Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_pilon, whole genome shotgun sequence
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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:566442 original size:35 final size:36
Alignment explanation
Indices: 566357--566444 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 36
566347 TAAGATACTA
* * *
566357 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
*
566392 CCTATAACATCACCATCTGCCATTACTA-TTGCACG
1 CCTATAACATAACCATCTGCCATTACTATTTGCACG
* *
566427 CCTATATCCTAACCATCT
1 CCTATAACATAACCATCT
566445 TTTTATCACC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 25 0.53
36 22 0.47
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
CCTATAACATAACCATCTGCCATTACTATTTGCACG
Found at i:566883 original size:13 final size:12
Alignment explanation
Indices: 566859--566899 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
566849 CAAAAGCAAC
566859 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
566871 AGAAAGAAGAAAA
1 AAAAAG-AGAAAA
566884 AAAAAGAGAAAGA
1 AAAAAGAGAAA-A
566897 AAA
1 AAA
566900 GACTCCTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:566951 original size:14 final size:14
Alignment explanation
Indices: 566932--566969 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
566922 TGCAAAAGAA
566932 AGAAAAAGAAAAAT
1 AGAAAAAGAAAAAT
566946 AGAAAAAGAAAAAT
1 AGAAAAAGAAAAAT
566960 AGAAAAAGAA
1 AGAAAAAGAA
566970 GAAAGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (14 bp):
AGAAAAAGAAAAAT
Found at i:567131 original size:16 final size:16
Alignment explanation
Indices: 567092--567150 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
567082 GAGTTGTAAG
567092 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
567109 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
* * *
567125 TTCTTTCATTTTTTTC
1 TTATTTCATTTCTTTA
567141 TTATTTCATT
1 TTATTTCATT
567151 ACCATATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 4 0.11
16 28 0.80
17 3 0.09
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:569559 original size:13 final size:12
Alignment explanation
Indices: 569504--569559 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
569494 ATTGGAGTGC
569504 AAAAAGAAAAG-
1 AAAAAGAAAAGA
** *
569515 AAAAA-TCAACA
1 AAAAAGAAAAGA
569526 AAAAAGAAAAGA
1 AAAAAGAAAAGA
569538 AGAAAAGAAAAGA
1 A-AAAAGAAAAGA
569551 AAAAGAGAA
1 AAAA-AGAA
569560 GTTCAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.06
11 10 0.29
12 7 0.20
13 16 0.46
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:575429 original size:17 final size:16
Alignment explanation
Indices: 575360--575431 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
575350 ATTCATGCAT
575360 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
* *
575377 GTTGGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* * *
575395 GTAGTTCAATCATCAAA
1 CTAGTTCATTAAT-AAA
575412 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
575429 CTA
1 CTA
575432 ACTCTTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
16 1 0.02
17 26 0.62
18 15 0.36
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:578220 original size:15 final size:15
Alignment explanation
Indices: 578200--578231 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
578190 CATTTTCGCG
578200 AAGAGTTGCCATTCC
1 AAGAGTTGCCATTCC
578215 AAGAGTTGCCATTCC
1 AAGAGTTGCCATTCC
578230 AA
1 AA
578232 AGGCTCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (15 bp):
AAGAGTTGCCATTCC
Found at i:583498 original size:15 final size:15
Alignment explanation
Indices: 583480--583515 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
583470 ATGAATAATT
583480 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
583495 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
583510 TAGAAT
1 AAGAAT
583516 AGTTATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:583695 original size:13 final size:12
Alignment explanation
Indices: 583676--583761 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
583666 ATATAGGCGT
583676 GATATGGTGATG
1 GATATGGTGATG
583688 GAATATGGTGAT-
1 G-ATATGGTGATG
*
583700 GATATAGGCG-T-
1 GATAT-GGTGATG
583711 GATAATGGTGATG
1 GAT-ATGGTGATG
583724 GACTATGGTGAT-
1 GA-TATGGTGATG
*
583736 GATATAGGCG-T-
1 GATAT-GGTGATG
583747 GATAATGGTGATG
1 GAT-ATGGTGATG
583760 GA
1 GA
583762 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:583731 original size:36 final size:36
Alignment explanation
Indices: 583658--583762 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
583648 ATTTATAAGT
* *
583658 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
583693 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
583729 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
583763 ATATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:588255 original size:36 final size:36
Alignment explanation
Indices: 588182--588286 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
588172 ATTTATAAGT
* * *
588182 TGGTGATAATATAGGCGTGAT-ATGGTGATGTAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
588217 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
588253 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
588287 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:589428 original size:560 final size:560
Alignment explanation
Indices: 588369--589497 Score: 2177
Period size: 560 Copynumber: 2.0 Consensus size: 560
588359 TAAGGGATGG
*
588369 TATGAAATGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
1 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
588434 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
66 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
588499 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
131 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
* * *
588564 AGATTTGTAAAGGCTTGGCCGAATAGATATATGCCTTTTCGGCAAATTACATGTCTTAAACGAAA
196 AGATTTGTAAAGGCTTGGCCAAATAGATATATGCCTTTTCGACAAAGTACATGTCTTAAACGAAA
588629 ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTAATCTTGG
261 ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTAATCTTGG
588694 CGCCAATTTAAAACAAGATGATGCTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
326 CGCCAATTTAAAACAAGATGATGCTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
588759 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
391 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
588824 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
456 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
*
588889 TGCATCTAGGTGACATGGTATTAATGGGACAGCAACTATT
521 TGCATCTAGGTGACATGGCATTAATGGGACAGCAACTATT
588929 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
1 TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
588994 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
66 ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
589059 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
131 AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
589124 AGATTTGTAAAGGCTTGGCCAAATAGATATATGCCTTTTCGACAAAGTACATGTCTTAAACGAAA
196 AGATTTGTAAAGGCTTGGCCAAATAGATATATGCCTTTTCGACAAAGTACATGTCTTAAACGAAA
*
589189 ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTCATCTTGG
261 ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTAATCTTGG
*
589254 CGCCAATTTGAAACAAGATGATGCTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
326 CGCCAATTTAAAACAAGATGATGCTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
*
589319 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGT
391 TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
589384 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
456 TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
*
589449 TGCATCTAGGTGACATGGCATTAATGGGACATCAACTATT
