Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 8 of 373
Found at i:2313678 original size:71 final size:72
Alignment explanation
Indices: 2313502--2313742 Score: 395
Period size: 71 Copynumber: 3.4 Consensus size: 72
2313492 ATTAAAAGGT
2313502 TCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA-AGAAATTGAAAATACCTC-GCGTG-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AAATACCTCAGCGTGT
*
2313563 CCCGAGGC
65 CCTGAGGC
2313571 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCGTGTC
2313636 CTGAGGC
66 CTGAGGC
2313643 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACA-AAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA-TACCTCAGCGTGT
2313706 CCTGAGGC
65 CCTGAGGC
*
2313714 TCAACTCACTTTCTCGCAATATGAGTTGA
1 TCAACTCAC-CTCTCGCAATATGAGTTGA
2313743 GTTATTTAAA
Statistics
Matches: 164, Mismatches: 2, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
69 34 0.21
70 22 0.13
71 55 0.34
72 53 0.32
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCGTGTC
CTGAGGC
Found at i:2313694 original size:199 final size:202
Alignment explanation
Indices: 2312761--2313694 Score: 1161
Period size: 199 Copynumber: 4.6 Consensus size: 202
2312751 CATGTGAACT
* * * *
2312761 GAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTAAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATTACCTCA
* * *
2312826 GCGTGTTCTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTG---AA-AAAGTAGAAATT
64 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAATT
** *
2312887 AAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTTGAAAGTAGAATTTGAAAATACCTC
129 AAAAGGTTCAACCCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAAATACCTC
*
2312952 GGCGTG-CCC
193 AGCGTGACCC
*
2312961 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTTAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAAATTACCTCAG
* *
2313026 CGTGTTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTGAAATAC
65 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAAT--
** * ** *
2313091 CTCAGCGTGTCCTGAGGCTCAACTCCATTTCTCGCAATATGAGTTGA-ATTTGAAAACA-AAATT
128 -T-A--------AAAGGTTCAAC-CCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT
* * *
2313154 GAAATTACCTCAGCGTGTCCT
182 GAAAATACCTCAGCGTGACCC
**
2313175 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAATTACCTCAG
2313240 CGTGTCCTGAGGCTCAACTCACCTCT-GCAATATGAGTTGATTTTGAAAAAC-----A-AAATTA
65 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAATTA
2313298 AAA-GTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTAAATTGAAAATACC
130 AAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAG----AAATTGAAAATACC
2313362 TCAGGCATGTGACCC
191 TCA-GC--GTGACCC
* *
2313377 GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-AAAACA-AAATTGAAAATACCTCAGC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGC
*
2313440 GTG-CC-GAGGCTCAACTCACCTCT-GCAATATGAGTTGATTTTG----A-AAAGTAGAAATTAA
66 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAATTAA
*
2313497 AAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-AGAAATTGAAAATACCTC-GC
131 AAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGC
2313560 GTG-CCC
196 GTGACCC
2313566 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA-TACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAAATTACCTCAG
*
2313630 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTGAAATTA
65 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAATTA
2313695 CCTCAGCGTG
Statistics
Matches: 645, Mismatches: 42, Indels: 95
0.82 0.05 0.12
Matches are distributed among these distances:
189 40 0.06
190 3 0.00
191 18 0.03
192 13 0.02
193 40 0.06
194 51 0.08
195 1 0.00
197 38 0.06
198 20 0.03
199 154 0.24
200 39 0.06
201 4 0.01
202 38 0.06
203 10 0.02
204 1 0.00
206 1 0.00
207 5 0.01
213 44 0.07
214 90 0.14
215 14 0.02
216 21 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (202 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGC
GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATAGAAATTAA
AAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGC
GTGACCC
Found at i:2314278 original size:1 final size:1
Alignment explanation
Indices: 2314272--2314305 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
2314262 TCAAATGAGT
* *
2314272 AAAAAAAAAAAGAAACAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2314306 TCGGCGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:2322757 original size:12 final size:12
Alignment explanation
Indices: 2322737--2322772 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2322727 TGGGATATGC
*
2322737 AATGTATGAATG
1 AATGCATGAATG
2322749 AATGCATGAATG
1 AATGCATGAATG
2322761 AATGCATGAATG
1 AATGCATGAATG
2322773 TCAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:2324311 original size:7 final size:7
Alignment explanation
Indices: 2324299--2324328 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2324289 ATAATAAAAT
2324299 ATATAAA
1 ATATAAA
2324306 ATATAAA
1 ATATAAA
2324313 ATATTAAA
1 ATA-TAAA
2324321 ATATAAA
1 ATATAAA
2324328 A
1 A
2324329 ATATTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATATAAA
Found at i:2324313 original size:16 final size:16
Alignment explanation
Indices: 2324292--2324332 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
2324282 GATGTGAATA
2324292 ATAAAATATATAAAAT
1 ATAAAATATATAAAAT
2324308 ATAAAATAT-TAAAAT
1 ATAAAATATATAAAAT
2324323 ATAAAA-ATAT
1 ATAAAATATAT
2324333 TAGAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAATATATAAAAT
Found at i:2324315 original size:24 final size:24
Alignment explanation
Indices: 2324288--2324343 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2324278 TAATGATGTG
2324288 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATATA-AAAATATTAA
* *
2324312 AATATTAAAATATAAAAATATTAG
1 AATAATAAAATATAAAAATATTAA
2324336 AATAATAA
1 AATAATAA
2324344 TAATTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATAAAAATATTAA
Found at i:2324322 original size:8 final size:8
Alignment explanation
Indices: 2324288--2324339 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2324278 TAATGATGTG
*
2324288 AATAATAA
1 AATATTAA
2324296 AATATATAA
1 AATAT-TAA
2324305 AATA-TAA
1 AATATTAA
2324312 AATATTAA
1 AATATTAA
*
2324320 AATATAAA
1 AATATTAA
*
2324328 AATATTAG
1 AATATTAA
2324336 AATA
1 AATA
2324340 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:2324333 original size:16 final size:15
Alignment explanation
Indices: 2324292--2324339 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2324282 GATGTGAATA
2324292 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
2324308 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
2324323 ATAAAAATATTAGAAT
1 AT-AAAATATTAAAAT
2324339 A
1 A
2324340 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2324369 original size:17 final size:16
Alignment explanation
Indices: 2324288--2324369 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 16
2324278 TAATGATGTG
2324288 AATAATAAAATATAT-AA
1 AATAA-AAAATAT-TGAA
*
2324305 AATATAAAATATT-AA
1 AATAAAAAATATTGAA
2324320 AATATAAAAATATTAGAA
1 AATA-AAAAATATT-GAA
2324338 TAATAATAATTAATATTGACA
1 -AATAA-AA--AATATTGA-A
2324359 AATAAAAAATA
1 AATAAAAAATA
2324370 AAATAGAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
15 7 0.13
16 15 0.27
17 8 0.15
18 3 0.05
19 8 0.15
20 7 0.13
21 7 0.13
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (16 bp):
AATAAAAAATATTGAA
Found at i:2324533 original size:22 final size:22
Alignment explanation
Indices: 2324500--2324555 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
2324490 AATATTAAAA
*
2324500 ATATGTACATAATATAGTGTTAA-
1 ATATATACATAATATA--GTTAAG
2324523 A-ATATACATAATATAGTTAAG
1 ATATATACATAATATAGTTAAG
2324544 ATATATACATAA
1 ATATATACATAA
2324556 GATAACATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
22 23 0.77
23 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
ATATATACATAATATAGTTAAG
Found at i:2324607 original size:25 final size:25
Alignment explanation
Indices: 2324488--2324704 Score: 113
Period size: 25 Copynumber: 9.0 Consensus size: 25
2324478 TAAATACGTG
* *
2324488 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
2324513 ATAGTGTT-AA-A-ATATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
2324535 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * * *
2324557 ATAACATGTAAAAAAAATATAAATAAT
1 ATAATAT-T-AAAGATATATACATAAT
*
2324584 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* *
