Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 12 of 54
Found at i:5563167 original size:33 final size:33
Alignment explanation
Indices: 5563064--5563172 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 33
5563054 AAAGCCGAAA
* * *
5563064 AGAGAGAGAAGAAAGGAA-AGGAAG-AGAAAAAAC
1 AGAGAGAGAAGGAAGGAAGA-AAAGTAG-AAAAAG
* * * *
5563097 AAAGAGAGAGGGAAGGAAGCAAAGTTGAAAAAGAAAG
1 AGAGAGAGAAGGAAGGAAGAAAAG-T--AGAA-AAAG
5563134 AGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAAG
1 AGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAAG
5563167 AGAGAG
1 AGAGAG
5563173 GAGATAGAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
33 28 0.47
34 3 0.05
36 3 0.05
37 25 0.42
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.03
Consensus pattern (33 bp):
AGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAAG
Found at i:5564539 original size:2 final size:2
Alignment explanation
Indices: 5564532--5564566 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5564522 ATAAAGGCAA
*
5564532 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5564567 ATCATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5564628 original size:27 final size:27
Alignment explanation
Indices: 5564591--5564644 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5564581 AAATTTATAA
5564591 GAAGATAAAAGAAAACCATGGTTAGTC
1 GAAGATAAAAGAAAACCATGGTTAGTC
5564618 NGAAGAT-AAAGAAAACCATGGTTAGTC
1 -GAAGATAAAAGAAAACCATGGTTAGTC
5564645 AAAAAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.19
Consensus pattern (27 bp):
GAAGATAAAAGAAAACCATGGTTAGTC
Found at i:5568269 original size:18 final size:17
Alignment explanation
Indices: 5568236--5568269 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5568226 CTGTGTTTTG
*
5568236 TGAGGCGATTCTGAGTT
1 TGAGGCGATGCTGAGTT
5568253 TGAGGCTGATGCTGAGT
1 TGAGGC-GATGCTGAGT
5568270 CGTTGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.12, G:0.38, T:0.32
Consensus pattern (17 bp):
TGAGGCGATGCTGAGTT
Found at i:5569899 original size:2 final size:2
Alignment explanation
Indices: 5569888--5569925 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5569878 AGTAAGAAAC
5569888 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5569926 AAATACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5582602 original size:33 final size:33
Alignment explanation
Indices: 5582560--5582628 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
5582550 CAAAAGTAAA
5582560 TTAAAAAAGTCAGCCACAAAATTTCTACTTTAT
1 TTAAAAAAGTCAGCCACAAAATTTCTACTTTAT
5582593 TTAAAAAAGTCAGCCACAAAATTTCTACTTTAT
1 TTAAAAAAGTCAGCCACAAAATTTCTACTTTAT
5582626 TTA
1 TTA
5582629 TTTACTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (33 bp):
TTAAAAAAGTCAGCCACAAAATTTCTACTTTAT
Found at i:5587331 original size:21 final size:20
Alignment explanation
Indices: 5587294--5587332 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5587284 TACTTAGAAA
*
5587294 AAAATGATAAATAAATAATT
1 AAAATGATAAACAAATAATT
*
5587314 AAAATGGATAAACCAATAA
1 AAAAT-GATAAACAAATAA
5587333 CCTTGTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAATGATAAACAAATAATT
Found at i:5591788 original size:13 final size:12
Alignment explanation
Indices: 5591766--5591799 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5591756 GATAGAAAAT
5591766 AATGAAGAAGAC
1 AATGAAGAAGAC
*
5591778 GAATTAAGAAGAC
1 -AATGAAGAAGAC
5591791 AATGAAGAA
1 AATGAAGAA
5591800 ACCAGCTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (12 bp):
AATGAAGAAGAC
Found at i:5592687 original size:2 final size:2
Alignment explanation
Indices: 5592671--5592724 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
5592661 CAAGTAAGAA
* *
5592671 AT AT AT -T AT AC AT AT AT AT AT AT AT AT -T AT AC 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
5592711 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
5592725 CAAACCTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5592697 original size:21 final size:21
Alignment explanation
Indices: 5592671--5592718 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5592661 CAAGTAAGAA
5592671 ATATATTATACATATATATAT
1 ATATATTATACATATATATAT
5592692 ATATATTATACATATATATAT
1 ATATATTATACATATATATAT
5592713 ATATAT
1 ATATAT
5592719 ATTATACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATATTATACATATATATAT
Found at i:5592708 original size:23 final size:22
Alignment explanation
Indices: 5592671--5592727 Score: 98
Period size: 23 Copynumber: 2.6 Consensus size: 22
5592661 CAAGTAAGAA
5592671 ATATATTATAC-ATATATATAT
1 ATATATTATACAATATATATAT
5592692 ATATATTATACATATATATATAT
1 ATATATTATACA-ATATATATAT
5592715 ATATATTATACAA
1 ATATATTATACAA
5592728 ACCTGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.32
22 1 0.03
23 22 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATTATACAATATATATAT
Found at i:5599483 original size:39 final size:39
Alignment explanation
Indices: 5599434--5599521 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
5599424 ATTCATTCTC
*
5599434 CCTTGTATGTTTCTTTTCCTTTCTTCAAGCACACGTGGT
1 CCTTGCATGTTTCTTTTCCTTTCTTCAAGCACACGTGGT
** *
5599473 CCTTGCATGTTTCTTTTCCTTTCTTCAAGGGCAGGTGGT
1 CCTTGCATGTTTCTTTTCCTTTCTTCAAGCACACGTGGT
*
5599512 GCTTGCATGT
1 CCTTGCATGT
5599522 AATTTATTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (39 bp):
CCTTGCATGTTTCTTTTCCTTTCTTCAAGCACACGTGGT
Found at i:5599580 original size:42 final size:42
Alignment explanation
Indices: 5599533--5599615 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
5599523 ATTTATTGCA
*
5599533 TATTTTCTTTTCCTCTCAAAGCTACACATGGAGTTCCTTTCG
1 TATTTTCTTTTCCTCTCAAAGCCACACATGGAGTTCCTTTCG
* * *
5599575 TATTTTCTTTTCTTCTCAAAGCCACACGTGGTGTTCCTTTC
1 TATTTTCTTTTCCTCTCAAAGCCACACATGGAGTTCCTTTC
5599616 ATGAACGTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.17, C:0.27, G:0.12, T:0.45
Consensus pattern (42 bp):
TATTTTCTTTTCCTCTCAAAGCCACACATGGAGTTCCTTTCG
Found at i:5601936 original size:20 final size:20
Alignment explanation
Indices: 5601913--5601981 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
5601903 AATTTAGTAA
5601913 AATTTATAATTATTTAAATT
1 AATTTATAATTATTTAAATT
* *
5601933 AA-TTATGATTTTATTAAGTTAATT
1 AATTTAT-A-ATTATT---TAAATT
5601957 AAATTTATAATTATTTAAATT
1 -AATTTATAATTATTTAAATT
5601978 AATT
1 AATT
5601982 AGAGTTTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 4 0.11
20 7 0.18
21 10 0.26
24 10 0.26
25 3 0.08
26 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTATAATTATTTAAATT
Found at i:5601963 original size:45 final size:44
Alignment explanation
Indices: 5601912--5601998 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
5601902 GAATTTAGTA
*
5601912 AAATTTATAATTATTTAAATTAATTATGA-TTTTATTAAGTTAATT
1 AAATTTATAATTATTTAAATTAATTA-GAGTTTTAGTAA-TTAATT
5601957 AAATTTATAATTATTTAAATTAATTAGAGTTTTAGTAATTAA
1 AAATTTATAATTATTTAAATTAATTAGAGTTTTAGTAATTAA
5601999 GTAATTAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 6 0.15
45 34 0.85
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.51
Consensus pattern (44 bp):
AAATTTATAATTATTTAAATTAATTAGAGTTTTAGTAATTAATT
Found at i:5604705 original size:37 final size:37
Alignment explanation
Indices: 5604605--5604740 Score: 145
Period size: 37 Copynumber: 3.8 Consensus size: 37
5604595 AATGATGCTG
* * *
5604605 AGATAAAACTGATTGCTTTTCTTTTTAAAACATGATA
1 AGATAAAACTAATTGATTTTCTTTTTAAAATATGATA
* * * * *
5604642 AGAT-TAACTAACT-A-CTT-TTTTTAAAATGTGCTA
1 AGATAAAACTAATTGATTTTCTTTTTAAAATATGATA
* *
5604675 AGATAAAATTGATTGATTTTCTTTTTAAAATATGATA
1 AGATAAAACTAATTGATTTTCTTTTTAAAATATGATA
*
5604712 AGGTAAAACTAATTGATTTTCTTTTTAAA
1 AGATAAAACTAATTGATTTTCTTTTTAAA
5604741 TGGATAATGT
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
33 17 0.22
34 7 0.09
35 1 0.01
36 8 0.10
37 44 0.57
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (37 bp):
AGATAAAACTAATTGATTTTCTTTTTAAAATATGATA
Found at i:5623419 original size:11 final size:11
Alignment explanation
Indices: 5623349--5623434 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
5623339 CTTATTTATA
5623349 TATTTATTTTGT
1 TATTTATTTT-T
*
5623361 CATTT-TTTTT
1 TATTTATTTTT
* ** *
5623371 CATGAATTATT
1 TATTTATTTTT
5623382 TATTTATTTTAT
1 TATTTATTTT-T
5623394 TA-TTATTATTAT
1 TATTTATT-TT-T
*
