Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 68 of 208
Found at i:25173670 original size:21 final size:21
Alignment explanation
Indices: 25173651--25173689 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
25173641 TTTTTTTTAA
25173651 AAATTTTTATA-AT-ATTTTT
1 AAATTTTTATATATGATTTTT
25173670 AAATTTTTATATATGATTTT
1 AAATTTTTATATATGATTTT
25173690 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 2 0.11
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AAATTTTTATATATGATTTTT
Found at i:25174380 original size:24 final size:23
Alignment explanation
Indices: 25174352--25174418 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
25174342 CAGCAAATGA
25174352 TTTTAAAATTATTAAAATTAATTT
1 TTTTAAAATTA-TAAAATTAATTT
***
25174376 TTTTATTCTTATAAAATTAATTT
1 TTTTAAAATTATAAAATTAATTT
**
25174399 TTTTAATTTTTATAAAATTA
1 TTTTAA-AATTATAAAATTA
25174419 TCATCATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 17 0.46
24 20 0.54
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAAATTATAAAATTAATTT
Found at i:25174390 original size:23 final size:24
Alignment explanation
Indices: 25174364--25174418 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
25174354 TTAAAATTAT
25174364 TAAAATTAATTTTTTT-ATTCTTA
1 TAAAATTAATTTTTTTAATTCTTA
*
25174387 TAAAATTAATTTTTTTAATTTTTA
1 TAAAATTAATTTTTTTAATTCTTA
25174411 TAAAATTA
1 TAAAATTA
25174419 TCATCATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TAAAATTAATTTTTTTAATTCTTA
Found at i:25174518 original size:3 final size:3
Alignment explanation
Indices: 25174510--25174536 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25174500 TCCACCAAGC
25174510 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
25174537 TATCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:25177056 original size:12 final size:12
Alignment explanation
Indices: 25177039--25177081 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
25177029 AATATAGAAC
25177039 AATATAATATAT
1 AATATAATATAT
*
25177051 AATATATTATAT
1 AATATAATATAT
* *
25177063 TATATAATAAAAT
1 AATATAAT-ATAT
25177076 AATATA
1 AATATA
25177082 CTAATATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAATATAT
Found at i:25177081 original size:15 final size:15
Alignment explanation
Indices: 25177028--25177087 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
25177018 TTAGTTTATT
* *
25177028 TAATATAGAACAATA
1 TAATATATAATAATA
25177043 TAATATATAATATATTA
1 TAATATATAATA-A-TA
* *
25177060 TATTATATAATAAAA
1 TAATATATAATAATA
25177075 TAATATACTAATA
1 TAATATA-TAATA
25177088 TTAAAAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 17 0.46
16 7 0.19
17 13 0.35
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (15 bp):
TAATATATAATAATA
Found at i:25177218 original size:23 final size:23
Alignment explanation
Indices: 25177192--25177236 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
25177182 ATTAATCTAT
25177192 AATTCAACTTTTATCCCTAATTC
1 AATTCAACTTTTATCCCTAATTC
* * * *
25177215 AATTTAGCTTTTTTTCCTAATT
1 AATTCAACTTTTATCCCTAATT
25177237 TCTCTTAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTCAACTTTTATCCCTAATTC
Found at i:25177515 original size:27 final size:27
Alignment explanation
Indices: 25177485--25177536 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
25177475 CCACTACAGA
*
25177485 CTCCAATTCTCTTTATTATTTTTCTGG
1 CTCCAATTCTCTTTATGATTTTTCTGG
25177512 CTCCAATTCTCTTTATGATTTTTCT
1 CTCCAATTCTCTTTATGATTTTTCT
25177537 CTGCCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (27 bp):
CTCCAATTCTCTTTATGATTTTTCTGG
Found at i:25178055 original size:21 final size:21
Alignment explanation
Indices: 25178029--25178084 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
25178019 AACAGCGGTG
*
25178029 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
25178050 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
25178071 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
25178085 AACAGCGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:25181084 original size:6 final size:6
Alignment explanation
Indices: 25181073--25181122 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
25181063 TTTGCAATCC
*
25181073 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAGGGG AAGGGG AAAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG
25181122 A
1 A
25181123 GAAGAAGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:25181129 original size:18 final size:17
Alignment explanation
Indices: 25181073--25181130 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
25181063 TTTGCAATCC
25181073 AAGGGGAAGGGGA-AAGGG
1 AAGGGGAAGGGGAGAA--G
**
25181091 AAGGGGAAGGGGAAGGGG
1 AAGGGGAAGGGG-AGAAG
25181109 AAGGGGAAAGGGGAGAAG
1 AAGGGG-AAGGGGAGAAG
25181127 AAGG
1 AAGG
25181131 TAACAGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGGAGAAG
Found at i:25186945 original size:32 final size:32
Alignment explanation
Indices: 25186904--25186976 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
25186894 TAGAGTATAA
*
25186904 CTTAAAAAAACCATGAAAAGTGAGGATATTCC
1 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
25186936 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
1 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
25186968 CTTAAAAAA
1 CTTAAAAAA
25186977 TTATTCGAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (32 bp):
CTTAAAAAAACCATAAAAAGTGAGGATATTCC
Found at i:25198006 original size:18 final size:18
Alignment explanation
Indices: 25197972--25198022 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
25197962 TAGGGTGTGC
25197972 AAAATTCGGTTAAAACCGAA
1 AAAATTCGGTT--AACCGAA
*
25197992 AAAATTCGGTTAACCGAC
1 AAAATTCGGTTAACCGAA
**
25198010 CGAATTCGGTTAA
1 AAAATTCGGTTAA
25198023 TCAGTCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 17 0.61
20 11 0.39
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAATTCGGTTAACCGAA
Found at i:25198229 original size:13 final size:13
Alignment explanation
Indices: 25198211--25198237 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25198201 CCTCCAGGCT
25198211 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
25198224 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
25198237 C
1 C
25198238 AATTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.15, T:0.07
Consensus pattern (13 bp):
CTAAGCCCAAGAA
Found at i:25198252 original size:7 final size:7
Alignment explanation
Indices: 25198240--25198298 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
25198230 CCAAGAACAA
25198240 TTCATGT
1 TTCATGT
25198247 TTCATGT
1 TTCATGT
25198254 TTCATGT
1 TTCATGT
*
25198261 TTCACGAT
1 TTCATG-T
25198269 TTCATGT
1 TTCATGT
**
25198276 TTCATAC
1 TTCATGT
*
25198283 TGCATGT
1 TTCATGT
25198290 TTCATGT
1 TTCATGT
25198297 TT
1 TT
25198299 TCTTCTGTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (7 bp):
TTCATGT
Found at i:25198588 original size:37 final size:37
Alignment explanation
Indices: 25198545--25198650 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
25198535 TGTGTTAAAG
*
25198545 ACTTATGTAATGTTTTTAATTATTTAGTGATTCAAAA
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
* * * *
25198582 ATTTATGTAATGTTTTTAGTTATGTAGTGATTCAAAG
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
*
25198619 ACTTATGTAATTTTTTTAATTATATAGTGATT
1 ACTTATGTAATGTTTTTAATTATATAGTGATT
25198651 TAAATCGGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
Found at i:25198669 original size:9 final size:9
Alignment explanation
Indices: 25198650--25198742 Score: 143
Period size: 9 Copynumber: 10.4 Consensus size: 9
25198640 ATATAGTGAT
25198650 TTAAATCGG
1 TTAAATCGG
* *
25198659 TTAAGTTGG
1 TTAAATCGG
25198668 TTAAATCGG
1 TTAAATCGG
25198677 TTAAATCGG
1 TTAAATCGG
25198686 TTAAATCGG
1 TTAAATCGG
25198695 TTAAATCGG
1 TTAAATCGG
*
25198704 TTAAGTCGG
1 TTAAATCGG
25198713 TT-AATCGG
1 TTAAATCGG
*
25198721 TTAAATAGG
1 TTAAATCGG
25198730 TTAAATCGG
1 TTAAATCGG
25198739 TTAA
1 TTAA
25198743 TTTTTAACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
8 7 0.09
9 68 0.91
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (9 bp):
TTAAATCGG
Found at i:25208303 original size:2 final size:2
Alignment explanation
Indices: 25208261--25208290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25208251 CTGTTGGCAA
25208261 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25208291 CATGTGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25213472 original size:18 final size:18
Alignment explanation
Indices: 25213449--25213486 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25213439 GATAATAAAG
25213449 AATGTAGAATAAA-ATTAA
1 AATGTAGAA-AAATATTAA
*
25213467 AATGTATAAAAATATTAA
1 AATGTAGAAAAATATTAA
25213485 AA
1 AA
25213487 CAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
AATGTAGAAAAATATTAA
Found at i:25213707 original size:18 final size:18
Alignment explanation
Indices: 25213684--25213728 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
25213674 AATAAACCAC
25213684 AACTTACAAGTCTAACAA
1 AACTTACAAGTCTAACAA
25213702 AACTTACAAGTCTAACAA
