Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_pilon, whole genome shotgun sequence
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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 19
Found at i:1056376 original size:24 final size:24
Alignment explanation
Indices: 1056344--1056390 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1056334 CTCTAAAATC
1056344 TAAAACTCTCAAACAT-TCAAACTT
1 TAAAACTCTCAAAC-TCTCAAACTT
*
1056368 TAAAACTCTTAAACTCTCAAACT
1 TAAAACTCTCAAACTCTCAAACT
1056391 AATAAAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAACTCTCAAACTCTCAAACTT
Found at i:1056396 original size:16 final size:16
Alignment explanation
Indices: 1056346--1056396 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1056336 CTAAAATCTA
1056346 AAACTCTCAAAC-ATT
1 AAACTCTCAAACTATT
* * *
1056361 CAAACTTTAAAACTCTT
1 -AAACTCTCAAACTATT
*
1056378 AAACTCTCAAACTAAT
1 AAACTCTCAAACTATT
1056394 AAA
1 AAA
1056397 ATGGCTCATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (16 bp):
AAACTCTCAAACTATT
Found at i:1059667 original size:57 final size:57
Alignment explanation
Indices: 1059603--1059743 Score: 237
Period size: 57 Copynumber: 2.5 Consensus size: 57
1059593 CTAAAGTAAA
* *
1059603 AAAGAAAAATATATGTGAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGCAT
1 AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT
*
1059660 AATGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT
1 AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT
* *
1059717 AAAGAAATATATGTGTAAAAGGAATTA
1 AAAGAAAAATATATGTAAAAGGAATTA
1059744 TTTTAGGCAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.24
Consensus pattern (57 bp):
AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT
Found at i:1059761 original size:37 final size:37
Alignment explanation
Indices: 1059708--1059780 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
1059698 GGCTAGAAAC
* *
1059708 TTTAGGAATAAAGAAATATATGTGTAAAAGGAATTAT
1 TTTAGGAATAAAGAAATATATATGTAAAAAGAATTAT
* *
1059745 TTTAGGCATAACGAAATATATATGTAAAAAGAATTA
1 TTTAGGAATAAAGAAATATATATGTAAAAAGAATTA
1059781 AACTAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (37 bp):
TTTAGGAATAAAGAAATATATATGTAAAAAGAATTAT
Found at i:1059831 original size:49 final size:49
Alignment explanation
Indices: 1059759--1059860 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
1059749 GGCATAACGA
1059759 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG
1 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG
* **
1059808 AATATATGTGTAAATGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG
1 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG
1059857 AATA
1 AATA
1059861 AAGAAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (49 bp):
AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG
Found at i:1059877 original size:143 final size:145
Alignment explanation
Indices: 1059606--1059879 Score: 435
Period size: 143 Copynumber: 1.9 Consensus size: 145
1059596 AAGTAAAAAA
* *
1059606 GAAAAATATATGTGAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGCATAATGAAAAATA
1 GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG-A-AAT----AATA
1059671 TATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAA
60 TATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAA
1059736 AGGAATTATTTTAGGCATAAC
125 AGGAATTATTTTAGGCATAAC
* *
1059757 GAAATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG-AAT-ATATGTGTA
1 GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAATAATATATGTA
*
1059820 AATGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAA
66 AAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAA
1059880 ATCATTATGT
Statistics
Matches: 118, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
143 67 0.57
148 3 0.03
151 48 0.41
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (145 bp):
GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAATAATATATGTA
AAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAAGGAAT
TATTTTAGGCATAAC
Found at i:1062469 original size:15 final size:15
Alignment explanation
Indices: 1062435--1062481 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1062425 CTTTCACCTA
*
1062435 ATTTTAAAAATA-AC
1 ATTTTAATAATATAC
*
1062449 ATTTTAATAATATAT
1 ATTTTAATAATATAC
*
1062464 ATTTTAATTATATAC
1 ATTTTAATAATATAC
1062479 ATT
1 ATT
1062482 ATAAATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTTAATAATATAC
Found at i:1063506 original size:20 final size:20
Alignment explanation
Indices: 1063483--1063527 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1063473 TAAAGTAGTG
1063483 TAAAATGTT-TTAAAATAAA
1 TAAAATGTTATTAAAATAAA
1063502 -ATAAATGTTATTAAAATAAA
1 TA-AAATGTTATTAAAATAAA
1063522 TAAAAT
1 TAAAAT
1063528 CAGATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 14 0.61
21 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
TAAAATGTTATTAAAATAAA
Found at i:1063509 original size:19 final size:19
Alignment explanation
Indices: 1063485--1063525 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1063475 AAGTAGTGTA
1063485 AAATGTT-TTAAAATAAAAT
1 AAATGTTATTAAAAT-AAAT
1063504 AAATGTTATTAAAATAAAT
1 AAATGTTATTAAAATAAAT
1063523 AAA
1 AAA
1063526 ATCAGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAATGTTATTAAAATAAAT
Found at i:1066868 original size:16 final size:16
Alignment explanation
Indices: 1066847--1066880 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1066837 TTTCTCCAAG
1066847 TCAATCGTAATTGACA
1 TCAATCGTAATTGACA
*
1066863 TCAATCTTAATTGACA
1 TCAATCGTAATTGACA
1066879 TC
1 TC
1066881 CACCCCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (16 bp):
TCAATCGTAATTGACA
Found at i:1074597 original size:2 final size:2
Alignment explanation
Indices: 1074590--1074615 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1074580 TTTTATTTTG
1074590 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1074616 GTTTTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1075237 original size:12 final size:12
Alignment explanation
Indices: 1075220--1075246 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1075210 TTGCAATGTC
1075220 TGGTCGTGGCGG
1 TGGTCGTGGCGG
1075232 TGGTCGTGGCGG
1 TGGTCGTGGCGG
1075244 TGG
1 TGG
1075247 AGGCCGTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.59, T:0.26
Consensus pattern (12 bp):
TGGTCGTGGCGG
Found at i:1075473 original size:30 final size:30
Alignment explanation
Indices: 1075383--1075550 Score: 165
Period size: 30 Copynumber: 5.3 Consensus size: 30
1075373 TACCCCGCCT
* * **
1075383 CCTCCTCAGTCGGCTCCAGCTCATCAACCA
1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA
1075413 CCTCCTCAGGCGCTCCGGCTCCGGCGGCTCGGCAACCA
1 CCTCCTCA-G-G---CGGCT-C--CGGCTCGGCAACCA
*
1075451 CCTCCTCAGACGGCTCCGGCTCGGCAACCA
1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA
* * * *
1075481 CCTCTTCAGGCGGCTCCGACTCGGCAATCT
1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA
* *
1075511 CCTCCCCAGGCGGCTCCGGCTCGGCAACCT
1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA
1075541 CCTCCTCAGG
1 CCTCCTCAGG
1075551 AGGTTCCTGC
Statistics
Matches: 115, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
30 82 0.71
31 1 0.01
32 1 0.01
33 5 0.04
35 5 0.04
36 1 0.01
37 1 0.01
38 19 0.17
ACGTcount: A:0.14, C:0.46, G:0.23, T:0.17
Consensus pattern (30 bp):
CCTCCTCAGGCGGCTCCGGCTCGGCAACCA
Found at i:1087058 original size:3 final size:3
Alignment explanation
Indices: 1087050--1087074 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1087040 ATCATGTTAT
1087050 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1087075 GTAGTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1089030 original size:101 final size:105
Alignment explanation
Indices: 1088857--1089114 Score: 339
Period size: 101 Copynumber: 2.5 Consensus size: 105
1088847 AACTTCCTCT
* *
1088857 TCCTT-TTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGATGCTGATATATCTC
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACAC-TTCTGGAAATGTTGATGATGATATATCTC
* * * *
1088921 TTTCTGTGATAGAATC-ACGCAAAATGTTGAACAAGTTC-T-
65 CTTATGTGATAGAATCGA-GCAAAAGGTTAAACAAGTTCTTC
* * *
1088960 T-C-TCTTCAGATGAATTATTCTCATTATGAACACTTCTGGAAATGTTGATGATGATCTATCTCC
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGATGATATATCTCC
**
1089023 TTATGTGATAGCGTCGAGCAAAAGGTTAAACAAGTTCTTC
66 TTATGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTC
*
1089063 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGAT
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGAT
1089115 CTTCAAAAGA
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
101 58 0.43
102 29 0.22
103 2 0.01
104 1 0.01
105 27 0.20
106 17 0.13
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (105 bp):
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGATGATATATCTCC
TTATGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTC
Found at i:1089383 original size:41 final size:40
Alignment explanation
Indices: 1089296--1089396 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
1089286 AAGGCTGAAC
* * * *
1089296 AAGTTCTTCTCACTATGAAC-TTCTTTTTCCTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTTCTTCTCCCTCTTCAAAT
1089335 AAGTTCTTCTCATTATGAACTTTCTTCTCCCTTCTTCAAAT
1 AAGTTCTTCTCATTATGAACTTTCTTCTCCC-TCTTCAAAT
*
1089376 GAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTCATTATGAACT
1089397 CTATCTGGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 19 0.35
40 8 0.15
41 28 0.51
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (40 bp):
AAGTTCTTCTCATTATGAACTTTCTTCTCCCTCTTCAAAT
Found at i:1089495 original size:113 final size:113
Alignment explanation
Indices: 1089338--1089657 Score: 514
Period size: 113 Copynumber: 2.8 Consensus size: 113
1089328 TTCAGATAAG
* * * *
1089338 TTCTTCTCATTATGAACTTTCTTCTCCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTATCT
1 TTCTTCTCATTATGAAC-TTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
* * *
1089403 GGCAATGCTGATCCATCAAGTGATAAATTCGAGCGAAAGGTTGAACAAA
65 GGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
*
1089452 TTCTTCTCATTTTGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* *
1089517 GCAATGTTGATCCCTCAAGTGATGAATTCGAGCAAAAGGTTGAACAAG
66 GCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
* * *
1089565 TTCTTCTCATTATGAACTTTCTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAGCTCTACCTG
1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1089630 GCAATGTTGATCCATCAAGTGATGAATT
66 GCAATGTTGATCCATCAAGTGATGAATT
1089658 TGAATATTTG
Statistics
Matches: 191, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
113 175 0.92
114 16 0.08
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
Found at i:1091636 original size:36 final size:36
Alignment explanation
Indices: 1091550--1091647 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
1091540 TTACTTCTTG
* *
1091550 CTGAGATGAGCCTCCAAGAATG-CCCAAATATTCATA
1 CTGACATGAGCCTTCAA-AATGCCCCAAATATTCATA
* * *
1091586 TTGTCGTGAGCCTTCAAAATGCCCCAAATATTCATA
1 CTGACATGAGCCTTCAAAATGCCCCAAATATTCATA
**
1091622 CTGACATG-GACCTTCAGGATGCCCCA
1 CTGACATGAG-CCTTCAAAATGCCCCA
1091648 CATGAATCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
35 5 0.10
36 45 0.90
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (36 bp):
CTGACATGAGCCTTCAAAATGCCCCAAATATTCATA
Found at i:1099231 original size:3 final size:3
Alignment explanation
Indices: 1099223--1099247 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1099213 ATCATGTTAT
1099223 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1099248 GTAGTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1099301 original size:3 final size:3
Alignment explanation
Indices: 1099293--1099321 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1099283 ATATGACTAC
1099293 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1099322 TAAATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1099350 original size:14 final size:13
Alignment explanation
Indices: 1099299--1099360 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 13
1099289 CTACATAATA
*
1099299 ATAATAATAATAAT
1 ATAAAAATAA-AAT
*
1099313 AATAATAATTAAATAT
1 -ATAA-AAATAAA-AT
1099329 ATTAAAAATAAACAT
1 A-TAAAAATAAA-AT
1099344 ATAAAAATAAAAT
1 ATAAAAATAAAAT
1099357 ATAA
1 ATAA
1099361 CTAAATGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 6 0.15
14 10 0.25
15 15 0.38
16 9 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATAAAAT
Found at i:1099366 original size:15 final size:14
Alignment explanation
Indices: 1099331--1099360 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1099321 TTAAATATAT
1099331 TAAAAATAAACATA
1 TAAAAATAAACATA
1099345 TAAAAATAAA-ATA
1 TAAAAATAAACATA
1099358 TAA
1 TAA
1099361 CTAAATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAAATAAACATA
Found at i:1103963 original size:48 final size:48
Alignment explanation
Indices: 1103892--1103986 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
1103882 AAAATAATGG
*
1103892 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCATCAACACAGCAA
1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA
*
1103940 CACTCTTTGAATCAGAAAGTGTTGTCTATGGTGGCACCAACACAGCA
1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCA
1103987 GCACCGGCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (48 bp):
CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA
Found at i:1106065 original size:20 final size:19
Alignment explanation
Indices: 1106048--1106085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1106038 AAATTTAATT
*
1106048 TTTTTAAATAATTATTAAAA
1 TTTTCAAATAATT-TTAAAA
1106068 TTTTCAAATAATTTTAAA
1 TTTTCAAATAATTTTAAA
1106086 TGATAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTCAAATAATTTTAAAA
Found at i:1106246 original size:23 final size:22
Alignment explanation
Indices: 1106214--1106277 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
1106204 AATTTTTAAA
1106214 TTTTAATAATTTTAA-AAATATT
1 TTTTAATAA-TTTAATAAATATT
1106236 TTTTACATAATTTAATAAATAATT
1 TTTTA-ATAATTTAATAAAT-ATT
* *
1106260 ATATAATTAATTTAATAA
1 TTTTAA-TAATTTAATAA
1106278 TAAAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.28
23 9 0.25
24 17 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAATAATTTAATAAATATT
Found at i:1119220 original size:48 final size:48
Alignment explanation
Indices: 1119147--1119241 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
1119137 TTGATGAAGT
1119147 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
* * * * *
1119195 ACGAGGCATCTCCTCGATATGCGTATGTATGTGTGTGTTTATGTATA
1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATA
1119242 TACCCAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (48 bp):
ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
Found at i:1120061 original size:31 final size:32
Alignment explanation
Indices: 1120005--1120070 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
1119995 GCTTAATAAA
* *
1120005 CTTAACGAGCAACGACTCGAGCAATAAATTTT
1 CTTAACGAGCAACAACTAGAGCAATAAATTTT
*
1120037 CTTAACGAG-AACAAGTAGAGCAATAAATTTT
1 CTTAACGAGCAACAACTAGAGCAATAAATTTT
1120068 CTT
1 CTT
1120071 TACAAGCACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (32 bp):
CTTAACGAGCAACAACTAGAGCAATAAATTTT
Found at i:1120563 original size:78 final size:78
Alignment explanation
Indices: 1120478--1120635 Score: 221
Period size: 78 Copynumber: 2.0 Consensus size: 78
1120468 AGAAAAAAAT
* *
1120478 AACATTTTAAG-TAGCGCCCAATATTAACATTTCCGGTAAAAAAATAATAATTT-AGATAACGCT
1 AACATTTT-AGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAG-TAACGCT
1120541 TTACCAGAAATGTTA
64 TTACCAGAAATGTTA
* * * *
1120556 AACATTTTAGTTAGCACCTAATATTAACATTTCTAGTAAAAAAATAATATTTTAAGTAACGTTTT
1 AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAGTAACGCTTT
*
1120621 ACTAGAAATGTTA
66 ACCAGAAATGTTA
1120634 AA
1 AA
1120636 AAATATTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
77 2 0.03
78 67 0.94
79 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (78 bp):
AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAGTAACGCTTT
ACCAGAAATGTTA
Found at i:1123688 original size:22 final size:23
Alignment explanation
Indices: 1123660--1123704 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1123650 GGAATAACAA
1123660 TGCCAGTGATTGGTGA-TTAAAG
1 TGCCAGTGATTGGTGATTTAAAG
1123682 TGCCAGTGATTGGTGATTTAAAG
1 TGCCAGTGATTGGTGATTTAAAG
1123705 ATTCTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33
Consensus pattern (23 bp):
TGCCAGTGATTGGTGATTTAAAG
Found at i:1126875 original size:21 final size:21
Alignment explanation
Indices: 1126799--1126880 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 21
1126789 AAATGACCAA
**
1126799 CAAATTCGCAACGCGA-ACTC
1 CAAATTCGCAACGCGATTTTC
* * *
1126819 CAATTTCGCAACTC-AGTTTC
1 CAAATTCGCAACGCGATTTTC
***
1126839 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
1126860 CAAATTCGCAACGCGAATTTT
1 CAAATTCGCAACGCG-ATTTT
1126881 GTTGTAGCAA
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 1 0.02
20 23 0.50
21 17 0.37
22 5 0.11
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:1130160 original size:18 final size:18
Alignment explanation
Indices: 1130137--1130172 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1130127 AAGCAAAAAG
*
1130137 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1130155 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1130173 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1130483 original size:20 final size:20
Alignment explanation
Indices: 1130460--1130541 Score: 83
Period size: 20 Copynumber: 4.1 Consensus size: 20
1130450 TCGCATTACA
*
1130460 AATTTGGCTTTCACGTTGCG
1 AATTTGACTTTCACGTTGCG
**
1130480 AATTTGACTTTTGCGTTGCG
1 AATTTGACTTTCACGTTGCG
* * ***
1130500 AATTTGACTATCGCAACGCG
1 AATTTGACTTTCACGTTGCG
*
1130520 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCACGTTGCG
1130540 AA
1 AA
1130542 AGTGTACCTT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
AATTTGACTTTCACGTTGCG
Found at i:1130734 original size:63 final size:64
Alignment explanation
Indices: 1130600--1130746 Score: 235
Period size: 63 Copynumber: 2.3 Consensus size: 64
1130590 ACTTTAAAAC
1130600 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
1130664 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1130727 AACAAATCAAC-TTTACAAAT
1 AACAAATCAACTTTTACAAAT
1130747 ACATCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
62 9 0.12
63 35 0.45
64 34 0.44
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:1132115 original size:21 final size:21
Alignment explanation
Indices: 1132089--1132224 Score: 112
Period size: 21 Copynumber: 6.5 Consensus size: 21
1132079 GTGAATCGGG
*
1132089 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
1132110 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1132131 CTCTTGAACTGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
** *
1132152 CTCTTGAA-GGATGATAGCGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * * *
1132173 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * *
1132194 CTTTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
1132215 CTCTTGAACG
1 CTCTTGAACG
1132225 ATGACAGGTG
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
20 1 0.01
21 91 0.98
22 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1132148 original size:42 final size:41
Alignment explanation
Indices: 1132089--1132223 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
1132079 GTGAATCGGG
* *
1132089 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACTGTGGGAGGG-CCTCTTGAACGATGACAGAGGC
* * *
1132131 CTCTTGAACTGTGGGAGGGGCCTCTTGAAGGATGATAGCGGC
1 CTCTTGAACTGTGGGA-GGGCCTCTTGAACGATGACAGAGGC
* * *
1132173 CTCTTGAA-TGATAGGAGAGGCCTTTTGAACGAT-AGGAGAGGC
1 CTCTTGAACTG-TGGGAG-GGCCTCTTGAACGATGA-CAGAGGC
1132215 CTCTTGAAC
1 CTCTTGAAC
1132224 GATGACAGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
41 4 0.05
42 72 0.91
43 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACTGTGGGAGGGCCTCTTGAACGATGACAGAGGC
Found at i:1134326 original size:20 final size:20
Alignment explanation
Indices: 1134281--1134326 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1134271 TTGTGTTGCG
* *
