Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1536070 original size:35 final size:35
Alignment explanation
Indices: 1536024--1536098 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1536014 AAAATACTTT
*
1536024 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGA
* * *
1536059 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGA
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGA
1536094 AATTT
1 AATTT
1536099 TGAACACGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGA
Found at i:1545745 original size:19 final size:19
Alignment explanation
Indices: 1545716--1545753 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1545706 GATAATCATC
1545716 AAAACTTATCAAAATATTAT
1 AAAACTTATCAAAAT-TTAT
1545736 AAAA-TTATCAAAATTTAT
1 AAAACTTATCAAAATTTAT
1545754 CACTATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAACTTATCAAAATTTAT
Found at i:1546088 original size:35 final size:35
Alignment explanation
Indices: 1546049--1546119 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1546039 TAAAATATTT
1546049 TTTGAAATTTATCATTTTAACGTGATAAATTTTAA
1 TTTGAAATTTATCATTTTAACGTGATAAATTTTAA
1546084 TTTGAAATTTATCATTTTAACGTGATAAATTTTAA
1 TTTGAAATTTATCATTTTAACGTGATAAATTTTAA
1546119 T
1 T
1546120 ATAATTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (35 bp):
TTTGAAATTTATCATTTTAACGTGATAAATTTTAA
Found at i:1547524 original size:18 final size:17
Alignment explanation
Indices: 1547493--1547530 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1547483 ATCAAATGGA
*
1547493 CTCGACTCGGACTCGAG
1 CTCGACTCGAACTCGAG
1547510 CTCGAGCTCGAACTCGAG
1 CTCGA-CTCGAACTCGAG
1547528 CTC
1 CTC
1547531 TGCTCGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.18, C:0.37, G:0.26, T:0.18
Consensus pattern (17 bp):
CTCGACTCGAACTCGAG
Found at i:1547612 original size:11 final size:11
Alignment explanation
Indices: 1547596--1547657 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
1547586 AAAATTACAT
1547596 TATTAAAAATA
1 TATTAAAAATA
1547607 TATT-AAAATA
1 TATTAAAAATA
* ***
1547617 CATTATTGATA
1 TATTAAAAATA
1547628 -ATTATAAAAT-
1 TATTA-AAAATA
1547638 T-TTAAAAATA
1 TATTAAAAATA
1547648 TATTAAAAAT
1 TATTAAAAAT
1547658 TCTATAATAC
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
9 5 0.13
10 17 0.44
11 17 0.44
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1547784 original size:7 final size:7
Alignment explanation
Indices: 1547764--1547859 Score: 63
Period size: 7 Copynumber: 13.7 Consensus size: 7
1547754 ATTTATAATG
1547764 AATCCTA
1 AATCCTA
**
1547771 ACGCCTA
1 AATCCTA
1547778 AATCCTA
1 AATCCTA
*
1547785 AA-CCTTG
1 AATCC-TA
*
1547792 AATCTTA
1 AATCCTA
*
1547799 AACCCTA
1 AATCCTA
*
1547806 AATCATA
1 AATCCTA
1547813 AATCCTA
1 AATCCTA
*
1547820 AATTCTA
1 AATCCTA
1547827 AA-CCTTA
1 AATCC-TA
*
1547834 AA-CCATG
1 AATCC-TA
1547841 AATCCTA
1 AATCCTA
*
1547848 AACCCTA
1 AATCCTA
1547855 AATCC
1 AATCC
1547860 GATTATGTGA
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
6 3 0.05
7 60 0.91
8 3 0.05
ACGTcount: A:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (7 bp):
AATCCTA
Found at i:1547855 original size:28 final size:28
Alignment explanation
Indices: 1547797--1547856 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1547787 CCTTGAATCT
* **
1547797 TAAACCCTAAATCATAAATCCTAAATTC
1 TAAACCCTAAACCATAAATCCTAAACCC
* *
1547825 TAAACCTTAAACCATGAATCCTAAACCC
1 TAAACCCTAAACCATAAATCCTAAACCC
1547853 TAAA
1 TAAA
1547857 TCCGATTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAACCATAAATCCTAAACCC
Found at i:1548554 original size:7 final size:7
Alignment explanation
Indices: 1548539--1548575 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
1548529 GAGCTTGAAT
*
1548539 TAAAACC
1 TAAACCC
1548546 TAAACCC
1 TAAACCC
1548553 TAAACCC
1 TAAACCC
1548560 TAAACCC
1 TAAACCC
1548567 TAAACCC
1 TAAACCC
1548574 TA
1 TA
1548576 TAAATTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:1548584 original size:21 final size:20
Alignment explanation
Indices: 1548536--1548584 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1548526 TACGAGCTTG
*
1548536 AATTAAAACCTAAACCCTAA
1 AATTAAACCCTAAACCCTAA
**
1548556 ACCCTAAACCCTAAACCCTATA
1 A-ATTAAACCCTAAACCCTA-A
1548578 AATTAAA
1 AATTAAA
1548585 GCCCAAACTC
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.05
21 19 0.86
22 2 0.09
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
AATTAAACCCTAAACCCTAA
Found at i:1548641 original size:11 final size:11
Alignment explanation
Indices: 1548625--1548718 Score: 95
Period size: 11 Copynumber: 8.5 Consensus size: 11
1548615 CGTGTGGTGA
*
1548625 TGAATCAAGCT
1 TGAATCGAGCT
1548636 TGAATCGAGCT
1 TGAATCGAGCT
* *
1548647 CGAATTGAG-T
1 TGAATCGAGCT
1548657 TCGAATCGAG-T
1 T-GAATCGAGCT
*
1548668 TCGAATCGAACT
1 T-GAATCGAGCT
1548680 TGAATCGAG-T
1 TGAATCGAGCT
1548690 TCGAATCGAGCT
1 T-GAATCGAGCT
*
1548702 TGAATCGAGTT
1 TGAATCGAGCT
1548713 TGAATC
1 TGAATC
1548719 TCGAGTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
10 3 0.04
11 64 0.90
12 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (11 bp):
TGAATCGAGCT
Found at i:1548662 original size:22 final size:21
Alignment explanation
Indices: 1548626--1548718 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 21
1548616 GTGTGGTGAT
* *
1548626 GAATCAAGCTTGAATCGAGCTC
1 GAATCGAG-TTGAATCGAGTTC
*
1548648 GAATTGAGTTCGAATCGAGTTC
1 GAATCGAGTT-GAATCGAGTTC
*
1548670 GAATCGAACTTGAATCGAGTTC
1 GAATCG-AGTTGAATCGAGTTC
*
1548692 GAATCGAGCTTGAATCGAGTTT
1 GAATCGAG-TTGAATCGAGTTC
1548714 GAATC
1 GAATC
1548719 TCGAGTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
21 3 0.05
22 55 0.90
23 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (21 bp):
GAATCGAGTTGAATCGAGTTC
Found at i:1548716 original size:33 final size:33
Alignment explanation
Indices: 1548626--1548718 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
1548616 GTGTGGTGAT
* * *
1548626 GAATCAAGCTTGAATCGAGCTCGAATTGAGTTC
1 GAATCGAGCTTGAATCGAGCTTGAATCGAGTTC
*
1548659 GAATCGAG-TTCGAATCGAACTTGAATCGAGTTC
1 GAATCGAGCTT-GAATCGAGCTTGAATCGAGTTC
*
1548692 GAATCGAGCTTGAATCGAGTTTGAATC
1 GAATCGAGCTTGAATCGAGCTTGAATC
1548719 TCGAGTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.04
33 48 0.92
34 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (33 bp):
GAATCGAGCTTGAATCGAGCTTGAATCGAGTTC
Found at i:1554402 original size:27 final size:26
Alignment explanation
Indices: 1554352--1554403 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1554342 ATTTGATCAT
*
1554352 TTAATTTTGATATTATTTCCTTTTTA
1 TTAATTTTGATATTATTTCATTTTTA
* *
1554378 TTAACTTTTTATATTATTTTATTTTT
1 TTAA-TTTTGATATTATTTCATTTTT
1554404 TATAACTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (26 bp):
TTAATTTTGATATTATTTCATTTTTA
Found at i:1570325 original size:17 final size:17
Alignment explanation
Indices: 1570303--1570355 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1570293 CATATCTAAT
1570303 TTTTAGTTTAAATTTCA
1 TTTTAGTTTAAATTTCA
* *
1570320 TTTTAGTATATA-TT-A
1 TTTTAGTTTAAATTTCA
**
1570335 TTAAAGTTTAAATTTCA
1 TTTTAGTTTAAATTTCA
1570352 TTTT
1 TTTT
1570356 GGTATCTATC
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 9 0.35
16 4 0.15
17 13 0.50
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTAGTTTAAATTTCA
Found at i:1570348 original size:32 final size:32
Alignment explanation
Indices: 1570307--1570369 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1570297 TCTAATTTTT
*
1570307 AGTTTAAATTTCATTTTAGTATATATTATTAA
1 AGTTTAAATTTCATTTTAGTATATATCATTAA
* *
1570339 AGTTTAAATTTCATTTTGGTATCTATCATTA
1 AGTTTAAATTTCATTTTAGTATATATCATTA
1570370 TAAACTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (32 bp):
AGTTTAAATTTCATTTTAGTATATATCATTAA
Found at i:1578574 original size:2 final size:2
Alignment explanation
Indices: 1578567--1578613 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1578557 CTTCAATTGC
*
1578567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
1578609 AT AT A
1 AT AT A
1578614 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1581774 original size:13 final size:13
Alignment explanation
Indices: 1581746--1581795 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1581736 TCTAATCTTA
*
1581746 ATTAAT-ATAAAC
1 ATTAATAATAAAT
1581758 ATTAATAATAAAT
1 ATTAATAATAAAT
1581771 ATTAACCTAATATAAT
1 ATTAA--TAATA-AAT
1581787 -TTAATAATA
1 ATTAATAATA
1581796 GTGTATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 6 0.18
13 15 0.45
15 9 0.27
16 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAATAATAAAT
Found at i:1592242 original size:6 final size:6
Alignment explanation
Indices: 1592231--1592269 Score: 50
Period size: 5 Copynumber: 7.2 Consensus size: 6
1592221 TTTCATCCTA
1592231 AACCCG AACCCG AACCCG AA-CC- AACCCG -ACCCG -ACCCG A
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG A
1592270 CCAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.07
5 14 0.47
6 14 0.47
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:1593420 original size:21 final size:20
Alignment explanation
Indices: 1593394--1593433 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1593384 TCCAATTTCG
1593394 CAACGTGAATAGTGAAAATCC
1 CAACGTGAATAGT-AAAATCC
1593415 CAACGTGAATAGTAAAATC
1 CAACGTGAATAGTAAAATC
1593434 GCAATGCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.20
Consensus pattern (20 bp):
CAACGTGAATAGTAAAATCC
Found at i:1593444 original size:20 final size:20
Alignment explanation
Indices: 1593391--1593458 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
1593381 GTTTCCAATT
*
1593391 TCGCAACGTGAATAGTGAAAA
1 TCGCAACGCGAATAGT-AAAA
* *
1593412 TCCCAACGTGAATAGTAAAA
1 TCGCAACGCGAATAGTAAAA
*
1593432 TCGCAATGCGAATTTAG-AAAA
1 TCGCAACGCGAA--TAGTAAAA
1593453 TCGCAA
1 TCGCAA
1593459 AATCGCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.32
21 25 0.61
22 3 0.07
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATAGTAAAA
Found at i:1593862 original size:21 final size:20
Alignment explanation
Indices: 1593808--1593896 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
1593798 CATATAGATT
* *
1593808 CGTTACGATTTTAATATTCA
1 CGTTGCGATTTTACTATTCA
1593828 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
1593848 CGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCA
* * *
1593869 CATTGCGAATTTGACT-TTCG
1 CGTTGCG-ATTTTACTATTCA
1593889 CGTTGCGA
1 CGTTGCGA
1593897 ATTTGAATTC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 35 0.57
21 24 0.39
22 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:1593867 original size:41 final size:40
Alignment explanation
Indices: 1593808--1593896 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
1593798 CATATAGATT
* * *
1593808 CGTTACGATTTTAATATTCACGTTGCG-ATTTTACTATTCA
1 CGTTGCGATTTTAATATTCACATTGCGAATTTGACT-TTCA
* *
1593848 CGTTGCGATTTTTACTATTCACATTGCGAATTTGACTTTCG
1 CGTTGCGA-TTTTAATATTCACATTGCGAATTTGACTTTCA
1593889 CGTTGCGA
1 CGTTGCGA
1593897 ATTTGAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 7 0.17
41 28 0.67
42 7 0.17
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (40 bp):
CGTTGCGATTTTAATATTCACATTGCGAATTTGACTTTCA
Found at i:1593897 original size:20 final size:20
Alignment explanation
Indices: 1593828--1593941 Score: 74
Period size: 20 Copynumber: 5.7 Consensus size: 20
1593818 TTAATATTCA
* *
1593828 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCG
* * *
1593848 CGTTGCGATTTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCG
*
1593869 CATTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCG
*
1593889 CGTTGCGAATTTGA-ATTCTG
1 CGTTGCGAATTTGACTTTC-G
* *
1593909 TGTTGCG-ATTT-ACAGATTCG
1 CGTTGCGAATTTGAC--TTTCG
1593929 CGTTGCGAATTTG
1 CGTTGCGAATTTG
1593942 GAAAATCGCA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 7 0.09
20 37 0.47
21 33 0.42
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:1593950 original size:21 final size:21
Alignment explanation
Indices: 1593933--1593980 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1593923 GATTCGCGTT
1593933 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
1593954 GCGAATTTGGAAAA-CGCAAT
1 GCGAATTTGGAAAATCGCAAC
1593974 GC-AATTT
1 GCGAATTT
1593981 ACATTTTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 7 0.27
21 14 0.54
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:1596124 original size:21 final size:22
Alignment explanation
Indices: 1596099--1596147 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1596089 AATCTAGTTA
*
1596099 ATTAGTTTGTTAGTATAAAT-T
1 ATTAGTTGGTTAGTATAAATAT
* *
1596120 ATTAGTTGGTTAGTTTAAGTAT
1 ATTAGTTGGTTAGTATAAATAT
1596142 ATTAGT
1 ATTAGT
1596148 AGTTTATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (22 bp):
ATTAGTTGGTTAGTATAAATAT
Found at i:1596150 original size:25 final size:26
Alignment explanation
Indices: 1596117--1596171 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
1596107 GTTAGTATAA
* *
1596117 ATTATTAGTTGGTTAGTTTAAG-TAT
1 ATTAGTAGTTGATTAGTTTAAGTTAT
*
1596142 ATTAGTAGTTTATTAGTTTAAGTTAT
1 ATTAGTAGTTGATTAGTTTAAGTTAT
1596168 ATTA
1 ATTA
1596172 TATTATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (26 bp):
ATTAGTAGTTGATTAGTTTAAGTTAT
Found at i:1596206 original size:40 final size:40
Alignment explanation
Indices: 1596147--1596236 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 40
1596137 AGTATATTAG
* *
1596147 TAGTTTATTAGTTTAAGTTA-TATTATATTATATAAAAA-AT
1 TAGTTAATTAGTTTAAGTTAGTATTA-AATATA-AAAAATAT
1596187 TAGTTAATTAGTTCT-AGTTAGTTATTAAATATAAAAAATAT
1 TAGTTAATTAGTT-TAAGTTAG-TATTAAATATAAAAAATAT
*
1596228 TAATTAATT
1 TAGTTAATT
1596237 TGTTAGTGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 22 0.51
41 16 0.37
42 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (40 bp):
TAGTTAATTAGTTTAAGTTAGTATTAAATATAAAAAATAT
Found at i:1596669 original size:15 final size:15
Alignment explanation
Indices: 1596649--1596700 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
1596639 TTCCGTTTTA
1596649 AAAAATATTGTGTTT
1 AAAAATATTGTGTTT
1596664 AAAAATATTTAGTGTTGTTT
1 AAAAATA--T--TG-TGTTT
*
1596684 AAAAATATTTTGTTT
1 AAAAATATTGTGTTT
1596699 AA
1 AA
1596701 TTTACATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 14 0.45
16 1 0.03
17 1 0.03
18 1 0.03
19 2 0.06
20 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
AAAAATATTGTGTTT
Found at i:1597004 original size:25 final size:26
Alignment explanation
Indices: 1596976--1597033 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1596966 AATCATTAAT
*
1596976 ATCAATCATTA-GATAATAGTAATCA
1 ATCAATCATTAGGATAATAGTAAGCA
* * *
1597001 ATC-ATTATTAGGTTTATAGTAAGCA
1 ATCAATCATTAGGATAATAGTAAGCA
1597026 ATCAATCA
1 ATCAATCA
1597034 AGTTAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 6 0.23
25 17 0.65
26 3 0.12
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (26 bp):
ATCAATCATTAGGATAATAGTAAGCA
Found at i:1599780 original size:26 final size:26
Alignment explanation
Indices: 1599752--1600226 Score: 324
Period size: 26 Copynumber: 19.2 Consensus size: 26
1599742 GATGATTTAG
**
1599752 TAATGATTTGATAATAATCATTATTG
1 TAATGATTTGATAATAATCATTATAA
1599778 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
1599804 TAATGATTT-AGTAATAATTATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
1599830 AAATGA-TT--TAATAATGATT-T-A
1 TAATGATTTGATAATAATCATTATAA
* * * * *
1599851 -AAT-ATTTAATGACTTGATGATT-TAG
1 TAATGATTTGAT-A-ATAATCATTATAA
*
1599876 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1599902 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1599928 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * * *
1599954 AAATAATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1599977 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
1600000 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1600026 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1600052 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1600078 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * *
1600101 T-ATTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
1600123 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
1600149 TAATGATTTTATAATAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
1600174 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1600198 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
1600223 TAAT
1 TAAT
1600227 TATAAATAAT
Statistics
Matches: 362, Mismatches: 55, Indels: 65
0.75 0.11 0.13
Matches are distributed among these distances:
19 1 0.00
20 9 0.02
21 8 0.02
22 12 0.03
23 30 0.08
24 37 0.10
25 46 0.13
26 211 0.58
27 8 0.02
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:1599916 original size:124 final size:124
Alignment explanation
Indices: 1599694--1600210 Score: 889
Period size: 124 Copynumber: 4.2 Consensus size: 124
1599684 ATGTATTTAT
*
1599694 TAATCATTATAAAAATAATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
1599759 TTGATAATAATCATTATTGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
1599818 TAATTATTATAAAAATGATTTAATAATGATTTAAATATTTAATGACTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1599883 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
1599942 TAATCATTATAAAAATAATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1600007 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1600066 TAATCATTATAAAAATGATTTAATAATGATTTAAATA-TTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
1600130 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
1600188 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
1600211 CTAATGATTT
Statistics
Matches: 377, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
120 18 0.05
122 17 0.05
123 65 0.17
124 277 0.73
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1600217 original size:14 final size:14
Alignment explanation
Indices: 1599752--1600226 Score: 149
Period size: 14 Copynumber: 35.1 Consensus size: 14
1599742 GATGATTTAG
*
1599752 TAATGATTTGATAA
1 TAATGATTTAATAA
* **
1599766 TAATCA-TT-ATTG
1 TAATGATTTAATAA
*
1599778 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1599792 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1599804 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
1599818 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
1599830 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
1599841 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
* *
1599857 TAATGACTTGATGATTTAG
1 TAATGA-TT--T-A-ATAA
*
1599876 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
1599890 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
1599902 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1599916 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1599928 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
1599942 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
1599954 AAAT-AATT--TAA
1 TAATGATTTAATAA
*
1599965 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
1599981 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
1600000 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
1600014 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
1600026 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1600040 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1600052 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
1600066 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1600078 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
1600089 TAATGATTTAAATAT
1 TAATGATTT-AATAA
*
1600104 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
1600123 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1600137 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1600149 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
1600163 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
1600175 T-ATTATTTAGTAA
1 TAATGATTTAATAA
1600188 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
1600198 TAATGATTTAATAC
1 TAATGATTTAATAA
1600212 TAATGATTTAATAA
1 TAATGATTTAATAA
1600226 T
1 T
1600227 TATAAATAAT
Statistics
Matches: 351, Mismatches: 63, Indels: 94
0.69 0.12 0.19
Matches are distributed among these distances:
10 4 0.01
11 37 0.11
12 95 0.27
13 39 0.11
14 103 0.29
15 16 0.05
16 19 0.05
17 3 0.01
18 3 0.01
19 28 0.08
20 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:1602609 original size:15 final size:14
Alignment explanation
Indices: 1602586--1602616 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1602576 TACAACACTA
1602586 AACTTTAATATAAT
1 AACTTTAATATAAT
1602600 AACTTATAATATAAT
1 AACTT-TAATATAAT
1602615 AA
1 AA
1602617 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1602624 original size:16 final size:16
Alignment explanation
Indices: 1602591--1602637 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1602581 CACTAAACTT
*
1602591 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1602606 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1602622 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1602638 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1602758 original size:32 final size:34
Alignment explanation
Indices: 1602678--1602759 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
1602668 CTAAACCCTT
*
1602678 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
1602711 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
1602744 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
1602760 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:1602875 original size:44 final size:44
Alignment explanation
Indices: 1602799--1602932 Score: 138
Period size: 44 Copynumber: 3.1 Consensus size: 44
1602789 TCAACAAACA
*
1602799 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTT
* *
1602846 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTT
1602889 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
1602930 AAT
1 AAT
1602933 TTTTGTATAC
Statistics
Matches: 78, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
38 5 0.06
39 2 0.03
40 8 0.10
41 12 0.15
42 6 0.08
43 11 0.14
44 16 0.21
45 5 0.06
46 6 0.08
47 7 0.09
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (44 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTT
Found at i:1602969 original size:22 final size:24
Alignment explanation
Indices: 1602929--1602974 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
1602919 AAATAATTTT
1602929 TAATTTTTGTATACTATAACTTAA
1 TAATTTTTGTATACTATAACTTAA
1602953 TAATTTTT-TA-ACTATAACTTAA
1 TAATTTTTGTATACTATAACTTAA
1602975 ACTAACAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.55
23 2 0.09
24 8 0.36
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATTTTTGTATACTATAACTTAA
Found at i:1603144 original size:21 final size:21
Alignment explanation
Indices: 1603114--1603166 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1603104 CCCTTTCTTC
*
1603114 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1603135 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1603156 TTCTTTCTTTC
1 TTCTTTCTTTC
1603167 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:1603157 original size:17 final size:16
Alignment explanation
Indices: 1603137--1603168 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1603127 TTCTCCCTTT
1603137 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1603154 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1603169 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1603201 original size:23 final size:23
Alignment explanation
Indices: 1603171--1603216 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1603161 TCTTTCTCGG
1603171 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1603194 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1603217 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:1603363 original size:27 final size:27
Alignment explanation
Indices: 1603333--1603388 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1603323 AATAATTCAC
1603333 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
1603360 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
1603387 GG
1 GG
1603389 GAGCTGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (27 bp):
GGCTCAAATGGTTCACATGCATGCATT
Found at i:1603493 original size:29 final size:29
Alignment explanation
Indices: 1603461--1603569 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 29
1603451 ATGGGAATGG
1603461 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
1603490 CGCCGGGACTACATGGTGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
1603519 CGTCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1603548 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1603570 CTCTATTCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
29 71 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1603655 original size:12 final size:13
Alignment explanation
Indices: 1603623--1603657 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1603613 GCTCGTATGG
1603623 CTCGTATGTCACC
1 CTCGTATGTCACC
1603636 CTCGTATGTCACC
1 CTCGTATGTCACC
1603649 C-CGTATGTC
1 CTCGTATGTC
1603658 GCCTGGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.31
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:1622465 original size:22 final size:23
Alignment explanation
Indices: 1622432--1622478 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1622422 ACCGAATTCG
1622432 ACGCCCCACATTCTTGAATTTTA
1 ACGCCCCACATTCTTGAATTTTA
*
1622455 ACGCCCC-CATTCTTGACTTTTA
1 ACGCCCCACATTCTTGAATTTTA
1622477 AC
1 AC
1622479 AATCTCCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (23 bp):
ACGCCCCACATTCTTGAATTTTA
Found at i:1623348 original size:22 final size:22
Alignment explanation