521 TGCATCTAGGTGACATGGCATTAATGGGACAGCAACTATT
589489 TATGAAAGG
1 TATGAAAGG
589498 TAACATTTGT
Statistics
Matches: 560, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
560 560 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (560 bp):
TATGAAAGGACTTTGACCCACTAGTTATTTAAACTAGGAACCAGAAGTATCAAGGTGAAGGAATG
ACGCCACAAGCTTTAGAAAGGCTTGTTTAATCGATATAGTTCTAAAAAGAACTTGAAGAGAGAAT
AATCTCACAAAGGATTTTTAATTGATCAAAGGGTTCATTACAAATGAATGCCAAACCCTATTTAT
AGATTTGTAAAGGCTTGGCCAAATAGATATATGCCTTTTCGACAAAGTACATGTCTTAAACGAAA
ATAAATGATGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTATCTCTTAATCTTGG
CGCCAATTTAAAACAAGATGATGCTTTGGCCGAATGGTTAGAAGCCTCTTCATTTTGGCGCCCAT
TTCATCCACATGCATGGAACATGTGTGGGCTGTTCATGAGGCACTCACATGGGTGGCATAGGGGC
TTATGGTGTGGCTTCTTCTTGGCGTGAATTTGAGCAGCAACTTAGGCATGACTTGGCATCAAACT
TGCATCTAGGTGACATGGCATTAATGGGACAGCAACTATT
Found at i:592752 original size:16 final size:16
Alignment explanation
Indices: 592718--592766 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
592708 GTAAGTTATC
* * *
592718 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
592734 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
592750 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
592767 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:595784 original size:19 final size:20
Alignment explanation
Indices: 595760--595802 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
595750 AGCATTTATC
*
595760 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
595779 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
595799 TTCA
1 TTCA
595803 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:597377 original size:22 final size:24
Alignment explanation
Indices: 597350--597401 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
597340 AAATCCAGCA
*
597350 AAGAAATCG-AAGCACT-CAAAAG
1 AAGAAATCGAAAGCACTAAAAAAG
*
597372 AAGAAATTGAAAGCACTAAAAAAG
1 AAGAAATCGAAAGCACTAAAAAAG
597396 AAGAAA
1 AAGAAA
597402 AAGAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 8 0.31
23 7 0.27
24 11 0.42
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.10
Consensus pattern (24 bp):
AAGAAATCGAAAGCACTAAAAAAG
Found at i:597407 original size:24 final size:23
Alignment explanation
Indices: 597359--597407 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
597349 AAAGAAATCG
* **
597359 AAGCACTCAAAAGAAGAAATTGA
1 AAGCACTAAAAAGAAGAAAAAGA
597382 AAGCACTAAAAAAGAAGAAAAAGA
1 AAGCACT-AAAAAGAAGAAAAAGA
597406 AA
1 AA
597408 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.65, C:0.10, G:0.16, T:0.08
Consensus pattern (23 bp):
AAGCACTAAAAAGAAGAAAAAGA
Found at i:597410 original size:5 final size:5
Alignment explanation
Indices: 597391--597438 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
597381 AAAGCACTAA
* *
597391 AAAAG AAGA- AAAAG AAAAG AAAAG AAAAG AAAAG GAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
597439 TTGAAGCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 7 0.18
5 31 0.82
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:597418 original size:15 final size:15
Alignment explanation
Indices: 597391--597438 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
597381 AAAGCACTAA
*
597391 AAAAGAAGA-AAAAG
1 AAAAGAAAAGAAAAG
597405 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
*
597420 AAAAGGAAAG-AAAG
1 AAAAGAAAAGAAAAG
597434 AAAAG
1 AAAAG
597439 TTGAAGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:599981 original size:14 final size:14
Alignment explanation
Indices: 599962--599994 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
599952 AGAAAGATAA
599962 AAGAGAAGTCTTAC
1 AAGAGAAGTCTTAC
*
599976 AAGAGAAGTCTTGC
1 AAGAGAAGTCTTAC
599990 AAGAG
1 AAGAG
599995 CAGCAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (14 bp):
AAGAGAAGTCTTAC
Found at i:603998 original size:8 final size:8
Alignment explanation
Indices: 603975--604028 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
603965 ATTGGAGTGC
603975 AAAAAGAA
1 AAAAAGAA
603983 AGAAAAGAA
1 A-AAAAGAA
603992 AAAAAGAA
1 AAAAAGAA
**
604000 AAAAATCA
1 AAAAAGAA
* *
604008 GAATAGAA
1 AAAAAGAA
*
604016 GAAAAGAA
1 AAAAAGAA
604024 AAAAA
1 AAAAA
604029 AAGAAGAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
8 29 0.78
9 8 0.22
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:604010 original size:24 final size:24
Alignment explanation
Indices: 603983--604028 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
603973 GCAAAAAGAA
603983 AGAAAAGAAAAAAAGAAAAAAATC
1 AGAAAAGAAAAAAAGAAAAAAATC
* *
604007 AGAATAGAAGAAAAGAAAAAAA
1 AGAAAAGAAAAAAAGAAAAAAA
604029 AAGAAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.04
Consensus pattern (24 bp):
AGAAAAGAAAAAAAGAAAAAAATC
Found at i:604049 original size:33 final size:31
Alignment explanation
Indices: 603974--604054 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
603964 AATTGGAGTG
603974 CAAAAAGAAAGAAAAGAAAAAAAGAAAAAAAT
1 CAAAAAG-AAGAAAAGAAAAAAAGAAAAAAAT
* *
604006 CAGAATAGAAGAAAAGAAAAAAA-AAGAAGAATTT
1 CA-AAAAGAAGAAAAGAAAAAAAGAA-AA-AA-AT
*
604040 CAAAAAGAAGCAAAG
1 CAAAAAGAAGAAAAG
604055 CCAAGGAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.05
32 19 0.46
33 17 0.41
34 3 0.07
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.06
Consensus pattern (31 bp):
CAAAAAGAAGAAAAGAAAAAAAGAAAAAAAT
Found at i:611110 original size:2 final size:2
Alignment explanation
Indices: 611103--611136 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
611093 AGTTATTTTC
611103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
611137 CCTATAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:612784 original size:20 final size:19
Alignment explanation
Indices: 612735--612801 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
612725 ATTGGAGTAC
612735 AAAAAGAAAGAAAAGACAA
1 AAAAAGAAAGAAAAGACAA
** *
612754 AAAGAAGAAAGAAAATTCAG
1 AAA-AAGAAAGAAAAGACAA
* *
612774 AAAAAGAAA-AGAAGAAAA
1 AAAAAGAAAGAAAAGACAA
612792 GAAAAAGAAA
1 -AAAAAGAAA
612802 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.11
19 18 0.47
20 16 0.42
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAGAAAAGACAA
Found at i:612792 original size:35 final size:31
Alignment explanation
Indices: 612741--612813 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 31
612731 GTACAAAAAG
612741 AAAGAAAAGACAAAAAGAAGAAAGAAAATTCAGAA
1 AAAGAAAAGACAAAAAGAA-AAAG-AAATTC--AA
612776 AAAGAAAAGA-AGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGACA-AAAAGAAAAAGAAATTCAA
612807 AAAGAAA
1 AAAGAAA
612814 TCAAGCCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
31 9 0.24
33 6 0.16
34 5 0.14
35 17 0.46
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.05
Consensus pattern (31 bp):
AAAGAAAAGACAAAAAGAAAAAGAAATTCAA
Found at i:615160 original size:25 final size:24
Alignment explanation
Indices: 615127--615178 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
615117 TTCTTTTTTT
* * *
615127 TTTTAATTTTTCGGAATTTGTTTC
1 TTTTAAATTTTCAGAATTCGTTTC
*
615151 TTTTAAATTTTCAGAATTCGTTTT
1 TTTTAAATTTTCAGAATTCGTTTC
615175 TTTT
1 TTTT
615179 CAAGATGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (24 bp):
TTTTAAATTTTCAGAATTCGTTTC
Found at i:616426 original size:11 final size:11
Alignment explanation
Indices: 616405--616446 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
616395 GTGCTGGAAT
616405 CAAGATAAAAA
1 CAAGATAAAAA
* *
616416 TAAGATTAAAA
1 CAAGATAAAAA
616427 CAAGATAAAGAA
1 CAAGATAAA-AA
616439 -AAGATAAA
1 CAAGATAAA
616447 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:620738 original size:10 final size:10
Alignment explanation
Indices: 620725--620790 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 10
620715 TTTTTTGAAA
*
