Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 3 of 109
Found at i:776139 original size:16 final size:16
Alignment explanation
Indices: 776093--776139 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
776083 CCTATTACGT
*
776093 CTCTATTCCATTACGC
1 CTCTATTCCATTACAC
* *
776109 ATCTATTTCATTACAC
1 CTCTATTCCATTACAC
776125 CTCTATTCCATTACA
1 CTCTATTCCATTACA
776140 ACGAACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.32, G:0.02, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAC
Found at i:778395 original size:16 final size:15
Alignment explanation
Indices: 778374--778412 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
778364 GGACTAGGTA
778374 TTCTTTTTTTTTCTT
1 TTCTTTTTTTTTCTT
*
778389 CTTCTTTTCTTTTCTT
1 -TTCTTTTTTTTTCTT
778405 TT-TTTTTT
1 TTCTTTTTT
778413 AACCACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 2 0.10
16 14 0.67
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTCTTTTTTTTTCTT
Found at i:778409 original size:13 final size:13
Alignment explanation
Indices: 778374--778411 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
778364 GGACTAGGTA
778374 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
*
778387 TTCTTCTTTTCTT-
1 TTCTT-TTTTTTTC
778400 TTCTTTTTTTTT
1 TTCTTTTTTTTT
778412 TAACCACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 6 0.27
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:778948 original size:17 final size:19
Alignment explanation
Indices: 778913--778955 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
778903 ATTACAAAAT
778913 ATTATAAAAAAAGTATAAA
1 ATTATAAAAAAAGTATAAA
778932 ATTATAAAAAAA-T-TAAA
1 ATTATAAAAAAAGTATAAA
*
778949 AATATAA
1 ATTATAA
778956 GACAAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
ATTATAAAAAAAGTATAAA
Found at i:779216 original size:45 final size:46
Alignment explanation
Indices: 779149--779296 Score: 230
Period size: 46 Copynumber: 3.3 Consensus size: 46
779139 TACGTAAGAT
*
779149 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
779192 CACCTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
779238 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
779284 TACTTATCACTTT
1 CACTTATCACTTT
779297 ATCAANNNNN
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
43 9 0.10
44 5 0.05
45 20 0.21
46 60 0.64
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:788471 original size:32 final size:32
Alignment explanation
Indices: 788427--788491 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
788417 TAATAAGGTA
788427 AGATTTCGATCCTTAATTATAAGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
* *
788459 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
788491 A
1 A
788492 ATAGAAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
AGATTTCGATCCTTAATTATAAGGATTCCAAC
Found at i:798995 original size:35 final size:35
Alignment explanation
Indices: 798927--798995 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
798917 AGCTGAAAAC
*
798927 TATAAAAAATACATTTATAATAAATTTTGCTATTT
1 TATAAAAAATAAATTTATAATAAATTTTGCTATTT
*
798962 TATAGAAAAATGAAATTT-TAAT-AATTTTTCTATT
1 TATA-AAAAAT-AAATTTATAATAAATTTTGCTATT
798996 AATTCAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.50
36 10 0.33
37 5 0.17
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (35 bp):
TATAAAAAATAAATTTATAATAAATTTTGCTATTT
Found at i:805239 original size:17 final size:18
Alignment explanation
Indices: 805217--805251 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
805207 TCGAACGGCG
805217 GAAAAGAAG-AAGGGAAA
1 GAAAAGAAGAAAGGGAAA
805234 GAAAAGAAGAAAGGGAAA
1 GAAAAGAAGAAAGGGAAA
805252 ATTGGGGATT
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAAGAAGAAAGGGAAA
Found at i:809977 original size:30 final size:32
Alignment explanation
Indices: 809934--810010 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
809924 TTTATAATTG
*
809934 TTAAAATATAA-TTTTACTAATTTTTAAAGGA
1 TTAAAATATAATTTTTACTAATTTTTAAAAGA
* * *
809965 TTAAATTA-AATTTTTATTATTTTTTAAAAGA
1 TTAAAATATAATTTTTACTAATTTTTAAAAGA
* *
809996 TTAAAGTGTAATTTT
1 TTAAAATATAATTTT
810011 ATCATTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 2 0.05
31 30 0.79
32 6 0.16
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (32 bp):
TTAAAATATAATTTTTACTAATTTTTAAAAGA
Found at i:810492 original size:23 final size:23
Alignment explanation
Indices: 810466--810512 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
810456 TATAAGATAG
810466 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
810489 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
810512 T
1 T
810513 TTGTTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (23 bp):
TCACTAAACTAATCGAATTTGTC
Found at i:810981 original size:162 final size:163
Alignment explanation
Indices: 810686--810989 Score: 459
Period size: 162 Copynumber: 1.9 Consensus size: 163
810676 TTCTTTTTTC
* * *
810686 TTTTCTTTGCGACATTTCACCTAAAACGCTAAAAAAATAAATTTATTAGTTAAGTTTGATAAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
* *
810751 AAATAGAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTCTTTT
66 AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
810816 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
131 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
* * *
810849 TTTTCTTTGTGACATTTTACCTAAAAAGCTACAAAAATAAATTTATCAGATATA-TTTGATAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATA-AGTTTGATAAAA
* * * * * *
810913 AAAA-CCAAGAAATAGGAACACCAGAAAGATCCAAAATAATATTTTTCATCTTTTTTCATTATTT
65 AAAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTT
810977 TAAAATTAACCCT
130 TAAAATTAACCCT
810990 CAATACACAA
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 65 0.52
163 60 0.48
164 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (163 bp):
TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
Found at i:818105 original size:2 final size:2
Alignment explanation
Indices: 818094--818127 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
818084 AAAATTTAAT
818094 TA TA -A 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
818128 GTTTCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:821426 original size:31 final size:31
Alignment explanation
Indices: 821366--821427 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
821356 AATAACAATC
*
821366 TAGTAACTTAAATGAAAATTTTCATATAGTT
1 TAGTAACTTAAATGAAAATTTTCAAATAGTT
821397 TAGTAACTTAAATGAAAATTTAT-AAATAGTT
1 TAGTAACTTAAATGAAAATTT-TCAAATAGTT
821428 CAGTGATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (31 bp):
TAGTAACTTAAATGAAAATTTTCAAATAGTT
Found at i:825583 original size:39 final size:39
Alignment explanation
Indices: 825539--825613 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
825529 TCCAAACAAA
825539 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
825578 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
825614 AGTAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (39 bp):
GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
Found at i:829472 original size:15 final size:15
Alignment explanation
Indices: 829452--829482 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
829442 CGCCAAACAG
829452 CTTTTTTATTCACAA
1 CTTTTTTATTCACAA
829467 CTTTTTTATTCACAA
1 CTTTTTTATTCACAA
829482 C
1 C
829483 GACCATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTTTTTATTCACAA
Found at i:840265 original size:22 final size:22
Alignment explanation
Indices: 840237--840278 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
840227 AGAATTTAAA
840237 TTTTATAAAGGGATATAAAATT
1 TTTTATAAAGGGATATAAAATT
840259 TTTTATAAAGGGATATAAAA
1 TTTTATAAAGGGATATAAAA
840279 ATTAAGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
TTTTATAAAGGGATATAAAATT
Found at i:841285 original size:13 final size:13
Alignment explanation
Indices: 841267--841291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
841257 CTAAAGCCCT
841267 TATAAACTAGAAG
1 TATAAACTAGAAG
841280 TATAAACTAGAA
1 TATAAACTAGAA
841292 ACCTTCCATA
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:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TATAAACTAGAAG
Found at i:850343 original size:55 final size:57
Alignment explanation
Indices: 850247--850428 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 57
850237 CTAGTAATAT
* * * * * * *
850247 CTAACTATTAGTAAATTATTTTTTGGTCACTCAATTGTGAAAAGTTACAAGATGGTTA
1 CTAATTATTAGT-AATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
* * *
850305 CCTAATTATTAGT-A-T-TTTTTTGGTCACCCAACCATGAAAAGCTACAAAATGATCA
1 -CTAATTATTAGTAATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
*
850360 CTAATTATTAGTAAATTTCTTTTTTGGTCACCTAACTATGAAAAGTTACAAAATGGTCA
1 CTAATTATTAGT-AA-TTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
850419 CTCAATTATT
1 CT-AATTATT
850429 CAATTTTTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
54 12 0.12
55 32 0.31
56 2 0.02
57 1 0.01
58 1 0.01
59 49 0.47
60 7 0.07
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (57 bp):
CTAATTATTAGTAATTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCA
Found at i:851676 original size:25 final size:27
Alignment explanation
Indices: 851648--851697 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
851638 GGACTCAAAT
851648 TTTGGAAATTT-T-AGAA-GAAAATAAG
