Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_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: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:532039 original size:45 final size:45
Alignment explanation
Indices: 531946--532217 Score: 454
Period size: 45 Copynumber: 6.0 Consensus size: 45
531936 ATAACATTTC
* * *
531946 TTACCAATATACTAACCATTTATTCTCACAAGCTCCTAAGCTTATT
1 TTACCAATATACTTACCATTTATTC-CATAAGCTCGTAAGCTTATT
*
531992 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGATTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
*
532037 TTACCAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
*
532082 TTACCAATATACTTACCATTTATTCCCTAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* * *
532127 TTACCAATATACTTACAATTTATTCCATAATCCCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
532172 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
532217 T
1 T
532218 GCATGGTTAC
Statistics
Matches: 211, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 187 0.89
46 24 0.11
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:533499 original size:13 final size:13
Alignment explanation
Indices: 533499--533592 Score: 83
Period size: 13 Copynumber: 7.3 Consensus size: 13
533489 CCGTTGACCC
533499 GACCCGACCCGTT
1 GACCCGACCCGTT
533512 GACCCGACCCGTT
1 GACCCGACCCGTT
533525 GACCCGACCC---
1 GACCCGACCCGTT
*
533535 GACCTGTTTACCC---
1 GACCCG---ACCCGTT
533548 GACCCGACCCGTT
1 GACCCGACCCGTT
533561 GACCCGACCCGTT
1 GACCCGACCCGTT
*
533574 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
533589 GACC
1 GACC
533593 GTTGACCGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
10 9 0.13
13 49 0.70
15 12 0.17
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:533500 original size:18 final size:18
Alignment explanation
Indices: 533477--533571 Score: 137
Period size: 18 Copynumber: 5.6 Consensus size: 18
533467 TCCGGTCACA
533477 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
533495 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
533512 ----GACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
533526 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTG
533544 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
533562 ACCCGACCCG
1 ACCCGACCCG
533572 TTGACCGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
13 13 0.19
18 55 0.81
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:533516 original size:31 final size:31
Alignment explanation
Indices: 533481--533592 Score: 131
Period size: 31 Copynumber: 3.5 Consensus size: 31
533471 GTCACAACCC
533481 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
533512 GACCCGACCCGTTGACCCGACCCGACCTGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
533543 TACCCGACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGACCCGTTGACCC---GACCCGACCCGTT
*
533574 GACCGTTGACCCGTTGACC
1 GACC--CGACCCGTTGACC
533593 GTTGACCGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.07
31 54 0.79
33 5 0.07
36 4 0.06
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:533530 original size:49 final size:49
Alignment explanation
Indices: 533477--533577 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
533467 TCCGGTCACA
533477 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
* *
533526 ACCCGACCCGACCTGTTTACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
533575 ACC
1 ACC
533578 GTTGACCCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.14
Consensus pattern (49 bp):
ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:533566 original size:8 final size:8
Alignment explanation
Indices: 533553--533599 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
533543 TACCCGACCC
533553 GACCCGTT
1 GACCCGTT
533561 GACCC---
1 GACCCGTT
533566 GACCCGTT
1 GACCCGTT
533574 GA-CCGTT
1 GACCCGTT
533581 GACCCGTT
1 GACCCGTT
533589 GA-CCGTT
1 GACCCGTT
533596 GACC
1 GACC
533600 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:533581 original size:7 final size:7
Alignment explanation
Indices: 533569--533600 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
533559 TTGACCCGAC
533569 CCGTTGA
1 CCGTTGA
533576 CCGTTGA
1 CCGTTGA
533583 CCCGTTGA
1 -CCGTTGA
533591 CCGTTGA
1 CCGTTGA
533598 CCG
1 CCG
533601 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:533586 original size:15 final size:15
Alignment explanation
Indices: 533553--533599 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
533543 TACCCGACCC
*
533553 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
533566 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
533581 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
533596 GACC
1 GACC
533600 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:536162 original size:24 final size:24
Alignment explanation
Indices: 536080--536174 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 24
536070 ATTTCTGCTT
* *
536080 TGAATTATGTTTTGACATTTGATC
1 TGAATTATGTTTTGATATCTGATC
* * * * *
536104 TGAAATCTGTTCTGAT-TCCTAACC
1 TGAATTATGTTTTGATAT-CTGATC
* * *
536128 TGGATTCTGTTATGATATCTGATC
1 TGAATTATGTTTTGATATCTGATC
*
536152 TGAATTATGTTTTGATTTCTGAT
1 TGAATTATGTTTTGATATCTGAT
536175 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 51 0.96
25 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTATGTTTTGATATCTGATC
Found at i:538316 original size:13 final size:13
Alignment explanation
Indices: 538316--538407 Score: 85
Period size: 13 Copynumber: 6.3 Consensus size: 13
538306 CCGTTGACCC
538316 GACCCGACCCGTT
1 GACCCGACCCGTT
*
538329 TACCCGACCCGTT
1 GACCCGACCCGTT
538342 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
538360 GACCCGACCCGTT
1 GACCCGACCCGTT
538373 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
538391 GACCCGACCCGTT
1 GACCCGACCCGTT
538404 GACC
1 GACC
538408 GTTGACCGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 20
0.75 0.02 0.22
Matches are distributed among these distances:
13 42 0.63
18 25 0.37
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:538317 original size:18 final size:18
Alignment explanation
Indices: 538294--538401 Score: 137
Period size: 18 Copynumber: 6.6 Consensus size: 18
538284 ACCGGTCACA
538294 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
538312 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
538329 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
538343 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
538360 ----GACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
538374 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
538392 ACCCGACCCG
1 ACCCGACCCG
538402 TTGACCGTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
13 25 0.32
18 53 0.68
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:538337 original size:31 final size:31
Alignment explanation
Indices: 538298--538407 Score: 211
Period size: 31 Copynumber: 3.5 Consensus size: 31
538288 GTCACAACCC
538298 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
538329 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
538360 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
538391 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
538408 GTTGACCGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:539756 original size:18 final size:18
Alignment explanation
Indices: 539730--539765 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
539720 TCGAAAGGAC
*
539730 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
539748 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
539766 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:540977 original size:24 final size:23
Alignment explanation
Indices: 540883--540988 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 23
540873 ATATTTTATC
* *
540883 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATG-TT
* * *
540907 TGACATCTGATCTGAAATCTGTT
1 TGATATCTGATCTGAATTATGTT
* * * *
540930 CTGAT-TCCTAACCTGGATTCTGTT
1 -TGATAT-CTGATCTGAATTATGTT
540954 ATGATATCTGATCTGAATTATGTT
1 -TGATATCTGATCTGAATTATGTT
*
540978 TGATTTCTGAT
1 TGATATCTGAT
540989 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 13 0.21
24 49 0.78
25 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (23 bp):
TGATATCTGATCTGAATTATGTT
Found at i:550751 original size:18 final size:18
Alignment explanation
Indices: 550716--550753 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
550706 GTGTGTTTTG
*
550716 ACTTATTTTCATGCAACA
1 ACTTATTTTCATGAAACA
550734 ACTTATTTTCCA-GAAACA
1 ACTTATTTT-CATGAAACA
550752 AC
1 AC
550754 GATAAAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (18 bp):
ACTTATTTTCATGAAACA
Found at i:560095 original size:20 final size:20
Alignment explanation
Indices: 560070--560109 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
560060 TTTTGGTGCA
*
560070 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
560090 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCTT
560110 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:562431 original size:16 final size:16
Alignment explanation
Indices: 562406--562438 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
562396 GAAGTGGTTT
*
562406 TAAGTTTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
562422 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
562438 T
1 T
562439 GATAAATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:565241 original size:452 final size:452
Alignment explanation
Indices: 564222--565580 Score: 2607
Period size: 452 Copynumber: 3.0 Consensus size: 452
564212 GATTCGAGAA
564222 GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
1 GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
*
564287 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCGTTGGAAGAAGTTTATGATGATATTTAT
