Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2366315 original size:185 final size:186
Alignment explanation
Indices: 2365964--2366319 Score: 642
Period size: 185 Copynumber: 1.9 Consensus size: 186
2365954 AGGCTTTGAA
** *
2365964 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGAA
*
2366029 AATAGTTTATTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
66 AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
** *
2366094 GAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 GAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAAC
2366150 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGAA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGAA
2366215 AATAGTTTACTAAGT-AAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
66 AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
2366279 GAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATT
131 GAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATT
2366320 CTGTTTTTTG
Statistics
Matches: 163, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
185 87 0.53
186 76 0.47
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (186 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGTGGAA
AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
GAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAAC
Found at i:2366915 original size:22 final size:22
Alignment explanation
Indices: 2366887--2366941 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2366877 CATAAAGCTT
2366887 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
**
2366909 TCATCTTAAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2366931 TCATCTTTGAA
1 TCATCTTTGAA
2366942 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2369572 original size:114 final size:114
Alignment explanation
Indices: 2369372--2369591 Score: 395
Period size: 114 Copynumber: 1.9 Consensus size: 114
2369362 GATCATGCAG
* *
2369372 TTCATCTTTCAATTCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAAATAACTCAAAGA
*
2369437 ACACTTCCAGAAGATGCTATTGGATCTCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
*
2369486 TTCATCTTTTAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAAATAACTCAAAGA
*
2369551 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTTTACTA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTA
2369592 CGAGAACGTG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAAATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
Found at i:2371754 original size:10 final size:9
Alignment explanation
Indices: 2371733--2371809 Score: 75
Period size: 9 Copynumber: 8.3 Consensus size: 9
2371723 ATTTCTCCCC
2371733 TTTTTC-TT
1 TTTTTCTTT
*
2371741 TTTTCCTTT
1 TTTTTCTTT
2371750 TTTTTCTTT
1 TTTTTCTTT
2371759 TTTTTCTTT
1 TTTTTCTTT
2371768 TTTTTCTTT
1 TTTTTCTTT
* * **
2371777 CTTTGCTGGA
1 TTTTTCT-TT
2371787 TTTTTCTTTT
1 TTTTTC-TTT
2371797 TTCTTTCTTT
1 TT-TTTCTTT
2371807 TTT
1 TTT
2371810 GGATGAGTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
8 5 0.09
9 34 0.62
10 11 0.20
11 5 0.09
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2371812 original size:26 final size:26
Alignment explanation
Indices: 2371740--2371813 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
2371730 CCCTTTTTCT
*
2371740 TTTTTCCTTTTT-TTTCTTTTTT---
1 TTTTTCTTTTTTCTTTCTTTTTTGGA
* **
2371762 TTCTT-TTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTTTTGGA
2371787 TTTTTCTTTTTTCTTTCTTTTTTGGA
1 TTTTTCTTTTTTCTTTCTTTTTTGGA
2371813 T
1 T
2371814 GAGTATAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 5 0.12
22 12 0.30
25 4 0.10
26 19 0.47
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.77
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTTTTGGA
Found at i:2374659 original size:15 final size:14
Alignment explanation
Indices: 2374631--2374669 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2374621 TAAAAGTATG
2374631 AATGCAAAATGAAA
1 AATGCAAAATGAAA
2374645 AATGCAAAGATGAAA
1 AATGCAAA-ATGAAA
2374660 AATG-AAAATG
1 AATGCAAAATG
2374670 CATATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 11 0.46
15 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:2374660 original size:21 final size:21
Alignment explanation
Indices: 2374636--2374681 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2374626 GTATGAATGC
2374636 AAAATGAAAAATGCAAAGATGA
1 AAAATG-AAAATGCAAAGATGA
* *
2374658 AAAATGAAAATGCATATATGA
1 AAAATGAAAATGCAAAGATGA
2374679 AAA
1 AAA
2374682 GGTGTTACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.63, C:0.04, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAATGAAAATGCAAAGATGA
Found at i:2376756 original size:16 final size:15
Alignment explanation
Indices: 2376721--2376772 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 15
2376711 AAAATACTTG
*
2376721 AATAAAATAAATA--
1 AATAAAATAAAAAGT
2376734 AATAAAATAAAAAGT
1 AATAAAATAAAAAGT
2376749 ATATAAAAATAAAAAGT
1 A-AT-AAAATAAAAAGT
2376766 AATAAAA
1 AATAAAA
2376773 AATTTGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 12 0.35
15 5 0.15
16 4 0.12
17 13 0.38
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAAAGT
Found at i:2376774 original size:18 final size:18
Alignment explanation
Indices: 2376730--2376774 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
2376720 GAATAAAATA
2376730 AATAAATAAAATAAAAAGT
1 AATAAA-AAAATAAAAAGT
*
2376749 -ATATAAAAATAAAAAGT
1 AATAAAAAAATAAAAAGT
2376766 AATAAAAAA
1 AATAAAAAA
2376775 TTTGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (18 bp):
AATAAAAAAATAAAAAGT
Found at i:2376775 original size:17 final size:17
Alignment explanation
Indices: 2376737--2376773 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2376727 ATAAATAAAT
2376737 AAAATAAAAAGTATATA
1 AAAATAAAAAGTATATA
2376754 AAAATAAAAAGTA-ATA
1 AAAATAAAAAGTATATA
2376770 AAAA
1 AAAA
2376774 ATTTGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAGTATATA
Found at i:2377414 original size:21 final size:22
Alignment explanation
Indices: 2377390--2377433 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2377380 AAATATTTTC
2377390 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
2377411 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
2377433 T
1 T
2377434 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:2377650 original size:2 final size:2
Alignment explanation
Indices: 2377643--2377674 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2377633 ATTATTTAAA
2377643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2377675 TTATGTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2377704 original size:17 final size:17
Alignment explanation
Indices: 2377684--2377717 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2377674 TTTATGTGAC
2377684 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
2377701 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
2377718 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:2377742 original size:16 final size:16
Alignment explanation
Indices: 2377723--2377755 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2377713 AATAACAAAT
2377723 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
2377739 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
2377755 T
1 T
2377756 TTAAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:2378011 original size:20 final size:20
Alignment explanation
Indices: 2377986--2378029 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2377976 TAAAAGTATA
2377986 TGGTTGGAGTAATAAATGAT
1 TGGTTGGAGTAATAAATGAT
2378006 TGGTTGGAGTAATAAATGAT
1 TGGTTGGAGTAATAAATGAT
2378026 TGGT
1 TGGT
2378030 CTCTGGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (20 bp):
TGGTTGGAGTAATAAATGAT
Found at i:2378046 original size:10 final size:10
Alignment explanation
Indices: 2378031--2378055 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2378021 ATGATTGGTC
2378031 TCTGGTAGCT
1 TCTGGTAGCT
2378041 TCTGGTAGCT
1 TCTGGTAGCT
2378051 TCTGG
1 TCTGG
2378056 AGTAAGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.32, T:0.40
Consensus pattern (10 bp):
TCTGGTAGCT
Found at i:2379118 original size:27 final size:28
Alignment explanation
Indices: 2379088--2379158 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
2379078 CATAAACAAC
2379088 ATTATCGATTCTAAGAGTTGCAA-CCCT
1 ATTATCGATTCTAAGAGTTGCAACCCCT
* * *
2379115 ATTAGCTA-T-TAA-ACTTGCAAGTCCCCT
1 ATTATCGATTCTAAGAGTTGCAA--CCCCT
2379142 ATTATCGATTCTAAGAG
1 ATTATCGATTCTAAGAG
2379159 AACGAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
24 7 0.22
25 3 0.09
26 1 0.03
27 16 0.50
28 1 0.03
29 3 0.09
30 1 0.03
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (28 bp):
ATTATCGATTCTAAGAGTTGCAACCCCT
Found at i:2379637 original size:3 final size:3
Alignment explanation
Indices: 2379629--2379688 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
2379619 TTTTACTTAA
** *
2379629 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
2379674 ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
2379689 AATAATTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2379670 original size:16 final size:14
Alignment explanation
Indices: 2379629--2379688 Score: 65
Period size: 13 Copynumber: 4.5 Consensus size: 14
2379619 TTTTACTTAA
*
2379629 ATTATTATTA-A-A
1 ATTATTATTATATT
2379641 ATTATTATTATTATT
1 ATTATTATTA-TATT
*
2379656 ATTATTA-AATATT
1 ATTATTATTATATT
2379669 ATTA-TATTATATT
1 ATTATTATTATATT
2379682 ATTATTA
1 ATTATTA
2379689 AATAATTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 12 0.30
13 17 0.43
14 4 0.10
15 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:2379696 original size:24 final size:26
Alignment explanation
Indices: 2379629--2379696 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
2379619 TTTTACTTAA
2379629 ATTATTATT-AA-AATTATTATTATT
1 ATTATTATTAAATAATTATTATTATT
2379653 ATTATTATTAAAT-ATTATTA-TATTAT
1 ATTATTATTAAATAATTATTATTA-T-T
2379679 ATTATTATTAAATAATTA
1 ATTATTATTAAATAATTA