5623406 TATTTGTTTTT
1 TATTTATTTTT
5623417 TATTTTATTTTT
1 TA-TTTATTTTT
5623429 TATTTA
1 TATTTA
5623435 GATCCATATC
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
10 4 0.07
11 26 0.44
12 25 0.42
13 4 0.07
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:5623427 original size:12 final size:12
Alignment explanation
Indices: 5623380--5623433 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
5623370 TCATGAATTA
5623380 TTTA-TTTATTT
1 TTTATTTTATTT
5623391 TATTATTATTA-TT
1 T-TTATT-TTATTT
* *
5623404 ATTA-TTTGTTT
1 TTTATTTTATTT
5623415 TTTATTTTATTT
1 TTTATTTTATTT
5623427 TTTATTT
1 TTTATTT
5623434 AGATCCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 19 0.56
13 3 0.09
14 3 0.09
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:5624630 original size:14 final size:14
Alignment explanation
Indices: 5624606--5624642 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5624596 CTTCTTTTCT
5624606 TTTCTCTCTCTTCAC
1 TTTC-CTCTCTTCAC
5624621 TTTCCTCTC-TCAC
1 TTTCCTCTCTTCAC
5624634 TTT-CTCTCT
1 TTTCCTCTCT
5624643 CATGCCGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 7 0.33
14 5 0.24
15 4 0.19
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTCCTCTCTTCAC
Found at i:5624640 original size:12 final size:12
Alignment explanation
Indices: 5624610--5624644 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5624600 TTTTCTTTTC
5624610 TCTCTCTTCACTT
1 TCTCTC-TCACTT
5624623 TCCTCTCTCACTT
1 T-CTCTCTCACTT
5624636 TCTCTCTCA
1 TCTCTCTCA
5624645 TGCCGCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 8 0.38
14 5 0.24
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTCTCTCACTT
Found at i:5624643 original size:14 final size:15
Alignment explanation
Indices: 5624606--5624643 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
5624596 CTTCTTTTCT
5624606 TTTCTCTCTCTTCAC
1 TTTCTCTCTCTTCAC
5624621 TTTC-CTCTC-TCAC
1 TTTCTCTCTCTTCAC
5624634 TTTCTCTCTC
1 TTTCTCTCTC
5624644 ATGCCGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 10 0.45
15 4 0.18
ACGTcount: A:0.05, C:0.42, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCTCTCTCTTCAC
Found at i:5632760 original size:15 final size:16
Alignment explanation
Indices: 5632740--5632769 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5632730 CTGTTATGCA
5632740 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
5632755 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
5632770 AAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:5632904 original size:85 final size:83
Alignment explanation
Indices: 5632813--5632981 Score: 293
Period size: 85 Copynumber: 2.0 Consensus size: 83
5632803 ATATAAGTTA
5632813 TAGTGTTACATTATTAATTGTTGTTTAAAATTTCACTAATATATTATTTTTTTATTAATCCTAAT
1 TAGTGTTACATTATTAATTGTTGTTTAAAATTTCACTAATATATTA-TTTTTTATTAATCCTAAT
5632878 TATATAAGAAAAAATTATC
65 TATATAAGAAAAAATTATC
** *
5632897 TNAGTGTTGTATTATTAGTTGTTGTTTAAAATTTCACTAATATATTATTTTTTATTAATCCTAAT
1 T-AGTGTTACATTATTAATTGTTGTTTAAAATTTCACTAATATATTATTTTTTATTAATCCTAAT
5632962 TATATAAGAAAAAATTATC
65 TATATAAGAAAAAATTATC
5632981 T
1 T
5632982 TGAGTATATT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
84 39 0.48
85 42 0.52
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (83 bp):
TAGTGTTACATTATTAATTGTTGTTTAAAATTTCACTAATATATTATTTTTTATTAATCCTAATT
ATATAAGAAAAAATTATC
Found at i:5634723 original size:27 final size:27
Alignment explanation
Indices: 5634673--5634787 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 27
5634663 AAGCGCCCAA
* ** *
5634673 AGGTGTTCTAAATGTATAAGCGTCCA-
1 AGGTGTTCCAAATGTGGAAACGTCCAG
* **
5634699 AGGGTGTTCTAAGCGTGGAAACGTCCAG
1 A-GGTGTTCCAAATGTGGAAACGTCCAG
5634727 AGGTGTTCCAAATGTGGAAACGTCCAG
1 AGGTGTTCCAAATGTGGAAACGTCCAG
*
5634754 AGGTGTTCCAAATGTGGAAACGCCCAG
1 AGGTGTTCCAAATGTGGAAACGTCCAG
*
5634781 GGGTGTT
1 AGGTGTT
5634788 TCAATCATGG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 75 0.97
28 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.24
Consensus pattern (27 bp):
AGGTGTTCCAAATGTGGAAACGTCCAG
Found at i:5656977 original size:15 final size:16
Alignment explanation
Indices: 5656946--5656992 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
5656936 ATAATTTTAT
*
5656946 TTAAAATTATTAATAAA
1 TTAAAA-TATTATTAAA
5656963 -TAAAATATTATTAAA
1 TTAAAATATTATTAAA
5656978 TTTAAAATATT-TTAA
1 -TTAAAATATTATTAA
5656993 CTCGAACTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 9 0.33
16 9 0.33
17 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATTATTAAA
Found at i:5665757 original size:2 final size:2
Alignment explanation
Indices: 5665750--5665892 Score: 180
Period size: 2 Copynumber: 71.5 Consensus size: 2
5665740 TGGCAGATTT
* *
5665750 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5665792 TA TA TA TG TA TA TA TG TA TA TA TA TA TA CA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5665834 TA TA TA TA CA TA TA TA TA GTA TA TA TA TA TA -A AA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
5665876 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
5665893 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
1 1 0.01
2 118 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5665939 original size:2 final size:2
Alignment explanation
Indices: 5665932--5666035 Score: 136
Period size: 2 Copynumber: 52.0 Consensus size: 2
5665922 NNNNNNNNNN
* * *
5665932 AT AT AT AT AC AT AT AT AT AT AT GT AT AT AT GT 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
* * * *
5665974 AC AT AT AT AC AT AT AT AT AT AT AC AT AT AT AT GT 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
*
5666016 AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5666036 TGTAAAAAGC
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5669111 original size:3 final size:3
Alignment explanation
Indices: 5669103--5669127 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5669093 AGTTGAAACC
5669103 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5669128 GCACCTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5678640 original size:2 final size:2
Alignment explanation
Indices: 5678635--5678662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5678625 TATAAAACTT
5678635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5678663 AGTATGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5679735 original size:12 final size:12
Alignment explanation
Indices: 5679718--5679755 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5679708 CTTTTTATGG
*
5679718 TATATATATATA
1 TATATATATGTA
5679730 TATATATATGTA
1 TATATATATGTA
*
5679742 TGTATATATGTA
1 TATATATATGTA
5679754 TA
1 TA
5679756 GATAATTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:5701546 original size:195 final size:195
Alignment explanation
Indices: 5701181--5701563 Score: 480
Period size: 195 Copynumber: 2.0 Consensus size: 195
5701171 CATTGCCACA
* * *
5701181 CTCAGGGGGTTTCACAGTTTGGGCAGTTCCTAAACCACCCTCATTCACACTACTCTCAGTAACCA
1 CTCAGGAGGTTTCACAGTTTGGGCAGTTCCTAAACCACCCTCATTCACACTACACTCAGAAACCA
* * *
5701246 ACTTAGCTTGAGAAAATTCTAGTGCAGCAGGTTCTTGATTTTGGGTGGTATAAGTATTAGGTGAT
66 ACTTAGCTTGAGAAAATTCTAGTGCAGCAGCTTCTCGATTTTGGGTAGTATAAGTATTAGGTGAT
** * ** ** * *
5701311 TCCTGTCTTATTCGCAATTTAACTGACTTTGGCCTATTAGAAATAGAATTGATAGCTGCACTGTT
131 TCCCATCCTATTCGCAAGGTAACCAACTTTGGCCTATTAGAAACAGAATTAATAGCTGCACTGTT
* * * **
5701376 CTCAGGAGGTTTCACAGTTTGGGCAGTTTCTAAACCACCCTCGTTCTCACTACACTTGGAAACCA
1 CTCAGGAGGTTTCACAGTTTGGGCAGTTCCTAAACCACCCTCATTCACACTACACTCAGAAACCA
* ** * * * *
5701441 ACTTGGCTTGAGAAGGTTCTTGTGCAGCAGCTTCTCGTTTTTGGGTAGTGTAAGTATTAGGTGCT
66 ACTTAGCTTGAGAAAATTCTAGTGCAGCAGCTTCTCGATTTTGGGTAGTATAAGTATTAGGTGAT
** *
5701506 TCCCATCCTATTCGTGAGGTAACCAAC-TTGGACTTATTAGAAACAGAATTAATAGCTG
131 TCCCATCCTATTCGCAAGGTAACCAACTTTGG-CCTATTAGAAACAGAATTAATAGCTG
5701564 TATTACCCTC
Statistics
Matches: 157, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
194 4 0.03
195 153 0.97
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (195 bp):
CTCAGGAGGTTTCACAGTTTGGGCAGTTCCTAAACCACCCTCATTCACACTACACTCAGAAACCA
ACTTAGCTTGAGAAAATTCTAGTGCAGCAGCTTCTCGATTTTGGGTAGTATAAGTATTAGGTGAT
TCCCATCCTATTCGCAAGGTAACCAACTTTGGCCTATTAGAAACAGAATTAATAGCTGCACTGTT
Found at i:5705598 original size:23 final size:23
