Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold276
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: 761718
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
File 4 of 6
Found at i:485613 original size:32 final size:32
Alignment explanation
Indices: 485564--485650 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
485554 AATTTAATTG
*
485564 ATTTAAA-TTAAATTAATTTAAAATCAAAATA
1 ATTTAAATTTAAAATAATTTAAAATCAAAATA
* * *
485595 ATTTAAATTTAAAATAATTTAAATTTAAAATT
1 ATTTAAATTTAAAATAATTTAAAATCAAAATA
*
485627 ACTTAAATTTAAAA-ATATTTAAAA
1 ATTTAAATTTAAAATA-ATTTAAAA
485651 ATTTTAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 8 0.17
32 40 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
ATTTAAATTTAAAATAATTTAAAATCAAAATA
Found at i:485663 original size:32 final size:32
Alignment explanation
Indices: 485577--485669 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
485567 TAAATTAAAT
* * *
485577 TAATTTAAAATCAAAATAATTTAAATTT-AAAA
1 TAATTTAAATTTAAAAT-ACTTAAATTTAAAAA
485609 TAATTTAAATTTAAAATTACTTAAATTTAAAAA
1 TAATTTAAATTTAAAA-TACTTAAATTTAAAAA
*
485642 T-ATTTAAAAATTTTAAA-ACTTAAATTTA
1 TAATTT--AAATTTAAAATACTTAAATTTA
485670 GTAACTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 38 0.72
33 6 0.11
34 9 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (32 bp):
TAATTTAAATTTAAAATACTTAAATTTAAAAA
Found at i:486173 original size:16 final size:14
Alignment explanation
Indices: 486139--486166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
486129 AATTAATATT
486139 TAAAATATATTTAA
1 TAAAATATATTTAA
486153 TAAAATATATTTAA
1 TAAAATATATTTAA
486167 AATAAAAAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:486744 original size:16 final size:16
Alignment explanation
Indices: 486723--486753 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
486713 TCATTTAGAG
486723 TTTAAGTCACTTTGGT
1 TTTAAGTCACTTTGGT
*
486739 TTTAAGTCATTTTGG
1 TTTAAGTCACTTTGG
486754 ATTCAAATTA
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:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTAAGTCACTTTGGT
Found at i:486920 original size:16 final size:16
Alignment explanation
Indices: 486882--486973 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
486872 TCGAGTTAAA
486882 TCATTTTGAGTTCAAGT
1 TCATTTTGAGTTC-AGT
*
486899 T-GTTTTGAGTTCAGT
1 TCATTTTGAGTTCAGT
* *
486914 TCATTTTGGGTTTAGT
1 TCATTTTGAGTTCAGT
* * *
486930 TCATTTTAAATTTAAG-
1 TCATTTT-GAGTTCAGT
* *
486946 TCATTATGAGTTCAAT
1 TCATTTTGAGTTCAGT
486962 TCATTTTGAGTT
1 TCATTTTGAGTT
486974 TAAGTTAGTT
Statistics
Matches: 58, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
15 8 0.14
16 45 0.78
17 5 0.09
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (16 bp):
TCATTTTGAGTTCAGT
Found at i:487934 original size:49 final size:49
Alignment explanation
Indices: 487881--487990 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 49
487871 TTTGCCAAAA
* * * *
487881 TGTATCGATACAAGGTCTCAATGGTCAAAAATTCAAAATTTTCACAATT
1 TGTATCGATACAAAGTCCCAACGGTCAAAAATTCAAAATTTTCACAACT
* *
487930 TGTATCGATACAAAGTCCCAACGGTCAAAAATTTAAAATTTTTACAACT
1 TGTATCGATACAAAGTCCCAACGGTCAAAAATTCAAAATTTTCACAACT
487979 TGTATCGATACA
1 TGTATCGATACA
487991 TTCTGAGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (49 bp):
TGTATCGATACAAAGTCCCAACGGTCAAAAATTCAAAATTTTCACAACT
Found at i:490519 original size:79 final size:78
Alignment explanation
Indices: 490327--490543 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 78
490317 AAATTTTTCA
* * * * **
490327 TCGAGAGGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTTCACCATT-GGGATACTC
1 TCGAG-GGATACTCCAACCCTGGTTTCATTTCTAAAACACTGATTTTTCACCATTGGGGATACTC
490391 CAATCCCATTATTT
65 CAATCCCATTATTT
* *
490405 TCGAGGGATACTCCAACTCTGGTTTCATTTTTAAAACACTGATTTTTCACCATTGGGGATACTCC
1 TCGAGGGATACTCCAACCCTGGTTTCATTTCTAAAACACTGATTTTTCACCATTGGGGATACTCC
***
490470 AA-CTTTGTTATTT
66 AATC-CCATTATTT
* * *
490483 TTGAGGAGATACTCCAACCCTGGTTTCATTTCTAAAACATTGATTTTTCACCATCGGGGAT
1 TCGAGG-GATACTCCAACCCTGGTTTCATTTCTAAAACACTGATTTTTCACCATTGGGGAT
490544 GTTTTTTTCA
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
77 42 0.35
78 28 0.23
79 50 0.42
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (78 bp):
TCGAGGGATACTCCAACCCTGGTTTCATTTCTAAAACACTGATTTTTCACCATTGGGGATACTCC
AATCCCATTATTT
Found at i:492269 original size:18 final size:19
Alignment explanation
Indices: 492242--492286 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
492232 CTCGAAAAAA
492242 TTTAATATTTTTA-ATTAAT
1 TTTAA-ATTTTTATATTAAT
* *
492261 TTTAAATTTTTATTTTATT
1 TTTAAATTTTTATATTAAT
492280 TTTAAAT
1 TTTAAAT
492287 AAAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAAATTTTTATATTAAT
Found at i:492513 original size:444 final size:444
Alignment explanation
Indices: 491697--493676 Score: 3621
Period size: 444 Copynumber: 4.5 Consensus size: 444
491687 TTTAGTTTTT
* * * * * * * * *
491697 ATTTTAA-TTTTT-ATTTGATTTTAAAATAATATATTTTAAA-AATTGATCGACATAAAAATTTA
1 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
* * * * * * *
491759 TAATTCAATTTAATATTTATATTTGACAT-AGT-TAAAAAAATTATTATTTTATAATTAATTTTA
66 TAGTTTAATTTAATATTCATATTTGA-ATCACTCGAAAAAATTTAATATTTT-TAATTAATTTTA
* *
491822 AATTTTTA-TTTATTTTTAATTAATATATTTAAAAAAATGATGATAATAATATTAAAATAATATA
129 AATTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATA
491886 TATTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGT
194 TATTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGT
491951 CAAACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACT
259 CAAACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACT
492016 TTTAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGT
324 TTTAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGT
492081 AGTTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
389 AGTTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
492137 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
1 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
492202 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
66 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
492267 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
131 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
492332 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
196 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
492397 AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
261 AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
492462 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
326 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
492527 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
391 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
492581 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
1 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
492646 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
66 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
492711 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
131 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
492776 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
196 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
492841 AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
261 AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
492906 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
326 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
492971 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
391 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
493025 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
1 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
493090 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
66 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
493155 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
131 TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
493220 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
196 TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
*
493285 AACTCTTGGCCTGACAGATGACAAGTACTAACTATTTCGATTTTTATTTTTAAGTTTTGTACTTT
261 AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
493350 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
326 TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
493415 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
391 TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
493469 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
1 ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
493534 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
66 TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
* * ** * * * * *
493599 TTTTTATTTTATTTTTAAATAATATACTTTAAATGAGTTAATGATCATAATATTGAAATGATGTA
131 TTTTTATTTTATTTTTAAATAAAATA-TTTAAA-AAAATGATGATAATAATATTAAAATAATATA
*
493664 TATTTTAATGTTG
194 TATTTTAACGTTG
493677 CTTCATATTG
Statistics
Matches: 1503, Mismatches: 29, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
440 7 0.00
441 5 0.00
442 27 0.02
443 61 0.04
444 1362 0.91
445 6 0.00
446 35 0.02
