Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1592455 original size:85 final size:86
Alignment explanation
Indices: 1592354--1592576 Score: 233
Period size: 85 Copynumber: 2.6 Consensus size: 86
1592344 AATTATTTTC
* * * *
1592354 TTTTCAATCTTATTTTTTA-TATTTATAATTGATGATCCT-ATGTTTTTCAATCCCACTTTGTAC
1 TTTTTAATCTCATTTTTTACT-TTTATAATTGAGGATCATAAT-TTTTTCAATCCCACTTTGTAC
*
1592417 ATT-TATAATTGA-GCTC-GTGATT
64 -TTATATAATTGAGGC-CACTGATT
* * * *
1592439 TTTTTAATCTCATTTTTTACTTTTATAGTTGAGGCTCATAATTTTTTCAATCCCATTTTTTACTT
1 TTTTTAATCTCATTTTTTACTTTTATAATTGAGGATCATAATTTTTTCAATCCCACTTTGTACTT
*
1592504 ATATAATTTAGGCCACTGATT
66 ATATAATTGAGGCCACTGATT
* * * *
1592525 TTTTTAATCTCACTTTTTACCTTAATAATTGAGG-TCCCTAATTTTTTCAATC
1 TTTTTAATCTCATTTTTTACTTTTATAATTGAGGAT-CATAATTTTTTCAATC
1592577 ATACTTTTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
84 2 0.02
85 60 0.51
86 55 0.47
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (86 bp):
TTTTTAATCTCATTTTTTACTTTTATAATTGAGGATCATAATTTTTTCAATCCCACTTTGTACTT
ATATAATTGAGGCCACTGATT
Found at i:1592557 original size:86 final size:84
Alignment explanation
Indices: 1592396--1592600 Score: 225
Period size: 86 Copynumber: 2.4 Consensus size: 84
1592386 TGATCCTATG
* * * * * *
1592396 TTTTTCAATCCCACTTTGTACATTTATAATTGAGCTCGTGATTTTTTTAATCTCATTTTTTACTT
1 TTTTTCAATCCCATTTTTTAC-TTTATAATTTAGCTCCTGATTTTTTTAATCTCACTTTTTACCT
* *
1592461 TTATAGTTGAGG-CTCATAAT
65 TAATAATTGAGGTC-CATAAT
1592481 TTTTTCAATCCCATTTTTTACTTATATAATTTAGGC-CACTGATTTTTTTAATCTCACTTTTTAC
1 TTTTTCAATCCCATTTTTTACTT-TATAATTTA-GCTC-CTGATTTTTTTAATCTCACTTTTTAC
*
1592545 CTTAATAATTGAGGTCCCTAAT
63 CTTAATAATTGAGGTCCATAAT
** *
1592567 TTTTTCAATCATACTTTTTTACTTTTATAGTTTA
1 TTTTTCAATCCCA-TTTTTTAC-TTTATAATTTA
1592601 AGCCCCTAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
84 2 0.02
85 28 0.27
86 53 0.52
87 17 0.17
88 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (84 bp):
TTTTTCAATCCCATTTTTTACTTTATAATTTAGCTCCTGATTTTTTTAATCTCACTTTTTACCTT
AATAATTGAGGTCCATAAT
Found at i:1592608 original size:44 final size:43
Alignment explanation
Indices: 1592354--1592612 Score: 165
Period size: 43 Copynumber: 6.0 Consensus size: 43
1592344 AATTATTTTC
* **
1592354 TTTTCAATCTTA-TTTTTTA-TATTTATAATTGATGATCCT-ATGT
1 TTTTCAATC-TACTTTTTTACT-TTTATAATTGAGGCCCCTAAT-T
* * * * * *
1592397 TTTTCAATCCCAC-TTTGTACATTTATAATTGA-GCTCGTGATT
1 TTTTCAAT-CTACTTTTTTACTTTTATAATTGAGGCCCCTAATT
* * * *
1592439 TTTTTAATCT-CATTTTTTACTTTTATAGTTGAGGCTCATAATT
1 TTTTCAATCTAC-TTTTTTACTTTTATAATTGAGGCCCCTAATT
* * * * *
1592482 TTTTCAATC-CCATTTTTTACTTATATAATTTAGGCCACTGATT
1 TTTTCAATCTAC-TTTTTTACTTTTATAATTGAGGCCCCTAATT
* * * *
1592525 TTTTTAATCTCAC-TTTTTACCTTAATAATTGAGGTCCCTAATT
1 TTTTCAATCT-ACTTTTTTACTTTTATAATTGAGGCCCCTAATT
* * *
1592568 TTTTCAATCATACTTTTTTACTTTTATAGTTTAAGCCCCTAATT
1 TTTTCAATC-TACTTTTTTACTTTTATAATTGAGGCCCCTAATT
1592612 T
1 T
1592613 AATCATTTTT
Statistics
Matches: 168, Mismatches: 36, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 28 0.17
43 110 0.65
44 27 0.16
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (43 bp):
TTTTCAATCTACTTTTTTACTTTTATAATTGAGGCCCCTAATT
Found at i:1593076 original size:22 final size:21
Alignment explanation
Indices: 1593041--1593092 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1593031 ATAATATTTT
1593041 TTTAGAG-TT-AAAGTTCAAG
1 TTTAGAGTTTAAAAGTTCAAG
* *
1593060 ATTTAGTGTTTAAAAGTTGAAG
1 -TTTAGAGTTTAAAAGTTCAAG
1593082 TTTAGAGTTTA
1 TTTAGAGTTTA
1593093 GTATTTAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 9 0.33
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (21 bp):
TTTAGAGTTTAAAAGTTCAAG
Found at i:1594418 original size:6 final size:6
Alignment explanation
Indices: 1594407--1594481 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
1594397 TCTCGTCTCG
** **
1594407 GGTCGT GGTCGT GGTCGT GGTAAT GGTAAT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
1594455 GGTAAT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1594482 AATGGTAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.08, C:0.12, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1594487 original size:12 final size:12
Alignment explanation
Indices: 1594430--1594487 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
1594420 GTCGTGGTAA
1594430 TGGTAATGGTCG
1 TGGTAATGGTCG
**
1594442 TGGTCGTGGTCG
1 TGGTAATGGTCG
1594454 TGGTAATGGTCG
1 TGGTAATGGTCG
**
1594466 TGGTCGTGGTCG
1 TGGTAATGGTCG
1594478 TGGTAATGGT
1 TGGTAATGGT
1594488 AATGGTAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.10, C:0.10, G:0.45, T:0.34
Consensus pattern (12 bp):
TGGTAATGGTCG
Found at i:1594493 original size:24 final size:24
Alignment explanation
Indices: 1594412--1594487 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
1594402 TCTCGGGTCG
**
1594412 TGGTCGTGGTCGTGGTAATGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
1594436 TGGTCGTGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
1594460 TGGTCGTGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
1594484 TGGT
1 TGGT
1594488 AATGGTAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.11, C:0.11, G:0.45, T:0.34
Consensus pattern (24 bp):
TGGTCGTGGTCGTGGTCGTGGTAA
Found at i:1594625 original size:21 final size:21
Alignment explanation
Indices: 1594599--1594649 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1594589 GAAATGGAAA
1594599 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1594620 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1594641 ATCGCAACG
1 ATCGCAACG
1594650 CGATTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:1596232 original size:18 final size:20
Alignment explanation
Indices: 1596199--1596238 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1596189 CCCTACTTGA
*
1596199 TTAAATATTTAATATTT-TT
1 TTAAATATTAAATATTTATT
1596218 TTAAAT-TTAAATATTTATT
1 TTAAATATTAAATATTTATT
1596237 TT
1 TT
1596239 TTGCATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAATATTAAATATTTATT
Found at i:1599663 original size:12 final size:12
Alignment explanation
Indices: 1599637--1599678 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1599627 TAATAAATTG
1599637 AAATAAA-AGAA
1 AAATAAAGAGAA
*
1599648 AAATAAAGATAA
1 AAATAAAGAGAA
1599660 AAATAAAG-GAA
1 AAATAAAGAGAA
1599671 AAACTAAA
1 AAA-TAAA
1599679 TGATTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (12 bp):
AAATAAAGAGAA
Found at i:1601669 original size:60 final size:60
Alignment explanation
Indices: 1601591--1601709 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
1601581 CAAGTGGTCA
* * * *
1601591 TTTTATAACTTTTGATAGTC-GAATGACTCAACAGAATAACATGTCATAGTTGAGAGACCG
1 TTTTATAACTTTTAATAGTCGGAA-GACTCAACAAAATAACATCTCATAGTCGAGAGACCG
* * * *
1601651 TTTTGTAACTTTTAATAGTCGGAAGACTTAACAAAATAATATCTTATAGTCGAGAGACC
1 TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACC
1601710 ATTCGTGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
60 47 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACCG
Found at i:1611320 original size:24 final size:24
Alignment explanation
Indices: 1611288--1611336 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1611278 TTTTAACATG
1611288 TAGCTTAAGCTCAAACAAATGACT
1 TAGCTTAAGCTCAAACAAATGACT
1611312 TAGCTTAAGCTCAAACAAATGACT
1 TAGCTTAAGCTCAAACAAATGACT
1611336 T
1 T
1611337 TTTGTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (24 bp):
TAGCTTAAGCTCAAACAAATGACT
Found at i:1613909 original size:92 final size:92
Alignment explanation
Indices: 1613750--1613933 Score: 350
Period size: 92 Copynumber: 2.0 Consensus size: 92
1613740 CTTTTGTTCT
*
1613750 TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGGCGGCATGGTCAATCTTTACAG
1 TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
1613815 AAAGTAAACAGAGGCATGATACTAGCC
66 AAAGTAAACAGAGGCATGATACTAGCC
*
1613842 TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGACGGCATGGTCAATCTTTAGAG
1 TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
1613907 AAAGTAAACAGAGGCATGATACTAGCC
66 AAAGTAAACAGAGGCATGATACTAGCC
1613934 CCTTTAGTAG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
AAAGTAAACAGAGGCATGATACTAGCC
Found at i:1615309 original size:20 final size:20
Alignment explanation
Indices: 1615284--1615328 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1615274 AGTTTAAGTC
1615284 GGTTAACTTTTTTGATTTAG
1 GGTTAACTTTTTTGATTTAG
1615304 GGTTAACTTTTTTGATTTAG
1 GGTTAACTTTTTTGATTTAG
1615324 GGTTA
1 GGTTA
1615329 GGGTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.53
Consensus pattern (20 bp):
