Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 116 of 126
Found at i:34768704 original size:6 final size:6
Alignment explanation
Indices: 34768688--34768727 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
34768678 CTCTTACCCT
* *
34768688 AGAGCC CGAGCT AGAGCC AGAGCC AGAGCC AGAGCC AGAG
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAG
34768728 GAAGAGGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.30, G:0.35, T:0.03
Consensus pattern (6 bp):
AGAGCC
Found at i:34769340 original size:15 final size:14
Alignment explanation
Indices: 34769290--34769346 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
34769280 ATAAACCTAA
* *
34769290 AACCCTAAACTATT
1 AACCCTAAAATACT
34769304 AA-CCTAAAATACT
1 AACCCTAAAATACT
* *
34769317 AACCTTAAAATTCT
1 AACCCTAAAATACT
34769331 AAACCCT-AAATACT
1 -AACCCTAAAATACT
34769345 AA
1 AA
34769347 ATTTCAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 13 0.37
14 17 0.49
15 5 0.14
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTAAAATACT
Found at i:34769347 original size:22 final size:22
Alignment explanation
Indices: 34769322--34769363 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34769312 ATACTAACCT
*
34769322 TAAAATTCTAAACCCTAAATAC
1 TAAAATTCAAAACCCTAAATAC
* *
34769344 TAAATTTCAAAACCTTAAAT
1 TAAAATTCAAAACCCTAAAT
34769364 TCATAACCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATTCAAAACCCTAAATAC
Found at i:34769366 original size:14 final size:14
Alignment explanation
Indices: 34769344--34769457 Score: 57
Period size: 14 Copynumber: 7.8 Consensus size: 14
34769334 CCCTAAATAC
34769344 TAAATTTCAAAACCT
1 TAAA-TTCAAAACCT
* *
34769359 TAAATTCATAACCC
1 TAAATTCAAAACCT
* * *
34769373 TATATTTAAAATCT
1 TAAATTCAAAACCT
** *
34769387 TAAACCCTAAACCTT
1 TAAATTCAAAACC-T
* *
34769402 TAAAATTCAATACTT
1 T-AAATTCAAAACCT
*
34769417 TTAATTCAAAACTCT
1 TAAATTCAAAAC-CT
* *
34769432 TAAATTTGAAACCCT
1 TAAA-TTCAAAACCT
*
34769447 AAAATTCAAAA
1 TAAATTCAAAA
34769458 TATACCCTTT
Statistics
Matches: 68, Mismatches: 27, Indels: 9
0.65 0.26 0.09
Matches are distributed among these distances:
14 38 0.56
15 17 0.25
16 13 0.19
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (14 bp):
TAAATTCAAAACCT
Found at i:34775364 original size:20 final size:20
Alignment explanation
Indices: 34775341--34775418 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
34775331 ATTTAATAAT
34775341 ATTTTTTATATATTTTTATG
1 ATTTTTTATATATTTTTATG
* * *
34775361 ATTTTTAATGA-AATTTTATT
1 ATTTTTTAT-ATATTTTTATG
* *
34775381 ATTTTTTATGTTTTTTTA-G
1 ATTTTTTATATATTTTTATG
* *
34775400 AATTTTTATATGTTTTTAT
1 ATTTTTTATATATTTTTAT
34775419 AAAATTATAT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
19 15 0.34
20 28 0.64
21 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (20 bp):
ATTTTTTATATATTTTTATG
Found at i:34775369 original size:29 final size:29
Alignment explanation
Indices: 34775295--34775418 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 29
34775285 ATTAGGGTTT
* * *
34775295 TTTTTATCATTTTT-ATAAGTTTATATAAA
1 TTTTTATGATTTTTAATAA-TTTTTATATA
* * *
34775324 TTTTAAT-ATTTAATAATATTTTTTATATA
1 TTTTTATGATTT-TTAATAATTTTTATATA
*
34775353 TTTTTATGATTTTTAATGAAATTTTAT-TA
1 TTTTTATGATTTTTAAT-AATTTTTATATA
* * * *
34775382 TTTTTTATGTTTTTTTAGAATTTTTATATG
1 -TTTTTATGATTTTTAATAATTTTTATATA
34775412 TTTTTAT
1 TTTTTAT
34775419 AAAATTATAT
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
28 4 0.05
29 42 0.56
30 29 0.39
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTTTATGATTTTTAATAATTTTTATATA
Found at i:34775424 original size:21 final size:20
Alignment explanation
Indices: 34775381--34775424 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
34775371 AAATTTTATT
* *
34775381 ATTTTTTATGTTTTTTTAGA
1 ATTTTTTATGTTTTTATAAA
34775401 ATTTTTATATGTTTTTATAAA
1 ATTTTT-TATGTTTTTATAAA
34775422 ATT
1 ATT
34775425 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
ATTTTTTATGTTTTTATAAA
Found at i:34775457 original size:25 final size:24
Alignment explanation
Indices: 34775419--34775467 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
34775409 ATGTTTTTAT
* *
34775419 AAAATTATATATATATTTGAATATA
1 AAAATTATAAATAT-TTTAAATATA
*
34775444 AAAATTTTAAATATTTTAAATATA
1 AAAATTATAAATATTTTAAATATA
34775468 CTTTATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AAAATTATAAATATTTTAAATATA
Found at i:34777069 original size:14 final size:15
Alignment explanation
Indices: 34777050--34777092 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
34777040 GAATGTGAAA
34777050 ATGATTT-TGTATTG
1 ATGATTTATGTATTG
*
34777064 ATGATTTAGTGTATTT
1 ATGATTTA-TGTATTG
34777080 ATGATATTATGTA
1 ATGAT-TTATGTA
34777093 GCTAACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (15 bp):
ATGATTTATGTATTG
Found at i:34778430 original size:21 final size:21
Alignment explanation
Indices: 34778406--34778446 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34778396 TCAATACCTT
*
34778406 TATTAATTCTACCGGTACAAA
1 TATTAATTCTACCGATACAAA
* *
34778427 TATTATTTTTACCGATACAA
1 TATTAATTCTACCGATACAA
34778447 GTCATGCAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (21 bp):
TATTAATTCTACCGATACAAA
Found at i:34779312 original size:52 final size:52
Alignment explanation
Indices: 34779154--34779386 Score: 308
Period size: 52 Copynumber: 4.5 Consensus size: 52
34779144 TTTCATTTAA
* * ** * * * *
34779154 TACTCACGATGACA-TATAGTCATCGGACCCCTTGTTTCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGAACCCTTTAATCCATAAAGG-ATTCATT
* * * * *
34779207 TACTCACGATGACACTGAGTCATCGGA-CCTTTAATTCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
*
34779258 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
34779310 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
34779362 TACTCACGATGACACTTAGTCATCG
1 TACTCACGATGACACTTAGTCATCG
34779387 GACTCTTTCG
Statistics
Matches: 162, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
51 31 0.19
52 106 0.65
53 24 0.15
54 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
Found at i:34782207 original size:11 final size:11
Alignment explanation
Indices: 34782191--34782220 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
34782181 TTTTTAACAT
34782191 TTTAAATTAAA
1 TTTAAATTAAA
34782202 TTTAAATTAAA
1 TTTAAATTAAA
34782213 TTTAAATT
1 TTTAAATT
34782221 TTCTCGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:34790221 original size:19 final size:20
Alignment explanation
Indices: 34790197--34790240 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
34790187 TATAGAATAA
*
34790197 TAAAAAAAATAAAAGA-ATT
1 TAAAAAAAATAAAAAATATT
**
34790216 TAAAAATTATAAAAAATATT
1 TAAAAAAAATAAAAAATATT
34790236 TAAAA
1 TAAAA
34790241 TTTATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAAAAATAAAAAATATT
Found at i:34790241 original size:19 final size:20
Alignment explanation
Indices: 34790205--34790247 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
34790195 AATAAAAAAA
34790205 ATAAAAGAATTTAAAAA-TT
1 ATAAAAGAATTTAAAAATTT
*
34790224 ATAAAA-AATATTTAAAATTT
1 ATAAAAGAAT-TTAAAAATTT
34790244 ATAA
1 ATAA
34790248 TAACTATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAGAATTTAAAAATTT
Found at i:34790600 original size:22 final size:22
Alignment explanation
Indices: 34790557--34790600 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34790547 TTTTTATAGA
*
34790557 TTTTATATAATTTTTAATTATT
1 TTTTATATAATTTTTAAATATT
34790579 TTTTA-ATAATTTTATAAATATT
1 TTTTATATAATTTT-TAAATATT
34790601 AAGTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATAATTTTTAAATATT
Found at i:34791323 original size:381 final size:381
Alignment explanation
Indices: 34790620--34791387 Score: 1473
Period size: 381 Copynumber: 2.0 Consensus size: 381
34790610 TTATTCTTTT
34790620 ATATTTTTAATTCTTTTTATAATTTCAAAATATATCTAAACAAATGAATGTTGAGATTCAAATGA
1 ATATTTTTAATTCTTTTTATAATTTCAAAATATATCTAAACAAATGAATGTTGAGATTCAAATGA
*