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (444 bp):
ATTTTAATTTTTTAATTTTATTTTAAAATAATAAATTCTAAATGATTGGTTGATATAGAAATTAA
TAGTTTAATTTAATATTCATATTTGAATCACTCGAAAAAATTTAATATTTTTAATTAATTTTAAA
TTTTTATTTTATTTTTAAATAAAATATTTAAAAAAATGATGATAATAATATTAAAATAATATATA
TTTTAACGTTGATTTGTACGATAATATTTTATATAATAAAAAAAGTGAAGGCATGATACATGTCA
AACTCTTGGCCTGACAGATGACAAGTACTAACCATTTCGATTTTTATTTTTAAGTTTTGTACTTT
TAAAAATTTTCTTTTAAAGTTTTAATTTATTTTTAAATTATATATTTTAACCTTAGTTTATGTAG
TTGATTTAATATTTATATTTGATTTATTTTAAAAAAATTAAAATATTTTTTAAA
Found at i:492713 original size:18 final size:19
Alignment explanation
Indices: 492686--492730 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
492676 CTCGAAAAAA
492686 TTTAATATTTTTA-ATTAAT
1 TTTAA-ATTTTTATATTAAT
* *
492705 TTTAAATTTTTATTTTATT
1 TTTAAATTTTTATATTAAT
492724 TTTAAAT
1 TTTAAAT
492731 AAAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAAATTTTTATATTAAT
Found at i:493157 original size:18 final size:19
Alignment explanation
Indices: 493130--493174 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
493120 CTCGAAAAAA
493130 TTTAATATTTTTA-ATTAAT
1 TTTAA-ATTTTTATATTAAT
* *
493149 TTTAAATTTTTATTTTATT
1 TTTAAATTTTTATATTAAT
493168 TTTAAAT
1 TTTAAAT
493175 AAAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAAATTTTTATATTAAT
Found at i:493601 original size:18 final size:19
Alignment explanation
Indices: 493574--493618 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
493564 CTCGAAAAAA
493574 TTTAATATTTTTA-ATTAAT
1 TTTAA-ATTTTTATATTAAT
* *
493593 TTTAAATTTTTATTTTATT
1 TTTAAATTTTTATATTAAT
493612 TTTAAAT
1 TTTAAAT
493619 AATATACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAAATTTTTATATTAAT
Found at i:493758 original size:14 final size:14
Alignment explanation
Indices: 493739--493770 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
493729 AAAATAGTCT
493739 TTTTTTTAATTTAA
1 TTTTTTTAATTTAA
493753 TTTTTTTAATTTAA
1 TTTTTTTAATTTAA
493767 TTTT
1 TTTT
493771 AAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTTTAATTTAA
Found at i:494017 original size:19 final size:20
Alignment explanation
Indices: 493979--494027 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
493969 TAAAAAAATT
493979 ATTTTAAATTTTTATATTTAA
1 ATTTTAAA-TTTTATATTTAA
494000 ATTTTAAATTTT-TATTTAA
1 ATTTTAAATTTTATATTTAA
*
494019 TTTTTAAAT
1 ATTTTAAAT
494028 AATGTAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.56
20 4 0.15
21 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTAAATTTTATATTTAA
Found at i:496239 original size:3 final size:3
Alignment explanation
Indices: 496231--496268 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
496221 CTTAAACAGG
496231 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
496269 AGAATCAATC
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:498061 original size:12 final size:13
Alignment explanation
Indices: 498018--498058 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
498008 AAAAACTCAC
*
498018 TAATCAATTTCTTT
1 TAATTAATTT-TTT
498032 TAACTTAATTTTTT
1 TAA-TTAATTTTTT
498046 TAATTAATTTTTT
1 TAATTAATTTTTT
498059 AATCTGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
14 9 0.36
15 6 0.24
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATTAATTTTTT
Found at i:503613 original size:20 final size:20
Alignment explanation
Indices: 503588--503663 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
503578 AAAAACCCAT
*
503588 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATTAGA
*
503608 AATGTATCGATACAATTATA
1 AATGTATCGATACAATTAGA
* *
503628 AGCATGTATCGATACATTTAGT
1 A--ATGTATCGATACAATTAGA
*
503650 AATGTATAGATACA
1 AATGTATCGATACA
503664 TTTCCTTGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 31 0.65
22 17 0.35
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATTAGA
Found at i:503708 original size:13 final size:13
Alignment explanation
Indices: 503690--503715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
503680 CAAGGTGATT
503690 TTGTATCGATACA
1 TTGTATCGATACA
503703 TTGTATCGATACA
1 TTGTATCGATACA
503716 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:503728 original size:19 final size:19
Alignment explanation
Indices: 503704--503753 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
503694 ATCGATACAT
503704 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
503723 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
* *
503742 TATATCAATACA
1 TGTATCGATACA
503754 TTTTCTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:505969 original size:17 final size:17
Alignment explanation
Indices: 505947--505981 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
505937 AAGTGAATTT
* *
505947 AGAGATGGAGAAGAAAA
1 AGAGATGAACAAGAAAA
505964 AGAGATGAACAAGAAAA
1 AGAGATGAACAAGAAAA
505981 A
1 A
505982 AAAGTGATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.29, T:0.06
Consensus pattern (17 bp):
AGAGATGAACAAGAAAA
Found at i:507421 original size:48 final size:48
Alignment explanation
Indices: 507335--507451 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 48
507325 CTAGACAATC
* * * * *
507335 CATAAAATTTAAACTATTCCTAAGGAGAAAATGCTTCTTTCCATAAGG
1 CATAAACTTCAAACTATTCTTAACGAGAAAATGCTTCTTTCCACAAGG
* * * *
507383 CATGAACTTCAAACTATTCTTAACGAGAAAATGTTTCTTTCTACGAGG
1 CATAAACTTCAAACTATTCTTAACGAGAAAATGCTTCTTTCCACAAGG
*
507431 CATAAACTTTAAACTATTCTT
1 CATAAACTTCAAACTATTCTT
507452 CCTCTCCACA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (48 bp):
CATAAACTTCAAACTATTCTTAACGAGAAAATGCTTCTTTCCACAAGG
Found at i:507790 original size:67 final size:67
Alignment explanation
Indices: 507703--507853 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 67
507693 ATTATACCAA
* * * * * **
507703 CTAAATATAGTTTAAAATCTTTAATCTTGT-TCTAATTTAACTAGGATTAATAT-CTCAATGATG
1 CTAAATATAGCTTAAAATCTTTAATCTTATGCCT-ACTTAACTAGGATTAACATCCT-AACAATG
507766 CTAG
64 CTAG
* *
507770 CTAAATATGGCTTAAAATCTTTAATCTTATGCCTACTTAACTAGGATTAACATCCTAACAATGTT
1 CTAAATATAGCTTAAAATCTTTAATCTTATGCCTACTTAACTAGGATTAACATCCTAACAATGCT
507835 AG
66 AG
507837 CTAAATA-AGCTTAAAAT
1 CTAAATATAGCTTAAAAT
507854 TTCGTGCAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
66 9 0.12
67 59 0.82
68 4 0.06
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (67 bp):
CTAAATATAGCTTAAAATCTTTAATCTTATGCCTACTTAACTAGGATTAACATCCTAACAATGCT
AG
Found at i:508178 original size:67 final size:67
Alignment explanation
Indices: 508017--508193 Score: 171
Period size: 67 Copynumber: 2.6 Consensus size: 67
508007 AATAACGTCC
* * * **
508017 TAATGGTGCTAGT-TAAGTAAGGCTTGAAACCTGTCATCTTATGCCAACTTTATAGGGCTTAGCA
1 TAATGGTGCTA-TCTAAGTAAGGCTTGAAACCTTTCACCTTATGCCAACTTAATAGAACTTAGCA
*
508081 TCC
65 TCA
* * * * * *
508084 TAATGATGCTAGCCAAGTGAA-GATTGAAACCTTTCACCTTATGCTAACTTAATTGAACTTAGCA
1 TAATGGTGCTATCTAAGT-AAGGCTTGAAACCTTTCACCTTATGCCAACTTAATAGAACTTAGCA
508148 TCA
65 TCA
* * *
508151 TAATGGTGCCATCTAAGTTAGGCTTGAAA-CTTCCCACCTTATG
1 TAATGGTGCTATCTAAGTAAGGCTTGAAACCTT-TCACCTTATG
508194 TCAATGATTC
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
66 4 0.05
67 81 0.93
68 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (67 bp):
TAATGGTGCTATCTAAGTAAGGCTTGAAACCTTTCACCTTATGCCAACTTAATAGAACTTAGCAT
CA
Found at i:509556 original size:60 final size:59
Alignment explanation
Indices: 509450--509561 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
509440 TCATGTTTTT
*
509450 CTCTAGATTCCTCGTTTTAAGGTTTTCACCTTAAAGCTCTATTTTTTCTTTTTTTCTTTA
1 CTCTAGATTCCTCGTTTTAAGGTTTTCACCTTAAAGCTCTACTTTTT-TTTTTTTCTTTA
* ** *
509510 CTCTAGATTGCTCGTTTTTTGGTTTTCAACC-TAGAGCT-TCACTTTTTTTTTT
1 CTCTAGATTCCTCGTTTTAAGGTTTTC-ACCTTAAAGCTCT-ACTTTTTTTTTT
509562 CTTTTTGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 6 0.13
60 36 0.80
61 3 0.07
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.54
Consensus pattern (59 bp):
CTCTAGATTCCTCGTTTTAAGGTTTTCACCTTAAAGCTCTACTTTTTTTTTTTTCTTTA
Found at i:510565 original size:20 final size:20
Alignment explanation
Indices: 510540--510588 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
510530 GGCATAATGT
*
510540 ATCGATACAAT-TCTTCATGA
1 ATCGATACAATGTC-CCATGA
*
510560 ATCGATACAATGTCCCATGT
1 ATCGATACAATGTCCCATGA
510580 ATCGATACA
1 ATCGATACA
510589 TTTCACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (20 bp):
ATCGATACAATGTCCCATGA
Found at i:510662 original size:19 final size:19
Alignment explanation
Indices: 510618--510672 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
510608 TGCTAATTTA
* *
510618 ATGTATCGATACAATTGTGT
1 ATGTATCGATACAA-TGAGC
510638 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
*
510657 ATGTATTGATACAATG
1 ATGTATCGATACAATG
510673 TATCGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACAATGAGC
Found at i:514587 original size:16 final size:16
Alignment explanation
Indices: 514566--514596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
514556 CAATGTTTCC
*
514566 TCTATTAAAACTTTTT
1 TCTATTAAAAATTTTT
514582 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
514597 GAAAACCTTT
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:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Found at i:520282 original size:368 final size:368
