Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 27 of 226
Found at i:12225904 original size:53 final size:53
Alignment explanation
Indices: 12225811--12225920 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 53
12225801 AAATCTCAAA
* * *
12225811 TTTTATATTTTTATAAATGATCTAAGTTTATATATTTTTGAAA-ATTTTTAAGGT
1 TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATA-TTTTAA-GT
*
12225865 TTTTAAATTTTTATAAAT-TTCTAAATTTATATATATTTGAAATATTTTAAGT
1 TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATATTTTAAGT
12225917 TTTT
1 TTTT
12225921 CTTTATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 6 0.12
53 27 0.53
54 18 0.35
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (53 bp):
TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATATTTTAAGT
Found at i:12230394 original size:3 final size:3
Alignment explanation
Indices: 12230388--12230413 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12230378 AATAATAATA
12230388 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
12230414 AAAAGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:12236025 original size:3 final size:3
Alignment explanation
Indices: 12236017--12236065 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
12236007 ATGTTATTAA
*
12236017 ATT ATT ATT ATT ATT ATT AAT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12236064 AT
1 AT
12236066 ATTGTGAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12236281 original size:13 final size:13
Alignment explanation
Indices: 12236249--12236291 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
12236239 TTAAATGTTA
*
12236249 AAATAATATAAAG
1 AAATAATAAAAAG
12236262 TAAATAATAAAAAG
1 -AAATAATAAAAAG
12236276 AAATAA-AACAAAG
1 AAATAATAA-AAAG
12236289 AAA
1 AAA
12236292 GAACAGAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 12 0.44
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (13 bp):
AAATAATAAAAAG
Found at i:12237365 original size:23 final size:23
Alignment explanation
Indices: 12237334--12237421 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
12237324 GCTTTGCCGA
*
12237334 TCAGACACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
12237357 TCAGGCACTTTATGTGTCATATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
12237380 TCAGGCACCTCGTGTGT--TGTT
1 TCAGGCACTTTATGTGTCGTATT
*
12237401 TCAGGCAC-TTATTTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
12237422 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.09
21 11 0.21
22 2 0.04
23 35 0.66
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:12239170 original size:27 final size:27
Alignment explanation
Indices: 12239118--12239170 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12239108 ATGCTTTTCA
* *
12239118 ATTTTTTAAAAATATAAAATATAAATT
1 ATTTTCTAAAAATATAAAATAAAAATT
12239145 ATTTTCTAAAAATA-AAAATGAAAAAT
1 ATTTTCTAAAAATATAAAAT-AAAAAT
12239171 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
ATTTTCTAAAAATATAAAATAAAAATT
Found at i:12243787 original size:22 final size:22
Alignment explanation
Indices: 12243759--12243869 Score: 150
Period size: 22 Copynumber: 5.0 Consensus size: 22
12243749 TTTATTGTTC
*
12243759 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
12243781 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
12243803 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
12243825 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
12243847 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
12243869 A
1 A
12243870 CAAATTTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:12246363 original size:3 final size:3
Alignment explanation
Indices: 12246355--12246381 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12246345 GAACATTCAC
12246355 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
12246382 AGGCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12246643 original size:4 final size:4
Alignment explanation
Indices: 12246636--12246680 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
12246626 TTACTTTAGG
* * * *
12246636 ATTA ATTA TTTA ATTA TTTA ATTA TTTA ATTA TTTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
12246681 CTTGGATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (4 bp):
ATTA
Found at i:12246650 original size:8 final size:8
Alignment explanation
Indices: 12246637--12246680 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
12246627 TACTTTAGGA
12246637 TTAATTAT
1 TTAATTAT
12246645 TTAATTAT
1 TTAATTAT
12246653 TTAATTAT
1 TTAATTAT
12246661 TTAATTAT
1 TTAATTAT
*
12246669 TTAATTAA
1 TTAATTAT
12246677 TTAA
1 TTAA
12246681 CTTGGATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTAATTAT
Found at i:12254346 original size:31 final size:31
Alignment explanation
Indices: 12254311--12254375 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12254301 AATAGGTATC
*
12254311 TAAACTTGACACTTTTTCCTAATTTGGTACT
1 TAAACTTGACACTTTTTCCTAAGTTGGTACT
*
12254342 TAAACTTGACACTTTTTCTTAAGTTGGTACT
1 TAAACTTGACACTTTTTCCTAAGTTGGTACT
12254373 TAA
1 TAA
12254376 TCTCTTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (31 bp):
TAAACTTGACACTTTTTCCTAAGTTGGTACT
Found at i:12258846 original size:7 final size:7
Alignment explanation
Indices: 12258834--12258864 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
12258824 ATGAAAACTT
12258834 TCTTATA
1 TCTTATA
12258841 TCTTATA
1 TCTTATA
12258848 TCTTATA
1 TCTTATA
12258855 TCTTATA
1 TCTTATA
12258862 TCT
1 TCT
12258865 ACCGTAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTTATA
Found at i:12268614 original size:23 final size:23
Alignment explanation
Indices: 12268570--12268632 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
12268560 TTGTGTGACG
* *
12268570 AATAAAATTT-ATATAAATAAATT
1 AATAAAATTTCAAATATATAAA-T
12268593 AATAAAATTTCAAATATA-AAAT
1 AATAAAATTTCAAATATATAAAT
* *
12268615 AGTAAAATATACAAATAT
1 AATAAAAT-TTCAAATAT
12268633 GAGACACACG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.24
23 21 0.62
24 5 0.15
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAAATTTCAAATATATAAAT
Found at i:12268620 original size:22 final size:23
Alignment explanation
Indices: 12268586--12268632 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12268576 ATTTATATAA
* *
12268586 ATAAATTAATAAAAT-TTCAAAT
1 ATAAAATAATAAAATATACAAAT
*
12268608 ATAAAATAGTAAAATATACAAAT
1 ATAAAATAATAAAATATACAAAT
12268631 AT
1 AT
12268633 GAGACACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAAATAATAAAATATACAAAT
Found at i:12269404 original size:3 final size:3
Alignment explanation
Indices: 12269389--12269443 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
12269379 GCGCAACTTG
* *
12269389 AAT AAT AAC AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12269437 AAT AAT A
1 AAT AAT A
12269444 TTATTATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12269448 original size:3 final size:3
Alignment explanation
Indices: 12269442--12269476 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12269432 ATAATAATAA
*
12269442 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12269477 GAAATAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12270066 original size:22 final size:22
Alignment explanation
Indices: 12270039--12270093 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
12270029 TTAAATATGG
12270039 ATTTGAGAGAAATTTG-GAAGGAA
1 ATTTGAGAGAAA-TTGAG-AGGAA
12270062 A-TTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
12270084 ATTTGAGAGA
1 ATTTGAGAGA
12270094 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:12270091 original size:12 final size:12
Alignment explanation