GGTTAACTTTTTTGATTTAG
Found at i:1622098 original size:60 final size:59
Alignment explanation
Indices: 1622023--1622144 Score: 165
Period size: 60 Copynumber: 2.1 Consensus size: 59
1622013 GTCTCCTGAT
* * *
1622023 TATAGGGTGATGCTTTGTTGAGTCTCC-TGACTATTAAAAGTTATAAAATGATCACTCGAC
1 TATAGAGTGATGCTTTGTTAAGTC-CCATGACTATTAAAAGTTA-AAAATGATCACTCAAC
* * *
1622083 TATAGAGTGTTGCTTTGTTAAGTCCCATGACTATTAAAAGTTACAAATGGTCACTCAAC
1 TATAGAGTGATGCTTTGTTAAGTCCCATGACTATTAAAAGTTAAAAATGATCACTCAAC
1622142 TAT
1 TAT
1622145 TCATATGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 18 0.33
60 37 0.67
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (59 bp):
TATAGAGTGATGCTTTGTTAAGTCCCATGACTATTAAAAGTTAAAAATGATCACTCAAC
Found at i:1624620 original size:17 final size:17
Alignment explanation
Indices: 1624600--1624637 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1624590 GAAAGTCAAC
* *
1624600 GGTCAACGGTTGGGTCG
1 GGTCAACAGTCGGGTCG
1624617 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1624634 GGTC
1 GGTC
1624638 GGTCAGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1624649 original size:9 final size:9
Alignment explanation
Indices: 1624637--1624726 Score: 81
Period size: 9 Copynumber: 9.4 Consensus size: 9
1624627 CGGGTCGGGT
*
1624637 CGGTCAGAC
1 CGGTCAAAC
1624646 CGGTCAAAC
1 CGGTCAAAC
**
1624655 CGGTTCTGAC
1 CGG-TCAAAC
1624665 CGGTCAAAC
1 CGGTCAAAC
*
1624674 CGGTTGAAAC
1 CGG-TCAAAC
1624684 CGGTCAAAC
1 CGGTCAAAC
1624693 CGGTCAGAAC
1 CGGTCA-AAC
*
1624703 CGGTTGAAAAC
1 CGG-T-CAAAC
*
1624714 CGGTTAAAC
1 CGGTCAAAC
1624723 CGGT
1 CGGT
1624727 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
9 37 0.55
10 22 0.33
11 7 0.10
12 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:1624667 original size:19 final size:19
Alignment explanation
Indices: 1624640--1624706 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
1624630 GTCGGGTCGG
1624640 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
1624659 TCTGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
1624678 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
1624696 TCAGAACCGGT
1 TCAG-ACCGGT
1624707 TGAAAACCGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 2 0.05
19 39 0.95
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1624695 original size:38 final size:39
Alignment explanation
Indices: 1624644--1624726 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 39
1624634 GGTCGGTCAG
* *
1624644 ACCGGTCAAACCGGTTCTG-ACCGG-T-CAAACCGGTTGAA
1 ACCGGTCAAACCGG-TCAGAACCGGTTGAAAACCGGTT-AA
1624682 ACCGGTCAAACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGGTCAGAACCGGTTGAAAACCGGTTAA
1624721 ACCGGT
1 ACCGGT
1624727 TTCCAGCAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
37 3 0.08
38 19 0.47
39 9 0.22
40 9 0.22
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (39 bp):
ACCGGTCAAACCGGTCAGAACCGGTTGAAAACCGGTTAA
Found at i:1629466 original size:2 final size:2
Alignment explanation
Indices: 1629459--1629494 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1629449 TCCATCTCTT
1629459 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
1629495 AGGATCTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1631643 original size:29 final size:29
Alignment explanation
Indices: 1631599--1631783 Score: 134
Period size: 29 Copynumber: 6.4 Consensus size: 29
1631589 TATCTTAACA
1631599 TTAAAAAATATATTTTATTTTATATTAAT
1 TTAAAAAATATATTTTATTTTATATTAAT
** * *
1631628 TTATTAAATATATTTTAAGTTTAT-TTTAT
1 TTAAAAAATATATTTT-ATTTTATATTAAT
* *
1631657 TTAAAAAATATATTTTACTCTTATTTTAA-
1 TTAAAAAATATATTTTA-TTTTATATTAAT
* * *
1631686 CTAAAAAATATATCTTATTCTTATATTACCT
1 TTAAAAAATATATTTTATT-TTATATTA-AT
* * *
1631717 TT-AAAAATATATCTTATCCTTATATTAAC
1 TTAAAAAATATATTTTAT-TTTATATTAAT
*
1631746 TT-AAAAATAGA---T-TTTTATATTAACT
1 TTAAAAAATATATTTTATTTTATATTAA-T
*
1631771 TTTAAAAATATAT
1 TTAAAAAATATAT
1631784 CTTAAATTAA
Statistics
Matches: 124, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
24 9 0.07
25 3 0.02
26 9 0.07
28 2 0.02
29 68 0.55
30 32 0.26
31 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (29 bp):
TTAAAAAATATATTTTATTTTATATTAAT
Found at i:1631739 original size:59 final size:55
Alignment explanation
Indices: 1631660--1631787 Score: 143
Period size: 59 Copynumber: 2.3 Consensus size: 55
1631650 ATTTTATTTA
* * *
1631660 AAAAATATATTTTACTCTTATTTTAACTAAAAAATATATCTTATTCTTATATT-ACCTTT
1 AAAAATATATCTTACTCTTATATTAACTAAAAAATAGA---T-TT-TTATATTAACCTTT
* *
1631719 AAAAATATATCTTA-TCCTTATATTAACTTAAAAATAGATTTTTATATTAACTTTT
1 AAAAATATATCTTACT-CTTATATTAACTAAAAAATAGATTTTTATATTAACCTTT
1631774 AAAAATATATCTTA
1 AAAAATATATCTTA
1631788 AATTAAAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
54 7 0.11
55 21 0.34
56 1 0.02
58 1 0.02
59 32 0.52
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (55 bp):
AAAAATATATCTTACTCTTATATTAACTAAAAAATAGATTTTTATATTAACCTTT
Found at i:1634551 original size:18 final size:18
Alignment explanation
Indices: 1634530--1634569 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1634520 AGACCCGGAG
*
1634530 GATGAGGAGGACGATGAA
1 GATGACGAGGACGATGAA
* *
1634548 GATGACGAGGATGATGAT
1 GATGACGAGGACGATGAA
1634566 GATG
1 GATG
1634570 GAGGTGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.17
Consensus pattern (18 bp):
GATGACGAGGACGATGAA
Found at i:1635759 original size:13 final size:13
Alignment explanation
Indices: 1635722--1635760 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1635712 TCGACCCGAC
**
1635722 TCGTTGACTTTAA
1 TCGTTGACTTTTT
1635735 TCGTTGACTTTTT
1 TCGTTGACTTTTT
1635748 TCGTTGACTTTTT
1 TCGTTGACTTTTT
1635761 CGATGACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.56
Consensus pattern (13 bp):
TCGTTGACTTTTT
Found at i:1635761 original size:12 final size:12
Alignment explanation
Indices: 1635722--1635768 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
1635712 TCGACCCGAC
*
1635722 TCGTTGACTTTAA
1 TCGTTGACTTT-T
1635735 TCGTTGACTTTTT
1 TCGTTGAC-TTTT
1635748 TCGTTGACTTTT
1 TCGTTGACTTTT
*
1635760 TCGATGACT
1 TCGTTGACT
1635769 GTTGACTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 12 0.39
13 16 0.52
14 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (12 bp):
TCGTTGACTTTT
Found at i:1636388 original size:30 final size:30
Alignment explanation
Indices: 1636346--1636443 Score: 133
Period size: 30 Copynumber: 3.3 Consensus size: 30
1636336 TTCTAATTAG
* *
1636346 GCATGGGATTAATTCCACGTTATGACATCT
1 GCATGAGATTAATTCCACGTTCTGACATCT
* * *
1636376 ACATGAGATTAATTCCTCTTTCTGACATCT
1 GCATGAGATTAATTCCACGTTCTGACATCT
* *
1636406 GCATGAGATTAATTCCCCGTTCTGACATTT
1 GCATGAGATTAATTCCACGTTCTGACATCT
1636436 GCATGAGA
1 GCATGAGA
1636444 ATATATCTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (30 bp):
GCATGAGATTAATTCCACGTTCTGACATCT
Found at i:1636458 original size:30 final size:30
Alignment explanation
Indices: 1636346--1636459 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 30
1636336 TTCTAATTAG
* * *
1636346 GCATGGGATTAATT-CCACGTTATGACATCT
1 GCATGAGAATAATTCCCA-GTTCTGACATCT
* * *
1636376 ACATGAGATTAATTCCTC-TTTCTGACATCT
1 GCATGAGAATAATTCC-CAGTTCTGACATCT
* * *
1636406 GCATGAGATTAATTCCCCGTTCTGACATTT
1 GCATGAGAATAATTCCCAGTTCTGACATCT
*
1636436 GCATGAGAAT-ATATCTCAGTTCTG
1 GCATGAGAATAAT-TCCCAGTTCTG
1636460 TTTCTGTTGG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.04
30 65 0.93
31 1 0.01
32 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (30 bp):
GCATGAGAATAATTCCCAGTTCTGACATCT
Found at i:1636656 original size:26 final size:26
Alignment explanation
Indices: 1636622--1636711 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1636612 ATATCTAAAT
1636622 TTTAATATTGTTCGATTAATATTTTG
1 TTTAATATTGTTCGATTAATATTTTG
* * * *
1636648 TTTATTATT-TTACG-GTAAAATATCTG
1 TTTAATATTGTT-CGATTAATAT-TTTG
*
1636674 AATTTTAATATTGTTCGATTATTATTTTG
1 ---TTTAATATTGTTCGATTAATATTTTG
*
1636703 TTTATTATT
1 TTTAATATT
1636712 TTATGTTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 7 0.15
26 21 0.45
29 13 0.28
30 6 0.13
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTAATATTGTTCGATTAATATTTTG
Found at i:1636672 original size:55 final size:55
Alignment explanation
Indices: 1636606--1636714 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
1636596 ACATTCTGCT
1636606 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
1 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
* *
1636661 GGTAAAATATCTGAATTTTAATATTGTTCGATTATTATTTTGTTTATTATTTTA
1 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTA
1636715 TGTTTGAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (55 bp):
GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
Found at i:1638242 original size:23 final size:23
Alignment explanation
Indices: 1638216--1638259 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1638206 TATGATCGAC
1638216 TCGACCCGTAGACTTTGACTGAA
1 TCGACCCGTAGACTTTGACTGAA
*
1638239 TCGACCCGTTGACTTTGACTG
1 TCGACCCGTAGACTTTGACTG
1638260 TTGACTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (23 bp):
TCGACCCGTAGACTTTGACTGAA
Found at i:1638899 original size:30 final size:30
Alignment explanation
Indices: 1638865--1638965 Score: 175
Period size: 30 Copynumber: 3.4 Consensus size: 30
1638855 TTCTAATTAG
**
1638865 GCATGGGATTAATTCCCTGTTCTGACATCT
1 GCATGGGATTAATTCCCAATTCTGACATCT
1638895 GCATGGGATTAATTCCCAATTCTGACATCT
1 GCATGGGATTAATTCCCAATTCTGACATCT
1638925 GCATGGGATTAATTCCCAATTCTGACATCT
1 GCATGGGATTAATTCCCAATTCTGACATCT
*
1638955 GCATGAGATTA
1 GCATGGGATTA
1638966 TATCTCCATT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (30 bp):
GCATGGGATTAATTCCCAATTCTGACATCT
Found at i:1649754 original size:21 final size:22
Alignment explanation
Indices: 1649730--1649776 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1649720 TACTATAATT
1649730 AATTTATAT-ATTTTCTTTA-AA
1 AATTTATATAATTTT-TTTACAA
1649751 AATTTATATAATTTTTTTACAA
1 AATTTATATAATTTTTTTACAA
1649773 AATT
1 AATT
1649777 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTTATATAATTTTTTTACAA
Found at i:1654538 original size:2 final size:2
Alignment explanation
Indices: 1654533--1654601 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
1654523 ATACATACAC
1654533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1654575 AT AC AT AC AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1654602 GTTGTTAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1654703 original size:9 final size:9
Alignment explanation
Indices: 1654689--1654722 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1654679 ATATTATTAG
1654689 TAAAAAATA
1 TAAAAAATA
1654698 TAAAAAATA
1 TAAAAAATA
*
1654707 TATAAAAATT
1 TA-AAAAATA
1654717 TAAAAA
1 TAAAAA
1654723 TTTTACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAAAATA
Found at i:1654834 original size:3 final size:3
Alignment explanation
Indices: 1654826--1654866 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1654816 GGAAGAGAGC
1654826 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1654867 ATCTTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1662949 original size:16 final size:17
Alignment explanation
Indices: 1662915--1662952 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1662905 GCATTTTAAT
* *
1662915 TTTTATATTTTTTCTAA
1 TTTTATATTTTTGCAAA
1662932 TTTT-TATTTTTGCAAA
1 TTTTATATTTTTGCAAA
1662948 TTTTA
1 TTTTA
1662953 AGTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATATTTTTGCAAA
Found at i:1689997 original size:42 final size:42
Alignment explanation
Indices: 1689946--1690162 Score: 375
Period size: 42 Copynumber: 5.2 Consensus size: 42
1689936 CATATTCGCA
* *
1689946 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
* *
1689988 TTGCGATAGTCGAAGTTCGTGTTGCGATTCATTCC-AATTCG
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
1690029 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCG
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
1690070 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
*
1690112 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTTCAAATTCG
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
1690154 TTGCGATAG
1 TTGCGATAG
1690163 TCCAAATATT
Statistics
Matches: 169, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
41 80 0.47
42 89 0.53
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (42 bp):
TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
Found at i:1690035 original size:83 final size:84
Alignment explanation
Indices: 1689946--1690164 Score: 379
Period size: 83 Copynumber: 2.6 Consensus size: 84
1689936 CATATTCGCA
* * *
1689946 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGTGTT
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1690011 GCGATTCATTCC-AATTCG
66 GCGATTCATTCCAAATTCG
*
1690029 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTTGCGATAGGCGAAGTTCGCGTT
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1690093 GCGATTCATTCCAAATTCG
66 GCGATTCATTCCAAATTCG
*
1690112 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTTCAAATTCGTTGCGATAGTC
1 TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGATAGTC
1690165 CAAATATTGC
Statistics
Matches: 128, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
82 39 0.30
83 73 0.57
84 16 0.12
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (84 bp):
TTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTCATTCCAAATTCG
Found at i:1691050 original size:19 final size:19
Alignment explanation
Indices: 1691026--1691093 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
1691016 CAAATGCAAT
1691026 ATTTGGACTATCGCAACGA
1 ATTTGGACTATCGCAACGA
*
1691045 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* *
1691068 ATTTCGCCTATCGCAACGA
1 ATTTGGACTATCGCAACGA
1691087 ATTTGGA
1 ATTTGGA
1691094 ATGAATCGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 16 0.41
21 14 0.36
23 9 0.23
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (19 bp):
ATTTGGACTATCGCAACGA
Found at i:1691160 original size:41 final size:42
Alignment explanation
Indices: 1691036--1691282 Score: 356
Period size: 42 Copynumber: 5.9 Consensus size: 42
1691026 ATTTGGACTA
* *
1691036 TCGCAACGAATTTGGAATGAATCGCAACGCGAATTTCGCCTA
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
*
1691078 TCGCAACGAATTTGGAATGAATCGCAACGCGAGCTTCGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* *
1691120 TCGCAACGAA-TTGGAATGAATCGCAATGCGAACTTTGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* *
1691161 TCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
** *
1691202 TCGCGTTGCGAA-TTGGAATGAATCGCAACGCGAGCTTCGCCTG
1 TCGC--AACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
*
1691245 TCGCAACGAATTTGGAATGAATCGCAACGTGAACTTCG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCG
1691283 ACTATCGCGT
Statistics
Matches: 183, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
41 73 0.40
42 74 0.40
43 36 0.20
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (42 bp):
TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
Found at i:1694503 original size:33 final size:33
Alignment explanation
Indices: 1694461--1694546 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
1694451 AGAAACTGCA
1694461 AAACCTGCAGCGGAAACCGAGCCAAAGATACCG
1 AAACCTGCAGCGGAAACCGAGCCAAAGATACCG
* * *
1694494 AAACCTGCAGCAGAAACTGAGCCAAGGATACCG
1 AAACCTGCAGCGGAAACCGAGCCAAAGATACCG
1694527 AAACCTGCAGCGGAAACCGA
1 AAACCTGCAGCGGAAACCGA
1694547 ACAGATGACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.40, C:0.29, G:0.24, T:0.07
Consensus pattern (33 bp):
AAACCTGCAGCGGAAACCGAGCCAAAGATACCG
Found at i:1705553 original size:24 final size:24
Alignment explanation
Indices: 1705526--1705626 Score: 175
Period size: 24 Copynumber: 4.2 Consensus size: 24
1705516 CTTTGGCTTA
*
1705526 TTTCTGCCACCTTTCATGTCTTCT
1 TTTCTACCACCTTTCATGTCTTCT
1705550 TTTCTACCACCTTTCATGTCTTCT
1 TTTCTACCACCTTTCATGTCTTCT
1705574 TTTCTACCACCTTTCATGTCTTCT
1 TTTCTACCACCTTTCATGTCTTCT
* *
1705598 ATTCTACCACCATTCATGTCTTCT
1 TTTCTACCACCTTTCATGTCTTCT
1705622 TTTCT
1 TTTCT
1705627 CTCTTCGATG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.13, C:0.33, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTCTACCACCTTTCATGTCTTCT
Found at i:1718525 original size:57 final size:57
Alignment explanation
Indices: 1718437--1718612 Score: 280
Period size: 57 Copynumber: 3.1 Consensus size: 57
1718427 ATCGAAAGGC
* * *
1718437 AGCCGCGACGAGGACGACGAGGAGAGGCGAGATCGTGATAAGGAACGCCATAGAAGA
1 AGCCGCGACGAAGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAGA
* * *
1718494 AGCCGGGATGAAGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAAA
1 AGCCGCGACGAAGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAGA
* *
1718551 AGCCGCGACGAGGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAGC
1 AGCCGCGACGAAGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAGA
1718608 AGCCG
1 AGCCG
1718613 TGATAGGGAG
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 108 1.00
ACGTcount: A:0.35, C:0.19, G:0.38, T:0.07
Consensus pattern (57 bp):
