Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 4 of 222
Found at i:1180999 original size:18 final size:17
Alignment explanation
Indices: 1180968--1181002 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1180958 GATTTAGGGT
1180968 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
1180985 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
1181003 AATATATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:1182179 original size:12 final size:12
Alignment explanation
Indices: 1182162--1182215 Score: 90
Period size: 12 Copynumber: 4.5 Consensus size: 12
1182152 AGCAACAAGG
*
1182162 TATAAACTAGAT
1 TATAAACCAGAT
1182174 TATAAACCAGAT
1 TATAAACCAGAT
*
1182186 TATAAACCAGAA
1 TATAAACCAGAT
1182198 TATAAACCAGAT
1 TATAAACCAGAT
1182210 TATAAA
1 TATAAA
1182216 ATTTCAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (12 bp):
TATAAACCAGAT
Found at i:1183619 original size:30 final size:31
Alignment explanation
Indices: 1183583--1183641 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1183573 AAAACAAGCT
*
1183583 TTTAGCGGCGCTTT-TTAGCGCCGCAAATAC
1 TTTAGCGGCGCTTTATAAGCGCCGCAAATAC
*
1183613 TTTAGCGGTGCTTTGATAAGCGCCGCAAA
1 TTTAGCGGCGCTTT-ATAAGCGCCGCAAA
1183642 AGATGCCGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
32 12 0.48
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (31 bp):
TTTAGCGGCGCTTTATAAGCGCCGCAAATAC
Found at i:1183827 original size:43 final size:43
Alignment explanation
Indices: 1183755--1183898 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
1183745 AGATTAAGAG
*
1183755 CTTTAGCGGCGTTTTTAATATAACTGCCGCTATAGAT-TGGTGT
1 CTTTAGCGGCGTTTTTAATATAACTGCCGCTATAGATCAGG-GT
**
1183798 CTTTAGCGGCGTTTTTGTTGA-AAGC-GCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTAAT-ATAA-CTGCCGCTATAGATCAGGGT
* * * * * *
1183841 CGTTAGCGGC-TTTTTTATATAAGC-ACCACTATAGATCATGGC
1 CTTTAGCGGCGTTTTTAATATAA-CTGCCGCTATAGATCAGGGT
*
1183883 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
1183899 CCCAAAAACG
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 33 0.39
43 46 0.55
44 4 0.05
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTAATATAACTGCCGCTATAGATCAGGGT
Found at i:1183933 original size:43 final size:42
Alignment explanation
Indices: 1183886--1184091 Score: 229
Period size: 43 Copynumber: 4.7 Consensus size: 42
1183876 TCATGGCCTT
1183886 TAGCGGCGCTTTTCCCAAAAACGCCGC-AATAGACCCTGATCTA
1 TAGCGGCGCTTTT-CCAAAAACGCCGCTAA-AGACCCTGATCTA
*
1183929 TAGCGGCGCTTTTCCAGAAAACACCGC-AATAGACCCTGATCTA
1 TAGCGGCGCTTTTCCA-AAAACGCCGCTAA-AGACCCTGATCTA
* * *
1183972 TAGCGGCGCTTATCCAGAAAACGCAGCTAAATACCCTTTG-TCTATA
1 TAGCGGCGCTTTTCCA-AAAACGCCGCTAAAGACCC--TGATC--TA
** *
1184018 TAGCGGCGCTTCGCGCAAAAACGCCGCTAAAGACCCTAATCTA
1 TAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGACCCTGATCTA
1184061 TAGCGGCGCTTTTACCAAAAACGCCGCTAAA
1 TAGCGGCGCTTTT-CCAAAAACGCCGCTAAA
1184092 TTTGGCAGAT
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.02
43 96 0.68
44 6 0.04
45 4 0.03
46 31 0.22
47 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (42 bp):
TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCTGATCTA
Found at i:1184052 original size:89 final size:89
Alignment explanation
Indices: 1183927--1184092 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 89
1183917 GACCCTGATC
** *
1183927 TATAGCGGCGCTTTTCCAGAAAACACCGCAATAGACCCTGATCTATAGCGGCGCTTAT-CCAGAA
1 TATAGCGGCGCTTCGCCAGAAAACACCGCAATAGACCCTAATCTATAGCGGCGCTTATACCA-AA
1183991 AACGCAGCTAAATACCCTTTGTCTA
65 AACGCAGCTAAATACCCTTTGTCTA
* *
1184016 TATAGCGGCGCTTCGCGCA-AAAACGCCGCTAA-AGACCCTAATCTATAGCGGCGCTTTTACCAA
1 TATAGCGGCGCTTCGC-CAGAAAACACCGC-AATAGACCCTAATCTATAGCGGCGCTTATACCAA
*
1184079 AAACGCCGCTAAAT
64 AAACGCAGCTAAAT
1184093 TTGGCAGATT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
89 61 0.90
90 7 0.10
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (89 bp):
TATAGCGGCGCTTCGCCAGAAAACACCGCAATAGACCCTAATCTATAGCGGCGCTTATACCAAAA
ACGCAGCTAAATACCCTTTGTCTA
Found at i:1184425 original size:21 final size:21
Alignment explanation
Indices: 1184399--1184510 Score: 125
Period size: 21 Copynumber: 5.3 Consensus size: 21
1184389 TTTGACGCTG
1184399 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
1184420 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
1184441 CTCTGCTTCCCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
1184462 CTGTTCTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
1184483 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
1184504 ATCTGCT
1 CTCTGCT
1184511 CTAAGCTGCT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:1184566 original size:66 final size:65
Alignment explanation
Indices: 1184487--1184627 Score: 187
Period size: 66 Copynumber: 2.2 Consensus size: 65
1184477 TGCCGCCTCT
* *
1184487 GCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAACC
1 GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT--TTGAACA
*
1184550 TTA
63 TCA
* * *
1184553 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTGAACATCA
1 GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTTTGAACATCA
1184618 GCTTCTCTCG
1 GCTTCTCTCG
1184628 ATGTTGCCTC
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
65 19 0.28
66 44 0.66
67 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (65 bp):
GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTTTGAACATCA
Found at i:1184643 original size:65 final size:65
Alignment explanation
Indices: 1184521--1184650 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 65
1184511 CTAAGCTGCT
* * * *
1184521 GCTGGAGTTCTTCATACTTTCGTTGAACCTTAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTC-TTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
1184586 A
65 A
* *
1184587 GCTGGAGTTCTTCATATCTTT-TTGAACATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 GCTGGAGTTCTTCATA-CTTTCTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
1184651 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
65 37 0.65
66 16 0.28
67 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (65 bp):
GCTGGAGTTCTTCATACTTTCTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTA
Found at i:1185809 original size:9 final size:9
Alignment explanation
Indices: 1185795--1185825 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1185785 TTTGGTTAAA
1185795 AATTAACCG
1 AATTAACCG
1185804 AATTAACCG
1 AATTAACCG
*
1185813 AATTAACCA
1 AATTAACCG
1185822 AATT
1 AATT
1185826 GAATCACTAC
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:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1188984 original size:44 final size:45
Alignment explanation
Indices: 1188899--1188987 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 45
1188889 CAATTGTCAA
1188899 AAGATAGACTAAAGTCTGGCATTTTTTACTGGATAAGAGTCCTCC
1 AAGATAGACTAAAGTCTGGCATTTTTTACTGGATAAGAGTCCTCC
1188944 AAGATAGACTAAAGTCTGGCA-TTTTTACTGGATAAGAGTCCTCC
1 AAGATAGACTAAAGTCTGGCATTTTTTACTGGATAAGAGTCCTCC
1188988 TCATCCATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 23 0.52
45 21 0.48
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (45 bp):
AAGATAGACTAAAGTCTGGCATTTTTTACTGGATAAGAGTCCTCC
Found at i:1192947 original size:88 final size:87
Alignment explanation
Indices: 1192767--1192951 Score: 214
Period size: 88 Copynumber: 2.1 Consensus size: 87
1192757 AAAATTTAAA
* * *
1192767 AATTAAGCCCCTCGTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAAT
1 AATTAAGCCCCTCGTTTTTTTTGCACTCAATAGAGCACTTGAACTTTCAAAATGCATAAAAAAAC
* *
1192832 CCCTCAAACTTCTTCAAAAAAATC
66 CCCTCAAAATTCTTC--AAAAAGC
* * *
1192856 AATTAAGCCCCTAC-TTTTTTTT-TACTCAATAGGGTACTTGAACTTTCAAAATGCATAAAAAAA
1 AATTAAGCCCCT-CGTTTTTTTTGCACTCAATAGAGCACTTGAACTTTCAAAATGCAT--AAAAA
*
1192919 AACCCCTTCAAAATTTTTC-AAAAGC
63 AACCCC-TCAAAATTCTTCAAAAAGC
1192944 AATTAAGC
1 AATTAAGC
1192952 TCCTGCTCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
88 43 0.52
89 20 0.24
90 10 0.12
91 10 0.12
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (87 bp):
AATTAAGCCCCTCGTTTTTTTTGCACTCAATAGAGCACTTGAACTTTCAAAATGCATAAAAAAAC
CCCTCAAAATTCTTCAAAAAGC
Found at i:1193030 original size:18 final size:18
Alignment explanation
Indices: 1192980--1193031 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1192970 TAGAAAAAAA
*
1192980 TTATAAAAATAATAAATT
1 TTATAAAAATATTAAATT
* *
1192998 TTAGAAAATTATTAAATT
1 TTATAAAAATATTAAATT
1193016 TTAATAAAAAT-TTAAA
1 TT-ATAAAAATATTAAA
1193032 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TTATAAAAATATTAAATT
Found at i:1193077 original size:17 final size:17
Alignment explanation
Indices: 1193055--1193087 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1193045 AATTTTTTTT
1193055 ATAAAAAATCGTAAAAA
1 ATAAAAAATCGTAAAAA
*
1193072 ATAAAAAATTGTAAAA
1 ATAAAAAATCGTAAAA
1193088 TTTTATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
ATAAAAAATCGTAAAAA
Found at i:1196823 original size:25 final size:24
Alignment explanation
Indices: 1196777--1196829 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1196767 TTAATTGTAC
