Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold328
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: 936272
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 4 of 6
Found at i:567946 original size:17 final size:18
Alignment explanation
Indices: 567911--567951 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
567901 ACATAAAATT
567911 TTTCTT-TTTTTCTTCTC
1 TTTCTTCTTTTTCTTCTC
*
567928 TTTCTTCTTTTT-TTTTC
1 TTTCTTCTTTTTCTTCTC
567945 TTT-TTCT
1 TTTCTTCT
567952 CATTTCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTCTTTTTCTTCTC
Found at i:567961 original size:2 final size:2
Alignment explanation
Indices: 567956--568026 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
567946 TTTTCTCATT
567956 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
567998 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
568027 ATATATATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:568031 original size:2 final size:2
Alignment explanation
Indices: 568026--568064 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
568016 TCTCTCTCTC
568026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
568065 CTCCCTCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:572294 original size:21 final size:22
Alignment explanation
Indices: 572255--572296 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
572245 TTATATTTTG
*
572255 ATGCTTTTCAAACTTTTCTTTC
1 ATGCTTTTCAAACTCTTCTTTC
*
572277 ATGC-TTTCAGACTCTTCTTT
1 ATGCTTTTCAAACTCTTCTTT
572297 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52
Consensus pattern (22 bp):
ATGCTTTTCAAACTCTTCTTTC
Found at i:572810 original size:23 final size:23
Alignment explanation
Indices: 572783--572829 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
572773 AATATAAGAC
*
572783 AACATAAAAAATAATATGAACAT
1 AACATAAAAAATAATACGAACAT
572806 AACATAAAAAATAATACGAACAT
1 AACATAAAAAATAATACGAACAT
572829 A
1 A
572830 TCAAAATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (23 bp):
AACATAAAAAATAATACGAACAT
Found at i:573675 original size:37 final size:33
Alignment explanation
Indices: 573607--573675 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
573597 TAATGTGAAT
* *
573607 ATAAAATGAATACATAAATATGTGAAAATATAC
1 ATAAAATAAATAAATAAATATGTGAAAATATAC
573640 ATAAAATAAATAAAATAAATAATTGTGAAAAATATA
1 ATAAAATAAAT-AAATAAAT-A-TGTG-AAAATATA
573676 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 10 0.33
34 7 0.23
35 1 0.03
36 4 0.13
37 8 0.27
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (33 bp):
ATAAAATAAATAAATAAATATGTGAAAATATAC
Found at i:573797 original size:10 final size:10
Alignment explanation
Indices: 573782--573821 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
573772 ATTGCTTTCC
573782 TTTTTTTCTT
1 TTTTTTTCTT
573792 TTTTTTTCTT
1 TTTTTTTCTT
573802 TTTTTTTCCTT
1 TTTTTTT-CTT
*
573813 TCTTTTTCT
1 TTTTTTTCT
573822 CACCTTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:573802 original size:18 final size:18
Alignment explanation
Indices: 573744--573806 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
573734 TCTCTCTTGC
573744 TTTTTTCATTTTTCTCTTTCT
1 TTTTTTC-TTTTT-T-TTTCT
** *
573765 TTTTTT-TATTGCTTTCCT
1 TTTTTTCT-TTTTTTTTCT
573783 TTTTTTCTTTTTTTTTCT
1 TTTTTTCTTTTTTTTTCT
573801 TTTTTT
1 TTTTTT
573807 TTCCTTTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 23 0.68
19 3 0.09
20 2 0.06
21 6 0.18
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTCTTTTTTTTTCT
Found at i:573807 original size:21 final size:21
Alignment explanation
Indices: 573744--573821 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
573734 TCTCTCTTGC
*
573744 TTTTTTCATTTTTCTCTTTCTTTT
1 TTTTTTC-TTTTT-TTTTTC-TTT
573768 TTTTATTGCTTTCCTTTTTTTCTTT
1 TTTT-TT-CTTT--TTTTTTTCTTT
*
573793 TTTTTTCTTTTTTTTTCCTTT
1 TTTTTTCTTTTTTTTTTCTTT
*
573814 CTTTTTCT
1 TTTTTTCT
573822 CACCTTTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
21 17 0.36
23 4 0.09
24 6 0.13
25 12 0.26
26 6 0.13
27 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTTCTTT
Found at i:575568 original size:21 final size:21
Alignment explanation
Indices: 575529--575568 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
575519 AGACGGTTGG
*
575529 GATTATCTCATAATTATTATC
1 GATTATCTCATAATAATTATC
575550 GATTATCT-ATAAATAATTA
1 GATTATCTCAT-AATAATTA
575569 GATTGAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (21 bp):
GATTATCTCATAATAATTATC
Found at i:576118 original size:18 final size:17
Alignment explanation
Indices: 576087--576120 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
576077 TCAAAAAATC
*
576087 TAAAAAAATCATTTTTT
1 TAAAAAAATAATTTTTT
576104 TAAAGAAAATAATTTTT
1 TAAA-AAAATAATTTTT
576121 AAAGTCAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAAAAAATAATTTTTT
Found at i:577281 original size:11 final size:11
Alignment explanation
Indices: 577260--577344 Score: 62
Period size: 12 Copynumber: 7.1 Consensus size: 11
577250 AAGCCACCTT
577260 TTTCTTTTTTTC
1 TTTC-TTTTTTC
*
577272 TTTCTTTTTTT
1 TTTCTTTTTTC
**
577283 TTTCTCTCATTC
1 TTTCT-TTTTTC
577295 TTTCCTTTTTCTTC
1 TTT-C-TTTT-TTC
577309 TTTCCTTTTTTC
1 TTT-CTTTTTTC
* *
577321 TTCCTTTTTTA
1 TTTCTTTTTTC
577332 TTCTCTTTTTTC
1 TT-TCTTTTTTC
577344 T
1 T
577345 CCCCCCTTCC
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
11 20 0.34
12 23 0.40
13 6 0.10
14 9 0.16
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:577285 original size:23 final size:23
Alignment explanation
Indices: 577258--577342 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 23
577248 CCAAGCCACC
577258 TTTTTCTTTTTTTCTTTCTTTTT
1 TTTTTCTTTTTTTCTTTCTTTTT
* **
577281 TTTTTCTCTCATTCTTTCCTTTTT
1 TTTTTCTTTTTTTCTTT-CTTTTT
* *
577305 CTTCTTTCCTTTTTTCTTCCTTTTT
1 -TT-TTTCTTTTTTTCTTTCTTTTT
*
577330 TATTCTCTTTTTT
1 T-TTTTCTTTTTT
577343 CTCCCCCCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 14 0.29
24 15 0.31
25 9 0.19
26 10 0.21
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTTTCTTTTT
Found at i:577295 original size:19 final size:18
Alignment explanation
Indices: 577257--577319 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
577247 CCCAAGCCAC
*
577257 CTTTTTCTTTTT-TTCTTT
1 CTTTTT-TTTTTCTTCATT
577275 CTTTTTTTTTTCTCTCATT
1 CTTTTTTTTTTCT-TCATT
** *
577294 CTTTCCTTTTTCTTCTTT
1 CTTTTTTTTTTCTTCATT
577312 CCTTTTTT
1 -CTTTTTT
577320 CTTCCTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 5 0.14
18 11 0.31
19 20 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTTTTTTTCTTCATT
Found at i:577311 original size:14 final size:15
Alignment explanation
Indices: 577292--577323 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
577282 TTTTCTCTCA
577292 TTCTTTCC-TTTTTC
1 TTCTTTCCTTTTTTC
577306 TTCTTTCCTTTTTTC
1 TTCTTTCCTTTTTTC
577321 TTC
1 TTC
577324 CTTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCTTTCCTTTTTTC
Found at i:578873 original size:14 final size:14
Alignment explanation
Indices: 578826--578874 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
578816 TTATAAAATT
578826 ATTTTTTAAATTTA
1 ATTTTTTAAATTTA
* * *
578840 ATTGTATTAAGTAATA
1 ATT-TTTTAAAT-TTA
578856 ATTTTTTAAATTTA
1 ATTTTTTAAATTTA
578870 ATTTT
1 ATTTT
578875 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 10 0.37
15 12 0.44