Alignment explanation
Indices: 519605--520338 Score: 1459
Period size: 368 Copynumber: 2.0 Consensus size: 368
519595 GAGGGTTGAC
519605 CTCTTCCATGCGGACCTACCTTTTTTAAGACCTATTTGTTTGCATCAAGATGACCGTTCACCTAC
1 CTCTTCCATGCGGACCTACCTTTTTTAAGACCTATTTGTTTGCATCAAGATGACCGTTCACCTAC
519670 ATGGTCGAAAGATTGCAATTTCGAAGTTCATAAAAAATAAACCTTAAATAAAAAAGACAAACATC
66 ATGGTCGAAAGATTGCAATTTCGAAGTTCATAAAAAATAAACCTTAAATAAAAAAGACAAACATC
519735 GAAGAAAAAAATTAGAGTTTAAATACTTTTTTTGTAGTTTTGAAATTTATTTTTAAATATAATAT
131 GAAGAAAAAAATTAGAGTTTAAATACTTTTTTTGTAGTTTTGAAATTTATTTTTAAATATAATAT
519800 TATGGGAAAATGTCTTATTTTTTGAAATTTTTGAAATCTTTTTTTGGGAATTTTATAAGTTGATC
196 TATGGGAAAATGTCTTATTTTTTGAAATTTTTGAAATCTTTTTTTGGGAATTTTATAAGTTGATC
519865 ATTGTATATTTCACTAATACTCATTCGGTATTAATGTTGATATTTACTCTAAAAAATCCAAAAAT
261 ATTGTATATTTCACTAATACTCATTCGGTATTAATGTTGATATTTACTCTAAAAAATCCAAAAAT
519930 GTTCAAAAAGGTACATATCAGTATTTATACCACAAGATATTTA
326 GTTCAAAAAGGTACATATCAGTATTTATACCACAAGATATTTA
519973 CTCTTCCATGCGGACCTACCTTTTTTAAGACCTATTTGTTTGCATCAAGATGACCGTTCACCTAC
1 CTCTTCCATGCGGACCTACCTTTTTTAAGACCTATTTGTTTGCATCAAGATGACCGTTCACCTAC
520038 ATGGTCGAAAGATTGCAATTTCGAAGTTCATAAAAAATAAACCTTAAATAAAAAAGACAAACATC
66 ATGGTCGAAAGATTGCAATTTCGAAGTTCATAAAAAATAAACCTTAAATAAAAAAGACAAACATC
520103 GAAGAAAAAAATTAGAGTTTAAATACTTTTTTTGTAGTTTTGAAATTTATTTTTAAATATAATAT
131 GAAGAAAAAAATTAGAGTTTAAATACTTTTTTTGTAGTTTTGAAATTTATTTTTAAATATAATAT
520168 TATGGGAAAATGTCTTATTTTTTGAAATTTTTGAAATCTTTTTTTGGGAATTTTATAAGTTGATC
196 TATGGGAAAATGTCTTATTTTTTGAAATTTTTGAAATCTTTTTTTGGGAATTTTATAAGTTGATC
520233 ATTGTATATTTCACTAATACTCATTCGGTATTAATGTTGATATTTACTCTAAAAAATCCAAAAAT
261 ATTGTATATTTCACTAATACTCATTCGGTATTAATGTTGATATTTACTCTAAAAAATCCAAAAAT
*
520298 GTTCAAAAAGGTACATATCAGTATTTATACTACAAGATATT
326 GTTCAAAAAGGTACATATCAGTATTTATACCACAAGATATT
520339 AAATTTTTGA
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
368 365 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (368 bp):
CTCTTCCATGCGGACCTACCTTTTTTAAGACCTATTTGTTTGCATCAAGATGACCGTTCACCTAC
ATGGTCGAAAGATTGCAATTTCGAAGTTCATAAAAAATAAACCTTAAATAAAAAAGACAAACATC
GAAGAAAAAAATTAGAGTTTAAATACTTTTTTTGTAGTTTTGAAATTTATTTTTAAATATAATAT
TATGGGAAAATGTCTTATTTTTTGAAATTTTTGAAATCTTTTTTTGGGAATTTTATAAGTTGATC
ATTGTATATTTCACTAATACTCATTCGGTATTAATGTTGATATTTACTCTAAAAAATCCAAAAAT
GTTCAAAAAGGTACATATCAGTATTTATACCACAAGATATTTA
Found at i:521530 original size:11 final size:11
Alignment explanation
Indices: 521516--521545 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
521506 CACAAGGCTT
521516 AAAAGAAATAA
1 AAAAGAAATAA
*
521527 AAAAAAAATAA
1 AAAAGAAATAA
521538 AAAAGAAA
1 AAAAGAAA
521546 AATTATAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAGAAATAA
Found at i:524460 original size:21 final size:19
Alignment explanation
Indices: 524436--524484 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
524426 CATATTTTTG
524436 CCTCTCTCTTTTTTCTCCTTC
1 CCTCTCTCTTTTTTCT--TTC
524457 CCTCT-T-TTTTTTCTTTC
1 CCTCTCTCTTTTTTCTTTC
*
524474 CCTTTCTCTTT
1 CCTCTCTCTTT
524485 ACTTTCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 1 0.04
19 11 0.44
20 1 0.04
21 5 0.20
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (19 bp):
CCTCTCTCTTTTTTCTTTC
Found at i:524463 original size:17 final size:17
Alignment explanation
Indices: 524441--524476 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
524431 TTTTGCCTCT
524441 CTCTTTTTTCTCCTTCC
1 CTCTTTTTTCTCCTTCC
* *
524458 CTCTTTTTTTTCTTTCC
1 CTCTTTTTTCTCCTTCC
524475 CT
1 CT
524477 TTCTCTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTCTTTTTTCTCCTTCC
Found at i:524490 original size:21 final size:20
Alignment explanation
Indices: 524475--524538 Score: 103
Period size: 21 Copynumber: 3.2 Consensus size: 20
524465 TTTTCTTTCC
*
524475 CTTTCTCTTTACTTTCCCTT
1 CTTTCTCTTTACTTTCCTTT
524495 CTTTCTCTTTACTTTCCCTTT
1 CTTTCTCTTTACTTT-CCTTT
524516 CTTTCTCTTTACTTT-CTTT
1 CTTTCTCTTTACTTTCCTTT
524535 CTTT
1 CTTT
524539 TTCTCTTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 8 0.19
20 15 0.36
21 19 0.45
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTCTCTTTACTTTCCTTT
Found at i:524500 original size:20 final size:21
Alignment explanation
Indices: 524475--524538 Score: 107
Period size: 20 Copynumber: 3.2 Consensus size: 21
524465 TTTTCTTTCC
524475 CTTTCTCTTTACTTTCCC-TT
1 CTTTCTCTTTACTTTCCCTTT
524495 CTTTCTCTTTACTTTCCCTTT
1 CTTTCTCTTTACTTTCCCTTT
524516 CTTTCTCTTTACTTT--CTTT
1 CTTTCTCTTTACTTTCCCTTT
524535 CTTT
1 CTTT
524539 TTCTCTTCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.19
20 18 0.42
21 17 0.40
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTTCTCTTTACTTTCCCTTT
Found at i:524541 original size:21 final size:21
Alignment explanation
Indices: 524466--524545 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
524456 CCCTCTTTTT
**
524466 TTTCTTTCCCTTTCTCTTTAC
1 TTTCTTTCTTTTTCTCTTTAC
*
524487 TTTC--CCTTCTTTCTCTTTAC
1 TTTCTTTCTT-TTTCTCTTTAC
524507 TTTCCCTTTC--TTTCTCTTTAC
1 TTT--CTTTCTTTTTCTCTTTAC
524528 TTTCTTTCTTTTTCTCTT
1 TTTCTTTCTTTTTCTCTT
524546 CTAGTCTCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
19 6 0.12
20 14 0.29
21 26 0.54
22 1 0.02
24 1 0.02
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTCTTTCTTTTTCTCTTTAC
Found at i:524738 original size:21 final size:20
Alignment explanation
Indices: 524714--524772 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
524704 AGCTTTAAAA
524714 ATTAATTTTAAATTAAATTTT
1 ATTAA-TTTAAATTAAATTTT
*
524735 ATTAAGTTATAATT--ATTTT
1 ATTAATTTA-AATTAAATTTT
524754 -TTAAATTTAAATTATAATT
1 ATT-AATTTAAATTA-AATT
524773 ATGAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
18 6 0.19
19 10 0.32
20 3 0.10
21 12 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTAATTTAAATTAAATTTT
Found at i:525447 original size:35 final size:33
Alignment explanation
Indices: 525380--525451 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
525370 AATATATTTT
*
525380 AATATTTTAAATAATTATATTTAAAGTAAAAATCA
1 AATATTTTAAATAATTATA-TTAAAATAAAAAT-A
*
525415 AATATTTATAATTAATTATA-TAAAATATAAAATA
1 AATATTT-TAAATAATTATATTAAAATA-AAAATA
525449 AAT
1 AAT
525452 TGAGATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 10 0.30
35 12 0.36
36 11 0.33
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (33 bp):
AATATTTTAAATAATTATATTAAAATAAAAATA
Found at i:525578 original size:15 final size:16
Alignment explanation
Indices: 525558--525587 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
525548 TTTTAAATGT
525558 AAAAAAATAA-AAAAC
1 AAAAAAATAATAAAAC
525573 AAAAAAATAATAAAA
1 AAAAAAATAATAAAA
525588 ACTAATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAATAATAAAAC
Found at i:525700 original size:17 final size:17
Alignment explanation
Indices: 525659--525701 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
525649 CTCTTTCTTT
*
525659 ATTTCTCTTTTTCTCTCC
1 ATTTC-CTTTGTCTCTCC
*
525677 ATCTCCTTTGTCTCTCC
1 ATTTCCTTTGTCTCTCC
*
525694 CTTTCCTT
1 ATTTCCTT
525702 ACCTCATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTCCTTTGTCTCTCC
Found at i:527078 original size:26 final size:26
Alignment explanation
Indices: 527029--527083 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
527019 TATCTTTAAA
* * *
527029 ATTTTTAAAATAATAGTAATTAATTT
1 ATTTTTAAAATAATAATAAATAATAT
527055 ATTTTT-AAATAATAATAACATAATAT
1 ATTTTTAAAATAATAATAA-ATAATAT
527081 ATT
1 ATT
527084 AATATCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTTTTAAAATAATAATAAATAATAT
Found at i:527931 original size:9 final size:10
Alignment explanation
Indices: 527917--527960 Score: 65
Period size: 9 Copynumber: 4.5 Consensus size: 10
527907 AAAAATTAGT
527917 TAAAAATA-A
1 TAAAAATATA
527926 TAAAAATA-A
1 TAAAAATATA
527935 TAAAAATATA
1 TAAAAATATA
527945 TAAAATATATA
1 TAAAA-ATATA
527956 TAAAA
1 TAAAA
527961 TAAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 17 0.52
10 6 0.18
11 10 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAATATA
Found at i:527938 original size:18 final size:21
Alignment explanation
Indices: 527901--527960 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
527891 CTGCGAACAC
*
527901 AATATAAAAAAT-TAGT-TAAA
1 AATATATAAAATATA-TATAAA
527921 AATA-ATAAAA-ATA-ATAAA
1 AATATATAAAATATATATAAA
527939 AATATATAAAATATATATAAA
1 AATATATAAAATATATATAAA
527960 A
1 A
527961 TAAATTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 8 0.24
19 13 0.38
20 7 0.21
21 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AATATATAAAATATATATAAA
Found at i:527990 original size:14 final size:16
Alignment explanation
Indices: 527952--527992 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
527942 ATATAAAATA
527952 TATATAAAATAAATTAT
1 TATAT-AAATAAATTAT
527969 TAATATAAA-AAATT-T
1 T-ATATAAATAAATTAT
527984 TATATAAAT
1 TATATAAAT
527993 TTATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.32
15 2 0.09
16 5 0.23
17 4 0.18
18 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATAAATTAT
Found at i:527999 original size:27 final size:25
Alignment explanation
Indices: 527960--528014 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 25