1 AACTTACAAGTCTAACAA
*
25213720 AATTTACAA
1 AACTTACAA
25213729 ACCCTATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24
Consensus pattern (18 bp):
AACTTACAAGTCTAACAA
Found at i:25213982 original size:29 final size:28
Alignment explanation
Indices: 25213935--25214036 Score: 75
Period size: 29 Copynumber: 3.7 Consensus size: 28
25213925 TATGCTATTC
* *
25213935 TATACATTAACTTTGAATTTGGGTAATTT
1 TATACATAAAATTTGAATTT-GGTAATTT
* **
25213964 TATACATAAAATTTTAATTT-G--ATCC
1 TATACATAAAATTTGAATTTGGTAATTT
* * * *
25213989 AATTCATGAACTTTGAATTTGTGTAATTT
1 TATACATAAAATTTGAATTTG-GTAATTT
*
25214018 TATACATAAAATTTTAATT
1 TATACATAAAATTTGAATT
25214037 AATTTGATCC
Statistics
Matches: 52, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
25 17 0.33
27 2 0.04
29 33 0.63
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (28 bp):
TATACATAAAATTTGAATTTGGTAATTT
Found at i:25214205 original size:31 final size:30
Alignment explanation
Indices: 25214170--25214255 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
25214160 ATTAAAAGTG
*
25214170 TATAATTGAATCAAAATTAAAGTTTCATATA
1 TATAATTGAA-CAAAATTAAAGTTTCACATA
* ** * *
25214201 TATAATTGAACCACAACCAAATTTTCACATG
1 TATAATTGAA-CAAAATTAAAGTTTCACATA
* *
25214232 TATAATTGTACCAAATTAAAGTTT
1 TATAATTGAACAAAATTAAAGTTT
25214256 AAGTATAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
30 9 0.21
31 33 0.79
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (30 bp):
TATAATTGAACAAAATTAAAGTTTCACATA
Found at i:25221946 original size:254 final size:254
Alignment explanation
Indices: 25221497--25221998 Score: 977
Period size: 254 Copynumber: 2.0 Consensus size: 254
25221487 TTGACCTCAC
25221497 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
1 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
*
25221562 CCTAAATGACTTATTAGGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
66 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
25221627 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
131 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
25221692 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
196 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
25221751 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
1 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
25221816 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
66 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
* *
25221881 CATTAAGAATACCCTACATAGCAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
131 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
25221946 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAA
196 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAA
25221999 TAAATAATAA
Statistics
Matches: 245, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
254 245 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (254 bp):
AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
Found at i:25226483 original size:33 final size:33
Alignment explanation
Indices: 25226345--25226588 Score: 118
Period size: 33 Copynumber: 7.3 Consensus size: 33
25226335 CCATCTAACC
* *
25226345 ATGGTCTTACGTTCATAGTGTCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
**
25226378 ATGGTCTTA---TCATGAGAATGCCATGGCCCAGCT
1 ATGGTCTTACGTTCAT-AG--TGCCATAACCCAGCT
* * * * * * * *
25226411 ATGGTCTTACATATAAACACTGCCATGATCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGCT
*
25226446 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
* * * **
25226479 ATGGTCTTATC-ATCAGAATGCCATAGTCCAGCT
1 ATGGTCTTA-CGTTCATAGTGCCATAACCCAGCT
* * * * * * *** * *
25226512 ATGATCTTACATATAAACACTGTCATGGTCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGCT
*
25226547 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
25226580 ATGGTCTTA
1 ATGGTCTTA
25226589 TCCATCAATT
Statistics
Matches: 152, Mismatches: 47, Indels: 24
0.68 0.21 0.11
Matches are distributed among these distances:
30 4 0.03
31 2 0.01
32 1 0.01
33 93 0.61
34 4 0.03
35 45 0.30
37 2 0.01
38 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
Found at i:25226488 original size:101 final size:101
Alignment explanation
Indices: 25226262--25226595 Score: 539
Period size: 101 Copynumber: 3.3 Consensus size: 101
25226252 TTTACATTTG
* * *
25226262 TAGTGCCATAACCCAGTTGTGGTCTTATCATCAGAATGTCATAGCCTAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
*
25226327 AAACACTGCC---ATCTAACCATGGTCTTACGTTCA
66 AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
* * *
25226360 TAGTGTCATAACCCAGTTATGGTCTTATCATGAGAATGCCATGGCCCAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
25226425 AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
66 AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
* *
25226461 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGTCCAGCTATGATCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
* *
25226526 AAACACTGTCATGGTCCAACCATGGTCTTACGTTCA
66 AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
25226562 TAGTGCCATAACCCAGTTATGGTCTTATCCATCA
1 TAGTGCCATAACCCAGTTATGGTCTTAT-CATCA
25226596 ATTCATCATT
Statistics
Matches: 218, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
98 69 0.32
101 144 0.66
102 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
Found at i:25229010 original size:43 final size:43
Alignment explanation
Indices: 25228962--25229050 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
25228952 CTTATGTCAA
* *
25228962 TTGTTAGAGTATATTATACTTATATCT-CAAAGGTATTATTTTC
1 TTGTTAGAATATATTATACTTATAT-TACAAAGGTATTATTCTC
* * *
25229005 TTGTTAGAATATGTTGTACTTATATTATAAAGGTATTATTCTC
1 TTGTTAGAATATATTATACTTATATTACAAAGGTATTATTCTC
25229048 TTG
1 TTG
25229051 GTATCATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.49
Consensus pattern (43 bp):
TTGTTAGAATATATTATACTTATATTACAAAGGTATTATTCTC
Found at i:25229620 original size:19 final size:20
Alignment explanation
Indices: 25229583--25229636 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
25229573 ACAAAAACTA
*
25229583 TAAAAATTTAAAATAATTT-
1 TAAAAATTCAAAATAATTTG
25229602 TCAAAAATTCAAAAT-ATTTG
1 T-AAAAATTCAAAATAATTTG
25229622 TAAAAATTCTAAAAT
1 TAAAAATTC-AAAAT
25229637 TGATATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAATTCAAAATAATTTG
Found at i:25233977 original size:15 final size:15
Alignment explanation
Indices: 25233957--25233987 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25233947 GTTCGTTCAA
25233957 TTTTATATATAAATT
1 TTTTATATATAAATT
*
25233972 TTTTATTTATAAATT
1 TTTTATATATAAATT
25233987 T
1 T
25233988 AATTGTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATATAAATT
Found at i:25237358 original size:42 final size:42
Alignment explanation
Indices: 25237310--25237408 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
25237300 GCTCTCGGTA
* *
25237310 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
* *
25237352 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
*
25237394 TCGTACACTTAGTGC
1 TCGCACACTTAGTGC
25237409 TGTTCATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
Found at i:25240288 original size:24 final size:24
Alignment explanation
Indices: 25240223--25240288 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
25240213 TTATATAGTA
*
25240223 TATTTAAA-TTTA-ATT-TGAATC
1 TATTTAAAGTTTATATTATCAATC
*
25240244 AATTTAAAGTTT-T-TTGAATCAATC
1 TATTTAAAGTTTATATT--ATCAATC
25240268 TATTTAAAGTTTATATTATCA
1 TATTTAAAGTTTATATTATCA
25240289 TTTAAAAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
21 9 0.26
22 3 0.09
24 20 0.57
25 1 0.03
26 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
TATTTAAAGTTTATATTATCAATC
Found at i:25240921 original size:71 final size:71
Alignment explanation
Indices: 25240833--25240977 Score: 263
Period size: 71 Copynumber: 2.0 Consensus size: 71
25240823 GAGAGTAAAC
*
25240833 ATTGAGGGCTAAAAAGTACACAATTAACAGCAAAAATGGTTAGCATTATTGATTGGACCAAACTA
1 ATTGAGGGCTAAAAAGTACACAATTAACAGCAAAAATGGTTAGCATGATTGATTGGACCAAACTA
25240898 AATCAA
66 AATCAA
* *
25240904 ATTGAGGGCTAAAAAGTACACAATTAACAGCAAAAATGGTTGGCATGATTGATTGGACCGAACTA
1 ATTGAGGGCTAAAAAGTACACAATTAACAGCAAAAATGGTTAGCATGATTGATTGGACCAAACTA
25240969 AATCAA
66 AATCAA
25240975 ATT
1 ATT
25240978 AAGTGCAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (71 bp):
ATTGAGGGCTAAAAAGTACACAATTAACAGCAAAAATGGTTAGCATGATTGATTGGACCAAACTA
AATCAA
Found at i:25251774 original size:25 final size:23
Alignment explanation
Indices: 25251730--25251777 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
25251720 ATTTAATTAA
**
25251730 TATTTTATTAAGATTTTTAATAT
1 TATTTTATTAAGATGATTAATAT
25251753 TATTTTATTATTAGATGATTAATAT
1 TATTTTATTA--AGATGATTAATAT
25251778 AAAAGGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TATTTTATTAAGATGATTAATAT
Found at i:25259119 original size:14 final size:13
Alignment explanation
Indices: 25259081--25259121 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
25259071 TTTTATAAAC
25259081 ATTTTAATTATTT
1 ATTTTAATTATTT
*
25259094 GTTTT-A-TATTT
