Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold245
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: 333457
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 3
Found at i:191554 original size:16 final size:16
Alignment explanation
Indices: 191533--191565 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
191523 TAGCACTTTA
191533 CCAACAGACCACATAG
1 CCAACAGACCACATAG
191549 CCAACAGACCACATAG
1 CCAACAGACCACATAG
191565 C
1 C
191566 TGTTGGCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.39, G:0.12, T:0.06
Consensus pattern (16 bp):
CCAACAGACCACATAG
Found at i:197683 original size:45 final size:45
Alignment explanation
Indices: 197632--197718 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
197622 CTAAAGGTAT
* * *
197632 AATGATATTTATGTCAAACTATTATATCAAAAATAACTGTGCCCG
1 AATGATACTTATGTCAAACTATTACACCAAAAATAACTGTGCCCG
* * * *
197677 AATGATACTTGTGTCAAAGTATTACACCAAAAGTAATTGTGC
1 AATGATACTTATGTCAAACTATTACACCAAAAATAACTGTGC
197719 TAAAAGTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (45 bp):
AATGATACTTATGTCAAACTATTACACCAAAAATAACTGTGCCCG
Found at i:198049 original size:3 final size:3
Alignment explanation
Indices: 198041--198084 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
198031 ACTTATAGCA
198041 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
198085 AGCATTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:198195 original size:3 final size:3
Alignment explanation
Indices: 198187--198233 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
198177 GAGAAAAAAC
198187 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
198233 T
1 T
198234 CTAAAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:199206 original size:15 final size:15
Alignment explanation
Indices: 199188--199229 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
199178 ATTAATTATT
* *
199188 TTTAAATTATTTTAA
1 TTTAAAATAATTTAA
199203 TTTAAAATAATTTAA
1 TTTAAAATAATTTAA
199218 --TAAAATAATTTA
1 TTTAAAATAATTTA
199230 TATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
15 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATAATTTAA
Found at i:199223 original size:13 final size:13
Alignment explanation
Indices: 199205--199229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199195 TATTTTAATT
199205 TAAAATAATTTAA
1 TAAAATAATTTAA
199218 TAAAATAATTTA
1 TAAAATAATTTA
199230 TATATTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATAATTTAA
Found at i:199376 original size:16 final size:17
Alignment explanation
Indices: 199339--199379 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
199329 TAAAATTAAT
*
199339 AAATATATTAATATACA
1 AAATTTATTAATATACA
*
199356 AAATTTATTAATAT-TA
1 AAATTTATTAATATACA
199372 AAATTTAT
1 AAATTTAT
199380 AAGATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATTAATATACA
Found at i:202086 original size:2 final size:2
Alignment explanation
Indices: 202079--202108 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202069 GCAAGTAGAA
202079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
202109 AAATTTATGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:205034 original size:13 final size:13
Alignment explanation
Indices: 205018--205042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
205008 ATAGCATATT
205018 AAAAAATTAATTA
1 AAAAAATTAATTA
205031 AAAAAATTAATT
1 AAAAAATTAATT
205043 TTATTTGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTAATTA
Found at i:205348 original size:16 final size:17
Alignment explanation
Indices: 205329--205361 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
205319 TTTTTAAGTT
205329 AATAATT-ATTTTTAAA
1 AATAATTAATTTTTAAA
*
205345 AATATTTAATTTTTAAA
1 AATAATTAATTTTTAAA
205362 TTTAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAATTAATTTTTAAA
Found at i:206022 original size:22 final size:22
Alignment explanation
Indices: 205966--206024 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 22
205956 ATAAACTAAA
*
205966 TAAAATATATAATGAATTAAAATAT
1 TAAAATA-A-AAT-AATTAAAAAAT
*
205991 TATAGA-AAAATAATTAAAAAAT
1 TA-AAATAAAATAATTAAAAAAT
206013 TAAAATAAAATA
1 TAAAATAAAATA
206025 TGATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.07
22 18 0.62
23 3 0.10
24 1 0.03
25 3 0.10
26 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (22 bp):
TAAAATAAAATAATTAAAAAAT
Found at i:206034 original size:17 final size:18
Alignment explanation
Indices: 206014--206048 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
206004 TTAAAAAATT
206014 AAAATAAAATATG-ATAA
1 AAAATAAAATATGCATAA
*
206031 AAAATAATATATGCATAA
1 AAAATAAAATATGCATAA
206049 TTTTTAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATAAAATATGCATAA
Found at i:208648 original size:2 final size:2
Alignment explanation
Indices: 208641--208674 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
208631 TAAATCACAA
208641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
208675 TCTAAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209447 original size:23 final size:24
Alignment explanation
Indices: 209416--209464 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
209406 TAAAATATAA
*
209416 TATAAAAAATATA-TATTAAAATT
1 TATAAAAAATAAATTATTAAAATT
* *
209439 TATATAAAATAAATTATTAATATT
1 TATAAAAAATAAATTATTAAAATT
209463 TA
1 TA
209465 CATTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAAAAAATAAATTATTAAAATT
Found at i:211889 original size:864 final size:859
Alignment explanation
Indices: 210332--211938 Score: 1893
Period size: 887 Copynumber: 1.8 Consensus size: 859
210322 AAAAAAAAAA
* *
210332 TTTTCTCAGCTTAATAAAAACAACAAATTTCTCAGATTAGTTTGGTCTCTTAACCCAGGGGTTTC
1 TTTTCTCAGCATAATAAAAACAACAAATTTCTCAGATTAGTTTGGTCTATTAACCCAGGGGTTTC
* *
210397 AGATTACTTTTGGCGTTGTACCTAAACCTGATTAAACCGGATTGGAGGTGGGTTGCACCTCCAGT
66 AAATTACTTTTGGCGTTGTACCTAAACCTGATTAAACCGCATTGGAGGTGGGTTGCACCTCCAGT
* *
210462 GAGGCACTAGTAGGACAAGAGAGACCAGCGGACGGACCCTTGTGGGGTGAAATTCTAACTCACCT
131 GAGGCACTAGAAGGACAAGAGAGACCAGCGGACGGACCATTGTGGGGTGAAATTCTAACTCACCT
210527 CTTTTTGTTTTTTAAACAATTTATTTTTATTTAAAAATCTTGAAATTATTTTATTTTATTTTTAT
196 CTTTTTGTTTTTTAAACAATTTATTTTTATTTAAAAATCTTGAAA-TA-TTTATTTTATTTTTAT
*
210592 TAATTTGTTTTTTAATTTTTTATGTAATGATTTTTAAATTGTTTATTTATTTAATATACAATATA
259 TAATTTATTTTTTAA--TTTTATGT-ATGA--TTTAAA----TTA--TATTTAATATACAATATA
* ** * *
210657 ATAAATGTATATATTTATATAATAATTAACTAACGAATTAAAATATTTATATAAATATATAATTA
313 ATAAATATATATATTTATATAATAATTAACTAAAAAATTAAAATATTTATATAAATATAAAATAA
* * *
210722 ATATGTTAAATTTTAAATATCATTAATATATAAGATAATTTATTAATATATTGTTACAAAATATT
378 ATATGTTAAATTTAAAATATCATTAATATATAAGATAATTTATTAATATACTGTTACAAAATATC
*
210787 TTTAATAATTATATTTATTTTATATCTTCACTATTATCTTTATATTTAAAAATACATCTACACTT
443 TTTAATAACTATATTTATTTTATATCTTCACTATTATCTTTATATTT-AAAATACATCTACACTT
* * * * *** * * * *
210852 ATAATTAATGTTTATTGATTCAAATAGTTTCGTACTTATTTTTTTTAAGTGAAATATCGAATTTA
507 ATAATGAAAGTTCATTGATTCAAATAATTTAACACTTATTTTTTTTAAATAAAATATCAAACTTA
* *
210917 AATTTTATAAATAAAAATAACTAGCATCAGAAGAAATCTATCTCAAAATTGACTAACTCAACTGA
572 AATCTTATAAATAAAAATAACTA-CATCAGAAGAAATCTATCTCAAAATTGACCAACTCAACTGA
* * * *
210982 CATTGAATTAGTGAGATTCAATAAATTTTTGAATATCAAAATTTTAATAAAAAAAATAAGTATAC
636 CA-TGAATTAGTAAAATTCAATAAATTTTTAAATATCAAAATTTTAAT-AAAAAAAT-A-CATAC
211047 AATA-CTTATATTTTTCAATATAATATTTAATTTTTTTACCACTGTTGTTCTTAATACTATTTTA
697 AATATC-TATATTTTTCAATATAATATTTAATTTTTTTACCACTGTTGTTCTTAATACTATTTTA
211111 AATTAAATAATCAATTATCTTAAAATTTAACTGATAGATATATTAGAATTTACTACCAAATAATA
761 AATTAAATAATCAATTATCTTAAAATTTAACTGATAGATATATTAGAATTTACTACCAAATAATA
211176 CAGTTTTGAATAGATTATTAATTTTTTTTTAATT
826 CAGTTTTGAATAGATTATTAATTTTTTTTTAATT
* *
211210 TTTTCTCAGCATAATAAAAACTACAAAATTTCTCAGATTAGTTTTGGTCTATTAAGCCAGGGCTT
1 TTTTCTCAGCATAATAAAAACAAC-AAATTTCTCAGATTAG-TTTGGTCTATTAACCCAGGG---
* *
211275 GAAATTTCAAATTACTTTTGGCGTTGTAACCTAAACGTGATTTAACCGCATTGGAGGTGGGTTGC
61 G---TTTCAAATTACTTTTGGCGTTGT-ACCTAAACCTGATTAAACCGCATTGGAGGTGGGTTGC
* * * * * *
211340 ATCTCCAGTGAGGCACTGGAAGGAGAAGGGAGGCCAGTGGACGGACCATTGTGGGGTGAAATTCT
122 ACCTCCAGTGAGGCACTAGAAGGACAAGAGAGACCAGCGGACGGACCATTGTGGGGTGAAATTCT
* * *
211405 AATTCACCTCTTTTTGTTTTTTTAAACGA-TTATTTTTATTTAAAAATCTT-TAA-A-TTATTTT
187 AACTCACCTCTTTTTG-TTTTTTAAACAATTTATTTTTATTTAAAAATCTTGAAATATTTATTTT
211466 ATTTTTA-TACATTTATTTTTTAA-TTT-T-T-T-A-TT-AA-TA-ATTTAATATACAATATAAT
251 ATTTTTATTA-ATTTATTTTTTAATTTTATGTATGATTTAAATTATATTTAATATACAATATAAT
*
211521 AAATATATATATTTATATAATAATTAGCTAAAAAATTAAAATATTTACT-TAAATATAAAATAAA
315 AAATATATATATTTATATAATAATTAACTAAAAAATTAAAATATTTA-TATAAATATAAAAT-AA
* * * ***
211585 ATATTTTAAAATTTAAAATATCATTAACATATATAAAAGATAATTTTTTAATGTACTGTTGTGTA
378 ATATGTT-AAATTTAAAATATCATT-A-ATATAT--AAGATAATTTATTAATATACTGTT-ACAA
* * * *
211650 AATGTCTTTAATAACTATATTTATTATTATCTCTTCATTATTA-CTTT-TATATT-CAA-A-ATC
437 AATATCTTTAATAACTATATTTATT-TTATATCTTCACTATTATCTTTATAT-TTAAAATACATC
* * * *
211710 -ACATTTATAATGAAAGTTCGTT-AGTTCAAATAATTTAACATTTATTTTTTTTAAATAAAATTT
500 TACACTTATAATGAAAGTTCATTGA-TTCAAATAATTTAACACTTATTTTTTTTAAATAAAATAT
