Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1692931 original size:20 final size:19
Alignment explanation
Indices: 1692902--1692959 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
1692892 CTTCTTTTCT
*
1692902 AAAAAAAAAACAAAAACAA
1 AAAAAAAAAAAAAAAACAA
1692921 AAAAAATAAAAAAAAAACAA
1 AAAAAA-AAAAAAAAAACAA
1692941 AAAACAAAACAAAGAAAAA
1 AAAA-AAAA-AAA-AAAAA
1692960 AGAGAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.18
20 18 0.53
21 5 0.15
22 5 0.15
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAACAA
Found at i:1692968 original size:1 final size:1
Alignment explanation
Indices: 1692902--1692960 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
1692892 CTTCTTTTCT
* * * * * * *
1692902 AAAAAAAAAACAAAAACAAAAAAAATAAAAAAAAAACAAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1692961 GAGAAAAAGA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1694213 original size:55 final size:55
Alignment explanation
Indices: 1694035--1694566 Score: 615
Period size: 55 Copynumber: 9.3 Consensus size: 55
1694025 TTCGCCCTTT
*
1694035 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
*
1694090 TAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 -AGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
* * * *
1694152 AATCCTCAAAAAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * **
1694207 AGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
1694262 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1694317 AGTCCTCAAAGAGCAGGACGCCTCTT-AAATCCCACGCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
*
1694372 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
* *
1694427 AGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACGC---C--TTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
** *
1694487 TAGTCCTCAAAGAGCAGGACGCCTTTCCTTCTCAAAGCCCACATGAGTTGGTGGCACTTTTT
1 -AGTCCTCAAAGAGCAGGACG-----CCTT-TCAAAGCCCACACAAGTTGGTGGCACTTTTC
1694549 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1694567 TGCACTTTAT
Statistics
Matches: 413, Mismatches: 37, Indels: 47
0.83 0.07 0.09
Matches are distributed among these distances:
54 6 0.01
55 234 0.57
56 24 0.06
58 1 0.00
60 4 0.01
61 110 0.27
62 32 0.08
63 1 0.00
66 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:1695447 original size:13 final size:13
Alignment explanation
Indices: 1695429--1695455 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1695419 ACAAACAGTA
1695429 AATGTATCGATAC
1 AATGTATCGATAC
1695442 AATGTATCGATAC
1 AATGTATCGATAC
1695455 A
1 A
1695456 TAAGTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1695525 original size:21 final size:21
Alignment explanation
Indices: 1695499--1695540 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1695489 AGCTACTACC
1695499 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1695520 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1695541 GGTCTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:1695610 original size:19 final size:21
Alignment explanation
Indices: 1695570--1695611 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
1695560 TCTGAAAATT
1695570 TTACCCAGATGTATCGATACA
1 TTACCCAGATGTATCGATACA
1695591 TTACCCA-ATGTATC-ATACA
1 TTACCCAGATGTATCGATACA
1695610 TT
1 TT
1695612 CAGGCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
TTACCCAGATGTATCGATACA
Found at i:1697961 original size:51 final size:50
Alignment explanation
Indices: 1697903--1698066 Score: 127
Period size: 51 Copynumber: 3.2 Consensus size: 50
1697893 TTTCATCTCT
1697903 GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATC
1 GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATC
* * * * * ** ** *
1697953 GAGGATACTCCAA-CTCCGATTTTA-TTTCTAAAGCCTCGATTTACCGCAACC
1 G-GGATACTCCAATC-CCGGTTTCATTTTC-AAAACATCAATTTTTCTTAATC
*** * *
1698004 GGGGATACTCCAATCTTAGTTTCATCTCCAAAACATCAA-TTTTCTTAATC
1 -GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATC
1698054 GGAGATACTCCAA
1 GG-GATACTCCAA
1698067 CTTCGATTTT
Statistics
Matches: 82, Mismatches: 25, Indels: 14
0.68 0.21 0.12
Matches are distributed among these distances:
49 2 0.02
50 22 0.27
51 54 0.66
52 4 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATC
Found at i:1698076 original size:101 final size:102
Alignment explanation
Indices: 1697903--1698085 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
1697893 TTTCATCTCT
* * *
1697903 GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
1 GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
1697968 CCGATTTTATTTCTAAAGCCTCGATTTACCGCAACCG
66 CCGATTTTATTTCTAAAGCCTCGATTTACCGCAACCG
**
1698005 GGGATACTCCAATCTTAGTTTCATCTCCAAAACATCAA-TTTTCTTAATCG-GAGATACTCCAAC
1 GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAG-GATACTCCAAC
*
1698068 TTCGATTTTATTTCTAAA
65 TCCGATTTTATTTCTAAA
1698086 ATACCAATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 1 0.01
101 40 0.54
102 33 0.45
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (102 bp):
GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
CCGATTTTATTTCTAAAGCCTCGATTTACCGCAACCG
Found at i:1698094 original size:50 final size:50
Alignment explanation
Indices: 1697927--1698096 Score: 132
Period size: 50 Copynumber: 3.4 Consensus size: 50
1697917 CCGGTTTCAT
* *
1697927 TTTC-AAAACATCAATTTTTCTTAATC-GAGGATACTCCAACTCCGATTTTA
1 TTTCTAAAACACCAA-TTTTCTTAATCGGA-GATACTCCAACTTCGATTTTA
* * * ** * * * *
1697977 TTTCTAAAGC-CTCGATTTACCGCAACCGGGGATACTCCAATCTTAG-TTTCA
1 TTTCTAAAACAC-CAATTT-TCTTAATCGGAGATACTCCAA-CTTCGATTTTA
* * *
1698028 TCTCCAAAACATCAATTTTCTTAATCGGAGATACTCCAACTTCGATTTTA
1 TTTCTAAAACACCAATTTTCTTAATCGGAGATACTCCAACTTCGATTTTA
*
1698078 TTTCTAAAATACCAATTTT
1 TTTCTAAAACACCAATTTT
1698097 TCACAATTGG
Statistics
Matches: 86, Mismatches: 27, Indels: 14
0.68 0.21 0.11
Matches are distributed among these distances:
49 4 0.05
50 42 0.49
51 36 0.42
52 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (50 bp):
TTTCTAAAACACCAATTTTCTTAATCGGAGATACTCCAACTTCGATTTTA
Found at i:1698109 original size:101 final size:102
Alignment explanation
Indices: 1697903--1698117 Score: 265
Period size: 101 Copynumber: 2.1 Consensus size: 102
1697893 TTTCATCTCT
* * *
1697903 GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
1 GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
* * *
1697968 CCGATTTTATTTCTAAAGCCTCGATTTACCGCAACCG
66 CCGATTTTATTTCTAAAGACTCAATTTACCACAACCG
**
1698005 GGGATACTCCAATCTTAGTTTCATCTCCAAAACATCAA-TTTTCTTAATCG-GAGATACTCCAAC
1 GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAG-GATACTCCAAC
* * ** **
1698068 TTCGATTTTATTTCTAAAATAC-CAATTTTTCACAATTG
65 TCCGATTTTATTTCT-AAAGACTCAATTTACCACAACCG
1698106 GGGATACTCCAA
1 GGGATACTCCAA
1698118 CCCCGTCACA
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
100 1 0.01
101 59 0.61
102 37 0.38
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (102 bp):
GGGATACTCCAATCCCAGTTTCATCTCCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
CCGATTTTATTTCTAAAGACTCAATTTACCACAACCG
Found at i:1698126 original size:26 final size:26
Alignment explanation
Indices: 1698097--1698149 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1698087 TACCAATTTT
* *
1698097 TCACAATTGGGGATACTCCAACCCCG
1 TCACAATCGGAGATACTCCAACCCCG
1698123 TCACAATCGGAGATACTCCAACCCCG
1 TCACAATCGGAGATACTCCAACCCCG
1698149 T
1 T
1698150 TATTTTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (26 bp):
TCACAATCGGAGATACTCCAACCCCG
Found at i:1707898 original size:79 final size:79
Alignment explanation
Indices: 1707806--1708336 Score: 425
Period size: 79 Copynumber: 6.8 Consensus size: 79
1707796 AAATTTAATA
* * *
1707806 TTTTGGAGATAAAAATGGAGTCAGAGTACCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCAGT
1 TTTTGGAAATAAAACTGGAGTCAGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCAGT
* *
1707870 GGTGGAAAATCGA-TG
65 TGTGAAAAAT-GAGTG
* * *
1707885 TTTTGGAAATAAAACTAGG-GTTCA-AGTATCCCTTCGAAAATAACGAGATTGGAGTATCCCC-G
1 TTTTGGAAATAAAACT-GGAG-TCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAG
*
1707947 ATTATGAAAAAT-AGGTG
64 -TTGTGAAAAATGA-GTG
* * * * *
1707964 TTTTGAAAATAAAGCCT----TGA-AGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAAT
1 TTTTGGAAATAAA-ACTGGAGTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGT
* *
1708024 TATGAAAAATTAGTG
65 TGTGAAAAATGAGTG
* ** *
1708039 TTTTGAAAATAAAACT-GAGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC-GA
1 TTTTGGAAATAAAACTGGA-GTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAG-
* *
1708102 CTGTGAAAAATTAGTG
64 TTGTGAAAAATGAGTG
* * * * * * **
1708118 TTTTGAAAATAAAACCGGGGTTAGAGTATCCTCTCGGAAATAATAGGGTTGGAGTATCCCC-GAT
1 TTTTGGAAATAAAACTGGAGTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAG-T
1708182 TGTGAAAAATGAGTG
65 TGTGAAAAATGAGTG
* * * * * *
1708197 TTTTGGAAATAAAA-TCGAGGCTGGAGTATCCCCTC-ATAAATAATGAGGTTGGAGTATCCCCAA
1 TTTTGGAAATAAAACTGGAGTC-AGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCAG
1708260 TTG-GAAAAAATTG-GTG
64 TTGTG-AAAAA-TGAGTG
* * ** *
1708276 TTTTCGAAATAAAACCT-GTGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCC
1 TTTTGGAAATAAAA-CTGGAGTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1708337 TCGGGAATAA
Statistics
Matches: 374, Mismatches: 54, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
74 2 0.01
75 62 0.17
76 1 0.00
77 1 0.00
78 5 0.01
79 288 0.77
80 14 0.04
81 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
TTTTGGAAATAAAACTGGAGTCAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTT
GTGAAAAATGAGTG
Found at i:1708222 original size:158 final size:154
Alignment explanation
Indices: 1707828--1708336 Score: 568
Period size: 158 Copynumber: 3.3 Consensus size: 154
1707818 AAATGGAGTC
* * *
1707828 AGAGTACCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCAGTGGTGGAAAATCGA-TGTTTTGG
1 AGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCA-TTGTGAAAAAT-GAGTGTTTTGG
* ** * *
1707891 AAATAAAACTAGGGTTCAAGTATCCCTTCGAAAATAACGAGATTGGAGTATCCCCGATTATGAAA
63 AAATAAAACGA-GGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAA
*
1707956 AA-TAGGTGTTTTGAAAATAAAGCC--TT
127 AATTA-GTGTTTTGAAAATAAAACCGGTT
* * * *
1707982 -GAAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATTAGTGTTTTGAA
1 AG-AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-ATTGTGAAAAATGAGTGTTTTGGA
* *
1708046 AATAAAACTGAGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGACTGTGAAAA
64 AATAAAAC-GAGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
1708111 ATTAGTGTTTTGAAAATAAAACCGGGGTT
128 ATTAGTGTTTTGAAAATAAAACC--GGTT
* * **
1708140 AGAGTATCCTCTCGGAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATGAGTGTTTTGGAA
1 AGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-ATTGTGAAAAATGAGTGTTTTGGAA
* * * *
1708205 ATAAAATCGAGGCTGGAGTATCCCCTC-ATAAATAATGAGGTTGGAGTATCCCCAATTG-GAAAA
65 ATAAAA-CGAGGTTGGAGTATCCCTTCGA-AAATAACGAGGTTGGAGTATCCCCGATTGTG-AAA
*
1708268 AATTGGTGTTTTCG-AAATAAAACCTGTGTT
127 AATTAGTGTTTT-GAAAATAAAACC-G-GTT
* *
1708298 GGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCC
1 AGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1708337 TCGGGAATAA
Statistics
Matches: 305, Mismatches: 34, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
153 2 0.01
154 124 0.41
155 5 0.02
157 3 0.01
158 168 0.55
159 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (154 bp):
AGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCATTGTGAAAAATGAGTGTTTTGGAAA
TAAAACGAGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
AGTGTTTTGAAAATAAAACCGGTT
Found at i:1710731 original size:20 final size:20
Alignment explanation
Indices: 1710706--1710760 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1710696 AAAATGCCTG
*
1710706 AATGTATCGATACATTGAGA-
1 AATGTATCGATACAATGA-AC
*
1710726 AATGTATCGTTACAATGAAC
1 AATGTATCGATACAATGAAC
1710746 AATGTATCGATACAA
1 AATGTATCGATACAA
1710761 ATTGTGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:1712726 original size:28 final size:28
Alignment explanation
Indices: 1712691--1712788 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
1712681 ACTGGGGTTG
*
1712691 GAGTATCCCCTCGGAAATAACGGGTTTA
1 GAGTATCCCCTTGGAAATAACGGGTTTA
*
1712719 GAGTATCCCCGATTGTGAAA-AATCGGTGTTTG
1 GAGTATCCCC--TTG-GAAATAA-CGG-GTTTA
* **
1712751 GAGCATCCCCTTGGAAATAACGGGGATA
1 GAGTATCCCCTTGGAAATAACGGGTTTA
1712779 GAGTATCCCC
1 GAGTATCCCC
1712789 GATTATGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
28 21 0.37
29 7 0.12
30 9 0.16
31 7 0.12
32 13 0.23
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (28 bp):
GAGTATCCCCTTGGAAATAACGGGTTTA
Found at i:1712781 original size:60 final size:60
Alignment explanation
Indices: 1712688--1712809 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
1712678 AAAACTGGGG
* ** * *
1712688 TTGGAGTATCCCCTCGGAAATAACGGGTTTAGAGTATCCCCGATTGTGAAAAATCGGTGT
1 TTGGAGCATCCCCTCGGAAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAGTGT
*
1712748 TTGGAGCATCCCCTTGGAAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAGTGT
1 TTGGAGCATCCCCTCGGAAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAGTGT
1712808 TT
1 TT
1712810 TAGAAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (60 bp):
TTGGAGCATCCCCTCGGAAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAGTGT
Found at i:1712896 original size:79 final size:79
Alignment explanation
Indices: 1712765--1713259 Score: 381
Period size: 79 Copynumber: 6.3 Consensus size: 79
1712755 ATCCCCTTGG
* * *
1712765 AAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAG-TGTTTTAGAAATAAAACTGGGGTT
1 AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACTGGGGTT
* *
1712829 GAAATATCATCTCAA
66 GAAGTATC-CCTCAA
* **
1712844 AAATAACAGGGTTAGAGTATCCTCGATGATGAAAAATCAG-TGTTTTAGAAATAAAACCAGGGTT
1 AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACTGGGGTT
*
1712908 GTAGTATCCCCTCAA
66 GAAGTAT-CCCTCAA
* * * * **
1712923 AAATAACGGGGTTGGAGTAT-CCCAATGGTGAAAAATC-GATGTTTTAGAAATAAAA-TCGAAGT
1 AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACT-GGGGT
* * *
1712985 TGGAGCATCCCTTCGA
65 TGAAGTATCCC-TCAA
* * * * * * **
1713001 AATTAACAGGGTTGGAGTATCCCCAATGTTGAAAAGTTAG-TGTTTTAGAAATAAAA-TCGAGTT
1 AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACT-G-GGG
*
1713064 TTG-AGTATCCCCTCGA
64 TTGAAGTAT-CCCTCAA
* * * * ** *
1713080 AAATAACAAGTTTAGAGTATCCCCGATGGT-AAAAAT-TGACATTTTAGAAATAAAACAGGGGTT
1 AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACTGGGGTT
1713143 -AGAGTATCTCCTCAGA
66 GA-AGTATC-CCTCA-A
** ** *
1713159 AAA-AATGGGGTT-GAAGTATCCCCGAT-AGTGAAAAATC-GATGTTTTAGAAATAAAACCAGAG
1 AAATAACAGGGTTAG-AGTATCCCCGATGA-TGAAAAATCAGATGTTTTAGAAATAAAACTGGGG
* *
1713220 TTGGAGTATCCCCTCGA
64 TTGAAGTAT-CCCTCAA
**
1713237 AAATAATGGGGTTAGAGTATCCC
1 AAATAACAGGGTTAGAGTATCCC
1713260 TTTGAAAATA
Statistics
Matches: 338, Mismatches: 56, Indels: 44
0.77 0.13 0.10
Matches are distributed among these distances:
77 10 0.03
78 110 0.33
79 208 0.62
80 10 0.03
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
AAATAACAGGGTTAGAGTATCCCCGATGATGAAAAATCAGATGTTTTAGAAATAAAACTGGGGTT
GAAGTATCCCTCAA
Found at i:1713043 original size:157 final size:154
Alignment explanation
Indices: 1712839--1713259 Score: 445
Period size: 157 Copynumber: 2.7 Consensus size: 154
1712829 GAAATATCAT
* * * *
1712839 CTCAAAAATAACAGGGTTAGAGTATCCTCGATGATGAAAAATCAGTGTTTTAGAAATAAAACCAG
1 CTCAGAAATAACAGGGTTGGAGTATCCCCGATG-TG-AAAATTAGTGTTTTAGAAATAAAACCAG
* * * **
1712904 GGTTGTAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCAATGGTGAAAAATCGATGTTTTA
64 AGTTGTAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCAATGGT-AAAAATCGACATTTTA
*
1712969 GAAATAAAATC-GAAGTTGGAGCATC-C
128 GAAATAAAA-CAGAAGTTAGAGCATCTC
* *
1712995 CTTC-GAAATTAACAGGGTTGGAGTATCCCCAATGTTGAAAAGTTAGTGTTTTAGAAATAAAATC
1 C-TCAGAAA-TAACAGGGTTGGAGTATCCCCGATG-TGAAAA-TTAGTGTTTTAGAAATAAAACC
* ** * * *
1713059 -GAGTTTTGAGTATCCCCTCGAAAATAACAAGTTTAGAGTATCCCCGATGGTAAAAATTGACATT
62 AGAGTTGT-AGTATCCCCTCGAAAATAACGGGGTTAGAGTAT-CCCAATGGTAAAAATCGACATT
** *
1713123 TTAGAAATAAAACAGGGGTTAGAGTATCTC
125 TTAGAAATAAAACAGAAGTTAGAGCATCTC
* ** * * *
1713153 CTCAGAAAAAATGGGGTTGAAGTATCCCCGATAGTGAAAAATCGATGTTTTAGAAATAAAACCAG
1 CTCAGAAATAACAGGGTTGGAGTATCCCCGAT-GTGAAAATTAG-TGTTTTAGAAATAAAACCAG
* *
1713218 AGTTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCC
64 AGTTGTAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCC
1713260 TTTGAAAATA
Statistics
Matches: 218, Mismatches: 36, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
156 19 0.09
157 179 0.82
158 20 0.09