Indices: 1623305--1623348 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1623295 AAAATATGGT
* *
1623305 ATGAACAGTACCGTCAATAGTA
1 ATGAACAATACCGTCAACAGTA
* *
1623327 ATGAACAATGCCGTGAACAGTA
1 ATGAACAATACCGTCAACAGTA
1623349 CCCTATTACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (22 bp):
ATGAACAATACCGTCAACAGTA
Found at i:1623430 original size:21 final size:21
Alignment explanation
Indices: 1623406--1623458 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1623396 AAACCGATTC
1623406 CCCTGCTACAGGGAACTGATA
1 CCCTGCTACAGGGAACTGATA
* *
1623427 CCCTGATACATGGAACTGATA
1 CCCTGCTACAGGGAACTGATA
1623448 CCCTGCTACAG
1 CCCTGCTACAG
1623459 TACTGCTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (21 bp):
CCCTGCTACAGGGAACTGATA
Found at i:1625764 original size:3 final size:3
Alignment explanation
Indices: 1625756--1625785 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1625746 GACTCTAGGA
1625756 AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
1625786 ATTAAGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1627837 original size:31 final size:31
Alignment explanation
Indices: 1627799--1627983 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
1627789 CCCGAAGGAC
* *
1627799 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1627830 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1627861 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1627892 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1627923 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1627954 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1627984 CCCTCGACCC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1628660 original size:21 final size:21
Alignment explanation
Indices: 1628636--1628680 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1628626 CTATGTTCGT
* * *
1628636 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1628657 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1628678 TTG
1 TTG
1628681 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1629426 original size:23 final size:23
Alignment explanation
Indices: 1629400--1629485 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
1629390 AATCTTATAT
*
1629400 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
**
1629423 GGCACTTTAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * * *
1629446 GACACTACGATGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
1629469 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
1629486 ATATGAGTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1629996 original size:23 final size:22
Alignment explanation
Indices: 1629958--1630006 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
1629948 AAGTTGTGGT
*
1629958 TAAAATAAAAAAAATAATTAAA
1 TAAAAGAAAAAAAATAATTAAA
1629980 TAAAAGAAAAAATAATAATTAAA
1 TAAAAGAAAAAA-AATAATTAAA
1630003 TAAA
1 TAAA
1630007 CAAATTAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAAAGAAAAAAAATAATTAAA
Found at i:1630690 original size:19 final size:19
Alignment explanation
Indices: 1630634--1630696 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1630624 CTATTTAAAC
**
1630634 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1630654 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1630674 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1630693 TAAA
1 TAAA
1630697 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1630724 original size:64 final size:65
Alignment explanation
Indices: 1630599--1630801 Score: 182
Period size: 64 Copynumber: 3.0 Consensus size: 65
1630589 TAAAACATCT
* *
1630599 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAA-A-AATA-ATATAATAT
1 TAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATA-C-AAAGATAA-AGATAAAATAT
1630661 -TC-
62 ATCA
1630663 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACAAAGATAAAG-------AT-AA
1630728 AATAATATCA
57 AAT-ATATCA
* * *
1630738 TAAAACTTAATTAAAATACTAAAAATATATTTAAACTAAAATACAAAGATAAAGATAAAATATA
1 TAAATCCTAATTAAAATACT-AAAA-CTATTTAAACTAAAATACAAAGATAAAGATAAAATATA
1630802 AAAAATATTT
Statistics
Matches: 117, Mismatches: 6, Indels: 29
0.77 0.04 0.19
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 37 0.32
67 3 0.03
68 5 0.04
69 2 0.02
71 2 0.02
72 4 0.03
73 2 0.02
74 2 0.02
75 18 0.15
76 31 0.26
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (65 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACAAAGATAAAGATAAAATATATCA
Found at i:1635669 original size:15 final size:15
Alignment explanation
Indices: 1635645--1635693 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
1635635 TTTCTCTTGT
*
1635645 TCTTCTTGATGTGCG
1 TCTTCCTGATGTGCG
*
1635660 TCTTCCTGATGTGTG
1 TCTTCCTGATGTGCG
1635675 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
1635690 TCTT
1 TCTT
1635694 TTTCTGCTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.06, C:0.22, G:0.24, T:0.47
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:1637387 original size:21 final size:22
Alignment explanation
Indices: 1637354--1637394 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1637344 GTTAAAATAA
1637354 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
1637376 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
1637395 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:1638056 original size:65 final size:68
Alignment explanation
Indices: 1637985--1638184 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 68
1637975 TAAAACATCT
*
1637985 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACTAAAAAAAATAATATAAT-AT
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATAC-AAAAAAAATAATATAATAAT
1638048 -T-C
65 ATCC
1638050 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAA-A-AAA-AT--AATAT--
1638114 AAATAATATCC
59 -AATAATATCC
* * * * *
1638125 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAA-AATATAAT
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAAAAAAATAATATAAT
1638185 GTTTAAAATA
Statistics
Matches: 116, Mismatches: 6, Indels: 24
0.79 0.04 0.16
Matches are distributed among these distances:
64 8 0.07
65 37 0.32
66 3 0.03
67 5 0.04
69 5 0.04
70 5 0.04
72 3 0.03
73 3 0.03
74 3 0.03
75 18 0.16
76 26 0.22
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAAAAAAATAATATAATAATA
TCC
Found at i:1638108 original size:76 final size:76
Alignment explanation
Indices: 1638028--1638177 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 76
1638018 ACTAAAATAC
* *
1638028 TAAAA-AAAATAATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAAT
1 TAAAATAAAA-AA-ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAAT
1638091 ACAAAGATAAAGA
64 ACAAAGATAAAGA
* *
1638104 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAAAATAAAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1638169 AAAGATAAA
66 AAAGATAAA
1638178 ATATAATGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
75 26 0.38
76 39 0.57
77 3 0.04
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (76 bp):
TAAAATAAAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
AAAGATAAAGA
Found at i:1639023 original size:24 final size:24
Alignment explanation
Indices: 1639007--1639090 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
1638997 GTATAAATTA
1639007 CACCGAAGTGCCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAATTTG
1639031 CACCGAAGTGCCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAATTTG
** * *
1639055 CACCGAAGTATCGCGTAGAA-ATG
1 CACCGAAGTGCCACGTAGAATTTG
*
1639078 CACCGTAGTGCCA
1 CACCGAAGTGCCA
1639091 TATAAGATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 11 0.21
24 41 0.79
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (24 bp):
CACCGAAGTGCCACGTAGAATTTG
Found at i:1639238 original size:23 final size:23
Alignment explanation
Indices: 1639202--1639245 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1639192 AATACATATA
1639202 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* * *
1639225 TGTCCGGAATGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
1639246 CCCTCTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:1644270 original size:22 final size:23
Alignment explanation
Indices: 1644238--1644282 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1644228 TCGAATTTGG
1644238 TGCCCCACATTCTTGAA-TTTTAA
1 TGCCCCACATTCTT-AACTTTTAA
1644261 TGCCCC-CATTCTTAACTTTTAA
1 TGCCCCACATTCTTAACTTTTAA
1644283 CAGGAGATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.10
22 13 0.62
23 6 0.29
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (23 bp):