AGCCGCGACGAAGACGATGAGGAGAGGCGAGACCGTGATAAGGAACGCCATAGAAGA
Found at i:1727307 original size:287 final size:287
Alignment explanation
Indices: 1726791--1727364 Score: 1139
Period size: 287 Copynumber: 2.0 Consensus size: 287
1726781 AAGAGAAGCA
1726791 TAAATACGAGACTGGCGTAGTTGCTAATCTGCAAGTGAGGCAGGAGTCCATGTTAGAAAAGACCC
1 TAAATACGAGACTGGCGTAGTTGCTAATCTGCAAGTGAGGCAGGAGTCCATGTTAGAAAAGACCC
*
1726856 GACTTAATACGTAGATGTTATAAGCAAAGCAATCAACCATGCAAAACAGGCACTTGCACTTTCTT
66 GACTAAATACGTAGATGTTATAAGCAAAGCAATCAACCATGCAAAACAGGCACTTGCACTTTCTT
1726921 ACAAACGAAAATACAAAACTCAACCGAGAAAGTGGGTTTTTTACCTCGGGAACAATAAACTGTCC
131 ACAAACGAAAATACAAAACTCAACCGAGAAAGTGGGTTTTTTACCTCGGGAACAATAAACTGTCC
1726986 GGTAAGGAGACAGATAGCCGGAAGGGTACAGTAAACAACCAACGGAATGGATGTCCATGGATATA
196 GGTAAGGAGACAGATAGCCGGAAGGGTACAGTAAACAACCAACGGAATGGATGTCCATGGATATA
1727051 CAACCGAGTTTATGTAGGAAAATCGTT
261 CAACCGAGTTTATGTAGGAAAATCGTT
1727078 TAAATACGAGACTGGCGTAGTTGCTAATCTGCAAGTGAGGCAGGAGTCCATGTTAGAAAAGACCC
1 TAAATACGAGACTGGCGTAGTTGCTAATCTGCAAGTGAGGCAGGAGTCCATGTTAGAAAAGACCC
1727143 GACTAAATACGTAGATGTTATAAGCAAAGCAATCAACCATGCAAAACAGGCACTTGCACTTTCTT
66 GACTAAATACGTAGATGTTATAAGCAAAGCAATCAACCATGCAAAACAGGCACTTGCACTTTCTT
1727208 ACAAACGAAAATACAAAACTCAACCGAGAAAGTGGGTTTTTTACCTCGGGAACAATAAACTGTCC
131 ACAAACGAAAATACAAAACTCAACCGAGAAAGTGGGTTTTTTACCTCGGGAACAATAAACTGTCC
1727273 GGTAAGGAGACAGATAGCCGGAAGGGTACAGTAAACAACCAACGGAATGGATGTCCATGGATATA
196 GGTAAGGAGACAGATAGCCGGAAGGGTACAGTAAACAACCAACGGAATGGATGTCCATGGATATA
1727338 CAACCGAGTTTATGTAGGAAAATCGTT
261 CAACCGAGTTTATGTAGGAAAATCGTT
1727365 CCAGCCATTT
Statistics
Matches: 286, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 286 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (287 bp):
TAAATACGAGACTGGCGTAGTTGCTAATCTGCAAGTGAGGCAGGAGTCCATGTTAGAAAAGACCC
GACTAAATACGTAGATGTTATAAGCAAAGCAATCAACCATGCAAAACAGGCACTTGCACTTTCTT
ACAAACGAAAATACAAAACTCAACCGAGAAAGTGGGTTTTTTACCTCGGGAACAATAAACTGTCC
GGTAAGGAGACAGATAGCCGGAAGGGTACAGTAAACAACCAACGGAATGGATGTCCATGGATATA
CAACCGAGTTTATGTAGGAAAATCGTT
Found at i:1728393 original size:20 final size:21
Alignment explanation
Indices: 1728368--1728408 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1728358 GTCATGATGG
*
1728368 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
1728388 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
1728409 TCGATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:1731515 original size:20 final size:21
Alignment explanation
Indices: 1731490--1731530 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1731480 GTCATGATGG
*
1731490 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
1731510 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
1731531 TCGATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:1734637 original size:20 final size:21
Alignment explanation
Indices: 1734612--1734652 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1734602 GTCATGATGG
*
1734612 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
1734632 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
1734653 TTGATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:1742637 original size:7 final size:7
Alignment explanation
Indices: 1742625--1742678 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
1742615 TTCCTTCACA
1742625 TTCCCTT
1 TTCCCTT
1742632 TTCCCTT
1 TTCCCTT
1742639 TTCCCTT
1 TTCCCTT
1742646 TTCCCTT
1 TTCCCTT
1742653 TTCCCTT
1 TTCCCTT
1742660 TTCCCTT
1 TTCCCTT
1742667 TTCCCTT
1 TTCCCTT
1742674 TTCCC
1 TTCCC
1742679 GTTCCCACTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCCCTT
Found at i:1745975 original size:15 final size:17
Alignment explanation
Indices: 1745950--1745981 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1745940 CAACATATCA
1745950 ATATGATACTT-ATTAT
1 ATATGATACTTAATTAT
1745966 ATAT-ATACTTAATTAT
1 ATATGATACTTAATTAT
1745982 TGGAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATGATACTTAATTAT
Found at i:1747282 original size:21 final size:21
Alignment explanation
Indices: 1747258--1747317 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1747248 AATTTTTCCA
*
1747258 GAAATGATCGATCTCTTAGGG
1 GAAAGGATCGATCTCTTAGGG
* *
1747279 GAAAGGATCAATCTCTTCGGG
1 GAAAGGATCGATCTCTTAGGG
*
1747300 GAAAGGATCGATCCCTTA
1 GAAAGGATCGATCTCTTA
1747318 CCAAAAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (21 bp):
GAAAGGATCGATCTCTTAGGG
Found at i:1750755 original size:2 final size:2
Alignment explanation
Indices: 1750748--1750794 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1750738 ATTGGCAGTA
1750748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1750790 AT AT A
1 AT AT A
1750795 AATCAAGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1750954 original size:2 final size:2
Alignment explanation
Indices: 1750947--1750972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1750937 TAGTTTAATA
1750947 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1750973 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1757884 original size:20 final size:20
Alignment explanation
Indices: 1757859--1757899 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1757849 TTAATGGTAC
1757859 TCATCACCGCTCGTCGAACG
1 TCATCACCGCTCGTCGAACG
1757879 TCATCACCGCTCGTCGAACG
1 TCATCACCGCTCGTCGAACG
1757899 T
1 T
1757900 GGAAGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (20 bp):
TCATCACCGCTCGTCGAACG
Found at i:1764753 original size:31 final size:30
Alignment explanation
Indices: 1764715--1764793 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
1764705 ATTTTGTATT
1764715 AAATAATAATAATA-AATGTCAT-ATTATACCA
1 AAATAATAATAATAGAAT-TCATAATTAT--CA
*
1764746 AAATAATAATAAAAGAATTCATAATTATCA
1 AAATAATAATAATAGAATTCATAATTATCA
*
1764776 AAATAAGAATAATTAGAA
1 AAATAATAATAA-TAGAA
1764794 AATTTATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 13 0.31
31 21 0.50
32 8 0.19
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATAATAATAATAGAATTCATAATTATCA
Found at i:1768178 original size:29 final size:29
Alignment explanation
Indices: 1768136--1768204 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
1768126 TGATTTTAAG
*
1768136 TTAGGTGATAATCTTGAACTTATAAAATT
1 TTAGGTGGTAATCTTGAACTTATAAAATT
*
1768165 TTAGGTGGTAATCTTGAACTTATTAAATT
1 TTAGGTGGTAATCTTGAACTTATAAAATT
1768194 TTAGGTGGTAA
1 TTAGGTGGTAA
1768205 AAACATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (29 bp):
TTAGGTGGTAATCTTGAACTTATAAAATT
Found at i:1769022 original size:26 final size:26
Alignment explanation
Indices: 1768993--1769044 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1768983 AAACTTAACA
1768993 CGCTTTGTACCTAAACTACTAGTTTT
1 CGCTTTGTACCTAAACTACTAGTTTT
1769019 CGCTTTGTACCTAAACTACTAGTTTT
1 CGCTTTGTACCTAAACTACTAGTTTT
1769045 GGCCCGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (26 bp):
CGCTTTGTACCTAAACTACTAGTTTT
Found at i:1769703 original size:24 final size:24
Alignment explanation
Indices: 1769652--1769703 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1769642 TCTATGTCCT
* * **
1769652 TGTGACATGATTTTTCTCTTCTTT
1 TGTGACATGAGTTTTCTCTGCTCA
*
1769676 TGTGACATGCGTTTTCTCTGCTCA
1 TGTGACATGAGTTTTCTCTGCTCA
1769700 TGTG
1 TGTG
1769704 GTACGATTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (24 bp):
TGTGACATGAGTTTTCTCTGCTCA
Found at i:1770430 original size:139 final size:139
Alignment explanation
Indices: 1770275--1770547 Score: 546
Period size: 139 Copynumber: 2.0 Consensus size: 139
1770265 TTAGAAATCA
1770275 ATCGATATATAAACACAAATATTATCAAAACTACTTTTTTAATATTTATTCTTTTAGTTGACTTT
1 ATCGATATATAAACACAAATATTATCAAAACTACTTTTTTAATATTTATTCTTTTAGTTGACTTT
1770340 TTCTTAATTAATATTGTTTGTTAAGGAATTTATTTTTATTAATCTGATCTATATTTAAGATAGTA
66 TTCTTAATTAATATTGTTTGTTAAGGAATTTATTTTTATTAATCTGATCTATATTTAAGATAGTA
1770405 TCCGGGTAT
131 TCCGGGTAT
1770414 ATCGATATATAAACACAAATATTATCAAAACTACTTTTTTAATATTTATTCTTTTAGTTGACTTT
1 ATCGATATATAAACACAAATATTATCAAAACTACTTTTTTAATATTTATTCTTTTAGTTGACTTT
1770479 TTCTTAATTAATATTGTTTGTTAAGGAATTTATTTTTATTAATCTGATCTATATTTAAGATAGTA
66 TTCTTAATTAATATTGTTTGTTAAGGAATTTATTTTTATTAATCTGATCTATATTTAAGATAGTA
1770544 TCCG
131 TCCG
1770548 TTTAAGAAAT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 134 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (139 bp):
ATCGATATATAAACACAAATATTATCAAAACTACTTTTTTAATATTTATTCTTTTAGTTGACTTT
TTCTTAATTAATATTGTTTGTTAAGGAATTTATTTTTATTAATCTGATCTATATTTAAGATAGTA
TCCGGGTAT
Found at i:1781521 original size:29 final size:30
Alignment explanation
Indices: 1781489--1781570 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