527950 TATATATAAA
527960 ATAAATTATTAATATAAAAAATTTTAT
1 ATAAATTATT-A-ATAAAAAATTTTAT
*
527987 ATAAATT-TATAATAATAAATTTTAT
1 ATAAATTAT-TAATAAAAAATTTTAT
528012 ATA
1 ATA
528015 TAAACAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 16 0.62
26 2 0.08
27 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAATTATTAATAAAAAATTTTAT
Found at i:528138 original size:10 final size:11
Alignment explanation
Indices: 528113--528154 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
528103 CTACTAACAC
528113 AATATAAAAAATT
1 AATAT-AAAAA-T
528126 AAT-TAAAAAT
1 AATATAAAAAT
*
528136 AATATTAAAAT
1 AATATAAAAAT
528147 AATATAAA
1 AATATAAA
528155 TATATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 18 0.69
12 1 0.04
13 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:528214 original size:27 final size:26
Alignment explanation
Indices: 528184--528246 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
528174 ATAAATTATT
*
528184 AATATAAAAAATTTTAG-ATAAGTTTA
1 AATATAAAAAATTTTAGAATAA-CTTA
*
528210 AA-ATAATAAATTTTTAGAATAACTTA
1 AATATAA-AAAATTTTAGAATAACTTA
528236 AATATAAAAAA
1 AATATAAAAAA
528247 AAAACTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 4 0.13
26 19 0.61
27 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
AATATAAAAAATTTTAGAATAACTTA
Found at i:529571 original size:21 final size:21
Alignment explanation
Indices: 529535--529582 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
529525 ATTTTAAAAT
*
529535 AATAAAAAAGACAAAAATTCTA
1 AATAAAAAACACAAAAATTC-A
529557 AATAAAAAACA-AAAAATTCA
1 AATAAAAAACACAAAAATTCA
529577 AA-AAAA
1 AATAAAA
529583 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 8 0.32
22 10 0.40
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (21 bp):
AATAAAAAACACAAAAATTCA
Found at i:531011 original size:12 final size:13
Alignment explanation
Indices: 530993--531032 Score: 66
Period size: 12 Copynumber: 3.2 Consensus size: 13
530983 TCATTTAAAT
530993 TAATTTTTTATAA
1 TAATTTTTTATAA
531006 -AATTTTTTA-AA
1 TAATTTTTTATAA
531017 TAATTTTTTATAA
1 TAATTTTTTATAA
531030 TAA
1 TAA
531033 ATATTAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 18 0.72
13 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATTTTTTATAA
Found at i:531025 original size:24 final size:25
Alignment explanation
Indices: 530977--531029 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
530967 TTTTTTTGAA
530977 ATAAAATCATTTAAATTAATTTTTT
1 ATAAAATCATTTAAATTAATTTTTT
**
531002 ATAAAATTTTTTAAA-TAATTTTTT
1 ATAAAATCATTTAAATTAATTTTTT
531026 ATAA
1 ATAA
531030 TAAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAAAATCATTTAAATTAATTTTTT
Found at i:531039 original size:24 final size:25
Alignment explanation
Indices: 530977--531039 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
530967 TTTTTTTGAA
530977 ATAAAATCAT-TTAAATTAATTTTTT
1 ATAAAAT-ATATTAAATTAATTTTTT
* *
531002 ATAAAATTTTTTAAA-TAATTTTTT
1 ATAAAATATATTAAATTAATTTTTT
531026 ATAATAA-ATATTAA
1 ATAA-AATATATTAA
531040 GATTCAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAAAATATATTAAATTAATTTTTT
Found at i:533996 original size:18 final size:17
Alignment explanation
Indices: 533964--534026 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 17
533954 ATCTAAGTTT
*
533964 TAAAAATTTTAAAAATA
1 TAAATATTTTAAAAATA
*
533981 TAAATTATTTTTAAAATA
1 TAAA-TATTTTAAAAATA
533999 TAAATA-TTT-AAAAT-
1 TAAATATTTTAAAAATA
534013 T--ATATTTTAAAAAT
1 TAAATATTTTAAAAAT
534027 CCATATCTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 3 0.07
13 3 0.07
14 6 0.15
15 5 0.12
16 3 0.07
17 6 0.15
18 15 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATTTTAAAAATA
Found at i:534125 original size:39 final size:40
Alignment explanation
Indices: 534044--534121 Score: 133
Period size: 38 Copynumber: 2.0 Consensus size: 40
534034 TATTTTTAAA
534044 AAATATTTTTAAAATATAAAAAATTTTAAATTATATTTTT
1 AAATATTTTTAAAATATAAAAAATTTTAAATTATATTTTT
*
534084 AAAT-TTTTTAAAATAT-TAAAATTTTAAATTATATTTTT
1 AAATATTTTTAAAATATAAAAAATTTTAAATTATATTTTT
534122 TAAAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 21 0.57
39 12 0.32
40 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (40 bp):
AAATATTTTTAAAATATAAAAAATTTTAAATTATATTTTT
Found at i:534158 original size:100 final size:98
Alignment explanation
Indices: 533988--534168 Score: 215
Period size: 100 Copynumber: 1.8 Consensus size: 98
533978 ATATAAATTA
* * **
533988 TTTTTAAAATATAAATATTTAAAATTATATTTTAAAAATCCATATCTATTTTTAAAAAATATTTT
1 TTTTTAAAATATAAATATTTAAAATTATATTTTAAAAATCAATATATATTTTT-AAAAATATTAA
*
534053 TAAAATATAAAAAATTTTAAATTATATTTTTAAAT
65 AAAAAT-TAAAAAATTTTAAATTATATTTTTAAAT
* *
534088 TTTTTAAAATATTAAA-ATTTTAAATTATATTTTTTAAAAATTAATATATGATTTTT-AAAA-AT
1 TTTTTAAAATA-TAAATATTTAAAATTATA--TTTTAAAAATCAATATAT-ATTTTTAAAAATAT
*
534150 TAAAAAAATTAAAACATTT
62 TAAAAAAATTAAAAAATTT
534169 AATGAAAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
99 9 0.13
100 31 0.45
101 8 0.12
102 15 0.22
103 6 0.09
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (98 bp):
TTTTTAAAATATAAATATTTAAAATTATATTTTAAAAATCAATATATATTTTTAAAAATATTAAA
AAAATTAAAAAATTTTAAATTATATTTTTAAAT
Found at i:534379 original size:9 final size:9
Alignment explanation
Indices: 534365--534394 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
534355 ATGTCTTTTT
*
534365 TCCTTTCTC
1 TCCTTTCCC
534374 TCCTTTCCC
1 TCCTTTCCC
534383 TCCTTTCCC
1 TCCTTTCCC
534392 TCC
1 TCC
534395 CAATCTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (9 bp):
TCCTTTCCC
Found at i:534433 original size:36 final size:36
Alignment explanation
Indices: 534392--534465 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
534382 CTCCTTTCCC
534392 TCCCAATCTCCTCCTTCGACTTCGTTCAGGCCATTT
1 TCCCAATCTCCTCCTTCGACTTCGTTCAGGCCATTT
534428 TCCCAATCTCCTCCTTCGACTTCGTTCAGGCCATTT
1 TCCCAATCTCCTCCTTCGACTTCGTTCAGGCCATTT
534464 TC
1 TC
534466 ACTTAACCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.39, G:0.11, T:0.36
Consensus pattern (36 bp):
TCCCAATCTCCTCCTTCGACTTCGTTCAGGCCATTT
Found at i:534778 original size:20 final size:20
Alignment explanation
Indices: 534753--534790 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
534743 AGGGAAAAAA
534753 TATTTTTATTTTAAAAATAT
1 TATTTTTATTTTAAAAATAT
*
534773 TATTTTTATTTTTAAAAT
1 TATTTTTATTTTAAAAAT
534791 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTATTTTAAAAATAT
Found at i:537051 original size:28 final size:27
Alignment explanation
Indices: 537010--537083 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
537000 TAGAAATATT
* * *
537010 AAATTAAATATATATAATAAATAATTAA
1 AAATTATATTTATAT-ATAAATAATAAA
537038 AAATTATATTTATAT-TAAATAATAAA
1 AAATTATATTTATATATAAATAATAAA
*
537064 ATATATTATACTTATATATA
1 A-A-ATTATATTTATATATA
537084 TTAAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 11 0.28
27 1 0.03
28 25 0.64
29 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATTATATTTATATATAAATAATAAA
Found at i:537513 original size:36 final size:36
Alignment explanation
Indices: 537390--537623 Score: 158
Period size: 36 Copynumber: 6.8 Consensus size: 36
537380 ATTTAAAATT
*
537390 ATTAAAATTATATTTATA-GAAATAATAAAATATAA
1 ATTAAAATTATATTTATATTAAATAATAAAATATAA
* * **
537425 A-T-AAATTATA-TTATTGTTAAATAATAATAAAAATTT
1 ATTAAAATTATATTTA-TATTAAATAAT-A-AAATATAA
*
537461 ATTAAAATTATGTTTATATTAAATAATAAAATATAA
1 ATTAAAATTATATTTATATTAAATAATAAAATATAA
** * *
537497 ATTAAAAAGATATTTATGTTAAATAATTATGAAT-T--
1 ATTAAAATTATATTTATATTAAATAA-TA-AAATATAA
* *
537532 ATTAAAATTATATTTAAATT-AA-AAT----TAT-C
1 ATTAAAATTATATTTATATTAAATAATAAAATATAA
* * * *
537561 TTTTAATTTATATTTATATTAAATAATAAAATATAT
1 ATTAAAATTATATTTATATTAAATAATAAAATATAA
*
537597 ATTAAAATCATA-TT-TATTAAATAATAA
1 ATTAAAATTATATTTATATTAAATAATAA
537624 TTAAAATTAT
Statistics
Matches: 153, Mismatches: 28, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 16 0.10
30 2 0.01
31 3 0.02
32 4 0.03
33 11 0.07
34 23 0.15
35 23 0.15
36 41 0.27
37 5 0.03
38 20 0.13
39 3 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (36 bp):
ATTAAAATTATATTTATATTAAATAATAAAATATAA
Found at i:537553 original size:71 final size:70
Alignment explanation
Indices: 537374--537554 Score: 217
Period size: 71 Copynumber: 2.6 Consensus size: 70
537364 TTATATATAA
* * **
537374 TAAATAAT-TTAAAATTATTAAAATTATATTTATA-GAAATAATAAAATATAAATAAATTATATT
1 TAAATAATATAAAAATTATTAAAATTATATTTATATTAAATAATAAAATATAAATAAAAGATATT
537437 ATTGT
66 ATTGT
*
537442 TAAATAATAATAAAAATTTATTAAAATTATGTTTATATTAAATAATAAAATATAAATTAAAAAGA
1 TAAATAAT-ATAAAAA-TTATTAAAATTATATTTATATTAAATAATAAAATATAAA-T-AAAAGA
537507 TATT-TATGT
62 TATTAT-TGT
** *
537516 TAAATAAT-TATGAATTATTAAAATTATATTTAAATTAAA
1 TAAATAATATAAAAATTATTAAAATTATATTTATATTAAA
537555 ATTATCTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
68 8 0.08
70 5 0.05
71 42 0.43
72 21 0.22
73 2 0.02
74 19 0.20
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (70 bp):
TAAATAATATAAAAATTATTAAAATTATATTTATATTAAATAATAAAATATAAATAAAAGATATT
ATTGT
Found at i:537554 original size:17 final size:17
Alignment explanation
Indices: 537532--537604 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