* * * ** * * * * *
211773 TAAACTTAAATCTTGTAAATAAAAA-AATTA-ATGTTGAA-AAAGTTTTATTTTATAGTTGACCA
564 CAAACTTAAATCTTATAAATAAAAATAACTACAT-CAGAAGAAA--TCTATCTCAAAATTGACCA
* * *
211835 A-TCCAACTTGTAC-TGAATTAATTAAAATTTAATAAATTTTTAAATATCAAAATTTTGATAAAA
626 ACT-CAAC-TG-ACATGAATT-AGTAAAATTCAATAAATTTTTAAATATCAAAATTTTAATAAAA
* *
211898 AAATACCTACAATATCTATATTTTTCACTATAATATTTAAT
687 AAATACATACAATATCTATATTTTTCAATATAATATTTAAT
211939 CTTATTATCA
Statistics
Matches: 623, Mismatches: 76, Indels: 77
0.80 0.10 0.10
Matches are distributed among these distances:
861 36 0.06
862 79 0.13
863 45 0.07
864 119 0.19
865 8 0.01
866 7 0.01
867 2 0.00
868 24 0.04
869 29 0.05
870 17 0.03
871 2 0.00
874 1 0.00
875 1 0.00
877 1 0.00
878 23 0.04
879 19 0.03
880 18 0.03
881 2 0.00
882 26 0.04
883 1 0.00
884 1 0.00
886 24 0.04
887 127 0.20
888 11 0.02
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (859 bp):
TTTTCTCAGCATAATAAAAACAACAAATTTCTCAGATTAGTTTGGTCTATTAACCCAGGGGTTTC
AAATTACTTTTGGCGTTGTACCTAAACCTGATTAAACCGCATTGGAGGTGGGTTGCACCTCCAGT
GAGGCACTAGAAGGACAAGAGAGACCAGCGGACGGACCATTGTGGGGTGAAATTCTAACTCACCT
CTTTTTGTTTTTTAAACAATTTATTTTTATTTAAAAATCTTGAAATATTTATTTTATTTTTATTA
ATTTATTTTTTAATTTTATGTATGATTTAAATTATATTTAATATACAATATAATAAATATATATA
TTTATATAATAATTAACTAAAAAATTAAAATATTTATATAAATATAAAATAAATATGTTAAATTT
AAAATATCATTAATATATAAGATAATTTATTAATATACTGTTACAAAATATCTTTAATAACTATA
TTTATTTTATATCTTCACTATTATCTTTATATTTAAAATACATCTACACTTATAATGAAAGTTCA
TTGATTCAAATAATTTAACACTTATTTTTTTTAAATAAAATATCAAACTTAAATCTTATAAATAA
AAATAACTACATCAGAAGAAATCTATCTCAAAATTGACCAACTCAACTGACATGAATTAGTAAAA
TTCAATAAATTTTTAAATATCAAAATTTTAATAAAAAAATACATACAATATCTATATTTTTCAAT
ATAATATTTAATTTTTTTACCACTGTTGTTCTTAATACTATTTTAAATTAAATAATCAATTATCT
TAAAATTTAACTGATAGATATATTAGAATTTACTACCAAATAATACAGTTTTGAATAGATTATTA
ATTTTTTTTTAATT
Found at i:212070 original size:33 final size:36
Alignment explanation
Indices: 212033--212101 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 36
212023 TATGTTTCAT
212033 TTATTAAAATAAAAT-AAAT-TTATAAT-ATAATAG
1 TTATTAAAATAAAATAAAATATTATAATAATAATAG
**
212066 TTATTTTAATAAAATAAAATAATTATAATAATAATA
1 TTATTAAAATAAAATAAAAT-ATTATAATAATAATA
212102 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 13 0.43
34 4 0.13
36 7 0.23
37 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
TTATTAAAATAAAATAAAATATTATAATAATAATAG
Found at i:212628 original size:18 final size:17
Alignment explanation
Indices: 212597--212631 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
212587 AAAATTTAAA
*
212597 TTTATAAAATATTATAT
1 TTTATAAAAAATTATAT
212614 TTTATAAAAAAATTATAT
1 TTTAT-AAAAAATTATAT
212632 AATTTCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATAAAAAATTATAT
Found at i:213126 original size:18 final size:16
Alignment explanation
Indices: 213087--213128 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
213077 CGATATTAAC
*
213087 ATAATATAATAAAAAT
1 ATAATATAATAAAAAA
213103 ATAATATAATATATAAAA
1 ATAATATAATA-A-AAAA
213121 ATAATATA
1 ATAATATA
213129 TATGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATATAATAAAAAA
Found at i:213227 original size:22 final size:22
Alignment explanation
Indices: 213193--213243 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
213183 TATAATATCT
* *
213193 TAAAATGATTATAATATAAAA-A
1 TAAAATAAATATAATA-AAAATA
213215 TAAAATAAATATAATAAAAATA
1 TAAAATAAATATAATAAAAATA
213237 TATAAAT
1 TA-AAAT
213244 TATTTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 17 0.68
23 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATATAATAAAAATA
Found at i:214285 original size:19 final size:19
Alignment explanation
Indices: 214251--214288 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
214241 TGTGAGTTTA
**
214251 GAATTTTTTATTTTTTATT
1 GAATTTTTTAAATTTTATT
214270 GAATTTTTTAAATTTTATT
1 GAATTTTTTAAATTTTATT
214289 AAATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
GAATTTTTTAAATTTTATT
Found at i:214417 original size:22 final size:20
Alignment explanation
Indices: 214390--214435 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
214380 TATAATTTTT
*
214390 TTAAAATATAAACTTATAAATA
1 TTAAAATATAAAATT-TAAA-A
*
214412 TTAAAATTTAAAATTTAAAA
1 TTAAAATATAAAATTTAAAA
214432 TTAA
1 TTAA
214436 CTTATAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAATATAAAATTTAAAA
Found at i:215539 original size:2 final size:2
Alignment explanation
Indices: 215528--215556 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
215518 CTATTTAAAT
215528 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
215557 ATCTGCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:217431 original size:3 final size:3
Alignment explanation
Indices: 217423--217451 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
217413 TAATATTCAA
217423 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
217452 CATTTATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:219156 original size:18 final size:18
Alignment explanation
Indices: 219116--219162 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
219106 ACAAAAATAT
219116 AAAATATTAATAATTATAC
1 AAAATATTAA-AATTATAC
219135 -AAATATTAAAATGTA-AC
1 AAAATATTAAAAT-TATAC
219152 AAAAT-TTAAAA
1 AAAATATTAAAA
219163 AAAATCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATATTAAAATTATAC
Found at i:220438 original size:24 final size:22
Alignment explanation
Indices: 220400--220462 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
220390 GTGCGTATTG
220400 ATTTATAATTT-AATATTTAAAA
1 ATTTA-AATTTGAATATTTAAAA
**
220422 ATTTTAAATATTGAATATTTTTAA
1 A-TTTAAAT-TTGAATATTTAAAA
220446 ATTTAAATTTG-ATATTT
1 ATTTAAATTTGAATATTT
220463 GTATATAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 6 0.17
22 7 0.19
23 13 0.36
24 10 0.28
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTAAATTTGAATATTTAAAA
Found at i:222712 original size:6 final size:6
Alignment explanation
Indices: 222681--222722 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
222671 TAATATAATT
*
222681 TTTATA TTTACA -TTATAA TATTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTAT-A T-TTATA TTTATA TTTATA TTTAT
222723 TCTTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 3 0.10
6 22 0.71
7 2 0.06
8 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:222785 original size:17 final size:17
Alignment explanation
Indices: 222765--222818 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
222755 AATATAAAAA
*
222765 TAAATGTATTATATAAT
1 TAAATATATTATATAAT
* * *
222782 TAAA-AAATTATAAAAA
1 TAAATATATTATATAAT
222798 TAAATATATTATATAAT
1 TAAATATATTATATAAT
222815 TAAA
1 TAAA
222819 AAAAACATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATATATTATATAAT
Found at i:222799 original size:33 final size:33
Alignment explanation
Indices: 222757--222821 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
222747 TATATATAAA
*
222757 TATAAAAATAAATGTATTATATAATTAAAAAAT
1 TATAAAAATAAATATATTATATAATTAAAAAAT
222790 TATAAAAATAAATATATTATATAATTAAAAAA
1 TATAAAAATAAATATATTATATAATTAAAAAA
222822 AACATATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (33 bp):
TATAAAAATAAATATATTATATAATTAAAAAAT
Found at i:222901 original size:19 final size:19
Alignment explanation
Indices: 222877--222927 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
222867 AGTTAGATCT
222877 ATTTTTTATATTTATTTTA
1 ATTTTTTATATTTATTTTA
*
222896 ATTTTTT-TATTAAATTTTA
1 ATTTTTTATATT-TATTTTA
*
222915 TTTTTTTA-ATTTA
1 ATTTTTTATATTTA
222928 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTTATATTTATTTTA
Found at i:222906 original size:14 final size:14
Alignment explanation
Indices: 222887--222947 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
222877 ATTTTTTATA
222887 TTTATTTTAATTTT
1 TTTATTTTAATTTT
*
222901 TTTATTAAATTTTATTTT
1 TTTA-T---TTTAATTTT
* *
222919 TTTAATTTAATATT
1 TTTATTTTAATTTT
*
222933 TTTATTTAAATTTT
1 TTTATTTTAATTTT
222947 T
1 T
222948 AAAATTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
14 23 0.64
15 1 0.03
18 12 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTTAATTTT
Found at i:222913 original size:32 final size:32
Alignment explanation
Indices: 222877--222947 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
222867 AGTTAGATCT
* *
222877 ATTTTTTATATTTATTTTAATTTTTTTA-TTAA
1 ATTTTTT-TATTTAATTTAATATTTTTATTTAA
*
222909 ATTTTATTTTTTTAATTTAATATTTTTATTTAA
1 ATTTT-TTTATTTAATTTAATATTTTTATTTAA
222942 ATTTTT
1 ATTTTT
222948 AAAATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (32 bp):
ATTTTTTTATTTAATTTAATATTTTTATTTAA
Found at i:222940 original size:18 final size:18
Alignment explanation
Indices: 222880--222941 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
222870 TAGATCTATT
* *
222880 TTTTATATTTATTTTAATT
1 TTTT-TATTTAATTTAATA
*
222899 TTTTTATTAAATTT--TA
1 TTTTTATTTAATTTAATA
222915 -TTTT-TTTAATTTAATA
1 TTTTTATTTAATTTAATA
222931 TTTTTATTTAA
1 TTTTTATTTAA
222942 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 7 0.20
15 4 0.11
16 3 0.09
17 4 0.11