Alignment explanation
Indices: 5705572--5705616 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5705562 AATAGAAACA
5705572 CCAATTTAACAGATAATTAGTAT
1 CCAATTTAACAGATAATTAGTAT
5705595 CCAATTTAACAGATAATTAGTA
1 CCAATTTAACAGATAATTAGTA
5705617 ATAAGGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (23 bp):
CCAATTTAACAGATAATTAGTAT
Found at i:5705932 original size:79 final size:79
Alignment explanation
Indices: 5705797--5705950 Score: 211
Period size: 79 Copynumber: 1.9 Consensus size: 79
5705787 TCTTGAGTGG
* * *
5705797 GGTCATTGGAAGAGGTGGAAACCATCTCCACAAAAAATGGGATTGGGAAATGATCTTGGTAATTC
1 GGTCATTGAAAAAGGTGGAAACCATCTCCACAAAAAATGGGATTGGGAAATAATCTTGGTAATTC
*
5705862 TTGTGTTGTCATGA
66 TTGTATTGTCATGA
* * * * *
5705876 GGTCATTGAAAAAGGTGGAAACCATCTCCATAAATAATTGGATTGGG-GATCAATCTTGGTGATT
1 GGTCATTGAAAAAGGTGGAAACCATCTCCACAAAAAATGGGATTGGGAAAT-AATCTTGGTAATT
5705940 CTTGTATTGTC
65 CTTGTATTGTC
5705951 CTATTTCCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 2 0.03
79 63 0.97
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (79 bp):
GGTCATTGAAAAAGGTGGAAACCATCTCCACAAAAAATGGGATTGGGAAATAATCTTGGTAATTC
TTGTATTGTCATGA
Found at i:5720204 original size:81 final size:81
Alignment explanation
Indices: 5720069--5720231 Score: 299
Period size: 81 Copynumber: 2.0 Consensus size: 81
5720059 TAGAAGTTGT
* *
5720069 GGCTTTTTGTAGTTTGTCGTAATTGTTCACCCATTTTTCAGGAAAAAGTTTAGCCAAATCATTTT
1 GGCTTTTTGTAGTTTGTCGTAATTGGTCACCCATTTTTCAAGAAAAAGTTTAGCCAAATCATTTT
5720134 TTGGAATTCTTTTAAG
66 TTGGAATTCTTTTAAG
*
5720150 GGCTTTTTGTAGTTTGTCGTAATTGGTCACCCATTTTTCAAGAAGAAGTTTAGCCAAATCATTTT
1 GGCTTTTTGTAGTTTGTCGTAATTGGTCACCCATTTTTCAAGAAAAAGTTTAGCCAAATCATTTT
5720215 TTGGAATTCTTTTAAG
66 TTGGAATTCTTTTAAG
5720231 G
1 G
5720232 ACAAATGAGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (81 bp):
GGCTTTTTGTAGTTTGTCGTAATTGGTCACCCATTTTTCAAGAAAAAGTTTAGCCAAATCATTTT
TTGGAATTCTTTTAAG
Found at i:5745272 original size:15 final size:17
Alignment explanation
Indices: 5745242--5745273 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5745232 GAATTAAATC
5745242 ATAAAATAATTTTATTA
1 ATAAAATAATTTTATTA
5745259 ATAAAA-AA-TTTATTA
1 ATAAAATAATTTTATTA
5745274 CGTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATAATTTTATTA
Found at i:5746441 original size:19 final size:17
Alignment explanation
Indices: 5746418--5746457 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
5746408 TTATAAATAA
5746418 ATTTTT-ATTTATATATAT
1 ATTTTTAATTT-T-TATAT
5746436 ATTTTTAATTTTTATAT
1 ATTTTTAATTTTTATAT
5746453 ATTTT
1 ATTTT
5746458 AATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTAATTTTTATAT
Found at i:5746451 original size:17 final size:18
Alignment explanation
Indices: 5746407--5746457 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5746397 AATAAATAAT
* *
5746407 TTTATAAATAAATTTTTA
1 TTTATATATATATTTTTA
5746425 TTTATATATATATTTTTAA
1 TTTATATATATATTTTT-A
5746444 TTT-T-TATATATTTT
1 TTTATATATATATTTT
5746458 AATATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 10 0.33
18 16 0.53
19 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATATATATTTTTA
Found at i:5751562 original size:2 final size:2
Alignment explanation
Indices: 5751557--5751600 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5751547 TAATTGAATT
*
5751557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5751599 TA
1 TA
5751601 CATGTATATT
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5754830 original size:80 final size:83
Alignment explanation
Indices: 5754717--5754881 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 83
5754707 TTCACACATA
5754717 TTTCTCTTTCTCTTCTCTTTTTGTTCTTTTATTTTACGTTACTCTCTCTTATATAATTAATTACT
1 TTTCTCTTTCTCTTCTCTTTTTGTTCTTTTATTTTACGTTACTCTCTCTTATATAATTAATTACT
*
5754782 -AAATACA-TTCATNCTT
66 AAAATACATTTCATTCTT
5754798 TTTCTCTTTCTCTTCTC-TTTTGTTCTTTTATTTTACGTTACTCTCTCTTATATAATTAATTACT
1 TTTCTCTTTCTCTTCTCTTTTTGTTCTTTTATTTTACGTTACTCTCTCTTATATAATTAATTACT
5754862 AAAATACATTTCATTCTT
66 AAAATACATTTCATTCTT
5754880 TT
1 TT
5754882 AAAGAGAGAT
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
80 47 0.58
81 24 0.30
82 10 0.12
ACGTcount: A:0.20, C:0.19, G:0.02, T:0.58
Consensus pattern (83 bp):
TTTCTCTTTCTCTTCTCTTTTTGTTCTTTTATTTTACGTTACTCTCTCTTATATAATTAATTACT
AAAATACATTTCATTCTT
Found at i:5757229 original size:44 final size:44
Alignment explanation
Indices: 5757179--5757288 Score: 220
Period size: 44 Copynumber: 2.5 Consensus size: 44
5757169 AGAAAGCAAG
5757179 AGTTTAAAGGAGGTTGTTGAATTTGGTTTGTCGAGGTAAGCTAA
1 AGTTTAAAGGAGGTTGTTGAATTTGGTTTGTCGAGGTAAGCTAA
5757223 AGTTTAAAGGAGGTTGTTGAATTTGGTTTGTCGAGGTAAGCTAA
1 AGTTTAAAGGAGGTTGTTGAATTTGGTTTGTCGAGGTAAGCTAA
5757267 AGTTTAAAGGAGGTTGTTGAAT
1 AGTTTAAAGGAGGTTGTTGAAT
5757289 CTGGAAGGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.36
Consensus pattern (44 bp):
AGTTTAAAGGAGGTTGTTGAATTTGGTTTGTCGAGGTAAGCTAA
Found at i:5762554 original size:14 final size:14
Alignment explanation
Indices: 5762528--5762575 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5762518 TAAAAATATG
5762528 TTACAATCAAATAAA
1 TTACAA-CAAATAAA
*
5762543 TTACACCAAATATAA
1 TTACAACAAATA-AA
*
5762558 ATA-AACAAATAAA
1 TTACAACAAATAAA
5762571 TTACA
1 TTACA
5762576 TAAATAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 4 0.15
14 14 0.52
15 9 0.33
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (14 bp):
TTACAACAAATAAA
Found at i:5762935 original size:29 final size:29
Alignment explanation
Indices: 5762895--5762952 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5762885 CCTAATTAAA
5762895 AAAAAAATCTAAACTAAAATTATTAATTT
1 AAAAAAATCTAAACTAAAATTATTAATTT
5762924 AAAAAAATCTAAACTAAAATTATTAATTT
1 AAAAAAATCTAAACTAAAATTATTAATTT
5762953 GACAAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAAAATCTAAACTAAAATTATTAATTT
Found at i:5762941 original size:15 final size:15
Alignment explanation
Indices: 5762895--5762942 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5762885 CCTAATTAAA
5762895 AAAAAAATCTAAACT
1 AAAAAAATCTAAACT
** **
5762910 AAAATTAT-TAATTT
1 AAAAAAATCTAAACT
5762924 AAAAAAATCTAAACT
1 AAAAAAATCTAAACT
5762939 AAAA
1 AAAA
5762943 TTATTAATTT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAAATCTAAACT
Found at i:5763071 original size:18 final size:18
Alignment explanation
Indices: 5763040--5763093 Score: 99
Period size: 18 Copynumber: 2.9 Consensus size: 18
5763030 TTAAATATAT
5763040 AAAATTATTAAATTAATTA
1 AAAATTATT-AATTAATTA
5763059 AAAATTATTAATTAATTA
1 AAAATTATTAATTAATTA
5763077 AAAATTATTAATTAATT
1 AAAATTATTAATTAATT
5763094 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTATTAATTAATTA
Found at i:5769331 original size:28 final size:28
Alignment explanation
Indices: 5769299--5769385 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
5769289 TTAAAAGGTA
5769299 AAACACAAATTTATCAATTCTTTCCTAC
1 AAACACAAATTTATCAATTCTTTCCTAC
******
5769327 AAACACATAA--T-T-AATTAAAAGGTA-
1 AAACACA-AATTTATCAATTCTTTCCTAC
5769351 AAACACAAATTTATCAATTCTTTCCTAC
1 AAACACAAATTTATCAATTCTTTCCTAC
5769379 AAACACA
1 AAACACA
5769386 CACACACACA
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
23 2 0.05
24 7 0.17
25 7 0.17
26 2 0.05
27 7 0.17
28 14 0.34
29 2 0.05
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (28 bp):
AAACACAAATTTATCAATTCTTTCCTAC
Found at i:5769357 original size:52 final size:52
Alignment explanation
Indices: 5769276--5769385 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
5769266 TAAACCAAAG
*
5769276 AACATATAATTAATTAAAAGGTAAAACACAAATTTATCAATTCTTTCCTACA
1 AACACATAATTAATTAAAAGGTAAAACACAAATTTATCAATTCTTTCCTACA
5769328 AACACATAATTAATTAAAAGGTAAAACACAAATTTATCAATTCTTTCCTACA
1 AACACATAATTAATTAAAAGGTAAAACACAAATTTATCAATTCTTTCCTACA
5769380 AACACA
1 AACACA
5769386 CACACACACA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (52 bp):
AACACATAATTAATTAAAAGGTAAAACACAAATTTATCAATTCTTTCCTACA
Found at i:5774664 original size:27 final size:28
Alignment explanation
Indices: 5774611--5774665 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
5774601 TATTAAAAAA
5774611 TATATTTAAGAAACGTTTTTCTTTTTTAT
1 TATATTTAAGAAAC-TTTTTCTTTTTTAT
*
5774640 TATATTTAATAAA-TTTTT-TTATTTTA
1 TATATTTAAGAAACTTTTTCTT-TTTTA