1 ATTTTAATTATTT
25259105 ATTTTAAATTATTT
1 ATTTT-AATTATTT
25259119 ATT
1 ATT
25259122 ATATTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.39
12 1 0.04
13 5 0.22
14 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
ATTTTAATTATTT
Found at i:25262921 original size:21 final size:22
Alignment explanation
Indices: 25262895--25262941 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
25262885 CTCTGCTCAA
*
25262895 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
25262916 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
25262938 ACTC
1 ACTC
25262942 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:25267835 original size:23 final size:22
Alignment explanation
Indices: 25267809--25267851 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
25267799 TAGAAATCGA
25267809 TAGAA-TTATTATTTCAAAAAAAT
1 TAGAATTTA-TATTT-AAAAAAAT
25267832 TAGAATTTATATTTAAAAAA
1 TAGAATTTATATTTAAAAAA
25267852 TAAATTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TAGAATTTATATTTAAAAAAAT
Found at i:25268218 original size:17 final size:17
Alignment explanation
Indices: 25268198--25268230 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
25268188 TTTAAATAAA
25268198 TAAATAATTTTCTCAAT
1 TAAATAATTTTCTCAAT
25268215 TAAATAATTTTCTCAA
1 TAAATAATTTTCTCAA
25268231 CCTGATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTTCTCAAT
Found at i:25269485 original size:56 final size:56
Alignment explanation
Indices: 25269399--25269518 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
25269389 ACAAGGGATG
25269399 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
25269455 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
25269511 ATGGGCAA
1 ATGGGCAA
25269519 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:25270592 original size:80 final size:79
Alignment explanation
Indices: 25270379--25270636 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 79
25270369 TCGAATGATG
* * * * * * *
25270379 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGTAT
1 TCCGGGCTAAATCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
25270442 TTGTGCGAGATACTAAT
64 TTGTGCGAG-TACTAAA
* * * *
25270459 TCCGGGCT-AAGCCCGAAGGCATTGGTGCGAGTTACTA-AATTCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
25270522 TGTGCGAGTTACTAAA
65 TGTGCGAG-TACTAAA
* *
25270538 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
** *
25270603 GAACGAGTAGCTATA
66 GTGCGAGTA-CTAAA
* *
25270618 TCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAATCCCGAAGG
25270637 TACGTGATTT
Statistics
Matches: 149, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.01
79 71 0.48
80 74 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTACTAAA
Found at i:25270610 original size:40 final size:40
Alignment explanation
Indices: 25270379--25270603 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
25270369 TCGAATGATG
* * * *
25270379 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
25270419 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25270459 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
25270498 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
25270538 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
25270579 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25270604 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.20
40 117 0.74
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:25270625 original size:119 final size:119
Alignment explanation
Indices: 25270386--25270636 Score: 269
Period size: 119 Copynumber: 2.1 Consensus size: 119
25270376 ATGTCCGGGC
* *
25270386 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* ** *
25270451 ATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATTCGGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATTCCGGT
* * * **
25270505 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAA-ATCCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * *
25270568 AGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA-TCCGGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAATTCCGGT
* *
25270624 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
25270637 TACGTGATTT
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
118 4 0.04
119 78 0.71
120 28 0.25
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATTCCGGT
Found at i:25278232 original size:40 final size:40
Alignment explanation
Indices: 25278001--25278225 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
25277991 TCGAATGATG
* * * * *
25278001 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
25278041 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25278081 TCCGGGTTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
25278120 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
25278160 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
25278201 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
25278226 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 35 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:25281391 original size:4 final size:4
Alignment explanation
Indices: 25281384--25281414 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
25281374 TTGCAAGGTA
*
25281384 ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
25281415 TATATTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:25291134 original size:36 final size:36
Alignment explanation
Indices: 25291076--25291167 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
25291066 ATGTCTCTAA
* * *
25291076 AATAGTAATAAAAATAATAATAAAACAACAGTTATAT
1 AATAGTAA-AATAATAACAATAAAACAACAGTAATAT
* * * *
25291113 AATATTCAAATAATAACAATAAAATAATAGTAATAT
1 AATAGTAAAATAATAACAATAAAACAACAGTAATAT
*
25291149 AATAGTAAAATAGTAACAA
1 AATAGTAAAATAATAACAA
25291168 AATAACATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 39 0.87
37 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (36 bp):
AATAGTAAAATAATAACAATAAAACAACAGTAATAT
Found at i:25298483 original size:23 final size:23
Alignment explanation
Indices: 25298453--25298501 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
25298443 AGCTTTTACC
25298453 ACATTTCCTGTTAAGTTTCATTA
1 ACATTTCCTGTTAAGTTTCATTA
25298476 ACATTTCCTGTTAAGTTTCATTA
1 ACATTTCCTGTTAAGTTTCATTA
25298499 ACA
1 ACA
25298502 AGATAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (23 bp):
ACATTTCCTGTTAAGTTTCATTA
Found at i:25300000 original size:26 final size:26
Alignment explanation
Indices: 25299964--25300016 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
25299954 GCAAGGAAAA
25299964 AGGGAACTTCAGAAACAAAGATAAAT
1 AGGGAACTTCAGAAACAAAGATAAAT
25299990 AGGGAACTTCAGAAACAAAGATAAAT
1 AGGGAACTTCAGAAACAAAGATAAAT
25300016 A
1 A
25300017 TATTATCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (26 bp):
AGGGAACTTCAGAAACAAAGATAAAT
Found at i:25302185 original size:61 final size:61
Alignment explanation
Indices: 25302120--25302241 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
25302110 CCACAACCTC
*
25302120 CAAGAACAACCAGTAATAGGAAAGTAAGAATGTAAAAAAAACTCACCACCTCCAAGAACAA
1 CAAGAACAACCAGAAATAGGAAAGTAAGAATGTAAAAAAAACTCACCACCTCCAAGAACAA
25302181 CAAGAACAACCAGAAATAGGAAAGTAAGAATGTAAAAAAAACTCACCACCTCCAAGAACAA
1 CAAGAACAACCAGAAATAGGAAAGTAAGAATGTAAAAAAAACTCACCACCTCCAAGAACAA
25302242 ACACCTTCAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (61 bp):
CAAGAACAACCAGAAATAGGAAAGTAAGAATGTAAAAAAAACTCACCACCTCCAAGAACAA
Found at i:25307305 original size:121 final size:125
Alignment explanation
Indices: 25306993--25307341 Score: 492
Period size: 126 Copynumber: 2.8 Consensus size: 125
25306983 TAATTTCGAG
** *
25306993 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTACCAGAATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTG
* *
25307058 AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGTAAGTCACGGAAG-AATAATTATTTTT
* * *
25307119 TTGACGTTTCTGAGCAAATAGTATAAGATCGCTTCTAGGAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTG
* * *
25307184 AAATCGCGGCCTCGTCAG-CGTGCTTTTGCTACAGTAAGTCATGTAAG-A-AA-T-TTTTT
66 AAATCGCGCCCTCGT-AGACGTGCTTTTGCTACAGTAAGTCACGGAAGAATAATTATTTTT
* *
25307240 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGAATACTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTG
* * **
25307305 AAATCGCGCCATCGTGGACGCACTTTTGCTACAGTAA
66 AAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGTAA
25307342 CATGTTTGGG
Statistics
Matches: 200, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
120 1 0.00
121 95 0.47
122 1 0.00
123 2 0.01
124 1 0.00
126 99 0.50
127 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGTAAGTCACGGAAGAATAATTATTTTT
Found at i:25310590 original size:116 final size:116
Alignment explanation
Indices: 25310377--25310614 Score: 404
Period size: 116 Copynumber: 2.1 Consensus size: 116
25310367 TGATAAATTG
* *
25310377 TATTCAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
*
25310442 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
* * *
25310493 TATTAAGTTAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