34790685 ACCTAGATAACCATTTATCTAGTTTCACTATATGCTTATTTTAAATTTTTTATTAATTTTTGAAT
66 ACCTAGATAACCATTTATCTAGTTTCACCATATGCTTATTTTAAATTTTTTATTAATTTTTGAAT
34790750 CGATGGAAACATGGCACTAACATGTCAGCAAATGGTGCTGACATCGCGTCTATTAACAATCACAT
131 CGATGGAAACATGGCACTAACATGTCAGCAAATGGTGCTGACATCGCGTCTATTAACAATCACAT
*
34790815 CAGCATTGTCATTAAACACTAACAATCAGCATTAAACAAAAGCTCTATTTAATTAATTTTGTTAG
196 CAGCATTGTCATTAAACACTAACAATCAACATTAAACAAAAGCTCTATTTAATTAATTTTGTTAG
34790880 TTTAAGTGCTCAATTGAATACAAAAAATTAAGTTTGAAAAAATTCGAATATTTATAATACCATTA
261 TTTAAGTGCTCAATTGAATACAAAAAATTAAGTTTGAAAAAATTCGAATATTTATAATACCATTA
*
34790945 AATGTATCAAATATACATTACTAAAACACAAATACCATACCAAAAACTTTAAATAC
326 AATGTATCAAATATACATTACTAAAACACAAATACCATACCAAAAACTTTAAACAC
*
34791001 ATATTTTTAATTCTTTTTATAATTTCAAAATATATCTAAACAAATGAATGTTGAGGTTCAAATGA
1 ATATTTTTAATTCTTTTTATAATTTCAAAATATATCTAAACAAATGAATGTTGAGATTCAAATGA
34791066 ACCTAGATAACCATTTATCTAGTTTCACCATATGCTTATTTTAAATTTTTTATTAATTTTTGAAT
66 ACCTAGATAACCATTTATCTAGTTTCACCATATGCTTATTTTAAATTTTTTATTAATTTTTGAAT
34791131 CGATGGAAACATGGCACTAACATGTCAGCAAATGGTGCTGACATCGCGTCTATTAACAATCACAT
131 CGATGGAAACATGGCACTAACATGTCAGCAAATGGTGCTGACATCGCGTCTATTAACAATCACAT
*
34791196 CAGCATTGTCATTAAACACTAACAATCAACATTAAACAAAAGCTCTATTTAGTTAATTTTGTTAG
196 CAGCATTGTCATTAAACACTAACAATCAACATTAAACAAAAGCTCTATTTAATTAATTTTGTTAG
*
34791261 TTTAAGTGCTCAATTGAATACAAAAAATTAAGTTTGAAAAAATTCGAATGTTTATAATACCATTA
261 TTTAAGTGCTCAATTGAATACAAAAAATTAAGTTTGAAAAAATTCGAATATTTATAATACCATTA
*
34791326 AATGTATCAAATATACATTACTAAAACACAAATACCATACCAAAAACTTTAAACAT
326 AATGTATCAAATATACATTACTAAAACACAAATACCATACCAAAAACTTTAAACAC
34791382 ATATTT
1 ATATTT
34791388 AAAGTAATCA
Statistics
Matches: 380, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
381 380 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (381 bp):
ATATTTTTAATTCTTTTTATAATTTCAAAATATATCTAAACAAATGAATGTTGAGATTCAAATGA
ACCTAGATAACCATTTATCTAGTTTCACCATATGCTTATTTTAAATTTTTTATTAATTTTTGAAT
CGATGGAAACATGGCACTAACATGTCAGCAAATGGTGCTGACATCGCGTCTATTAACAATCACAT
CAGCATTGTCATTAAACACTAACAATCAACATTAAACAAAAGCTCTATTTAATTAATTTTGTTAG
TTTAAGTGCTCAATTGAATACAAAAAATTAAGTTTGAAAAAATTCGAATATTTATAATACCATTA
AATGTATCAAATATACATTACTAAAACACAAATACCATACCAAAAACTTTAAACAC
Found at i:34798321 original size:3 final size:3
Alignment explanation
Indices: 34798315--34798359 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
34798305 CAACAACAGC
* *
34798315 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
34798360 GGCCAAAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34799319 original size:99 final size:99
Alignment explanation
Indices: 34799083--34799378 Score: 553
Period size: 99 Copynumber: 3.0 Consensus size: 99
34799073 GCTGAAGAAG
34799083 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
*
34799148 CC---TTTAAGGACGCAAGCTCCTTCTTTAAAGA
66 CCTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
34799179 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
34799244 CCTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
66 CCTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
34799278 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
1 ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
*
34799343 CCTTTTTTAAGGACGCATTCTCCTTCTTTAAAGA
66 CCTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
34799377 AT
1 AT
34799379 TATTTTCTTC
Statistics
Matches: 195, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
96 67 0.34
99 128 0.66
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (99 bp):
ATCATTCCTCAACTTCTCAATCTCTTTTTCTTGATCTCTCAAAGTTTGATTCATCAAAGAATAAT
CCTTTTTTAAGGACGCAATCTCCTTCTTTAAAGA
Found at i:34801688 original size:3 final size:3
Alignment explanation
Indices: 34801682--34801732 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
34801672 CAGCAGCAAC
* *
34801682 AAG AAG AAG AAG AAG AAG AAG AAG ATG AAG AAG AAG AAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
34801730 AAG
1 AAG
34801733 GGCCAAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:34803093 original size:2 final size:2
Alignment explanation
Indices: 34803086--34803120 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34803076 ATACTTTAGA
34803086 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
34803121 AAAACCTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34806405 original size:24 final size:25
Alignment explanation
Indices: 34806368--34806414 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
34806358 CAAAAGATGA
* *
34806368 AAAAATAACTAAACCCTGAAAACCC
1 AAAAATAACAAAACCCTCAAAACCC
*
34806393 AAAAATAA-AAAACTCTCAAAAC
1 AAAAATAACAAAACCCTCAAAAC
34806415 GTAAACACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.62, C:0.23, G:0.02, T:0.13
Consensus pattern (25 bp):
AAAAATAACAAAACCCTCAAAACCC
Found at i:34806595 original size:28 final size:28
Alignment explanation
Indices: 34806563--34806619 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
34806553 TAAAACAAAT
34806563 AAACAAAGTTTAATTAAAACAAATAAAC
1 AAACAAAGTTTAATTAAAACAAATAAAC
*
34806591 AAACAAAGTTTAATTGAAACAAATAAAC
1 AAACAAAGTTTAATTAAAACAAATAAAC
34806619 A
1 A
34806620 GGGTTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (28 bp):
AAACAAAGTTTAATTAAAACAAATAAAC
Found at i:34806656 original size:24 final size:24
Alignment explanation
Indices: 34806543--34806657 Score: 122
Period size: 24 Copynumber: 4.6 Consensus size: 24
34806533 TAGACTAATA
* *
34806543 AGAGTTTAACTAAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
34806567 AAAGTTTAATTAAAACAAATAAACAAAC
1 AGAGTTTAATTGAAACAAAT----AAAC
*
34806595 AAAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
34806619 AGGGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
34806643 TGAGTTTAACTGAAA
1 AGAGTTTAATTGAAA
34806658 GATTATTTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
24 56 0.71
28 23 0.29
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:34808539 original size:24 final size:25
Alignment explanation
Indices: 34808511--34808569 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
34808501 TAGACTAATA
34808511 AGAGTTTAACTT-AAACAAATAAAC
1 AGAGTTTAACTTGAAACAAATAAAC
34808535 AGAGTTTAA-TTGAAACAAATAAAC
1 AGAGTTTAACTTGAAACAAATAAAC
*
34808559 AAAGTTTAACT
1 AGAGTTTAACT
34808570 AAAAGATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (25 bp):
AGAGTTTAACTTGAAACAAATAAAC
Found at i:34809786 original size:20 final size:20
Alignment explanation
Indices: 34809761--34809844 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
34809751 ATTATATTAT
34809761 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
* **
34809781 TGTTTTGGTTGCTATTTTTTGT
1 TGTTTTGG-TG-TTTTTTTTAC
* *
34809803 TGTTTT--TGTGTTTTTTAT
1 TGTTTTGGTGTTTTTTTTAC
* *
34809821 TGTTTTGGTGCTTTTTTAAC
1 TGTTTTGGTGTTTTTTTTAC
34809841 TGTT
1 TGTT
34809845 GGTTGTTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 14 0.27
19 2 0.04
20 20 0.39
21 2 0.04
22 13 0.25
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:34809818 original size:18 final size:19
Alignment explanation
Indices: 34809757--34809838 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 19
34809747 AAAAATTATA
*
34809757 TTATTGTTTTGGTGTTTTTT
1 TTATTGTTTTGGTG-CTTTT
*
34809777 TTACTGTTTTGGTTGCTATTTT
1 TTATTGTTTTGG-TGC--TTTT
* *
34809799 TTGTTGTTTTTGTG-TTTT
1 TTATTGTTTTGGTGCTTTT
34809817 TTATTGTTTTGGTGCTTTT
1 TTATTGTTTTGGTGCTTTT
34809836 TTA
1 TTA
34809839 ACTGTTGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
18 16 0.31
19 7 0.14
20 11 0.22
21 4 0.08
22 13 0.25
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.71
Consensus pattern (19 bp):
TTATTGTTTTGGTGCTTTT
Found at i:34809827 original size:60 final size:60
Alignment explanation
Indices: 34809752--34809883 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
34809742 AATAAAAAAA
* * * *
34809752 TTATATTATTGTTTTGGTGTTTTTTTTACTGTTTTGGTTGCTATTTT-TTGTTGTTTTTGT-G
1 TTAT-TTATTGTTTTGGTGCTTTTTTAACTG--TTGGTTGCTATTTTCGTATTGTTTTTGTCG
* *
