 47 0.26
30 85 0.47
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAAGGGTTAAAATGTAA
Found at i:12646603 original size:86 final size:87
Alignment explanation
Indices: 12646462--12646716 Score: 302
Period size: 86 Copynumber: 2.9 Consensus size: 87
12646452 GAGAATATAG
* * *
12646462 GGTCAAAACATAATTTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTTTAAGGGTT
1 GGTCAAAATACAA-TTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTT
*
12646527 AAAATGCAATTTTTGAAAAGTTTA
64 AAAATGAAATTTTTGAAAAGTTTA
* * *
12646551 -GTCAAAATGCAATTTTGGAAAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTTAA
1 GGTCAAAATACAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAA
* *
12646615 AAT-ATAATTTTAGAAAATTTTA
66 AATGA-AATTTTTGAAAAGTTTA
* * * * * *
12646637 GGGTTAAAATATAATTTT--AAAAGTTTAAGGGTTAAAATGTAAATTTAGAAAAATTTGAGGGTT
1 -GGTCAAAATACAATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTT
12646700 AAAATGAAATTTTTGAA
64 AAAATGAAATTTTTGAA
12646717 GAAAATAGGG
Statistics
Matches: 142, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
86 60 0.42
87 59 0.42
88 23 0.16
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (87 bp):
GGTCAAAATACAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAA
AATGAAATTTTTGAAAAGTTTA
Found at i:12646726 original size:29 final size:30
Alignment explanation
Indices: 12646607--12646711 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 30
12646597 GAAAAGTTTA
* * * *
12646607 AGGGTTAAAATATAATTTTAG-AAAATTTT
1 AGGGTTAAAATGTAAATTTAGAAAAATATG
* * * * *
12646636 AGGGTTAAAATAT-AATTT-TAAAAGTTTA
1 AGGGTTAAAATGTAAATTTAGAAAAATATG
*
12646664 AGGGTTAAAATGTAAATTTAGAAAAATTTG
1 AGGGTTAAAATGTAAATTTAGAAAAATATG
12646694 AGGGTTAAAATG-AAATTT
1 AGGGTTAAAATGTAAATTT
12646712 TTGAAGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 22 0.34
29 24 0.37
30 19 0.29
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (30 bp):
AGGGTTAAAATGTAAATTTAGAAAAATATG
Found at i:12650985 original size:22 final size:22
Alignment explanation
Indices: 12650959--12651008 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
12650949 CAACAAGAAA
*
12650959 GTTTAGTCTACAACTACTTCTT
1 GTTTAGTCTAAAACTACTTCTT
12650981 GTTTAGTCTAAAACTACTTCTT
1 GTTTAGTCTAAAACTACTTCTT
12651003 GTTTAG
1 GTTTAG
12651009 ATTAATTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (22 bp):
GTTTAGTCTAAAACTACTTCTT
Found at i:12651846 original size:38 final size:38
Alignment explanation
Indices: 12651695--12651881 Score: 178
Period size: 38 Copynumber: 4.9 Consensus size: 38
12651685 CGAAAATCTT
* * *
12651695 ATTCAGTATAATCAGTGGATAAT-GCTCGTTTAAGCAAGC
1 ATTCAGTATAATCAGTGGAT--TCACTCGTTTGAGCAAAC
* * * *
12651734 ATTCAATATAACCAGTAGTTATCACTCGTTTGAGCAAAC
1 ATTCAGTATAATCAGTGGAT-TCACTCGTTTGAGCAAAC
* * * * * *
12651773 ATTCAATAAAATCAGTGGATTCGCACATTTAAGCAAAC
1 ATTCAGTATAATCAGTGGATTCACTCGTTTGAGCAAAC
* *
12651811 ATTCAGTATAATCAATGGATTCACTTGTTTGAGCAAAC
1 ATTCAGTATAATCAGTGGATTCACTCGTTTGAGCAAAC
* * *
12651849 ATTCAGTATGATTAGTGGATTCGCTCGTTTGAG
1 ATTCAGTATAATCAGTGGATTCACTCGTTTGAG
12651882 AAAATGTTCA
Statistics
Matches: 119, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
38 74 0.62
39 45 0.38
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (38 bp):
ATTCAGTATAATCAGTGGATTCACTCGTTTGAGCAAAC
Found at i:12651892 original size:38 final size:38
Alignment explanation
Indices: 12651755--12651902 Score: 118
Period size: 38 Copynumber: 3.9 Consensus size: 38
12651745 CCAGTAGTTA
* * ** *
12651755 TCACTCGTTTGAGCAAACATTCAATAAAATCAGTGGAT
1 TCACTCGTTTGAGAAAACATTCAGTATGATTAGTGGAT
* * * * * * * *
12651793 TCGCACATTTAAGCAAACATTCAGTATAATCAATGGAT
1 TCACTCGTTTGAGAAAACATTCAGTATGATTAGTGGAT
* *
12651831 TCACTTGTTTGAGCAAACATTCAGTATGATTAGTGGAT
1 TCACTCGTTTGAGAAAACATTCAGTATGATTAGTGGAT
* **