18 13 0.37
19 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTTAATTTAATA
Found at i:222941 original size:13 final size:12
Alignment explanation
Indices: 222887--222948 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
222877 ATTTTTTATA
*
222887 TTTATTTTAATT
1 TTTATTTAAATT
*
222899 TTTTTATTAAA-T
1 TTTAT-TTAAATT
222911 TTTATTT---TT
1 TTTATTTAAATT
*
222920 TTAATTTAATATT
1 TTTATTTAA-ATT
222933 TTTATTTAAATT
1 TTTATTTAAATT
222945 TTTA
1 TTTA
222949 AAATTAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
9 7 0.18
11 2 0.05
12 16 0.41
13 14 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTTAAATT
Found at i:222967 original size:18 final size:19
Alignment explanation
Indices: 222938--222978 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
222928 ATATTTTTAT
222938 TTAAATTTTTAAAATTAAA
1 TTAAATTTTTAAAATTAAA
* *
222957 TTAAA-TTTTAAATTTAAG
1 TTAAATTTTTAAAATTAAA
222975 TTAA
1 TTAA
222979 CTCAGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAATTTTTAAAATTAAA
Found at i:223526 original size:27 final size:26
Alignment explanation
Indices: 223494--223572 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 26
223484 TTTAATTATT
223494 ATTTAATAATAAAAATAATTATTAAAA
1 ATTTAAT-ATAAAAATAATTATTAAAA
*
223521 ATTTAAT-TATAAAAT-A-TA-TAAAT
1 ATTTAATATA-AAAATAATTATTAAAA
*
223544 A-TTAATATAAAAATAATTTTTAAAA
1 ATTTAATATAAAAATAATTATTAAAA
223569 ATTT
1 ATTT
223573 TATTAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
22 10 0.23
23 8 0.19
24 3 0.07
25 8 0.19
26 7 0.16
27 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTTAATATAAAAATAATTATTAAAA
Found at i:223529 original size:15 final size:16
Alignment explanation
Indices: 223508--223548 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
223498 AATAATAAAA
223508 ATAATTATTAAAA-AT
1 ATAATTATTAAAATAT
*
223523 TTAATTA-TAAAATAT
1 ATAATTATTAAAATAT
*
223538 ATAAATATTAA
1 ATAATTATTAA
223549 TATAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATTATTAAAATAT
Found at i:224138 original size:26 final size:26
Alignment explanation
Indices: 224109--224158 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
224099 GCTAATGAAA
224109 ATTTAAAATTAAAT-TATTATTAAAGT
1 ATTTAAAATTAAATATA-TATTAAAGT
* *
224135 ATTTTAATTTAAATATATATTAAA
1 ATTTAAAATTAAATATATATTAAA
224159 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTTAAAATTAAATATATATTAAAGT
Found at i:226261 original size:29 final size:28
Alignment explanation
Indices: 226228--226282 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
226218 TAAAAATAAA
226228 AAATATAATAAACATAATATAATATATTT
1 AAATATAATAAACATAAT-TAATATATTT
* *
226257 AAATATAATTAATATAATTAATATAT
1 AAATATAATAAACATAATTAATATAT
226283 CATATTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATATAATAAACATAATTAATATATTT
Found at i:226272 original size:9 final size:9
Alignment explanation
Indices: 226229--226281 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
226219 AAAAATAAAA
*
226229 AATATAATA
1 AATATAATT
*
226238 AACATAATAT
1 AATATAAT-T
*
226248 AATATATTT
1 AATATAATT
226257 AAATATAATT
1 -AATATAATT
226267 AATATAATT
1 AATATAATT
226276 AATATA
1 AATATA
226282 TCATATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 23 0.62
10 14 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
AATATAATT
Found at i:226277 original size:19 final size:20
Alignment explanation
Indices: 226200--226287 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 20
226190 AAGTAAAATA
*
226200 TAAATATAATAT-ATTTAA-
1 TAAATATAATATAATATAAT
* *
226218 TAAAAATAA-AAAATATAA-
1 TAAATATAATATAATATAAT
* *
226236 TAAACATAATATAATATATT
1 TAAATATAATATAATATAAT
226256 TAAATATAAT-TAATATAAT
1 TAAATATAATATAATATAAT
*
226275 TAATATATCATAT
1 TAA-ATATAATAT
226288 TTAACACATA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 1 0.02
18 21 0.38
19 18 0.32
20 15 0.27
21 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATAATATAATATAAT
Found at i:226351 original size:15 final size:16
Alignment explanation
Indices: 226331--226363 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
226321 TTAAAAAATT
226331 TATTAAT-TTATATTA
1 TATTAATATTATATTA
226346 TATTAATACTTATATTA
1 TATTAATA-TTATATTA
226363 T
1 T
226364 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATATTATATTA
Found at i:227676 original size:20 final size:20
Alignment explanation
Indices: 227647--227685 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
227637 AAAGTTTTAG
* *
227647 ATTATTTATTTATTTAATAT
1 ATTATATATTTATATAATAT
227667 ATTATATATTTATATAATA
1 ATTATATATTTATATAATA
227686 AATAGTTAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATATATTTATATAATAT
Found at i:228436 original size:22 final size:23
Alignment explanation
Indices: 228400--228458 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
228390 AAAAATTGGT
*
228400 TTAAAAGATTCGAATTTTTTTTA
1 TTAAAAGATTCGAATATTTTTTA
228423 TTAAAAG-TTCGAATATTTTTTA
1 TTAAAAGATTCGAATATTTTTTA
* *
228445 -TAAAAAATTTGAAT
1 TTAAAAGATTCGAAT
228459 CTTACAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.16
22 20 0.62
23 7 0.22
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (23 bp):
TTAAAAGATTCGAATATTTTTTA
Found at i:230317 original size:23 final size:23
Alignment explanation
Indices: 230291--230336 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
230281 TGGATATTTT
230291 AAATTTATATAAATTTTAATATG
1 AAATTTATATAAATTTTAATATG
*
230314 AAATTTATATAAATTTTGATATG
1 AAATTTATATAAATTTTAATATG
230337 TTAATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
AAATTTATATAAATTTTAATATG
Found at i:230323 original size:11 final size:10
Alignment explanation
Indices: 230290--230329 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
230280 TTGGATATTT
230290 TAAATTTATA
1 TAAATTTATA
230300 TAAATTTTAATA
1 TAAA-TTT-ATA
230312 TGAAATTTATA
1 T-AAATTTATA
230323 TAAATTT
1 TAAATTT
230330 TGATATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.37
11 7 0.26
12 7 0.26
13 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
TAAATTTATA
Found at i:230335 original size:12 final size:11
Alignment explanation
Indices: 230290--230335 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
230280 TTGGATATTT
230290 TAAA-TTTATA
1 TAAATTTTATA
230300 TAAATTTTAATA
1 TAAATTTT-ATA
230312 TGAAA-TTTATA
1 T-AAATTTTATA
230323 TAAATTTTGATA
1 TAAATTTT-ATA
230335 T
1 T
230336 GTTAATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.23
11 10 0.32
12 11 0.35
13 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (11 bp):
TAAATTTTATA
Found at i:232272 original size:21 final size:21
Alignment explanation
Indices: 232235--232274 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
232225 AATATATATT
232235 TATATTAAAAATATAAAAAAA
1 TATATTAAAAATATAAAAAAA
*
232256 TATA-TAAAACATTTAAAAA
1 TATATTAAAA-ATATAAAAA
232275 GATAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TATATTAAAAATATAAAAAAA
Found at i:232667 original size:27 final size:27
Alignment explanation
Indices: 232630--232685 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
232620 TTAAGATGTA
232630 TTAAAAATAAATTATGAAATTTA-ATTT
1 TTAAAAATAAA-TATGAAATTTAGATTT
* *
232657 TTAAAATTAAATATGATATTTAGATTT
1 TTAAAAATAAATATGAAATTTAGATTT
232684 TT
1 TT
232686 TACACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
TTAAAAATAAATATGAAATTTAGATTT
Found at i:232721 original size:20 final size:18
Alignment explanation
Indices: 232685--232723 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
232675 TTTAGATTTT
232685 TTACACATAAAAAAATTA
1 TTACACATAAAAAAATTA
232703 TTACATCATAAAAATAATTA
1 TTACA-CATAAAAA-AATTA
232723 T
1 T
232724 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
TTACACATAAAAAAATTA
Found at i:233120 original size:17 final size:18
Alignment explanation
Indices: 233098--233132 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
233088 ATTATTAATT
233098 AATTAAATA-TTTATAAA
1 AATTAAATATTTTATAAA
233115 AATTAAATATTTTATAAA
1 AATTAAATATTTTATAAA
233133 TTTATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATATTTTATAAA
Found at i:233147 original size:39 final size:40
Alignment explanation
Indices: 233103--233198 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 40
233093 TAATTAATTA
233103 AATATTTATAAAAATTAAATA-TTTTATAAATTTATTA-AT
1 AATATTTATAAAAATTAAATATTTTTA-AAATTTATTATAT
** *
233142 AATA-TTATAAAAATATTTATATTTTTAAAATTTTTTATAT
1 AATATTTATAAAAAT-TAAATATTTTTAAAATTTATTATAT
233182 AATTTATTTA-AAAAATT
1 AA--TATTTATAAAAATT
233199 TATGAACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
38 10 0.21
39 17 0.35
40 9 0.19
41 1 0.02
42 8 0.17
43 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
AATATTTATAAAAATTAAATATTTTTAAAATTTATTATAT
Found at i:233158 original size:20 final size:20
Alignment explanation
Indices: 233103--233158 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
233093 TAATTAATTA
*
233103 AATATTTATAAAAAT-TAAAT
1 AATA-TTATAAAAATATTAAT
* **
233123 -ATTTTATAAATTTATTAAT
1 AATATTATAAAAATATTAAT
233142 AATATTATAAAAATATT
