Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 146 of 182
Found at i:45068504 original size:21 final size:21
Alignment explanation
Indices: 45068474--45068521 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
45068464 TGTTCTTGAA
* *
45068474 TTTCAGCAGCAATCTATTAAT
1 TTTCAACAGCAAACTATTAAT
*
45068495 TTTCAACAGCAAACTATTGAT
1 TTTCAACAGCAAACTATTAAT
45068516 TTTCAA
1 TTTCAA
45068522 AAGAGAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTCAACAGCAAACTATTAAT
Found at i:45069701 original size:15 final size:15
Alignment explanation
Indices: 45069681--45069729 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
45069671 AGGCAACCCA
*
45069681 ATTTTTAATTTTATT
1 ATTTTTTATTTTATT
45069696 ATTTTTTATTTT-TCT
1 ATTTTTTATTTTAT-T
45069711 ATTTATTTA-TTTATT
1 ATTT-TTTATTTTATT
45069726 ATTT
1 ATTT
45069730 GTCCAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 24 0.80
16 5 0.17
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTATTTTATT
Found at i:45074322 original size:27 final size:27
Alignment explanation
Indices: 45074287--45074341 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
45074277 ATTTAATACC
*
45074287 TAATGCCTATTATACCCTTAATGCCCT
1 TAATACCTATTATACCCTTAATGCCCT
45074314 TAATACCTATTATACCCTTAATGCCCT
1 TAATACCTATTATACCCTTAATGCCCT
45074341 T
1 T
45074342 CTCAATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.05, T:0.38
Consensus pattern (27 bp):
TAATACCTATTATACCCTTAATGCCCT
Found at i:45079035 original size:2 final size:2
Alignment explanation
Indices: 45079028--45079055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45079018 TGGTAAGAAA
45079028 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
45079056 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:45092708 original size:17 final size:18
Alignment explanation
Indices: 45092672--45092709 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
45092662 ACTTATTACG
* *
45092672 TCTTTTGCATCATCTTTC
1 TCTTTTGCAACATATTTC
45092690 TCTTTTGCAAC-TATTTC
1 TCTTTTGCAACATATTTC
45092707 TCT
1 TCT
45092710 CACCATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.26, G:0.05, T:0.55
Consensus pattern (18 bp):
TCTTTTGCAACATATTTC
Found at i:45094540 original size:6 final size:6
Alignment explanation
Indices: 45094529--45094616 Score: 68
Period size: 6 Copynumber: 14.2 Consensus size: 6
45094519 TGGCAATCTC
* * * * *
45094529 TTCTTT TTCTTT TTCTTT ATCTTT TCCTTT TTCTTC ATCTTT TACCTTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T-TC-TTT
* * * *
45094579 CTTCTGT TTCTGT TTCTGT TTCTTT TTCCTT TTCTTT T
1 -TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T
45094617 ACTTCATCTG
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
6 57 0.88
7 3 0.05
8 4 0.06
9 1 0.02
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (6 bp):
TTCTTT
Found at i:45098422 original size:29 final size:29
Alignment explanation
Indices: 45098384--45098448 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
45098374 TTAAAAAAAA
45098384 TTTAAGTAAAGTAATAGAAAAAATAAGTAT
1 TTTAA-TAAAGTAATAGAAAAAATAAGTAT
45098414 TTTAATAAAGTAATAGAAAAAATAAGTAT
1 TTTAATAAAGTAATAGAAAAAATAAGTAT
45098443 TTTAAT
1 TTTAAT
45098449 GGGATGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (29 bp):
TTTAATAAAGTAATAGAAAAAATAAGTAT
Found at i:45098543 original size:25 final size:25
Alignment explanation
Indices: 45098515--45098563 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
45098505 AATTTTTAAA
*
45098515 ATTTTA-ATTTTTTTATATATTTTAG
1 ATTTTATAATTTTTTATA-ATTTTAG
45098540 ATTTTATTAATTTTTTATAATTTT
1 ATTTTA-TAATTTTTTATAATTTT
45098564 TATAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 5 0.24
27 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTTATAATTTTTTATAATTTTAG
Found at i:45098605 original size:26 final size:25
Alignment explanation
Indices: 45098558--45098625 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 25
45098548 AATTTTTTAT
* *
45098558 AATTTTTATAAAATATAAAATTTGA
1 AATTTTTATAAAATTTTAAATTTGA
* *
45098583 AATTTTTATAAATATTTTTAATTTTA
1 AATTTTTATAAA-ATTTTAAATTTGA
* *
45098609 ATTTTTTTTAAAATTTT
1 AATTTTTATAAAATTTT
45098626 GATTGGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 17 0.47
26 19 0.53
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
AATTTTTATAAAATTTTAAATTTGA
Found at i:45099751 original size:7 final size:7
Alignment explanation
Indices: 45099739--45099763 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45099729 TGAGTCGAAA
45099739 TTAAATT
1 TTAAATT
45099746 TTAAATT
1 TTAAATT
45099753 TTAAATT
1 TTAAATT
45099760 TTAA
1 TTAA
45099764 TAGTCTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:45121690 original size:11 final size:12
Alignment explanation
Indices: 45121675--45121707 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
45121665 TATAAAAAAT
45121675 ATAAATTTAAT-
1 ATAAATTTAATA
*
45121686 TTAAATTTAATA
1 ATAAATTTAATA
45121698 ATAAATTTAA
1 ATAAATTTAA
45121708 AAACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAAATTTAATA
Found at i:45122106 original size:21 final size:21
Alignment explanation
Indices: 45122088--45122164 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
45122078 GATAATGATG
45122088 AGAGTTATAAA-ACTTATGAGA
1 AGAGTTATAAACA-TTATGAGA
45122109 AGAGTTATAAACATTATGAGA
1 AGAGTTATAAACATTATGAGA
* *
45122130 AGAGTTACAAACATTATGAGG
1 AGAGTTATAAACATTATGAGA
*
45122151 AGAGTTACAAACAT
1 AGAGTTATAAACAT
45122165 AATGTTTTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 52 0.98
22 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (21 bp):
AGAGTTATAAACATTATGAGA
Found at i:45128775 original size:28 final size:28
Alignment explanation
Indices: 45128743--45128796 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
45128733 GCTTGACAAC
*
45128743 TTGTTCAATAATTCAAGAGGTTGGCCAG
1 TTGTTCAATAAATCAAGAGGTTGGCCAG
* *
45128771 TTGTTCAATAAATGAGGAGGTTGGCC
1 TTGTTCAATAAATCAAGAGGTTGGCC
45128797 GTGTGGGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (28 bp):
TTGTTCAATAAATCAAGAGGTTGGCCAG
Found at i:45130204 original size:50 final size:49
Alignment explanation
Indices: 45130121--45130215 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 49
45130111 TGCATGACTT
* *
45130121 GATTTAATGATGCATTTAACTAATATGGGAGTTACATAATGCATGATAG
1 GATTTAATGATGCATTTAACTAACATGGAAGTTACATAATGCATGATAG
* * *
45130170 GATTT-ATGATGCATATTTAACTAACATGTAAGTTACTTCATGCATG
1 GATTTAATGATGC--ATTTAACTAACATGGAAGTTACATAATGCATG
45130216 TCATTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 7 0.18
49 5 0.13
50 27 0.69
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (49 bp):
GATTTAATGATGCATTTAACTAACATGGAAGTTACATAATGCATGATAG
Found at i:45130477 original size:16 final size:16
Alignment explanation
Indices: 45130456--45130487 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45130446 CTTATTAAAC
45130456 TGAAATAAAATAAAAA
1 TGAAATAAAATAAAAA
45130472 TGAAATAAAATAAAAA
1 TGAAATAAAATAAAAA
45130488 GTCCTTAAAA
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:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (16 bp):
TGAAATAAAATAAAAA
Found at i:45132994 original size:29 final size:28
Alignment explanation
Indices: 45132962--45133038 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
45132952 TTTTAATTCG
45132962 ATTTTTTTCTTCTTTTTTACAA-ACTTT-GA
1 ATTTTTTTCTT-TTTTTT-CAATA-TTTAGA
**
45132991 ATTTTCTTTGATTTTTTTCAATATTTAGA
1 ATTTT-TTTCTTTTTTTTCAATATTTAGA
*
45133020 TTTTTTTTCTTTTTTTTCA
1 ATTTTTTTCTTTTTTTTCA
45133039 CTTTTTCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 18 0.45
29 18 0.45
30 4 0.10
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.68
Consensus pattern (28 bp):
ATTTTTTTCTTTTTTTTCAATATTTAGA
Found at i:45135131 original size:21 final size:21
Alignment explanation
Indices: 45135091--45135131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45135081 ATCAAACCCT
*
45135091 TCTTGCATCATCCTTCGCATC
1 TCTTGCATCATACTTCGCATC
45135112 TCTTGCATCATGACTT-GCAT
1 TCTTGCATCAT-ACTTCGCAT
45135132 TTGAAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.17, C:0.32, G:0.12, T:0.39
Consensus pattern (21 bp):
TCTTGCATCATACTTCGCATC
Found at i:45135513 original size:18 final size:17
Alignment explanation
Indices: 45135492--45135527 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
45135482 TTTTTAATAC
*
45135492 TCGATTTTTTTTCTTCTT
1 TCGATTCTTTTT-TTCTT
45135510 TCGATTCTTTTTTTCTT
1 TCGATTCTTTTTTTCTT
45135527 T
1 T
45135528 TTTAATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (17 bp):
TCGATTCTTTTTTTCTT
Found at i:45135535 original size:19 final size:20
Alignment explanation
Indices: 45135497--45135552 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
45135487 AATACTCGAT
*
45135497 TTTTTTTCTTCTTTCGATTC
1 TTTTTTTCTTCTTTCAATTC
*
45135517 TTTTTTTCTT-TTTTAATTC
1 TTTTTTTCTTCTTTCAATTC
45135536 GAATTTTTTTCTTCTTT
1 ---TTTTTTTCTTCTTT
45135553 TTTTCAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.23
20 10 0.33
22 10 0.33
23 3 0.10