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (154 bp):
CTCAGAAATAACAGGGTTGGAGTATCCCCGATGTGAAAATTAGTGTTTTAGAAATAAAACCAGAG
TTGTAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCAATGGTAAAAATCGACATTTTAGAA
ATAAAACAGAAGTTAGAGCATCTC
Found at i:1713048 original size:236 final size:235
Alignment explanation
Indices: 1712748--1713259 Score: 592
Period size: 236 Copynumber: 2.2 Consensus size: 235
1712738 AAATCGGTGT
* * *
1712748 TTGGAGCATCCCCTTGGAAATAACGGGGATAGAGTATCCCCGATTATGAAAAATCAGTGTTTTAG
1 TTGGAGCAT-CCCTTCGAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCAGTGTTTTAG
* * *
1712813 AAATAAAA-CTG-GGGTTGAAATATCATCTCAAAAATAACAGGGTTAGAGTATCCTCGATGATGA
65 AAATAAAATC-GAGGGTTG-AATATCACCTCAAAAATAACAAGGTTAGAGTATCCCCGATGAT-A
**
1712876 AAAATCAG-TGTTTTAGAAATAAAACCA-GGGTT-GTAGTATCCCCTCA-AAAATAACGGGGTTG
127 AAAAT-AGACATTTTAGAAATAAAA-CAGGGGTTAG-AGTATCCCCTCAGAAAA-AACGGGGTTG
* * *
1712937 GAGTAT-CCCAATGGTGAAAAATCGATGTTTTAGAAATAAAATC-GAAG
188 AAGTATCCCCAATAGTGAAAAATCGATGTTTTAGAAATAAAACCAG-AG
* * * *
1712984 TTGGAGCATCCCTTCGAAATTAACAGGGTTGGAGTATCCCCAATGT-TGAAAAGTTAGTGTTTTA
1 TTGGAGCATCCCTTCGAAA-TAACGGGGTTAGAGTATCCCCAAT-TATGAAAAATCAGTGTTTTA
** * * * * *
1713048 GAAATAAAATCGAGTTTTGAGTATCCCCTCGAAAATAACAAGTTTAGAGTATCCCCGATGGTAAA
64 GAAATAAAATCGAGGGTTGAATATCACCTCAAAAATAACAAGGTTAGAGTATCCCCGATGATAAA
* * *
1713113 AATTGACATTTTAGAAATAAAACAGGGGTTAGAGTATCTCCTCAGAAAAAATGGGGTTGAAGTAT
129 AATAGACATTTTAGAAATAAAACAGGGGTTAGAGTATCCCCTCAGAAAAAACGGGGTTGAAGTAT
*
1713178 CCCCGATAGTGAAAAATCGATGTTTTAGAAATAAAACCAGAG
194 CCCCAATAGTGAAAAATCGATGTTTTAGAAATAAAACCAGAG
* * *
1713220 TTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCC
1 TTGGAGCATCCCTTCG-AAATAACGGGGTTAGAGTATCCC
1713260 TTTGAAAATA
Statistics
Matches: 234, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
234 3 0.01
235 59 0.25
236 162 0.69
237 10 0.04
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (235 bp):
TTGGAGCATCCCTTCGAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCAGTGTTTTAGA
AATAAAATCGAGGGTTGAATATCACCTCAAAAATAACAAGGTTAGAGTATCCCCGATGATAAAAA
TAGACATTTTAGAAATAAAACAGGGGTTAGAGTATCCCCTCAGAAAAAACGGGGTTGAAGTATCC
CCAATAGTGAAAAATCGATGTTTTAGAAATAAAACCAGAG
Found at i:1713288 original size:28 final size:28
Alignment explanation
Indices: 1713219--1713288 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1713209 TAAAACCAGA
* **
1713219 GTTGGAGTATCCCCTCGAAAATAATGGG
1 GTTGGAGTATCCCTTCGAAAATAACAGG
* *
1713247 GTTAGAGTATCCCTTTGAAAATAACAGG
1 GTTGGAGTATCCCTTCGAAAATAACAGG
1713275 GTTGGAGTATCCCT
1 GTTGGAGTATCCCT
1713289 AGTGGTGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (28 bp):
GTTGGAGTATCCCTTCGAAAATAACAGG
Found at i:1717298 original size:15 final size:15
Alignment explanation
Indices: 1717280--1717321 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
1717270 CATTAGTAAT
1717280 TGTATCGATACAATA
1 TGTATCGATACAATA
*
1717295 TGTATCAATACAATA
1 TGTATCGATACAATA
1717310 TGTATCGATACA
1 TGTATCGATACA
1717322 TTATTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (15 bp):
TGTATCGATACAATA
Found at i:1721179 original size:88 final size:87
Alignment explanation
Indices: 1721070--1721246 Score: 327
Period size: 88 Copynumber: 2.0 Consensus size: 87
1721060 CCTGCATATG
*
1721070 TAAGATGCATCATATAGTTGGTTTGGTTTTACAAAGAAATTCTTGAAATGAGTTTTTTTTTCAAT
1 TAAGATGCATCATATAGTTGGTTTGGTTTTACAAAGAAATTCTTGAAA-GAGTTTCTTTTTCAAT
1721135 TCCATTATAACCTAAACCATCTT
65 TCCATTATAACCTAAACCATCTT
1721158 TAAGATGCATCATATAGTTGGTTTGGTTTTACAAAGAAATTCTTGAAAGAGTTTCTTTTTCAATT
1 TAAGATGCATCATATAGTTGGTTTGGTTTTACAAAGAAATTCTTGAAAGAGTTTCTTTTTCAATT
*
1721223 CCATTATAGCCTAAACCATCTT
66 CCATTATAACCTAAACCATCTT
1721245 TA
1 TA
1721247 TCAAAGAAAG
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 39 0.45
88 48 0.55
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (87 bp):
TAAGATGCATCATATAGTTGGTTTGGTTTTACAAAGAAATTCTTGAAAGAGTTTCTTTTTCAATT
CCATTATAACCTAAACCATCTT
Found at i:1723210 original size:16 final size:16
Alignment explanation
Indices: 1723191--1723268 Score: 75
Period size: 16 Copynumber: 4.9 Consensus size: 16
1723181 TCGGATTTGA
* *
1723191 GCTTATTCGGGTTTAG
1 GCTTTTTCGGGTTCAG
* *
1723207 GCTTTTTTGGGTTCGG
1 GCTTTTTCGGGTTCAG
* *
1723223 GTTTTTTCAGGTTCAG
1 GCTTTTTCGGGTTCAG
* * *
1723239 ACTTATTCAGGTTCAG
1 GCTTTTTCGGGTTCAG
1723255 GCTTTTTCGGGTTC
1 GCTTTTTCGGGTTC
1723269 GGGTCGATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.46
Consensus pattern (16 bp):
GCTTTTTCGGGTTCAG
Found at i:1723221 original size:48 final size:48
Alignment explanation
Indices: 1723168--1723271 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
1723158 GGCTCATTCA
* * * *
1723168 GGTTCGGGCACTTTC-GGATT-TGAGCTTATTCGGGTTTAGGCTTTTTTG
1 GGTTCGGGCACTTTCAGG-TTCAGA-CTTATTCAGGTTCAGGCTTTTTCG
***
1723216 GGTTCGGGTTTTTTCAGGTTCAGACTTATTCAGGTTCAGGCTTTTTCG
1 GGTTCGGGCACTTTCAGGTTCAGACTTATTCAGGTTCAGGCTTTTTCG
1723264 GGTTCGGG
1 GGTTCGGG
1723272 TCGATTTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 43 0.91
49 4 0.09
ACGTcount: A:0.11, C:0.15, G:0.32, T:0.42
Consensus pattern (48 bp):
GGTTCGGGCACTTTCAGGTTCAGACTTATTCAGGTTCAGGCTTTTTCG
Found at i:1723491 original size:18 final size:18
Alignment explanation
Indices: 1723452--1723491 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1723442 ATATTTATAT
*
1723452 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
*
1723470 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTGTTAA
1723488 ATAA
1 ATAA
1723492 TTTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:1723654 original size:9 final size:10
Alignment explanation
Indices: 1723638--1723681 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
1723628 TAACTGAATT
1723638 AATATTTAAA
1 AATATTTAAA
1723648 AAT-TTTAAA
1 AATATTTAAA
1723657 ATATATTTAATAA
1 A-ATATTT-A-AA
1723670 AATATTTAAA
1 AATATTTAAA
1723680 AA
1 AA
1723682 CTCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.23
10 9 0.30
11 4 0.13
12 7 0.23
13 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTTAAA
Found at i:1723674 original size:12 final size:11
Alignment explanation
Indices: 1723638--1723681 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
1723628 TAACTGAATT
1723638 AATATTT-AAA
1 AATATTTAAAA
1723648 AAT-TTTAAAA
1 AATATTTAAAA
*
1723658 TATATTTAATAA
1 AATATTTAA-AA
1723670 AATATTTAAAA
1 AATATTTAAAA
1723681 A
1 A
1723682 CTCATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 3 0.10
10 8 0.28
11 8 0.28
12 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:1723691 original size:24 final size:22
Alignment explanation
Indices: 1723639--1723680 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1723629 AACTGAATTA
1723639 ATATTT-A-AAAATTTTAAAAT
1 ATATTTAATAAAATTTTAAAAT
1723659 ATATTTAATAAAATATTTAAAA
1 ATATTTAATAAAAT-TTTAAAA
1723681 ACTCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 5 0.26
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATTTAATAAAATTTTAAAAT
Found at i:1724198 original size:16 final size:15
Alignment explanation
Indices: 1724170--1724200 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1724160 TATGTTAACT
1724170 TTATATTCTATTCTA
1 TTATATTCTATTCTA
1724185 TTATATTACTATTCTA
1 TTATATT-CTATTCTA
1724201 AGTGTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATTCTATTCTA
Found at i:1724328 original size:3 final size:3
Alignment explanation
Indices: 1724320--1724364 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1724310 CATTACTTGA
*
1724320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAG AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1724365 TTCAAATAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1724373 original size:17 final size:16
Alignment explanation
Indices: 1724319--1724376 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
1724309 TCATTACTTG
*
1724319 AAATAATAATAATAAT
1 AAATAAGAATAATAAT
*
1724335 -AATAATAATAATAAT
1 AAATAAGAATAATAAT
*
1724350 AATATAAGAATAATATT
1 AA-ATAAGAATAATAAT
1724367 CAAATAAGAA
1 -AAATAAGAA
1724377 CTTAAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 15 0.41
16 1 0.03
17 19 0.51
18 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAAGAATAATAAT
Found at i:1724755 original size:16 final size:17
Alignment explanation
Indices: 1724723--1724795 Score: 55