1781479 TATTCCTTAA
* *
1781489 AATA-TAATATAATATAATATTCTTATTTT
1 AATAGTAATATAATATAATAATATTATTTT
* * *
1781518 AATATTAATAT-TTTTAATAATATTATTTT
1 AATAGTAATATAATATAATAATATTATTTT
1781547 AATAAGTAAT-TAATATAATTAATA
1 AAT-AGTAATATAATATAA-TAATA
1781571 ATATATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 22 0.52
30 15 0.36
31 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
AATAGTAATATAATATAATAATATTATTTT
Found at i:1781522 original size:14 final size:14
Alignment explanation
Indices: 1781503--1781550 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1781493 TAATATAATA
*
1781503 TAATATTCTTATTT
1 TAATATTATTATTT
*
1781517 TAATATTAATATTTT
1 TAATATTATTA-TTT
*
1781532 TAATAATATTATTT
1 TAATATTATTATTT
1781546 TAATA
1 TAATA
1781551 AGTAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATTATTATTT
Found at i:1781534 original size:15 final size:14
Alignment explanation
Indices: 1781512--1781556 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1781502 ATAATATTCT
*
1781512 TATTTTAATATTAA
1 TATTTTAATAATAA
*
1781526 TATTTTTAATAATAT
1 TA-TTTTAATAATAA
1781541 TATTTTAATAAGTAA
1 TATTTTAATAA-TAA
1781556 T
1 T
1781557 TAATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:1781551 original size:14 final size:14
Alignment explanation
Indices: 1781511--1781551 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1781501 TATAATATTC
*
1781511 TTATTTTAATATTA
1 TTATTTTAATAATA
*
1781525 ATATTTTTAATAATA
1 TTA-TTTTAATAATA
1781540 TTATTTTAATAA
1 TTATTTTAATAA
1781552 GTAATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTTAATAATA
Found at i:1781760 original size:24 final size:24
Alignment explanation
Indices: 1781709--1781778 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
1781699 AAATAATAGT
* *
1781709 AAATAA-ATTATTCTAATATTTTAA
1 AAATAATATTATT-TATTATATTAA
*
1781733 AAATAATATTA-TTATTTTATTAA
1 AAATAATATTATTTATTATATTAA
1781756 TAAATAATATTATTTATTATATT
1 -AAATAATATTATTTATTATATT
1781779 TGATGTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 8 0.21
24 18 0.46
25 13 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATAATATTATTTATTATATTAA
Found at i:1782087 original size:33 final size:33
Alignment explanation
Indices: 1782045--1782111 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1782035 GAGGTCCTTA
1782045 GAGGATCATATCCATATATCTATATCCAAACAT
1 GAGGATCATATCCATATATCTATATCCAAACAT
1782078 GAGGATCATATCCATATATCTATATCCAAACAT
1 GAGGATCATATCCATATATCTATATCCAAACAT
1782111 G
1 G
1782112 TCTTGGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (33 bp):
GAGGATCATATCCATATATCTATATCCAAACAT
Found at i:1787752 original size:13 final size:13
Alignment explanation
Indices: 1787734--1787771 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
1787724 GGAATAATTT
1787734 AATAATTTATTAA
1 AATAATTTATTAA
1787747 AATAATTTATTAA
1 AATAATTTATTAA
1787760 AATAATATTATT
1 AATAAT-TTATT
1787772 CCATTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATAATTTATTAA
Found at i:1789342 original size:16 final size:17
Alignment explanation
Indices: 1789317--1789357 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1789307 TAAATTTAAC
1789317 ATTTAATTTAA-AAAAT
1 ATTTAATTTAATAAAAT
*
1789333 ATTTATTTTAATAAAA-
1 ATTTAATTTAATAAAAT
1789349 ATGTTAATT
1 AT-TTAATT
1789358 AAATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTAATTTAATAAAAT
Found at i:1798744 original size:234 final size:232
Alignment explanation
Indices: 1798338--1798805 Score: 857
Period size: 234 Copynumber: 2.0 Consensus size: 232
1798328 CCTAGATATC
*
1798338 ACAGTTTCGAACACTAGCAACTGCAATAGTGATTGAACATTTATTGTCAAATTGTTGAAGATATT
1 ACAGTTTCGAACACTAGCAACTGCAAGAGTGATTGAACATTTATTGTCAAATTGTTGAAGATATT
1798403 TAAAACATATATAATTTTATAATCACCTTAACTTAATAAAATAAAATAAAAAAACCAAGAGCACT
66 TAAAACATATATAATTTTATAATCACCTTAACTTAATAAAATAAAATAAAAAAACCAAGAGCACT
1798468 ACATTTCCTTTAATGACACATAATAAGTAAAAATGGATAATTACTATTTAACAACTCAGAATAAA
131 ACATTTCCTTTAATGACACATAATAAGTAAAAATGGATAATTACTATTTAACAACTCAGAATAAA
1798533 TTAAGTGACATTT-AAAATAAAAGAACTCGGAATAAA
196 TTAAGTGACATTTAAAAATAAAAGAACTCGGAATAAA
*
1798569 ACAGTTTCGAACACTAGCAACTGCAACAGGAGTGATTGAGCATTTATTGTCAAATTGTTGAAGAT
1 ACAGTTTCGAACACTAGCAACTGC-A-A-GAGTGATTGAACATTTATTGTCAAATTGTTGAAGAT
*
1798634 ATTTAAAACATATATAATTTTATAATCACCTTAACTTAATAAAATAAAATAAAAAAACCAATAGC
63 ATTTAAAACATATATAATTTTATAATCACCTTAACTTAATAAAATAAAATAAAAAAACCAAGAGC
1798699 ACTACATTTCCTTTAATGACACATAATAAGTAAAAATGGATAATTACTATTTAACAACTCAGAAT
128 ACTACATTTCCTTTAATGACACATAATAAGTAAAAATGGATAATTACTATTTAACAACTCAGAAT
*
1798764 AAATTAAGTTACATTTAAAAAATAAAAGAACTCGGAATAAA
193 AAATTAAGTGACATTT-AAAAATAAAAGAACTCGGAATAAA
1798805 A
1 A
1798806 TTAATTATTA
Statistics
Matches: 228, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
231 24 0.11
232 1 0.00
233 1 0.00
234 178 0.78
236 24 0.11
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (232 bp):
ACAGTTTCGAACACTAGCAACTGCAAGAGTGATTGAACATTTATTGTCAAATTGTTGAAGATATT
TAAAACATATATAATTTTATAATCACCTTAACTTAATAAAATAAAATAAAAAAACCAAGAGCACT
ACATTTCCTTTAATGACACATAATAAGTAAAAATGGATAATTACTATTTAACAACTCAGAATAAA
TTAAGTGACATTTAAAAATAAAAGAACTCGGAATAAA
Found at i:1803369 original size:183 final size:182
Alignment explanation
Indices: 1802744--1803398 Score: 764
Period size: 180 Copynumber: 3.6 Consensus size: 182
1802734 TTTTCACTAT
* * * * *
1802744 TGTTGTTTATCTGTCCACCTTCAGAATCCAACTGCTTCTCATCCTTCTTAGACACGTCCAATTTA
1 TGTTGTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCGTCCAACTTA
* * *
1802809 TTCTCTTCAGTGA-T---CTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCATCATCTTTAGCCA
66 CTCTCTTCAGT-ATTCCCCTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCACCATCCTTAGCCA
* * * * * *
1802870 CACTCGCATTCGA-ATCCCCTTTCGTAT-CTTCCTCGGATAAATTCT---TACCAC
130 CACTCACATTTGAGA-CCCCTATC-TTTGCATCCTCGG-TAAATTCTCACCACCAC
** * *
1802921 TGTTGTTTGTCTGTCCACCTTCAGAATTTAATTGCTTCTTATCTTTCTTGGACT-GATCCAACTT
1 TGTTGTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCG-TCCAACTT
* * * * *
1802985 ACTCTCTTCAGTGTTCCCCTTGTTTTCTTGTGTGTTTGAGTTGCCACTGCCACCATCGTTAGCCA
65 ACTCTCTTCAGTATTCCCCTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCACCATCCTTAGCCA
* * * *
1803050 CACTCACGTTTGAGTCCCCTAT-TCTTGCA-CCCCTGAGTAAATTCTCACC-CTA-
130 CACTCACATTTGAGACCCCTATCT-TTGCATCCTC-G-GTAAATTCTCACCACCAC
* * * *
1803102 TG-TGTTTGACTGTCCACCTTCAGAATCCAATTGCTTCTTATCTTTCTTGGACTCATCCAACTTA
1 TGTTGTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCGTCCAACTTA
*** * * *
1803166 CTCTCTTCAGCGGTCCCCTTGTTTTCTTGTGTGTTTAAGTTTCCAGTGCCACCATCCTTAGCCCC
66 CTCTCTTCAGTATTCCCCTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCACCATCCTTAGCCAC
*
1803231 ACTCACTTTTGAGACCCCTATCTTTGCATCCTCGGCTAAATTCTCACCACCAC
131 ACTCACATTTGAGACCCCTATCTTTGCATCCTCGG-TAAATTCTCACCACCAC
*
1803284 TGTTGTTTGTCTGTCCACCTTGAGAATCCAATTGCTTCTTATCCTTCTTAGACTCGTCCAACTTA
1 TGTTGTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCGTCCAACTTA
*
1803349 CTCTCTTCAGTATTCCCCTTGTTTTCTTGTGTACTTAAGTTGCCAGTGCC
66 CTCTCTTCAGTATTCCCCTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCC
1803399 CTTGCCATCA
Statistics
Matches: 406, Mismatches: 52, Indels: 34
0.83 0.11 0.07
Matches are distributed among these distances:
176 1 0.00
177 65 0.16
178 1 0.00
179 5 0.01
180 220 0.54
181 9 0.02
182 4 0.01
183 101 0.25
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (182 bp):
TGTTGTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCGTCCAACTTA
CTCTCTTCAGTATTCCCCTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCACCATCCTTAGCCAC
ACTCACATTTGAGACCCCTATCTTTGCATCCTCGGTAAATTCTCACCACCAC
Found at i:1803595 original size:66 final size:66
Alignment explanation
Indices: 1803489--1803617 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 66
1803479 ATTGAACGTT
* *
1803489 GTTGCTCTTGTCATTGCTATTATCGGTTACCGGTGTAACCTGATCATCAACTTGGTTTTTCTTTT
1 GTTGCTCCTGTCATTGCTATTATCGATTACCGGTGTAACCTGATCATCAACTTGGTTTTTCTTTT
1803554 C
66 C
* *
1803555 GTTGCTCCTGTCATTGCTATTATCGATTACCGGTGTAACCTGATCATCGAGTTGGTTTTTCTT
1 GTTGCTCCTGTCATTGCTATTATCGATTACCGGTGTAACCTGATCATCAACTTGGTTTTTCTT
1803618 ATCATGAGCC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
GTTGCTCCTGTCATTGCTATTATCGATTACCGGTGTAACCTGATCATCAACTTGGTTTTTCTTTT
C
Found at i:1806481 original size:26 final size:26
Alignment explanation
Indices: 1806451--1806507 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1806441 TCCTAAACAC
1806451 CTCTAGATGAAAATGAATGAGGCAAT
1 CTCTAGATGAAAATGAATGAGGCAAT
1806477 CTCTAGATGAAAATGAATGAGGCAAT
1 CTCTAGATGAAAATGAATGAGGCAAT
1806503 CTCTA
1 CTCTA