537522 ATTATGAATT
537532 ATTAAAATTATATTTAA
1 ATTAAAATTATATTTAA
* *
537549 ATTAAAATTATCTTTTA
1 ATTAAAATTATATTTAA
* *
537566 ATTTATATT-TATATTAA
1 ATTAAAATTATAT-TTAA
*
537583 ATAATAAAATATATATTAAA
1 AT--TAAAAT-TATATTTAA
537603 AT
1 AT
537605 CATATTTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
16 2 0.05
17 27 0.64
19 4 0.10
20 6 0.14
21 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAAAATTATATTTAA
Found at i:537604 original size:12 final size:12
Alignment explanation
Indices: 537587--537652 Score: 52
Period size: 12 Copynumber: 5.6 Consensus size: 12
537577 TATTAAATAA
537587 TAAAATATATAT
1 TAAAATATATAT
537599 TAAAATCATAT-T
1 TAAAAT-ATATAT
537611 TATTAAATA-ATAAT
1 TA--AAATATAT-AT
537625 TAAAAT-TATAT
1 TAAAATATATAT
*
537636 TAAAA-AT-TAA
1 TAAAATATATAT
537646 TAAAATA
1 TAAAATA
537653 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
10 7 0.16
11 9 0.20
12 17 0.38
13 5 0.11
14 7 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAATATATAT
Found at i:537636 original size:22 final size:21
Alignment explanation
Indices: 537611--537651 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
537601 AAATCATATT
537611 TATTAAATAA-TAATTAAAATTA
1 TATTAAA-AATTAA-TAAAATTA
537633 TATTAAAAATTAATAAAAT
1 TATTAAAAATTAATAAAAT
537652 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTAAAAATTAATAAAATTA
Found at i:537655 original size:100 final size:99
Alignment explanation
Indices: 537468--537655 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 99
537458 TTTATTAAAA
* * * *
537468 TTATGTTTATATTAAATAATAAAATATAAATTAAAAAGATATTTATGTTAAATAATTATGAATTA
1 TTATATTTATATTAAATAATAAAATATAAATTAAAAACATATTTATGTAAAATAATTATAAATTA
*
537533 TTAAAATTATATTTAAATTAAAATTATCTTTTAAT
66 TTAAAATTATA-TTAAAATAAAATTATCTTTTAAT
* *
537568 TTATATTTATATTAAATAATAAAATATATATTAAAATCATATTTAT-TAAATAATAATTA-AAAT
1 TTATATTTATATTAAATAATAAAATATAAATTAAAAACATATTTATGT-AA-AATAATTATAAA-
537631 TATATTAAAAATTA-A-TAAAATAAAA
63 T-TATT-AAAATTATATTAAAATAAAA
537656 ATAAAAATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
99 1 0.01
100 54 0.71
101 9 0.12
102 5 0.07
103 7 0.09
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (99 bp):
TTATATTTATATTAAATAATAAAATATAAATTAAAAACATATTTATGTAAAATAATTATAAATTA
TTAAAATTATATTAAAATAAAATTATCTTTTAAT
Found at i:538040 original size:28 final size:29
Alignment explanation
Indices: 538004--538059 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
537994 AATAAAATTA
538004 TTTATTTATTAAAT-ATAATATTAATAAAT
1 TTTATTTATTAAATAATAA-ATTAATAAAT
*
538033 TTTA-TTATTATATAATAAATTAATAAA
1 TTTATTTATTAAATAATAAATTAATAAA
538060 AATATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTATTTATTAAATAATAAATTAATAAAT
Found at i:538087 original size:33 final size:35
Alignment explanation
Indices: 538026--538093 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
538016 ATATAATATT
538026 AATAAATTTTATTATTATATAATAAATT-AATAAA
1 AATAAATTTTATTATTATATAATAAATTAAATAAA
* * *
538060 AATATATTTT-TTATTATATGATTAATTAAATAAA
1 AATAAATTTTATTATTATATAATAAATTAAATAAA
538094 TAATTACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
AATAAATTTTATTATTATATAATAAATTAAATAAA
Found at i:538183 original size:28 final size:28
Alignment explanation
Indices: 538135--538196 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
538125 ATTAATTTTA
* *
538135 TTAATTTATTTTTTAACATAAATATAATT
1 TTAA-TTATTATTTAACATAAATAAAATT
*
538164 TTAATTATTATTTAATATAAATAAAATT
1 TTAATTATTATTTAACATAAATAAAATT
538192 TTAAT
1 TTAAT
538197 ATTTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAATTATTATTTAACATAAATAAAATT
Found at i:538215 original size:21 final size:22
Alignment explanation
Indices: 538179--538219 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
538169 TATTATTTAA
538179 TATAAATAAAATTTTAATATTT
1 TATAAATAAAATTTTAATATTT
*
538201 TATAAAT-ATATTTTAATAT
1 TATAAATAAAATTTTAATAT
538220 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAAATAAAATTTTAATATTT
Found at i:538230 original size:14 final size:16
Alignment explanation
Indices: 538201--538232 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
538191 TTTAATATTT
538201 TATAAATATATTTTAA
1 TATAAATATATTTTAA
538217 TATAAA-AT-TTTTAA
1 TATAAATATATTTTAA
538231 TA
1 TA
538233 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAAATATATTTTAA
Found at i:538267 original size:24 final size:24
Alignment explanation
Indices: 538235--538281 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
538225 TTTTAATAAT
*
538235 TATTTTTATTATAATTTAT-TTTAC
1 TATTATTATTAT-ATTTATATTTAC
538259 TATTATTATTATATTTATATTTA
1 TATTATTATTATATTTATATTTA
538282 AATATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTATTATTATATTTATATTTAC
Found at i:538275 original size:18 final size:17
Alignment explanation
Indices: 538230--538279 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
538220 AAAATTTTTA
538230 ATAA-TTATTTT-TATT
1 ATAATTTATTTTATATT
538245 ATAATTTATTTTACTATT
1 ATAATTTATTTTA-TATT
*
538263 ATTA-TTATATTTATATT
1 ATAATTTAT-TTTATATT
538280 TAAATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 8 0.27
18 11 0.37
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATAATTTATTTTATATT
Found at i:538320 original size:47 final size:45
Alignment explanation
Indices: 538252--538349 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 45
538242 ATTATAATTT
* *
538252 ATTTTACTATTATTATTATATTTATATTTAAATATATATCAATA-CTA
1 ATTTTAATATTATTATAATATTTA-ATTTAAATAT-TA-CAATATCTA
* *
538299 ATTTTAATATTATTATAATATTTAATTTTATTATTACAATATCTA
1 ATTTTAATATTATTATAATATTTAATTTAAATATTACAATATCTA
538344 ATTTTA
1 ATTTTA
538350 CTACTAAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 5 0.11
45 11 0.24
46 8 0.17
47 22 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (45 bp):
ATTTTAATATTATTATAATATTTAATTTAAATATTACAATATCTA
Found at i:538322 original size:18 final size:17
Alignment explanation
Indices: 538297--538332 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
538287 ATATCAATAC
538297 TAATTTTAATATTATTA
1 TAATTTTAATATTATTA
*
538314 TAATATTTAATTTTATTA
1 TAAT-TTTAATATTATTA
538332 T
1 T
538333 TACAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTTAATATTATTA
Found at i:538325 original size:24 final size:24
Alignment explanation
Indices: 538188--538349 Score: 86
Period size: 21 Copynumber: 7.3 Consensus size: 24
538178 ATATAAATAA
*
538188 AATTTTAATATT-TTATAA-ATAT
1 AATTTTAATATTATTATAATATTT
*
538210 -ATTTTAATA-TA--A-AATTTTT
1 AATTTTAATATTATTATAATATTT
* * *
538229 AATAATTATTTTTATTAT-A-ATTT
1 AAT-TTTAATATTATTATAATATTT
* *
538252 -ATTTTACTATTATTATTATATTT
1 AATTTTAATATTATTATAATATTT
* *
538275 ATATTTAAATA-TA-TATCAATA-CT
1 A-ATTTTAATATTATTAT-AATATTT
538298 AATTTTAATATTATTATAATATTT
1 AATTTTAATATTATTATAATATTT
* *
538322 AA-TTT--TATTATTACAATATCT
1 AATTTTAATATTATTATAATATTT
538343 AATTTTA
1 AATTTTA
538350 CTACTAAAGC
Statistics
Matches: 105, Mismatches: 17, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 3 0.03
21 40 0.38
22 16 0.15
23 21 0.20
24 13 0.12
25 7 0.07
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
AATTTTAATATTATTATAATATTT
Found at i:540123 original size:2 final size:2
Alignment explanation
Indices: 540111--540142 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
540101 CGTGCGTGCA
*
540111 TG TG GG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
540143 ATAGATAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:542942 original size:2 final size:2
Alignment explanation
Indices: 542935--542967 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
542925 AGTAATGCAC
542935 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 T
542968 ATTGGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:546827 original size:22 final size:22
Alignment explanation
Indices: 546812--546866 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
546802 TTTATATTTA
546812 GATTATTTTAAATTTAAGTTAT
1 GATTATTTTAAATTTAAGTTAT
** *
546834 TTTTATTTTAAATTTAAGATAT
1 GATTATTTTAAATTTAAGTTAT
**
546856 TTTTATTTTAA
1 GATTATTTTAA
546867 TAATCGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
GATTATTTTAAATTTAAGTTAT
Found at i:546843 original size:16 final size:17
Alignment explanation
Indices: 546797--546844 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
546787 AGTGTAAGTT
546797 TTATTTTTATATTT-AGA
1 TTATTTTTAT-TTTAAGA
* *
546814 TTATTTTAAATTTAAG-
1 TTATTTTTATTTTAAGA
546830 TTATTTTTATTTTAA
1 TTATTTTTATTTTAA
546845 ATTTAAGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTATTTTTATTTTAAGA
Found at i:547752 original size:16 final size:17
Alignment explanation
Indices: 547718--547766 Score: 84
Period size: 16 Copynumber: 3.0 Consensus size: 17
547708 TATGATGAAG
547718 TAAATTTTAAATAATTT
1 TAAATTTTAAATAATTT
547735 TAAATTTTAAAT-ATTT
1 TAAATTTTAAATAATTT
547751 TAAATTTT-AATAATTT
1 TAAATTTTAAATAATTT
547767 CAAACTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.10
16 16 0.52
17 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTTTAAATAATTT
Found at i:547786 original size:32 final size:33
Alignment explanation
Indices: 547718--547789 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