ACGTcount: A:0.09, C:0.14, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTTTTTCTTCTTTCAATTC
Found at i:45135536 original size:24 final size:25
Alignment explanation
Indices: 45135509--45135555 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
45135499 TTTTTCTTCT
45135509 TTCG-ATTCTTTTT-TTCTTTTTTAA
1 TTCGAATT-TTTTTCTTCTTTTTTAA
45135533 TTCGAATTTTTTTCTTCTTTTTT
1 TTCGAATTTTTTTCTTCTTTTTT
45135556 TCAAACTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.72
Consensus pattern (25 bp):
TTCGAATTTTTTTCTTCTTTTTTAA
Found at i:45135556 original size:28 final size:27
Alignment explanation
Indices: 45135509--45135615 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
45135499 TTTTTCTTCT
*
45135509 TTCGATTCTTTTT-TTCTTTTTT--AA-
1 TTCGATT-TTTTTATTTTTTTTTCAAAC
*
45135533 TTCGAATTTTTTTCTTCTTTTTTTCAAAC
1 TTCG-ATTTTTTTATT-TTTTTTTCAAAC
* *
45135562 TTCGATTTTTTTATTTTTTTCTCAATAT
1 TTCGATTTTTTTATTTTTTTTTCAA-AC
45135590 TTCGATTTTTTT-TTTTCTTTTTCAAA
1 TTCGATTTTTTTATTTT-TTTTTCAAA
45135616 TTTTTTTCAC
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
24 9 0.13
25 5 0.07
26 6 0.09
27 14 0.20
28 32 0.46
29 4 0.06
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.67
Consensus pattern (27 bp):
TTCGATTTTTTTATTTTTTTTTCAAAC
Found at i:45136183 original size:17 final size:17
Alignment explanation
Indices: 45136163--45136195 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45136153 TTTAAGGACT
45136163 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
45136180 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
45136196 TAAGTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:45136474 original size:50 final size:50
Alignment explanation
Indices: 45136390--45136542 Score: 125
Period size: 50 Copynumber: 3.1 Consensus size: 50
45136380 TGACATCCAT
* * * *
45136390 TAACTCTCATGATTAGTTAAGTTTGCAGCATAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAATGACATGCATTAAG
* ** ** *
45136441 TAACTTACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCGCTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATGA-CATGCATTAAG
* * *
45136491 TAACTCCCATGTTAGTT-AA-ATGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTTAAATATGCATCA-TAAAT-AATGACATGCATTAAG
45136540 TAA
1 TAA
45136543 TCCATTAGTT
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
48 8 0.10
49 18 0.23
50 44 0.56
51 9 0.11
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATGACATGCATTAAG
Found at i:45137827 original size:20 final size:21
Alignment explanation
Indices: 45137787--45137843 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
45137777 AAGTTTTAAA
* *
45137787 AAAGAAGAAAAAAATTCGAATTT
1 AAAGAAGAAAAAAA--AGAATCT
45137810 AAA-AAGAAAAAAAAGAATCT
1 AAAGAAGAAAAAAAAGAATCT
45137830 AAAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
45137844 GTTGAGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.26
21 10 0.32
22 10 0.32
23 3 0.10
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAGAAGAAAAAAAAGAATCT
Found at i:45137844 original size:20 final size:20
Alignment explanation
Indices: 45137787--45137844 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
45137777 AAGTTTTAAA
*
45137787 AAAGAAGAAAAAAATTCGAATTT
1 AAAGAAGAAAAAAA---GAATCT
45137810 AAA-AAGAAAAAAAAGAATCT
1 AAAGAAG-AAAAAAAGAATCT
45137830 AAAGAAGAAAAAAAG
1 AAAGAAGAAAAAAAG
45137845 TTGAGTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 16 0.50
21 3 0.09
22 3 0.09
23 10 0.31
ACGTcount: A:0.71, C:0.03, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAGAAGAAAAAAAGAATCT
Found at i:45138808 original size:42 final size:39
Alignment explanation
Indices: 45138728--45138815 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 39
45138718 AATAAAGAAA
45138728 GAAAAAAAGAGAATGTGAATAAAAAAAGAAAACAGAATT
1 GAAAAAAAGAGAATGTGAATAAAAAAAGAAAACAGAATT
45138767 GAAAAGAAAGAGAGATGTGTAA-AAAAGAAATGAAAA-AGAATT
1 GAAAA-AAAGAGA-ATGTG-AATAAAA-AAA-GAAAACAGAATT
45138809 GAAAAAA
1 GAAAAAA
45138816 GAAATGAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
39 5 0.11
40 7 0.16
41 11 0.25
42 16 0.36
43 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.20, T:0.12
Consensus pattern (39 bp):
GAAAAAAAGAGAATGTGAATAAAAAAAGAAAACAGAATT
Found at i:45138813 original size:10 final size:11
Alignment explanation
Indices: 45138788--45138824 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
45138778 GAGATGTGTA
45138788 AAAAAGAAATG
1 AAAAAGAAATG
*
45138799 AAAAAGAATTG
1 AAAAAGAAATG
45138810 AAAAAAGAAATG
1 -AAAAAGAAATG
45138822 AAA
1 AAA
45138825 GTGAAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (11 bp):
AAAAAGAAATG
Found at i:45138814 original size:12 final size:12
Alignment explanation
Indices: 45138787--45138824 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
45138777 AGAGATGTGT
45138787 AAAAAAGAAATG
1 AAAAAAGAAATG
*
45138799 -AAAAAGAATTG
1 AAAAAAGAAATG
45138810 AAAAAAGAAATG
1 AAAAAAGAAATG
45138822 AAA
1 AAA
45138825 GTGAAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (12 bp):
AAAAAAGAAATG
Found at i:45140308 original size:17 final size:17
Alignment explanation
Indices: 45140288--45140320 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45140278 TTTAAGGACT
45140288 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
45140305 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
45140321 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:45140599 original size:50 final size:51
Alignment explanation
Indices: 45140533--45140670 Score: 165
Period size: 50 Copynumber: 2.7 Consensus size: 51
45140523 ATGATCAGGT
* * *
45140533 AAGTTTGCATAATAAATAGTGA-CATGCATTAAGTAACTTACATGTTAGTTA
1 AAGTATGCATCATAAATACT-ATCATGCATTAAGTAACTTACATGTTAGTTA
*
45140584 AA-TATGCATCATAAATCCTATCATGCATTAAGTAACTTACATGTTAGTTA
1 AAGTATGCATCATAAATACTATCATGCATTAAGTAACTTACATGTTAGTTA
* * *
45140634 AAGTTTGCATCATTAAAT-CAAGTCATGCATTTAGTAA
1 AAGTATGCATCA-TAAATACTA-TCATGCATTAAGTAA
45140671 TCCATTAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.01
50 44 0.58
51 12 0.16
52 19 0.25
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (51 bp):
AAGTATGCATCATAAATACTATCATGCATTAAGTAACTTACATGTTAGTTA
Found at i:45141884 original size:18 final size:18
Alignment explanation
Indices: 45141861--45141913 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
45141851 TTCGTATTTC
*
45141861 GAAAAAGTGAAAAAAATT
1 GAAAAAATGAAAAAAATT
*
45141879 GAAAAAAAGAAAAAAA-T
1 GAAAAAATGAAAAAAATT
* *
45141896 CAAAATATTGAAAAAAAT
1 GAAAA-AATGAAAAAAAT
45141914 AAAAAAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (18 bp):
GAAAAAATGAAAAAAATT
Found at i:45141900 original size:26 final size:26
Alignment explanation
Indices: 45141871--45141947 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 26
45141861 GAAAAAGTGA
45141871 AAAAAATTGAAAAAAAGAAAAAAATC
1 AAAAAATTGAAAAAAAGAAAAAAATC
* *
45141897 AAAATATTGAAAAAAATAAAAAAATC
1 AAAAAATTGAAAAAAAGAAAAAAATC
**
45141923 -AAAGTTTGGAAAAAAAGAAGAAAAA
1 AAAAAATT-GAAAAAAAGAA-AAAAA
45141948 ATTCAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 5 0.11
26 34 0.77
27 5 0.11
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAATTGAAAAAAAGAAAAAAATC
Found at i:45142680 original size:19 final size:18
Alignment explanation
Indices: 45142639--45142683 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
45142629 AGAGTGTGAG
*
45142639 AAAAGAGATCGAAATTGA
1 AAAAGAAATCGAAATTGA
45142657 AAAAGAAATCGAGAA-TGAA
1 AAAAGAAATCGA-AATTG-A
45142676 AAAAGAAA
1 AAAAGAAA
45142684 AGAAAGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.64, C:0.04, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAAGAAATCGAAATTGA
Found at i:45145016 original size:12 final size:12
Alignment explanation
Indices: 45144999--45145033 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
45144989 TCAAAATTGA
45144999 AAGTGAAAGTGG
1 AAGTGAAAGTGG
*
45145011 AAGTGAAATTGG
1 AAGTGAAAGTGG
*
45145023 AATTGAAAGTG
1 AAGTGAAAGTG
45145034 ATATGCATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (12 bp):
AAGTGAAAGTGG
Found at i:45150766 original size:6 final size:6
Alignment explanation
Indices: 45150751--45150801 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
45150741 TGATCAAAAT
* * * * *
45150751 TGAAAG TGAAAC TGAATG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
45150799 TGA
1 TGA
45150802 TATGAATTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (6 bp):
TGAAAG
Found at i:45153202 original size:27 final size:26
Alignment explanation
Indices: 45153172--45153241 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
45153162 AAAACTTTTT
45153172 AAAAAAAGAAAAAAATCGA-AATATTGA
1 AAAAAAAGAAAAAAATC-ATAAT-TTGA
* *
45153199 AAAAAAATAAAAAAAATCATAGTTTGA
1 AAAAAAA-GAAAAAAATCATAATTTGA
45153226 AAAAAAAGAAGAAAAA
1 AAAAAAAGAA-AAAAA
45153242 AATTCAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.05
27 24 0.65
28 11 0.30
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAAAGAAAAAAATCATAATTTGA
Found at i:45154314 original size:18 final size:18
Alignment explanation