1 TTTGG-AATTTATAAGAAGGAAAATAAG
851673 TTTGGAATTTATAAGAAGGAAAATA
1 TTTGGAATTTATAAGAAGGAAAATA
851698 TTTGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 4 0.18
27 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (27 bp):
TTTGGAATTTATAAGAAGGAAAATAAG
Found at i:851701 original size:25 final size:23
Alignment explanation
Indices: 851644--851701 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
851634 CCAGGGACTC
851644 AAAT-TTTGGAAATTTTAGAAGA
1 AAATATTTGGAAATTTTAGAAGA
851666 AAATAAGTTTGG-AATTTATAAGAAGGA
1 AAAT-A-TTTGGAAATTT-T-AGAA-GA
851693 AAATATTTG
1 AAATATTTG
851702 AATAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 4 0.13
24 5 0.17
25 10 0.33
26 5 0.17
27 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (23 bp):
AAATATTTGGAAATTTTAGAAGA
Found at i:860102 original size:14 final size:14
Alignment explanation
Indices: 860083--860112 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
860073 TTTTTGAGAA
860083 TTTAGTCATTTTAC
1 TTTAGTCATTTTAC
860097 TTTAGTCATTTTAC
1 TTTAGTCATTTTAC
860111 TT
1 TT
860113 GCCTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAGTCATTTTAC
Found at i:862187 original size:60 final size:60
Alignment explanation
Indices: 862094--862663 Score: 575
Period size: 60 Copynumber: 9.6 Consensus size: 60
862084 CTCAAGGTAA
* ** * *
862094 TAATTTGTCGTTAGCTTAAA-TCCCAGCATTAAGCCTTTTGTATTGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * *
862154 TAATTTGTTGTTAGCTTAAA-TACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * * *
862214 TAATTTGTTGTTAGCTTAAA-TCCCTGCATTAA--ATGTTCGCAATGTGCTCCACGTGTTGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCT-TTTGTAACGTGTTCCACGTGATGT
* ** * * *
862273 TAATTTCTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTCATGACATGTTCCACGTGATAT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * *
862333 TAATTTGTTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
** * *
862393 TAATTTGCCGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * *
862453 TAATTTGCTGTTAGCTTAAAGTCCAGCCTTAGGCCTTTTGTAACGAGTTCCACGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * * *
862513 TAATTTGTTGTTTGCTTAAA-TCCCAGCATTAAACCTTCTG--ATGTGCTCCGCGTG-TCAT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGAT-GT
* * ** ** * *
862571 TAGTTTGTTGTTAACTTAAAGTCTTGCATTAAGCCTTTCATAACGTGCTCCACATGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
862631 TAATTTGTTGTTAGCTTAAA-TCCTAGCATTAAG
1 TAATTTGTTGTTAGCTTAAAGTCC-AGCATTAAG
862664 TCTTCTCCAA
Statistics
Matches: 428, Mismatches: 71, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
57 1 0.00
58 41 0.10
59 51 0.12
60 333 0.78
61 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (60 bp):
TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
Found at i:880353 original size:17 final size:18
Alignment explanation
Indices: 880326--880359 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
880316 ACTTGTTTTA
880326 AAAATATTTTAAAATATT
1 AAAATATTTTAAAATATT
880344 AAAA-ATTTTAAAATAT
1 AAAATATTTTAAAATAT
880360 AATTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATTTTAAAATATT
Found at i:886042 original size:29 final size:31
Alignment explanation
Indices: 885989--886052 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
885979 TGAGAAGCCT
*
885989 TTATTTGAACACTTTTGAAAATGTTTGACCC
1 TTATTTGAACACTTTTGAAAATGTTTAACCC
* *
886020 TTATTTGACCA-TTTT-AAAATGTTTAACTC
1 TTATTTGAACACTTTTGAAAATGTTTAACCC
886049 TTAT
1 TTAT
886053 GTAAGCAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATTTGAACACTTTTGAAAATGTTTAACCC
Found at i:886623 original size:41 final size:41
Alignment explanation
Indices: 886566--886646 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
886556 AAACCTGGGT
886566 CCTTTAGTTCAATGTAA-GCTAAAAACTAGTGTAACTAGGGC
1 CCTTTAGTTCAATGTAATG-TAAAAACTAGTGTAACTAGGGC
886607 CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGG
1 CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGG
886647 ATGGCAATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (41 bp):
CCTTTAGTTCAATGTAATGTAAAAACTAGTGTAACTAGGGC
Found at i:894767 original size:90 final size:90
Alignment explanation
Indices: 894586--895024 Score: 400
Period size: 89 Copynumber: 4.8 Consensus size: 90
894576 CAAAATACTA
* * * * ** *
894586 GAACTAAATCAGTTACAAAACTCATCTCCAAAATTACAGAGCCAACAAAAAAAAAAAACTCTAGA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAG-C--C---AAATTAAAACTCTATA
* **
894651 ATTCAAACTTTTTAAAAAAAAAATTCAAATATTT
60 ATTCAAAC-ATTT--AAAAAAAATTCAAATATGC
* * *
894685 GAACTGAATCACTTACAAAATTCATCTGCATAATTACAAAGCCAAATTAAAACTCTATAATTTAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
894750 ACATTTAAAAAAAATTCAAATATGC
66 ACATTTAAAAAAAATTCAAATATGC
* * * *
894775 GAAGTGGATCACTTACAAGACTCATCTGCAAAATTACAAAGCTAAATTAAAACTC---AATTCAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
* * * * *
894837 ACTTTTTTTTTTACAAAAATTCAAATACGT
66 AC-----ATTTAAAAAAAATTCAAATATGC
* * * * * *
894867 GAACGGAACCACTTACGAAACTCATCTGCAAAATTACAAAGCCAAATAAAAACTCTAGAATACAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
*****
894932 ACATTT-TTTTTAATTCAAATATGC
66 ACATTTAAAAAAAATTCAAATATGC
* * *
894956 GAACTGAATCACTTACAAAACTTATCTGCAAAATTACAAAGCTAAATTAAACCTCTATAATTCAA
1 GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
895021 ACAT
66 ACAT
895025 GAAAGAGAAA
Statistics
Matches: 281, Mismatches: 51, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
87 8 0.03
89 71 0.25
90 69 0.25
92 68 0.24
93 20 0.07
95 8 0.03
96 1 0.00
98 1 0.00
99 35 0.12
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (90 bp):
GAACTGAATCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATTAAAACTCTATAATTCAA
ACATTTAAAAAAAATTCAAATATGC
Found at i:894882 original size:182 final size:181
Alignment explanation
Indices: 894669--895006 Score: 487
Period size: 182 Copynumber: 1.9 Consensus size: 181
894659 TTTTTAAAAA
** * * * * *
894669 AAAAATTCAAATATTTGAACTGAATCACTTACAAAATTCATCTGCATAATTACAAAGCCAAATTA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
* ** * * *
894734 AAACTCTATAATTTAAACATTTAAAAAAAATTCAAATATGCGAAGTGGATCACTTACAAGACTCA
66 AAACTCTAGAATACAAACATTT-AAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCA
894799 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
130 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
*
894851 AAAAATTCAAATACGTGAACGGAACCACTTACGAAACTCATCTGCAAAATTACAAAGCCAAATAA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
***** *
894916 AAACTCTAGAATACAAACATTTTTTTTAATTCAAATATGCGAACTGAATCACTTACAAAACTTAT
66 AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
894981 CTGCAAAATTACAAAGCTAAATTAAA
131 CTGCAAAATTACAAAGCTAAATTAAA
895007 CCTCTATAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
181 60 0.44
182 76 0.56
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (181 bp):
AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
CTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
Found at i:896505 original size:25 final size:24
Alignment explanation
Indices: 896477--896524 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
896467 TTTACATGAT
*
896477 GATAGTGTAAATTTGTCACTATATG
1 GATAGTG-AAATTTCTCACTATATG
*
896502 GATATTGAAATTTCTCACTATAT
1 GATAGTGAAATTTCTCACTATAT
896525 TTATTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (24 bp):
GATAGTGAAATTTCTCACTATATG
Found at i:896888 original size:27 final size:27
Alignment explanation
Indices: 896836--896889 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
896826 AAACTTCTAA
*
896836 TATAAAACACATTACTTTATTTTATTT
1 TATAAAACACATTACTTTATTATATTT
* *
896863 TATAAATCACATT-TTTTATTAATATTT
1 TATAAAACACATTACTTTATT-ATATTT
896890 AATATTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
TATAAAACACATTACTTTATTATATTT
Found at i:902154 original size:44 final size:44
Alignment explanation
Indices: 902106--902200 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 44
902096 TTATACAGTC
*
902106 AAATTATGTTCATGTCATATTTGCACTTTCATTTTGGTCATTCA
1 AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
*
902150 AAATTATGTTCATATCATATTTGCATTTTCATTTTGGTCATTCA
1 AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
902194 ATAATTA
1 A-AATTA
902201 GGTCGGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 43 0.90
45 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (44 bp):
AAATTATGTTCATATCATATTTGCACTTTCATTTTGGTCATTCA
Found at i:905350 original size:22 final size:22
Alignment explanation
Indices: 905325--905372 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
905315 AATATTTTTT
* *
905325 TATAAAATTTAATTATAAAA-TA
1 TATAAAATTCAA-TACAAAATTA
905347 TATAAAATTCAATACAAAATTA
1 TATAAAATTCAATACAAAATTA
905369 TATA
1 TATA
905373 TTTTTAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAAATTCAATACAAAATTA
Found at i:913025 original size:31 final size:31
Alignment explanation
Indices: 912990--913055 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
912980 AGATATGATC
912990 TTTTAAATACACGAAAATATTAGAACTCGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
* *
913021 TTTTAAATACACGAAATTATTAGAACTTGAA
1 TTTTAAATACACGAAAATATTAGAACTCGAA
913052 TTTT
1 TTTT
913056 TTGTATTACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
TTTTAAATACACGAAAATATTAGAACTCGAA
Found at i:915360 original size:2 final size:2