Indices: 12270039--12270092 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
12270029 TTAAATATGG
12270039 ATTTGAGA-GAA
1 ATTTGAGAGGAA
12270050 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
12270062 A-TTGAGAGCAA
1 ATTTGAGAGGAA
12270073 A-TTGAGAGGAA
1 ATTTGAGAGGAA
12270084 ATTTGAGAG
1 ATTTGAGAG
12270093 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 24 0.65
12 12 0.32
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:12271603 original size:20 final size:20
Alignment explanation
Indices: 12271553--12271603 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
12271543 CTATTTCTTT
*
12271553 TAAATTGAAAATTACATTTA
1 TAAAATGAAAATTACATTTA
* * *
12271573 TAAAATAAAAATT-TATTTT
1 TAAAATGAAAATTACATTTA
12271592 TAATAATGAAAA
1 TAA-AATGAAAA
12271604 ATGTGAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAATGAAAATTACATTTA
Found at i:12280074 original size:9 final size:9
Alignment explanation
Indices: 12280060--12280099 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
12280050 TCTTCATATC
12280060 TTTATTATT
1 TTTATTATT
12280069 TTTATTATT
1 TTTATTATT
*
12280078 TTTATCATTT
1 TTTATTA-TT
*
12280088 TTTATTCTT
1 TTTATTATT
12280097 TTT
1 TTT
12280100 GGGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTATT
Found at i:12284183 original size:14 final size:13
Alignment explanation
Indices: 12284151--12284184 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
12284141 TTGATTCTAG
12284151 AAAAT-GAAACAA
1 AAAATAGAAACAA
12284163 AAAATAGAAACAA
1 AAAATAGAAACAA
12284176 ACAAATAGA
1 A-AAATAGA
12284185 GCCGAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAATAGAAACAA
Found at i:12284644 original size:14 final size:14
Alignment explanation
Indices: 12284627--12284656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12284617 AGGTGAACTA
12284627 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
12284641 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
12284655 GC
1 GC
12284657 TGCAATCTTT
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:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:12284705 original size:33 final size:33
Alignment explanation
Indices: 12284668--12284732 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
12284658 GCAATCTTTA
12284668 GGTGAAGAGAGTGAAAAGA-GAAGCTGTGGAAAG
1 GGTGAAGAGAGTGAAAAGATG-AGCTGTGGAAAG
*
12284701 GGTGAAGAGAGTGAAGAGATGAGCTGTGGAAA
1 GGTGAAGAGAGTGAAAAGATGAGCTGTGGAAA
12284733 ATGTCTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.43, T:0.14
Consensus pattern (33 bp):
GGTGAAGAGAGTGAAAAGATGAGCTGTGGAAAG
Found at i:12286676 original size:114 final size:113
Alignment explanation
Indices: 12286488--12286695 Score: 312
Period size: 114 Copynumber: 1.8 Consensus size: 113
12286478 ATCAGTTTAG
* * * * *
12286488 GATATTTTGATTTTTATTCTATATGATTTTAATTTCAAAAATAAAAAATTGAATAAAAGGATTTG
1 GATATTTAGATTTTTATTCTATACGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATTG
*
12286553 ATTCATTTTTTAATCTAAAAATCAAATTAAAATCGTATTATTAATTTCA
66 ATTCATTTTTT-ATCCAAAAATCAAATTAAAATCGTATTATTAATTTCA
*
12286602 GATATTTAGATTTTTATTCTATACCG-TTTTAATTTCAAAAAT-GAAAATCGAATAAAACGAATT
1 GATATTTAGATTTTTATTCTATA-CGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATT
*
12286665 GATTCATTTTTTATCCAAAATTCAAATTAAA
65 GATTCATTTTTTATCCAAAAATCAAATTAAA
12286696 CTAAACCAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
112 17 0.20
113 29 0.34
114 38 0.45
115 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (113 bp):
GATATTTAGATTTTTATTCTATACGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATTG
ATTCATTTTTTATCCAAAAATCAAATTAAAATCGTATTATTAATTTCA
Found at i:12287731 original size:31 final size:31
Alignment explanation
Indices: 12287696--12287755 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12287686 ATTAACAACC
12287696 CAATGAATTAAATAAAAACTTTCAAATAGCT
1 CAATGAATTAAATAAAAACTTTCAAATAGCT
* * *
12287727 CAATGACTTACATAAAAACTTTCGAATAG
1 CAATGAATTAAATAAAAACTTTCAAATAG
12287756 TTTAGTGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (31 bp):
CAATGAATTAAATAAAAACTTTCAAATAGCT
Found at i:12297508 original size:18 final size:16
Alignment explanation
Indices: 12297477--12297512 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
12297467 ATTAGTTAGA
12297477 ATTTTTTATTAATTTG
1 ATTTTTTATTAATTTG
12297493 ATTTTTTAGTTAAATTTG
1 ATTTTTTA-TT-AATTTG
12297511 AT
1 AT
12297513 ATTCAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (16 bp):
ATTTTTTATTAATTTG
Found at i:12297563 original size:24 final size:22
Alignment explanation
Indices: 12297535--12297580 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12297525 TAAAAAAGTT
*
12297535 AAATTTGATTATAATTTTTTTTAA
1 AAATTT-ATT-TAATATTTTTTAA
*
12297559 AAATTTATTTACTATTTTTTAA
1 AAATTTATTTAATATTTTTTAA
12297581 TAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 3 0.15
24 6 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATTTATTTAATATTTTTTAA
Found at i:12297590 original size:23 final size:22
Alignment explanation
Indices: 12297551--12297595 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
12297541 GATTATAATT
** *
12297551 TTTTTTAAAAATTTATTTACTA
1 TTTTTTAAAAAAATATTGACTA
12297573 TTTTTTAATAAAAATATTGACTA
1 TTTTTTAA-AAAAATATTGACTA
12297596 AAAAGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTTAAAAAAATATTGACTA
Found at i:12297683 original size:17 final size:17
Alignment explanation
Indices: 12297656--12297698 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12297646 TTTATGCTAT
*
12297656 TTTTTTAATTTGTATAAA
1 TTTTTT-ATTTATATAAA
*
12297674 TTTTTTATTTATTTAAA
1 TTTTTTATTTATATAAA
*
12297691 TATTTTAT
1 TTTTTTAT
12297699 AATCTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTTATTTATATAAA
Found at i:12297890 original size:18 final size:18
Alignment explanation
Indices: 12297869--12297910 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12297859 AATTTTACTA
12297869 AAAAATATT-CACAACATT
1 AAAAATATTGCA-AACATT
* *
12297887 AAAAAAATTGTAAACATT
1 AAAAATATTGCAAACATT
12297905 AAAAAT
1 AAAAAT
12297911 TAAATTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATATTGCAAACATT
Found at i:12306010 original size:5 final size:5
Alignment explanation
Indices: 12305990--12306047 Score: 80
Period size: 5 Copynumber: 11.2 Consensus size: 5
12305980 TTTTTATGTT
* *
12305990 TTATA TATATTA TTATA TTATA TTATA TTATA TTATA TTGTA TTGTA TTATA
1 TTATA T-TA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
12306042 TTATA T
1 TTATA T
12306048 AAGTAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 42 0.86
6 4 0.08
7 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:12306082 original size:16 final size:16
Alignment explanation
Indices: 12306048--12306080 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
12306038 TATATTATAT
12306048 AAGTAAAAATAAAAAA
1 AAGTAAAAATAAAAAA
12306064 AAGT-AAAATAAAAAA
1 AAGTAAAAATAAAAAA
12306079 AA
1 AA
12306081 AGATGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGTAAAAATAAAAAA
Found at i:12306765 original size:3 final size:3
Alignment explanation
Indices: 12306757--12306821 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
12306747 AATAAGAATT
* * * *
12306757 TTA TTA TTA TTA TTA TTG TTA ATA TAA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
12306805 ATA TAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
12306822 TTTAATGATT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12306795 original size:27 final size:27
Alignment explanation
Indices: 12306757--12306821 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
12306747 AATAAGAATT
12306757 TTATTATTATTATTATTGTTAATATAA