1196777 TTTCAATTGTAATTTAGATTTCT-
1 TTTCAATTGTAATTTAGATTTCTA
* *
1196800 TTTCAGTTGTAATTTTTAGTTTTCTA
1 TTTCAATTGTAA--TTTAGATTTCTA
1196826 TTTC
1 TTTC
1196830 GTTCTTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
25 10 0.40
26 4 0.16
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTCAATTGTAATTTAGATTTCTA
Found at i:1198418 original size:23 final size:23
Alignment explanation
Indices: 1198389--1198463 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1198379 GTGTTATTGA
1198389 TCAGTGGTAGCTTCGGCTACAGT
1 TCAGTGGTAGCTTCGGCTACAGT
* *
1198412 TCGGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACAGT
1198435 TCAGTGGTAGCTTCGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACAGT
1198457 ATCAGTG
1 -TCAGTG
1198464 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACAGT
Found at i:1202527 original size:17 final size:17
Alignment explanation
Indices: 1202488--1202529 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1202478 TTTTTTTAAG
1202488 TTTATA-ATTCTTTATA
1 TTTATATATTCTTTATA
1202504 TTATATATATT-TTTATA
1 TT-TATATATTCTTTATA
1202521 TATTATATA
1 T-TTATATA
1202530 ATTTACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATTCTTTATA
Found at i:1202638 original size:17 final size:16
Alignment explanation
Indices: 1202609--1202648 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1202599 TGTTAAGATG
* *
1202609 ATTATATAAAAAATTC
1 ATTAAATAAAAAAATC
1202625 ATTAAATAAAAAAATC
1 ATTAAATAAAAAAATC
1202641 ATTAAATA
1 ATTAAATA
1202649 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAATAAAAAAATC
Found at i:1202668 original size:22 final size:23
Alignment explanation
Indices: 1202625--1202672 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1202615 TAAAAAATTC
1202625 ATTAAATAAAAAAATCATTAAAT
1 ATTAAATAAAAAAATCATTAAAT
*
1202648 ATTAAATTAAAAGAA-CA-TAAAT
1 ATTAAA-TAAAAAAATCATTAAAT
1202670 ATT
1 ATT
1202673 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTAAATAAAAAAATCATTAAAT
Found at i:1211407 original size:10 final size:10
Alignment explanation
Indices: 1211388--1211462 Score: 73
Period size: 10 Copynumber: 7.6 Consensus size: 10
1211378 TTATCTTATA
1211388 TTTT-TAATT
1 TTTTATAATT
1211397 TTTTATAA-T
1 TTTTATAATT
*
1211406 TTTTATACTT
1 TTTTATAATT
*
1211416 TTTTATAATA
1 TTTTATAATT
*
1211426 TTTTGTAATT
1 TTTTATAATT
1211436 TTTTATTAATT
1 TTTTA-TAATT
* *
1211447 TATTAAAATT
1 TTTTATAATT
*
1211457 TATTAT
1 TTTTAT
1211463 TTTCTATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
9 12 0.22
10 33 0.61
11 9 0.17
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1211484 original size:19 final size:21
Alignment explanation
Indices: 1211460--1211506 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1211450 TAAAATTTAT
1211460 TATTTTCT-ATATTTTTA-AA
1 TATTTTCTCATATTTTTACAA
*
1211479 TATTTT-TCATTTTTTTACAA
1 TATTTTCTCATATTTTTACAA
1211499 TATTTTCT
1 TATTTTCT
1211507 TTTTGCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 8 0.33
21 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTCTCATATTTTTACAA
Found at i:1211652 original size:9 final size:9
Alignment explanation
Indices: 1211631--1211690 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
1211621 CAATAAGTTT
*
1211631 TTTTTGTAA
1 TTTTTATAA
1211640 TTTTTAT-A
1 TTTTTATAA
*
1211648 TTTTTGTATA
1 TTTTTATA-A
1211658 TTTTTATAA
1 TTTTTATAA
**
1211667 TGATTATAA
1 TTTTTATAA
*
1211676 TTTTTATTA
1 TTTTTATAA
1211685 TTTTTA
1 TTTTTA
1211691 ATAAAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 7 0.17
9 26 0.63
10 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1211700 original size:28 final size:27
Alignment explanation
Indices: 1211643--1211700 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1211633 TTTGTAATTT
* **
1211643 TTATATTTTTGTATATTTTTATAATGA
1 TTATATTTTTATATATTTTTATAAAAA
1211670 TTATAATTTTTAT-TATTTTTAATAAAAA
1 TTAT-ATTTTTATATATTTTT-ATAAAAA
1211698 TTA
1 TTA
1211701 GTTTTCACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATATTTTTATATATTTTTATAAAAA
Found at i:1223776 original size:8 final size:8
Alignment explanation
Indices: 1223754--1223786 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1223744 CTTTTCAACA
1223754 AAAAAAAT
1 AAAAAAAT
1223762 AAGAAAAAT
1 AA-AAAAAT
1223771 -AAAAAAT
1 AAAAAAAT
1223778 AAAAAAAT
1 AAAAAAAT
1223786 A
1 A
1223787 CTCCTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.26
8 11 0.48
9 6 0.26
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1224412 original size:29 final size:32
Alignment explanation
Indices: 1224361--1224420 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 32
1224351 AATTTTGTGC
*
1224361 AGGAATACAATTTGGGGCTAAA-TAGAAGAAAA
1 AGGAATACAATTTGGGGCCAAATTA-AAGAAAA
1224393 AGGAA-ACAA-TT-GGGCCAAATTAAAGAAA
1 AGGAATACAATTTGGGGCCAAATTAAAGAAA
1224421 GAAGCAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 13 0.50
30 4 0.15
31 4 0.15
32 5 0.19
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCCAAATTAAAGAAAA
Found at i:1237119 original size:21 final size:22
Alignment explanation
Indices: 1237070--1237119 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1237060 ATATTATTTT
* *
1237070 AAATT-TTTTAATATTTATATT
1 AAATTATTTCAATATTTATATA
*
1237091 ATATTATTTCAATATTTA-ATA
1 AAATTATTTCAATATTTATATA
1237112 AAATTATT
1 AAATTATT
1237120 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATTTCAATATTTATATA
Found at i:1237469 original size:11 final size:12
Alignment explanation
Indices: 1237455--1237483 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1237445 AAAATTTAAA
1237455 TTAAAT-ATTAT
1 TTAAATAATTAT
1237466 TTAAATAATTAT
1 TTAAATAATTAT
1237478 TTAAAT
1 TTAAAT
1237484 TAAGGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATAATTAT
Found at i:1243404 original size:21 final size:21
Alignment explanation
Indices: 1243378--1243418 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1243368 ATCTGCTCAA
* *
1243378 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1243399 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1243419 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1246461 original size:20 final size:21
Alignment explanation
Indices: 1246411--1246462 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1246401 CGCTTGGAGT
*
1246411 ACTCTTTTCGATATTACTCTA
1 ACTCTTTTCAATATTACTCTA
* *
1246432 ACTTTTTTCAATATTATTCTA
1 ACTCTTTTCAATATTACTCTA
1246453 A-TCTTTTCAA
1 ACTCTTTTCAA
1246463 ATCTGGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (21 bp):
ACTCTTTTCAATATTACTCTA
Found at i:1250602 original size:18 final size:18
Alignment explanation
Indices: 1250579--1250635 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
1250569 TACGACCGTT
1250579 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
1250597 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
1250615 TACGGTACTATTCACATA
1 TACGGCACTATTCACGTA
1250633 TAC
1 TAC
1250636 AGTAGTTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:1265121 original size:14 final size:14
Alignment explanation
Indices: 1265102--1265128 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1265092 CATCATTTGC
1265102 CTATAACCAAAACT
1 CTATAACCAAAACT
1265116 CTATAACCAAAAC
1 CTATAACCAAAAC
1265129 CCAAAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.19
Consensus pattern (14 bp):
CTATAACCAAAACT
Found at i:1268296 original size:30 final size:30
Alignment explanation
Indices: 1268255--1268336 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
1268245 CATATTTATG
* *
1268255 GAAAATCAAAGACATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
1268285 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
1268315 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
1268337 GAGATATTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:1268308 original size:15 final size:15
Alignment explanation
Indices: 1268259--1268336 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
1268249 TTTATGGAAA
*
1268259 ATCAAAGACATGGGT
1 ATCAAAGATATGGGT
* * **
1268274 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
1268288 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
1268304 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
1268318 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
1268334 ATC
1 ATC
1268337 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:1272941 original size:15 final size:15
Alignment explanation
Indices: 1272921--1272968 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1272911 TTTATGGAAA
1272921 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
1272936 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
1272950 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
1272966 ATC
1 ATC
1272969 GAGATATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:1272949 original size:30 final size:31
Alignment explanation
Indices: 1272915--1272978 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