34809813 TTTTTTATTGTTTTGGTGCTTTTTTAACTGTTGGTTGTTATTTTCGTATTGTTTTTGTCG
1 TTATTTATTGTTTTGGTGCTTTTTTAACTGTTGGTTGCTATTTTCGTATTGTTTTTGTCG
34809873 TTATTT-TTGTT
1 TTATTTATTGTT
34809884 GTTATTTTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 13 0.21
59 16 0.26
60 30 0.48
61 3 0.05
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (60 bp):
TTATTTATTGTTTTGGTGCTTTTTTAACTGTTGGTTGCTATTTTCGTATTGTTTTTGTCG
Found at i:34809895 original size:12 final size:12
Alignment explanation
Indices: 34809846--34809898 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
34809836 TTAACTGTTG
*
34809846 GTTGTTATTTTC
1 GTTGTTATTTTT
* *
34809858 G-TATTGTTTTT
1 GTTGTTATTTTT
*
34809869 GTCGTTATTTTT
1 GTTGTTATTTTT
34809881 GTTGTTATTTTT
1 GTTGTTATTTTT
34809893 GTTGTT
1 GTTGTT
34809899 TTTAATGTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 8 0.24
12 25 0.76
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.70
Consensus pattern (12 bp):
GTTGTTATTTTT
Found at i:34816411 original size:8 final size:8
Alignment explanation
Indices: 34816379--34816443 Score: 57
Period size: 7 Copynumber: 8.5 Consensus size: 8
34816369 AAATGATTAT
34816379 ATATAAAA
1 ATATAAAA
* *
34816387 TTTTAAAA
1 ATATAAAA
34816395 A-ATAAAA
1 ATATAAAA
34816402 ATATAAAA
1 ATATAAAA
*
34816410 ATAT-TAA
1 ATATAAAA
34816417 AT-TAAAA
1 ATATAAAA
34816424 AT-TAAAA
1 ATATAAAA
*
34816431 ATTATATAA
1 A-TATAAAA
34816440 ATAT
1 ATAT
34816444 GTTTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
6 1 0.02
7 20 0.43
8 20 0.43
9 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATATAAAA
Found at i:34816425 original size:22 final size:23
Alignment explanation
Indices: 34816383--34816441 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
34816373 GATTATATAT
* * *
34816383 AAAATTTTAAAAAATAAAAA-TA
1 AAAATTATATAAATTAAAAATTA
*
34816405 TAAAAATAT-TAAATTAAAAATTA
1 -AAAATTATATAAATTAAAAATTA
34816428 AAAATTATATAAAT
1 AAAATTATATAAAT
34816442 ATGTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATTATATAAATTAAAAATTA
Found at i:34822492 original size:29 final size:28
Alignment explanation
Indices: 34822435--34822502 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
34822425 TTTAATAGTC
* *
34822435 TATATTTTTATAATTTTTAAAAATTAAA
1 TATAATTTTATAATTTTAAAAAATTAAA
*
34822463 TCA-AATTTTATCATTTTAAAAAATTAAAA
1 T-ATAATTTTATAATTTTAAAAAATT-AAA
34822492 TATAATTTTAT
1 TATAATTTTAT
34822503 TTTTATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAATTTTATAATTTTAAAAAATTAAA
Found at i:34822590 original size:3 final size:3
Alignment explanation
Indices: 34822582--34822614 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
34822572 AGAAATATGA
34822582 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34822615 TTCTTGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34828349 original size:91 final size:90
Alignment explanation
Indices: 34828191--34828372 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 90
34828181 GCTGACTGTA
* * *
34828191 AAGAAAAAGAACAAAGAAGGATAGAAGCAAGTAACTTAGAGTAAGATGAATAAATATCTAGTTAT
1 AAGAAAAAGAACAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAG-CAT
*
34828256 CCTCTGGAGAATAAATTAGAAATTCT
65 CCTCTAGAGAATAAATTAGAAATTCT
* *
34828282 AAGAAAAAGCACAAAGAAGGTATAAAAGCAAGGAACTTAGAGTGAAGATGAATACATATCTA-CA
1 AAGAAAAAGAACAAAGAAGG-ATAAAAGCAAGGAACTTAGAGT-AAGATGAATAAATATCTAGCA
34828346 TCCTCTAGAGAATAAATTAGAAATTCT
64 TCCTCTAGAGAATAAATTAGAAATTCT
34828373 TAGTCGATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
91 46 0.55
92 20 0.24
93 17 0.20
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (90 bp):
AAGAAAAAGAACAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAGCATC
CTCTAGAGAATAAATTAGAAATTCT
Found at i:34841473 original size:12 final size:12
Alignment explanation
Indices: 34841456--34841480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34841446 AAAATCTAAG
34841456 AAATCTAAATTA
1 AAATCTAAATTA
34841468 AAATCTAAATTA
1 AAATCTAAATTA
34841480 A
1 A
34841481 TTTGAGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCTAAATTA
Found at i:34846838 original size:10 final size:9
Alignment explanation
Indices: 34846716--34846848 Score: 60
Period size: 9 Copynumber: 14.1 Consensus size: 9
34846706 ATAACAAAAT
34846716 TTTTTAT-A
1 TTTTTATAA
34846724 TTTTTATAA
1 TTTTTATAA
*
34846733 CTTTTAAATAAA
1 -TTTT-TAT-AA
34846745 TTTTTA-ACA
1 TTTTTATA-A
* *
34846754 TTTTATTTAG
1 TTTT-TATAA
34846764 TTTTTATAA
1 TTTTTATAA
* *
34846773 TTTCTAAAA
1 TTTTTATAA
* *
34846782 TTTTAATTA
1 TTTTTATAA
*
34846791 TTTTCCAT-A
1 TTTT-TATAA
34846800 TTTTTCATAA
1 TTTTT-ATAA
34846810 TATTTTAATCAA
1 T-TTTT-AT-AA
34846822 -TTTTATAA
1 TTTTTATAA
34846830 TTTTCTATAA
1 TTTT-TATAA
34846840 -TTTTATAA
1 TTTTTATAA
34846848 T
1 T
34846849 ATGTTAATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
8 15 0.16
9 40 0.42
10 23 0.24
11 13 0.14
12 4 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34846840 original size:30 final size:29
Alignment explanation
Indices: 34846765--34846849 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
34846755 TTTATTTAGT
*
34846765 TTTTATAA-TTTCTA-AA-ATTTTAATTA
1 TTTTATAATTTTCTATAATATTTTAATAA
*
34846791 TTTTCCATATTTTTC-ATAATATTTTAATCAA
1 TTTT--ATAATTTTCTATAATATTTTAAT-AA
34846822 TTTTATAATTTTCTATAAT-TTTATAATA
1 TTTTATAATTTTCTATAATATTT-TAATA
34846850 TGTTAATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.08
28 4 0.08
29 18 0.38
30 17 0.35
31 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATAATTTTCTATAATATTTTAATAA
Found at i:34846841 original size:18 final size:18
Alignment explanation
Indices: 34846765--34846848 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 18
34846755 TTTATTTAGT
*
34846765 TTTTATAA-TTTCTAAAA
1 TTTTATAATTTTCTATAA
* * *
34846782 TTTTAATTATTTTCCATAT
1 TTTT-ATAATTTTCTATAA
34846801 TTTTCATAATATTT-TAATCAA
1 TTTT-ATAAT-TTTCT-AT-AA
34846822 TTTTATAATTTTCTATAA
1 TTTTATAATTTTCTATAA
34846840 TTTTATAAT
1 TTTTATAAT
34846849 ATGTTAATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 4 0.08
18 14 0.26
19 19 0.36
20 11 0.21
21 5 0.09
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATAATTTTCTATAA
Found at i:34847881 original size:22 final size:24
Alignment explanation
Indices: 34847838--34847896 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
34847828 AATTTATTTT
34847838 TATATTTTATTTATAATATATTAGA
1 TATATTTTATTTATAATATATT-GA
34847863 -ATATTATT-TTTAT-AT-TATTGA
1 TATATT-TTATTTATAATATATTGA
34847884 TATATTTCTATTT
1 TATATTT-TATTT
34847897 TATTTATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
21 3 0.10
22 10 0.33
23 5 0.17
24 10 0.33
25 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (24 bp):
TATATTTTATTTATAATATATTGA
Found at i:34847916 original size:39 final size:39
Alignment explanation
Indices: 34847869--34847945 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
34847859 TAGAATATTA
*
34847869 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
* *
34847908 TTTTTATATTATTTATCTATTTCTATTTCATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTC
34847946 ATTTGCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
Found at i:34847921 original size:20 final size:19
Alignment explanation
Indices: 34847867--34847942 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
34847857 ATTAGAATAT
*
34847867 TATTTTTATATTATTGATA
1 TATTTTTATATTATTTATA
* * *
34847886 TATTTCTATTTTATTTATT
1 TATTTTTATATTATTTATA
* *
34847905 TCCTTTTTATATTATTTATC
1 T-ATTTTTATATTATTTATA
*
34847925 TATTTCTAT-TTCATTTAT
1 TATTTTTATATT-ATTTAT
34847943 TTCATTTGCA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 2 0.04
19 28 0.62
20 15 0.33
ACGTcount: A:0.24, C:0.08, G:0.01, T:0.67
Consensus pattern (19 bp):
TATTTTTATATTATTTATA
Found at i:34849793 original size:16 final size:15
Alignment explanation
Indices: 34849763--34849797 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34849753 TTCTATTGTC
34849763 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