12651869 TCGCTCGTTTGAGAAAATGTTCAGTA-GAATTAGT
1 TCACTCGTTTGAGAAAACATTCAGTATG-ATTAGT
12651903 ATTCCACTTT
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 1 0.01
38 88 0.99
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (38 bp):
TCACTCGTTTGAGAAAACATTCAGTATGATTAGTGGAT
Found at i:12652563 original size:36 final size:36
Alignment explanation
Indices: 12652517--12652589 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
12652507 CATAACATCG
* *
12652517 AATTAACTAATTATCATATATCAATCAGTTTGATTC
1 AATTAACTAATTATCATATATCAATCAATTTAATTC
* *
12652553 AATTTACTAATTGTCATATATCAATCAATTTAATTC
1 AATTAACTAATTATCATATATCAATCAATTTAATTC
12652589 A
1 A
12652590 TTTGTAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (36 bp):
AATTAACTAATTATCATATATCAATCAATTTAATTC
Found at i:12657912 original size:3 final size:3
Alignment explanation
Indices: 12657904--12657948 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12657894 AAATCCACAA
12657904 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12657949 TGAGCTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12658181 original size:3 final size:3
Alignment explanation
Indices: 12658173--12658214 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
12658163 TTATTCTTAA
12658173 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12658215 ATCAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12658416 original size:17 final size:17
Alignment explanation
Indices: 12658394--12658427 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12658384 TAAAATAAGT
12658394 TAAATTCTCAATTTGTA
1 TAAATTCTCAATTTGTA
12658411 TAAATTCTCAATTTGTA
1 TAAATTCTCAATTTGTA
12658428 GTAGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (17 bp):
TAAATTCTCAATTTGTA
Found at i:12662410 original size:21 final size:21
Alignment explanation
Indices: 12662381--12662422 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12662371 GATACCTAAT
12662381 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATCGATACTTTTTG
*
12662402 AAAAGGTATCGATACTTTTTG
1 AAAAAGTATCGATACTTTTTG
12662423 TCATTGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAAAGTATCGATACTTTTTG
Found at i:12662586 original size:17 final size:18
Alignment explanation
Indices: 12662564--12662598 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12662554 TGTTTGAAAA
12662564 TATCAGAGG-GTATCGAT
1 TATCAGAGGAGTATCGAT
12662581 TATCAGAGGAGTATCGAT
1 TATCAGAGGAGTATCGAT
12662599 ATCTCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (18 bp):
TATCAGAGGAGTATCGAT
Found at i:12662601 original size:17 final size:16
Alignment explanation
Indices: 12662563--12662601 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 16
12662553 TTGTTTGAAA
12662563 ATATCAGAGGGTATCG
1 ATATCAGAGGGTATCG
12662579 ATTATCAGAGGAGTATCG
1 A-TATCAGAGG-GTATCG
12662597 ATATC
1 ATATC
12662602 TCATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (16 bp):
ATATCAGAGGGTATCG
Found at i:12664302 original size:3 final size:3
Alignment explanation
Indices: 12664294--12664339 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
12664284 GCCTATCCTT
12664294 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
12664340 CCCTCTCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:12668006 original size:42 final size:41
Alignment explanation
Indices: 12667915--12667994 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 41
12667905 TGGTGGTGAA
*
12667915 GCTTCTGTTCGAGCCCAAAGCCAGGTCCAACAAGGTCCCCTT
1 GCTTCTGTTCGAGCCCAAAACCAGGTCCAACAAGG-CCCCTT
*
12667957 GCTTCTGTT-GAAGCCCAAAATCA-GTCTCAACAAGGCCC
1 GCTTCTGTTCG-AGCCCAAAACCAGGTC-CAACAAGGCCC
12667995 TATCGCTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 7 0.21
42 27 0.79
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (41 bp):