1134281 AGTTTCGCGTTGCGATTTTC
1 AGTTTCGCGTTGCGAATTTA
* *
1134301 ATTTTCGTGTTGCGAATTTA
1 AGTTTCGCGTTGCGAATTTA
1134321 AGTTTC
1 AGTTTC
1134327 AAATAGTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (20 bp):
AGTTTCGCGTTGCGAATTTA
Found at i:1134668 original size:22 final size:22
Alignment explanation
Indices: 1134642--1134699 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1134632 GATGAAGATA
1134642 GACGGATTTCGCCGGAGATAAG
1 GACGGATTTCGCCGGAGATAAG
* **
1134664 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATAAG
*
1134686 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1134700 TAAAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATAAG
Found at i:1135123 original size:22 final size:22
Alignment explanation
Indices: 1135096--1135143 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1135086 GGAGATAAAT
1135096 GGATTTCACCGGAGATGGGGAC
1 GGATTTCACCGGAGATGGGGAC
**
1135118 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCACCGGAGATGGGGAC
1135140 GGAT
1 GGAT
1135144 GTCGCCATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21
Consensus pattern (22 bp):
GGATTTCACCGGAGATGGGGAC
Found at i:1135301 original size:451 final size:451
Alignment explanation
Indices: 1134455--1135307 Score: 1483
Period size: 451 Copynumber: 1.9 Consensus size: 451
1134445 ATTTACTAAG
1134455 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT
1 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT
1134520 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT
66 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT
* *
1134585 TGATTTTCCATTTCTGACCGTGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAGACGGATT
131 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT
* *
1134650 TCGCCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCGTAAAGAGTGAAAGAT
196 TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAAAGAT
* * *
1134715 GGAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATATTGTATATATTT
261 GAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATTT
*
1134780 GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGTG
326 GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGCG
1134845 CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA
391 CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA
*
1134906 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAGTAT
1 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT
*
1134971 GAAAAATCTAATAATAATACAAAATTTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT
66 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT
* *
1135036 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGGAGATAAATGGATT
131 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT
** *
1135101 TCACCGGAGATGGGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAGAGAGT-AAGAGA
196 TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAA-AGA
* * *
1135165 TGAAGATGGGACTGAGTTGTGATTTAGGGTTTTAAGTTATGATTTACGATTATACTATTTATATT
260 TGAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATT
** * * *
1135230 TGTGTTGCGAAATAAATATTGTGTTTTGAATTCGAAATTAAAATTCGCGTTGCGAAAATAAACGC
325 TGTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGC
1135295 GCTTTGCGAATTT
390 GCTTTGCGAATTT
1135308 AACTTGTGTT
Statistics
Matches: 378, Mismatches: 23, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
450 2 0.01
451 376 0.99
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (451 bp):
CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT
GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT
TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT
TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAAAGAT
GAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATTT
GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGCG
CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA
Found at i:1135324 original size:18 final size:20
Alignment explanation
Indices: 1135298--1135345 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1135288 TAAACGCGCT
1135298 TTGCGAATTTAAC-T-TGTG
1 TTGCGAATTTAACTTATGTG
* *
1135316 TTGCAAATTTGACTTATGTG
1 TTGCGAATTTAACTTATGTG
1135336 TTGCGAATTT
1 TTGCGAATTT
1135346 GGAAACTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 13 0.52
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTAACTTATGTG
Found at i:1141856 original size:11 final size:12
Alignment explanation
Indices: 1141828--1141860 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1141818 GTATTATGAA
1141828 TTTTCAAATATTG
1 TTTTCAAATA-TG
1141841 TTTTCAAATA-G
1 TTTTCAAATATG
1141852 TTTTCAAAT
1 TTTTCAAAT
1141861 CCAAATCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (12 bp):
TTTTCAAATATG
Found at i:1145365 original size:23 final size:23
Alignment explanation
Indices: 1145337--1145405 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1145327 ACATCTTATA
*
1145337 TGGCACTTCGGTGCATTTCTATAC-
1 TGGCACTTAGGTGCATTT-T-TACG
*
1145361 T-GCACTTAGGTGCAATTTTACG
1 TGGCACTTAGGTGCATTTTTACG
* *
1145383 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTAGGTGCATTTTTACG
1145406 AGCTGTGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 32 0.84
24 1 0.03
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (23 bp):
TGGCACTTAGGTGCATTTTTACG
Found at i:1150637 original size:23 final size:23
Alignment explanation
Indices: 1150609--1150677 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1150599 ACATCTTATA
1150609 TGGCACTTCGGTGCATTTCTATAC-
1 TGGCACTTCGGTGCATTT-T-TACG
* *
1150633 T-GCACTTAGGTGCAATTTTACG
1 TGGCACTTCGGTGCATTTTTACG
*
1150655 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTTTACG
1150678 AGCTGTGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 32 0.84
24 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTTTACG
Found at i:1151584 original size:20 final size:20
Alignment explanation
Indices: 1151559--1151596 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1151549 CTATATATAT
1151559 ATTTGGTTTTGATT-GTTTGA
1 ATTTGG-TTTGATTAGTTTGA
1151579 ATTTGGTTTGATTAGTTT
1 ATTTGGTTTGATTAGTTT
1151597 ATATTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61
Consensus pattern (20 bp):
ATTTGGTTTGATTAGTTTGA
Found at i:1157781 original size:24 final size:25
Alignment explanation
Indices: 1157736--1157787 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1157726 CCATAAGGAT
*
1157736 TGTGACACAAGAAAAG-AGAAAACG
1 TGTGACACAAGAAAAGAAAAAAACG
* * *
1157760 TGTGCCACAAGAACATAAAAAAACG
1 TGTGACACAAGAAAAGAAAAAAACG
1157785 TGT
1 TGT
1157788 TACAAGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.13
Consensus pattern (25 bp):
TGTGACACAAGAAAAGAAAAAAACG
Found at i:1158554 original size:10 final size:10
Alignment explanation
Indices: 1158541--1158573 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1158531 TTTCTTTTTC
1158541 TTTTTTATTT
1 TTTTTTATTT
1158551 TTTTTTA-TT
1 TTTTTTATTT
*
1158560 TTTTTAATTT
1 TTTTTTATTT
1158570 TTTT
1 TTTT
1158574 AACAAGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1158574 original size:9 final size:9
Alignment explanation
Indices: 1158541--1158575 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1158531 TTTCTTTTTC
*
1158541 TTTTTTATT
1 TTTTTTAAT
*
1158550 TTTTTTTAT
1 TTTTTTAAT
1158559 TTTTTTAAT
1 TTTTTTAAT
1158568 TTTTTTAA
1 TTTTTTAA
1158576 CAAGTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:1164009 original size:24 final size:24
Alignment explanation
Indices: 1163940--1164000 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1163930 CCATAAGGAT
1163940 TGTGCCACAAGAAAAGAGAAAACG
1 TGTGCCACAAGAAAAGAGAAAACG
1163964 TGTGCCACAAGAAAAGAGAAAACG
1 TGTGCCACAAGAAAAGAGAAAACG
1163988 TGTGCCACAAGAA
1 TGTGCCACAAGAA
1164001 CATAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.25, T:0.10
Consensus pattern (24 bp):
TGTGCCACAAGAAAAGAGAAAACG
Found at i:1170197 original size:24 final size:25
Alignment explanation
Indices: 1170152--1170203 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1170142 CCATAAGGAT
*
1170152 TGTGCCACAAGAAAAG-AGAAAACG
1 TGTGCCACAAGAAAAGAAAAAAACG
* *
1170176 TGTGCCACAAGAACATAAAAAAACG
1 TGTGCCACAAGAAAAGAAAAAAACG
1170201 TGT
1 TGT
1170204 TACAAGGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.13
Consensus pattern (25 bp):
TGTGCCACAAGAAAAGAAAAAAACG
Found at i:1171403 original size:19 final size:21
Alignment explanation
Indices: 1171360--1171405 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1171350 TTCTTCTTTT
*
1171360 AAATTTTTGTTTTAGATCTTT
1 AAATTTTTGTTTTAGATCTTC
*
1171381 AAATTTTTTTTTTA-A-CTTC
1 AAATTTTTGTTTTAGATCTTC
1171400 AAATTT
1 AAATTT
1171406 CTTATAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 1 0.04
21 13 0.57
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (21 bp):
AAATTTTTGTTTTAGATCTTC
Found at i:1173750 original size:18 final size:18
Alignment explanation
Indices: 1173727--1173763 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1173717 TATGCTTTTC
1173727 GCTGATGACATTGTCATA
1 GCTGATGACATTGTCATA
*
1173745 GCTGATGACATTGTTATA
1 GCTGATGACATTGTCATA
1173763 G
1 G
1173764 TTGCTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (18 bp):
GCTGATGACATTGTCATA
Found at i:1176969 original size:41 final size:41
Alignment explanation
Indices: 1176904--1177060 Score: 208
Period size: 41 Copynumber: 3.8 Consensus size: 41
1176894 GGAAGTTTAG
* *
1176904 TGGATTTACCATTCGGGATAAATTTCACTTTGGAATATTAA
1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA
* * * * *
1176945 TGGGTTCACCATTCAGGATGAATTTCAC-TTCGAATTATTAG
1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAA-TATTAA
* *
1176986 TGGATTCACCCTTCGGGATTAATTTCACTTTAGAATATTAA
1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA
*
1177027 TGGATTCACCCTTCGGGATTAATTTCACTTTGGA
1 TGGATTCACCATTCGGGATTAATTTCACTTTGGA
1177061 TTATCACTGC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.05
41 91 0.90
42 5 0.05
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (41 bp):
TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA
Found at i:1177047 original size:22 final size:22
Alignment explanation