1 AATATTATAAAAATATT
233159 TATATTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTATAAAAATATTAAT
Found at i:233292 original size:20 final size:18
Alignment explanation
Indices: 233269--233312 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
233259 TACCATTCCC
233269 AAAAAACATATCAATCTCTT
1 AAAAAAC-TATCAATC-CTT
*
233289 AAAAAACTATCACTCCTT
1 AAAAAACTATCAATCCTT
233307 AAAAAA
1 AAAAAA
233313 TTACTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 7 0.30
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAACTATCAATCCTT
Found at i:233540 original size:26 final size:26
Alignment explanation
Indices: 233480--233541 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
233470 GAAAATTAAA
*
233480 AAAATTAAAAAATAAAAAATTTATTTT
1 AAAATT-AAAAATAAAAAATATATTTT
**
233507 AATTTTAAAAATAAAAAA-ATATTTT
1 AAAATTAAAAATAAAAAATATATTTT
233532 GAAAATTAAA
1 -AAAATTAAA
233542 GTAATTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 6 0.21
26 19 0.66
27 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAATTAAAAATAAAAAATATATTTT
Found at i:234063 original size:112 final size:111
Alignment explanation
Indices: 233738--234064 Score: 618
Period size: 111 Copynumber: 2.9 Consensus size: 111
233728 ATGACTTAGT
233738 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGCAGTGGCTAGCGGCACTAAC
1 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGCAGTGGCTAGCGGCACTAAC
*
233803 TAGTGGCTAGTTCCACCAACTTGAAACCTAACAGAATCAGGAAGAG
66 TAGTGGCTAGTTCCACCAACTTGAAACCTAAGAGAATCAGGAAGAG
233849 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGCAGTGGCTAGCGGCACTAAC
1 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGCAGTGGCTAGCGGCACTAAC
233914 TAGTGGCTAGTTCCACCAACTTGAAACCTAAGAGAATCAGGAAGAG
66 TAGTGGCTAGTTCCACCAACTTGAAACCTAAGAGAATCAGGAAGAG
*
233960 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCTAGCTAGTGGCTAGCGGCACTAA
1 TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGC-AGTGGCTAGCGGCACTAA
*
234025 CTAGTGCCTAGTTCCACCAACTTGAAACCTAAGAGAATCA
65 CTAGTGGCTAGTTCCACCAACTTGAAACCTAAGAGAATCA
234065 AGGAGAACGG
Statistics
Matches: 212, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
111 155 0.73
112 57 0.27
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (111 bp):
TTTAGGCCTATCTGAGTTATTGACACCAAGTCCGACCTCTCCGAGCAGTGGCTAGCGGCACTAAC
TAGTGGCTAGTTCCACCAACTTGAAACCTAAGAGAATCAGGAAGAG
Found at i:234105 original size:46 final size:46
Alignment explanation
Indices: 234033--234127 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
234023 AACTAGTGCC
*
234033 TAGTTCCACCAACTTGAAACCTAAGAGAATCAAGGAGAACGGGAGA
1 TAGTCCCACCAACTTGAAACCTAAGAGAATCAAGGAGAACGGGAGA
* * *
234079 TAGTCCCACCAACTTGAAACCTAAGAGAATTACGGAGAAGGGGAGA
1 TAGTCCCACCAACTTGAAACCTAAGAGAATCAAGGAGAACGGGAGA
234125 TAG
1 TAG
234128 AAAGGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (46 bp):
TAGTCCCACCAACTTGAAACCTAAGAGAATCAAGGAGAACGGGAGA
Found at i:234603 original size:8 final size:7
Alignment explanation
Indices: 234582--234622 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
234572 TATTTTATTT
234582 ATAAAAA
1 ATAAAAA
* *
234589 TTGAAAA
1 ATAAAAA
234596 ATAAAAA
1 ATAAAAA
234603 ATAAAAA
1 ATAAAAA
234610 ATAACAAA
1 ATAA-AAA
234618 ATAAA
1 ATAAA
234623 TTTTTTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:240995 original size:16 final size:16
Alignment explanation
Indices: 240931--240995 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
240921 ACACCCACAT
240931 TGATTCGAACTCGAAA
1 TGATTCGAACTCGAAA
**
240947 TGACCCGAAC-CTGAAA
1 TGATTCGAACTC-GAAA
*
240963 TGA-TCAGAATTCGAAA
1 TGATTC-GAACTCGAAA
*
240979 TGATTCGAACTCAAAA
1 TGATTCGAACTCGAAA
240995 T
1 T
240996 TACTTGAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.05
16 34 0.87
17 3 0.08
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (16 bp):
TGATTCGAACTCGAAA
Found at i:244921 original size:22 final size:23
Alignment explanation
Indices: 244887--244931 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
244877 GGGATCGAAA
244887 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
244909 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
244932 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:245324 original size:11 final size:11
Alignment explanation
Indices: 245286--245326 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
245276 AAATTTAGGT
245286 AAAAAAGAAAG
1 AAAAAAGAAAG
*
245297 AAAGAAGATGAAG
1 AAAAAAGA--AAG
245310 AAAAAAGAAAG
1 AAAAAAGAAAG
245321 AAAAAA
1 AAAAAA
245327 AAATATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:245721 original size:2 final size:2
Alignment explanation
Indices: 245708--245744 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
245698 TTATTTTATT
*
245708 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
245745 TTTGAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:253178 original size:30 final size:31
Alignment explanation
Indices: 253138--253195 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
253128 GTACTGTGAC
*
253138 CTTTTCAAAGTCCACGACT-CAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCCA-TGGCATTTT
253169 CTTTT-AAAGTCCACAACTCCATGGCAT
1 CTTTTCAAAGTCCACAACTCCATGGCAT
253196 CCTTTTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCCATGGCATTTT
Found at i:253230 original size:46 final size:46
Alignment explanation
Indices: 253163--253251 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
253153 GACTCAGTGG
*
253163 CATTTTCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAGTTCA
1 CATTTTCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTTCA
*
253209 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CATTTTCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGT
253252 CCCCAACTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (46 bp):
CATTTTCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTTCA
Found at i:253258 original size:27 final size:27
Alignment explanation
Indices: 253215--253789 Score: 943
Period size: 27 Copynumber: 21.0 Consensus size: 27
253205 TTCACATTTT
253215 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
253243 CTTTTAAGTCCCCAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
253270 CTTTCAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
253297 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253324 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
253352 TTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253379 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253406 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
253433 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253460 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
253488 CTTTTAAGTCCACAACTCCGTGGCCCCC
1 CTTTTAAGTCCACAACTCCGTGG-CACC
253516 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253543 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
253571 CTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253598 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
253626 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253653 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
253681 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253708 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
253735 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
253762 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
253789 C
1 C
253790 ATTCCAAAGC
Statistics
Matches: 511, Mismatches: 30, Indels: 13
0.92 0.05 0.02
Matches are distributed among these distances:
27 354 0.69
28 156 0.31
29 1 0.00
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:253381 original size:55 final size:55
Alignment explanation
Indices: 253215--253786 Score: 940
Period size: 55 Copynumber: 10.5 Consensus size: 55
253205 TTCACATTTT
* *
253215 CTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCCCAACTTCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
253270 CTTTCAAGTCCACAACTCCGTGGCAT-TCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* *
253324 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
253379 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
253433 CTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCA-CC
**
253488 CTTTTAAGTCCACAACTCCGTGGCCCCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* *
253543 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
*
253598 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
253653 CTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
*
253708 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* *
253762 CTTTTAAATCCACAACTCTGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
253787 CCCATTCCAA
Statistics
Matches: 486, Mismatches: 25, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
54 218 0.45
55 222 0.46
56 46 0.09
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:253830 original size:32 final size:32
Alignment explanation
Indices: 253772--254755 Score: 1318