1272905 TCCATATTTA
1272915 TGGAAAATCAAAGATATGGGTATC-AAATAT
1 TGGAAAATCAAAGATATGGGTATCGAAATAT
* *
1272945 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAATCAAAGATATGGGTATCGAAATAT
1272976 TGG
1 TGG
1272979 CATAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (31 bp):
TGGAAAATCAAAGATATGGGTATCGAAATAT
Found at i:1280930 original size:21 final size:21
Alignment explanation
Indices: 1280906--1280946 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280896 CCAATGAGTA
*
1280906 TTTAAGGTTTAGGGTTTAAAG
1 TTTAAGGTTTAGGATTTAAAG
1280927 TTTAAGGTTTAGGATTTAAA
1 TTTAAGGTTTAGGATTTAAA
1280947 TTTGATTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (21 bp):
TTTAAGGTTTAGGATTTAAAG
Found at i:1282615 original size:24 final size:24
Alignment explanation
Indices: 1282571--1282618 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1282561 GATTCATCCA
**
1282571 TACTAAAATAAATTATTTTAAAAT
1 TACTAAAATAAATTAAGTTAAAAT
1282595 TACTAAAAATAAA-TAAGTTAAAAT
1 TACT-AAAATAAATTAAGTTAAAAT
1282619 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TACTAAAATAAATTAAGTTAAAAT
Found at i:1282873 original size:20 final size:21
Alignment explanation
Indices: 1282833--1282873 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1282823 ATAATCATTA
1282833 TAAAAATATACAAAAATATTT
1 TAAAAATATACAAAAATATTT
1282854 TAAAAAT-TACAAGAAA-ATTT
1 TAAAAATATACAA-AAATATTT
1282874 ATTGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAAATATACAAAAATATTT
Found at i:1282959 original size:33 final size:33
Alignment explanation
Indices: 1282917--1282983 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1282907 AAATTGTTAT
1282917 AAATAAAAATAAAATAATTA-A-AAACTTGCAAAA
1 AAATAAAAATAAAA-AATTATATAAA-TTGCAAAA
* *
1282950 AAATTAAAATTAAAAATTATATAAATTGCAAAA
1 AAATAAAAATAAAAAATTATATAAATTGCAAAA
1282983 A
1 A
1282984 TAAAATATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 5 0.17
33 22 0.73
34 3 0.10
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.25
Consensus pattern (33 bp):
AAATAAAAATAAAAAATTATATAAATTGCAAAA
Found at i:1282999 original size:17 final size:17
Alignment explanation
Indices: 1282979--1283017 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1282969 TATAAATTGC
1282979 AAAAAT-AAAATATTGTA
1 AAAAATAAAAATATT-TA
1282996 AAAAATGAAAAATATTTA
1 AAAAAT-AAAAATATTTA
1283014 AAAA
1 AAAA
1283018 TGTAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAAATAAAAATATTTA
Found at i:1283006 original size:24 final size:23
Alignment explanation
Indices: 1282947--1283009 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
1282937 AAAACTTGCA
* *
1282947 AAAAAATTAAAATTAAAAATTAT
1 AAAAAATGAAAAATAAAAATTAT
* * *
1282970 ATAAATTGCAAAAATAAAATATTGT
1 AAAAAATG-AAAAATAAAA-ATTAT
1282995 AAAAAATGAAAAATA
1 AAAAAATGAAAAATA
1283010 TTTAAAAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 5 0.16
24 16 0.52
25 10 0.32
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AAAAAATGAAAAATAAAAATTAT
Found at i:1283089 original size:18 final size:18
Alignment explanation
Indices: 1283061--1283107 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1283051 AAAAATTACA
*
1283061 AAAATATTATAAAAAGTAT
1 AAAA-ATTATAAAAAATAT
*
1283080 AAAAATTATAAAAAATTT
1 AAAAATTATAAAAAATAT
1283098 AAAAA-TATAA
1 AAAAATTATAA
1283108 GACAGACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 5 0.19
18 17 0.65
19 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATTATAAAAAATAT
Found at i:1283094 original size:11 final size:10
Alignment explanation
Indices: 1283026--1283102 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1283016 AATGTAGAAA
*
1283026 ATAATAAATT
1 ATAAAAAATT
* *
1283036 TTAATAAATT
1 ATAAAAAATT
1283046 AATAAAAAAATT
1 -AT-AAAAAATT
*
1283058 ACAAAAATATT
1 ATAAAAA-ATT
*
1283069 AT-AAAAAGT
1 ATAAAAAATT
1283078 AT-AAAAATT
1 ATAAAAAATT
1283087 ATAAAAAATT
1 ATAAAAAATT
1283097 -TAAAAA
1 ATAAAAA
1283103 TATAAGACAG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
9 18 0.32
10 25 0.45
11 6 0.11
12 7 0.12
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:1283302 original size:27 final size:26
Alignment explanation
Indices: 1283269--1283319 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1283259 TTTATACAAA
1283269 TTGTTTTCATG-TTTATAATTTTTATAG
1 TTGTTTT-ATGATTT-TAATTTTTATAG
*
1283296 TTGTTTTATGATTTTATTTTTTAT
1 TTGTTTTATGATTTTAATTTTTAT
1283320 GATTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.69
Consensus pattern (26 bp):
TTGTTTTATGATTTTAATTTTTATAG
Found at i:1298351 original size:22 final size:22
Alignment explanation
Indices: 1298326--1298372 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
1298316 ATTTTTTAAA
1298326 AATATTT-ATG-TTCTTTTAATTT
1 AATATTTAATGATT-TTTT-ATTT
1298348 AATATTTAATGATTTTTTATTT
1 AATATTTAATGATTTTTTATTT
1298370 AAT
1 AAT
1298373 GAATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.61
23 7 0.30
24 2 0.09
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
AATATTTAATGATTTTTTATTT
Found at i:1298384 original size:17 final size:15
Alignment explanation
Indices: 1298350--1298381 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1298340 TTTAATTTAA
1298350 TATTTAATGATTTTT
1 TATTTAATGATTTTT
1298365 TATTTAATGAATTTTT
1 TATTTAATG-ATTTTT
1298381 T
1 T
1298382 TATATAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TATTTAATGATTTTT
Found at i:1302547 original size:23 final size:23
Alignment explanation
Indices: 1302521--1302596 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
1302511 ATAAGTGCCA
1302521 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1302544 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1302567 CACCGA-ACTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
1302590 CACTGAT
1 CACTGAT
1302597 CAATAACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1304193 original size:25 final size:24
Alignment explanation
Indices: 1304154--1304206 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1304144 CACAAAGAAC
1304154 GAAATAGAAAACTAAAAATTACAACT
1 GAAATAGAAAACT--AAATTACAACT
* *
1304180 GAAA-AGAAATCTAAATTACAATT
1 GAAATAGAAAACTAAATTACAACT
1304203 GAAA
1 GAAA
1304207 GTACAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
25 7 0.28
26 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (24 bp):
GAAATAGAAAACTAAATTACAACT
Found at i:1307944 original size:38 final size:37
Alignment explanation
Indices: 1307888--1308000 Score: 95
Period size: 38 Copynumber: 3.0 Consensus size: 37
1307878 ACTAGGGGTC
*
1307888 ATTTTTTTATGA-TATTTATAAAATTTTACAATTTTTT
1 ATTTTTTTA-GATTTTTTATAAAATTTTACAATTTTTT
** *
1307925 ATTTTTTTACGATTTTTTATAAAAAAAATT-CTATTTTTT
1 ATTTTTTTA-GATTTTTTAT--AAAATTTTACAATTTTTT
* * * *
1307964 AATTTTTTAAATTTTTTATTAAAATTTAATAATTTTT
1 ATTTTTTTAGATTTTTTA-TAAAATTTTACAATTTTT
1308001 CTAAAATTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
37 16 0.27
38 20 0.34
39 17 0.29
40 6 0.10
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (37 bp):
ATTTTTTTAGATTTTTTATAAAATTTTACAATTTTTT
Found at i:1308146 original size:89 final size:87
Alignment explanation
Indices: 1308052--1308237 Score: 223
Period size: 88 Copynumber: 2.1 Consensus size: 87
1308042 AAGAGCAGGA
* * *
1308052 GCTTAATTG-CTTTTTGAAAAATTTTGAAGGGGTTTTTTTTTATGCATTTTGAAAGTTCAAGTAC
1 GCTTAATTGACTTTTTGAAAAAGTTTG-A-GGG-ATTTTTTGATGCATTTTGAAAGTTCAAGTAC
*
1308116 CCTATTGAGT-AAAAAAAAAGTAGGG
63 CCAATTGAGTCAAAAAAAAAG-AGGG
* * * *
1308141 GCTTAATTGATTTTTTTGAAGAAGTTTGAGGGATTTTTTGATGCATTTTGAAAGTTCAAGTGCTC
1 GCTTAATTGA-CTTTTTGAAAAAGTTTGAGGGATTTTTTGATGCATTTTGAAAGTTCAAGTACCC
*
1308206 AATTGAGTGCAAAAAAAACGAGGG
65 AATTGAGT-CAAAAAAAAAGAGGG
1308230 GCTTAATT
1 GCTTAATT
1308238 TTTAAATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 36 0.43
89 24 0.29
90 10 0.12
91 14 0.17
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (87 bp):
GCTTAATTGACTTTTTGAAAAAGTTTGAGGGATTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
ATTGAGTCAAAAAAAAAGAGGG
Found at i:1312077 original size:45 final size:45
Alignment explanation
Indices: 1312026--1312115 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1312016 AGATGGATGA
1312026 GGAGGACTCTTATCCAGTAAAAAATGCCAGACTTTAGTCTATCTT
1 GGAGGACTCTTATCCAGTAAAAAATGCCAGACTTTAGTCTATCTT
1312071 GGAGGACTCTTATCCAGTAAAAAATGCCAGACTTTAGTCTATCTT
1 GGAGGACTCTTATCCAGTAAAAAATGCCAGACTTTAGTCTATCTT
1312116 TTGACAATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (45 bp):
GGAGGACTCTTATCCAGTAAAAAATGCCAGACTTTAGTCTATCTT
Found at i:1315216 original size:9 final size:9
Alignment explanation
Indices: 1315199--1315229 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1315189 GTAGTGATTC
*
1315199 AATTTGGTT
1 AATTCGGTT
1315208 AATTCGGTT
1 AATTCGGTT
1315217 AATTCGGTT
1 AATTCGGTT
1315226 AATT
1 AATT
1315230 TTTAACCAAA
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:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1316472 original size:66 final size:65
Alignment explanation