Period size: 16 Copynumber: 4.5 Consensus size: 17
1724713 GTTTGGATTC
1724723 TTTCGGGTTC-AAGCTT
1 TTTCGGGTTCGAAGCTT
*
1724739 TTTCGGGTTCGGA-CTT
1 TTTCGGGTTCGAAGCTT
* * *
1724755 TCTCGAGTTCG-AGCTA
1 TTTCGGGTTCGAAGCTT
* * *
1724771 TCTCGAGTTCG-AGCTA
1 TTTCGGGTTCGAAGCTT
1724787 TTTCGGGTT
1 TTTCGGGTT
1724796 TGAGTAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.02
16 47 0.96
17 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (17 bp):
TTTCGGGTTCGAAGCTT
Found at i:1725243 original size:20 final size:20
Alignment explanation
Indices: 1725217--1725274 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
1725207 CGTTGAACTC
1725217 AATGTATCGATACATTTATG
1 AATGTATCGATACATTTATG
*
1725237 GATGTATCGATACA-TTATG
1 AATGTATCGATACATTTATG
1725256 AACTGTATCGATACATTTA
1 AA-TGTATCGATACATTTA
1725275 CATGTGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 6 0.18
20 25 0.74
21 3 0.09
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTTATG
Found at i:1725282 original size:20 final size:19
Alignment explanation
Indices: 1725219--1725290 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
1725209 TTGAACTCAA
1725219 TGTATCGATACATTT-ATGG
1 TGTATCGATACATTTAAT-G
*
1725238 ATGTATCGATACATTATGAA-C
1 -TGTATCGATACATT-T-AATG
1725259 TGTATCGATACATTTACATG
1 TGTATCGATACATTTA-ATG
*
1725279 TGTATCAATACA
1 TGTATCGATACA
1725291 AATAAGGGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 39 0.89
21 1 0.02
23 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATTTAATG
Found at i:1725435 original size:20 final size:20
Alignment explanation
Indices: 1725410--1725450 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1725400 ACCAACCATA
1725410 TGTATCGATACATACAGTAT
1 TGTATCGATACATACAGTAT
*
1725430 TGTATCGATACATTCAGTAT
1 TGTATCGATACATACAGTAT
1725450 T
1 T
1725451 TTTACTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACAGTAT
Found at i:1727148 original size:25 final size:22
Alignment explanation
Indices: 1727118--1727162 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
1727108 AATTTTTTAT
1727118 TTTTATTTTTAAAATTTTAAATTAT
1 TTTTATTTTTAAAATTTT---TTAT
1727143 TTTTATTTTTAAAATTTTTT
1 TTTTATTTTTAAAATTTTTT
1727163 TTGACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 2 0.10
25 18 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTTTTAAAATTTTTTAT
Found at i:1727858 original size:3 final size:3
Alignment explanation
Indices: 1727850--1727884 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1727840 CAAAGTCAAA
*
1727850 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1727885 ATTTTTTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1730090 original size:24 final size:25
Alignment explanation
Indices: 1730063--1730109 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1730053 GATATAATAC
*
1730063 AAACATAACATA-AAAAAATAATTA
1 AAACATAAAATATAAAAAATAATTA
1730087 AAACATAAAATATAAAAAATAAT
1 AAACATAAAATATAAAAAATAAT
1730110 ATGAATGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (25 bp):
AAACATAAAATATAAAAAATAATTA
Found at i:1730271 original size:32 final size:35
Alignment explanation
Indices: 1730216--1730281 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 35
1730206 ATACACAAAC
* *
1730216 TTTTCTTTCTTCTTTTCTATCCTCT-T-TTCTTTT
1 TTTTCTGTCTTCTTTCCTATCCTCTCTCTTCTTTT
*
1730249 TTTTCTGT-TTCTTTCCTGTCCTCTCTCTTCTTT
1 TTTTCTGTCTTCTTTCCTATCCTCTCTCTTCTTT
1730282 ACTTTCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 14 0.50
33 8 0.29
34 6 0.21
ACGTcount: A:0.02, C:0.27, G:0.03, T:0.68
Consensus pattern (35 bp):
TTTTCTGTCTTCTTTCCTATCCTCTCTCTTCTTTT
Found at i:1732013 original size:12 final size:12
Alignment explanation
Indices: 1731989--1732035 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
1731979 AAAAAAATCG
1731989 TATTATA-TTTA
1 TATTATATTTTA
*
1732000 TATTATTTTTTA
1 TATTATATTTTA
1732012 TATTATATTTTA
1 TATTATATTTTA
*
1732024 TATTACATTTTA
1 TATTATATTTTA
1732036 ATTTTTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 6 0.19
12 26 0.81
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1733841 original size:22 final size:24
Alignment explanation
Indices: 1733785--1733841 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
1733775 TGGGTAGAGC
1733785 TAATAATT-TTGACTCTTAAATAAA
1 TAATAATTATT-ACTCTTAAATAAA
* *
1733809 T-TTAATAATTACT-TTAAA-AAA
1 TAATAATTATTACTCTTAAATAAA
1733830 TAATAATTATTA
1 TAATAATTATTA
1733842 AATTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
21 4 0.15
22 13 0.48
23 7 0.26
24 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATAATTATTACTCTTAAATAAA
Found at i:1736085 original size:2 final size:2
Alignment explanation
Indices: 1736080--1736127 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1736070 TTGTGTGTAT
*
1736080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1736122 TA TA TA
1 TA TA TA
1736128 ATCAAATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1736789 original size:2 final size:2
Alignment explanation
Indices: 1736782--1736817 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1736772 TCACCACCTA
1736782 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
1736818 TGAAGTCGGC
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):
AT
Found at i:1738483 original size:20 final size:22
Alignment explanation
Indices: 1738460--1738501 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1738450 TTAAAATTAA
1738460 AATTAAA-TAA-GAAAAATATT
1 AATTAAATTAACGAAAAATATT
*
1738480 AATTAAATTAACGAAAATTATT
1 AATTAAATTAACGAAAAATATT
1738502 TAAATAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AATTAAATTAACGAAAAATATT
Found at i:1739367 original size:37 final size:38
Alignment explanation
Indices: 1739294--1739367 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
1739284 ATTTAATAAG
* * *
1739294 ATAATATTTAATTATTTATTTTATATTTTTATATTTTT
1 ATAATATTTAATTATTTATTTTACATTTTAAAATTTTT
1739332 ATAATATTTTAA-T-TTTATTTTACATTTTAAAATTTT
1 ATAATA-TTTAATTATTTATTTTACATTTTAAAATTTT
1739368 AAATTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 20 0.62
38 7 0.22
39 5 0.16
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
ATAATATTTAATTATTTATTTTACATTTTAAAATTTTT
Found at i:1739397 original size:18 final size:19
Alignment explanation
Indices: 1739355--1739402 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1739345 TTTATTTTAC
*
1739355 ATTTTAAAATTTTAAATTT
1 ATTTTAAAAATTTAAATTT
*
1739374 -TGTTAAAAATTT-AATTT
1 ATTTTAAAAATTTAAATTT
*
1739391 ATTTTAATAATT
1 ATTTTAAAAATT
1739403 AGACATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTAAAAATTTAAATTT
Found at i:1740053 original size:18 final size:19
Alignment explanation
Indices: 1740022--1740069 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
1740012 ATTAAATTGA
1740022 TAAATATT--AAATAAATT
1 TAAATATTAAAAATAAATT
1740039 TAAAT-TTAAAAATAAATT
1 TAAATATTAAAAATAAATT
1740057 TAAATATTAAAAA
1 TAAATATTAAAAA
1740070 AATGGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.07
17 5 0.18
18 14 0.50
19 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATATTAAAAATAAATT
Found at i:1744070 original size:20 final size:20
Alignment explanation
Indices: 1744032--1744070 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1744022 ATTAATTTTA
*
1744032 ATAATAAATAAATATTAAAT
1 ATAATAAATAAATAATAAAT
* *
1744052 ATAATTAATAATTAATAAA
1 ATAATAAATAAATAATAAA
1744071 ATACATATTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATAAATAAATAATAAAT
Found at i:1744214 original size:16 final size:15
Alignment explanation
Indices: 1744193--1744226 Score: 59
Period size: 15 Copynumber: 2.2 Consensus size: 15
1744183 CAAAATGAGG
1744193 AAAAAAAACTTAAAAA
1 AAAAAAAAC-TAAAAA
1744209 AAAAAAAACTAAAAA
1 AAAAAAAACTAAAAA
1744224 AAA
1 AAA
1744227 GGATCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAAAACTAAAAA
Found at i:1744798 original size:4 final size:4
Alignment explanation
Indices: 1744784--1744818 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1744774 GTGACAATGA
1744784 TAAT T-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1744819 AATCATCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:1746030 original size:30 final size:30
Alignment explanation
Indices: 1745996--1746054 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1745986 ATTTAAATTA