GCTTCTGTTCGAGCCCAAAACCAGGTCCAACAAGGCCCCTT
Found at i:12673930 original size:23 final size:24
Alignment explanation
Indices: 12673895--12673952 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
12673885 CGTTTGTTTA
**
12673895 ATGTTCACAAACAT-TAAGCGAAC
1 ATGTTCATGAACATATAAGCGAAC
* **
12673918 ATGTTCATGAACATATGATTGAAC
1 ATGTTCATGAACATATAAGCGAAC
12673942 ATGTTCATGAA
1 ATGTTCATGAA
12673953 TAATATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATGTTCATGAACATATAAGCGAAC
Found at i:12674412 original size:26 final size:25
Alignment explanation
Indices: 12674379--12674453 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
12674369 TTCACTATTA
* *
12674379 ATTTAATTTAATTATATTATATAAC
1 ATTTAATTTAATTAAATTACATAAC
* *
12674404 ATTTTAATTTAATCAAATTACATAAT
1 A-TTTAATTTAATTAAATTACATAAC
* *
12674430 AATTAATTTAATTTAATTATCATA
1 ATTTAATTTAATTAAATTA-CATA
12674454 TTATATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 16 0.39
26 25 0.61
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTAATTTAATTAAATTACATAAC
Found at i:12679550 original size:16 final size:17
Alignment explanation
Indices: 12679515--12679552 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12679505 AATATATATT
*
12679515 TAAAAATTAAAAATACA
1 TAAAAATTAAAAAAACA
*
12679532 TAAAAA-TAAAAAAATA
1 TAAAAATTAAAAAAACA
12679548 TAAAA
1 TAAAA
12679553 TTTGGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAATTAAAAAAACA
Found at i:12689638 original size:34 final size:34
Alignment explanation
Indices: 12689584--12689684 Score: 134
Period size: 34 Copynumber: 3.0 Consensus size: 34
12689574 GTGTCATTTT
* *
12689584 TACATACTAA-TTCTTCAGTTTGAAAA-TTTCAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTAC-AA
12689617 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
* * *
12689651 TACATATTGATTTCTTGAGCTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
12689685 AATGAGTTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
33 10 0.16
34 48 0.79
35 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (34 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTACAA
Found at i:12690694 original size:30 final size:30
Alignment explanation
Indices: 12690597--12690696 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 30
12690587 GATTATATTT
12690597 AAATATTTAAAATATAATTTATATATTCTAATT-
1 AAATATTTAAAAT-TAA--TAT-TATTCTAATTA
* *
12690630 AAAT-TTTATAAATAAATATTATT-TACTTA
1 AAATATTTA-AAATTAATATTATTCTAATTA
12690659 GAAATATTTAAAATTAATATT-TTCTATATTA
1 -AAATATTTAAAATTAATATTATTCTA-ATTA
12690690 AAATATT
1 AAATATT
12690697 AATAATAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
28 4 0.07
29 6 0.11
30 26 0.46
31 7 0.12
32 6 0.11
33 8 0.14
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (30 bp):
AAATATTTAAAATTAATATTATTCTAATTA
Found at i:12691142 original size:18 final size:18
Alignment explanation
Indices: 12691106--12691144 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12691096 ATTGCGTCTT
**
12691106 AAAAATACTTTTGGGATA
1 AAAAATACTTTTGAAATA
12691124 AAAAATACTTTTGAAATA
1 AAAAATACTTTTGAAATA
12691142 AAA
1 AAA
12691145 GCATTACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (18 bp):
AAAAATACTTTTGAAATA
Found at i:12698492 original size:57 final size:57
Alignment explanation
Indices: 12698404--12698518 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
12698394 TACCGTTAGC
* **
12698404 ACCTATATCAATGCCATGCATGTAGCCTAGTTTCCTACGAATCGATTCCATTCTTTT
1 ACCTACATCAATGCCATGCACATAGCCTAGTTTCCTACGAATCGATTCCATTCTTTT
* *
12698461 ACCTACATCAATGTCATGCACATAGCCTAGTTTCCTACGAATCGATTCCTTTCTTTT
1 ACCTACATCAATGCCATGCACATAGCCTAGTTTCCTACGAATCGATTCCATTCTTTT
12698518 A
1 A
12698519 TCATTAACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (57 bp):
ACCTACATCAATGCCATGCACATAGCCTAGTTTCCTACGAATCGATTCCATTCTTTT
Done.