Alignment explanation
Indices: 915353--915408 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
915343 TATGCTCAAG
915353 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
915395 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
915409 GAGTGAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:927605 original size:13 final size:14
Alignment explanation
Indices: 927589--927622 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
927579 AATAAATATA
927589 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
927602 TATTTTTTAATTTT
1 TATTTTTTAATTTT
927616 TAATTTT
1 T-ATTTT
927623 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:933864 original size:17 final size:17
Alignment explanation
Indices: 933842--933875 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
933832 CATTTACGAG
933842 CCAAATGTCGTTTTTAA
1 CCAAATGTCGTTTTTAA
*
933859 CCAAATGTGGTTTTTAA
1 CCAAATGTCGTTTTTAA
933876 AAGATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
CCAAATGTCGTTTTTAA
Found at i:934817 original size:21 final size:21
Alignment explanation
Indices: 934769--934810 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
934759 TTTTCCTAGG
* *
934769 ATGTGAATTAGATTGAATTGA
1 ATGTAAATTAGATTAAATTGA
*
934790 ATGTAAATTATATTAAATTGA
1 ATGTAAATTAGATTAAATTGA
934811 TGCTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGTAAATTAGATTAAATTGA
Found at i:935300 original size:26 final size:25
Alignment explanation
Indices: 935270--935335 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
935260 GCAACTCTTA
* *
935270 TGAGCGTCCCGTTATATGGCTC-TTCG
1 TGAGCTTCCCGTTA-AAGGCTCATT-G
*
935296 TGAGCTTCTCGATTAAAGGCTCATTG
1 TGAGCTTCCCG-TTAAAGGCTCATTG
935322 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
935336 GTGTGCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.09
26 26 0.76
27 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTAAAGGCTCATTG
Found at i:935400 original size:24 final size:24
Alignment explanation
Indices: 935373--935431 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
935363 GCTATCTGAT
*
935373 GCTACCTGTTAATTGCTCTTCGAA
1 GCTACCCGTTAATTGCTCTTCGAA
* * *
935397 GCTACCCATTGATTGCTCTTCGGA
1 GCTACCCGTTAATTGCTCTTCGAA
935421 GCTACCCGTTA
1 GCTACCCGTTA
935432 TAGGCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (24 bp):
GCTACCCGTTAATTGCTCTTCGAA
Found at i:937660 original size:36 final size:36
Alignment explanation
Indices: 937612--937683 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
937602 GGTTGGTGTC
*
937612 GGTGTTTGAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
937648 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
1 GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
937684 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (36 bp):
GGTGTTTCAGGGTCAAGCTAAATCTGAGCTTAGATT
Found at i:939900 original size:10 final size:11
Alignment explanation
Indices: 939874--939899 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
939864 TTAAAAATAA
939874 AAAAATATTTT
1 AAAAATATTTT
939885 AAAAATATTTT
1 AAAAATATTTT
939896 AAAA
1 AAAA
939900 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:940597 original size:17 final size:18
Alignment explanation
Indices: 940576--940610 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
940566 TGAAAAATAA
940576 ATTTTT-AATT-TTTTTT
1 ATTTTTAAATTATTTTTT
940592 ATTTTTAAATTATTTTTT
1 ATTTTTAAATTATTTTTT
940610 A
1 A
940611 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTAAATTATTTTTT
Found at i:945141 original size:18 final size:18
Alignment explanation
Indices: 945114--945149 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
945104 GTATAAAGAG
*
945114 AATTAAATAAAATGTTTT
1 AATTAAATAAAATATTTT
*
945132 AATTAGATAAAATATTTT
1 AATTAAATAAAATATTTT
945150 TTATAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTAAATAAAATATTTT
Found at i:960585 original size:809 final size:809
Alignment explanation
Indices: 959028--960638 Score: 2769
Period size: 809 Copynumber: 2.0 Consensus size: 809
959018 GCTTGATTTA
*
959028 CAGCAGATGCAGCAGCAACATATTCAGCTTCCGCTTTTGACTGTGCTACCAGACTTTGCTTTTTA
1 CAGCAGATGCAGCAGCAACATATTCAGCTTCCGCTGTTGACTGTGCTACCAGACTTTGCTTTTTA
*
959093 GAACTCCAGCAAAACATGCCTGAGCCAAGACTAAAGGCATATCCAGATGTGCTCCTCATGTCATC
66 GAACTCCAGCAAAACATGCATGAGCCAAGACTAAAGGCATATCCAGATGTGCTCCTCATGTCATC
959158 ACAAGATCCAGCCCAGTCACTATCAACATAGCCTATCAGCTTCATGTTTTCAGCCCTTTTGAACA
131 ACAAGATCCAGCCCAGTCACTATCAACATAGCCTATCAGCTTCATGTTTTCAGCCCTTTTGAACA
959223 ATACACCATGATCAATGGTGCCTTTGATGTATCTTAGCACTCTTTTAGCTGCTTGAAAGTGCTGA
196 ATACACCATGATCAATGGTGCCTTTGATGTATCTTAGCACTCTTTTAGCTGCTTGAAAGTGCTGA
*
959288 TCATTGCAGCAATTCATGTATCTCGATAGCACACTAACAGCAAACATGATATCGGGTCTTGTTGC
261 TCATTGCAGCAATTCATGTATCTCGATAGCACACTAACAGCAAACATGATATCGGGTCTTGTTAC
959353 AGTCAAATACAACAGACTACCAATGAGACTCTTGTACATAGTCTCACAAATTGGTTCACCACTCC
326 AGTCAAATACAACAGACTACCAATGAGACTCTTGTACATAGTCTCACAAATTGGTTCACCACTCC
959418 CTTGCCTCGAAAGCTTCACTCCAACAGCCATTGGTGTGCTTGTTGGCTTGCAGTTCTTCATAGAG
391 CTTGCCTCGAAAGCTTCACTCCAACAGCCATTGGTGTGCTTGTTGGCTTGCAGTTCTTCATAGAG
* * * *
959483 AACTTACCCAGAATCTTCATAGTAAAGGAACTCTGACTGAGAAAGATTTCTTTTGCTGTTTGCTT
456 AACTTACCCAGAATCTTCATAGTAAAAGAACTCTGACTAAGAAAGATTCCCTTTGCTGTTTGCTT
* * *
959548 CACCTCTATTCCAAGGAAGTAGTTCATTCTGCCTAGATCAGACATTTCAAACATCTCTATCATTT
521 CACCTCCATTCCAAGGAAGTAGTTCATTCTGCCTAAATCAGACATTTCAAACATCTCCATCATTT
* * *
959613 TTCTTTTGAAGTCCTGTAGCATTCTTTTATCTCCTCCTGTCACCAATAAATCATCAACATAGAGT
586 TTCTTTTGAAATCCTGTAGCATTCTTCTATCTCCTCCAGTCACCAATAAATCATCAACATAGAGT
* * *
959678 GATAAAATGAGCTGAGTTTCAGCTTGATCTTTCTTTACATACAATGTTGGTTCACTGGCACTTCT
651 GACAAAATAAGCTGAGTTTCAGCTTGATCTTTCTTCACATACAATGTTGGTTCACTGGCACTTCT
* ** * * *
959743 CTCGAATTCCAAACTGATTAGATAGGAGTCAATTTGAGCATACCAGACTCGAGGTGCCTGCTTCA
716 CTCAAATTCCAAACTGACAAGATAAGAGTCAATTCGAGCATACCAGACTCGAGGAGCCTGCTTCA
*
959808 GGCCATACAAGGCCTTTTTCAGCCTATAC
781 GGCCATACAAAGCCTTTTTCAGCCTATAC
*
959837 CAGCAGATGCAGCAGCAACATATTCAGCTTCTGCTGTTGACTGTGCTACCAGACTTTGCTTTTTA
1 CAGCAGATGCAGCAGCAACATATTCAGCTTCCGCTGTTGACTGTGCTACCAGACTTTGCTTTTTA
*
959902 GAACTCCAGCAAAACATGCATGAGCCAAGACTAAATGCATATCCAGATGTGCTCCTCATGTCATC
66 GAACTCCAGCAAAACATGCATGAGCCAAGACTAAAGGCATATCCAGATGTGCTCCTCATGTCATC
*
959967 ACAAGATCCAGCCCAGTCACTATCAACATAGCCTATCAGCTTCATGTTTTCTGCCCTTTTGAACA
131 ACAAGATCCAGCCCAGTCACTATCAACATAGCCTATCAGCTTCATGTTTTCAGCCCTTTTGAACA
*
960032 ATACGCCATGATCAATGGTGCCTTTGATGTATCTTAGCACTCTTTTAGCTGCTTGAAAGTGCTGA
196 ATACACCATGATCAATGGTGCCTTTGATGTATCTTAGCACTCTTTTAGCTGCTTGAAAGTGCTGA
*
960097 TCATTGCAGCAATTCATGTATCTGGATAGCACACTAACAGCAAACATGATATCGGGTCTTGTTAC
261 TCATTGCAGCAATTCATGTATCTCGATAGCACACTAACAGCAAACATGATATCGGGTCTTGTTAC
* **
960162 AGTCAAATACAACAGACTACCAATGAGACTTTTGTACATAGTCTCGTAAATTGGTTCACCACTCC
326 AGTCAAATACAACAGACTACCAATGAGACTCTTGTACATAGTCTCACAAATTGGTTCACCACTCC
960227 CTTGCCTCGAAAGCTTCACTCCAACAGCCATTGGTGTGCTTGTTGGCTTGCAGTTCTTCATAGAG
391 CTTGCCTCGAAAGCTTCACTCCAACAGCCATTGGTGTGCTTGTTGGCTTGCAGTTCTTCATAGAG
* *
960292 AACTTATCCAGGATCTTCATAGTAAAAGAACTCTGACTAAGAAAGATTCCCTTTGCTGTTTGCTT
456 AACTTACCCAGAATCTTCATAGTAAAAGAACTCTGACTAAGAAAGATTCCCTTTGCTGTTTGCTT
* *
960357 CACTTCCATTCCAAGGAAGTAGTTCATTCTGCCTAAATCAGACATTTCAAACATTTCCATCATTT
521 CACCTCCATTCCAAGGAAGTAGTTCATTCTGCCTAAATCAGACATTTCAAACATCTCCATCATTT
* *
960422 TTCTTTTGAAATCTTCG-AGCATTCTTCTATCTCCTCCAGTTACCAATAAATCATCAACATAGAG
586 TTCTTTTGAAATCCT-GTAGCATTCTTCTATCTCCTCCAGTCACCAATAAATCATCAACATAGAG
** * * *
960486 TGACAGGATAAGCTGAGTTTCAGCTTGGT-TCTTCTTCACATACAGTGTTGGTTCACTGGGACTT
650 TGACAAAATAAGCTGAGTTTCAGCTTGATCT-TTCTTCACATACAATGTTGGTTCACTGGCACTT
* *
960550 CTCTCAAATTCCAAACTGAGCAAG-TAAGAGTCAATTCGAGCATACCAGGCTCGAGGAGCCTGTT
714 CTCTCAAATTCCAAACTGA-CAAGATAAGAGTCAATTCGAGCATACCAGACTCGAGGAGCCTGCT
*
960614 TCAGGCCATATAAAGCCTTTTTCAG
778 TCAGGCCATACAAAGCCTTTTTCAG
960639 TCTGTACACC
Statistics
Matches: 754, Mismatches: 45, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
808 1 0.00
809 750 0.99
810 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (809 bp):
CAGCAGATGCAGCAGCAACATATTCAGCTTCCGCTGTTGACTGTGCTACCAGACTTTGCTTTTTA
GAACTCCAGCAAAACATGCATGAGCCAAGACTAAAGGCATATCCAGATGTGCTCCTCATGTCATC
ACAAGATCCAGCCCAGTCACTATCAACATAGCCTATCAGCTTCATGTTTTCAGCCCTTTTGAACA
ATACACCATGATCAATGGTGCCTTTGATGTATCTTAGCACTCTTTTAGCTGCTTGAAAGTGCTGA
TCATTGCAGCAATTCATGTATCTCGATAGCACACTAACAGCAAACATGATATCGGGTCTTGTTAC
AGTCAAATACAACAGACTACCAATGAGACTCTTGTACATAGTCTCACAAATTGGTTCACCACTCC
CTTGCCTCGAAAGCTTCACTCCAACAGCCATTGGTGTGCTTGTTGGCTTGCAGTTCTTCATAGAG
AACTTACCCAGAATCTTCATAGTAAAAGAACTCTGACTAAGAAAGATTCCCTTTGCTGTTTGCTT
CACCTCCATTCCAAGGAAGTAGTTCATTCTGCCTAAATCAGACATTTCAAACATCTCCATCATTT
TTCTTTTGAAATCCTGTAGCATTCTTCTATCTCCTCCAGTCACCAATAAATCATCAACATAGAGT
GACAAAATAAGCTGAGTTTCAGCTTGATCTTTCTTCACATACAATGTTGGTTCACTGGCACTTCT
CTCAAATTCCAAACTGACAAGATAAGAGTCAATTCGAGCATACCAGACTCGAGGAGCCTGCTTCA
GGCCATACAAAGCCTTTTTCAGCCTATAC
Found at i:968775 original size:21 final size:21
Alignment explanation
Indices: 968733--968780 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
968723 CATCCTTATC
* *
968733 TCCTCCACCCTCACCTGTTAG
1 TCCTCCACCCCCACCTGCTAG
* *
968754 TTCTCCACCCCCAGCTGCTAG
1 TCCTCCACCCCCACCTGCTAG
968775 TCCTCC
1 TCCTCC
968781 GCCACAGTCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.12, C:0.50, G:0.10, T:0.27
Consensus pattern (21 bp):