16 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTTTTAAATTTA
Found at i:578955 original size:17 final size:17
Alignment explanation
Indices: 578918--578955 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
578908 GATACAGATC
* *
578918 TTAAATTAACTTGTTAG
1 TTAAATTAACTTATTAA
578935 TTAAATTAACTTATTAA
1 TTAAATTAACTTATTAA
578952 TTAA
1 TTAA
578956 TATGTTATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (17 bp):
TTAAATTAACTTATTAA
Found at i:579982 original size:16 final size:17
Alignment explanation
Indices: 579952--579991 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
579942 ATATGAGAAA
579952 ATAAT-TAAAATATAAT
1 ATAATATAAAATATAAT
579968 ATAATATAAAA-ATAAT
1 ATAATATAAAATATAAT
579984 ATTAATAT
1 A-TAATAT
579992 GATACGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATAAAATATAAT
Found at i:579987 original size:29 final size:28
Alignment explanation
Indices: 579936--580025 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 28
579926 ACATGACATA
579936 AATATAATATGAGAAAATA-ATTAAAATAT
1 AATATAATAT-A-AAAATATATTAAAATAT
579965 AATATAATATAAAAATAATATT--AATAT
1 AATATAATATAAAAAT-ATATTAAAATAT
* * *
579992 GATACGAATAT-AAAATATATTAAAATCT
1 AATA-TAATATAAAAATATATTAAAATAT
580020 -ATATAA
1 AATATAA
580026 AATGAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
26 7 0.13
27 21 0.40
28 11 0.21
29 13 0.25
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (28 bp):
AATATAATATAAAAATATATTAAAATAT
Found at i:582197 original size:21 final size:22
Alignment explanation
Indices: 582172--582235 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
582162 ATATATTATT
* *
582172 TATATAATAAAAAT-TACTTAA
1 TATATAATAAAAATAAAATTAA
*
582193 TATATAA-AAATATAAAATTAA
1 TATATAATAAAAATAAAATTAA
*
582214 TATATTATAAAATTATAAAATT
1 TATATAATAAAA--ATAAAATT
582236 GGTCAAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.15
21 18 0.53
22 3 0.09
24 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TATATAATAAAAATAAAATTAA
Found at i:583457 original size:15 final size:15
Alignment explanation
Indices: 583437--583480 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
583427 TAAAAAATAA
583437 TAATAAATAATTATT
1 TAATAAATAATTATT
*
583452 TAATAAA-ATTTAATT
1 TAATAAATAATT-ATT
583467 TAA-AAATAATTATT
1 TAATAAATAATTATT
583481 ATTAGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAAATAATTATT
Found at i:584010 original size:2 final size:2
Alignment explanation
Indices: 584003--584038 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
583993 ACATCTCAGC
584003 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
584039 TAAATGGTGA
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:585989 original size:56 final size:56
Alignment explanation
Indices: 585903--586014 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
585893 ATTTTTGTGT
585903 AAGTATGATTCACATAGGAGCTTGGATTTGCGCATAAACAAGTTAAGAGGATAACA
1 AAGTATGATTCACATAGGAGCTTGGATTTGCGCATAAACAAGTTAAGAGGATAACA
585959 AAGTATGATTCACATAGGAGCTTGGATTTGCGCATAAACAAGTTAAGAGGATAACA
1 AAGTATGATTCACATAGGAGCTTGGATTTGCGCATAAACAAGTTAAGAGGATAACA
586015 CTGCAGTAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (56 bp):
AAGTATGATTCACATAGGAGCTTGGATTTGCGCATAAACAAGTTAAGAGGATAACA
Found at i:589827 original size:51 final size:52
Alignment explanation
Indices: 589763--589878 Score: 180
Period size: 51 Copynumber: 2.2 Consensus size: 52
589753 TCTGAAAAGA
* *
589763 AAATATATCGATACTTTTTTTATTGTATCGATACATTCTAAG-TTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCGATACATTCTAAGTTTTTGACCC
* *
589814 AAATATATTGATACATTTTTCATTGTATCGATACATTCTGAGTTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCGATACATTCTAAGTTTTTGACCC
*
589866 AAATGTATCGATA
1 AAATATATCGATA
589879 TATTCTTCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 38 0.66
52 20 0.34
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (52 bp):
AAATATATCGATACATTTTTCATTGTATCGATACATTCTAAGTTTTTGACCC
Found at i:589900 original size:52 final size:51
Alignment explanation
Indices: 589763--589901 Score: 154
Period size: 51 Copynumber: 2.7 Consensus size: 51
589753 TCTGAAAAGA
* * * *
589763 AAATATATCGATACTTTTTTTATTGTATCGATACATTCTAAGTTTTGACCC
1 AAATATATCGATACATTCTTCATTGTATCAATACATTCTAAGTTTTGACCC
* * * *
589814 AAATATATTGATACATTTTTCATTGTATCGATACATTCTGAGTTTTTGACCC
1 AAATATATCGATACATTCTTCATTGTATCAATACATTCTAAG-TTTTGACCC
* * *
589866 AAATGTATCGATATATTCTTCGA-TGTATTAATACAT
1 AAATATATCGATACATTCTTC-ATTGTATCAATACAT
589902 GTAAGTTATT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
51 38 0.50
52 37 0.49
53 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (51 bp):
AAATATATCGATACATTCTTCATTGTATCAATACATTCTAAGTTTTGACCC
Found at i:591192 original size:52 final size:52
Alignment explanation
Indices: 591112--591216 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
591102 CCTTGCATGG
* * *
591112 AGATTAGCATGGATTTAAGGTTTCCATGAGCTGGTTTTTCAACCTTTGAGGA
1 AGATTAGCATGAACTTAAGGTTTCCATGAGCTGGTTTTCCAACCTTTGAGGA
* *
591164 AGATTAGCATGAACTTAAGGTTTTCATGAGTTGGTTTTCCAACCTTTGAGGA
1 AGATTAGCATGAACTTAAGGTTTCCATGAGCTGGTTTTCCAACCTTTGAGGA
591216 A
1 A
591217 AAAGCAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (52 bp):
AGATTAGCATGAACTTAAGGTTTCCATGAGCTGGTTTTCCAACCTTTGAGGA
Found at i:592781 original size:190 final size:190
Alignment explanation
Indices: 592420--592792 Score: 570
Period size: 190 Copynumber: 2.0 Consensus size: 190
592410 GATACTCCAA
* *
592420 CTCATCAATTTCGAGGGGATGCTCTAACCCCGTTTTTACTTCTAAAATATTGAATTTCTTCATCT
1 CTCATCAATTTCGAGGGGATACTCTAACCCCGTTTTTACTTCTAAAACATTGAATTTCTTCATCT
* * *
592485 CTGGGGATATTCTAACCCTATCATTTCTAAAGGATACTCCAATCCCATTTTTATTTTCCAAAACA
66 ATGGGGATACTCTAACCCCATCATTTCTAAAGGATACTCCAATCCCATTTTTATTTTCCAAAACA
* *
592550 TCAAAATTTTCATCTTAAGGGATATTCTAACCCCTACCATTTTCGAGGAGATATTCTAAT
131 TCAAAATTTTCATCTTAAGGGACACTCTAACCCCTACCATTTTCGAGGAGATATTCTAAT
* *
592610 CTCATCAATTGT-GAGGGGATACTTTAACCCCGTTTTTACTTTTAAAACATTGAATTTCTTCATC
1 CTCATCAATT-TCGAGGGGATACTCTAACCCCGTTTTTACTTCTAAAACATTGAATTTCTTCATC
*
592674 TATGGGGATACTCTAACCCCATCATTTTTAAAGGGATACTCCAATCCCATTTTTATTTTCCAAAA
65 TATGGGGATACTCTAACCCCATCATTTCTAAA-GGATACTCCAATCCCATTTTTATTTTCCAAAA
** * * * *
592739 CATTGAAATTTTCATCTTAGGGGACACTCTAATCCC-ACCATTTTTGAGGGGATA
129 CATCAAAATTTTCATCTTAAGGGACACTCTAACCCCTACCATTTTCGAGGAGATA
592793 CTCCAACCCT
Statistics
Matches: 165, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
190 102 0.62
191 63 0.38
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (190 bp):
CTCATCAATTTCGAGGGGATACTCTAACCCCGTTTTTACTTCTAAAACATTGAATTTCTTCATCT
ATGGGGATACTCTAACCCCATCATTTCTAAAGGATACTCCAATCCCATTTTTATTTTCCAAAACA
TCAAAATTTTCATCTTAAGGGACACTCTAACCCCTACCATTTTCGAGGAGATATTCTAAT
Found at i:593965 original size:31 final size:31
Alignment explanation
Indices: 593930--594027 Score: 110
Period size: 31 Copynumber: 3.1 Consensus size: 31
593920 AAATTTAATG
*
593930 AATTACTTGTAAATTTGATGAATGTTAAAAA
1 AATTACTTGTAAATTTGATGAATATTAAAAA
* * *
593961 AATTACTTGTAAATTTGACGAATATTAGACAT
1 AATTACTTGTAAATTTGATGAATATTA-AAAA
*
593993 AATTA-TTCATAAATTTGAT-AATTATTAAAAA
1 AATTACTT-GTAAATTTGATGAA-TATTAAAAA
594024 AATT
1 AATT
594028 TCAACCTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 35 0.62
32 21 0.38
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (31 bp):
AATTACTTGTAAATTTGATGAATATTAAAAA