620725 TTTTGGCTTT
1 TTTTGGTTTT
620735 TTTTGTGTTTT
1 TTTTG-GTTTT
620746 TTTTGTGTTTTT
1 TTTTG-G-TTTT
*
620758 TTTTGCCTTTT
1 TTTTG-GTTTT
620769 TTTT-GTTTT
1 TTTTGGTTTT
620778 TTTTGGTTTT
1 TTTTGGTTTT
620788 TTT
1 TTT
620791 GAAAAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.16
10 13 0.27
11 19 0.39
12 9 0.18
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (10 bp):
TTTTGGTTTT
Found at i:620745 original size:9 final size:10
Alignment explanation
Indices: 620732--620791 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
620722 AAATTTTGGC
620732 TTTTTTTGTG
1 TTTTTTTGTG
620742 TTTTTTTTGTG
1 -TTTTTTTGTG
*
620753 TTTTTTTTTG
1 TTTTTTTGTG
620763 CCTTTTTTT-TG
1 --TTTTTTTGTG
620774 TTTTTTT-TGG
1 TTTTTTTGT-G
620784 TTTTTTTG
1 TTTTTTTG
620792 AAAAAAATAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 8 0.18
10 17 0.39
11 12 0.27
12 7 0.16
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (10 bp):
TTTTTTTGTG
Found at i:620748 original size:11 final size:11
Alignment explanation
Indices: 620732--620790 Score: 79
Period size: 11 Copynumber: 5.5 Consensus size: 11
620722 AAATTTTGGC
620732 TTTTTTTGTGT
1 TTTTTTTGTGT
620743 TTTTTTTGTGT
1 TTTTTTTGTGT
*
620754 TTTTTTT-TGCC
1 TTTTTTTGTG-T
620765 TTTTTTT-TGT
1 TTTTTTTGTGT
620775 TTTTTTTG-GT
1 TTTTTTTGTGT
620785 TTTTTT
1 TTTTTT
620791 GAAAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 17 0.39
11 27 0.61
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:620762 original size:23 final size:22
Alignment explanation
Indices: 620732--620781 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
620722 AAATTTTGGC
**
620732 TTTTTTTGTGTTTTTTTTGTGTT
1 TTTTTTTGCCTTTTTTTTGT-TT
620755 TTTTTTTGCCTTTTTTTTGTTT
1 TTTTTTTGCCTTTTTTTTGTTT
620777 TTTTT
1 TTTTT
620782 GGTTTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (22 bp):
TTTTTTTGCCTTTTTTTTGTTT
Found at i:620789 original size:32 final size:33
Alignment explanation
Indices: 620725--620790 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
620715 TTTTTTGAAA
*
620725 TTTTGGCTTTTTTTGTGTTTTTTTTGTGTTTTT
1 TTTTGCCTTTTTTTGTGTTTTTTTTGTGTTTTT
620758 TTTTGCCTTTTTTT-TGTTTTTTTTG-GTTTTT
1 TTTTGCCTTTTTTTGTGTTTTTTTTGTGTTTTT
620789 TT
1 TT
620791 GAAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 8 0.25
32 11 0.34
33 13 0.41
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (33 bp):
TTTTGCCTTTTTTTGTGTTTTTTTTGTGTTTTT
Found at i:621146 original size:22 final size:21
Alignment explanation
Indices: 621118--621163 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
621108 TATGTGCTGG
621118 AATCAAGATAAA-AATAAGATTA
1 AATCAAGATAAAGAA-AAGA-TA
621140 AATCAAGATAAAGAAAAGATA
1 AATCAAGATAAAGAAAAGATA
621161 AAT
1 AAT
621164 GAATTGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 16 0.70
23 2 0.09
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (21 bp):
AATCAAGATAAAGAAAAGATA
Found at i:622458 original size:28 final size:28
Alignment explanation
Indices: 622418--622473 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
622408 CGTGAATTAA
622418 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
*
622446 CAAAACAAATGATGAACATGTTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
622474 TGAATGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGCTGTTATG
Found at i:622785 original size:27 final size:27
Alignment explanation
Indices: 622744--622799 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
622734 ACCTTGTGGC
* * *
622744 ATGACTTCGGGATCTGATGTGGGCTTG
1 ATGACTTCGAGATCTGATATGGGCGTG
*
622771 ATGACTTCGATATCTGATATGGGCGTG
1 ATGACTTCGAGATCTGATATGGGCGTG
622798 AT
1 AT
622800 CATATAATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (27 bp):
ATGACTTCGAGATCTGATATGGGCGTG
Found at i:625181 original size:11 final size:11
Alignment explanation
Indices: 625157--625201 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
625147 TTGGTGTTGG
625157 AAACAAGATAA
1 AAACAAGATAA
* *
625168 AAATAAGATTA
1 AAACAAGATAA
625179 AAACAAGATAA
1 AAACAAGATAA
625190 AGAA-AAGATAA
1 A-AACAAGATAA
625201 A
1 A
625202 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:625185 original size:22 final size:22
Alignment explanation
Indices: 625157--625198 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
625147 TTGGTGTTGG
625157 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
625179 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
625199 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:630785 original size:20 final size:21
Alignment explanation
Indices: 630760--630810 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
630750 TATCATATCG
**
630760 TTTCTTTCTTCCATTTCCT-A
1 TTTCTTTCTTCCATTTAATCA
630780 TTTCTTAT-TTCCATTTAATCA
1 TTTCTT-TCTTCCATTTAATCA
630801 TTTCTTTCTT
1 TTTCTTTCTT
630811 TTTAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCTTTCTTCCATTTAATCA
Found at i:637762 original size:17 final size:17
Alignment explanation
Indices: 637740--637772 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
637730 TAAGATTTGA
637740 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
637757 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
637773 TTTCCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:640302 original size:33 final size:33
Alignment explanation
Indices: 640260--640328 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
640250 GTTGATGAAT
*
640260 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
640293 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
640326 GAA
1 GAA
640329 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:643340 original size:16 final size:16
Alignment explanation
Indices: 643315--643354 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
643305 TGATAGGAAC
643315 CTTTTT-TTTCTTTTT
1 CTTTTTCTTTCTTTTT
643330 -TTTCTTCTTTCTTTTT
1 CTTT-TTCTTTCTTTTT
643346 CTTTTTCTT
1 CTTTTTCTT
643355 GCAGCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 2 0.09
16 14 0.64
17 3 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (16 bp):
CTTTTTCTTTCTTTTT
Found at i:643548 original size:22 final size:22
Alignment explanation
Indices: 643523--643591 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
643513 TAAAAAGAAA
643523 GAAATGATTAAAATGGAAATAT
1 GAAATGATTAAAATGGAAATAT
* *
643545 GAAA-CA--AGAAATGGAAGA-AA
1 GAAATGATTA-AAATGGAA-ATAT
643565 GAAATGATTAAAATGGAAATAT
1 GAAATGATTAAAATGGAAATAT
643587 GAAAT
1 GAAAT
643592 AAGAAATGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 1 0.03
20 13 0.35
21 4 0.11
22 18 0.49
23 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.20, T:0.20
Consensus pattern (22 bp):
GAAATGATTAAAATGGAAATAT
Found at i:643558 original size:20 final size:20
Alignment explanation
Indices: 643533--643602 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
643523 GAAATGATTA
643533 AAATGGAAATATGAAACAAG
1 AAATGGAAATATGAAACAAG
* *
643553 AAATGGAAGA-AAGAAATGATTA-
1 AAATGGAA-ATATGAAA-CA--AG
*
643575 AAATGGAAATATGAAATAAG
1 AAATGGAAATATGAAACAAG
643595 AAATGGAA
1 AAATGGAA
643603 GAAAGAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
19 1 0.03
20 21 0.52
21 4 0.10
22 13 0.32
23 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGGAAATATGAAACAAG
Found at i:643576 original size:42 final size:42
Alignment explanation
Indices: 643517--643613 Score: 185
Period size: 42 Copynumber: 2.3 Consensus size: 42
643507 CATAATTAAA
643517 AAGAAAGAAATGATTAAAATGGAAATATGAAACAAGAAATGG
1 AAGAAAGAAATGATTAAAATGGAAATATGAAACAAGAAATGG
*
643559 AAGAAAGAAATGATTAAAATGGAAATATGAAATAAGAAATGG
1 AAGAAAGAAATGATTAAAATGGAAATATGAAACAAGAAATGG
643601 AAGAAAGAAATGA
1 AAGAAAGAAATGA
643614 AATTATAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.61, C:0.01, G:0.22, T:0.16
Consensus pattern (42 bp):