1806508 ATTTCGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (26 bp):
CTCTAGATGAAAATGAATGAGGCAAT
Found at i:1810324 original size:40 final size:40
Alignment explanation
Indices: 1810270--1810345 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1810260 TGTTGCTAGT
1810270 ATGGCCCCTTGGTTT-CTTTTACC-AGTCTGCTACTAGATG
1 ATGGCCCCTTGGTTTAC-TTTACCAAGTCTGCTACTAGATG
*
1810309 ATGGCCCCCTTGGTTTACTTTACCAAGTCTTCTACTA
1 ATGG-CCCCTTGGTTTACTTTACCAAGTCTGCTACTA
1810346 CATTCGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
39 4 0.12
40 17 0.52
41 12 0.36
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (40 bp):
ATGGCCCCTTGGTTTACTTTACCAAGTCTGCTACTAGATG
Found at i:1811026 original size:14 final size:14
Alignment explanation
Indices: 1810973--1811030 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
1810963 CAGTAATTTT
*
1810973 TTTATAAATACTGAA
1 TTTATATATA-TGAA
1810988 TTTATAT-TA--AA
1 TTTATATATATGAA
* *
1810999 TGTAAATATATGAA
1 TTTATATATATGAA
*
1811013 TTTATATATTTGAA
1 TTTATATATATGAA
1811027 TTTA
1 TTTA
1811031 ATTTAGGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
11 7 0.21
12 2 0.06
14 19 0.56
15 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTATATATATGAA
Found at i:1818474 original size:12 final size:12
Alignment explanation
Indices: 1818457--1818481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1818447 TTTGAAAATC
1818457 ATTTATTTAAAA
1 ATTTATTTAAAA
1818469 ATTTATTTAAAA
1 ATTTATTTAAAA
1818481 A
1 A
1818482 AGGGTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTATTTAAAA
Found at i:1824666 original size:31 final size:31
Alignment explanation
Indices: 1824629--1824688 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1824619 GAGAGAAGGA
*
1824629 AAAAGGGTAAATTACACCATGAGTTATTAGG
1 AAAAGGGTAAATTACACCATGAGTCATTAGG
1824660 AAAAGGGTAAATTACACCATGAGTCATTA
1 AAAAGGGTAAATTACACCATGAGTCATTA
1824689 AACTTTGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAGGGTAAATTACACCATGAGTCATTAGG
Found at i:1825750 original size:20 final size:22
Alignment explanation
Indices: 1825706--1825753 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
1825696 TGCATGGTAG
1825706 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATG-T-AAGAA
1825730 TGCATCGATGCAC-TG-AAGAA
1 TGCATCGATGCACATGTAAGAA
1825750 TGCA
1 TGCA
1825754 CCGACACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.38
23 2 0.08
24 13 0.54
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCACATGTAAGAA
Found at i:1825763 original size:20 final size:20
Alignment explanation
Indices: 1825725--1825763 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1825715 GCACATGTTA
* **
1825725 AAGAATGCATCGATGCACTG
1 AAGAATGCACCGACACACTG
1825745 AAGAATGCACCGACACACT
1 AAGAATGCACCGACACACT
1825764 TCAATGGGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
AAGAATGCACCGACACACTG
Found at i:1829779 original size:20 final size:20
Alignment explanation
Indices: 1829746--1829784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1829736 GCATATGTTA
* * *
1829746 AAGAATGTATCGATGCACTG
1 AAGAATGCACCGATACACTG
1829766 AAGAATGCACCGATACACT
1 AAGAATGCACCGATACACT
1829785 TCAATGAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGAATGCACCGATACACTG
Found at i:1841978 original size:166 final size:164
Alignment explanation
Indices: 1841698--1842029 Score: 580
Period size: 166 Copynumber: 2.0 Consensus size: 164
1841688 GTATCGCAAC
* *
1841698 AACTTACGGTGTCGAAACCTATAATCTGTGGAGCATGTCCATGCATCGCGCTTCTAACCAGAACA
1 AACTTACGGTGTCGAAACCTATAATCTATGGAGCATGTCCATGCATCGCGCTTCTAACCAGAAAA
1841763 AACTCAGATTTTTCGATGGAACATGTCGAAAGGATGATTATGAGGGTCTGATGCAGTCTCAGTGG
66 AACTCAGATTTTTCGATGGAACATGTCGAAAGGATGATTATGAGGGTCTGATGCAGTCTCAGTGG
1841828 GAGCGCTGCAATGCTTTGGTTCTCTCAT-GATCCTG
131 GA--GCTGCAATGCTTTGGTTCTCTCATGGATCCTG
1841863 AACTTACCGGTGTCGAAACCTATAATCTATGGAGCATGTCCATGCGCATCGCGCTTCT-ACCAGA
1 AACTTA-CGGTGTCGAAACCTATAATCTATGGAGCATGTCCAT--GCATCGCGCTTCTAACCAGA
1841927 AAAAACTCAGATTTTTCGATGGAACATGTC-AAAGGATGATTATGAGGGTCTGATGCAGTCTCAG
63 AAAAACTCAGATTTTTCGATGGAACATGTCGAAAGGATGATTATGAGGGTCTGATGCAGTCTCAG
1841991 TGGGAGCTGCAATGCTTTGGTTCTCTCATGGATCCTG
128 TGGGAGCTGCAATGCTTTGGTTCTCTCATGGATCCTG
1842028 AA
1 AA
1842030 TCTGTTAGTC
Statistics
Matches: 161, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
164 24 0.15
165 15 0.09
166 74 0.46
167 35 0.22
168 13 0.08
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (164 bp):
AACTTACGGTGTCGAAACCTATAATCTATGGAGCATGTCCATGCATCGCGCTTCTAACCAGAAAA
AACTCAGATTTTTCGATGGAACATGTCGAAAGGATGATTATGAGGGTCTGATGCAGTCTCAGTGG
GAGCTGCAATGCTTTGGTTCTCTCATGGATCCTG
Found at i:1846008 original size:29 final size:26
Alignment explanation
Indices: 1845963--1846024 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
1845953 TAGTATTCTC
1845963 ATTCATAT-TAAAAAAGAAGAGGTATT
1 ATTCA-ATCTAAAAAAGAAGAGGTATT
1845989 ATTCAATCTAAAAAAGAAGAGGTATT
1 ATTCAATCTAAAAAAGAAGAGGTATT
1846015 ATTCAATCTA
1 ATTCAATCTA
1846025 GCTTTTACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 2 0.06
26 33 0.94
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (26 bp):
ATTCAATCTAAAAAAGAAGAGGTATT
Found at i:1850210 original size:127 final size:126
Alignment explanation
Indices: 1849976--1850228 Score: 481
Period size: 127 Copynumber: 2.0 Consensus size: 126
1849966 TTAACATGTA
1849976 TAAGTGTTATATTTAATATGTTAATTAATCGAACCGTTAATACTAAATGGTTTCGATTAATTGAG
1 TAAGTGTTATATTTAATATGTTAATTAATCGAACCGTTAATACTAAATGGTTTCGATTAATTGAG
1850041 CCTAAAAATTATGGTTAATCATTAACAAATTAAATTTATAATTATATTTCTAATTTATTAT
66 CCTAAAAATTATGGTTAATCATTAACAAATTAAATTTATAATTATATTTCTAATTTATTAT
1850102 TAAGTGTTATATTTAAT-TGTTAATTAATCGAACCGTTAATACTAAATGGTTTCGATTAATTGAG
1 TAAGTGTTATATTTAATATGTTAATTAATCGAACCGTTAATACTAAATGGTTTCGATTAATTGAG
1850166 CCGCTAAAAATTATGGTTAATCATTAACAAATTAAATTTATAATTATATTTCTAATTTATTAT
66 -C-CTAAAAATTATGGTTAATCATTAACAAATTAAATTTATAATTATATTTCTAATTTATTAT
1850229 ATTTTACACA
Statistics
Matches: 125, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
125 47 0.38
126 18 0.14
127 60 0.48
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (126 bp):
TAAGTGTTATATTTAATATGTTAATTAATCGAACCGTTAATACTAAATGGTTTCGATTAATTGAG
CCTAAAAATTATGGTTAATCATTAACAAATTAAATTTATAATTATATTTCTAATTTATTAT
Found at i:1863390 original size:60 final size:60
Alignment explanation
Indices: 1863318--1863454 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
1863308 ATAAATGGGT
* ** *
1863318 GACCATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAGCAAT-TCTCTATAGTTGGTG
1 GACCATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAGCATTATCT-TATAGTCAGAG
* ** * *
1863378 GACCATTTTGTAACTTTTAATAGTCTGGTGATTCAACAAAGCATTATCTTATAGTCAGAG
1 GACCATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAGCATTATCTTATAGTCAGAG
1863438 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
1863455 ACCCTTCAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 60 0.91
61 6 0.09
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAGCATTATCTTATAGTCAGAG
Found at i:1870680 original size:43 final size:43
Alignment explanation
Indices: 1870632--1870742 Score: 222
Period size: 43 Copynumber: 2.6 Consensus size: 43
1870622 ACATAAATAA
1870632 TATGATGAACCTGATATTTCTGAAGATAAGAAAATAGGAAGTG
1 TATGATGAACCTGATATTTCTGAAGATAAGAAAATAGGAAGTG
1870675 TATGATGAACCTGATATTTCTGAAGATAAGAAAATAGGAAGTG
1 TATGATGAACCTGATATTTCTGAAGATAAGAAAATAGGAAGTG
1870718 TATGATGAACCTGATATTTCTGAAG
1 TATGATGAACCTGATATTTCTGAAG
1870743 TTGCAAACTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.30
Consensus pattern (43 bp):
TATGATGAACCTGATATTTCTGAAGATAAGAAAATAGGAAGTG
Found at i:1874844 original size:22 final size:21
Alignment explanation
Indices: 1874819--1874859 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
1874809 TAAAGGTTAA
1874819 ATGTATAATATTAATA-AAAATT
1 ATGTA-AA-ATTAATAGAAAATT
1874841 ATGTAAAATTAATAGAAAA
1 ATGTAAAATTAATAGAAAA
1874860 AATAACACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
ATGTAAAATTAATAGAAAATT
Found at i:1881008 original size:15 final size:16
Alignment explanation
Indices: 1880988--1881026 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1880978 ACATTCAGTG
*
1880988 AATTAAGTAATA-ATT
1 AATTAAATAATATATT
*
1881003 AATTAAATAATATTTT
1 AATTAAATAATATATT
1881019 AATTAAAT
1 AATTAAAT
1881027 GTGTACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAAATAATATATT
Found at i:1881878 original size:19 final size:19
Alignment explanation
Indices: 1881842--1881878 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1881832 TTTAGGCTTC
