Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1128108 original size:29 final size:30
Alignment explanation
Indices: 1128076--1128135 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1128066 TACTTAAATT
1128076 TTTA-TTTATA-CTCAAATAAATCATTAACC
1 TTTAGTTTATATC-CAAATAAATCATTAACC
* *
1128105 TTTAGTTTTTATCCAAATAAATTATTAACC
1 TTTAGTTTATATCCAAATAAATCATTAACC
1128135 T
1 T
1128136 CTTTTAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 22 0.81
31 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTAGTTTATATCCAAATAAATCATTAACC
Found at i:1128886 original size:2 final size:2
Alignment explanation
Indices: 1128879--1128903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1128869 AACCCTACAT
1128879 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 T
1128904 GAAAAAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1139954 original size:120 final size:120
Alignment explanation
Indices: 1139824--1140063 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 120
1139814 AATATATAAG
1139824 GACGATAAAAAAATACCTAAAAAGTAACTATCGAAAACCTTAGAGCTTCTATAAATAAAAAAAAT
1 GACGATAAAAAAATACCTAAAAAGTAACTATCGAAAACCTTAGAGCTTCTATAAATAAAAAAAAT
1139889 TCAATTTTTTAAAATAAAATATTAACTTAAACATCAAAACATATATTAAAATCTA
66 TCAATTTTTTAAAATAAAATATTAACTTAAACATCAAAACATATATTAAAATCTA
*
1139944 GACGATAAAAAAATACCTAAAAAGTAACTATCGAAAACCTTAGAGCTTTTATAAATAAAAAAAAT
1 GACGATAAAAAAATACCTAAAAAGTAACTATCGAAAACCTTAGAGCTTCTATAAATAAAAAAAAT
1140009 TCAATTTTTTAAAATAAAATATTAACTTAAACATCAAAACATATATTAAAATCTA
66 TCAATTTTTTAAAATAAAATATTAACTTAAACATCAAAACATATATTAAAATCTA
1140064 AACTCTGATC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (120 bp):
GACGATAAAAAAATACCTAAAAAGTAACTATCGAAAACCTTAGAGCTTCTATAAATAAAAAAAAT
TCAATTTTTTAAAATAAAATATTAACTTAAACATCAAAACATATATTAAAATCTA
Found at i:1140613 original size:28 final size:28
Alignment explanation
Indices: 1140581--1140638 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1140571 AATAATTAAT
1140581 TAATTTATTA-AATATTTATTTTATAAAA
1 TAATTTATTATAAT-TTTATTTTATAAAA
1140609 TAATTTATTATAATTTTATTTTATAAAA
1 TAATTTATTATAATTTTATTTTATAAAA
1140637 TA
1 TA
1140639 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATTTATTATAATTTTATTTTATAAAA
Found at i:1140616 original size:17 final size:16
Alignment explanation
Indices: 1140584--1140640 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1140574 AATTAATTAA
*
1140584 TTTATTAAATATTTAT
1 TTTATAAAATATTTAT
1140600 TTTATAAAATAATTTA-
1 TTTATAAAAT-ATTTAT
1140616 -TTAT--AAT-TTTAT
1 TTTATAAAATATTTAT
1140628 TTTATAAAATATT
1 TTTATAAAATATT
1140641 AAAATAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
11 4 0.12
13 7 0.21
15 7 0.21
16 11 0.32
17 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATAAAATATTTAT
Found at i:1140654 original size:28 final size:29
Alignment explanation
Indices: 1140591--1140677 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 29
1140581 TAATTTATTA
**
1140591 AATATTTATTTTATAAAATAATTTATTAT
1 AATATTTATTTTATAAAATAATTTAAAAT
1140620 AAT-TTTATTTTATAAAAT-A-TTAAAAT
1 AATATTTATTTTATAAAATAATTTAAAAT
* *
1140646 AATTATTTAAATTTTA-AATATAATATAAAAT
1 AA-TATTT--ATTTTATAAAATAATTTAAAAT
1140677 A
1 A
1140678 TTTTAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
26 7 0.15
27 2 0.04
28 18 0.38
29 7 0.15
30 7 0.15
31 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTTATTTTATAAAATAATTTAAAAT
Found at i:1140662 original size:20 final size:19
Alignment explanation
Indices: 1140633--1140687 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1140623 TTTATTTTAT
* *
1140633 AAAATATTAAAATAATTATT
1 AAAATTTTAAAATAA-TATA
*
1140653 TAAATTTTAAATATAATATA
1 AAAATTTTAAA-ATAATATA
1140673 AAATATTTTAAAATA
1 AAA-ATTTTAAAATA
1140688 TTTTAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTTAAAATAATATA
Found at i:1140676 original size:19 final size:19
Alignment explanation
Indices: 1140629--1140679 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1140619 TAATTTTATT
1140629 TTATAAAATATTAAAATAA
1 TTATAAAATATTAAAATAA
* *
1140648 TTATTTAAATTTTAAATATAA
1 TTA-TAAAATATTAAA-ATAA
1140669 -TATAAAATATT
1 TTATAAAATATT
1140680 TTAAAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATAAAATATTAAAATAA
Found at i:1140770 original size:20 final size:20
Alignment explanation
Indices: 1140725--1140778 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1140715 TTTTATCATA
1140725 TTTTATTTTATAA-ATTAAAT
1 TTTTA-TTTATAATATTAAAT
** *
1140745 AATTATTTATAATATTATAT
1 TTTTATTTATAATATTAAAT
1140765 TTTTATTT-TAATAT
1 TTTTATTTATAATAT
1140779 AATTTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAATATTAAAT
Found at i:1141413 original size:2 final size:2
Alignment explanation
Indices: 1141406--1141461 Score: 78
Period size: 2 Copynumber: 28.0 Consensus size: 2
1141396 TATATGTTAT
* *
1141406 GA GA GA GA TA GA CG- GA GA GA GA GA GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1141448 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
1141462 TTTGAAGAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.46, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1145663 original size:29 final size:29
Alignment explanation
Indices: 1145590--1145667 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
1145580 TTTATATTTT
*
1145590 TTTATATTATA-AT-TATA-ATTAAAATA
1 TTTATATTATATATATATATATTTAAATA
* * * * *
1145616 -TTATATAAAATTTAAATATATTTATATA
1 TTTATATTATATATATATATATTTAAATA
1145644 TTTATATTATATATATATATATTT
1 TTTATATTATATATATATATATTT
1145668 TTTTTTATGT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
25 8 0.21
26 1 0.03
27 3 0.08
28 7 0.18
29 19 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTATATTATATATATATATATTTAAATA
Found at i:1147632 original size:2 final size:2
Alignment explanation
Indices: 1147627--1147665 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1147617 AGAGAGATGT
1147627 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
1147666 CTTGTGAAGA
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:1148024 original size:10 final size:9
Alignment explanation
Indices: 1148007--1148036 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1147997 TGCATGAATT
1148007 TTAAAAAAA
1 TTAAAAAAA
1148016 TTAAAAAAA
1 TTAAAAAAA
1148025 TTAAAAAAA
1 TTAAAAAAA
1148034 TTA
1 TTA
1148037 CGTTTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1152752 original size:2 final size:2
Alignment explanation
Indices: 1152745--1152772 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1152735 TCTAATATTA
1152745 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
1152773 GTGTGTGTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153210 original size:2 final size:2
Alignment explanation
Indices: 1153203--1153236 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1153193 GGCCAATCTA
1153203 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
1153237 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153418 original size:462 final size:462
Alignment explanation
Indices: 1152584--1153969 Score: 2681
Period size: 462 Copynumber: 3.0 Consensus size: 462
1152574 TTAATATTTT
1152584 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
1 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
*
1152649 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGTTTTTTTAACGACAAGGAACTTCATTTTTAT
66 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
1152714 ATAATGAATGCAATCGGCCAATCTAATATTAATATATATATATATATATATATATATATGTGTGT
131 ATAATGAATGCAATCGGCCAATCTAATA-T-ATATATATATATATATATATATATATATGTGTGT
1152779 GTGTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTC
194 GTGTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTC
1152844 TTTGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCAC
259 TTTGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCAC
1152909 TGCCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAA
324 TGCCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAA
1152974 CTTTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGT
389 CTTTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGT
1153039 ATTCTCCAC
454 ATTCTCCAC
1153048 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
1 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
1153113 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
66 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
*
1153178 ATAATGAATGCAATCGGCCAATCTAATATATATATATATATATATATATATATATATATGTGTGT
131 ATAATGAATGCAATCGGCCAATCTAATATATATATATATATATATATATATATATATGTGTGTGT
*
1153243 GTGTGTGTGTGATGCCTTTAACCAGCACTTAAACTTTCACTTTCACTTGAGAAGTGCTTTTTCTT
196 GTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTCTT
1153308 TGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCACTG
261 TGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCACTG
1153373 CCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAACT
326 CCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAACT
1153438 TTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGTAT
391 TTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGTAT
1153503 TCTCCAC
456 TCTCCAC
1153510 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
1 TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
1153575 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
66 GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
* *
1153640 ATAATGAATGCAATCGGCCAATC---TA-ATATATATATATATATATATATATGTGTGTGTGTGT
131 ATAATGAATGCAATCGGCCAATCTAATATATATATATATATATATATATATATATATGTGTGTGT
1153701 GTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTCTT
196 GTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTCTT
1153766 TGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCACTG
261 TGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCACTG
1153831 CCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAACT
326 CCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAACT
1153896 TTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGTAT
391 TTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGTAT
1153961 TCTCCAC
456 TCTCCAC
1153968 TA
1 TA
1153970 CCTTGTTTAT
Statistics
Matches: 915, Mismatches: 7, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
458 301 0.33
459 2 0.00
462 454 0.50
463 1 0.00
464 157 0.17
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (462 bp):
TATTTAAATCTTTTAAATATAGAAACTTTTCATTTATAACCAGGCACTTGAATGGAAAATTATAT
GAGATCTGAGAATCAAAACCCAAATCAGAAAAGGCTTTTTTAACGACAAGGAACTTCATTTTTAT
ATAATGAATGCAATCGGCCAATCTAATATATATATATATATATATATATATATATATGTGTGTGT
GTGTGTGTGTGATGCCTTTAACCAGCACTTGAACTTTCACTTTCACTTGAGAAGTGCTTTTTCTT
TGTTCCCTGATTAAAACTTCCCTTTCCAAGTGTCATCCCTTACCAAATTTACCTCTCAGCCACTG
CCTTCATAATATTAAACAAATGAAAAGGCAACAAGCTAGATTTCCCCATTTGATTTGTTTAAACT
TTAAATGAAAAAAGAACCAAATTGTTTGTTTGGCACAATATCATGCATTATTATGTTTCAAGTAT
TCTCCAC
Found at i:1162465 original size:12 final size:12
Alignment explanation
Indices: 1162427--1162498 Score: 76
Period size: 12 Copynumber: 5.9 Consensus size: 12
1162417 TTTTCAAATT
1162427 AATATAATATTAA
1 AATATAATA-TAA
*
1162440 AAAATAAT-TAA
1 AATATAATATAA
* *
1162451 AATGTGATATAA
1 AATATAATATAA
1162463 AATATAATATAA
1 AATATAATATAA
1162475 ATATATAATA-AA
1 A-ATATAATATAA
1162487 AATATTAATATA
1 AATA-TAATATA
1162499 TTTAAATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
11 11 0.22
12 22 0.45
13 16 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
AATATAATATAA
Found at i:1162514 original size:31 final size:31
Alignment explanation
Indices: 1162476--1162543 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1162466 ATAATATAAA
1162476 TATATAATA-AAAATATTAATATATTTAAATT
1 TATATAATATAAAATATTAATATA-TTAAATT
* *
1162507 TATATAATATAAATTATTAATTTATTAAATT
1 TATATAATATAAAATATTAATATATTAAATT
1162538 TATATA
1 TATATA
1162544 TGGTGCAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATAATATAAAATATTAATATATTAAATT
Found at i:1163003 original size:3 final size:3
Alignment explanation
Indices: 1162989--1163032 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1162979 TGTTTAGATG
*
1162989 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1163033 GGGCATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1163716 original size:2 final size:2
Alignment explanation
Indices: 1163709--1163740 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1163699 CTAGAAATTT
1163709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1163741 CACACACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1165365 original size:15 final size:15
Alignment explanation
Indices: 1165328--1165374 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1165318 ATTTTAAAAG
*
1165328 ATTTTTAAATATAAA
1 ATTTTTTAATATAAA
**
1165343 ATAATTTAATATAAA
1 ATTTTTTAATATAAA
*
1165358 ATTTTTTATTA-AAA
1 ATTTTTTAATATAAA
1165372 ATT
1 ATT
1165375 AAAATAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTTTTAATATAAA
Found at i:1166112 original size:14 final size:12
Alignment explanation
Indices: 1166076--1166213 Score: 53
Period size: 12 Copynumber: 11.6 Consensus size: 12
1166066 TTTAAATTTA
1166076 AATAA-AAATA-
1 AATAATAAATAT
1166086 AAT-ATAAA-AT
1 AATAATAAATAT
*
1166096 AATTA-AAATAT
1 AATAATAAATAT
1166107 AATAATAAATAT
1 AATAATAAATAT
1166119 AATTTAATGTAAATA-
1 AA--TAA--TAAATAT
1166134 AATATATAAATAT
1 AATA-ATAAATAT
** *
1166147 TTTAA-ATTATAT
1 AATAATA-AATAT
*
1166159 AATATATTTAATAT
1 AATA-A-TAAATAT
*
1166173 AATTATAATATAT
1 AATAATAA-ATAT
*
1166186 AA-AATATATA-
1 AATAATAAATAT
1166196 AATAAT-AATAT
1 AATAATAAATAT
*
1166207 AAAAATA
1 AATAATA
1166214 CTGATTACCA
Statistics
Matches: 95, Mismatches: 14, Indels: 36
0.66 0.10 0.25
Matches are distributed among these distances:
9 2 0.02
10 17 0.18
11 19 0.20
12 26 0.27
13 12 0.13
14 11 0.12
15 2 0.02
16 6 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:1166114 original size:49 final size:49
Alignment explanation
Indices: 1166054--1166201 Score: 126
Period size: 49 Copynumber: 2.9 Consensus size: 49
1166044 AATATTTTAT
1166054 AATT-TATAATAATTTAAATTTAAATAAAAATAAATATA-AAATAATTAA
1 AATTATATAATAATTTAAATTT-AATAAAAATAAATATATAAATAATTAA
* ** * *
1166102 AA-TATAATAATAA-ATATAATTTAATGTAAATAAATATATAAATATTTTA
1 AATTAT-ATAATAATTTA-AATTTAATAAAAATAAATATATAAATAATTAA
*
1166151 AATTATATAATATATTTAATATAATT-ATAATATATAAAATATATAAATAAT
1 AATTATATAATA-ATTTAA-AT--TTAATAA-AAAT-AAATATATAAATAAT
1166202 AATATAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
47 1 0.01
48 19 0.24
49 28 0.36
50 5 0.06
51 4 0.05
52 2 0.03
53 5 0.06
54 14 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.41
Consensus pattern (49 bp):
AATTATATAATAATTTAAATTTAATAAAAATAAATATATAAATAATTAA
Found at i:1166115 original size:28 final size:28
Alignment explanation
Indices: 1166074--1166146 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1166064 AATTTAAATT
1166074 TAAATA-AA-AATAAATATAAAATAAT-
1 TAAATATAATAATAAATATAAAATAATG
**
1166099 TAAAATATAATAATAAATATAATTTAATG
1 T-AAATATAATAATAAATATAAAATAATG
1166128 TAAATA-AATATATAAATAT
1 TAAATATAATA-ATAAATAT
1166147 TTTAAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.02
26 5 0.12
27 6 0.15
28 28 0.68
29 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
TAAATATAATAATAAATATAAAATAATG
Found at i:1166191 original size:20 final size:20
Alignment explanation
Indices: 1166156--1166193 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1166146 TTTTAAATTA
**
1166156 TATAATATATTTAATATAAT
1 TATAATATATAAAATATAAT
1166176 TATAATATATAAAATATA
1 TATAATATATAAAATATA
1166194 TAAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATATATAAAATATAAT
Found at i:1166198 original size:45 final size:42