2379697 CAAGCCCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.28
25 10 0.26
26 14 0.36
27 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTATTATTAAATAATTATTATTATT
Found at i:2381162 original size:3 final size:3
Alignment explanation
Indices: 2381154--2381207 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
2381144 TATTTTATTT
* * * *
2381154 ATA ATA ATA GTA ATA ATTA ATTA CTC ATA ATA ATA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
2381201 ATA ATA A
1 ATA ATA A
2381208 AGTCTGGACG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2381588 original size:93 final size:92
Alignment explanation
Indices: 2381429--2381630 Score: 234
Period size: 93 Copynumber: 2.2 Consensus size: 92
2381419 GTCAGACTTG
* * *
2381429 TTCCACTGTTACTCA--AATATCAAATCTTAAAAGAAAGTGATTTGTTCCACTTCTTCCTGTGGG
1 TTCCACTGTTACTCATGAATATCAAATCATAAAAGAAAGTGATTTGTTCCACTTCTTCCTGAGAG
* * *
2381492 AAAATCAAATCCAGGGATGTTGATTTA
66 AAAATCAAATACAGGGATATTGATTCA
* *
2381519 TTCCACTATTACTCATGGAATATCAAATCATGAAAGAGAA-TGATCTAT-TTCC-CTTCTTCCTG
1 TTCCACTGTTACTCAT-GAATATCAAATCATAAAAGA-AAGTGAT-T-TGTTCCACTTCTTCCTG
* * *
2381581 AGAGAAAATTAGATATAGGGATATTGATTCA
62 AGAGAAAATCAAATACAGGGATATTGATTCA
2381612 TTCCACTGTTACTCATGAA
1 TTCCACTGTTACTCATGAA
2381631 AGAATGAATC
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
90 14 0.15
92 3 0.03
93 69 0.73
94 7 0.07
95 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (92 bp):
TTCCACTGTTACTCATGAATATCAAATCATAAAAGAAAGTGATTTGTTCCACTTCTTCCTGAGAG
AAAATCAAATACAGGGATATTGATTCA
Found at i:2381773 original size:134 final size:134
Alignment explanation
Indices: 2381519--2381777 Score: 317
Period size: 134 Copynumber: 1.9 Consensus size: 134
2381509 TGTTGATTTA
* * *
2381519 TTCCACTATTACTCATGGAATATCAAATCATGAAAGAGAATGATCTATTTCCCTTCTTCCTGAGA
1 TTCCACTATTACTCAAGGAATATCAAATCATGAAAGAGAAGGATCTATTTCCCTTCTTACTGAGA
* * *
2381584 GAAAATTAGATATAGGGATATTGATTCATTCCACTGTTACTCATGAAAGAATGAATCAAGACAGA
66 GAAAATCAGATATAGGAATATTGATTCATTCCACTGTTACTCAAGAAAGAATGAATCAAGACAGA
2381649 CTTG
131 CTTG
* * *
2381653 TTCCACTATTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATCTA-TTCCGCTTCTTATTGAG
1 TTCCACTATTACTCAAGGAATATCAAATCATGAAAGAGAAGGATCTATTTCC-CTTCTTACTGAG
* * * * * * * *
2381717 GGAAAATCAGATCT-GGAAATGTTGATTTATTCTATTGTT-CTTCAAGGAAGATTGAATCAAG
65 AGAAAATCAGATATAGG-AATATTGATTCATTCCACTGTTAC-TCAAGAAAGAATGAATCAAG
2381778 TTCGATTTGC
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
133 7 0.07
134 98 0.93
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (134 bp):
TTCCACTATTACTCAAGGAATATCAAATCATGAAAGAGAAGGATCTATTTCCCTTCTTACTGAGA
GAAAATCAGATATAGGAATATTGATTCATTCCACTGTTACTCAAGAAAGAATGAATCAAGACAGA
CTTG
Found at i:2382589 original size:233 final size:231
Alignment explanation
Indices: 2382113--2382699 Score: 732
Period size: 233 Copynumber: 2.5 Consensus size: 231
2382103 TTACCCAAAG
* ** * *
2382113 GACTTA-TGGATGGCCCGAAGGACTTACCAATTTTTGTTATGGTTTACTAGGTAATAAACTTTTC
1 GACTTACT-GATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTC
* * * * * *
2382177 TTACTTTTCAAAAATTTCAATGTTC-TGATTTAAATAAGAAATTTTTCTCATTTGTTTGACAGGC
65 TTACTTTTCAAAATTTTCAATTTTCAT-ATTTAAAT--GAGATCTTTCTCATTT-TTTGAAAGAC
* *
2382241 AGGTGAAAACATCCTGACCAAAGGTTTTATGCATGGCCCGAAGGACTTATCATCTTGCTCGAAAG
126 AGGTGAAAACATCCTGACCAAAGGTCTTATGCATGGCCCGAAGGACTTATCATCTTGCTCAAAAG
* * * * *
2382306 ACTTATAGATGACTCGAAGGATTTAAGTATCATGCTCGAAA
191 ACATACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAA
* * *
2382347 GACTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAGGAAACTTTTCT
1 GACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCT
*
2382412 TACTTTTCAAAATTTTCAATTTTCATATTTAAATGAGACTCCTTTCTCATTTTTTGAAAGACATG
66 TACTTTTCAAAATTTTCAATTTTCATATTTAAATGAGA-T-CTTTCTCATTTTTTGAAAGACAGG
* * * *
2382477 TGAAAACATCCT-ACCCAAAGGTCTTATGGATGGCCTGAATGACTTATCATCTTGCTCAAAATAC
129 TGAAAACATCCTGA-CCAAAGGTCTTATGCATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAC
* *
2382541 ATACATATAACCCGAAGGATTTAAGCATCATGCTTGAAA
193 ATACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAA
* * *
2382580 GACTTACTGATGGCCCGAGGGCCTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTCCT
1 GACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCT
* * * *
2382645 TACTTTTCAACAATTTTC-ATTTTTAGATTTAAACGAGAAACTGTTCTCATTTTTT
66 TACTTTTCAA-AATTTTCAATTTTCATATTTAAATGAG-ATCT-TTCTCATTTTTT
2382700 AACTTATAAA
Statistics
Matches: 307, Mismatches: 38, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
232 6 0.02
233 196 0.64
234 103 0.34
235 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (231 bp):
GACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCT
TACTTTTCAAAATTTTCAATTTTCATATTTAAATGAGATCTTTCTCATTTTTTGAAAGACAGGTG
AAAACATCCTGACCAAAGGTCTTATGCATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACATA
CAGATAACCCGAAGGATTTAAGCATCATGCTCGAAA
Found at i:2384512 original size:31 final size:30
Alignment explanation
Indices: 2384466--2384527 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
2384456 TCTTTCTTTA
2384466 TCTTTATTTTTTTTCTTTATTCTTTTTCTT
1 TCTTTATTTTTTTTCTTTATTCTTTTTCTT
*
2384496 TCTTTATTCTTTTTTCTTTTTTCTTTTTCTT
1 TCTTTATT-TTTTTTCTTTATTCTTTTTCTT
2384527 T
1 T
2384528 TTTCAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (30 bp):
TCTTTATTTTTTTTCTTTATTCTTTTTCTT
Found at i:2384514 original size:44 final size:43
Alignment explanation
Indices: 2384405--2384529 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 43
2384395 CTTATCTATC
* *
2384405 CTTTCTTTCATTCTTTTTCCTTTTCATTTTCCTTTTCATTTTCCTTTT
1 CTTTCTTT-ATTCTTTTTTC-TTT-ATTTT--TTTTCTTTTTCCTTTT
* *
2384453 CTTTC--T-TTC-TTTATCTTTATTTTTTTTCTTTATTCTTTTT
1 CTTTCTTTATTCTTTTTTCTTTATTTTTTTTCTTT-TTCCTTTT
2384493 CTTTCTTTATTCTTTTTTCTTT-TTTCTTTTTCTTTTT
1 CTTTCTTTATTCTTTTTTCTTTATTT-TTTTTCTTTTT
2384530 TCAAGTGTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
39 7 0.11
40 12 0.18
41 5 0.08
42 4 0.06
43 12 0.18
44 20 0.30
46 1 0.02
48 5 0.08
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (43 bp):
CTTTCTTTATTCTTTTTTCTTTATTTTTTTTCTTTTTCCTTTT
Found at i:2384515 original size:6 final size:6
Alignment explanation
Indices: 2384415--2384529 Score: 90
Period size: 6 Copynumber: 18.3 Consensus size: 6
2384405 CTTTCTTTCA
* * * * *
2384415 TTCTTT TTCCTT TTCATT TTCCTT TTCATT TTCCTT TTCTTTCT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TT-T TTCTTT
* *
2384465 ATCTTT ATTTTTT TTCTTT ATTCTTT TTC--T TTCTTT ATTCTTTT TTCTTTT
1 TTCTTT -TTCTTT TTCTTT -TTCTTT TTCTTT TTCTTT -TTC-TTT TTC-TTT
2384516 TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TT
2384530 TCAAGTGTGG
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
4 4 0.04
6 54 0.59
7 26 0.29
8 7 0.08
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:2384528 original size:13 final size:13
Alignment explanation
Indices: 2384443--2384531 Score: 81
Period size: 13 Copynumber: 6.4 Consensus size: 13
2384433 TTCCTTTTCA
*
2384443 TTTTCCTTTTCTT
1 TTTTCTTTTTCTT
*
2384456 TCTTTCTTTATCTT
1 T-TTTCTTTTTCTT
2384470 TATTT-TTTTTCTT
1 T-TTTCTTTTTCTT
*
2384483 TATTCTTTTTCTTTCT
1 TTTTCTTTTTC--T-T
2384499 TTATTCTTTTTTCTT
1 TT-TTC-TTTTTCTT
2384514 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
2384527 TTTTC
1 TTTTC
2384532 AAGTGTGGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
12 2 0.03
13 28 0.44
14 17 0.27
15 4 0.06
16 3 0.05
17 3 0.05
18 6 0.10
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:2384529 original size:7 final size:7
Alignment explanation
Indices: 2384449--2384531 Score: 73
Period size: 7 Copynumber: 11.7 Consensus size: 7
2384439 TTCATTTTCC
2384449 TTTTCTT
1 TTTTCTT
2384456 TCTTTC-T
1 T-TTTCTT
*
2384463 TTATCTT
1 TTTTCTT
*
2384470 TATT-TT
1 TTTTCTT
2384476 TTTTCTT
1 TTTTCTT
*
2384483 TATTCTTTT
1 T-TT-TCTT
2384492 TCTTTCTT
1 T-TTTCTT
*
2384500 TATTCTT
1 TTTTCTT
2384507 TTTTCTT
1 TTTTCTT
2384514 TTTTC-T
1 TTTTCTT
2384520 TTTTCTT
1 TTTTCTT
2384527 TTTTC
1 TTTTC
2384532 AAGTGTGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
6 14 0.23
7 31 0.51
8 10 0.16
9 6 0.10
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:2395420 original size:10 final size:9
Alignment explanation
Indices: 2395402--2395463 Score: 92
Period size: 9 Copynumber: 7.0 Consensus size: 9
2395392 TTCTTTGAAG
2395402 ATGAAAAAA
1 ATGAAAAAA
2395411 ATGAAAAAAA
1 ATG-AAAAAA
2395421 ATGAAAAAA
1 ATGAAAAAA
2395430 ATG-AAAAA
1 ATGAAAAAA
2395438 ATG-AAAAA
1 ATGAAAAAA
2395446 ATGAAAAAA
1 ATGAAAAAA
*
2395455 AGGAAAAAA
1 ATGAAAAAA
2395464 GAAGGAGGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
8 16 0.32
9 25 0.50
10 9 0.18
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:2395426 original size:19 final size:19
Alignment explanation
Indices: 2395402--2395455 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
2395392 TTCTTTGAAG
2395402 ATGAAAAAAATGAAAAAAA
1 ATGAAAAAAATGAAAAAAA
2395421 ATGAAAAAAATG--AAAAA
1 ATGAAAAAAATGAAAAAAA
2395438 ATG-AAAAAATGAAAAAAA
1 ATGAAAAAAATGAAAAAAA
2395456 GGAAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.24
17 8 0.24
18 5 0.15
19 12 0.36
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
ATGAAAAAAATGAAAAAAA
Found at i:2395427 original size:7 final size:8
Alignment explanation
Indices: 2395406--2395454 Score: 71
Period size: 8 Copynumber: 5.8 Consensus size: 8
2395396 TTGAAGATGA
2395406 AAAAAATG
1 AAAAAATG
2395414 AAAAAAAATG
1 --AAAAAATG
2395424 AAAAAAATG
1 -AAAAAATG
2395433 AAAAAATG
1 AAAAAATG
2395441 AAAAAATG
1 AAAAAATG
2395449 AAAAAA
1 AAAAAA
2395455 AGGAAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 22 0.56
9 9 0.23
10 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:2395436 original size:17 final size:17
Alignment explanation
Indices: 2395406--2395463 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
2395396 TTGAAGATGA
2395406 AAAAAATGAAAAAAAATG
1 AAAAAATG-AAAAAAATG
2395424 AAAAAAATG-AAAAAATG
1 -AAAAAATGAAAAAAATG
*
2395441 AAAAAATGAAAAAAAGG
1 AAAAAATGAAAAAAATG
2395458 AAAAAA
1 AAAAAA