Found at i:595632 original size:16 final size:16
Alignment explanation
Indices: 595613--595662 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
595603 TTGAATTTAA
595613 TTGGATTTAAGTCT-TT
1 TTGGATTTAAGT-TATT
* *
595629 TTGGGTTGAAGTTATT
1 TTGGATTTAAGTTATT
*
595645 TTGGATTTAAGTAATT
1 TTGGATTTAAGTTATT
595661 TT
1 TT
595663 TTATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (16 bp):
TTGGATTTAAGTTATT
Found at i:600935 original size:13 final size:13
Alignment explanation
Indices: 600917--600943 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
600907 ACATACTGCT
600917 TTGTATCGATACA
1 TTGTATCGATACA
600930 TTGTATCGATACA
1 TTGTATCGATACA
600943 T
1 T
600944 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:600940 original size:33 final size:32
Alignment explanation
Indices: 600898--600962 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
600888 CACTTCCAGA
*
600898 TGTATCGATACATACTGCTTTGTATCGATACAT
1 TGTATCGATACATACT-CATTGTATCGATACAT
*
600931 TGTATCGATACATGCTCATTGTATCGATACAT
1 TGTATCGATACATACTCATTGTATCGATACAT
600963 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATACTCATTGTATCGATACAT
Found at i:600973 original size:20 final size:19
Alignment explanation
Indices: 600927--600983 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
600917 TTGTATCGAT
600927 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
600946 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
600965 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
600984 AGATTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:601051 original size:13 final size:13
Alignment explanation
Indices: 601033--601081 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
601023 CATGGGATAA
601033 TGTATCGATACAT
1 TGTATCGATACAT
601046 TGTATCGATACA-
1 TGTATCGATACAT
*
601058 TG-AT--A-AAAT
1 TGTATCGATACAT
601067 TGTATCGATACAT
1 TGTATCGATACAT
601080 TG
1 TG
601082 CTTGTAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 3 0.10
10 2 0.07
11 2 0.07
12 3 0.10
13 17 0.59
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:606061 original size:20 final size:20
Alignment explanation
Indices: 606015--606065 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
606005 ATTGGGCTCA
* *
606015 ATATATCGATACATTTCACC
1 ATATATCGATACAATCCACC
* **
606035 ATGTATCGATACAATCCTTC
1 ATATATCGATACAATCCACC
606055 ATATATCGATA
1 ATATATCGATA
606066 TAATGTATCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (20 bp):
ATATATCGATACAATCCACC
Found at i:607005 original size:23 final size:22
Alignment explanation
Indices: 606946--607007 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
606936 ATACGACATG
* *
606946 AATATAATATAAGAATAATTAA
1 AATACAATATAAAAATAATTAA
* *
606968 AATACAATACGAAAAGTAA-TATA
1 AATACAATA-TAAAAATAATTA-A
606991 AATACAATATAAAAATA
1 AATACAATATAAAAATA
607008 CACAAATATG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (22 bp):
AATACAATATAAAAATAATTAA
Found at i:607698 original size:28 final size:28
Alignment explanation
Indices: 607652--607707 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
607642 TTGAATATAC
607652 AAAAAATAACATGAATATAA-ATACAATA
1 AAAAAATAACATGAATATAATATA-AATA
* *
607680 AAAAAATAACATTACTATAATATAAATA
1 AAAAAATAACATGAATATAATATAAATA
607708 TGAAAATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAAAATAACATGAATATAATATAAATA
Found at i:607871 original size:21 final size:22
Alignment explanation
Indices: 607818--607864 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
607808 ATCAATATGG
607818 TACTTTT-AT-TTTAAAAATAT
1 TACTTTTGATATTTAAAAATAT
*
607838 TAGTTTTGATATTTAAAAAT-T
1 TACTTTTGATATTTAAAAATAT
607859 TACTTT
1 TACTTT
607865 GTGTATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TACTTTTGATATTTAAAAATAT
Found at i:608008 original size:21 final size:21
Alignment explanation
Indices: 607984--608023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
607974 CAAAAATAAT
*
607984 TATTTAATTAAATATAAAATA
1 TATTTAATTAAAAATAAAATA
**
608005 TATTTTTTTAAAAATAAAA
1 TATTTAATTAAAAATAAAA
608024 ATAAACAGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAATTAAAAATAAAATA
Found at i:609032 original size:21 final size:21
Alignment explanation
Indices: 609003--609046 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
608993 GATGTGTGAA
*
609003 AATTAAAATTTTTTTAATTTT
1 AATTAAAATTTTTATAATTTT
* *
609024 AATTTAAATTTTTATATTTTT
1 AATTAAAATTTTTATAATTTT
609045 AA
1 AA
609047 AATATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTAAAATTTTTATAATTTT
Found at i:609241 original size:21 final size:20
Alignment explanation
Indices: 609198--609249 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
609188 ATGTTATGTT
609198 AATAAATAACTTGATAGTATAA
1 AATAAA-AA-TTGATAGTATAA
* * *
609220 ATATTAAAATTGATATTTTAA
1 A-ATAAAAATTGATAGTATAA
609241 AATAAAAAT
1 AATAAAAAT
609250 ATTATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.28
21 11 0.44
22 3 0.12
23 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (20 bp):
AATAAAAATTGATAGTATAA
Found at i:609589 original size:11 final size:11
Alignment explanation
Indices: 609568--609596 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
609558 CGCTCTTTAT
609568 ATATTTT-TTA
1 ATATTTTATTA
609578 ATATTTTATTA
1 ATATTTTATTA
609589 ATATTTTA
1 ATATTTTA
609597 CATTTAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATATTTTATTA
Found at i:609720 original size:22 final size:22
Alignment explanation
Indices: 609678--609722 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
609668 TTTAGAAGAT
* *
609678 AAATTATTTATATTATTATATA
1 AAATAATTTATATTATAATATA
609700 AAATAATTATATATTA-AATATA
1 AAATAATT-TATATTATAATATA
609722 A
1 A
609723 TACATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATTTATATTATAATATA
Found at i:609724 original size:20 final size:21
Alignment explanation
Indices: 609685--609751 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
609675 GATAAATTAT
* *
609685 TTATATTATTATATAAAATA-A
1 TTATA-TATTAAATATAATACA
609706 TTATATATTAAATATAATACA
1 TTATATATTAAATATAATACA
* * * *
609727 TAATATA-AAAATATATTATA
1 TTATATATTAAATATAATACA
609747 TTATA
1 TTATA
609752 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 26 0.68
21 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATATTAAATATAATACA
Found at i:609766 original size:18 final size:19
Alignment explanation
Indices: 609745--609793 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
609735 AAATATATTA
609745 TATTATAAAATTTTAAAT-
1 TATTATAAAATTTTAAATG
*
609763 TATTA-AATAAATTTAAATG
1 TATTATAA-AATTTTAAATG
609782 TATTTATAAAAT
1 TA-TTATAAAAT
609794 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 14 0.56
19 2 0.08
20 5 0.20
21 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTATAAAATTTTAAATG
Found at i:609860 original size:17 final size:16
Alignment explanation
Indices: 609840--609926 Score: 60
Period size: 17 Copynumber: 5.6 Consensus size: 16
609830 ATTTATTCGA
609840 TAATTAATTTTAAAAAT
1 TAATTAA-TTTAAAAAT
609857 TAA-TAA-TT---AAT
1 TAATTAATTTAAAAAT
*
609868 TAAATTAAATTAATAAAT
1 T-AATTAATTTAA-AAAT
*
609886 AAATTAAATTTAAAAAT
1 TAATT-AATTTAAAAAT
*
609903 TAATTAAATT-AAAAT
1 TAATTAATTTAAAAAT
*
609918 AAATTAATT
1 TAATTAATT
609927 AAATTCAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 3 0.05