2324609 ATAGTA-TAATATATATATACACGTAAT
1 ATAATATTAA-AGATATATACA--TAAT
* *
2324636 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
2324659 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
2324681 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
2324704 A
1 A
2324705 ACAAAAAAGG
Statistics
Matches: 149, Mismatches: 26, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.03
21 5 0.03
22 36 0.24
23 20 0.13
24 12 0.08
25 41 0.28
26 2 0.01
27 26 0.17
28 2 0.01
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:2325286 original size:30 final size:30
Alignment explanation
Indices: 2325193--2325337 Score: 177
Period size: 30 Copynumber: 4.8 Consensus size: 30
2325183 TAGGTACAAG
* *
2325193 TGGTGCTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGT
* ** *
2325223 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGT
2325253 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
* *
2325283 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
*
2325313 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGT
2325338 TGAGAAAAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 2 0.02
30 100 0.98
ACGTcount: A:0.21, C:0.05, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
Found at i:2325911 original size:27 final size:27
Alignment explanation
Indices: 2325872--2325925 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2325862 GGACTAGCTC
*
2325872 AATTCAATTTAAACAATA-AAAAGTCAA
1 AATTCAATTTAAAAAATATAAAA-TCAA
2325899 AATT-AATTATAAAAAATATAAAATCAA
1 AATTCAATT-TAAAAAATATAAAATCAA
2325926 TAAAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (27 bp):
AATTCAATTTAAAAAATATAAAATCAA
Found at i:2327291 original size:30 final size:29
Alignment explanation
Indices: 2327199--2327294 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
2327189 TTCCCTTGAA
* ** *
2327199 AATTGTTAAAAATTTTAATTTGGCC-TCC
1 AATTTTTAAAAATTTTAATTAAGCCTTCT
* * *
2327227 AATTTTTTTAAAAATTTTCATTATGCCTTTT
1 AA--TTTTTAAAAATTTTAATTAAGCCTTCT
* *
2327258 AATTTTTGAAAATTTTAATTAAAGTCTTCT
1 AATTTTTAAAAATTTTAATT-AAGCCTTCT
2327288 AATTTTT
1 AATTTTT
2327295 TTTTCGAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
28 2 0.04
29 16 0.30
30 32 0.60
31 3 0.06
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (29 bp):
AATTTTTAAAAATTTTAATTAAGCCTTCT
Found at i:2328275 original size:31 final size:29
Alignment explanation
Indices: 2328240--2328305 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
2328230 TTAACTGTTT
2328240 AGTGACTAAAATATTACA-ATTCGATAACATA
1 AGTGACTAAAATA-TA-ATATTCGA-AACATA
*
2328271 AGTGACTAAAATATAATATTTGAAACATA
1 AGTGACTAAAATATAATATTCGAAACATA
2328300 AGTGAC
1 AGTGAC
2328306 AAGATGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 13 0.39
30 7 0.21
31 13 0.39
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (29 bp):
AGTGACTAAAATATAATATTCGAAACATA
Found at i:2330030 original size:20 final size:20
Alignment explanation
Indices: 2330005--2330048 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2329995 TTTTAATTTT
*
2330005 TATAAAAATATTAGTTTC-AA
1 TATAAAAATAATA-TTTCAAA
*
2330025 TATAAATATAATATTTCAAA
1 TATAAAAATAATATTTCAAA
2330045 TATA
1 TATA
2330049 TATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAAAAATAATATTTCAAA
Found at i:2333146 original size:19 final size:19
Alignment explanation
Indices: 2333122--2333211 Score: 159
Period size: 19 Copynumber: 4.9 Consensus size: 19
2333112 ATAATCTTCA
2333122 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2333141 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2333160 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2333177 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2333195 ATGATATGCAATCTTAG
1 ATGATATGCAATCTTAG
2333212 GAGATATAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2333193 original size:35 final size:37
Alignment explanation
Indices: 2333122--2333211 Score: 148
Period size: 35 Copynumber: 2.4 Consensus size: 37
2333112 ATAATCTTCA
2333122 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
2333160 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
2333195 ATGATATGCAATCTTAG
1 ATGATA-GCAATCTTAG
2333212 GAGATATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 19 0.38
36 16 0.32
37 9 0.18
38 6 0.12
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:2337645 original size:39 final size:39
Alignment explanation
Indices: 2337602--2337741 Score: 226
Period size: 39 Copynumber: 3.6 Consensus size: 39
2337592 GCTCTGATGA
*
2337602 GCTTCAGTTAGCCTTCGGGATTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
2337641 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
2337680 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
2337719 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
2337742 AGATCACGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:2342021 original size:17 final size:17
Alignment explanation
Indices: 2341995--2342028 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2341985 GATATAATTG
*
2341995 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
2342012 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
2342029 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:2343424 original size:24 final size:24
Alignment explanation
Indices: 2343317--2343425 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
2343307 ATGACATTGA
* * *
2343317 CACTATGTGTGTGGATTTGAATGG
1 CACTATGTGTGCGGATTAGCATGG
* * ***
2343341 CACTATGTATGTGGATTTTAATGG
1 CACTATGTGTGCGGATTAGCATGG
* *
2343365 CACTACGTGTGCGGATTAGCAAGG
1 CACTATGTGTGCGGATTAGCATGG
2343389 CACTATGTGTGCAGGA-TAGCATGG
1 CACTATGTGTGC-GGATTAGCATGG
2343413 CACTATGTGTGCG
1 CACTATGTGTGCG
2343426 AATTTCCTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
23 1 0.01
24 69 0.95
25 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (24 bp):
CACTATGTGTGCGGATTAGCATGG
Found at i:2348459 original size:8 final size:8
Alignment explanation
Indices: 2348446--2348471 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2348436 AATCCACTTG
2348446 TTTAGTTC
1 TTTAGTTC
2348454 TTTAGTTC
1 TTTAGTTC
2348462 TTTAGTTC
1 TTTAGTTC
2348470 TT
1 TT
2348472 AAGGAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (8 bp):
TTTAGTTC
Found at i:2349490 original size:78 final size:78
Alignment explanation
Indices: 2349382--2349832 Score: 699
Period size: 78 Copynumber: 5.8 Consensus size: 78
2349372 CGAAGAAACA
** * *
2349382 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
2349447 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
2349460 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAAAGCAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
2349524 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
** * * * * *
2349538 GATTTGGCATCTCCATATTCGACGGAGAGAAGATCAAAGACATAGCAGATTTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
2349603 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
2349616 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
2349681 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
2349694 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
2349758 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
*
2349772 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCCGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
2349833 GTGTTTACAT
Statistics
Matches: 337, Mismatches: 32, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
77 2 0.01
78 334 0.99
79 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:2349925 original size:45 final size:46
Alignment explanation
Indices: 2349772--2350045 Score: 271
Period size: 45 Copynumber: 6.1 Consensus size: 46
2349762 GATCCAAGAT
*
2349772 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-GAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAG--ATAACA
** * * * * * * *
2349819 GATCCGACCT-TCATGTGTTTACATC--GAAGCAGATC-TAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCAGAAGATAACA
*
2349864 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG-AGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAGATAACA
* * *
2349909 GATTTGGCATCTCTGTATTAGACGGAGAGCAGAT-TGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAGATAACA
*
2349953 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATC-GAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAGATAACA
* * *