1745996 ATTATTTTAAAATTAAA-AATTTTTATTTAT
1 ATTATTTTAAAATTAAATAA-TTTTATTTAT
*
1746026 ATTATTTTAAATTTAAATAATTTTATTTA
1 ATTATTTTAAAATTAAATAATTTTATTTA
1746055 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTATTTTAAAATTAAATAATTTTATTTAT
Found at i:1746039 original size:16 final size:15
Alignment explanation
Indices: 1745987--1746065 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
1745977 ATTAATTTGA
*
1745987 TTTAAA-TTAATTAT
1 TTTAAATTTAATAAT
* *
1746001 TTTAAAATTAAAAAT
1 TTTAAATTTAATAAT
* *
1746016 TTT-TATTTATATTAT
1 TTTAAATTTA-ATAAT
1746031 TTTAAATTTAAATAAT
1 TTTAAATTT-AATAAT
1746047 TTT--ATTTAA-AA-
1 TTTAAATTTAATAAT
1746058 TTTAAATT
1 TTTAAATT
1746066 ATTTAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.06
12 2 0.04
13 5 0.10
14 14 0.27
15 15 0.29
16 11 0.22
17 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAATTTAATAAT
Found at i:1746053 original size:21 final size:21
Alignment explanation
Indices: 1746027--1746078 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1746017 TTTATTTATA
1746027 TTATTTTAAATTTAAATAATT
1 TTATTTTAAATTTAAATAATT
* *
1746048 TTATTTAAAATTTAAATTATT
1 TTATTTTAAATTTAAATAATT
* *
1746069 TAAATTTAAA
1 TTATTTTAAA
1746079 CTAGGTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTTTAAATTTAAATAATT
Found at i:1746073 original size:15 final size:16
Alignment explanation
Indices: 1746048--1746078 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1746038 TTAAATAATT
1746048 TTATTTAAAATTTAAA
1 TTATTTAAAATTTAAA
1746064 TTATTT-AAATTTAAA
1 TTATTTAAAATTTAAA
1746079 CTAGGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTTAAAATTTAAA
Found at i:1747548 original size:9 final size:9
Alignment explanation
Indices: 1747536--1747577 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1747526 ATTTTTTTTA
1747536 TTTTTAAAT
1 TTTTTAAAT
1747545 TTTTT--AT
1 TTTTTAAAT
1747552 TTTTTAAAT
1 TTTTTAAAT
*
1747561 TTTTTGACAT
1 TTTTT-AAAT
1747571 TTTTTAA
1 TTTTTAA
1747578 TGATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:1747549 original size:16 final size:16
Alignment explanation
Indices: 1747528--1747602 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
1747518 CTTATATCAT
1747528 TTTTTTTATTTTTAAA
1 TTTTTTTATTTTTAAA
1747544 -TTTTTTATTTTTTAAA
1 TTTTTTTA-TTTTTAAA
* *
1747560 TTTTTTGACATTTTTTAA
1 TTTTTT--TATTTTTAAA
** *
1747578 TGATTTTATTTTTTAA
1 TTTTTTTATTTTTAAA
*
1747594 TTATTTTAT
1 TTTTTTTAT
1747603 ACCTATGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
15 7 0.14
16 25 0.51
17 5 0.10
18 11 0.22
19 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTTATTTTTAAA
Found at i:1751700 original size:32 final size:32
Alignment explanation
Indices: 1751645--1751742 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
1751635 TTCAACGATT
*
1751645 TGTATCGATACATAAAGTGTTGTATCGATATAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1751678 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1751710 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1751742 T
1 T
1751743 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1751702 original size:19 final size:18
Alignment explanation
Indices: 1751643--1751740 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1751633 AATTCAACGA
1751643 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1751662 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
1751678 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1751694 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1751710 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1751726 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1751741 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
15 6 0.09
17 4 0.06
18 2 0.03
19 24 0.36
20 10 0.15
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1751720 original size:13 final size:13
Alignment explanation
Indices: 1751665--1751721 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1751655 CATAAAGTGT
*
1751665 TGTATCGATATAA
1 TGTATCGATACAA
1751678 TGTATCGATACATAA
1 TGTATCGATAC--AA
1751693 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1751710 TGTATCGATACA
1 TGTATCGATACA
1751722 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1751801 original size:13 final size:13
Alignment explanation
Indices: 1751783--1751807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1751773 ATTACTCAAA
1751783 TGTATCGATACAT
1 TGTATCGATACAT
1751796 TGTATCGATACA
1 TGTATCGATACA
1751808 CTGATATTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1751872 original size:52 final size:52
Alignment explanation
Indices: 1751816--1751996 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
1751806 CACTGATATT
1751816 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
1751868 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
1751920 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
1751972 TGTATCGATACATGCAGACAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1751997 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1752699 original size:17 final size:17
Alignment explanation
Indices: 1752677--1752712 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1752667 TCTGCTTATA
1752677 TATTATCATCATTTTAG
1 TATTATCATCATTTTAG
1752694 TATTATCATCATTTTAG
1 TATTATCATCATTTTAG
1752711 TA
1 TA
1752713 ATCCTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTATCATCATTTTAG
Found at i:1757387 original size:126 final size:124
Alignment explanation
Indices: 1757202--1757455 Score: 393
Period size: 126 Copynumber: 2.0 Consensus size: 124
1757192 AGCATGGGGT
* *
1757202 ATTGTTATGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
1 ATTGTTATGATCCACTTATATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGCTATATATGGAC
* *
1757267 TTAGGCTCTCCCACCCTAATAGCTAGCTTTTGGGGTGTGGTTCTCTAAAAAGTCCGTATCA
66 TTAGGCTCTCCCACCCTAATAGCTAGCTTTTAGGGTGTGATTCT-T-AAAAGTCCGTATCA
*
1757328 ATTGTTGTGATCCACTTATATCCCACATCGAAAGATAAAGGCTTTCCTTGT-GCTCATATATGGA
1 ATTGTTATGATCCACTTATATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGCT-ATATATGGA
** * *
1757392 CTTAGGCTCTCTTACCCTAATAGCTAGCTTTTAGGGTGTGATTCTTCAAAGTCCGTATTA
65 CTTAGGCTCTCCCACCCTAATAGCTAGCTTTTAGGGTGTGATTCTTAAAAGTCCGTATCA
1757452 ATTG
1 ATTG
1757456 ATATCAGAGC
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
124 16 0.14
125 3 0.03
126 99 0.84
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (124 bp):
ATTGTTATGATCCACTTATATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGCTATATATGGAC
TTAGGCTCTCCCACCCTAATAGCTAGCTTTTAGGGTGTGATTCTTAAAAGTCCGTATCA
Found at i:1757745 original size:34 final size:34
Alignment explanation
Indices: 1757700--1757769 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1757690 ATAGTTAGCT
*
1757700 TTTGGGATGTGGTTCTCCACAAAGTCCGTATCAA
1 TTTGGGATGTGGTTCTCCAAAAAGTCCGTATCAA
*
1757734 TTTGGGGTGTGGTTCTCCAAAAAGTCCGTATCAA
1 TTTGGGATGTGGTTCTCCAAAAAGTCCGTATCAA
1757768 TT
1 TT
1757770 GGTATCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (34 bp):
TTTGGGATGTGGTTCTCCAAAAAGTCCGTATCAA
Found at i:1757905 original size:15 final size:15
Alignment explanation
Indices: 1757882--1757911 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1757872 AAAGGGGTGC
*
1757882 TAGCTGTGACCAACG
1 TAGCCGTGACCAACG
1757897 TAGCCGTGACCAACG
1 TAGCCGTGACCAACG
1757912 AGGACGTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (15 bp):
TAGCCGTGACCAACG
Found at i:1758164 original size:126 final size:125
Alignment explanation
Indices: 1757939--1758193 Score: 465
Period size: 126 Copynumber: 2.0 Consensus size: 125
1757929 AGCATGGGGT
1757939 ATTGTTGTGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
1 ATTGTTGTGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
*
1758004 TTAGGCTCTCCCACCCTAATAGCTAGCTTTTGGGGTGTGTTTCTCCAAAAAGTCCGTATAA
66 TTAGGCTCTCCCACCCTAATAGCTAGCTTTTGGGGTGTGATTCTCC-AAAAGTCCGTATAA
1758065 ATTGTTGTGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
1 ATTGTTGTGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
* * *
1758130 TTAGGCTCTCTCACCCTAATAGCTAGCTTTTGGGGTGTGATTCTCCAAAAGTCCTTATCA
66 TTAGGCTCTCCCACCCTAATAGCTAGCTTTTGGGGTGTGATTCTCCAAAAGTCCGTATAA
1758190 ATTG
1 ATTG
1758194 ATATCAGAGC
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