TGCCCCACATTCTTAACTTTTAA
Found at i:1644475 original size:29 final size:29
Alignment explanation
Indices: 1644433--1644500 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
1644423 TTCTTCCGAG
*
1644433 AAGGGTTGGTGATATTGCTCAGCTAGTTA
1 AAGGGTTGGTGATATTGCTCAGCTAGATA
* * *
1644462 AAGGGTTGGTGATATTGTTTATCTAGATA
1 AAGGGTTGGTGATATTGCTCAGCTAGATA
1644491 AAGGGTTGGT
1 AAGGGTTGGT
1644501 TGGTTTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37
Consensus pattern (29 bp):
AAGGGTTGGTGATATTGCTCAGCTAGATA
Found at i:1644597 original size:28 final size:28
Alignment explanation
Indices: 1644558--1644628 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
1644548 TTTTTGCTCC
*
1644558 TTTTGGTTTGTTTTAGTTATGTTGGGTTG
1 TTTT-GTTTGTTTTAGTTATGTTGGGTTA
1644587 TTTTGTTTGTTTTAGTTATGTTGGGTTA
1 TTTTGTTTGTTTTAGTTATGTTGGGTTA
1644615 TTTTGTTTGTTTTA
1 TTTTGTTTGTTTTA
1644629 TTCTTTGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.08, C:0.00, G:0.25, T:0.66
Consensus pattern (28 bp):
TTTTGTTTGTTTTAGTTATGTTGGGTTA
Found at i:1645210 original size:21 final size:21
Alignment explanation
Indices: 1645184--1645226 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1645174 GATTCTCAAC
1645184 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1645205 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
1645226 G
1 G
1645227 TAAATCGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:1645263 original size:21 final size:21
Alignment explanation
Indices: 1645239--1645325 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
1645229 AATCGCAATA
*
1645239 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCATTG
*
1645260 CGAT-TTAC-ATA-TTCGCATTG
1 CGATAGT-CGA-AGTTCGCATTG
*
1645280 CGATAGTCCAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
1645301 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCATTG
1645322 CGAT
1 CGAT
1645326 TTATTCCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.29
21 40 0.71
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCATTG
Found at i:1645482 original size:5 final size:6
Alignment explanation
Indices: 1645443--1645479 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1645433 GACACGTATT
1645443 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1645480 CGAGACGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1645975 original size:5 final size:5
Alignment explanation
Indices: 1645961--1645991 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1645951 CCGCCGCCGC
1645961 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1645992 GGTCGGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:1646008 original size:6 final size:6
Alignment explanation
Indices: 1645992--1646065 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
1645982 TCTCGTCTCG
1645992 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1646039 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1646066 AATGGTAATG
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1646288 original size:41 final size:40
Alignment explanation
Indices: 1646234--1646537 Score: 284
Period size: 41 Copynumber: 7.4 Consensus size: 40
1646224 GCGATTTACA
1646234 TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTCGGC
1 TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTC--C
1646276 TA-TCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAC
1 TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTC--C
*
1646317 TA-TCGCATTCCGATTTACATATTCGCATTGCGATAGTCC
1 TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
* *
1646356 AAGTTCGCATTGCGATAGT-CGA-AGTTCGCATTGCGATAGTCC
1 TA-TTCGCATTGCGAT-TTAC-ATA-TTCGCATTGCGATAGTCC
* * * * *
1646398 AAGTTCGCGTTGCGATAGT-CGACTA-TCGCATTGCGAT-TTACA
1 TA-TTCGCATTGCGAT-TTAC-A-TATTCGCATTGCGATAGT-CC
* *
1646440 TATTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAC
1 TATTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTC--C
1646483 TA-TCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
*
1646522 AAGTTCGCATTGCGAT
1 TA-TTCGCATTGCGAT
1646538 AGTCGAAGTT
Statistics
Matches: 230, Mismatches: 15, Indels: 35
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.02
41 150 0.65
42 72 0.31
43 2 0.01
44 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (40 bp):
TATTCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
Found at i:1646385 original size:62 final size:61
Alignment explanation
Indices: 1646255--1646578 Score: 290
Period size: 62 Copynumber: 5.2 Consensus size: 61
1646245 CGATTTACAT
* *
1646255 ATTCGCATTGCGATAGT-C-GGCTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCGA
1 ATTCGCATTGCGATAGTCCAAG-T-TCGCATTGCGATAGT-CA-ACTTCGCATTGCGATAGTCGA
* * * * *
1646316 CTATCGCATTCCGAT-TTACATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
1 AT-TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGT-CAACTTCGCATTGCGATAGTCGA
* * *
1646378 AGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGACTATCGCATTGCGAT-TTAC-A
1 A-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACT-TCGCATTGCGATAGT-CGA
* *
1646440 TATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGAT-TTAC-A
1 -ATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACT-TCGCATTGCGATAGT-CGA
* * *
1646502 TATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTTGCATTACGATAGTCGA
1 -ATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-AACTTCGCATTGCGATAGTCGA
*
1646565 AGTTCGCGTTGCGA
1 A-TTCGCATTGCGA
1646579 ATTTGGAAAC
Statistics
Matches: 226, Mismatches: 21, Indels: 30
0.82 0.08 0.11
Matches are distributed among these distances:
61 15 0.07
62 163 0.72
63 48 0.21
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (61 bp):
ATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTTCGCATTGCGATAGTCGA
Found at i:1646432 original size:145 final size:145
Alignment explanation
Indices: 1646256--1646564 Score: 430
Period size: 145 Copynumber: 2.1 Consensus size: 145
1646246 GATTTACATA
* *
1646256 TTCGCATTGCGATAGTCGGCTATCGCATTGCGATTTACATATTCGCATTGCGATAGT-CGACTAT
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACT-T
* * *
1646320 CGCATTCCGAT--T-TACATATTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
65 CGCATTCCGATAGTCGAC-TA-TCGCATTGCGAT-GTACATA-TTCGCATTGCGATAGTCCAAGT
1646381 TCGCATTGCGATAGTCCAAG
126 TCGCATTGCGATAGTCCAAG
* *
1646401 TTCGCGTTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTC
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTTC
* *
1646466 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCA
66 GCATTCCGATAGTCGACTATCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCGCA
*
1646531 TTGCGATAGTCGAAG
131 TTGCGATAGTCCAAG
* *
1646546 TTTGCATTACGATAGTCGA
1 TTCGCATTGCGATAGTCGA
1646565 AGTTCGCGTT
Statistics
Matches: 146, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
145 125 0.86
146 16 0.11
147 3 0.02
148 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (145 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTTC
GCATTCCGATAGTCGACTATCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCGCA
TTGCGATAGTCCAAG
Found at i:1646435 original size:104 final size:103
Alignment explanation
Indices: 1646210--1646537 Score: 461
Period size: 104 Copynumber: 3.2 Consensus size: 103
1646200 AACGCGAACT
* * *
1646210 TCGACTATCGCAATGCGATTTACATATTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTC
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTC
*
1646273 G-GCTATCGCATTGCGATTTACATATTCGCATTGCGATAG
65 GAG-TATCGCATTGCGATGTACATATTCGCATTGCGATAG
*
1646312 TCGACTATCGCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
* *
1646377 AAGT-TCGCATTGCGATAGTCCA-AGTTCGCGTTGCGATAG
66 -AGTATCGCATTGCGAT-GTACATA-TTCGCATTGCGATAG
1646416 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
* *
1646481 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
66 AGTATCGCATTGCGATGTACATATTCGCATTGCGATAG
* *
1646519 TCCAAGT-TCGCATTGCGAT
1 T-CGACTATCGCATTGCGAT
1646538 AGTCGAAGTT
Statistics
Matches: 203, Mismatches: 14, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
102 38 0.19
103 66 0.33
104 98 0.48
105 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (103 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
AGTATCGCATTGCGATGTACATATTCGCATTGCGATAG
Found at i:1646546 original size:21 final size:21
Alignment explanation
Indices: 1646256--1646578 Score: 266
Period size: 21 Copynumber: 15.6 Consensus size: 21
1646246 GATTTACATA
1646256 TTCGCATTGCGATAGTCG--G
1 TTCGCATTGCGATAGTCGAAG
*
1646275 CTATCGCATTGCGAT-TTAC-ATA-
1 -T-TCGCATTGCGATAGT-CGA-AG
*