2349998 GATTTGGCGTCTCTGTATTAGACGAGGAGCAGATCA-AAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAGATAACA
2350043 GAT
1 GAT
2350046 ATCGCCTTCC
Statistics
Matches: 187, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 45 0.24
45 111 0.59
46 4 0.02
47 21 0.11
48 4 0.02
49 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (46 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAGAAGATAACA
Found at i:2349982 original size:89 final size:90
Alignment explanation
Indices: 2349772--2350045 Score: 301
Period size: 89 Copynumber: 3.0 Consensus size: 90
2349762 GATCCAAGAT
* * ** * *
2349772 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCCGACCT-TCATGTG
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAG--ATAACAGATTTGGCATCTC-TGT-
* * *
2349836 TTTACATCGA--AGCAGATCTAAGAT-GACA
62 ATTAGA-CGAGGAGCAGATCAAAGATAG-CA
2349864 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATC-AGAGATAACAGATTTGGCATCTCTGTATT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGA-AGATAACAGATTTGGCATCTCTGTATT
**
2349928 AGACG-GAGAGCAGATTGAAGA-AGCA
65 AGACGAG-GAGCAGATCAAAGATAGCA
* * *
2349953 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
2350018 GACGAGGAGCAGATCAAAGATAGCA
66 GACGAGGAGCAGATCAAAGATAGCA
2350043 GAT
1 GAT
2350046 ATCGCCTTCC
Statistics
Matches: 158, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
88 2 0.01
89 82 0.52
90 35 0.22
91 3 0.02
92 36 0.23
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (90 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
GACGAGGAGCAGATCAAAGATAGCA
Found at i:2350427 original size:36 final size:36
Alignment explanation
Indices: 2350387--2350497 Score: 94
Period size: 36 Copynumber: 3.2 Consensus size: 36
2350377 ATGGAAATAT
*
2350387 AATCTTTAATGATATGTAATTTTAGATATGATATGC
1 AATCTTTAATGATATGTAATCTTAGATATGATATGC
2350423 AATC-TT-A-GATATGATACAATCTTAGATATGATA--C
1 AATCTTTAATGATATG-T--AATCTTAGATATGATATGC
* *
2350457 AATCTTAGATATGAT-TGCAATCTTAG--ATGATATGC
1 AATCTT-TA-ATGATATGTAATCTTAGATATGATATGC
2350492 AATCTT
1 AATCTT
2350498 AGAAGATATG
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
33 12 0.19
34 7 0.11
35 18 0.29
36 19 0.31
38 3 0.05
39 3 0.05
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (36 bp):
AATCTTTAATGATATGTAATCTTAGATATGATATGC
Found at i:2350507 original size:17 final size:19
Alignment explanation
Indices: 2350395--2350500 Score: 145
Period size: 17 Copynumber: 5.9 Consensus size: 19
2350385 ATAATCTTTA
* *
2350395 ATGATATGTAATTTTAGAT
1 ATGATATGCAATCTTAGAT
2350414 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2350433 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2350450 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2350467 ATGAT-TGCAATCTTAG--
1 ATGATATGCAATCTTAGAT
2350483 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
2350501 AGATATGATT
Statistics
Matches: 81, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
16 5 0.06
17 44 0.54
18 9 0.11
19 23 0.28
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2361611 original size:134 final size:134
Alignment explanation
Indices: 2361461--2361702 Score: 367
Period size: 134 Copynumber: 1.8 Consensus size: 134
2361451 GAATGAATTT
* * *
2361461 TTGAAGGGATACTCGATCATTTTAAGCAAACGTGAAATTGCAACGCAACACGTTAAGGCACTATT
1 TTGAAGGGACACTCGATCATTTTAAGCAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATT
*
2361526 CCGCGAATTGCAAAATATCGAATTTCGCCTTCATTTTAAAGAATTATTTTAAAAGGCATGAGGGA
66 CCGCGAATTGCAAAATATCGAATTTCACCTTCATTTTAAAGAATTATTTTAAAAGGCATGAGGGA
2361591 AATC
131 AATC
* * * * *
2361595 TTGAAGGGACATTCGATTATTTTGAGCAAACGCGAAATTGCCACCCAACACGTTAGGGCACTATT
1 TTGAAGGGACACTCGATCATTTTAAGCAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATT
* * * *
2361660 CCGCGGATTGCCAAATATCGGATTTCACCTTCGTTTTAAAGAA
66 CCGCGAATTGCAAAATATCGAATTTCACCTTCATTTTAAAGAA
2361703 AATTGTTTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
134 95 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (134 bp):
TTGAAGGGACACTCGATCATTTTAAGCAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATT
CCGCGAATTGCAAAATATCGAATTTCACCTTCATTTTAAAGAATTATTTTAAAAGGCATGAGGGA
AATC
Found at i:2362139 original size:2 final size:2
Alignment explanation
Indices: 2362132--2362169 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2362122 CTAAGGCTAG
*
2362132 AT AT AT AT AT AT A- AT AT AT AT A- AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2362170 TTGAAATGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2362150 original size:9 final size:9
Alignment explanation
Indices: 2362132--2362162 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2362122 CTAAGGCTAG
2362132 ATAT-ATAT
1 ATATAATAT
2362140 ATATAATAT
1 ATATAATAT
2362149 ATATAATAT
1 ATATAATAT
2362158 ATATA
1 ATATA
2362163 TGTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATAATAT
Found at i:2362150 original size:11 final size:10
Alignment explanation
Indices: 2362132--2362169 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
2362122 CTAAGGCTAG
2362132 ATATATATAT
1 ATATATATAT
2362142 ATA-ATATAT
1 ATATATATAT
2362151 ATA-ATATAT
1 ATATATATAT
*
2362160 ATATGTATAT
1 ATATATATAT
2362170 TTGAAATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATATAT
Found at i:2364591 original size:18 final size:19
Alignment explanation
Indices: 2364568--2364603 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2364558 TTTCCCTGAT
*
2364568 TTTTTTTATAT-ATTTTAA
1 TTTTTTTAAATAATTTTAA
2364586 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
2364604 GTACCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:2366880 original size:18 final size:18
Alignment explanation
Indices: 2366857--2366892 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2366847 TAATGTTTTT
2366857 TTAAAAAATCAT-AAAATA
1 TTAAAAAAT-ATGAAAATA
2366875 TTAAAAAATATGAAAATA
1 TTAAAAAATATGAAAATA
2366893 GAGATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAATATGAAAATA
Found at i:2368402 original size:6 final size:6
Alignment explanation
Indices: 2368391--2368423 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2368381 AAACTACCCA
2368391 AGCATG AGCATG AGCATG AGCATG AGCATG AGC
1 AGCATG AGCATG AGCATG AGCATG AGCATG AGC
2368424 CACCTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.15
Consensus pattern (6 bp):
AGCATG
Found at i:2373511 original size:20 final size:20
Alignment explanation
Indices: 2373457--2373502 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2373447 CTGAAATAAC
2373457 GATTTACCAATATTTCTAAG
1 GATTTACCAATATTTCTAAG
2373477 GATTTACCAATATTTCTAAG
1 GATTTACCAATATTTCTAAG
2373497 GATTTA
1 GATTTA
2373503 TTGAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
GATTTACCAATATTTCTAAG
Found at i:2375421 original size:23 final size:23
Alignment explanation
Indices: 2375395--2375464 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
2375385 AGGCTCGCCC
*
2375395 ATATTATTTTTTTTTTAATATTT
1 ATATTATTTTTATTTTAATATTT
*
2375418 ATATTA-TATTATTTTAATATTT
1 ATATTATTTTTATTTTAATATTT
* **
2375440 A-ATAATTTTATATTTTTTTATTT
1 ATATTATTTT-TATTTTAATATTT
2375463 AT
1 AT
2375465 TGAAAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.08
22 17 0.45
23 18 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATATTATTTTTATTTTAATATTT
Found at i:2375458 original size:26 final size:22
Alignment explanation
Indices: 2375395--2375459 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 22
2375385 AGGCTCGCCC
*
2375395 ATATTATTTTTTTTTTAATATTT
1 ATATTA-TATTTTTTTAATATTT
*
2375418 ATATTATATTATTTTAATATTT
1 ATATTATATTTTTTTAATATTT
2375440 AATAATTTTATATTTTTTTA
1 -AT-A--TTATATTTTTTTA
2375460 TTTATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 14 0.40
23 8 0.23
24 1 0.03
26 12 0.34
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
ATATTATATTTTTTTAATATTT
Found at i:2375472 original size:26 final size:26
Alignment explanation
Indices: 2375421--2375474 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2375411 AATATTTATA
*
2375421 TTATATTATTTTAATATTTAATAATT
1 TTATATTATTTTAATATTGAATAATT
* *
2375447 TTATATTTTTTTATTTATTGAA-AATT
1 TTATATTATTTTA-ATATTGAATAATT
2375473 TT
1 TT
2375475 TTATATAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATATTATTTTAATATTGAATAATT
Found at i:2376545 original size:18 final size:18
Alignment explanation
Indices: 2376522--2376560 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2376512 CAACCTCAAA
*
2376522 TTTTTTCCTACTTTGATT
1 TTTTTTCCAACTTTGATT
* *
2376540 TTTTTTTCAACTTTTATT