*
1881842 TTTAAATATATATATTTTT
1 TTTAAATATAAATATTTTT
1881861 TTTAAATATAAA-ATTTTT
1 TTTAAATATAAATATTTTT
1881879 AAAACTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAATATAAATATTTTT
Found at i:1882717 original size:66 final size:67
Alignment explanation
Indices: 1882577--1882728 Score: 209
Period size: 66 Copynumber: 2.3 Consensus size: 67
1882567 AACAATACTT
* * * *
1882577 AATGGAGGTAATGACATTCCCAGTAATATACTCCAAAAAATCCACTATTGGTAATCTTACATTAC
1 AATGGAGGTAATGATATTCCCAATAATATACTCCAAAAAATCCACTATTAGTAATCGTACATTAC
1882642 CA
66 CA
* * *
1882644 TAGGGAGGTAATGATATTCCCAATAATATA-TCTTAAAAAAT-CACTATTAGTAATCGTACATTA
1 AATGGAGGTAATGATATTCCCAATAATATACTC-CAAAAAATCCACTATTAGTAATCGTACATTA
1882707 CCA
65 CCA
*
1882710 AATGGAGGTAATAATATTC
1 AATGGAGGTAATGATATTC
1882729 TTATATGAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
66 41 0.55
67 33 0.45
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (67 bp):
AATGGAGGTAATGATATTCCCAATAATATACTCCAAAAAATCCACTATTAGTAATCGTACATTAC
CA
Found at i:1882803 original size:23 final size:23
Alignment explanation
Indices: 1882773--1882821 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1882763 TAAGCCAACC
1882773 CTTCATATGTGATACGGTTTACA
1 CTTCATATGTGATACGGTTTACA
1882796 CTTCATATGTGATACGGTTTACA
1 CTTCATATGTGATACGGTTTACA
1882819 CTT
1 CTT
1882822 TACATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (23 bp):
CTTCATATGTGATACGGTTTACA
Found at i:1883109 original size:22 final size:21
Alignment explanation
Indices: 1883075--1883115 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1883065 ATAATTATTT
1883075 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
1883096 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1883116 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:1884164 original size:20 final size:21
Alignment explanation
Indices: 1884139--1884179 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1884129 AAAATCTAAA
*
1884139 AATAATAAA-TTATTAAATAT
1 AATAATAAATTTATAAAATAT
1884159 AATAATAAATTTATAAAATAT
1 AATAATAAATTTATAAAATAT
1884180 TTTGAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATAAATTTATAAAATAT
Found at i:1885501 original size:12 final size:12
Alignment explanation
Indices: 1885484--1885510 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1885474 TTACTAAAGT
1885484 TGATAATGTTAG
1 TGATAATGTTAG
1885496 TGATAATGTTAG
1 TGATAATGTTAG
1885508 TGA
1 TGA
1885511 GTATTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
TGATAATGTTAG
Found at i:1891120 original size:80 final size:82
Alignment explanation
Indices: 1891022--1891185 Score: 224
Period size: 83 Copynumber: 2.0 Consensus size: 82
1891012 CGTTGAATTT
* * *
1891022 TAGATGATACATTGTTTATATCATTCAAACTTCA-AT-TTTTTTAATTGTAGCATTAAATTTTAA
1 TAGATGATACATTGTTTATATCATTCAAACTTCATATATTTTTTAATTATAACAGTAAATTTTAA
*
1891085 TTTTAACTTCAATTATG
66 TTTTAACTTCAATCATG
* * * *
1891102 TAGATGATACATTGTTTATATCATTCAAATTTTATTTTATTTTTTAATTATAACAGTAAATTTTG
1 TAGATGATACATTGTTTATATCATTCAAACTTCA-TATATTTTTTAATTATAACAGTAAATTTTA
*
1891167 ATTTTAATTTCAATCATG
65 ATTTTAACTTCAATCATG
1891185 T
1 T
1891186 CATTGTGCTA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
80 32 0.44
82 1 0.01
83 39 0.54
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.51
Consensus pattern (82 bp):
TAGATGATACATTGTTTATATCATTCAAACTTCATATATTTTTTAATTATAACAGTAAATTTTAA
TTTTAACTTCAATCATG
Found at i:1910854 original size:22 final size:22
Alignment explanation
Indices: 1910829--1910878 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1910819 GCAGCACGGC
* *
1910829 TCTCTGGATTCACCCACACGCT
1 TCTCTCGATGCACCCACACGCT
1910851 TCTCTCGATGCACCCACACGCT
1 TCTCTCGATGCACCCACACGCT
1910873 TCTCTC
1 TCTCTC
1910879 AAGTCAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.28
Consensus pattern (22 bp):
TCTCTCGATGCACCCACACGCT
Found at i:1926666 original size:22 final size:22
Alignment explanation
Indices: 1926638--1926700 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1926628 TTTTGGTGCA
*
1926638 GAGGGAATCGATCCCCCCTCAT
1 GAGGGAACCGATCCCCCCTCAT
* * *
1926660 GAGGGAACCGATTCCCCAT-TT
1 GAGGGAACCGATCCCCCCTCAT
1926681 GAAGGGAACCGATTCCCCCC
1 G-AGGGAACCGA-TCCCCCC
1926701 ACAGGGGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 26 0.79
23 5 0.15
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (22 bp):
GAGGGAACCGATCCCCCCTCAT
Found at i:1929152 original size:21 final size:21
Alignment explanation
Indices: 1929119--1929159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1929109 TTCTGGGCAA
* *
1929119 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1929140 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1929160 ACGACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1929637 original size:2 final size:2
Alignment explanation
Indices: 1929630--1929690 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1929620 CATGAGTTAG
* *
1929630 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1929672 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1929691 GGAATTGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1930504 original size:32 final size:32
Alignment explanation
Indices: 1930463--1930558 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
1930453 GAGTCGAGGA
1930463 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1930495 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1930526 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1930558 T
1 T
1930559 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1930645 original size:29 final size:30
Alignment explanation
Indices: 1930550--1930642 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
1930540 AAGGAACATA
1930550 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1930580 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1930610 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1930639 TGGA
1 TGGA
1930643 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 17 0.29
30 42 0.71
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1933582 original size:21 final size:21
Alignment explanation
Indices: 1933556--1933600 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1933546 GATTTCTGGG
* *
1933556 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1933577 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1933598 CAA
1 CAA
1933601 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1934080 original size:2 final size:2
Alignment explanation
Indices: 1934073--1934105 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1934063 CATGAGTTAG
1934073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1934106 GAATTGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1934918 original size:32 final size:32
Alignment explanation
Indices: 1934877--1934973 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
1934867 GAGTCGAGGA
1934877 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1934909 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1934940 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1934972 TT
1 TT
1934974 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1934949 original size:31 final size:31
Alignment explanation
Indices: 1934877--1934976 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
1934867 GAGTCGAGGA
1934877 TTTACCTATGTTCT-ACGGAACATATGGACAG
1 TTTACCTATGTTCTAAC-GAACATATGGACAG
**
1934908 TTTTACCTATG-TCTTTCGAGACATATGGACAG
1 -TTTACCTATGTTCTAACGA-ACATATGGACAG
* *
1934940 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTATGTTCTAACGAACATATGGACAG
1934971 TTTACC
1 TTTACC
1934977 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTCTAACGAACATATGGACAG
Found at i:1935008 original size:30 final size:30
Alignment explanation
Indices: 1934964--1935057 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
1934954 AAGGAACATA
1934964 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1934995 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1935025 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1935054 TGGA
1 TGGA
1935058 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1937675 original size:18 final size:20
Alignment explanation
Indices: 1937647--1937717 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
1937637 AAATTGGTCT
*
1937647 CGAATGACCAC-TA-TGTCC
1 CGAAGGACCACGTATTGTCC
*
1937665 CGTAGGACCACTGTATTGTCC
1 CGAAGGACCAC-GTATTGTCC
** *
1937686 CGAAGGACCATTTTATTATCC
1 CGAAGGACCA-CGTATTGTCC
1937707 CGAAGGACCAC
1 CGAAGGACCAC