Indices: 1316378--1316543 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 65
1316368 GAGCAAATTA
* * * * * *
1316378 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAG-TATGAAGAACTCCA
1316442 G
65 G
*
1316443 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCA
1316508 G
65 G
* * * *
1316509 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGC
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGC
1316544 AGAGGCGGCA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 81 0.93
67 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:1316546 original size:21 final size:21
Alignment explanation
Indices: 1316520--1316631 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
1316510 AGCAGCTTAG
*
1316520 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
1316541 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
* * * *
1316562 AGAACAGGCTGCAGCAAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
*** * *
1316583 AGCAGAGGCTAAAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
* * *
1316604 AGCAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
1316625 AGCAGAG
1 AGCAGAG
1316632 CAGCGTCAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.36, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:1316576 original size:42 final size:42
Alignment explanation
Indices: 1316530--1316631 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
1316520 AGCAGATGCG
* **
1316530 GCAGCAAGAGAAGCAGAGGCGGCAGCGAGAGAAGAACAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
* * * *
1316572 GCAGCAAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
*
1316614 GCAGCGAGGGAAGCAGAG
1 GCAGCAAGGGAAGCAGAG
1316632 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.43, T:0.03
Consensus pattern (42 bp):
GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
Found at i:1316986 original size:43 final size:42
Alignment explanation
Indices: 1316938--1317143 Score: 229
Period size: 43 Copynumber: 4.7 Consensus size: 42
1316928 ATCTGCCAAA
*
1316938 TTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTC
1 TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTATAGATCAGGGTC
** *
1316981 TTTAGCGGCGTTTTTGCGCGAAGCGCCGCTATATAGA-CAAAGGGTA
1 TTTAGCGGCGTTTTTG-GAAAAGCGCCGC--TATAGATC--AGGGTC
* *
1317027 TTTAGCTGCGTTTTCTGGATAAGCGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTT-TGGAAAAGCGCCGCTATAGATCAGGGTC
*
1317070 TATT-GCGGTGTTTTCTGGAAAAGCGCCGCTATAGATCAGGGTC
1 T-TTAGCGGCGTTTT-TGGAAAAGCGCCGCTATAGATCAGGGTC
1317113 TATT-GCGGCGTTTTTGGGAAAAGCGCCGCTA
1 T-TTAGCGGCGTTTTT-GGAAAAGCGCCGCTA
1317144 AAGGCCATGA
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.01
43 95 0.67
44 9 0.06
45 7 0.05
46 28 0.20
47 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTATAGATCAGGGTC
Found at i:1317094 original size:89 final size:89
Alignment explanation
Indices: 1316937--1317143 Score: 241
Period size: 89 Copynumber: 2.4 Consensus size: 89
1316927 AATCTGCCAA
* **
1316937 ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTCTTTAGCGGCGTTTTTGCGCGA
1 ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTTTGCGAAA
1317002 AGCGCCGCTATATAGACAAAGGGT
66 AGCGCCGCTATATAGACAAAGGGT
* * *
1317026 ATTTAGCTGCGTTTTCTGG-ATAAGCGCCGCTATAGATCAGGGTCTATT-GCGGTGTTTTCTG-G
1 ATTTAGCGGCGTTTT-TGGTAAAAGCGCCGCTATAGATCAGGGTCT-TTAGCGGCGTTTT-TGCG
1317088 AAAAGCGCCGC--TATAGATC--AGGGT
63 AAAAGCGCCGCTATATAGA-CAAAGGGT
* *
1317112 CTATT-GCGGCGTTTTTGGGAAAAGCGCCGCTA
1 AT-TTAGCGGCGTTTTTGGTAAAAGCGCCGCTA
1317144 AAGGCCATGA
Statistics
Matches: 103, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
85 3 0.03
86 27 0.26
87 8 0.08
88 1 0.01
89 57 0.55
90 7 0.07
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (89 bp):
ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTTTGCGAAA
AGCGCCGCTATATAGACAAAGGGT
Found at i:1317445 original size:31 final size:33
Alignment explanation
Indices: 1317389--1317450 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
1317379 AGCGGCATCT
*
1317389 TTTGCGGCGCTTATCAAAGCACCGCTAAAAGTA
1 TTTGCGGCGCTTATAAAAGCACCGCTAAAAGTA
*
1317422 TTTGCGGCGC-TA-AAAAGCGCCGCTAAAAG
1 TTTGCGGCGCTTATAAAAGCACCGCTAAAAG
1317451 CTTGTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 15 0.56
32 2 0.07
33 10 0.37
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (33 bp):
TTTGCGGCGCTTATAAAAGCACCGCTAAAAGTA
Found at i:1318834 original size:12 final size:12
Alignment explanation
Indices: 1318819--1318872 Score: 90
Period size: 12 Copynumber: 4.5 Consensus size: 12
1318809 TATTTGAAAT
1318819 TTTATAATCTGG
1 TTTATAATCTGG
*
1318831 TTTATATTCTGG
1 TTTATAATCTGG
1318843 TTTATAATCTGG
1 TTTATAATCTGG
*
1318855 TTTATAATCTAG
1 TTTATAATCTGG
1318867 TTTATA
1 TTTATA
1318873 CCTTGTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:1320055 original size:18 final size:17
Alignment explanation
Indices: 1320032--1320066 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1320022 GAATATATTT
1320032 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
1320050 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
1320067 ACCCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:1320908 original size:18 final size:16
Alignment explanation
Indices: 1320885--1320920 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
1320875 GTTTAAAATT
1320885 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
1320903 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
1320919 TT
1 TT
1320921 CTCATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:1323510 original size:22 final size:21
Alignment explanation
Indices: 1323462--1323519 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
1323452 ATAATCATTA
*
1323462 TAAAAATATACAAAAATATTT
1 TAAAAATATACAAAAAAATTT
1323483 TAAAAAT-TACAAAAAAATTAAT
1 TAAAAATATACAAAAAAATT--T
* *
1323505 TGAAAATATAGAAAA
1 TAAAAATATACAAAA
1323520 GTGCACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 7 0.23
23 6 0.19
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
TAAAAATATACAAAAAAATTT
Found at i:1323562 original size:22 final size:23
Alignment explanation
Indices: 1323526--1323570 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1323516 AAAAGTGCAC
1323526 AAAAATGATAAAATTATTATAAAT
1 AAAAATGATAAAATTA-TATAAAT
1323550 AAAAAT-A-AAAATTATATAAAT
1 AAAAATGATAAAATTATATAAAT
1323571 TGCAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 1 0.05
24 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAATGATAAAATTATATAAAT
Found at i:1323583 original size:24 final size:23
Alignment explanation
Indices: 1323525--1323583 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1323515 GAAAAGTGCA
1323525 CAAAAATGATAAAATTATTATAAAT
1 CAAAAA-GA-AAAATTATTATAAAT
*
1323550 -AAAAATAAAAATTA-TATAAATT
1 CAAAAAGAAAAATTATTATAAA-T
1323572 GCAAAAAGAAAA
1 -CAAAAAGAAAA
1323584 TATTGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 1 0.03
24 14 0.48
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (23 bp):
CAAAAAGAAAAATTATTATAAAT
Found at i:1323613 original size:19 final size:20
Alignment explanation
Indices: 1323578--1323624 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
1323568 AATTGCAAAA
1323578 AGAAAATATTGTAAAAA-AT
1 AGAAAATATTGTAAAAATAT
1323597 ATGAAAATATT-TAAAAATAT
1 A-GAAAATATTGTAAAAATAT
1323617 AGAAAATA
1 AGAAAATA
1323625 ATAAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
AGAAAATATTGTAAAAATAT
Found at i:1323684 original size:9 final size:9
Alignment explanation
Indices: 1323435--1323687 Score: 61
Period size: 9 Copynumber: 26.7 Consensus size: 9
1323425 TAATTTTTAT
*
1323435 TAAAAATAA
1 TAAAAATTA
1323444 TAAAAATTA
1 TAAAAATTA
**
1323453 TAATCATTA
1 TAAAAATTA
1323462 TAAAAATATA
1 TAAAAAT-TA
* *
1323472 CAAAAATATTT
1 -TAAAA-ATTA
1323483 TAAAAATTACA
1 TAAAAATT--A
*
1323494 AAAAAATTAA
1 TAAAAATT-A
*
1323504 TTGAAAA-TA
1 -TAAAAATTA
*
1323513 TAGAAAAGTGCA
1 TA-AAAA-T-TA
* *
1323525 CAAAAATGA
1 TAAAAATTA
1323534 TAAAATTATTA
1 TAAAA--ATTA
**
1323545 TAAATAAAAA
1 TAAA-AATTA
1323555 TAAAAATTA
1 TAAAAATTA
* *
1323564 TATAAATTG
1 TAAAAATTA
* *
1323573 CAAAAA-GA
1 TAAAAATTA
* *
1323581 -AAATATTG
1 TAAAAATTA
*
1323589 TAAAAAATA
1 TAAAAATTA
1323598 TGAAAATATT-
1 T-AAAA-ATTA
1323608 TAAAAA-TA
1 TAAAAATTA
1323616 TAGAAAA-TA
1 TA-AAAATTA
* *
1323625 -ATAAATTT
1 TAAAAATTA
1323633 TAATAAATTA
1 TAA-AAATTA
1323643 GTAAAAATTA
1 -TAAAAATTA
*
1323653 CAAAATATTA
1 TAAAA-ATTA
**
1323663 TAAAAAAGCA
1 T-AAAAATTA
1323673 TAAAAATTA
1 TAAAAATTA
1323682 TAAAAA
1 TAAAAA
1323688 AACTTTAAAA
Statistics
Matches: 173, Mismatches: 46, Indels: 50
0.64 0.17 0.19
Matches are distributed among these distances:
7 8 0.05
8 6 0.03
9 80 0.46
10 38 0.22
11 36 0.21
12 5 0.03
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1323697 original size:19 final size:19
Alignment explanation
Indices: 1323637--1323703 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
1323627 AAATTTTAAT
*
1323637 AAATTAGTAAAAATTACA-AA
1 AAATTA-TAAAAA-AACATAA
* *
1323657 ATATTATAAAAAAGCATAA
1 AAATTATAAAAAAACATAA