66 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
564352 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
131 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
564417 CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
196 CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
564482 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGA--TG
261 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGATGTG
564545 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAA-AACCAATAAAGGTGATGTCTCTAT
326 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
564609 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
391 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
564671 GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
1 GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
564736 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
66 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
564801 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
131 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
564866 CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
196 CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
* * *
564931 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTAAAATGCGAAGGACATGTG
261 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGATGTG
564996 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
326 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
565061 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
391 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
* *
565123 GAGTTAAATCAATAAAGATGGTGTCCACTTTCGATTCATTCCCCATGGAAGAATCCAGACCAATT
1 GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
565188 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
66 GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
565253 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
131 CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
* ** *
565318 CAAAGAAGTGGAGTAATCAAGAACATAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTT
196 CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
565383 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGATGTG
261 TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGATGTG
565448 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
326 GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
565513 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
391 TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
565575 GAGTTA
1 GAGTTA
565581 CAAGATGCTT
Statistics
Matches: 894, Mismatches: 13, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
449 317 0.35
451 42 0.05
452 535 0.60
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (452 bp):
GAGTTAAATCGATAAAGATGGTGTCCACTTTCGGTTCATTCCCCATGGAAGAATCCAGACCAATT
GATGTGTCTCCACACTTCAATGGAAGAAATTATCATCATTGGAAGAAGTTTATGATGATATTTAT
CCAAGGATTTGATATGGAAGCTTGGATGATGATCGAGAAAGGATATTTTTGTCCTACGAAGAAGG
CAAAGAACTGGAGTAATCAAGAACGGAAGAAAGCTCAACAAAATACAAAGGCTATGCACATGTTG
TGTTGTGCAATTGATCCTAATGTATATACAGGAGTTTCTTCTTGTTCAAATGCCAAGGAGATGTG
GGATAAGCTTGAGGATATCTATAGAGACAAGGAAGAAGAAGAACCAATAAAGGTGATGTCTCTAT
TAGCTCTCACAGAGCCAAAGGTATCTTCTAACTTAAATAGATTAAATTCAAAATATTTTAAT
Found at i:571249 original size:17 final size:18
Alignment explanation
Indices: 571222--571266 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
571212 ACTGTTGCTA
571222 AAAAGGAAAAAAGGAAAA-G
1 AAAA-GAAAAAA-GAAAAGG
571241 -AAAG-AAAAAGAAAAGG
1 AAAAGAAAAAAGAAAAGG
571257 AAAAGAAAAA
1 AAAAGAAAAA
571267 GTAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 5 0.22
18 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAGG
Found at i:571260 original size:11 final size:11
Alignment explanation
Indices: 571230--571265 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
571220 TAAAAAGGAA
571230 AAAAGGAAAAG
1 AAAAGGAAAAG
*
571241 -AAAGAAAAAG
1 AAAAGGAAAAG
571251 AAAAGGAAAAG
1 AAAAGGAAAAG
571262 AAAA
1 AAAA
571266 AGTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGGAAAAG
Found at i:571267 original size:17 final size:15
Alignment explanation
Indices: 571229--571285 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 15
571219 CTAAAAAGGA
571229 AAAAAGGAAAAGAAAG
1 AAAAA-GAAAAGAAAG
571245 AAAAAGAAAAGGAAAAG
1 AAAAAGAAAA-G-AAAG
571262 AAAAAGTAAAA-AAA-
1 AAAAAG-AAAAGAAAG
*
571276 AATAAGAAAA
1 AAAAAGAAAA
571286 TCCAAAGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 8 0.22
16 6 0.16
17 10 0.27
18 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAGAAAG
Found at i:576441 original size:55 final size:55
Alignment explanation
Indices: 576336--576448 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
576326 ATTATTTTTT
* *
576336 ATATTAAAAGTATTCAACAAATTTGATTAAAATATGATTTTTAAATTAATACCAG
1 ATATTAAAAGTATTCAACAAATTTGATTAAAATATAATGTTTAAATTAATACCAG
* * * *
576391 ATATTAAAAGTATTCAACTAATTTGATTTAAATCTAACTGTTTAAA-TAATATCAG
1 ATATTAAAAGTATTCAACAAATTTGATTAAAATATAA-TGTTTAAATTAATACCAG
576446 ATA
1 ATA
576449 ATGTATGAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 44 0.86
56 7 0.14
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (55 bp):
ATATTAAAAGTATTCAACAAATTTGATTAAAATATAATGTTTAAATTAATACCAG
Found at i:578508 original size:21 final size:21
Alignment explanation
Indices: 578469--578508 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
578459 TCCCTTAGCA
* *
578469 AAAGAATTGATTCCTTTGACC
1 AAAGAATTGATCCCCTTGACC
*
578490 AAAGGATTGATCCCCTTGA
1 AAAGAATTGATCCCCTTGA
578509 GAAATTATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
AAAGAATTGATCCCCTTGACC
Found at i:578569 original size:21 final size:21
Alignment explanation
Indices: 578543--578589 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
578533 AGTAAATTTT
* *
578543 GGATCGACCCCTTTTAGAAAA
1 GGATCGACCCCTCTAAGAAAA
*
578564 GGATCGATCCCTCTAAGAAAA
1 GGATCGACCCCTCTAAGAAAA
578585 GGATC
1 GGATC
578590 CATCTCTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GGATCGACCCCTCTAAGAAAA
Found at i:588299 original size:27 final size:27
Alignment explanation
Indices: 588268--588326 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
588258 CTAAACTTTC
588268 AATTTATTAATTTTATTCACTAGCCAA
1 AATTTATTAATTTTATTCACTAGCCAA
* *
588295 CATTTATTAATTTTGTTCACTAGCCAA
1 AATTTATTAATTTTATTCACTAGCCAA
588322 AATTT
1 AATTT
588327 TGAGGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (27 bp):
AATTTATTAATTTTATTCACTAGCCAA
Found at i:591289 original size:59 final size:59
Alignment explanation
Indices: 591182--591298 Score: 180
Period size: 59 Copynumber: 2.0 Consensus size: 59
591172 TTGTGCAAAG
* ** * *
591182 GGTCGATCCCTTTTATTTTCCAGAAAAATGATCGATCCGTTTGTAAAAAGGATCGATCT
1 GGTCAATCCCTTGCATTTTCCAGAAAAATGATCGATCCCTTTGCAAAAAGGATCGATCT
*
591241 GGTCAATCCCTTGCATTTTCCAGAAAAATGATCGATCCCTTTGCAAAAAGGATTGATC
1 GGTCAATCCCTTGCATTTTCCAGAAAAATGATCGATCCCTTTGCAAAAAGGATCGATC
591299 CATTTTTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (59 bp):
GGTCAATCCCTTGCATTTTCCAGAAAAATGATCGATCCCTTTGCAAAAAGGATCGATCT
Found at i:597553 original size:81 final size:81
Alignment explanation
Indices: 597460--597633 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 81
597450 TTGTTAGACA
* *
597460 TTTAGTCTTTTACCCAAAGTTATTTAACCTTTCATCTAACTGGCAAGATTGACACCTTTCTGCCA
1 TTTAGTCTTTTACCCAAAGGTATTTAACATTTCATCTAACTGGCAAGATTGACACCTTTCTGCCA
*
597525 AAGGCACAGTTAGGCT
66 AAGGCACAATTAGGCT
* * * * * *
597541 TTTAGTGTTTTACTCGAAGGTATTTAACATTTCATCTAATTGGCATGATTGAGACCTTTCTGCCA
1 TTTAGTCTTTTACCCAAAGGTATTTAACATTTCATCTAACTGGCAAGATTGACACCTTTCTGCCA
597606 AAGGCACAATTAGGCT
66 AAGGCACAATTAGGCT
*
597622 TTTAATCTTTTA
1 TTTAGTCTTTTA
597634 GTTTAGAACA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (81 bp):
TTTAGTCTTTTACCCAAAGGTATTTAACATTTCATCTAACTGGCAAGATTGACACCTTTCTGCCA
AAGGCACAATTAGGCT
Found at i:598032 original size:46 final size:46
Alignment explanation
Indices: 597965--598402 Score: 660
Period size: 46 Copynumber: 9.5 Consensus size: 46
597955 TTATTCGTTA
* * * * *
597965 ATTTCAGTTATGACATCCTTTCTTGCCTTAATGCATCATTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* ** *
598011 ATTTCATTTATGGCATCCTTTCATACCTTAATATATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
598057 ATTTCATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
598103 ATTTCATTTATGGTATCATTTCATTCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
598149 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
598195 ATTTCATTTATGGTATCATTTCATTCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
598241 ATTTTATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
598287 ATTTCGTTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCAAGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
598333 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
598379 ATTTCATTTATGGCATCCTTTCAT
1 ATTTCATTTATGGCATCCTTTCAT
598403 CCATTTCATT
Statistics
Matches: 353, Mismatches: 39, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 353 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:598503 original size:21 final size:21
Alignment explanation
Indices: 598457--598495 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
598447 ATTCATTTCA
*
598457 TTTATGGCATCCTTTCATGAC
1 TTTATGGCATCCTTTAATGAC
598478 TTTAT-GCATCCTTTAATG
1 TTTATGGCATCCTTTAATG
598496 CATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTATGGCATCCTTTAATGAC
Found at i:598532 original size:45 final size:46
Alignment explanation
Indices: 598391--598553 Score: 211
Period size: 46 Copynumber: 3.6 Consensus size: 46
598381 TTCATTTATG
* * * *
598391 GCATCCTTTCATCCATTTCATTTATGGCATCCTTTCGTTCCTTAAT
1 GCATCCTTTAATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* * * *
598437 GCATCTTTTAATTCATTTCATTTATGGCATCCTTTCATGACTTTAT