125 16 0.13
126 109 0.87
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (125 bp):
ATTGTTGTGATCCACTTGTATCCCACATCGAAAGATAAAGGCTTTCCTTGTGGGTATATATGGAC
TTAGGCTCTCCCACCCTAATAGCTAGCTTTTGGGGTGTGATTCTCCAAAAGTCCGTATAA
Found at i:1758310 original size:15 final size:15
Alignment explanation
Indices: 1758290--1758328 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1758280 AGGTGCCAGT
*
1758290 CGTGACCAACGTAGC
1 CGTGACCAACGTAAC
1758305 CGTGACCAACGTAAC
1 CGTGACCAACGTAAC
1758320 CGTGACCAA
1 CGTGACCAA
1758329 TGAGGACGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
CGTGACCAACGTAAC
Found at i:1767274 original size:43 final size:43
Alignment explanation
Indices: 1767217--1767315 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
1767207 TTTTATAATT
* * * * *
1767217 AAATTTAAATAAAAATATATTTTTTACTATTAACA-TTCGAATCC
1 AAATTTATA-AAAAATATATTTTTTAATATTAA-AGGTCAAACCC
*
1767261 AAATTTATAAAAAATTTATTTTTTAATATTAAAGGTCAAACCC
1 AAATTTATAAAAAATATATTTTTTAATATTAAAGGTCAAACCC
1767304 AAATTTATAAAA
1 AAATTTATAAAA
1767316 TTTTTATCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.02
43 39 0.81
44 8 0.17
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (43 bp):
AAATTTATAAAAAATATATTTTTTAATATTAAAGGTCAAACCC
Found at i:1769663 original size:3 final size:3
Alignment explanation
Indices: 1769649--1769680 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1769639 ATGGTTAAAT
*
1769649 TCA TCA TAA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1769681 GTCTTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1774584 original size:7 final size:7
Alignment explanation
Indices: 1774572--1774603 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1774562 GAACACACGC
1774572 AAAACCA
1 AAAACCA
1774579 AAAACCA
1 AAAACCA
1774586 AAAACCA
1 AAAACCA
*
1774593 AAAGCCA
1 AAAACCA
1774600 AAAA
1 AAAA
1774604 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.72, C:0.25, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAACCA
Found at i:1775418 original size:28 final size:25
Alignment explanation
Indices: 1775373--1775435 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 25
1775363 TTTTAAGTAA
**
1775373 ATTAAAAAATTTTAATTATTTATTT
1 ATTAAAAAATTTTAATTAAATATTT
1775398 GA-TAAAAAATTTTAATTATTAAATATTT
1 -ATTAAAAAATTTT-A--ATTAAATATTT
1775426 ATTAAAAAAT
1 ATTAAAAAAT
1775436 AATATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 11 0.35
26 2 0.06
27 1 0.03
28 17 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTAAAAAATTTTAATTAAATATTT
Found at i:1776445 original size:2 final size:2
Alignment explanation
Indices: 1776438--1776465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1776428 AGCTTTACTG
1776438 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
1776466 TCCTCTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1776941 original size:20 final size:20
Alignment explanation
Indices: 1776858--1776942 Score: 54
Period size: 20 Copynumber: 4.2 Consensus size: 20
1776848 TTGCATGTTA
1776858 AATTATTTTAAATTTTAAATTT
1 AATTATTTTAAA-TTTAAA-TT
1776880 AA-TA-TTTAAA-TT-AATT
1 AATTATTTTAAATTTAAATT
** * *
1776896 AGATTTAAATT-ATTTTAAAATA
1 A-A-TTATTTTAAATTT-AAATT
1776918 AATTATTTTAAATTTAAATT
1 AATTATTTTAAATTTAAATT
1776938 AATTA
1 AATTA
1776943 AATCTAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
16 3 0.06
17 3 0.06
18 2 0.04
19 3 0.06
20 24 0.50
21 7 0.15
22 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
AATTATTTTAAATTTAAATT
Found at i:1776943 original size:15 final size:16
Alignment explanation
Indices: 1776855--1776945 Score: 77
Period size: 15 Copynumber: 6.0 Consensus size: 16
1776845 TATTTGCATG
*
1776855 TTAAATTATTTTAAATT
1 TTAAATTATATTAAA-T
*
1776872 TTAAATT-TA--ATAT
1 TTAAATTATATTAAAT
*
1776885 TTAAATTA-ATTAGAT
1 TTAAATTATATTAAAT
*
1776900 TTAAATTATTTTAAA-
1 TTAAATTATATTAAAT
* *
1776915 ATAAATTATTTTAAAT
1 TTAAATTATATTAAAT
1776931 TTAAATTA-ATTAAAT
1 TTAAATTATATTAAAT
1776946 CTAATATTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
13 9 0.15
14 2 0.03
15 31 0.51
16 12 0.20
17 7 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TTAAATTATATTAAAT
Found at i:1777022 original size:15 final size:15
Alignment explanation
Indices: 1777004--1777045 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1776994 ATTTTATCAT
*
1777004 GTTTAATTATTTTGA
1 GTTTAATTATTTTAA
1777019 GTTTAAATTA-TTTAA
1 GTTT-AATTATTTTAA
*
1777034 GATTAATTATTT
1 GTTTAATTATTT
1777046 ATGTCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
GTTTAATTATTTTAA
Found at i:1777100 original size:16 final size:16
Alignment explanation
Indices: 1777081--1777124 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1777071 GAGTTAAAGC
1777081 CATTTCAAATTTAAAT
1 CATTTCAAATTTAAAT
*
1777097 CATTTTAAATTTAAAT
1 CATTTCAAATTTAAAT
1777113 CATTTCAAATTT
1 CATTTCAAATTT
1777125 GATTTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (16 bp):
CATTTCAAATTTAAAT
Found at i:1777222 original size:20 final size:20
Alignment explanation
Indices: 1777193--1777237 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1777183 GGTTAAGGTG
* *
1777193 GTTT-AGTTAAATTTTATGA
1 GTTTAAGTTAAAATTTATAA
1777212 GTTTAAGTTAAAATTTATAA
1 GTTTAAGTTAAAATTTATAA
1777232 GTTTAA
1 GTTTAA
1777238 TTGGAACGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
GTTTAAGTTAAAATTTATAA
Found at i:1778146 original size:2 final size:2
Alignment explanation
Indices: 1778134--1778169 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1778124 ATTTCAAAAC
*
1778134 AT AT AT GT 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
1778170 TTGTTCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1780962 original size:142 final size:141
Alignment explanation
Indices: 1780765--1781113 Score: 400
Period size: 142 Copynumber: 2.5 Consensus size: 141
1780755 TAAAAAAATG
* * ** * *
1780765 AAAAGTTTTGAAGATTTCTATACCTTTACAAAAAATCATTGGAATATTAGAAATCTTGAAAAATT
1 AAAAGTTTTTAAAATTTCTATACCCCTACAAAAAATCATAGGAATATTAAAAATCTTGAAAAATT
** * * * *
1780830 ATTATAATAATTTTTATTTAATATTTTAATTTTTAAAAAATTTATTTCATA-CATTAATGGAGAA
66 AAGATAATAATTTTTATTTAATA-TTTAATCTTCAAAAAAATCATTTCATATC-TTAATGGAGAA
*
1780894 TTGAAAAGATACA
129 TCGAAAAGATACA
*
1780907 AAAAGTTTTTAAAATTTCTATACCCCTACAAAAAA-CTATAGGAATATTAAAAATCTTTAAAAAT
1 AAAAGTTTTTAAAATTTCTATACCCCTACAAAAAATC-ATAGGAATATTAAAAATCTTGAAAAAT
**
1780971 TAAGATAATAATTTTTATTTAATATTTAATCTTCAAAAAAATCATTTTGTATCTTAATGGAGAAT
65 TAAGATAATAATTTTTATTTAATATTTAATCTTCAAAAAAATCATTTCATATCTTAATGGAGAAT
1781036 CGAAAAGATACA
130 CGAAAAGATACA
* * * ** * * * **
1781048 ACAAG-TTTTAAAGATTT-TATATCCTTATGAAATATCATAAGAATATTAGAAATCTAAAAAAAT
1 AAAAGTTTTTAAA-ATTTCTATACCCCTACAAAAAATCATAGGAATATTAAAAATCTTGAAAAAT
1781111 TAA
65 TAA
1781114 CCAAAAGTCA
Statistics
Matches: 177, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
140 45 0.25
141 54 0.31
142 78 0.44
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (141 bp):
AAAAGTTTTTAAAATTTCTATACCCCTACAAAAAATCATAGGAATATTAAAAATCTTGAAAAATT
AAGATAATAATTTTTATTTAATATTTAATCTTCAAAAAAATCATTTCATATCTTAATGGAGAATC
GAAAAGATACA
Found at i:1781881 original size:20 final size:20
Alignment explanation
Indices: 1781845--1781896 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1781835 TTTAGCTTAT
*
1781845 TTTTTCTTAT-TTTCTCTCT-
1 TTTTTCTT-TCTTCCTCTCTC
*
1781864 TTTTTCGTTTCTTCCTCTTTC
1 TTTTTC-TTTCTTCCTCTCTC
1781885 TTTTTCTTTCTT
1 TTTTTCTTTCTT
1781897 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTCTTTCTTCCTCTCTC
Found at i:1781906 original size:16 final size:17
Alignment explanation
Indices: 1781844--1781907 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 17
1781834 GTTTAGCTTA
*
1781844 TTTTTTCTTATTTTCTCTC
1 TTTTTTCTT-TCTT-TCTC
*
1781863 TTTTTTCGTTTCTTCCTC
1 TTTTTTC-TTTCTTTCTC
*
1781881 TTTCTT-TTTCTTTCT-
1 TTTTTTCTTTCTTTCTC
1781896 TTTTTTCTTTCT
1 TTTTTTCTTTCT
1781908 ACTTGTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 5 0.13
16 13 0.34
18 8 0.21
19 10 0.26
20 2 0.05
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTCTTTCTTTCTC
Found at i:1782906 original size:153 final size:152
Alignment explanation
Indices: 1782715--1783199 Score: 611
Period size: 153 Copynumber: 3.2 Consensus size: 152
1782705 AAAAATTATG
* * * *