*
25310558 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAACAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
*
25310609 TGTTAA
1 TATTAA
25310615 CTTAGTTTAG
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:25310637 original size:23 final size:23
Alignment explanation
Indices: 25310611--25311172 Score: 321
Period size: 23 Copynumber: 22.0 Consensus size: 23
25310601 TGTAACATTG
* *
25310611 TTAACTTAGTTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
25310634 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
*
25310657 TTAAATTAGGTTAAGGTTAGGGTTT--
1 TTAAATTAGGTTAGGGTT----TTTAA
*
25310682 TTAAGTTAAGGGTTTAGGGTTTTTAA
1 TTAAATT-A-GG-TTAGGGTTTTTAA
*
25310708 TTAAACTAGGTTAGGATTTGTGTTTTTAA
1 TTAAATTAGGTTA-G----G-GTTTTTAA
*
25310737 TTAAGTTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
*
25310760 TTAAATTAGGTTAGGGTTCTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
*
25310783 TTAAATTAGGTTAAGGTTAATGTTAGA
1 TTAAATTAGGTTAGGGTT--T-TTA-A
* *
25310810 GTT--TTTAAGTTAAGGGTTTAGGGTTTTTAA
1 -TTAAATTAGGTT-A-------GGGTTTTTAA
25310840 TTAAATTAGGTTAGGGTTAAGGTTTTTAA
1 TTAAATTAGGTTA--G----GGTTTTTAA
25310869 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
* *
25310892 TTAAATTATGTTAGAGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
25310915 TTAAATTAGGTTA-GGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
25310937 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
25310960 TTAAATTAGGTTAGAGTTAGGGTTTTTAA
1 TT-AA--A--TTAG-GTTAGGGTTTTTAA
25310989 TTAATTTAAGTTAGGGGTTAGGGTTTTTAA
1 TT-A---AA-TTA--GGTTAGGGTTTTTAA
* *
25311019 TTAAATTAGGTTAGGGTTAGGGTTAGGGTT
1 TTAAATTAGGTTAGGGTT---TTTA----A
*
25311049 TTTAATTAATTTAGGTTAGGGTTAGGGTTCTTAA
1 TTAAATTA-----GGTTAGGG-T----TT-TTAA
25311083 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
* *
25311106 TTAAATTAAGTTAGGGTTTTAAA
1 TTAAATTAGGTTAGGGTTTTTAA
25311129 TTAAATTAGGTTAGGG--TTTAA
1 TTAAATTAGGTTAGGGTTTTTAA
*
25311150 GGTTAAATTA-GTTAGGATTTTTA
1 --TTAAATTAGGTTAGGGTTTTTA
25311173 TTACATCAAA
Statistics
Matches: 436, Mismatches: 35, Indels: 135
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.01
22 27 0.06
23 198 0.45
24 15 0.03
25 11 0.03
26 21 0.05
27 8 0.02
28 16 0.04
29 74 0.17
30 26 0.06
31 10 0.02
32 2 0.00
34 11 0.03
35 8 0.02
36 1 0.00
38 3 0.01
40 1 0.00
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (23 bp):
TTAAATTAGGTTAGGGTTTTTAA
Found at i:25310678 original size:52 final size:50
Alignment explanation
Indices: 25310616--25311143 Score: 404
Period size: 52 Copynumber: 10.1 Consensus size: 50
25310606 CATTGTTAAC
*
25310616 TTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AATTAGG
* *
25310667 TTAAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTTTTAATTAAACTAGG
1 TT-AGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATT-AATTAGG
* * *
25310718 TTAGGATTTGTGTTTTTAATTAAGTTAGGTTAGGGTTTTTAATTAA--A--
1 TTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTAGG
* * * *
25310765 TTAGGTTAGGGTTCTTAATTAAATTAGGTTAAGGTTAATGTTAGAGTT-TTTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT--T-TTA-A-TTAATTAGG
**
25310819 TTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTT--TTAATTAAA
1 TT-A-GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTAATTAATTAGG
* *
25310874 TTAGGTTAGGGTTTTTAATTAAATTATGTTAGAGTTTTTAATTAA--A--
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTAGG
25310920 TTAGGTTA-GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AATTAGG
25310970 TTAGAGTTAGGGTTTTTAATTAATTTAAGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAG-GTTAGGGTTTTTAATT-A---AA-TTA--GGTTAGGGTTTTTAATT--A--A--TTA-GG
* * * **
25311035 TTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTT-CTTAATTAAA
1 TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT---TTTAATTAATTAGG
* *
25311088 TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTAAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AATTAGG
25311139 TTAGG
1 TTAGG
25311144 GTTTAAGGTT
Statistics
Matches: 392, Mismatches: 35, Indels: 100
0.74 0.07 0.19
Matches are distributed among these distances:
45 32 0.08
46 36 0.09
47 5 0.01
48 6 0.02
49 5 0.01
50 18 0.05
51 56 0.14
52 104 0.27
53 10 0.03
54 8 0.02
55 7 0.02
56 5 0.01
57 32 0.08
58 13 0.03
59 18 0.05
60 7 0.02
61 3 0.01
62 1 0.00
64 4 0.01
65 21 0.05
66 1 0.00
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (50 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTAGG
Found at i:25310701 original size:22 final size:20
Alignment explanation
Indices: 25310666--25310711 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
25310656 ATTAAATTAG
25310666 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
25310686 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
25310708 -TTAA
1 GTTAA
25310712 ACTAGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:25310852 original size:132 final size:132
Alignment explanation
Indices: 25310611--25311036 Score: 539
Period size: 132 Copynumber: 3.3 Consensus size: 132
25310601 TGTAACATTG
* *
25310611 TTAACTTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTA
1 TTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTA
* *
25310676 -G---G-GTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAACTAGGTTAGGATT-TGTGTTTTT
66 TGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGATTAAGTGTTTTT
25310735 AA
131 AA
*
25310737 TTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTCTTAATTAAATTAGGTTAAGGTTA
1 TTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTT-
*
25310802 ATGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAG-GTTTT
65 ATGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGATTAAGTGTTTT
25310866 TAA
130 TAA
* * *
25310869 TTAAATTAGGTTAGGGTTTTTAATTAAATTATGTTAGAGTTTTTAATTAAATTAGGTT-AGGTT-
1 TTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTA
* * *
25310932 T-TTA-A----TTAAATT-A-GG-TTAGGGTTTTTAATTAAATTAGGTTA-GAGTTAGGGTTTTT
66 TGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGA-TTA-AGTGTTT
25310987 AATTAA
129 --TTAA
25310993 TTTAAGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 -TTAAGTTA--GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
25311037 AGGGTTAGGG
Statistics
Matches: 268, Mismatches: 17, Indels: 29
0.85 0.05 0.09
Matches are distributed among these distances:
119 1 0.00
120 29 0.11
121 3 0.01
122 4 0.01
123 6 0.02
124 4 0.01
125 7 0.03
126 61 0.23
127 33 0.12
128 4 0.01
129 1 0.00
131 6 0.02
132 108 0.40
133 1 0.00
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (132 bp):
TTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTA
TGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGATTAAGTGTTTTT
AA
Found at i:25311014 original size:59 final size:60
Alignment explanation
Indices: 25310933--25311096 Score: 228
Period size: 59 Copynumber: 2.7 Consensus size: 60
25310923 GGTTAGGTTT
*
25310933 TTAA-TTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAG-A-GTTAGGGTTTTTAA
1 TTAATTTAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGTAGGTTAGGGTTTTTAA
25310989 TTAATTTAAGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAA
1 TTAATTTAAGTTA-GGGTTAGGGTTTTTAATTAAATTAGGTTA--G-TA-GGTTAGGGTTTTTAA
* *
25311054 TTAATTTAGGTTAGGGTTAGGGTTCTTAATTAAATTAGGTTAG
1 TTAATTTAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
25311097 GGTTTTTAAT
Statistics
Matches: 96, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
56 4 0.04
57 7 0.07
59 28 0.29
61 1 0.01
62 1 0.01
63 1 0.01
64 28 0.29
65 26 0.27
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.45
Consensus pattern (60 bp):
TTAATTTAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGTAGGTTAGGGTTTTTAA
Found at i:25311042 original size:35 final size:34
Alignment explanation
Indices: 25310945--25311097 Score: 172
Period size: 29 Copynumber: 4.9 Consensus size: 34
25310935 AATTAAATTA
25310945 GGTTAGGGTTTTTAATTAAATTAGGTTA-G--A-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
* *
25310975 -GTTAGGGTTTTTAATTAATTTAAGTTA-G---G
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
25311004 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAG
25311039 GGTTAGGGTTTTTAATT-AA-T---TTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
*
25311068 GGTTAGGGTTCTTAATTAAATTAGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGG
25311098 GTTTTTAATT
Statistics
Matches: 106, Mismatches: 5, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
29 48 0.45
30 30 0.28
31 1 0.01
32 1 0.01
33 1 0.01
34 7 0.07
35 18 0.17
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (34 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
Found at i:25311063 original size:94 final size:87
Alignment explanation
Indices: 25310945--25311123 Score: 259
Period size: 94 Copynumber: 2.0 Consensus size: 87
25310935 AATTAAATTA
*
25310945 GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAATTTAAGTTAGGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTCTTAATT-A---AA-TTA--GGTTAG
*