5774666 AAATTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.08
27 10 0.42
29 12 0.50
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (28 bp):
TATATTTAAGAAACTTTTTCTTTTTTAT
Found at i:5778408 original size:13 final size:14
Alignment explanation
Indices: 5778381--5778409 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5778371 TCACAACCTC
5778381 TACAATAAGATATA
1 TACAATAAGATATA
5778395 TACAATAA-ATATA
1 TACAATAAGATATA
5778408 TA
1 TA
5778410 TGTTAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (14 bp):
TACAATAAGATATA
Found at i:5780815 original size:20 final size:20
Alignment explanation
Indices: 5780786--5780823 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5780776 TATATTTTAA
*
5780786 TTTAATCATGTTAATCGTGT
1 TTTAAGCATGTTAATCGTGT
5780806 TTTAAGCATGTTAATCGT
1 TTTAAGCATGTTAATCGT
5780824 ATCAATTGTA
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:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTAAGCATGTTAATCGTGT
Found at i:5782927 original size:13 final size:14
Alignment explanation
Indices: 5782904--5782936 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5782894 AAGGCATGAG
5782904 TTTTA-TCATT-AA
1 TTTTATTCATTAAA
5782916 TTTTATTCATTAAA
1 TTTTATTCATTAAA
5782930 TTTTATT
1 TTTTATT
5782937 ATTGTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 5 0.26
14 9 0.47
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTCATTAAA
Found at i:5788488 original size:18 final size:18
Alignment explanation
Indices: 5788465--5788510 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5788455 ACACGTTTAC
*
5788465 TTAATCGTGTTATTGTGT
1 TTAATCGTGTTATCGTGT
5788483 TTAATCGTGTTATCGTGT
1 TTAATCGTGTTATCGTGT
*
5788501 TTAAACGTGT
1 TTAATCGTGT
5788511 ATATATGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.50
Consensus pattern (18 bp):
TTAATCGTGTTATCGTGT
Found at i:5827279 original size:2 final size:2
Alignment explanation
Indices: 5827272--5827372 Score: 117
Period size: 2 Copynumber: 54.0 Consensus size: 2
5827262 CAGGTATACA
5827272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5827311 AT -T AT -T AT -T AT -T NT 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
* * *
5827349 AT AT AT TT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
5827373 CGTTATTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
1 7 0.08
2 78 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:5831612 original size:28 final size:28
Alignment explanation
Indices: 5831575--5831638 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
5831565 AACTCACAAG
5831575 AAAAATATAAAAATTTAATTAAATATAAT
1 AAAAA-ATAAAAATTTAATTAAATATAAT
* **
5831604 AAAAAATAAAAATTTATTTAAATATTTT
1 AAAAAATAAAAATTTAATTAAATATAAT
5831632 AAAAAAT
1 AAAAAAT
5831639 TTTATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAAATAAAAATTTAATTAAATATAAT
Found at i:5833531 original size:37 final size:37
Alignment explanation
Indices: 5833489--5833561 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
5833479 ACTTGAATCT
*
5833489 GCTAGTGGTTTGCCCTTCTCTCCCTTACATGGTGCTC
1 GCTAGTGGTTTGCCCTTCCCTCCCTTACATGGTGCTC
* *
5833526 GCTAGTGGTTTGCCTTTCCCTCGCTTACATGGTGCT
1 GCTAGTGGTTTGCCCTTCCCTCCCTTACATGGTGCT
5833562 TGCTTCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.08, C:0.30, G:0.23, T:0.38
Consensus pattern (37 bp):
GCTAGTGGTTTGCCCTTCCCTCCCTTACATGGTGCTC
Found at i:5842821 original size:20 final size:21
Alignment explanation
Indices: 5842781--5842828 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5842771 TTGGGACTCC
*
5842781 CCCGATGCTCCCCTTAGGGAA
1 CCCGATGCTCCCCTTAAGGAA
*
5842802 CCCGATGCT-CTCTTAAGGAA
1 CCCGATGCTCCCCTTAAGGAA
5842822 CTCCGAT
1 C-CCGAT
5842829 CGGGCTCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
CCCGATGCTCCCCTTAAGGAA
Found at i:5842850 original size:21 final size:23
Alignment explanation
Indices: 5842826--5842868 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5842816 AAGGAACTCC
5842826 GATCGG-GCTCCCC-ATGGGGAG
1 GATCGGTGCTCCCCAATGGGGAG
5842847 GATCGGTGCTCCCCAATGGGGA
1 GATCGGTGCTCCCCAATGGGGA
5842869 TCTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.16, C:0.28, G:0.40, T:0.16
Consensus pattern (23 bp):
GATCGGTGCTCCCCAATGGGGAG
Found at i:5847427 original size:2 final size:2
Alignment explanation
Indices: 5847422--5847485 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
5847412 ATAAATAAAN
* * *
5847422 AT AT AT AT AA AT AA AT AA 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
5847464 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5847486 TCAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5847430 original size:20 final size:20
Alignment explanation
Indices: 5847405--5847485 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
5847395 AGTCAAGGAT
*
5847405 TATATAAATAAATAAANATA
1 TATATAAATAAATAAATATA
5847425 TATATAAATAAATAAATATA
1 TATATAAATAAATAAATATA
* * *
5847445 TATATATATATATATATATA
1 TATATAAATAAATAAATATA
* * *
5847465 TATATATATATATATATATA
1 TATATAAATAAATAAATATA
5847485 T
1 T
5847486 TCAAATTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAAATAAATAAATATA
Found at i:5847431 original size:16 final size:16
Alignment explanation
Indices: 5847405--5847478 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
5847395 AGTCAAGGAT
*
5847405 TATATAAATAAATAAA
1 TATATATATAAATAAA
*
5847421 NATATATATAAATAAA
1 TATATATATAAATAAA
* * *
5847437 TAAATATATATATATA
1 TATATATATAAATAAA
* *
5847453 TATATATATATATATA
1 TATATATATAAATAAA
5847469 TATATATATA
1 TATATATATA
5847479 TATATATTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATATAAATAAA
Found at i:5849514 original size:17 final size:17
Alignment explanation
Indices: 5849492--5849554 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
5849482 CCTCCCATTC
5849492 TCTTTCTTTTCCTCTTT
1 TCTTTCTTTTCCTCTTT
*
5849509 TCTTTCTTTATCTTCCTTT
1 TCTTTCTTT-TCCT-CTTT
5849528 T-TTT-TTTTCCTCTTTT
1 TCTTTCTTTTCCTC-TTT
5849544 TCCTTTCTTTT
1 T-CTTTCTTTT
5849555 TCTCAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 7 0.18
17 12 0.32
18 9 0.24
19 9 0.24
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (17 bp):
TCTTTCTTTTCCTCTTT
Found at i:5855749 original size:15 final size:15
Alignment explanation
Indices: 5855712--5855759 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5855702 TAGACAAAAA
*
5855712 TATAAAAT-TTTATT
1 TATAAAATATATATT
* *
5855726 TTTAGAATATATATT
1 TATAAAATATATATT
*
5855741 TATAAAATATATATA
1 TATAAAATATATATT
5855756 TATA
1 TATA
5855760 TATAGCCCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TATAAAATATATATT
Found at i:5860544 original size:3 final size:3
Alignment explanation
Indices: 5860536--5860563 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5860526 GGGCGTGTGA
5860536 AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG A
5860564 TGGGGTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:5872691 original size:45 final size:45
Alignment explanation
Indices: 5872636--5872785 Score: 132
Period size: 45 Copynumber: 3.4 Consensus size: 45
5872626 ATAATAATAA
5872636 TTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCTCTTATT
1 TTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCTCTTATT
* * * * ** **
5872681 TTTTTCAAATTAATAAAAAATTAGTAAAA---AT-GATATAATAGTA--
1 TTTTTAAAATTAAT---AAA-GAGTAAAATTGATCGGTGTTCTCTTATT
*
5872724 ATTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCTCTTATT
1 TTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCTCTTATT
*
5872769 TTTTTCAAATTAATAAA
1 TTTTTAAAATTAATAAA
5872786 AAATTAGTAA
Statistics
Matches: 76, Mismatches: 19, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
39 7 0.09
40 3 0.04
42 2 0.03
43 18 0.24
45 34 0.45
46 2 0.03
48 3 0.04
49 7 0.09
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (45 bp):
TTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCTCTTATT
Found at i:5872773 original size:89 final size:88
Alignment explanation
Indices: 5872609--5872838 Score: 408
Period size: 88 Copynumber: 2.6 Consensus size: 88
5872599 TTTTTTTTTT
* *
5872609 AAATTAATAAAAAAT-ATATAATAATAATTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTT
1 AAATTAGT-AAAAATGATATAATAGTAA-TTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTT
5872673 CTCTTATTTTTTTCAAATTAATAAA