2395464 GAAGGAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 8 0.22
17 21 0.57
19 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAAAATGAAAAAAATG
Found at i:2396870 original size:55 final size:55
Alignment explanation
Indices: 2396744--2397279 Score: 722
Period size: 55 Copynumber: 9.8 Consensus size: 55
2396734 GTGAAGCAAA
* * *
2396744 TGAAGATTGTTCGAGTCTTATACTCTTTGAAGAAATAGGG-GCATACACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* * * *
2396798 TGAAGATTATTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCATACACGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* * *
2396853 TGAAGATTGCTCAAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* * * * *
2396908 TGAATATTGTTCGAGTCTTAAACTCTCTAAAGAAATAGGGAGCAGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* *
2396963 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCGGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* * *
2397018 TGAAGATTGTTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACATGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* *
2397073 TGAAGATTGCTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACGATTAT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
* *
2397128 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATG-CATGATTAA
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCA-GACACGATTAT
* * * * * * *
2397183 TGAAGGTTGTTCGAGTCTTATACTCTTTGAAAAAATAGGGAACAAACACGATTGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
*
2397238 TGAAG-TTGTTCGAGATC-CATACT-TCCTGAAGCAATAGGGAGC
1 TGAAGATTGTTCGAG-TCTCATACTCT-CTGAAGAAATAGGGAGC
2397280 GAACCCGCTG
Statistics
Matches: 429, Mismatches: 48, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 65 0.15
55 362 0.84
56 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTAT
Found at i:2397443 original size:3 final size:3
Alignment explanation
Indices: 2397427--2397499 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
2397417 AAGAGAAGAA
* * * * *
2397427 ATT A-T ATT ACT ATT ATT ATT ATA ACT ATT A-T ATT ATA ATAC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
*
2397471 ATT ATT ATT ATT ATT GCTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT A
2397500 CATATTTTGC
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.85
4 4 0.07
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:2397509 original size:22 final size:22
Alignment explanation
Indices: 2397468--2397509 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2397458 ATTATAATAC
*
2397468 ATTATTATTATTATTATTGCTT
1 ATTATTATTAATATTATTGCTT
2397490 ATTATTATTACATATT-TTGC
1 ATTATTATTA-ATATTATTGC
2397510 AGCACCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTATTATTAATATTATTGCTT
Found at i:2401331 original size:75 final size:75
Alignment explanation
Indices: 2401234--2401373 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
2401224 CATTTCGTAG
* *
2401234 GTTTTATTATACTTTTTCATATAAGCAAATGTACCCGTATTCATATAAATAAAA-ATATA-TAAT
1 GTTTTATTATACTTATTCATATAAGAAAATGTA-CCGTATTCATATAAATAAAATATATACTAAT
2401297 TTTTTTTCACA
65 TTTTTTTCACA
* * * * *
2401308 GTTTTCTTAATACTTATTGATATAAGAAAATGTACCTTTTTCATATAATTAAAATATATACTAAT
1 GTTTTATT-ATACTTATTCATATAAGAAAATGTACCGTATTCATATAAATAAAATATATACTAAT
2401373 T
65 T
2401374 ATTCATAGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 24 0.43
75 27 0.48
76 5 0.09
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (75 bp):
GTTTTATTATACTTATTCATATAAGAAAATGTACCGTATTCATATAAATAAAATATATACTAATT
TTTTTTCACA
Found at i:2407925 original size:2 final size:2
Alignment explanation
Indices: 2407918--2407973 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2407908 ATCCTTTCAA
2407918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2407960 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2407974 CCCTTGTTGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2408186 original size:4 final size:4
Alignment explanation
Indices: 2408177--2408253 Score: 99
Period size: 4 Copynumber: 19.8 Consensus size: 4
2408167 AAATACATAA
*
2408177 AAAG AAAG -AAG AAAG AAAG AAA- AAAG AAGAG AAA- AAAT AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG
2408223 AAAG AAAAG AAAG AAAG AAAG -AAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAA
2408254 ATCGATCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
3 12 0.18
4 46 0.70
5 8 0.12
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:2408193 original size:11 final size:11
Alignment explanation
Indices: 2408177--2408253 Score: 91
Period size: 11 Copynumber: 6.6 Consensus size: 11
2408167 AAATACATAA
2408177 AAAGAAAGAAG
1 AAAGAAAGAAG
*
2408188 AAAGAAAGAAA
1 AAAGAAAGAAG
*
2408199 AAAGAAGAGAAA
1 AAAGAA-AGAAG
*
2408211 AAATAAAGAAAG
1 AAAGAAAG-AAG
2408223 AAAGAAAAGAAAG
1 AAAG-AAAG-AAG
2408236 AAAGAAAGAAG
1 AAAGAAAGAAG
2408247 AAAGAAA
1 AAAGAAA
2408254 ATCGATCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
11 28 0.47
12 19 0.32
13 12 0.20
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (11 bp):
AAAGAAAGAAG
Found at i:2408206 original size:21 final size:22
Alignment explanation
Indices: 2408175--2408252 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
2408165 CCAAATACAT
2408175 AAAAAGAAAGAAGAAAGAAAGA
1 AAAAAGAAAGAAGAAAGAAAGA
* *
2408197 AAAAAGAAGAGAAAAAATAAAGA
1 AAAAAGAA-AGAAGAAAGAAAGA
2408220 AAGAAAG-AA-AAGAAAGAAAGA
1 AA-AAAGAAAGAAGAAAGAAAGA
*
2408241 AAGAAGAAAGAA
1 AAAAAGAAAGAA
2408253 AATCGATCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 3 0.06
21 14 0.30
22 11 0.23
23 15 0.32
24 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (22 bp):
AAAAAGAAAGAAGAAAGAAAGA
Found at i:2410795 original size:5 final size:5
Alignment explanation
Indices: 2410766--2410842 Score: 50
Period size: 6 Copynumber: 13.8 Consensus size: 5
2410756 TAACCTTAAT
2410766 TAAAA -AAAA TTAAAA TAATAAA TAAAA TAAAA -AAACA TAAACA TAAACA
1 TAAAA TAAAA -TAAAA T-A-AAA TAAAA TAAAA TAAA-A TAAA-A TAAA-A
2410815 TAGAAACA TAAAA TAAAAA TAAAA TAAA
1 T--AAA-A TAAAA T-AAAA TAAAA TAAA
2410843 CCTAAATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
4 7 0.11
5 20 0.32
6 26 0.41
7 4 0.06
8 6 0.10
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:2410823 original size:14 final size:12
Alignment explanation
Indices: 2410776--2410842 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 12
2410766 TAAAAAAAAT
2410776 TAAAATAATAA-A
1 TAAAATAA-AACA
2410788 TAAAATAAAA-A
1 TAAAATAAAACA
*
2410799 -AACAT-AAACA
1 TAAAATAAAACA
2410809 TAAACATAGAAACA
1 TAAA-ATA-AAACA
2410823 TAAAATAAAA-A
1 TAAAATAAAACA
2410834 TAAAATAAA
1 TAAAATAAA
2410843 CCTAAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 15 0.31
12 13 0.27
13 3 0.06
14 9 0.19
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.18
Consensus pattern (12 bp):
TAAAATAAAACA
Found at i:2410848 original size:11 final size:11
Alignment explanation
Indices: 2410776--2410853 Score: 61
Period size: 11 Copynumber: 6.7 Consensus size: 11
2410766 TAAAAAAAAT
*
2410776 TAAAATAATAAA
1 TAAAATAA-ACA
2410788 TAAAATAAA-A
1 TAAAATAAACA
2410798 -AAACATAAACA
1 TAAA-ATAAACA
2410809 TAAACATAGAAACA
1 TAAA-AT--AAACA
*
2410823 TAAAATAAAAA
1 TAAAATAAACA
*
2410834 TAAAATAAACC
1 TAAAATAAACA
2410845 TAAATATAA
1 TAAA-ATAA
2410854 GGACCTAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
9 3 0.05
10 6 0.11
11 19 0.33
12 18 0.32
13 2 0.04
14 9 0.16
ACGTcount: A:0.72, C:0.08, G:0.01, T:0.19
Consensus pattern (11 bp):
TAAAATAAACA
Found at i:2412643 original size:39 final size:39
Alignment explanation
Indices: 2412571--2412701 Score: 176
Period size: 39 Copynumber: 3.4 Consensus size: 39
2412561 AAGAAGAACA
*
2412571 ATCTCAAGTGAGAT-AAATCTTCCATTTCGAGTGAAACT
1 ATCTCAAGTGAGATAAAATCTTCTATTTCGAGTGAAACT
* * *
2412609 ATCTCAAGTGAGATAAAATCTTCTATTCCAAGTGAATCT
1 ATCTCAAGTGAGATAAAATCTTCTATTTCGAGTGAAACT
* *
2412648 ATCTCAA-TCGAGATAAAATATTCTGTTTCGAGTGAAACT
1 ATCTCAAGT-GAGATAAAATCTTCTATTTCGAGTGAAACT
*
2412687 ATCTCAAGTAAGATA
1 ATCTCAAGTGAGATA
2412702 TTGATCCCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 15 0.19
39 64 0.80
40 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (39 bp):
ATCTCAAGTGAGATAAAATCTTCTATTTCGAGTGAAACT
Found at i:2412809 original size:23 final size:23
Alignment explanation
Indices: 2412777--2412853 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
2412767 TCTTCTCATT
2412777 ATGATCTTCTTCTCCCTCTATCGA
1 ATGA-CTTCTTCTCCCTCTATCGA
* *
2412801 ATGAGTTCTTCT-CAT-TAT-G-
1 ATGACTTCTTCTCCCTCTATCGA
2412820 A--ACTTCTTCTCCCTCTATCGA
1 ATGACTTCTTCTCCCTCTATCGA
*
2412841 ATGATTTCTTCTC
1 ATGACTTCTTCTC
2412854 ATTATGAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
19 4 0.10
20 2 0.05
21 4 0.10
22 2 0.05
23 16 0.38
24 4 0.10
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (23 bp):
ATGACTTCTTCTCCCTCTATCGA
Found at i:2412826 original size:40 final size:40
Alignment explanation
Indices: 2412767--2412863 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
2412757 TCTAACAAGC
*
2412767 TCTTCTCATTATGATCTTCTTCTCCCTCTATCGAATGAGT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGT
*
2412807 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGATT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGT
2412847 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
2412864 CTCCATTTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.45
Consensus pattern (40 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGT
Found at i:2417564 original size:24 final size:24
Alignment explanation
Indices: 2417536--2417594 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
2417526 GATCTTTATT
2417536 TAATTTGAAAATCATTACGGATGC
1 TAATTTGAAAATCATTACGGATGC
2417560 TAATTTGAAAATCATTACGGATGC
1 TAATTTGAAAATCATTACGGATGC
* *
2417584 AAAATTGAAAA
1 TAATTTGAAAA
2417595 GGGTATTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (24 bp):
TAATTTGAAAATCATTACGGATGC
Found at i:2420598 original size:51 final size:53
Alignment explanation
Indices: 2420535--2420662 Score: 167