1782715 AAAATAAA-TAAAATTTGCAAAACTGATTTAATATCAATTAAACAATAATATGTAAAGAATTTTA
1 AAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
*
1782779 AAAATTATAAACTTAGAAAAATCTTATCGAAAAATTTATGAAGAAGAAAACTTTGTATTTCGATA
66 AAAATTATAAACTTAGAAAAATCTTA-CCAAAAATTTATGAAGAAGAAAACTTTGTATTTCGATA
1782844 ACAGAAAAAATT-TCAAAACTCAT
130 ACAGAAAAAATTCT-AAAACTCAT
* *
1782867 AAAATAAATTTAATTTTTCAAAACTGATTTAATACCAATTAAACAATAATATTTGAAGAATTTT-
1 AAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* * * * * *
1782931 GAAATTACAAACTTAGAGATATCTTACCAAAAATTCAT-AGAGTAGAAAACTTTGTATTTCGATA
66 AAAATTATAAACTTAGAAAAATCTTACCAAAAATTTATGA-AGAAGAAAACTTTGTATTTCGATA
* *
1782995 ATAGGAAAAATTCTAAAACTCAT
130 ACAGAAAAAATTCTAAAACTCAT
* * * * * *
1783018 AAAACAAATTGAATTTTTCAAAACTAATTTAATATCAATTGAATAGTAATATTTGAAGAATTTTA
1 AAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
* * * * ** *
1783083 AAAATTATAAACTTAAAAAAATCTTACCTAAAAAATTACGAAGAAAAAAACTTCATATTTTGATA
66 AAAATTATAAACTTAGAAAAATCTTACC-AAAAATTTATGAAGAAGAAAACTTTGTATTTCGATA
* *
1783148 ACA-AGAAGAATTCTAAAACACAT
130 ACAGA-AAAAATTCTAAAACTCAT
*
1783171 AAAATAAATTAAATTTTTCAAAATTGATT
1 AAAATAAATTAAATTTTTCAAAACTGATT
1783200 CTATGGTGAT
Statistics
Matches: 283, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
150 1 0.00
151 109 0.39
152 54 0.19
153 118 0.42
154 1 0.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (152 bp):
AAAATAAATTAAATTTTTCAAAACTGATTTAATATCAATTAAACAATAATATTTGAAGAATTTTA
AAAATTATAAACTTAGAAAAATCTTACCAAAAATTTATGAAGAAGAAAACTTTGTATTTCGATAA
CAGAAAAAATTCTAAAACTCAT
Found at i:1785113 original size:18 final size:19
Alignment explanation
Indices: 1785071--1785113 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1785061 GCAGATTTCT
*
1785071 AGATTTCCTGAATTCTAGT
1 AGATTTCCTGAATTCTAGC
* *
1785090 AGATTTCCTG-ATTTTTGC
1 AGATTTCCTGAATTCTAGC
1785108 AGATTT
1 AGATTT
1785114 TTAGATCTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (19 bp):
AGATTTCCTGAATTCTAGC
Found at i:1789882 original size:18 final size:19
Alignment explanation
Indices: 1789840--1789884 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1789830 TGCAAATTTC
1789840 CAGATTTCCTGAATTCTAG
1 CAGATTTCCTGAATTCTAG
*
1789859 CAGATTTCCTGATTTCTA-
1 CAGATTTCCTGAATTCTAG
1789877 CAGATTTC
1 CAGATTTC
1789885 TAAATCTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.40
Consensus pattern (19 bp):
CAGATTTCCTGAATTCTAG
Found at i:1789913 original size:16 final size:16
Alignment explanation
Indices: 1789894--1789924 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1789884 CTAAATCTGC
1789894 AAATTTATTGATTTTG
1 AAATTTATTGATTTTG
*
1789910 AAATTTTTTGATTTT
1 AAATTTATTGATTTT
1789925 CTAGATATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (16 bp):
AAATTTATTGATTTTG
Found at i:1795242 original size:2 final size:2
Alignment explanation
Indices: 1795235--1795271 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1795225 TCATAAAATG
*
1795235 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1795272 CTATCTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1795423 original size:76 final size:76
Alignment explanation
Indices: 1795331--1795507 Score: 189
Period size: 76 Copynumber: 2.3 Consensus size: 76
1795321 GCACGATTCG
* *
1795331 AAACGAAAACTATTATTCTAAA-TCGATGGCACAGTTCAAAACAAAAATC-ACTATTCTAAACCA
1 AAACAAAAATTATTATTCTAAACT-GATGGCACAGTTCAAAACAAAAA-CAACTATTCTAAACCA
*
1795394 ATGG-TACAGTTTA
64 ATGGCT-CAGTTCA
* * ** * * *
1795407 AAACAAAAATTATTATTCTTAACTGGTGGCAGGGTTCAATATAAAAACAACTATTCTTAACCAAT
1 AAACAAAAATTATTATTCTAAACTGATGGCACAGTTCAAAACAAAAACAACTATTCTAAACCAAT
1795472 GGCTCAGTTCA
66 GGCTCAGTTCA
* * *
1795483 ATACAAAAATCATTATTCTTAACTG
1 AAACAAAAATTATTATTCTAAACTG
1795508 GTGACATGGC
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
75 1 0.01
76 83 0.97
77 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (76 bp):
AAACAAAAATTATTATTCTAAACTGATGGCACAGTTCAAAACAAAAACAACTATTCTAAACCAAT
GGCTCAGTTCA
Found at i:1795502 original size:38 final size:38
Alignment explanation
Indices: 1795342--1795505 Score: 150
Period size: 38 Copynumber: 4.3 Consensus size: 38
1795332 AACGAAAACT
* * *
1795342 ATTATTCTAAATCGATGGCACAGTTCAAAACAAAAATC
1 ATTATTCTTAACCAATGGCACAGTTCAAAACAAAAATC
* * * * *
1795380 ACTATTCTAAACCAATGGTACAGTTTAAAACAAAAATT
1 ATTATTCTTAACCAATGGCACAGTTCAAAACAAAAATC
*** ** * *
1795418 ATTATTCTTAACTGGTGGCAGGGTTCAATATAAAAA-C
1 ATTATTCTTAACCAATGGCACAGTTCAAAACAAAAATC
* * *
1795455 AACTATTCTTAACCAATGGCTCAGTTCAATACAAAAATC
1 -ATTATTCTTAACCAATGGCACAGTTCAAAACAAAAATC
1795494 ATTATTCTTAAC
1 ATTATTCTTAAC
1795506 TGGTGACATG
Statistics
Matches: 97, Mismatches: 27, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
38 96 0.99
39 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (38 bp):
ATTATTCTTAACCAATGGCACAGTTCAAAACAAAAATC
Found at i:1796322 original size:20 final size:20
Alignment explanation
Indices: 1796272--1796323 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1796262 AAATAGAGAT
* *
1796272 AAATTCATAAATATATATTA
1 AAATTAATAAAAATATATTA
* *
1796292 AAA-TATGTAAAAATTTATTA
1 AAATTA-ATAAAAATATATTA
1796312 AAATTAATAAAA
1 AAATTAATAAAA
1796324 CTGAAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTAATAAAAATATATTA
Found at i:1796351 original size:21 final size:22
Alignment explanation
Indices: 1796322--1796371 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1796312 AAATTAATAA
*
1796322 AACTGAAATTTATATTATTTTT
1 AACTGAAATATATATTATTTTT
*
1796344 AACT-AAATATATTTTA-TTTT
1 AACTGAAATATATATTATTTTT
*
1796364 AGCTGAAA
1 AACTGAAA
1796372 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
AACTGAAATATATATTATTTTT
Found at i:1796412 original size:24 final size:21
Alignment explanation
Indices: 1796369--1796414 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
1796359 ATTTTAGCTG
*
1796369 AAAATAATTTTTAAATAATTC
1 AAAATAATTTTTAAAAAATTC
1796390 AAAATAAATTTTTTAAAAAAATTC
1 AAAAT-AA-TTTTT-AAAAAATTC
1796414 A
1 A
1796415 TTCAACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 5 0.24
24 9 0.43
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATAATTTTTAAAAAATTC
Found at i:1797337 original size:31 final size:31
Alignment explanation
Indices: 1797276--1797339 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1797266 TATATATCTT
*
1797276 ATAAAAAAATATATTCTATAAATATAAATAA
1 ATAAAAAAATATATTCTAAAAATATAAATAA
* *
1797307 ATAATAAAAAT-TATTTTAAAAATATTAATAA
1 ATAA-AAAAATATATTCTAAAAATATAAATAA
1797338 AT
1 AT
1797340 CTCAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
ATAAAAAAATATATTCTAAAAATATAAATAA
Found at i:1798060 original size:21 final size:22
Alignment explanation
Indices: 1798020--1798078 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 22
1798010 TTATGTGTGA
1798020 TAAATTAATTTTTAAAAATTAAA-
1 TAAATTAA--TTTAAAAATTAAAT
*
1798043 TAAA-TAATATTAATAATTAAAT
1 TAAATTAAT-TTAAAAATTAAAT
1798065 TAAATTAATTTAAA
1 TAAATTAATTTAAA
1798079 TTTAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
22 11 0.35
23 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTAATTTAAAAATTAAAT
Found at i:1798312 original size:32 final size:29
Alignment explanation
Indices: 1798270--1798332 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 29
1798260 AAAGTTGCAT
1798270 AATTTTTTA-TTTAAATTTAAATCTAAATTTA
1 AATTTTTTATTTTAAA-TTAAAT-T-AATTTA
1798301 AATTTTATTATTTTAAATTAAATTAATTTA
1 AATTTT-TTATTTTAAATTAAATTAATTTA
1798331 AA
1 AA
1798333 ATAATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 8 0.27
31 7 0.23
32 9 0.30
33 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
AATTTTTTATTTTAAATTAAATTAATTTA
Found at i:1798352 original size:19 final size:21
Alignment explanation
Indices: 1798323--1798370 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
1798313 TTAAATTAAA
1798323 TTAATTTAAAATAATA-ATTT
1 TTAATTTAAAATAATATATTT
1798343 TTAA-TTAAAATAATATA-TT
1 TTAATTTAAAATAATATATTT
1798362 TT-ATTTAAA
1 TTAATTTAAA
1798371 TTTAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 20 0.77
20 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTTAAAATAATATATTT
Found at i:1798362 original size:49 final size:49
Alignment explanation
Indices: 1798309--1798411 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
1798299 TAAATTTTAT
* *
1798309 TATTTTAAATTAAA-TTAATT-TAAAATA-ATAATTTTTAATTAAAATAATA