Indices: 45154293--45154336 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
45154283 AGAGTGTGAG
*
45154293 AAAAGAGATCGA-AATTGA
1 AAAAGAAATCGAGAA-TGA
45154311 AAAAGAAATCGAGAATGA
1 AAAAGAAATCGAGAATGA
45154329 AAAAGAAA
1 AAAAGAAA
45154337 AGAAAGAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.64, C:0.05, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAAGAAATCGAGAATGA
Found at i:45155747 original size:17 final size:17
Alignment explanation
Indices: 45155727--45155759 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45155717 TTTAAGGACT
45155727 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
45155744 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
45155760 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:45156031 original size:50 final size:50
Alignment explanation
Indices: 45155954--45156074 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
45155944 TGACATCCAT
* * * * *
45155954 TAACTCTCATGATCAGTTAAGTTTGCATAATAAATAATGGCATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATAATAAATAATAGCATGCATTAAG
* * ** * *
45156005 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATAATAAATAATAGCATGCATTAAG
*
45156055 TAACTCCCATGTTAGTTAAA
1 TAACTCACATGTTAGTTAAA
45156075 GTTTGCATCA
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
50 48 0.84
51 9 0.16
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATAATAAATAATAGCATGCATTAAG
Found at i:45159292 original size:39 final size:40
Alignment explanation
Indices: 45159233--45159312 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
45159223 AAGAGGTACG
*
45159233 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
*
45159273 TCCAATTTGAAAAGG-TTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
45159312 T
1 T
45159313 TAAGTGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 24 0.63
40 14 0.37
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:45160713 original size:14 final size:13
Alignment explanation
Indices: 45160694--45160724 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
45160684 TTATGCAATC
45160694 TTTTCTTTAAATAT
1 TTTTCTTTAAAT-T
45160708 TTTTCTTTAAATT
1 TTTTCTTTAAATT
45160721 TTTT
1 TTTT
45160725 AAACATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCTTTAAATT
Found at i:45161167 original size:19 final size:19
Alignment explanation
Indices: 45161118--45161167 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
45161108 ATCTTTTTAT
*
45161118 TTCTT-TATTTTATTTTTC
1 TTCTTCTATTTTATTTCTC
**
45161136 TTCTTCTCCTTTATTTCTC
1 TTCTTCTATTTTATTTCTC
45161155 TTC-TCATATTTTA
1 TTCTTC-TATTTTA
45161168 CATTATAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTCTATTTTATTTCTC
Found at i:45161504 original size:19 final size:17
Alignment explanation
Indices: 45161480--45161516 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
45161470 TTGTTTTTGT
45161480 TTTTATTTTATTATTATAA
1 TTTTA-TTTATT-TTATAA
45161499 TTTTATTTATTTTATAA
1 TTTTATTTATTTTATAA
45161516 T
1 T
45161517 GAAAATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTATTTTATAA
Found at i:45162354 original size:24 final size:24
Alignment explanation
Indices: 45162327--45162384 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
45162317 GAGAGGAAAA
45162327 AAAAGAAGAAGTAAAA-G-TTTTTTT
1 AAAA-AAGAAG-AAAATGATTTTTTT
*
45162351 AAAATAAGATGAAAATGATTTTTTT
1 AAAA-AAGAAGAAAATGATTTTTTT
*
45162376 TAAAAAGAA
1 AAAAAAGAA
45162385 TTTTGGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 14 0.50
25 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (24 bp):
AAAAAAGAAGAAAATGATTTTTTT
Found at i:45165102 original size:29 final size:30
Alignment explanation
Indices: 45165055--45165165 Score: 111
Period size: 30 Copynumber: 3.8 Consensus size: 30
45165045 CCTTAATTTT
* * * *
45165055 AAAATTGTTTTTTGACCCTTAATCTATCCA
1 AAAATTATATTTTGACCCTCAAACTATCCA
45165085 AAAATTATATTTT-ACCCTCAAACTATCCA
1 AAAATTATATTTTGACCCTCAAACTATCCA
** * *
45165114 AAAATTATGCTTTGA-CCTACAAACTTTTCA
1 AAAATTATATTTTGACCCT-CAAACTATCCA
*
45165144 AAAATTATGTTTTGACCC-CAAA
1 AAAATTATATTTTGACCCTCAAA
45165166 GTTTCTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 32 0.46
30 35 0.51
31 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTCAAACTATCCA
Found at i:45165176 original size:29 final size:29
Alignment explanation
Indices: 45165084--45165178 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
45165074 TAATCTATCC
* * *
45165084 AAAAATTATATTTT-ACCCTCAAACTATCC
1 AAAAATTATGTTTTGACCC-CAAACTTTCT
* *
45165113 AAAAATTATGCTTTGACCTACAAACTTT-T
1 AAAAATTATGTTTTGACC-CCAAACTTTCT
*
45165142 CAAAAATTATGTTTTGACCCCAAAGTTTCT
1 -AAAAATTATGTTTTGACCCCAAACTTTCT
45165172 AAAAATT
1 AAAAATT
45165179 CCCAATTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 26 0.48
30 28 0.52
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTATGTTTTGACCCCAAACTTTCT
Found at i:45174682 original size:27 final size:27
Alignment explanation
Indices: 45174652--45174706 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
45174642 TGAAACCGAA
45174652 TGTACTCCTAAAGATAAAAGAAGAGGT
1 TGTACTCCTAAAGATAAAAGAAGAGGT
45174679 TGTACTCCTAAAGATAAAAGAAGAGGT
1 TGTACTCCTAAAGATAAAAGAAGAGGT
45174706 T
1 T
45174707 CGAAAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (27 bp):
TGTACTCCTAAAGATAAAAGAAGAGGT
Found at i:45178132 original size:12 final size:12
Alignment explanation
Indices: 45178115--45178145 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
45178105 ACATTTATTG
45178115 TTTTGATTAATA
1 TTTTGATTAATA
*
45178127 TTTTGACTAATA
1 TTTTGATTAATA
45178139 TTTTGAT
1 TTTTGAT
45178146 ATCTTCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (12 bp):
TTTTGATTAATA
Found at i:45195148 original size:64 final size:64
Alignment explanation
Indices: 45195040--45195166 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
45195030 GACGATTGCG
* * * * *
45195040 GGTATTTTCAGTGGAAATTAAGCGCATACAGTTTGACTATATTATGCCGCCACGCATTAGGATA
1 GGTATTTTCACTGGAAATTAAACGCATACAATTTGACTAGATTATGACGCCACGCATTAGGATA
* *
45195104 GGTATTTTCTCTGGAAATTAAACGCATACAATTTGATTAGATTATGACGCCACGCATTAGGAT
1 GGTATTTTCACTGGAAATTAAACGCATACAATTTGACTAGATTATGACGCCACGCATTAGGAT
45195167 TCACTTTTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (64 bp):
GGTATTTTCACTGGAAATTAAACGCATACAATTTGACTAGATTATGACGCCACGCATTAGGATA
Found at i:45195615 original size:28 final size:28
Alignment explanation
Indices: 45195567--45195635 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
45195557 CCAAATGATT
*
45195567 GAGGAGGTTGGCAACTCGTTCAATAAGTC
1 GAGGAGGTTGGCCACTCGTTCAATAA-TC
*
45195596 -AGGAGGTTGGCCACTTGTTCAATAATC
1 GAGGAGGTTGGCCACTCGTTCAATAATC
45195623 GAGGAGGTTGGCC
1 GAGGAGGTTGGCC
45195636 GTGTGGGCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GAGGAGGTTGGCCACTCGTTCAATAATC
Found at i:45198634 original size:37 final size:37
Alignment explanation
Indices: 45198527--45198676 Score: 106
Period size: 37 Copynumber: 4.1 Consensus size: 37
45198517 TTGTTAGTAA
* * * *
45198527 GAAATCGGACTATGTGCCT-GACAAGCTTCATGCCGGT
1 GAAATCGGGCTATATGCCTAG-CAGGCTTCGTGCCGGT
* * * *** *
45198564 GAAAACGGGCTGTGTGCCTAGCAAATTTTGTGCCGGT
1 GAAATCGGGCTATATGCCTAGCAGGCTTCGTGCCGGT
* *
45198601 GAAATCGGGCTATATGGCTAGCAGGCTTCGTGCCGAT
1 GAAATCGGGCTATATGCCTAGCAGGCTTCGTGCCGGT
* * * * *
45198638 G-TATCGAGCTTTATGCCTAGCAGGCCTTTGTGTCGGT
1 GAAATCGGGCTATATGCCTAGCAGG-CTTCGTGCCGGT
45198675 GA
1 GA
45198677 TTTACATATA
Statistics
Matches: 87, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
36 19 0.22
37 67 0.77
38 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (37 bp):
GAAATCGGGCTATATGCCTAGCAGGCTTCGTGCCGGT
Found at i:45207430 original size:2 final size:2
Alignment explanation
Indices: 45207423--45207453 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45207413 TACATAGTAA
45207423 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 A
45207454 ATTGTCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45209005 original size:21 final size:21
Alignment explanation
Indices: 45208981--45209020 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45208971 TCGAGTTTAG
*
45208981 GATTCTAGGATCAATGTTTGA
1 GATTCAAGGATCAATGTTTGA
*
45209002 GATTCAAGGTTCAATGTTT
1 GATTCAAGGATCAATGTTT
45209021 ATGTTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (21 bp):
GATTCAAGGATCAATGTTTGA
Found at i:45212796 original size:21 final size:21
Alignment explanation
Indices: 45212771--45212832 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
45212761 GAGAATCGAG
45212771 GTTCAAGATTTAAAATTTAAT
1 GTTCAAGATTTAAAATTTAAT
** *
45212792 GTTCAAGATTTAAGGTTAAAT
1 GTTCAAGATTTAAAATTTAAT
* * *
45212813 GTTCAAAATTCAAAACTTAA
1 GTTCAAGATTTAAAATTTAA
45212833 AATTAAGTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (21 bp):
GTTCAAGATTTAAAATTTAAT
Found at i:45212881 original size:7 final size:7
Alignment explanation
Indices: 45212869--45212910 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
45212859 ATTGAAATTC
45212869 AAATTTA
1 AAATTTA
45212876 AAATTTA
1 AAATTTA
45212883 AAATTTA