1 TTATTATTATTATTATTGTTAATATAA
12306784 TTATTATTATTATTATTGTTAATATAA
1 TTATTATTATTATTATTGTTAATATAA
12306811 TTATTATTATT
1 TTATTATTATT
12306822 TTTAATGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TTATTATTATTATTATTGTTAATATAA
Found at i:12309100 original size:42 final size:42
Alignment explanation
Indices: 12309022--12309119 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
12309012 GCTCTCAGTA
* *
12309022 TCGCACACTTAGTGCCCGTTATTCAACATCTCCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATCCAACATCTCCATTTTAATC
* * *
12309064 TCGCACACTTAGTGCCCTTTATCCAACCTCGT-CATTTTAGTC
1 TCGCACACTTAGTGCCCGTTATCCAACATC-TCCATTTTAATC
12309106 TCGCACACTTAGTG
1 TCGCACACTTAGTG
12309120 TTGTTCATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATCCAACATCTCCATTTTAATC
Found at i:12324155 original size:39 final size:39
Alignment explanation
Indices: 12324074--12324285 Score: 183
Period size: 45 Copynumber: 5.0 Consensus size: 39
12324064 ATTTGCCGGC
* * * *
12324074 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
12324112 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
12324151 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
12324196 TTACTGTTATCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTG
1 TTAC-----T-GATTCGGCACTTTGTGTGTCGAATAC---T---GTTACTG
* * *
12324247 TTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
12324286 CTACCGTTAC
Statistics
Matches: 148, Mismatches: 11, Indels: 29
0.79 0.06 0.15
Matches are distributed among these distances:
38 14 0.09
39 31 0.21
42 2 0.01
45 87 0.59
47 2 0.01
48 1 0.01
51 11 0.07
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:12324169 original size:45 final size:45
Alignment explanation
Indices: 12324101--12324300 Score: 310
Period size: 45 Copynumber: 4.4 Consensus size: 45
12324091 ATGTGCCGAC
*
12324101 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
12324146 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
12324191 TACTGTTACTGTTATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
12324236 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
12324281 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACCGATT
12324301 ACTGTATACT
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 142 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:12325202 original size:11 final size:11
Alignment explanation
Indices: 12325186--12325210 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12325176 GGGGTGTTAC
12325186 AAGTTTTGGCT
1 AAGTTTTGGCT
12325197 AAGTTTTGGCT
1 AAGTTTTGGCT
12325208 AAG
1 AAG
12325211 CAATATTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (11 bp):
AAGTTTTGGCT
Found at i:12335037 original size:21 final size:21
Alignment explanation
Indices: 12335011--12335213 Score: 113
Period size: 21 Copynumber: 9.7 Consensus size: 21
12335001 ATGAGAGCTA
*
12335011 AACGGAAACCCATAAGGGTTG
1 AACGGAAACTCATAAGGGTTG
* ** * *
12335032 AACGGAAGCTTGTAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
*
12335053 AACGGAAAC-CTATAAGGGTTA
1 AACGGAAACTC-ATAAGGGTTG
** * * * *
12335074 AATTGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
* * *
12335095 AACAGAAACCCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTG
* * * * *
12335116 AACTGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
* * *
12335137 AACAGAAACCCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTG
* * * *
12335158 AAC-TAAAGCTCAAAAGAGCTG
1 AACGGAAA-CTCATAAGGGTTG
*
12335179 AACGGAAACTCATTAGGGTTG
1 AACGGAAACTCATAAGGGTTG
12335200 AACGGAAACTCATA
1 AACGGAAACTCATA
12335214 TGAGTTAACA
Statistics
Matches: 125, Mismatches: 53, Indels: 8
0.67 0.28 0.04
Matches are distributed among these distances:
20 3 0.02
21 118 0.94
22 4 0.03
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
AACGGAAACTCATAAGGGTTG
Found at i:12335057 original size:42 final size:42
Alignment explanation
Indices: 12334994--12335198 Score: 275
Period size: 42 Copynumber: 4.9 Consensus size: 42
12334984 AGGCTTAACA
** * * *
12334994 GAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGTTGAACG
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*** * *
12335036 GAAGCTTGTAAGAGCTGAACGGAAACCTATAAGGGTTAAATT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*
12335078 GAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*
12335120 GAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
* * *
12335162 AAAGCTCAAAAGAGCTGAACGGAAACTCATTAGGGTT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTT
12335199 GAACGGAAAC
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 145 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
Found at i:12335325 original size:24 final size:24
Alignment explanation
Indices: 12335298--12335369 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
12335288 TACTTGAGTA
* *
12335298 ATTTGCCGTCAATTTATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
12335322 ATTTACCGTCAATTCATTCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
12335346 ATTTACTGTCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
12335370 CACAGAACGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCCTTTGC
Found at i:12344493 original size:19 final size:19
Alignment explanation
Indices: 12344458--12344495 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12344448 ACACATAAGC
*
12344458 ATTTAAATAAATTTTTTAA
1 ATTTAAATAAATATTTTAA
12344477 ATTTAAA-AAATAATTTTAA
1 ATTTAAATAAAT-ATTTTAA
12344496 TGATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAATATTTTAA
Found at i:12344504 original size:29 final size:30
Alignment explanation
Indices: 12344458--12344550 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 30
12344448 ACACATAAGC
*
12344458 ATTTAAATAAATTTTTTAAATTTAAAAAATA
1 ATTTTAAT-AATTTTTTAAATTTAAAAAATA
* * *
12344489 ATTTTAATGA-TTTTTAATTTTTAAAAATA
1 ATTTTAATAATTTTTTAAATTTAAAAAATA
* * *
12344518 GTTTTTATAATTTTTTGAAATTTTAAAATATA
1 ATTTTAATAATTTTTT-AAA-TTTAAAAAATA
12344550 A
1 A
12344551 AAATTAATTA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 24 0.50
30 6 0.12
31 9 0.19
32 9 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTAATAATTTTTTAAATTTAAAAAATA
Found at i:12348317 original size:2 final size:2
Alignment explanation
Indices: 12348310--12348338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12348300 CCACCACCTT
12348310 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
12348339 TACTAGTTTC
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:12350997 original size:23 final size:25
Alignment explanation
Indices: 12350959--12351145 Score: 180
Period size: 25 Copynumber: 7.8 Consensus size: 25
12350949 ATGAGGAACC
* *
12350959 TTAGCGCTATCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
12350984 TTAGTGCTC-C-GATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* * *
12351007 TCAGTGTTATCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* *
12351032 TCAGGGCTCTCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* *
12351057 TTAATGCTCTCTGATTATTAGCACG
1 TTAGTGCTCTCTGATTATTAGCACA
*
12351082 TTAGTGCTCTCCG---ATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
12351104 TCT-GTGCTCTCTG--TA-TAGCAC-
1 T-TAGTGCTCTCTGATTATTAGCACA
*
12351125 TTTGTGCTCTCTG-TTCATTAG
1 TTAGTGCTCTCTGATT-ATTAG
12351146 TGCATAATAA
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.01
21 11 0.08
22 25 0.18
23 22 0.16
24 5 0.04
25 74 0.54
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (25 bp):
TTAGTGCTCTCTGATTATTAGCACA
Found at i:12351101 original size:22 final size:20
Alignment explanation
Indices: 12351073--12351135 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 20