14 4 0.07
15 12 0.21
16 7 0.12
17 15 0.27
18 9 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTAATTTAAAAAT
Found at i:609875 original size:5 final size:5
Alignment explanation
Indices: 609861--609942 Score: 72
Period size: 5 Copynumber: 17.8 Consensus size: 5
609851 AAAAATTAAT
*
609861 AATT- AATTA AATTA AATT- AA-TA AA-TA AATTA AATTT AA--A AATT-
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA
* *
609904 AATTA AATTA AAATA AATT- AATTA AATTCA ATTTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATT-A AATTA AATT
609943 GATTGTTGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
3 3 0.05
4 20 0.31
5 37 0.58
6 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:609904 original size:39 final size:41
Alignment explanation
Indices: 609856--609940 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 41
609846 ATTTTAAAAA
* *
609856 TTAATAATTAATTAAATT-AAATTAA-TAAATAAATTAAAT
1 TTAAAAATTAATTAAATTAAAATAAATTAAATAAATTAAAT
* *
609895 TTAAAAATTAATTAAATTAAAATAAATTAATTAAATTCAAT
1 TTAAAAATTAATTAAATTAAAATAAATTAAATAAATTAAAT
609936 TTAAA
1 TTAAA
609941 TTGATTGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 17 0.43
40 6 0.15
41 17 0.43
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (41 bp):
TTAAAAATTAATTAAATTAAAATAAATTAAATAAATTAAAT
Found at i:609941 original size:11 final size:9
Alignment explanation
Indices: 609860--609942 Score: 75
Period size: 9 Copynumber: 9.1 Consensus size: 9
609850 TAAAAATTAA
609860 TAATT-AAT
1 TAATTAAAT
609868 TAAATTAAAT
1 T-AATTAAAT
609878 TAA-TAAAT
1 TAATTAAAT
*
609886 AAATTAAATT
1 TAATTAAA-T
609896 TAA--AAAT
1 TAATTAAAT
609903 TAATTAAAT
1 TAATTAAAT
*
609912 TAAAATAAAT
1 T-AATTAAAT
609922 TAATTAAAT
1 TAATTAAAT
609931 TCAATTTAAAT
1 T-AA-TTAAAT
609942 T
1 T
609943 GATTGTTGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
7 4 0.06
8 11 0.18
9 23 0.37
10 17 0.27
11 7 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATTAAAT
Found at i:611181 original size:1 final size:1
Alignment explanation
Indices: 611175--611201 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
611165 AATGTAATGG
611175 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
611202 ATGCAAGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:618140 original size:21 final size:19
Alignment explanation
Indices: 618095--618141 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 19
618085 ATAAAAACTA
618095 AAAATATTATATTAATATTT
1 AAAA-ATTATATTAATATTT
*
618115 TAAAATTATATTAATATATAT
1 AAAAATTATATTAATAT-T-T
618136 AAAAAT
1 AAAAAT
618142 ATAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTATATTAATATTT
Found at i:618421 original size:2 final size:2
Alignment explanation
Indices: 618416--618443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
618406 CACACACACA
618416 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
618444 AGCACTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:619169 original size:15 final size:15
Alignment explanation
Indices: 619149--619186 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
619139 AAAATTTTTA
*
619149 ATTAAATTTAATATT
1 ATTAAATTTAATAAT
*
619164 ATTAAATTAAATAAT
1 ATTAAATTTAATAAT
619179 A-TAAATTT
1 ATTAAATTT
619187 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAATTTAATAAT
Found at i:622407 original size:178 final size:179
Alignment explanation
Indices: 622184--622547 Score: 658
Period size: 178 Copynumber: 2.0 Consensus size: 179
622174 GTTTTGGAAA
*
622184 AGCTTGGGAGGTATATTTTCTAGTCTTTTTCCTTTTGAGTAAGTCTTTATGTTATCTTTAAGATT
1 AGCTTGGGAGGTATATTTTCTAGCCTTTTTCCTTTTGAGTAAGTCTTTATGTTATCTTTAAGATT
*
622249 ATCTTGCTTCCATAATGTTATTCATAAATAGATTTCAAAGAAAATAAGGCCATTTACTCATGCAT
66 ATCTTACTTCCATAATGTTATTCATAAATAGATTTCAAAGAAAATAAGGCCATTTACTCATGCAT
*
622314 TCTCACATATTCATGCAC-TTTTTTTCATGAGATTAATTCATGTGGATG
131 TCTCACATATTCATGCACTTTTTTTTCATGAGATTAATACATGTGGATG
*
622362 AGCTTGGGAGGTATATTTTCTAGCCTTTTTCCTTTTGATTAAGTCTTTATGTTATCTTTAAGATT
1 AGCTTGGGAGGTATATTTTCTAGCCTTTTTCCTTTTGAGTAAGTCTTTATGTTATCTTTAAGATT
* *
622427 ATCTTACTTCCATAATGTTGTTCATAAATAGATTTCAAAGAAAATGAGGCCATTTACTCATGCAT
66 ATCTTACTTCCATAATGTTATTCATAAATAGATTTCAAAGAAAATAAGGCCATTTACTCATGCAT
622492 TCTCACATATTCATGCACTTTTTTTTTCATGAGATTAATACATGTGGATG
131 TCTCACATATTCATGCAC-TTTTTTTTCATGAGATTAATACATGTGGATG
622542 AGCTTG
1 AGCTTG
622548 ATGATTTCCC
Statistics
Matches: 178, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
178 143 0.80
180 35 0.20
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (179 bp):
AGCTTGGGAGGTATATTTTCTAGCCTTTTTCCTTTTGAGTAAGTCTTTATGTTATCTTTAAGATT
ATCTTACTTCCATAATGTTATTCATAAATAGATTTCAAAGAAAATAAGGCCATTTACTCATGCAT
TCTCACATATTCATGCACTTTTTTTTCATGAGATTAATACATGTGGATG
Found at i:627561 original size:4 final size:4
Alignment explanation
Indices: 627501--627574 Score: 57
Period size: 4 Copynumber: 19.0 Consensus size: 4
627491 ATACAAAACA
* * * *
627501 AAAG AAA- ATAG AAAG TAAG -AAG -AAG AAA- AAAG AAAA AAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
627545 AGAAA AAAGG AAAG AAAG AAAG AAAG AAAG
1 A-AAG AAA-G AAAG AAAG AAAG AAAG AAAG
627575 GAAAAGAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
3 11 0.19
4 41 0.71
5 6 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:630395 original size:34 final size:35
Alignment explanation
Indices: 630325--630397 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
630315 CTGGTGTTTG
*
630325 TGAAAGAATAAGCACAAAGGAATACAAATGAGCTT
1 TGAAAGAATAAGCACAAAGGAATACAAAAGAGCTT
**
630360 TGAAAGAATAA-CAACAAA-GAATACAAAAGCTCTT
1 TGAAAGAATAAGC-ACAAAGGAATACAAAAGAGCTT
630394 TGAA
1 TGAA
630398 GTGTAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 18 0.53
35 16 0.47
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.18
Consensus pattern (35 bp):
TGAAAGAATAAGCACAAAGGAATACAAAAGAGCTT
Found at i:630673 original size:20 final size:20
Alignment explanation
Indices: 630648--630700 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
630638 GTTGGGCTCA
630648 ATGTATTGATACATTTCATC
1 ATGTATTGATACATTTCATC
630668 ATGTATTGATACATTTCATC
1 ATGTATTGATACATTTCATC
*
630688 ATGTATGGATACA
1 ATGTATTGATACA
630701 ATCTTTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATTGATACATTTCATC
Found at i:630821 original size:19 final size:19
Alignment explanation
Indices: 630769--630823 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
630759 TATTTTAGTG
**
630769 TGTATCGATACAATAAACA
1 TGTATCGATACAATGTACA
630788 TGTATCGATACAATGTACA
1 TGTATCGATACAATGTACA
630807 TGTATCGATACAATGTA
1 TGTATCGATACAATGTA
630824 TCGATACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAATGTACA
Found at i:630822 original size:13 final size:13
Alignment explanation
Indices: 630806--630832 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
630796 TACAATGTAC
630806 ATGTATCGATACA
1 ATGTATCGATACA
630819 ATGTATCGATACA
1 ATGTATCGATACA
630832 A
1 A
630833 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:632409 original size:13 final size:13
Alignment explanation
Indices: 632391--632415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
632381 CATTTTATGG
632391 TGTATCGATACAA
1 TGTATCGATACAA
632404 TGTATCGATACA
1 TGTATCGATACA
632416 TACTATGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:632410 original size:33 final size:32
Alignment explanation