1 AAATTTA
*
45212890 AAGTTTA
1 AAATTTA
*
45212897 AAGTTTA
1 AAATTTA
*
45212904 AAGTTTA
1 AAATTTA
45212911 GGATTTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:45212888 original size:14 final size:14
Alignment explanation
Indices: 45212869--45212910 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
45212859 ATTGAAATTC
*
45212869 AAATTTAAAATTTA
1 AAATTTAAAGTTTA
45212883 AAATTTAAAGTTTA
1 AAATTTAAAGTTTA
*
45212897 AAGTTTAAAGTTTA
1 AAATTTAAAGTTTA
45212911 GGATTTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AAATTTAAAGTTTA
Found at i:45212917 original size:21 final size:20
Alignment explanation
Indices: 45212863--45212910 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
45212853 TTCATGATTG
*
45212863 AAATTCAAATTTAAAATTTA
1 AAATTTAAATTTAAAATTTA
*
45212883 AAATTTAAAGTTTAAAGTTTA
1 AAATTTAAA-TTTAAAATTTA
*
45212904 AAGTTTA
1 AAATTTA
45212911 GGATTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (20 bp):
AAATTTAAATTTAAAATTTA
Found at i:45213408 original size:28 final size:30
Alignment explanation
Indices: 45213355--45213410 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
45213345 ATTTAAATCA
*
45213355 AATTTTTATTTTTTAATAGTGTTAAAATAT
1 AATTTTTATTTTTTAATAATGTTAAAATAT
*
45213385 AATTTTTA-TTTTTATTAAT-TTAAAAT
1 AATTTTTATTTTTTAATAATGTTAAAAT
45213411 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (30 bp):
AATTTTTATTTTTTAATAATGTTAAAATAT
Found at i:45213920 original size:14 final size:16
Alignment explanation
Indices: 45213887--45213927 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
45213877 GCAACTTGCA
*
45213887 TATTTTTAATTATTTT
1 TATTTTTAATTATATT
45213903 TATTTTT-A-TATATT
1 TATTTTTAATTATATT
*
45213917 TATTTTAAATT
1 TATTTTTAATT
45213928 GGTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 11 0.52
15 2 0.10
16 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTAATTATATT
Found at i:45215847 original size:2 final size:2
Alignment explanation
Indices: 45215840--45215886 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
45215830 TTCCTTAATC
45215840 TA TA TA TA 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 TA TA TA TA
45215882 TA TA T
1 TA TA T
45215887 GAATTTAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45217379 original size:15 final size:15
Alignment explanation
Indices: 45217359--45217387 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45217349 ATATTTTCGG
45217359 TTTTTTTTTTGTTGT
1 TTTTTTTTTTGTTGT
45217374 TTTTTTTTTTGTTG
1 TTTTTTTTTTGTTG
45217388 AATTAGCTGA
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:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTGTTGT
Found at i:45241100 original size:16 final size:16
Alignment explanation
Indices: 45241065--45241099 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
45241055 TAAATTGATT
45241065 AAAATAAAAAACAATA
1 AAAATAAAAAACAATA
*
45241081 AAAATAAATAA-AATA
1 AAAATAAAAAACAATA
45241096 AAAA
1 AAAA
45241100 AACGGAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAACAATA
Found at i:45256585 original size:4 final size:4
Alignment explanation
Indices: 45256576--45256605 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
45256566 ATCAATCTAT
45256576 CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
45256606 ATTTTATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:45262501 original size:9 final size:9
Alignment explanation
Indices: 45262482--45262513 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
45262472 TTATAAAAAA
45262482 AATTCTTAAT
1 AATT-TTAAT
45262492 AATTTTAAT
1 AATTTTAAT
45262501 AATTTTAAT
1 AATTTTAAT
45262510 AATT
1 AATT
45262514 ATTCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTTAAT
Found at i:45262620 original size:26 final size:28
Alignment explanation
Indices: 45262561--45262620 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 28
45262551 TTGATAATCT
*
45262561 TTCATCAATACATTACTATTTTTTTGGTA
1 TTCAT-AATACATTACTATTTTATTGGTA
*
45262590 --AATAATACATTACTA-TTTATT-GTA
1 TTCATAATACATTACTATTTTATTGGTA
45262614 TTCATAA
1 TTCATAA
45262621 GACTCATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
24 3 0.12
25 5 0.19
26 16 0.62
27 2 0.08
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (28 bp):
TTCATAATACATTACTATTTTATTGGTA
Found at i:45263920 original size:9 final size:9
Alignment explanation
Indices: 45263902--45263940 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
45263892 CAAATCTGTT
*
45263902 AATTACAAA
1 AATTAAAAA
45263911 AATTAAAAA
1 AATTAAAAA
* *
45263920 AACTACAAA
1 AATTAAAAA
45263929 AATTAAAAA
1 AATTAAAAA
45263938 AAT
1 AAT
45263941 ATTATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:45263928 original size:18 final size:18
Alignment explanation
Indices: 45263905--45263939 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
45263895 ATCTGTTAAT
45263905 TACAAAAATTAAAAAAAC
1 TACAAAAATTAAAAAAAC
45263923 TACAAAAATTAAAAAAA
1 TACAAAAATTAAAAAAA
45263940 TATTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
TACAAAAATTAAAAAAAC
Found at i:45275858 original size:26 final size:28
Alignment explanation
Indices: 45275808--45275861 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
45275798 AATTTCCATT
45275808 TATTTTTATCAAATTAATAAATGTCATTTG
1 TATTTTTATCAAATT-AT-AATGTCATTTG
45275838 TATTTTTATCAAATT-T-ATGTCATT
1 TATTTTTATCAAATTATAATGTCATT
45275862 CCTCATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 8 0.33
28 1 0.04
30 15 0.62
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (28 bp):
TATTTTTATCAAATTATAATGTCATTTG
Found at i:45275939 original size:28 final size:28
Alignment explanation
Indices: 45275906--45275961 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
45275896 TTTTAGAGAT
*
45275906 TAAAATTA-AATTATATT-TTTATAATAA
1 TAAAAATATAATTATATTATTT-TAATAA
*
45275933 TAAAAATATAATTTTATTATTTTAATAA
1 TAAAAATATAATTATATTATTTTAATAA
45275961 T
1 T
45275962 TTATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 15 0.60
29 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAAAATATAATTATATTATTTTAATAA
Found at i:45275942 original size:22 final size:24
Alignment explanation
Indices: 45275917--45275976 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
45275907 AAAATTAAAT
45275917 TATATTTTTATAATAATAA-AA-A
1 TATATTTTTATAATAATAATAATA
* * ** *
45275939 TATAATTTTATTATTTTAATAATT
1 TATATTTTTATAATAATAATAATA
45275963 TATATTTTTATAAT
1 TATATTTTTATAAT
45275977 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
24 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTTTTATAATAATAATAATA
Found at i:45275970 original size:15 final size:16
Alignment explanation
Indices: 45275940--45275978 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
45275930 TAATAAAAAT
45275940 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
45275957 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
45275972 ATAATTT
1 ATAATTT
45275979 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:45276034 original size:32 final size:29
Alignment explanation
Indices: 45275936--45276044 Score: 86
Period size: 32 Copynumber: 3.8 Consensus size: 29
45275926 ATAATAATAA
*
45275936 AAATATAATTTTATTA-TTTT-AATAATT
1 AAATATAATTTTATTATTTTTAAAAAATT
* *
45275963 ---TATATTTTTATAATTTTTAAAAAATT
1 AAATATAATTTTATTATTTTTAAAAAATT
* *
45275989 AAATAAAATTTTTATTATTTTTATAAGAGATT
1 AAATATAA-TTTTATTATTTTTA-AA-AAATT
45276021 AAAGTATAATTTTATT-TTTATTAA
1 AAA-TATAATTTTATTATTT-TTAA
45276045 TTTAAAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
24 11 0.17
25 4 0.06
26 6 0.09
29 3 0.05
30 13 0.20
31 6 0.09
32 17 0.27
33 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
AAATATAATTTTATTATTTTTAAAAAATT
Found at i:45283306 original size:3 final size:3
Alignment explanation
Indices: 45283298--45283331 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
45283288 CAAAATCCAA
45283298 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45283332 GAATATTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45284421 original size:7 final size:7
Alignment explanation
Indices: 45284398--45284535 Score: 97
Period size: 7 Copynumber: 20.4 Consensus size: 7
45284388 TTTTCAAAAA
45284398 GTCAACG
1 GTCAACG
*
45284405 GTCAA-A
1 GTCAACG
45284411 GTCAACG
1 GTCAACG
*
45284418 GTCAA-A
1 GTCAACG
45284424 GTCAACG
1 GTCAACG
*
45284431 GTCAATG
1 GTCAACG
* *
45284438 ATCAA-A
1 GTCAACG
*
45284444 GTCAACA
1 GTCAACG
*
45284451 GTCAACA
1 GTCAACG
*
45284458 ATCAACG
1 GTCAACG
45284465 GTCAACG
1 GTCAACG
**
45284472 GTCAATA
1 GTCAACG
45284479 GTCAACG
1 GTCAACG
45284486 GTCAACG
1 GTCAACG
45284493 GTCAA-G
1 GTCAACG
* *
45284499 GTAAATG
1 GTCAACG
*
45284506 GTCAACA
1 GTCAACG
* *
45284513 ATCAATG
1 GTCAACG
*
45284520 GTCAA-A
1 GTCAACG
45284526 GTCAACG
1 GTCAACG
45284533 GTC
1 GTC
45284536 GGTCAACGAT
Statistics
Matches: 101, Mismatches: 25, Indels: 10
0.74 0.18 0.07
Matches are distributed among these distances:
6 24 0.24
7 77 0.76
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:45284489 original size:55 final size:54