12351063 CTCTCTGATT
12351073 ATTAGCACGTTAGTGCTCTCCG
1 ATTAGCAC-TT-GTGCTCTCCG
*
12351095 ATTAGCACATCTGTGCTCTCTG
1 ATTAGCAC-T-TGTGCTCTCCG
12351117 -TATAGCACTTTGTGCTCTC
1 AT-TAGCAC-TTGTGCTCTC
12351136 TGTTCATTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.28
22 25 0.69
23 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTAGCACTTGTGCTCTCCG
Found at i:12358269 original size:17 final size:18
Alignment explanation
Indices: 12358247--12358280 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12358237 AATCCATACA
12358247 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
12358264 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
12358281 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:12360545 original size:15 final size:15
Alignment explanation
Indices: 12360525--12360553 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12360515 GATAATAGAC
12360525 TAACAATCTCTATAT
1 TAACAATCTCTATAT
12360540 TAACAATCTCTATA
1 TAACAATCTCTATA
12360554 CTCTAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
TAACAATCTCTATAT
Found at i:12375722 original size:28 final size:28
Alignment explanation
Indices: 12375682--12375738 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12375672 AGAAAGAATG
12375682 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
12375710 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
12375738 A
1 A
12375739 CTCCATTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATCTAGCATTATACTATAATCCTTTT
Found at i:12379571 original size:22 final size:22
Alignment explanation
Indices: 12379543--12379650 Score: 144
Period size: 22 Copynumber: 4.9 Consensus size: 22
12379533 TTTATTGTTC
*
12379543 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
12379565 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
12379587 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
12379609 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
12379631 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
12379651 ATCCAAACTG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:12393615 original size:26 final size:26
Alignment explanation
Indices: 12393554--12393617 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
12393544 TTTGAAATTT
*
12393554 AAATAC-ATTTTTATAATTTTTTACA
1 AAATACAATTTTTAAAATTTTTTACA
*
12393579 AAA-AAATATTTTTAAAATTTTTTA-A
1 AAATACA-ATTTTTAAAATTTTTTACA
12393604 AAGATACAATTTTT
1 AA-ATACAATTTTT
12393618 TTATAGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 23 0.72
27 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (26 bp):
AAATACAATTTTTAAAATTTTTTACA
Found at i:12393670 original size:20 final size:19
Alignment explanation
Indices: 12393624--12393677 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
12393614 TTTTTTATAG
* *
12393624 TTTTATAATTTTTTCATTT
1 TTTTATAATTTATTAATTT
**
12393643 TTAAATAATATTATTAATTT
1 TTTTATAAT-TTATTAATTT
12393663 TTTTATAATCTTATT
1 TTTTATAAT-TTATT
12393678 GTATTTTTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTATTAATTT
Found at i:12393716 original size:16 final size:15
Alignment explanation
Indices: 12393679--12393715 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12393669 AATCTTATTG
* *
12393679 TATTTTTGTAAACTT
1 TATTTTTATAAACTA
12393694 TATTTTTATAAACTA
1 TATTTTTATAAACTA
12393709 TATTTTT
1 TATTTTT
12393716 TTCTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTTTATAAACTA
Found at i:12401786 original size:14 final size:14
Alignment explanation
Indices: 12401767--12401793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12401757 TCAAAGCAGA
12401767 TCACTTTTGCAAAG
1 TCACTTTTGCAAAG
12401781 TCACTTTTGCAAA
1 TCACTTTTGCAAA
12401794 CAATGTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
TCACTTTTGCAAAG
Found at i:12418165 original size:22 final size:22
Alignment explanation
Indices: 12418139--12418183 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12418129 TGAGATAAAG
* * *
12418139 AAAAGCTCAAGTATCAATTTGA
1 AAAAGATCAAGTACCAAATTGA
12418161 AAAAGATCAAGTACCAAATTGA
1 AAAAGATCAAGTACCAAATTGA
12418183 A
1 A
12418184 CATTAAAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (22 bp):
AAAAGATCAAGTACCAAATTGA
Found at i:12420192 original size:2 final size:2
Alignment explanation
Indices: 12420187--12420216 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12420177 ACACACACAC
12420187 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 A
12420217 ACAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12426128 original size:3 final size:3
Alignment explanation
Indices: 12426122--12426150 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12426112 TAAGAAACCA
12426122 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12426151 AAGTCTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12434736 original size:23 final size:24
Alignment explanation
Indices: 12434710--12434761 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
12434700 AGAATTAGAA
12434710 AAATTT-TGTAAATGTTAAAAATT-
1 AAATTTAT-TAAATGTTAAAAATTC
* *
12434733 AAATTTATTAAATTTTTAAAATTC
1 AAATTTATTAAATGTTAAAAATTC
12434757 AAATT
1 AAATT
12434762 AAAATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTATTAAATGTTAAAAATTC
Found at i:12434782 original size:21 final size:23
Alignment explanation
Indices: 12434758--12434805 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
12434748 TTAAAATTCA
*
12434758 AATTAAAAT-GATAAAT-TTTAT
1 AATTAAAATAGATAAATATTTAG
*
12434779 AATTAAAATATATAAATATTTAG
1 AATTAAAATAGATAAATATTTAG
12434802 AATT
1 AATT
12434806 TATGATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 6 0.26
23 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AATTAAAATAGATAAATATTTAG
Found at i:12443761 original size:9 final size:9
Alignment explanation
Indices: 12443743--12443800 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
12443733 TTTGGTTAAA
12443743 AATTAACCG
1 AATTAACCG
*
12443752 AATTATCCG
1 AATTAACCG
12443761 AATTAACCG
1 AATTAACCG
* *
12443770 AATTACCCA
1 AATTAACCG
*
12443779 AATTACCCG
1 AATTAACCG
*
12443788 AATTAACCT
1 AATTAACCG
12443797 AATT
1 AATT
12443801 GAATCATACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:12443782 original size:27 final size:27
Alignment explanation
Indices: 12443743--12443800 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12443733 TTTGGTTAAA
* *
12443743 AATTAACCGAATTATCCGAATTAACCG
1 AATTAACCAAATTACCCGAATTAACCG
* *
12443770 AATTACCCAAATTACCCGAATTAACCT
1 AATTAACCAAATTACCCGAATTAACCG
12443797 AATT
1 AATT
12443801 GAATCATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTACCCGAATTAACCG
Found at i:12443920 original size:13 final size:13
Alignment explanation
Indices: 12443902--12443936 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12443892 TATGATTGGG
12443902 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
*
12443915 TTGGGTTTGGTAA
1 TTGGGTTGGGTAA
12443928 TTGGGTTGG
1 TTGGGTTGG
12443937 ATTGAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:12443932 original size:31 final size:29
Alignment explanation
Indices: 12443895--12443963 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
12443885 TAATTTTTAT
* **
12443895 GATTGGGTTGGGTTGGGTAATTGGGTTTG
1 GATTGGGTTGGATTGAATAATTGGGTTTG
*
12443924 GTAATTGGGTTGGATTGAATACTTGGGTTTG
1 G--ATTGGGTTGGATTGAATAATTGGGTTTG
12443955 GATTGGGTT
1 GATTGGGTT
12443964 TAGGTGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 9 0.26
31 25 0.74
ACGTcount: A:0.14, C:0.01, G:0.42, T:0.42
Consensus pattern (29 bp):
GATTGGGTTGGATTGAATAATTGGGTTTG
Found at i:12446273 original size:25 final size:25
Alignment explanation