Indices: 632368--632435 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
632358 CGTTACAAGC
** *
632368 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCAATA
632401 CAATGTATCGATACATACTATGTGTATCAATA
1 CAATGTATCGATACATACTATGTGTATCAATA
632433 CAA
1 CAA
632436 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCAATA
Found at i:632514 original size:20 final size:20
Alignment explanation
Indices: 632489--632551 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
632479 TCTTTTTCAA
632489 GTATCGATACTATGCAACAT
1 GTATCGATACTATGCAACAT
632509 GTATCG--A-TA--C-A-AT
1 GTATCGATACTATGCAACAT
632522 GTATCGATACTATGCAACAT
1 GTATCGATACTATGCAACAT
632542 GTATCGATAC
1 GTATCGATAC
632552 ATTTAAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 1 0.03
20 18 0.50
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACTATGCAACAT
Found at i:632525 original size:13 final size:13
Alignment explanation
Indices: 632507--632531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
632497 ACTATGCAAC
632507 ATGTATCGATACA
1 ATGTATCGATACA
632520 ATGTATCGATAC
1 ATGTATCGATAC
632532 TATGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:632526 original size:33 final size:33
Alignment explanation
Indices: 632489--632552 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
632479 TCTTTTTCAA
632489 GTATCGATACTATGCAACATGTATCGATACAAT
1 GTATCGATACTATGCAACATGTATCGATACAAT
632522 GTATCGATACTATGCAACATGTATCGATACA
1 GTATCGATACTATGCAACATGTATCGATACA
632553 TTTAAATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (33 bp):
GTATCGATACTATGCAACATGTATCGATACAAT
Found at i:634996 original size:13 final size:13
Alignment explanation
Indices: 634978--635016 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
634968 ATAATCCCCT
634978 TGTATCGATACAG
1 TGTATCGATACAG
*
634991 TGTATCGATACAA
1 TGTATCGATACAG
635004 TGTATCGATACAG
1 TGTATCGATACAG
635017 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:641198 original size:13 final size:13
Alignment explanation
Indices: 641180--641204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
641170 CATTTTATGG
641180 TGTATCGATACAA
1 TGTATCGATACAA
641193 TGTATCGATACA
1 TGTATCGATACA
641205 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:641220 original size:32 final size:33
Alignment explanation
Indices: 641157--641224 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
641147 CGTTACAAGC
**
641157 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
641190 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
641222 CAA
1 CAA
641225 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:641303 original size:20 final size:21
Alignment explanation
Indices: 641256--641307 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
641246 GCCAATGACC
**
641256 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
641277 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
641297 TGTATCGATAC
1 TGTATCGATAC
641308 TATGCAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:641318 original size:20 final size:20
Alignment explanation
Indices: 641295--641360 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
641285 TACATTTGGT
641295 CATGTATCGATACTATGCAA
1 CATGTATCGATACTATGCAA
641315 CATGTATCG--A-TA--C-A
1 CATGTATCGATACTATGCAA
641329 -ATGTATCGATACTATGCAA
1 CATGTATCGATACTATGCAA
641348 CATGTATCGATAC
1 CATGTATCGATAC
641361 ATTTAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 8 0.21
14 1 0.03
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 1 0.03
20 21 0.54
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACTATGCAA
Found at i:641334 original size:13 final size:13
Alignment explanation
Indices: 641316--641340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
641306 ACTATGCAAC
641316 ATGTATCGATACA
1 ATGTATCGATACA
641329 ATGTATCGATAC
1 ATGTATCGATAC
641341 TATGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:641338 original size:33 final size:33
Alignment explanation
Indices: 641296--641361 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
641286 ACATTTGGTC
641296 ATGTATCGATACTATGCAACATGTATCGATACA
1 ATGTATCGATACTATGCAACATGTATCGATACA
641329 ATGTATCGATACTATGCAACATGTATCGATACA
1 ATGTATCGATACTATGCAACATGTATCGATACA
641362 TTTAAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACTATGCAACATGTATCGATACA
Found at i:643467 original size:34 final size:33
Alignment explanation
Indices: 643424--643488 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
643414 AATAGTACCT
*
643424 ATGTATCGATGCTAAGAAAAGCAGTATCGATACA
1 ATGTATCGATACTAAG-AAAGCAGTATCGATACA
* *
643458 ATGTATCGATACTAAGAATGCAGTATTGATA
1 ATGTATCGATACTAAGAAAGCAGTATCGATA
643489 TATTTGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACTAAGAAAGCAGTATCGATACA
Found at i:648050 original size:12 final size:12
Alignment explanation
Indices: 648033--648059 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
648023 TTCGAGTCAA
648033 CTTCATCATCAT
1 CTTCATCATCAT
648045 CTTCATCATCAT
1 CTTCATCATCAT
648057 CTT
1 CTT
648060 TGATGGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTCATCATCAT
Found at i:649385 original size:34 final size:35
Alignment explanation
Indices: 649315--649387 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
649305 CTGGTGTTTG
* *
649315 TGAAAGAATAAGCACAAAGGAATACAAATGAGCTT
1 TGAAAGAATAACCACAAAGGAATACAAAAGAGCTT
**
649350 TGAAAGAAT-ACCAACAAA-GAATACAAAAGCTCTT
1 TGAAAGAATAACC-ACAAAGGAATACAAAAGAGCTT
649384 TGAA
1 TGAA
649388 GTGTAGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.58
35 14 0.42
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (35 bp):
TGAAAGAATAACCACAAAGGAATACAAAAGAGCTT
Found at i:649697 original size:13 final size:13
Alignment explanation
Indices: 649679--649709 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
649669 ACAATCTTCC
*
649679 ATGTATCGATATA
1 ATGTATCGATACA
649692 ATGTATCGATACA
1 ATGTATCGATACA
649705 ATGTA
1 ATGTA
649710 AGTTTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:649777 original size:19 final size:19
Alignment explanation
Indices: 649753--649800 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
649743 TATTTTAGTG
649753 TGTATCGATACAATAAACA
1 TGTATCGATACAATAAACA
**
649772 TGTATCGATACAATGTACA
1 TGTATCGATACAATAAACA
649791 TGTATCGATA
1 TGTATCGATA
649801 TATGTACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAATAAACA
Found at i:652407 original size:2 final size:2
Alignment explanation
Indices: 652395--652438 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
652385 TCACTTACAC
* * *
652395 AT AT GT AT AT AT AT AT AC AT AT AT AT AT AT AT AT GT 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
652437 AT
1 AT
652439 CTTTTGCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:654007 original size:16 final size:17
Alignment explanation
Indices: 653988--654054 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 17
653978 AAATATATTT
653988 TAAAAT-TTATATAATA
1 TAAAATATTATATAATA
*
654004 TAAATTATTATA-AAT-
1 TAAAATATTATATAATA
654019 TAAAAT-TTATATAAATA
1 TAAAATATTATAT-AATA
*
654036 TAAAATATT-TTTAATA
1 TAAAATATTATATAATA
654052 TAA
1 TAA
654055 TTAAAACATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 18 0.42
17 13 0.30
18 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATATTATATAATA
Found at i:661370 original size:18 final size:20