1646297 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
* *
1646317 TATCGCATTCCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
1646338 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
1646359 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1646380 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
* *
1646401 TTCGCGTTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
1646421 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
1646442 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
1646463 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
1646483 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
1646504 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
1646525 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* *
1646546 TTTGCATTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1646567 TTCGCGTTGCGA
1 TTCGCATTGCGA
1646579 ATTTGGAAAC
Statistics
Matches: 250, Mismatches: 24, Indels: 57
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.00
20 64 0.26
21 182 0.73
22 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:1646600 original size:83 final size:82
Alignment explanation
Indices: 1646236--1646578 Score: 344
Period size: 83 Copynumber: 4.1 Consensus size: 82
1646226 GATTTACATA
* * * *
1646236 TTCGCATTGCGATTTACATATTCGCATTGCGATAGT-C-GGCTATCGCATTGCGAT-TTAC-ATA
1 TTCGCGTTGCGATTTAGATA-TCGCATTGCGATAGTCCAAG-T-TCGCATTGCGATAGT-CGA-A
*
1646297 -TTCGCATTGCGATAGTCG-AC
61 GTTCGCATTGCGATAGTCGAAG
* * *
1646317 TATCGCATTCCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTT
1 T-TCGCGTTGCGATTTAGATA-TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTT
*
1646382 CGCATTGCGATAGTCCAAG
64 CGCATTGCGATAGTCGAAG
* * * * *
1646401 TTCGCGTTGCGATAGTCGACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAGT
1 TTCGCGTTGCGAT-TTAGA-TATCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
*
1646464 TCGCATTGCGATAGTCG-AC
63 TCGCATTGCGATAGTCGAAG
* *
1646483 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTT
1 T-TCGCGTTGCGATTTAGATA-TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTT
* *
1646548 TGCATTACGATAGTCGAAG
64 CGCATTGCGATAGTCGAAG
1646567 TTCGCGTTGCGA
1 TTCGCGTTGCGA
1646579 ATTTGGAAAC
Statistics
Matches: 221, Mismatches: 26, Indels: 28
0.80 0.09 0.10
Matches are distributed among these distances:
81 3 0.01
82 65 0.29
83 131 0.59
84 20 0.09
85 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (82 bp):
TTCGCGTTGCGATTTAGATATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCG
CATTGCGATAGTCGAAG
Found at i:1652894 original size:507 final size:507
Alignment explanation
Indices: 1651941--1652958 Score: 2018
Period size: 507 Copynumber: 2.0 Consensus size: 507
1651931 AATTGTGCTT
1651941 CATGGTTGAAGGGCTTAATCACTTTTGGCCTACATTCTTTTCTTCTTTTGTTTGGCTTTGTAGGC
1 CATGGTTGAAGGGCTTAATCACTTTTGGCCTACATTCTTTTCTTCTTTTGTTTGGCTTTGTAGGC
1652006 GCCTTTCCAAATGCTGTGGTGTCCAGCTGTTAATGAGTTGTCACGTGTGCTGTGTGCCTCTAGGC
66 GCCTTTCCAAATGCTGTGGTGTCCAGCTGTTAATGAGTTGTCACGTGTGCTGTGTGCCTCTAGGC
1652071 AGTGATGAAGGTTCCAGATTTTACTCATGCTTTCACACTTGAGGAGGTTCTGATGCATGCCTTCT
131 AGTGATGAAGGTTCCAGATTTTACTCATGCTTTCACACTTGAGGAGGTTCTGATGCATGCCTTCT
1652136 GTTACAATGGATTTGCTGAGTTTAGGCTTTGCGTATTAATCCTTATTTTTCAATAGAGAGAGCAA
196 GTTACAATGGATTTGCTGAGTTTAGGCTTTGCGTATTAATCCTTATTTTTCAATAGAGAGAGCAA
1652201 GGTTTTTAATTTTGAGGTCGTGGGATCGAATTTTACGGAGGGTATTTTATAATTCGGAAATCTCC
261 GGTTTTTAATTTTGAGGTCGTGGGATCGAATTTTACGGAGGGTATTTTATAATTCGGAAATCTCC
1652266 CACGGAAGCTGTTCTTAATCTGACGTTAGAGGCCAGCCTATTATCTTACTTCCCTCTTACCCCAT
326 CACGGAAGCTGTTCTTAATCTGACGTTAGAGGCCAGCCTATTATCTTACTTCCCTCTTACCCCAT
1652331 TATATATGAGAATAAAGATCAACTAATTTATTTTCAACAACTAATGTCAACGTAAGAAAATATTT
391 TATATATGAGAATAAAGATCAACTAATTTATTTTCAACAACTAATGTCAACGTAAGAAAATATTT
*
1652396 CAACATTTTCATAAATTCGAAATATAAAACCGACATAAATTAATTAGCCCTC
456 CAACATTTTCATAAATTCGAAATATAAAACCGACATAAATTAATTAGACCTC
1652448 CATGGTTGAAGGGCTTAATCACTTTTGGCCTACATTCTTTTCTTCTTTTGTTTGGCTTTGTAGGC
1 CATGGTTGAAGGGCTTAATCACTTTTGGCCTACATTCTTTTCTTCTTTTGTTTGGCTTTGTAGGC
1652513 GCCTTTCCAAATGCTGTGGTGTCCAGCTGTTAATGAGTTGTCACGTGTGCTGTGTGCCTCTAGGC
66 GCCTTTCCAAATGCTGTGGTGTCCAGCTGTTAATGAGTTGTCACGTGTGCTGTGTGCCTCTAGGC
1652578 AGTGATGAAGGTTCCAGATTTTACTCATGCTTTCACACTTGAGGAGGTTCTGATGCATGCCTTCT
131 AGTGATGAAGGTTCCAGATTTTACTCATGCTTTCACACTTGAGGAGGTTCTGATGCATGCCTTCT
*
1652643 GTTACAATGGATTTGCTGAGTTTAGGCTTTGCGTATTAATCCTTATTTTTCAATATAGAGAGCAA
196 GTTACAATGGATTTGCTGAGTTTAGGCTTTGCGTATTAATCCTTATTTTTCAATAGAGAGAGCAA
1652708 GGTTTTTAATTTTGAGGTCGTGGGATCGAATTTTACGGAGGGTATTTTATAATTCGGAAATCTCC
261 GGTTTTTAATTTTGAGGTCGTGGGATCGAATTTTACGGAGGGTATTTTATAATTCGGAAATCTCC
1652773 CACGGAAGCTGTTCTTAATCTGACGTTAGAGGCCAGCCTATTATCTTACTTCCCTCTTACCCCAT
326 CACGGAAGCTGTTCTTAATCTGACGTTAGAGGCCAGCCTATTATCTTACTTCCCTCTTACCCCAT
1652838 TATATATGAGAATAAAGATCAACTAATTTATTTTCAACAACTAATGTCAACGTAAGAAAATATTT
391 TATATATGAGAATAAAGATCAACTAATTTATTTTCAACAACTAATGTCAACGTAAGAAAATATTT
1652903 CAACATTTTCATAAATTCGAAATATAAAACCGACATAAATTAATTAGACCTC
456 CAACATTTTCATAAATTCGAAATATAAAACCGACATAAATTAATTAGACCTC
1652955 CATG
1 CATG
1652959 TTAAAATTTG
Statistics
Matches: 509, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
507 509 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (507 bp):
CATGGTTGAAGGGCTTAATCACTTTTGGCCTACATTCTTTTCTTCTTTTGTTTGGCTTTGTAGGC
GCCTTTCCAAATGCTGTGGTGTCCAGCTGTTAATGAGTTGTCACGTGTGCTGTGTGCCTCTAGGC
AGTGATGAAGGTTCCAGATTTTACTCATGCTTTCACACTTGAGGAGGTTCTGATGCATGCCTTCT
GTTACAATGGATTTGCTGAGTTTAGGCTTTGCGTATTAATCCTTATTTTTCAATAGAGAGAGCAA
GGTTTTTAATTTTGAGGTCGTGGGATCGAATTTTACGGAGGGTATTTTATAATTCGGAAATCTCC
CACGGAAGCTGTTCTTAATCTGACGTTAGAGGCCAGCCTATTATCTTACTTCCCTCTTACCCCAT
TATATATGAGAATAAAGATCAACTAATTTATTTTCAACAACTAATGTCAACGTAAGAAAATATTT
CAACATTTTCATAAATTCGAAATATAAAACCGACATAAATTAATTAGACCTC
Found at i:1659327 original size:2 final size:2
Alignment explanation
Indices: 1659320--1659344 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1659310 ATGAAACTAC
1659320 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 A
1659345 GAGCTTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1660284 original size:16 final size:18
Alignment explanation
Indices: 1660253--1660289 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
1660243 TCAATCAATA
1660253 AAATAAATATTAATAATT
1 AAATAAATATTAATAATT
1660271 AAATAAA-A-TAATAATT
1 AAATAAATATTAATAATT
1660287 AAA
1 AAA
1660290 GAATCGAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 1 0.05
18 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAAATATTAATAATT
Found at i:1660589 original size:3 final size:3
Alignment explanation
Indices: 1660583--1660649 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
1660573 ATTTTTGTTT
**
1660583 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
1660628 -TA TTA TTA TTA -TA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1660650 CAAAGCCCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.11
3 45 0.83
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1661958 original size:16 final size:17
Alignment explanation
Indices: 1661932--1661971 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1661922 TTATTTACAA
1661932 TATTATTTTATCATTAT
1 TATTATTTTATCATTAT
*
1661949 TATT-TTTTATTATTAT
1 TATTATTTTATCATTAT
*
1661965 TTTTATT
1 TATTATT
1661972 ATTTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTTATCATTAT
Found at i:1661960 original size:13 final size:13
Alignment explanation
Indices: 1661932--1661974 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
1661922 TTATTTACAA
*
1661932 TATTATTTTATCAT
1 TATTATTTT-TTAT
1661946 TATTATTTTTTAT
1 TATTATTTTTTAT
1661959 TATTA-TTTTTAT
1 TATTATTTTTTAT
1661971 TATT
1 TATT
1661975 TATATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 8 0.29
14 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTTTTTAT
Found at i:1661977 original size:16 final size:14
Alignment explanation
Indices: 1661932--1661974 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1661922 TTATTTACAA
*
1661932 TATTATTTTATCAT
1 TATTATTTTATTAT
1661946 TATTATTTT-TTAT
1 TATTATTTTATTAT
1661959 TATTATTTTTATTAT
1 TATTA-TTTTATTAT
1661974 T
1 T
1661975 TATATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:1661998 original size:18 final size:16
Alignment explanation
Indices: 1661975--1662009 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1661965 TTTTATTATT
1661975 TATATA-AATAAATATA
1 TATATATAATAAATA-A
1661991 TATATATAATAAATAA
1 TATATATAATAAATAA
1662007 TAT
1 TAT
1662010 TTGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:1662192 original size:20 final size:19