547708 TATGATGAAG
* * **
547718 TAAATTTTAAATAATTTTAAATTTTAAATATTT
1 TAAATTTTAAATAATTTCAAATCTTAAATACCT
547751 TAAATTTT-AATAATTTCAAA-CTTAAATTACCT
1 TAAATTTTAAATAATTTCAAATCTTAAA-TACCT
547783 TAAATTT
1 TAAATTT
547790 AAGGTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.15
32 21 0.62
33 8 0.24
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (33 bp):
TAAATTTTAAATAATTTCAAATCTTAAATACCT
Found at i:548324 original size:2 final size:2
Alignment explanation
Indices: 548267--548313 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
548257 AAAAATAATA
548267 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
548309 AG AG A
1 AG AG A
548314 TGTGTGAGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:549490 original size:30 final size:29
Alignment explanation
Indices: 549456--549515 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
549446 GACCTATCAT
* *
549456 GATAGAACCAATATCTAGAGTATTTTAAAA
1 GATAGAACCAATACCTAGAGCA-TTTAAAA
*
549486 GATAGATCCAATACCTAGAGCATTTAAAA
1 GATAGAACCAATACCTAGAGCATTTAAAA
549515 G
1 G
549516 GTGTTGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (29 bp):
GATAGAACCAATACCTAGAGCATTTAAAA
Found at i:551010 original size:3 final size:3
Alignment explanation
Indices: 550996--551038 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
550986 CCCTTTCGCT
* * *
550996 TTA TTG TTA TTA TTA TTA CTA AT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
551039 CCCTTTCTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:564113 original size:2 final size:2
Alignment explanation
Indices: 564106--564134 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
564096 TGAAAGGCAT
564106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
564135 TCTTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:566397 original size:21 final size:21
Alignment explanation
Indices: 566371--566447 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
566361 AAAAAATTCA
566371 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
566392 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
566413 AATGTATTGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
566434 AATGTATCGATACA
1 AATGTATCGATACA
566448 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:566507 original size:19 final size:19
Alignment explanation
Indices: 566483--566550 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
566473 AATTCAACAA
566483 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
566502 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
566517 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
566534 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
566551 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:566522 original size:13 final size:13
Alignment explanation
Indices: 566504--566528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566494 ACATAAGTTT
566504 TGTATCGATACAA
1 TGTATCGATACAA
566517 TGTATCGATACA
1 TGTATCGATACA
566529 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566526 original size:32 final size:32
Alignment explanation
Indices: 566485--566547 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
566475 TTCAACAATT
*
566485 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
566517 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
566548 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:567251 original size:52 final size:53
Alignment explanation
Indices: 567171--567328 Score: 180
Period size: 52 Copynumber: 3.0 Consensus size: 53
567161 AAAACCATTT
* * *
567171 CCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 CCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGGGGATACTCCAA
* * **
567223 CCCCGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATCGGGGATACTCCAA
1 CCCCGGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATCGGGGATACTCCAA
* * * *
567275 CTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCCAA
1 CCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGGGGATACTCCAA
567327 CC
1 CC
567329 TTGTTATTTC
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
51 6 0.07
52 66 0.75
53 12 0.14
54 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.32
Consensus pattern (53 bp):
CCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGGGGATACTCCAA
Found at i:567453 original size:107 final size:107
Alignment explanation
Indices: 567262--567466 Score: 243
Period size: 107 Copynumber: 1.9 Consensus size: 107
567252 TCCTTTAATC
* * *
567262 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
**
567327 CCTTGTTATTTCATCGGGGATACTCCAACCCCGGTACTTTCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGGTACTTTCGA
* * *** * * *
567370 GGGGATACTCCAACCCCGGCTTTA-TTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
567434 CCCCGTTATTTTCGA-GGGGATACTCCAATCCCG
66 CCCCGTTA-TTTC-ACGGGGATACTCCAACCCCG
567467 ATTTTTTTTC
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 55 0.68
108 25 0.31
109 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGGTACTTTCGA
Found at i:567517 original size:78 final size:78
Alignment explanation
Indices: 567341--567544 Score: 239
Period size: 78 Copynumber: 2.6 Consensus size: 78
567331 GTTATTTCAT
* * *
567341 CGGGGATACTCCAACCCCGGTACTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCT-AAATAT
* * *
567406 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * * *
567420 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCT-AATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAT-AT
567484 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * * *
567498 CGGGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
567545 TTATTATCTC
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
77 3 0.03
78 53 0.50
79 50 0.47
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAATATC
GATTTCTCACAAC
Found at i:579944 original size:11 final size:11
Alignment explanation
Indices: 579928--579986 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
579918 CATTCTCTTC
579928 AAAAAAAAAAG
1 AAAAAAAAAAG
579939 AAAAAAAAAAG
1 AAAAAAAAAAG
579950 AAACAAAACAAAG
1 AAA-AAAA-AAAG
** *
579963 AAAAAGGAGAG
1 AAAAAAAAAAG
*
579974 AAAAGAAAAAG
1 AAAAAAAAAAG
579985 AA
1 AA
579987 CCTGCTTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 26 0.67
12 6 0.15
13 7 0.18
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:581100 original size:59 final size:59
Alignment explanation
Indices: 580953--581709 Score: 771
Period size: 59 Copynumber: 13.3 Consensus size: 59
580943 TCCGCTTTTT
* * **
580953 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
581014 AGTCCTCAAAGAACGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
581073 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * * *
581133 AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
581192 AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
581251 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
581310 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* ** **
581371 AGTCCCCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* ** **
581426 AGTCCCCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
581481 AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGATGG------C
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
581529 A-TCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * **
581583 AGTCC-CAATGAGCAGGACTCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * * *
581637 AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
*
581692 AGTCCTCAAAGAACAGGA
1 AGTCCTCAAAGAGCAGGA
581710 TACGCTTTAT
Statistics
Matches: 625, Mismatches: 47, Indels: 54
0.86 0.06 0.07
Matches are distributed among these distances:
45 2 0.00
47 40 0.06
48 2 0.00
53 2 0.00
54 49 0.08
55 171 0.27
56 11 0.02
59 198 0.32
60 110 0.18
61 40 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:581121 original size:119 final size:117
Alignment explanation
Indices: 580953--581709 Score: 794
Period size: 119 Copynumber: 6.7 Consensus size: 117
580943 TCCGCTTTTT
* *
580953 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTC
* *
581018 CTCAAAGAACGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
64 CTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
581073 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCC
* * * *
581138 TCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT
65 TCAAAGAGCAGGACGC-CTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
581192 AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCT
* *
581257 CAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
66 CAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
581310 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA--TTTTCAGT
* ** **
581374 CCCCAAAGAGCAGGAC-CC---CTTTCGAAGCCCACACAAGTTGGTGGCATTTTTC
63 CCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
* **
581426 AGTCCCCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCC
* *
581486 TCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGATGG------C
65 TCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