Alignment explanation
Indices: 45284411--45284524 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 54
45284401 AACGGTCAAA
* *
45284411 GTCAACGGTCAAAGTCAACGGTCAATGATCAAAGTCAACAGTCAACAATCAACG
1 GTCAACGGTCAAAGTCAACGGTCAACGATCAAAGTAAACAGTCAACAATCAACG
* * ** *
45284465 GTCAACGGTCAATAGTCAACGGTCAACGGTCAAGGTAAATGGTCAACAATCAATG
1 GTCAACGGTCAA-AGTCAACGGTCAACGATCAAAGTAAACAGTCAACAATCAACG
45284520 GTCAA
1 GTCAA
45284525 AGTCAACGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
54 12 0.23
55 40 0.77
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (54 bp):
GTCAACGGTCAAAGTCAACGGTCAACGATCAAAGTAAACAGTCAACAATCAACG
Found at i:45284529 original size:20 final size:20
Alignment explanation
Indices: 45284411--45284535 Score: 101
Period size: 20 Copynumber: 6.2 Consensus size: 20
45284401 AACGGTCAAA
*
45284411 GTCAACGGTCAAAGTCAACG
1 GTCAATGGTCAAAGTCAACG
* *
45284431 GTCAATGATCAAAGTCAACA
1 GTCAATGGTCAAAGTCAACG
*** *
45284451 GTCAACAATCAACGGTCAACG
1 GTCAATGGTCAA-AGTCAACG
* *
45284472 GTCAATAGTCAACGGTCAACG
1 GTCAATGGTCAA-AGTCAACG
*
45284493 GTCAA-GGT-AAATGGTCAACA
1 GTCAATGGTCAAA--GTCAACG
*
45284513 ATCAATGGTCAAAGTCAACG
1 GTCAATGGTCAAAGTCAACG
45284533 GTC
1 GTC
45284536 GGTCAACGAT
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 47 0.55
21 33 0.39
22 3 0.04
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
GTCAATGGTCAAAGTCAACG
Found at i:45284535 original size:13 final size:13
Alignment explanation
Indices: 45284395--45284490 Score: 104
Period size: 13 Copynumber: 7.2 Consensus size: 13
45284385 GGTTTTTCAA
45284395 AAAGTCAACGGTC
1 AAAGTCAACGGTC
45284408 AAAGTCAACGGTC
1 AAAGTCAACGGTC
45284421 AAAGTCAACGGTC
1 AAAGTCAACGGTC
* *
45284434 AATGATCAA-AGTC
1 AAAG-TCAACGGTC
**
45284447 AACAGTCAACAATC
1 AA-AGTCAACGGTC
*
45284461 AACGGTCAACGGTC
1 AA-AGTCAACGGTC
45284475 AATAGTCAACGGTC
1 AA-AGTCAACGGTC
45284489 AA
1 AA
45284491 CGGTCAAGGT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
13 38 0.54
14 33 0.46
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:45284542 original size:11 final size:11
Alignment explanation
Indices: 45284526--45284587 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
45284516 AATGGTCAAA
45284526 GTCAACGGTCG
1 GTCAACGGTCG
* *
45284537 GTCAACGATTG
1 GTCAACGGTCG
45284548 GTCAACGGTCG
1 GTCAACGGTCG
* **
45284559 GTTAACGACCG
1 GTCAACGGTCG
*
45284570 ATCAACGGTCG
1 GTCAACGGTCG
45284581 GTCAACG
1 GTCAACG
45284588 ACCGATCAAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:45284551 original size:22 final size:22
Alignment explanation
Indices: 45284526--45284598 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
45284516 AATGGTCAAA
**
45284526 GTCAACGGTCGGTCAACGATTG
1 GTCAACGGTCGGTCAACGACCG
*
45284548 GTCAACGGTCGGTTAACGACCG
1 GTCAACGGTCGGTCAACGACCG
*
45284570 ATCAACGGTCGGTCAACGACCG
1 GTCAACGGTCGGTCAACGACCG
*
45284592 ATCAACG
1 GTCAACG
45284599 ATTTGACTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (22 bp):
GTCAACGGTCGGTCAACGACCG
Found at i:45284718 original size:25 final size:25
Alignment explanation
Indices: 45284689--45284751 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
45284679 ATTGGATCAA
45284689 AATTTGGGCTTAGAGATTTTAAAAG
1 AATTTGGGCTTAGAGATTTTAAAAG
** * *
45284714 AATTTGGG-TTATTTGGTTTTAATAG
1 AATTTGGGCTTA-GAGATTTTAAAAG
45284739 AATTTGGGCTTAG
1 AATTTGGGCTTAG
45284752 GAACAATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 3 0.10
25 25 0.81
26 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.25, T:0.43
Consensus pattern (25 bp):
AATTTGGGCTTAGAGATTTTAAAAG
Found at i:45290531 original size:24 final size:23
Alignment explanation
Indices: 45290500--45290548 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
45290490 AATTAATAAT
* *
45290500 AAAATAAATTAATTAAAACTCCCA
1 AAAATAAAAT-ATCAAAACTCCCA
*
45290524 AAAATAAAATATCAAAAGTCCCA
1 AAAATAAAATATCAAAACTCCCA
45290547 AA
1 AA
45290549 GTGCATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAATAAAATATCAAAACTCCCA
Found at i:45290600 original size:3 final size:3
Alignment explanation
Indices: 45290592--45290633 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
45290582 CAAAATCCGA
45290592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45290634 GAATATTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45291726 original size:7 final size:7
Alignment explanation
Indices: 45291703--45291829 Score: 57
Period size: 7 Copynumber: 18.7 Consensus size: 7
45291693 CAAAAAAAAA
45291703 GTCAACG
1 GTCAACG
*
45291710 GTCAA-A
1 GTCAACG
*
45291716 GTCAATG
1 GTCAACG
**
45291723 GTCAATA
1 GTCAACG
*
45291730 GTCAA-A
1 GTCAACG
45291736 GTCAACG
1 GTCAACG
* *
45291743 ATCAACA
1 GTCAACG
45291750 GTCAACG
1 GTCAACG
* *
45291757 ATCAATG
1 GTCAACG
45291764 GTCAACG
1 GTCAACG
*
45291771 GTCAA-A
1 GTCAACG
*
45291777 GTCAATG
1 GTCAACG
**
45291784 GTCAATA
1 GTCAACG
*
45291791 GTCAACA
1 GTCAACG
*
45291798 GTCAA-A
1 GTCAACG
*
45291804 GTCAATG
1 GTCAACG
*
45291811 G-CTAACA
1 GTC-AACG
45291818 GTCAACG
1 GTCAACG
45291825 GTCAA
1 GTCAA
45291830 AGTCAACGAT
Statistics
Matches: 94, Mismatches: 20, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
6 23 0.24
7 70 0.74
8 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:45291732 original size:27 final size:28
Alignment explanation
Indices: 45291702--45291835 Score: 130
Period size: 27 Copynumber: 4.7 Consensus size: 28
45291692 TCAAAAAAAA
45291702 AGTCAACGGTCAAAGTCAATGGTCAATAGT
1 AGTCAACGGTCAAAGTCAATGGTCAA-A-T
* * *
45291732 CAAAGTCAACGATCAACAGTCAACGATC-AAT
1 ---AGTCAACGGTCAA-AGTCAATGGTCAAAT
*
45291763 GGTCAACGGTCAAAGTCAATGGTC-AAT
1 AGTCAACGGTCAAAGTCAATGGTCAAAT
* * *
45291790 AGTCAACAGTCAAAGTCAATGG-CTAAC
1 AGTCAACGGTCAAAGTCAATGGTCAAAT
45291817 AGTCAACGGTCAAAGTCAA
1 AGTCAACGGTCAAAGTCAA
45291836 CGATTGGTCA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
26 1 0.01
27 52 0.59
28 11 0.12
31 1 0.01
32 1 0.01
33 13 0.15
34 9 0.10
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (28 bp):
AGTCAACGGTCAAAGTCAATGGTCAAAT
Found at i:45291822 original size:20 final size:20
Alignment explanation
Indices: 45291703--45291802 Score: 119
Period size: 20 Copynumber: 4.9 Consensus size: 20
45291693 CAAAAAAAAA
*
45291703 GTCAACGGTCAAAGTCAATG
1 GTCAACAGTCAAAGTCAATG
* *
45291723 GTCAATAGTCAAAGTCAACG
1 GTCAACAGTCAAAGTCAATG
* *
45291743 ATCAACAGTCAACGATCAATG
1 GTCAACAGTCAAAG-TCAATG
*
45291764 GTCAACGGTCAAAGTCAATG
1 GTCAACAGTCAAAGTCAATG
*
45291784 GTCAATAGTCAACAGTCAA
1 GTCAACAGTCAA-AGTCAA
45291803 AGTCAATGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 44 0.67
21 22 0.33
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
GTCAACAGTCAAAGTCAATG
Found at i:45292463 original size:11 final size:11
Alignment explanation
Indices: 45292433--45292466 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
45292423 AAAAAGAATG
45292433 AAGGAAAAAGA
1 AAGGAAAAAGA
45292444 AA-GAAAAAGA
1 AAGGAAAAAGA
*
45292454 AAGGATAAAGA
1 AAGGAAAAAGA
45292465 AA
1 AA
45292467 TAAGGATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAGGAAAAAGA
Found at i:45297319 original size:41 final size:38
Alignment explanation
Indices: 45297219--45297322 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
45297209 TTCGAAGCAA
* *
45297219 TAAAGTGACACCCAGTGTCTCATCG-GCCTAACCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
* ** ** * *
45297256 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
45297294 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
45297323 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
Found at i:45298223 original size:11 final size:12
Alignment explanation
Indices: 45298190--45298257 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 12
45298180 ATATTAGTTA
45298190 ATAATAATAA-T
1 ATAATAATAATT
*
45298201 ATAATACTAATT
1 ATAATAATAATT
45298213 A-AATAATAATTT
1 ATAATAATAA-TT
* *
45298225 ATATTATTATATT
1 ATAATAATA-ATT
*
45298238 ATAATATTAA-T
1 ATAATAATAATT
45298249 A-AATAATAA
1 ATAATAATAA
45298258 AAAAATCAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
10 7 0.15
11 18 0.38
12 6 0.13
13 15 0.32
14 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:45298672 original size:6 final size:6
Alignment explanation
Indices: 45298654--45298762 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
45298644 TTAAATTGAT
* *
45298654 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
45298701 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAACA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
*
45298750 TTAAAAA TTTAAA
1 TT-TAAA TTTAAA
45298763 AGTCCAAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 15 0.18
8 6 0.07
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:45298684 original size:17 final size:15
Alignment explanation
Indices: 45298658--45298722 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
45298648 ATTGATTTTA
45298658 AATTTATTTAAATTT
1 AATTTATTTAAATTT
45298673 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
45298690 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