1 GCATCCTTTAATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
598483 GCATCCTTTAATGCATTTTATTTATGGTAT-CTTTCATGCCTTAAT
1 GCATCCTTTAATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
598528 GCATCCTTTCATGAATTTCATTTATG
1 GCATCCTTTAATGCATTTCATTTATG
598554 ATTCATTTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
45 36 0.36
46 65 0.64
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (46 bp):
GCATCCTTTAATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
Found at i:598547 original size:91 final size:93
Alignment explanation
Indices: 598385--598553 Score: 234
Period size: 91 Copynumber: 1.8 Consensus size: 93
598375 ATGCATTTCA
* * * * *
598385 TTTATGGCATCCTTTCATCCATTTCATTTATGGCATCCTTTCGTTCCTTAATGCATCTTTTAATT
1 TTTATGGCATCCTTTAATCCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTAATG
*
598450 CATTTCATTTATGGCATCCTTTCATGAC
66 AATTTCATTTATGGCATCCTTTCATGAC
* * * *
598478 TTTAT-GCATCCTTTAATGCATTTTATTTATGGTAT-CTTTCATGCCTTAATGCATCCTTTCATG
1 TTTATGGCATCCTTTAATCCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTAATG
598541 AATTTCATTTATG
66 AATTTCATTTATG
598554 ATTCATTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
91 35 0.53
92 26 0.39
93 5 0.08
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.49
Consensus pattern (93 bp):
TTTATGGCATCCTTTAATCCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTAATG
AATTTCATTTATGGCATCCTTTCATGAC
Found at i:599032 original size:42 final size:41
Alignment explanation
Indices: 598986--599078 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
598976 CCCTACCATG
* * * * *
598986 GTATCGATACTTCTATATTATGGTACGGATAC-CTTTCTCTCA
1 GTATCGATACTACTATACTACGGTACCGATACTCTAT-T-TCA
*
599028 GTATCGATACTACTGTACTACGGTACCGATACTCTATTTCA
1 GTATCGATACTACTATACTACGGTACCGATACTCTATTTCA
599069 GTATCGATAC
1 GTATCGATAC
599079 CATTTTGACA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 13 0.30
42 28 0.64
43 3 0.07
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (41 bp):
GTATCGATACTACTATACTACGGTACCGATACTCTATTTCA
Found at i:600976 original size:2 final size:2
Alignment explanation
Indices: 600969--600995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
600959 CCAGAAAAGC
600969 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
600996 GACATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:603288 original size:81 final size:81
Alignment explanation
Indices: 603196--603450 Score: 447
Period size: 81 Copynumber: 3.1 Consensus size: 81
603186 CCGTTAGACA
* * *
603196 TTTAGTCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTACCA
1 TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCA
*
603261 AAGGTACAATTAGGCT
66 AAGGCACAATTAGGCT
*
603277 TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGCCA
1 TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCA
*
603342 AAGGCACAGTTAGGCT
66 AAGGCACAATTAGGCT
603358 TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCA
1 TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCA
603423 AAGGCACAATTAGGCT
66 AAGGCACAATTAGGCT
*
603439 TTTAATCTTTTA
1 TTTAGTCTTTTA
603451 TTTTAGAATA
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 165 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (81 bp):
TTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCA
AAGGCACAATTAGGCT
Found at i:603434 original size:162 final size:162
Alignment explanation
Indices: 603145--603450 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 162
603135 CAATTAATCC
* * * * *
603145 TTCATCCAACTTGGATTATTGGCATCTTTCTTCCAAATACACCGTTAGACATTTAGTCTTTTACC
1 TTCATCCAACTTGGATGATTGACATCTTTCTGCCAAAGACACAGTTAGACATTTAGTCTTTTACC
* *
603210 CAAAGGTATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGGTACAATTAGG
66 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGGCACAATTAGG
*
603275 CTTTTAGTCTTTTACTCAAAGGTATTTAACCT
131 CTTTTAATCTTTTACTCAAAGGTATTTAACCT
* * * *
603307 TTCATCTAAC-TGGCATGATTGACATCTTTCTGCCAAAGGCACAGTTAGGCTTTTAGTCTTTTAC
1 TTCATCCAACTTGG-ATGATTGACATCTTTCTGCCAAAGACACAGTTAGACATTTAGTCTTTTAC
* *
603371 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAAGGCACAATTAG
65 CCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGGCACAATTAG
603436 GCTTTTAATCTTTTA
130 GCTTTTAATCTTTTA
603451 TTTTAGAATA
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
161 3 0.02
162 126 0.98
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (162 bp):
TTCATCCAACTTGGATGATTGACATCTTTCTGCCAAAGACACAGTTAGACATTTAGTCTTTTACC
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTACCAAAGGCACAATTAGG
CTTTTAATCTTTTACTCAAAGGTATTTAACCT
Found at i:603644 original size:55 final size:55
Alignment explanation
Indices: 603585--603693 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
603575 ACATGGGTTA
*
603585 CACACCCACTACCAATACA-AAAATTCATAAACTTATTATGAATTTCTTAGTTTTG
1 CACACACACTACCAATA-AGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTG
* * * * * * *
603640 CACACATATTGCCCATAAGGAATTTCATAACCTTATTATGAATTTCTTAGTTTT
1 CACACACACTACCAATAAGAAAATTCATAAACTTATTATGAATTTCTTAGTTTT
603694 TGAAATAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
54 1 0.02
55 44 0.98
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (55 bp):
CACACACACTACCAATAAGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTG
Found at i:603874 original size:20 final size:20
Alignment explanation
Indices: 603845--604088 Score: 110
Period size: 26 Copynumber: 10.7 Consensus size: 20
603835 TTCATTTATG
603845 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
603865 GCATCATTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
603890 GGCATCCTTTTATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
603911 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
603936 GGCATCCTTTCATGCATTTCATTTAT
1 -GCATCCTTTCATGC----C-TTAAT
*
603962 GACATCCTTCCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
603983 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
604008 GACATCTTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
604029 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
* *
604054 GGAACCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
604075 GCATCATTTCATGC
1 GCATCCTTTCATGC
604089 ATTTCATTTA
Statistics
Matches: 178, Mismatches: 21, Indels: 50
0.71 0.08 0.20
Matches are distributed among these distances:
20 61 0.34
21 18 0.10
22 4 0.02
24 4 0.02
25 18 0.10
26 73 0.41
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:603905 original size:46 final size:46
Alignment explanation
Indices: 603833--603950 Score: 218
Period size: 46 Copynumber: 2.6 Consensus size: 46
603823 TTATTCGTTA
603833 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
603879 ATTTCATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
603925 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
603951 ATTTCATTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:603951 original size:72 final size:72
Alignment explanation
Indices: 603865--604022 Score: 262
Period size: 72 Copynumber: 2.2 Consensus size: 72
603855 ATGCCTTAAT
* **
603865 GCATCATTTCATGCATTTCATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTC
1 GCATCATTTCATGCATTTCATTTATGACATCCTTCCATGCCTTAATGCATCCTTTCATGCATTTC
603930 ATTTATG
66 ATTTATG
*
603937 GCATCCTTTCATGCATTTCATTTATGACATCCTTCCATGCCTTAATGCATCCTTTCATGCATTTC
1 GCATCATTTCATGCATTTCATTTATGACATCCTTCCATGCCTTAATGCATCCTTTCATGCATTTC
604002 ATTTATG
66 ATTTATG
* *
604009 ACATCTTTTCATGC
1 GCATCATTTCATGC
604023 CTTAATGCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (72 bp):
GCATCATTTCATGCATTTCATTTATGACATCCTTCCATGCCTTAATGCATCCTTTCATGCATTTC
ATTTATG
Found at i:604041 original size:118 final size:118
Alignment explanation
Indices: 603833--604068 Score: 402
Period size: 118 Copynumber: 2.0 Consensus size: 118
603823 TTATTCGTTA
* * *
603833 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCT
1 ATTTCATTTATGACATCCTTCCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACATCCT
* *
603898 TTTATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
66 TTTATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGAACCCTTTCATGC
*
603951 ATTTCATTTATGACATCCTTCCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACAT-CT
1 ATTTCATTTATGACATCCTTCCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACATCCT
604015 TTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGAACCCTTTCATGC
66 TTT-ATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGAACCCTTTCATGC
604069 CTTAATGCAT
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 5 0.05
118 106 0.95
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (118 bp):
ATTTCATTTATGACATCCTTCCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACATCCT
TTTATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGAACCCTTTCATGC
Found at i:604102 original size:46 final size:46
Alignment explanation
Indices: 603937--604100 Score: 276
Period size: 46 Copynumber: 3.6 Consensus size: 46
603927 TTCATTTATG
*
603937 GCATCCTTTCATGCATTTCATTTATGACATCCTTCCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAAT
*
603983 GCATCCTTTCATGCATTTCATTTATGACATCTTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAAT
*
604029 GCATCCTTTCATGCATTTCATTTATGGA-ACCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTAT-GACATCCTTTCATGCCTTAAT
*
604075 GCATCATTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
604101 GATTCATTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
45 1 0.01
46 109 0.97
47 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAAT
Found at i:604550 original size:22 final size:22
Alignment explanation
Indices: 604524--604601 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
604514 TACCCCTACC
604524 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
604546 ATGGTA-CTGATACCTT-TCT-CT