Period size: 51 Copynumber: 2.5 Consensus size: 53
2420525 AGGGGTTAAA
* * *
2420535 AGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGT-TTT-CAAATG-TGTTTT-T
1 AGAAACTAAGCCTAATTTTTAGGGTTTCTTGAT-TATTTCCAAA-GAAGTTTTAG
2420586 AGAAACTAAGCCT-ATTTTTAAGGGTTTCTTGATTATTTCCAAAGAAGTTTTAG
1 AGAAACTAAGCCTAATTTTT-AGGGTTTCTTGATTATTTCCAAAGAAGTTTTAG
2420639 AGAAACTAAGCCTAATTTTTAGGG
1 AGAAACTAAGCCTAATTTTTAGGG
2420663 GTTTGTGATC
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
50 7 0.10
51 29 0.43
52 9 0.13
53 17 0.25
54 6 0.09
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (53 bp):
AGAAACTAAGCCTAATTTTTAGGGTTTCTTGATTATTTCCAAAGAAGTTTTAG
Found at i:2420955 original size:19 final size:19
Alignment explanation
Indices: 2420933--2420991 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
2420923 ATCTCGCTTA
2420933 AGATAGTTTCACTCGAAAC
1 AGATAGTTTCACTCGAAAC
* **
2420952 AGATTA-TTTAATCTCGTTTA-
1 AGA-TAGTTTCA-CTCG-AAAC
2420972 AGATAGTTTCACTCGAAAC
1 AGATAGTTTCACTCGAAAC
2420991 A
1 A
2420992 TAAGATTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 13 0.45
21 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (19 bp):
AGATAGTTTCACTCGAAAC
Found at i:2420977 original size:39 final size:39
Alignment explanation
Indices: 2420922--2421517 Score: 745
Period size: 39 Copynumber: 15.3 Consensus size: 39
2420912 GAGGGATCAA
* **
2420922 TATCTCGCTTAAGATAGTTTCACTCGAAACAGATTATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * * *
2420961 AATCTCGTTTAAGATAGTTTCACTCGAAACATAAGA-TT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * *
2420999 TACCTCGCTTGAGATGGTTTCACTCGAAACATAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * *
2421038 TATTTCGCTT--GATATTTTCACTTGAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* *
2421075 TATCTCGCTTGAGATGGTTTCACTCGAAATAGAAGATTTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
2421115 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * * *
2421154 TATCTCACTTGAGATAGTTTCACTTGAAGCAAAAGA-TT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * * *
2421192 TATCTCGCTGGAGATGGTTTCACTTGAAATAGAAGATTTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
*
2421232 TATCTCGCTTGATATAGTTTCACTCGAAACAGAAGATTTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
* * *
2421272 TATCTCGCTTCATATAATTTCACTCGAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* *
2421311 TATCTCGCTTGAGATAGTTTCAATCCAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
** *
2421350 TATCTCATTTAAGATAGTTTCACTCGAAACAGAAGATTTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
* * * *
2421390 TATCTCTCTTGAGATAGTTTCACTTGAAATAGAAAATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* *
2421429 TATCTCGCTTGAGATAGTTTCACTTGAAATAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
2421468 T-TACTCGCTTGAGATTGTTTCACTCGAAACAGAAGA-TT
1 TAT-CTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
2421506 TATCTCACTTGA
1 TATCTCGCTTGA
2421518 TATTGTTTTT
Statistics
Matches: 486, Mismatches: 62, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
37 32 0.07
38 77 0.16
39 236 0.49
40 141 0.29
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (39 bp):
TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
Found at i:2421035 original size:22 final size:21
Alignment explanation
Indices: 2420970--2421035 Score: 52
Period size: 22 Copynumber: 3.3 Consensus size: 21
2420960 TAATCTCGTT
2420970 TAAGATAGTTTCACTCGAAACA
1 TAAGAT-GTTTCACTCGAAACA
* *
2420992 TAAGAT-TTAC-CTCG---CT
1 TAAGATGTTTCACTCGAAACA
*
2421008 TGAGATGGTTTCACTCGAAACA
1 TAAGAT-GTTTCACTCGAAACA
2421030 TAAGAT
1 TAAGAT
2421036 TTTATTTCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
16 6 0.19
18 3 0.09
19 8 0.25
20 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (21 bp):
TAAGATGTTTCACTCGAAACA
Found at i:2421275 original size:157 final size:157
Alignment explanation
Indices: 2420922--2421517 Score: 767
Period size: 157 Copynumber: 3.8 Consensus size: 157
2420912 GAGGGATCAA
* ** * * *
2420922 TATCTCGCTTAAGATAGTTTCACTCGAAACAGATTA-TTTAATCTCGTTTAAGATAGTTTCACTC
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
* * * * *
2420986 GAAACATAAGA-TTTACCTCGCTTGAGATGGTTTCACTCGAAACATAAGATTTTATTTCGCTTGA
66 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGA
*
2421050 TAT-TTTCACTTGAAACAGAAGA-TTT
131 GATGTTTCACTTGAAACAGAAGATTTT
* *
2421075 TATCTCGCTTGAGATGGTTTCACTCGAAATAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
* * * * *
2421140 GAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTTGAAGCAAAAGA-TTTATCTCGCTGGA
66 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGA
*
2421204 GATGGTTTCACTTGAAATAGAAGATTTT
131 GAT-GTTTCACTTGAAACAGAAGATTTT
* * * *
2421232 TATCTCGCTTGATATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTCATATAATTTCACTC
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
* * ** *
2421297 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCAATCCAAACAGAAGATTTTATCTCATTTAA
66 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGA
*
2421362 GATAGTTTCACTCGAAACAGAAGATTTT
131 GAT-GTTTCACTTGAAACAGAAGATTTT
* * * * *
2421390 TATCTCTCTTGAGATAGTTTCACTTGAAATAGAA-AATTTTATCTCGCTTGAGATAGTTTCACTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
* * *
2421454 GAAATAGAAGATTTT-TACTCGCTTGAGATTGTTTCACTCGAAACAGAAGA-TTTATCTCACTTG
66 GAAACAGAAGATTTTAT-CTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTG
2421517 A
130 A
2421518 TATTGTTTTT
Statistics
Matches: 383, Mismatches: 53, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
153 31 0.08
154 49 0.13
155 32 0.08
156 31 0.08
157 175 0.46
158 65 0.17
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (157 bp):
TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTC
GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGA
GATGTTTCACTTGAAACAGAAGATTTT
Found at i:2421367 original size:118 final size:118
Alignment explanation
Indices: 2420922--2421506 Score: 761
Period size: 118 Copynumber: 5.0 Consensus size: 118
2420912 GAGGGATCAA
* * ** * * *
2420922 TATCTCGCTTAAGATAGTTTCACTCGAAACAGATTATTTAATCTCGTTTAAGATAGTTTCACTCG
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
* * * * *
2420987 AAACATAAGA-TTTACCTCGCTTGAGATGGTTTCACTCGAAACATAAGA-TTT
66 AAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
2421038 TATTTCGCTT--GATATTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATGGTTTCACTCG
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
2421101 AAATAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
66 AAATAGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * * * *
2421154 TATCTCACTTGAGATAGTTTCACTTGAAGCAAAAGA-TTTATCTCGCTGGAGATGGTTTCACTTG
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
*
2421218 AAATAGAAGATTTTTATCTCGCTTGATATAGTTTCACTCGAAACAGAAGATTTT
66 AAATAGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * * * *
2421272 TATCTCGCTTCATATAATTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCAATCC
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
* ** *
2421337 AAACAGAAGATTTTATCTCATTTAAGATAGTTTCACTCGAAACAGAAGATTTT
66 AAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
2421390 TATCTCTCTTGAGATAGTTTCACTTGAAATAGAAAATTTTATCTCGCTTGAGATAGTTTCACTTG
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
*
2421455 AAATAGAAGATTTT-TACTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTT
66 AAATAGAAGATTTTAT-CTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
2421507 ATCTCACTTG
Statistics
Matches: 408, Mismatches: 54, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
114 53 0.13
116 55 0.13
117 76 0.19
118 192 0.47
119 32 0.08
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (118 bp):
TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
AAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:2421641 original size:58 final size:59
Alignment explanation
Indices: 2421539--2421658 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 59
2421529 TTAAAACGAA
* * *
2421539 CAACACCCTACCAGAGGGGTTAATATTTCCTAGTGCTCGATCACAACACTTTGAATCAG
1 CAACACCCCACCAGAGGGGTTAACATTTCCTAGTGCTCGATCACAACACTTCGAATCAG
* * *
2421598 CAACGCCCCACCAGA-GGGTTTACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAG
1 CAACACCCCACCAGAGGGGTTAACATTTCCTAGTGCTCGA-TCACAACACTTCGAATCAG
2421656 CAA
1 CAA
2421659 TGTATTACTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
57 7 0.13
58 34 0.63
59 13 0.24
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (59 bp):
CAACACCCCACCAGAGGGGTTAACATTTCCTAGTGCTCGATCACAACACTTCGAATCAG
Found at i:2423022 original size:109 final size:109
Alignment explanation
Indices: 2422786--2422991 Score: 317
Period size: 109 Copynumber: 1.9 Consensus size: 109
2422776 GTTTTAAGTC
* * * * *
2422786 CCCCAAACTTTCTAGTGTT-TTTACAAATTGGTCACTGTCAGGGAACGTTTTTATAATTTTCCCA
1 CCCCAAACTTTCTCGTGTTCTTGA-AAAATAGTCACTGTCAGGGAACGTTTTCATAATTTTCCCA
* *
2422850 TTTCTATGTATGCTTTGTATTTTTTGGTAAAATCGAATTCCAGGT
65 TTTATATGCATGCTTTGTATTTTTTGGTAAAATCGAATTCCAGGT
2422895 CCCCAAACTTTCTCGTGTTCTTGAAAAATAGTCACTGTCAGGG-ACTGTTTTCATAATTTTCCCA
1 CCCCAAACTTTCTCGTGTTCTTGAAAAATAGTCACTGTCAGGGAAC-GTTTTCATAATTTTCCCA
2422959 TTTATATGCATGCTTTGTATTTTTTGGTAAAAT
65 TTTATATGCATGCTTTGTATTTTTTGGTAAAAT
2422992 TTCATTCTAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
108 2 0.02
109 83 0.94
110 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (109 bp):
CCCCAAACTTTCTCGTGTTCTTGAAAAATAGTCACTGTCAGGGAACGTTTTCATAATTTTCCCAT
TTATATGCATGCTTTGTATTTTTTGGTAAAATCGAATTCCAGGT
Found at i:2426562 original size:133 final size:132
Alignment explanation
Indices: 2426369--2426778 Score: 432
Period size: 132 Copynumber: 3.1 Consensus size: 132
2426359 ATGAGAAACA
* * * *
2426369 TTGATTCATTCCACT-GTTCTTCAGGGAAA-ATTGAATTGAGTCAGACTTATTCCACTGTTACTC
1 TTGATTCATTCCACTGGTAC-TCA-GGAAAGATTAAATCGAGGCAGACTTATTCCACTGTTACTC
*
2426432 AGGGAATATAAAATCTTGAAAAAAGGGATTTGTTATGCTTCTTC-CTACGGGAAAATCAGATCTG
64 AGGGAATATCAAATCTTGAAAAAAGGGATTTGTT-TGCTTCTTCTCTA-GGGAAAATCAGATCTG
2426496 GGGACG