Alignment explanation
Indices: 1166071--1166207 Score: 116
Period size: 45 Copynumber: 3.0 Consensus size: 42
1166061 AATAATTTAA
*
1166071 ATTTAAATAAAAATAAATATA-AAATAATTAAAATATAATAATAAATAT
1 ATTT-AATATAAATAAATATATAAAT-ATT---ATA-AATAAT-AATAT
* *
1166119 AATTTAATGTAAATAAATATATAAATATTTTAAATTATATAATAT
1 -ATTTAATATAAATAAATATATAAATATTATAAA-TA-ATAATAT
*
1166164 ATTTAATATAATTATAATATATAAA-ATATATAAATAATAATAT
1 ATTTAATATAAATA-AATATATAAATAT-TATAAATAATAATAT
1166207 A
1 A
1166208 AAAATACTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
43 8 0.10
44 18 0.23
45 24 0.31
46 2 0.03
48 17 0.22
49 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (42 bp):
ATTTAATATAAATAAATATATAAATATTATAAATAATAATAT
Found at i:1166200 original size:20 final size:20
Alignment explanation
Indices: 1166081--1166210 Score: 64
Period size: 18 Copynumber: 6.8 Consensus size: 20
1166071 ATTTAAATAA
1166081 AAATAA-ATATAAAATA-AT
1 AAATAATATATAAAATATAT
*
1166099 TAA-AATATAATAATAA-ATAT
1 AAATAATAT-ATAA-AATATAT
* * *
1166119 AATTTAATGTAAATAAATATAT
1 AA-ATAATATATA-AAATATAT
* *
1166141 AAAT-AT-TTTAAATTATAT
1 AAATAATATATAAAATATAT
* *
1166159 -AAT-ATATTTAATATA-AT
1 AAATAATATATAAAATATAT
*
1166176 -TATAATATATAAAATATAT
1 AAATAATATATAAAATATAT
1166195 AAATAATAATATAAAA
1 AAATAAT-ATATAAAA
1166211 ATACTGATTA
Statistics
Matches: 84, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
17 11 0.13
18 28 0.33
19 9 0.11
20 12 0.14
21 13 0.15
22 11 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAATAATATATAAAATATAT
Found at i:1166207 original size:23 final size:21
Alignment explanation
Indices: 1166169--1166213 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
1166159 AATATATTTA
*
1166169 ATATAATTATAATATATAAAAT
1 ATATAATAATAATATA-AAAAT
1166191 ATATAAATAATAATATAAAAAT
1 ATAT-AATAATAATATAAAAAT
1166213 A
1 A
1166214 CTGATTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAATAATAATATAAAAAT
Found at i:1166213 original size:11 final size:11
Alignment explanation
Indices: 1166167--1166213 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
1166157 ATAATATATT
**
1166167 TAATATAATTA
1 TAATATAAAAA
1166178 TAATATATAAAA
1 TAATATA-AAAA
1166190 T-ATATAAATAA
1 TAATATAAA-AA
1166201 TAATATAAAAA
1 TAATATAAAAA
1166212 TA
1 TA
1166214 CTGATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 2 0.06
11 19 0.61
12 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATAAAAA
Found at i:1175142 original size:2 final size:2
Alignment explanation
Indices: 1175135--1175184 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
1175125 TATTAATGAA
* *
1175135 AT AT AT AT AT AT AT AT A- AA AT AT AT CAT AT A- AA 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
1175176 AT AT AT AT A
1 AT AT AT AT A
1175185 AATCAACATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1175166 original size:14 final size:13
Alignment explanation
Indices: 1175141--1175178 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
1175131 TGAAATATAT
1175141 ATATATATATAAA
1 ATATATATATAAA
1175154 ATATATCATATAAA
1 ATATAT-ATATAAA
1175168 ATATATATATA
1 ATATATATATA
1175179 TATATAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATATATATAAA
Found at i:1175977 original size:11 final size:11
Alignment explanation
Indices: 1175961--1176053 Score: 72
Period size: 11 Copynumber: 8.7 Consensus size: 11
1175951 TAATGATTTA
1175961 TATATTTATAT
1 TATATTTATAT
1175972 TATATTTATAT
1 TATATTTATAT
* *
1175983 TAT-TTTTTAA
1 TATATTTATAT
1175993 TAT-TTTATAT
1 TATATTTATAT
* *
1176003 CATA-TTAAAT
1 TATATTTATAT
1176013 T-T-TTTATAT
1 TATATTTATAT
1176022 TATATTCGTATCA-
1 TATATT--TAT-AT
*
1176035 TATAATTATAT
1 TATATTTATAT
1176046 TATATTTA
1 TATATTTA
1176054 AAGTTATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
9 7 0.11
10 22 0.34
11 26 0.41
13 8 0.12
14 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1175980 original size:19 final size:19
Alignment explanation
Indices: 1175956--1176053 Score: 64
Period size: 19 Copynumber: 5.3 Consensus size: 19
1175946 CATATTAATG
1175956 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
1175975 ATTTATATTATTT-T-TTAAT
1 ATTTATA-TATTTATATT-AT
* *
1175994 ATTT-TATA-TCATATTAA
1 ATTTATATATTTATATTAT
* *
1176011 ATTT-TTTATATTATATTCGT
1 ATTTATATAT-TTATATT-AT
* *
1176031 A-TCATATAATTATATTAT
1 ATTTATATATTTATATTAT
1176049 ATTTA
1 ATTTA
1176054 AAGTTATTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
16 1 0.02
17 11 0.19
18 8 0.14
19 30 0.51
20 9 0.15
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:1176027 original size:31 final size:31
Alignment explanation
Indices: 1175957--1176027 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
1175947 ATATTAATGA
* *
1175957 TTTATATATTTATATTATATTTATATTATTTT
1 TTTATAT-TTTATATCATATTTAAATTATTTT
*
1175989 TTAATATTTTATATCATA-TTAAATT-TTTT
1 TTTATATTTTATATCATATTTAAATTATTTT
1176018 ATATTATATT
1 -T-TTATATT
1176028 CGTATCATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 4 0.12
30 7 0.21
31 16 0.48
32 6 0.18
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTATATTTTATATCATATTTAAATTATTTT
Found at i:1176377 original size:19 final size:17
Alignment explanation
Indices: 1176350--1176393 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1176340 GAGACCATTA
*
1176350 ATTTCTCTTTCTTTCTTT
1 ATTTTTCTTTCTTTC-TT
*
1176368 CATTTTTCTTTTTTTCTT
1 -ATTTTTCTTTCTTTCTT
1176386 ATTTTTCT
1 ATTTTTCT
1176394 CATTTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 2 0.09
19 13 0.57
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTCTTTCTTTCTT
Found at i:1181833 original size:24 final size:24
Alignment explanation
Indices: 1181806--1181880 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
1181796 GTTTATGACT
1181806 TGAATTGAATCTTAGTAAGGGCAA
1 TGAATTGAATCTTAGTAAGGGCAA
* * *
1181830 TGAATTG-ATGTTA-T---GAC-T
1 TGAATTGAATCTTAGTAAGGGCAA
1181848 TGAATTGAATCTTAGTAAGGGCAA
1 TGAATTGAATCTTAGTAAGGGCAA
1181872 TGAATTGAA
1 TGAATTGAA
1181881 GTAATAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 7 0.18
19 7 0.18
20 1 0.03
22 1 0.03
23 7 0.18
24 16 0.41
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (24 bp):
TGAATTGAATCTTAGTAAGGGCAA
Found at i:1181845 original size:42 final size:42
Alignment explanation
Indices: 1181798--1181879 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
1181788 TTATCTGTGT
1181798 TTATGACTTGAATTGAATCTTAGTAAGGGCAATGAATTGATG
1 TTATGACTTGAATTGAATCTTAGTAAGGGCAATGAATTGATG
1181840 TTATGACTTGAATTGAATCTTAGTAAGGGCAATGAATTGA
1 TTATGACTTGAATTGAATCTTAGTAAGGGCAATGAATTGA
1181880 AGTAATAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (42 bp):
TTATGACTTGAATTGAATCTTAGTAAGGGCAATGAATTGATG
Found at i:1182314 original size:16 final size:17
Alignment explanation
Indices: 1182286--1182320 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1182276 TCCCACTCCC
1182286 GTTCCCTTCTTGATGGA
1 GTTCCCTTCTTGATGGA
*
1182303 GTTCCC-TCTTGATTGA
1 GTTCCCTTCTTGATGGA
1182319 GT
1 GT
1182321 AGGAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (17 bp):
GTTCCCTTCTTGATGGA
Found at i:1185906 original size:23 final size:23
Alignment explanation
Indices: 1185880--1185944 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
1185870 TTGAAATATA
1185880 ACAATATGTAGAATATGTATTAG
1 ACAATATGTAGAATATGTATTAG
1185903 ACAATA-G--GAA-A--TA-TA-
1 ACAATATGTAGAATATGTATTAG
1185918 ACAATATGTAGAATATGTATTAG
1 ACAATATGTAGAATATGTATTAG
1185941 ACAA
1 ACAA
1185945 CATGATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 2 0.06
18 3 0.09
19 2 0.06
20 3 0.09
21 2 0.06
22 3 0.09
23 10 0.29
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.29
Consensus pattern (23 bp):
ACAATATGTAGAATATGTATTAG
Found at i:1185914 original size:38 final size:38
Alignment explanation