45298704 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
45298721 AA
1 AA
45298723 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:45298700 original size:31 final size:31
Alignment explanation
Indices: 45298662--45298725 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45298652 ATTTTAAATT
*
45298662 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
45298693 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
45298724 TA
1 TA
45298726 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:45298708 original size:11 final size:11
Alignment explanation
Indices: 45298644--45298724 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
45298634 GACTTTTGAG
* *
45298644 TTAAATTGATT
1 TTAAATTTAAT
45298655 TTAAATTT-AT
1 TTAAATTTAAT
45298665 TTAAATTTAGAT
1 TTAAATTTA-AT
*
45298677 TT-ATTTTAAAT
1 TTAAATTT-AAT
45298688 TTAAA--T-AT
1 TTAAATTTAAT
45298696 TTAAATTTAAT
1 TTAAATTTAAT
*
45298707 TTGAATTTAAAT
1 TTAAATTT-AAT
45298719 TTAAAT
1 TTAAAT
45298725 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 7 0.12
10 11 0.20
11 24 0.43
12 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:45298721 original size:42 final size:41
Alignment explanation
Indices: 45298654--45298747 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
45298644 TTAAATTGAT
* ** * *
45298654 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
45298695 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
45298736 TATTAAATTTAA
1 T-TTAAATTTAA
45298748 CATTAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:45298761 original size:20 final size:18
Alignment explanation
Indices: 45298710--45298762 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
45298700 ATTTAATTTG
*
45298710 AATTTAAATTTAAATAAA
1 AATTAAAATTTAAATAAA
*
45298728 AATTAAAATATTAAATTTAA
1 AATTAAAAT-TTAAA-TAAA
*
45298748 CATTAAAAATTTAAA
1 AATT-AAAATTTAAA
45298763 AGTCCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.28
19 5 0.17
20 11 0.38
21 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAATTTAAATAAA
Found at i:45299898 original size:24 final size:24
Alignment explanation
Indices: 45299866--45299920 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
45299856 ACGAGCTGAC
*
45299866 CGGCGCGTGACCGCGTCGACCGGA
1 CGGCGCGTGACCGCGTCGACCGAA
45299890 CGGCGCGTGACCGCGTCGACCGAA
1 CGGCGCGTGACCGCGTCGACCGAA
45299914 CGGCGCG
1 CGGCGCG
45299921 ACCGAGGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.13, C:0.38, G:0.42, T:0.07
Consensus pattern (24 bp):
CGGCGCGTGACCGCGTCGACCGAA
Found at i:45300405 original size:29 final size:29
Alignment explanation
Indices: 45300371--45300492 Score: 115
Period size: 30 Copynumber: 4.2 Consensus size: 29
45300361 ATCATCTTTC
*
45300371 GACCCCGAAACTTTTCCAAATTACATTTT
1 GACCCCCAAACTTTTCCAAATTACATTTT
** *
45300400 -ACCCCCAAAACTTTTTTAAAATTATATTTT
1 GACCCCC-AAAC-TTTTCCAAATTACATTTT
* *
45300430 GACACCCAAACTTTTCCAAAATTATATTTTT
1 GACCCCCAAACTTTTCC-AAATTACA-TTTT
* *
45300461 GA-CCTCAAACTTTTCCAAATTAC-TGTT
1 GACCCCCAAACTTTTCCAAATTACATTTT
45300488 GACCC
1 GACCC
45300493 TAAAACTTCC
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.07
28 7 0.09
29 14 0.18
30 39 0.51
31 11 0.14
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
GACCCCCAAACTTTTCCAAATTACATTTT
Found at i:45300461 original size:31 final size:29
Alignment explanation
Indices: 45300371--45300479 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 29
45300361 ATCATCTTTC
*
45300371 GACCCCGAAACTTTTCC-AAATTACATTTT
1 GACCCC-AAACTTTTCCAAAATTATATTTT
**
45300400 -ACCCCCAAAACTTTTTTAAAATTATATTTT
1 GA-CCCC-AAACTTTTCCAAAATTATATTTT
45300430 GACACCCAAACTTTTCCAAAATTATATTTTT
1 GAC-CCCAAACTTTTCCAAAATTATA-TTTT
*
45300461 GACCTCAAACTTTTCCAAA
1 GACCCCAAACTTTTCCAAA
45300480 TTACTGTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.01
29 12 0.18
30 44 0.65
31 11 0.16
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
GACCCCAAACTTTTCCAAAATTATATTTT
Found at i:45300608 original size:62 final size:60
Alignment explanation
Indices: 45300501--45300766 Score: 240
Period size: 62 Copynumber: 4.4 Consensus size: 60
45300491 CCTAAAACTT
* **
45300501 CCAAAAATTACCATTTTACCCCCGAATTCTAAATTGCA-CCATTTTATTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAA-TCTATATTAAATCCA-TTT-TTTAACCCCGATTTCA
* *
45300563 CCAAAAATTACCATTTTACCCCTGAATCT-TTTTAAATCCA-TTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAATCTATATTAAATCCATTTTTTAACCCCGATTTCA
* * * * **
45300621 CCGAAAATTA-CATCTTTACCCCCGAAGCT-TCTAAAATCACGGTTTTTAACCCCTTGATTTCA
1 CCAAAAATTACCAT-TTTACCCCCGAATCTATATTAAATC-CATTTTTTAACCCC--GATTTCA
* * * * *
45300683 TCGAAAATTACCATTTTACCCCCGAA-CTCTATTAAGATTCCATTTTTCAACCTCGATTAT-A
1 CCAAAAATTACCATTTTACCCCCGAATCTATATTAA-A-TCCATTTTTTAACCCCGATT-TCA
*
45300744 CCAAAAATTACCATTTTGCCCCC
1 CCAAAAATTACCATTTTACCCCC
45300767 CCGAAGTATC
Statistics
Matches: 172, Mismatches: 21, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
57 3 0.02
58 45 0.26
59 3 0.02
60 14 0.08
61 33 0.19
62 58 0.34
63 14 0.08
64 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (60 bp):
CCAAAAATTACCATTTTACCCCCGAATCTATATTAAATCCATTTTTTAACCCCGATTTCA
Found at i:45300631 original size:120 final size:121
Alignment explanation
Indices: 45300501--45300766 Score: 305
Period size: 120 Copynumber: 2.2 Consensus size: 121
45300491 CCTAAAACTT
* **
45300501 CCAAAAATTACCATTTTACCCCCGAA-TTCTAAATTGCACCATTTTATTTAACCCC-GATTTCAC
1 CCAAAAATTACCATTTTACCCCCGAACTTCTAAAAT-CA-C-GGTT-TTTAACCCCTGATTTCAC
* *
45300564 CAAAAATTACCATTTTACCCCTGAA-TCTTTTTAA-A-TCCATTTTT-AACCCCGATT-TCA
62 CAAAAATTACCATTTTACCCCCGAACTC-TATTAAGATTCCATTTTTCAACCCCGATTAT-A
* *
45300621 CCGAAAATTA-CATCTTTACCCCCGAAGCTTCTAAAATCACGGTTTTTAACCCCTTGATTTCATC
1 CCAAAAATTACCAT-TTTACCCCCGAA-CTTCTAAAATCACGGTTTTTAACCCC-TGATTTCACC
* *
45300685 GAAAATTACCATTTTACCCCCGAACTCTATTAAGATTCCATTTTTCAACCTCGATTATA
63 AAAAATTACCATTTTACCCCCGAACTCTATTAAGATTCCATTTTTCAACCCCGATTATA
*
45300744 CCAAAAATTACCATTTTGCCCCC
1 CCAAAAATTACCATTTTACCCCC
45300767 CCGAAGTATC
Statistics
Matches: 124, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
118 9 0.07
119 5 0.04
120 57 0.46
121 5 0.04
122 17 0.14
123 27 0.22
124 4 0.03
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (121 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCTAAAATCACGGTTTTTAACCCCTGATTTCACCAAA
AATTACCATTTTACCCCCGAACTCTATTAAGATTCCATTTTTCAACCCCGATTATA
Found at i:45312733 original size:31 final size:30
Alignment explanation
Indices: 45312692--45313148 Score: 142
Period size: 31 Copynumber: 13.6 Consensus size: 30
45312682 ACACGTCTTT
45312692 ATCT-CTGAAATTGAAGTAAGAGCAACGTC
1 ATCTCCTGAAATTGAAGTAAGAGCAACGTC
**
45312721 ATCTCCTCGAAATTGAAGTAGAGTGGATAACACGTC
1 ATCTCCT-GAAATTGAAGTA-A---GAGCA-ACGTC
45312757 TTTATCT-CTGAAATTGAAGTAAGAGCAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
* * *
45312789 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
1 AT-CTCCTGAAATTGAAGTA-AG-AGCA-A-C--GTC
45312826 TTTATCT-CTGAAATTGAAG--A-AGCAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
* * *
45312855 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
1 AT-CTCCTGAAATTGAAGTA-AG-AGCA-A-C--GTC
45312892 TTTATCT-CTGAAATTGAAGTAAGAGCAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
* * *
45312924 ATCTCCTCGAAATTGAAGTGGAGTGGATAACATGTC
1 ATCTCCT-GAAATTGAAGT-AAG-AG-CAAC--GTC
45312960 TTTATCT-CTGAAATTGAAGTAAGAGCAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
* * *
45312992 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
1 AT-CTCCTGAAATTGAAGTA-AG-AGCA-A-C--GTC
*
45313029 TTTATCT-CTGAAATTGAAGTAAGAACAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
* * **
45313061 GTCCTCTTGAAATTGAAGTAGAGTGGATAACACGTC
1 AT-CTCCTGAAATTGAAGTA-A---GAGCA-ACGTC
45313097 TTTATCT-CTGAAATTGAAGTAAGAGCAACGTC
1 ---ATCTCCTGAAATTGAAGTAAGAGCAACGTC
*
45313129 ATCCTCTTGAAATTGAAGTA
1 AT-CTCCTGAAATTGAAGTA
45313149 GAGTTGGATA
Statistics
Matches: 322, Mismatches: 38, Indels: 134
0.65 0.08 0.27
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 11 0.03
29 18 0.06
30 12 0.04
31 77 0.24
32 28 0.09
33 15 0.05
34 11 0.03
35 13 0.04
36 20 0.06
37 49 0.15
38 43 0.13
39 15 0.05
40 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (30 bp):
ATCTCCTGAAATTGAAGTAAGAGCAACGTC
Found at i:45312759 original size:68 final size:69
Alignment explanation
Indices: 45312645--45313305 Score: 1013
Period size: 69 Copynumber: 9.7 Consensus size: 69
45312635 CTGCAGGTCT
* *
45312645 CAACGTCAT-CTCCTCGAAATTGAAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAG
1 CAACGTCATCCT-CTTGAAATTG-AAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
45312708 TAAGAG
64 TAAGAG
* *
45312714 CAACGTCAT-CTCCTCGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGT
1 CAACGTCATCCT-CTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
45312777 AAGAG
65 AAGAG
*
45312782 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAG--
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45312845 A-AG
66 AGAG
*