AAGAAAGAAATGATTAAAATGGAAATATGAAACAAGAAATGG
Found at i:645768 original size:5 final size:5
Alignment explanation
Indices: 645716--645747 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
645706 AGCACTCAAG
*
645716 AAGAA AAGAA AAGAA AAAAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
645748 AGAATATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:650459 original size:30 final size:31
Alignment explanation
Indices: 650424--650483 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
650414 CTTAGCTTTA
**
650424 TATTATGGTTACATATGTTTTAGAT-TCATT
1 TATTATGGTTACATATCATTTAGATATCATT
* *
650454 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGGTTACATATCATTTAGATATCAT
650484 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (31 bp):
TATTATGGTTACATATCATTTAGATATCATT
Found at i:651405 original size:19 final size:20
Alignment explanation
Indices: 651381--651431 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
651371 CGGCCAAGAG
* *
651381 CATGTATCTTCATTAAAA-T
1 CATGTATTTTCATCAAAACT
651400 CATGTATTTTCATCAAAACT
1 CATGTATTTTCATCAAAACT
651420 CATGTATTTTCA
1 CATGTATTTTCA
651432 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAACT
Found at i:651825 original size:22 final size:22
Alignment explanation
Indices: 651785--651826 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
651775 ACCATCTTCA
*
651785 ATCCATCATCAACATCATCAAC
1 ATCCATCATCAACACCATCAAC
* *
651807 ATCCTTCATCAAGACCATCA
1 ATCCATCATCAACACCATCA
651827 TCAATCCCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (22 bp):
ATCCATCATCAACACCATCAAC
Found at i:652154 original size:11 final size:11
Alignment explanation
Indices: 652138--652195 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 11
652128 ATTGGAGTGC
652138 AAAAAGAAAAG
1 AAAAAGAAAAG
652149 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
652163 AAGAATCAGAAAA-
1 AA-AA--AGAAAAG
652176 AAAAAGAAAAG
1 AAAAAGAAAAG
652187 AAAAAGAAA
1 AAAAAGAAA
652196 TTCAAAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
10 6 0.15
11 15 0.38
12 2 0.05
13 2 0.05
14 11 0.28
15 2 0.05
17 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:652193 original size:27 final size:28
Alignment explanation
Indices: 652142--652194 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
652132 GAGTGCAAAA
*
652142 AGAAAAGAAAAAGACAAAAAGAAGAATC
1 AGAAAAGAAAAAGACAAAAAAAAGAATC
652170 AGAAAA-AAAAAGA-AAAGAAAAAGAA
1 AGAAAAGAAAAAGACAAA-AAAAAGAA
652195 ATTCAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 14 0.61
28 6 0.26
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (28 bp):
AGAAAAGAAAAAGACAAAAAAAAGAATC
Found at i:654576 original size:19 final size:20
Alignment explanation
Indices: 654552--654602 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
654542 CGGCCAAGAG
* *
654552 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
654571 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
654591 CATGTATTTTCA
1 CATGTATTTTCA
654603 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:656919 original size:12 final size:12
Alignment explanation
Indices: 656902--656930 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
656892 TTGGCTTTTT
656902 TGATCCCCCTTC
1 TGATCCCCCTTC
656914 TGATCCCCCTTC
1 TGATCCCCCTTC
656926 TGATC
1 TGATC
656931 TCACCCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.45, G:0.10, T:0.34
Consensus pattern (12 bp):
TGATCCCCCTTC
Found at i:657385 original size:16 final size:17
Alignment explanation
Indices: 657364--657398 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
657354 GTATTTCTTA
657364 TTTC-TTTTTTTCTTTT
1 TTTCTTTTTTTTCTTTT
657380 TTTCTTTTTTTTCTTTT
1 TTTCTTTTTTTTCTTTT
657397 TT
1 TT
657399 CTTGTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTCTTTTTTTTCTTTT
Found at i:657399 original size:16 final size:16
Alignment explanation
Indices: 657357--657401 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
657347 TCTTTTTGTA
*
657357 TTTCTTATTTC-TTTT
1 TTTCTTTTTTCTTTTT
657372 TTTCTTTTTTTCTTTTT
1 TTTC-TTTTTTCTTTTT
657389 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
657402 GTTGCTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTT
Found at i:657401 original size:7 final size:8
Alignment explanation
Indices: 657364--657398 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
657354 GTATTTCTTA
657364 TTTCTTTT
1 TTTCTTTT
657372 TTTCTTTT
1 TTTCTTTT
657380 TTTCTTTTT
1 TTTC-TTTT
657389 TTTCTTTT
1 TTTCTTTT
657397 TT
1 TT
657399 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTCTTTT
Found at i:657640 original size:16 final size:16
Alignment explanation
Indices: 657578--657632 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
657568 ATTAAAGAAA
* *
657578 GAAATGATTA-AAAAT
1 GAAATGATAAGAAAAG
657593 GAATATGA-AAGAAGAATG
1 GAA-ATGATAAGAA-AA-G
657611 GAAATGATAAGAAAAG
1 GAAATGATAAGAAAAG
657627 GAAATG
1 GAAATG
657633 GATAGAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.12
16 13 0.39
17 8 0.24
18 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (16 bp):
GAAATGATAAGAAAAG
Found at i:659032 original size:22 final size:22
Alignment explanation
Indices: 658992--659033 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
658982 AAATATGTGG
*
658992 TTCATAATAATAACTTCATACA
1 TTCATAATAATAACATCATACA
* *
659014 TTCATAATATTATCATCATA
1 TTCATAATAATAACATCATA
659034 ACTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATAACATCATACA
Found at i:661904 original size:21 final size:20
Alignment explanation
Indices: 661878--661917 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
661868 GCATCAAGGT
*
661878 TTTTGTTGAGGCCATGAAATC
1 TTTTGTCGAGGCCAT-AAATC
661899 TTTTGTCGAGGCCATAAAT
1 TTTTGTCGAGGCCATAAAT
661918 TCATGCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (20 bp):
TTTTGTCGAGGCCATAAATC
Found at i:665611 original size:17 final size:16
Alignment explanation
Indices: 665583--665629 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
665573 TGGAAATAAG
665583 AAAT-GAAAGAAATGA
1 AAATGGAAAGAAATGA
*
665598 AAATTGATAAGAAATG-
1 AAATGGA-AAGAAATGA
665614 AAATGGAAAGAAATGA
1 AAATGGAAAGAAATGA
665630 TATCAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 12 0.43
16 8 0.29
17 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (16 bp):
AAATGGAAAGAAATGA
Found at i:679590 original size:6 final size:6
Alignment explanation
Indices: 679579--679621 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
679569 GATATAGGAG
* *
679579 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TCGTTT GCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
679622 GTTGCAGCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:680913 original size:58 final size:58
Alignment explanation
Indices: 680841--681470 Score: 915
Period size: 58 Copynumber: 10.9 Consensus size: 58
680831 GTGTGGTGTT
680841 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* * * * * *
680899 GAAATCATATTAAGTGTATAAATTTCCATTTAGGACATTTTGTACGCTAAAATGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* * * *
680957 GAAATCATATTAAGTGTATGAATTTCCATATAGGACGTTTAGTACGCTAAATTGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* * * * *
681015 GAAATCATACTAAGTGTATGGATTTACATATAGGGCGTTTCGTTCGTTAAAATTTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* *
681073 GAAATCATACTATGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTAAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* ** * * *
681131 GAAAGCATACTAAGTAAATGAATTTCCATATAGGGCATATCGTACGCTAAAATGTTTA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* * *
681189 GAAATTATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTAGGCTAAATTGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* *
681247 GAAATCATATTAAGTGTATGAATTTCCATATAGGGCTTTTCGTACGCTAAAATGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* *