Indices: 1176981--1177049 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
1176971 ACTTCGAATT
*
1176981 ATTAGTGGATTCACCCTTCGGG
1 ATTAATGGATTCACCCTTCGGG
* * **
1177003 ATTAAT---TTCA-CTTTAGAAT
1 ATTAATGGATTCACCCTTCG-GG
1177022 ATTAATGGATTCACCCTTCGGG
1 ATTAATGGATTCACCCTTCGGG
1177044 ATTAAT
1 ATTAAT
1177050 TTCACTTTGG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
22 15 0.45
23 4 0.12
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTAATGGATTCACCCTTCGGG
Found at i:1177064 original size:82 final size:82
Alignment explanation
Indices: 1176900--1177056 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 82
1176890 TCGAGGAAGT
* * *
1176900 TTAGTGGATTTACCATTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCATTCAGGATG
1 TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG
1176965 AATTTCACTTCGAATTA
66 AATTTCACTTCGAATTA
* * * * *
1176982 TTAGTGGATTCACCCTTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCCTTCGGGATT
1 TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG
1177047 AATTTCACTT
66 AATTTCACTT
1177057 TGGATTATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (82 bp):
TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG
AATTTCACTTCGAATTA
Found at i:1177080 original size:41 final size:41
Alignment explanation
Indices: 1176915--1177081 Score: 120
Period size: 41 Copynumber: 4.1 Consensus size: 41
1176905 GGATTTACCA
* * * ** * *
1176915 TTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCA
1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC
* * * * * * *
1176956 TTCAGGATGAATTTCAC-TTCGAATTATTAGTGGATTCACCC
1 TTCGGGATTAATTTCACTTTAGAA-TATCAATGCATCCACCC
* * *
1176997 TTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCC
1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC
* * * * *
1177038 TTCGGGATTAATTTCACTTTGGATTATCACTGCCTCCTCCC
1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC
1177079 TTC
1 TTC
1177082 AAGACAGACT
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 5 0.05
41 96 0.91
42 5 0.05
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (41 bp):
TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC
Found at i:1177080 original size:82 final size:82
Alignment explanation
Indices: 1176915--1177081 Score: 208
Period size: 82 Copynumber: 2.0 Consensus size: 82
1176905 GGATTTACCA
* *
1176915 TTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCATTCAGGATGAATTTCACTTCGAAT
1 TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT
* * * *
1176980 TATTAGTGGATTCACCC
66 TATCACTGCATCCACCC
* * * * * *
1176997 TTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCCTTCGGGATTAATTTCACTTTGGAT
1 TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT
* *
1177062 TATCACTGCCTCCTCCC
66 TATCACTGCATCCACCC
1177079 TTC
1 TTC
1177082 AAGACAGACT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (82 bp):
TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT
TATCACTGCATCCACCC
Found at i:1177576 original size:21 final size:21
Alignment explanation
Indices: 1177546--1177593 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1177536 TAATTTTCAA
*
1177546 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1177567 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1177588 ACATTG
1 ACATTG
1177594 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1182193 original size:21 final size:21
Alignment explanation
Indices: 1182163--1182210 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1182153 TAATTTTCAA
*
1182163 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1182184 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1182205 ACATTG
1 ACATTG
1182211 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1183326 original size:40 final size:40
Alignment explanation
Indices: 1183271--1183356 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
1183261 TTACCACTCG
* * * *
1183271 GGATGAATTTTACTTTGGATTATTAGTGTATTCACCTTTC
1 GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC
*
1183311 GGATGAATTTCACTTTGGAATATTAGTGGGTTCACCATTC
1 GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC
1183351 GAGATG
1 G-GATG
1183357 TTTAAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (40 bp):
GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC
Found at i:1184073 original size:21 final size:21
Alignment explanation
Indices: 1184038--1184079 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1184028 GCACTAATAC
*
1184038 ACTAAAGTGCCTTAGCGTTGA
1 ACTAAAGTGCCTTAGCATTGA
**
1184059 ACTAAAGTGTTTTAGCATTGA
1 ACTAAAGTGCCTTAGCATTGA
1184080 TGGGTGAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTAAAGTGCCTTAGCATTGA
Found at i:1187050 original size:76 final size:77
Alignment explanation
Indices: 1186883--1187174 Score: 333
Period size: 77 Copynumber: 3.8 Consensus size: 77
1186873 AAAAGCTGAA
* * * * **
1186883 AATGTCATGGTTCACTGAGAAACATGTTGCGATCTAGAATTTTACTATTTTTATTAATAAAATAA
1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG
* *
1186948 CTTGCGCCCAAG
66 GTTGCGCACAAG
* * *
1186960 AATGTCATGATTCACTGAGAAATATGTTACGATCTAGAATGTTAATA-TTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG
* *
1187024 GTTGCGCTCAAT
66 GTTGCGCACAAG
* * * * *
1187036 AATGTCATGGTTCACTAATAAATAGGTTGCGATTTGGAATGTTAATATTTTTATAAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG
*
1187101 GTTGCACACAAG
66 GTTGCGCACAAG
*
1187113 AATGTTATGGTTCACTAAGAAAGTGA-GTTGCGATCT-GTAATGTTAAT-TTTTCTATT-ATAAA
1 AATGTCATGGTTCACTAAGAAA-T-ATGTTGCGATCTAG-AATGTTAATATTTT-TATTAATAAA
1187174 A
62 A
1187175 AATTCGAAAG
Statistics
Matches: 185, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
76 64 0.35
77 98 0.53
78 22 0.12
79 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (77 bp):
AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG
GTTGCGCACAAG
Found at i:1187436 original size:123 final size:124
Alignment explanation
Indices: 1187276--1187499 Score: 342
Period size: 124 Copynumber: 1.8 Consensus size: 124
1187266 TTTACAAAAA
1187276 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTAT-AAATTCAAAAGTAT
1 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT
* *
1187340 CGATACTTTTGAAAAAATATTCATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG
66 AGATACTTTTGAAAAAATATACATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG
* * * ** * *
1187399 TATCGATACTTTTAACTTTGAAATTTAAAATATCATTTTTTATTTTTTTTAAAATTCAAAATTAT
1 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT
* *
1187464 AGATACTTTTGAAAAAGTATACTTACTTTCGAATTT
66 AGATACTTTTGAAAAAATATACATACTTTCGAATTT
1187500 TTTATAATAG
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
123 44 0.49
124 45 0.51
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (124 bp):
TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT
AGATACTTTTGAAAAAATATACATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG
Found at i:1187553 original size:17 final size:17
Alignment explanation
Indices: 1187531--1187564 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1187521 TTTCAGATCG
1187531 CAACTTGTTTTCTTTGT
1 CAACTTGTTTTCTTTGT
1187548 CAACTTGTTTTCTTTGT
1 CAACTTGTTTTCTTTGT
1187565 GAATCATAAT
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:0.12, C:0.18, G:0.12, T:0.59
Consensus pattern (17 bp):
CAACTTGTTTTCTTTGT
Found at i:1187763 original size:77 final size:77
Alignment explanation
Indices: 1187592--1187924 Score: 363
Period size: 77 Copynumber: 4.4 Consensus size: 77
1187582 TGTGCAGTCT
* * * *
1187592 ATTTTATTTATAAAATTATTAACATTCCATATCACAACTTATTTATTAGTG-ATCATTGACA-T-
1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCA-TGACATTC
* *
1187654 TTGGGCGCAACCC
65 TTGGACGCAACTC
* * * *
1187667 ATTTTATTAATAAAAATATTAATATTCCATATCGCATCCTATTTATTAATGAACCATGACATTCT
1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT
* *
1187732 TGGGCGTAACTC
66 TGGACGCAACTC
* * * * * *
1187744 ATTTTATTAATAAAAATATTAACATTTCAGATCACAACCTTTTTCTTAGTAAATCATGACATTCT
1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT
*
1187809 TGAACGCAACAT-
66 TGGACGCAAC-TC
* *** * *
1187821 ATTTTATTAATAAAAATATTAACATTCCAAATTGTAACCTAATTCTTAATGAAAT-ATGACATTC
1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATG-AATCATGACATTC
1187885 TTGGACGCAAC-C
65 TTGGACGCAACTC
1187897 AATTTTATTAATAAAAATATTAACATTC
1 -ATTTTATTAATAAAAATATTAACATTC
1187925 TAGATTATAT
Statistics
Matches: 218, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
75 49 0.22
76 4 0.02
77 161 0.74
78 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (77 bp):
ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT
TGGACGCAACTC
Found at i:1187884 original size:154 final size:152
Alignment explanation
Indices: 1187592--1187929 Score: 412
Period size: 154 Copynumber: 2.2 Consensus size: 152
1187582 TGTGCAGTCT
* * * *
1187592 ATTTTATTTATAAAATTATTAACATTCCATATCACAACTTATTTATTAGTGATCATTGACATTTG
1 ATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTATTAGTAATCATTGACATTTG
** * * * * * *
1187657 GGCGCAACCCATTTTATTAATAAAAATATTAATATTCCATATCGCATCCTATTTATTAATGAACC
66 AACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATGAAAC
* *
1187722 ATGACATTCTTGGGCGTAACTC-
131 ATGACATTCTTGGACGCAAC-CA
* *
1187744 ATTTTATTAATAAAAATATTAACATTTCAGATCACAACCTT-TTTCTTAGTAAATCA-TGACATT
1 ATTTTATTAATAAAAATATTAACATTCCAGATCACAA-CTTATTTATTAGT-AATCATTGACA-T
* * * *
1187807 CTTGAACGCAACATATTTTATTAATAAAAATATTAACATTCCAAATTGTAACCTAATTCTTAATG
63 -TTGAACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATG
*
1187872 AAATATGACATTCTTGGACGCAACCA
127 AAACATGACATTCTTGGACGCAACCA
*
1187898 ATTTTATTAATAAAAATATTAACATTCTAGAT
1 ATTTTATTAATAAAAATATTAACATTCCAGAT
1187930 TATATGTTTC
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
152 46 0.29
153 9 0.06
154 103 0.65
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (152 bp):
ATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTATTAGTAATCATTGACATTTG
AACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATGAAAC
ATGACATTCTTGGACGCAACCA
Found at i:1187924 original size:40 final size:40
Alignment explanation
Indices: 1187725--1187925 Score: 102