1 TTTTTTCCAACTTTGATT
2376558 TTT
1 TTT
2376561 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTCCAACTTTGATT
Found at i:2376567 original size:24 final size:24
Alignment explanation
Indices: 2376537--2376586 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
2376527 TCCTACTTTG
*
2376537 ATTTTTTTTTCAACTTTTATTTTTA
1 ATTTTTTTTCCAAC-TTTATTTTTA
*
2376562 ATTTTTTTTCCAACTTTCTTTTTA
1 ATTTTTTTTCCAACTTTATTTTTA
2376586 A
1 A
2376587 GGTGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTTTCCAACTTTATTTTTA
Found at i:2377165 original size:101 final size:101
Alignment explanation
Indices: 2376984--2377191 Score: 263
Period size: 101 Copynumber: 2.1 Consensus size: 101
2376974 TCCTTTGTGA
* * * * *
2376984 ATCTTGGGTAGTGTCCAATTGGTTGATTGTAATTGGTCATCAAAATAATCTGACAATAGCAATAC
1 ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTGGTCATCAAAATAATCTGACAATAGCAATAC
* * * * * *
2377049 TAAGTTGTCAGTATTGATGATTGATCTAGGTGATGC
66 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
* * * * * *
2377085 ATCTTTGGTAATGTCTAATTAGTTGATCGGAATTTGTCGTTAAAATAATTTGACAATAGCAATGC
1 ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTGGTCATCAAAATAATCTGACAATAGCAATAC
2377150 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
66 TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
2377186 ATCTTT
1 ATCTTT
2377192 AATATAATAT
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (101 bp):
ATCTTTGGTAATGTCCAATTAGTTGATCGGAATTGGTCATCAAAATAATCTGACAATAGCAATAC
TAAGATGCCACTATTGATGATTCACCTAAGTGATGC
Found at i:2377788 original size:14 final size:14
Alignment explanation
Indices: 2377769--2377797 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2377759 CTTCTTTAGA
2377769 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2377783 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2377797 C
1 C
2377798 GTAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAAATGTTAGCAC
Found at i:2377982 original size:14 final size:14
Alignment explanation
Indices: 2377963--2377991 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2377953 CTTCTTTAGA
2377963 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2377977 CAAAATGTTAGCAC
1 CAAAATGTTAGCAC
2377991 C
1 C
2377992 GTAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAAATGTTAGCAC
Found at i:2378004 original size:194 final size:193
Alignment explanation
Indices: 2377666--2378023 Score: 698
Period size: 194 Copynumber: 1.8 Consensus size: 193
2377656 TTCTATTAAA
2377666 GAAAATATAAAAGTTGCCACACGAATGAAGGAAGCATTTCATTAATGCTAACAGGTGCCATCCAC
1 GAAAATATAAAAGTTGCCACACGAATGAAGGAAGCATTTCATTAATGCTAACAGGTGCCATCCAC
2377731 TACAATAGTAATTACTATTGTGTTAGATCTTCTTTAGACAAAATGTTAGCACCAAAATGTTAGCA
66 TACAATAGTAATTACTATTGTGTTAGATCTTCTTTAGACAAAATGTTAGCACCAAAATGTTAGCA
2377796 CCGTAAAACAAAATTTGATATAAAACTTAACAAAAGCATAACATGAATAAAATAGGAAACAAT
131 CCGTAAAACAAAATTTGATATAAAACTTAACAAAAGCATAACATGAATAAAATAGGAAACAAT
*
2377859 GAAAATGTAGAAAGTTGCCACACGAATGAAGGAAGCATTTCATTAATGCTAACAGGTGCCATCCA
1 GAAAATATA-AAAGTTGCCACACGAATGAAGGAAGCATTTCATTAATGCTAACAGGTGCCATCCA
2377924 CTACAATAGTAATTACTATTGTGTTAGATCTTCTTTAGACAAAATGTTAGCACCAAAATGTTAGC
65 CTACAATAGTAATTACTATTGTGTTAGATCTTCTTTAGACAAAATGTTAGCACCAAAATGTTAGC
2377989 ACCGTAAAACAAAATTTGATATAAAACTTAACAAA
130 ACCGTAAAACAAAATTTGATATAAAACTTAACAAA
2378024 TTAAATCTGT
Statistics
Matches: 163, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
193 8 0.05
194 155 0.95
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (193 bp):
GAAAATATAAAAGTTGCCACACGAATGAAGGAAGCATTTCATTAATGCTAACAGGTGCCATCCAC
TACAATAGTAATTACTATTGTGTTAGATCTTCTTTAGACAAAATGTTAGCACCAAAATGTTAGCA
CCGTAAAACAAAATTTGATATAAAACTTAACAAAAGCATAACATGAATAAAATAGGAAACAAT
Found at i:2380347 original size:14 final size:15
Alignment explanation
Indices: 2380316--2380349 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2380306 AAATGCAAAA
2380316 AAAAACAAATTAAAT
1 AAAAACAAATTAAAT
*
2380331 AAAAACAAA-TAATT
1 AAAAACAAATTAAAT
2380345 AAAAA
1 AAAAA
2380350 GAATATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAACAAATTAAAT
Found at i:2382692 original size:16 final size:16
Alignment explanation
Indices: 2382671--2382702 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2382661 TGAAGAACAC
2382671 TTATAAGAATTATCAA
1 TTATAAGAATTATCAA
2382687 TTATAAGAATTATCAA
1 TTATAAGAATTATCAA
2382703 AAACATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TTATAAGAATTATCAA
Found at i:2386679 original size:88 final size:86
Alignment explanation
Indices: 2386572--2386735 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 86
2386562 TTGTGTGCGC
* *
2386572 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGGCCCTCAAACTTCTTTAAAAAAAGTAA
1 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTT-TTT-AAAAAAGCAA
*
2386637 TTAAGCCCCTGCTTTTTTTTCAA
64 TTAAGCCACTGCTTTTTTTTCAA
** * * * * * * *
2386660 TCAATTGGGTACTTGAACTTTCAAAATACATCAAAACGACCCTTAAAGTTTTTCAAAAAGCAATT
1 TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTTTTTAAAAAAGCAATT
2386725 AAGCCACTGCT
66 AAGCCACTGCT
2386736 CTTATTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
86 20 0.31
87 3 0.05
88 41 0.64
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (86 bp):
TCAATTGAATACTTAAACTTTCAAAATAAATAAAAAAGACCCTCAAACTTTTTAAAAAAGCAATT
AAGCCACTGCTTTTTTTTCAA
Found at i:2387136 original size:25 final size:25
Alignment explanation
Indices: 2387102--2387149 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2387092 TAAAATTTTA
*
2387102 TAATTTTTTTCTAATTTTAAATATT
1 TAATATTTTTCTAATTTTAAATATT
*
2387127 TAATATTTTTCTAATTTTTAATA
1 TAATATTTTTCTAATTTTAAATA
2387150 AAAGCATGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TAATATTTTTCTAATTTTAAATATT
Found at i:2392826 original size:3 final size:3
Alignment explanation
Indices: 2392820--2392850 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2392810 AAACATACAT
*
2392820 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2392851 GACGACGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2392931 original size:44 final size:45
Alignment explanation
Indices: 2392882--2392966 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 45
2392872 AACAATACTA
* * *
2392882 ATATATTAAGTTACAAAAGTAAAATAATAA-TAATGATAATGATG
1 ATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAATGATG
* * *
2392926 ATATATCAGGTAACTATAGTAAAATAATAAGTAATAATAAT
1 ATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAAT
2392967 AACGTGTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 25 0.74
45 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (45 bp):
ATATATCAAGTAACAAAAGTAAAATAATAAGTAATAATAATGATG
Found at i:2393529 original size:10 final size:10
Alignment explanation
Indices: 2393501--2393543 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
2393491 CGGACCGTCC
*
2393501 CCGTCTGCCA
1 CCGTCGGCCA
*
2393511 -CGCCGGCCA
1 CCGTCGGCCA
2393520 CCGTCGGCCA
1 CCGTCGGCCA
2393530 CCGTCGGCCA
1 CCGTCGGCCA
2393540 CCGT
1 CCGT
2393544 AGCCGGCCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.09, C:0.51, G:0.28, T:0.12
Consensus pattern (10 bp):
CCGTCGGCCA
Found at i:2399570 original size:15 final size:15
Alignment explanation
Indices: 2399550--2399578 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2399540 TGATAAATTG
2399550 AAAAATTAAGTGTTT
1 AAAAATTAAGTGTTT
2399565 AAAAATTAAGTGTT
1 AAAAATTAAGTGTT
2399579 ACAGGCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
AAAAATTAAGTGTTT
Found at i:2400878 original size:3 final size:3
Alignment explanation
Indices: 2400838--2400862 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2400828 CTTTAATTTA
2400838 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2400863 GTTTACGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2401121 original size:21 final size:19
Alignment explanation
Indices: 2401085--2401133 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
2401075 TCTTCTGTAC
2401085 TATTATATATATTTTCTAA
1 TATTATATATATTTTCTAA
2401104 TATTACTATATATATTTCTAA
1 TATTA-TATATAT-TTTCTAA
2401125 TA-TATATAT
1 TATTATATAT
2401134 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATATATATTTTCTAA
Found at i:2401226 original size:11 final size:11
Alignment explanation
Indices: 2401210--2401240 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2401200 TCTAAATGTA
2401210 TGTATATATTG
1 TGTATATATTG
*
2401221 TGTATATTTTG
1 TGTATATATTG
2401232 TGTATATAT
1 TGTATATAT