1937718 TGTAACCCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.21
20 2 0.05
21 31 0.74
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24
Consensus pattern (20 bp):
CGAAGGACCACGTATTGTCC
Found at i:1937686 original size:21 final size:21
Alignment explanation
Indices: 1937660--1937721 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1937650 ATGACCACTA
*
1937660 TGTCCCGTAGGACCACTGTAT
1 TGTCCCGAAGGACCACTGTAT
* *
1937681 TGTCCCGAAGGACCATTTTAT
1 TGTCCCGAAGGACCACTGTAT
*
1937702 TATCCCGAAGGACCACTGTA
1 TGTCCCGAAGGACCACTGTA
1937722 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGTAT
Found at i:1939446 original size:27 final size:27
Alignment explanation
Indices: 1939416--1939508 Score: 186
Period size: 27 Copynumber: 3.4 Consensus size: 27
1939406 CAAAATAGTG
1939416 CTGAATGATTCATCACAGAAGTACATT
1 CTGAATGATTCATCACAGAAGTACATT
1939443 CTGAATGATTCATCACAGAAGTACATT
1 CTGAATGATTCATCACAGAAGTACATT
1939470 CTGAATGATTCATCACAGAAGTACATT
1 CTGAATGATTCATCACAGAAGTACATT
1939497 CTGAATGATTCA
1 CTGAATGATTCA
1939509 AATCCGTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (27 bp):
CTGAATGATTCATCACAGAAGTACATT
Found at i:1950479 original size:2 final size:2
Alignment explanation
Indices: 1950472--1950537 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1950462 GATCCTAACC
1950472 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
1950514 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
1950538 CAATATTTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1960035 original size:2 final size:2
Alignment explanation
Indices: 1960028--1960057 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1960018 AAATCCTTAA
1960028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1960058 TGATAGTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1968797 original size:3 final size:3
Alignment explanation
Indices: 1968789--1968814 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1968779 TTATAATTTC
1968789 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1968815 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1968832 original size:15 final size:16
Alignment explanation
Indices: 1968814--1968845 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1968804 ATTATTATTA
1968814 TGTTGTTGTTGT-TTT
1 TGTTGTTGTTGTGTTT
1968829 TGTTGTTGTTGTGTTT
1 TGTTGTTGTTGTGTTT
1968845 T
1 T
1968846 TAAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (16 bp):
TGTTGTTGTTGTGTTT
Found at i:1969889 original size:41 final size:41
Alignment explanation
Indices: 1969830--1969969 Score: 113
Period size: 41 Copynumber: 3.6 Consensus size: 41
1969820 TATCTATAGT
* *
1969830 GGCGTTTTTCCAATAAACGCCACTATAGATAGACTTATTGC
1 GGCGTTTTTTCAAAAAACGCCACTATAGATAGACTTATTGC
*
1969871 GGCGTTTTTTCAAAAAACGTCACTAT---T--A-TTA---C
1 GGCGTTTTTTCAAAAAACGCCACTATAGATAGACTTATTGC
* * * *
1969903 AGC-TTTTATTGAAATAACGCTACTATAGATAGACTTATTGC
1 GGCGTTTT-TTCAAAAAACGCCACTATAGATAGACTTATTGC
*
1969944 GGCG-TTTATCAAAAAAACGCCACTAT
1 GGCGTTTTTTC-AAAAAACGCCACTAT
1969970 TGTTGTCCCA
Statistics
Matches: 74, Mismatches: 13, Indels: 24
0.67 0.12 0.22
Matches are distributed among these distances:
31 4 0.05
32 17 0.23
35 4 0.05
36 1 0.01
37 1 0.01
38 4 0.05
40 1 0.01
41 42 0.57
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (41 bp):
GGCGTTTTTTCAAAAAACGCCACTATAGATAGACTTATTGC
Found at i:1972407 original size:31 final size:31
Alignment explanation
Indices: 1972342--1972420 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
1972332 TAAACAATGA
* *
1972342 TTTTATTAAAAATATTATTTTTTATTAATAT
1 TTTTACTAAAAATATTATTTTATATTAATAT
1972373 TTTTGA-TAAAAATATTATTTATAATATT-AT-T
1 TTTT-ACTAAAAATATTATTT-T-ATATTAATAT
*
1972404 TTTTACTTAAAATATTA
1 TTTTACTAAAAATATTA
1972421 ATATTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 1 0.02
31 33 0.79
32 4 0.10
33 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTACTAAAAATATTATTTTATATTAATAT
Found at i:1972408 original size:15 final size:15
Alignment explanation
Indices: 1972352--1972408 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
1972342 TTTTATTAAA
*
1972352 AATATTATTTTTTAT
1 AATAATATTTTTTAT
*
1972367 --TAATATTTTTGAT
1 AATAATATTTTTTAT
* *
1972380 AAAAATATTATTTAT
1 AATAATATTTTTTAT
*
1972395 AATATTATTTTTTA
1 AATAATATTTTTTA
1972409 CTTAAAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 11 0.34
15 21 0.66
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATAATATTTTTTAT
Found at i:1972576 original size:20 final size:21
Alignment explanation
Indices: 1972539--1972577 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1972529 TAAAACGCTC
*
1972539 AATAATAATATTTTCAATAGA
1 AATAATAATATCTTCAATAGA
1972560 AATAATAA-ATCTTCAATA
1 AATAATAATATCTTCAATA
1972578 AATTTTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (21 bp):
AATAATAATATCTTCAATAGA
Found at i:1972899 original size:49 final size:49
Alignment explanation
Indices: 1972846--1972966 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 49
1972836 TTAGCAGTAA
* * * * *
1972846 GCGCCCCTGTACCGCGCTATACGATGA-TTTAGCGTCACGTGGGTATAGC
1 GCGCCCCTGCACCGCGCTATACGATGAGCTGA-CGCCACGTGGATATAGC
* * * *
1972895 GCGCCCTTGCACCACGCTATACGGTGAGCTGACGCCACGTGGATATAGT
1 GCGCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGATATAGC
*
1972944 GCGGCCCCTGCAGCGCGCTATAC
1 GC-GCCCCTGCACCGCGCTATAC
1972967 CTGTATATCT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
49 39 0.67
50 19 0.33
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (49 bp):
GCGCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGATATAGC
Found at i:1973123 original size:20 final size:20
Alignment explanation
Indices: 1973078--1973117 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1973068 TTATCACACC
*
1973078 AAATTT-TCTCAAATTCTCT
1 AAATTTATCTCAAATACTCT
1973097 AAATTTATCTCAAATACTCT
1 AAATTTATCTCAAATACTCT
1973117 A
1 A
1973118 TTTTTAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTTATCTCAAATACTCT
Found at i:1975251 original size:9 final size:9
Alignment explanation
Indices: 1975237--1975267 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1975227 ACCTGCGCAA
*
1975237 GACGACGAC
1 GACGACGAT
1975246 GACGACGAT
1 GACGACGAT
1975255 GACGACGAT
1 GACGACGAT
1975264 GACG
1 GACG
1975268 GTGATGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.26, G:0.35, T:0.06
Consensus pattern (9 bp):
GACGACGAT
Found at i:1975471 original size:26 final size:24
Alignment explanation
Indices: 1975398--1975471 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1975388 TTATATTTGT
1975398 ATTTACTTTATTTTGTTAAATTATA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
1975423 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1975447 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1975472 GTTGGAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1979167 original size:2 final size:2
Alignment explanation
Indices: 1979160--1979192 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1979150 ATTACCGATC
*
1979160 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1979193 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1990676 original size:2 final size:2
Alignment explanation
Indices: 1990669--1990724 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1990659 AAGGAGTGAA
1990669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1990711 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1990725 GATGGTGAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2021818 original size:120 final size:122
Alignment explanation
Indices: 2021617--2021846 Score: 331
Period size: 120 Copynumber: 1.9 Consensus size: 122
2021607 AGACATTATA
* * * * *
2021617 TATGATTTTTAAAAAATTAAAAGTTTAGGTCTTAAAACAGACCAAAACTTATAGTTTAGATACTA
1 TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAAACTTATAGTTTAGATACTA
* *
2021682 AATGCGTAACTTACCCATGTATTTATTTCATTCTTTTAATCAAAACTAAACATCAAG
66 AATGCATAACTTACCCATGTATTTATTTCATTCTTTGAATCAAAACTAAACATCAAG
* *
2021739 TATGATTTTGAAAAAA-AAAAAATTTAAGTATTAAAACAGACC-AAA-TTAATAGTTTAGGTATT
1 TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAAACTT-ATAGTTTAGATACT
* *
2021801 AAATGTATAATTTACCCATGTATTTATTTCATTCTTTGAATCAAAA
65 AAATGCATAACTTACCCATGTATTTATTTCATTCTTTGAATCAAAA
2021847 TTGATATGTT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 2 0.02
120 57 0.59
121 22 0.23
122 15 0.16
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (122 bp):
TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAAACTTATAGTTTAGATACTA
AATGCATAACTTACCCATGTATTTATTTCATTCTTTGAATCAAAACTAAACATCAAG
Done.