Indices: 1185872--1185944 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
1185862 ATTAATAATT
1185872 GAAATATAACAATATGTAGAATATGTATTAGACAATAG
1 GAAATATAACAATATGTAGAATATGTATTAGACAATAG
1185910 GAAATATAACAATATGTAGAATATGTATTAGACAA
1 GAAATATAACAATATGTAGAATATGTATTAGACAA
1185945 CATGATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (38 bp):
GAAATATAACAATATGTAGAATATGTATTAGACAATAG
Found at i:1188572 original size:14 final size:14
Alignment explanation
Indices: 1188553--1188580 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1188543 AAACAGGGCC
1188553 TTCCCATTAGTGTG
1 TTCCCATTAGTGTG
1188567 TTCCCATTAGTGTG
1 TTCCCATTAGTGTG
1188581 CAATGACGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
TTCCCATTAGTGTG
Found at i:1191836 original size:2 final size:2
Alignment explanation
Indices: 1191831--1191859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1191821 TTTTTTTTTA
1191831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1191860 ATTTTTCTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1192259 original size:34 final size:34
Alignment explanation
Indices: 1192213--1192397 Score: 266
Period size: 34 Copynumber: 5.5 Consensus size: 34
1192203 GTAAAAACCA
*
1192213 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1192247 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
1192281 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1192315 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1192349 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1192382 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1192398 TCTCCCACTT
Statistics
Matches: 137, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
33 18 0.13
34 115 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1192355 original size:102 final size:101
Alignment explanation
Indices: 1192213--1192397 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
1192203 GTAAAAACCA
1192213 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1192278 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
1192315 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1192380 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
1192398 TCTCCCACTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 16 0.20
102 63 0.80
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:1196857 original size:34 final size:34
Alignment explanation
Indices: 1196811--1196993 Score: 262
Period size: 34 Copynumber: 5.4 Consensus size: 34
1196801 GTAAAAACCA
*
1196811 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1196845 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
1196879 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1196913 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1196947 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1196980 CCATTTAATCAACA
1 CCATTTAATCAACA
1196994 CTAATTTCAT
Statistics
Matches: 135, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
33 16 0.12
34 115 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1196953 original size:102 final size:101
Alignment explanation
Indices: 1196811--1196993 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
1196801 GTAAAAACCA
1196811 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1196876 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
1196913 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1196978 CACCATTTAATCAACA
66 CACCATTTAATCAACA
1196994 CTAATTTCAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 63 0.82
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:1199275 original size:3 final size:3
Alignment explanation
Indices: 1199267--1199296 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1199257 AGTTTGCAGC
1199267 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1199297 TTAGACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1200178 original size:3 final size:3
Alignment explanation
Indices: 1200170--1200201 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1200160 AGAGTACAAT
1200170 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1200202 CAGCGCGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1200444 original size:23 final size:22
Alignment explanation
Indices: 1200408--1200453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1200398 ATACATACAT
*
1200408 AAAATTTTAAATTTTAAATTATA
1 AAAATATTAAATTTTAAA-TATA
*
1200431 AAAATATTATATTTTAAATATA
1 AAAATATTAAATTTTAAATATA
1200453 A
1 A
1200454 TTGTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATATTAAATTTTAAATATA
Found at i:1202025 original size:25 final size:26
Alignment explanation
Indices: 1202003--1202092 Score: 91
Period size: 24 Copynumber: 3.7 Consensus size: 26
1201993 AATATAAATT
1202003 TTATATTTAAAA-TAATAATTAAAAA
1 TTATATTTAAAATTAATAATTAAAAA
**
1202028 TTATATTTAAAATTAAT-A-CCAAAA
1 TTATATTTAAAATTAATAATTAAAAA
* *
1202052 TAATATTTAAAATTAAT-A-TCAAAA
1 TTATATTTAAAATTAATAATTAAAAA
* *
1202076 TAATATTTAAAAATAAT
1 TTATATTTAAAATTAAT
1202093 TTATTACATA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
24 42 0.71
25 13 0.22
26 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
TTATATTTAAAATTAATAATTAAAAA
Found at i:1202027 original size:13 final size:13
Alignment explanation
Indices: 1202011--1202092 Score: 55
Period size: 13 Copynumber: 6.6 Consensus size: 13
1202001 TTTTATATTT
1202011 AAAATAATAATTA
1 AAAATAATAATTA
* *
1202024 AAAATTATATTTA
1 AAAATAATAATTA
* **
1202037 AAATTAAT-A-CC
1 AAAATAATAATTA
*
1202048 AAAATAATATTTA
1 AAAATAATAATTA
* *
1202061 AAATTAAT-A-TC
1 AAAATAATAATTA
*
1202072 AAAATAATATTTA
1 AAAATAATAATTA
1202085 AAAATAAT
1 AAAATAAT
1202093 TTATTACATA
Statistics
Matches: 48, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
11 15 0.31
13 33 0.69
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATAATAATTA
Found at i:1202057 original size:24 final size:24
Alignment explanation
Indices: 1202024--1202092 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
1202014 ATAATAATTA
*
1202024 AAAATTATATTTAAAATTAATACC
1 AAAATAATATTTAAAATTAATACC
*
1202048 AAAATAATATTTAAAATTAATATC
1 AAAATAATATTTAAAATTAATACC
*
1202072 AAAATAATATTTAAAAATAAT
1 AAAATAATATTTAAAATTAAT
1202093 TTATTACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAATATTTAAAATTAATACC
Found at i:1202081 original size:11 final size:12
Alignment explanation
Indices: 1202036--1202081 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1202026 AATTATATTT
*
1202036 AAAATTAATACC
1 AAAATTAATATC
*
1202048 AAAA-TAATATTT
1 AAAATTAATA-TC
1202060 AAAATTAATATC
1 AAAATTAATATC
1202072 AAAA-TAATAT
1 AAAATTAATAT
1202082 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 11 0.38
12 13 0.45
13 5 0.17
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATC
Found at i:1206645 original size:22 final size:22
Alignment explanation
Indices: 1206615--1206657 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1206605 AAGCTAACAA
* *
1206615 AGCAGAAATGAAATGCAGTAAG
1 AGCAAAAATGAAATACAGTAAG
*
1206637 AGCAAAAATGAAGTACAGTAA
1 AGCAAAAATGAAATACAGTAA
1206658 CAAGGGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.23, T:0.14
Consensus pattern (22 bp):
AGCAAAAATGAAATACAGTAAG
Found at i:1208354 original size:11 final size:11
Alignment explanation
Indices: 1208338--1208362 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1208328 ACACCAGTGT
1208338 TCAACACATTG
1 TCAACACATTG
1208349 TCAACACATTG
1 TCAACACATTG
1208360 TCA
1 TCA
1208363 GATATGCATT
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:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (11 bp):
TCAACACATTG
Found at i:1211421 original size:36 final size:36
Alignment explanation
Indices: 1211342--1211454 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
1211332 TAAAATTATC