25311010 GGTTTTTAATTAAATTAGGTTAGGGTTAG
59 GGTTTTTAATTAAATTAAGTTAGGGTTAG
* *
25311039 GGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTCTTAATTAAATTAGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTCTTAATTAAATTAGGTTAGGGTTTTT
25311104 AATTAAATTAAGTTAGGGTT
66 AATTAAATTAAGTTAGGGTT
25311124 TTAAATTAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
87 32 0.40
89 3 0.04
90 2 0.02
93 1 0.01
94 43 0.53
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (87 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTCTTAATTAAATTAGGTTAGGGTTTTT
AATTAAATTAAGTTAGGGTTAG
Found at i:25311247 original size:45 final size:45
Alignment explanation
Indices: 25311178--25311266 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
25311168 TTTTATTACA
* * *
25311178 TCAAATAAACTTCTATTTTATTACATCAAATAATATGAAAATAAC
1 TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATAAC
*
25311223 TCAAA-AAAATTCTATTTTTTTTACATAAAATAATATCAAAATAA
1 TCAAATAAAATTCTA-TTTTATTACATAAAATAATATCAAAATAA
25311267 TTAAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 8 0.21
45 31 0.79
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (45 bp):
TCAAATAAAATTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:25311993 original size:355 final size:355
Alignment explanation
Indices: 25311322--25312019 Score: 1135
Period size: 355 Copynumber: 2.0 Consensus size: 355
25311312 ATGCCCGGGG
* * * *
25311322 GATTCAGTTCCACATGGCGGCCGTCGACGGTTACGCGCTGGATTCCTGCTTTCTCTAGCTTCCGG
1 GATTCAGTGCCACATGGCGGCCATCGACGGTTACGCGCTGGATTCCTACTTTATCTAGCTTCCGG
* *
25311387 CGGTGGTTGTTGTTCCTCCAGTGGGGATTCTGGTTCTTCCAGTTCGACATCTGGTTGTCAGACTT
66 CGGCGGTTGTTGTTCCTCCAGTGGGGATTCTGGTTCTTCCAGTTCGACATCTGGTTATCAGACTT
* *
25311452 GGGACGATGATCCACCTTCAAATAATAGTGTATGTGGAGTTGTTTGCATCAGGAACGACGACGGT
131 GGAACGATGATCCACCTTCAAAGAATAGTGTATGTGGAGTTGTTTGCATCAGGAACGACGACGGT
* * *
25311517 ATTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCTCAACGGCCCCCATTGCGA
196 ATTTGAAACCCATACGTTGGTGGGGACTGGTAAAAAGGAGAGCTCCCCAACGGCCCCCATTGCGA
* * * * *
25311582 TCCCTCGTGTGCCGTTGGCCTATACATCGGTGGTCCGCTCGGCGTAACAGGAAATGGAGCTAAAC
261 TCCCTCGTGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGCATAACAAGAAATGGAGCTAAAC
*
25311647 CGGGCATTTGGCTCCAACCTGCTTTCTCTA
326 CGGGCATTCGGCTCCAACCTGCTTTCTCTA
* *
25311677 GATTCAGTGCCACATGGCGGCCATTGACGGTTACGCGCTGGATTCCTACTTTATTTAGCTTCCGG
1 GATTCAGTGCCACATGGCGGCCATCGACGGTTACGCGCTGGATTCCTACTTTATCTAGCTTCCGG
* * ** * *
25311742 TGGCGGTTGTTGTTCCTCCGGTGGGGATTCTGGTTCTTCTGGTTCGGCATCTGGTTATCGGACTT
66 CGGCGGTTGTTGTTCCTCCAGTGGGGATTCTGGTTCTTCCAGTTCGACATCTGGTTATCAGACTT
25311807 GGAACGATGATCCACCTTCAAAGAATAGTGTATGTGGAGTTGTTTGCATCAGGAACGACGACGGT
131 GGAACGATGATCCACCTTCAAAGAATAGTGTATGTGGAGTTGTTTGCATCAGGAACGACGACGGT
* *
25311872 GTTTGAAACCCATACGTTGGTGGGGACTGGTAAAAAGGAGAGCTCCCCGACGGCCCCCATTGCGA
196 ATTTGAAACCCATACGTTGGTGGGGACTGGTAAAAAGGAGAGCTCCCCAACGGCCCCCATTGCGA
* *
25311937 TCCCTCGTGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGCATAATAAGAAATGGAGCTGAAC
261 TCCCTCGTGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGCATAACAAGAAATGGAGCTAAAC
25312002 CGGGCATTCGGCTCCAAC
326 CGGGCATTCGGCTCCAAC
25312020 TTGCCAGAGG
Statistics
Matches: 314, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
355 314 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (355 bp):
GATTCAGTGCCACATGGCGGCCATCGACGGTTACGCGCTGGATTCCTACTTTATCTAGCTTCCGG
CGGCGGTTGTTGTTCCTCCAGTGGGGATTCTGGTTCTTCCAGTTCGACATCTGGTTATCAGACTT
GGAACGATGATCCACCTTCAAAGAATAGTGTATGTGGAGTTGTTTGCATCAGGAACGACGACGGT
ATTTGAAACCCATACGTTGGTGGGGACTGGTAAAAAGGAGAGCTCCCCAACGGCCCCCATTGCGA
TCCCTCGTGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGCATAACAAGAAATGGAGCTAAAC
CGGGCATTCGGCTCCAACCTGCTTTCTCTA
Found at i:25312066 original size:18 final size:18
Alignment explanation
Indices: 25312043--25312077 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25312033 TGGAAAAGGA
*
25312043 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
25312061 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
25312078 AAACGCACCT
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:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:25312723 original size:7 final size:7
Alignment explanation
Indices: 25312713--25312758 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
25312703 TTATATACAT
25312713 AATACTA
1 AATACTA
25312720 AATACTA
1 AATACTA
25312727 AATACTA
1 AATACTA
25312734 AATACTA
1 AATACTA
25312741 AATACTA
1 AATACTA
25312748 AATACTA
1 AATACTA
25312755 AATA
1 AATA
25312759 TCAGTCGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:25313708 original size:22 final size:21
Alignment explanation
Indices: 25313683--25313734 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
25313673 AAATATGGAT
25313683 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAA-TTGAG-AGGAAA
*
25313705 TTGAGAGGAATTGAGAGGAAA
1 TTGAGAGAAATTGAGAGGAAA
25313726 TATGAGAGA
1 T-TGAGAGA
25313735 GGATTTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (21 bp):
TTGAGAGAAATTGAGAGGAAA
Found at i:25313733 original size:12 final size:11
Alignment explanation
Indices: 25313699--25313733 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
25313689 GAAATTTGGA
25313699 AGGAAATTGAG
1 AGGAAATTGAG
25313710 AGG-AATTGAG
1 AGGAAATTGAG
25313720 AGGAAATATGAG
1 AGGAAAT-TGAG
25313732 AG
1 AG
25313734 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:25315932 original size:16 final size:17
Alignment explanation
Indices: 25315900--25315934 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25315890 GTTCATGTAT
*
25315900 TTTTATTTTTTTATAAA
1 TTTTAGTTTTTTATAAA
25315917 TTTTAGTTTTTT-TAAA
1 TTTTAGTTTTTTATAAA
25315933 TT
1 TT
25315935 AAGACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAGTTTTTTATAAA
Found at i:25327440 original size:2 final size:2
Alignment explanation
Indices: 25327433--25327457 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25327423 CAACAGTAGA
25327433 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25327458 CATAGATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25331954 original size:20 final size:20
Alignment explanation
Indices: 25331929--25331978 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
25331919 TGGCTTAAAA
25331929 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
25331949 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
25331966 GTGGTAGTGGATT
1 TTGGTAGTGGATT
25331979 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:25336592 original size:20 final size:20
Alignment explanation
Indices: 25336567--25336616 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
25336557 TGGCTTAAAA
25336567 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
25336587 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
25336604 GTGGTAGTGGATT
1 TTGGTAGTGGATT
25336617 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:25350688 original size:22 final size:22
Alignment explanation
Indices: 25350660--25350703 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25350650 AACCACGAAT
25350660 TTTAGTATTTGGTCTCTTTAAG
1 TTTAGTATTTGGTCTCTTTAAG
25350682 TTTAGTATTTGGTCTCTTTAAG
1 TTTAGTATTTGGTCTCTTTAAG
25350704 AAGTTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (22 bp):
TTTAGTATTTGGTCTCTTTAAG
Found at i:25351727 original size:20 final size:18
Alignment explanation
Indices: 25351704--25351760 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
25351694 TTATATATAT
25351704 TTTAAAAAAAATTAAGATAA
1 TTTAAAAAAAATTAA-A-AA
* *
25351724 TTTAAAGAAAGTT-AAAA
1 TTTAAAAAAAATTAAAAA
*
25351741 TATAAAAAAAATTATAAAA
1 TTTAAAAAAAATTA-AAAA
25351760 T
1 T
25351761 AATAATTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 12 0.40
18 1 0.03
19 6 0.20
20 11 0.37
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TTTAAAAAAAATTAAAAA
Found at i:25356781 original size:29 final size:31
Alignment explanation
Indices: 25356725--25356783 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
25356715 AGGGGTGGGA
25356725 TGGGAAGAGAGTAAAAGTTTTAGAGGGAAAG
1 TGGGAAGAGAGTAAAAGTTTTAGAGGGAAAG
* * *
25356756 TGGGAA-ATAGTAAAA-TTTTGGGGGGAAA
1 TGGGAAGAGAGTAAAAGTTTTAGAGGGAAA
25356784 ATAAAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 8 0.32
31 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (31 bp):
TGGGAAGAGAGTAAAAGTTTTAGAGGGAAAG
Found at i:25360105 original size:27 final size:27
Alignment explanation
Indices: 25360040--25360107 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
25360030 AAATAGAGAG
* * *
25360040 ACTGTCACAGGCAGCACCAATGGTGTC
1 ACTGTCACAGGCGGCACCAAAGGTGCC
* * *
25360067 AGTGGCAGAGGCGGCACCAAAGGTGCC
1 ACTGTCACAGGCGGCACCAAAGGTGCC
*
25360094 ACTGTCATAGGCGG
1 ACTGTCACAGGCGG
25360108 TACCCTTCTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.34, T:0.15
Consensus pattern (27 bp):
ACTGTCACAGGCGGCACCAAAGGTGCC
Found at i:25360422 original size:156 final size:157
Alignment explanation
Indices: 25360182--25360557 Score: 526
Period size: 157 Copynumber: 2.4 Consensus size: 157