Alignment explanation
Indices: 661333--661373 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
661323 ATATTATTAA
661333 ATTTTTATTATTAATAAATTT
1 ATTTTTATTA-TAATAAATTT
*
661354 ATTTTTATTA-AATAATTTT
1 ATTTTTATTATAATAAATTT
661373 A
1 A
661374 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTATTATAATAAATTT
Found at i:661901 original size:40 final size:42
Alignment explanation
Indices: 661848--661930 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 42
661838 TTATATTATT
* * *
661848 AATTTTATTTTAAAT-TTTTTAATTAATAAATTCACTT-ATATA
1 AATTTTA-TTTAAATAATTTTAA-TAAAAAATTAACTTAATATA
661890 AATTTTA-TTAAATAATTTTAATAAAAAATTAACTTAATATA
1 AATTTTATTTAAATAATTTTAATAAAAAATTAACTTAATATA
661931 TACATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 18 0.50
41 11 0.31
42 7 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (42 bp):
AATTTTATTTAAATAATTTTAATAAAAAATTAACTTAATATA
Found at i:662075 original size:22 final size:23
Alignment explanation
Indices: 662020--662072 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
662010 AAAATTACTA
662020 AATAATATTAAT-ATAAATAATTT
1 AATAATATTAATAATAAA-AATTT
*
662043 AA-ATTATTAATAATAAAAATTT
1 AATAATATTAATAATAAAAATTT
662065 AATAATAT
1 AATAATAT
662073 AATTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATATTAATAATAAAAATTT
Found at i:662078 original size:13 final size:14
Alignment explanation
Indices: 662049--662082 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
662039 ATTTAAATTA
662049 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
662063 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
662076 TTAATAA
1 TTAATAA
662083 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:662495 original size:15 final size:15
Alignment explanation
Indices: 662475--662511 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
662465 TTTAAATATT
*
662475 AATATAATATTTATA
1 AATATAATATTAATA
662490 AATATAATATTAATA
1 AATATAATATTAATA
662505 AA-ATAAT
1 AATATAAT
662512 TAAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATAATATTAATA
Found at i:662502 original size:26 final size:25
Alignment explanation
Indices: 662469--662531 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
662459 ATTTAATTTA
*
662469 AATATTAATATAATATTTATAAATAT
1 AATATTAATATAATAATTA-AAATAT
*
662495 AATATTAATAAAATAATTAAAATAT
1 AATATTAATATAATAATTAAAATAT
*
662520 AAT-TAAATATAA
1 AATATTAATATAA
662532 CACGAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 7 0.21
25 9 0.27
26 17 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATTAATATAATAATTAAAATAT
Found at i:662566 original size:16 final size:15
Alignment explanation
Indices: 662547--662626 Score: 58
Period size: 16 Copynumber: 5.2 Consensus size: 15
662537 AAATATATTT
662547 TAAAATTTATATAATA
1 TAAAATTTATA-AATA
*
662563 TAAATTATTATAAATA
1 TAAAAT-TTATAAATA
*
662579 TAAAATTTTTTAAATA
1 TAAAA-TTTATAAATA
*
662595 T--AA-TTATGATATAA
1 TAAAATTTAT-AAAT-A
*
662609 TAAAATATATAAATA
1 TAAAATTTATAAATA
662624 TAA
1 TAA
662627 TATACGAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 4 0.08
15 4 0.08
16 27 0.54
17 9 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
TAAAATTTATAAATA
Found at i:662585 original size:32 final size:31
Alignment explanation
Indices: 662547--662626 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
662537 AAATATATTT
*
662547 TAAAATTTATATAATATAAATTATTATAAATA
1 TAAAATTTATATAATATAAATTATGATAAA-A
* *
662579 TAAAATTT-TTTAA-ATATAATTATGATATAA
1 TAAAATTTATATAATATA-AATTATGATAAAA
*
662609 TAAAATATATA-AATATAA
1 TAAAATTTATATAATATAA
662627 TATACGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
30 14 0.35
31 18 0.45
32 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAATTTATATAATATAAATTATGATAAAA
Found at i:664981 original size:257 final size:255
Alignment explanation
Indices: 664524--665009 Score: 595
Period size: 257 Copynumber: 1.9 Consensus size: 255
664514 ATCTAAGTGT
* * *
664524 ATCTAAATGCTTACAGAAATCATCTCCAAAATACATACATGAAATAGGCACACCAGAATGACAAT
1 ATCTAAATGCTTACAGAAACCATCTCCAAAATACATACATGAAATAGACACACCAGAATCACAAT
* * *
664589 TAGCTGCATCGTTTTACTAAAATTCAGAGAAAATGTTGGCTTTTCAATCTATCTAAGTGCACTTA
66 TAGCTGCATCATTTTACTAAAATTCAGAGAAAATGTTGGCTTTTCAATCCATCTAAGTGAACTTA
* ***
664654 AATGCTATACTATGAAGGCATATAACCTTATTTTTTAAAATATTTAGGCGCATCGATATTTAATT
131 AATGCTATACCATGAAGGCATATAACCTTATACCTTAAAATATTTAGGCGCATCGATATTTAATT
* * *
664719 TCAGTGTGCTTTTTTCGTAAAGTTCAGAGAAAAGCCATCCTCCTAATACCATTTAAACAC
196 TCAGTGTACCTTTTTCGTAAAGTTCAAAGAAAAGCCATCCTCCTAATACCATTTAAACAC
* * * ** *
664779 ATCTAAATGCTTTATAGAAACCATCTTCAAAATACATACATGAAATAGACGCACTTGTATCA-AA
1 ATCTAAATGC-TTACAGAAACCATCTCCAAAATACATACATGAAATAGACACACCAGAATCACAA
* * * * *
664843 TTTAGGTGCGTCATTTTACTAAAGTTTAGAGAAAATGTTGGATTTTTCAATCCATCTAAGTGAA-
65 -TTAGCTGCATCATTTTACTAAAATTCAGAGAAAATGTTGG-CTTTTCAATCCATCTAAGTGAAC
* * * * * *
664907 TCTCAATGTTTTACCATGAAGGCATATATCCTTAATACCTT-CAATATTT-GG-GCATGCTAGTA
128 T-TAAATGCTATACCATGAAGGCATATAACCTT-ATACCTTAAAATATTTAGGCGCAT-CGA-TA
*
664969 TTTAATTTCAGTGTACCTTTTTCGTAGAGTTCAAAGAAAAG
189 TTTAATTTCAGTGTACCTTTTTCGTAAAGTTCAAAGAAAAG
665010 GCGTGCTTCG
Statistics
Matches: 193, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
255 16 0.08
256 82 0.42
257 91 0.47
258 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (255 bp):
ATCTAAATGCTTACAGAAACCATCTCCAAAATACATACATGAAATAGACACACCAGAATCACAAT
TAGCTGCATCATTTTACTAAAATTCAGAGAAAATGTTGGCTTTTCAATCCATCTAAGTGAACTTA
AATGCTATACCATGAAGGCATATAACCTTATACCTTAAAATATTTAGGCGCATCGATATTTAATT
TCAGTGTACCTTTTTCGTAAAGTTCAAAGAAAAGCCATCCTCCTAATACCATTTAAACAC
Found at i:666251 original size:14 final size:14
Alignment explanation
Indices: 666232--666258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
666222 AATTAAGATA
666232 AAAATCTTGAATAT
1 AAAATCTTGAATAT
666246 AAAATCTTGAATA
1 AAAATCTTGAATA
666259 ATTTTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAATCTTGAATAT
Found at i:666650 original size:20 final size:18
Alignment explanation
Indices: 666627--666670 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
666617 AAAGAAAACT
666627 TTAAATAAAGTTAAAAAATC
1 TTAAATAAAG-T-AAAAATC
*
666647 TTAATTAAAGTAAAAATC
1 TTAAATAAAGTAAAAATC
666665 -TAAATA
1 TTAAATA
666671 TCACTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 1 0.05
20 9 0.41
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
TTAAATAAAGTAAAAATC
Found at i:668694 original size:12 final size:12
Alignment explanation
Indices: 668654--668698 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
668644 AAAATTTCTT
*
668654 TTTTTATAAATA
1 TTTTAATAAATA
668666 TTTTGAAT-AA-A
1 TTTT-AATAAATA
668677 -TTTAATAAATA
1 TTTTAATAAATA
668688 TTTTAATAAAT
1 TTTTAATAAAT
668699 GAAAATCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
9 3 0.11
10 5 0.18
11 2 0.07
12 16 0.57
13 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTTAATAAATA
Found at i:669090 original size:21 final size:21
Alignment explanation
Indices: 669064--669105 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
669054 TAAAAATTTC
669064 AATATTAT-ATTTTTTAAAATT
1 AATATT-TGATTTTTTAAAATT
669085 AATATTTGATTTTTTAAAATT
1 AATATTTGATTTTTTAAAATT
669106 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATATTTGATTTTTTAAAATT
Found at i:669103 original size:64 final size:63