1 ATGGTATC-GATA-CTTCTATACT
* * *
604567 CT-GTATCGATACTACTACACT
1 ATGGTATCGATACTTCTATACT
*
604588 GTGGTATCGATACT
1 ATGGTATCGATACT
604602 CTCTTTCAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.05
20 8 0.18
21 8 0.18
22 23 0.52
23 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:607899 original size:16 final size:16
Alignment explanation
Indices: 607874--607916 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
607864 TGCTTATCTC
* *
607874 TATGTTTTGATGGTAG
1 TATGTGTTGATGCTAG
607890 TATGTGTTGATGCTAG
1 TATGTGTTGATGCTAG
607906 TATGTGTTGAT
1 TATGTGTTGAT
607917 TGTATTTGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (16 bp):
TATGTGTTGATGCTAG
Found at i:609512 original size:13 final size:13
Alignment explanation
Indices: 609470--609519 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
609460 CTCTCCTTTA
*
609470 TTTATTTTCAAGT
1 TTTATTTTTAAGT
*
609483 TTTCATTTTT--TT
1 TTT-ATTTTTAAGT
609495 CTTTATTTTTAAGT
1 -TTTATTTTTAAGT
609509 TTTATTTTTAA
1 TTTATTTTTAA
609520 ATATGCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 7 0.23
13 17 0.57
14 6 0.20
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (13 bp):
TTTATTTTTAAGT
Found at i:610106 original size:16 final size:18
Alignment explanation
Indices: 610079--610116 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
610069 ACCGTATTGA
*
610079 TTTTCAACTTTACAAT-C
1 TTTTCAACTTTAAAATGC
610096 TTTTC-ACTTTAAAATGC
1 TTTTCAACTTTAAAATGC
610113 TTTT
1 TTTT
610117 ATTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTCAACTTTAAAATGC
Found at i:614464 original size:21 final size:19
Alignment explanation
Indices: 614424--614466 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
614414 TCTAGAAAAC
*
614424 TAAGATAAGAATATAAGAT
1 TAAGATAAGAAAATAAGAT
614443 TAAGATTAAGAAAATGAAGAT
1 TAAGA-TAAGAAAAT-AAGAT
614464 TAA
1 TAA
614467 AACAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (19 bp):
TAAGATAAGAAAATAAGAT
Found at i:614568 original size:17 final size:17
Alignment explanation
Indices: 614543--614576 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
614533 CTTAGCCAAA
*
614543 ATTAGGGTAGTGGTGAT
1 ATTAAGGTAGTGGTGAT
614560 ATTAAGGTAGTGGTGAT
1 ATTAAGGTAGTGGTGAT
614577 GATGGATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (17 bp):
ATTAAGGTAGTGGTGAT
Found at i:614614 original size:23 final size:24
Alignment explanation
Indices: 614573--614619 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
614563 AAGGTAGTGG
614573 TGATGATGGATGATAATGGTGATT
1 TGATGATGGATGATAATGGTGATT
*
614597 TGATGAT-GATGATGATGGTGATT
1 TGATGATGGATGATAATGGTGATT
614620 GAGAGATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (24 bp):
TGATGATGGATGATAATGGTGATT
Found at i:615166 original size:25 final size:25
Alignment explanation
Indices: 615130--615186 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
615120 TAGTTCCTGA
615130 CATTGGATTGACGCATTCTAAGTAC
1 CATTGGATTGACGCATTCTAAGTAC
*
615155 CGTTGGATTGACGCATTCTAAGTAC
1 CATTGGATTGACGCATTCTAAGTAC
615180 CATTGGA
1 CATTGGA
615187 AAGCTAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (25 bp):
CATTGGATTGACGCATTCTAAGTAC
Found at i:616199 original size:7 final size:7
Alignment explanation
Indices: 616187--616228 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
616177 ACTTTCGGTC
616187 AATCGAA
1 AATCGAA
616194 AATCGAA
1 AATCGAA
616201 AATCGAA
1 AATCGAA
616208 AATCGAA
1 AATCGAA
616215 AATCGAA
1 AATCGAA
616222 AATCGAA
1 AATCGAA
616229 TAGAAGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
AATCGAA
Found at i:623715 original size:2 final size:2
Alignment explanation
Indices: 623708--623733 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
623698 AAGTAATACT
623708 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
623734 ACAGATAGGT
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):
TA
Found at i:624949 original size:67 final size:67
Alignment explanation
Indices: 624841--624967 Score: 191
Period size: 67 Copynumber: 1.9 Consensus size: 67
624831 CCTTAGATCC
** * * * * *
624841 ATAAGGAATTATTAGTCGGTGTTGAACCTATTCAAGGAATTACCAACAGCGACTGAACCTGCCAA
1 ATAAGGAATTACCAGTCGATGCTAAACCTATACAAGGAATTACCAACAACGACTGAACCTGCCAA
624906 AG
66 AG
624908 ATAAGGAATTACCAGTCGATGCTAAACCTATACAAGGAATTACCAACAACGACTGAACCT
1 ATAAGGAATTACCAGTCGATGCTAAACCTATACAAGGAATTACCAACAACGACTGAACCT
624968 ACCAGACTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (67 bp):
ATAAGGAATTACCAGTCGATGCTAAACCTATACAAGGAATTACCAACAACGACTGAACCTGCCAA
AG
Found at i:624967 original size:31 final size:31
Alignment explanation
Indices: 624863--624968 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
624853 TAGTCGGTGT
* *
624863 TGAACCTATTCAAGGAATTACCAACAGCGAC
1 TGAACCTATACAAGGAATTACCAACAACGAC
* * * * *
624894 TGAACCTGCCAAAGATAAGGAATTACCAGTCGATG-C
1 TGAACCT-----ATACAAGGAATTACCA-ACAACGAC
*
624930 TAAACCTATACAAGGAATTACCAACAACGAC
1 TGAACCTATACAAGGAATTACCAACAACGAC
624961 TGAACCTA
1 TGAACCTA
624969 CCAGACTCTT
Statistics
Matches: 54, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
30 3 0.06
31 29 0.54
36 20 0.37
37 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (31 bp):
TGAACCTATACAAGGAATTACCAACAACGAC
Found at i:626943 original size:14 final size:14
Alignment explanation
Indices: 626899--626943 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
626889 AACGGTTTAC
626899 GGTCAAAGTCAATG
1 GGTCAAAGTCAATG
*
626913 AGTCAAAGTCAATG
1 GGTCAAAGTCAATG
*
626927 GGTCAAAGTCAACG
1 GGTCAAAGTCAATG
626941 GGT
1 GGT
626944 TGACTCAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (14 bp):
GGTCAAAGTCAATG
Found at i:626959 original size:14 final size:14
Alignment explanation
Indices: 626942--626991 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
626932 AAGTCAACGG
626942 GTTGACTCAGATAA
1 GTTGACTCAGATAA
* *
626956 GTTGACTTAGATGA
1 GTTGACTCAGATAA
* *
626970 GTTGACTAAGATAG
1 GTTGACTCAGATAA
626984 GTTGACTC
1 GTTGACTC
626992 TGACGAGTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (14 bp):
GTTGACTCAGATAA
Found at i:626999 original size:28 final size:28
Alignment explanation
Indices: 626942--627001 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
626932 AAGTCAACGG
* *
626942 GTTGACTCAGATAAGTTGACTTAGATGA
1 GTTGACTAAGATAAGTTGACTTAGACGA
*
626970 GTTGACTAAGATAGGTTGACTCT-GACGA
1 GTTGACTAAGATAAGTTGACT-TAGACGA
626998 GTTG
1 GTTG
627002 GGGTTGACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
GTTGACTAAGATAAGTTGACTTAGACGA
Found at i:627006 original size:20 final size:21
Alignment explanation
Indices: 626983--627021 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
626973 GACTAAGATA
*
626983 GGTTGACTCTGA-CGAGTTGG
1 GGTTGACTCAGATCGAGTTGG
627003 GGTTGACTCAGATCGAGTT
1 GGTTGACTCAGATCGAGTT
627022 TACTCGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (21 bp):
GGTTGACTCAGATCGAGTTGG
Found at i:630464 original size:21 final size:21
Alignment explanation
Indices: 630438--630484 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
630428 TTTATTTTAT
630438 ACTTAATTACTAGAATTAGGG
1 ACTTAATTACTAGAATTAGGG
630459 ACTTAATTACTAGAATTAGGG
1 ACTTAATTACTAGAATTAGGG
630480 A-TTAA
1 ACTTAA
630485 ATCGAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (21 bp):
ACTTAATTACTAGAATTAGGG
Found at i:633068 original size:17 final size:17
Alignment explanation
Indices: 633046--633088 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
633036 TGTTATAATC
633046 CAATTCCTCCTTAAAAT
1 CAATTCCTCCTTAAAAT
633063 CAATTCCTCCTTAAAAT
1 CAATTCCTCCTTAAAAT
633080 CAATTCCTC
1 CAATTCCTC
633089 AAACCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (17 bp):
CAATTCCTCCTTAAAAT
Found at i:634597 original size:131 final size:131
Alignment explanation
Indices: 634268--634605 Score: 387
Period size: 131 Copynumber: 2.6 Consensus size: 131
634258 ATTTTAAGAG
* * * * * * *
634268 TGAAAACGATAAGATCTAATTATTTTCAACCGAGAATAAATGACCTTTCGTGCATTAAAACT-GT
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAA-TAGT
* * * * * *
634332 CAGTTATTACTCCAATAGAAACAAAGAGATATTACTATTTCGTCTTAAAATTCAATATTGATTCG
65 CATTTATTACTCCAATAGAAACAAAGAGATATCACTATTTCATCCTAAAATCCAATATTAATTCG
634397 AA
130 AA
* * * *
634399 TGAAAATGATAATATCTAATGATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGACA-T
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAA-ATAGT
* * ** *
634463 CATTTATTGCTCCAATTGAAATGAAGAGGTATCACTATTTCATCCTAAGAA-CCAATATTAATTC
65 CATTTATTACTCCAATAGAAACAAAGAGATATCACTATTTCATCCTAA-AATCCAATATTAATTC
634527 GAGA
129 GA-A
* *
634531 -GAAAACGACAATATCAAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAATAGTC
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAATAGTC
*
634595 ATTTATCACTC
66 ATTTATTACTC
634606 ATAGCGAAAT
Statistics
Matches: 172, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
130 2 0.01
131 166 0.97
132 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (131 bp):
TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAATAGTC
ATTTATTACTCCAATAGAAACAAAGAGATATCACTATTTCATCCTAAAATCCAATATTAATTCGA
A
Found at i:635980 original size:20 final size:20
Alignment explanation
Indices: 635957--636002 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
635947 AAAAATCCCT
635957 AAAAACTCTATAAAAGCCCC
1 AAAAACTCTATAAAAGCCCC
635977 AAAAACTCTATAAAAGCCCC
1 AAAAACTCTATAAAAGCCCC
635997 AAAAAC
1 AAAAAC
636003 ACGCCCCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.28, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAACTCTATAAAAGCCCC
Found at i:636470 original size:19 final size:19
Alignment explanation
Indices: 636442--636486 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
636432 CTGCTTCATG
*
636442 TGGGCATGGAAGGGCATTA
1 TGGGCTTGGAAGGGCATTA
636461 TGGGCTTGGAAGGGCATTA
1 TGGGCTTGGAAGGGCATTA
636480 TGGGCTT
1 TGGGCTT