34849778 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
34849794 TATA
1 TATA
34849798 CAAGATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:34854832 original size:37 final size:38
Alignment explanation
Indices: 34854788--34854863 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
34854778 TCATCTCCTT
*
34854788 TTGCTTCTTTTC-TTTCTCCCCCC-TCTAATCAAACGTG
1 TTGCTTCTTGTCTTTTC-CCCCCCTTCTAATCAAACGTG
34854825 TTGCTTCTTGTCTTTTCCCCCCCTTCTAATCAAACGTG
1 TTGCTTCTTGTCTTTTCCCCCCCTTCTAATCAAACGTG
34854863 T
1 T
34854864 AACTTCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 17 0.47
38 19 0.53
ACGTcount: A:0.13, C:0.34, G:0.09, T:0.43
Consensus pattern (38 bp):
TTGCTTCTTGTCTTTTCCCCCCCTTCTAATCAAACGTG
Found at i:34854856 original size:38 final size:37
Alignment explanation
Indices: 34854788--34854863 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 37
34854778 TCATCTCCTT
*
34854788 TTGCTTCTTTTCTTTCTCCCCCCTCTAATCAAACGTG
1 TTGCTTCTTGTCTTTCTCCCCCCTCTAATCAAACGTG
34854825 TTGCTTCTTGTCTTT-TCCCCCCCTTCTAATCAAACGTG
1 TTGCTTCTTGTCTTTCT-CCCCCC-TCTAATCAAACGTG
34854863 T
1 T
34854864 AACTTCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 1 0.03
37 20 0.56
38 15 0.42
ACGTcount: A:0.13, C:0.34, G:0.09, T:0.43
Consensus pattern (37 bp):
TTGCTTCTTGTCTTTCTCCCCCCTCTAATCAAACGTG
Found at i:34856541 original size:2 final size:2
Alignment explanation
Indices: 34856534--34856579 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
34856524 AAAATAAGAC
34856534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34856576 AT AT
1 AT AT
34856580 TGCCATTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34858256 original size:19 final size:18
Alignment explanation
Indices: 34858232--34858304 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
34858222 AAAATTTATC
*
34858232 ATTTTTATACTTTTTAAAT
1 ATTTTT-TAATTTTTAAAT
*
34858251 ATTTTTTAATTTTTAAAA
1 ATTTTTTAATTTTTAAAT
* *
34858269 ATGATTTTTGATTTTT-GAT
1 AT--TTTTTAATTTTTAAAT
* *
34858288 TTTTTTTAAATTTTAAA
1 ATTTTTTAATTTTTAAA
34858305 AATTGATTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
17 10 0.24
18 13 0.31
19 8 0.19
20 11 0.26
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTTTTAATTTTTAAAT
Found at i:34868519 original size:21 final size:20
Alignment explanation
Indices: 34868476--34868520 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
34868466 GGTTAAACCT
* *
34868476 AAAACAAACAAATCCTAAAG
1 AAAACAAACAAAGCATAAAG
*
34868496 AAAACAAACCAAAGCATAATG
1 AAAACAAA-CAAAGCATAAAG
34868517 AAAA
1 AAAA
34868521 AGAAGGGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAACAAACAAAGCATAAAG
Found at i:34869253 original size:15 final size:15
Alignment explanation
Indices: 34869233--34869266 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
34869223 TTCATGAGAT
34869233 AGATAACTATATAAA
1 AGATAACTATATAAA
34869248 AGATAACTATATAAA
1 AGATAACTATATAAA
34869263 AGAT
1 AGAT
34869267 GTGACAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (15 bp):
AGATAACTATATAAA
Found at i:34871848 original size:18 final size:20
Alignment explanation
Indices: 34871814--34871859 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
34871804 CTAAAAATAA
*
34871814 TCAAAATAATTT-TTAAAAT
1 TCAAAATAATTTATAAAAAT
34871833 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
34871852 TCCAAAAT
1 T-CAAAAT
34871860 CTAAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 14 0.58
20 6 0.25
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:34874943 original size:19 final size:19
Alignment explanation
Indices: 34874919--34874955 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34874909 AATGATCAGA
34874919 TTGATTCATATTTTATTAT
1 TTGATTCATATTTTATTAT
*
34874938 TTGATTCGTATTTTATTA
1 TTGATTCATATTTTATTA
34874956 GACAATCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTGATTCATATTTTATTAT
Found at i:34878883 original size:7 final size:7
Alignment explanation
Indices: 34878854--34878899 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
34878844 AACTTTTTCG
34878854 AAATAT-
1 AAATATA
34878860 AAATATA
1 AAATATA
*
34878867 AAATGGTA
1 AAAT-ATA
34878875 AAATATA
1 AAATATA
34878882 AAATATA
1 AAATATA
34878889 AAATATA
1 AAATATA
34878896 AAAT
1 AAAT
34878900 TTATAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 6 0.17
7 24 0.67
8 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:34884285 original size:30 final size:31
Alignment explanation
Indices: 34884249--34884308 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
34884239 TAATTCTAAT
* *
34884249 TTTTAAC-AAGGAAGAAATAAAGAGAAAAAC
1 TTTTAACAAAGAAAAAAATAAAGAGAAAAAC
34884279 TTTTAACAAAGAAAAAAATAAAGAGAAAAA
1 TTTTAACAAAGAAAAAAATAAAGAGAAAAA
34884309 AGTGGTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.17
Consensus pattern (31 bp):
TTTTAACAAAGAAAAAAATAAAGAGAAAAAC
Found at i:34886681 original size:3 final size:3
Alignment explanation
Indices: 34886673--34886702 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34886663 CAAAAAGAGC
34886673 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
34886703 CAGCAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34902423 original size:12 final size:13
Alignment explanation
Indices: 34902387--34902424 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
34902377 AATTATATTT
34902387 AAATAATTTTGAATA
1 AAATAA-TTT-AATA
34902402 AAATAATTTAATA
1 AAATAATTTAATA
34902415 AAA-AATTTAA
1 AAATAATTTAA
34902425 AAGATTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 3 0.13
15 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
AAATAATTTAATA
Found at i:34909388 original size:2 final size:2
Alignment explanation
Indices: 34909381--34909414 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34909371 GATCAAAAAC
34909381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34909415 AACTGTATCT
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):
TA
Found at i:34915557 original size:27 final size:27
Alignment explanation
Indices: 34915502--34915558 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
34915492 TAAAAGATTC
* * *
34915502 AAATATATATATATATATAATCTAGAA
1 AAATATATATATAAATAAAATCTAAAA
34915529 AAATATATATTATAAATAAAAT-TAAAA
1 AAATATATA-TATAAATAAAATCTAAAA
34915556 AAA
1 AAA
34915559 ACACGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATATATATATAAATAAAATCTAAAA
Found at i:34915683 original size:55 final size:55
Alignment explanation
Indices: 34915588--34915691 Score: 129
Period size: 55 Copynumber: 1.9 Consensus size: 55
34915578 ATTAGTTGAA
* * ** *
34915588 TTAAAAATATTATTTCAAAAAATTGTAAATTTTTTTAAAAATTTTTAAAAAAGGT
1 TTAAAAATATTATTTCAAAAAATTCTAAATTTCTAAAAAAATATTTAAAAAAGGT
* *
34915643 TTAAAAATAATT-TTTTATAAAATTCTAAATTTCTAAAAAAATATTTAAA
1 TTAAAAAT-ATTATTTCAAAAAATTCTAAATTTCTAAAAAAATATTTAAA
34915692 TTTAAGTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
55 38 0.93
56 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (55 bp):
TTAAAAATATTATTTCAAAAAATTCTAAATTTCTAAAAAAATATTTAAAAAAGGT
Found at i:34919519 original size:16 final size:17
Alignment explanation
Indices: 34919495--34919527 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
34919485 ATGGTAAATA
34919495 TATATACTACTATTTTT
1 TATATACTACTATTTTT
*
34919512 TATA-ACTATTATTTTT
1 TATATACTACTATTTTT
34919528 GAAAAACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATACTACTATTTTT
Found at i:34920324 original size:27 final size:25
Alignment explanation
Indices: 34920287--34920355 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 25
34920277 TATATGTGAA
*
34920287 TTTTTATAATTTTTAAACTTATTTCAT
1 TTTTTATAATTTTTAAACTT-TCT-AT
34920314 TTTTTATAATTTATTTTAAACTTTCTAT
1 TTTTTATAA--T-TTTTAAACTTTCTAT
34920342 TTTTTAGTAATTTT
1 TTTTTA-TAATTTT
34920356 CTACAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 3 0.08
27 10 0.27
28 8 0.22
29 6 0.16
30 10 0.27
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTTTATAATTTTTAAACTTTCTAT