TCCTCCACCCCCACCTGCTAG
Found at i:974316 original size:42 final size:42
Alignment explanation
Indices: 974265--974393 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 42
974255 AGCTAAACAA
*
974265 AAACTCATAAGGGTTGAACGAAAGCTCGTAAGAGCTGAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
* **
974307 AAACCCATAAGGGTTAAATAAAAGCTC--AATGGAGCTGAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAA--GAGCTGAACGG
* * * *
974349 AAACTCATATGAGTTAAACGAAAGCTCGTGAGAGCTAAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
974391 AAA
1 AAA
974394 GTAAACATGA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.03
42 69 0.96
44 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (42 bp):
AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
Found at i:974368 original size:21 final size:22
Alignment explanation
Indices: 974327--974394 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
974317 GGGTTAAATA
*
974327 AAAGCTCAATG-GAGCTGAACGG
1 AAAGCTC-ATGAGAGCTAAACGG
*
974349 AAA-CTCAT-ATGAGTTAAAC-G
1 AAAGCTCATGA-GAGCTAAACGG
*
974369 AAAGCTCGTGAGAGCTAAACGG
1 AAAGCTCATGAGAGCTAAACGG
974391 AAAG
1 AAAG
974395 TAAACATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
20 6 0.16
21 22 0.59
22 9 0.24
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16
Consensus pattern (22 bp):
AAAGCTCATGAGAGCTAAACGG
Found at i:978649 original size:27 final size:28
Alignment explanation
Indices: 978606--978678 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
978596 TCGTGACAAG
* * * *
978606 TTTA-AAAAATATGAAAATTTATATAAA
1 TTTATAAAAATATAAAAAATCATAAAAA
978633 TTTATAAAAAT-TAAAAAATCATAAAAA
1 TTTATAAAAATATAAAAAATCATAAAAA
*
978660 TTTATAAAAGTAATAAAAA
1 TTTATAAAAAT-ATAAAAA
978679 CATATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 26 0.68
28 6 0.16
29 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (28 bp):
TTTATAAAAATATAAAAAATCATAAAAA
Found at i:978676 original size:36 final size:36
Alignment explanation
Indices: 978607--978678 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
978597 CGTGACAAGT
* * *
978607 TTAAAAAATATGAAAATTTATATAAATTTATAAAAA
1 TTAAAAAATATAAAAATTTATATAAAGTAATAAAAA
978643 TTAAAAAATCATAAAAATTTATA-AAAGTAATAAAAA
1 TTAAAAAAT-ATAAAAATTTATATAAAGTAATAAAAA
978679 CATATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (36 bp):
TTAAAAAATATAAAAATTTATATAAAGTAATAAAAA
Found at i:978707 original size:31 final size:30
Alignment explanation
Indices: 978654--978731 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
978644 TAAAAAATCA
*
978654 TAAAA-ATTTATAAAAGTAATAAAAACATATT
1 TAAAATATTTA-AAAATTAATAAAAACATA-T
* *
978685 TAAAATATTTAAAAATTTATAAAAACGTAT
1 TAAAATATTTAAAAATTAATAAAAACATAT
*
978715 TAAAATACTATAAAAAT
1 TAAAATA-TTTAAAAAT
978732 CATAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.20
31 28 0.68
32 5 0.12
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (30 bp):
TAAAATATTTAAAAATTAATAAAAACATAT
Found at i:978719 original size:20 final size:19
Alignment explanation
Indices: 978696--978788 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
978686 AAAATATTTA
978696 AAAATTTATAAAAACGTATT
1 AAAATTTATAAAAACGTA-T
*
978716 AAAATACTATAAAAA--TCAT
1 AAAAT-TTATAAAAACGT-AT
*
978735 AAAA-TTATAAAAAAAGTATT
1 AAAATTTAT-AAAAACGTA-T
* * *
978755 AAAATTGATATAAACTTAT
1 AAAATTTATAAAAACGTAT
*
978774 AAAAATTATAAAAAC
1 AAAATTTATAAAAAC
978789 AATATATAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
17 3 0.05
18 5 0.09
19 20 0.35
20 18 0.32
21 11 0.19
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATTTATAAAAACGTAT
Found at i:978729 original size:40 final size:39
Alignment explanation
Indices: 978685--978788 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 39
978675 AAAACATATT
978685 TAAAATATTTAAAAATTTATAAAAACGTATTAAAATACTA
1 TAAAATATTTAAAAA-TTATAAAAACGTATTAAAATACTA
* *
978725 TAAAA-A-TCATAAAATTATAAAAAAAGTATTAAAATTGA-TA
1 TAAAATATTTA-AAAATTAT-AAAAACGTATTAAAA-T-ACTA
* *
978765 TAAACT-TATAAAAATTATAAAAAC
1 TAAAATATTTAAAAATTATAAAAAC
978789 AATATATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
38 6 0.12
39 24 0.46
40 20 0.38
41 2 0.04
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (39 bp):
TAAAATATTTAAAAATTATAAAAACGTATTAAAATACTA
Found at i:978749 original size:11 final size:10
Alignment explanation
Indices: 978608--978801 Score: 59
Period size: 9 Copynumber: 19.7 Consensus size: 10
978598 GTGACAAGTT
978608 TAAAAAA-TA
1 TAAAAAATTA
* *
978617 TGAAAATTTA
1 TAAAAAATTA
* *
978627 TATAAATTTA
1 TAAAAAATTA
978637 T-AAAAA-T-
1 TAAAAAATTA
*
978644 TAAAAAATCA
1 TAAAAAATTA
*
978654 TAAAAATTTA
1 TAAAAAATTA
* *
978664 T-AAAAGTAA
1 TAAAAAATTA
*
978673 TAAAAACATATT
1 TAAAAA-AT-TA
*
978685 TAAAATATT-
1 TAAAAAATTA
*
978694 TAAAAATTTA
1 TAAAAAATTA
**
978704 TAAAAACGTA
1 TAAAAAATTA
* *
978714 TTAAAATACTA
1 -TAAAAAATTA
*
978725 T-AAAAATCA
1 TAAAAAATTA
978734 T--AAAATTA
1 TAAAAAATTA
*
978742 TAAAAAAAGTA
1 T-AAAAAATTA
*
978753 T-TAAAATTGA
1 TAAAAAATT-A
* *
978763 TATAAACTTA
1 TAAAAAATTA
978773 T-AAAAATTA
1 TAAAAAATTA
978782 TAAAAACAATATA
1 T-AAAA-AAT-TA
978795 TAAAAAA
1 TAAAAAA
978802 CTTGAATTGG
Statistics
Matches: 135, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
7 1 0.01
8 13 0.10
9 40 0.30
10 38 0.28
11 28 0.21
12 12 0.09
13 3 0.02
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:978787 original size:9 final size:9
Alignment explanation
Indices: 978608--978787 Score: 87
Period size: 10 Copynumber: 18.7 Consensus size: 9
978598 GTGACAAGTT
*
978608 TAAAAAATA
1 TAAAAATTA
*
978617 TGAAAATTTA
1 T-AAAAATTA
*
978627 TATAAATTTA
1 TA-AAAATTA
978637 TAAAAATTA
1 TAAAAATTA
*
978646 -AAAAATCA
1 TAAAAATTA
978654 TAAAAATTTA
1 TAAAAA-TTA
* *
978664 TAAAAGTAA
1 TAAAAATTA
*
978673 TAAAAACATATT
1 T-AAAA-AT-TA
978685 TAAAATATT-
1 TAAAA-ATTA
978694 TAAAAATTTA
1 TAAAAA-TTA
*
978704 TAAAAACGTA
1 TAAAAA-TTA
*
978714 TTAAAATACTA
1 -TAAAA-ATTA
*
978725 TAAAAATCA
1 TAAAAATTA
978734 T-AAAATTA
1 TAAAAATTA
*
978742 TAAAAAAAGTA
1 T--AAAAATTA
*
978753 TTAAAATTGA
1 TAAAAATT-A
*
978763 TATAAACTTA
1 TA-AAAATTA
978773 TAAAAATTA
1 TAAAAATTA
978782 TAAAAA
1 TAAAAA
978788 CAATATATAA
Statistics
Matches: 132, Mismatches: 23, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
8 15 0.11
9 43 0.33
10 46 0.35
11 26 0.20
12 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:978794 original size:20 final size:20
Alignment explanation
Indices: 978735--978799 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
978725 TAAAAATCAT
*
978735 AAAATTATAAAAA-AAGTATT
1 AAAATTATAAAAACAA-TATA
* *
978755 AAAATTGATATAAAC-TTATA
1 AAAATT-ATAAAAACAATATA
978775 AAAATTATAAAAACAATATA
1 AAAATTATAAAAACAATATA
978795 TAAAA
1 -AAAA
978800 AACTTGAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.19
20 19 0.53
21 10 0.28
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATTATAAAAACAATATA
Found at i:979380 original size:17 final size:17
Alignment explanation
Indices: 979328--979396 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 17
979318 NNNNNNNNNN
*
979328 ATTTTT-TAAAATTTA-
1 ATTTTTATAATATTTAT
*
979343 ATTTTTATTAGAGTTTTTAT
1 ATTTTTA-TA-A-TATTTAT
979363 ATTTTTATAATATTTAT
1 ATTTTTATAATATTTAT
979380 ATGTTTTTATAAT-TTTA
1 A--TTTTTATAATATTTA
979397 ATAAGTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.14
17 9 0.20
18 6 0.14
19 16 0.36
20 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTTTATAATATTTAT
Found at i:979395 original size:9 final size:9
Alignment explanation
Indices: 979341--979454 Score: 54
Period size: 9 Copynumber: 11.9 Consensus size: 9
979331 TTTTAAAATT
979341 TAATTTTTA
1 TAATTTTTA
979350 TTAGAGTTTTTA
1 -TA-A-TTTTTA
979362 T-ATTTTTA
1 TAATTTTTA
*
979370 TAATATTTA
1 TAATTTTTA
*
979379 TATGTTTTTA
1 TA-ATTTTTA
*
979389 TAATTTTAA
1 TAATTTTTA
*
979398 TAAGTTTATA
1 TAA-TTTTTA
979408 TCAA-TTTTA
1 T-AATTTTTA
*
979417 TTA-TTTTA
1 TAATTTTTA
*
979425 TTATATTTTTG
1 -TA-ATTTTTA
*
979436 TGATTTTTTTA
1 T-A-ATTTTTA
979447 TAATTTTT
1 TAATTTTT
979455 TAAAGATTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
8 13 0.16
9 28 0.35
10 17 0.21
11 16 0.20
12 6 0.08
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:979405 original size:27 final size:27
Alignment explanation
Indices: 979355--979408 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
979345 TTTTATTAGA
*
979355 GTTTTTATATTTTTATAATATTTATAT
1 GTTTTTATATTTTAATAATATTTATAT
*
979382 GTTTTTATAATTTTAATAA-GTTTATAT
1 GTTTTTAT-ATTTTAATAATATTTATAT
979409 CAATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
GTTTTTATATTTTAATAATATTTATAT
Found at i:979434 original size:19 final size:20
Alignment explanation
Indices: 979345--979454 Score: 65
Period size: 19 Copynumber: 5.8 Consensus size: 20
979335 AAAATTTAAT
* *
979345 TTTTATTAGAGTTTTTAT-A
1 TTTTATTATAATTTTTATGA
*
979364 -TTT-TTATAATATTTAT-A
1 TTTTATTATAATTTTTATGA
* *
979381 TGTTT-TTATAATTTTAATAA
1 T-TTTATTATAATTTTTATGA
* *
979401 GTTTA-TATCAA-TTTTATTA
1 TTTTATTAT-AATTTTTATGA
*
979420 TTTTATTAT-ATTTTTGTGA
1 TTTTATTATAATTTTTATGA
*
979439 TTTTTTTATAATTTTT
1 TTTTATTATAATTTTT
979455 TAAAGATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
17 11 0.15
18 4 0.06
19 44 0.62
20 12 0.17
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATTATAATTTTTATGA
Found at i:980689 original size:11 final size:11