636487 CAACCGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.11, G:0.42, T:0.27
Consensus pattern (19 bp):
TGGGCTTGGAAGGGCATTA
Found at i:637147 original size:134 final size:134
Alignment explanation
Indices: 636873--637268 Score: 388
Period size: 134 Copynumber: 3.0 Consensus size: 134
636863 ATTGAGGTGG
* * * * * *
636873 ACTTGTTCCACTGATACTCAGGGAAAATGAAATCTTGAAAGAGA--GATATATT-CCGCTT-TTT
1 ACTTGTTCCACAGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTACC-CTTCTTC
* * * * * * ** * * * *
636934 TTTAGGGAAAATAATATTTGGGGACGTTGATTTATTTTACTGTT-CTTTAGGGAAGATTGAATCG
65 TTGAGGGAAAATCAGATATGGGGATGTTGATTCATTCCATTGTTAC-TCAAGGAAGATTGAATCA
* *
636998 AGGCAG
129 AGTCAA
* * * * * * **
637004 ACCTATTCCACTGTTACTCAGGGAATCTCAAATCTTGAAAGATATGGATATGTTATGCTTCTTCT
1 ACTTGTTCCACAGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTACCCTTCTTCT
** * *
637069 TGAGGGAAAATTGGATCTGGGGATGTTGATTCATTCCATTGTTACTCAAGGAATATTGAATCAAG
66 TGAGGGAAAATCAGATATGGGGATGTTGATTCATTCCATTGTTACTCAAGGAAGATTGAATCAAG
637134 TCAA
131 TCAA
* * * * *
637138 ACTTGTTCCACAGTTACTTAGGGAATATCAAATCTTGAAAGGGAGGGATTTGTTCCCCTTCTTTT
1 ACTTGTTCCACAGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTACCCTTCTTCT
* *
637203 TGAGGGAAAATCATATATGGGGATGTTGATTCATTCCATTGTTACTCAGGGAAGATTGAATCAAG
66 TGAGGGAAAATCAGATATGGGGATGTTGATTCATTCCATTGTTACTCAAGGAAGATTGAATCAAG
637268 T
131 T
637269 TCGATTTGCT
Statistics
Matches: 214, Mismatches: 46, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
131 37 0.17
133 10 0.05
134 166 0.78
135 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (134 bp):
ACTTGTTCCACAGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTACCCTTCTTCT
TGAGGGAAAATCAGATATGGGGATGTTGATTCATTCCATTGTTACTCAAGGAAGATTGAATCAAG
TCAA
Found at i:645304 original size:20 final size:21
Alignment explanation
Indices: 645279--645328 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
645269 GACCAACAAA
645279 ATCGCAACGCAATCTCCA-AT
1 ATCGCAACGCAATCTCCAGAT
** *
645299 ATCGCAAATCAATTTCCAGAT
1 ATCGCAACGCAATCTCCAGAT
645320 -TCGCAACGC
1 ATCGCAACGC
645329 GATTTTGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCAATCTCCAGAT
Found at i:646045 original size:19 final size:19
Alignment explanation
Indices: 646013--646106 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 19
646003 AAATCGTAAC
646013 GCGATTTTAGTTTC-TCGTT
1 GCGATTTTAGTTTCAT-GTT
646032 GCGATTTT-GATTTCATGTT
1 GCGATTTTAG-TTTCATGTT
* * * *
646051 GCGATAGTCATTTTCGTGTT
1 GCGAT-TTTAGTTTCATGTT
* **
646071 GCGATTTTCATTTTTGTGTT
1 GCGATTTT-AGTTTCATGTT
*
646091 GTGATTTTAAGTTTCA
1 GCGATTTT-AGTTTCA
646107 GAAACTATTC
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 21 0.36
20 36 0.62
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.52
Consensus pattern (19 bp):
GCGATTTTAGTTTCATGTT
Found at i:646096 original size:20 final size:20
Alignment explanation
Indices: 646029--646098 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
646019 TTAGTTTCTC
* *
646029 GTTGCGATTTTGA-TTTCAT
1 GTTGCGATTTTCATTTTCGT
**
646048 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
646068 GTTGCGATTTTCATTTTTGT
1 GTTGCGATTTTCATTTTCGT
*
646088 GTTGTGATTTT
1 GTTGCGATTTT
646099 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:648017 original size:20 final size:20
Alignment explanation
Indices: 647994--648042 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
647984 GAAACTTAAA
*
647994 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
648014 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
648034 ATCGCAACG
1 ATCGCAACG
648043 GGCTAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:648099 original size:20 final size:20
Alignment explanation
Indices: 648076--648113 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
648066 AATCGCAACG
*
648076 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
648096 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
648114 TTTAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:648145 original size:19 final size:19
Alignment explanation
Indices: 648118--648154 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
648108 CGCGAATTTA
*
648118 GTTTTGCGTTGTGATTTTG
1 GTTTCGCGTTGTGATTTTG
648137 GTTTCGCGTTGTGATTTT
1 GTTTCGCGTTGTGATTTT
648155 TATTTCGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.08, G:0.30, T:0.57
Consensus pattern (19 bp):
GTTTCGCGTTGTGATTTTG
Found at i:648160 original size:19 final size:19
Alignment explanation
Indices: 648123--648162 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
648113 ATTTAGTTTT
*
648123 GCGTTGTGATTTTGGTTTC
1 GCGTTGTGATTTTGATTTC
*
648142 GCGTTGTGATTTTTATTTC
1 GCGTTGTGATTTTGATTTC
648161 GC
1 GC
648163 ATTGCGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (19 bp):
GCGTTGTGATTTTGATTTC
Found at i:648242 original size:19 final size:19
Alignment explanation
Indices: 648182--648242 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
648172 ATCTTGTTGT
*
648182 GATAGTCAAATTT-GCGTTGC
1 GATAGTC-ATTTTCGCGTT-C
648202 GATAGTCATTTCTGCGCG--C
1 GATAGTCATTT-T-CGCGTTC
648221 GATAGTCATTTTCGCGTTC
1 GATAGTCATTTTCGCGTTC
648240 GAT
1 GAT
648243 TTTAAGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 19 0.54
20 8 0.23
22 3 0.09
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (19 bp):
GATAGTCATTTTCGCGTTC
Found at i:648252 original size:19 final size:20
Alignment explanation
Indices: 648230--648272 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
648220 CGATAGTCAT
*
648230 TTTCGCGTT-CGATTTTAAG
1 TTTCGCGTTGCGATTTTAAA
*
648249 TTTCGTGTTGCGATTTTAAA
1 TTTCGCGTTGCGATTTTAAA
648269 TTTC
1 TTTC
648273 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAA
Found at i:648839 original size:21 final size:21
Alignment explanation
Indices: 648744--648851 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
648734 GCCCGACTCA
648744 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
648765 TCT-CCTATCATTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
648786 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
648807 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
648828 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
648849 CCT
1 CCT
648852 TCCACCATTC
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:648845 original size:42 final size:42
Alignment explanation
Indices: 648744--648866 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
648734 GCCCGACTCA
* * * *
648744 CCTGTCATCGTTCAAGAGGCCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCATTCAAGAGGCC
* ** *
648786 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCATTCAAGAGGCC
* *
648828 CCTGTCATCGTTGAAGAGGT-CCCTTCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCACCATTCAAGAG
648867 CTCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:648865 original size:21 final size:21
Alignment explanation
Indices: 648797--648866 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
648787 CTATCATCCC
*
648797 TCAAGA-GTCCCCTCCCACCGT
1 TCAAGAGGT-CCCTTCCACCGT
* *
648818 TCAAGAGGCCCCTGT-CATCGT
1 TCAAGAGGTCCCT-TCCACCGT
* *
648839 TGAAGAGGTCCCTTCCACCAT
1 TCAAGAGGTCCCTTCCACCGT
648860 TCAAGAG
1 TCAAGAG
648867 CTCGATTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
TCAAGAGGTCCCTTCCACCGT
Found at i:650236 original size:20 final size:20
Alignment explanation
Indices: 650211--650288 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
650201 AGGTACACTT
*
650211 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
650231 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
650251 TTGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
650271 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
650289 TTCGCGTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:650352 original size:20 final size:20
Alignment explanation
Indices: 650278--650457 Score: 134
Period size: 20 Copynumber: 9.7 Consensus size: 20
650268 AAATCGCAAC
*
650278 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
650297 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
650317 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
650331 GCGATAGTCAAATTCCCGTT
1 GCGATAGTCAAATTCGCGTT
* *
650351 GCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
* * *
650371 GCAATAGACAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
*
650391 GCGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
*
650405 GCGATAGTCATATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
650425 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
650445 GTGATATTCAAAT
1 GCGATAGTCAAAT
650458 GAATGTGTAA
Statistics
Matches: 126, Mismatches: 22, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
14 21 0.17
16 2 0.02
18 1 0.01
19 8 0.06
20 94 0.75
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:650353 original size:34 final size:34
Alignment explanation
Indices: 650293--650429 Score: 123
Period size: 34 Copynumber: 3.9 Consensus size: 34
650283 AGTCAATTCG
* * *
650293 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
650327 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* * *
650367 CGTTGCAATAGACAAATTCGTGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
650400 GCGTTGCGATAGTCATATTCGCGTTGCGAT
1 -CGTTGCGATAGTCAAATTCGCGTTGCGAT
650430 AGTCAAATTC
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
34 52 0.63
36 1 0.01
38 1 0.01
40 28 0.34
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:650457 original size:74 final size:74
Alignment explanation
Indices: 650278--650457 Score: 222
Period size: 74 Copynumber: 2.4 Consensus size: 74
650268 AAATCGCAAC
* *
650278 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAA
650342 ATTCCCGTT
66 ATTCCCGTT
* * * * *
650351 GCGATAATCAAATTCACGTTGCAATAGACAAATTCG-TGTTGCGATTTT-TGCGTTGCGATAGTC