681305 AAAATCATAATAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
* *
681363 GAAAT-ATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACG-GATAAATTTTAA
1 GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTA-AAATGTTAA
* *
681420 GAAATCATACTAAGTAG-ATGAATTTTCATATATGGCGTTTCGTACGCTAAA
1 GAAATCATACTAAGT-GTATGAATTTCCATATAGGGCGTTTCGTACGCTAAA
681471 GTGTATGAAT
Statistics
Matches: 509, Mismatches: 59, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
56 1 0.00
57 52 0.10
58 454 0.89
59 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (58 bp):
GAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAA
Found at i:681537 original size:96 final size:96
Alignment explanation
Indices: 681373--681566 Score: 284
Period size: 96 Copynumber: 2.0 Consensus size: 96
681363 GAAATATACT
* *
681373 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGGATAAATTTTAAGAAATCATACTAAGTAGA
1 AAGTGTATGAATTTCCATATAGGGCATTTCGTACGGATAAATGTTAAGAAATCATACTAAGTAGA
* * *
681438 TGAATTTTCATATATGGCGTTTCGTACGCTA
66 TGAATTTGCATATAGGGCGTTCCGTACGCTA
* *
681469 AAGTGTATGAATTTCCATATAGGGCATTTCTTAC-GCTAAACTGTTAAGAAATCATACTAAGT-G
1 AAGTGTATGAATTTCCATATAGGGCATTTCGTACGGATAAA-TGTTAAGAAATCATACTAAGTAG
*
681532 TATGAATTTGCATATAGGGCGTTCCGTACGTTA
65 -ATGAATTTGCATATAGGGCGTTCCGTACGCTA
681565 AA
1 AA
681567 ATGTTAAGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 6 0.07
96 82 0.93
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (96 bp):
AAGTGTATGAATTTCCATATAGGGCATTTCGTACGGATAAATGTTAAGAAATCATACTAAGTAGA
TGAATTTGCATATAGGGCGTTCCGTACGCTA
Found at i:681572 original size:58 final size:58
Alignment explanation
Indices: 681469--682326 Score: 1329
Period size: 58 Copynumber: 14.8 Consensus size: 58
681459 TCGTACGCTA
* * *
681469 AAGTGTATGAATTTCCATATAGGGCATTTCTTACGCTAAACTGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * *
681527 AAGTGTATGAATTTGCATATAGGGCGTTCCGTACGTTAAAATGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* *
681585 AAGTGTATGAATTTCCATATAGGGTGTTTCGTACGCTAAAATGTTAAGAAAGCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* *
681643 AAGTGTATGAATTTCCATATAGGGTGTTTCGTACGCTAAAATGTTAATAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * * *
681701 AAGTGTATGAATTTTCATATAAGGCGTTTTGTACGATAAAATGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
*
681759 AAGTGTATGAATTTCCATATAGGGCGTTTCGTTCGCTAAAATGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * * *
681817 AAGTGTATGAATTTCCATATAGGGCGTTTAGTGCGCTAAAATGGTAAGAAAGCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * *
681875 AAGTTTATGAATTTCCATATAGGGCGTTTCGTATGCTAAAATGGTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * *
681933 AAGTGTATGAATTTCCATATAGGCCATTTCGTATGCTAAAATGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
** * *
681991 AAGTGTATGAATTTCCATATAGGGTATATCGTACGCTAAAATGTTAAGAAATCATTCT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * *
682049 AAGTGTATGAATTTCCATATAAGGCGTTTCGTGCGCTAAAATGTTAAAAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* *
682107 AAGTGTATGAATTTCCATATAGGGCATTTCGTATGCTAAAATGTTAAGAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* * * *
682165 AAGTGTATGAATTTCCATACAGGGTGTTTCATACGCTAAAATGTTAAGAAATCATTCT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
** *
682223 AAGTGTATGAATTTCCATATAGGGCGTTTCGTTTGCTAAAATGTTAAAAAATCATACT
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
* *
682281 AAGTGTATGAATTTCCATATAGGGCATTTCGTATGCTAAAATGTTA
1 AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTA
682327 GATGAATGGT
Statistics
Matches: 731, Mismatches: 69, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 731 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (58 bp):
AAGTGTATGAATTTCCATATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACT
Found at i:682420 original size:2 final size:2
Alignment explanation
Indices: 682413--682438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
682403 ATTAAGGGGT
682413 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
682439 ATGTACAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:684982 original size:19 final size:20
Alignment explanation
Indices: 684941--684991 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
684931 GAAACCCCTT
*
684941 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
684961 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
684980 TGAAGATACATG
1 TGAAAATACATG
684992 CTCTTAGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:685934 original size:20 final size:20
Alignment explanation
Indices: 685909--685947 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
685899 CCATGATATG
685909 TAAATG-ATATACAAACATAA
1 TAAATGAATATA-AAACATAA
685929 TAAATGAATATAAAACATA
1 TAAATGAATATAAAACATA
685948 CGTAAGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:688180 original size:13 final size:12
Alignment explanation
Indices: 688156--688214 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
688146 CTTTTTGAAT
688156 TTTTC-TTTTTC
1 TTTTCTTTTTTC
688167 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
688180 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
688194 TCTTCTTTTGTC
1 TTTTCTTTTTTC
688206 TTTTTCTTT
1 -TTTTCTTT
688215 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:688180 original size:19 final size:19
Alignment explanation
Indices: 688158--688214 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
688148 TTTTGAATTT
688158 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
688177 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
688196 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
688215 CTTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:688183 original size:33 final size:34
Alignment explanation
Indices: 688143--688221 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 34
688133 CATTGGCTTG
*
688143 CTTCTTTTTGAATTTTTCT-TT-TTCTTTTC-TTTT
1 CTTCTTTTTG-ATTTTTCTCTTCTT-TTGTCTTTTT
688176 CTTCTTTTCTGATTTTTCTCTTCTTTTGTCTTTTT
1 CTTCTTTT-TGATTTTTCTCTTCTTTTGTCTTTTT
688211 CTTTCTTTTTG
1 C-TTCTTTTTG
688222 CACTTCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
33 16 0.40
34 8 0.20
35 9 0.22
36 7 0.17
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (34 bp):
CTTCTTTTTGATTTTTCTCTTCTTTTGTCTTTTT
Found at i:688577 original size:20 final size:21
Alignment explanation
Indices: 688540--688578 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
688530 GATGGTCTTG
*
688540 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
688561 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
688579 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:688956 original size:19 final size:20
Alignment explanation
Indices: 688915--688965 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
688905 GAAACCCCTT
*
688915 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
688935 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
688954 TGAAGATACATG
1 TGAAAATACATG
688966 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:689916 original size:20 final size:20
Alignment explanation
Indices: 689891--689929 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
689881 CCATGATATG
689891 TAAATG-ATATACAAACATAA
1 TAAATGAATATA-AAACATAA
689911 TAAATGAATATAAAACATA
1 TAAATGAATATAAAACATA
689930 CGTAAGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:692150 original size:18 final size:17
Alignment explanation
Indices: 692129--692208 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
692119 CATTGGCTTG
692129 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
692147 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
692163 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