127 GGGACG
* * * * * * * *
2426502 TTTATTTATTCCACTGTTACTCATGAAAGATTGAATCGAGGTATACTTGTTCCACTGTTACTCAG
1 TTGATTCATTCCACTGGTACTCAGGAAAGATTAAATCGAGGCAGACTTATTCCACTGTTACTCAG
** * * * *
2426567 AAAATATCAAATCGTGAAAAAA-GGATTTGTTTCGCTTCTTCTTTAGGGAAAATTAGATTTGGGG
66 GGAATATCAAATCTTGAAAAAAGGGATTTGTTT-GCTTCTTCTCTAGGGAAAATCAGATCTGGGG
2426631 ACG
130 ACG
* * *
2426634 TTGATTCATTCCACTGGTACTCAGGGAAGATTAAATCGAGGCAGACTTCTTCCACTGTTACTCAA
1 TTGATTCATTCCACTGGTACTCAGGAAAGATTAAATCGAGGCAGACTTATTCCACTGTTACTCAG
* * * * ** * * *
2426699 GGAATATCAAGTCTTGAAAGAAAGAGATATGTTCCGCTTCTTCTCGGGGGGAAATCTGATCTGGA
66 GGAATATCAAATCTTGAAA-AAAGGGATTTGTT-TGCTTCTTCTCTAGGGAAAATCAGATCTGGG
* *
2426764 AAAG
129 GACG
2426768 TTGATTCATTC
1 TTGATTCATTC
2426779 TGCTGTTCTT
Statistics
Matches: 226, Mismatches: 44, Indels: 13
0.80 0.16 0.05
Matches are distributed among these distances:
131 1 0.00
132 111 0.49
133 70 0.31
134 44 0.19
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (132 bp):
TTGATTCATTCCACTGGTACTCAGGAAAGATTAAATCGAGGCAGACTTATTCCACTGTTACTCAG
GGAATATCAAATCTTGAAAAAAGGGATTTGTTTGCTTCTTCTCTAGGGAAAATCAGATCTGGGGA
CG
Found at i:2427604 original size:232 final size:230
Alignment explanation
Indices: 2427134--2427694 Score: 716
Period size: 232 Copynumber: 2.4 Consensus size: 230
2427124 TTGCCTGAAT
* * * * *
2427134 GACTTACTAATTTTTGAAACT-GTTTACTAGGAAAAAAACTTTTCTTACTTTTCCAAAATTTCAA
1 GACTTACCAATTTTGGAAA-TAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAA
* * ** *
2427198 TTTTCAGATTTAAATAAGAAA-CTCTCTCATTTTTTGATAGGTATGTGAAACATCCTGCCCAAAG
65 TTTTCAGATTTAAATGAGAAATCTTTCTCA-TTTTTGATAGACATGTGAAACATCCTACCCAAAG
* * * *
2427262 GTTTTGTGGAGGCCCGAAAGACTTATCATCTTGCTCGAAAGACTTACACACGAACCGAAGAATTT
129 GTCTTATGGAGGCCCGAAAGACTTATCATCTTGCTCAAAAGACTTACAAACGAACCGAAGAATTT
* * ** *
2427327 AAGCATCATGCTTGAAAGACTTACTGGTGGCCCGAGG
194 AAGCATCATGCTCGAAAGACGTACTAATGGCCCAAGG
*
2427364 GACTTACCAATTTTGGAAATAGTTTAGTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAT
1 GACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAT
* * *
2427429 TTTCAGATTTAAATGAGAAATCTTTCTTATTTTTGAGT-GACATGTGAAAACATCCTACTCGAAG
66 TTTCAGATTTAAATGAGAAATCTTTCTCATTTTTGA-TAGACATGTG-AAACATCCTACCCAAAG
* * * * * * *
2427493 GTCTTATGGATGGCCCGAAGGACTTATCATTTTTCTCAAAAGACTTACAAATGACCCGTAGGATT
129 GTCTTATGGA-GGCCCGAAAGACTTATCATCTTGCTCAAAAGACTTACAAACGAACCGAAGAATT
*
2427558 TATGCATCATGCTCGAAAGACGTACTAATGGCCCAAGG
193 TAAGCATCATGCTCGAAAGACGTACTAATGGCCCAAGG
** * *
2427596 GACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTCCCTTACTTTTCAATAATTTCCAT
1 GACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAT
*
2427661 TTTCAGATTTAAACGAGAAAAT-TTTCTCATTTTT
66 TTTCAGATTTAAATGAG-AAATCTTTCTCATTTTT
2427695 TAACTTATAA
Statistics
Matches: 287, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
229 1 0.00
230 89 0.31
231 29 0.10
232 164 0.57
233 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (230 bp):
GACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAT
TTTCAGATTTAAATGAGAAATCTTTCTCATTTTTGATAGACATGTGAAACATCCTACCCAAAGGT
CTTATGGAGGCCCGAAAGACTTATCATCTTGCTCAAAAGACTTACAAACGAACCGAAGAATTTAA
GCATCATGCTCGAAAGACGTACTAATGGCCCAAGG
Found at i:2429374 original size:8 final size:7
Alignment explanation
Indices: 2429362--2429469 Score: 71
Period size: 7 Copynumber: 14.6 Consensus size: 7
2429352 TTATCTATCC
2429362 TTTCTTT
1 TTTCTTT
2429369 CTTTCTTT
1 -TTTCTTT
2429377 CTTT-TTT
1 -TTTCTTT
2429384 TTT-TATT
1 TTTCT-TT
2429391 TTTCTTT
1 TTTCTTT
2429398 TTTCTTAT
1 TTTCTT-T
2429406 TTTCTTT
1 TTTCTTT
2429413 GTCTT-TATT
1 -T-TTCT-TT
*
2429422 TTTATTT
1 TTTCTTT
2429429 TTTCTTAT
1 TTTCTT-T
*
2429437 TTTCCTT
1 TTTCTTT
*
2429444 TTCCTTT
1 TTTCTTT
2429451 TAATTC-TT
1 T--TTCTTT
2429459 TTTCTTT
1 TTTCTTT
2429466 TTTC
1 TTTC
2429470 GAGTATGGTA
Statistics
Matches: 84, Mismatches: 5, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
6 7 0.08
7 39 0.46
8 32 0.38
9 6 0.07
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:2429461 original size:31 final size:32
Alignment explanation
Indices: 2429392--2429469 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 32
2429382 TTTTTTATTT
**
2429392 TTCTTTTTTCTTATTTT-CTTTGTCTTTATTT
1 TTCTTTTTTCTTATTTTCCTTTGTCTTTATAA
*
2429423 TTATTTTTTCTTATTTTCCTTT-TCCTTT-TAA
1 TTCTTTTTTCTTATTTTCCTTTGT-CTTTATAA
2429454 TTC-TTTTTCTT-TTTTC
1 TTCTTTTTTCTTATTTTC
2429470 GAGTATGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.12
30 8 0.20
31 20 0.49
32 8 0.20
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (32 bp):
TTCTTTTTTCTTATTTTCCTTTGTCTTTATAA
Found at i:2434966 original size:15 final size:15
Alignment explanation
Indices: 2434946--2434978 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2434936 AGGAATCAAG
2434946 ATTATTGAATAAAAT
1 ATTATTGAATAAAAT
*
2434961 ATTATTGAATAAATT
1 ATTATTGAATAAAAT
2434976 ATT
1 ATT
2434979 CATGGAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTATTGAATAAAAT
Found at i:2439255 original size:37 final size:36
Alignment explanation
Indices: 2439174--2439484 Score: 242
Period size: 39 Copynumber: 8.4 Consensus size: 36
2439164 TCAAAAACCA
* * *
2439174 TTTTAAAAACTATATACTATATGTTTTCAAAAA-TA
1 TTTTCAAAACTATATATTATATGTTTTCAAAAATTG
* *
2439209 TTTTAAAAACTATATATTAGATGTTTTCAAAAATGTG
1 TTTTCAAAACTATATATTATATGTTTTCAAAAAT-TG
* **
2439246 TTTTCAAAAC----TA-TATATGTTTTCCAAAACCG
1 TTTTCAAAACTATATATTATATGTTTTCAAAAATTG
* *
2439277 ATTTTTAAAAAATATATATTATATATGTTTT-AAGAAATGTG
1 --TTTTCAAAACTATATA-T-TATATGTTTTCAA-AAAT-TG
*
2439318 TTTTCAAAACTATATATTATATGTTTTCAAAAGCTTG
1 TTTTCAAAACTATATATTATATGTTTTCAAAA-ATTG
* * * *
2439355 TTTTCAAAACCATATTATATATATATTTTCGAAAACTG
1 TTTTCAAAACTATA-TAT-TATATGTTTTCAAAAATTG
* *
2439393 ATTTTAAAAAACTATATATTATATTGCTTTCAAAAATTG
1 -TTTT-CAAAACTATATATTATA-TGTTTTCAAAAATTG
* *
2439432 TTTTCTAAAAACTATATATTATATATTTTTCAAAAA-TA
1 TTTTC--AAAACTATATATTATAT-GTTTTCAAAAATTG
2439470 TTTTCAAAAACTATA
1 TTTTC-AAAACTATA
2439485 CTATATTATT
Statistics
Matches: 222, Mismatches: 31, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
31 1 0.00
32 14 0.06
33 10 0.05
35 31 0.14
37 49 0.22
38 24 0.11
39 71 0.32
40 21 0.09
41 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATGTTTTCAAAAATTG
Found at i:2439406 original size:77 final size:76
Alignment explanation
Indices: 2439161--2439484 Score: 227
Period size: 72 Copynumber: 4.4 Consensus size: 76
2439151 ATACATTAAA
* * * *
2439161 TTTTCAAAAACCATTTT-AAAAACTATATACTATA-TGTTTTCAAAAA-T-ATTT-TAAAAACTA
1 TTTTCAAAAA-TATTTTAAAAAACTATATATTATATTGCTTTCAAAAATTGTTTTCTAAAAACTA
* *
2439221 TATATTAGAT-G
65 TATATTATATAT
* ** ** *
2439232 TTTTCAAAAATGTGTTTTCAAAACTATATATGT-T-TT-C---C-AAAACCGATTTT-TAAAAAA
1 TTTTCAAAAATAT-TTTAAAAAACTATATAT-TATATTGCTTTCAAAAATTG-TTTTCTAAAAAC
2439289 TATATATTATATAT
63 TATATATTATATAT
* ** * *
2439303 GTTTT-AAGAAATGTGTTTTCAAAACTATATATTATA-TGTTTTCAAAAGCTTGTTTTC--AAAA
1 -TTTTCAA-AAATAT-TTTAAAAAACTATATATTATATTGCTTTCAAAA-ATTGTTTTCTAAAAA
*
2439364 CCATAT-TATATATAT
62 CTATATAT-TATATAT
*
2439379 ATTTTCGAAAACTGATTTTAAAAAACTATATATTATATTGCTTTCAAAAATTGTTTTCTAAAAAC
1 -TTTTC-AAAAAT-ATTTTAAAAAACTATATATTATATTGCTTTCAAAAATTGTTTTCTAAAAAC
2439444 TATATATTATATAT
63 TATATATTATATAT
*
2439458 TTTTCAAAAATATTTTCAAAAACTATA
1 TTTTCAAAAATATTTTAAAAAACTATA
2439485 CTATATTATT
Statistics
Matches: 200, Mismatches: 26, Indels: 49
0.73 0.09 0.18
Matches are distributed among these distances:
67 4 0.02
68 1 0.00
70 21 0.10
71 16 0.08
72 43 0.22
73 1 0.00
75 1 0.00
76 35 0.17
77 42 0.21
78 19 0.09
79 16 0.08
80 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (76 bp):
TTTTCAAAAATATTTTAAAAAACTATATATTATATTGCTTTCAAAAATTGTTTTCTAAAAACTAT
ATATTATATAT
Found at i:2439480 original size:116 final size:115
Alignment explanation
Indices: 2439160--2439490 Score: 295
Period size: 116 Copynumber: 3.0 Consensus size: 115
2439150 CATACATTAA
* * * * * *
2439160 ATTTTCAAAAACC-A-TTTTAAAAACTATATACTATATGT-TTTCAA-AAA--TATTTTAAAAAC
1 ATTTTCCAAAACCGATTTTTAAAAAATATATATTATATATGTTTCAAGAAATGTGTTTTCAAAAC
* *
2439219 TATATATTAGATGTTTTCAAAA-ATGTGTTTTC--AA--A-AC--TATATAT
66 TATATATTATATGTTTTCAAAACA--TATTTTCAAAACCATACTATATATAT
* *
2439263 GTTTTCCAAAACCGATTTTTAAAAAATATATATTATATATGTTTTAAGAAATGTGTTTTCAAAAC
1 ATTTTCCAAAACCGATTTTTAAAAAATATATATTATATATGTTTCAAGAAATGTGTTTTCAAAAC
* * *
2439328 TATATATTATATGTTTTCAAAAGCTTGTTTTCAAAACCATATTATATATAT
66 TATATATTATATGTTTTCAAAA-CATATTTTCAAAACCATACTATATATAT
* *
2439379 ATTTTCGAAAACTGA-TTTTAAAAAACTATATATTATAT-TGCTTTCAA-AAAT-TGTTTTCTAA
1 ATTTTCCAAAACCGATTTTTAAAAAA-TATATATTATATATG-TTTCAAGAAATGTGTTTTC--A
* *
2439440 AAACTATATATTATATATTTTTCAAAA-ATATTTTCAAAAACTATACTATAT
62 AAACTATATATTATAT-GTTTTCAAAACATATTTTC-AAAACCATACTATAT
2439491 TATTATATAT
Statistics
Matches: 187, Mismatches: 20, Indels: 29
0.79 0.08 0.12
Matches are distributed among these distances:
103 11 0.06
104 1 0.01
105 21 0.11
106 5 0.03
107 3 0.02
109 38 0.20
111 2 0.01
113 1 0.01
114 8 0.04
115 22 0.12
116 66 0.35
117 9 0.05
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (115 bp):
ATTTTCCAAAACCGATTTTTAAAAAATATATATTATATATGTTTCAAGAAATGTGTTTTCAAAAC
TATATATTATATGTTTTCAAAACATATTTTCAAAACCATACTATATATAT
Found at i:2440261 original size:202 final size:203
Alignment explanation
Indices: 2439862--2440279 Score: 477
Period size: 202 Copynumber: 2.1 Consensus size: 203
2439852 CAGACATCTT
* * ** * * * *
2439862 TTCTCGACTTAAGTTATTCTATAAATTAGGTTGGGAGGTAGTTTCTTGTTGCTAAATCGCAACCG
1 TTCTCGCCTTGAGTTACACTATAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAACCA
* * **
2439927 ACCTAAGTATTCTTCTAGGCTTAAAAGACCTCAGTTTAAAATTAAACCGGCAAGTAGTTCCTAGC
66 ACCTAAGTATTCTTCTAGACTTAAAAGACCTCAGCTTAAAATTAAACCGAAAAGTAGTTCCTAGC
* * * ** *
2439992 TGCTACCATGCGGTTTGATATGCCATCGAGCTAAATAGAATTGAACATAAAATTTTTCGTTGACA
131 TGCTACCATGCGGTTTGATACGCCATCAAGATAAATAGAATCAAACATAAAATTTTTCGTCGACA
2440057 GATAGCCC
196 GATAGCCC
* *
2440065 TTCTCGCCTTGAGTTACACTATAAATTCGGCTGGGATATAGTTCCTTGTTGCTAAATCG-AAGCC
1 TTCTCGCCTTGAGTTACACTATAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAA-CC