2401241 ATTATACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (11 bp):
TGTATATATTG
Found at i:2406530 original size:17 final size:17
Alignment explanation
Indices: 2406498--2406529 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2406488 CAAATATAAA
2406498 AACGATAAACCCAAAAG
1 AACGATAAACCCAAAAG
2406515 AACGA-AAACCCAAAA
1 AACGATAAACCCAAAA
2406530 AAAAATAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.25, G:0.09, T:0.03
Consensus pattern (17 bp):
AACGATAAACCCAAAAG
Found at i:2410523 original size:35 final size:35
Alignment explanation
Indices: 2410477--2410543 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2410467 ATTAGATGAA
* *
2410477 CCAAAAACTTGAATATACGAAGCAAAGAAAGCGAG
1 CCAAAAACTTGAAGATACGAAGCAAAAAAAGCGAG
*
2410512 CCAAACACTTGAAGATACGAAGCAAAAAAAGC
1 CCAAAAACTTGAAGATACGAAGCAAAAAAAGC
2410544 AAACTAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.52, C:0.19, G:0.18, T:0.10
Consensus pattern (35 bp):
CCAAAAACTTGAAGATACGAAGCAAAAAAAGCGAG
Found at i:2410827 original size:18 final size:18
Alignment explanation
Indices: 2410804--2410862 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
2410794 TATTTTACAT
2410804 TTTTGTAAGAATTGAGTA
1 TTTTGTAAGAATTGAGTA
* * *
2410822 TTTTGTTACAAAATTGCGTT
1 TTTTG-TA-AGAATTGAGTA
*
2410842 TTTTCTAAGAATTTGAGTA
1 TTTTGTAAGAA-TTGAGTA
2410861 TT
1 TT
2410863 GACAAAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 8 0.26
19 11 0.35
20 12 0.39
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (18 bp):
TTTTGTAAGAATTGAGTA
Found at i:2420647 original size:21 final size:21
Alignment explanation
Indices: 2420613--2420653 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2420603 AATTAACTAC
*
2420613 TTTTAGATTATTTATTTTAAT
1 TTTTAGATTATTTAATTTAAT
2420634 TTTTA-ATTATTTTAATTTAA
1 TTTTAGATTA-TTTAATTTAA
2420654 AATTGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTAGATTATTTAATTTAAT
Found at i:2420657 original size:16 final size:16
Alignment explanation
Indices: 2420624--2420657 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2420614 TTTAGATTAT
**
2420624 TTATTTTAATTTTTAA
1 TTATTTTAATTTAAAA
2420640 TTATTTTAATTTAAAA
1 TTATTTTAATTTAAAA
2420656 TT
1 TT
2420658 GTTAAAAATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTAATTTAAAA
Found at i:2422726 original size:11 final size:11
Alignment explanation
Indices: 2422710--2422735 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2422700 ACCTTAAAAC
2422710 TATTGATGTTA
1 TATTGATGTTA
2422721 TATTGATGTTA
1 TATTGATGTTA
2422732 TATT
1 TATT
2422736 AATCAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
TATTGATGTTA
Found at i:2424147 original size:36 final size:36
Alignment explanation
Indices: 2424100--2424199 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
2424090 ATCTATGCGC
2424100 CTAATTACTAAAATTATAACCACATATTTAGATGTA
1 CTAATTACTAAAATTATAACCACATATTTAGATGTA
* *
2424136 CTAATTACTAAAATTATAAGCACATATTTAGATGTT
1 CTAATTACTAAAATTATAACCACATATTTAGATGTA
*
2424172 CTAATTACTACAATTATAACCACATATT
1 CTAATTACTAAAATTATAACCACATATT
2424200 ATCCTTTGAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (36 bp):
CTAATTACTAAAATTATAACCACATATTTAGATGTA
Found at i:2425734 original size:25 final size:25
Alignment explanation
Indices: 2425706--2425753 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2425696 CAATATGCAA
* *
2425706 TTCAATTCCACAATCCAATTTCACT
1 TTCAATTCAAAAATCCAATTTCACT
* *
2425731 TTCATTTCAAAAATCCACTTTCA
1 TTCAATTCAAAAATCCAATTTCA
2425754 AAATCAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (25 bp):
TTCAATTCAAAAATCCAATTTCACT
Found at i:2426238 original size:22 final size:24
Alignment explanation
Indices: 2426196--2426239 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2426186 TAACTAAGGT
2426196 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
2426220 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
2426240 TCTAGCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:2426578 original size:11 final size:12
Alignment explanation
Indices: 2426564--2426595 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2426554 TTAGTTTCAC
2426564 CTTT-TTCTTTT
1 CTTTCTTCTTTT
2426575 CTTTCTTC-TTT
1 CTTTCTTCTTTT
2426586 CTTTCTTCTT
1 CTTTCTTCTT
2426596 ATTTCTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTCTTCTTTT
Found at i:2426964 original size:31 final size:32
Alignment explanation
Indices: 2426929--2427001 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
2426919 TATTTATCAT
* * *
2426929 ATAAAAATCTTATAA-TATAATAAT-TTAATTA
1 ATAAATATCTTATAACT-TAATAATAATAAATA
*
2426960 ATAAATATCTTTTAACTTAATAATAATAAATA
1 ATAAATATCTTATAACTTAATAATAATAAATA
2426992 ATAAATATCT
1 ATAAATATCT
2427002 ACTTACCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (32 bp):
ATAAATATCTTATAACTTAATAATAATAAATA
Found at i:2428641 original size:12 final size:12
Alignment explanation
Indices: 2428624--2428649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2428614 AAAATAGGGC
2428624 TTTAGCGGCGTT
1 TTTAGCGGCGTT
2428636 TTTAGCGGCGTT
1 TTTAGCGGCGTT
2428648 TT
1 TT
2428650 ATCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:2428784 original size:41 final size:41
Alignment explanation
Indices: 2428705--2428972 Score: 412
Period size: 41 Copynumber: 6.6 Consensus size: 41
2428695 CGATTTACCA
* * ** *
2428705 AAAACGCCGTTAAAA-ACTGAGCAATAGCGGCGTTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
2428745 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
* *
2428786 AAAACGCCGCTAAAAGAAAGAGCTTTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
* *
2428827 AAAACACCGGTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
* *
2428868 AAAACGCCGCTAAAAGAAAGAGCTTTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
* *
2428909 AAAACACCGGTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
2428950 AAAACGCCGCTAAAAGACAGAGC
1 AAAACGCCGCTAAAAGACAGAGC
2428973 AGTAGTTACA
Statistics
Matches: 206, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
40 14 0.07
41 192 0.93
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
Found at i:2429643 original size:46 final size:46
Alignment explanation
Indices: 2429576--2429670 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
2429566 ACTTAATAAT
*
2429576 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTTTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
*
2429622 ATTTGATTTATTCTAAATATTTATAATCTTTAATTATAATTGTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
2429668 ATT
1 ATT
2429671 CAATTCATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (46 bp):
ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
Found at i:2430420 original size:32 final size:32
Alignment explanation
Indices: 2430373--2430456 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 32
2430363 TAGAATTAAT
*
2430373 TTTTTGGTTGTATTTTAATGCTAAATTTGCTG
1 TTTTTGGTTGCATTTTAATGCTAAATTTGCTG
* * * *
2430405 TTTTTGGCTGCATTTT-ATACTATATTTGTTG
1 TTTTTGGTTGCATTTTAATGCTAAATTTGCTG
* * *
2430436 TATTTGGTTGGAATTTAATGC
1 TTTTTGGTTGCATTTTAATGC
2430457 AGGAAGGGCT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 24 0.59
32 17 0.41
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (32 bp):
TTTTTGGTTGCATTTTAATGCTAAATTTGCTG
Found at i:2437158 original size:20 final size:20
Alignment explanation
Indices: 2437121--2437158 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2437111 ATGATGGGAG
*
2437121 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
2437141 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
2437159 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:2438027 original size:17 final size:16
Alignment explanation
Indices: 2437995--2438028 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2437985 AATGATGGAG
*
2437995 AATGAAATATTGATAT
1 AATGAAATAATGATAT
2438011 AATGAAATGAATGATAT
1 AATGAAAT-AATGATAT
2438028 A
1 A
2438029 TGCTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (16 bp):
AATGAAATAATGATAT
Found at i:2441958 original size:57 final size:57
Alignment explanation
Indices: 2441889--2442002 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
2441879 TTCTCATTTA
2441889 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
1 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
2441946 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
1 TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
2442003 ACTCCAACCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.37