692180 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
692198 CTTTCTTTTTG
1 CTTTCTTTTTG
692209 CACTTCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 12 0.24
18 23 0.45
19 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:692167 original size:13 final size:12
Alignment explanation
Indices: 692143--692201 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
692133 CTTTTTGAAT
692143 TTTTC-TTTTTC
1 TTTTCTTTTTTC
692154 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
692167 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
692181 TCTTCTTTTGTC
1 TTTTCTTTTTTC
692193 TTTTTCTTT
1 -TTTTCTTT
692202 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:692167 original size:19 final size:19
Alignment explanation
Indices: 692145--692201 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
692135 TTTTGAATTT
692145 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
692164 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
692183 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
692202 CTTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:692564 original size:20 final size:21
Alignment explanation
Indices: 692527--692565 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
692517 GATGGTCTTG
*
692527 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
692548 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
692566 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:692943 original size:19 final size:20
Alignment explanation
Indices: 692902--692952 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
692892 GAAACCCCTT
*
692902 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
692922 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
692941 TGAAGATACATG
1 TGAAAATACATG
692953 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:695547 original size:50 final size:52
Alignment explanation
Indices: 695472--695609 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 52
695462 CACACTCCAA
*
695472 TTTTCCTTTTCATTGCGACTAGGAGGGTT-GG-TTAGAGCCATATTATCGAG
1 TTTTCCATTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
* *
695522 TTTTCCATTTCATTGCAACTTGGAGGGTTCTATAGGACACTTAGAGCCATATTATCGAG
1 TTTTCCATTTCATTGCGACTAGGAGGG---T-TAGG--A-TTAGAGCCATATTATCGAG
*
695581 TTTGCCATTTCATTGCGACTAGGAGGGTT
1 TTTTCCATTTCATTGCGACTAGGAGGGTT
695610 CGATAGGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
50 24 0.33
53 1 0.01
54 1 0.01
55 3 0.04
56 1 0.01
59 43 0.59
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (52 bp):
TTTTCCATTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
Found at i:695595 original size:59 final size:59
Alignment explanation
Indices: 695503--695620 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
695493 GGAGGGTTGG
* * *
695503 TTAGAGCCATATTATCGAGTTTTCCATTTCATTGCAACTTGGAGGGTTCTATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCATTTCATTGCAACTAGGAGGGTTCGATAGGACAC
*
695562 TTAGAGCCATATTATCGAGTTTGCCATTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCATTTCATTGCAACTAGGAGGGTTCGATAGGACAC
695621 CTATACATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCATTTCATTGCAACTAGGAGGGTTCGATAGGACAC
Found at i:701227 original size:36 final size:35
Alignment explanation
Indices: 701131--701242 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
701121 TTGATGGTTA
* * * **
701131 TATAGGCGTGAAATGATGATAGAAGTTGATGATAA
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
* * *
701166 TATAGGCGTGCAATGGAGATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
701201 TATAGGCGTGAAAATGGTGATAGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTGATGT
701237 TATAGG
1 TATAGG
701243 TAGGAGCAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
35 37 0.57
36 28 0.43
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
Found at i:706932 original size:17 final size:17
Alignment explanation
Indices: 706910--706949 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
706900 TTAAATCACT
*
706910 ATGTTCTCCTTGAGAAG
1 ATGTTCTCCTTGAAAAG
*
706927 ATGTTCTCCTTGAAAAT
1 ATGTTCTCCTTGAAAAG
706944 ATGTTC
1 ATGTTC
706950 CACGTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (17 bp):
ATGTTCTCCTTGAAAAG
Found at i:728447 original size:33 final size:35
Alignment explanation
Indices: 728373--728468 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 35
728363 TACTATTTTC
* *
728373 ATCACCATAATCCATCTCCCATTATCACGCCTATATC
1 ATCACCATAATCCATC-ACCATTATCAC-CCTATATA
*
728410 ATCACCATAGTCCATCACCATTA-CA-CCTATATA
1 ATCACCATAATCCATCACCATTATCACCCTATATA
*
728443 ATCACCATATTCCATCACCA-TATCAC
1 ATCACCATAATCCATCACCATTATCAC
728469 GCCAATAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.04
33 28 0.53
35 2 0.04
36 6 0.11
37 15 0.28
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (35 bp):
ATCACCATAATCCATCACCATTATCACCCTATATA
Found at i:730623 original size:15 final size:18
Alignment explanation
Indices: 730587--730626 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
730577 GATGCCAAGG
730587 GACATGATCATTCAAGCA
1 GACATGATCATTCAAGCA
730605 -ACATG-TC-TTCAA-CA
1 GACATGATCATTCAAGCA
730619 GACATGAT
1 GACATGAT
730627 TTTTATCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 3 0.15
17 5 0.25
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (18 bp):
GACATGATCATTCAAGCA
Found at i:732361 original size:36 final size:36
Alignment explanation
Indices: 732309--732421 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
732299 AAGATACTTT
*
732309 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
732345 TCATCACCATAGTCCATCACCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
732381 TAATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
732416 ACATCA
1 TCATCA
732422 TCTACCATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 15 0.22
36 53 0.78
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:732405 original size:13 final size:13
Alignment explanation
Indices: 732309--732405 Score: 68
Period size: 13 Copynumber: 7.9 Consensus size: 13
732299 AAGATACTTT
732309 TCATCACCATA-A
1 TCATCACCATATA
*
732321 TCCATCTCCAT-TA
1 T-CATCACCATATA
*
732334 TCA-CGCC-TATA
1 TCATCACCATATA
732345 TCATCACCATAGT-
1 TCATCACCATA-TA
*
732358 CCATCACCAT-TA
1 TCATCACCATATA
732370 TCA-CACC-TATA
1 TCATCACCATATA
*
732381 TAATCACCATAT-
1 TCATCACCATATA
732393 TCCATCACCATAT
1 T-CATCACCATAT
732406 CACGCCAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
10 2 0.03
11 17 0.25
12 13 0.19
13 34 0.51
14 1 0.01
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (13 bp):
TCATCACCATATA
Found at i:732896 original size:25 final size:26
Alignment explanation
Indices: 732856--732912 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
732846 AATTTGGAGT
732856 GCAAAAGAAAGAAAAGAAAAAGAGAA
1 GCAAAAGAAAGAAAAGAAAAAGAGAA
* * *
732882 TCAAAA-AAAGCAAAGAAAAAGTGAA
1 GCAAAAGAAAGAAAAGAAAAAGAGAA
732907 GCAAAA
1 GCAAAA
732913 TTGCAAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.70, C:0.07, G:0.19, T:0.04
Consensus pattern (26 bp):
GCAAAAGAAAGAAAAGAAAAAGAGAA
Found at i:736279 original size:36 final size:36
Alignment explanation
Indices: 736227--736314 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
736217 GATACTATTT
* *
736227 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
*
736263 TCATCACCATAGTCCATCACCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
* *
736299 TAATCACCATATTCCA
1 TCATCACCATAATCCA
736315 CCATATCACG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACACCTATA
Found at i:740209 original size:36 final size:36
Alignment explanation
Indices: 740157--740269 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
740147 AGAGATATTT
*
740157 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
740193 TCATCACCATAGTCCATCACCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
740229 TAATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
740264 ACATCA
1 TCATCA
740270 TCCTACCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 15 0.22
36 53 0.78
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:740253 original size:13 final size:13
Alignment explanation
Indices: 740157--740253 Score: 68
Period size: 13 Copynumber: 7.9 Consensus size: 13
740147 AGAGATATTT
740157 TCATCACCATA-A
1 TCATCACCATATA
*
740169 TCCATCTCCAT-TA
1 T-CATCACCATATA
*
740182 TCA-CGCC-TATA
1 TCATCACCATATA
740193 TCATCACCATAGT-
1 TCATCACCATA-TA
*
740206 CCATCACCAT-TA
1 TCATCACCATATA
740218 TCA-CACC-TATA
1 TCATCACCATATA
*
740229 TAATCACCATAT-
1 TCATCACCATATA
740241 TCCATCACCATAT
1 T-CATCACCATAT
740254 CACGCCAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
10 2 0.03
11 17 0.25
12 13 0.19
13 34 0.51
14 1 0.01
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (13 bp):
TCATCACCATATA
Found at i:741412 original size:21 final size:23
Alignment explanation
Indices: 741386--741427 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
741376 TTTCACCAAT
741386 TGTTCCT-TATG-CTCTCCTTAG
1 TGTTCCTATATGACTCTCCTTAG
*
741407 TGTTCCTATATGAGTCTCCTT
1 TGTTCCTATATGACTCTCCTT
741428 GCTGTAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (23 bp):
TGTTCCTATATGACTCTCCTTAG
Found at i:747745 original size:27 final size:27
Alignment explanation
Indices: 747707--747760 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
747697 TGTTTCACCT
747707 ATAGGAATCAACAAACAAATAAAGTAA
1 ATAGGAATCAACAAACAAATAAAGTAA
747734 ATAGGAATCAACAAACAAATAAAGTAA
1 ATAGGAATCAACAAACAAATAAAGTAA
747761 GCAATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.15
Consensus pattern (27 bp):
ATAGGAATCAACAAACAAATAAAGTAA
Found at i:748987 original size:15 final size:15
Alignment explanation
Indices: 748967--749003 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
748957 AGAAGTATTA
748967 GGGTGACATAGATAG
1 GGGTGACATAGATAG
748982 GGGTGACATAGATAG
1 GGGTGACATAGATAG
748997 GGGTGAC
1 GGGTGAC
749004 GCCACAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.43, T:0.19
Consensus pattern (15 bp):
GGGTGACATAGATAG
Found at i:750447 original size:15 final size:15
Alignment explanation
Indices: 750427--750469 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
750417 GAAATATGAA
750427 ATAAGAAAGGAAATG
1 ATAAGAAAGGAAATG
750442 ATAAGAAAGGAAATG
1 ATAAGAAAGGAAATG
750457 -TAAATGAAAGGAA
1 AT-AA-GAAAGGAA
750470 TTGAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.04
15 17 0.65
16 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (15 bp):
ATAAGAAAGGAAATG
Found at i:767053 original size:16 final size:16
Alignment explanation
Indices: 767021--767068 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
767011 TAAGGTAGTA
767021 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
* *
767039 AATAAGGAAATGAAAT
1 AATAAGAAAATGAAAG
*
767055 AGTAAGAAAATGAA
1 AATAAGAAAATGAA
767069 GATAACTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 18 0.69
17 2 0.08
18 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:773296 original size:15 final size:15
Alignment explanation
Indices: 773285--773314 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
773275 ACTCAAAAAG
773285 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
773300 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
773314 A
1 A
773315 TTGAAGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:779739 original size:24 final size:21
Alignment explanation
Indices: 779705--779747 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
779695 TCCACAAGAC
*
779705 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
779727 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
779748 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:781736 original size:20 final size:19
Alignment explanation
Indices: 781693--781742 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
781683 CGGCGAAGAG
*
781693 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
*
781712 CATGTTTTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
781732 CATGTAATTTT
1 CATGT-ATTTT
781743 TGGAAGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 13 0.50
20 9 0.35
21 4 0.15
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:790185 original size:12 final size:12
Alignment explanation
Indices: 790163--790248 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 12
790153 TATTATGCTT
790163 AGAAG-AAAAGA
1 AGAAGAAAAAGA
790174 AGAAGAAAAAGA
1 AGAAGAAAAAGA
*
790186 A-AA-AAGAA-A
1 AGAAGAAAAAGA
*
790195 AG--GAAAGAGA
1 AGAAGAAAAAGA
790205 A-AAGAAAAAAGA
1 AGAAG-AAAAAGA
* *
790217 GAGAA-AATAAGC
1 -AGAAGAAAAAGA
790229 AGAAGAAAAAGAA
1 AGAAGAAAAAG-A
790242 AGAAGAA
1 AGAAGAA
790249 TAGAAAATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
9 5 0.09
10 6 0.11
11 12 0.21
12 23 0.41
13 8 0.14
14 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:790193 original size:24 final size:24
Alignment explanation
Indices: 790165--790216 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
790155 TTATGCTTAG
790165 AAGAAAAGAAGAAGA-AAAAGAAAA
1 AAGAAAAGAA-AAGAGAAAAGAAAA
*
790189 AAGAAAAGGAAAGAGAAAAGAAAA
1 AAGAAAAGAAAAGAGAAAAGAAAA
790213 AAGA
1 AAGA
790217 GAGAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAGAAAAGAAAAGAGAAAAGAAAA
Found at i:790235 original size:14 final size:12
Alignment explanation
Indices: 790182--790248 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
790172 GAAGAAGAAA
*
790182 AAGAAAAAAGAA
1 AAGAAAAAAGAG
* * *
790194 AAGGAAAGAGAA
1 AAGAAAAAAGAG
790206 AAGAAAAAAGAG
1 AAGAAAAAAGAG
790218 -AGAAAATAAGCAG
1 AAGAAAA-AAG-AG
*
790231 AAGAAAAAGAAAG
1 AAGAAAAA-AGAG
790244 AAGAA
1 AAGAA
790249 TAGAAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.13
12 22 0.49
13 10 0.22
14 7 0.16
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (12 bp):
AAGAAAAAAGAG
Found at i:814123 original size:22 final size:22
Alignment explanation
Indices: 814097--814138 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
814087 TATTTATAGC
814097 TATGATGATGA-TATTATGAATG
1 TATGATG-TGATTATTATGAATG
*
814119 TATGATGTTATTATTATGAA
1 TATGATGTGATTATTATGAA
814139 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (22 bp):
TATGATGTGATTATTATGAATG
Found at i:816035 original size:16 final size:17
Alignment explanation
Indices: 816007--816040 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
815997 CCATTATACC
816007 TATACCATAACCATTTA
1 TATACCATAACCATTTA
816024 TATACC-TAACCATTTA
1 TATACCATAACCATTTA
816040 T
1 T
816041 TTTAAGCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (17 bp):
TATACCATAACCATTTA
Found at i:828449 original size:22 final size:22
Alignment explanation
Indices: 828423--828464 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
828413 TATTTATAGC
828423 TATGATGATGA-TATTATGAATG
1 TATGATG-TGATTATTATGAATG
*
828445 TATGATGTTATTATTATGAA
1 TATGATGTGATTATTATGAA
828465 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (22 bp):
TATGATGTGATTATTATGAATG
Found at i:830359 original size:16 final size:17
Alignment explanation
Indices: 830330--830362 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
830320 TCCATTATAC
830330 CTATACCATAACCATTT
1 CTATACCATAACCATTT
830347 CTATACC-TAACCATTT
1 CTATACCATAACCATTT
830363 ATTTTAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:848332 original size:20 final size:19
Alignment explanation
Indices: 848289--848339 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
848279 CGAATAAGAG
* *
848289 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATTAAAAT
*
848308 AATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