*
1323676 AAATTATAAAAAAACTTTAA
1 AAATTATAAAAAAAC-ATAA
1323696 AAA-TATAA
1 AAATTATAA
1323704 GACAAACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 26 0.67
20 11 0.28
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATTATAAAAAAACATAA
Found at i:1323711 original size:20 final size:20
Alignment explanation
Indices: 1323654--1323703 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1323644 TAAAAATTAC
* *
1323654 AAAATATTATAAAAAAGC-AT
1 AAAA-ATTATAAAAAAACTTT
1323674 AAAAATTATAAAAAAACTTT
1 AAAAATTATAAAAAAACTTT
1323694 AAAAA-TATAA
1 AAAAATTATAA
1323704 GACAAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATAAAAAAACTTT
Found at i:1336848 original size:21 final size:21
Alignment explanation
Indices: 1336823--1336866 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1336813 TTTTGTTACA
1336823 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
1336844 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
1336865 AT
1 AT
1336867 TCTTTGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (21 bp):
ATGGCTTCTACAGATTCATCC
Found at i:1355357 original size:6 final size:6
Alignment explanation
Indices: 1355348--1355394 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
1355338 CATGTTCATA
1355348 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATAT
1355395 TTAAGGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:1355640 original size:17 final size:18
Alignment explanation
Indices: 1355615--1355650 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1355605 CTGATCAGGC
*
1355615 ATTGGTTCGTC-AGTCTA
1 ATTGATTCGTCTAGTCTA
1355632 ATTGATTCGTCTAGTCTA
1 ATTGATTCGTCTAGTCTA
1355650 A
1 A
1355651 CCACTTCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (18 bp):
ATTGATTCGTCTAGTCTA
Found at i:1358358 original size:22 final size:22
Alignment explanation
Indices: 1358305--1358367 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
1358295 AATTATAATC
*
1358305 ATTA-TAAAAATATACAAAAAT
1 ATTATTAAAAATATACAAAAAA
*
1358326 ATTTTTAAAAAT-TACAAAAGAA
1 ATTATTAAAAATATACAAAA-AA
*
1358348 ATTATTGAAAAA-ATAGAAAA
1 ATTATT-AAAAATATACAAAA
1358368 TTGCACAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 10 0.29
22 13 0.38
23 11 0.32
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (22 bp):
ATTATTAAAAATATACAAAAAA
Found at i:1360913 original size:78 final size:78
Alignment explanation
Indices: 1360784--1360941 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
1360774 GTCCTGGTAA
1360784 GAAAAAACAAAATCAAGAAAGCCAGTTGATACTTCCAGTTGATACCAATGAAAGAAGCTCAACGT
1 GAAAAAACAAAATCAAGAAAGCCAGTTGATACTTCCAGTTGATACCAATGAAAGAAGCTCAACGT
*
1360849 TTTATCAAGAAAG
66 TTGATCAAGAAAG
*
1360862 GAAAAAACAAAATCAAGAAAGCCAGTTGATACTTCCAGTTGATACCAATGAAAGAAGCTCAATGT
1 GAAAAAACAAAATCAAGAAAGCCAGTTGATACTTCCAGTTGATACCAATGAAAGAAGCTCAACGT
1360927 TTGATCAAGAAAG
66 TTGATCAAGAAAG
1360940 GA
1 GA
1360942 GTCACTTGGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (78 bp):
GAAAAAACAAAATCAAGAAAGCCAGTTGATACTTCCAGTTGATACCAATGAAAGAAGCTCAACGT
TTGATCAAGAAAG
Found at i:1364070 original size:21 final size:22
Alignment explanation
Indices: 1364021--1364071 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1364011 TATCCTGCCA
* *
1364021 AAAATTATTGGTATTTTTAAAT
1 AAAATTATTAGTATTATTAAAT
* *
1364043 GAAATTATTAGTA-TATTATAT
1 AAAATTATTAGTATTATTAAAT
1364064 AAAATTAT
1 AAAATTAT
1364072 ATAAAGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
AAAATTATTAGTATTATTAAAT
Found at i:1372557 original size:7 final size:7
Alignment explanation
Indices: 1372533--1372660 Score: 50
Period size: 7 Copynumber: 17.7 Consensus size: 7
1372523 ATTATTTTAA
1372533 ATTATAT
1 ATTATAT
*
1372540 TTTATAGT
1 ATTATA-T
1372548 ATTATAT
1 ATTATAT
1372555 ATTATGAT
1 ATTAT-AT
* *
1372563 TTTAGTAA
1 ATTA-TAT
1372571 ATTCATAT
1 ATT-ATAT
*
1372579 AATA-AT
1 ATTATAT
1372585 ATT-TAAT
1 ATTAT-AT
* *
1372592 ACTACATAG
1 A-T-TATAT
*
1372601 ATTATAA
1 ATTATAT
1372608 ATTATAT
1 ATTATAT
1372615 -TTA-AT
1 ATTATAT
1372620 AATTAT-T
1 -ATTATAT
* *
1372627 ATTTTAA
1 ATTATAT
1372634 ATTATAT
1 ATTATAT
*
1372641 TTTATAGT
1 ATTATA-T
1372649 ATTATAT
1 ATTATAT
1372656 ATTAT
1 ATTAT
1372661 GATTTTAGTA
Statistics
Matches: 88, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
5 2 0.02
6 11 0.12
7 44 0.50
8 26 0.30
9 4 0.05
10 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:1372607 original size:101 final size:101
Alignment explanation
Indices: 1372481--1372696 Score: 391
Period size: 101 Copynumber: 2.2 Consensus size: 101
1372471 TATTCTATTG
*
1372481 AGAA-ATTTAA-ACAACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1372544 TAGTATTATATATTATGATTTTAGTAAATTCATATA
66 TAGTATTATATATTATGATTTTAGTAAATTCATATA
* *
1372580 ATAATATTTAATACTACATAGATTATAAATTATATTTAATAATTATTATTTTAAATTATATTTTA
1 AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1372645 TAGTATTATATATTATGATTTTAGTAAATTCATATA
66 TAGTATTATATATTATGATTTTAGTAAATTCATATA
1372681 AGAATATTTAATACTA
1 AGAATATTTAATACTA
1372697 AGAATTTTAT
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 3 0.03
100 6 0.05
101 102 0.92
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (101 bp):
AGAATATTTAATACTACATAGATTATAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
TAGTATTATATATTATGATTTTAGTAAATTCATATA
Found at i:1372640 original size:26 final size:26
Alignment explanation
Indices: 1372500--1372660 Score: 95
Period size: 26 Copynumber: 6.2 Consensus size: 26
1372490 AACAACATAG
*
1372500 ATTATAAATTATATTTAATAATAATT
1 ATTATAAATTATATTTAATAATTATT
* *
1372526 ATTTTAAATTATATTT--T-A-TAGT
1 ATTATAAATTATATTTAATAATTATT
* *
1372548 ATTATATATTATGATTTTAGTAA--ATT
1 ATTATAAATTAT-A-TTTAATAATTATT
* * * *
1372574 CA-TAT-AATAATATTTAATACTACATAG
1 -ATTATAAATTATATTTAATAAT-TAT-T
1372601 ATTATAAATTATATTTAATAATTATT
1 ATTATAAATTATATTTAATAATTATT
* *
1372627 ATTTTAAATTATATTTTATAGTATTATAT
1 ATTATAAATTATATTTAATA--ATTAT-T
1372656 ATTAT
1 ATTAT
1372661 GATTTTAGTA
Statistics
Matches: 102, Mismatches: 18, Indels: 27
0.69 0.12 0.18
Matches are distributed among these distances:
22 12 0.12
23 8 0.08
24 5 0.05
25 4 0.04
26 42 0.41
27 7 0.07
28 19 0.19
29 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATAAATTATATTTAATAATTATT
Found at i:1372763 original size:12 final size:12
Alignment explanation
Indices: 1372724--1372764 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
1372714 TATATTTTTA
1372724 TTAAATTATATT
1 TTAAATTATATT
*
1372736 TTATAATAATTATT
1 TTA-AATTA-TATT
1372750 TTAAATTATATT
1 TTAAATTATATT
1372762 TTA
1 TTA
1372765 TAGTATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 8 0.32
14 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTATATT
Found at i:1372805 original size:18 final size:17
Alignment explanation
Indices: 1372782--1372833 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
1372772 ACATATTATG
1372782 ATTTTAGTAAATTCATAT
1 ATTTTAGTAAATT-ATAT
*
1372800 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
*
1372817 ATTTTTATTAAATTATA
1 A-TTTTAGTAAATTATA
1372834 ATAATTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 5 0.16
18 27 0.84
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:1373083 original size:16 final size:15
Alignment explanation
Indices: 1373062--1373114 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1373052 ATATTTACCT
1373062 ATTACGTCTCTATTTC
1 ATTACG-CTCTATTTC
*
1373078 ATTACGCATTTATTTC
1 ATTACGC-TCTATTTC
* *
1373094 ATTACACCTCTATTCC
1 ATTAC-GCTCTATTTC
1373110 ATTAC
1 ATTAC
1373115 AGCGAACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.04, T:0.45
Consensus pattern (15 bp):
ATTACGCTCTATTTC
Found at i:1373115 original size:16 final size:16
Alignment explanation
Indices: 1373069--1373115 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1373059 CCTATTACGT
*
1373069 CTCTATTTCATTACGC
1 CTCTATTTCATTACAC
* *
1373085 ATTTATTTCATTACAC
1 CTCTATTTCATTACAC
*
1373101 CTCTATTCCATTACA
1 CTCTATTTCATTACA
1373116 GCGAACCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.45
Consensus pattern (16 bp):
CTCTATTTCATTACAC
Found at i:1375847 original size:20 final size:20
Alignment explanation
Indices: 1375823--1375862 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 20
1375813 AAAATAATAC
1375823 AAAAATATACAAAAAAATTTT
1 AAAAAT-TACAAAAAAATTTT
1375844 AAAAATTACAAAAAAATTT
1 AAAAATTACAAAAAAATTT
1375863 ATTGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTACAAAAAAATTTT
Found at i:1376017 original size:21 final size:20
Alignment explanation
Indices: 1375983--1376026 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1375973 TTGCAAAAAG
* *
1375983 AAAATGTTTTAAAAAATATGA
1 AAAATATTTAAAAAAATA-GA
*
1376004 AAAATATTTAAAAATATAGA
1 AAAATATTTAAAAAAATAGA
1376024 AAA
1 AAA
1376027 TAATAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAATATTTAAAAAAATAGA
Found at i:1376099 original size:19 final size:19
Alignment explanation
Indices: 1376049--1376101 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1376039 ATAAGTTAAT