* * * *
2440129 AACCTAAGTCTTCTTCTTGACTT-AAAGACCTCAGCTTAAACTTCAACCGAAAAGTAGTTCCTCA
65 AACCTAAGTATTCTTCTAGACTTAAAAGACCTCAGCTTAAAATTAAACCGAAAAGTAGTTCCT-A
** * * * * *
2440193 -CTGCTACGTTGCGG-TTGATACGCCCTCAAGATGAATATAGTCAAAC-TCAAAAGTTTTTTGTC
129 GCTGCTACCATGCGGTTTGATACGCCATCAAGATAAATAGAATCAAACAT-AAAA-TTTTTCGTC
2440255 GACAGATAGCCC
192 GACAGATAGCCC
*
2440267 TTTTCGCCTTGAG
1 TTCTCGCCTTGAG
2440280 CTATACAGTG
Statistics
Matches: 179, Mismatches: 32, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
200 1 0.01
201 27 0.15
202 79 0.44
203 72 0.40
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (203 bp):
TTCTCGCCTTGAGTTACACTATAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAACCA
ACCTAAGTATTCTTCTAGACTTAAAAGACCTCAGCTTAAAATTAAACCGAAAAGTAGTTCCTAGC
TGCTACCATGCGGTTTGATACGCCATCAAGATAAATAGAATCAAACATAAAATTTTTCGTCGACA
GATAGCCC
Found at i:2448056 original size:18 final size:18
Alignment explanation
Indices: 2447998--2448056 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
2447988 AAAATAAGAT
* *
2447998 TAATAACAATATAATATAA
1 TAATAAAAATA-AAAATAA
2448017 T-ATAATAAATGAAAAATAAA
1 TAATAA-AAAT-AAAAAT-AA
2448037 TAATAAAAATAAAAATAA
1 TAATAAAAATAAAAATAA
2448055 TA
1 TA
2448057 TGTATACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.24
19 14 0.41
20 8 0.24
21 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
TAATAAAAATAAAAATAA
Found at i:2448109 original size:34 final size:34
Alignment explanation
Indices: 2448070--2448137 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2448060 ATACTATATT
2448070 TATTTTAAAAACTATATACTACATGTTTTCAAAA
1 TATTTTAAAAACTATATACTACATGTTTTCAAAA
* *
2448104 TATTTTAAAAACTATATATTATATGTTTTCAAAA
1 TATTTTAAAAACTATATACTACATGTTTTCAAAA
2448138 ATGTGTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (34 bp):
TATTTTAAAAACTATATACTACATGTTTTCAAAA
Found at i:2448222 original size:23 final size:24
Alignment explanation
Indices: 2448184--2448230 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2448174 ATTTTTAAGA
2448184 ACTATATATTACATATGTTTTCAAT
1 ACTATATATTA-ATATGTTTTCAAT
2448209 ACTATATATT-ATATGTTTTCAA
1 ACTATATATTAATATGTTTTCAA
2448231 AAGCGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.55
25 10 0.45
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (24 bp):
ACTATATATTAATATGTTTTCAAT
Found at i:2448364 original size:37 final size:39
Alignment explanation
Indices: 2448265--2448381 Score: 120
Period size: 39 Copynumber: 3.0 Consensus size: 39
2448255 TATAATTTTT
* *
2448265 TTTCAAAAACCGATTTTTAAAAAACTATATATTA-T-ATTA
1 TTTCAAAAATC-A-TTTTCAAAAACTATATATTATTAATTA
2448304 CTTTCAAAAATCATTTTCTAAAAACTATATATTATTAATT-
1 -TTTCAAAAATCATTTTC-AAAAACTATATATTATTAATTA
*
2448344 TTTGAAAAAT-ATTTTCAAAAACTATACTA-TATT-ATTA
1 TTTCAAAAATCATTTTCAAAAACTATA-TATTATTAATTA
2448381 T
1 T
2448382 ATATACTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
36 3 0.04
37 15 0.22
38 12 0.17
39 25 0.36
40 11 0.16
41 3 0.04
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (39 bp):
TTTCAAAAATCATTTTCAAAAACTATATATTATTAATTA
Found at i:2449813 original size:159 final size:159
Alignment explanation
Indices: 2449524--2449813 Score: 476
Period size: 159 Copynumber: 1.8 Consensus size: 159
2449514 AAATAATAGT
*
2449524 AAAAAATATTAAAATTTCATTCTAAAGTTCATTATTAATTCAAAATAACAATACCCAAAATAATT
1 AAAAAATATTAAAATTTCATTCTAAAGTTCATTATTAATTCAAAATAACAACACCCAAAATAATT
* * *
2449589 TTAAGAAAGAAAATAATAATATCTAATTATTTACAATCGAGAATAAACGACCTCTCATACCTTAA
66 TTAAGAAAGAAAATAAAAATATATAATTATTTACAATCAAGAATAAACGACCTCTCATACCTTAA
2449654 AGCAATCAATTCTTACTCTAAATGAAATA
131 AGCAATCAATTCTTACTCTAAATGAAATA
*
2449683 AAAAAATATTAAAA-TTCGATTCTAAAGTTCATTATTAATTCCAAATAACAACACCCAAAATAAT
1 AAAAAATATTAAAATTTC-ATTCTAAAGTTCATTATTAATTCAAAATAACAACACCCAAAATAAT
* * *
2449747 TTTAAGAGAA-AAAATAAAAATATATAATTATTTCCAATCAAGAATAAACGATCTCTCATACTTT
65 TTTAAGA-AAGAAAATAAAAATATATAATTATTTACAATCAAGAATAAACGACCTCTCATACCTT
2449811 AAA
129 AAA
2449814 ATAGTCATTT
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
158 3 0.02
159 116 0.96
160 2 0.02
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (159 bp):
AAAAAATATTAAAATTTCATTCTAAAGTTCATTATTAATTCAAAATAACAACACCCAAAATAATT
TTAAGAAAGAAAATAAAAATATATAATTATTTACAATCAAGAATAAACGACCTCTCATACCTTAA
AGCAATCAATTCTTACTCTAAATGAAATA
Found at i:2451933 original size:3 final size:3
Alignment explanation
Indices: 2451925--2452002 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
2451915 TATTTTATTT
* * * * *
2451925 ATA ATA ATA GTA ATA ATTA ATTA CTC ATA ATA CTA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
2451972 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2452003 AGTTGGGACA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 58 0.91
4 6 0.09
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2456968 original size:5 final size:6
Alignment explanation
Indices: 2456939--2456968 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2456929 CTGAGATGAG
2456939 GGGTTA GGGTTA GGGTTA GGGTTA -GGTTA G
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA G
2456969 ATGTTTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
GGGTTA
Found at i:2457088 original size:3 final size:3
Alignment explanation
Indices: 2457082--2457147 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
2457072 ATATTTTTAA
*
2457082 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2457130 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
2457148 GTAAGGCAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2471593 original size:21 final size:20
Alignment explanation
Indices: 2471542--2471593 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
2471532 GTGTTTATGC
*
2471542 TTATTTTTTACTTTTTTATT
1 TTATTTTTTTCTTTTTTATT
*
2471562 TTGTTTTTTTTCTTTTTT-TT
1 TT-ATTTTTTTCTTTTTTATT
2471582 ATTATTTATTTT
1 -TTATTT-TTTT
2471594 AATTAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.83
Consensus pattern (20 bp):
TTATTTTTTTCTTTTTTATT
Found at i:2478420 original size:3 final size:3
Alignment explanation
Indices: 2478405--2478448 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2478395 ATGTTAATAA
* *
2478405 ATT ATT TTT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2478449 AAATTATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2480337 original size:54 final size:56
Alignment explanation
Indices: 2480265--2480559 Score: 193
Period size: 56 Copynumber: 5.3 Consensus size: 56
2480255 TTACCCGGCT
* *
2480265 AATGCAATTTTT-TAGAAACTAAGTCCGATTTTCAATGGTTTCTTGATATT-TTT-A
1 AATG-AATTTTTAAAGAAACTAAGTCCGATTTTCAAGGGTTTCTTGATATTATTTCA
* ** * ** *
2480319 AATGAGTTTTTAAAGAAACTAAGTATGATTTTC-AGAAGTTTCTT-A-ACGATTTTA
1 AATGAATTTTTAAAGAAACTAAGTCCGATTTTCAAG-GGTTTCTTGATATTATTTCA
* * * * * * * *
2480373 AATGAGTTTTCAGAGAATCCAAATCTGATATTTCAAGGGTTTCTTGATGATTATTTCC
1 AATGAATTTTTAAAGAAACTAAGTCCGAT-TTTCAAGGGTTTCTTGAT-ATTATTTCA
* *
2480431 CATGAA-TTTTAAAGAATA-TAAG-CCTGATTTTCAAGGGTTTCCTT-ATTATTATTTCT
1 AATGAATTTTTAAAGAA-ACTAAGTCC-GATTTTCAAGGGTTT-CTTGA-TATTATTTCA
* * * *
2480487 AAT-AAATTTTAAAGAAACTAAG-CCTGATTTTCAGGGGTTTATTGATGATTGTTTCCA
1 AATGAATTTTTAAAGAAACTAAGTCC-GATTTTCAAGGGTTTCTTGAT-ATTATTT-CA
2480544 AA-GAATTTTTAAAGAA
1 AATGAATTTTTAAAGAA
2480560 GATAAGCCTA
Statistics
Matches: 188, Mismatches: 34, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
52 1 0.01
53 11 0.06
54 53 0.28
55 17 0.09
56 65 0.35
57 32 0.17
58 9 0.05
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (56 bp):
AATGAATTTTTAAAGAAACTAAGTCCGATTTTCAAGGGTTTCTTGATATTATTTCA
Found at i:2480468 original size:56 final size:55
Alignment explanation
Indices: 2480397--2480574 Score: 214
Period size: 56 Copynumber: 3.1 Consensus size: 55
2480387 GAATCCAAAT
*
2480397 CTGATATTTCAAGGGTTTCTTGATGATTATTTCCCATGAATTTTAAAGAATATAAGC
1 CTGAT-TTTCAAGGGTTTCTTGATGATTATTTCCAATGAATTTTAAAGAA-ATAAGC
* * *
2480454 CTGATTTTCAAGGGTTTCCTT-ATTATTATTTCTAATAAATTTTAAAGAAACTAAGC
1 CTGATTTTCAAGGGTTT-CTTGATGATTATTTCCAATGAATTTTAAAGAAA-TAAGC
* * * *
2480510 CTGATTTTCAGGGGTTTATTGATGATTGTTTCCAAAGAATTTTTAAAGAAGATAAGC
1 CTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATGAA-TTTTAAAGAA-ATAAGC
*
2480567 CTAATTTT
1 CTGATTTT
2480575 AGGGGGTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
55 3 0.03
56 70 0.67
57 30 0.29
58 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (55 bp):
CTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATGAATTTTAAAGAAATAAGC
Found at i:2480976 original size:176 final size:175
Alignment explanation
Indices: 2480675--2480993 Score: 532
Period size: 176 Copynumber: 1.8 Consensus size: 175
2480665 TCAGTAAATG
* *
2480675 TTTCGATCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGAAAAGTTTT
1 TTTCGAGCATCATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGAAAAGTTTT
* * * *
2480740 CGGGTCATCCTTAAGACCTTCGGGCAGGATGTTTTCGAATGATTTTTGAAAAAAGAGAAAGTGAT
66 CGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCGAATGATTTTCGAAAAAAGAGAAAGCGAT
2480805 TTCCAAAGTTTCTTGCTAAGTAGTCCTTCGAGCCATCAACAAGTC
131 TTCCAAAGTTTCTTGCTAAGTAGTCCTTCGAGCCATCAACAAGTC
* *
2480850 TTTCGAGCATCATGCTTAAATTCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCTT
1 TTTCGAGCATCATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGAAAAGT-TT
*
2480915 TCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTC-ACATGATTTTCGAAAAATGAGAAAGCG
65 TCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCGA-ATGATTTTCGAAAAAAGAGAAAGCG
2480979 ATTTCCAAAGTTTCT
129 ATTTCCAAAGTTTCT
2480994 CATTTAAATA
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
175 59 0.44
176 74 0.56
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (175 bp):
TTTCGAGCATCATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGAAAAGTTTT
CGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCGAATGATTTTCGAAAAAAGAGAAAGCGAT
TTCCAAAGTTTCTTGCTAAGTAGTCCTTCGAGCCATCAACAAGTC
Found at i:2481171 original size:41 final size:41
Alignment explanation