* *
1211342 ATTAAAAATATTATATTAATA-TATATATATAATAAAT
1 ATTAAAAA-ATTATATTTATATTAAATA-ATAATAAAT
* *
1211379 AATAAAAAATTATATTTATATTAAATAATAATAAGT
1 ATTAAAAAATTATATTTATATTAAATAATAATAAAT
* *
1211415 GTT-AAAAA-TATATTTACATTAAATAATAATTTAAAT
1 ATTAAAAAATTATATTTATATTAAATAATAA--TAAAT
1211451 ATTA
1 ATTA
1211455 TTATGTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
34 20 0.32
35 5 0.08
36 26 0.41
37 12 0.19
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (36 bp):
ATTAAAAAATTATATTTATATTAAATAATAATAAAT
Found at i:1220619 original size:30 final size:27
Alignment explanation
Indices: 1220564--1220628 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
1220554 TTTAACAATC
*
1220564 ATTATAATATAAAAAAATAATTAATAA
1 ATTAAAATATAAAAAAATAATTAATAA
* *
1220591 ATATAAAATATAAGATAAATATATTAATAT
1 AT-TAAAATATAA-AAAAATA-ATTAATAA
1220621 ATTAAAAT
1 ATTAAAAT
1220629 TTATAGGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 9 0.28
29 12 0.38
30 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTAAAATATAAAAAAATAATTAATAA
Found at i:1235911 original size:15 final size:15
Alignment explanation
Indices: 1235888--1235923 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1235878 TTTTTTTATA
1235888 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
*
1235903 ATTTTAATTTAAATT
1 ATTTAAATTTAAATT
*
1235918 AATTAA
1 ATTTAA
1235924 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:1235978 original size:30 final size:29
Alignment explanation
Indices: 1235927--1235991 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
1235917 TAATTAATAA
1235927 ATTTTTAAAATTTTATAAAATATATAATC
1 ATTTTTAAAATTTTATAAAATATATAATC
*
1235956 ATTTTTATAAACTTTT-TAAAATATTTAAT-
1 ATTTTTA-AAA-TTTTATAAAATATATAATC
1235985 -TTTTTAA
1 ATTTTTAA
1235992 TTCGAGTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.03
28 6 0.18
29 7 0.21
30 15 0.45
31 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTTAAAATTTTATAAAATATATAATC
Found at i:1245482 original size:24 final size:26
Alignment explanation
Indices: 1245455--1245513 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
1245445 TAAAAATAAT
1245455 TAATTTAAATTTA-AGTAATTTTT-A
1 TAATTTAAATTTATAGTAATTTTTAA
** *
1245479 TAATTTATTTTTATATTAATTTTTAA
1 TAATTTAAATTTATAGTAATTTTTAA
*
1245505 AAATTTAAA
1 TAATTTAAA
1245514 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 11 0.41
25 9 0.33
26 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TAATTTAAATTTATAGTAATTTTTAA
Found at i:1245500 original size:12 final size:13
Alignment explanation
Indices: 1245470--1245503 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1245460 TAAATTTAAG
1245470 TAATTTTTATAAT
1 TAATTTTTATAAT
*
1245483 TTATTTTTAT-AT
1 TAATTTTTATAAT
1245495 TAATTTTTA
1 TAATTTTTA
1245504 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTTATAAT
Found at i:1245700 original size:15 final size:16
Alignment explanation
Indices: 1245680--1245717 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1245670 TAATTTGGTA
1245680 AAAATTTAA-TAATTT
1 AAAATTTAATTAATTT
1245695 AAAA-TTAATTAATTT
1 AAAATTTAATTAATTT
1245710 -AAATTTAA
1 AAAATTTAA
1245718 AAATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATTTAATTAATTT
Found at i:1245733 original size:21 final size:21
Alignment explanation
Indices: 1245682--1245733 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1245672 ATTTGGTAAA
*
1245682 AATTT-AAT-AATTTAAAATT
1 AATTTAAATAAATTTAAAAAT
*
1245701 AA-TTAATTTAAATTTAAAAAT
1 AATTTAA-ATAAATTTAAAAAT
1245722 AATTTAAATAAA
1 AATTTAAATAAA
1245734 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 1 0.04
21 16 0.62
22 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAAATAAATTTAAAAAT
Found at i:1245785 original size:16 final size:15
Alignment explanation
Indices: 1245688--1245802 Score: 80
Period size: 16 Copynumber: 7.7 Consensus size: 15
1245678 TAAAAATTTA
1245688 ATAATTTAAAATTAAT
1 ATAATTT-AAATTAAT
*
1245704 -TAATTTAAATTTAAAA
1 ATAATTTAAA-TT-AAT
1245720 ATAATTTAAA-TAA-
1 ATAATTTAAATTAAT
* *
1245733 AAAATTTAAA-TATT
1 ATAATTTAAATTAAT
1245747 A-AATTT-AATTAAT
1 ATAATTTAAATTAAT
* *
1245760 ATGAACTTAAATTTATT
1 AT-AATTTAAA-TTAAT
*
1245777 ATAATTTAAATTTAAA
1 ATAATTTAAA-TTAAT
1245793 ATAATTTAAA
1 ATAATTTAAA
1245803 ATAAAAATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
12 2 0.02
13 20 0.25
14 6 0.07
15 13 0.16
16 25 0.31
17 15 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
ATAATTTAAATTAAT
Found at i:1245809 original size:16 final size:16
Alignment explanation
Indices: 1245777--1245812 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1245767 TAAATTTATT
* *
1245777 ATAATTTAAATTTAAA
1 ATAATTTAAAATAAAA
1245793 ATAATTTAAAATAAAA
1 ATAATTTAAAATAAAA
1245809 ATAA
1 ATAA
1245813 CATAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATTTAAAATAAAA
Found at i:1247868 original size:2 final size:2
Alignment explanation
Indices: 1247861--1247893 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1247851 GAACCATTAC
*
1247861 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1247894 GCAGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1248062 original size:22 final size:22
Alignment explanation
Indices: 1248023--1248064 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1248013 GTGGGGAGTA
*
1248023 TTTTTAAATAATAGAATAATAT
1 TTTTTAAATAATAAAATAATAT
1248045 TTTTTAAAATAA-AAAATAAT
1 TTTTT-AAATAATAAAATAAT
1248065 TAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTTTAAATAATAAAATAATAT
Found at i:1248271 original size:15 final size:15
Alignment explanation
Indices: 1248242--1248280 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1248232 TTTATTTTTT
*
1248242 AATAT-AAATAATTA
1 AATATAAAAAAATTA
*
1248256 AATCTAAAAAAATTA
1 AATATAAAAAAATTA
1248271 AATATAAAAA
1 AATATAAAAA
1248281 TCAAATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATAAAAAAATTA
Found at i:1251283 original size:8 final size:8
Alignment explanation
Indices: 1251260--1251358 Score: 65
Period size: 8 Copynumber: 12.0 Consensus size: 8
1251250 AACATAAATT
1251260 AATATATA
1 AATATATA
* *
1251268 ATTTTATA
1 AATATATA
1251276 AATATATA
1 AATATATA
* *
1251284 AAAACATA
1 AATATATA
*
1251292 TATATATA
1 AATATATA
*
1251300 TATATATA
1 AATATATA
1251308 AATAACTTATA
1 AAT-A--TATA
1251319 AATATATA
1 AATATATA
* *
1251327 AAAAAATTA
1 AATATA-TA
*
1251336 AATATATT
1 AATATATA
*
1251344 TATAT-TA
1 AATATATA
1251351 AATATATA
1 AATATATA
1251359 TCCATTATCG
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
7 5 0.07
8 48 0.71
9 7 0.10
10 1 0.01
11 7 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
AATATATA
Found at i:1251342 original size:19 final size:20
Alignment explanation
Indices: 1251271--1251342 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 20
1251261 ATATATAATT
1251271 TTATAA-ATATATAAAAACATA
1 TTATAATATATATAAAAA-A-A
* *
1251292 TATATATATATATATAAATAAC
1 T-TATA-ATATATATAAAAAAA
1251314 TTATAA-ATATATAAAAAAA
1 TTATAATATATATAAAAAAA
1251333 TTA-AATATAT
1 TTATAATATAT
1251343 TTATATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 2 0.05
19 18 0.42
20 1 0.02
21 5 0.12
22 5 0.12
23 2 0.05
24 10 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTATAATATATATAAAAAAA
Found at i:1253665 original size:17 final size:18
Alignment explanation
Indices: 1253640--1253681 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1253630 TGAATATGGC
1253640 TGAAAAAAAAGCATCCCA
1 TGAAAAAAAAGCATCCCA
1253658 TGAAAAAAAAGCATCCCA
1 TGAAAAAAAAGCATCCCA
1253676 TGAAAA
1 TGAAAA
1253682 GCAGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.12
Consensus pattern (18 bp):
TGAAAAAAAAGCATCCCA
Found at i:1256199 original size:23 final size:22
Alignment explanation
Indices: 1256134--1256199 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 22