Period size: 40 Copynumber: 5.2 Consensus size: 40
1187715 ATGAACCATG
* *
1187725 ACATTCTTGGGCGTAACTC-ATTTTATTAATAAAAATATTA
1 ACATTCTTGGACGCAAC-CAATTTTATTAATAAAAATATTA
** * * * * *
1187765 ACATT-TCAGATCACAACC-TTTTTCTTAGT--AAATCA-TG
1 ACATTCTTGGA-CGCAACCAATTTTATTAATAAAAAT-ATTA
*
1187802 ACATTCTTGAACGCAA-CATATTTTATTAATAAAAATATTA
1 ACATTCTTGGACGCAACCA-ATTTTATTAATAAAAATATTA
*** * * * * *
1187842 ACATTC-CAAATTGTAACCTAA--TTCTTAAT-GAAATA-TG
1 ACATTCTTGGA-CGCAACC-AATTTTATTAATAAAAATATTA
1187879 ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA
1 ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA
1187919 ACATTCT
1 ACATTCT
1187926 AGATTATATG
Statistics
Matches: 113, Mismatches: 32, Indels: 32
0.64 0.18 0.18
Matches are distributed among these distances:
36 3 0.03
37 26 0.23
38 24 0.21
39 26 0.23
40 31 0.27
41 2 0.02
42 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.37
Consensus pattern (40 bp):
ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA
Found at i:1205754 original size:24 final size:24
Alignment explanation
Indices: 1205722--1205770 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1205712 GAAACAACTT
1205722 GTAACAGATGAGATTAAAAGAGTA
1 GTAACAGATGAGATTAAAAGAGTA
1205746 GTAACAGATGAGATTAAAAGAGTA
1 GTAACAGATGAGATTAAAAGAGTA
1205770 G
1 G
1205771 CAAGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (24 bp):
GTAACAGATGAGATTAAAAGAGTA
Found at i:1206134 original size:20 final size:20
Alignment explanation
Indices: 1206109--1206240 Score: 108
Period size: 20 Copynumber: 6.6 Consensus size: 20
1206099 AACACAGAAA
1206109 TCAAATTCGCAACGC-GATAG
1 TCAAATTCGCAACGCGGA-AG
* * * *
1206129 TCAAATTCGTAACACAGAAT
1 TCAAATTCGCAACGCGGAAG
* * * **
1206149 TCAAATTTGTAACACAAAAG
1 TCAAATTCGCAACGCGGAAG
*
1206169 TCAAATT-GATAACGC-GATAG
1 TCAAATTCG-CAACGCGGA-AG
* *
1206189 TCAAATTCACAATGCGGAAG
1 TCAAATTCGCAACGCGGAAG
1206209 TCAAATTCGCAACGCGGAAG
1 TCAAATTCGCAACGCGGAAG
1206229 TCAAATTCGCAA
1 TCAAATTCGCAA
1206241 AGCAGAACAA
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.02
20 88 0.94
21 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (20 bp):
TCAAATTCGCAACGCGGAAG
Found at i:1206153 original size:40 final size:39
Alignment explanation
Indices: 1206095--1206240 Score: 125
Period size: 40 Copynumber: 3.7 Consensus size: 39
1206085 TATTTGTAAA
*
1206095 TCGTAACACAGAAATCAAATTCGCAACGCGATAGTCAAAT
1 TCGTAACACAGAAGTCAAATTCGCAACGCGA-AGTCAAAT
* * * * *
1206135 TCGTAACACAGAATTCAAATTTGTAACACAAAAGTCAAAT
1 TCGTAACACAGAAGTCAAATTCGCAACGC-GAAGTCAAAT
* * *
1206175 T-GATAACGC-GATAGTCAAATTCACAATGCGGAAGTCAAAT
1 TCG-TAACACAGA-AGTCAAATTCGCAACGC-GAAGTCAAAT
* * *
1206215 TCGCAACGCGGAAGTCAAATTCGCAA
1 TCGTAACACAGAAGTCAAATTCGCAA
1206241 AGCAGAACAA
Statistics
Matches: 85, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
39 3 0.04
40 78 0.92
41 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (39 bp):
TCGTAACACAGAAGTCAAATTCGCAACGCGAAGTCAAAT
Found at i:1206213 original size:60 final size:60
Alignment explanation
Indices: 1206097--1206240 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 60
1206087 TTTGTAAATC
** *
1206097 GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCGTAACACAGAATTCAAATTT
1 GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT
* ** * *
1206157 GTAACACA-AAAGTCAAATT-GATAACGCGATAGTCAAATTCACAATGCGGAAGTCAAATTC
1 GTAACACAGAAA-TCAAATTCG-CAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT
* * * *
1206217 GCAACGCGGAAGTCAAATTCGCAA
1 GTAACACAGAAATCAAATTCGCAA
1206241 AGCAGAACAA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
59 4 0.06
60 60 0.90
61 3 0.04
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (60 bp):
GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT
Found at i:1206385 original size:22 final size:20
Alignment explanation
Indices: 1206350--1206392 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1206340 TCACTCTCTA
*
1206350 CGGCGACATCCGTCCCTATCTC
1 CGGCGAAATCCGT--CTATCTC
*
1206372 CGGCGAAATTCGTCTATCTC
1 CGGCGAAATCCGTCTATCTC
1206392 C
1 C
1206393 ATCTCTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.16, C:0.40, G:0.19, T:0.26
Consensus pattern (20 bp):
CGGCGAAATCCGTCTATCTC
Found at i:1209005 original size:21 final size:21
Alignment explanation
Indices: 1208958--1209056 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
1208948 GATGCACCTA
* **
1208958 TCATCATTCAAGAGTCATCTC
1 TCATCATTCAAGAGGCCCCTC
1208979 -CTATCATTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
*
1209000 TCATCA-TCGAAGAAGCCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * * *
1209021 CCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
*
1209042 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
1209057 TCCCGCCCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:1209005 original size:42 final size:41
Alignment explanation
Indices: 1208958--1209055 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 41
1208948 GATGCACCTA
* * *
1208958 TCATCATTCAAGAGTCATCTCCTATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAG-CACCTCCCACCATTCAAGAGGCCCCTC
* * *
1209000 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAG-AGCACCTCCCACCATTCAAGAGGCCCCTC
*
1209042 TCATCGTTCAAGAG
1 TCATCATTCAAGAG
1209056 GTCCCGCCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
41 4 0.09
42 38 0.83
43 4 0.09
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (41 bp):
TCATCATTCAAGAGCACCTCCCACCATTCAAGAGGCCCCTC
Found at i:1209070 original size:42 final size:42
Alignment explanation
Indices: 1208985--1209076 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1208975 TCTCCTATCA
*
1208985 TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACCG
* * * * *
1209027 TTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGCCCGCCG
1 TTCAAGAGGCCCCTCTCATC-ATCGAAGAAGCCCCGCCCACCG
1209069 TTCAAGAG
1 TTCAAGAG
1209077 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACCG
Found at i:1210551 original size:66 final size:65
Alignment explanation
Indices: 1210392--1210567 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
1210382 TGGTGTACAC
1210392 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
1210456 TAATTA
60 TAATTA
* *
1210462 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAATAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAATAATT
1210526 A
65 A
1210527 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1210568 GTTTTAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 40 0.40
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTA
Found at i:1210678 original size:20 final size:20
Alignment explanation
Indices: 1210630--1210678 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1210620 ACAAATTCAT
1210630 AACGCGAAAGGTAAATTCGC
1 AACGCGAAAGGTAAATTCGC
* *
1210650 AAAGTGAAA-GTAAAATTCGC
1 AACGCGAAAGGT-AAATTCGC
1210670 AACGCGAAA
1 AACGCGAAA
1210679 TAAGCGCTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (20 bp):
AACGCGAAAGGTAAATTCGC
Found at i:1213453 original size:24 final size:24
Alignment explanation
Indices: 1213402--1213455 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1213392 ACATCATCAT
** *
1213402 TGACTAAGATCAAAGTCCGGGTAT
1 TGACTAAGATCAAAGTCCGAATAC
* *
1213426 TGACTAAGATCAAATTTCGAATAC
1 TGACTAAGATCAAAGTCCGAATAC
1213450 TGACTA
1 TGACTA
1213456 GTACTCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (24 bp):
TGACTAAGATCAAAGTCCGAATAC
Found at i:1213586 original size:12 final size:12
Alignment explanation
Indices: 1213565--1213598 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1213555 GGTTGTGGGT
*
1213565 TTTGAGATTGTG
1 TTTGATATTGTG
1213577 TTTGATATTGTG
1 TTTGATATTGTG
*
1213589 TTTGGTATTG
1 TTTGATATTG
1213599 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1214412 original size:19 final size:18
Alignment explanation
Indices: 1214369--1214415 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1214359 CAAAACATTT
1214369 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
1214387 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
1214406 GTGTTGCGAA
1 GTGTTGCGAA
1214416 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:1214449 original size:19 final size:19
Alignment explanation
Indices: 1214408--1214459 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1214398 TTAAATTCGT
*
1214408 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTG-AAATCTA
1214428 GTTGCGAATTTGAAAT-TAA
1 GTTGCGAATTTGAAATCT-A
*
1214447 GTTACGAATTTGA
1 GTTGCGAATTTGA
1214460 CTTTTGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.03
19 17 0.59
20 11 0.38
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATCTA
Found at i:1214476 original size:20 final size:20
Alignment explanation
Indices: 1214451--1214493 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1214441 AATTAAGTTA
*
1214451 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTCTGTGTTG
1214471 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
1214491 CGA
1 CGA
1214494 TTTACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (20 bp):
CGAATTTGACTTCTGTGTTG
Found at i:1214536 original size:20 final size:20
Alignment explanation
Indices: 1214511--1214560 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1214501 ATTCGCGTTG
1214511 CGAAATTGGAAACTGTGTTA
1 CGAAATTGGAAACTGTGTTA
*
1214531 CGAAATTGGAAACTGTGTTG
1 CGAAATTGGAAACTGTGTTA
1214551 CGAAATTGGA
1 CGAAATTGGA
1214561 GTTTGCGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (20 bp):
CGAAATTGGAAACTGTGTTA
Found at i:1214570 original size:20 final size:20
Alignment explanation
Indices: 1214505--1214574 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1214495 TTACAAATTC
1214505 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* *
1214525 GTGTTACGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* ***
1214545 GTGTTGCGAAATTGGAGTTT
1 GCGTTGCGAAATTGGAAACT
1214565 GCGTTGCGAA
1 GCGTTGCGAA
1214575 TTTGTTGGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:1216922 original size:2 final size:2
Alignment explanation
Indices: 1216915--1216950 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1216905 GAGGGAAAAC