581529 A-TCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCC
* * **
581588 -CAATGAGCAGGACTCCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
65 TCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
581637 AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCC
*
581697 TCAAAGAACAGGA
65 TCAAAGAGCAGGA
581710 TACGCTTTAT
Statistics
Matches: 565, Mismatches: 46, Indels: 62
0.84 0.07 0.09
Matches are distributed among these distances:
101 38 0.07
102 45 0.08
103 7 0.01
104 1 0.00
108 6 0.01
109 51 0.09
110 69 0.12
111 8 0.01
114 1 0.00
115 26 0.05
116 20 0.04
118 85 0.15
119 167 0.30
120 39 0.07
121 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (117 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCT
CAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:581430 original size:55 final size:56
Alignment explanation
Indices: 580948--581709 Score: 643
Period size: 55 Copynumber: 13.4 Consensus size: 56
580938 CTCCTTCCGC
* *
580948 TTTTT-AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACG----C-CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
581008 TTTTCCAGTCCTCAAAGAACGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
581068 -CCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC----CTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
581127 TTTTCCAGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGC----CCTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
581187 CCTTT-AGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGC----CCTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
581246 -CCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
581305 -CCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGC-----CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
581365 CCTTTT-AGTCCCCAAAGAGCAGGAC-CCCTTTCGAAGCCCACACAAGTTGGTGGCA
1 -TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
581420 TTTTTCAGTCCCCAAAGAGCAGGAC-CCCTTTCGAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
581475 TTTTCCAGTCCTCAAAGAGCAGGAC-ACCTTTCAAAGCCCACACAAGTTGATGG--
1 TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
581528 -----CA-TCCTCAAAGAGCAGGAC-ACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCCCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * *
581577 CCTTTCAGTCC-CAATGAGCAGGAC-TCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
581631 TTTTCCAGTCCTCAAAGAGCAGGAC-ACCTTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
581686 CTTTTT-AGTCCTCAAAGAACAGGA
1 -TTTTTCAGTCCTCAAAGAGCAGGA
581710 TACGCTTTAT
Statistics
Matches: 617, Mismatches: 50, Indels: 75
0.83 0.07 0.10
Matches are distributed among these distances:
47 41 0.07
48 4 0.01
53 2 0.00
54 52 0.08
55 184 0.30
56 5 0.01
57 1 0.00
58 3 0.00
59 179 0.29
60 109 0.18
61 34 0.06
62 2 0.00
64 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (56 bp):
TTTTTCAGTCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:581558 original size:47 final size:47
Alignment explanation
Indices: 581483--581685 Score: 194
Period size: 47 Copynumber: 4.0 Consensus size: 47
581473 CATTTTCCAG
581483 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
1 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
*
581530 TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGATGGCA
* *
581577 -CCTTTCAGTCCCAATGAGCAGGACTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
1 TCC--TCA-----AA-GAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGG-------CA
* *
581638 GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCA
1 -TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
581686 CTTTTTAGTC
Statistics
Matches: 133, Mismatches: 4, Indels: 37
0.76 0.02 0.21
Matches are distributed among these distances:
46 2 0.02
47 43 0.32
48 7 0.05
53 4 0.03
54 33 0.25
55 35 0.26
56 2 0.02
61 5 0.04
63 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (47 bp):
TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
Found at i:581778 original size:42 final size:41
Alignment explanation
Indices: 581693--581781 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
581683 GCACTTTTTA
* * *
581693 GTCCTCAAAGAACAGGATACGCTTTATTTTCCTCTTTCTTTT
1 GTCCTCAAAGAACAGGA-ACGATTTATTTCCCTCTTTCCTTT
* *
581735 GTCCTCAAAGAGCAGG-ACGTATTTCATTTCCCTTTTTCCTTT
1 GTCCTCAAAGAACAGGAACG-ATTT-ATTTCCCTCTTTCCTTT
581777 GTCCT
1 GTCCT
581782 TGGAAAATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 3 0.08
41 3 0.08
42 34 0.85
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (41 bp):
GTCCTCAAAGAACAGGAACGATTTATTTCCCTCTTTCCTTT
Found at i:582500 original size:21 final size:21
Alignment explanation
Indices: 582453--582506 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
582443 AAAAAAAATT
*
582453 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
582474 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
582495 CAAATGTATCGA
1 CAAATGTATCGA
582507 AACAGGGTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:582573 original size:19 final size:19
Alignment explanation
Indices: 582546--582613 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
582536 AATTCAAGAA
582546 TTTGCATCGATACATAAGT
1 TTTGCATCGATACATAAGT
*
582565 TTTGTATCGATAC--AA--
1 TTTGCATCGATACATAAGT
582580 --TGCATCGATACATAAGT
1 TTTGCATCGATACATAAGT
* *
582597 ATTGTATCGATACATAA
1 TTTGCATCGATACATAA
582614 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
17 2 0.05
19 26 0.65
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
TTTGCATCGATACATAAGT
Found at i:582584 original size:32 final size:32
Alignment explanation
Indices: 582548--582610 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
582538 TTCAAGAATT
*
582548 TGCATCGATACATAAGTTTTGTATCGATACAA
1 TGCATCGATACATAAGTATTGTATCGATACAA
582580 TGCATCGATACATAAGTATTGTATCGATACA
1 TGCATCGATACATAAGTATTGTATCGATACA
582611 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TGCATCGATACATAAGTATTGTATCGATACAA
Found at i:582658 original size:20 final size:20
Alignment explanation
Indices: 582633--582687 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
582623 GCCAAGGAAA
*
582633 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
582653 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
582673 TGTATCGATACATTT
1 TGTATCGATACATTT
582688 GAAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:585322 original size:13 final size:13
Alignment explanation
Indices: 585304--585329 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585294 CAATTTTTTG
585304 TGTATCGATACAT
1 TGTATCGATACAT
585317 TGTATCGATACAT
1 TGTATCGATACAT
585330 ACTTGATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:586050 original size:21 final size:21
Alignment explanation
Indices: 586009--586052 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
585999 CTCCCCTTTA
* *
586009 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
586030 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
586051 TC
1 TC
586053 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:586069 original size:25 final size:25
Alignment explanation
Indices: 586041--586092 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
586031 CTCCCCCTTA
586041 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
586066 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
586091 AT
1 AT
586093 TTGCACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (25 bp):
ATCAAGTAATTCATATCAAAAATTT
Found at i:586084 original size:14 final size:14
Alignment explanation
Indices: 586041--586084 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
586031 CTCCCCCTTA
586041 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
*
586055 ATCAA-AAATT--T
1 ATCAAGTAATTCAT
586066 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
586080 ATCAA
1 ATCAA
586085 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (14 bp):
ATCAAGTAATTCAT
Found at i:587901 original size:13 final size:13
Alignment explanation
Indices: 587883--587908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
587873 ATAATCACCC
587883 TGTATCGATACAA
1 TGTATCGATACAA
587896 TGTATCGATACAA
1 TGTATCGATACAA
587909 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:590007 original size:15 final size:15
Alignment explanation
Indices: 589987--590017 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
589977 ATTTCGTTTG
*
589987 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
590002 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
590017 G
1 G
590018 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:591850 original size:21 final size:21
Alignment explanation
Indices: 591821--591865 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
591811 AAGTTTTCAT
*
591821 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
591841 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
591863 TTT
1 TTT
591866 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:594098 original size:13 final size:13
Alignment explanation
Indices: 594080--594105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
594070 CAATTTTTTG
594080 TGTATCGATACAT
1 TGTATCGATACAT
594093 TGTATCGATACAT
1 TGTATCGATACAT