45312848 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45312913 AGAG
66 AGAG
* * *
45312917 CAACGTCAT-CTCCTCGAAATTGAAGTGGAG-TGGATAACATGTCTTTATCTCTGAAATTGAAGT
1 CAACGTCATCCT-CTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
45312980 AAGAG
65 AAGAG
*
45312985 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
*
45313050 AGAA
66 AGAG
* *
45313054 CAACGTCGTCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45313118 AGAG
66 AGAG
*
45313122 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
*
45313187 AGAA
66 AGAG
* *
45313191 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45313256 AGAG
66 AGAG
* * * *
45313260 CAACATCATCC-CTCGAAATTGAAATAGAG-TGGATAACACGTCTTTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA
45313306 ATTGAAGTGA
Statistics
Matches: 555, Mismatches: 28, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
66 65 0.12
67 16 0.03
68 216 0.39
69 258 0.46
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (69 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
AGAG
Found at i:45312829 original size:137 final size:137
Alignment explanation
Indices: 45312645--45313305 Score: 1025
Period size: 137 Copynumber: 4.8 Consensus size: 137
45312635 CTGCAGGTCT
* *
45312645 CAACGTCAT-CTCCTCGAAATTGAAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGT
1 CAACGTCATCCT-CTTGAAATTG-AAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
* * *
45312709 AAGAGCAACGTCAT-CTCCTCGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
64 AAGAGCAACGTCATCCT-CTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATT
*
45312772 GAAGTAAGAG
128 GAAGTAAGAA
*
45312782 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAG--
1 CAACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45312845 A-AGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
65 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
*
45312909 AGTAAGAG
130 AGTAAGAA
* * *
45312917 CAACGTCAT-CTCCTCGAAATTGAAGTGGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCT-CTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
45312981 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
65 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
45313046 AGTAAGAA
130 AGTAAGAA
* *
45313054 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAA
45313119 GAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
66 GAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
45313184 GTAAGAA
131 GTAAGAA
* *
45313191 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
* * * * *
45313256 AGAGCAACATCATCC-CTCGAAATTGAAATAGAG-TGGATAACACGTCTTTA
65 AGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA
45313306 ATTGAAGTGA
Statistics
Matches: 492, Mismatches: 22, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
134 60 0.12
135 64 0.13
136 24 0.05
137 294 0.60
138 50 0.10
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (137 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAA
Found at i:45313678 original size:6 final size:6
Alignment explanation
Indices: 45313669--45313767 Score: 78
Period size: 6 Copynumber: 16.2 Consensus size: 6
45313659 ATTTTAATTT
* * *
45313669 ATTTAA ATTTAG ATTT-A TTTTAA ATTTAAA TATTTAA ATTT-A ATTTGA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA -ATTTAA ATTTAA ATTTAA
* * *
45313717 ATTTAA ATTTAA A-TAAA ATTAAA ATATTAA ATTTAA CATTAAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA -ATT-TAA ATTTAA
45313767 A
1 A
45313768 AGTCCAAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
5 12 0.16
6 43 0.57
7 15 0.20
8 6 0.08
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:45313704 original size:31 final size:31
Alignment explanation
Indices: 45313668--45313731 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45313658 GATTTTAATT
*
45313668 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
45313699 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
45313730 TA
1 TA
45313732 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:45313709 original size:25 final size:25
Alignment explanation
Indices: 45313661--45313724 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
45313651 TTAAATTGAT
*
45313661 TTTAATTT--ATTT-AA-ATTTAGA
1 TTTAATTTAAATTTAAATATTTAAA
*
45313682 TTTATTTTAAATTTAAATATTTAAA
1 TTTAATTTAAATTTAAATATTTAAA
*
45313707 TTTAATTTGAATTTAAAT
1 TTTAATTTAAATTTAAAT
45313725 TTAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.20
23 4 0.11
24 2 0.06
25 22 0.63
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTAATTTAAATTTAAATATTTAAA
Found at i:45313722 original size:11 final size:11
Alignment explanation
Indices: 45313659--45313730 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
45313649 AGTTAAATTG
*
45313659 ATTTTAATTT-
1 ATTTAAATTTA
45313669 ATTTAAATTTA
1 ATTTAAATTTA
*
45313680 GATTT-ATTTTAA
1 -ATTTAAATTT-A
45313692 ATTTAAA--T-
1 ATTTAAATTTA
45313700 ATTTAAATTTA
1 ATTTAAATTTA
*
45313711 ATTTGAATTTAA
1 ATTTAAATTT-A
45313723 ATTTAAAT
1 ATTTAAAT
45313731 AAAATTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
8 7 0.14
10 11 0.22
11 17 0.35
12 14 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:45313728 original size:17 final size:15
Alignment explanation
Indices: 45313661--45313728 Score: 84
Period size: 17 Copynumber: 4.3 Consensus size: 15
45313651 TTAAATTGAT
45313661 TTTAATTTATTTAAA
1 TTTAATTTATTTAAA
45313676 TTTAGATTTATTTTAAA
1 TTTA-ATTTA-TTTAAA
*
45313693 TTTAA-ATATTTAAA
1 TTTAATTTATTTAAA
45313707 TTTAATTTGAATTTAAA
1 TTTAATTT--ATTTAAA
45313724 TTTAA
1 TTTAA
45313729 ATAAAATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.24
15 7 0.15
16 6 0.13
17 22 0.48
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTAATTTATTTAAA
Found at i:45313766 original size:20 final size:17
Alignment explanation
Indices: 45313716--45313767 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 17
45313706 ATTTAATTTG
*
45313716 AATTTAAATTTAAATAA
1 AATTAAAATTTAAATAA
45313733 AATTAAAATATTAAATTTAA
1 AATTAAAAT-TTAAA--TAA
*
45313753 CATTAAAAATTTAAA
1 AATT-AAAATTTAAA
45313768 AGTCCAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
20 11 0.38
21 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAAATTTAAATAA
Found at i:45313939 original size:13 final size:13
Alignment explanation
Indices: 45313921--45313952 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
45313911 TCTGCTGCCA
*
45313921 CCACCAGCTCCAT
1 CCACCAGCTCCAC
45313934 CCACCAGCTCCAC
1 CCACCAGCTCCAC
45313947 CCACCA
1 CCACCA
45313953 TGCCCTGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.59, G:0.06, T:0.09
Consensus pattern (13 bp):
CCACCAGCTCCAC
Found at i:45315399 original size:30 final size:30
Alignment explanation
Indices: 45315354--45315597 Score: 336
Period size: 30 Copynumber: 8.2 Consensus size: 30
45315344 ATCATCTTTC
*
45315354 GACCCCGAAACTTTTCCAAAATTACATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
* * *
45315384 -ACCCTAAAACTTTTTCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
*
45315413 GACCCCAAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
* ** *
45315443 AACCCTGAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
45315473 GACCCCAAAACTTTTCCAAAATTACATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
* *
45315503 CA-CCCAAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
45315532 GACCCCAAAACTTTTCCAAAATTACATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
45315562 GACCCCAAAAC--TTCCAAAAATTACCATTTT
1 GACCCCAAAACTTTTCC-AAAATTA-CATTTT
45315592 -ACCCCA
1 GACCCCA
45315598 GAAGCTTCTA
Statistics
Matches: 193, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
28 4 0.02
29 65 0.34
30 124 0.64
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
GACCCCAAAACTTTTCCAAAATTACATTTT
Found at i:45315424 original size:59 final size:60
Alignment explanation
Indices: 45315354--45315574 Score: 365
Period size: 59 Copynumber: 3.7 Consensus size: 60
45315344 ATCATCTTTC
* *
45315354 GACCCCGAAACTTTTCCAAAATTACATTTT-ACCCTAAAACTTTTTCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTT
* *
45315413 GACCCCAAAACTTTTCCAAAATTATATTTTAACCCTGAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTT
*
45315473 GACCCCAAAACTTTTCCAAAATTACATTTTCACCC-AAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTT
* *
45315532 GACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTT
1 GACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTT
45315575 CCAAAAATTA
Statistics
Matches: 152, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
59 85 0.56
60 67 0.44
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (60 bp):
GACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTT
Found at i:45315509 original size:89 final size:88
Alignment explanation
Indices: 45315355--45315595 Score: 353
Period size: 89 Copynumber: 2.7 Consensus size: 88
45315345 TCATCTTTCG
* * *
45315355 ACCCCGAAACTTTTCCAAAATTACATTTT-ACCCTAAAACTTTTTCAAAATTATATTTTGACCCC
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT-A-CCC
45315419 AAAACTTTTCCAAAATTATATTTTA