Indices: 2481065--2481171 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 41
2481055 TCTTACTGAG
* * *
2481065 TAAGTCCTTCGGGCCATCAATAAGTGTTTCGAGTATGATGCT
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGAT-CT
* * *
2481107 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGAT-T
1 TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGATCT
*
2481147 ATAAGTCCTTCGGGCCATCCATAAG
1 -TAAGTCCTTCGGGCCATCAATAAG
2481172 ACCTTCGGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 21 0.38
42 33 0.60
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAAAGATCT
Found at i:2481207 original size:241 final size:241
Alignment explanation
Indices: 2480795--2481964 Score: 1668
Period size: 241 Copynumber: 4.9 Consensus size: 241
2480785 TTGAAAAAAG
* * * * * *
2480795 AGAAAGTGATTTCCAAAGTTTCTTGCTAAGT-AGTCCTTCGAGCCATCAACAAGTCTTTCGAGCA
1 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
* * * *
2480859 TCATGCTTAAATTCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCAT
66 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCAT
*
2480924 CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAAAG
131 CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAAG
*
2480989 TTTCTCATTTAAATAATTTCTAAAAATTGTTTTTTCTTGAAAAGTA
196 TTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
* * *
2481035 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCCTTCGGGCCATCAATAAGTGTTTCGAGTA
1 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
*
2481100 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATTATAAGTCCTTCGGGCCAT
66 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCAT
*
2481165 CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAAAG
131 CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAAG
2481230 TTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
196 TTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
* *
2481276 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTGTTTCGAGAA
1 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
* * *
2481341 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGTAAGATTATAAGTCATTCGGGCCAT
66 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCAT
* * *
2481406 CCATAAGACCTTCGGGCAGGATGTTTTCACATGAGTTTCTAAAAATGAGAAAACGATTTCCAAAA
131 CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAAG
* * * **
2481471 TTTCTCATTTAAATATTTTCTAAAAATTAATTTTTCTTTAAAACCA
196 TTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
* * * *
2481517 AGAAAGCGATTTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAGTAAGTCTTTCTAGCA
1 AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
* * * *
2481582 TGATGCGTAAATTCTTCGGGTCATTTATAAGTCTTTCGA-ACAAGATGATAAGTTCTTCGGGCCA
66 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGA-AAGATGATAAGTCCTTCGGGCCA
* ** * * *
2481646 TCCATAAGACCTTCGGGCAGGATGCTTTCACATGATTTTCGAAAAAAAAGGAAACAATTTCAAAA
130 TCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAA
* *
2481711 GTTTCT-ATTTAAATATTTTCTAAAAACTGATTTTTCTTGAAAAGTA
195 GTTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
* * * * ** * *
2481757 AGAAAGTG-ATTCCCAAAGTTTCTTAATGCGTAAGTCTTTAGATCCGTCAGTAAGTCTTTCGAGC
1 AGAAAGTGAATT-CCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGC
** * ** * * * *
2481821 ATGATGAGTAAATGCTTCCAGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGG-CA
65 ATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCA
* * * * *
2481885 TCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTCGGAAAACGAGAAAATG-TTTCAAAA
130 TCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAA
2481949 GTTTCTCATTTAAATA
195 GTTTCTCATTTAAATA
2481965 TTTTTTGAAG
Statistics
Matches: 844, Mismatches: 81, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
238 14 0.02
239 61 0.07
240 165 0.20
241 604 0.72
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (241 bp):
AGAAAGTGAATTCCAAAGTTTCTTACTGAGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCTTCGGGCCAT
CCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAAG
TTTCTCATTTAAATAATTTCTAAAAATTGATTTTTCTTGAAAAGTA
Found at i:2481653 original size:41 final size:41
Alignment explanation
Indices: 2481554--2481653 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
2481544 GAGTAAGTCA
* * * *
2481554 TTCGGGCCATCAGTAAGTCTTTCTAGCATGATGCGTAAATTC
1 TTCGGGCCATCA-TAAGTCTTTCGAACAAGATGCATAAATTC
* * *
2481596 TTCGGGTCATTTATAAGTCTTTCGAACAAGATG-ATAAGTTC
1 TTCGGGCCA-TCATAAGTCTTTCGAACAAGATGCATAAATTC
2481637 TTCGGGCCATCCATAAG
1 TTCGGGCCAT-CATAAG
2481654 ACCTTCGGGC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.02
41 19 0.40
42 25 0.53
43 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
TTCGGGCCATCATAAGTCTTTCGAACAAGATGCATAAATTC
Found at i:2483367 original size:20 final size:20
Alignment explanation
Indices: 2483342--2483408 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
2483332 TTTATTTATG
*
2483342 CAACATCGATAACTATTGAA
1 CAACATCGATAACCATTGAA
*
2483362 CAACATCGATAACCATTAAA
1 CAACATCGATAACCATTGAA
2483382 CAACATCGATAACCATTGAA
1 CAACATCGATAACCATTGAA
2483402 CAACATC
1 CAACATC
2483409 AACATTCATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (20 bp):
CAACATCGATAACCATTGAA
Found at i:2494552 original size:23 final size:25
Alignment explanation
Indices: 2494508--2494553 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2494498 TGGAAAGTTT
*
2494508 AAATATTTATATAATCATATTAAGA
1 AAATATTCATATAATCATATTAAGA
2494533 AAATATTCA-ATAA-CATATTAA
1 AAATATTCATATAATCATATTAA
2494554 TATATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATATTCATATAATCATATTAAGA
Found at i:2495060 original size:23 final size:23
Alignment explanation
Indices: 2494994--2495061 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
2494984 AATAATTTAA
** *
2494994 TATAATAAAATAAAAAATAAAAC
1 TATAATAATTTAAAATATAAAAC
* * * *
2495017 TATAAT-TTTTAGAATTCTAAAAT
1 TATAATAATTTA-AAATATAAAAC
2495040 TATAATAATTTAAAATATAAAA
1 TATAATAATTTAAAATATAAAA
2495062 ATAACAATAG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
22 2 0.06
23 27 0.82
24 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (23 bp):
TATAATAATTTAAAATATAAAAC
Found at i:2505553 original size:17 final size:17
Alignment explanation
Indices: 2505531--2505563 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2505521 TTTTTTTTAA
2505531 AATATTATTAAAATTAC
1 AATATTATTAAAATTAC
*
2505548 AATATTATTATAATTA
1 AATATTATTAAAATTA
2505564 TGTATACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTATTAAAATTAC
Found at i:2515264 original size:13 final size:13
Alignment explanation
Indices: 2515234--2515274 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2515224 TAACTTTTTG
**
2515234 GGTCAAAGTCAGT
1 GGTCAAAGTCAAC
*
2515247 AGTCAAAGTCAAC
1 GGTCAAAGTCAAC
2515260 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
2515273 GG
1 GG
2515275 GTTGACTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2533306 original size:24 final size:24
Alignment explanation
Indices: 2533279--2533332 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2533269 CATTGGGTAA
2533279 TCCTGTATCAGTGCAATTATGCAC
1 TCCTGTATCAGTGCAATTATGCAC
*
2533303 TCCTGTATCAGTGTAATTATGCAC
1 TCCTGTATCAGTGCAATTATGCAC
2533327 TCCTGT
1 TCCTGT
2533333 GCTAATGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (24 bp):
TCCTGTATCAGTGCAATTATGCAC
Found at i:2536930 original size:25 final size:25
Alignment explanation
Indices: 2536874--2536965 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 25
2536864 ATTGTTGTAC
* *
2536874 TAGTGCATTCGTCCACTCCTGTAC--
1 TAGTGCATTTGTGCACTCCTG-ACAT
2536898 TAGTGCATTTGTGCACTCCTGACAT
1 TAGTGCATTTGTGCACTCCTGACAT
2536923 TAGTGCATTTGTGCACTCCTGACAT
1 TAGTGCATTTGTGCACTCCTGACAT
*
2536948 TAGTGCA-TTGTACACTCC
1 TAGTGCATTTGTGCACTCC
2536966 CATATTAGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
23 2 0.03
24 29 0.46
25 32 0.51
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (25 bp):
TAGTGCATTTGTGCACTCCTGACAT
Found at i:2537834 original size:59 final size:59
Alignment explanation
Indices: 2537737--2537864 Score: 211
Period size: 59 Copynumber: 2.2 Consensus size: 59
2537727 GTATACGGGT
* * * *
2537737 CAAGGTTGTTACATTTATTGGTATCAGAGCTACATGTTTAGTTGATTCTAGGCCTAAAC
1 CAAGCTTGTTACATTTATTGGTATCAAAGCTACATGTTTAGCTAATTCTAGGCCTAAAC
2537796 CAAGCTTGTTACATTTATTGGTATCAAAGCTACATGTTTAGCTAATTCTAGGCCTAAAC
1 CAAGCTTGTTACATTTATTGGTATCAAAGCTACATGTTTAGCTAATTCTAGGCCTAAAC
*
2537855 CGAGCTTGTT
1 CAAGCTTGTT
2537865 TTGTGTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (59 bp):
CAAGCTTGTTACATTTATTGGTATCAAAGCTACATGTTTAGCTAATTCTAGGCCTAAAC
Found at i:2540521 original size:25 final size:24
Alignment explanation
Indices: 2540483--2540707 Score: 82
Period size: 24 Copynumber: 9.3 Consensus size: 24
2540473 AAACCCATCA
* *
2540483 TATTAGTGCATTTGTTGCACTCTTG
1 TATTAGTACATTTG-TGCACTCCTG
* *
2540508 TATTAGTACCTTTGTGTACTCCTG
1 TATTAGTACATTTGTGCACTCCTG
* * * * **
2540532 TATCAGTACAATTATGCATTGTTG
1 TATTAGTACATTTGTGCACTCCTG
* *
2540556 TATTAGTACATTCGTGCACT-TTAG
1 TATTAGTACATTTGTGCACTCCT-G
* * * *
2540580 TACTAGTGCATTCGTGCACTTCTG
1 TATTAGTACATTTGTGCACTCCTG
* * * *
2540604 AAATTAGTGCA-TTGTACACTCCCG
1 -TATTAGTACATTTGTGCACTCCTG
* **
2540628 TATTAGCATCAATTTGT--ACTTATG
1 TATTAGTA-C-ATTTGTGCACTCCTG
* * *
2540652 TATTAGTGCAATTT-TGTACTCCTA
1 TATTAGTAC-ATTTGTGCACTCCTG
* ** **
2540676 AATTAGTGTATTCATGCACTCCTG
1 TATTAGTACATTTGTGCACTCCTG
2540700 TATTAGTA
1 TATTAGTA
2540708 TCGTTGTGTA
Statistics
Matches: 147, Mismatches: 44, Indels: 19
0.70 0.21 0.09
Matches are distributed among these distances:
22 1 0.01
23 16 0.11
24 104 0.71
25 22 0.15
26 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (24 bp):
TATTAGTACATTTGTGCACTCCTG
Found at i:2544196 original size:9 final size:9
Alignment explanation
Indices: 2544182--2544206 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2544172 AAACCCAACT
2544182 ATGGCCACC
1 ATGGCCACC
2544191 ATGGCCACC
1 ATGGCCACC
2544200 ATGGCCA
1 ATGGCCA
2544207 AACTCTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (9 bp):