594106 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:595125 original size:28 final size:27
Alignment explanation
Indices: 595055--595130 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
595045 TTTCTTCACA
*
595055 ATCGGGGATACTCCAACCCCATTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
595082 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
595108 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
595131 GTTTTATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.50
28 18 0.41
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:595183 original size:52 final size:51
Alignment explanation
Indices: 595115--595283 Score: 189
Period size: 52 Copynumber: 3.3 Consensus size: 51
595105 ATTTTCGAGG
*
595115 GGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGA
1 GGATACTCCAACCCCGGTTTTATT-CTAAAACACCAATTTTTCCACAATCGA
* * ** *
595167 GGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATCGG
1 GGATACTCCAACCCCGGTTTTATTCT-AAAACACCAATTTTTCC-ACAATCGA
* * * *
595219 GGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
1 GGATACTCCAACCCCGGTTTTA-TT-CTAAAACACCAATTTTTCCACAATCGA
595271 GGATACTCCAACC
1 GGATACTCCAACC
595284 TTGTTATTTC
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 7 0.07
52 74 0.77
53 11 0.11
54 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCGGTTTTATTCTAAAACACCAATTTTTCCACAATCGA
Found at i:595266 original size:104 final size:103
Alignment explanation
Indices: 594946--595283 Score: 308
Period size: 104 Copynumber: 3.2 Consensus size: 103
594936 CTCAATTCTC
* * * * * *
594946 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAATACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAACCCCG-TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
595010 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * ** * * * ** **
595051 CACAATCGGGGATACTCCAACCCC-ATTAATCATCGGGGATACTCCAA--CCCCGTTATTTTCGA
1 CACAATCGAGGATACTCCAACCCCGTTTTATTTTC---AAAACACCAATTTTCC-TT-TAATC--
* * * * *
595113 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
595157 CCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAACCCC-GTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
595222 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
595262 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
595284 TTGTTATTTC
Statistics
Matches: 180, Mismatches: 39, Indels: 29
0.73 0.16 0.12
Matches are distributed among these distances:
103 6 0.03
104 44 0.24
105 39 0.22
106 18 0.10
107 40 0.22
108 5 0.03
109 28 0.16
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAACCCCGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:595311 original size:212 final size:212
Alignment explanation
Indices: 594941--595393 Score: 642
Period size: 212 Copynumber: 2.1 Consensus size: 212
594931 AGTTTCTCAA
* * * *
594941 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAATACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
*
595006 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * * *
595071 CCCCATTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTT
131 CCCCATTAATCATCGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCTTT
*
595136 ATTGCTAAAACACTAAT
196 ATTCCTAAAACACTAAT
* * * * *
595153 TTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCG
*
595218 GGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCA
65 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCA
*** *
595281 ACCTTGTTATTTCATCGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCT
130 ACCCCATTA-ATCATCGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCT
* * *
595346 TTATTCCTAAAATATTGAT
194 TTATTCCTAAAACACTAAT
* *
595365 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATCGGGGATACTCCAACCCCG
595394 TTATTTTCGA
Statistics
Matches: 212, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
211 48 0.23
212 128 0.60
213 36 0.17
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCATTAATCATCGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:595408 original size:107 final size:107
Alignment explanation
Indices: 595004--595421 Score: 295
Period size: 107 Copynumber: 3.9 Consensus size: 107
594994 TTCTATAATC
* * * *
595004 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * * * *
595069 AACCCCATTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGA
64 AACCCCGTTATTTCA-CGGGGATACTCCAACCCCGGTACTTCCGA
** * * * * *
595113 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCT-CACAATCGAGGATACTCCA
* * ** ** *
595177 ACCCCGGTTTTATTTTCA-----AAACGCCAATTTTCCTTTA-AT-C--
65 ACCCC-G--TTA-TTTCACGGGGATACTCCAA--CCCCGGTACTTCCGA
* * *
595217 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
**
595282 CCTTGTTATTTCATCGGGGATACTCCAACCCCGGTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGGTACTTCCGA
* * *** * * *
595325 GGGGATACTCCAACCCCGGCTTTA-TTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
595389 CCCCGTTATTTTCGA-GGGGATACTCCAATCCCG
66 CCCCGTTA-TTTC-ACGGGGATACTCCAACCCCG
595422 ATTTTTTTTC
Statistics
Matches: 244, Mismatches: 44, Indels: 44
0.73 0.13 0.13
Matches are distributed among these distances:
100 5 0.02
101 3 0.01
103 1 0.00
104 48 0.20
105 17 0.07
106 17 0.07
107 91 0.37
108 33 0.14
109 23 0.09
110 3 0.01
112 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGGTACTTCCGA
Found at i:595472 original size:78 final size:78
Alignment explanation
Indices: 595296--595499 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 78
595286 GTTATTTCAT
* * * *
595296 CGGGGATACTCCAACCCCGGTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCT-AAATAT
* * *
595361 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * * *
595375 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCT-AATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAT-AT
595439 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * * *
595453 CGGGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
595500 TTATTATCTC
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 3 0.03
78 53 0.50
79 49 0.47
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAATATC
GATTTCTCACAAC
Found at i:596616 original size:20 final size:20
Alignment explanation
Indices: 596593--596642 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
596583 TAAAGAAAAT
*
596593 TGTATCGATACATTTAGAAA
1 TGTATCGATACATTTACAAA
**
596613 TGTATCGATACATTTACTTA
1 TGTATCGATACATTTACAAA
596633 TGTATCGATA
1 TGTATCGATA
596643 TAATTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTACAAA
Found at i:597218 original size:2 final size:2
Alignment explanation
Indices: 597211--597236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
597201 AAACAACAAC
597211 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
597237 TGAGTAAATA
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):
AT
Found at i:598424 original size:34 final size:36
Alignment explanation
Indices: 598361--598437 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
598351 ATATGGAATA
598361 ATATT-TTTATTAAAATAATAAATAATAAATATTAT
1 ATATTATTTATTAAAATAATAAATAATAAATATTAT
* *
598396 TTATTATTTATTATAA-AAT-AATAATAAATATTAT
1 ATATTATTTATTAAAATAATAAATAATAAATATTAT
598430 ATATTATT
1 ATATTATT
598438 AAAATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 22 0.58
35 7 0.18
36 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
ATATTATTTATTAAAATAATAAATAATAAATATTAT
Found at i:598892 original size:2 final size:2
Alignment explanation
Indices: 598885--598957 Score: 76
Period size: 2 Copynumber: 36.0 Consensus size: 2
598875 AAGGAAATGG
* * * * *
598885 AT AT AT AT AT AT AT AC ACT AT AT GA- AT AC GT AT AT GT AT AT GT
1 AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT
598928 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
598958 GCATTTGTGT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:603527 original size:47 final size:48
Alignment explanation
Indices: 603436--603528 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
603426 AGTATGTCAG
* *
603436 ATAATAATTTTGAAAATAATAAAATTTTAAGATAAAAATATAATATAA
1 ATAAAAATTTTGAAAATAATAAAAATTTAAGATAAAAATATAATATAA
* * *
603484 ATAAAAATATTTGAATAT-ATAAAAATTT-ATATAAATATATAATAT
1 ATAAAAAT-TTTGAAAATAATAAAAATTTAAGATAAAAATATAATAT
603529 TTTAAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 15 0.38
48 16 0.41
49 8 0.21
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (48 bp):
ATAAAAATTTTGAAAATAATAAAAATTTAAGATAAAAATATAATATAA
Found at i:603532 original size:20 final size:21
Alignment explanation
Indices: 603497--603547 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
603487 AAAATATTTG
* *
603497 AATATATAAAAATTTATATA-
1 AATATATAATAATTTAAATAT
*
603517 AATATATAATATTTTAAATAT
1 AATATATAATAATTTAAATAT
603538 AAT-TATAATA
1 AATATATAATA
603548 CTTAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATATAATAATTTAAATAT
Found at i:604149 original size:2 final size:2
Alignment explanation
Indices: 604142--604170 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
604132 GAAGCACCTG
604142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
604171 CCACTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.