25360172 TATGTTTATG
* * * * *
25360182 AAAA-AATAAAAAACGAAAATAGTATATTTACTGAAATTAATAAAATCCGAAAAAAAAGAGAAAA
1 AAAATAATAAAATACGAAAATAGTATATTT-TTTAAAATAATAAAATCC-AAAAATAAGA-AAAA
25360246 ATAACAAATGGCCAAAATAAAGG-TTTTCCACTAAATTTATATAAAAA-ACACACTAAAATAATA
63 ATAACAAATGGCCAAAATAAAGGTTTTTCCACTAAATTTATATAAAAACACACACTAAAATAATA
*
25360309 CATTTCAAACATTATGTACT-AAATAATAT
128 CATTTCAAACATTATGTAATAAAATAATAT
25360338 AAAATAATAAAATACGAAAATAGTATATTTTTTAAAATAATAAAATCCAAAAATAAGAAAAATAT
1 AAAATAATAAAATACGAAAATAGTATATTTTTTAAAATAATAAAATCCAAAAATAAGAAAAA-AT
** * *
25360403 GAACAAATGGCCAAAATAAAGGTTTTTTTATTAAATTTATATAAAAACACACACTAAATTAATAC
65 -AACAAATGGCCAAAATAAAGGTTTTTCCACTAAATTTATATAAAAACACACACTAAAATAATAC
* *
25360468 ATTTTAAACTTTATGTAATAAAATAATAT
129 ATTTCAAACATTATGTAATAAAATAATAT
* ** *
25360497 AAAATAATAAAATATGAAAATAACATATTTTTTGAAAGTAATAAAATCCAAAAATAAGAAA
1 AAAATAATAAAATACGAAAATAGTATATTTTTT-AAAATAATAAAATCCAAAAATAAGAAA
25360558 TGTATTAATT
Statistics
Matches: 197, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
154 4 0.02
155 11 0.06
156 40 0.20
157 45 0.23
158 32 0.16
159 39 0.20
160 26 0.13
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (157 bp):
AAAATAATAAAATACGAAAATAGTATATTTTTTAAAATAATAAAATCCAAAAATAAGAAAAAATA
ACAAATGGCCAAAATAAAGGTTTTTCCACTAAATTTATATAAAAACACACACTAAAATAATACAT
TTCAAACATTATGTAATAAAATAATAT
Found at i:25360891 original size:16 final size:15
Alignment explanation
Indices: 25360845--25360894 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
25360835 TTTTTATTTC
25360845 TTTTCATATTTTATT
1 TTTTCATATTTTATT
***
25360860 TTTTCATAAACATATT
1 TTTTCAT-ATTTTATT
25360876 TTTTCGATATTTTATT
1 TTTTC-ATATTTTATT
25360892 TTT
1 TTT
25360895 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 7 0.26
16 18 0.67
17 2 0.07
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTCATATTTTATT
Found at i:25364221 original size:158 final size:158
Alignment explanation
Indices: 25363933--25364251 Score: 485
Period size: 158 Copynumber: 2.0 Consensus size: 158
25363923 ATAATTACTT
* * ** *
25363933 TTTATTAAGTAAAGCTAAAAATCAGTATAAGATAATTTTAATGTAATTCCATAAGAGCCTCGATA
1 TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
* * * * * *
25363998 TAACCCAATGCCTTTAAATATGGAGAGTGATTCTACTTGATCCTCAAGTAACCATTTTTCAAGTT
66 TAAACCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
*
25364063 TTCAACCTTAACTCAACTGGTATTCATG
131 TTCAACCTTAACTCAACTGATATTCATG
* *
25364091 TTTATAAAGTAAAACTAAAAATCAACATAGGATAATTTTGATGTAATTCCATAAGAGCCTCAATA
1 TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
*
25364156 TAAACCAATGCCTTTAAACATGGAAAATGACTCTACTTGATTATCAAGTAACCATTTTTCAAGTT
66 TAAACCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
* *
25364221 TTCAACCTTAACTCAATTGATCTTCATG
131 TTCAACCTTAACTCAACTGATATTCATG
25364249 TTT
1 TTT
25364252 TGAGTTCTAA
Statistics
Matches: 144, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
158 144 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (158 bp):
TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
TAAACCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
TTCAACCTTAACTCAACTGATATTCATG
Found at i:25366166 original size:7 final size:7
Alignment explanation
Indices: 25366154--25366180 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25366144 TGTTATGTTT
25366154 AAATTTG
1 AAATTTG
25366161 AAATTTG
1 AAATTTG
25366168 AAATTTG
1 AAATTTG
25366175 AAATTT
1 AAATTT
25366181 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
AAATTTG
Found at i:25367333 original size:58 final size:58
Alignment explanation
Indices: 25367260--25367378 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
25367250 CTTTCTTTTT
* *
25367260 AGTCGAAAGAGAGAAAGATTCGTCTTTACATAGTGACTAGTCATCTTGTTCCTAAGCC
1 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGTCATATTGTTCCTAAGCC
*
25367318 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGGCTAGTCATATTGTTCCTAAGCC
1 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGTCATATTGTTCCTAAGCC
25367376 AGT
1 AGT
25367379 AGCATATTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (58 bp):
AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGTCATATTGTTCCTAAGCC
Found at i:25368005 original size:20 final size:19
Alignment explanation
Indices: 25367966--25368005 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
25367956 AAATAGTGAG
* *
25367966 AATTTATTTTCTAAGTATA
1 AATTTATTTTCCAAGAATA
25367985 AATTCTATTTTCCAAGAATA
1 AATT-TATTTTCCAAGAATA
25368005 A
1 A
25368006 CGATTCTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTTATTTTCCAAGAATA
Found at i:25370042 original size:24 final size:24
Alignment explanation
Indices: 25370015--25370066 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25370005 TTAGTAAGTC
* *
25370015 AAATAAACTATGCTAATAAATATT
1 AAATAAACTATACTAATAAATACT
* *
25370039 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
25370063 AAAT
1 AAAT
25370067 CTTCTAAAAT
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:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:25382090 original size:12 final size:12
Alignment explanation
Indices: 25382075--25382127 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
25382065 TAAGTAATAA
25382075 AAAGAAATAAAG
1 AAAGAAATAAAG
*
25382087 AAAGAAATATAG
1 AAAGAAATAAAG
*
25382099 AAATG-AA-ACAG
1 AAA-GAAATAAAG
25382110 AAA-AAATAAAG
1 AAAGAAATAAAG
25382121 AAAGAAA
1 AAAGAAA
25382128 AAGAAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 2 0.06
11 12 0.35
12 19 0.56
13 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (12 bp):
AAAGAAATAAAG
Found at i:25382116 original size:22 final size:21
Alignment explanation
Indices: 25382083--25382149 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
25382073 AAAAAGAAAT
*
25382083 AAAGAAAGAAATATAGAAATGAA
1 AAAGAAA-AAATAAAGAAA-GAA
*
25382106 ACAGAAAAAATAAAGAAAGAA
1 AAAGAAAAAATAAAGAAAGAA
**
25382127 AAAGAAAAAGGGAAAGAAAGAA
1 AAAGAAAAA-ATAAAGAAAGAA
25382149 A
1 A
25382150 GGAGAAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 11 0.29
22 21 0.55
23 6 0.16
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.06
Consensus pattern (21 bp):
AAAGAAAAAATAAAGAAAGAA
Found at i:25382549 original size:38 final size:39
Alignment explanation
Indices: 25382507--25382583 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
25382497 AAATGTGAAG
25382507 AATAAAAATTAGTCTCGA-TTTGGGACTAAATTGAAATT
1 AATAAAAATTAGTCTCGATTTTGGGACTAAATTGAAATT
25382545 AATAAAAATTAGTCTCGATTTTGGGACTAAATTGAAATT
1 AATAAAAATTAGTCTCGATTTTGGGACTAAATTGAAATT
25382584 TAGGCAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 18 0.47
39 20 0.53
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (39 bp):
AATAAAAATTAGTCTCGATTTTGGGACTAAATTGAAATT
Found at i:25383508 original size:29 final size:29
Alignment explanation
Indices: 25383475--25383536 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
25383465 TGAGTATGGC
*
25383475 ATGAAATGATGTATTTATGAGTTGAATAT
1 ATGAAATGATGTATTCATGAGTTGAATAT
*
25383504 ATGAAATGATGTATTCATGAGTTGAGTAT
1 ATGAAATGATGTATTCATGAGTTGAATAT
25383533 -TGAA
1 ATGAA
25383537 TGGTTAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
ATGAAATGATGTATTCATGAGTTGAATAT
Found at i:25385962 original size:24 final size:24
Alignment explanation
Indices: 25385888--25386013 Score: 143
Period size: 22 Copynumber: 5.3 Consensus size: 24
25385878 ACTTTAGTGC
25385888 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATT-TTAGCACGTTAGT
* *
25385913 GCTCTCTAATTATTAGCATGTTAGT
1 GCTCTCTGATT-TTAGCACGTTAGT
*
25385938 GCTCTCTGATTTTAGCACGTCAGT
1 GCTCTCTGATTTTAGCACGTTAGT
* *
25385962 GCTCTCTG--TTTAGCACATTTGT
1 GCTCTCTGATTTTAGCACGTTAGT
* *
25385984 GCTCTCTG--TATAGCACTTTAGT
1 GCTCTCTGATTTTAGCACGTTAGT
25386006 GCTCTCTG
1 GCTCTCTG
25386014 TTCATTAGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
22 38 0.42
24 19 0.21
25 33 0.37
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.41
Consensus pattern (24 bp):
GCTCTCTGATTTTAGCACGTTAGT
Found at i:25390304 original size:18 final size:18
Alignment explanation
Indices: 25390281--25390317 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25390271 AATCTTTCTT
25390281 TCTTTCTTCC-TCTGTTTC
1 TCTTTC-TCCTTCTGTTTC
25390299 TCTTTCTCCTTCTGTTTC
1 TCTTTCTCCTTCTGTTTC
25390317 T
1 T
25390318 GTTACTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.62
Consensus pattern (18 bp):
TCTTTCTCCTTCTGTTTC
Found at i:25397497 original size:29 final size:29
Alignment explanation
Indices: 25397455--25397511 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
25397445 AGCCCCGTGA
* *
25397455 CAAGTGGTATCCGAGCTGTTGGTTCGAAC
1 CAAGTGATATCCGAGCTATTGGTTCGAAC
* *
25397484 CAAGTGATGTCCGAGTTATTGGTTCGAA
1 CAAGTGATATCCGAGCTATTGGTTCGAA
25397512 GGCACCGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (29 bp):
CAAGTGATATCCGAGCTATTGGTTCGAAC
Found at i:25398291 original size:25 final size:25
Alignment explanation
Indices: 25398254--25398370 Score: 91
Period size: 25 Copynumber: 4.7 Consensus size: 25
25398244 CCCATATGAG