Period size: 32 Copynumber: 31.8 Consensus size: 32
253762 CTTTTAAATC
* * *
253772 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
253803 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
253835 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
253865 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
253895 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
253923 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
253951 CACAAGTCGGTGGCAATCTATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
253981 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254011 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254043 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
254075 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254107 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254139 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254170 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254202 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254234 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
254264 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254294 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254322 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
254350 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
254380 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254410 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254442 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254474 CACAAGTCGGTGGTAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254506 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254538 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
254569 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254601 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
254633 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254665 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
254697 CACAAGTCGGGGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** ** *
254729 TGCAAGTTAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
254756 TCACCATTTT
Statistics
Matches: 868, Mismatches: 64, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
28 113 0.13
29 23 0.03
30 136 0.16
31 80 0.09
32 516 0.59
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:253895 original size:28 final size:29
Alignment explanation
Indices: 253215--254698 Score: 823
Period size: 32 Copynumber: 50.6 Consensus size: 29
253205 TTCACATTTT
*
253215 CTTTT-AAAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * *
253243 CTTTT--AAGTCCCCAACTTCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* **
253270 C-TTTC-AAGTCCACAACTCCGTGGCATT
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* *
253297 CTTTT--AAGTCCACAACTCTGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* *
253324 CTTTT--AAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * *
253351 CTTTT-TAAGTCCACAACTCCGTGGCCCC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253379 CTTTT--AAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253406 CTTTT--AAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* *
253433 CTTTT--AAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253460 CTTTT--AAGTCCACAACTCCGTGGCATCC
1 CTTTTCAAAGTCCACAAGTCCGTGGCA-CC
* *
253488 CTTTT--AAGTCCACAACTCCGTGGCCCCC
1 CTTTTCAAAGTCCACAAGTCCGTGG-CACC
*
253516 CTTTT--AAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253543 CTTTT--AAGTCCACAACTCCGTGGCATCC
1 CTTTTCAAAGTCCACAAGTCCGTGGCA-CC
*
253571 CTTTT--AAGTCCAC-AGCTCCGTGGCATC
1 CTTTTCAAAGTCCACAAG-TCCGTGGCACC
*
253598 CTTTT--AAGTCCACAACTCCGTGGCATCC
1 CTTTTCAAAGTCCACAAGTCCGTGGCA-CC
* *
253626 CTTTT--AAGTCCACAACTCTGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253653 CTTTT-AAAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253681 CTTTT--AAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
*
253708 CTTTT--AAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* *
253735 CTTTT--AAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* *
253762 CTTTT-AAA-TCCACAACTCTGTGGCACC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * * *
253789 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
253821 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * * *
253853 CATTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
** *
253881 CTTTTCAAAGTCCACACAAGTTGGTGGCATC
1 CTTTTCAAAGT-C-CACAAGTCCGTGGCACC
* * *
253912 C-TTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * **
253940 C-TTTCAAAGCCCACAAGTCGGTGGCAAT
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* ** *
253968 CTATTTCAAAGCCCACAAGTTAGTGGCA-T
1 CT-TTTCAAAGTCCACAAGTCCGTGGCACC
* * * *
253997 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254029 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254061 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * * *
254093 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254125 CATTTCAAAGCCCACACAAGTCGGTGGCACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGCACC
* * *
254156 CATTTCAAAGCCCACATAAGTCGGTGGCAACC
1 CTTTTCAAAGTCCAC--AAGTCCGTGGC-ACC
* * * *
254188 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254220 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * * *
254252 CATTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
** *
254280 CTTTTCAAAGTCCACACAAGTTGGTGGCATC
1 CTTTTCAAAGT-C-CACAAGTCCGTGGCACC
* * *
254311 C-TTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * *
254339 C-TTTCAAAGCCCACAAGTCGGTGGCAATC
1 CTTTTCAAAGTCCACAAGTCCGTGGC-ACC
* * ** *
254368 CATTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTTCAAAGTCCACAAGTCCGTGGCACC
* * * *
254396 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254428 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * * *
254460 CATTTCAAAGCCCACACAAGTCGGTGGTAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGG-CACC
* * * *
254492 CATTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254524 CATTTCAAAGCCCACACAAGTCGGTGGCACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGCACC
* * *
254555 CATTTCAAAGCCCACATAAGTCGGTGGCAACC
1 CTTTTCAAAGTCCAC--AAGTCCGTGGC-ACC
* * *
254587 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254619 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
* * *
254651 CATTTCAAAGCCCACACAAGTCGGTGGCGACC
1 CTTTTCAAAG-TC-CACAAGTCCGTGGC-ACC
*
254683 CTTTTCAAAGCCCACA
1 CTTTTCAAAGTCCACA
254699 CAAGTCGGGG
Statistics
Matches: 1327, Mismatches: 83, Indels: 90
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.00
27 347 0.26
28 277 0.21
29 24 0.02
30 146 0.11
31 70 0.05
32 450 0.34
33 4 0.00
34 6 0.00
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (29 bp):
CTTTTCAAAGTCCACAAGTCCGTGGCACC
Found at i:254524 original size:399 final size:399
Alignment explanation
Indices: 253781--254703 Score: 1749
Period size: 399 Copynumber: 2.3 Consensus size: 399
253771 CCACAACTCT
253781 GTGGC-ACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
253845 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
66 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
*
253910 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCTATTTC
131 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
253975 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
196 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
254040 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
261 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
254105 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
326 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
254170 CATAAGTCG
391 CATAAGTCG
254179 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
254244 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
66 TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
254309 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
131 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
254374 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
196 AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
254439 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGTAACCCATTCCAAAGCC
261 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
254504 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
326 CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
254569 CATAAGTCG
391 CATAAGTCG
*
254578 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
* * *
254643 TGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCGACCCTTTTCAAAGCCCACACAAGT
66 TGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCACACAAGT
254704 CGGGGGCAAC
Statistics
Matches: 514, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
398 5 0.01
399 473 0.92
400 2 0.00
401 13 0.03
402 1 0.00
403 20 0.04
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (399 bp):
GTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
TGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCA
TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCAATCCATTTC
AAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCC
CACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCA
CATAAGTCG
Found at i:254839 original size:45 final size:47
Alignment explanation
Indices: 254788--254906 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 47
254778 GTCCGATATT
*
254788 GCTGGCCTTGAATCAGCATATTGG-CACCTTT-CTAAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
* * * *
254833 GCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTC
1 GCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCTAAGCCCAATGTC
* *
254882 GCTGACCTTGAAAT-GGCACATTGGC
1 GCTGGCCTTG-AATCAGCACATTGGC
254907 ATTCCTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 22 0.36
47 6 0.10
48 1 0.02
49 30 0.49
50 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (47 bp):
GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
Found at i:255624 original size:22 final size:23
Alignment explanation
Indices: 255590--255634 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
255580 AGGGATCGAA
255590 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
255612 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
255635 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:256027 original size:11 final size:11
Alignment explanation
Indices: 255989--256029 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
255979 AAATTTAGGT
255989 AAAAAAGAAAG
1 AAAAAAGAAAG
*
256000 AAAGAAGATGAAG
1 AAAAAAGA--AAG
256013 AAAAAAGAAAG
1 AAAAAAGAAAG
256024 AAAAAA
1 AAAAAA
256030 AAATATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:256424 original size:2 final size:2
Alignment explanation
Indices: 256411--256445 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
256401 TTATTTTATT
*
256411 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
256446 TTTGAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259832 original size:22 final size:21
Alignment explanation
Indices: 259802--259854 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
259792 ACCATAACAA
*
259802 AAAAAAAAACTACAAATTAATG
1 AAAACAAAA-TACAAATTAATG
** *
259824 AAAACAAAATAGTAGTTAATG
1 AAAACAAAATACAAATTAATG
259845 AAAACGAAAA
1 AAAAC-AAAA
259855 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.66, C:0.08, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAACAAAATACAAATTAATG
Found at i:260268 original size:17 final size:18
Alignment explanation
Indices: 260248--260282 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
260238 TATTTATAAG
260248 TAAT-TATATTTTAAAAA
1 TAATATATATTTTAAAAA
*
260265 TAATATATTTTTTAAAAA
1 TAATATATATTTTAAAAA
260283 AACTTTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATATATTTTAAAAA
Found at i:260271 original size:16 final size:16
Alignment explanation
Indices: 260230--260275 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
260220 AAAATTAATG
260230 AAAATAA-ATA-TTTA
1 AAAATAATATATTTTA
* *
260244 TAAGTAATTATATTTTA
1 AAAATAA-TATATTTTA
260261 AAAATAATATATTTT
1 AAAATAATATATTTT
260276 TTAAAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.20
16 11 0.44
17 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAAATAATATATTTTA
Found at i:261449 original size:32 final size:32
Alignment explanation
Indices: 261407--261479 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
261397 GATTTGAACT
*
261407 CGAAACAACCCGAACCCGAAATGA-CCAAAAC
1 CGAAATAACCCGAACCCGAAATGATCCAAAAC
* * * *
261438 CTGAAATAACCCGAATCTGAAATGATCCGAATC
1 C-GAAATAACCCGAACCCGAAATGATCCAAAAC
261471 CGAAATAAC
1 CGAAATAAC
261480 TTGAACTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.03
32 28 0.80
33 6 0.17
ACGTcount: A:0.45, C:0.29, G:0.14, T:0.12
Consensus pattern (32 bp):
CGAAATAACCCGAACCCGAAATGATCCAAAAC
Found at i:261457 original size:16 final size:16
Alignment explanation
Indices: 261438--261479 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
261428 TGACCAAAAC
261438 CTGAAATAACCCGAAT
1 CTGAAATAACCCGAAT
* *
261454 CTGAAATGATCCGAAT
1 CTGAAATAACCCGAAT
*
261470 CCGAAATAAC
1 CTGAAATAAC
261480 TTGAACTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (16 bp):
CTGAAATAACCCGAAT
Found at i:262031 original size:2 final size:2
Alignment explanation
Indices: 262024--262053 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
262014 GGAATTGCTA
*
262024 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
262054 TTCTCACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:264193 original size:265 final size:265
Alignment explanation
Indices: 263831--264351 Score: 762
Period size: 265 Copynumber: 2.0 Consensus size: 265
263821 TCCAAAGAGA
* * * *
263831 ATGACAACAAATCTTGAAGAACAACCAGAAAAGAAGAAGAATTACAAAGTATAGCAGCAAAAAAA
1 ATGACAACAAATCTTGAAAAACAACCAGAAAAGAAGAAGAATAAAAAAATATAGCAGCAAAAAAA
* *
263896 ACCAAGAAGGGAAATTAGAAAACCTATAAAGTATGTAGACTTTATTGAGGTTATTGA-TGTTAAT
66 ACCAAGAAGGGAAATCAGAAAACCTATAAAGTATGCAGACTTTATTGAGGTTATT-ATTGTTAAT
* *
263960 CCTATTGCTTATGCCTTAGTAGTTGTAGAGAGCATTATTTTTGATGAACCAAGGTCATATAAAAA
130 CATATTGCTTATGCCTTAGTAGTTGTAGAGAGCATTATTTCTGATGAACCAAGGTCATATAAAAA
* * * *** *
264025 GGCAGTACAGAGT-AAAAAAGCAATTAAAATGATTGATTGGTATGAATGAAGAGATGTAGTCTCT
195 GGCAATACAGAGTAAAAAAAAC-ATCAAAATGATTGATTACCATGAATGAAGAGATGCAGTCTCT
264089 AAAGATG
259 AAAGATG
*
264096 ATGACAACAAATCTT-AAAATACAACCTAGAAAAGAAGAAGAATAAAAAAATATAGCAGC-AAAG
1 ATGACAACAAATCTTGAAAA-ACAACC-AGAAAAGAAGAAGAATAAAAAAATATAGCAGCAAAAA
* * * *
264159 AAACCAAGAAGGGTAATCAGAAAATCTCTAAAGTATGCAGACTTTATTGTGGTTATTATTGTTAA
64 AAACCAAGAAGGGAAATCAGAAAACCTATAAAGTATGCAGACTTTATTGAGGTTATTATTGTTAA
* * *
264224 TCATGTTGCTTATGCCTTAGTAGTTGTAGAGAGCATTGTTTCTGATGAACCAAGGTCATATAAAG
129 TCATATTGCTTATGCCTTAGTAGTTGTAGAGAGCATTATTTCTGATGAACCAAGGTCATATAAAA
*
264289 AGGCAATACAGAGTAAAAAAAACATCAAAATGGTTGATTACCATGAATGAAGAGATGCAGTCT
194 AGGCAATACAGAGTAAAAAAAACATCAAAATGATTGATTACCATGAATGAAGAGATGCAGTCT
264352 ATTACAAAAA
Statistics
Matches: 228, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
264 4 0.02
265 188 0.82
266 36 0.16
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (265 bp):
ATGACAACAAATCTTGAAAAACAACCAGAAAAGAAGAAGAATAAAAAAATATAGCAGCAAAAAAA
ACCAAGAAGGGAAATCAGAAAACCTATAAAGTATGCAGACTTTATTGAGGTTATTATTGTTAATC
ATATTGCTTATGCCTTAGTAGTTGTAGAGAGCATTATTTCTGATGAACCAAGGTCATATAAAAAG
GCAATACAGAGTAAAAAAAACATCAAAATGATTGATTACCATGAATGAAGAGATGCAGTCTCTAA
AGATG
Found at i:266106 original size:26 final size:26
Alignment explanation
Indices: 266050--266106 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
266040 TATAGAGATA
*
266050 GGATTGATAAAGTTCAACTTTATATG
1 GGATTAATAAAGTTCAACTTTATATG
* *
266076 AGATTAATAAAGTTCAACTTTATCTG
1 GGATTAATAAAGTTCAACTTTATATG
266102 GGATT
1 GGATT
266107 CTAAATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (26 bp):
GGATTAATAAAGTTCAACTTTATATG
Found at i:273182 original size:6 final size:6
Alignment explanation
Indices: 273167--273197 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
273157 TGGTTTTCAG
*
273167 TTTTCA TTTTCC TTTTCC TTTTCC TTTTCC T
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC T
273198 GTAACATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCC
Found at i:277422 original size:13 final size:13
Alignment explanation
Indices: 277393--277440 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
277383 GAGGTGAGAC
277393 AAGAAAAATACAAA
1 AAGAAAAA-ACAAA
277407 AAGAAAAAA-AATA
1 AAGAAAAAACAA-A
*
277420 AAGAAAAAATAAA
1 AAGAAAAAACAAA
277433 AAGGAAAA
1 AA-GAAAA
277441 GGAAATAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.06
13 14 0.45
14 15 0.48
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.06
Consensus pattern (13 bp):
AAGAAAAAACAAA
Found at i:279318 original size:5 final size:5
Alignment explanation
Indices: 279308--279341 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
279298 ATACGGCATA
279308 AATAT AATAT AAATAT AAATAT AATAT AATAT AA
1 AATAT AATAT -AATAT -AATAT AATAT AATAT AA
279342 ACGTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:279321 original size:11 final size:11
Alignment explanation
Indices: 279305--279342 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
279295 TAGATACGGC
279305 ATAAATATAAT
1 ATAAATATAAT
279316 ATAAATATAA-
1 ATAAATATAAT
279326 ATATAATATAAT
1 ATA-AATATAAT
279338 ATAAA
1 ATAAA
279343 CGTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:279325 original size:17 final size:16
Alignment explanation
Indices: 279305--279342 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
279295 TAGATACGGC
279305 ATAAATATAATATAAAT
1 ATAAATATAATAT-AAT
279322 ATAAATATAATATAAT
1 ATAAATATAATATAAT
279338 ATAAA
1 ATAAA
279343 CGTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATATAATATAAT
Found at i:279793 original size:9 final size:8
Alignment explanation
Indices: 279686--279793 Score: 60
Period size: 8 Copynumber: 13.1 Consensus size: 8
279676 TGTATTATAA
279686 TAATATTT
1 TAATATTT
*
279694 AAAATATTT
1 -TAATATTT
279703 T-ATATTT