1216915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1216951 AACTTAACAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1218375 original size:21 final size:21
Alignment explanation
Indices: 1218345--1218397 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1218335 TTTAAACAAT
*
1218345 AACTAAAATAAATGAAAT-TAA
1 AACTATAATAAATGAAATAT-A
*
1218366 AACTATAAT-ATTGAAATATA
1 AACTATAATAAATGAAATATA
*
1218386 AACAATAATAAA
1 AACTATAATAAA
1218398 ATTTGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (21 bp):
AACTATAATAAATGAAATATA
Found at i:1219779 original size:3 final size:3
Alignment explanation
Indices: 1219766--1219817 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1219756 ATTTATTATT
* *
1219766 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA -AA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1219812 TAA TAA
1 TAA TAA
1219818 ATCAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1219780 original size:9 final size:8
Alignment explanation
Indices: 1219773--1219831 Score: 57
Period size: 9 Copynumber: 6.9 Consensus size: 8
1219763 ATTTAATAAA
1219773 AATAATAAT
1 AATAA-AAT
1219782 AATAATAAT
1 AATAA-AAT
1219791 AATAAAAT
1 AATAAAAT
1219799 AATAAAAT
1 AATAAAAT
*
1219807 AATTATAAT
1 AA-TAAAAT
1219816 AAATCAAAA-
1 -AAT-AAAAT
1219825 AATAAAA
1 AATAAAA
1219832 CACAAATGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
7 4 0.09
8 16 0.36
9 20 0.44
10 5 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:1221028 original size:80 final size:79
Alignment explanation
Indices: 1220929--1221083 Score: 247
Period size: 80 Copynumber: 1.9 Consensus size: 79
1220919 TTGCGCGTTC
* *
1220929 TTGATTTGAGTATTTTGTTTAGGGTTGCGAGATCTATATAAAATTTGGGTTAGATTTAAGTAATG
1 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAA-TTAGGTTAGATTTAAGTAATG
*
1220994 TTTGCATTTTGGTTA
65 TTTACATTTTGGTTA
* * *
1221009 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATGTAAAATTAGGTTTGATTTACGTAATGT
1 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGT
1221074 TTACATTTTG
66 TTACATTTTG
1221084 TTTACTAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 28 0.41
80 41 0.59
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.47
Consensus pattern (79 bp):
TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGT
TTACATTTTGGTTA
Found at i:1223390 original size:18 final size:18
Alignment explanation
Indices: 1223358--1223392 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1223348 TTCATTGCCA
**
1223358 TGGATTACATGACTGTTC
1 TGGATTACAAAACTGTTC
1223376 TGGATTACAAAACTGTT
1 TGGATTACAAAACTGTT
1223393 TTTGCATAAT
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:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
TGGATTACAAAACTGTTC
Found at i:1227940 original size:34 final size:34
Alignment explanation
Indices: 1227897--1227963 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1227887 GATGAACTAT
*
1227897 CAATTTAGGGCATTGAATATCGGAACTCTATGTC
1 CAATTTAGGGCATTGAATATCGGAACCCTATGTC
*
1227931 CAATTTAGGGTATTGAATATCGGAACCCTATGT
1 CAATTTAGGGCATTGAATATCGGAACCCTATGT
1227964 GCTTGCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (34 bp):
CAATTTAGGGCATTGAATATCGGAACCCTATGTC
Found at i:1241119 original size:18 final size:18
Alignment explanation
Indices: 1241093--1241138 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1241083 TCACGGAATG
* *
1241093 TAAGATTACTGGCGTGAA
1 TAAGATTACTGACGAGAA
* *
1241111 TAGGATTACCGACGAGAA
1 TAAGATTACTGACGAGAA
1241129 TAAGATTACT
1 TAAGATTACT
1241139 AGGAATGTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (18 bp):
TAAGATTACTGACGAGAA
Found at i:1241844 original size:20 final size:20
Alignment explanation
Indices: 1241805--1241845 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1241795 CCAGATCAGT
**
1241805 CCAAGATGTAGGGTGTAAGC
1 CCAAGATGTAGGGTCAAAGC
*
1241825 CCAAGATGTTGGGTCAAAGC
1 CCAAGATGTAGGGTCAAAGC
1241845 C
1 C
1241846 TTACCCCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (20 bp):
CCAAGATGTAGGGTCAAAGC
Found at i:1245195 original size:18 final size:19
Alignment explanation
Indices: 1245172--1245209 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1245162 CGCTTCTTCT
1245172 CTACTTAT-AGTATCGATA
1 CTACTTATCAGTATCGATA
*
1245190 CTACTTTTCAGTATCGATA
1 CTACTTATCAGTATCGATA
1245209 C
1 C
1245210 CTATTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (19 bp):
CTACTTATCAGTATCGATA
Found at i:1251232 original size:22 final size:22
Alignment explanation
Indices: 1251183--1251232 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1251173 CAACATGTTC
*
1251183 TTCATACACCCAAATCATGTAA
1 TTCATCCACCCAAATCATGTAA
1251205 TTCATCCACCCAAATCATGTAA
1 TTCATCCACCCAAATCATGTAA
1251227 TTCATC
1 TTCATC
1251233 ATTCAGGCAT
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:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (22 bp):
TTCATCCACCCAAATCATGTAA
Found at i:1257884 original size:22 final size:22
Alignment explanation
Indices: 1257855--1257914 Score: 59
Period size: 27 Copynumber: 2.5 Consensus size: 22
1257845 GTGTAAATTA
1257855 TTTTGGTTGTTTGA-TGTTTTG
1 TTTTGGTTGTTTGATTGTTTTG
1257876 TTTTCGGTTGTTAGCTTGATTGTTTTG
1 TTTT-GGTTG-T---TTGATTGTTTTG
1257903 TTTTTGGTTGTT
1 -TTTTGGTTGTT
1257915 GGCTTGACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
21 4 0.12
22 5 0.16
23 2 0.06
26 5 0.16
27 12 0.38
28 4 0.12
ACGTcount: A:0.05, C:0.03, G:0.27, T:0.65
Consensus pattern (22 bp):
TTTTGGTTGTTTGATTGTTTTG
Found at i:1257902 original size:27 final size:26
Alignment explanation
Indices: 1257865--1257931 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 26
1257855 TTTTGGTTGT
1257865 TTGATGTTTTGTTTTCGGTTGTTAGC
1 TTGATGTTTTGTTTTCGGTTGTTAGC
* *
1257891 TTGATTGTTTTGTTTTTGGTTGTTGGC
1 TTGA-TGTTTTGTTTTCGGTTGTTAGC
1257918 TTGACTGTTTTGTT
1 TTGA-TGTTTTGTT
1257932 GTAGCATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.06, C:0.06, G:0.27, T:0.61
Consensus pattern (26 bp):
TTGATGTTTTGTTTTCGGTTGTTAGC
Found at i:1258449 original size:29 final size:29
Alignment explanation
Indices: 1258414--1258497 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
1258404 TTAAATTTTT
**
1258414 AAAAGTTATAAAATCGTTATTG-AAGTTTC
1 AAAAGTTATAAAATAATTATTGTAA-TTTC
* *
1258443 AGAAGTTATAAAATAATTATTGTAATTTT
1 AAAAGTTATAAAATAATTATTGTAATTTC
1258472 AAAAGTTATAAAATAATTATT-TAATT
1 AAAAGTTATAAAATAATTATTGTAATT
1258498 AATCGGACTG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.10
29 42 0.86
30 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (29 bp):
AAAAGTTATAAAATAATTATTGTAATTTC
Found at i:1259118 original size:20 final size:20
Alignment explanation
Indices: 1259093--1259166 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
1259083 ATCCGACTCG
1259093 AAATATTATATTTATTAAAA
1 AAATATTATATTTATTAAAA
*
1259113 AAATATTATTTTTATTCAATAA
1 AAATATTATATTTATT-AA-AA
* *
1259135 AAATA-GAGATTTAATTAAAA
1 AAATATTATATTT-ATTAAAA
*
1259155 ATAATAATATAT
1 A-AATATTATAT
1259167 AAAAAGATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 18 0.42
21 12 0.28
22 13 0.30
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATTATATTTATTAAAA
Found at i:1259834 original size:188 final size:188
Alignment explanation
Indices: 1259517--1259892 Score: 752
Period size: 188 Copynumber: 2.0 Consensus size: 188
1259507 TTTCCCCAGG
1259517 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT
1 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT
1259582 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG
66 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG
1259647 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT
131 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT
1259705 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT
1 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT
1259770 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG
66 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG
1259835 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT
131 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT
1259893 CCTCCTGCGA
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 188 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (188 bp):
TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT
TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG
AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT
Found at i:1261591 original size:84 final size:85
Alignment explanation
Indices: 1261450--1261609 Score: 313
Period size: 84 Copynumber: 1.9 Consensus size: 85
1261440 TGGAAGAAAA
1261450 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACC-AAACG
1 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG
1261514 ATGAAGACGTAAATGCATAG
66 ATGAAGACGTAAATGCATAG
1261534 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG
1 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG
1261599 ATGAAGACGTA
66 ATGAAGACGTA
1261610 GAAATATGCA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 59 0.79
85 16 0.21
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (85 bp):
AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG
ATGAAGACGTAAATGCATAG
Found at i:1264215 original size:17 final size:18
Alignment explanation
Indices: 1264178--1264216 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1264168 ATATTTTGTA
1264178 TTTAAATTATTTAAGTAT
1 TTTAAATTATTTAAGTAT
*
1264196 TTTAATTTATTTAA-TAT
1 TTTAAATTATTTAAGTAT
1264213 TTTA
1 TTTA
1264217 CTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAAATTATTTAAGTAT
Found at i:1265968 original size:50 final size:50
Alignment explanation
Indices: 1265894--1265993 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
1265884 AGCAGCCACC
*
1265894 GTATCCAGCGACTTACATACCGCAACCATAAATGATGCCGCCA-CGCCTT
1 GTATCCAGCGACCTACATACCGCAACCATAAATGATGCCGCCACCGCCTT
1265943 GTATCCAGCGACACTACATACCGCAACCATAAATGATGCCGCCACCGCCTT
1 GTATCCAGCGAC-CTACATACCGCAACCATAAATGATGCCGCCACCGCCTT
1265994 TCCATTACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 12 0.25
50 30 0.62
51 6 0.12