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCT-TTGCGATTTTCT-CGTTGCGATAGTC
* *
650414 ATATTCGCGTT
64 AAATTCCCGTT
* *
650425 GCGATAGTCAAATTCGCGTTGTGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
650458 GAATGTGTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
73 9 0.10
74 80 0.90
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (74 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAA
ATTCCCGTT
Found at i:650656 original size:126 final size:128
Alignment explanation
Indices: 650428--650683 Score: 471
Period size: 126 Copynumber: 2.0 Consensus size: 128
650418 TCGCGTTGCG
* *
650428 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAA-GTGTAATAAGTGATAACAACTGAACAGATCA
650493 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
65 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
650557 ATAGTCAAATTCGCGTTGCGATATTCAAATGAA-TGTAATAAGTGATAACAA-TGAACAGATCAT
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAAGTGTAATAAGTGATAACAACTGAACAGATCAT
650620 AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
650683 A
1 A
650684 AATACTCATA
Statistics
Matches: 125, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
126 75 0.60
127 18 0.14
129 32 0.26
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (128 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAAGTGTAATAAGTGATAACAACTGAACAGATCAT
AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
Found at i:650776 original size:18 final size:18
Alignment explanation
Indices: 650753--650787 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
650743 AAGCCGGTTG
*
650753 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
650771 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
650788 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:651481 original size:331 final size:332
Alignment explanation
Indices: 650878--651543 Score: 1300
Period size: 331 Copynumber: 2.0 Consensus size: 332
650868 ATTGGTGATC
650878 CACATGTCAACCTTGTATGACCACTTTCCTTGCACCGACTACATGTCAATCTCTTCTTCTCTTCA
1 CACATGTCAACCTTGTATGACCACTTTCCTTGCACCGACTACATGTCAATCTCTTCTTCTCTTCA
650943 CCCTTAGACGGTATACGATCGTGACTTTTTGGTCGGCCAGGTAGCCTTCTGTCCATGGCTGGTGG
66 CCCTTAGACGGTATACGATCGTGACTTTTTGGTCGGCCAGGTAGCCTTCTGTCCATGGCTGGTGG
651008 CAAAACTGTTTGTAAGTCATCTGGTATGTCCCACTCAGAAGGATGTGGAATAGGGTAGATAATCT
131 CAAAACTGTTTGTAAGTCATCTGGTATGTCCCACTCAGAAGGATGTGGAATAGGGTAGATAATCT
*
651073 CGGCATAAGTCTACCGATATTCTTCTGTAGTGTAGCAATCCATAGTGTATACGCTTGAATCATCT
196 CGGCATAAGTCTACCGATATACTTCTGTAGTGTAGCAATCCATAGTGTATACGCTTGAATCATCT
651138 TGGTTTAGATGAAGAGCAACTTTTATAACATGGCCACATGGATAACCAGATGTTTGTCATTTCAT
261 TGGTTTAGATGAAGAGCAACTTTTATAACATGGCCACATGGATAACCAGATGTTTGTCATTTCAT
651203 ACAACTA
326 ACAACTA
651210 CACATGTCAACCTTGTATGACCACTTTCCTTGCACCGACTACATGTCAATCTCTTCTTCTCTTCA
1 CACATGTCAACCTTGTATGACCACTTTCCTTGCACCGACTACATGTCAATCTCTTCTTCTCTTCA
651275 -CCTTAGACGGTATACGATCGTGAC-TTTTGGTTCGGCCAGGTAGCCTTCTGTCCATGGCTGGTG
66 CCCTTAGACGGTATACGATCGTGACTTTTTGG-TCGGCCAGGTAGCCTTCTGTCCATGGCTGGTG
651338 GCAAAACTGTTTGTAAGTCATCTGGTATGTCCCACTCAGAAGGATGTGGAATAGGGTAGATAATC
130 GCAAAACTGTTTGTAAGTCATCTGGTATGTCCCACTCAGAAGGATGTGGAATAGGGTAGATAATC
651403 TCGGCATAAGTCTACCGATATACTTCTGTAGTGTAGCAATCCATAGTGTATACGCTTGAATCATC
195 TCGGCATAAGTCTACCGATATACTTCTGTAGTGTAGCAATCCATAGTGTATACGCTTGAATCATC
651468 TTGGTTTAGATGAAGAGCAACTTTTATAACATGGCCACATGGATAACCAGATGTTTGTCATTTCA
260 TTGGTTTAGATGAAGAGCAACTTTTATAACATGGCCACATGGATAACCAGATGTTTGTCATTTCA
651533 TACAACTA
325 TACAACTA
651541 CAC
1 CAC
651544 GTCTTTGCAT
Statistics
Matches: 332, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
330 6 0.02
331 261 0.79
332 65 0.20
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (332 bp):
CACATGTCAACCTTGTATGACCACTTTCCTTGCACCGACTACATGTCAATCTCTTCTTCTCTTCA
CCCTTAGACGGTATACGATCGTGACTTTTTGGTCGGCCAGGTAGCCTTCTGTCCATGGCTGGTGG
CAAAACTGTTTGTAAGTCATCTGGTATGTCCCACTCAGAAGGATGTGGAATAGGGTAGATAATCT
CGGCATAAGTCTACCGATATACTTCTGTAGTGTAGCAATCCATAGTGTATACGCTTGAATCATCT
TGGTTTAGATGAAGAGCAACTTTTATAACATGGCCACATGGATAACCAGATGTTTGTCATTTCAT
ACAACTA
Found at i:653174 original size:14 final size:13
Alignment explanation
Indices: 653143--653177 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
653133 ACTCCGTTGC
653143 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
*
653156 CTTTCTTCGGGGA
1 TTTTCTTCGGGGA
653169 TTTTTCTTC
1 -TTTTCTTC
653178 TTCTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.06, C:0.20, G:0.23, T:0.51
Consensus pattern (13 bp):
TTTTCTTCGGGGA
Found at i:653406 original size:24 final size:24
Alignment explanation
Indices: 653379--653425 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
653369 CAAAATCCGA
653379 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
653403 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
653426 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:653434 original size:24 final size:24
Alignment explanation
Indices: 653383--653434 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
653373 ATCCGAGTAT
** *
653383 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
653407 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
653431 TGAC
1 TGAC
653435 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:654151 original size:20 final size:20
Alignment explanation
Indices: 654126--654214 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
654116 GAAATTCAGT
*
654126 GTTGCGATAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
654146 GTTGCGATAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
* **
654166 GTTGCGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAGAATCGC
654187 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
654207 GTTGCGAT
1 GTTGCGAT
654215 TATGTATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 39 0.68
21 12 0.21
22 3 0.05
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:654186 original size:41 final size:41
Alignment explanation
Indices: 654141--654235 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
654131 GATAGTTAGA
*
654141 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
*
654182 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
654223 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
654236 TTACATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
Found at i:654190 original size:21 final size:21
Alignment explanation
Indices: 654161--654237 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
654151 GATAGTCAGA
*
654161 ATCGAGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
654182 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
654202 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTTTGTATT
654223 ATCGCGTTGCGATTT
1 ATCGCGTTGCGATTT
654238 ACATATTTGC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 26 0.59
22 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:654253 original size:61 final size:61
Alignment explanation
Indices: 654127--654255 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 61
654117 AAATTCAGTG
* ** *
654127 TTGCGATAGTTAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTTCATATTATCGCA
** *
654188 TTGCGATAGTCAGAATCGCGTTGCGATTATGT-ATTATCGCGTTGCGATTTACATATT-T-GCA
1 TTGCGATAGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGAGTTGCGATTT-CATATTATCGCA
654249 TTGCGAT
1 TTGCGAT
654256 TTTCTAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
61 34 0.59
62 18 0.31
63 6 0.10
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (61 bp):
TTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTTCATATTATCGCA
Found at i:659108 original size:51 final size:51
Alignment explanation
Indices: 659051--659153 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
659041 TAGAAAAATA
659051 ATATAAAATCAAATGATTCTCAATTATCCAACATAACGAGACGATGATATC
1 ATATAAAATCAAATGATTCTCAATTATCCAACATAACGAGACGATGATATC
659102 ATATAAAATCAAATGATTCTCAATTATCCAACATAACGAGACGATGATATC
1 ATATAAAATCAAATGATTCTCAATTATCCAACATAACGAGACGATGATATC
659153 A
1 A
659154 CTTGATAGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (51 bp):
ATATAAAATCAAATGATTCTCAATTATCCAACATAACGAGACGATGATATC
Found at i:659810 original size:4 final size:4
Alignment explanation
Indices: 659795--659823 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
659785 GACTACTTCC
659795 TTAT TT-T TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
659824 TTATTCTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:662294 original size:3 final size:3
Alignment explanation
Indices: 662286--662324 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
662276 AAAATTTATT
*
662286 TAA TAA TAA TAAA TAA TAA TAA TAA TAA -GA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
662325 ATAAATAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 28 0.88
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:662713 original size:17 final size:17
Alignment explanation
Indices: 662691--662753 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
662681 GTTGAACAAG
662691 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
662708 TTCTTCTTCCTATTCA-GATTAG
1 TTCTTC-T-C-ATT-ATGA--AC
662730 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
662747 TTCTTCT
1 TTCTTCT
662754 GAAAATGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 14 0.38
18 2 0.05
19 6 0.16
20 6 0.16
21 2 0.05
22 7 0.19
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.51
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:662716 original size:137 final size:138
Alignment explanation
Indices: 662545--662901 Score: 479
Period size: 137 Copynumber: 2.6 Consensus size: 138
662535 TAGCAAAAGA
* * *
662545 TTGAATAAGTTCTTCTCATTAGGAACCTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * * *
662610 TCCTTCTGGAAATGTTGATCCTTAAGAAAGG-T-GTCGTTGATTCAACTTCATATCTGATGAATT
66 T-CTTCTGGAAATGTTGATCCTCAAGAAAGGTTAGTCGTTCATTCAACTCCATAGCTGATGAATC
662673 AAGGC-AAGG
130 AA-GCTAAGG
* *
662682 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATTAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * * *
662747 TTCTTCTGAAAATGTTGATCCTCAAGAGAGGTTATTCTTTCATTCAACTCCATAGGTGATGAATC
66 -TCTTCTGGAAATGTTGATCCTCAAGAAAGGTTAGTCGTTCATTCAACTCCATAGCTGATGAATC
662812 AAGCTAAGG
130 AAGCTAAGG
* * *
662821 TCGAACAAGTTCTTCTCAATATGAACTT-TTCTTCCTCTTCAGATGAGTTCTTTTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
*
662885 TTTATCTGGAAATGTTG
66 TCT-TCTGGAAATGTTG
662902 GTGTTGATCT
Statistics
Matches: 193, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
137 88 0.46
138 49 0.25
139 56 0.29
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (138 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
TCTTCTGGAAATGTTGATCCTCAAGAAAGGTTAGTCGTTCATTCAACTCCATAGCTGATGAATCA
AGCTAAGG
Found at i:663125 original size:123 final size:123
Alignment explanation
Indices: 662817--663151 Score: 519
Period size: 123 Copynumber: 2.7 Consensus size: 123
662807 GAATCAAGCT
* *
662817 AAGGTCGAACAAGTTCTTCTCAATATGAACTTTTCTTCCTCTTCAGATGAGTTCTTTTCATTATG
1 AAGGTCGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
* * * *
662882 AACTTTATCTGGAAATGTTGGTGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAA
66 AACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGC-AAA
* *
662941 AAGGTCGAATAAGTTCTTCTCATTATGAACTTTTCCTTCCTCTTCAGACGAGTTCTTCTCATTAT
1 AAGGTCGAACAAGTTCTTCTCATTATGAACTTTT-CTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
663006 GAACTCTACCTGGCAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGC-AA
65 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAA
* * *
663064 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGT
1 AAGGTCGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
663129 GAACTCTTCCTGGAAATGTTGAT
65 GAACTCTACCTGGAAATGTTGAT
663152 CTATCGAGTG
Statistics
Matches: 193, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
123 80 0.41
124 34 0.18
125 79 0.41
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (123 bp):
AAGGTCGAACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
AACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAA
Found at i:663556 original size:22 final size:22
Alignment explanation
Indices: 663528--663670 Score: 180
Period size: 22 Copynumber: 6.5 Consensus size: 22
663518 AATAAAGCTT
*
663528 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
663550 TCATCTTTGAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCTA
*
663572 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
663594 TCATCTTTGAAAATATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
663616 TCATCTTTGAAGAGTGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
* *
663638 TCATTTTTGAAGAA-TGAATCTA
1 TCATCTTTGAA-AAGAGAATCTA
663660 TCATCTTTGAA
1 TCATCTTTGAA
663671 GAATATAGAT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 103 0.99
23 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:663641 original size:66 final size:66
Alignment explanation
Indices: 663528--663677 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 66
663518 AATAAAGCTT
* *
663528 TCATCTTTGAAAAGAGAATATATCATCTTTGAAAAGAGAATCCATCATCTTTGAAGAGA-GAATC
1 TCATCTTTGAAAATATAATATATCATCTTTGAAAAGAGAATCCATCATCTTTGAAGA-ATGAATC
663592 TA
65 TA
* * * ** *
663594 TCATCTTTGAAAATATAATCTATCATCTTTGAAGAGTGAATTTATCATTTTTGAAGAATGAATCT
1 TCATCTTTGAAAATATAATATATCATCTTTGAAAAGAGAATCCATCATCTTTGAAGAATGAATCT
663659 A
66 A
663660 TCATCTTTGAAGAATATA
1 TCATCTTTGAA-AATATA
663678 GATGTAGATA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 67 0.91
67 6 0.08
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (66 bp):
TCATCTTTGAAAATATAATATATCATCTTTGAAAAGAGAATCCATCATCTTTGAAGAATGAATCT
A
Found at i:664587 original size:21 final size:22
Alignment explanation
Indices: 664563--664603 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
664553 AGATGTTTAT
664563 AAAAGAATAAA-TT-GAATTTCG
1 AAAAG-ATAAACTTGGAATTTCG
664584 AAAAGATAAACTTGGAATTT
1 AAAAGATAAACTTGGAATTT
664604 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (22 bp):
AAAAGATAAACTTGGAATTTCG
Found at i:664975 original size:13 final size:13
Alignment explanation
Indices: 664959--664999 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
664949 TTTTTTTATA
664959 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
*
664972 TTTTTTCTTCTCT
1 TTTTTTCTTTTCT
*
664985 TTTTTCCTTTT-T
1 TTTTTTCTTTTCT
664997 TTT
1 TTT
665000 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:674482 original size:16 final size:16
Alignment explanation
Indices: 674463--674496 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
674453 CATACTTACT
674463 ATAATCCCTAATTCAC
1 ATAATCCCTAATTCAC
**
674479 ATAATTTCTAATTCAC
1 ATAATCCCTAATTCAC
674495 AT
1 AT
674497 GCATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATCCCTAATTCAC
Found at i:677168 original size:3 final size:3
Alignment explanation
Indices: 677160--677216 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
677150 TGAAATTTAT
*
677160 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
677206 -GA TAA TAA TAA
1 TAA TAA TAA TAA
677217 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.11
3 42 0.89
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:677187 original size:11 final size:11
Alignment explanation
Indices: 677160--677220 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
677150 TGAAATTTAT
677160 TAATAATAATAA
1 TAATAATAAT-A
677172 TAATAATAATA
1 TAATAATAATA
677183 TAATAATAATA
1 TAATAATAATA
*
677194 TAATAATAGTA
1 TAATAATAATA
677205 -AGATAATAATA
1 TA-ATAATAATA
677216 -AATAA
1 TAATAA
677221 ATAAATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 5 0.11
11 31 0.67
12 10 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
TAATAATAATA
Found at i:677187 original size:14 final size:14
Alignment explanation
Indices: 677160--677216 Score: 71
Period size: 14 Copynumber: 4.0 Consensus size: 14
677150 TGAAATTTAT
677160 TAATAATAATAATAA
1 TAAT-ATAATAATAA
677175 TAATA-ATATAATAA
1 TAATATA-ATAATAA
*
677189 TAATATAATAATAG
1 TAATATAATAATAA
*
677203 TAAGATAATAATAA
1 TAATATAATAATAA
677217 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 1 0.03
14 31 0.84
15 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:677221 original size:4 final size:4
Alignment explanation
Indices: 677212--677237 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
677202 GTAAGATAAT
677212 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
677238 ATGGGCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:677223 original size:11 final size:10
Alignment explanation
Indices: 677160--677232 Score: 78
Period size: 11 Copynumber: 7.0 Consensus size: 10
677150 TGAAATTTAT
677160 TAAT-AATAA
1 TAATAAATAA
677169 TAAT-AATAA
1 TAATAAATAA
677178 TAATATAATAA
1 TAATA-AATAA
677189 TAATATAATAA
1 TAATA-AATAA
*
677200 TAGTAAGATAA
1 TAATAA-ATAA
677211 TAATAAATAAA
1 TAATAAAT-AA
677222 TAAATAAATAA
1 T-AATAAATAA
677233 ATAAAATGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
9 13 0.23
10 3 0.05
11 34 0.60
12 7 0.12
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (10 bp):
TAATAAATAA
Found at i:679030 original size:14 final size:14
Alignment explanation
Indices: 678993--679030 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
678983 TTCATTTTAA
*
678993 TTTTAATTTTTTTG
1 TTTTCATTTTTTTG
679007 TTTTCATTTTTGTTG
1 TTTTCATTTTT-TTG
679022 TTTTC-TTTT
1 TTTTCATTTT
679031 CATGAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTCATTTTTTTG
Found at i:683434 original size:15 final size:16
Alignment explanation
Indices: 683411--683440 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
683401 AAATGTAAAT
683411 AATACAAATATATTAG
1 AATACAAATATATTAG
683427 AATA-AAATATATTA
1 AATACAAATATATTA
683441 TTTTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AATACAAATATATTAG
Found at i:686973 original size:41 final size:42
Alignment explanation
Indices: 686914--687007 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 42
686904 ACATTCTTCC
* ** * * * *
686914 CGAAAGTCTTATGGATGGCCTGAAAGTCTTAT-CATCTTTCT
1 CGAAAGACTTATAAATGGCCCGAAAGACTTATGCATCATGCT
*
686955 CGAAAGACTTATAAATGGCCCGAAGGACTTATGCATCATGCT
1 CGAAAGACTTATAAATGGCCCGAAAGACTTATGCATCATGCT
686997 CGAAAGACTTA
1 CGAAAGACTTA
687008 CTGATGACCC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 26 0.59
42 18 0.41
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (42 bp):
CGAAAGACTTATAAATGGCCCGAAAGACTTATGCATCATGCT
Found at i:687322 original size:113 final size:114
Alignment explanation
Indices: 687029--687336 Score: 503
Period size: 114 Copynumber: 2.7 Consensus size: 114
687019 AATGACTTAC
* *
687029 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTCAGTTGTCATCAAGGAACCCCTACATATC
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATC
* *
687094 ACGTTGGTCCCTCTAGCATAGTTTTTTTTATAAAAATTCATTAAAAATCA
66 ACGTTGGTCCCTCGAGCATAG-TTTTATTATAAAAATTCATTAAAAATCA
687144 TCATCAAGAAACCCCT-AAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATC
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATC
* * *
687208 ACGTTGGTTCCTCGAGCTTAG-TTTATTATAAAAATTCATTGAAAATCA
66 ACGTTGGTCCCTCGAGCATAGTTTTATTATAAAAATTCATTAAAAATCA
* * *
687256 TCATCAAGAAACCCCTGAAAATCAGGCATAGTTTCTTAGTTGTCATCAAGGAACCCCTACAAATC
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATC
687321 ACGTTGGTCCCTCGAG
66 ACGTTGGTCCCTCGAG
687337 TCAGGCATAA
Statistics
Matches: 181, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
112 41 0.23
113 60 0.33
114 65 0.36
115 15 0.08
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (114 bp):
TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATC
ACGTTGGTCCCTCGAGCATAGTTTTATTATAAAAATTCATTAAAAATCA
Found at i:687442 original size:39 final size:39
Alignment explanation
Indices: 687387--688007 Score: 816
Period size: 39 Copynumber: 15.9 Consensus size: 39
687377 ATAAATATTT
* * *
687387 TGTTTCCAGTGAAACTATCTCAAGTGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
687426 TGTTTCAAGTGG-AACTATCTCAGGCGAGATAAAATCTTC
1 TGTTTCAAG-GGAAACTATCTCAAGCGAGATAAAATCTTC
*
687465 TATTTCAAGGGAAACTATCTCAAGCGAGACT-AAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGA-TAAAATCTTC
* *
687504 TGTTTCGAGGGAAACTATCTCAAGCAAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
687543 TGTTTCAGGGGAAACAATCTCAACCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
687582 TGTTTCGAGGGAAACTATCTCAAGCCAGATAACATCTTA
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
** * * *
687621 TGTTTTGAGGGAAACTATCTCAAGAGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
687660 TGTTTCAAGTGAAACTATCTCAAGTGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
687699 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
687738 TGTTTCAAGGGAAATTATCTCAAGGGAGACAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
687777 TGTTTCGAGGGAAACTATCTCAAGCTAGATAAAATATTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
** *
687816 TGTTTCAAGGGAAACTATCTCAAGTTAGATAAAATTTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
687855 TGTTTCAAGTGAAACTATCTCAAGCAAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
687894 TGTTT-GAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
687932 TTTTTCGAGAGAAAATATCTCAAGCGAGACAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
687971 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCT
688008 GGTTTTAAGA
Statistics
Matches: 509, Mismatches: 68, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
38 37 0.07
39 470 0.92
40 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:688084 original size:37 final size:36
Alignment explanation
Indices: 688043--688172 Score: 95
Period size: 37 Copynumber: 3.5 Consensus size: 36
688033 AAATGAATCT
*
688043 TCTTGTTTTGAGTAAAAACTGTCTTAAGCGAGAAAAA
1 TCTTGTTTTAAG-AAAAACTGTCTTAAGCGAGAAAAA
** * *
688080 TCTTGTTTTAAGAAAAAC-AACATGT-AGTGAAATGAAATA
1 TCTTGTTTTAAGAAAAACTGTC-T-TAAGCG--A-GAAAAA
* * *
688119 TCTTATTTTGAGTAAAAACTGTCTCAAGCGAGACAAAA
1 TCTTGTTTTAAG-AAAAACTGTCTTAAGCGAGA-AAAA
688157 TC-TGTTTTAAGAAAAA
1 TCTTGTTTTAAGAAAAA
688173 TAATCTTGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
35 1 0.01
36 15 0.21
37 21 0.30
38 7 0.10
39 15 0.21
40 10 0.14
41 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (36 bp):
TCTTGTTTTAAGAAAAACTGTCTTAAGCGAGAAAAA
Found at i:688128 original size:76 final size:77
Alignment explanation
Indices: 687982--688396 Score: 437
Period size: 75 Copynumber: 5.5 Consensus size: 77
687972 GTTTCAAGTG
* * * * *
687982 AAACTATCTCAAGCGAGATAAAATCTGGTTTTAAGAAAAA-AACCTTGAGTGAAATG-AATCTTC
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAAT-GTC
*
688045 TTGTTTTGAGTAA
65 TTCTTTTGAGTAA
* * *
688058 AAACTGTCTTAAGCGAGA-AAAATCTTGTTTTAAGAAAAACAA-CATGTAGTGAAATGAAATATC
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTG-AGTGAAATGAAATGTC
*
688121 TTATTTTGAGTAA
65 TTCTTTTGAGTAA
* * *
688134 AAACTGTCTCAAGCGAGACAAAATC-TGTTTTAAGAAAAATAATCTTGATTGAAATGAAATGTAT
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
*
688198 TCTTTCGAGTAA
66 TCTTTTGAGTAA
* * *
688210 AAA-TGTCTTAAGAGAGAC-AAATCTTGTTTTAAGAAAAACAATCTTGAGTCAAATGAAATGTCT
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
688273 TCTTTCT-AGT-A
66 TCTTT-TGAGTAA
* * ** * *
688284 AAACCGTCTCAAGCGAGACAAAGTC-TGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAA--TCC
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
* *
688345 TCTGTATTAAAT-A
66 TCT-T-TTGAGTAA
*
688358 AGACTGTCTCAAGCGAGACAAAAT-TTGTTTCTAAGAAAA
1 AAACTGTCTCAAGCGAGACAAAATCTTGTTT-TAAGAAAA
688397 CTAGTCTCGA
Statistics
Matches: 291, Mismatches: 34, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
72 5 0.02
73 2 0.01
74 42 0.14
75 125 0.43
76 105 0.36
77 12 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (77 bp):
AAACTGTCTCAAGCGAGACAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
TCTTTTGAGTAA
Found at i:688264 original size:151 final size:150
Alignment explanation
Indices: 687973--688328 Score: 459
Period size: 151 Copynumber: 2.4 Consensus size: 150
687963 AAATCTTCTG
* * * * *
687973 TTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTGGTTTTAAGAAAAAAACCTTGAGTGAAATG
1 TTTCTAGTAAAACTGTCTCAAGCGAGACAAAATCT-GTTTTAAGAAAAAAATCTTGAGTGAAATG
* * * * *
688038 AATCTTCTTGTTTTGAGTAAAAACTGTCTTAAGCGAGAAAAATCTTGTTTTAAGAAAAACAACAT
65 AATCGTATTCTTTCGAGTAAAAACTGTCTTAAGAGAGAAAAATCTTGTTTTAAGAAAAACAACAT
*
688103 GTAGTGAAATGAAATATCTTA
130 GTAGTCAAATGAAATATCTTA
*
688124 TTT-TGAGTAAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAATAATCTTGATTGAAA
1 TTTCT-AGT-AAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAA-AATCTTGAGTGAAA
*
688188 TGAAAT-GTATTCTTTCGAGTAAAAA-TGTCTTAAGAGAGACAAATCTTGTTTTAAGAAAAACAA
63 TG-AATCGTATTCTTTCGAGTAAAAACTGTCTTAAGAGAGAAAAATCTTGTTTTAAGAAAAACAA
* * *
688251 TCTTG-AGTCAAATGAAATGTCTTC
127 -CATGTAGTCAAATGAAATATCTTA
* *
688275 TTTCTAGTAAAACCGTCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAACAATCT
1 TTTCTAGTAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAA-AATCT
688329 CAAGTGAGAT
Statistics
Matches: 180, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
150 43 0.24
151 77 0.43
152 57 0.32
153 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (150 bp):
TTTCTAGTAAAACTGTCTCAAGCGAGACAAAATCTGTTTTAAGAAAAAAATCTTGAGTGAAATGA
ATCGTATTCTTTCGAGTAAAAACTGTCTTAAGAGAGAAAAATCTTGTTTTAAGAAAAACAACATG
TAGTCAAATGAAATATCTTA
Found at i:688323 original size:36 final size:36
Alignment explanation
Indices: 688283--688413 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 36
688273 TCTTTCTAGT
* *
688283 AAAACCGTCTCAAGCGAGACAAAGTCTGTTTTAAGA
1 AAAACAGTCTCAAGCGAGACAAAATCTGTTTTAAGA
* * * * *
688319 AAAACAATCTCAAGTGAGATAAATCCTCTGTATTAA-A
1 AAAACAGTCTCAAGCGAGACAAA--ATCTGTTTTAAGA
* * *
688356 TAAGACTGTCTCAAGCGAGACAAAATTTGTTTCTAAG-
1 -AAAACAGTCTCAAGCGAGACAAAATCTGTTT-TAAGA
*
688393 AAAACTAGTCTCGAGCGAGAC
1 AAAAC-AGTCTCAAGCGAGAC
688414 GACTCTTTGT
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
36 28 0.39
37 17 0.24
38 27 0.38
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (36 bp):
AAAACAGTCTCAAGCGAGACAAAATCTGTTTTAAGA
Found at i:689586 original size:10 final size:10
Alignment explanation
Indices: 689571--689626 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 10
689561 TCTTGTCCTA
*
689571 TTTTTCTTTG
1 TTTTTCTTTC
689581 TTTTTCTTTTC
1 TTTTTC-TTTC
689592 TTTTTCTTTC
1 TTTTTCTTTC
689602 TTCTTTGCTTT-
1 TT-TTT-CTTTC
*
689613 TTATTTTTTTC
1 TT-TTTCTTTC
689624 TTT
1 TTT
689627 GCTCTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 16 0.41
11 19 0.49
12 4 0.10
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:689590 original size:15 final size:15
Alignment explanation
Indices: 689572--689626 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
689562 CTTGTCCTAT
689572 TTTTCTTTGTT-TTTC
1 TTTTCTTT-TTCTTTC
689587 TTTTCTTTTTCTTTC
1 TTTTCTTTTTCTTTC
*
689602 TTCTTTGCTTTTTATTT-
1 -T-TTT-CTTTTTCTTTC
689619 TTTTCTTT
1 TTTTCTTT
689627 GCTCTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 6 0.17
15 15 0.43
16 2 0.06
17 3 0.09
18 9 0.26
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTTC
Found at i:689605 original size:28 final size:26
Alignment explanation
Indices: 689574--689626 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
689564 TGTCCTATTT
* *
689574 TTCTTTGTTTTTCTTTTCTTTTTCTTTC
1 TTCTTTGCTTTT-TATT-TTTTTCTTTC
689602 TTCTTTGCTTTTTATTTTTTTCTTT
1 TTCTTTGCTTTTTATTTTTTTCTTT
689627 GCTCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 3 0.13
28 11 0.48
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (26 bp):
TTCTTTGCTTTTTATTTTTTTCTTTC
Found at i:689624 original size:19 final size:18
Alignment explanation
Indices: 689581--689629 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
689571 TTTTTCTTTG
*
689581 TTTTTCTTTTCTTTTTCT
1 TTTTTCTTTGCTTTTTCT
* *
689599 TTCTTCTTTGCTTTTTATT
1 TTTTTCTTTGCTTTTT-CT
689618 TTTTTCTTTGCT
1 TTTTTCTTTGCT
689630 CTATTTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTGCTTTTTCT
Found at i:689636 original size:14 final size:15
Alignment explanation
Indices: 689618--689658 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
689608 GCTTTTTATT
689618 TTTTTCTTTGCTCTA
1 TTTTTCTTTGCTCTA
689633 TTTTTCTTTGCTCT-
1 TTTTTCTTTGCTCTA
689647 TTTTTCTTTGCT
1 TTTTTCTTTGCT
689659 TTTATCCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (15 bp):
TTTTTCTTTGCTCTA
Found at i:698800 original size:41 final size:40
Alignment explanation
Indices: 698755--698959 Score: 139
Period size: 40 Copynumber: 5.0 Consensus size: 40
698745 AAACATACTT
* *
698755 TAGTGGTGTTTATGTAGAAAACACCGCTATAGCCAGATATA
1 TAGTGGCGTTTATGTA-AAAACGCCGCTATAGCCAGATATA
* * * *
698796 TAGTGGCGATTT-TATAAAAACGCCGCTAAAACCTCG-TACTA
1 TAGTGGCG-TTTATGTAAAAACGCCGCTATAGCC-AGATA-TA
*
698837 TAGTGGCGTTTATGTAAAAA-GCCTCTATAGCCAGATATA
1 TAGTGGCGTTTATGTAAAAACGCCGCTATAGCCAGATATA
* * ** * * ** *
698876 TAGTGACGTTTTTGTGTAAACGCCACTAAAGTAAGAGTACTT
1 TAGTGGCGTTTATGTAAAAACGCCGCTATAGCCAGA-TA-TA
* * * *
698918 TAGTGGCGTTTATGTTAAAATGCC-ATGATAGCCCGATATA
1 TAGTGGCGTTTATGTAAAAACGCCGCT-ATAGCCAGATATA
698958 TA
1 TA
698960 ACACCATTTG
Statistics
Matches: 124, Mismatches: 31, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
39 19 0.15
40 44 0.35
41 33 0.27
42 28 0.23
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (40 bp):
TAGTGGCGTTTATGTAAAAACGCCGCTATAGCCAGATATA
Done.