1256124 TTTTAGTTTT
*
1256134 ATTTTATATATAATATAAATAAA
1 ATTTTATATATAATAT-ATTAAA
* *
1256157 ATATATTATAT-T-TTAAATTAAA
1 AT-T-TTATATATAATATATTAAA
1256179 ATTTTATAATATAATATATTA
1 ATTTTAT-ATATAATATATTA
1256200 TTTTATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 8 0.24
23 10 0.30
24 2 0.06
25 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTATATATAATATATTAAA
Found at i:1256210 original size:33 final size:35
Alignment explanation
Indices: 1256146--1256227 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 35
1256136 TTTATATATA
*
1256146 ATATAAATAAAATATATTATATTTTAAATTAAAATT
1 ATAT-AATATAATATATTATATTTTAAATTAAAATT
* * *
1256182 TTATAATATAATATA-T-TATTTTATATTAACATT
1 ATATAATATAATATATTATATTTTAAATTAAAATT
1256215 ATATAATATAATA
1 ATATAATATAATA
1256228 CATAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 27 0.66
34 1 0.02
35 10 0.24
36 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATAATATAATATATTATATTTTAAATTAAAATT
Found at i:1260426 original size:26 final size:25
Alignment explanation
Indices: 1260397--1260473 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
1260387 TAAACATGTC
1260397 AAGTATGGTGACGTTAAAACTCTTTA
1 AAGTATGGTGACGTTAAAAC-CTTTA
* * *
1260423 AAGT-T--TGGC-TTATAAACATTTC
1 AAGTATGGTGACGTTA-AAACCTTTA
1260445 AAGTATGGTGACGTTAAAACGCTTTA
1 AAGTATGGTGACGTTAAAAC-CTTTA
1260471 AAG
1 AAG
1260474 CGTGGTTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
22 10 0.26
23 8 0.21
25 8 0.21
26 13 0.33
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (25 bp):
AAGTATGGTGACGTTAAAACCTTTA
Found at i:1260447 original size:48 final size:48
Alignment explanation
Indices: 1260379--1260473 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
1260369 ATGATTTAAC
*
1260379 TTGGCTTATAAACATGTCAAGTATGGTGACGTTAAAACTCTTTAAAGT
1 TTGGCTTATAAACATGTCAAGTATGGTGACGTTAAAACGCTTTAAAGT
*
1260427 TTGGCTTATAAACATTTCAAGTATGGTGACGTTAAAACGCTTTAAAG
1 TTGGCTTATAAACATGTCAAGTATGGTGACGTTAAAACGCTTTAAAG
1260474 CGTGGTTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (48 bp):
TTGGCTTATAAACATGTCAAGTATGGTGACGTTAAAACGCTTTAAAGT
Found at i:1260448 original size:22 final size:23
Alignment explanation
Indices: 1260379--1260450 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 23
1260369 ATGATTTAAC
*
1260379 TTGGCTTATAAACATGTCAAGTA
1 TTGGCTTATAAACATTTCAAGTA
* * *
1260402 TGGTGACGTTA-AAACTCTTTAAAGT-
1 T--TGGC-TTATAAAC-ATTTCAAGTA
1260427 TTGGCTTATAAACATTTCAAGTA
1 TTGGCTTATAAACATTTCAAGTA
1260450 T
1 T
1260451 GGTGACGTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
22 10 0.28
23 9 0.25
25 8 0.22
26 9 0.25
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (23 bp):
TTGGCTTATAAACATTTCAAGTA
Found at i:1261465 original size:143 final size:143
Alignment explanation
Indices: 1261207--1261467 Score: 387
Period size: 143 Copynumber: 1.8 Consensus size: 143
1261197 TGTCAGGTTC
* * * *
1261207 CATAATTATTGAAGAGTTAAAGAGGCATTCGTGTATCATTTATTAATTGCATCACGTATTATTTT
1 CATAATTATTGAAAAATTAAAGAGGCATTCGCGTATCATTTATTAATTACATCACGTATTATTTT
* * * * *
1261272 GTAATTAAAGCTTAATGGTTAATGGTATAGATGATCTTGTCATAGTAGTCGGAGGTTAATGCTTT
66 ATAATTAAAACTTAATGATTAATAGTATAGATAATCTTGTCATAGTAGTCGGAGGTTAATGCTTT
1261337 AGACATCAGTCTA
131 AGACATCAGTCTA
* * *
1261350 CATAATTATTGAAAAATTAAAGAGGTATTCGCGTATCATTTATTAATTATATCATGTATTATTTT
1 CATAATTATTGAAAAATTAAAGAGGCATTCGCGTATCATTTATTAATTACATCACGTATTATTTT
* **
1261415 ATAATTAAAATTTGGTGATTAATAGTATAGATAATCTTGTCATAGTAGTCGGA
66 ATAATTAAAACTTAATGATTAATAGTATAGATAATCTTGTCATAGTAGTCGGA
1261468 AGTTGGAGAC
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
143 103 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (143 bp):
CATAATTATTGAAAAATTAAAGAGGCATTCGCGTATCATTTATTAATTACATCACGTATTATTTT
ATAATTAAAACTTAATGATTAATAGTATAGATAATCTTGTCATAGTAGTCGGAGGTTAATGCTTT
AGACATCAGTCTA
Found at i:1262187 original size:18 final size:18
Alignment explanation
Indices: 1262160--1262194 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1262150 ATCATAAATA
* *
1262160 AAAAATAACAGATATATT
1 AAAAAGAACAAATATATT
1262178 AAAAAGAACAAATATAT
1 AAAAAGAACAAATATAT
1262195 AATAATTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAAGAACAAATATATT
Found at i:1269012 original size:96 final size:96
Alignment explanation
Indices: 1268848--1269036 Score: 290
Period size: 96 Copynumber: 2.0 Consensus size: 96
1268838 CTATACCTGG
* * * * * *
1268848 ACATATACAAGTACAACAAGGCTGCTATTTTGTTTCTATTTTAGGCTTGGAATGTTTTAAGCAGA
1 ACATAGACAAGTACAACAAGACTGCTATCTCGTTTCTATTTTAAGCTTGGAACGTTTTAAGCAGA
1268913 TGAATAAGATAAGATAAATTAGAATCTGTTA
66 TGAATAAGATAAGATAAATTAGAATCTGTTA
* *
1268944 ACATAGACAAGTATAACCAGACTGCTATCTCGTTTCTATTTTAAG-TTCGGAACGTTTTAAGCAG
1 ACATAGACAAGTACAACAAGACTGCTATCTCGTTTCTATTTTAAGCTT-GGAACGTTTTAAGCAG
1269008 ATGAATAAGATAAGATAAATTAGAATCTG
65 ATGAATAAGATAAGATAAATTAGAATCTG
1269037 ACTGTATATT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 2 0.02
96 82 0.98
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (96 bp):
ACATAGACAAGTACAACAAGACTGCTATCTCGTTTCTATTTTAAGCTTGGAACGTTTTAAGCAGA
TGAATAAGATAAGATAAATTAGAATCTGTTA
Found at i:1271544 original size:3 final size:3
Alignment explanation
Indices: 1271536--1271561 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1271526 TTCACTATAT
1271536 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1271562 TCTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1276575 original size:23 final size:21
Alignment explanation
Indices: 1276543--1276584 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1276533 GAATAAAATA
1276543 TTTAAATTAAAAGTATTTATAAG
1 TTTAAATTAAAA-T-TTTATAAG
*
1276566 TTTAATTTAAAATTTTATA
1 TTTAAATTAAAATTTTATA
1276585 TTATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAAATTAAAATTTTATAAG
Found at i:1276593 original size:20 final size:19
Alignment explanation
Indices: 1276570--1276637 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
1276560 TATAAGTTTA
1276570 ATTTAAAATTTTATATTATT
1 ATTTAAAATTTTATATTA-T
* *
1276590 ATTTAAAATATTAT-TTAA
1 ATTTAAAATTTTATATTAT
* *
1276608 ATATAAAAATTTATATTAAT
1 ATTTAAAATTTTATATT-AT
*
1276628 ATTTATAATT
1 ATTTAAAATT
1276638 AAAATTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 11 0.30
19 5 0.14
20 21 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAAAATTTTATATTAT
Found at i:1276619 original size:26 final size:27
Alignment explanation
Indices: 1276589--1276672 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 27
1276579 TTTATATTAT
1276589 TATTTAAAATATTATTTA-AATATAAAA
1 TATTTAAAATATTATTTATAAT-TAAAA
* * *
1276616 -ATTTATATTAATATTTATAATTAAAA
1 TATTTAAAATATTATTTATAATTAAAA
* * *
1276642 TTTTTAAAATTTTATTATATAAATAATAA
1 TATTTAAAATATTATT-TATAATTAA-AA
1276671 TA
1 TA
1276673 CAAGTTAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
26 19 0.44
27 13 0.30
28 8 0.19
29 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTTAAAATATTATTTATAATTAAAA
Found at i:1276749 original size:26 final size:26
Alignment explanation
Indices: 1276706--1276755 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1276696 TACTACAAAA
* *
1276706 AAATTTATTCAATATAAATTAATTAT
1 AAATTAATTCAATATAAATAAATTAT
* *
1276732 AAATTAATTTAATTTAAATAAATT
1 AAATTAATTCAATATAAATAAATT
1276756 TATATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTAATTCAATATAAATAAATTAT
Found at i:1276766 original size:15 final size:15
Alignment explanation
Indices: 1276706--1276764 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1276696 TACTACAAAA
*
1276706 AAATTT-ATTCAATAT
1 AAATTTAATTTAA-AT
1276721 AAA-TTAATTATAAAT
1 AAATTTAATT-TAAAT
*
1276736 TAATTTAATTTAAAT
1 AAATTTAATTTAAAT
1276751 AAATTTATATTTAA
1 AAATTTA-ATTTAA
1276765 TATTCAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.05
15 21 0.57
16 14 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTAATTTAAAT
Found at i:1277496 original size:24 final size:24
Alignment explanation
Indices: 1277469--1277515 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1277459 ATTTAATTAA
1277469 TTTAT-AAAATTTAAATTTTAAAAT
1 TTTATGAAAA-TTAAATTTTAAAAT
* *
1277493 TTTATGTAAATTAATTTTTAAAA
1 TTTATGAAAATTAAATTTTAAAA
1277516 ATAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATGAAAATTAAATTTTAAAAT
Found at i:1278130 original size:12 final size:12
Alignment explanation
Indices: 1278115--1278157 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1278105 ATTTTAAATA
1278115 TAAATTTATTTT
1 TAAATTTATTTT
1278127 TAAATTTATTATTT
1 TAAATTTA-T-TTT
* *
1278141 TAAAATTAATTT
1 TAAATTTATTTT
1278153 TAAAT
1 TAAAT
1278158 AAAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 15 0.58
13 1 0.04
14 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATTTATTTT
Found at i:1278274 original size:16 final size:16
Alignment explanation
Indices: 1278247--1278323 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 16
1278237 AAAATTTTAG
* *
1278247 TTATTTTTAAAATT-T
1 TTATTATTAAAATTAA
1278262 TTAATTATTAAAATTAA
1 TT-ATTATTAAAATTAA
1278279 TTATTATT-AAATTAAA
1 TTATTATTAAAATT-AA
1278295 TTATTATT-AAATTATA
1 TTATTATTAAAATTA-A
1278311 TT-TTAATTAAAAT
1 TTATT-ATTAAAAT
1278324 ACATGTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.19
16 38 0.70
17 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTATTAAAATTAA
Found at i:1278422 original size:23 final size:24
Alignment explanation
Indices: 1278377--1278427 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1278367 AATTTTGAAA
* *
1278377 TAAATTTATTAAAATATTTTTATT
1 TAAATTAATTAAAATATTATTATT
*
1278401 TAAATTAATT-AATTATTATTATT
1 TAAATTAATTAAAATATTATTATT
1278424 TAAA
1 TAAA
1278428 AAATTAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATTAATTAAAATATTATTATT
Found at i:1278876 original size:18 final size:19
Alignment explanation
Indices: 1278835--1278876 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1278825 TTTAACTTAA
1278835 TAATAATTAAAAATAATTT
1 TAATAATTAAAAATAATTT
1278854 T-ATAATTAAAAAT-ATTT
1 TAATAATTAAAAATAATTT
1278871 TAATAA
1 TAATAA
1278877 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATAATTAAAAATAATTT
Found at i:1279671 original size:16 final size:16
Alignment explanation
Indices: 1279652--1279682 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1279642 TAACAAATAC
*
1279652 AATTTATATTAAATTA
1 AATTTAAATTAAATTA
1279668 AATTTAAATTAAATT
1 AATTTAAATTAAATT
1279683 TATGTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAAATTAAATTA
Found at i:1279690 original size:11 final size:11
Alignment explanation
Indices: 1279660--1279684 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1279650 ACAATTTATA
1279660 TTAAATTAAAT
1 TTAAATTAAAT
1279671 TTAAATTAAAT
1 TTAAATTAAAT
1279682 TTA
1 TTA
1279685 TGTTAATTTA
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:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:1280751 original size:10 final size:10
Alignment explanation
Indices: 1280678--1280751 Score: 52
Period size: 9 Copynumber: 7.8 Consensus size: 10
1280668 ATATTTAAAT
1280678 TATTATAT-A
1 TATTATATAA
*
1280687 TTTTATATAA
1 TATTATATAA
*
1280697 T-TT-TATTA
1 TATTATATAA
1280705 TATTA-ATAAA
1 TATTATAT-AA
*
1280715 TTATTATAAAA
1 -TATTATATAA
*
1280726 TATAATAT-A
1 TATTATATAA
1280735 T-TTATATAA
1 TATTATATAA
1280744 TATTATAT
1 TATTATAT
1280752 TTTAATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
8 10 0.20
9 17 0.34
10 15 0.30
11 7 0.14
12 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTATATAA
Found at i:1282095 original size:21 final size:22
Alignment explanation
Indices: 1282057--1282097 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1282047 TTTATAAATG
* *
1282057 TAAATAATGATAATTAATATAT
1 TAAATAATAATAAATAATATAT
1282079 TAAA-AATAATAAATAATAT
1 TAAATAATAATAAATAATAT
1282098 CTTTATCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAATAATAATAAATAATATAT
Found at i:1288240 original size:2 final size:2
Alignment explanation
Indices: 1288233--1288271 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1288223 AATCTTCCAG
1288233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1288272 ATACTTTTAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1295610 original size:19 final size:20
Alignment explanation
Indices: 1295569--1295611 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1295559 ATATATAAGG
*
1295569 AAAATTATTAAAAAAAACTA
1 AAAATTATTAAAAAAAACAA
1295589 AAAATTA-TAAATAAAAA-AA
1 AAAATTATTAAA-AAAAACAA
1295608 AAAA
1 AAAA
1295612 CTAAGGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATTATTAAAAAAAACAA
Found at i:1295611 original size:20 final size:20
Alignment explanation
Indices: 1295569--1295611 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1295559 ATATATAAGG
**
1295569 AAAATTATTAAAAAAAACTA
1 AAAATTATTAAAAAAAAAAA
*
1295589 AAAATTA-TAAATAAAAAAA
1 AAAATTATTAAAAAAAAAAA
1295608 AAAA
1 AAAA
1295612 CTAAGGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATTATTAAAAAAAAAAA
Found at i:1305818 original size:2 final size:2
Alignment explanation
Indices: 1305813--1305849 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1305803 TATATATATA
1305813 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1305850 ATTTGAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1306386 original size:3 final size:3
Alignment explanation
Indices: 1306378--1306408 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1306368 CCTATATACA
*
1306378 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1306409 TAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1306657 original size:2 final size:2
Alignment explanation
Indices: 1306650--1306685 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1306640 AAACTTAAAA
1306650 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
1306686 GTATCCTTCG
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:1318093 original size:101 final size:101
Alignment explanation
Indices: 1317866--1318145 Score: 343
Period size: 101 Copynumber: 2.8 Consensus size: 101
1317856 TTAGCATAAA
* *
1317866 AATTTTCCAGATTTTAATTTCCTACT-GCTTTAAAATATTGCTAAGTGGAAATCT-AATCATCAA
1 AATTTTCCAGATTTTAATTTCCTA-TGGCTTTAAAATATTGCTAAGTTGTAATCTCAA-CATCAA
* * *
1317929 CTCAAAGCAGACTCCCACCAATTCTATTGGTTAAGGAAC
64 CTCAAAGCAG-CTCACACCAATTCAATTGGATAAGGAAC
* * *
1317968 AATTTTCCAGATTTTAATTTCCTATGGCTATAAAATATTACTAAGTTGTAATCTCAGCATCAACT
1 AATTTTCCAGATTTTAATTTCCTATGGCTTTAAAATATTGCTAAGTTGTAATCTCAACATCAACT
*
1318033 CAAAACAGCTCACACCAATAT-AATTGGATAAGGAAC
66 CAAAGCAGCTCACACCAAT-TCAATTGGATAAGGAAC
* * * * * * *
1318069 AATTTTCCAGATCTAAATTCCCTATGCCTTTCAAATACTGCTAAGTTACT-ATCTCAACATCAAC
1 AATTTTCCAGATTTTAATTTCCTATGGCTTTAAAATATTGCTAAGTT-GTAATCTCAACATCAAC
1318133 TCAAAGCAGCTCA
65 TCAAAGCAGCTCA
1318146 AAGGAAATAA
Statistics
Matches: 154, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
101 88 0.57
102 65 0.42
103 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (101 bp):
AATTTTCCAGATTTTAATTTCCTATGGCTTTAAAATATTGCTAAGTTGTAATCTCAACATCAACT
CAAAGCAGCTCACACCAATTCAATTGGATAAGGAAC
Found at i:1319425 original size:2 final size:2
Alignment explanation
Indices: 1319418--1319448 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1319408 AATACATGTA
1319418 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1319449 ATCAGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1321235 original size:20 final size:21
Alignment explanation
Indices: 1321205--1321259 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
1321195 TTAATTAAAT
1321205 AATATAATATATTAAA-A-TTTA
1 AATA-AATATA-TAAATATTTTA
1321226 AATAAATATA-AAATATTTTA
1 AATAAATATATAAATATTTTA
1321246 AATAAATTATATAA