Consensus pattern (57 bp):
TCTCTTATCTTGTTGGTTACCCACAAGCCTCTAAACAGCCTTTCTATACACATCTTG
Found at i:2443507 original size:20 final size:21
Alignment explanation
Indices: 2443472--2443518 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2443462 TTTTAGGGTT
2443472 TTTTATAGAAAATTTT-AGAA
1 TTTTATAGAAAATTTTAAGAA
2443492 TTTTA-AGAAAAGTTTTAAGAA
1 TTTTATAGAAAA-TTTTAAGAA
2443513 TTTTAT
1 TTTTAT
2443519 GGTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
TTTTATAGAAAATTTTAAGAA
Found at i:2443820 original size:19 final size:19
Alignment explanation
Indices: 2443776--2443825 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2443766 TTATAATTTC
*
2443776 TATTTTTTAATATTTTTGGA
1 TATTTTTTAA-ATTTTTGAA
*
2443796 TGTTTTTTAAATTTTT-AA
1 TATTTTTTAAATTTTTGAA
2443814 TTATTTTTTAAA
1 -TATTTTTTAAA
2443826 AAATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
TATTTTTTAAATTTTTGAA
Found at i:2444264 original size:26 final size:28
Alignment explanation
Indices: 2444214--2444269 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
2444204 TGAAAGTAAG
2444214 AGACCAAACCGATAAAAAAAGATAT-AA
1 AGACCAAACCGATAAAAAAAGATATCAA
*
2444241 AGACCAAACTGATAAAAAAA-ATATCAA
1 AGACCAAACCGATAAAAAAAGATATCAA
2444268 AG
1 AG
2444270 TGATGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.62, C:0.14, G:0.11, T:0.12
Consensus pattern (28 bp):
AGACCAAACCGATAAAAAAAGATATCAA
Found at i:2446687 original size:7 final size:7
Alignment explanation
Indices: 2446670--2446699 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2446660 GAGGTAAGGG
2446670 TTTTA-T
1 TTTTATT
2446676 TTTTATT
1 TTTTATT
2446683 TTTTATT
1 TTTTATT
2446690 TTTTATT
1 TTTTATT
2446697 TTT
1 TTT
2446700 CGAATCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:2452266 original size:11 final size:11
Alignment explanation
Indices: 2452252--2452291 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2452242 GTTTTGACCC
2452252 TATTTTGCTAT
1 TATTTTGCTAT
*
2452263 TATTTTACTAT
1 TATTTTGCTAT
* *
2452274 TATGTTGCTAC
1 TATTTTGCTAT
2452285 TATTTTG
1 TATTTTG
2452292 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:2456954 original size:17 final size:17
Alignment explanation
Indices: 2456934--2456976 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
2456924 AAATAATCTT
2456934 AAAGTAGTCAAA-ACCA
1 AAAGTAGTCAAAGACCA
2456950 GAAAGTA-TCAAAGACCA
1 -AAAGTAGTCAAAGACCA
2456967 AAGAGTAGTC
1 AA-AGTAGTC
2456977 TAGTCCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.51, C:0.16, G:0.19, T:0.14
Consensus pattern (17 bp):
AAAGTAGTCAAAGACCA
Found at i:2459807 original size:63 final size:62
Alignment explanation
Indices: 2459698--2459822 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 62
2459688 TAAAGTTTTT
2459698 GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
1 GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
2459760 GATGTTGTTTGGTTAGATATGAAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
1 GATGTTGTTTGGTTAGATATG-AAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
2459823 TATAGGAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 21 0.34
63 41 0.66
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.38
Consensus pattern (62 bp):
GATGTTGTTTGGTTAGATATGAAAAAGGACTAGTTTGTAAAGTAAAAATTGTTAATTTTGAC
Found at i:2461718 original size:12 final size:12
Alignment explanation
Indices: 2461701--2461726 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2461691 ACTTTGGAAA
2461701 TTGTTTTTTTTT
1 TTGTTTTTTTTT
2461713 TTGTTTTTTTTT
1 TTGTTTTTTTTT
2461725 TT
1 TT
2461727 ATAAATTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:2462562 original size:45 final size:45
Alignment explanation
Indices: 2462458--2462570 Score: 113
Period size: 45 Copynumber: 2.5 Consensus size: 45
2462448 CTTAAACAGT
* * *
2462458 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTA
1 AATCAATAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTA
** * * * *
2462503 AATCTGTAATAGTAA-AGGTAACAGTATTCGACCCACAAAGTG-TCG
1 AATCAATAACAGTAACA-GTAACAGTATTCAACACACAAAGTGCT-A
2462548 AATCAATAACAGTAACAGTAACA
1 AATCAATAACAGTAACAGTAACA
2462571 ATAGTCAGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
44 2 0.04
45 52 0.95
46 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
AATCAATAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTA
Found at i:2462833 original size:40 final size:40
Alignment explanation
Indices: 2462782--2462859 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2462772 CTTCGATAAT
* *
2462782 TTCACAGTTCAATGCAGTACACATAACAATATTCAGTAAC
1 TTCACAATTCAATGCAGTACACAAAACAATATTCAGTAAC
* **
2462822 TTCACAATTCAATTCAGTACTTAAAACAATATTCAGTA
1 TTCACAATTCAATGCAGTACACAAAACAATATTCAGTA
2462860 TTCTATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCACAATTCAATGCAGTACACAAAACAATATTCAGTAAC
Found at i:2463617 original size:45 final size:45
Alignment explanation
Indices: 2463566--2463754 Score: 141
Period size: 46 Copynumber: 4.2 Consensus size: 45
2463556 TCCCATCCAC
* * *
2463566 GGTCTTATTTATCTTTGACATAATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTCATCTTTGACATAATGCCATAGTATCTTTCAACCAT
* * * ** *
2463611 GGTCTTACTCATTTTTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATCTTTGACATAATGCCATAGTATCTTTCAACCAT
* *** *
2463656 GGTCTTATTCAT-TTCATGTCACGCTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATCTT--TGACATAATGCCATAGTATCTTTCAACCAT
* * ** *
2463702 GGTCTTACTT-AT-TTCCCGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTA-TTCATCTT--TGACATAATGCCATAGTATCTTTCAACCAT
2463748 GGTCTTA
1 GGTCTTA
2463755 CACGTTTCAT
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 2 0.02
45 47 0.38
46 74 0.59
47 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (45 bp):
GGTCTTATTCATCTTTGACATAATGCCATAGTATCTTTCAACCAT
Found at i:2463693 original size:46 final size:46
Alignment explanation
Indices: 2463589--2463861 Score: 359
Period size: 46 Copynumber: 6.0 Consensus size: 46
2463579 TTTGACATAA
* * * * * *
2463589 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT-TTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
** * *
2463634 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
** ** *
2463680 TGCCATGGTATCTTTCAACCATGGTCTTACTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
* * *
2463726 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
2463772 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
2463818 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAG
2463862 AGAGCACACT
Statistics
Matches: 204, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
45 32 0.16
46 172 0.84
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:2463861 original size:92 final size:92
Alignment explanation
Indices: 2463589--2463861 Score: 404
Period size: 92 Copynumber: 3.0 Consensus size: 92
2463579 TTTGACATAA
* * * *
2463589 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT-TTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
** * *
2463653 CATGGTCTTATTCATTTCATGTCACGC
66 CATGGTCTTACACATTTCATATCAGGC
* **
2463680 TGCCATGGTATCTTTCAACCATGGTCTTACTTATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
*
2463745 CATGGTCTTACACGTTTCATATCAGGC
66 CATGGTCTTACACATTTCATATCAGGC
* * *
2463772 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
2463837 CATGGTCTTACACATTTCATATCAG
66 CATGGTCTTACACATTTCATATCAG
2463862 AGAGCACACT
Statistics
Matches: 163, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
91 32 0.20
92 131 0.80
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGC
Found at i:2466025 original size:23 final size:22
Alignment explanation
Indices: 2465997--2466058 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
2465987 TAATTAATAA
*
2465997 TAAAATAATAATAAATATCTCAT
1 TAAAATAAT-ATAAATATCTAAT
2466020 TAAAATAATAT--ATATCTAAT
1 TAAAATAATATAAATATCTAAT
2466040 T-AAATAATCATAAAATATC
1 TAAAATAAT-AT-AAATATC
2466059 ATCAACATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 7 0.21
20 11 0.32
22 2 0.06
23 14 0.41
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAATATAAATATCTAAT
Found at i:2466028 original size:20 final size:19
Alignment explanation
Indices: 2466003--2466047 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2465993 ATAATAAAAT
*
2466003 AATAATAAATATCTCATTAA
1 AATAATAAATATCTAATT-A
*
2466023 AATAATATATATCTAATTA
1 AATAATAAATATCTAATTA
2466042 AATAAT
1 AATAAT