Alignment explanation
Indices: 1662159--1662208 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1662149 TAAATATCCT
1662159 ATTTTTTAAATTATATATTA
1 ATTTTTT-AATTATATATTA
* *
1662179 ATTGTTTTAATTATTTATTT
1 ATT-TTTTAATTATATATTA
1662199 ATTTTTTAAT
1 ATTTTTTAAT
1662209 ATCAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:1662819 original size:28 final size:26
Alignment explanation
Indices: 1662788--1662845 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
1662778 TAATTCTTTC
*
1662788 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA--TATTA
* * *
1662816 TTTTTATAATATTTATATGTATATTA
1 TTTTCAAAATATTTATATATATATTA
1662842 TTTT
1 TTTT
1662846 ATTAATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATATTTATATATATATTA
Found at i:1672120 original size:22 final size:22
Alignment explanation
Indices: 1672092--1672168 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
1672082 ATCTACACAC
1672092 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1672114 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1672136 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1672158 TTCAAAGATGA
1 TTCAAAGATGA
1672169 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1672944 original size:76 final size:76
Alignment explanation
Indices: 1672845--1673178 Score: 614
Period size: 76 Copynumber: 4.4 Consensus size: 76
1672835 CTATTTCCTA
*
1672845 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1672910 AGCCTTAGGGT
66 AGCCTTAGGGT
1672921 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1672986 AGCCTTAGGGT
66 AGCCTTAGGGT
1672997 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1673062 AGCCTTATGGT
66 AGCCTTAGGGT
* *
1673073 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGTGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1673138 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1673149 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
1673179 TTAGGACCTC
Statistics
Matches: 251, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 251 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1673346 original size:3 final size:3
Alignment explanation
Indices: 1673338--1673401 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
1673328 ATTTTTGTTT
* **
1673338 TTA TTA TTA TCA TTA AAA TTA TTA TTA TTA TTA -TA TATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
1673382 TTA TTA TTA -TA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1673402 CAAAGCCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1673361 original size:18 final size:20
Alignment explanation
Indices: 1673338--1673401 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1673328 ATTTTTGTTT
*
1673338 TTATTATTATCATTA-A-AA
1 TTATTATTATTATTATATAA
1673356 TTATTATTATTATTATATATA
1 TTATTATTATTATTATATA-A
1673377 TTA-TATTATTATTATATAA
1 TTATTATTATTATTATATAA
1673396 TTATTA
1 TTATTA
1673402 CAAAGCCCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
18 14 0.34
19 5 0.12
20 18 0.44
21 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATTATTATATAA
Found at i:1674669 original size:16 final size:17
Alignment explanation
Indices: 1674643--1674682 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1674633 TTATTTGCAA
1674643 TATTATTTTATCATTAT
1 TATTATTTTATCATTAT
*
1674660 TATT-TTTTATTATTAT
1 TATTATTTTATCATTAT
*
1674676 TTTTATT
1 TATTATT
1674683 ATTTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTTATCATTAT
Found at i:1674673 original size:13 final size:13
Alignment explanation
Indices: 1674643--1674685 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
1674633 TTATTTGCAA
*
1674643 TATTATTTTATCAT
1 TATTATTTT-TTAT
1674657 TATTATTTTTTAT
1 TATTATTTTTTAT
1674670 TATTA-TTTTTAT
1 TATTATTTTTTAT
1674682 TATT
1 TATT
1674686 TATATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 8 0.29
14 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTTTTTAT
Found at i:1674688 original size:16 final size:14
Alignment explanation
Indices: 1674643--1674685 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1674633 TTATTTGCAA
*
1674643 TATTATTTTATCAT
1 TATTATTTTATTAT
1674657 TATTATTTT-TTAT
1 TATTATTTTATTAT
1674670 TATTATTTTTATTAT
1 TATTA-TTTTATTAT
1674685 T
1 T
1674686 TATATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:1674898 original size:20 final size:19
Alignment explanation
Indices: 1674868--1674916 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1674858 AATATCCTAT
1674868 TTTTTTAAATTATATATTAA
1 TTTTTT-AATTATATATTAA
* *
1674888 TTGTTTTAATTATTTATTTA
1 TT-TTTTAATTATATATTAA
1674908 TTTTTTAAT
1 TTTTTTAAT
1674917 ATCAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 15 0.58
21 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTATATATTAA
Found at i:1675002 original size:27 final size:27
Alignment explanation
Indices: 1674972--1675026 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1674962 ATATTTATAA
*
1674972 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAAGATTTT-TTTCATAAATAT
* *
1674999 ATAAATTAAGATTTTTTTCATAATTAT
1 ATAAATAAAGATTTTTTTCATAAATAT
1675026 A
1 A
1675027 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAAATAAAGATTTTTTTCATAAATAT
Found at i:1676722 original size:19 final size:19
Alignment explanation
Indices: 1676698--1676738 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1676688 TCTTCAAGCC
* *
1676698 TTTCAACTAGGTTCTCTGT
1 TTTCAACTACGATCTCTGT
*
1676717 TTTCAATTACGATCTCTGT
1 TTTCAACTACGATCTCTGT
1676736 TTT
1 TTT
1676739 GTAAATTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (19 bp):
TTTCAACTACGATCTCTGT
Found at i:1680054 original size:2 final size:2
Alignment explanation
Indices: 1680047--1680109 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1680037 TCATAAAATT
1680047 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
1680089 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1680110 TACAAAATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1682816 original size:20 final size:20
Alignment explanation
Indices: 1682791--1682836 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1682781 GGGTTGCCAT
*
1682791 TTTTTGACAGAACGTGCGAA
1 TTTTTGACAGAACGTACGAA
*
1682811 TTTTTGACAGAACGTATGAA
1 TTTTTGACAGAACGTACGAA
1682831 TTTTTG
1 TTTTTG
1682837 CATTTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTTTGACAGAACGTACGAA
Found at i:1685548 original size:90 final size:89
Alignment explanation
Indices: 1685391--1685563 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
1685381 ACACACCCTT
1685391 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATCTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATCTA
* *
1685456 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
1685480 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATCT
1685545 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
1685564 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATCTA
ATTAATTGAAATTAAATAATCCTC
Found at i:1686908 original size:19 final size:19
Alignment explanation
Indices: 1686836--1686909 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
1686826 TTTATGGGTG
* * *
1686836 CAAAGTTTCGAAACTTTTG
1 CAAAGTTTCAAAACTCTTA
*
1686855 TAAAGTTTCAAAACTCTTAA
1 CAAAGTTTCAAAACTCTT-A
* * *
1686875 TAAAAATTTCTAAACTCTTA
1 -CAAAGTTTCAAAACTCTTA
*
1686895 CAAAGTTTCCAAACT
1 CAAAGTTTCAAAACT
1686910 AAGAACAATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 27 0.63
20 1 0.02
21 15 0.35
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.35
Consensus pattern (19 bp):
CAAAGTTTCAAAACTCTTA
Found at i:1687004 original size:20 final size:20
Alignment explanation
Indices: 1686979--1687023 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1686969 ATTTTTCATA
*
1686979 TTTAAAAAGTTTAAATAC-AT
1 TTTAAAAACTTTAAAT-CTAT
*
1686999 TTTAAACACTTTAAATCTAT
1 TTTAAAAACTTTAAATCTAT
1687019 TTTAA
1 TTTAA
1687024 TTAACTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAAAAACTTTAAATCTAT
Found at i:1687893 original size:2 final size:2
Alignment explanation
Indices: 1687888--1687912 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1687878 TTTTATGATC
1687888 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 A
1687913 ATCTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1692799 original size:3 final size:3
Alignment explanation
Indices: 1692791--1692858 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1692781 TATGCTACAG
1692791 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1692839 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