1 AATAAA-TATATAA
1321260 TAAAACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 16 0.53
21 8 0.27
22 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAATATATAAATATTTTA
Found at i:1321240 original size:27 final size:28
Alignment explanation
Indices: 1321195--1321247 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1321185 TAAATTTAAA
* *
1321195 TTAATTAAATAATATAATATATTAAAAT
1 TTAAATAAATAATAAAATATATTAAAAT
*
1321223 TTAAATAAAT-ATAAAATATTTTAAA
1 TTAAATAAATAATAAAATATATTAAA
1321248 TAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAATAAATAATAAAATATATTAAAAT
Found at i:1321859 original size:16 final size:15
Alignment explanation
Indices: 1321838--1321894 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1321828 ACGATATGAT
*
1321838 ATTTATATATTTAAAA
1 ATTTATATA-ATAAAA
1321854 ATTTATATAATAAAA
1 ATTTATATAATAAAA
*
1321869 A-TTATTAAAATATTAAA
1 ATTTA-TATAATA--AAA
1321886 ATTTATATA
1 ATTTATATA
1321895 TATATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 12 0.35
16 9 0.26
17 7 0.21
18 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTATATAATAAAA
Found at i:1324227 original size:16 final size:16
Alignment explanation
Indices: 1324206--1324239 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1324196 GATATGGTGA
1324206 TTTATTATATATAAAC
1 TTTATTATATATAAAC
1324222 TTTATTATATATAAAC
1 TTTATTATATATAAAC
1324238 TT
1 TT
1324240 AAATGCTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTATATATAAAC
Found at i:1327678 original size:21 final size:21
Alignment explanation
Indices: 1327642--1327717 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
1327632 GAAAATGTTT
*
1327642 TTTTAATAAAACAAATTTATAA
1 TTTTAA-AAAATAAATTTATAA
*
1327664 TTTTAAAAAATAAA-TAATAAA
1 TTTTAAAAAATAAATTTAT-AA
* *
1327685 TATTAAAATATAAATTT-TAA
1 TTTTAAAAAATAAATTTATAA
*
1327705 TTTTTATAAAATA
1 -TTTTAAAAAATA
1327718 TTTTTTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.12
21 31 0.72
22 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAAAAAATAAATTTATAA
Found at i:1329017 original size:3 final size:3
Alignment explanation
Indices: 1329009--1329046 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1328999 AAGATTACCG
1329009 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1329047 TTATTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1329741 original size:22 final size:22
Alignment explanation
Indices: 1329696--1329742 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1329686 AATATATATT
** *
1329696 TATACTATTAATAATGCTATAC
1 TATACTATTAATAATAATACAC
*
1329718 TATACTATTATTAATAATACAC
1 TATACTATTAATAATAATACAC
1329740 TAT
1 TAT
1329743 TATATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
TATACTATTAATAATAATACAC
Found at i:1329896 original size:32 final size:33
Alignment explanation
Indices: 1329860--1329929 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
1329850 TTTTATATAT
1329860 TTATATAAAATTTGATAGATTAATA-ATTGATA
1 TTATATAAAATTTGATAGATTAATATATTGATA
* * *
1329892 TTATATAAATTTTGATATATTAATATATTTATA
1 TTATATAAAATTTGATAGATTAATATATTGATA
1329925 TTATA
1 TTATA
1329930 CTTATTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (33 bp):
TTATATAAAATTTGATAGATTAATATATTGATA
Found at i:1329908 original size:17 final size:19
Alignment explanation
Indices: 1329860--1329929 Score: 54
Period size: 16 Copynumber: 4.3 Consensus size: 19
1329850 TTTTATATAT
1329860 TTATATAA-A-ATTTGATA
1 TTATATAATATATTTGATA
*
1329877 -GAT-TAATA-A-TTGATA
1 TTATATAATATATTTGATA
1329892 TTATATAA-AT-TTTGATA
1 TTATATAATATATTTGATA
1329909 -TAT-TAATATATTT-ATA
1 TTATATAATATATTTGATA
1329925 TTATA
1 TTATA
1329930 CTTATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
15 12 0.29
16 15 0.36
17 15 0.36
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTATATAATATATTTGATA
Found at i:1336211 original size:19 final size:19
Alignment explanation
Indices: 1336187--1336242 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1336177 AATTATAAAT
*
1336187 AATAAAATTTAATTTTATA
1 AATAAAATATAATTTTATA
*
1336206 AAT-AAATATCAA-ATTATTA
1 AATAAAATAT-AATTTTA-TA
*
1336225 AATAAAATATATTTTTAT
1 AATAAAATATAATTTTAT
1336243 TAATTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
18 8 0.28
19 12 0.41
20 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAAATATAATTTTATA
Found at i:1336887 original size:30 final size:29
Alignment explanation
Indices: 1336828--1336888 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
1336818 TAAATTTAGA
* *
1336828 TTATAATTTCAAAATTTTATATATGAAAT
1 TTATAATTTCAAAATTTTAAATATAAAAT
*
1336857 TTATAATTTTCAAAGTTTTAAAT-TCAAAAT
1 TTATAA-TTTCAAAATTTTAAATAT-AAAAT
1336887 TT
1 TT
1336889 TTTGTTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATAATTTCAAAATTTTAAATATAAAAT
Found at i:1337638 original size:11 final size:11
Alignment explanation
Indices: 1337597--1337645 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
1337587 TTTATTAATT
*
1337597 TTAAAGATTCAA
1 TTAAAAATT-AA
*
1337609 TTAAAAAATAA
1 TTAAAAATTAA
1337620 TTAAAAATTAA
1 TTAAAAATTAA
*
1337631 TTAAAAATTAT
1 TTAAAAATTAA
1337642 TTAA
1 TTAA
1337646 TTATTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
11 26 0.79
12 7 0.21
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (11 bp):
TTAAAAATTAA
Found at i:1339145 original size:24 final size:27
Alignment explanation
Indices: 1339090--1339145 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
1339080 TCATTATTAA
*
1339090 TATTATTATTTAAATTATAATCTTAAT
1 TATTATTATTTAAATTATAATCATAAT
*
1339117 T-TTATT-TTT-AATTATAA-CATATT
1 TATTATTATTTAAATTATAATCATAAT
1339140 TATTAT
1 TATTAT
1339146 AATTACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 12 0.46
25 3 0.12
26 5 0.19
27 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTATTATTTAAATTATAATCATAAT
Found at i:1339639 original size:23 final size:25
Alignment explanation
Indices: 1339592--1339641 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1339582 CTAAGATTTA
*
1339592 TTAAGGAAAAAATGTTGATGTTATT
1 TTAAGGAAAAAATGTTGATGATATT
*
1339617 TTAAGGAAAAAAT-TTTAT-ATATT
1 TTAAGGAAAAAATGTTGATGATATT
1339640 TT
1 TT
1339642 TTAGTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 4 0.17
25 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (25 bp):
TTAAGGAAAAAATGTTGATGATATT
Found at i:1339643 original size:25 final size:26
Alignment explanation
Indices: 1339587--1339644 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1339577 CCAAGCTAAG
* *
1339587 ATTTATTAAGGAAAAAATGTTGATGT
1 ATTTTTTAAGGAAAAAATGTTGATAT
* *
1339613 -TATTTTAAGGAAAAAAT-TTTATAT
1 ATTTTTTAAGGAAAAAATGTTGATAT
1339637 ATTTTTTA
1 ATTTTTTA
1339645 GTTTAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (26 bp):
ATTTTTTAAGGAAAAAATGTTGATAT
Found at i:1339699 original size:13 final size:14
Alignment explanation
Indices: 1339677--1339710 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1339667 AATATAAAGA
1339677 ATTAATTTAAAAAT
1 ATTAATTTAAAAAT
*
1339691 ATTAATTAAAAAAT
1 ATTAATTTAAAAAT
*
1339705 TTTAAT
1 ATTAAT
1339711 CAAAGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATTTAAAAAT
Found at i:1349973 original size:2 final size:2
Alignment explanation
Indices: 1349966--1349995 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1349956 CAAAGTAGTC
1349966 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
1349996 TTACTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351403 original size:19 final size:20
Alignment explanation
Indices: 1351360--1351404 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1351350 GATTCAGATG
*
1351360 ATAAATTTATAAAAAATTAT
1 ATAAATTAATAAAAAATTAT
* *
1351380 ATAAATTAATTAAATATT-T
1 ATAAATTAATAAAAAATTAT
1351399 ATAAAT
1 ATAAAT
1351405 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAATTAATAAAAAATTAT
Done.