* *
25398254 CATATAATGGGGAAACTCTTTCGAGC
1 CATATAA-CGGGAAGCTCTTTCGAGC
25398280 CATGA-AACGGGAAGCT-TATGT-GAGC
1 CAT-ATAACGGGAAGCTCT-T-TCGAGC
*
25398305 CATATAACGGGAAGCTCTTGCGAGC
1 CATATAACGGGAAGCTCTTTCGAGC
** * *
25398330 CA-ATTATTGGGAAGCTCATACGAGC
1 CATA-TAACGGGAAGCTCTTTCGAGC
25398355 CATA-AACGGGAAGCTC
1 CATATAACGGGAAGCTC
25398371 AAGAGAGCCA
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
24 13 0.18
25 52 0.70
26 8 0.11
27 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
CATATAACGGGAAGCTCTTTCGAGC
Found at i:25398329 original size:50 final size:50
Alignment explanation
Indices: 25398246--25398370 Score: 130
Period size: 50 Copynumber: 2.5 Consensus size: 50
25398236 CAGTTATGCC
* * *
25398246 CATATGAG-CATATAATGGGGAAACTCTTTCGAGCC-ATGAAACGGGAAGCT
1 CATATGAGCCATATAA-CGGGAAGCTCTTGCGAGCCAAT-AAACGGGAAGCT
* * * **
25398296 TATGTGAGCCATATAACGGGAAGCTCTTGCGAGCCAATTATTGGGAAGCT
1 CATATGAGCCATATAACGGGAAGCTCTTGCGAGCCAATAAACGGGAAGCT
*
25398346 CATACGAGCCATA-AACGGGAAGCTC
1 CATATGAGCCATATAACGGGAAGCTC
25398371 AAGAGAGCCA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
49 12 0.19
50 41 0.66
51 9 0.15
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (50 bp):
CATATGAGCCATATAACGGGAAGCTCTTGCGAGCCAATAAACGGGAAGCT
Found at i:25398393 original size:49 final size:50
Alignment explanation
Indices: 25398290--25398421 Score: 133
Period size: 49 Copynumber: 2.7 Consensus size: 50
25398280 CATGAAACGG
* * ** * * ***
25398290 GAAGCTTATGTGAGCCATATAACGGGAAGCTCTTGCGAGCCAATTATTGG
1 GAAGCTCATGAGAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCAA
25398340 GAAGCTCAT-ACGAGCCATA-AACGGGAAGCTCAAGAGAGCCAAATATCAA
1 GAAGCTCATGA-GAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCAA
* * *
25398389 GAAGCTCATGAGAGCCATGTAATGGGATGCTCA
1 GAAGCTCATGAGAGCCATATAACGGGAAGCTCA
25398422 TAAGAGTTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
49 39 0.58
50 28 0.42
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (50 bp):
GAAGCTCATGAGAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCAA
Found at i:25398393 original size:74 final size:75
Alignment explanation
Indices: 25398275--25398423 Score: 176
Period size: 74 Copynumber: 2.0 Consensus size: 75
25398265 GAAACTCTTT
* * * * ** * * *
25398275 CGAGCCATGAAACGGGAAGCTTATGTGAGCCATATAACGGGAAGCTCTTGCGAGCCAAT-TATTG
1 CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAAGAAGCTCATGAGAGCC-ATGTAATG
25398339 GGAAGCTCATA
65 GGAAGCTCATA
*
25398350 CGAGCCAT-AAACGGGAAGCTCAAGAGAGCCAAATATCAAGAAGCTCATGAGAGCCATGTAATGG
1 CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAAGAAGCTCATGAGAGCCATGTAATGG
*
25398414 GATGCTCATA
66 GAAGCTCATA
25398424 AGAGTTAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
73 2 0.03
74 52 0.84
75 8 0.13
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (75 bp):
CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAAGAAGCTCATGAGAGCCATGTAATGG
GAAGCTCATA
Found at i:25398420 original size:25 final size:25
Alignment explanation
Indices: 25398326--25398445 Score: 66
Period size: 25 Copynumber: 4.8 Consensus size: 25
25398316 AAGCTCTTGC
* * * *
25398326 GAGCCAATTATTGGGAAGCTCATAC
1 GAGCCAAATAATGGGATGCTCATAA
* * *
25398351 GAGCCATA-AACGGGAAGCTCA-AGA
1 GAGCCAAATAATGGGATGCTCATA-A
** * *
25398375 GAGCCAAAT-ATCAAGAAGCTCATGA
1 GAGCCAAATAAT-GGGATGCTCATAA
**
25398400 GAGCCATGTAATGGGATGCTCATAA
1 GAGCCAAATAATGGGATGCTCATAA
**
25398425 GAGTTAAATAATGGGATGCTC
1 GAGCCAAATAATGGGATGCTC
25398446 TTGCGAGCTG
Statistics
Matches: 70, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
23 1 0.01
24 19 0.27
25 48 0.69
26 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (25 bp):
GAGCCAAATAATGGGATGCTCATAA
Found at i:25401831 original size:16 final size:16
Alignment explanation
Indices: 25401798--25401831 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25401788 TTGTACTGTT
* *
25401798 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
25401814 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
25401830 AA
1 AA
25401832 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:25404663 original size:21 final size:21
Alignment explanation
Indices: 25404629--25404669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25404619 AGACGAGCAA
* * *
25404629 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTAGAGTG
25404650 TACTCCAAAACAGGTAGAGT
1 TACTCCAAAACAGGTAGAGT
25404670 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:25406608 original size:16 final size:16
Alignment explanation
Indices: 25406575--25406608 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25406565 GGAGATTGTT
* *
25406575 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
25406591 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
25406607 AA
1 AA
25406609 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:25409284 original size:48 final size:48
Alignment explanation
Indices: 25409200--25409293 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
25409190 TTTCTTGGCT
****
25409200 TAAAAACGCCTAAGTCAGCCTAACTTCCCTTGATAAAGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
*
25409248 TAAAAACGCCTAAGTCAG-CTCAACTTGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTCCAACAATAAAGGATTCAAC
25409294 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:25414673 original size:14 final size:14
Alignment explanation
Indices: 25414654--25414693 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
25414644 TTGATTGCTA
25414654 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
*
25414668 GTAAAATGATTTCT
1 GTAAAATGTTTTCT
*
25414682 GGAAAATGTTTT
1 GTAAAATGTTTT
25414694 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:25414702 original size:20 final size:20
Alignment explanation
Indices: 25414677--25414716 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25414667 TGTAAAATGA
*
25414677 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
25414697 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
25414717 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:25414705 original size:34 final size:35
Alignment explanation
Indices: 25414662--25414728 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
25414652 TAGTAAAATG
*
25414662 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
25414696 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
25414729 CTGGTGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:25414732 original size:14 final size:15
Alignment explanation
Indices: 25414656--25414732 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
25414646 GATTGCTAGT
*
25414656 AAAATG-TTTTCTGT
1 AAAATGATTTTCTGG
25414670 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
25414684 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
25414704 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
25414719 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
25414733 TGTTTAATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 26 0.51
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:25414846 original size:20 final size:19
Alignment explanation
Indices: 25414821--25414867 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
25414811 ACATATATTA
25414821 ATATATATTAATAAATTTTT
1 ATATATATTAAT-AATTTTT
* *
25414841 ATATAT-TAAATTATTTTT
1 ATATATATTAATAATTTTT
*
25414859 ACATATATT
1 ATATATATT
25414868 GCAATGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATATTAATAATTTTT
Found at i:25416814 original size:24 final size:24
Alignment explanation
Indices: 25416761--25416806 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
25416751 TCTTTTTAGA
*
25416761 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGTATAAT
25416785 ATATTTAGCATTTATTAGTATA
1 ATATTTAGCATTTATTAGTATA
25416807 GTTTATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGTATAAT
Found at i:25439925 original size:21 final size:21
Alignment explanation
Indices: 25439899--25439939 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25439889 ATCTGCTCAA
* *
25439899 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
25439920 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
25439940 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:25444100 original size:2 final size:2
Alignment explanation
Indices: 25444093--25444119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25444083 TACGATGGCA
25444093 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
25444120 ACTAATACAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25446648 original size:29 final size:29
Alignment explanation
Indices: 25446595--25446654 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
25446585 TGCTATAAGT
25446595 TTTTATACTCTTTATTTATCTGAATTTTAG
1 TTTTATACTCTTTATTTATCTGAA-TTTAG
*
25446625 TTTTATACT-TTTATTT-TTTAGAATTTAG
1 TTTTATACTCTTTATTTATCT-GAATTTAG
25446653 TT
1 TT
25446655 CCTCTACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 10 0.36
30 9 0.32
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (29 bp):
TTTTATACTCTTTATTTATCTGAATTTAG