1692859 TGTAGTAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1701818 original size:2 final size:2
Alignment explanation
Indices: 1701811--1701842 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1701801 TTTTGTTTGA
1701811 AT AT AT AT AT AT AT AT -T 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 A
1701843 GGAATACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1701832 original size:13 final size:13
Alignment explanation
Indices: 1701814--1701839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1701804 TGTTTGAATA
1701814 TATATATATATAT
1 TATATATATATAT
1701827 TATATATATATAT
1 TATATATATATAT
1701840 ATAGGAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:1701832 original size:15 final size:15
Alignment explanation
Indices: 1701812--1701841 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1701802 TTTGTTTGAA
1701812 TATATATATATATAT
1 TATATATATATATAT
1701827 TATATATATATATAT
1 TATATATATATATAT
1701842 AGGAATACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:1705802 original size:47 final size:47
Alignment explanation
Indices: 1705732--1705836 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
1705722 ATTTTTATAG
* **
1705732 ATTTTGTTATTATTGGACTCTTTACC-GATTTTGATAAAGCACTACCA
1 ATTTTGTTATTATTGGACGCTTTACCGGA-TTTGATAAAAAACTACCA
* *
1705779 GTTTTGTTATTATT-GAGCGCTTTACCGGATTTGTTAAAAAACTACCA
1 ATTTTGTTATTATTGGA-CGCTTTACCGGATTTGATAAAAAACTACCA
1705826 ATTTTGTTATT
1 ATTTTGTTATT
1705837 TTTTCTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 2 0.04
47 46 0.92
48 2 0.04
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (47 bp):
ATTTTGTTATTATTGGACGCTTTACCGGATTTGATAAAAAACTACCA
Found at i:1705908 original size:21 final size:21
Alignment explanation
Indices: 1705882--1705926 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1705872 CTGAAAATGT
1705882 TAAAAA-AATTAATATTTTAAG
1 TAAAAATAA-TAATATTTTAAG
*
1705903 TAAAAATAATAATGTTTTAAG
1 TAAAAATAATAATATTTTAAG
1705924 TAA
1 TAA
1705927 TTTTTTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:1732708 original size:36 final size:36
Alignment explanation
Indices: 1732661--1732732 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1732651 TTATATATAT
1732661 ATATATATATAATGATATAAACATTGGTGGAGAATG
1 ATATATATATAATGATATAAACATTGGTGGAGAATG
1732697 ATATATATATAATGATATAAACATTGGTGGAGAATG
1 ATATATATATAATGATATAAACATTGGTGGAGAATG
1732733 CCTATATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (36 bp):
ATATATATATAATGATATAAACATTGGTGGAGAATG
Found at i:1736579 original size:28 final size:28
Alignment explanation
Indices: 1736539--1736595 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1736529 AAGAGCCAAT
* *
1736539 GGAGAGGTCGCCATGCAGTCTTATACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
1736567 GGAGAGGTCGCCATGCAGGCTTAGACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
1736595 G
1 G
1736596 TCGTACGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.37, T:0.18
Consensus pattern (28 bp):
GGAGAGGTCGCCATGCAGGCTTAGACGA
Found at i:1736664 original size:29 final size:29
Alignment explanation
Indices: 1736614--1736722 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
1736604 GCCAATAGAG
* *
1736614 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
1736643 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1736672 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
1736701 AGGTCGCCATGTAATCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
1736723 CCATTCCCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1736830 original size:27 final size:27
Alignment explanation
Indices: 1736798--1736853 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1736788 CCTACAGCTC
1736798 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
1736825 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
1736852 CC
1 CC
1736854 GTGAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:1737026 original size:27 final size:23
Alignment explanation
Indices: 1736999--1737044 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1736989 AAAAGAAAGA
1736999 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1737022 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1737045 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:1737059 original size:25 final size:23
Alignment explanation
Indices: 1736999--1737059 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1736989 AAAAGAAAGA
**
1736999 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
1737022 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
1737045 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
1737060 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:1737302 original size:46 final size:48
Alignment explanation
Indices: 1737239--1737330 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
1737229 TTATATAGTT
*
1737239 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
*
1737284 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1737331 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 15 0.37
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:1737407 original size:32 final size:33
Alignment explanation
Indices: 1737371--1737447 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
1737361 TTAGTTAGTA
1737371 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
1737403 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
1737437 ATTTTATTAGT
1 AGTTTATTAGT
1737448 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:1739815 original size:28 final size:28
Alignment explanation
Indices: 1739783--1739850 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
1739773 ATAATATATA
*
1739783 TAATAATATATAACTTAAACTAATAAAC
1 TAATAATATATAACTTAAACTAACAAAC
1739811 TAAT-ATAATATAACTTAAACTAACAAAC
1 TAATAAT-ATATAACTTAAACTAACAAAC
*
1739839 TAATAATTTATA
1 TAATAATATATA
1739851 CTAACAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 32 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATAATATATAACTTAAACTAACAAAC
Found at i:1739853 original size:21 final size:21
Alignment explanation
Indices: 1739820--1739868 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1739810 CTAATATAAT
1739820 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1739841 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1739862 ATTAACT
1 A-TAACT
1739869 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1739993 original size:14 final size:15
Alignment explanation
Indices: 1739971--1740003 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1739961 ATGTTTGAGC
1739971 CTTTATCTT-CTTTT
1 CTTTATCTTCCTTTT
*
1739985 CTTTTTCTTCCTTTT
1 CTTTATCTTCCTTTT
1740000 CTTT
1 CTTT
1740004 CTCTCGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTATCTTCCTTTT
Found at i:1740522 original size:29 final size:29
Alignment explanation
Indices: 1740480--1740541 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1740470 AAATACACAC
*
1740480 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1740509 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1740538 AGGT
1 AGGT
1740542 TACTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:1746578 original size:17 final size:17
Alignment explanation
Indices: 1746541--1746577 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1746531 ACATAATATT
*
1746541 AAAACACTCGAACTCAA
1 AAAACACTCAAACTCAA
1746558 AAAAC-CTCAAACTCAA
1 AAAACACTCAAACTCAA
1746574 AAAA
1 AAAA
1746578 AATCAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.59, C:0.27, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAACACTCAAACTCAA
Found at i:1747090 original size:14 final size:14
Alignment explanation
Indices: 1747070--1747103 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1747060 TGGTAGTATG
1747070 CATTTTAAATTATT
1 CATTTTAAATTATT
* *
1747084 TATTTTAATTTATT
1 CATTTTAAATTATT
1747098 CATTTT
1 CATTTT
1747104 TTAGTAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
CATTTTAAATTATT
Found at i:1747424 original size:21 final size:21
Alignment explanation
Indices: 1747400--1747473 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
1747390 TATTTTAGGG
1747400 TTTAGGGTTTAGTATTAATGA
1 TTTAGGGTTTAGTATTAATGA
*
1747421 TTTAAGGTTTA-TGATTTAA-GA
1 TTTAGGGTTTAGT-A-TTAATGA
* * *
1747442 TTTAGGATTTAGTGTTTAT-A
1 TTTAGGGTTTAGTATTAATGA
1747462 GTTTAGGGTTTA
1 -TTTAGGGTTTA
1747474 AGGTTCATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 5 0.12
21 32 0.76
22 5 0.12
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTAGTATTAATGA
Done.