Alignment explanation
Indices: 980673--980697 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
980663 CAGATCTACC
980673 ATTAAAAATTG
1 ATTAAAAATTG
980684 ATTAAAAATTG
1 ATTAAAAATTG
980695 ATT
1 ATT
980698 CTATACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTAAAAATTG
Found at i:987271 original size:20 final size:20
Alignment explanation
Indices: 987220--987273 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
987210 NNTTTATAAA
**
987220 TATTTT-TAATTTTAAAATT
1 TATTTTGTAATTTTTGAATT
*
987239 TATTTTG-ATTTTTTGAATT
1 TATTTTGTAATTTTTGAATT
*
987258 TTTTTTGTAATTTTTG
1 TATTTTGTAATTTTTG
987274 TTGAAAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (20 bp):
TATTTTGTAATTTTTGAATT
Found at i:989022 original size:15 final size:14
Alignment explanation
Indices: 989002--989035 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
988992 AATCATTAAC
*
989002 AATTATCTTAATATT
1 AATTATCCTAATA-T
989017 AATTATCCTAATAT
1 AATTATCCTAATAT
989031 AATTA
1 AATTA
989036 AAATAGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATCCTAATAT
Found at i:992642 original size:29 final size:29
Alignment explanation
Indices: 992610--992667 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
992600 GCTAGGGAGA
*
992610 AAGGGAAAGCACGCAATTCAATCTAATCC
1 AAGGGAAAGCACACAATTCAATCTAATCC
* *
992639 AAGGGAAAGCACACAATTTAATCTGATCC
1 AAGGGAAAGCACACAATTCAATCTAATCC
992668 TCAGTTACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (29 bp):
AAGGGAAAGCACACAATTCAATCTAATCC
Found at i:995740 original size:19 final size:19
Alignment explanation
Indices: 995712--995753 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
995702 TCATCAATTA
995712 ATTTAATAAT-ATTACTATT
1 ATTTAATAATCA-TACTATT
* *
995731 ATTTATTAATCATATTATT
1 ATTTAATAATCATACTATT
995750 ATTT
1 ATTT
995754 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATCATACTATT
Found at i:1008657 original size:19 final size:17
Alignment explanation
Indices: 1008633--1008676 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
1008623 ATAGTCTTTG
1008633 TTATTATCATTATTTTTA
1 TTATTAT-ATTATTTTTA
1008651 TTTATTAATATTATTTTTA
1 -TTATT-ATATTATTTTTA
1008670 TTATTAT
1 TTATTAT
1008677 TGTCAATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 5 0.21
19 15 0.62
20 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATATTATTTTTA
Found at i:1012237 original size:41 final size:41
Alignment explanation
Indices: 1012180--1012315 Score: 245
Period size: 41 Copynumber: 3.3 Consensus size: 41
1012170 CATTGAATGT
* *
1012180 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1012221 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
*
1012262 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1012303 AAGGGGTTGCTAA
1 AAGGGGTTGCTAA
1012316 CTGATCGAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
Found at i:1012321 original size:22 final size:22
Alignment explanation
Indices: 1012293--1012339 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1012283 TCCCCGAATC
*
1012293 ACTGATCGAAAAGGGGTTGCTA
1 ACTGATCGAAAAGGGATTGCTA
1012315 ACTGATCGAAAAGGGATTGCTA
1 ACTGATCGAAAAGGGATTGCTA
1012337 ACT
1 ACT
1012340 ACAGATTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (22 bp):
ACTGATCGAAAAGGGATTGCTA
Found at i:1012355 original size:63 final size:63
Alignment explanation
Indices: 1012254--1012378 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
1012244 CCCGAATCAT
* * *
1012254 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
1 TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
*
1012317 TGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAA
1 TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAA
1012379 TTGTAGATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (63 bp):
TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
Found at i:1012376 original size:41 final size:41
Alignment explanation
Indices: 1012317--1012594 Score: 439
Period size: 41 Copynumber: 6.8 Consensus size: 41
1012307 GGTTGCTAAC
* * * * *
1012317 TGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCAC
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
* *
1012358 TGATCGAAAAGGGGTTGCTAATTGTAGATTCCCCGAATCAT
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
1012399 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
*
1012440 TGATCGAAAAAGGGTTGCTAAGTGCAGATTCCCCGAATCAT
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
* *
1012481 TGATCGAAAAAGGGTTGCTAAGTGCAGATTCCCCTAATCAT
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
* *
1012522 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCTCCGAATCAC
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
*
1012563 TGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
1 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCC
1012595 TCGAGGGGTT
Statistics
Matches: 221, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 221 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (41 bp):
TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT
Found at i:1012391 original size:104 final size:104
Alignment explanation
Indices: 1012211--1012419 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 104
1012201 TCCCCGAATC
* * * *
1012211 ACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAAAAGGGGTTGCTAAG
1 ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
1012276 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
66 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
* * *
1012315 ACTGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAAT
1 ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
* *
1012380 TGTAGATTCCCCGAATCATTGATCGAAAAGGGGTTGCTA
66 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
1012419 A
1 A
1012420 GTGCAGATTC
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (104 bp):
ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
Found at i:1014945 original size:15 final size:14
Alignment explanation
Indices: 1014911--1014946 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1014901 AATTTAGAGT
1014911 AAAT-AATAATTTA
1 AAATAAATAATTTA
1014924 AAATAAATAATTTA
1 AAATAAATAATTTA
1014938 AGAATAAAT
1 A-AATAAAT
1014947 CAAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 10 0.48
15 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAATAAATAATTTA
Found at i:1018446 original size:20 final size:20
Alignment explanation
Indices: 1018421--1018461 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1018411 AAGGAGAGTG
1018421 TTGAGAAGAAAGTAGACAGT
1 TTGAGAAGAAAGTAGACAGT
1018441 TTGAGAAGAAAGTAGACAGT
1 TTGAGAAGAAAGTAGACAGT
1018461 T
1 T
1018462 AGCTGAGTAC
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:0.44, C:0.05, G:0.29, T:0.22
Consensus pattern (20 bp):
TTGAGAAGAAAGTAGACAGT
Found at i:1019240 original size:14 final size:14
Alignment explanation
Indices: 1019221--1019249 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1019211 TGGGATTTGG
1019221 ATCACACAACTCTA
1 ATCACACAACTCTA
1019235 ATCACACAACTCTA
1 ATCACACAACTCTA
1019249 A
1 A
1019250 CAACATACAT
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:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
ATCACACAACTCTA
Found at i:1020411 original size:22 final size:23
Alignment explanation
Indices: 1020368--1020416 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1020358 TAAAACAAGC
*
1020368 ATATATATAATAAATATTAAAATT
1 ATATATATAATAAATA-TAAAAAT
* *
1020392 ATATTTATATTAAATA-AAAAAT
1 ATATATATAATAAATATAAAAAT
1020414 ATA
1 ATA
1020417 AACTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATATATAATAAATATAAAAAT
Found at i:1025469 original size:11 final size:11
Alignment explanation
Indices: 1025453--1025487 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
1025443 ATCTGAAAAG
1025453 AAAATATCTAA
1 AAAATATCTAA
1025464 AAAATATCTAA
1 AAAATATCTAA
1025475 AAAATATCTAA
1 AAAATATCTAA
1025486 AA
1 AA
1025488 TTTTAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATATCTAA
Found at i:1025544 original size:8 final size:8
Alignment explanation
Indices: 1025533--1025575 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
1025523 TATATGTAAC
1025533 TAAAAAAA
1 TAAAAAAA
1025541 TAAAAAAA
1 TAAAAAAA
*
1025549 TATTACAAAA
1 TA--AAAAAA
*
1025559 TAAAAATA
1 TAAAAAAA
1025567 TAAAAAAA
1 TAAAAAAA
1025575 T
1 T
1025576 TCAAGTTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1026113 original size:31 final size:29
Alignment explanation
Indices: 1026077--1026180 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 29
1026067 TATATGTATT
1026077 TGAGGATCAAATTGATAGAATTTGTAAATA
1 TGAGGATCAAATTGATA-AATTTGTAAATA
* * *
1026107 TGGAGGATTAAATTTATTAAATTATTTAGAAT-
1 T-GAGGATCAAATTGA-TAAATT-TGTA-AATA
* *
1026139 T-AGGATCAAATTGATAAAATGTGTAAGTA
1 TGAGGATCAAATTGAT-AAATTTGTAAATA
*
1026168 TTGAGGATTAAAT
1 -TGAGGATCAAAT
1026181 GTGTTATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.04
29 4 0.07
30 17 0.30
31 25 0.44
32 6 0.11
33 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (29 bp):
TGAGGATCAAATTGATAAATTTGTAAATA
Found at i:1028325 original size:309 final size:309
Alignment explanation
Indices: 1027766--1028385 Score: 1224
Period size: 309 Copynumber: 2.0 Consensus size: 309
1027756 AAATACGAGG