Found at i:34920333 original size:30 final size:29
Alignment explanation
Indices: 34920297--34920354 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
34920287 TTTTTATAAT
*
34920297 TTTTAAACTTATTTCATTTTTTA-TAATTTA
1 TTTTAAACTT-TCT-ATTTTTTAGTAATTTA
34920327 TTTTAAACTTTCTATTTTTTAGTAATTT
1 TTTTAAACTTTCTATTTTTTAGTAATTT
34920355 TCTACAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 8 0.31
30 10 0.38
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTAAACTTTCTATTTTTTAGTAATTTA
Found at i:34933337 original size:14 final size:14
Alignment explanation
Indices: 34933320--34933348 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34933310 ATTTAATATC
34933320 TAATTTTTATATTT
1 TAATTTTTATATTT
34933334 TAATTTTTATATTT
1 TAATTTTTATATTT
34933348 T
1 T
34933349 TATAATGTTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TAATTTTTATATTT
Found at i:34935447 original size:20 final size:20
Alignment explanation
Indices: 34935410--34935463 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
34935400 TTGCCTTGGG
* * * *
34935410 ACTTCTACCGGTAAAACTTC
1 ACTTCTACTGATACAACTAC
34935430 ACTTCTACTGATACAACTAC
1 ACTTCTACTGATACAACTAC
* *
34935450 AGTTTTACTGATAC
1 ACTTCTACTGATAC
34935464 CTTGAAAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (20 bp):
ACTTCTACTGATACAACTAC
Found at i:34937346 original size:23 final size:25
Alignment explanation
Indices: 34937318--34937364 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
34937308 TCAAATTCAA
34937318 AAAATA-GAAG-GACTAAATTCTTG
1 AAAATACGAAGAGACTAAATTCTTG
* *
34937341 AAAATACTAAGATACTAAATTCTT
1 AAAATACGAAGAGACTAAATTCTT
34937365 AATATAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (25 bp):
AAAATACGAAGAGACTAAATTCTTG
Found at i:34939169 original size:16 final size:16
Alignment explanation
Indices: 34939118--34939173 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
34939108 CGTTTGGTTC
*
34939118 GTTGTAACGGAAT-GAA
1 GTTGTAATGGAATAG-A
*
34939134 GCTGTAATGGAATAGA
1 GTTGTAATGGAATAGA
*
34939150 GTTGTAATGGAATAGG
1 GTTGTAATGGAATAGA
34939166 GTTGTAAT
1 GTTGTAAT
34939174 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 34 0.97
17 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (16 bp):
GTTGTAATGGAATAGA
Found at i:34939408 original size:58 final size:59
Alignment explanation
Indices: 34939346--34939508 Score: 206
Period size: 58 Copynumber: 2.7 Consensus size: 59
34939336 TTTTAATAAG
* *
34939346 ATTATTATTAAATATAATTTAATAAAAATAATAAATAAATTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAAATTAATAATATTTTTAACATA
* * *
34939404 ATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAAATTAATAATATTTTTAACATA
*
34939462 ATTATTATTAAAATATGAA-TTAGTAAAATTATAATATATAATATTAA
1 ATTATTATT-AAATAT-AATTTAATAAAA--ATAATATATAA-ATTAA
34939509 AAAAATAATA
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
57 21 0.23
58 40 0.44
59 9 0.10
60 5 0.06
62 11 0.12
63 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAAATTAATAATATTTTTAACATA
Found at i:34946435 original size:20 final size:20
Alignment explanation
Indices: 34946410--34946450 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
34946400 CTGCTCAGTC
34946410 AATTTAATCCTTTAAAAATT
1 AATTTAATCCTTTAAAAATT
34946430 AATTTAATCCTTTAAAAATT
1 AATTTAATCCTTTAAAAATT
34946450 A
1 A
34946451 TAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAATCCTTTAAAAATT
Found at i:34946477 original size:24 final size:23
Alignment explanation
Indices: 34946444--34946514 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 23
34946434 TAATCCTTTA
34946444 AAAATTATAAAAATATATATTATT
1 AAAATTATAAAAATATATATT-TT
* *
34946468 AAAATAATAAAATTATAT-TTTT
1 AAAATTATAAAAATATATATTTT
** *
34946490 ATTATTATAAAAATATACATTTT
1 AAAATTATAAAAATATATATTTT
34946513 AA
1 AA
34946515 TTCGAGTCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 15 0.39
23 7 0.18
24 16 0.42
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATAAAAATATATATTTT
Found at i:34946499 original size:22 final size:22
Alignment explanation
Indices: 34946444--34946506 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
34946434 TAATCCTTTA
34946444 AAAATTATAAAAATATATATTATT
1 AAAATTAT-AAAAT-TATATTATT
* *
34946468 AAAATAATAAAATTATATTTTT
1 AAAATTATAAAATTATATTATT
** *
34946490 ATTATTATAAAAATATA
1 AAAATTATAAAATTATA
34946507 CATTTTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 21 0.64
23 5 0.15
24 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTATAAAATTATATTATT
Found at i:34950156 original size:6 final size:6
Alignment explanation
Indices: 34950145--34950190 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
34950135 ATTAAAGACG
*
34950145 TTATAT TTATAT TTACAT TTATAT TTATAT TTATAT TTATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
34950191 GAATGATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:34951347 original size:18 final size:18
Alignment explanation
Indices: 34951326--34951363 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34951316 TAAATTTTTG
34951326 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
*
34951344 AATTCTAATAAACCGAAT
1 AATTCGAATAAACCGAAT
34951362 AA
1 AA
34951364 AACTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:34951701 original size:31 final size:31
Alignment explanation
Indices: 34951661--34951733 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
34951651 TATTCGATTC
*
34951661 GATTTGATTCGATTCAAATTCTATCTCACTT
1 GATTCGATTCGATTCAAATTCTATCTCACTT
*
34951692 GATTCGATTCGATTCGAATTCTATCTCACTT
1 GATTCGATTCGATTCAAATTCTATCTCACTT
34951723 GATTCGATTCG
1 GATTCGATTCG
34951734 TAAAAATTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (31 bp):
GATTCGATTCGATTCAAATTCTATCTCACTT
Found at i:34955568 original size:20 final size:20
Alignment explanation
Indices: 34955524--34955568 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
34955514 TTATTTTTAA
*
34955524 GTTTGAGGTTTAGGTTTCAT
1 GTTTAAGGTTTAGGTTTCAT
* * *
34955544 ATTTAAGGTTTGGGTTTGAT
1 GTTTAAGGTTTAGGTTTCAT
34955564 GTTTA
1 GTTTA
34955569 GGATAAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.51
Consensus pattern (20 bp):
GTTTAAGGTTTAGGTTTCAT
Found at i:34956670 original size:26 final size:27
Alignment explanation
Indices: 34956621--34956676 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
34956611 TAAATTAGTC
*
34956621 TCTTTATTATTAAATAAATTAATTTAAT
1 TCTTTATTATTAAATAAA-TAATTAAAT
34956649 TCTTATATTATTAAA-AAA-AATTAAAT
1 TCTT-TATTATTAAATAAATAATTAAAT
34956675 TC
1 TC
34956677 AAATTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
28 7 0.27
29 10 0.38
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (27 bp):
TCTTTATTATTAAATAAATAATTAAAT
Found at i:34968874 original size:2 final size:2
Alignment explanation
Indices: 34968867--34968902 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34968857 TTTGAATTTA
34968867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34968903 TAATAACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34969022 original size:14 final size:14
Alignment explanation
Indices: 34969005--34969038 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
34968995 AACTTTTAAA
34969005 CCTAAACTTGGGAC
1 CCTAAACTTGGGAC
34969019 CCTAAACTTGGGAC
1 CCTAAACTTGGGAC
34969033 CCTAAA
1 CCTAAA
34969039 TTCAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (14 bp):
CCTAAACTTGGGAC
Found at i:34972120 original size:22 final size:23
Alignment explanation
Indices: 34972092--34972141 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
34972082 TAGTTCAATG
34972092 ATTTAATGAAA-ATTTT-TAAATA
1 ATTTAAT-AAATATTTTGTAAATA
*
34972114 ATTTAATAAATATTTTGTAATTA
1 ATTTAATAAATATTTTGTAAATA
34972137 ATTTA
1 ATTTA
34972142 GTCTTTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 12 0.48
23 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTTAATAAATATTTTGTAAATA
Found at i:34976831 original size:17 final size:16