2466048 CATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATAAATATCTAATTA
Found at i:2470060 original size:21 final size:21
Alignment explanation
Indices: 2470031--2470082 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
2470021 AAATGTAAGA
*
2470031 AAATATATACAAT-TATATTAC
1 AAATGTATA-AATATATATTAC
2470052 AAATGTATAAATACATATATTAC
1 AAATGTATAAAT--ATATATTAC
*
2470075 ACATGTAT
1 AAATGTAT
2470083 TTTATCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
23 15 0.58
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (21 bp):
AAATGTATAAATATATATTAC
Found at i:2470172 original size:70 final size:70
Alignment explanation
Indices: 2470091--2470232 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
2470081 ATTTTATCAT
* *
2470091 ATCCATACAATTGGCATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATG
1 ATCCATACAATTGACATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
2470156 AATTC
66 AATTC
*
2470161 ATCCATACAATTGACATATTTTGATTTATTTAATAATATAATGTCATTGTAATTTAATTATCATA
1 ATCCATACAATTGACATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
2470226 AATTC
66 AATTC
2470231 AT
1 AT
2470233 ATAATTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (70 bp):
ATCCATACAATTGACATATTTTGATTTATTTAATAATATAATGTCATTATAATTTAATTATCATA
AATTC
Found at i:2470232 original size:25 final size:23
Alignment explanation
Indices: 2470188--2470248 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
2470178 ATTTTGATTT
* *
2470188 ATTTAATAATATAATGTCATTGTA
1 ATTTAATTATATAATGTCA-TATA
2470212 ATTTAATTATCATAAAT-TCATATA
1 ATTTAATTAT-AT-AATGTCATATA
2470236 ATTTAAATTATAT
1 ATTT-AATTATAT
2470249 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 11 0.34
26 3 0.09
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (23 bp):
ATTTAATTATATAATGTCATATA
Found at i:2470889 original size:25 final size:25
Alignment explanation
Indices: 2470850--2470909 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
2470840 AATATAAAAA
2470850 TAAATAACATATCTTTCAAAATTCAT
1 TAAATAA-ATATCTTTCAAAATTCAT
2470876 TAAATAAATATCTTTCAAAATTCAT
1 TAAATAAATATCTTTCAAAATTCAT
2470901 TAAATAAAT
1 TAAATAAAT
2470910 CACCTTACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATAAATATCTTTCAAAATTCAT
Found at i:2472348 original size:9 final size:9
Alignment explanation
Indices: 2472329--2472365 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2472319 TGAGTTTTCG
*
2472329 AATTGGAAT
1 AATTCGAAT
*
2472338 AACTCGAAT
1 AATTCGAAT
2472347 AATTCGAAT
1 AATTCGAAT
2472356 AATTCGAAT
1 AATTCGAAT
2472365 A
1 A
2472366 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2472649 original size:7 final size:7
Alignment explanation
Indices: 2472637--2472669 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2472627 TCCCTTCCCA
2472637 TCCCACC
1 TCCCACC
2472644 TCCCACC
1 TCCCACC
2472651 TCCCACC
1 TCCCACC
2472658 TCCCACC
1 TCCCACC
2472665 TCCCA
1 TCCCA
2472670 TCTACCCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.70, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCACC
Found at i:2494497 original size:16 final size:17
Alignment explanation
Indices: 2494471--2494502 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2494461 TTTAATTAAC
2494471 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
2494488 TAAA-TAATTTCTCAA
1 TAAATTAATTTCTCAA
2494503 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:2499681 original size:30 final size:30
Alignment explanation
Indices: 2499645--2499702 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2499635 TGTACATTTT
*
2499645 TGGAAAGCTAATTGCCTAACAACCTAGTAG
1 TGGAAAGCTAATAGCCTAACAACCTAGTAG
**
2499675 TGGAAAGCTTGTAGCCTAACAACCTAGT
1 TGGAAAGCTAATAGCCTAACAACCTAGT
2499703 TTCCACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (30 bp):
TGGAAAGCTAATAGCCTAACAACCTAGTAG
Found at i:2513188 original size:22 final size:21
Alignment explanation
Indices: 2513156--2513209 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2513146 CATATATGTA
* *
2513156 TAGTCTTGAGACAATTGATCT
1 TAGTCTCGAGACAAGTGATCT
*
2513177 TAAGTCTCGAGACAAGTGGTCT
1 T-AGTCTCGAGACAAGTGATCT
*
2513199 TTGTCTCGAGA
1 TAGTCTCGAGA
2513210 TAGAGGTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (21 bp):
TAGTCTCGAGACAAGTGATCT
Found at i:2515579 original size:31 final size:31
Alignment explanation
Indices: 2515544--2515604 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2515534 ATTTAGTATC
2515544 TAAATTTAACTCTAATATTCAATTTGATACT
1 TAAATTTAACTCTAATATTCAATTTGATACT
* * *
2515575 TAAATTTAATTTTAATATTCATTTTGATAC
1 TAAATTTAACTCTAATATTCAATTTGATAC
2515605 GTAATCACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (31 bp):
TAAATTTAACTCTAATATTCAATTTGATACT
Found at i:2521188 original size:23 final size:23
Alignment explanation
Indices: 2521161--2521225 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
2521151 TTTAATGTTC
**
2521161 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCA-CAAACATTAA
*
2521184 TCGAACATGTTCACAAACATTAA
1 ACGAACATGTTCACAAACATTAA
*
2521207 ACGAACATGTTCACGAACA
1 ACGAACATGTTCACAAACA
2521226 ATGTTAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (23 bp):
ACGAACATGTTCACAAACATTAA
Found at i:2526283 original size:26 final size:26
Alignment explanation
Indices: 2526253--2526322 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 26
2526243 ATACATATTT
2526253 AATTATTTATATTTAGTCATATAATA
1 AATTATTTATATTTAGTCATATAATA
* ** *
2526279 AATTATTAATATGATTTATTGTTTTAATA
1 AATTATT--TAT-ATTTAGTCATATAATA
2526308 AATTATTTAATATTT
1 AATTATTT-ATATTT
2526323 TAATTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 5 0.14
29 19 0.53
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTAGTCATATAATA
Found at i:2526296 original size:29 final size:30
Alignment explanation
Indices: 2526263--2526320 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
2526253 AATTATTTAT
2526263 ATTTAGTCATATAATAAATTA-TTAATATG
1 ATTTAGTCATATAATAAATTATTTAATATG
* ** *
2526292 ATTTATTGTTTTAATAAATTATTTAATAT
1 ATTTAGTCATATAATAAATTATTTAATAT
2526321 TTTAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
ATTTAGTCATATAATAAATTATTTAATATG
Found at i:2526349 original size:16 final size:16
Alignment explanation
Indices: 2526328--2526361 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2526318 TATTTTAATT
2526328 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
2526344 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
2526360 TA
1 TA
2526362 TTCTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:2526354 original size:25 final size:26
Alignment explanation
Indices: 2526300--2526355 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
2526290 TGATTTATTG
* * **
2526300 TTTTAATAAATTATTTAATATTTTAA
1 TTTTAATAAATTATTAAAAATAATAA
2526326 -TTTAATAAATT-TTAAAAATAATAA
1 TTTTAATAAATTATTAAAAATAATAA
2526350 TTTTAA
1 TTTTAA
2526356 ATAATATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTAATAAATTATTAAAAATAATAA
Found at i:2529575 original size:14 final size:15
Alignment explanation
Indices: 2529556--2529585 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2529546 AATTCAAAAG
2529556 AATGTTTTT-AATTA
1 AATGTTTTTAAATTA
2529570 AATGTTTTTAAATTA
1 AATGTTTTTAAATTA
2529585 A
1 A
2529586 TTTAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AATGTTTTTAAATTA
Found at i:2530525 original size:286 final size:286
Alignment explanation
Indices: 2530009--2530530 Score: 638
Period size: 286 Copynumber: 1.8 Consensus size: 286
2529999 ACATTAAGTG
* *
2530009 TGCATAATAAAATTAAAATGTATAAAAATGTTAAAATAAAACTTTAGATTAGTGGTAAATTAAAG
1 TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTAGATTAGTGGTAAATTAAAA
* * * *** * *
2530074 GTTTTAGTATTGCAGTTGGTGTGGATTTAAATCCCACCATATGAATATTTTTATTTGGTTAAGTG
66 GTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTATTTGGTTAAGTG
* * * ** *
2530139 AAAAAAATTAAAAGATCCTCAGAAAATATTACTTATTTTAATTACGAAAGGGTATTCTTGTAATT
131 AAAAAAATTAAAAGACCCTCAAAAAATATTACTTATTTTAATTACGAAAAGACATTCTTGTAACT
* * **
2530204 TTCTAGCCAAGTTAGTGACCCAATTGATTATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
196 TTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
2530269 TAGATATATAACTGATGGAGGTAGTA
261 TAGATATATAACTGATGGAGGTAGTA
* *
2530295 TGCATAATAAAATTAAAATGTAT-AAAATATTAAAAT-AAAGTTATAGATTAGTGGTACATTAAA
1 TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTT-TAGATTAGTGGTAAATTAAA
* * * * **
2530358 AGTTTTACTAATGTAATTGGCCAGGGTTCAAATTCCAACATATGTATATTTTTATTATTTTTTAA