848328 CATGTATTTTCA
1 CATGTATTTTCA
848340 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:849155 original size:6 final size:6
Alignment explanation
Indices: 849144--849187 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
849134 CAAAAGCAAC
* *
849144 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
849188 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:849169 original size:25 final size:24
Alignment explanation
Indices: 849141--849187 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
849131 TAACAAAAGC
849141 AACAAAAAGAAAAAGAAAGAAGAAA
1 AACAAAAAGAAAAAGAAA-AAGAAA
*
849166 AACAAAAAGAGAAAGAAAAAGA
1 AACAAAAAGAAAAAGAAAAAGA
849188 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAAAAAGAAAAAGAAA
Found at i:849172 original size:19 final size:18
Alignment explanation
Indices: 849144--849185 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
849134 CAAAAGCAAC
*
849144 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAA-AAG
*
849163 AAAAACAAAAAGAGAAAG
1 AAAAACAAAAAGAAAAAG
849181 AAAAA
1 AAAAA
849186 GACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:849227 original size:11 final size:11
Alignment explanation
Indices: 849227--849253 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
849217 AAAGGAAAAG
849227 AAGAAAATGAA
1 AAGAAAATGAA
849238 AAGAAAATGAA
1 AAGAAAATGAA
849249 AAGAA
1 AAGAA
849254 GCAATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (11 bp):
AAGAAAATGAA
Found at i:849232 original size:14 final size:14
Alignment explanation
Indices: 849213--849242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
849203 TGGAGTGCAA
849213 AAGAAAAGGAAAAG
1 AAGAAAAGGAAAAG
*
849227 AAGAAAATGAAAAG
1 AAGAAAAGGAAAAG
849241 AA
1 AA
849243 AATGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (14 bp):
AAGAAAAGGAAAAG
Found at i:852500 original size:19 final size:19
Alignment explanation
Indices: 852476--852525 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
852466 CGACCAAGAG
* **
852476 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATCAAAAT
852495 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
852514 CATGTATTTTCA
1 CATGTATTTTCA
852526 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:858944 original size:35 final size:34
Alignment explanation
Indices: 858899--859012 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 34
858889 TGGTAAGGGA
*
858899 ATGGTGATGATATAGGCGTGAAATGGTGATAGAGG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
* * *
858934 ATGGTGATGATATGGGCGTGCAATGGGGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
*
858969 ATGGTGATGTTATAGGCGTGAAAATGGTGATGAAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATG-AAG
859005 ATGGTGAT
1 ATGGTGAT
859013 AAACAAATAG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
35 49 0.72
36 19 0.28
ACGTcount: A:0.30, C:0.04, G:0.40, T:0.26
Consensus pattern (34 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGAAG
Found at i:861031 original size:16 final size:14
Alignment explanation
Indices: 861012--861045 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
861002 GTGCTGCAAC
861012 AAGATGAAAAAGAAA
1 AAGATG-AAAAGAAA
861027 GAAGATGAAAAGAAA
1 -AAGATGAAAAGAAA
861042 AAGA
1 AAGA
861046 AAAGAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (14 bp):
AAGATGAAAAGAAA
Found at i:861113 original size:24 final size:25
Alignment explanation
Indices: 861086--861132 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
861076 GTACAAAAAG
861086 AAAGAAAAGAAAAA-AGAAGAATCA
1 AAAGAAAAGAAAAAGAGAAGAATCA
* *
861110 AAAGCAAAGAAAAAGTGAAGAAT
1 AAAGAAAAGAAAAAGAGAAGAAT
861133 AGTTGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (25 bp):
AAAGAAAAGAAAAAGAGAAGAATCA
Found at i:868619 original size:13 final size:14
Alignment explanation
Indices: 868596--868624 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
868586 ATAAGATACT
868596 ATCTGTCCATCACC
1 ATCTGTCCATCACC
868610 ATCT-TCCATCACC
1 ATCTGTCCATCACC
868623 AT
1 AT
868625 TTCACGCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.31
Consensus pattern (14 bp):
ATCTGTCCATCACC
Found at i:869893 original size:17 final size:17
Alignment explanation
Indices: 869875--869932 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
869865 CTATTAAATG
*
869875 AACTAGTTTTATCAATG
1 AACTAGTTTTATCAATA
* *
869892 AACTAGTTTAATTAATA
1 AACTAGTTTTATCAATA
**
869909 AACTAACTTTATTCAATA
1 AACTAGTTTTA-TCAATA
869927 AACTAG
1 AACTAG
869933 ATGCATGAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 22 0.69
18 10 0.31
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (17 bp):
AACTAGTTTTATCAATA
Found at i:870234 original size:88 final size:89
Alignment explanation
Indices: 870071--870250 Score: 281
Period size: 88 Copynumber: 2.0 Consensus size: 89
870061 CATGCAGCTA
* *
870071 ATAAACTCACGAAAATTCATGCAATGAATTATATCATATGACACACTAGATGTTTTAAATGTAAT
1 ATAAACTCACGAAAATTAATACAATGAATTATATCA-ATGACACACTAGATGTTTTAAATGTAAT
870136 GCATGCTTAAATGAACATCACACTT
65 GCATGCTTAAATGAACATCACACTT
* *
870161 ATAAACTCATGAAAATTAATACAATGAATTATATC-ATGATACACTAGATGTTTTAAATGTAATG
1 ATAAACTCACGAAAATTAATACAATGAATTATATCAATGACACACTAGATGTTTTAAATGTAATG
* * *
870225 CATGTTTAAATGTACATTACACTT
66 CATGCTTAAATGAACATCACACTT
870249 AT
1 AT
870251 TAAATGCAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 51 0.61
90 32 0.39
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (89 bp):
ATAAACTCACGAAAATTAATACAATGAATTATATCAATGACACACTAGATGTTTTAAATGTAATG
CATGCTTAAATGAACATCACACTT
Found at i:874151 original size:17 final size:17
Alignment explanation
Indices: 874103--874158 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
874093 TAAGAGTTAA
*
874103 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAC
* *
874120 TTTGATGAATGAACTAC
1 TTTAATAAATGAACTAC
* *
874137 TTTAATTAATAAACTAAC
1 TTTAATAAATGAACT-AC
874155 TTTA
1 TTTA
874159 TTCAATTAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAC
Found at i:876961 original size:17 final size:17
Alignment explanation
Indices: 876910--876980 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
876900 ACTTAAGAGT
876910 TAATTTAATAAATGAAC
1 TAATTTAATAAATGAAC
* * *
876927 TAGTTTGATGAATGAAC
1 TAATTTAATAAATGAAC
* *
876944 TAATTTAATTAATAAAC
1 TAATTTAATAAATGAAC
* *
876961 TAACTTTATTCAATGAAC
1 TAA-TTTAATAAATGAAC
876979 TA
1 TA
876981 GATACATGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (17 bp):
TAATTTAATAAATGAAC
Found at i:880022 original size:81 final size:81
Alignment explanation
Indices: 879881--880204 Score: 396
Period size: 81 Copynumber: 4.0 Consensus size: 81
879871 TTATACTTCC
* * * * * * * * * ***
879881 TTTAGTCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATGATTGATACTTTTCTGTAA
1 TTTA-TCTTTTACTCAACGGTATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCA
879946 AATGCACAGCTAGGCCA
65 AATGCACAGCTAGGCCA
*
879963 TTTATCTTTTACTCAACGATATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
1 TTTATCTTTTACTCAACGGTATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
*
880028 ATGCACAGCTATGCCA
66 ATGCACAGCTAGGCCA
* **
880044 TTTATCTTTTACTCAATGGTATTGAACCGTTCATCTAACTGATATAATTGACACCTTTCTACCAA
1 TTTATCTTTTACTCAACGGTATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
* *
880109 ATGCACAACTAGTCCA
66 ATGCACAGCTAGGCCA
* * * * * **
880125 TTTATCTTTTACTCAACGGTATTGAACCATTTATCTAACTGTCATAATTGACTCATTTCTGTCAA
1 TTTATCTTTTACTCAACGGTATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
*
880190 ATGCACAGTTAGGCC
66 ATGCACAGCTAGGCC
880205 TCAAAGGAAC
Statistics
Matches: 209, Mismatches: 33, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
81 205 0.98
82 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGTATTGAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
ATGCACAGCTAGGCCA
Done.