Indices: 12446229--12446311 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
12446219 ATGTATGCTT
*
12446229 ATACGAGCATGTA-AACGGGAAGCTC
1 ATACGAGC-TGTATAAAGGGAAGCTC
*
12446254 -TTCTGAGCTGTATAAAGGGAAGCTC
1 ATAC-GAGCTGTATAAAGGGAAGCTC
**
12446279 ATACGAGCTGTATATTGGGAAGCTC
1 ATACGAGCTGTATAAAGGGAAGCTC
*
12446304 ATGCGAGC
1 ATACGAGC
12446312 CATTTATCGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 6 0.12
25 41 0.84
26 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (25 bp):
ATACGAGCTGTATAAAGGGAAGCTC
Found at i:12446323 original size:25 final size:25
Alignment explanation
Indices: 12446270--12446331 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
12446260 GCTGTATAAA
** *
12446270 GGGAAGCTCATACGAGCTGTATATT
1 GGGAAGCTCATACGAGCCATATATC
* *
12446295 GGGAAGCTCATGCGAGCCATTTATC
1 GGGAAGCTCATACGAGCCATATATC
12446320 GGGAAGCTCATA
1 GGGAAGCTCATA
12446332 AGAGTTGTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (25 bp):
GGGAAGCTCATACGAGCCATATATC
Found at i:12446370 original size:50 final size:50
Alignment explanation
Indices: 12446270--12446389 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
12446260 GCTGTATAAA
* * ** * * * **
12446270 GGGAAGCTCATACGAGCTGTATATTGGGAAGCTCATGCGAGCCATTTATC
1 GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
*
12446320 GGGAAGCTCATAAGAGTTGTAAATTAAGAAACTCATGCAACCCAAATATC
1 GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
*
12446370 GAGAAGCTCA-AGAGAGCTGT
1 GGGAAGCTCATA-AGAGCTGT
12446390 GGTGTGTCCA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.02
50 56 0.98
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
Found at i:12448630 original size:20 final size:20
Alignment explanation
Indices: 12448607--12448670 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
12448597 TAAAATTAGA
12448607 AAAAAATTGTAAAAAAATTT
1 AAAAAATTGTAAAAAAATTT
*
12448627 AAAAAATTGT--AAAATTTT
1 AAAAAATTGTAAAAAAATTT
*
12448645 ATAAAAATCGTAAAAAAATTAT
1 A-AAAAATTGTAAAAAAATT-T
12448667 AAAA
1 AAAA
12448671 TTTTATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 10 0.27
21 9 0.24
22 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAAATTGTAAAAAAATTT
Found at i:12448630 original size:39 final size:39
Alignment explanation
Indices: 12448587--12448738 Score: 125
Period size: 39 Copynumber: 3.9 Consensus size: 39
12448577 TAAATTTTAA
* *
12448587 TAAAAAATATTAAAATTAGAAAAAAATTGTAAAAAAATT
1 TAAAAAATATTAAAATTATAAAAAAATTATAAAAAAATT
* * **
12448626 TAAAAAAT-TGTAAAATTTTATAAAAATCGTAAAAAAA-T
1 TAAAAAATAT-TAAAATTATAAAAAAATTATAAAAAAATT
* * * * *
12448664 TATAAAATTTTATAAAGCTATAAGAAAATTAT-AAAAAATG
1 TAAAAAATATTA-AAA-TTATAAAAAAATTATAAAAAAATT
12448704 TAAAGAAATA-TAAAATTCAT-AAAAAATTATAAAAA
1 TAAA-AAATATTAAAATT-ATAAAAAAATTATAAAAA
12448739 TTATCTTACC
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
38 21 0.24
39 50 0.56
40 14 0.16
41 4 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (39 bp):
TAAAAAATATTAAAATTATAAAAAAATTATAAAAAAATT
Found at i:12448650 original size:30 final size:30
Alignment explanation
Indices: 12448559--12448679 Score: 84
Period size: 30 Copynumber: 4.0 Consensus size: 30
12448549 GAAAATCAAT
* * *
12448559 AAAAGGTATAAAAATTATTAAATTTTA-ATA
1 AAAAAGTAAAAAAATTATAAAATTTTATA-A
** * ** *
12448589 AAAAA-TATTAAAATTAGAAAAAAATTGTAA
1 AAAAAGTAAAAAAATTA-TAAAATTTTATAA
* * *
12448619 AAAAATTTAAAAAATTGTAAAATTTTATAA
1 AAAAAGTAAAAAAATTATAAAATTTTATAA
**
12448649 AAATCGTAAAAAAATTATAAAATTTTATAA
1 AAAAAGTAAAAAAATTATAAAATTTTATAA
12448679 A
1 A
12448680 GCTATAAGAA
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
29 10 0.15
30 50 0.74
31 8 0.12
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAAGTAAAAAAATTATAAAATTTTATAA
Found at i:12448731 original size:11 final size:10
Alignment explanation
Indices: 12448586--12448742 Score: 68
Period size: 11 Copynumber: 16.2 Consensus size: 10
12448576 TTAAATTTTA
12448586 ATAAAAAA-T
1 ATAAAAAATT
*
12448595 AT-TAAAATT
1 ATAAAAAATT
*
12448604 AGAAAAAAATT
1 A-TAAAAAATT
*
12448615 GTAAAAAAATT
1 AT-AAAAAATT
12448626 -TAAAAAATT
1 ATAAAAAATT
* **
12448635 GTAAAATTTT
1 ATAAAAAATT
12448645 AT-AAAAATCGT
1 ATAAAAAAT--T
12448656 A-AAAAAATT
1 ATAAAAAATT
12448665 AT--AAAATT
1 ATAAAAAATT
* * **
12448673 TTATAAAGCT
1 ATAAAAAATT
12448683 ATAAGAAAATT
1 ATAA-AAAATT
12448694 ATAAAAAATGT
1 ATAAAAAAT-T
*
12448705 A-AAGAAA-T
1 ATAAAAAATT
12448713 AT--AAAATT
1 ATAAAAAATT
12448721 CATAAAAAATT
1 -ATAAAAAATT
12448732 AT-AAAAATT
1 ATAAAAAATT
12448741 AT
1 AT
12448743 CTTACCAAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
7 3 0.03
8 14 0.13
9 29 0.26
10 27 0.24
11 38 0.34
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:12448935 original size:10 final size:10
Alignment explanation
Indices: 12448922--12449002 Score: 53
Period size: 10 Copynumber: 8.3 Consensus size: 10
12448912 TTTTGATACA
12448922 TTTTATAATT
1 TTTTATAATT
*
12448932 TTTTATGA-T
1 TTTTATAATT
**
12448941 TTTTATAAAA
1 TTTTATAATT
*
12448951 TTTTACAATT
1 TTTTATAATT
*
12448961 TCTTAT-ATAT
1 TTTTATAAT-T
* *
12448971 TTCTACAA-T
1 TTTTATAATT
12448980 TTTTATAATT
1 TTTTATAATT
12448990 TTTT-TATATT
1 TTTTATA-ATT
12449000 TTT
1 TTT
12449003 CACTAAATTT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
9 19 0.36
10 33 0.62
11 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12448944 original size:19 final size:19
Alignment explanation
Indices: 12448922--12448993 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
12448912 TTTTGATACA
**
12448922 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTACAAT
**
12448941 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
*
12448960 TTCTTAT-ATATTTCTACAAT
1 TT-TTATAAT-TTTTTACAAT
12448980 TTTTATAATTTTTT
1 TTTTATAATTTTTT
12448994 TATATTTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:12449018 original size:30 final size:29
Alignment explanation
Indices: 12448921--12449022 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 29
12448911 TTTTTGATAC
12448921 ATTTTATAATTTTTTATGATTTTT-A-TAAA
1 ATTTTATAATTTTTTAT-ATTTTTCACT-AA
* * *
12448950 ATTTTACAATTTCTTATATATTTCTAC-AA
1 ATTTTATAATTTTTTATATTTTTC-ACTAA
*
12448979 TTTTTATAATTTTTTTATATTTTTCACTAA
1 ATTTTATAA-TTTTTTATATTTTTCACTAA
*
12449009 ATTTAATAATTTTT
1 ATTTTATAATTTTT
12449023 ATAAACTTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
28 5 0.08
29 31 0.53
30 23 0.39
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTATAATTTTTTATATTTTTCACTAA
Found at i:12450486 original size:2 final size:2
Alignment explanation
Indices: 12450479--12450513 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12450469 AATTTTGTTT
12450479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12450514 GTNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12450775 original size:22 final size:21
Alignment explanation
Indices: 12450745--12450808 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
12450735 AAATTTTTAA
*
12450745 ATTTATATATATATTTTATTTT
1 ATTTTTATAT-TATTTTATTTT
12450767 ATTTTTATATT-TTATTCATTTT
1 ATTTTTATATTATT-TT-ATTTT
12450789 ATTTATT-TATT-TATTTATTT
1 ATTT-TTATATTAT-TTTATTT
12450809 ACGTTTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 25 0.68
23 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTTATATTATTTTATTTT
Found at i:12450795 original size:4 final size:4
Alignment explanation
Indices: 12450745--12450809 Score: 51
Period size: 4 Copynumber: 15.2 Consensus size: 4
12450735 AAATTTTTAA
* * *
12450745 ATTT ATAT ATAT ATTTT ATTTT ATTT -TTAT ATTTT ATTC ATTTT ATTT
1 ATTT ATTT ATTT A-TTT A-TTT ATTT ATT-T A-TTT ATTT A-TTT ATTT
12450793 ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT A