65 AGTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTA-T-TTGGTTAA
* * * * *
2530423 GTG-AAAAGATTAAAATACCCT-AAAATAATATTACTTATTTTAATTATGAAAATACATTTTTGT
128 GTGAAAAAAATTAAAAGACCCTCAAAA-AATATTACTTATTTTAATTACGAAAAGACATTCTTGT
* * * **
2530486 GACTTTCTAACTAAGTTAGTGATCCGGTTAAAGATGACACCAACT
192 AACTTTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACT
2530531 TAACCAAGGT
Statistics
Matches: 194, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
284 5 0.03
285 75 0.39
286 105 0.54
287 9 0.05
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (286 bp):
TGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTAGATTAGTGGTAAATTAAAA
GTTTTACTAATGCAATTGGCCAGGATTCAAATCCCAACATATGAATATTTTTATTTGGTTAAGTG
AAAAAAATTAAAAGACCCTCAAAAAATATTACTTATTTTAATTACGAAAAGACATTCTTGTAACT
TTCTAACCAAGTTAGTGACCCAATTAAAGATGACACCAACTCAGTAAGGGATTTTATTAGTAGTA
TAGATATATAACTGATGGAGGTAGTA
Found at i:2541532 original size:19 final size:20
Alignment explanation
Indices: 2541489--2541554 Score: 86
Period size: 19 Copynumber: 3.4 Consensus size: 20
2541479 AATCTTTCTT
2541489 TTTATTTTTATTT-TTATTTA
1 TTTATTTTT-TTTATTATTTA
2541509 TTTATTTTTTTTATTATTTA
1 TTTATTTTTTTTATTATTTA
2541529 -TTATTTTTTTTA-T-TTTA
1 TTTATTTTTTTTATTATTTA
2541546 TTTTATTTT
1 -TTTATTTT
2541555 AGTTAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 22 0.51
20 16 0.37
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTATTTTTTTTATTATTTA
Found at i:2541554 original size:16 final size:16
Alignment explanation
Indices: 2541487--2541555 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
2541477 CCAATCTTTC
2541487 TTTTTATTT-TTATTT
1 TTTTTATTTATTATTT
2541502 TTATTTATTTATT-TTT
1 TT-TTTATTTATTATTT
2541518 TTTATTATTTATTATTT
1 TTT-TTATTTATTATTT
2541535 TTTTTA-TT-TTATTT
1 TTTTTATTTATTATTT
2541549 TATTTTA
1 T-TTTTA
2541556 GTTAAATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.14
15 10 0.20
16 24 0.49
17 8 0.16
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATTTATTATTT
Found at i:2541555 original size:10 final size:10
Alignment explanation
Indices: 2541488--2541555 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 10
2541478 CAATCTTTCT
2541488 TTTTATTTTTA
1 TTTTA-TTTTA
2541499 TTTT-TATTTA
1 TTTTAT-TTTA
2541509 -TTTATTTT-
1 TTTTATTTTA
2541517 TTTTATTATT-
1 TTTTATT-TTA
*
2541527 TATTATTTT-
1 TTTTATTTTA
2541536 TTTTATTTTA
1 TTTTATTTTA
2541546 TTTTATTTTA
1 TTTTATTTTA
2541556 GTTAAATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
9 23 0.46
10 23 0.46
11 4 0.08
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:2542722 original size:118 final size:118
Alignment explanation
Indices: 2542537--2542749 Score: 354
Period size: 118 Copynumber: 1.8 Consensus size: 118
2542527 GTTTAGATCA
* *
2542537 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTTGCGTCAAAAGGTGGTG
1 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGAGTCAAAAGGTGGTG
*
2542602 TGACGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGAGTATGGCTCAAATCG
66 TGACGTGACAAGTAAAACTCCGCTAACCGAGGTTATGAGTATGGCTCAAATCG
*
2542655 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGAGTCAAAAGGTTGTG
1 TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGAGTCAAAAGGTGGTG
****
2542720 TGACGTGTTGGGTAAAACTCCGCTAACCGA
66 TGACGTGACAAGTAAAACTCCGCTAACCGA
2542750 AAATAAATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 87 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (118 bp):
TGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGAGTCAAAAGGTGGTG
TGACGTGACAAGTAAAACTCCGCTAACCGAGGTTATGAGTATGGCTCAAATCG
Found at i:2545690 original size:24 final size:24
Alignment explanation
Indices: 2545663--2545725 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
2545653 TATTAAAAGT
2545663 TATTTTAT-TTAAATTTAATTACTA
1 TATTTTATATTAAATTTAATTA-TA
* * *
2545687 TA-TTTATATAAAATTTATTTATT
1 TATTTTATATTAAATTTAATTATA
2545710 TATTTTAATATTAAAT
1 TATTTT-ATATTAAAT
2545726 AAATAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 8 0.25
24 16 0.50
25 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTATATTAAATTTAATTATA
Found at i:2549717 original size:18 final size:20
Alignment explanation
Indices: 2549677--2549717 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2549667 TTATTTGTAT
*
2549677 AATATTTTAAACTTTTACAA
1 AATATTATAAACTTTTACAA
2549697 AATATTATAAA-TTTT-CAA
1 AATATTATAAACTTTTACAA
2549715 AAT
1 AAT
2549718 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 4 0.20
20 10 0.50
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTATAAACTTTTACAA
Found at i:2558693 original size:68 final size:68
Alignment explanation
Indices: 2558585--2558729 Score: 290
Period size: 68 Copynumber: 2.1 Consensus size: 68
2558575 CTTAAGAGGA
2558585 AAAAAAAATAAAAGGCAAAAGCTTTAGAGAGAATGAATTGGTCGGCTAAGGAGAGTATTATATAT
1 AAAAAAAATAAAAGGCAAAAGCTTTAGAGAGAATGAATTGGTCGGCTAAGGAGAGTATTATATAT
2558650 ATG
66 ATG
2558653 AAAAAAAATAAAAGGCAAAAGCTTTAGAGAGAATGAATTGGTCGGCTAAGGAGAGTATTATATAT
1 AAAAAAAATAAAAGGCAAAAGCTTTAGAGAGAATGAATTGGTCGGCTAAGGAGAGTATTATATAT
2558718 ATG
66 ATG
2558721 AAAAAAAAT
1 AAAAAAAAT
2558730 TATGATTTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.23
Consensus pattern (68 bp):
AAAAAAAATAAAAGGCAAAAGCTTTAGAGAGAATGAATTGGTCGGCTAAGGAGAGTATTATATAT
ATG
Found at i:2559075 original size:21 final size:21
Alignment explanation
Indices: 2559042--2559086 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2559032 TGGTTATTTA
*
2559042 ATTTTAAAATTTTATAAAATT
1 ATTTGAAAATTTTATAAAATT
* *
2559063 ATTTGAAATTTTTATTAAATT
1 ATTTGAAAATTTTATAAAATT
2559084 ATT
1 ATT
2559087 GATCAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTGAAAATTTTATAAAATT
Found at i:2562242 original size:25 final size:25
Alignment explanation
Indices: 2562208--2562260 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2562198 GGAGGTGTAA
2562208 TAAGAAGAGAGGAGAAAATGGATGC
1 TAAGAAGAGAGGAGAAAATGGATGC
2562233 TAAGAAGAGAGGAGAAAATGGATGC
1 TAAGAAGAGAGGAGAAAATGGATGC
2562258 TAA
1 TAA
2562261 TGAGTTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.34, T:0.13
Consensus pattern (25 bp):
TAAGAAGAGAGGAGAAAATGGATGC
Found at i:2566201 original size:19 final size:22
Alignment explanation
Indices: 2566162--2566204 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
2566152 TACTCCGTAT
2566162 TTTTTATAATTTGTGAATTTAA
1 TTTTTATAATTTGTGAATTTAA
2566184 TTTTTAT-ATTT-T-AATTTAA
1 TTTTTATAATTTGTGAATTTAA
2566203 TT
1 TT
2566205 AATATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 4 0.19
22 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTTATAATTTGTGAATTTAA
Found at i:2566403 original size:44 final size:46
Alignment explanation
Indices: 2566323--2566417 Score: 151
Period size: 44 Copynumber: 2.1 Consensus size: 46
2566313 TAGTAAAATT
*
2566323 TAATTTTTTATTATATCTTATATATATTAATTG-TTTTTATCATAAA
1 TAATTTTTTATTATA-CTTATATATATTAATTGTTTTTTACCATAAA
2566369 TAATTTTTTATTATA-TTATATATATTAATTGTTTTTTACCATAAA
1 TAATTTTTTATTATACTTATATATATTAATTGTTTTTTACCATAAA
2566414 -AATT
1 TAATT
2566418 ATCGAATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 20 0.43
45 12 0.26
46 15 0.32
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (46 bp):
TAATTTTTTATTATACTTATATATATTAATTGTTTTTTACCATAAA
Found at i:2568552 original size:3 final size:3
Alignment explanation
Indices: 2568544--2568584 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2568534 CCATGTCTCG
*
2568544 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT- TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
2568585 GATTTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2573868 original size:20 final size:20
Alignment explanation
Indices: 2573843--2573881 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2573833 TGTAATTGTC
2573843 CAATTACATAAAATATTATT
1 CAATTACATAAAATATTATT
* *
2573863 CAATTACATGAATTATTAT
1 CAATTACATAAAATATTAT
2573882 AACATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
CAATTACATAAAATATTATT
Found at i:2575078 original size:7 final size:7
Alignment explanation
Indices: 2575068--2575105 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2575058 TAACACAAAT
2575068 TTAAAAA
1 TTAAAAA
2575075 TTAAAAA
1 TTAAAAA
2575082 -T--AAA
1 TTAAAAA
2575086 TTAAAAA
1 TTAAAAA
2575093 TTAAAAA
1 TTAAAAA
2575100 TTAAAA
1 TTAAAA
2575106 TATTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.11
5 1 0.04
6 1 0.04
7 23 0.82
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Done.