Alignment explanation
Indices: 668960--669147 Score: 166
Period size: 64 Copynumber: 2.9 Consensus size: 63
668950 CTTTAATTCC
* * *
668960 ATATTTTACTTTTTAAAATTTATTTAAAAGTA-AAAATAATTAAAATTATATTTTAAAAATTA
1 ATATTTCATTTTTTAAAATTTATTTAAAAATATAAAATAATTAAAATTATATTTTAAAAATTA
* * * * * * *
669022 ATA-TCCATTTTAATAAAATATATTGAAAAATATAAAA-ATTTCAATATTATATTTTTTAAAATT
1 ATATTTCATTTT-TTAAAATTTATTTAAAAATATAAAATAATT-AAAATTATA-TTTTAAAAATT
669085 A
63 A
* * * *
669086 ATATTTGATTTTTTAAAATTTTTTTAAAAACTATAAAATTATTTTAAAATTAAAATTTTAAA
1 ATATTTCATTTTTTAAAATTTATTTAAAAA-TATAAAA-TA-ATTAAAATT-ATATTTTAAA
669148 TATATAACTA
Statistics
Matches: 97, Mismatches: 19, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
61 5 0.05
62 22 0.23
63 12 0.12
64 28 0.29
65 13 0.13
67 12 0.12
68 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (63 bp):
ATATTTCATTTTTTAAAATTTATTTAAAAATATAAAATAATTAAAATTATATTTTAAAAATTA
Found at i:669154 original size:33 final size:35
Alignment explanation
Indices: 669107--669182 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
669097 TTTAAAATTT
* *
669107 TTTTAAAAACTATAA-AATTATTTTAAA-ATTAAAA
1 TTTTAAATACTATAACAATT-TTTTAAATATAAAAA
*
669141 TTTTAAATA-TATAACTATTTTTTAAATATAAAAA
1 TTTTAAATACTATAACAATTTTTTAAATATAAAAA
*
669175 TATTAAAT
1 TTTTAAAT
669183 GTGCCTGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.33
34 24 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (35 bp):
TTTTAAATACTATAACAATTTTTTAAATATAAAAA
Found at i:669178 original size:19 final size:19
Alignment explanation
Indices: 669141--669178 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
669131 AAAATTAAAA
* *
669141 TTTTAAATATATAACTATT
1 TTTTAAATATAAAAATATT
669160 TTTTAAATATAAAAATATT
1 TTTTAAATATAAAAATATT
669179 AAATGTGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAAATATAAAAATATT
Found at i:675398 original size:16 final size:17
Alignment explanation
Indices: 675377--675413 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
675367 AATATTAGGT
675377 TATTTATTAATATA-TA
1 TATTTATTAATATATTA
*
675393 TATTTATTAATTTATTA
1 TATTTATTAATATATTA
675410 TATT
1 TATT
675414 ACACTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTATTAATATATTA
Found at i:681369 original size:20 final size:20
Alignment explanation
Indices: 681344--681397 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
681334 GTTATAAGCA
*
681344 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
681364 ATGTATTGATACAATGTACC
1 ATGTATCGATACAATGTACC
681384 ATGTATCGATACAA
1 ATGTATCGATACAA
681398 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:681734 original size:13 final size:13
Alignment explanation
Indices: 681716--681741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
681706 AATCCTTGAA
681716 TGTATCGATACAT
1 TGTATCGATACAT
681729 TGTATCGATACAT
1 TGTATCGATACAT
681742 GAATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:683381 original size:3 final size:3
Alignment explanation
Indices: 683373--683408 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
683363 TCAACCATCA
* *
683373 ATG ATG ATG AAG ATG ATA ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
683409 GTGACTCGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:687588 original size:22 final size:23
Alignment explanation
Indices: 687561--687610 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
687551 GTTATCTTGA
*
687561 TAAATAAAATTAATAA-TTTAAT
1 TAAATAAAATTAAAAATTTTAAT
*
687583 TAAATAGAATTAAAAATTTTAAT
1 TAAATAAAATTAAAAATTTTAAT
687606 TAAAT
1 TAAAT
687611 TATGTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATAAAATTAAAAATTTTAAT
Found at i:690436 original size:23 final size:23
Alignment explanation
Indices: 690395--690438 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
690385 CAATGTCAAT
*
690395 ATTTTTTTATATAAATTTTTAAG
1 ATTTTTTAATATAAATTTTTAAG
* *
690418 ATTTTTTAATTTAATTTTTTA
1 ATTTTTTAATATAAATTTTTA
690439 CTTATAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTTTTAATATAAATTTTTAAG
Found at i:690498 original size:26 final size:26
Alignment explanation
Indices: 690441--690498 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
690431 ATTTTTTACT
690441 TATAAAATTTTAATTTTATTTAAATA
1 TATAAAATTTTAATTTTATTTAAATA
* *
690467 TTTAAAATTATTGA-TTTATTT-AATA
1 TATAAAATT-TTAATTTTATTTAAATA
690492 TAATAAA
1 T-ATAAA
690499 TAAATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TATAAAATTTTAATTTTATTTAAATA
Found at i:690808 original size:21 final size:22
Alignment explanation
Indices: 690783--690831 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
690773 ATCATTAATT
690783 TTAATTTTATTATTACAA-AAC
1 TTAATTTTATTATTACAATAAC
*
690804 TTAATTTTATTATTATAATAAC
1 TTAATTTTATTATTACAATAAC
690826 -TAATTT
1 TTAATTT
690832 CGTAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTTTATTATTACAATAAC
Found at i:692426 original size:6 final size:6
Alignment explanation
Indices: 692415--692459 Score: 62
Period size: 5 Copynumber: 8.2 Consensus size: 6
692405 ATTAAATTTA
692415 TATATT TATA-T TATATT TATA-T TAT-TT TATATT TATATT T-TATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
692459 T
1 T
692460 TAAAAGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 18 0.50
6 18 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:692431 original size:11 final size:11
Alignment explanation
Indices: 692415--692458 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
692405 ATTAAATTTA
692415 TATATTTATAT
1 TATATTTATAT
692426 TATATTTATAT
1 TATATTTATAT
692437 TAT-TTTATATT
1 TATATTTATA-T
692448 TATATTT-TAT
1 TATATTTATAT
692458 T
1 T
692459 TTAAAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.26
11 20 0.65
12 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:692444 original size:16 final size:16
Alignment explanation
Indices: 692415--692458 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
692405 ATTAAATTTA
692415 TATATTTATATTATATT
1 TATA-TTATATTATATT
*
692432 TATATTATTTTATATT
1 TATATTATATTATATT
*
692448 TATATTTTATT
1 TATATTATATT
692459 TTAAAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTATATTATATT
Found at i:692459 original size:11 final size:11
Alignment explanation
Indices: 692410--692459 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
692400 AATGAATTAA
692410 ATTTATATATTT
1 ATTTATAT-TTT
692422 ATATTATA-TTT
1 AT-TTATATTTT
692433 ATATTAT-TTTAT
1 AT-TTATATTT-T
692445 ATTTATATTTT
1 ATTTATATTTT
692456 ATTT
1 ATTT
692460 TAAAAGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 21 0.62
12 8 0.24
13 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTATATTTT
Found at i:694031 original size:21 final size:19
Alignment explanation
Indices: 694007--694045 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
693997 TTTTTTTGGG
694007 TATTTATATAATTTCAAAAAA
1 TATTTATA-AATTT-AAAAAA
*
694028 TATTTTTAAATTTAAAAA
1 TATTTATAAATTTAAAAA
694046 TTTAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTATAAATTTAAAAAA
Found at i:694122 original size:29 final size:27
Alignment explanation
Indices: 694090--694157 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 27
694080 AATATAAAAA
* *
694090 TTATTAGTAAAACTATTTATATCATATTT
1 TTATTA-TAAAA-TATTGATACCATATTT
694119 TTATTA-AAAATATTGATACCATATTT
1 TTATTATAAAATATTGATACCATATTT
694145 TTATATATAAAAT