*
1376049 AAAAATATAAAATATTATAA
1 AAAAATATAAAA-GTTATAA
1376069 AAAAAGTATAAAAGTTATAA
1 AAAAA-TATAAAAGTTATAA
*
1376089 AAAAATTTAAAAG
1 AAAAATATAAAAG
1376102 GATAAGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 7 0.23
20 16 0.53
21 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAAGTTATAA
Found at i:1376269 original size:21 final size:20
Alignment explanation
Indices: 1376243--1376287 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1376233 TTGTTGAATA
1376243 TTTTTTTGTAAT-TTTATACAT
1 TTTTTTTG-AATGTTTATA-AT
*
1376264 TTTTTTTGCATGTTTATAAT
1 TTTTTTTGAATGTTTATAAT
1376284 TTTT
1 TTTT
1376288 ATAGTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTTTTGAATGTTTATAAT
Found at i:1377230 original size:19 final size:19
Alignment explanation
Indices: 1377155--1377232 Score: 51
Period size: 19 Copynumber: 4.3 Consensus size: 19
1377145 TTAATACAAT
*
1377155 TAACAATTAATAATTTGA-
1 TAACAATTAATAATTTTAC
* *
1377173 TATA-ATTTGATAATTTTAC
1 TA-ACAATTAATAATTTTAC
* *
1377192 TAATAATTAATACA----AT
1 TAACAATTAATA-ATTTTAC
1377208 TAACAATTAATAATTTTAC
1 TAACAATTAATAATTTTAC
1377227 TAACAA
1 TAACAA
1377233 AATGTTAGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
15 1 0.02
16 12 0.27
18 14 0.32
19 16 0.36
20 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
TAACAATTAATAATTTTAC
Found at i:1377250 original size:86 final size:85
Alignment explanation
Indices: 1377155--1377326 Score: 235
Period size: 86 Copynumber: 2.0 Consensus size: 85
1377145 TTAATACAAT
*
1377155 TAACAATTAATAATTTGATATAATTTG-ATAATTTTACTAATAATTAAT-ACAATT-A-ACAATT
1 TAACAATTAATAA-TT-A-ATAATTTGAATAATTTGA-TAAT-ATTAATAACAATTAATACAATT
1377216 AATAATTTTACTAACAAAATGTTAG
61 AATAATTTTACTAACAAAATGTTAG
* *
1377241 TAACAATTAATAATTAATAATTTGATATAATTTGATAATTTTAGTAACAATTAATACAATTAATA
1 TAACAATTAATAATTAATAATTTGA-ATAATTTGATAATATTAATAACAATTAATACAATTAATA
1377306 ATTTTACTAACAAAATGTTAG
65 ATTTTACTAACAAAATGTTAG
1377327 ATTTTACAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
83 12 0.15
84 11 0.14
85 11 0.14
86 44 0.56
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (85 bp):
TAACAATTAATAATTAATAATTTGAATAATTTGATAATATTAATAACAATTAATACAATTAATAA
TTTTACTAACAAAATGTTAG
Found at i:1377351 original size:17 final size:17
Alignment explanation
Indices: 1377315--1377354 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1377305 AATTTTACTA
*
1377315 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
1377332 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
1377349 ACAAAA
1 ACAAAA
1377355 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:1377391 original size:16 final size:16
Alignment explanation
Indices: 1377372--1377428 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
1377362 AATTTGATAC
*
1377372 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
1377388 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
1377404 AATTTTAATAACATTT
1 AATTTTAATAACAATT
*
1377420 AGTTTTAAT
1 AATTTTAAT
1377429 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:1377452 original size:23 final size:23
Alignment explanation
Indices: 1377402--1377463 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1377392 TTGATAACAA
* * *
1377402 TTAATTTTAAT-AACATTTAGTT
1 TTAATTTTAATAAAAATATAATT
1377424 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
1377447 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
1377464 AGGGCCGGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 11 0.31
23 18 0.51
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:1378908 original size:45 final size:46
Alignment explanation
Indices: 1378841--1378988 Score: 230
Period size: 46 Copynumber: 3.3 Consensus size: 46
1378831 TACGTAAGAT
*
1378841 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
1378884 CACCTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1378930 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1378976 TACTTATCACTTT
1 CACTTATCACTTT
1378989 ATCAACACTT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
43 9 0.10
44 5 0.05
45 20 0.21
46 60 0.64
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1379027 original size:62 final size:64
Alignment explanation
Indices: 1378928--1379050 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 64
1378918 AGCTAAAGCT
*
1378928 AACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTTATC
1 AACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
*
1378992 AACACTTATCAC-TTGTTC-C-TGATCAGATAAGTGTAGCTAAAGCTACCATTTATCACTTT
1 AACACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1379051 GTCACTTGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
62 38 0.68
63 4 0.07
64 14 0.25
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (64 bp):
AACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
Found at i:1380194 original size:5 final size:6
Alignment explanation
Indices: 1380183--1380209 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1380173 AAATTTAATT
1380183 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1380210 TTTGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:1393312 original size:20 final size:20
Alignment explanation
Indices: 1393276--1393313 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1393266 AAAACATATG
*
1393276 ATATTAGATTTTTAATAATT
1 ATATTAGATTTTGAATAATT
1393296 ATATTAG-TTCTTGAATAA
1 ATATTAGATT-TTGAATAA
1393314 ATTCGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
ATATTAGATTTTGAATAATT
Found at i:1400667 original size:17 final size:18
Alignment explanation
Indices: 1400645--1400679 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1400635 TCGAACGGCG
1400645 GAAAAGAAG-AAGGGAAA
1 GAAAAGAAGAAAGGGAAA
1400662 GAAAAGAAGAAAGGGAAA
1 GAAAAGAAGAAAGGGAAA
1400680 ATTGGGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAAAGAAGAAAGGGAAA
Found at i:1402402 original size:17 final size:18
Alignment explanation
Indices: 1402371--1402405 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1402361 AAATCCCTAA
*
1402371 TTTTCCTTTTCTTCTTTT
1 TTTTCCCTTTCTTCTTTT
1402389 TTTTCCCTTT-TTCTTTT
1 TTTTCCCTTTCTTCTTTT
1402406 CCGCCGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTT
Found at i:1403876 original size:20 final size:21
Alignment explanation
Indices: 1403839--1403882 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1403829 ATATTCTAAG
1403839 TATTAAAATATTCATAACA-A
1 TATTAAAATATTCATAACATA
*
1403859 TATTAAAAATATT-TTAACATA
1 TATT-AAAATATTCATAACATA
1403880 TAT
1 TAT
1403883 AATAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTAAAATATTCATAACATA
Found at i:1405969 original size:23 final size:23
Alignment explanation
Indices: 1405943--1405989 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1405933 TATAAGATAG
1405943 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
1405966 TCACTAAACTAATCGAATTTGTC
1 TCACTAAACTAATCGAATTTGTC
1405989 T
1 T
1405990 TTGTTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (23 bp):
TCACTAAACTAATCGAATTTGTC
Found at i:1406456 original size:162 final size:163
Alignment explanation
Indices: 1406161--1406464 Score: 459
Period size: 162 Copynumber: 1.9 Consensus size: 163
1406151 TTCTTTTTTC
* * *
1406161 TTTTCTTTGCGACATTTCACCTAAAACGCTAAAAAAATAAATTTATTAGTTAAGTTTGATAAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
* *
1406226 AAATAGAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTCTTTT
66 AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
1406291 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
131 AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
* * *
1406324 TTTTCTTTGTGACATTTTACCTAAAAAGCTACAAAAATAAATTTATCAGATATA-TTTGATAAAA
1 TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATA-AGTTTGATAAAA
* * * * * *
1406388 AAAA-CCAAGAAATAGGAACACCAGAAAGATCCAAAATAATATTTTTCATCTTTTTTCATTATTT
65 AAAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTT
1406452 TAAAATTAACCCT
130 TAAAATTAACCCT
1406465 CAATACACAA
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 65 0.52
163 60 0.48
164 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (163 bp):
TTTTCTTTGCGACATTTCACCTAAAAAGCTAAAAAAATAAATTTATCAGATAAGTTTGATAAAAA
AAATACAAAAAATAAGAACACCACAAAGATCCAAAATAATACTTTTCATCTTTTCTCATTATTTT
AAAATTAACCCTTAATGTCACGAGAAAAGCAAT
Found at i:1408582 original size:298 final size:298
Alignment explanation
Indices: 1408008--1408759 Score: 856
Period size: 298 Copynumber: 2.5 Consensus size: 298
1407998 GAGGATTTTT
* *
1408008 ACGGTAGTGATTGG-AAAGAAGAAGGTTCTGGAAGTTTTTGGTCAAACAGTTTGACTGTAGTGTA
1 ACGGTAGTGATAGGAAAAGAAGAA---TCTGGAA-ATTTTGGTCAAACAGTTTGACTGTAGT-TA
* *
1408072 TTGTGCTTTTAATTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTGGAATTGATTTAT
61 TTGTGCTTGTAATTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATTGATTTAT
* * * *
1408137 TTTGAGTGAAGTGTGATTGCTTATG-AAAATGATATTCAATTTTTTTTTTTTGTTTTCTGGAATG
126 TTTGAGTAAAGTGTGATTGCTTATGAAAAATGATATTCAATTTTTATTTTTTGTTTTCTAGAATA