64 CTCTTATTTTTTTCAAATTAATAAA
5872698 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCT
1 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCT
5872763 CTTATTTTTTTCAAATTAATAAA
66 CTTATTTTTTTCAAATTAATAAA
*
5872786 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAAAGTAAAATT
1 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAGAGTAAAATT
5872839 ATTATTTCAA
Statistics
Matches: 137, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
88 119 0.87
89 18 0.13
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (88 bp):
AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCT
CTTATTTTTTTCAAATTAATAAA
Found at i:5872796 original size:49 final size:49
Alignment explanation
Indices: 5872654--5872802 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 49
5872644 ATTAATAAAG
5872654 AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
1 AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
* * ** ** * * *
5872703 AGTAAAA---AT-GATATAATAGTA--ATTTTAAAATTAAT---AAA-G
1 AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
5872742 AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
1 AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
*
5872791 AGTAAAAATGAT
1 AGTAAAATTGAT
5872803 ATAATAGTAA
Statistics
Matches: 71, Mismatches: 19, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
39 7 0.10
40 3 0.04
42 2 0.03
43 18 0.25
45 18 0.25
46 2 0.03
48 3 0.04
49 18 0.25
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (49 bp):
AGTAAAATTGATCGGTGTTCTCTTATTTTTTTCAAATTAATAAAAAATT
Found at i:5872830 original size:43 final size:43
Alignment explanation
Indices: 5872682--5872830 Score: 126
Period size: 43 Copynumber: 3.4 Consensus size: 43
5872672 TCTCTTATTT
*
5872682 TTTTCAAATTAATAAAAAATTAGTAAAAATGATATAATAGTAA
1 TTTTAAAATTAATAAAAAATTAGTAAAAATGATATAATAGTAA
* * * ** ** *
5872725 TTTTAAAATTAAT---AAA-GAGTAAAATTGATCGGTGTTCTCTTATTT
1 TTTTAAAATTAATAAAAAATTAGTAAAA---AT-GATATAATAGTA--A
*
5872770 TTTTCAAATTAATAAAAAATTAGTAAAAATGATATAATAGTAA
1 TTTTAAAATTAATAAAAAATTAGTAAAAATGATATAATAGTAA
5872813 TTTTAAAATTAATAAAAA
1 TTTTAAAATTAATAAAAA
5872831 GTAAAATTAT
Statistics
Matches: 77, Mismatches: 19, Indels: 20
0.66 0.16 0.17
Matches are distributed among these distances:
39 7 0.09
40 3 0.04
42 2 0.03
43 35 0.45
45 18 0.23
46 2 0.03
48 3 0.04
49 7 0.09
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.38
Consensus pattern (43 bp):
TTTTAAAATTAATAAAAAATTAGTAAAAATGATATAATAGTAA
Found at i:5872876 original size:88 final size:88
Alignment explanation
Indices: 5872609--5872881 Score: 293
Period size: 88 Copynumber: 3.1 Consensus size: 88
5872599 TTTTTTTTTT
* * * *
5872609 AAATTAATAAAAAAT-ATATAATAATAATTTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTT
1 AAATTAGT-AAAAATGATATAATAGTAA-TTTTAAAATTAATAAAAAGTAAAATTGATCGATGTT
* ****
5872673 CTCTTATTTTTTTCAAATTAATAAA
64 CTATTATTAACATCAAATTAATAAA
* *
5872698 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAGAGTAAAATTGATCGGTGTTCT
1 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAAAGTAAAATTGATCGATGTTCT
* ****
5872763 CTTATTTTTTTCAAATTAATAAA
66 ATTATTAACATCAAATTAATAAA
*
5872786 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAAAGTAAAATT-AT-TAT-TTCA
1 AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAAAGTAAAATTGATCGATGTTC-
*
5872848 ATATTATTACAACATCAAATTAACAAA
65 -TATTATT--AACATCAAATTAATAAA
5872875 AACATTA
1 AA-ATTA
5872882 AAGATTACCT
Statistics
Matches: 167, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
85 3 0.02
86 1 0.01
87 8 0.05
88 119 0.71
89 32 0.19
90 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (88 bp):
AAATTAGTAAAAATGATATAATAGTAATTTTAAAATTAATAAAAAGTAAAATTGATCGATGTTCT
ATTATTAACATCAAATTAATAAA
Found at i:5877822 original size:34 final size:34
Alignment explanation
Indices: 5877784--5877860 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
5877774 ACTGGTGGTG
* * *
5877784 AAACTTTAACCTTAACGTGTAACATCTAGTGCTA
1 AAACTTTAACCTTAACATATAACATCTAGTACTA
* ** *
5877818 AAACTTTGACCTTGGCATATAACATCTAGTACTG
1 AAACTTTAACCTTAACATATAACATCTAGTACTA
5877852 AAACTTTAA
1 AAACTTTAA
5877861 TTTTGGTGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (34 bp):
AAACTTTAACCTTAACATATAACATCTAGTACTA
Found at i:5883718 original size:14 final size:14
Alignment explanation
Indices: 5883699--5883727 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5883689 AATATTGTAN
5883699 AAATTAATTATTTT
1 AAATTAATTATTTT
5883713 AAATTAATTATTTT
1 AAATTAATTATTTT
5883727 A
1 A
5883728 TAAAATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTAATTATTTT
Found at i:5883735 original size:17 final size:15
Alignment explanation
Indices: 5883699--5883741 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
5883689 AATATTGTAN
5883699 AAATTAATTA-TTTT
1 AAATTAATTATTTTT
5883713 AAATTAATTATTTTAT
1 AAATTAATTATTTT-T
*
5883729 AAAATTAACTATT
1 -AAATTAATTATT
5883742 AATATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 1 0.04
17 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTAATTATTTTT
Found at i:5883850 original size:20 final size:20
Alignment explanation
Indices: 5883825--5883864 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5883815 AGTATATTTG
5883825 ATATTTTTTGAAAAATGTCT
1 ATATTTTTTGAAAAATGTCT
5883845 ATATTTTTTGAAAAATGTCT
1 ATATTTTTTGAAAAATGTCT
5883865 TACGCCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
ATATTTTTTGAAAAATGTCT
Found at i:5891404 original size:20 final size:19
Alignment explanation
Indices: 5891381--5891434 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5891371 TAATTAATTT
5891381 TTTTTTATTATAAATTCATA
1 TTTTTTATTATAAATT-ATA
* *
5891401 TTTTTAATTTAAAAATTATA
1 TTTTTTA-TTATAAATTATA
* *
5891421 ATATTTATTATAAA
1 TTTTTTATTATAAA
5891435 AAATAACTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTATTATAAATTATA
Found at i:5891771 original size:16 final size:15
Alignment explanation
Indices: 5891752--5891785 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5891742 ATGTCTCGTT
*
5891752 AAAACCTTATAAGAAA
1 AAAACCTCATAA-AAA
5891768 AAAACCTCATAAAAA
1 AAAACCTCATAAAAA
5891783 AAA
1 AAA
5891786 TCTGAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAACCTCATAAAAA
Found at i:5896500 original size:5 final size:5
Alignment explanation
Indices: 5896486--5896528 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
5896476 TTCCTTGTTA
*
5896486 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
5896529 CTCTCCCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:5896716 original size:34 final size:33
Alignment explanation
Indices: 5896660--5896725 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
5896650 TTAATTTTTA
5896660 AGCAGCTAAAGTTGCTTATTTTTGCTTCAAAATC
1 AGCAGCTAAAGTTGCTTATTTTTGCTT-AAAATC
* * *
5896694 AGCAGCT-ATGTTGCTCTGTTTTTTCTTAAAAT
1 AGCAGCTAAAGTTGCT-TATTTTTGCTTAAAAT
5896726 TTCAGCAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (33 bp):
AGCAGCTAAAGTTGCTTATTTTTGCTTAAAATC
Found at i:5896882 original size:34 final size:34
Alignment explanation
Indices: 5896844--5896926 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
5896834 ACAGTTTTTG
5896844 GCCTCCAAAACCAGCAGAAAAATGGCACTTTCCA
1 GCCTCCAAAACCAGCAGAAAAATGGCACTTTCCA
* * *
5896878 GCCTCCAAAACTAGCAGAAAAATGGCTCTTTTCA
1 GCCTCCAAAACCAGCAGAAAAATGGCACTTTCCA
*
5896912 GCCTCTAAAACCAGC
1 GCCTCCAAAACCAGC
5896927 CCTTAAATGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.18
Consensus pattern (34 bp):
GCCTCCAAAACCAGCAGAAAAATGGCACTTTCCA
Found at i:5900785 original size:23 final size:22
Alignment explanation
Indices: 5900753--5900800 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5900743 CCTGTTATGA
5900753 AAAAAAAACTTAAAAGAACAAAT
1 AAAAAAAAC-TAAAAGAACAAAT
* * *
5900776 AAAAATAACTGAAAGAACAATT
1 AAAAAAAACTAAAAGAACAAAT
5900798 AAA
1 AAA
5900801 GAAAGGAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAAAAACTAAAAGAACAAAT
Found at i:5912715 original size:38 final size:38
Alignment explanation
Indices: 5912664--5912741 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5912654 GAAGTAAGCA
5912664 ATTAATCTCATAAGTTGAAATATGTGAGATACTTAGAG
1 ATTAATCTCATAAGTTGAAATATGTGAGATACTTAGAG
5912702 ATTAATCTCATAAGTTGAAATATGTGAGATACTTAGAG