1 TAATATTT
279710 ATATATATTT
1 -TA-ATATTT
*
279720 TAATAATT
1 TAATATTT
*
279728 TAATAATT
1 TAATATTT
*
279736 T-ATATTA
1 TAATATTT
*
279743 TATAGATTT
1 TA-ATATTT
*
279752 TAAAATATT
1 TAATAT-TT
* *
279761 T-GTATAT
1 TAATATTT
279768 TAATATTT
1 TAATATTT
*
279776 TTATATTT
1 TAATATTT
279784 TAATTATTT
1 TAA-TATTT
279793 T
1 T
279794 TTATATATAT
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
7 13 0.17
8 33 0.43
9 24 0.32
10 6 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TAATATTT
Found at i:279818 original size:14 final size:14
Alignment explanation
Indices: 279799--279838 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
279789 ATTTTTTATA
279799 TATATTTATATAAT
1 TATATTTATATAAT
* *
279813 TATATTTTTATTAT
1 TATATTTATATAAT
*
279827 TAAATTTATATA
1 TATATTTATATA
279839 CAAGCGATGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTTATATAAT
Found at i:279825 original size:56 final size:56
Alignment explanation
Indices: 279702--279825 Score: 125
Period size: 56 Copynumber: 2.2 Consensus size: 56
279692 TTAAAATATT
*
279702 TTATATTTATA-T-ATATTTTAATAATTTAATAATTTATATTATATAGATTTTAAA
1 TTATATTTTTATTAATATTTTAATAATTTAATAATTTATATTATATAGATTTTAAA
* * * *
279756 --ATATTTGTATATTAATATTTTTATATTTTAATTATTT-T-TTATATATATTTATATAA
1 TTATATTT-T-TATTAATATTTTAATAATTTAATAATTTATATTATATAGATTT-TA-AA
279812 TTATATTTTTATTA
1 TTATATTTTTATTA
279826 TTAAATTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
52 6 0.11
54 13 0.23
55 4 0.07
56 27 0.47
57 1 0.02
58 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (56 bp):
TTATATTTTTATTAATATTTTAATAATTTAATAATTTATATTATATAGATTTTAAA
Found at i:281042 original size:24 final size:24
Alignment explanation
Indices: 280987--281044 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
280977 AGTAGTTTGT
* *
280987 TTTTTCAAAATTATTTTATTAATTA
1 TTTTT-AAAAATATTTTATTAATAA
281012 TTTTTAAAAATATTTTATTAA-AA
1 TTTTTAAAAATATTTTATTAATAA
281035 TTTATTAAAA
1 TTT-TTAAAA
281045 GATAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 4 0.13
24 21 0.70
25 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTAAAAATATTTTATTAATAA
Found at i:281717 original size:18 final size:16
Alignment explanation
Indices: 281668--281719 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
281658 AATTTAAATT
281668 ATTAAATTTAATTT-A
1 ATTAAATTTAATTTAA
281683 ATTAAATTTAAACTTTAA
1 ATTAAATTT-AA-TTTAA
281701 ATTAAATTTTATATTTAA
1 ATTAAA-TTTA-ATTTAA
281719 A
1 A
281720 ATTTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.28
16 2 0.06
17 3 0.09
18 14 0.44
19 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATTTAATTTAA
Found at i:281723 original size:7 final size:6
Alignment explanation
Indices: 281658--281719 Score: 51
Period size: 5 Copynumber: 10.3 Consensus size: 6
281648 TTTAAATAAT
281658 AATTTA AATTATTA AATTT- AATTT- AA-TTA AATTTA AACTTTA AA-TTA
1 AATTTA AA-T-TTA AATTTA AATTTA AATTTA AATTTA AA-TTTA AATTTA
*
281705 AATTTTA TATTTA AA
1 AA-TTTA AATTTA AA
281720 ATTTTTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 2 0.04
5 14 0.30
6 14 0.30
7 12 0.26
8 5 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:281782 original size:2 final size:2
Alignment explanation
Indices: 281775--281813 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
281765 CAAACAGCTC
*
281775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
281814 CATTTCAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:281988 original size:52 final size:52
Alignment explanation
Indices: 281882--281989 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 52
281872 TCTGTCTGAT
* * * * * *
281882 TAAAATAATATTAAAAAATTTAAATAATTAATTAATTATTTTTTAAAGTTTA
1 TAAAAAAATATTAAAAAATATAAATAATTAATTAATTATTTATAAAAATCTA
*
281934 TAAAAAAATATATAAAAAATATAATTAA-TAATTAATT-TTTAATAAAAATCTA
1 TAAAAAAATAT-TAAAAAATATAAATAATTAATTAATTATTT-ATAAAAATCTA
281986 TAAA
1 TAAA
281990 TATTATAAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
51 3 0.06
52 30 0.64
53 14 0.30
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (52 bp):
TAAAAAAATATTAAAAAATATAAATAATTAATTAATTATTTATAAAAATCTA
Found at i:282382 original size:36 final size:35
Alignment explanation
Indices: 282290--282385 Score: 86
Period size: 36 Copynumber: 2.7 Consensus size: 35
282280 ATCTTTTTAT
* * ** *
282290 TATAAAATAATATTATTATTTTTTTCAATAGTAACA
1 TATAAATTAAT-TTAATATTTTTTTCAATAAAAAAA
* * *
282326 TAAAAATTTTATGTAA-ATTTTTATTCAATAAAAAAA
1 TATAAA-TTAATTTAATATTTTT-TTCAATAAAAAAA
282362 TATAAATTAATTTAATATTTTTTT
1 TATAAATTAATTTAATATTTTTTT
282386 ATTTATACAA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
35 15 0.33
36 28 0.61
37 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (35 bp):
TATAAATTAATTTAATATTTTTTTCAATAAAAAAA
Found at i:282583 original size:22 final size:20
Alignment explanation
Indices: 282547--282586 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
282537 ATTGTTAATT
282547 TATTTTTAAAATTTATTAAA
1 TATTTTTAAAATTTATTAAA
282567 TATTATTTATAAATTTATTA
1 TATT-TTTA-AAATTTATTA
282587 TAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTAAAATTTATTAAA
Found at i:282598 original size:22 final size:22
Alignment explanation
Indices: 282551--282601 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
282541 TTAATTTATT
* *
282551 TTTA-AAATTTATTAAATATTA
1 TTTATAAATTTATTAAAAAATA
282572 TTTATAAATTTATTATAAAAATA
1 TTTATAAATTTATTA-AAAAATA
282595 -TTATAAA
1 TTTATAAA
282602 AATTGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATAAATTTATTAAAAAATA
Found at i:282626 original size:13 final size:14
Alignment explanation
Indices: 282608--282637 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
282598 TAAAAATTGA
282608 TATTTTT-ATTTAT
1 TATTTTTAATTTAT
282621 TATTTTTAATTTAT
1 TATTTTTAATTTAT
282635 TAT
1 TAT
282638 AAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTAATTTAT
Found at i:282854 original size:18 final size:18
Alignment explanation
Indices: 282831--282880 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
282821 TTAATATAAA
282831 TTTATTAATTTTTTTATT
1 TTTATTAATTTTTTTATT
*
282849 TTTATT-TTTATTTTTATT
1 TTTATTAATT-TTTTTATT
* *
282867 ATTATAAATTTTTT
1 TTTATTAATTTTTT
282881 AATTGAGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTAATTTTTTTATT
Found at i:282856 original size:5 final size:6
Alignment explanation
Indices: 282841--282871 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
282831 TTTATTAATT
*
282841 TTTTTA TTTTTA TTTTTA TTTTTA TTATTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
282872 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:283376 original size:11 final size:11
Alignment explanation
Indices: 283356--283406 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
283346 TAATTTTAAT
*
283356 ATATATATATA
1 ATATACATATA
283367 ATATACATATA
1 ATATACATATA
* *
283378 A-AGACATCTA
1 ATATACATATA
* *
283388 ATATATATCTA
1 ATATACATATA
283399 ATATACAT
1 ATATACAT
283407 TAAAAATATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 8 0.24
11 25 0.76
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATACATATA
Found at i:283621 original size:19 final size:19
Alignment explanation
Indices: 283597--283667 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
283587 AATATACATT
283597 AAAAATATATGAGAAAATA
1 AAAAATATATGAGAAAATA
* * ** * *
283616 AAAAATATTTAAGGGATTT
1 AAAAATATATGAGAAAATA
*
283635 AAAAATATCTGAGAAAATA
1 AAAAATATATGAGAAAATA
*
283654 TAAAATATATGAGA
1 AAAAATATATGAGA
283668 TTTTAGTATG
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.27
Consensus pattern (19 bp):
AAAAATATATGAGAAAATA
Found at i:283960 original size:116 final size:116
Alignment explanation
Indices: 283401--284206 Score: 1222
Period size: 115 Copynumber: 7.0 Consensus size: 116
283391 TATATCTAAT
* *
283401 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATATAATTTTGGTGTA-C
1 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
* * * *
283465 AATTAATATACATTAAGAATATATGAGAAAATAAAAAATATTTAAGGGGTA
66 TATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
* * * *
283516 ATACCTTAAAAATACCTTAGAAAATAAAAAAAATATATGAGATTTTAGTATGTGATTTTGGTGTA
1 ATACATTAAAAATATCTGAGAAAAT--ATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTA
*
283581 TCTATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGG---
64 CCTATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
*
283631 AT---TTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTCTGGTGTACC
1 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
**
283693 TATCCCTATACATT-AAAATATATGAGAAAATAAAAAATATTTAAGGGATA
66 TATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
* * *
283743 ATACATTAAAAATATCTGAAAAAATATAAAATATATGAGATTTTAGTATGTTATTCTGGTGTACC
1 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
*
283808 TATCAATATACATTAAAAACATATGAGAAAATAAAAAATATTTAAGGGATA
66 TATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
*
283859 ATACATTAAAAATA-CATGAGAAAATA-AAAAAATATGAGATTTTAGTATGTGATTTTGGTGTAC