12450810 CGTTTTCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 2 0.04
4 35 0.67
5 13 0.25
6 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:12454837 original size:55 final size:56
Alignment explanation
Indices: 12454774--12454884 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
12454764 AATTTTTAAG
12454774 AAATATAT-AAAAATACGTAAATATTTTTAAATATATATATAA-TAA-TAAAATTTTA
1 AAATATATAAAAAATACGTAAATATTTTTAAA-ATATA-ATAATTAATTAAAATTTTA
* *
12454829 AAATATATAAAAAATACTTAAATATTTTTAAAATATAATAATTAATTTAAATTTTA
1 AAATATATAAAAAATACGTAAATATTTTTAAAATATAATAATTAATTAAAATTTTA
12454885 TATTAATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
54 4 0.08
55 16 0.31
56 31 0.61
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (56 bp):
AAATATATAAAAAATACGTAAATATTTTTAAAATATAATAATTAATTAAAATTTTA
Found at i:12454837 original size:57 final size:56
Alignment explanation
Indices: 12454761--12454884 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 56
12454751 ATCTTAATCC
12454761 TAAAATTTTTAAGAAATATATAAAAATACGTAAATATTTTTAAATATATATATAA-TAA-
1 TAAAA-TTTTAAGAAATATA-AAAAATACGTAAATATTTTTAAA-ATATA-ATAATTAAT
*
12454819 TAAAATTTTAA-AATATATAAAAAATACTTAAATATTTTTAAAATATAATAATTAAT
1 TAAAATTTTAAGAA-ATATAAAAAATACGTAAATATTTTTAAAATATAATAATTAAT
*
12454875 TTAAATTTTA
1 TAAAATTTTA
12454885 TATTAATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
54 4 0.07
55 8 0.13
56 33 0.54
57 11 0.18
58 5 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (56 bp):
TAAAATTTTAAGAAATATAAAAAATACGTAAATATTTTTAAAATATAATAATTAAT
Found at i:12454917 original size:25 final size:25
Alignment explanation
Indices: 12454884--12454931 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
12454874 TTTAAATTTT
*
12454884 ATATTAATATTTAATAAAAATAATG
1 ATATTAATATTAAATAAAAATAATG
*
12454909 ATATTAATATTAAATAATAATAA
1 ATATTAATATTAAATAAAAATAA
12454932 AACCCTCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATTAATATTAAATAAAAATAATG
Found at i:12455522 original size:25 final size:25
Alignment explanation
Indices: 12455488--12455537 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12455478 GGAGACGGGG
*
12455488 TTATTTTTATTTAATATGAATATAA
1 TTATTTTTATTAAATATGAATATAA
*
12455513 TTATTTTTATTAAATATTAATATAA
1 TTATTTTTATTAAATATGAATATAA
12455538 AATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTTTTATTAAATATGAATATAA
Found at i:12455568 original size:29 final size:28
Alignment explanation
Indices: 12455535--12455695 Score: 96
Period size: 26 Copynumber: 6.0 Consensus size: 28
12455525 AATATTAATA
*
12455535 TAAAATTTAAATATATTA-TTATATATTTT
1 TAAAATTT-TATATATTATTTATATA-TTT
*
12455564 TAAAATATTTATGTA-TATTTATATATTT
1 TAAAAT-TTTATATATTATTTATATATTT
*
12455592 TAAAATTTTATATATTA-TT-TCT-TTT
1 TAAAATTTTATATATTATTTATATATTT
* *
12455617 CAATAATATTTCT-TATT-TTTATATATTTT
1 TAA-AAT-TTTATATATTATTTATATA-TTT
*
12455646 TAAAA-TTTAT-TATTA--TATCT-TTT
1 TAAAATTTTATATATTATTTATATATTT
* *
12455669 AAAAATATTTATATACT-TTTATATATT
1 TAAAAT-TTTATATATTATTTATATATT
12455696 GAATTGAGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
23 7 0.07
25 14 0.14
26 22 0.21
27 19 0.18
28 17 0.17
29 22 0.21
30 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
TAAAATTTTATATATTATTTATATATTT
Found at i:12455569 original size:23 final size:23
Alignment explanation
Indices: 12455543--12455680 Score: 71
Period size: 23 Copynumber: 5.5 Consensus size: 23
12455533 TATAAAATTT
12455543 AAATATATTATTATATATTTTTA
1 AAATATATTATTATATATTTTTA
*
12455566 AAATATTTATGTATATTTATATATTTTA
1 AAATA--TAT-TAT-TATATAT-TTTTA
* * * *
12455594 AAATTTTATATATTATTTCTTTTCA
1 AAA-TATAT-TATTATATATTTTTA
*
12455619 ATAATATTTCTTATTTTTATATATTTTTA
1 A-AATA-----TATTATTATATATTTTTA
* * *
12455648 AAATTTATTATTATATCTTTTAA
1 AAATATATTATTATATATTTTTA
12455671 AAATAT-TTAT
1 AAATATATTAT
12455681 ATACTTTTAT
Statistics
Matches: 86, Mismatches: 17, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
22 4 0.05
23 25 0.29
25 9 0.10
26 9 0.10
27 12 0.14
28 11 0.13
29 13 0.15
30 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (23 bp):
AAATATATTATTATATATTTTTA
Found at i:12455571 original size:21 final size:21
Alignment explanation
Indices: 12455514--12455581 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
12455504 TGAATATAAT
*
12455514 TATTTTTATTAAATATTAATATA
1 TATTTTTA--AAATATTATTATA
**
12455537 -AAATTTAAATATATTATTATA
1 TATTTTTAAA-ATATTATTATA
12455558 TATTTTTAAAATATTTATGTATA
1 TATTTTTAAAATA-TTAT-TATA
12455581 T
1 T
12455582 TTATATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 16 0.44
23 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATATTATTATA
Found at i:12455574 original size:31 final size:29
Alignment explanation
Indices: 12455535--12455695 Score: 93
Period size: 27 Copynumber: 6.0 Consensus size: 29
12455525 AATATTAATA
*
12455535 TAAAAT-TTAAATATATTATTATATATTTT
1 TAAAATATTTAATATATTATTATATA-TTT
*
12455564 TAAAATATTT-ATGTA-TATTTATATATTT
1 TAAAATATTTAATATATTA-TTATATATTT
*
12455592 TAAAAT-TTT-ATATATTATT-TCT-TTT
1 TAAAATATTTAATATATTATTATATATTT
* * *
12455617 CAATAATATTT-CT-TATTTTTATATATTT
1 TAA-AATATTTAATATATTATTATATATTT
* *
12455645 TTAAA-ATTT-AT-TATTA-TATCT-TTT
1 TAAAATATTTAATATATTATTATATATTT
*
12455669 AAAAATATTT-ATATACTT-TTATATATT
1 TAAAATATTTAATATA-TTATTATATATT
12455696 GAATTGAGAT
Statistics
Matches: 104, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
24 6 0.06
25 15 0.14
26 22 0.21
27 23 0.22
28 19 0.18
29 17 0.16
30 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
TAAAATATTTAATATATTATTATATATTT
Found at i:12455626 original size:54 final size:49
Alignment explanation
Indices: 12455543--12455695 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 49
12455533 TATAAAATTT
* * *
12455543 AAATATATTATTATATATTTTTAAAATATTTATGTATATTTATATATTTTA
1 AAATTTATTATTATATCTTTTAAAAATATTTAT-TAT-TTTATATATTTTA
* * *
12455594 AAATTTTATATATTATTTCTTTTCAATAATATTTCTTATTTTTATATATTTTTA
1 AAA-TTTAT-TATTATATCTTTT-AAAAATATTTATTA-TTTTATATA-TTTTA
12455648 AAATTTATTATTATATCTTTTAAAAATATTTATATACTTTTATATATT
1 AAATTTATTATTATATCTTTTAAAAATATTTAT-TA-TTTTATATATT
12455696 GAATTGAGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
51 15 0.17
52 27 0.31
53 26 0.30
54 18 0.21
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (49 bp):
AAATTTATTATTATATCTTTTAAAAATATTTATTATTTTATATATTTTA
Found at i:12455645 original size:10 final size:10
Alignment explanation
Indices: 12455630--12455695 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
12455620 TAATATTTCT
12455630 TATTTTTATA
1 TATTTTTATA
12455640 TATTTTTA-A
1 TATTTTTATA
*
12455649 AATTTATTATTA
1 TATTT-TTA-TA
*
12455661 TATCTTTTAAA
1 TAT-TTTTATA
* *
12455672 AATATTTATA
1 TATTTTTATA
*
12455682 TACTTTTATA
1 TATTTTTATA
12455692 TATT
1 TATT
12455696 GAATTGAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.62
11 3 0.07
12 6 0.14
13 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTTTATA
Found at i:12455677 original size:21 final size:20
Alignment explanation
Indices: 12455638--12455689 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
12455628 CTTATTTTTA
*
12455638 TATAT-TTTTAAAATTTATTAT
1 TATATCTTTTAAAATATA-T-T
12455659 TATATCTTTTAAAA-ATATT
1 TATATCTTTTAAAATATATT
12455678 TATATACTTTTA
1 TATAT-CTTTTA
12455690 TATATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 7 0.25
21 7 0.25
22 8 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATCTTTTAAAATATATT
Found at i:12466488 original size:26 final size:27
Alignment explanation
Indices: 12466459--12466515 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
12466449 TTACTAAATG
12466459 TAAATACACAT-TAAAAAATATAAAAA