64 AAAACTTTTCCAAAATTATATTTTA
* *
45315444 ACCCTGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTCACCCA
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT-ACCCA
*
45315509 AAACTTTTCCAAAATTATATTTTG
65 AAACTTTTCCAAAATTATATTTTA
*
45315533 ACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAAC--TTCCAAAAATTACCATTTTACCC
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC-AAAATTA-CATTTTACCC
45315596 CAGAAGCTTC
Statistics
Matches: 139, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
87 4 0.03
88 11 0.08
89 97 0.70
90 27 0.19
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.35
Consensus pattern (88 bp):
ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTACCCAA
AACTTTTCCAAAATTATATTTTA
Found at i:45315610 original size:29 final size:29
Alignment explanation
Indices: 45315549--45315801 Score: 149
Period size: 29 Copynumber: 8.6 Consensus size: 29
45315539 AAACTTTTCC
* * * *
45315549 AAAATTA-CATTTTGACCCCAAAACTTCCA
1 AAAATTACCATTTTAACCCCGAATCTT-CT
*
45315578 AAAATTACCATTTT-ACCCCAGAAGCTTCT
1 AAAATTACCATTTTAACCCC-GAATCTTCT
* * ** *
45315607 AAAATT-CTATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTAACCCCGA-ATCTTCT
* *
45315637 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTAACCCCGAATCTTCT
* * ** *
45315666 AAAATT-CCATTTTTAACCTCGATTTCACCG
1 AAAATTACCA-TTTTAACCCCGA-ATCTTCT
* *
45315696 AAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTACCATTTTAACCCCGAATCTTCT
* ** *
45315725 AAAATT-CCATTTTTAACCCCGATTTCACCG
1 AAAATTACCA-TTTTAACCCCGA-ATCTTCT
* *
45315755 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTAACCCCGAATCTTCT
*
45315784 AAGATT-CCATTTTCAACC
1 AAAATTACCATTTT-AACC
45315802 TCGATTACAC
Statistics
Matches: 167, Mismatches: 44, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
28 15 0.09
29 72 0.43
30 72 0.43
31 8 0.05
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGAATCTTCT
Found at i:45315626 original size:89 final size:87
Alignment explanation
Indices: 45315355--45315628 Score: 340
Period size: 89 Copynumber: 3.1 Consensus size: 87
45315345 TCATCTTTCG
* * *
45315355 ACCCCGAAACTTTTCCAAAATTACATTTT-ACCCTAAAACTTTTTCAAAATTATATTTTGACCCC
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAAC-TTTCCAAAATTACATTTT-ACCCC
45315419 AAAACTTTTCCAAAATTATATTTTA
64 AAAAC-TTTCCAAAATTATATTTTA
* *
45315444 ACCCTGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTT-CACCC
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAAC-TTTCCAAAATTACATTTTAC-CCC
*
45315508 AAAACTTTTCCAAAATTATATTTTG
64 AAAAC-TTTCCAAAATTATATTTTA
*
45315533 ACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAAC-TTCCAAAAATTACCATTTTACCCC
1 ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCC-AAAATTA-CATTTTACCCC
* * *
45315597 AGAAGC-TTCTAAAATTCTATTTTTA
64 A-AAACTTTCCAAAATTATA-TTTTA
45315622 ACCCCGA
1 ACCCCGA
45315629 TTTCACCAAA
Statistics
Matches: 164, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
87 4 0.02
88 19 0.12
89 111 0.68
90 30 0.18
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (87 bp):
ACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAATTACATTTTACCCCAA
AACTTTCCAAAATTATATTTTA
Found at i:45315638 original size:59 final size:59
Alignment explanation
Indices: 45315575--45315826 Score: 380
Period size: 59 Copynumber: 4.3 Consensus size: 59
45315565 CCCAAAACTT
* *
45315575 CCAAAAATTACCATTTTACCCCAGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
45315634 CCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
45315693 CCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * * * * * *
45315752 CCGAAAATTACCATTTTACCCCCGAATCTTTTAAGATTCCATTTTCAACCTCGATTACA
1 CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
45315811 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
45315827 GCCCTCGGGT
Statistics
Matches: 178, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
58 14 0.08
59 164 0.92
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:45315641 original size:30 final size:30
Alignment explanation
Indices: 45315607--45315776 Score: 134
Period size: 30 Copynumber: 5.7 Consensus size: 30
45315597 AGAAGCTTCT
* *
45315607 AAAATTCTATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCG
* * ****
45315637 AAAATTACCA-TTTTACCCCCGA-ATCTTTT
1 AAAATT-CCATTTTTAACCCCGATTTCACCG
*
45315666 AAAATTCCATTTTTAACCTCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTCACCG
* ** ** *
45315696 AAAATTACCA-TTTTACCCCCGA-AGCTTCT
1 AAAATT-CCATTTTTAACCCCGATTTCACCG
45315725 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTCACCG
*
45315755 AAAATTACCA-TTTTACCCCCGA
1 AAAATT-CCATTTTTAACCCCGA
45315777 ATCTTTTAAG
Statistics
Matches: 105, Mismatches: 28, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
28 6 0.06
29 37 0.35
30 54 0.51
31 8 0.08
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:45315700 original size:118 final size:117
Alignment explanation
Indices: 45315578--45315826 Score: 435
Period size: 118 Copynumber: 2.1 Consensus size: 117
45315568 AAAACTTCCA
*
45315578 AAAATTACCATTTTACCCCAGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCAGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* *
45315643 ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCACC
66 ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTCAACCTCGATTACACC
* *
45315695 GAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAAT
1 -AAAATTACCATTTTACCCCAGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
*
45315760 TACCATTTTACCCCCGAATCTTTTAAGATTCCATTTTCAACCTCGATTACACC
65 TACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTCAACCTCGATTACACC
45315813 AAAATTACCATTTT
1 AAAATTACCATTTT
45315827 GCCCTCGGGT
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
117 14 0.11
118 111 0.89
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCAGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTCAACCTCGATTACACC
Found at i:45315826 original size:30 final size:28
Alignment explanation
Indices: 45315607--45315826 Score: 97
Period size: 30 Copynumber: 7.5 Consensus size: 28
45315597 AGAAGCTTCT
* *
45315607 AAAATTCTATTTTTAACCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTACACC
* * ***
45315636 AAAAATTACCATTTTACCCCCGAAT-CTTTT
1 -AAAATT-CCATTTTAACCCCGATTAC-ACC
* *
45315666 AAAATTCCATTTTTAACCTCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTACACC
* * *
45315695 GAAAATTACCATTTTACCCCCGA--AGCTTCT
1 -AAAATT-CCATTTTAACCCCGATTA-C-ACC
*
45315725 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTACACC
* * ***
45315754 GAAAATTACCATTTTACCCCCGAAT-CTTTT
1 -AAAATT-CCATTTTAACCCCGATTAC-ACC
* *
45315784 AAGATTCCATTTTCAACCTCGATTACACC
1 AAAATTCCATTTT-AACCCCGATTACACC
45315813 AAAATTACCATTTT
1 AAAATT-CCATTTT
45315827 GCCCTCGGGT
Statistics
Matches: 139, Mismatches: 34, Indels: 34
0.67 0.16 0.16
Matches are distributed among these distances:
28 13 0.09
29 55 0.40
30 63 0.45
31 8 0.06
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGATTACACC
Found at i:45319168 original size:28 final size:27
Alignment explanation
Indices: 45319136--45319196 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
45319126 AAAACGGGAC
45319136 TTTTGAATATCCAGGGGC-AAAATGGTAA
1 TTTTGAATATCCA-GGGCAAAAAT-GTAA
* * *
45319164 TTTTGACTCTCGAGGGCAAAAATGTAA
1 TTTTGAATATCCAGGGCAAAAATGTAA
45319191 TTTTGA
1 TTTTGA
45319197 GAAAATTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (27 bp):
TTTTGAATATCCAGGGCAAAAATGTAA
Found at i:45319234 original size:29 final size:29
Alignment explanation
Indices: 45319181--45319570 Score: 104
Period size: 30 Copynumber: 13.2 Consensus size: 29
45319171 TCTCGAGGGC
* * *
45319181 AAAAATGTAATTTTGAGAAAATTTGGGGT
1 AAAAATGGAGTTTTGAGAAAGTTTGGGGT
45319210 CAAAAATGGAGTTTTG-GAAAGTTTGGGGGT
1 -AAAAATGGAGTTTTGAGAAAGTTT-GGGGT
* * * * *
45319240 AAAACA-GTAATTTTTGGTGAAA-TTAGGGTT
1 AAAA-ATG-GAGTTTT-GAGAAAGTTTGGGGT
45319270 AAAAATGGAGTTTTG-GAAAGTTTGGGGT
1 AAAAATGGAGTTTTGAGAAAGTTTGGGGT
* * * *
45319298 -AAAATAGTAATTTTTGATGAAA--TCGAGGTT
1 AAAAAT-G-GAGTTTTGA-GAAAGTTTG-GGGT
* *
45319328 AAAAATGGAATTTTG-GAAAGTTCGGGG-
1 AAAAATGGAGTTTTGAGAAAGTTTGGGGT
* *
45319355 ATAAAACGGTAATTTTTGATGAAA--TTGGGGTT
1 A-AAAATGG--AGTTTTGA-GAAAGTTTGGGG-T
*
45319387 AAAAAT-GAGATTTTG-GAAAGTTCGAGGGT
1 AAAAATGGAG-TTTTGAGAAAGTTTG-GGGT
* * * *
45319416 AAAACTGTAATTTTTGATGAAA--TCGGGGTT
1 AAAAATG-GAGTTTTGA-GAAAGTTTGGGG-T
45319446 AAAAATGG-GATTTTG-GAAAGTTTAGGGGT
1 AAAAATGGAG-TTTTGAGAAAGTTT-GGGGT
* * *
45319475 -AAAATGGTAATTTTTGGTGAAA-ATTGGGGTT
1 AAAAATGG--AGTTTT-GAGAAAGTTTGGGG-T
* **
45319506 AAAAATGGAATTTTG-GAAAGTTCAGGG-
1 AAAAATGGAGTTTTGAGAAAGTTTGGGGT
* *
45319533 ATAAAATGGTAATTTTCA-AAAGTTTCGGGGT
1 A-AAAATGG-AGTTTTGAGAAAGTTT-GGGGT
*
45319564 CAAAATG
1 AAAAATG
45319571 TAATTTTTTG
Statistics
Matches: 271, Mismatches: 41, Indels: 96
0.66 0.10 0.24
Matches are distributed among these distances:
27 23 0.08
28 35 0.13
29 75 0.28
30 93 0.34
31 21 0.08
32 24 0.09
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAAATGGAGTTTTGAGAAAGTTTGGGGT
Done.