ATGGCCACC
Found at i:2546053 original size:22 final size:20
Alignment explanation
Indices: 2546031--2546078 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2546021 AATAACAAAT
2546031 AATAAAAACTAATAAAAT--A
1 AATAAAAAC-AATAAAATAAA
2546050 AATAAAAA-AATAAAATAAA
1 AATAAAAACAATAAAATAAA
2546069 AATAAAAACA
1 AATAAAAACA
2546079 CAACGCTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (20 bp):
AATAAAAACAATAAAATAAA
Found at i:2547299 original size:23 final size:23
Alignment explanation
Indices: 2547273--2547340 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2547263 ATTTGTTTTT
2547273 AAAAACTATATATATATATATAA
1 AAAAACTATATATATATATATAA
* * *
2547296 AAAAACTAGATAGTATATATTTTAT
1 AAAAACTATATA-TATATA-TATAA
2547321 AAAAA-TAT-TATA-ATATATAA
1 AAAAACTATATATATATATATAA
2547341 TATAATACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 2 0.05
23 13 0.35
24 8 0.22
25 8 0.22
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (23 bp):
AAAAACTATATATATATATATAA
Found at i:2548673 original size:11 final size:10
Alignment explanation
Indices: 2548649--2548675 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2548639 TGCTATTTAC
2548649 TTTTTGTCGA
1 TTTTTGTCGA
2548659 TTTTTGTCGA
1 TTTTTGTCGA
2548669 TTTTTGT
1 TTTTTGT
2548676 ATACACTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (10 bp):
TTTTTGTCGA
Found at i:2549541 original size:13 final size:14
Alignment explanation
Indices: 2549513--2549541 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2549503 CTGGACCAAG
2549513 CCGTTGACTGTTGA
1 CCGTTGACTGTTGA
2549527 CCGTTGACT-TTGA
1 CCGTTGACTGTTGA
2549540 CC
1 CC
2549542 AAAAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.14, C:0.28, G:0.24, T:0.34
Consensus pattern (14 bp):
CCGTTGACTGTTGA
Found at i:2554683 original size:27 final size:28
Alignment explanation
Indices: 2554653--2554720 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
2554643 AAAATTATAG
*
2554653 AAATATCTCTAAAGGGTAAAAT-GACCA
1 AAATACCTCTAAAGGGTAAAATGGACCA
* * * *
2554680 AAATGCCCCTAAAGTGTAAAATGGACTA
1 AAATACCTCTAAAGGGTAAAATGGACCA
*
2554708 AATTACCTCTAAA
1 AAATACCTCTAAA
2554721 CCCTGGAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.24
Consensus pattern (28 bp):
AAATACCTCTAAAGGGTAAAATGGACCA
Found at i:2559049 original size:27 final size:27
Alignment explanation
Indices: 2559019--2559078 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2559009 CGAAATTGAA
*
2559019 TAAAATTAT-AGAAATATCTCTAAAGGG
1 TAAAATTATCA-AAATACCTCTAAAGGG
* * *
2559046 TAAAAATATCAAAATGCCTCTAAAGTG
1 TAAAATTATCAAAATACCTCTAAAGGG
2559073 TAAAAT
1 TAAAAT
2559079 GGCCTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (27 bp):
TAAAATTATCAAAATACCTCTAAAGGG
Found at i:2568042 original size:17 final size:17
Alignment explanation
Indices: 2568020--2568080 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
2568010 AACGGTCAAC
2568020 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2568037 GGTCAACGGTTGGGTCGGGTTG
1 GGTCAAC-----GGTCGGGTCG
2568059 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2568076 GGTCA
1 GGTCA
2568081 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 21 0.57
22 16 0.43
ACGTcount: A:0.11, C:0.20, G:0.48, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2568055 original size:22 final size:22
Alignment explanation
Indices: 2568027--2568079 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2568017 AACGGTCAAC
*
2568027 GGTCGGGTCGGGTCAACGGTTG
1 GGTCGGGTCGGGTCAACGGTCG
*
2568049 GGTCGGGTTGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
2568071 GGTCGGGTC
1 GGTCGGGTC
2568080 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.19, G:0.51, T:0.23
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:2568100 original size:19 final size:19
Alignment explanation
Indices: 2568078--2568155 Score: 97
Period size: 19 Copynumber: 4.1 Consensus size: 19
2568068 TCGGGTCGGG
2568078 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2568097 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2568116 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
2568135 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
2568155 T
1 T
2568156 GAAAATCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.06
19 39 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2568106 original size:10 final size:9
Alignment explanation
Indices: 2568076--2568154 Score: 86
Period size: 10 Copynumber: 8.3 Consensus size: 9
2568066 GGTCGGGTCG
*
2568076 GGTCAGACC
1 GGTCAAACC
2568085 GGTCAAACC
1 GGTCAAACC
*
2568094 GGTTCAGACC
1 GG-TCAAACC
2568104 GGTCAAACC
1 GGTCAAACC
*
2568113 GGTTCGAACC
1 GG-TCAAACC
*
2568123 GGTTGAAACC
1 GG-TCAAACC
2568133 GGTCAAACC
1 GGTCAAACC
2568142 GGTCAGAACC
1 GGTCA-AACC
2568152 GGT
1 GGT
2568155 TGAAAATCGG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
9 29 0.48
10 31 0.52
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2568133 original size:29 final size:28
Alignment explanation
Indices: 2568077--2568174 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
2568067 GTCGGGTCGG
* *
2568077 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTAAGACCG
*
2568105 GTCAAACCGGTTCGAACCGGTTGAA-ACCG
1 GTCAAACCGG-TCAAACCGGTT-AAGACCG
* *
2568134 GTCAAACCGGTCAGAACCGGTTGAAAATCG
1 GTCAAACCGGTCA-AACCGGTT-AAGACCG
*
2568164 GTTAAACCGGT
1 GTCAAACCGGT
2568175 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.18
29 35 0.58
30 14 0.23
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.17
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAAGACCG
Found at i:2575376 original size:17 final size:17
Alignment explanation
Indices: 2575354--2575393 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2575344 AACGGTCAAC
2575354 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2575371 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
2575388 GGTCAA
1 GGTCAA
2575394 ACCGGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.20, G:0.45, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2575381 original size:7 final size:7
Alignment explanation
Indices: 2575334--2575364 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2575324 GTCAAAGAAA
2575334 GTCAACG
1 GTCAACG
2575341 GTCAACG
1 GTCAACG
2575348 GTCAACG
1 GTCAACG
2575355 GTCAACG
1 GTCAACG
2575362 GTC
1 GTC
2575365 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2575416 original size:19 final size:19
Alignment explanation
Indices: 2575393--2575447 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
2575383 GGTTGGGTCA
2575393 AACCGGTCAAACCGGTTCG
1 AACCGGTCAAACCGGTTCG
*
2575412 GACCGGTCAAACCGGTTCG
1 AACCGGTCAAACCGGTTCG
*
2575431 AACCGGTTGAAACCGGT
1 AACCGG-TCAAACCGGT
2575448 CAAACTTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (19 bp):
AACCGGTCAAACCGGTTCG
Found at i:2575418 original size:10 final size:10
Alignment explanation
Indices: 2575393--2575447 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
2575383 GGTTGGGTCA
*
2575393 AACCGG-TCA
1 AACCGGTTCG
2575402 AACCGGTTCG
1 AACCGGTTCG
* *
2575412 GACCGG-TCA
1 AACCGGTTCG
2575421 AACCGGTTCG
1 AACCGGTTCG
2575431 AACCGGTT-G
1 AACCGGTTCG
2575440 AAACCGGT
1 -AACCGGT
2575448 CAAACTTGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
9 14 0.37
10 24 0.63
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:2584556 original size:7 final size:8
Alignment explanation
Indices: 2584540--2584567 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2584530 CTTTCTCATA
2584540 TTTTATTT
1 TTTTATTT
2584548 TTTTATTT
1 TTTTATTT
2584556 TTTTATTT
1 TTTTATTT
2584564 TTTT
1 TTTT
2584568 CTTGTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTATTT
Found at i:2584575 original size:16 final size:16
Alignment explanation
Indices: 2584540--2584575 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2584530 CTTTCTCATA
*
2584540 TTTTATTTTTTTATTT
1 TTTTATTTTTTTATTG
*
2584556 TTTTATTTTTTTCTTG
1 TTTTATTTTTTTATTG
2584572 TTTT
1 TTTT
2584576 CTAGTTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTATTTTTTTATTG
Found at i:2587328 original size:42 final size:41
Alignment explanation
Indices: 2587212--2587329 Score: 107
Period size: 42 Copynumber: 2.9 Consensus size: 41
2587202 TTAAACCTTA
*
2587212 TATTTTATCTTTGTTTAGGTATTTTAGTTTAAAT-AGATGT
1 TATTTTATCTTTGTTTAGGTATTTTAGTTTAAATAACATGT
** * ** * *
2587252 TAGCATT-TCTTAGGATTTAGG-ACATTATTTTAAATAACATTT
1 TA-TTTTATCTT-TG-TTTAGGTATTTTAGTTTAAATAACATGT
2587294 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA
1 TATTTTATCTTTG-TTTAGGTATTTTAGTTTAAATA
2587330 GTTTTAAGTG
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
40 6 0.11
41 23 0.40
42 28 0.49
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (41 bp):
TATTTTATCTTTGTTTAGGTATTTTAGTTTAAATAACATGT
Found at i:2596189 original size:20 final size:21
Alignment explanation
Indices: 2596144--2596189 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
2596134 TTTTCCCTTA
*
2596144 TTTTTGTTTTTAATTTCATGC
1 TTTTTGTTTTTAATTTCATAC
*
2596165 ATTTTG-TTTTAATTATC-TAC
1 TTTTTGTTTTTAATT-TCATAC
2596185 TTTTT
1 TTTTT
2596190 AACATGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTGTTTTTAATTTCATAC
Found at i:2596395 original size:18 final size:19
Alignment explanation
Indices: 2596353--2596394 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2596343 CTATGCTTTG
2596353 TTTTTATTTTGTTTACAAT
1 TTTTTATTTTGTTTACAAT
*
2596372 TTTTTATTTT-TTTTCTAAT
1 TTTTTATTTTGTTTAC-AAT
2596391 TTTT
1 TTTT
2596395 AATAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTGTTTACAAT
Found at i:2596415 original size:5 final size:5
Alignment explanation
Indices: 2596405--2596440 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
2596395 AATAATTTAA
2596405 ATTTT ATTTT ATTTT ATTTT A-TTT -TTTT A-TTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
2596441 GTCCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 10 0.36
5 18 0.64
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Done.