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19
Consensus pattern (50 bp):
GTATCCAGCGACCTACATACCGCAACCATAAATGATGCCGCCACCGCCTT
Found at i:1269727 original size:34 final size:34
Alignment explanation
Indices: 1269684--1269768 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1269674 TATGATTGAT
1269684 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
1269718 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
1269752 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
1269769 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:1269874 original size:23 final size:23
Alignment explanation
Indices: 1269844--1269887 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1269834 TTGAGCAGGG
1269844 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
1269867 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
1269888 GCATGCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:1269894 original size:23 final size:22
Alignment explanation
Indices: 1269841--1269894 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
1269831 GGGTTGAGCA
1269841 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
1269863 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
1269886 GGGCATGCA
1 GGGC-TGCA
1269895 ATTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:1270099 original size:41 final size:41
Alignment explanation
Indices: 1270042--1270119 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1270032 GAGACTGCTA
*
1270042 GGGCTAAGGCAATTCACAATTACAGAAGTAGTGAGAGTTTG
1 GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
*
1270083 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1 GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAG
1270120 CCTGAGAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.21
Consensus pattern (41 bp):
GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
Found at i:1270617 original size:20 final size:20
Alignment explanation
Indices: 1270592--1270632 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1270582 TTATAAAAAG
*
1270592 TTAGTA-TACTATGCTTGAAT
1 TTAGTATTAATATGCTT-AAT
1270612 TTAGTATTAATATGCTTAAT
1 TTAGTATTAATATGCTTAAT
1270632 T
1 T
1270633 GGTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (20 bp):
TTAGTATTAATATGCTTAAT
Found at i:1270649 original size:172 final size:173
Alignment explanation
Indices: 1270362--1270720 Score: 564
Period size: 172 Copynumber: 2.1 Consensus size: 173
1270352 TTGTAAAGTT
* * *
1270362 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGATAT
1 TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATAT
*
1270427 ACTATGCTGAAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
1270490 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* *
1270534 TTAGGGATCGTTTTGTAAAATTTGAGAAATTTAAGGAATTAGAGTAAATTATAAAAAGTT-AGTA
1 TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGA-TA
*
1270598 TACTATGCTTG-AATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA
65 TACTATGC-TGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTA
* *
1270662 GTGATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
129 GTGATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
1270707 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
1270721 ATATTTGATG
Statistics
Matches: 172, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
171 1 0.01
172 108 0.63
173 62 0.36
174 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATAT
ACTATGCTGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:1272976 original size:14 final size:14
Alignment explanation
Indices: 1272959--1273642 Score: 99
Period size: 14 Copynumber: 48.3 Consensus size: 14
1272949 AAGTCAAGTA
1272959 ATTATTATTAAATC
1 ATTATTATTAAATC
**
1272973 ATTAAAATTAAATC
1 ATTATTATTAAATC
** * *
1272987 ATTAAAATTAAGTA
1 ATTATTATTAAATC
1273001 ATTATTATT-AA--
1 ATTATTATTAAATC
1273012 ATTATTA--AAAT-
1 ATTATTATTAAATC
* * * *
1273023 A-AATCATTAAGTA
1 ATTATTATTAAATC
1273036 ATTATTATTAAATC
1 ATTATTATTAAATC
*
1273050 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
*
1273066 ATTAATCATT-AA--
1 ATT-ATTATTAAATC
*
1273078 ATTATTATTAAAGC
1 ATTATTATTAAATC
*
1273092 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
1273106 ---ATTA--AAGTA
1 ATTATTATTAAATC
1273115 ATTATTATTAAATC
1 ATTATTATTAAATC
* * *
1273129 ATTAAATCTTAAAGTA
1 ATT-ATTATTAAA-TC
*
1273145 ATTATTATTAAAAC
1 ATTATTATTAAATC
*
1273159 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* * *
1273173 ATTA-AAGTAATTATT
1 ATTATTATTAA--ATC
* *
1273188 ATTAATCATTAAAGTA
1 ATT-ATTATTAAA-TC
1273204 ATTATTATTAAATC
1 ATTATTATTAAATC
*
1273218 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
1273232 ATTAAATCATTAAATT
1 ATT--ATTATTAAATC
* * * *
1273248 A-AATCATTAAGTA
1 ATTATTATTAAATC
1273261 ATTATTATTAAATC
1 ATTATTATTAAATC
**
1273275 ATTAAAATT-AATC
1 ATTATTATTAAATC
* * *
1273288 ATTA-AAGTAATTATT
1 ATTATTATTAA--ATC
* *
1273303 ATTAATCATTAAAGTT
1 ATT-ATTATTAAA-TC
* * *
1273319 A-AATCATTAAAGTA
1 ATTATTATTAAA-TC
1273333 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
1273347 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
1273361 ATTATTA-TAAATC
1 ATTATTATTAAATC
*
1273374 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* * *
1273388 ATTA-AAGTAATATT
1 ATTATTATTAA-ATC
*
1273402 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
1273418 ATAAATCATTAAAGT-
1 AT-TATTATTAAA-TC
1273433 ATTATTATTAAATC
1 ATTATTATTAAATC
*
1273447 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
1273461 ATTAATCATTAAAATTAAATC
1 A-T--T-ATT---ATTAAATC
*
1273482 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
*
1273496 ATTAAATCATTAAA--
1 ATT--ATTATTAAATC
* *
1273510 ATTAATCATTAAAGTA
1 ATT-ATTATTAAA-TC
1273526 ATTATTATTAAATC
1 ATTATTATTAAATC
** *
1273540 ATTAAAATTCAATC
1 ATTATTATTAAATC
* *
1273554 ATTAAAGTATT--ATT
1 ATT--ATTATTAAATC
* * *
1273568 ATTAATCATTAAGTT
1 ATT-ATTATTAAATC
* *
1273583 A-AATTATTAAAGTA
1 ATTATTATTAAA-TC
1273597 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
1273611 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
1273625 ATTATTATTAAATC
1 ATTATTATTAAATC
1273639 ATTA
1 ATTA
1273643 AAGTTATAAT
Statistics
Matches: 499, Mismatches: 98, Indels: 146
0.67 0.13 0.20
Matches are distributed among these distances:
9 3 0.01
10 5 0.01
11 14 0.03
12 17 0.03
13 66 0.13
14 230 0.46
15 83 0.17
16 53 0.11
17 16 0.03
18 2 0.00
20 1 0.00
21 8 0.02
22 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:1272978 original size:8 final size:8
Alignment explanation
Indices: 1272965--1273559 Score: 216
Period size: 8 Copynumber: 81.8 Consensus size: 8
1272955 AGTAATTATT
1272965 ATTAAATC
1 ATTAAATC
1272973 ATTAAA--
1 ATTAAATC
1272979 ATTAAATC
1 ATTAAATC
1272987 ATTAAA--
1 ATTAAATC
* *
1272993 ATTAAGTA
1 ATTAAATC
*
1273001 ATT--ATT
1 ATTAAATC
*
1273007 ATTAAATT
1 ATTAAATC
1273015 ATTAAA--
1 ATTAAATC
1273021 A-TAAATC
1 ATTAAATC
* *
1273028 ATTAAGTA
1 ATTAAATC
*
1273036 ATT--ATT
1 ATTAAATC
1273042 ATTAAATC
1 ATTAAATC
1273050 ATTAAATC
1 ATTAAATC
1273058 ATTAAATC
1 ATTAAATC
1273066 ATT-AATC
1 ATTAAATC
*
1273073 ATTAAATTATT
1 ATT-AA--ATC
*
1273084 ATTAAAGC
1 ATTAAATC
1273092 ATTAAA--
1 ATTAAATC
*
1273098 GTTAAATC
1 ATTAAATC
*
1273106 ATTAAAGTA
1 ATTAAA-TC
*
1273115 ATT--ATT
1 ATTAAATC
1273121 ATTAAATC
1 ATTAAATC
1273129 ATTAAATC
1 ATTAAATC
*
1273137 -TTAAAGTA
1 ATTAAA-TC
*
1273145 ATT--ATT
1 ATTAAATC
*
1273151 ATTAAAAC
1 ATTAAATC
1273159 ATTAAA--
1 ATTAAATC
*
1273165 GTTAAATC
1 ATTAAATC
*
1273173 ATTAAAGTA
1 ATTAAA-TC
*
1273182 ATT--ATT
1 ATTAAATC
1273188 ATT-AATC
1 ATTAAATC
*
1273195 ATTAAAGTA
1 ATTAAA-TC
*
1273204 ATT--ATT
1 ATTAAATC
1273210 ATTAAATC
1 ATTAAATC
1273218 ATTAAA--
1 ATTAAATC
*
1273224 GTTAAATC
1 ATTAAATC
1273232 ATTAAATC
1 ATTAAATC
1273240 ATT-AA--
1 ATTAAATC
1273245 ATTAAATC
1 ATTAAATC
* *
1273253 ATTAAGTA
1 ATTAAATC
*
1273261 ATT--ATT
1 ATTAAATC
1273267 ATTAAATC
1 ATTAAATC
1273275 ATTAAA--
1 ATTAAATC
1273281 ATT-AATC
1 ATTAAATC
*
1273288 ATTAAAGTA
1 ATTAAA-TC
*
1273297 ATT--ATT
1 ATTAAATC
1273303 ATT-AATC
1 ATTAAATC
1273310 ATTAAA--
1 ATTAAATC
*
1273316 GTTAAATC
1 ATTAAATC
*
1273324 ATTAAAGTA
1 ATTAAA-TC
*
1273333 ATT--ATT
1 ATTAAATC
1273339 ATTAAATC
1 ATTAAATC
1273347 ATTAAA--
1 ATTAAATC
* *
1273353 GTTAAATA
1 ATTAAATC
*
1273361 ATT--ATT
1 ATTAAATC
1273367 A-TAAATC
1 ATTAAATC
1273374 ATTAAA--
1 ATTAAATC
*
1273380 GTTAAATC
1 ATTAAATC
1273388 ATTAAAGT-
1 ATTAAA-TC
* *
1273396 A--ATATT
1 ATTAAATC
1273402 ATTAAATC
1 ATTAAATC
1273410 ATTAAATC
1 ATTAAATC
1273418 A-TAAATC
1 ATTAAATC
1273425 ATTAAAGT-
1 ATTAAA-TC
*
1273433 ATT--ATT
1 ATTAAATC
1273439 ATTAAATC
1 ATTAAATC
1273447 ATTAAA--
1 ATTAAATC
*
1273453 GTTAAATC
1 ATTAAATC
1273461 ATT-AATC
1 ATTAAATC
1273468 ATTAAA--
1 ATTAAATC
1273474 ATTAAATC
1 ATTAAATC
1273482 ATTAAA--
1 ATTAAATC
*
1273488 GTTAAATC
1 ATTAAATC
1273496 ATTAAATC
1 ATTAAATC
1273504 ATTAAA--
1 ATTAAATC
1273510 ATT-AATC
1 ATTAAATC
*
1273517 ATTAAAGTA
1 ATTAAA-TC
*
1273526 ATT--ATT
1 ATTAAATC
1273532 ATTAAATC
1 ATTAAATC
1273540 ATTAAA--
1 ATTAAATC
*
1273546 ATTCAATC
1 ATTAAATC
1273554 ATTAAA
1 ATTAAA
1273560 GTATTATTAT
Statistics
Matches: 444, Mismatches: 62, Indels: 162
0.66 0.09 0.24
Matches are distributed among these distances:
5 14 0.03
6 121 0.27
7 55 0.12
8 218 0.49
9 29 0.07
10 2 0.00
11 5 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:1273172 original size:36 final size:37
Alignment explanation
Indices: 1273130--1273524 Score: 426
Period size: 35 Copynumber: 11.0 Consensus size: 37
1273120 TATTAAATCA
*
1273130 TTAAATC-TTAAAGTAATTATTATTAAAACATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273166 TTAAATCATTAAAGTAATTATTATT-AATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
1273202 TAATTATTATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAA-
1 ---------TTAAATCATTAAAG-TAATTATTATTAAATCATTAAAG
*
1273246 TTAAATCATT-AAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273282 TT-AATCATTAAAGTAATTATTATT-AATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273317 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273354 --------TTAAA-TAATTATTA-TAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273381 TTAAATCATTAAAGTAA-TATTATTAAATCATTAAA-