1027766 ATCGAAAAATAAGCTTGGGTAAAATTTAAGGTCCGCTTTCTATATAGGTCGGGCCTTGGGCAAGA
1 ATCGAAAAATAAGCTTGGGTAAAATTTAAGGTCCGCTTTCTATATAGGTCGGGCCTTGGGCAAGA
1027831 TTTTTTTAGCCTAAGCCTAGCCATGCCCAAATATATTATGTTATAAAAAACATTATATTAATTAT
66 TTTTTTTAGCCTAAGCCTAGCCATGCCCAAATATATTATGTTATAAAAAACATTATATTAATTAT
1027896 ATATGTTAAATAATAATTATATATTTTTATACTTATATTAAATCACTAATCTAATAACAATTAAA
131 ATATGTTAAATAATAATTATATATTTTTATACTTATATTAAATCACTAATCTAATAACAATTAAA
1027961 CCCATTACCCAAAATCTAAAAAATAACTTATCCAAATAAATAACTCAACCCAAAATATAAAATTT
196 CCCATTACCCAAAATCTAAAAAATAACTTATCCAAATAAATAACTCAACCCAAAATATAAAATTT
1028026 TAAAAATTATATTTAATACAATAAAAACACTTATTATATTTTTTTTGTT
261 TAAAAATTATATTTAATACAATAAAAACACTTATTATATTTTTTTTGTT
1028075 ATCGAAAAATAAGCTTGGGTAAAATTTAAGGTCCGCTTTCTATATAGGTCGGGCCTTGGGCAAGA
1 ATCGAAAAATAAGCTTGGGTAAAATTTAAGGTCCGCTTTCTATATAGGTCGGGCCTTGGGCAAGA
1028140 TTTTTTTAGCCTAAGCCTAGCCATGCCCAAATATATTATGTTATAAAAAAACATTAT-TTAATTA
66 TTTTTTTAGCCTAAGCCTAGCCATGCCCAAATATATTATGTTAT-AAAAAACATTATATTAATTA
1028204 TATATGTTAAATAATAATTATATATTTTTATACTTATATTAAATCACTAATCTAATAACAATTAA
130 TATATGTTAAATAATAATTATATATTTTTATACTTATATTAAATCACTAATCTAATAACAATTAA
1028269 ACCCATTACCCAAAATCTAAAAAATAACTTATCCAAATAAATAACTCAACCCAAAATATAAAATT
195 ACCCATTACCCAAAATCTAAAAAATAACTTATCCAAATAAATAACTCAACCCAAAATATAAAATT
1028334 TTAAAAATTATATTTAATACAATAAAAACACTTATTATATTTTTTTTGTT
260 TTAAAAATTATATTTAATACAATAAAAACACTTATTATATTTTTTTTGTT
1028384 AT
1 AT
1028386 ATAAATACTT
Statistics
Matches: 310, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
309 298 0.96
310 12 0.04
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (309 bp):
ATCGAAAAATAAGCTTGGGTAAAATTTAAGGTCCGCTTTCTATATAGGTCGGGCCTTGGGCAAGA
TTTTTTTAGCCTAAGCCTAGCCATGCCCAAATATATTATGTTATAAAAAACATTATATTAATTAT
ATATGTTAAATAATAATTATATATTTTTATACTTATATTAAATCACTAATCTAATAACAATTAAA
CCCATTACCCAAAATCTAAAAAATAACTTATCCAAATAAATAACTCAACCCAAAATATAAAATTT
TAAAAATTATATTTAATACAATAAAAACACTTATTATATTTTTTTTGTT
Found at i:1032821 original size:9 final size:9
Alignment explanation
Indices: 1032778--1032843 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
1032768 ATAGGAGGAT
1032778 ATTTTTTAA
1 ATTTTTTAA
* *
1032787 AATTTTAAA
1 ATTTTTTAA
**
1032796 TATTTTTTTGG
1 -A-TTTTTTAA
1032807 ATTTTTATAA
1 ATTTTT-TAA
1032817 ATTTTTT-A
1 ATTTTTTAA
*
1032825 CTTTTTTAA
1 ATTTTTTAA
1032834 ATTTTTTAA
1 ATTTTTTAA
1032843 A
1 A
1032844 ATTAATTAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
8 7 0.16
9 23 0.53
10 9 0.21
11 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:1032829 original size:17 final size:17
Alignment explanation
Indices: 1032809--1032841 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1032799 TTTTTTGGAT
1032809 TTTTATAAATTTTTTAC
1 TTTTATAAATTTTTTAC
*
1032826 TTTTTTAAATTTTTTA
1 TTTTATAAATTTTTTA
1032842 AAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATAAATTTTTTAC
Found at i:1033645 original size:16 final size:16
Alignment explanation
Indices: 1033624--1033657 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1033614 TTTTCCTCTC
1033624 TTTTTTTAA-ATATTTA
1 TTTTTTTAACAT-TTTA
1033640 TTTTTTTAACATTTTA
1 TTTTTTTAACATTTTA
1033656 TT
1 TT
1033658 AGACCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTAACATTTTA
Found at i:1034915 original size:22 final size:22
Alignment explanation
Indices: 1034888--1034929 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1034878 TTTTTTTTTT
*
1034888 TTTTTTTTTTTTTA-AACTTTG
1 TTTTTTTCTTTTTACAACTTTG
1034909 TTTTTTTCTTTTTACAACTTT
1 TTTTTTTCTTTTTACAACTTT
1034930 CGGTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTCTTTTTACAACTTTG
Found at i:1034936 original size:22 final size:21
Alignment explanation
Indices: 1034890--1034942 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1034880 TTTTTTTTTT
* *
1034890 TTTTTTTTTTTAAACTTTGTT
1 TTTTTCTTTTTAAACTTTGTG
1034911 TTTTTCTTTTTACAACTTTCG-G
1 TTTTTCTTTTTA-AACTTT-GTG
*
1034933 TTTTGCTTTT
1 TTTTTCTTTT
1034943 CGTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.41
22 15 0.56
23 1 0.04
ACGTcount: A:0.11, C:0.11, G:0.08, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTTTAAACTTTGTG
Found at i:1036391 original size:13 final size:16
Alignment explanation
Indices: 1036361--1036392 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1036351 GTTGAACTAG
1036361 TTTTTACTATATATTT
1 TTTTTACTATATATTT
1036377 TTTTTACT-TA-ATTT
1 TTTTTACTATATATTT
1036391 TT
1 TT
1036393 AACAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTACTATATATTT
Found at i:1038441 original size:9 final size:10
Alignment explanation
Indices: 1038408--1038441 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1038398 TGAAGGTAAT
1038408 AAATTTTATA
1 AAATTTTATA
1038418 AAATTTTATA
1 AAATTTTATA
1038428 AAATTTTA-A
1 AAATTTTATA
1038437 AAATT
1 AAATT
1038442 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTTTATA
Found at i:1040572 original size:27 final size:28
Alignment explanation
Indices: 1040542--1040601 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
1040532 ATGCAAAAAG
* *
1040542 AAAATTAAGGTTATAAAAAAAAT-TTAT
1 AAAAATAAGATTATAAAAAAAATGTTAT
*
1040569 AAAAATAATATTATAAAAAAAATGTTAT
1 AAAAATAAGATTATAAAAAAAATGTTAT
1040597 AAAAA
1 AAAAA
1040602 ATAATAGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAAATAAGATTATAAAAAAAATGTTAT
Found at i:1040573 original size:14 final size:14
Alignment explanation
Indices: 1040552--1040607 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
1040542 AAAATTAAGG
1040552 TTATAAAAAAAAT-
1 TTATAAAAAAAATA
*
1040565 TTATAAAAATAATA
1 TTATAAAAAAAATA
*
1040579 TTATAAAAAAAATG
1 TTATAAAAAAAATA
1040593 TTATAAAAAATAATA
1 TTATAAAAAA-AATA
1040608 GCATATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.32
14 22 0.59
15 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
TTATAAAAAAAATA
Found at i:1040601 original size:29 final size:27
Alignment explanation
Indices: 1040552--1040607 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
1040542 AAAATTAAGG
1040552 TTATAAAAAAAATTTATAAAAATAATA
1 TTATAAAAAAAATTTATAAAAATAATA
1040579 TTATAAAAAAAATGTTATAAAAAATAATA
1 TTATAAAAAAAAT-TTAT-AAAAATAATA
1040608 GCATATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 13 0.48
28 4 0.15
29 10 0.37
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
TTATAAAAAAAATTTATAAAAATAATA
Found at i:1046916 original size:13 final size:13
Alignment explanation
Indices: 1046898--1046922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1046888 ACCAATACGA
1046898 CGTCGTTTTGAGT
1 CGTCGTTTTGAGT
1046911 CGTCGTTTTGAG
1 CGTCGTTTTGAG
1046923 CCTAAGCTTC
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:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (13 bp):
CGTCGTTTTGAGT
Found at i:1049084 original size:24 final size:23
Alignment explanation
Indices: 1049046--1049107 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
1049036 GGAAGAACCA
*
1049046 TATATCGGAAAGCTCAAGAGAGCT
1 TATATCGGGAAGCTCAAGAGAG-T
* * *
1049070 TATATCGGGATGCTCATGTGAGT
1 TATATCGGGAAGCTCAAGAGAGT
* *
1049093 TATAGCGGGACGCTC
1 TATATCGGGAAGCTC
1049108 TTACGATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (23 bp):
TATATCGGGAAGCTCAAGAGAGT
Found at i:1059062 original size:28 final size:29
Alignment explanation
Indices: 1059012--1059080 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1059002 AATAGCCTAT
*
1059012 ATTTTTATAATTTTAAAGAATT-AAATGAA
1 ATTTTTATTATTTTAAAGAATTAAAAT-AA
* *
1059041 ATTTTTATTATTTTGAA-AATTAAAATAT
1 ATTTTTATTATTTTAAAGAATTAAAATAA
1059069 ATTTTTATTATT
1 ATTTTTATTATT
1059081 ACTAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.47
29 19 0.53
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
ATTTTTATTATTTTAAAGAATTAAAATAA
Found at i:1060230 original size:20 final size:20
Alignment explanation
Indices: 1060205--1060250 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1060195 ATTTAAAGAA
1060205 AATTTTTAATCAACTCAATC
1 AATTTTTAATCAACTCAATC
* *
1060225 AATTTTTTATCAATTCAATC
1 AATTTTTAATCAACTCAATC
1060245 AATTTT
1 AATTTT
1060251 GCATCGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTTTAATCAACTCAATC
Found at i:1060264 original size:20 final size:20
Alignment explanation
Indices: 1060221--1060264 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1060211 TAATCAACTC
** *
1060221 AATCAATTTTTTATCAATTC
1 AATCAATTTTGCATCAATTA
*
1060241 AATCAATTTTGCATCGATTA
1 AATCAATTTTGCATCAATTA
1060261 AATC
1 AATC
1060265 TTTTTTAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (20 bp):
AATCAATTTTGCATCAATTA
Found at i:1061721 original size:24 final size:22
Alignment explanation
Indices: 1061694--1061740 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1061684 TTTCTTTGAA
*
1061694 ATTTTTATGAACTTATTTATTTTT
1 ATTTTTATGAA-TTA-TAATTTTT
*
1061718 ATTTTTTTGAATTATAATTTTT
1 ATTTTTATGAATTATAATTTTT
1061740 A
1 A
1061741 AATTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
ATTTTTATGAATTATAATTTTT
Found at i:1063854 original size:17 final size:18
Alignment explanation
Indices: 1063832--1063872 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1063822 TTCAAAATGC
1063832 AATTAATTTAAA-TT-TTT
1 AATTAA-TTAAATTTATTT
1063849 AATTAATTAAATTTATTT
1 AATTAATTAAATTTATTT
1063867 AATTAA
1 AATTAA
1063873 AAACTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTAATTAAATTTATTT
Found at i:1064796 original size:23 final size:23
Alignment explanation
Indices: 1064770--1064822 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1064760 TGGGCCAATC
*
1064770 ACTGTAATATCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
1064793 ACTGTAATACCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
1064816 ACAGTAA
1 ACTGTAA
1064823 GAAAGTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (23 bp):
ACTGTAATACCCCGAAAATTACT
Found at i:1072100 original size:15 final size:16
Alignment explanation
Indices: 1072080--1072110 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1072070 TAATTATAAA
1072080 AATATAAG-AGATATT
1 AATATAAGAAGATATT
1072095 AATATAAGAAGATATT
1 AATATAAGAAGATATT
1072111 TTTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
AATATAAGAAGATATT
Found at i:1074832 original size:31 final size:31
Alignment explanation
Indices: 1074795--1074860 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1074785 AACAACCCAA
*
1074795 TGACTTAAAT-AATAACTTTCGAATAGTTCAG
1 TGACTTAAATGAA-AACTTTCAAATAGTTCAG
*
1074826 TGACTTAAATGAAAACTTTTAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
1074857 TGAC
1 TGAC
1074861 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:1081977 original size:31 final size:31
Alignment explanation
Indices: 1081940--1082005 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1081930 TTACAAAATG
*
1081940 GTCACTGAACTATTTAAAAGTT-TTCATTTAA
1 GTCACTGAACTATTCAAAAGTTATT-ATTTAA
*
1081971 GTCACTGAACTATTCGAAAGTTATTATTTAA
1 GTCACTGAACTATTCAAAAGTTATTATTTAA
1082002 GTCA
1 GTCA
1082006 TTGGGTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTATTATTTAA
Found at i:1085043 original size:31 final size:31
Alignment explanation
Indices: 1085006--1085071 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1084996 AACAACCCAA
*
1085006 TGACTTAAAT-AATAACTTTCGAATAGTTCAG
1 TGACTTAAATGAA-AACTTTCAAATAGTTCAG
*
1085037 TGACTTAAATGAAAACTTTTAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
1085068 TGAC
1 TGAC
1085072 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:1093995 original size:89 final size:88
Alignment explanation
Indices: 1093882--1094176 Score: 256
Period size: 89 Copynumber: 3.3 Consensus size: 88
1093872 CATAGCAAGC
* * *
1093882 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCCTATCTCTCCGAAGTTGCAG
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCCGAAGTTGCAG
1093947 TGGAGCAGACTGAAGATAGCGAAT
66 TGGAGCAGACT-AAGATAGCGAAT
* * * * * * * * **
1093971 CTTATTTTCCTGAAGTTTCAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAA
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAA---AT-TACT--AG-TCTTATCTCTCCGAA
* * * * *
1094036 GTTGTAGTAGAGCAGA-T--TATAGCAAAC
59 GTTGCAGTGGAGCAGACTAAGATAGCGAAT
* * * *
1094063 CTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTC-CCTGAAGTTGCA
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCC-GAAGTTGCA
* *
1094127 GTGGAGTAAACTAAAGATAGCGAAT
65 GTGGAGCAGACT-AAGATAGCGAAT
1094152 CTTATATCCCTAAAGTTGCAGTGGA
1 CTTATATCCCTAAAGTTGCAGTGGA
1094177 ACGAATTGAA
Statistics
Matches: 158, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
84 1 0.01
85 23 0.15
86 3 0.02
88 1 0.01
89 61 0.39
92 38 0.24
93 2 0.01
95 3 0.02
96 26 0.16
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (88 bp):
CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCCGAAGTTGCAG
TGGAGCAGACTAAGATAGCGAAT
Found at i:1094356 original size:44 final size:44
Alignment explanation
Indices: 1094239--1094594 Score: 207
Period size: 44 Copynumber: 7.9 Consensus size: 44
1094229 CTGATCATAG
* * * *
1094239 CAAACCTTATCTCCCTGAAA-TTGTAGTGGAGCAGACTGAAGATAA
1 CAAACCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAG-CAA
* * * * *
1094284 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * * * **
1094328 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACA-AGTTAAAAATAAA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TT--AAAGCAA
* * * * *
1094374 CCAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATGGGCTA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAA-A---GCAA
* * *
1094423 CAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATTAAAGCCA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * *
1094467 TAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAG-ATA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCA-A
* * * * * * * * * *
1094511 CCAATCTCATCTCTCTGAAGTTGTAGTGGATCAAATTGAAGCTA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * ** *
1094555 CTAATCC-CATCTCCCCGAAGTTGCAGTGGAGCGGATTAAA
1 C-AAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
1094595 ACGATGAATC
Statistics
Matches: 237, Mismatches: 62, Indels: 25
0.73 0.19 0.08
Matches are distributed among these distances:
43 1 0.00
44 131 0.55
45 35 0.15
46 31 0.13
47 3 0.01
48 3 0.01
49 33 0.14
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (44 bp):
CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
Found at i:1094356 original size:89 final size:90
Alignment explanation
Indices: 1094239--1094500 Score: 232
Period size: 90 Copynumber: 2.9 Consensus size: 90
1094229 CTGATCATAG
* * * * * *
1094239 CAAACCTTATCTCCCTGAAATTGTAGTGGAGC-AGACTGAAGAT-AACCAATCTTATCTCTCTGA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAG-CTAAAAATAAACCAATCTTATCTCCCTAA
1094302 AGTTGCAGTGGAGCAGATTAAAGCCA
65 AGTTGCAGTGGAGCAGATTAAAGCCA
* * *
1094328 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACAAGTTAAAAATAAACCAATCTTATCTCCCTAAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAGCTAAAAATAAACCAATCTTATCTCCCTAAA
* * *
1094393 GTTGCAGTGGAGTAGACTGAAGATGGGCTA
66 GTTGCAGTGGAGCAGA-TTAA-A---GCCA
* * * * * *
1094423 CAAATCTTATCTCCCTAAAATTGCAGTGGAGC-AGATTAAAGCCATAAA-C---CTTATCTCCCT
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAG-CTAAA--AATAAACCAATCTTATCTCCCT
1094483 AAAGTTGCAGTGGAGCAG
63 AAAGTTGCAGTGGAGCAG
1094501 GTTGAAGATA
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
89 33 0.23
90 36 0.25
91 3 0.02
92 1 0.01
93 28 0.20
94 2 0.01
95 34 0.24
96 1 0.01
97 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (90 bp):
CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAGCTAAAAATAAACCAATCTTATCTCCCTAAA
GTTGCAGTGGAGCAGATTAAAGCCA
Found at i:1094358 original size:181 final size:182
Alignment explanation
Indices: 1093868--1094360 Score: 593
Period size: 181 Copynumber: 2.7 Consensus size: 182
1093858 GATGGATTGA
* * * * *
1093868 AGATCATAGCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTACTAGTCCTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
* * * * *
1093932 TCTCCGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTTCCTGAAGTTTCAGTGGAA
66 TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
** *
1093997 CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTGTAGTAGAGC
131 CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
* *
1094049 AGATTATAGCAAACCTTATCTCCCT-AAAGTTACAGTGGAGCAGGTTGAAG-TTA-CAAGTCTTA
1 AGATCATAGCAAACCTTATCTCCCTGAAA-TTGCAGTGGAGCAGGTTGAAGATTACCAA-TCTTA
* * * *
1094111 TCTCCCTGAAGTTGCAGTGGAGTAAACTAAAGATAGCGAATCTTATATCCCTAAAGTTGCAGTGG
64 TCTCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGG
* * * *
1094176 AAC-GAATTGAAGTTATAAATTGTAGGTCTTATCTCTCTGAAGTTACAATAGAGC
129 AACAG-ATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
* * ** *
1094230 TGATCATAGCAAACCTTATCTCCCTGAAATTGTAGTGGAGCAGACTGAAGATAACCAATCTTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
* ** * * * * *
1094295 TCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAAACCTTGTCTCCCTGAAGTTGAAGTGGAA
66 TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
1094359 CA
131 CA
1094361 AGTTAAAAAT
Statistics
Matches: 262, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
180 4 0.02
181 216 0.82
182 39 0.15
183 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (182 bp):
AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
Found at i:1094399 original size:90 final size:89
Alignment explanation
Indices: 1094239--1094500 Score: 244
Period size: 95 Copynumber: 2.9 Consensus size: 89
1094229 CTGATCATAG
* * * * * *
1094239 CAAACCTTATCTCCCTGAAATTGTAGTGGAGCAGACTGAAGATAACCAATCTTATCTCTCTGAAG
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAAAATAACCAATCTTATCTCCCTAAAG
1094304 TTGCAGTGGAGCAGATTAAAGCCA
66 TTGCAGTGGAGCAGATTAAAGCCA
* * *
1094328 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACA-AGTTAAAAATAAACCAATCTTATCTCCCTAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGA-CTAAAAAT-AACCAATCTTATCTCCCTAA
* * *
1094392 AGTTGCAGTGGAGTAGACTGAAGATGGGCTA
64 AGTTGCAGTGGAGCAGA-TTAA-A---GCCA
* * * * * * *
1094423 CAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATTAAAGCCAT-A--AACCTTATCTCCCTAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAA--AATAACCAATCTTATCTCCCTAA
1094485 AGTTGCAGTGGAGCAG
64 AGTTGCAGTGGAGCAG
1094501 GTTGAAGATA
Statistics
Matches: 142, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
88 1 0.01
89 34 0.24
90 34 0.24
91 3 0.02
92 1 0.01
93 30 0.21
95 36 0.25
96 1 0.01
97 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (89 bp):
CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAAAATAACCAATCTTATCTCCCTAAAG
TTGCAGTGGAGCAGATTAAAGCCA
Found at i:1094495 original size:139 final size:133
Alignment explanation