1 ATTAATCTCATAAGTTGAAATATGTGAGATACTTAGAG
5912740 AT
1 AT
5912742 AGTATGTAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.35
Consensus pattern (38 bp):
ATTAATCTCATAAGTTGAAATATGTGAGATACTTAGAG
Found at i:5923430 original size:14 final size:14
Alignment explanation
Indices: 5923411--5923527 Score: 61
Period size: 13 Copynumber: 8.5 Consensus size: 14
5923401 ATATATTTGT
5923411 ATTTTTTATTATTA
1 ATTTTTTATTATTA
5923425 ATTTTTATATAATATT-
1 ATTTTT-TAT--TATTA
*
5923441 ATTTTTTA--AATA
1 ATTTTTTATTATTA
*
5923453 TATTTTTAATT-TTA
1 -ATTTTTTATTATTA
* *
5923467 TATATTTTATT-TTT
1 -ATTTTTTATTATTA
*
5923481 ATTTTTTAATA-TA
1 ATTTTTTATTATTA
5923494 ATTTTTTA-TATTA
1 ATTTTTTATTATTA
* *
5923507 TATATTCTATT-TTA
1 -ATTTTTTATTATTA
5923521 ATTTTTT
1 ATTTTTT
5923528 TACCTATATT
Statistics
Matches: 79, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 31 0.39
14 28 0.35
15 6 0.08
16 6 0.08
17 4 0.05
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTTATTATTA
Found at i:5923461 original size:60 final size:59
Alignment explanation
Indices: 5923359--5923502 Score: 134
Period size: 57 Copynumber: 2.4 Consensus size: 59
5923349 GAGTTTAATG
* * * * *
5923359 TTAATTTTTAAAATTATTTTTATTTATTAAAATATAAATTTAATATATTTGTATTTTTTATTA
1 TTAATTTTTAATA-TAATATTATTTATTAAAATATAAATTT-A-AT-TTTATATATTTTATTA
* ** *
5923422 TTAATTTTT-ATATAATATTATTT-TTTAAATATATTTTTAATTTTATATATTTTATTT
1 TTAATTTTTAATATAATATTATTTATTAAAATATAAATTTAATTTTATATATTTTATTA
*
5923479 TTATTTTTTAATATAAT-TT-TTTAT
1 TTAATTTTTAATATAATATTATTTAT
5923503 ATTATATATT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.04
57 24 0.35
58 9 0.13
59 1 0.01
60 12 0.17
61 9 0.13
62 2 0.03
63 9 0.13
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.65
Consensus pattern (59 bp):
TTAATTTTTAATATAATATTATTTATTAAAATATAAATTTAATTTTATATATTTTATTA
Found at i:5923486 original size:40 final size:40
Alignment explanation
Indices: 5923439--5923617 Score: 130
Period size: 40 Copynumber: 4.2 Consensus size: 40
5923429 TTATATAATA
*
5923439 TTATTTTTTAAATATATTTTTAATTTTATATATTTTATTT
1 TTATTTTTTAAATATATTTTTAATATTATATATTTTATTT
* *
5923479 TTATTTTTT-AATATAATTTTTTATATTATATATTCTATTT
1 TTATTTTTTAAATAT-ATTTTTAATATTATATATTTTATTT
* ** * *
5923519 TAATTTTTTTACCTATATTATATAA-ATTTTA-ATTTCTTATATT
1 TTA-TTTTTTAAATATATT-TTTAATATTATATA-TT-TTAT-TT
* * *
5923562 TTATTTTATTTTAATTTTTATTTTTTATATTATATATTTTATTT
1 TTA--TT-TTTTAA-ATATATTTTTAATATTATATATTTTATTT
5923606 TAATATTTTTTA
1 T--TATTTTTTA
5923618 TTTTAATTAT
Statistics
Matches: 108, Mismatches: 17, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
39 5 0.05
40 34 0.31
41 16 0.15
42 9 0.08
43 9 0.08
44 8 0.07
45 12 0.11
46 14 0.13
47 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (40 bp):
TTATTTTTTAAATATATTTTTAATATTATATATTTTATTT
Found at i:5923499 original size:20 final size:20
Alignment explanation
Indices: 5923439--5923502 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
5923429 TTATATAATA
5923439 TTATTTTTTAA-ATATATTTT
1 TTATTTTTTAATATA-ATTTT
* * **
5923459 TAATTTTAT-ATATTTTATTT
1 TTATTTTTTAATATAAT-TTT
5923479 TTATTTTTTAATATAATTTT
1 TTATTTTTTAATATAATTTT
5923499 TTAT
1 TTAT
5923503 ATTATATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 2 0.06
20 26 0.79
21 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTTTAATATAATTTT
Found at i:5923529 original size:54 final size:54
Alignment explanation
Indices: 5923471--5923597 Score: 125
Period size: 54 Copynumber: 2.3 Consensus size: 54
5923461 ATTTTATATA
* * *
5923471 TTTTATTTTTATT-TTTTAA-TATAATTTTTTATATTATATATTCTATTTTAATTT
1 TTTTATTTTTATTATATAAATTATAATTTCTTATATT-T-TATTCTATTTTAATTT
** * * *
5923525 TTTTACCTATATTATATAAATTTTAATTTCTTATATTTTATTTTATTTTAATTT
1 TTTTATTTTTATTATATAAATTATAATTTCTTATATTTTATTCTATTTTAATTT
5923579 TTATT-TTTTATATTATATA
1 TT-TTATTTT-TATTATATA
5923598 TTTTATTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
54 28 0.48
55 16 0.28
56 14 0.24
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (54 bp):
TTTTATTTTTATTATATAAATTATAATTTCTTATATTTTATTCTATTTTAATTT
Found at i:5923560 original size:89 final size:88
Alignment explanation
Indices: 5923456--5923617 Score: 240
Period size: 87 Copynumber: 1.8 Consensus size: 88
5923446 TTAAATATAT
5923456 TTTTAATTTTATATATTTTATTTTTATTTTTTAA-TATAATTTTTTATATTATATATTCTATTTT
1 TTTTAATTTTATATATTTTA-TTTTA--TTTTAATTATAATTTTTTATATTATATATTCTATTTT
5923520 AAT-TTTTTTACCTATATTATATAAA
63 AATATTTTTTACCTATATTATATAAA
* * *
5923545 TTTTAATTTCT-TATATTTTATTTTATTTTAATTTTTATTTTTTATATTATATATTTTATTTTAA
1 TTTTAATTT-TATATATTTTATTTTATTTTAATTATAATTTTTTATATTATATATTCTATTTTAA
5923609 TATTTTTTA
65 TATTTTTTA
5923618 TTTTAATTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
86 6 0.09
87 30 0.45
88 12 0.18
89 18 0.27
90 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (88 bp):
TTTTAATTTTATATATTTTATTTTATTTTAATTATAATTTTTTATATTATATATTCTATTTTAAT
ATTTTTTACCTATATTATATAAA
Found at i:5923568 original size:5 final size:5
Alignment explanation
Indices: 5923544--5923622 Score: 54
Period size: 5 Copynumber: 15.2 Consensus size: 5
5923534 TATTATATAA
* * * *
5923544 ATTTT AATTT CTTAT ATTTT ATTTT ATTTT AATTTTT ATTTT -TTAT ATTATAT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -A-TTTT ATTTT ATTTT ATT-T-T
*
5923597 ATTTT ATTTT AATATT -TTTT ATTTT A
1 ATTTT ATTTT -ATTTT ATTTT ATTTT A
5923623 ATTATAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
4 6 0.11
5 36 0.63
6 7 0.12
7 8 0.14
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:5923589 original size:7 final size:7
Alignment explanation
Indices: 5923570--5923621 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
5923560 TTTTATTTTA
*
5923570 TTTTAAT
1 TTTTATT
5923577 TTTTATT
1 TTTTATT
*
5923584 TTTTATA
1 TTTTATT
* *
5923591 TTATATA
1 TTTTATT
5923598 TTTTATT
1 TTTTATT
*
5923605 TTAATATT
1 TT-TTATT
5923613 TTTTATT
1 TTTTATT
5923620 TT
1 TT
5923622 AATTATAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTATT
Found at i:5923605 original size:33 final size:33
Alignment explanation
Indices: 5923543--5923633 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
5923533 ATATTATATA
* *
5923543 AATTTTAATTTCTTATATT-T-TATTTTATTTT
1 AATTTTTATTTTTTATATTATATATTTTATTTT
5923574 AATTTTTATTTTTTATATTATATATTTTATTTT
1 AATTTTTATTTTTTATATTATATATTTTATTTT
5923607 AATATTTT-TTATTTTA-ATTATAATATT
1 AAT-TTTTATT-TTTTATATTAT-ATATT
5923634 ATAAAATATT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
31 17 0.32
32 1 0.02
33 21 0.40
34 14 0.26
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
AATTTTTATTTTTTATATTATATATTTTATTTT
Found at i:5925784 original size:31 final size:31
Alignment explanation
Indices: 5925749--5925809 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
5925739 ACGAATTTAA
5925749 AATTTTACATGAAAAATTACTAGAAATGATT
1 AATTTTACATGAAAAATTACTAGAAATGATT
5925780 AATTTTACATGAAAAATTACTAGAAATGAT
1 AATTTTACATGAAAAATTACTAGAAATGAT
5925810 AATAACAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (31 bp):
AATTTTACATGAAAAATTACTAGAAATGATT
Found at i:5927522 original size:6 final size:6
Alignment explanation
Indices: 5927511--5927543 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5927501 CTGCCTCTGT
*
5927511 TTCAGC TACAGC TTCAGC TTCAGC TTCAGC TTC
1 TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTC
5927544 TGGGATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
TTCAGC
Found at i:5927725 original size:6 final size:6
Alignment explanation
Indices: 5927714--5927747 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5927704 TTTTCAGCTC
* *
5927714 CTTCCT CTTCCT CTTCCT CTTCTT CTTCTT CTTC
1 CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTC
5927748 TTCATCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
CTTCCT
Found at i:5927748 original size:12 final size:12
Alignment explanation
Indices: 5927714--5927750 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5927704 TTTTCAGCTC
*
5927714 CTTCCTCTTCCT
1 CTTCCTCTTCTT
5927726 CTTCCTCTTCTT
1 CTTCCTCTTCTT
*
5927738 CTTCTTCTTCTT
1 CTTCCTCTTCTT
5927750 C
1 C
5927751 ATCTTTAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (12 bp):
CTTCCTCTTCTT
Found at i:5936131 original size:2 final size:2
Alignment explanation