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273416 TCATAAATCATTAAAGT-ATTATTATTAAATCATTAAAG
1 T--TAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* **
1273454 TTAAATCATT-AA-TCATTAAAATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* **
1273489 TTAAATCATTAAA-TCATTAAAATT-AATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273524 T
1 T
1273525 AATTATTATT
Statistics
Matches: 319, Mismatches: 6, Indels: 69
0.81 0.02 0.18
Matches are distributed among these distances:
27 13 0.04
28 9 0.03
29 5 0.02
33 3 0.01
34 4 0.01
35 99 0.31
36 93 0.29
37 60 0.19
38 1 0.00
44 5 0.02
45 24 0.08
46 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:1273194 original size:22 final size:22
Alignment explanation
Indices: 1273169--1273317 Score: 140
Period size: 22 Copynumber: 6.5 Consensus size: 22
1273159 ATTAAAGTTA
1273169 AATCATTAAAGTAATTATTATT
1 AATCATTAAAGTAATTATTATT
1273191 AATCATTAAAGTAATTATTATT
1 AATCATTAAAGTAATTATTATT
*
1273213 AAATCATTAAAGTTAA--ATCATT
1 -AATCATTAAAG-TAATTATTATT
* * *
1273235 AAATCATTAAATTAAATCATTAAGT
1 -AATCATTAAAGT-AATTATT-ATT
* * * **
1273260 AATTATTATTAAATCATTAAAATT
1 AATCATTA--AAGTAATTATTATT
1273284 AATCATTAAAGTAATTATTATT
1 AATCATTAAAGTAATTATTATT
1273306 AATCATTAAAGT
1 AATCATTAAAGT
1273318 TAAATCATTA
Statistics
Matches: 103, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 62 0.60
23 11 0.11
24 21 0.20
25 5 0.05
26 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (22 bp):
AATCATTAAAGTAATTATTATT
Found at i:1273341 original size:129 final size:130
Alignment explanation
Indices: 1272993--1273628 Score: 718
Period size: 129 Copynumber: 4.9 Consensus size: 130
1272983 AATCATTAAA
* *
1272993 ATTAAGTAATTATTATTAAATTATTAAAATAAATCATT-AAGTAATTATTATTAAATCATTAAAT
1 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAA-
* * * * *
1273057 CATTAAATCATTAATCATTAAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTA
65 -GTTAAATCATTAA--AGT-AATTATTATTAAATCATTAAAGTTAAATCATTAAA-TCATTA-AA
1273122 TTAAATC
124 TTAAATC
* * * ** * * *
1273129 ATT-A--AA-TCTTA--AAGTAATTATTATTAAAACATTAAAGTTAA--ATCATTAAAGTAATTA
1 ATTAAGTAATTATTATTAAATCATTAAAATT-AATCATTAAAG-TAATTATTATTAAA-TCATTA
*
1273186 TTA-TT-AATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTA
63 -AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTA
1273249 AATC
127 AATC
1273253 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATT-AATCATTAAAG
1 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
1273317 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATAAATCATTAAAGT
66 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTT--A-AATCA-T-TAAATCATTAAA-T
1273382 TAAATC
125 TAAATC
*
1273388 ATTAAAGTAA-TATTATTAAATCATTAAATCATAAATCATTAAAGT-ATTATTATTAAATCATTA
1 ATT-AAGTAATTATTATTAAATCATTAAA--ATTAATCATTAAAGTAATTATTATTAAATCATTA
* **
1273451 AAGTTAAATCATT-AA-TCATTAAAATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATT-
63 AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATT-AAATTA
1273513 AATC
127 AATC
1273517 ATTAAAGTAATTATTATTAAATCATTAAAATTCAATCATTAAAGT-ATTATTATT-AATCATT-A
1 ATT-AAGTAATTATTATTAAATCATTAAAATT-AATCATTAAAGTAATTATTATTAAATCATTAA
* *
1273579 AGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
64 AGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1273629 TTATTAAATC
Statistics
Matches: 435, Mismatches: 35, Indels: 67
0.81 0.07 0.12
Matches are distributed among these distances:
124 11 0.03
125 6 0.01
126 34 0.08
127 17 0.04
128 25 0.06
129 122 0.28
130 55 0.13
131 19 0.04
132 20 0.05
133 8 0.02
134 12 0.03
135 51 0.12
136 20 0.05
137 35 0.08
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (130 bp):
ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTAAATC
Found at i:1273597 original size:71 final size:73
Alignment explanation
Indices: 1273402--1273675 Score: 272
Period size: 71 Copynumber: 3.9 Consensus size: 73
1273392 AAGTAATATT
** *
1273402 ATTAAATCATTAAA-TCATAAATCATTAAAGT-ATTATTATTAAATCATTAAAGTTAA--ATCAT
1 ATTAAATCATTAAAGT--TAAATCATTAAA-TCATTAAAATTAAATCATTAAAG-TAATTATTAT
1273463 T-AATCATTAAA
62 TAAATCATTAAA
1273474 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATT-AATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1273538 TCATTAAA
66 TCATTAAA
* * * * *
1273546 ATTCAATCATTAAAG-TATTATTATT-AATCATT-AAGTTAAATTATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTTA-AATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA
1273608 ATCATTAAA
65 ATCATTAAA
* * * * *
1273617 GTTAAATAATTATTA-TTAAATCATTAAA--GTTATAATTAAAT--TTAAA-TAATTATTATTAA
1 ATTAAATCATTA-AAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA
1273676 TATGTACTCG
Statistics
Matches: 174, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
68 13 0.07
69 8 0.05
70 18 0.10
71 86 0.49
72 48 0.28
73 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (73 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCATTAAA
Found at i:1273626 original size:28 final size:29
Alignment explanation
Indices: 1273589--1273648 Score: 113
Period size: 28 Copynumber: 2.1 Consensus size: 29
1273579 AGTTAAATTA
1273589 TTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAAGTAATTATTATTAAATCATTAAAG
1273618 TTAAA-TAATTATTATTAAATCATTAAAG
1 TTAAAGTAATTATTATTAAATCATTAAAG
1273646 TTA
1 TTA
1273649 TAATTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TTAAAGTAATTATTATTAAATCATTAAAG
Found at i:1273633 original size:229 final size:227
Alignment explanation
Indices: 1273043--1273644 Score: 759
Period size: 229 Copynumber: 2.7 Consensus size: 227
1273033 GTAATTATTA
*
1273043 TTAAATCATTAAATCATTAAATCATTAATCATT--A--AATTATTATTAAAGCATTAAAGTTAAA
1 TTAAATCATTAAATCATTAAA--ATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAA
* * *
1273104 TCATTAAAGTAATTATTATTAA--A-TCA-TTAAA-TCTTAAAGTAATTATTATTAAAACATTAA
64 TCATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAA
* * * *
1273164 AGTTAAATCATTA-AAGT-AATTATT--ATTAATCATTAAAGTAATTATTATTAAATCATTAAAG
129 AGTTAAATAATTATTATTAAATCATTAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG
1273225 TTAAATCATTAAATCATTAAATTAAATCATTAAG
194 TTAAATCATTAAATCATTAAATTAAATCATTAAG
*
1273259 -TAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATT-AATCATTAAAGTTAAA
1 TTAA--ATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAA
* * *
1273322 TCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATAAATCATTA-AAGTTAAA
64 TCATTAAAGTAATTATTATT-AATCATT-AAGTT--A-AATTATTA-AAGTAATTATTA-TTAAA
1273386 TCATTAAAG-----TAA-TATTATTAAATCATTAAATCATAAATCATTAAAGT-ATTATTATTAA
122 TCATTAAAGTTAAATAATTATTATTAAATCATTAAAT--T-AATCATTAAAGTAATTATTATTAA
1273444 ATCATTAAAGTTAAATCATT-AATCATTAAAATTAAATCATTAAAG
184 ATCATTAAAGTTAAATCATTAAATCATT-AAATTAAATCATT-AAG
* *
1273489 TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAATTCAATC
1 TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATC
1273554 ATTAAAGT-ATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG
66 ATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG
1273618 TTAAATAATTATTATTAAATCATTAAA
131 TTAAATAATTATTATTAAATCATTAAA
1273645 GTTATAATTA
Statistics
Matches: 332, Mismatches: 18, Indels: 59
0.81 0.04 0.14
Matches are distributed among these distances:
215 13 0.04
217 17 0.05
218 35 0.11
219 12 0.04
221 1 0.00
222 1 0.00
223 24 0.07
224 15 0.05
225 7 0.02
226 1 0.00
227 9 0.03
228 22 0.07
229 133 0.40
230 39 0.12
231 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (227 bp):
TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATC
ATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG
TTAAATAATTATTATTAAATCATTAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTT
AAATCATTAAATCATTAAATTAAATCATTAAG
Found at i:1273636 original size:20 final size:19
Alignment explanation
Indices: 1273611--1273675 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
1273601 TTATTAAATC
1273611 ATTAAAGTTAAATAATTATT
1 ATTAAA-TTAAATAATTATT
* * *
1273631 ATTAAATCATTAA-AGTTATA
1 ATTAAAT--TAAATAATTATT
1273651 ATTAAATTTAAATAATTATT
1 ATTAAA-TTAAATAATTATT
1273671 ATTAA
1 ATTAA
1273676 TATGTACTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTAAATTAAATAATTATT
Found at i:1273675 original size:14 final size:14
Alignment explanation
Indices: 1273585--1273675 Score: 66
Period size: 14 Copynumber: 6.6 Consensus size: 14
1273575 ATTAAGTTAA
1273585 ATTATTAAAGTAATT
1 ATTATTAAA-TAATT
*
1273600 ATTATTAAATCATT
1 ATTATTAAATAATT
*
1273614 A-AAGTTAAATAATT
1 ATTA-TTAAATAATT
*
1273628 ATTATTAAATCATT
1 ATTATTAAATAATT
*
1273642 A-AAGTT--ATAATT
1 ATTA-TTAAATAATT
*
1273654 A-AATTTAAATAATT
1 ATTA-TTAAATAATT
1273668 ATTATTAA
1 ATTATTAA
1273676 TATGTACTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
12 10 0.16
13 2 0.03
14 38 0.62
15 11 0.18
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTATTAAATAATT
Found at i:1277073 original size:42 final size:42
Alignment explanation
Indices: 1277014--1277101 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
1277004 AACAAATCTC
* *
1277014 ACGCTTCAGGCGAATCTCACGCTTCGACC-CTAAAGCATACAG
1 ACGCTTCAGACGAATCTCACGCTTCGACCAC-AAAGAATACAG
1277056 ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG
1 ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG
1277098 ACGC
1 ACGC
1277102 ATGCAGAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (42 bp):
ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG
Found at i:1279423 original size:23 final size:22
Alignment explanation
Indices: 1279390--1279457 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
1279380 TGCCATATAA
*
1279390 AATGTCTCGAAGGACCTCGTAG
1 AATGTCCCGAAGGACCTCGTAG
* *
1279412 AATTGTCCCGAAGGACCACATA-
1 AA-TGTCCCGAAGGACCTCGTAG
* *
1279434 TATATCCCGAAGGACCTCGTAG
1 AATGTCCCGAAGGACCTCGTAG
1279456 AA
1 AA
1279458 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 16 0.44
22 4 0.11
23 16 0.44
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (22 bp):
AATGTCCCGAAGGACCTCGTAG
Done.