Alignment explanation
Indices: 34976797--34976832 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34976787 TATTACAACC
*
34976797 TATGTAATACTTTTTT
1 TATGTAATACTATTTT
34976813 TATGTAATACTCATTTT
1 TATGTAATACT-ATTTT
34976830 TAT
1 TAT
34976833 CATTTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (16 bp):
TATGTAATACTATTTT
Found at i:34978525 original size:7 final size:7
Alignment explanation
Indices: 34978513--34978537 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34978503 ACTGAAAATG
34978513 AAAATAT
1 AAAATAT
34978520 AAAATAT
1 AAAATAT
34978527 AAAATAT
1 AAAATAT
34978534 AAAA
1 AAAA
34978538 ATTAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:34978543 original size:14 final size:14
Alignment explanation
Indices: 34978491--34978543 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
34978481 TAAAATTTAA
*
34978491 AAAAATTAAATTACT
1 AAAAATTAAAATA-T
* *
34978506 GAAAATGAAAATAT
1 AAAAATTAAAATAT
34978520 -AAAATATAAAATAT
1 AAAAAT-TAAAATAT
34978534 AAAAATTAAA
1 AAAAATTAAA
34978544 TTCTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 12 0.38
15 15 0.47
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAAATTAAAATAT
Found at i:34979062 original size:18 final size:19
Alignment explanation
Indices: 34979020--34979063 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
34979010 CAGATCTCCA
34979020 ATTAAGTCATTATTAATTT
1 ATTAAGTCATTATTAATTT
** *
34979039 GGTAAGTC-TTATTTATTT
1 ATTAAGTCATTATTAATTT
34979057 ATTAAGT
1 ATTAAGT
34979064 GTTGGATGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (19 bp):
ATTAAGTCATTATTAATTT
Found at i:34985712 original size:25 final size:25
Alignment explanation
Indices: 34985684--34985766 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
34985674 TTCGAGATCT
34985684 TTAAGCTTTCAAAATAATATAAAGA
1 TTAAGCTTTCAAAATAATATAAAGA
** ***
34985709 TTAAATTTATCGTTATAATA-AAAGGA
1 TTAAGCTT-TCAAAATAATATAAA-GA
*
34985735 TTTTTAAGCTTTCAAAATAATATAGAGA
1 ---TTAAGCTTTCAAAATAATATAAAGA
34985763 TTAA
1 TTAA
34985767 ATTTAATAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
25 13 0.32
26 10 0.24
28 10 0.24
29 8 0.20
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (25 bp):
TTAAGCTTTCAAAATAATATAAAGA
Found at i:34985764 original size:28 final size:28
Alignment explanation
Indices: 34985677--34985764 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
34985667 ATATCAATTC
*
34985677 GAGATCTTTAAGCTTTCAAAATAATATA
1 GAGATTTTTAAGCTTTCAAAATAATATA
* * * *
34985705 AAGATTAAATTT-ATCGTT-ATAATAA-A-A
1 GAGATT---TTTAAGCTTTCAAAATAATATA
34985732 G-GATTTTTAAGCTTTCAAAATAATATA
1 GAGATTTTTAAGCTTTCAAAATAATATA
34985759 GAGATT
1 GAGATT
34985765 AAATTTAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 16
0.63 0.13 0.24
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 6 0.14
26 5 0.12
27 3 0.07
28 9 0.21
29 6 0.14
30 4 0.09
31 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (28 bp):
GAGATTTTTAAGCTTTCAAAATAATATA
Found at i:34986246 original size:12 final size:12
Alignment explanation
Indices: 34986212--34986261 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
34986202 TGCGGCAGGT
*
34986212 GCTGAAGCTGAA
1 GCTGAAGCTGGA
* *
34986224 GCTGCACCTGGA
1 GCTGAAGCTGGA
34986236 GCTGAAGCTGGA
1 GCTGAAGCTGGA
* *
34986248 GATGGAGCTGGA
1 GCTGAAGCTGGA
34986260 GC
1 GC
34986262 GGCGCCAGCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.40, T:0.16
Consensus pattern (12 bp):
GCTGAAGCTGGA
Found at i:34986253 original size:18 final size:18
Alignment explanation
Indices: 34986217--34986257 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34986207 CAGGTGCTGA
*
34986217 AGCTGAAGCTGCACCTGG
1 AGCTGAAGCTGCACATGG
* *
34986235 AGCTGAAGCTGGAGATGG
1 AGCTGAAGCTGCACATGG
34986253 AGCTG
1 AGCTG
34986258 GAGCGGCGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.39, T:0.17
Consensus pattern (18 bp):
AGCTGAAGCTGCACATGG
Found at i:34992691 original size:11 final size:11
Alignment explanation
Indices: 34992653--34992696 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
34992643 GCCCAACTTG
34992653 AATTTTAAATT
1 AATTTTAAATT
*
34992664 AAGTTTGAAATT
1 AA-TTTTAAATT
34992676 AATTTTAAATT
1 AATTTTAAATT
*
34992687 TA-TTTAAATT
1 AATTTTAAATT
34992697 TAAATTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
12 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:34992696 original size:17 final size:17
Alignment explanation
Indices: 34992656--34992718 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
34992646 CAACTTGAAT
*
34992656 TTTAAA-TTAAGTTTGAA
1 TTTAAATTTAAATTTG-A
* *
34992673 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
34992689 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
34992706 TTTAAATTTAAAT
1 TTTAAATTTAAAT
34992719 ACATTTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.37
17 17 0.45
18 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:34992702 original size:27 final size:28
Alignment explanation
Indices: 34992662--34992738 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
34992652 GAATTTTAAA
*
34992662 TTAAGTTTGAAATTAATTTTAAATTTAT
1 TTAAATTTGAAATTAATTTTAAATTTAT
** *
34992690 TTAAATTT-AAATTTGTTTTAAATTTAA
1 TTAAATTTGAAATTAATTTTAAATTTAT
* * *
34992717 ATACATTTGAAA-TAACTTTAAA
1 TTAAATTTGAAATTAATTTTAAA
34992739 CTTAAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 29 0.74
28 10 0.26
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
TTAAATTTGAAATTAATTTTAAATTTAT
Found at i:34993930 original size:21 final size:21
Alignment explanation
Indices: 34993904--34993944 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34993894 GTTTTAAACA
*
34993904 AAAAAGATTTTTAAAAGAAAG
1 AAAAAGATTTTCAAAAGAAAG
* *
34993925 AAAAAGGTTTTCAAAGGAAA
1 AAAAAGATTTTCAAAAGAAA
34993945 AATCAAAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.02, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAAAGATTTTCAAAAGAAAG
Found at i:34993957 original size:24 final size:23
Alignment explanation
Indices: 34993925--34993969 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34993915 TAAAAGAAAG
*
34993925 AAAAAGGTTTTCAAAGGAAAAATC
1 AAAAAGG-TTTCAAAGAAAAAATC
*
34993949 AAAACGGTTTCAAAGAAAAAA
1 AAAAAGGTTTCAAAGAAAAAA
34993970 GAAAGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAAAGGTTTCAAAGAAAAAATC
Found at i:34994764 original size:30 final size:30
Alignment explanation
Indices: 34994730--34994824 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
34994720 CCTGATTTCA
34994730 CCAAAAACCACCATTTTACCCCCGAACTTT
1 CCAAAAACCACCATTTTACCCCCGAACTTT
* * * * *
34994760 CCAAAATTCCA--TTTTTA-GCCCTAATTTT
1 CCAAAA-ACCACCATTTTACCCCCGAACTTT
*
34994788 ACCAAAAATCACCATTTTACCCCCGAACTTT
1 -CCAAAAACCACCATTTTACCCCCGAACTTT
34994819 CCAAAA
1 CCAAAA
34994825 TCCCATTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 10 0.20
29 11 0.22
30 17 0.35
31 11 0.22
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (30 bp):
CCAAAAACCACCATTTTACCCCCGAACTTT
Found at i:34994801 original size:59 final size:59
Alignment explanation
Indices: 34994685--34994912 Score: 296
Period size: 59 Copynumber: 3.9 Consensus size: 59
34994675 TAAATTATAT
* *
34994685 TTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCTGATTTCACCAAAAACCACCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATCACCA
* * *
34994743 TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAGCCCTAATTTTACCAAAAATCACCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATCACCA
* * ** * * *
34994802 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTTACCAAAAATTACCG
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATCACCA
* * * * *
34994861 TTTCACCCGCAAACTTTCCAAGATTCCATTTTTGACCCTACTTTCACCAAAA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAA
34994913 GTTACATTTT
Statistics
Matches: 148, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 27 0.18
59 121 0.82
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (59 bp):
TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAAATCACCA
Found at i:34994855 original size:30 final size:29
Alignment explanation
Indices: 34994704--34994855 Score: 114
Period size: 29 Copynumber: 5.2 Consensus size: 29
34994694 CAAACTTTCC
* * *
34994704 AAAATTCCATTTTAACCCTGATTTCACCA
1 AAAATCCCATTTTAACCCCGATTTTACCA
* * *
34994733 AAAACCACCATTTTACCCCCGAACTTT-CC-
1 AAAATC-CCATTTTAACCCCG-ATTTTACCA
* * **
34994762 AAAATTCCATTTTTAGCCCTAATTTTACCA
1 AAAATCCCA-TTTTAACCCCGATTTTACCA
* *
34994792 AAAATCACCATTTTACCCCCGAACTTT-CC-
1 AAAATC-CCATTTTAACCCCG-ATTTTACCA
34994821 AAAATCCCATTTTTAACCCCGATTTTACCA
1 AAAATCCCA-TTTTAACCCCGATTTTACCA
34994851 AAAAT
1 AAAAT
34994856 TACCGTTTCA
Statistics
Matches: 94, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
28 14 0.15
29 36 0.38
30 34 0.36
31 10 0.11
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATCCCATTTTAACCCCGATTTTACCA
Found at i:34998009 original size:6 final size:6
Alignment explanation
Indices: 34998000--34998057 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
34997990 TGGGGCAGCT
* * * * * *
34998000 GCTGAA GCTGAA GCTGAA GCTGCA CCTGGA GCTGAT GCTGGA GCTGGA
1 GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA GCTGAA
*
34998048 GCTGGA GCTG
1 GCTGAA GCTG
34998058 TGCCAGCAGC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (6 bp):
GCTGAA
Found at i:34998017 original size:12 final size:12
Alignment explanation
Indices: 34998000--34998057 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
34997990 TGGGGCAGCT
*
34998000 GCTGAAGCTGAA
1 GCTGGAGCTGAA
* *
34998012 GCTGAAGCTGCA
1 GCTGGAGCTGAA
* *
34998024 CCTGGAGCTGAT
1 GCTGGAGCTGAA
*
34998036 GCTGGAGCTGGA
1 GCTGGAGCTGAA
34998048 GCTGGAGCTG
1 GCTGGAGCTG
34998058 TGCCAGCAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (12 bp):
GCTGGAGCTGAA
Found at i:34999426 original size:19 final size:18
Alignment explanation
Indices: 34999404--34999454 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
34999394 ATTATATAAC
*
34999404 TTAAAACATATTTAAGTAT
1 TTAAAACATATTTAA-AAT
* *
34999423 TTAATACATAATTAAAAT
1 TTAAAACATATTTAAAAT
34999441 TATAAAA-ATATTTA
1 T-TAAAACATATTTA
34999455 CATATTGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAAACATATTTAAAAT
Found at i:35008335 original size:26 final size:25
Alignment explanation
Indices: 35008305--35008385 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
35008295 GTTAAAAAAA
*
35008305 TTTAATTTTTAAAGGTTAAAATTTT
1 TTTAACTTTTAAAGGTTAAAATTTT
*
35008330 TCTTAACTTTTAAAGGGTTTAAATTTT
1 T-TTAACTTTTAAA-GGTTAAAATTTT
* *
35008357 TTATAACTTTTAAAGGTTCAACTTTT
1 TT-TAACTTTTAAAGGTTAAAATTTT
35008383 TTT
1 TTT
35008386 TTTAAGATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.04
26 24 0.49
27 23 0.47
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (25 bp):
TTTAACTTTTAAAGGTTAAAATTTT
Found at i:35009583 original size:49 final size:48
Alignment explanation
Indices: 35009528--35009621 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 48
35009518 AACATGGAAC
*
35009528 TGTAATAATATTTTAATTTAACATATTTTTTTTTAATTTAACTCAACAA
1 TGTAATAATATTTTAATTTAACATA-ATTTTTTTAATTTAACTCAACAA
35009577 TGTAATAATATTTTAATTTAACATAATTTTTTTAATTTAACTCAA
1 TGTAATAATATTTTAATTTAACATAATTTTTTTAATTTAACTCAA
35009622 ATAATTTTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 19 0.43
49 25 0.57
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (48 bp):
TGTAATAATATTTTAATTTAACATAATTTTTTTAATTTAACTCAACAA
Found at i:35009608 original size:18 final size:19
Alignment explanation
Indices: 35009581--35009617 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35009571 CAACAATGTA
35009581 ATAA-TATTTTAATTTAAC
1 ATAATTATTTTAATTTAAC
*
35009599 ATAATTTTTTTAATTTAAC
1 ATAATTATTTTAATTTAAC
35009618 TCAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAATTATTTTAATTTAAC
Found at i:35020429 original size:16 final size:16
Alignment explanation
Indices: 35020390--35020435 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
35020380 TTAAAATTTA
*
35020390 TTATT-AATAACACTG
1 TTATTAAATAATACTG
35020405 TATATTAAATAATACTG
1 T-TATTAAATAATACTG
35020422 TTATTAAAATAATA
1 TTATT-AAATAATA
35020436 AATAGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 18 0.67
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (16 bp):
TTATTAAATAATACTG
Found at i:35020446 original size:18 final size:19
Alignment explanation
Indices: 35020423--35020469 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
35020413 ATAATACTGT
35020423 TATTAAAATAATAA-ATAG
1 TATTAAAATAATAATATAG
* * *
35020441 TATT-AATTAATAATTTAT
1 TATTAAAATAATAATATAG
35020459 TATTAAAATAA
1 TATTAAAATAA
35020470 GATTATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATAATATAG
Found at i:35027697 original size:21 final size:21
Alignment explanation
Indices: 35027673--35027712 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35027663 ATTAAAGTGT
35027673 AATTTTATTATTATTAATTTA
1 AATTTTATTATTATTAATTTA
35027694 AATTTTATTATTATTAATT
1 AATTTTATTATTATTAATT
35027713 AATTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTTATTATTATTAATTTA
Found at i:35027718 original size:24 final size:20
Alignment explanation
Indices: 35027672--35027716 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
35027662 GATTAAAGTG
35027672 TAATTTTATTATTATTAATT
1 TAATTTTATTATTATTAATT
35027692 TAAATTTTATTATTATTAA-T
1 T-AATTTTATTATTATTAATT
35027712 TAATT
1 TAATT
35027717 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.17
20 3 0.12
21 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTATTATTATTAATT
Found at i:35028019 original size:15 final size:14
Alignment explanation
Indices: 35027984--35028019 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
35027974 TAATCCCTTT
35027984 TAATTTTATTTTCA
1 TAATTTTATTTTCA
*
35027998 AAATTTTATTTTCTA
1 TAATTTTATTTTC-A
35028013 TAATTTT
1 TAATTTT
35028020 CCAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTATTTTCA
Found at i:35028815 original size:3 final size:3
Alignment explanation
Indices: 35028807--35028854 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
35028797 GAACATTGCA
35028807 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35028855 CAAATCTACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35031365 original size:127 final size:126
Alignment explanation
Indices: 35031121--35031368 Score: 424
Period size: 127 Copynumber: 2.0 Consensus size: 126
35031111 GGAGTATAGA
*
35031121 AATCATTGTGGCCAAAGTAGGAAATATGGAAGTTATGTGAATATATGGAAAACATGGCAAAACAA
1 AATCATTGTGGCAAAAGTAGGAAATATGGAAGTTATGTGAATATATGGAAAACATGGCAAAACAA
* *
35031186 TGAAGGATTAATAGGAAATTTACTTATATTATTAGCAGTGGCAGAACTACGTTAAGGTCCT
66 TGAAGGATTAATAGGAAATTTACTTACATTATTAGCAGTGGCAGAACCACGTTAAGGTCCT
* *
35031247 AATCATTGTGGCAAAAAGTAGGAAATATGGAAGTTTTGTGAATATATGGAAAAGATGGCAAAACA
1 AATCATTGTGGC-AAAAGTAGGAAATATGGAAGTTATGTGAATATATGGAAAACATGGCAAAACA
* *
35031312 ATGAAGGATTAATAGGAAATTTACTTACATTATTAGCAGTGGCGGAGCCACGTTAAG
65 ATGAAGGATTAATAGGAAATTTACTTACATTATTAGCAGTGGCAGAACCACGTTAAG
35031369 ACCTATGGCC
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
126 12 0.11
127 102 0.89
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (126 bp):
AATCATTGTGGCAAAAGTAGGAAATATGGAAGTTATGTGAATATATGGAAAACATGGCAAAACAA
TGAAGGATTAATAGGAAATTTACTTACATTATTAGCAGTGGCAGAACCACGTTAAGGTCCT
Found at i:35067176 original size:20 final size:20
Alignment explanation
Indices: 35067139--35067177 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35067129 TCTTAACCAT
* * *
35067139 TTTTATATTCTTATATATTA
1 TTTTACATTATTACATATTA
35067159 TTTTACATTATTACATATT
1 TTTTACATTATTACATATT
35067178 TAATTCGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTACATTATTACATATTA
Found at i:35075757 original size:31 final size:31
Alignment explanation
Indices: 35075721--35075783 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
35075711 ATTTGGTTAT
*
35075721 TGAACTATTCGAAAGTTTTCATTTAAGTCAC