* * ** * * *
1408201 CTTTTGGATTTAATTTGTTCTTTGCAGAGTAGCCAAAAAGTTTCTGTTCCATTCTTTTAGGATTT
191 CTTTTGGATTTAATTTGTTCTTAGCAAACCAGCCAAAAAATTTATGTTCCATTCTTTTAGAATTT
* ** * *
1408266 AGTAACGAAAAGTTTGTAGTTAAACCAAACATAAAGGATTTTTG
256 AGTAACGAAAAGTTTGTAGCTAAACCAAACATAAAGG-GGTCTA
* * *
1408310 A-GGTATTGATAGGAAAATAAGAATCTGGAAATTTTGGTCAAATAGTTTGACTGTAGCTTATTGT
1 ACGGTAGTGATAGGAAAAGAAGAATCTGGAAATTTTGGTCAAACAGTTTGACTGTAG-TTATTGT
* * * *
1408374 GCTTGTATTTATCGTTTTCAATGATGGATCCTATGTATTTCAATGATTTGTATTTATTTATTTTG
65 GCTTGTAATTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATTGATTTATTTTG
* * *
1408439 AGTAAAGTGTGATTGCTTATGAAAAATGATATTCGATTTTTCATTTTTTG-TTTCTAGAGTATTT
130 AGTAAAGTGTGATTGCTTATGAAAAATGATATTCAATTTTT-ATTTTTTGTTTTCTAGAATACTT
* * *
1408503 TTGGA-TTAATTTGTTCTTAGCAAACCAG-TAAAGAAATTTATATTTTC-TTCTTTTAGAATTTA
194 TTGGATTTAATTTGTTCTTAGCAAACCAGCCAAA-AAATTTAT-GTTCCATTCTTTTAGAATTTA
* * ** *
1408565 GTGAAGGAACA-TTTGTAGCTAAATTAAACATAGAGGGGTCTA
257 GT-AACGAAAAGTTTGTAGCTAAACCAAACATAAAGGGGTCTA
* * * * * * * *
1408607 ACTGTAGTGATAGGAAAAGAAGATTCTAGAAGTTTTGGTCAAACAGTTTGACTGGA-TCATTATA
1 ACGGTAGTGATAGGAAAAGAAGAATCTGGAAATTTTGGTCAAACAGTTTGACTGTAGTTATTGTG
* *** * * *
1408671 CTTGTAGTTATCACGTTCGATGATGGATCCTGTATATTTGAATGATTTGAATTGATTTATTTTGA
66 CTTGTAATTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATTGATTTATTTTGA
*
1408736 GTAAAGTGTGATTACTTATGAAAA
131 GTAAAGTGTGATTGCTTATGAAAA
1408760 GATTTTTGAT
Statistics
Matches: 382, Mismatches: 60, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
296 83 0.22
297 6 0.02
298 217 0.57
299 50 0.13
300 7 0.02
301 10 0.03
302 9 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (298 bp):
ACGGTAGTGATAGGAAAAGAAGAATCTGGAAATTTTGGTCAAACAGTTTGACTGTAGTTATTGTG
CTTGTAATTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATTGATTTATTTTGA
GTAAAGTGTGATTGCTTATGAAAAATGATATTCAATTTTTATTTTTTGTTTTCTAGAATACTTTT
GGATTTAATTTGTTCTTAGCAAACCAGCCAAAAAATTTATGTTCCATTCTTTTAGAATTTAGTAA
CGAAAAGTTTGTAGCTAAACCAAACATAAAGGGGTCTA
Found at i:1413759 original size:3 final size:3
Alignment explanation
Indices: 1413753--1413779 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1413743 ATTATTATTA
1413753 TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG
1413780 GTTATTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:1417006 original size:31 final size:31
Alignment explanation
Indices: 1416971--1417032 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1416961 AATAACAATC
* * *
1416971 TAGTAACTTAAATGAAAATTTTTATATAGTT
1 TAGTAACTTAAATAAAAATTTATAAATAGTT
1417002 TAGTAACTTAAATAAAAATTTATAAATAGTT
1 TAGTAACTTAAATAAAAATTTATAAATAGTT
1417033 CAGTGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (31 bp):
TAGTAACTTAAATAAAAATTTATAAATAGTT
Found at i:1421216 original size:39 final size:39
Alignment explanation
Indices: 1421172--1421246 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
1421162 TCCAAACAAA
1421172 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
1421211 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
1 GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACC
1421247 AGTAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (39 bp):
GGGTTGAACCGATTGAATCAAAAACTGCTTGAAACCTTT
Found at i:1425090 original size:14 final size:14
Alignment explanation
Indices: 1425071--1425098 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1425061 CCAAACAGCT
1425071 TTTTTATTCACAAC
1 TTTTTATTCACAAC
1425085 TTTTTATTCACAAC
1 TTTTTATTCACAAC
1425099 GCCCATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTATTCACAAC
Found at i:1427736 original size:34 final size:34
Alignment explanation
Indices: 1427693--1427762 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1427683 ACTAACATGA
1427693 TTGTGACATGTAATATATTTAATTGTGTTACATT
1 TTGTGACATGTAATATATTTAATTGTGTTACATT
1427727 TTGTGACATGTAATATATTTAATTGTGTTACATT
1 TTGTGACATGTAATATATTTAATTGTGTTACATT
1427761 TT
1 TT
1427763 TTGTTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (34 bp):
TTGTGACATGTAATATATTTAATTGTGTTACATT
Found at i:1435850 original size:21 final size:21
Alignment explanation
Indices: 1435826--1435872 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1435816 ATCAGAATTT
1435826 AAATTTTATAAAGGGATATAA
1 AAATTTTATAAAGGGATATAA
1435847 AAATTTTATAAAGGGATATAA
1 AAATTTTATAAAGGGATATAA
1435868 AAATT
1 AAATT
1435873 AAGGAATGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTTTATAAAGGGATATAA
Found at i:1436876 original size:13 final size:13
Alignment explanation
Indices: 1436858--1436882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1436848 CTAAAGCCCT
1436858 TATAAACTAGAAG
1 TATAAACTAGAAG
1436871 TATAAACTAGAA
1 TATAAACTAGAA
1436883 ACCTTCCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TATAAACTAGAAG
Found at i:1445875 original size:59 final size:59
Alignment explanation
Indices: 1445810--1445986 Score: 220
Period size: 59 Copynumber: 3.1 Consensus size: 59
1445800 ATCATCTAAC
* * *
1445810 TATTAGTAAATTATTTTTTGGTCACCCAATTATGAAAAGTTACAAGATGGTTACCCAAT
1 TATTAGTAAATTATTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCACCCAAT
* * * *
1445869 TATTAGT--A-T-TTTTTTGGTCACCCAACCATGAAAAGCTACAAAATGATCA-CTAAT
1 TATTAGTAAATTATTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCACCCAAT
* * *
1445923 TATTAGTAAATTTATTTTTTGGTCACCTAACTATGAAAAGTTACAAAATAGTCACTCAAT
1 TATTAGTAAA-TTATTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCACCCAAT
1445983 TATT
1 TATT
1445987 CAATTATTTC
Statistics
Matches: 98, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
54 11 0.11
55 34 0.35
56 2 0.02
57 1 0.01
58 1 0.01
59 42 0.43
60 7 0.07
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (59 bp):
TATTAGTAAATTATTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCACCCAAT
Found at i:1457751 original size:60 final size:60
Alignment explanation
Indices: 1457658--1458228 Score: 595
Period size: 60 Copynumber: 9.6 Consensus size: 60
1457648 CTCAAGGTAA
* ** * *
1457658 TAATTTGTCGTTAGCTTAAA-TCCCAGCATTAAGCCTTTTGTATTGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * *
1457718 TAATTTGTTGTTAGCTTAAA-TACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * * *
1457778 TAATTTGTTGTTAGCTTAAA-TCCCTGCATTAA--ATGTTCGCAATGTGCTCCACGTGTTGT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCT-TTTGTAACGTGTTCCACGTGATGT
* ** * * *
1457837 TAATTTCTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTCATGACATGTTCCACGTGATAT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * *
1457897 TAATTTGTTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
** * *
1457957 TAATTTGCCGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGTTCCATGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* *
1458017 TAATTTGCTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGTTCCACGTGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
* * * * * *
1458077 TAATTTGTTGTTTGCTTAAA-TCCCAGCATTAAACCTTTCTG--ATGTGCTCCGCGTG-TCAT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTT-TGTAACGTGTTCCACGTGAT-GT
* * ** ** * *
1458136 TAGTTTGTTGTTAACTTAAAGTCTTGCATTAAGCCTTTCATAACGTGCTCCACATGATGT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
1458196 TAATTTGTTGTTAGCTTAAA-TCCTAGCATTAAG
1 TAATTTGTTGTTAGCTTAAAGTCC-AGCATTAAG
1458229 TCTTCTCCAA
Statistics
Matches: 434, Mismatches: 65, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
58 2 0.00
59 92 0.21
60 336 0.77
61 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (60 bp):
TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGTTCCACGTGATGT
Found at i:1458145 original size:239 final size:238
Alignment explanation
Indices: 1457658--1458228 Score: 686
Period size: 239 Copynumber: 2.4 Consensus size: 238
1457648 CTCAAGGTAA
* ** * * *
1457658 TAATTTGTCGTTAGCTTAAA-TCCCAGCATTAAGCCTTTTGTATTGAGTTCCATGTGATGTTAAT
1 TAATTTGTTGTTAGCTTAAAGT-CCAGCATTAAGCCTTTTGTAACGTGCTCCACGTGATGTTAAT
*
1457722 TTGTTGTTAGCTTAAATACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGTTAATTTGTT
65 TTGTTGTTAGCTTAAAT-CCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGTTAATTTGCT
* * *
1457787 GTTAGCTTAAATCCCTGCATTAAATGTTCGCAATGTGCTCCACGTGTTGTTAATTTCTTGTTAGC
129 GTTAGCTTAAATCCCAGCATTAAATGTTCGCAACGTGCTCCACGTGATGTTAATTTCTTGTTAGC
* *
1457852 TTAAAGTCCAGCATTAAGCCTTTCATGACATGTTCCACGTGATAT
194 TTAAAGTCCAGCATTAAACCTTTCATGACATGCTCCACGTGATAT
* *
1457897 TAATTTGTTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTCCACGTGAGGTTAATT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGCTCCACGTGATGTTAATT
** * * * *
1457962 TGCCGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGTTCCATGTGATGTTAATTTGCTG
66 TGTTGTTAGCTTAAA-TCCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGTTAATTTGCTG
* * * * * * *
1458027 TTAGCTTAAAGT-CCAGCCTTAAGCCT-TTTGTAACGTGTTCCACGTGATGTTAATTTGTTGTTT
130 TTAGCTTAAA-TCCCAGCATTAA--ATGTTCGCAACGTGCTCCACGTGATGTTAATTTCTTGTTA
** *
1458090 GCTTAAA-TCCCAGCATTAAACCTTTC-TGATGTGCTCCGCGTG-TCAT
192 GCTTAAAGT-CCAGCATTAAACCTTTCATGACATGCTCCACGTGAT-AT