1 TAAATACACATATAAAAAATATAAAAA
* * *
12466485 TAAATATACATATATAAAATCTAAAAA
1 TAAATACACATATAAAAAATATAAAAA
12466512 -AAAT
1 TAAAT
12466516 CTAAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (27 bp):
TAAATACACATATAAAAAATATAAAAA
Found at i:12466544 original size:15 final size:16
Alignment explanation
Indices: 12466509--12466546 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12466499 TAAAATCTAA
*
12466509 AAAAAATCTAAATTTT
1 AAAAAATATAAATTTT
12466525 -AAAAATAT-AATTTT
1 AAAAAATATAAATTTT
12466539 AAAAAATA
1 AAAAAATA
12466547 CAATAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAATATAAATTTT
Found at i:12471652 original size:18 final size:18
Alignment explanation
Indices: 12471615--12471653 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12471605 ATTATTATTT
*
12471615 TAAAATTTACTATTAGAA
1 TAAAATTTAATATTAGAA
12471633 TAAAATTTAAATATTA-AA
1 TAAAATTT-AATATTAGAA
12471651 TAA
1 TAA
12471654 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTAATATTAGAA
Found at i:12497391 original size:2 final size:2
Alignment explanation
Indices: 12497384--12497416 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12497374 NNNNNNNNNN
12497384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12497417 CACATTATGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12501389 original size:12 final size:12
Alignment explanation
Indices: 12501372--12501398 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12501362 TATGTGTATA
12501372 ATTATTATAATT
1 ATTATTATAATT
12501384 ATTATTATAATT
1 ATTATTATAATT
12501396 ATT
1 ATT
12501399 CATTCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTATAATT
Found at i:12501733 original size:20 final size:19
Alignment explanation
Indices: 12501700--12501751 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
12501690 AATTAAACAT
*
12501700 AAAGTAAAATAAAACAAAGCA
1 AAAG-AAAAGAAAACAAAG-A
*
12501721 AAAGAAAAGAAAAGAAAGA
1 AAAGAAAAGAAAACAAAGA
*
12501740 AACAGAATAGAA
1 AA-AGAAAAGAA
12501752 GGAGACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 20 0.74
21 4 0.15
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAGAAAAGAAAACAAAGA
Found at i:12502851 original size:39 final size:39
Alignment explanation
Indices: 12502789--12502903 Score: 151
Period size: 39 Copynumber: 3.0 Consensus size: 39
12502779 TTACTGATCA
* *
12502789 GGCAC-TTATGTGCCGACTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
* *
12502827 GGCACTTTGTGTGTCGAATACTGTTACTGTTACCAATTC
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
* * * *
12502866 GGCACTTGGTGTGGCGAATACTGTTACCGTTACTGATT
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATT
12502904 ACTGCTACTG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
38 5 0.07
39 62 0.93
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (39 bp):
GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
Found at i:12511698 original size:16 final size:17
Alignment explanation
Indices: 12511677--12511708 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12511667 TTCTTATAAT
12511677 TTTAAAAATTA-AAAAC
1 TTTAAAAATTAGAAAAC
12511693 TTTAAAAATTAGAAAA
1 TTTAAAAATTAGAAAA
12511709 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TTTAAAAATTAGAAAAC
Found at i:12511769 original size:21 final size:20
Alignment explanation
Indices: 12511725--12511775 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
12511715 AAATTTTATT
*
12511725 TTTATAAAAGTACATAAGAT
1 TTTATAAAAGTACATAAGAA
12511745 TTTATAAAAGTTACATACA-AA
1 TTTATAAAAG-TACATA-AGAA
12511766 TTTATCAAAA
1 TTTAT-AAAA
12511776 TATTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTATAAAAGTACATAAGAA
Found at i:12511854 original size:18 final size:18
Alignment explanation
Indices: 12511831--12511867 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12511821 TTTATTTATT
*
12511831 AAAATAATAATTTTATAA
1 AAAATAATAATCTTATAA
12511849 AAAATAATAATCTTATAA
1 AAAATAATAATCTTATAA
12511867 A
1 A
12511868 TAAAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAATAATCTTATAA
Found at i:12511856 original size:15 final size:17
Alignment explanation
Indices: 12511825--12511864 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
12511815 ATAAAATTTA
12511825 TTTATTAAAATAATAAT
1 TTTATTAAAATAATAAT
*
12511842 TTTATAAAAAATAATAAT
1 TTTAT-TAAAATAATAAT
*
12511860 CTTAT
1 TTTAT
12511865 AAATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATTAAAATAATAAT
Found at i:12514203 original size:70 final size:71
Alignment explanation
Indices: 12514085--12514228 Score: 245
Period size: 70 Copynumber: 2.0 Consensus size: 71
12514075 AAGCCAACTA
* *
12514085 ACTGCTGTCTTGTTTTGATATATATGTTGCTTGTTAAACATGATTTCATGTGCTGTAATGATGCT
1 ACTGCTGTCTTGTTTTGA-ATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCT
12514150 TAATCCT
65 TAATCCT
*
12514157 ACTGCTGTCTTGTTTTG-ATATATGTTGCTTGTTAAACATGACTTCATGTGTTGCAATGATGCTT
1 ACTGCTGTCTTGTTTTGAATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCTT
12514221 AATCCT
66 AATCCT
12514227 AC
1 AC
12514229 CTTTGAATCT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 52 0.75
72 17 0.25
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.44
Consensus pattern (71 bp):
ACTGCTGTCTTGTTTTGAATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCTT
AATCCT
Found at i:12514832 original size:17 final size:17
Alignment explanation
Indices: 12514797--12514841 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12514787 ATAAATTTAA
*
12514797 TTATTATTTAACATATT
1 TTATTATTTAAAATATT
12514814 TTATT-TTTAAAATATTT
1 TTATTATTTAAAATA-TT
12514831 TTAATTATTTA
1 TT-ATTATTTA
12514842 TTCTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 9 0.38
18 3 0.12
19 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATTTAAAATATT
Found at i:12516505 original size:46 final size:46
Alignment explanation
Indices: 12516375--12516513 Score: 199
Period size: 46 Copynumber: 3.0 Consensus size: 46
12516365 ACATTGTTAT
* * * *
12516375 AACTCAGTATGGTTTTCTTCACTGAAACACCATACTTAATTTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
12516421 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
12516467 AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
12516513 A
1 A
12516514 CTTTGCCATG
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 81 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:12517774 original size:16 final size:17
Alignment explanation
Indices: 12517728--12517775 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
12517718 AAATTCTTTT
12517728 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
12517745 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
12517762 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
12517776 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:12517966 original size:24 final size:24
Alignment explanation
Indices: 12517932--12517977 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12517922 TTGGCTTCGG
* **
12517932 TGAGATTGAAAATGTCAGTGGCGA
1 TGAGATCGAAAATCACAGTGGCGA
12517956 TGAGATCGAAAATCACAGTGGC
1 TGAGATCGAAAATCACAGTGGC
12517978 AGACTCAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (24 bp):
TGAGATCGAAAATCACAGTGGCGA
Found at i:12518129 original size:22 final size:23
Alignment explanation
Indices: 12518079--12518145 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 23
12518069 AGTTGTTAAA
12518079 AATAATTATCAATATATAATAATT
1 AATAATTA-CAATATATAATAATT
* *
12518103 -A-AATTA-AATTTATATTAATT
1 AATAATTACAATATATAATAATT
*
12518123 AATAATTATTAATATATAATAAT
1 AATAATTA-CAATATATAATAAT
12518146 AAAAATCTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 12 0.34
21 1 0.03