1 ATACATTAAAAATATC-TGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTAC
* * *
283922 CTATCAATATACATTAAAAACATATGAGAAAATAAAAAATATTTAAAGGAGA
65 CTATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
*
283974 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTCAGTATGTGATTTTGGTGTACC
1 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
* *
284039 TACCAATATACATTAAAAATATATGATAAAATAAAAAAATATTTAAGAGG-TA
66 TATCAATATACATTAAAAATATATGAGAAAAT-AAAAAATATTTAAG-GGATA
** *
284091 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGAAATTTTGATGTACC
1 ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
*
284156 TATCAATATACATTAAAAATATATGATAAAAT-AAAAATATTTAAGGGATA
66 TATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
284206 A
1 A
284207 GACAATAATT
Statistics
Matches: 636, Mismatches: 39, Indels: 32
0.90 0.06 0.05
Matches are distributed among these distances:
109 33 0.05
110 49 0.08
112 20 0.03
114 2 0.00
115 219 0.34
116 124 0.19
117 141 0.22
118 48 0.08
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (116 bp):
ATACATTAAAAATATCTGAGAAAATATAAAATATATGAGATTTTAGTATGTGATTTTGGTGTACC
TATCAATATACATTAAAAATATATGAGAAAATAAAAAATATTTAAGGGATA
Found at i:284365 original size:2 final size:2
Alignment explanation
Indices: 284346--284386 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
284336 TTATTATTTT
* *
284346 TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
284387 AGCAATCCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:284915 original size:23 final size:23
Alignment explanation
Indices: 284880--284923 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
284870 TTAATAAATT
284880 TTAATTTTATAATATTTGTTATCG
1 TTAATTTTATAAT-TTTGTTATCG
*
284904 TTAA-TTTATAATTTTTTTAT
1 TTAATTTTATAATTTTGTTAT
284924 ATTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTAATTTTATAATTTTGTTATCG
Found at i:284943 original size:21 final size:20
Alignment explanation
Indices: 284911--284953 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
284901 TCGTTAATTT
* * *
284911 ATAATTTTTTTATATTAAAA
1 ATAATTTATTTAGATAAAAA
284931 ATAATTATATTTAGATAAAAA
1 ATAATT-TATTTAGATAAAAA
284952 AT
1 AT
284954 TTAAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAATTTATTTAGATAAAAA
Found at i:286403 original size:20 final size:20
Alignment explanation
Indices: 286360--286396 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
286350 ATCAAAACTT
*
286360 TTAATAATATTTTTATGTGA
1 TTAATAATATTTCTATGTGA
286380 TTAATAATA-TTCTATGT
1 TTAATAATATTTCTATGT
286397 TTATTAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTAATAATATTTCTATGTGA
Found at i:286446 original size:21 final size:21
Alignment explanation
Indices: 286422--286462 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
286412 TATTTTTATA
286422 TAAAT-TTAATTATAAAATATC
1 TAAATATTAATT-TAAAATATC
286443 TAAATATTAATTTAAAATAT
1 TAAATATTAATTTAAAATAT
286463 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATATTAATTTAAAATATC
Found at i:286529 original size:16 final size:16
Alignment explanation
Indices: 286468--286530 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
286458 AATATTTTTT
286468 AATATTTTAA-TAT-A
1 AATATTTTAAGTATAA
* *
286482 AAT-TATTATGTATTAA
1 AATATTTTAAGTA-TAA
* *
286498 AATTTATTTAAATATAA
1 AATAT-TTTAAGTATAA
286515 AATATTTTAAGTATAA
1 AATATTTTAAGTATAA
286531 TTTTAATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 1 0.03
16 14 0.38
17 8 0.22
18 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATATTTTAAGTATAA
Found at i:287151 original size:35 final size:34
Alignment explanation
Indices: 287086--287155 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 34
287076 ATATTTAAAA
**
287086 TTTATTTAAATTATTATTTAATCATAAAAATTATT
1 TTTATTTAAATTATTATAAAATCATAAAAA-TATT
287121 TTTATTTAAATTTAATTATAAAAT-AT-AAAATATT
1 TTTATTTAAA-TT-ATTATAAAATCATAAAAATATT
287155 T
1 T
287156 ATATACTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 5 0.16
35 14 0.45
36 4 0.13
37 8 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (34 bp):
TTTATTTAAATTATTATAAAATCATAAAAATATT
Found at i:287339 original size:19 final size:18
Alignment explanation
Indices: 287315--287352 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
287305 ATGCCCATGT
287315 TTTTTAATGGAAAAATCAA
1 TTTTTAAT-GAAAAATCAA
*
287334 TTTTTAATGTAAAATCAA
1 TTTTTAATGAAAAATCAA
287352 T
1 T
287353 CATTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTTTAATGAAAAATCAA
Found at i:287910 original size:14 final size:14
Alignment explanation
Indices: 287891--287919 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
287881 ATAAAAAATC
287891 AAAAAATATTTTTA
1 AAAAAATATTTTTA
287905 AAAAAATATTTTTA
1 AAAAAATATTTTTA
287919 A
1 A
287920 TTTTATTTAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATATTTTTA
Found at i:288405 original size:20 final size:21
Alignment explanation
Indices: 288382--288427 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
288372 TACTAATATT
*
288382 AAAAATATATTA-AAAAAATA
1 AAAAATATAATATAAAAAATA
*
288402 AAAAATATAATATTAAAAATA
1 AAAAATATAATATAAAAAATA
288423 AAAAA
1 AAAAA
288428 CATTTTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATATAATATAAAAAATA
Found at i:290506 original size:120 final size:121
Alignment explanation
Indices: 290286--290527 Score: 405
Period size: 120 Copynumber: 2.0 Consensus size: 121
290276 CTTTCGACAA
* * *
290286 GCAAATTATTCCAGTTAGAATGATCGCGAAAAAGATATATATCCACGCCATCTTGTCAACTTTGA
1 GCAAATTATTCCAGTTAGAATGATCGAGAAAAAGATATATA-CAACGCAATCTTGTCAACTTTGA
* *
290351 TTAAAAGGTTAAAATCTAAATTATGGTTAAGGACATTAAGTGATTAGCGGAGCTAAT
65 TTAAAAGATTAAAATCTAAATGATGGTTAAGGACATTAAGTGATTAGCGGAGCTAAT
*
290408 GCAAATTATTTCAGTTAGAATGATCGAGAAAAAGATATATA-AACGCAATCTTGTCAACTTTGAT
1 GCAAATTATTCCAGTTAGAATGATCGAGAAAAAGATATATACAACGCAATCTTGTCAACTTTGAT
*
290472 TAAAAGATTAAAATCTAAATGATGGTTAATGACATTAAGTGATTAGCGGAGCTAAT
66 TAAAAGATTAAAATCTAAATGATGGTTAAGGACATTAAGTGATTAGCGGAGCTAAT
290528 TTAGAATATT
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
120 74 0.65
122 39 0.35
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (121 bp):
GCAAATTATTCCAGTTAGAATGATCGAGAAAAAGATATATACAACGCAATCTTGTCAACTTTGAT
TAAAAGATTAAAATCTAAATGATGGTTAAGGACATTAAGTGATTAGCGGAGCTAAT
Found at i:290661 original size:14 final size:14
Alignment explanation
Indices: 290629--290669 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
290619 AAAAATTTTA
290629 TAAATAATAT-AAA-
1 TAAA-AATATAAAAT
290642 TAAAAATATAAAAT
1 TAAAAATATAAAAT
*
290656 TAAAAAAATAAAAT
1 TAAAAATATAAAAT
290670 CAATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 13 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAAAATATAAAAT
Found at i:290965 original size:28 final size:28
Alignment explanation
Indices: 290933--290988 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
290923 AAATTTTTTC
290933 AAAAATTTT-TATTTATAAAAT-TTAAAAT
1 AAAAATTTTAT-TTTA-AAAATATTAAAAT
290961 AAAAATTTTATTTTAAAAATATTAAAAT
1 AAAAATTTTATTTTAAAAATATTAAAAT
290989 TTTTTCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.19
28 20 0.77
29 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAAATTTTATTTTAAAAATATTAAAAT
Found at i:291172 original size:2 final size:2
Alignment explanation
Indices: 291167--291220 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
291157 ATCTACATTG
291167 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
291209 CT CT CT CT CT CT
1 CT CT CT CT CT CT
291221 TCTTTTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:293373 original size:16 final size:16
Alignment explanation
Indices: 293349--293379 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
293339 ATATATTTTT
293349 TATTAATTATTTATTA
1 TATTAATTATTTATTA
*
293365 TATTTATTATTTATT
1 TATTAATTATTTATT
293380 TACTATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTAATTATTTATTA
Found at i:293423 original size:16 final size:17
Alignment explanation
Indices: 293389--293424 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
293379 TTACTATTAA
293389 AAAATTATTTTATATTT
1 AAAATTATTTTATATTT
293406 AAAATTATTTTA-ATTT
1 AAAATTATTTTATATTT
293422 AAA
1 AAA
293425 TTAATTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATTATTTTATATTT
Found at i:295159 original size:24 final size:22
Alignment explanation
Indices: 295132--295176 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
295122 GGAAAATCAT
*
295132 AATAACAATAAAATAATTAATATG
1 AATAAAAATAAAA-AA-TAATATG
295156 AATAAAAATAAAAAATAATAT
1 AATAAAAATAAAAAATAATAT
295177 TATTATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 12 0.60
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAAAAATAAAAAATAATATG
Found at i:297300 original size:20 final size:21
Alignment explanation
Indices: 297260--297302 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
297250 TTTTATTCTC
* *
297260 AATTTATAATTTTTTTATAAA
1 AATTTATAATATTTATATAAA
297281 AATTTA-AATATTTATATAAA
1 AATTTATAATATTTATATAAA
297301 AA
1 AA
297303 AATCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTATAATATTTATATAAA
Done.