1 TTAT-TATAAAAT
694158 TAATAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 18 0.51
27 6 0.17
28 5 0.14
29 6 0.17
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (27 bp):
TTATTATAAAATATTGATACCATATTT
Found at i:695081 original size:18 final size:19
Alignment explanation
Indices: 695047--695083 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
695037 ATTATATATA
*
695047 TTCTTTATATAATAAAAAT
1 TTCTTAATATAATAAAAAT
695066 TTCTTAATAT-ATAAAAAT
1 TTCTTAATATAATAAAAAT
695084 ATGAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTCTTAATATAATAAAAAT
Found at i:705425 original size:20 final size:21
Alignment explanation
Indices: 705380--705435 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
705370 CAATAGAAAA
*
705380 TGTATCGATACATGCTTACAAT
1 TGTATCGATACAT-TTTACAAT
*
705402 TGTATCGATACATTTTTC-AT
1 TGTATCGATACATTTTACAAT
705422 TGTATCGATACATT
1 TGTATCGATACATT
705436 CTGAGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 16 0.50
21 3 0.09
22 13 0.41
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
TGTATCGATACATTTTACAAT
Found at i:707910 original size:79 final size:79
Alignment explanation
Indices: 707768--708132 Score: 307
Period size: 79 Copynumber: 4.6 Consensus size: 79
707758 CTTAATCTTG
* * * *
707768 GTTTTATTTTTAAAACACTGATTTTCTACCATCGGGGATACTCCAATCCC-GTTATTTTCGAGGG
1 GTTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAA-CCCTGTTATTTTCGAGGG
*
707832 GATACTCTAACCCTA
65 GATACTCTAACCCTC
* * * *
707847 GTTTTATTTTTAAAACACCAATTTTCCACCAT-TGAGATACTCTAACCCTGTTATTTTCAGAGGG
1 GTTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCTGTTATTTTC-GAGGG
*
707911 GATACTTCT-A-CTTC
65 GATAC-TCTAACCCTC
* * * * * ** * *
707925 GATTTTATTTCTAAAATACCGATTTTTCACTATCAGAGATACTCTAACCCCATTA-TTTCTAAAG
1 G-TTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCTGTTATTTTC-GAGG
* *
707989 GGATACTGC-AACACTG
64 GGATACT-CTAACCCTC
* * * *
708005 GTTTTATTTCTAAAACATCGATTTTCAACCATCGGGGACACTCCAA-CCTCGTTATTTTCGAGGG
1 GTTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCT-GTTATTTTCGAGGG
*
708069 GATACTCCAACCC-C
65 GATACTCTAACCCTC
* * * * *
708083 GATTTTATTTCTAAAACATCAATTTTTCACTAT-TGAGGATACTCCAACCC
1 G-TTTTATTTCTAAAACACCGATTTTCCACCATCGGA-GATACTCCAACCC
708133 CGTTTTCACT
Statistics
Matches: 228, Mismatches: 44, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
77 3 0.01
78 28 0.12
79 168 0.74
80 29 0.13
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
GTTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCTGTTATTTTCGAGGGG
ATACTCTAACCCTC
Found at i:707992 original size:158 final size:158
Alignment explanation
Indices: 707803--708133 Score: 375
Period size: 158 Copynumber: 2.1 Consensus size: 158
707793 CTACCATCGG
* * * * * *
707803 GGATACTCCAATCCCGTTATTT-TCGAGGGGATACT-CTAACCCTAGTTTTATTTTTAAAACACC
1 GGATACTCCAACCCCATTATTTCT-AAAGGGATACTGC-AACACTAGTTTTATTTCTAAAACACC
* * * * * * **
707866 AATTTTCCACCAT-TGAGATACTCTAACC-CTGTTATTTTCAGAGGGGATACTTCTACTTCGATT
64 AATTTTCAACCATCGGAGACACTCCAACCTC-GTTATTTTC-GAGGGGATACTCCAACCCCGATT
* *
707929 TTATTTCTAAAATACCGATTTTTCACTATCAGA
127 TTATTTCTAAAACACCAATTTTTCACTAT-AGA
* * * *
707962 -GATACTCTAACCCCATTATTTCTAAAGGGATACTGCAACACTGGTTTTATTTCTAAAACATCGA
1 GGATACTCCAACCCCATTATTTCTAAAGGGATACTGCAACACTAGTTTTATTTCTAAAACACCAA
*
708026 TTTTCAACCATCGGGGACACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
66 TTTTCAACCATCGGAGACACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
* *
708091 TTCTAAAACATCAATTTTTCACTATTGA
131 TTCTAAAACACCAATTTTTCACTATAGA
708119 GGATACTCCAACCCC
1 GGATACTCCAACCCC
708134 GTTTTCACTT
Statistics
Matches: 143, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
157 2 0.01
158 118 0.83
159 22 0.15
160 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (158 bp):
GGATACTCCAACCCCATTATTTCTAAAGGGATACTGCAACACTAGTTTTATTTCTAAAACACCAA
TTTTCAACCATCGGAGACACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTAT
TTCTAAAACACCAATTTTTCACTATAGA
Found at i:714974 original size:17 final size:17
Alignment explanation
Indices: 714943--714977 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
714933 CCATAATTTT
714943 AATTAATTATTAATTAA
1 AATTAATTATTAATTAA
714960 AATTAATT-TTGAATTAA
1 AATTAATTATT-AATTAA
714977 A
1 A
714978 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTAATTATTAATTAA
Found at i:716984 original size:2 final size:2
Alignment explanation
Indices: 716977--717021 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
716967 AAAGCTCTGT
*
716977 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
717019 TC T
1 TC T
717022 GCTTTTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:719090 original size:2 final size:2
Alignment explanation
Indices: 719083--719109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
719073 TTGGGCCTTT
719083 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 T
719110 TATTACTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:721204 original size:2 final size:2
Alignment explanation
Indices: 721197--721225 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
721187 GTCGTATCAT
721197 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 T
721226 GTCTGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:723322 original size:21 final size:21
Alignment explanation
Indices: 723304--723363 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
723294 TATTAAAAGT
723304 TGCATTTTTTCATCCAAAAAA
1 TGCATTTTTTCATCCAAAAAA
**
723325 TGCATTTTTTCATCCAACCAA
1 TGCATTTTTTCATCCAAAAAA
723346 TGCATTATTTT-ATCCAAA
1 TGCATT-TTTTCATCCAAA
723364 TACACATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
TGCATTTTTTCATCCAAAAAA
Found at i:726657 original size:21 final size:20
Alignment explanation
Indices: 726617--726673 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
726607 TTAAAAGTTA
726617 CATTTTTTCATCCAAAAATG
1 CATTTTTTCATCCAAAAATG
*
726637 CATTTTTTCATCCAACTAATG
1 CATTTTTTCATCCAA-AAATG
*
726658 CATCATTTT-ATCCAAA
1 CAT-TTTTTCATCCAAA
726674 TACACTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
21 13 0.41
22 4 0.12
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (20 bp):
CATTTTTTCATCCAAAAATG
Found at i:734941 original size:52 final size:52
Alignment explanation
Indices: 734863--734990 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
734853 CAAAATATGA
* *
734863 AAATTTGCCTACATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
734915 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
734967 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
734991 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:735003 original size:51 final size:50
Alignment explanation
Indices: 734863--735010 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
734853 CAAAATATGA
* *
734863 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
734915 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
734967 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
735011 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:735017 original size:13 final size:13
Alignment explanation
Indices: 734999--735023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
734989 CAAAGATCAG
734999 TGTATCGATACAA
1 TGTATCGATACAA
735012 TGTATCGATACA
1 TGTATCGATACA
735024 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.