22 10 0.29
23 1 0.03
24 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
AATAATTACAATATATAATAATT
Found at i:12524403 original size:11 final size:11
Alignment explanation
Indices: 12524389--12524431 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12524379 TTCTACGTTC
12524389 TTCTTTTCTTT
1 TTCTTTTCTTT
*
12524400 TTCTTTTGTTT
1 TTCTTTTCTTT
* *
12524411 TTTTTTTCATT
1 TTCTTTTCTTT
*
12524422 TTCCTTTCTT
1 TTCTTTTCTT
12524432 CACTATAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:12528467 original size:50 final size:51
Alignment explanation
Indices: 12528353--12528479 Score: 161
Period size: 50 Copynumber: 2.5 Consensus size: 51
12528343 CGGATATCCG
* ** *
12528353 GTGGCCTGCACATAGTACCACTTTTGTAGTCAAAGCTACCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAA
* *
12528404 GTGGCGC-TCACATAGTACCACACTTGT-GACCAAAGCTATC-TCTTCTCAAA
1 GTGGC-CTTCACATAGTACCACACTTGTAG-CCAAAGCTACCTTCTTCACAAA
12528454 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
12528480 AGTCACTAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
49 1 0.01
50 34 0.51
51 31 0.46
52 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAA
Found at i:12530156 original size:53 final size:53
Alignment explanation
Indices: 12530076--12530182 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
12530066 ACTGAACCTG
12530076 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
*
12530129 TATAACCAAGATACACCCAAATATATTATTAATACAACCCGAATCAAATTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
12530182 T
1 T
12530183 TACACTTCCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.24
Consensus pattern (53 bp):
TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
Found at i:12531384 original size:2 final size:2
Alignment explanation
Indices: 12531379--12531462 Score: 147
Period size: 2 Copynumber: 43.5 Consensus size: 2
12531369 TAACACACAC
12531379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12531421 AT AT AT AT AT AT AT -T AT -T AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12531460 AT A
1 AT A
12531463 GTACGTACGN
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 76 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12541057 original size:23 final size:23
Alignment explanation
Indices: 12541027--12541075 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
12541017 TATTTGTAGA
12541027 TAAAAAGAAGAAGAAGATATGTT
1 TAAAAAGAAGAAGAAGATATGTT
12541050 TAAAAAGAAGAAGAAGATATGTT
1 TAAAAAGAAGAAGAAGATATGTT
12541073 TAA
1 TAA
12541076 GAATTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.22
Consensus pattern (23 bp):
TAAAAAGAAGAAGAAGATATGTT
Found at i:12555453 original size:28 final size:28
Alignment explanation
Indices: 12555421--12555475 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
12555411 TTTAAGTGTT
*
12555421 AAAGTTGTTATTCTGCTATTTTTAAAAA
1 AAAGTTGTTATTATGCTATTTTTAAAAA
12555449 AAAGTTGTTATTATGCTATTTTTAAAA
1 AAAGTTGTTATTATGCTATTTTTAAAA
12555476 GCTGACACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.47
Consensus pattern (28 bp):
AAAGTTGTTATTATGCTATTTTTAAAAA
Found at i:12561503 original size:2 final size:2
Alignment explanation
Indices: 12561496--12561528 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12561486 ACGTACCCTT
12561496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12561529 TTGTTGTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12561728 original size:21 final size:21
Alignment explanation
Indices: 12561687--12561728 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12561677 CATAGATTAC
* *
12561687 ATTGTTTATTATTTTTTTGCT
1 ATTGTTTACTATTTTTCTGCT
12561708 ATTGTTT-CTATTGTTTCTGCT
1 ATTGTTTACTATT-TTTCTGCT
12561729 TTCGTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (21 bp):
ATTGTTTACTATTTTTCTGCT
Found at i:12563948 original size:39 final size:39
Alignment explanation
Indices: 12563889--12563974 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
12563879 GAGCTCAACC
*
12563889 TTTTAGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
1 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
12563928 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
1 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
12563967 TTTTTGAT
1 TTTTTGAT
12563975 GGGTAGCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (39 bp):
TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
Found at i:12568364 original size:21 final size:22
Alignment explanation
Indices: 12568320--12568368 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
12568310 ATTTTTAAAT
12568320 TTAATAAATTAAAAAATAGATAA
1 TTAA-AAATTAAAAAATAGATAA
12568343 TTAAAAATTAAAATAA-AG-TAA
1 TTAAAAATTAAAA-AATAGATAA
12568364 TTAAA
1 TTAAA
12568369 CCATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
TTAAAAATTAAAAAATAGATAA
Found at i:12568589 original size:21 final size:21
Alignment explanation
Indices: 12568551--12568591 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12568541 ACCGTTAATT
* **
12568551 TTATTTTTAAATTTAATGTAA
1 TTATTTATAAATAAAATGTAA
12568572 TTATTTATAAATAAAATGTA
1 TTATTTATAAATAAAATGTA
12568592 GAATATTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTTATAAATAAAATGTAA
Found at i:12569265 original size:21 final size:20
Alignment explanation
Indices: 12569240--12569279 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12569230 AAAATTACAA
12569240 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
* *
12569260 AAAAAATTCCAAATTTTTAT
1 AAAAAATTCAAAATATTTAT
12569280 TTTAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:12569319 original size:22 final size:23
Alignment explanation
Indices: 12569293--12569336 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12569283 AAGAAATTAT
*
12569293 ATATATTTAAA-AAATCTAAAAA
1 ATATATATAAAGAAATCTAAAAA
*
12569315 ATATATATAAAGAAATTTAAAA
1 ATATATATAAAGAAATCTAAAA
12569337 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
ATATATATAAAGAAATCTAAAAA
Found at i:12573068 original size:2 final size:2
Alignment explanation
Indices: 12573056--12573099 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12573046 TGTAAATATT
*
12573056 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12573098 CA
1 CA
12573100 TTACCAATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12575555 original size:113 final size:114
Alignment explanation
Indices: 12575357--12575575 Score: 422
Period size: 113 Copynumber: 1.9 Consensus size: 114
12575347 CCATCAAGAA
*
12575357 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGTCCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
12575422 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCT-GTCATTAGAGGAGT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATTAGAGGAGT
12575470 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
12575535 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATT
12575576 CCCATGCTTC
Statistics
Matches: 104, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
113 98 0.94
114 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (114 bp):
ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATTAGAGGAGT
Found at i:12578610 original size:22 final size:21
Alignment explanation
Indices: 12578584--12578644 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
12578574 ATCTAAATTC
*
12578584 AAATTAAATAATAAAATTATCT
1 AAATTAAAT-ATAAAATTATAT
* *
12578606 AAATTTAAGTATAAAAATATAT
1 AAA-TTAAATATAAAATTATAT
*
12578628 AAATATTAATATAAAAT
1 AAAT-TAAATATAAAAT
12578645 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.81
23 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTAAATATAAAATTATAT
Done.