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAC
*
35075752 TGAACTATTCAAAAGTTTTTATTTAAGTCAC
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAC
35075783 T
1 T
35075784 AGGCTGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTCAC
Found at i:35081070 original size:27 final size:27
Alignment explanation
Indices: 35081036--35081088 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
35081026 ACATCCCAAC
35081036 TTTACTATTTCCATCAATAGCGGCTTT
1 TTTACTATTTCCATCAATAGCGGCTTT
35081063 TTTACTATTTCCATCAATAGCGGCTT
1 TTTACTATTTCCATCAATAGCGGCTT
35081089 CCCCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTACTATTTCCATCAATAGCGGCTTT
Found at i:35081702 original size:25 final size:25
Alignment explanation
Indices: 35081644--35081695 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
35081634 ATAGAAGTAC
*
35081644 TTTACTTAATTATTTTTTAAGTTAG
1 TTTAATTAATTATTTTTTAAGTTAG
35081669 TTTAATTAATT-TTTTTTGAAGTTAG
1 TTTAATTAATTATTTTTT-AAGTTAG
35081694 TT
1 TT
35081696 ATTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.62
Consensus pattern (25 bp):
TTTAATTAATTATTTTTTAAGTTAG
Found at i:35081979 original size:5 final size:5
Alignment explanation
Indices: 35081965--35082003 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
35081955 AAAATTACTT
* *
35081965 ATATA GTATA ATATA ATATA ATACAA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATA-TA ATATA ATATA ATA
35082004 GAGGTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:35088351 original size:23 final size:23
Alignment explanation
Indices: 35088317--35088466 Score: 78
Period size: 23 Copynumber: 6.4 Consensus size: 23
35088307 ACGCTAGCGC
* **
35088317 GCTTACTATTTCGCATTTTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
35088340 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
* * *
35088363 GCCTACTGATTT-GC-GCTATGTGC
1 GCTTACTG-TTTCGCACCT-TGTGT
* * *
35088386 GCCTACTGATT-ACA-CTGTGTGT
1 GCTTACTGTTTCGCACCT-TGTGT
* *
35088408 GCCTACTGGATT-GCA-CTGTGTGT
1 GCTTACT-GTTTCGCACCT-TGTGT
*
35088431 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT-CGCA-C-CTTGTGT
35088457 GCTTACTGTT
1 GCTTACTGTT
35088467 AAGTACTTCG
Statistics
Matches: 104, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
22 21 0.20
23 61 0.59
24 5 0.05
26 15 0.14
27 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTTGTGT
Found at i:35088438 original size:45 final size:46
Alignment explanation
Indices: 35088335--35088438 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
35088325 TTTCGCATTT
* * *
35088335 TGTGTGCTTACTGTTTCGCACCTTGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCTTACTGATTCACACCTTGTGTGCCTACTGATTTGCACTA
* * *
35088381 TGTGCGCCTACTGATT-ACA-CTGTGTGTGCCTACTGGA-TTGCACTG
1 TGTGTGCTTACTGATTCACACCT-TGTGTGCCTACT-GATTTGCACTA
35088426 TGTGTGCTTACTG
1 TGTGTGCTTACTG
35088439 TTTCCCCAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.04
45 31 0.65
46 15 0.31
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.38
Consensus pattern (46 bp):
TGTGTGCTTACTGATTCACACCTTGTGTGCCTACTGATTTGCACTA
Found at i:35091299 original size:36 final size:36
Alignment explanation
Indices: 35091259--35091329 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
35091249 GATATATGTC
35091259 GTTTTTGTAGAGAGAAAGGAAAATGCGTCCTATAAA
1 GTTTTTGTAGAGAGAAAGGAAAATGCGTCCTATAAA
*
35091295 GTTTTTGTAGAGAGAAAGGAAAATGCGTTCTATAA
1 GTTTTTGTAGAGAGAAAGGAAAATGCGTCCTATAA
35091330 GGTACGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (36 bp):
GTTTTTGTAGAGAGAAAGGAAAATGCGTCCTATAAA
Found at i:35092040 original size:15 final size:16
Alignment explanation
Indices: 35092016--35092049 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35092006 AAAATTTTTA
35092016 TTTTATTTTTTAAAAT
1 TTTTATTTTTTAAAAT
35092032 TTTTA-TTTTTAAAAT
1 TTTTATTTTTTAAAAT
35092047 TTT
1 TTT
35092050 AAGAATCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTTTAAAAT
Found at i:35093155 original size:17 final size:19
Alignment explanation
Indices: 35093133--35093178 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
35093123 TATCAAGATA
35093133 AATATTAAAATAA-A-TTT
1 AATATTAAAATAACACTTT
*
35093150 AATATTAAGATAATCACTTT
1 AATATTAAAATAA-CACTTT
35093170 AATATTAAA
1 AATATTAAA
35093179 CTAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.50
19 1 0.04
20 11 0.46
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
AATATTAAAATAACACTTT
Found at i:35093173 original size:69 final size:71
Alignment explanation
Indices: 35093091--35093228 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 71
35093081 TGATTAAACT
* * * *
35093091 TAATCACTTTAATATTAAATTAAT-ATAATAT-TTA-TCAAGATAAATATTAAAATAAATTTAAT
1 TAATCACTTTAATATTAAACTAATAATAAAATACTAGT-AAAATAAATATTAAAATAAATTTAAT
35093153 ATTAAGA
65 ATTAAGA
* *
35093160 TAATCACTTTAATATTAAACTAATAATAAAATACTAGTAAAATAAGTATTAAATTAAATTTAATA
1 TAATCACTTTAATATTAAACTAATAATAAAATACTAGTAAAATAAATATTAAAATAAATTTAATA
35093225 TTAA
66 TTAA
35093229 ACTGTTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
69 23 0.38
70 6 0.10
71 30 0.50
72 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (71 bp):
TAATCACTTTAATATTAAACTAATAATAAAATACTAGTAAAATAAATATTAAAATAAATTTAATA
TTAAGA
Found at i:35094535 original size:16 final size:16
Alignment explanation
Indices: 35094514--35094544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35094504 CTATGCATGC
*
35094514 AAAATATAAAAGACAA
1 AAAATAAAAAAGACAA
35094530 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
35094545 TAATAGTGAA
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:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAA
Found at i:35094945 original size:33 final size:34
Alignment explanation
Indices: 35094906--35094987 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 34
35094896 TTTCTTAATA
*
35094906 TATTTTTTTGAATTTTTATAAAATTAT-TA-AGTT
1 TATTTTTTTGAAATTTTA-AAAATTATATATAGTT
* *
35094939 T-TTTTTTTCAAATTTTAAATATTATATATAGTTT
1 TATTTTTTTGAAATTTTAAAAATTATATATAG-TT
35094973 TAATTTTTTTGAAAT
1 T-ATTTTTTTGAAAT
35094988 AGTTACAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 7 0.17
32 16 0.40
33 3 0.08
34 3 0.08
36 11 0.28
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (34 bp):
TATTTTTTTGAAATTTTAAAAATTATATATAGTT
Found at i:35095023 original size:9 final size:9
Alignment explanation
Indices: 35094998--35095065 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
35094988 AGTTACAATT
35094998 TTTTTAA-A
1 TTTTTAATA
35095006 TTTTT--TA
1 TTTTTAATA
35095013 TTTTTAATA
1 TTTTTAATA
*
35095022 TTTTAAATA
1 TTTTTAATA
35095031 CTATTTTGAATTA
1 -T-TTTT-AA-TA
*
35095044 TTTTTAAAA
1 TTTTTAATA
35095053 TTTTTAAT-
1 TTTTTAATA
35095061 TTTTT
1 TTTTT
35095066 TTGAATTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
7 6 0.12
8 10 0.20
9 18 0.37
10 3 0.06
11 7 0.14
12 3 0.06
13 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTAATA
Found at i:35095045 original size:31 final size:30
Alignment explanation
Indices: 35095010--35095086 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
35095000 TTTAAATTTT
35095010 TTATTTTTAATATTTTAAATACTATTTTGAA
1 TTATTTTTAATATTTTAAAT-CTATTTTGAA
* * * *
35095041 TTATTTTTAAAATTTTTAATTTTTTTTGAA
1 TTATTTTTAATATTTTAAATCTATTTTGAA
**
35095071 TT-TTCATAATATTTTA
1 TTATTTTTAATATTTTA
35095087 GCAATATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 10 0.26
30 10 0.26
31 18 0.47
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
TTATTTTTAATATTTTAAATCTATTTTGAA
Found at i:35097003 original size:15 final size:15
Alignment explanation
Indices: 35096966--35097009 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
35096956 ACTCTCAAAT
35096966 TTTCTTTTTCCTTTTCA
1 TTTC-TTTTCC-TTTCA
**
35096983 AATCTTTTCCTTTCA
1 TTTCTTTTCCTTTCA
35096998 TTTCTTTTCCTT
1 TTTCTTTTCCTT
35097010 GCATATACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 15 0.65
16 6 0.26
17 2 0.09
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTCTTTTCCTTTCA
Done.