Found at i:25450676 original size:2 final size:2
Alignment explanation
Indices: 25450669--25450697 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25450659 AGAAAGGAAA
25450669 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25450698 TAGACCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25455114 original size:23 final size:23
Alignment explanation
Indices: 25455066--25455114 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
25455056 AATATAATTA
*
25455066 TAATATCCCGAAAATTACTACTG
1 TAATATCCCGAAAATTACTACAG
25455089 TAATATCCCGAAAATTACTACAG
1 TAATATCCCGAAAATTACTACAG
25455112 TAA
1 TAA
25455115 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (23 bp):
TAATATCCCGAAAATTACTACAG
Found at i:25463212 original size:13 final size:12
Alignment explanation
Indices: 25463182--25463220 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
25463172 GAAATTATAG
25463182 CAAAACAATAACAA
1 CAAAACAA-AA-AA
25463196 CAAAACAACAAAA
1 CAAAACAA-AAAA
25463209 CAAAACAAAAAA
1 CAAAACAAAAAA
25463221 TTAAGCTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.17
13 10 0.42
14 10 0.42
ACGTcount: A:0.77, C:0.21, G:0.00, T:0.03
Consensus pattern (12 bp):
CAAAACAAAAAA
Found at i:25464367 original size:3 final size:3
Alignment explanation
Indices: 25464359--25464390 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
25464349 AGCCAACTAG
25464359 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
25464391 GATTCTCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:25478639 original size:24 final size:24
Alignment explanation
Indices: 25478612--25478661 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
25478602 TTTGATATTC
*
25478612 TTAT-TTTTATTTAGCAATATTAAT
1 TTATATTTAATTT-GCAATATTAAT
**
25478636 TTATATTTAATTTTTAATATTAAT
1 TTATATTTAATTTGCAATATTAAT
25478660 TT
1 TT
25478662 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATTTAATTTGCAATATTAAT
Found at i:25478686 original size:21 final size:21
Alignment explanation
Indices: 25478654--25478720 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
25478644 AATTTTTAAT
*
25478654 ATTAATTTTAATAAAAAATATA
1 ATTAAATTTAATAAAAAATA-A
*
25478676 ATTAGA-TTAATCAAATAAATAA
1 ATTAAATTTAAT-AAA-AAATAA
25478698 ATTAAATTTACATAAAAAA-AA
1 ATTAAATTTA-ATAAAAAATAA
25478719 AT
1 AT
25478721 CTAGTAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 9 0.24
22 16 0.42
23 11 0.29
24 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (21 bp):
ATTAAATTTAATAAAAAATAA
Found at i:25482477 original size:22 final size:23
Alignment explanation
Indices: 25482443--25482487 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
25482433 TTAAGAATTT
*
25482443 AATTTTATATTTATATTTTTAAA
1 AATTTAATATTTATATTTTTAAA
*
25482466 AATTTAAT-TTTATTTTTTTAAA
1 AATTTAATATTTATATTTTTAAA
25482488 TTAATTTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTTAATATTTATATTTTTAAA
Found at i:25482488 original size:20 final size:21
Alignment explanation
Indices: 25482440--25482494 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
25482430 AAATTAAGAA
*
25482440 TTTAATTTTATATTTATATTTT
1 TTTAAATTTA-ATTTATATTTT
**
25482462 TAAAAATTTAATTT-TATTTT
1 TTTAAATTTAATTTATATTTT
25482482 TTTAAA-TTAATTT
1 TTTAAATTTAATTT
25482495 CTGTACTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 4 0.14
22 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAAATTTAATTTATATTTT
Found at i:25489762 original size:18 final size:18
Alignment explanation
Indices: 25489694--25489767 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
25489684 TATTTTTTAA
*
25489694 TTATAACATATATTTAATT
1 TTATAATATATATTT-ATT
* *
25489713 TTAT-ATATATCTTTGTT
1 TTATAATATATATTTATT
* *
25489730 TTA-AATTTTTATTTATT
1 TTATAATATATATTTATT
*
25489747 TTATAATATATATTTAGT
1 TTATAATATATATTTATT
25489765 TTA
1 TTA
25489768 ATTTTGCCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
17 17 0.40
18 22 0.51
19 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATAATATATATTTATT
Found at i:25489768 original size:35 final size:34
Alignment explanation
Indices: 25489704--25489772 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
25489694 TTATAACATA
*
25489704 TATTTAATTTTATATATATCTTTGTTTTAAATTTT
1 TATTTAATTTTATATATATATTTGTTTT-AATTTT
25489739 TATTT-ATTTTATAATATATATTTAG-TTTAATTTT
1 TATTTAATTTTAT-ATATATATTT-GTTTTAATTTT
25489773 GCCAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 13 0.42
35 17 0.55
36 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (34 bp):
TATTTAATTTTATATATATATTTGTTTTAATTTT
Found at i:25492309 original size:26 final size:26
Alignment explanation
Indices: 25492280--25492342 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
25492270 AAACAATCTA
25492280 AATATATTCCATAAC-C-AATTTTAAAT
1 AATATATT-CA-AACGCTAATTTTAAAT
*
25492306 AATATA-TCAAACGCTTATTTTAAAT
1 AATATATTCAAACGCTAATTTTAAAT
25492331 AATATA-TCAAAC
1 AATATATTCAAAC
25492343 ACTCATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 22 0.65
26 6 0.18
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.37
Consensus pattern (26 bp):
AATATATTCAAACGCTAATTTTAAAT
Found at i:25492350 original size:25 final size:25
Alignment explanation
Indices: 25492297--25492350 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
25492287 TCCATAACCA
* *
25492297 ATTTTAAATAATATATCAAACGCTT
1 ATTTTAAATAATATATCAAACACTC
25492322 ATTTTAAATAATATATCAAACACTC
1 ATTTTAAATAATATATCAAACACTC
25492347 ATTT
1 ATTT
25492351 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTTTAAATAATATATCAAACACTC
Found at i:25492879 original size:21 final size:21
Alignment explanation
Indices: 25492838--25492892 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
25492828 AAATGGAAAT
*
25492838 AAATATATAAAAAATTCAGAA
1 AAATATATATAAAATTCAGAA
*
25492859 AAATATATATATAA-TCTAGAA
1 AAATATATATAAAATTC-AGAA
25492880 AAA-ATCATATAAA
1 AAATAT-ATATAAA
25492893 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATATATATAAAATTCAGAA
Found at i:25493042 original size:14 final size:15
Alignment explanation
Indices: 25493012--25493042 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25493002 TTTTGTATAA
25493012 AATTCTAAAATTTAT
1 AATTCTAAAATTTAT
25493027 AATTCTAAAA-TTAT
1 AATTCTAAAATTTAT
25493041 AA
1 AA
25493043 AAAGGTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTCTAAAATTTAT
Found at i:25495856 original size:23 final size:23
Alignment explanation
Indices: 25495830--25495880 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
25495820 ATTGATTATT
25495830 TCAAATTGATTAAATGAAATTAA
1 TCAAATTGATTAAATGAAATTAA
25495853 TCAAATTGATTAAATGAAATTAA
1 TCAAATTGATTAAATGAAATTAA
25495876 TCAAA
1 TCAAA
25495881 ATACTCGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (23 bp):
TCAAATTGATTAAATGAAATTAA
Found at i:25506508 original size:15 final size:15
Alignment explanation
Indices: 25506462--25506509 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
25506452 ATGTAAAATG
* *
25506462 AAATTAAAAGATATA
1 AAATTAAAATATAAA
*
25506477 AAATTCAAATAATAAA
1 AAATTAAAAT-ATAAA
*
25506493 AAATTAAAATAGAAA
1 AAATTAAAATATAAA
25506508 AA
1 AA
25506510 TAAGATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (15 bp):
AAATTAAAATATAAA
Found at i:25506509 original size:16 final size:16
Alignment explanation
Indices: 25506462--25506503 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
25506452 ATGTAAAATG
* *
25506462 AAATTAAAA-GATATA
1 AAATTAAAATAATAAA
*
25506477 AAATTCAAATAATAAA
1 AAATTAAAATAATAAA
25506493 AAATTAAAATA
1 AAATTAAAATA
25506504 GAAAAATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATTAAAATAATAAA
Found at i:25508602 original size:97 final size:97
Alignment explanation
Indices: 25508488--25508682 Score: 363
Period size: 97 Copynumber: 2.0 Consensus size: 97
25508478 TGCCATTAGC
25508488 AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTAAAACAATTTAAATC
1 AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTAAAACAATTTAAATC
**
25508553 ATTTTTATATTTTAAAAATGTTTTTTGTACTT
66 ATTTTTATATTTTAAAAATAATTTTTGTACTT
*
25508585 AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTTAAACAATTTAAATC
1 AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTAAAACAATTTAAATC
25508650 ATTTTTATATTTTAAAAATAATTTTTGTACTT
66 ATTTTTATATTTTAAAAATAATTTTTGTACTT
25508682 A
1 A
25508683 TTTTTATATT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (97 bp):
AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTAAAACAATTTAAATC
ATTTTTATATTTTAAAAATAATTTTTGTACTT
Found at i:25508637 original size:28 final size:28
Alignment explanation
Indices: 25508606--25508669 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
25508596 GTTTTTAAAA
25508606 TTAAAATATTT-AAT-ATATTTTATACTTT
1 TTAAAATATTTAAATCAT-TTTTATA-TTT
25508634 TTAAACA-ATTTAAATCATTTTTATATTT
1 TTAAA-ATATTTAAATCATTTTTATATTT
*
25508662 TAAAAATA
1 TTAAAATA
25508670 ATTTTTGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 1 0.03
28 17 0.55
29 11 0.35
30 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAAATATTTAAATCATTTTTATATTT
Done.