* * ** ** *
1458136 TAGTTTGTTGTTAACTTAAAGTCTTGCATTAAGCCTTTCATAACGTGCTCCACATGATGTTAATT
1 TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGCTCCACGTGATGTTAATT
1458201 TGTTGTTAGCTTAAATCCTAGCATTAAG
66 TGTTGTTAGCTTAAATCC-AGCATTAAG
1458229 TCTTCTCCAA
Statistics
Matches: 282, Mismatches: 42, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
238 4 0.01
239 221 0.78
240 56 0.20
241 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (238 bp):
TAATTTGTTGTTAGCTTAAAGTCCAGCATTAAGCCTTTTGTAACGTGCTCCACGTGATGTTAATT
TGTTGTTAGCTTAAATCCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGTTAATTTGCTGT
TAGCTTAAATCCCAGCATTAAATGTTCGCAACGTGCTCCACGTGATGTTAATTTCTTGTTAGCTT
AAAGTCCAGCATTAAACCTTTCATGACATGCTCCACGTGATAT
Found at i:1458201 original size:299 final size:298
Alignment explanation
Indices: 1457658--1458228 Score: 801
Period size: 299 Copynumber: 1.9 Consensus size: 298
1457648 CTCAAGGTAA
* **
1457658 TAATTTGTCGTTAGCTTAAATCCCAGCATTAAGCCTTTTGTATTGAGTTCCATGTGATGTTAATT
1 TAATTTGCCGTTAGCTTAAATCCCAGCATTAAGCCTTTTGTAACGAGTTCCATGTGATGTTAATT
* *
1457723 TGTTGTTAGCTTAAATACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATGTTAATTTGTTG
66 TGCTGTTAGCTTAAATACCAGCATTAAGCCTTTCGCAACGAGTTCCACGTGATGTTAATTTGTTG
* ** *
1457788 TTAGCTTAAATCCCTGCATTAAATGTTCGCAATGTGCTCCACGTGTTGTTAATTTCTTGTTAGCT
131 TTAGCTTAAATCCCAGCATTAAATGTTCG-AATGTGCTCCACGTGTCATTAATTTCTTGTTAACT
* * *
1457853 TAAAGTCCAGCATTAAGCCTTTCATGACATGTTCCACGTGATATTAATTTGTTGTTAGCTTAAAG
195 TAAAGTCCAGCATTAAGCCTTTCATAACATGCTCCACATGATATTAATTTGTTGTTAGCTTAAA-
*
1457918 TCC-AGCCTTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
259 TCCTAGCATTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
* *
1457957 TAATTTGCCGTTAGCTTAAAGT-CCAGCCTTAAGCCTTTTGTAACGTGTTCCATGTGATGTTAAT
1 TAATTTGCCGTTAGCTTAAA-TCCCAGCATTAAGCCTTTTGTAACGAGTTCCATGTGATGTTAAT
* * * *
1458021 TTGCTGTTAGCTTAAAGT-CCAGCCTTAAGCCTTTTGTAACGTGTTCCACGTGATGTTAATTTGT
65 TTGCTGTTAGCTTAAA-TACCAGCATTAAGCCTTTCGCAACGAGTTCCACGTGATGTTAATTTGT
* * * *
1458085 TGTTTGCTTAAATCCCAGCATTAAACCT-TTCTG-ATGTGCTCCGCGTGTCATTAGTTTGTTGTT
129 TGTTAGCTTAAATCCCAGCATTAAA--TGTTC-GAATGTGCTCCACGTGTCATTAATTTCTTGTT
** * *
1458148 AACTTAAAGTCTTGCATTAAGCCTTTCATAACGTGCTCCACATGATGTTAATTTGTTGTTAGCTT
191 AACTTAAAGTCCAGCATTAAGCCTTTCATAACATGCTCCACATGATATTAATTTGTTGTTAGCTT
1458213 AAATCCTAGCATTAAG
256 AAATCCTAGCATTAAG
1458229 TCTTCTCCAA
Statistics
Matches: 239, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
298 3 0.01
299 229 0.96
300 5 0.02
301 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (298 bp):
TAATTTGCCGTTAGCTTAAATCCCAGCATTAAGCCTTTTGTAACGAGTTCCATGTGATGTTAATT
TGCTGTTAGCTTAAATACCAGCATTAAGCCTTTCGCAACGAGTTCCACGTGATGTTAATTTGTTG
TTAGCTTAAATCCCAGCATTAAATGTTCGAATGTGCTCCACGTGTCATTAATTTCTTGTTAACTT
AAAGTCCAGCATTAAGCCTTTCATAACATGCTCCACATGATATTAATTTGTTGTTAGCTTAAATC
CTAGCATTAAGCCTTTTGTAACGTGCTCCACGTGAGGT
Found at i:1475838 original size:30 final size:28
Alignment explanation
Indices: 1475762--1475843 Score: 67
Period size: 30 Copynumber: 2.8 Consensus size: 28
1475752 AAATTATGAA
*
1475762 TTTAGTACTTATA-TTTTAATTTTATCAAT
1 TTTAGT-CTTATATTTTTAA-TTGATCAAT
* * *
1475791 TTTAGTATTACACTTTTTGAATTGATCATT
1 TTTAGTCTTATA-TTTTT-AATTGATCAAT
1475821 TTTAGTCCTTATATTTTTCAATT
1 TTTAGT-CTTATATTTTT-AATT
1475844 TTTAAAATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 4 0.10
29 6 0.14
30 26 0.62
31 6 0.14
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTAGTCTTATATTTTTAATTGATCAAT
Found at i:1480773 original size:41 final size:41
Alignment explanation
Indices: 1480716--1480796 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
1480706 AAACCTGGGT
*
1480716 CCTTTAGTTCAATGTAA-GCTAAAAACTAGTGTAACTAGGGC
1 CCTTTAGTTCAATGTAATG-TAAAAAATAGTGTAACTAGGGC
1480757 CCTTTAGTTCAATGTAATGTAAAAAATAGTGTAACTAGGG
1 CCTTTAGTTCAATGTAATGTAAAAAATAGTGTAACTAGGG
1480797 ATGGCAATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (41 bp):
CCTTTAGTTCAATGTAATGTAAAAAATAGTGTAACTAGGGC
Found at i:1488975 original size:90 final size:90
Alignment explanation
Indices: 1488852--1489236 Score: 400
Period size: 89 Copynumber: 4.2 Consensus size: 90
1488842 AAAAAAAAAA
* * **
1488852 AAAACTCTAGAATTCAAACTTTTTAAAAAAAAAATTCAAATATTTGAACTGAATCACTTACAAAA
1 AAAACTCTATAATTCAAAC-ATTT--AAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAA
* *
1488917 TTCATCTGCATAATTACAAAGCCAAATT
63 CTCATCTGCAAAATTACAAAGCCAAATT
* * * *
1488945 AAAACTCTATAATTTAAACATTTAAAAAAAATTCAAATATGCGAAGTGGATCACTTACAAGACTC
1 AAAACTCTATAATTCAAACATTTAAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTC
*
1489010 ATCTGCAAAATTACAAAGCTAAATT
66 ATCTGCAAAATTACAAAGCCAAATT
* * * * * * * *
1489035 AAAACTC---AATTCAAACTTTTTTTTTTACAAAAATTCAAATACGTGAACGGAACCACTTACGA
1 AAAACTCTATAATTCAAAC-----ATTTAAAAAAAATTCAAATATGCGAACTGAATCACTTACAA
*
1489097 AACTCATCTGCAAAATTACAAAGCCAAATA
61 AACTCATCTGCAAAATTACAAAGCCAAATT
* * ***** *
1489127 AAAACTCTAGAATACAAACATTT-TTTTTAATTCAAATATGCGAACTGAATCACTTACAAAACTT
1 AAAACTCTATAATTCAAACATTTAAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTC
*
1489191 ATCTGCAAAATTACAAAGCTAAATT
66 ATCTGCAAAATTACAAAGCCAAATT
*
1489216 AAACCTCTATAATTCAAACAT
1 AAAACTCTATAATTCAAACAT
1489237 GAAAGAGAAA
Statistics
Matches: 241, Mismatches: 43, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
87 8 0.03
89 71 0.29
90 69 0.29
92 68 0.28
93 17 0.07
95 8 0.03
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (90 bp):
AAAACTCTATAATTCAAACATTTAAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTC
ATCTGCAAAATTACAAAGCCAAATT
Found at i:1489094 original size:182 final size:181
Alignment explanation
Indices: 1488881--1489218 Score: 487
Period size: 182 Copynumber: 1.9 Consensus size: 181
1488871 TTTTTAAAAA
** * * * * *
1488881 AAAAATTCAAATATTTGAACTGAATCACTTACAAAATTCATCTGCATAATTACAAAGCCAAATTA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
* ** * * *
1488946 AAACTCTATAATTTAAACATTTAAAAAAAATTCAAATATGCGAAGTGGATCACTTACAAGACTCA
66 AAACTCTAGAATACAAACATTT-AAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCA
1489011 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
130 TCTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
*
1489063 AAAAATTCAAATACGTGAACGGAACCACTTACGAAACTCATCTGCAAAATTACAAAGCCAAATAA
1 AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
***** *
1489128 AAACTCTAGAATACAAACATTTTTTTTAATTCAAATATGCGAACTGAATCACTTACAAAACTTAT
66 AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
1489193 CTGCAAAATTACAAAGCTAAATTAAA
131 CTGCAAAATTACAAAGCTAAATTAAA
1489219 CCTCTATAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
181 60 0.44
182 76 0.56
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (181 bp):
AAAAATTCAAATACGTGAACGGAACCACTTACAAAACTCATCTGCAAAATTACAAAGCCAAATAA
AAACTCTAGAATACAAACATTTAAAAAAATTCAAATATGCGAACTGAATCACTTACAAAACTCAT
CTGCAAAATTACAAAGCTAAATTAAAACTCAATTCAAACTTTTTTTTTTAC
Found at i:1489974 original size:14 final size:14
Alignment explanation
Indices: 1489955--1489984 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1489945 TTTCATAAAT
1489955 TTATAATTTAATCC
1 TTATAATTTAATCC
*
1489969 TTATAATTTAGTCC
1 TTATAATTTAATCC
1489983 TT
1 TT
1489985 TTAACTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53
Consensus pattern (14 bp):
TTATAATTTAATCC
Found at i:1490732 original size:25 final size:24
Alignment explanation
Indices: 1490704--1490751 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1490694 TTTACATCAT
1490704 GATAGTGTAAATTTGTCACTATATG
1 GATAGTG-AAATTTGTCACTATATG
* *
1490729 GATATTGAAATTTGTCGCTATAT
1 GATAGTGAAATTTGTCACTATAT
1490752 TTATTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (24 bp):
GATAGTGAAATTTGTCACTATATG
Found at i:1496552 original size:14 final size:15
Alignment explanation
Indices: 1496533--1496573 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1496523 AAATTTAAGT
1496533 AAATATAAAT-TTTA
1 AAATATAAATATTTA
*
1496547 AAATATATATATTTA
1 AAATATAAATATTTA
1496562 AACATA-AAATAT
1 AA-ATATAAATAT
1496574 ATTGTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 11 0.48
16 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAAATATTTA
Found at i:1497266 original size:13 final size:13
Alignment explanation
Indices: 1497250--1497274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1497240 TAAAAGAATA
1497250 AATTAAACCGATC
1 AATTAAACCGATC
1497263 AATTAAACCGAT
1 AATTAAACCGAT
1497275 AACTCTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
AATTAAACCGATC
Found at i:1498926 original size:29 final size:32
Alignment explanation
Indices: 1498874--1498932 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 32
1498864 TAGTAAAAAT
1498874 AAAATTTCACTTTAATCCCCT-AAAATTATTA
1 AAAATTTCACTTTAATCCCCTAAAAATTATTA
**
1498905 AAAATTT-A-TTTAATCCTTTAAAAATTAT
1 AAAATTTCACTTTAATCCCCTAAAAATTAT
1498933 AAAGATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 9 0.36
31 7 0.28
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTTCACTTTAATCCCCTAAAAATTATTA
Done.