Indices: 5936120--5936152 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5936110 TGGGTTTTAG
5936120 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5936153 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:5936157 original size:2 final size:2
Alignment explanation
Indices: 5936152--5936185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5936142 TCTCTCTCTC
5936152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5936186 AGGAGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5951336 original size:14 final size:14
Alignment explanation
Indices: 5951301--5951334 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
5951291 AAATCATAAA
5951301 AAAAATTTATTAAT
1 AAAAATTTATTAAT
5951315 AGAAAATTTATTAACT
1 A-AAAATTTATTAA-T
5951331 AAAA
1 AAAA
5951335 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.06
15 15 0.83
16 2 0.11
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAAATTTATTAAT
Found at i:5951656 original size:27 final size:28
Alignment explanation
Indices: 5951618--5951703 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
5951608 TATTTTCACC
* *
5951618 ATTCATCAACTTTTAGT-GAGTTGAAA-T
1 ATTCATCTACTTTTAGTAG-GTTAAAAGT
*
5951645 ATTCATCTACTTTTTGTAGGTTAAAAGT
1 ATTCATCTACTTTTAGTAGGTTAAAAGT
* *
5951673 ATTTATCTACTTCTTA-TGGGTTAAAAGT
1 ATTCATCTACTT-TTAGTAGGTTAAAAGT
5951701 ATT
1 ATT
5951704 TTTATTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 21 0.42
28 27 0.54
29 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (28 bp):
ATTCATCTACTTTTAGTAGGTTAAAAGT
Found at i:5951963 original size:17 final size:17
Alignment explanation
Indices: 5951941--5951974 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5951931 TGTTATAAAA
5951941 TAGATATCATACAAAGT
1 TAGATATCATACAAAGT
*
5951958 TAGATATCATATAAAGT
1 TAGATATCATACAAAGT
5951975 CAATTTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (17 bp):
TAGATATCATACAAAGT
Found at i:5960572 original size:2 final size:2
Alignment explanation
Indices: 5960565--5960603 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5960555 TAAGAATCCA
5960565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5960604 AAAGATTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5962102 original size:24 final size:24
Alignment explanation
Indices: 5962075--5962126 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5962065 GGCTGAAGTG
* *
5962075 GAGGAAGAGGAAGAAGAAGAGTCT
1 GAGGAAGAAGAAGAAGAAGAATCT
* *
5962099 GAGGAGGAAGTAGAAGAAGAATCT
1 GAGGAAGAAGAAGAAGAAGAATCT
5962123 GAGG
1 GAGG
5962127 TCATTATCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.42, T:0.10
Consensus pattern (24 bp):
GAGGAAGAAGAAGAAGAAGAATCT
Found at i:5967837 original size:23 final size:23
Alignment explanation
Indices: 5967802--5967849 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5967792 ATGATATTAT
* *
5967802 TATAATATTTTAATA-AATAATAA
1 TATAACATATTAATACAA-AATAA
5967825 TATAACATATTAATACAAAATAA
1 TATAACATATTAATACAAAATAA
5967848 TA
1 TA
5967850 ACATAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TATAACATATTAATACAAAATAA
Found at i:5975861 original size:45 final size:45
Alignment explanation
Indices: 5975797--5975895 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
5975787 AACACGCTAT
*
5975797 GTTGTTACATGTCATGTACAAAAACATATGATACG-CTATGGTTAA
1 GTTGTTACATGTCATGTACAAAAACATATGACACGTC-ATGGTTAA
* * *
5975842 GTTGTTACATGTCATGTACAAAAATATGTGACATGTCATGGTTAA
1 GTTGTTACATGTCATGTACAAAAACATATGACACGTCATGGTTAA
5975887 GTTGTTACA
1 GTTGTTACA
5975896 CGTTATGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (45 bp):
GTTGTTACATGTCATGTACAAAAACATATGACACGTCATGGTTAA
Found at i:5975968 original size:45 final size:45
Alignment explanation
Indices: 5975918--5976075 Score: 120
Period size: 45 Copynumber: 3.4 Consensus size: 45
5975908 AAAAAATACT
5975918 GTTGTTACACGTCATGTACAAAAACATGTTACACGCCATGGTTAG
1 GTTGTTACACGTCATGTACAAAAACATGTTACACGCCATGGTTAG
* * * * *** *
5975963 GTTGTTACATG-CTATGTACAAAAACATCTGATATATCATGATTAG
1 GTTGTTACACGTC-ATGTACAAAAACATGTTACACGCCATGGTTAG
** * *
5976008 GTTGTTACTTGTCATGTTAAAAAAAAATGTTATTGTTACACGCCATGGTTAG
1 GTTGTTACACGTCATG-T--ACAAAAA---CA-TGTTACACGCCATGGTTAG
*
5976060 GTTGTTACACGCCATG
1 GTTGTTACACGTCATG
5976076 GTTAGGTTGT
Statistics
Matches: 83, Mismatches: 21, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
44 1 0.01
45 48 0.58
46 2 0.02
48 6 0.07
51 1 0.01
52 25 0.30
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (45 bp):
GTTGTTACACGTCATGTACAAAAACATGTTACACGCCATGGTTAG
Found at i:5976012 original size:121 final size:121
Alignment explanation
Indices: 5975796--5976054 Score: 331
Period size: 121 Copynumber: 2.1 Consensus size: 121
5975786 TAACACGCTA
* * *
5975796 TGTTGTTACATGTCATGTACAAAAACATATGATACGCTATGGTTAAGTTGTTACATGTCATGTAC
1 TGTTGTTACACGTCATGTACAAAAACATATGACACGCCATGGTTAAGTTGTTACATGTCATGTAC
* * * * *
5975861 AAAAATATGTGACATGTCATGGTTAAGTTGTTACACGTTATGTTAAAAAAAAATAC
66 AAAAACATCTGACATATCATGATTAAGTTGTTACACGTCATGTTAAAAAAAAATAC
* * *
5975917 TGTTGTTACACGTCATGTACAAAAACATGTTACACGCCATGGTTAGGTTGTTACATG-CTATGTA
1 TGTTGTTACACGTCATGTACAAAAACATATGACACGCCATGGTTAAGTTGTTACATGTC-ATGTA
* * ** **
5975981 CAAAAACATCTGATATATCATGATTAGGTTGTTACTTGTCATGTTAAAAAAAAATGT
65 CAAAAACATCTGACATATCATGATTAAGTTGTTACACGTCATGTTAAAAAAAAATAC
* *
5976038 TATTGTTACACGCCATG
1 TGTTGTTACACGTCATG
5976055 GTTAGGTTGT
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
120 1 0.01
121 117 0.99
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (121 bp):
TGTTGTTACACGTCATGTACAAAAACATATGACACGCCATGGTTAAGTTGTTACATGTCATGTAC
AAAAACATCTGACATATCATGATTAAGTTGTTACACGTCATGTTAAAAAAAAATAC
Found at i:5976065 original size:21 final size:21
Alignment explanation
Indices: 5976040--5976096 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
5976030 AAAAATGTTA
5976040 TTGTTACACGCCATGGTTAGG
1 TTGTTACACGCCATGGTTAGG
5976061 TTGTTACACGCCATGGTTAGG
1 TTGTTACACGCCATGGTTAGG
5976082 TTGTTACACGCCATG
1 TTGTTACACGCCATG
5976097 TTGAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGTTACACGCCATGGTTAGG
Found at i:5976216 original size:29 final size:29
Alignment explanation
Indices: 5976184--5976246 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
5976174 TATGTTGAAA
*
5976184 AAAAAATATTGTTGTTACATGCCATATTG
1 AAAAAATATTGTTGTTACACGCCATATTG
* *
5976213 AAAAAATATTGTTGTTACACGTCATATTT
1 AAAAAATATTGTTGTTACACGCCATATTG
5976242 AAAAA
1 AAAAA
5976247 CAATTTGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGCCATATTG
Found at i:5976217 original size:30 final size:30
Alignment explanation
Indices: 5976183--5976255 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
5976173 TTATGTTGAA
*
5976183 AAAAAAATATTGTTGTTACATGCCATATTG
1 AAAAAAATATTGTTGTTACACGCCATATTG
* *
5976213 -AAAAAATATTGTTGTTACACGTCATATTT
1 AAAAAAATATTGTTGTTACACGCCATATTG
5976242 AAAAACAAT-TTGTT
1 AAAAA-AATATTGTT
5976256 ACACTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 26 0.68
30 9 0.24
31 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (30 bp):
AAAAAAATATTGTTGTTACACGCCATATTG
Found at i:5981597 original size:43 final size:43
Alignment explanation
Indices: 5981478--5981598 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 43
5981468 CAATGATTGC
* **
5981478 TTCTGATATGATTATGACCCATGTCACAAGGGTTAATTGTGGT
1 TTCTGATATGATTATGACCCATGTCATAAGGGTTAATAATGGT
* *
5981521 TTC-GATACGATTATGACCCATGCCACTAA-GGTTAATAATGGT
1 TTCTGATATGATTATGACCCATGTCA-TAAGGGTTAATAATGGT
* * * *
5981563 TTCTGCTATAATTATGACCTATGTCGTAAGGGTTAA
1 TTCTGATATGATTATGACCCATGTCATAAGGGTTAA
5981599 GTATGACCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 37 0.58
43 27 0.42
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (43 bp):
TTCTGATATGATTATGACCCATGTCATAAGGGTTAATAATGGT
Found at i:5984374 original size:16 final size:16
Alignment explanation
Indices: 5984353--5984384 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5984343 AACAACATTT
5984353 ATGAAAAAAGGATGCA
1 ATGAAAAAAGGATGCA
5984369 ATGAAAAAAGGATGCA
1 ATGAAAAAAGGATGCA
5984385 GATGCATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (16 bp):
ATGAAAAAAGGATGCA
Found at i:5988289 original size:17 final size:16
Alignment explanation
Indices: 5988238--5988291 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
5988228 TATTTTTTTG