Indices: 1094244--1094594 Score: 364
Period size: 139 Copynumber: 2.6 Consensus size: 133
1094234 CATAGCAAAC
* * * *
1094244 CTTATCTCCCTGAAA-TTGTAGTGGAGCAGACTGAAGATAACCAATCTTATCTCTCTGAAGTTGC
1 CTTATCTCCCT-AAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGC
* *
1094308 AGTGGAGCAGATTAAAGCCACAAACCTTGTCTCCCTGAAGTTGAAGTGGAACAAGTTAAAAATAA
65 AGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAAT--
1094373 ACCAAT
128 ACCAAT
* * *
1094379 CTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATGGGCTACAAATCTTATCTCCCTAAAAT
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGAT----AACAAATCTTATCTCCCTAAAAT
* * * * * *
1094444 TGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGA
62 TGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAA
1094509 TACCAAT
127 TACCAAT
* * * * * * * * ** ** *
1094516 CTCATCTCTCTGAAGTTGTAGTGGATCAAATTGAAGCT-ACTAATCCCATCTCCCCGAAGTTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGCA
*
1094580 GTGGAGCGGATTAAA
66 GTGGAGCAGATTAAA
1094595 ACGATGAATC
Statistics
Matches: 180, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
132 34 0.19
134 3 0.02
135 32 0.18
137 35 0.19
139 76 0.42
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (133 bp):
CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGCA
GTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAATACC
AAT
Found at i:1102607 original size:118 final size:120
Alignment explanation
Indices: 1102467--1102708 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 120
1102457 TGTTTGAATG
*
1102467 AATATGAACTTGAATTTTCATATAGTGTGTAC-AA-ATAGATTTTTTATGTCATTTTTCTTGTAT
1 AATATGAACTTGAATTTTCATATAGTGTGTACAAATATAGATTTTTTATGTCAATTTTCTTGTAT
1102530 GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
66 GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
*
1102585 AATATGAACTTGAATTTTCATATAGTGTGTACAAATTATAGATTTTTTATGTTAATTTTCTTGTA
1 AATATGAACTTGAATTTTCATATAGTGTGTACAAA-TATAGATTTTTTATGTCAATTTTCTTGTA
*
1102650 TGAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATATT
65 TGAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
1102706 AAT
1 AAT
1102709 GTCACATTAA
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
118 32 0.27
119 2 0.02
121 84 0.71
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (120 bp):
AATATGAACTTGAATTTTCATATAGTGTGTACAAATATAGATTTTTTATGTCAATTTTCTTGTAT
GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
Found at i:1102719 original size:11 final size:11
Alignment explanation
Indices: 1102703--1102728 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1102693 CCTACCTTAT
1102703 ATTAATGTCAC
1 ATTAATGTCAC
1102714 ATTAATGTCAC
1 ATTAATGTCAC
1102725 ATTA
1 ATTA
1102729 CTTAATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
ATTAATGTCAC
Found at i:1105632 original size:14 final size:15
Alignment explanation
Indices: 1105608--1105648 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1105598 TGGGATAGTG
1105608 TTTTATCTTTTTTA-T
1 TTTTAT-TTTTTTATT
1105623 TTTTA-TTTTTTATT
1 TTTTATTTTTTTATT
1105637 TTTTATTTTTTT
1 TTTTATTTTTTT
1105649 CAAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTTTATT
Found at i:1105647 original size:7 final size:7
Alignment explanation
Indices: 1105615--1105647 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1105605 GTGTTTTATC
1105615 TTTTTTA
1 TTTTTTA
1105622 -TTTTTA
1 TTTTTTA
1105628 TTTTTTA
1 TTTTTTA
1105635 TTTTTTA
1 TTTTTTA
1105642 TTTTTT
1 TTTTTT
1105648 TCAAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1106413 original size:18 final size:18
Alignment explanation
Indices: 1106382--1106430 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1106372 GGCCAATCTA
*
1106382 GGCGTGT-TGGCCACACG
1 GGCGTGTGTGCCCACACG
1106399 GGCGTGTGTGCCCACACG
1 GGCGTGTGTGCCCACACG
* * *
1106417 AGCATGTGGGCCCA
1 GGCGTGTGTGCCCA
1106431 TAATTCTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.14, C:0.31, G:0.39, T:0.16
Consensus pattern (18 bp):
GGCGTGTGTGCCCACACG
Found at i:1111634 original size:2 final size:2
Alignment explanation
Indices: 1111627--1111667 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1111617 GTTAGGTGAC
* *
1111627 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1111668 CTATNNNNNN
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1111644 original size:12 final size:12
Alignment explanation
Indices: 1111627--1111667 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
1111617 GTTAGGTGAC
*
1111627 TATATATATATA
1 TATATACATATA
1111639 TATATACATATA
1 TATATACATATA
1111651 TATATACATATA
1 TATATACATATA
1111663 TATAT
1 TATAT
1111668 CTATNNNNNN
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TATATACATATA
Found at i:1114107 original size:99 final size:99
Alignment explanation
Indices: 1113936--1114129 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 99
1113926 TATATGTTTC
* * * *
1113936 GACAGCACATAGTAATTGAATGAGTGTAATAATTCTTAGGGTAGTAATTACACTCTCTTGTAATT
1 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
*
1114001 ACAAAGAATTAG-AATTCCCTAGATGTGTTTTTTG
66 ACAAAGAATT-GTAATTCCCTAGACGTGTTTTTTG
1114035 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
1 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
*
1114100 ATAAAGAATTGTAATTCCCTAGACGTGTTT
66 ACAAAGAATTGTAATTCCCTAGACGTGTTT
1114130 AGCTAGCAGA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 1 0.01
99 87 0.99
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (99 bp):
GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
ACAAAGAATTGTAATTCCCTAGACGTGTTTTTTG
Found at i:1114240 original size:16 final size:17
Alignment explanation
Indices: 1114219--1114263 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1114209 TATATTTTTA
1114219 AAAAAATAATTACTAT-
1 AAAAAATAATTACTATG
* *
1114235 AAAAAATTATTAGTATG
1 AAAAAATAATTACTATG
1114252 ATAAAAATAATT
1 A-AAAAATAATT
1114264 TCTGGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAAAATAATTACTATG
Found at i:1116788 original size:67 final size:67
Alignment explanation
Indices: 1116680--1116814 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
1116670 GTAATTGTCG
*
1116680 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1116745 TC
66 TC
* *
1116747 TTGCATGGGATTTAGCCTAGACTGGTAATCCTGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1116812 TC
66 TC
1116814 T
1 T
1116815 AAATTGGAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (67 bp):
TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:1119570 original size:113 final size:114
Alignment explanation
Indices: 1119422--1119663 Score: 459
Period size: 113 Copynumber: 2.1 Consensus size: 114
1119412 TATATATTGT
*
1119422 TATAACTTTATAAAATACACAAATTGTTTTTATAATAAATTATTTTGGAATTTATAATATAATAA
1 TATAATTTTATAAAATACACAAATTGTTTTTATAATAAATTATTTTGGAATTTATAATATAATAA
1119487 ATCTTTGGTCATAACTATCCCAAATACTCATATGTGTTCAAGCTTATAA
66 ATCTTTGGTCATAACTATCCCAAATACTCATATGTGTTCAAGCTTATAA
1119536 TATAATTTTATAAAATAC-CAAATTGTTTTTATAATAAATTATTTTGGAATTTATAATATAATAA
1 TATAATTTTATAAAATACACAAATTGTTTTTATAATAAATTATTTTGGAATTTATAATATAATAA
1119600 ATCTTTGGTCATAACTATCCCAAATACTCATATGTGTTCAAGCTTATAA
66 ATCTTTGGTCATAACTATCCCAAATACTCATATGTGTTCAAGCTTATAA
1119649 TATAATTTTCATAAA
1 TATAATTTT-ATAAA
1119664 TTGTATAAAA
Statistics
Matches: 126, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
113 104 0.83
114 22 0.17
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (114 bp):
TATAATTTTATAAAATACACAAATTGTTTTTATAATAAATTATTTTGGAATTTATAATATAATAA
ATCTTTGGTCATAACTATCCCAAATACTCATATGTGTTCAAGCTTATAA
Found at i:1120034 original size:11 final size:11
Alignment explanation
Indices: 1120018--1120042 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1120008 TCATTTACTA
1120018 AAAAAATGGAC
1 AAAAAATGGAC
1120029 AAAAAATGGAC
1 AAAAAATGGAC
1120040 AAA
1 AAA
1120043 TTAGTCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAAATGGAC
Found at i:1125574 original size:30 final size:30
Alignment explanation
Indices: 1125530--1125592 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1125520 ACTTAACAAG
1125530 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
1125560 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
1125590 CAA
1 CAA
1125593 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:1133780 original size:1 final size:1
Alignment explanation
Indices: 1133774--1133798 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1133764 CCAAGACTTC
1133774 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1133799 GGGTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1133786 original size:72 final size:72
Alignment explanation
Indices: 1133673--1133809 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
1133663 TTAGAAAAGC
1133673 TATTTTGATATGGAAGTCCAAGTACTTCTTTATTTTTTTTTTTTTTTTTTTTTTGGGTAAAAAAA
1 TATTTTGATATGGAAGTCCAAGTACTTCTTTATTTTTTTTTTTTTTTTTTTTTTGGGTAAAAAAA
1133738 AAAATTT
66 AAAATTT
*
1133745 TATTTTGATATGGAGAAGTCCAAG-ACTTCTTT-TTTTTTTTTTTTTTTTTTTTTTGGGTAATAA
1 TATTTTGATAT-G-GAAGTCCAAGTACTTCTTTATTTTTTTTTTTTTTTTTTTTTTGGGTAAAAA
1133808 AA
64 AA
1133810 CAACTGTTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
72 43 0.69
73 9 0.15
74 10 0.16
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (72 bp):
TATTTTGATATGGAAGTCCAAGTACTTCTTTATTTTTTTTTTTTTTTTTTTTTTGGGTAAAAAAA
AAAATTT
Done.