5988238 TTATTATTAAT-TATTT
1 TTATTA-TAATATATTT
*
5988254 TTATTTTAATATATATT
1 TTATTATAATATAT-TT
*
5988271 TTATTATCATACTATTT
1 TTATTATAATA-TATTT
5988288 TTAT
1 TTAT
5988292 GTATTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 17 0.53
18 3 0.09
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATAATATATTT
Found at i:5988320 original size:16 final size:16
Alignment explanation
Indices: 5988228--5988322 Score: 52
Period size: 17 Copynumber: 5.7 Consensus size: 16
5988218 CAATTATCTA
*
5988228 TATTTTTTTGTTATTAT
1 TATTTTATT-TTATTAT
*
5988245 TA-ATTATTTTTATT-T
1 TATTTTA-TTTTATTAT
*
5988260 TAATATATATTTTATTAT
1 T-AT-TTTATTTTATTAT
* **
5988278 CATACTATTTTTATGTAT
1 TATTTTA-TTTTAT-TAT
5988296 T-TTTATATTTTATTAT
1 TATTT-TATTTTATTAT
5988312 TATTTTATTTT
1 TATTTTATTTT
5988323 TCATAAGCGA
Statistics
Matches: 59, Mismatches: 10, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
15 2 0.03
16 20 0.34
17 29 0.49
18 8 0.14
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTATTAT
Found at i:5988477 original size:16 final size:17
Alignment explanation
Indices: 5988447--5988495 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
5988437 CAATGCTTAA
*
5988447 TTTTAAATTAGTTATTT
1 TTTTATATTAGTTATTT
5988464 TTTTATATTA-TTATTT
1 TTTTATATTAGTTATTT
* *
5988480 ATTTAT-TTATTTATTT
1 TTTTATATTAGTTATTT
5988496 AATGTCATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 17 0.59
17 9 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTATATTAGTTATTT
Found at i:5988483 original size:4 final size:4
Alignment explanation
Indices: 5988458--5988496 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
5988448 TTTAAATTAG
*
5988458 TTAT TTTT TTAT ATTA- TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTA
5988497 ATGTCATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:5988604 original size:13 final size:13
Alignment explanation
Indices: 5988588--5988617 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5988578 TATTATTTAT
5988588 TTTTATCAAGTAA
1 TTTTATCAAGTAA
5988601 TTTTATCAAGTAA
1 TTTTATCAAGTAA
5988614 TTTT
1 TTTT
5988618 TTTATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTTATCAAGTAA
Found at i:5989288 original size:30 final size:32
Alignment explanation
Indices: 5989225--5989291 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
5989215 CATCTCCAGA
*
5989225 TCTGGTGCCGCGCCAGCCGTCGCTCCTCTCTC
1 TCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTC
5989257 TCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTC
1 TCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTC
5989289 TCT
1 TCT
5989292 TCCTCCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.03, C:0.48, G:0.24, T:0.25
Consensus pattern (32 bp):
TCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTC
Found at i:5989442 original size:52 final size:52
Alignment explanation
Indices: 5989360--5989471 Score: 172
Period size: 52 Copynumber: 2.2 Consensus size: 52
5989350 TCTCTGGTGC
*
5989360 CGCGCCAGCCGCCGCTCCTCTCTCTATTCCTCCGCTCAGCTCTTCCTT-CCCT
1 CGCGCCAGCCGCCGCTCCTCTCTCTATTCCTCCGCTCAGCGC-TCCTTCCCCT
* * *
5989412 CGCGCCAGCCGCCGCTCCTCTCTCTTTTCCTCCGTTCGGCGCTCCTTCCCCT
1 CGCGCCAGCCGCCGCTCCTCTCTCTATTCCTCCGCTCAGCGCTCCTTCCCCT
5989464 CGCGCCAG
1 CGCGCCAG
5989472 ATCTTCACTG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 5 0.09
52 50 0.91
ACGTcount: A:0.04, C:0.52, G:0.17, T:0.27
Consensus pattern (52 bp):
CGCGCCAGCCGCCGCTCCTCTCTCTATTCCTCCGCTCAGCGCTCCTTCCCCT
Found at i:5993286 original size:2 final size:2
Alignment explanation
Indices: 5993279--5993325 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
5993269 CATTAAACAA
5993279 AT AT AT AT AT AT AT AT AT AT AT A- ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
5993321 GT AT A
1 AT AT A
5993326 GTTCAAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5996779 original size:29 final size:29
Alignment explanation
Indices: 5996711--5996780 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
5996701 AGTTATAAGA
* * *
5996711 ACTTATTTGATCCAAAATAAAAATATAAGG
1 ACTTATTTGA-ACAAAATAAAAAAATAAAG
* *
5996741 ATTTGA-TTGAACACAATAAAAAAATAAAG
1 ACTT-ATTTGAACAAAATAAAAAAATAAAG
5996770 ACTTATTTGAA
1 ACTTATTTGAA
5996781 TTTTCTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.03
29 23 0.72
30 7 0.22
31 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (29 bp):
ACTTATTTGAACAAAATAAAAAAATAAAG
Found at i:6004549 original size:35 final size:35
Alignment explanation
Indices: 6004500--6004773 Score: 302
Period size: 35 Copynumber: 7.8 Consensus size: 35
6004490 TCCTTAAGAA
*** *
6004500 GCCCAATTAACTTAATTATTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAACAATTTAATTAATTAG
*
6004536 GCCCAATAACTTAATTAAACAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAACAATTTAATTAATTAG
* * *
6004571 GCCCAACAATTTAATTAAACAATTTTAATCAATTAG
1 GCCCAATAACTTAATTAAACAA-TTTAATTAATTAG
* *
6004607 GCCCAATGACTTAATTAAACAAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAAC-AATTTAATTAATTAG
****
6004643 GCCCAATAACTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAACAATTTAATTAATTAG
* *
6004678 GCCTAATGACTTAATTAAACAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAACAATTTAATTAATTAG
* * *
6004713 GCCCAATGATTTAATTAAATAATTTAATTAATTA-
1 GCCCAATAACTTAATTAAACAATTTAATTAATTAG
* *
6004747 -CAC-ACAACTTAATTAAACAATTCTAAT
1 GCCCAATAACTTAATTAAACAATT-TAAT
6004774 CAAGTGCTTG
Statistics
Matches: 203, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
32 15 0.07
33 6 0.03
35 118 0.58
36 62 0.31
37 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.36
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAACAATTTAATTAATTAG
Found at i:6004598 original size:71 final size:70
Alignment explanation
Indices: 6004500--6004773 Score: 320
Period size: 71 Copynumber: 3.9 Consensus size: 70
6004490 TCCTTAAGAA
* **
6004500 GCCCAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATT
1 GCCCAA-TAATTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATT
*
6004565 AATTAA
65 AATTAG
* * *
6004571 GCCCAACAATTTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAAT
1 GCCCAATAATTTAATTAAATAA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAAT
*
6004636 CAATTAG
64 TAATTAG
* *** * * *
6004643 GCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCTAATGACTTAATTAAACAATTTAATTA
1 GCCCAATAATTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
6004708 ATTAG
66 ATTAG
* * * *
6004713 GCCCAATGATTTAATTAAATAATTTAATTAATTA--CAC-ACAACTTAATTAAACAATTCTAAT
1 GCCCAATAATTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATT-TAAT
6004774 CAAGTGCTTG
Statistics
Matches: 174, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
67 17 0.10
68 5 0.03
70 54 0.31
71 69 0.40
72 29 0.17
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.36
Consensus pattern (70 bp):
GCCCAATAATTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
ATTAG
Found at i:6012877 original size:42 final size:43
Alignment explanation
Indices: 6012817--6012920 Score: 131
Period size: 42 Copynumber: 2.4 Consensus size: 43
6012807 CAATGGTTGC
* * * *
6012817 TTCTGATACGATTGTGACCCATGCCA-TAGGGGTTAATTGTGGT
1 TTCTGATATGATTATGACCCATGCCACT-GAGGTTAATTGTGAT
*
6012860 TT-TGATATGATTATGACCCGTGCCACTGAGGTTAATTGTGAT
1 TTCTGATATGATTATGACCCATGCCACTGAGGTTAATTGTGAT
*
6012902 TTCTGCTATGATTATGACC
1 TTCTGATATGATTATGACC
6012921 TATGTCGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 35 0.66
43 18 0.34
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (43 bp):
TTCTGATATGATTATGACCCATGCCACTGAGGTTAATTGTGAT
Found at i:6012936 original size:43 final size:43
Alignment explanation
Indices: 6012820--6012937 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 43
6012810 TGGTTGCTTC
* * * *
6012820 TGATACGATTGTGACCCATGCCA-TAGGGGTTAATTGTGGTTT
1 TGATATGATTATGACCCATGCCACTAAGGGTTAATTGTGATTT
* *
6012862 TGATATGATTATGACCCGTGCCACTGA-GGTTAATTGTGATTT
1 TGATATGATTATGACCCATGCCACTAAGGGTTAATTGTGATTT
* * * *
6012904 CTGCTATGATTATGACCTATGTC-GTAAGGGTTAA
1 -TGATATGATTATGACCCATGCCACTAAGGGTTAA
6012938 GTATGGCCAT
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
42 36 0.59
43 25 0.41
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (43 bp):
TGATATGATTATGACCCATGCCACTAAGGGTTAATTGTGATTT
Done.