1 TATTTT-AATTAAATTTAATTATAAAATATATAAATATTAA-TAAAA-AATA
*
1798358 TATTTTATTTAAATTTAATTATAAAATATATAAATATTAATAAAAAATA
1 TATTTTAATTAAATTTAATTATAAAATATATAAATATTAATAAAAAATA
1798407 -ATTTT
1 TATTTT
1798412 TTAATATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
48 11 0.23
49 16 0.33
50 12 0.25
51 9 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (49 bp):
TATTTTAATTAAATTTAATTATAAAATATATAAATATTAATAAAAAATA
Found at i:1798391 original size:21 final size:21
Alignment explanation
Indices: 1798367--1798406 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1798357 ATATTTTATT
*
1798367 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1798388 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
1798407 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1798481 original size:18 final size:19
Alignment explanation
Indices: 1798453--1798496 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1798443 TTAAATCAAG
1798453 TTAAA-TTAAATATAAA-T
1 TTAAATTTAAATATAAATT
*
1798470 TTAAATTTAAATTTAAATT
1 TTAAATTTAAATATAAATT
1798489 TTAAATTT
1 TTAAATTT
1798497 TATCAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTTAAATATAAATT
Found at i:1798488 original size:12 final size:12
Alignment explanation
Indices: 1798453--1798533 Score: 64
Period size: 12 Copynumber: 6.8 Consensus size: 12
1798443 TTAAATCAAG
1798453 TTAAA-TTAAAT
1 TTAAATTTAAAT
*
1798464 ATAAATTTAAAT
1 TTAAATTTAAAT
1798476 TTAAATTTAAATT
1 TTAAATTTAAA-T
*
1798489 TTAAATTTTATCAAA
1 TTAAA-TTTA--AAT
1798504 TTATAATTT-AAT
1 TTA-AATTTAAAT
1798516 TT-AATTT-AAT
1 TTAAATTTAAAT
1798526 TT-AATTTA
1 TTAAATTTA
1798534 TAAATATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
10 15 0.25
11 4 0.07
12 20 0.34
13 6 0.10
14 4 0.07
15 6 0.10
16 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:1798493 original size:7 final size:6
Alignment explanation
Indices: 1798453--1798533 Score: 64
Period size: 5 Copynumber: 13.5 Consensus size: 6
1798443 TTAAATCAAG
* *
1798453 TTAAA- TTAAAT ATAAAT TTAAAT TTAAAT TTAAATT TTAAATT TTATCAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA-T TTA--AAT
1798504 TTATAAT TT-AAT TT-AAT TT-AAT TT-AAT TTA
1 TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTA
1798534 TAAATATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
5 25 0.38
6 21 0.32
7 15 0.23
8 3 0.05
9 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:1799719 original size:3 final size:3
Alignment explanation
Indices: 1799700--1799758 Score: 82
Period size: 3 Copynumber: 18.7 Consensus size: 3
1799690 TTACTCACTT
1799700 TAA TGAA TAA GTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
1799748 TAA CAA TAA TA
1 TAA TAA TAA TA
1799759 CTATTAACTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
3 42 0.82
4 9 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1799863 original size:18 final size:18
Alignment explanation
Indices: 1799840--1799898 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
1799830 TTAATTTAAT
1799840 TTAAAATAATAT-TTTTAA
1 TTAAAATAATATATTTT-A
1799858 TTAAAATAATATATTTTA
1 TTAAAATAATATATTTTA
1799876 TTAAAATAATATATTTTA
1 TTAAAATAATATATTTTA
1799894 TTAAA
1 TTAAA
1799899 TTTAATTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 36 0.90
19 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATAATATATTTTA
Found at i:1799919 original size:21 final size:21
Alignment explanation
Indices: 1799895--1799934 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1799885 TATATTTTAT
1799895 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
1799916 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1799935 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1799951 original size:48 final size:49
Alignment explanation
Indices: 1799846--1799973 Score: 126
Period size: 46 Copynumber: 2.7 Consensus size: 49
1799836 TAATTTAAAA
* ** * *
1799846 TAATATTTTTAATTAAAATAATATATTTTATTAAAATAATATATTTTAT
1 TAATATTTTTAATTATAATAATATATAATATTAAAATAAAATAATTTAT
*
1799895 TAA-A--TTTAATTATAA-AATATATAAATATTAATATAAAATAATTT-T
1 TAATATTTTTAATTATAATAATATAT-AATATTAAAATAAAATAATTTAT
*
1799940 TAATATTTTTAATAATAATAA-ATAATAAT-TTAAA
1 TAATATTTTTAATTATAATAATAT-ATAATATTAAA
1799974 TTTATAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
45 11 0.17
46 27 0.42
47 4 0.06
48 16 0.25
49 7 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (49 bp):
TAATATTTTTAATTATAATAATATATAATATTAAAATAAAATAATTTAT
Found at i:1799956 original size:29 final size:30
Alignment explanation
Indices: 1799923--1800010 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
1799913 ATATAAATAT
* *
1799923 TAATATAAAATAAT-TTTTAATATTT-TTAA
1 TAATATAAAATAATAATTTAA-ATTTATAAA
1799952 TAATA-ATAAATAATAATTTAAATTTATAAA
1 TAATATA-AAATAATAATTTAAATTTATAAA
* *
1799982 TTATATAAAATTA-AATTTAAATTTA-AAA
1 TAATATAAAATAATAATTTAAATTTATAAA
1800010 T
1 T
1800011 TTAAAACCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 5 0.10
29 28 0.55
30 17 0.33
31 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATATAAAATAATAATTTAAATTTATAAA
Found at i:1800388 original size:19 final size:18
Alignment explanation
Indices: 1800366--1800439 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 18
1800356 TTAAATCTAA
1800366 AATTATAACATAA-AAAATT
1 AATTATAA-ATAATAAAA-T
*
1800385 AATTAAAATATAATAAAAT
1 AATTATAA-ATAATAAAAT
1800404 AA-TATAAATAATATAAAAT
1 AATTATAAAT-A-ATAAAAT
*
1800423 ATAATATAAATATATAA
1 A-ATTATAAATA-ATAA
1800440 TATATTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 2 0.04
18 5 0.11
19 22 0.47
20 11 0.23
21 7 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTATAAATAATAAAAT
Found at i:1800442 original size:5 final size:5
Alignment explanation
Indices: 1800391--1800469 Score: 55
Period size: 5 Copynumber: 16.8 Consensus size: 5
1800381 AATTAATTAA
1800391 AATAT AATA- AA-AT AATAT AA-AT AATAT AAAATAT AATAT AA-AT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT --AATAT AATAT AATAT AATAT
* * * *
1800438 AATAT ATTAA AATTT TATAT AA-AT -ATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
1800470 CTTTAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
3 3 0.05
4 16 0.28
5 33 0.58
7 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1800442 original size:13 final size:13
Alignment explanation
Indices: 1800390--1800469 Score: 72
Period size: 13 Copynumber: 5.9 Consensus size: 13
1800380 AAATTAATTA
*
1800390 AAATATAATAAAAT
1 AAATAT-ATAATAT
*
1800404 AATATAAATAATAT
1 AA-ATATATAATAT
1800418 AAA-ATATAATAT
1 AAATATATAATAT
1800430 AAATATATAATAT
1 AAATATATAATAT
* * *
1800443 ATTAAAATTTTATAT
1 A--AATATATAATAT
1800458 AAATATATAATA
1 AAATATATAATA
1800470 CTTTAAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
12 11 0.21
13 19 0.36
14 10 0.19
15 13 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATATAATAT
Found at i:1800450 original size:28 final size:28
Alignment explanation
Indices: 1800386--1800486 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 28
1800376 TAAAAAATTA
1800386 ATTAAAATATAATA-AAATAATATAA-AT
1 ATTAAAATATAATATAAAT-ATATAATAT
1800413 AATATAAAATATAATATAAATATATAATAT
1 -AT-TAAAATATAATATAAATATATAATAT
* *
1800443 ATTAAAATTTTATATAAATATATAATACT
1 ATTAAAATATAATATAAATATATAATA-T
1800472 -TTAAAAAATATAATA
1 ATT--AAAATATAATA
1800487 AAAAAATTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
28 27 0.43
29 21 0.33
30 15 0.24
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTAAAATATAATATAAATATATAATAT
Found at i:1800474 original size:20 final size:18
Alignment explanation
Indices: 1800414--1800486 Score: 51
Period size: 20 Copynumber: 3.8 Consensus size: 18
1800404 AATATAAATA
*
1800414 ATATAAAATATAATATAAAT
1 ATATAAAATATAATAT--TT
* *
1800434 ATATAATATATTAAAATTTT
1 ATATAAAATA-TAATA-TTT
1800454 ATATAAATATATAATACTTT
1 ATATAAA-ATATAATA-TTT
1800474 A-A-AAAATATAATA
1 ATATAAAATATAATA
1800487 AAAAAATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 8 0.18
18 3 0.07
19 1 0.02
20 24 0.55
21 7 0.16
22 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAAATATAATATTT
Found at i:1800927 original size:29 final size:28
Alignment explanation
Indices: 1800870--1800953 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
1800860 GAGATATAAT
**
1800870 TTTTTATTTAAA-TTAATT-T-AATTTAA
1 TTTTTATTTAAATTTAATTATAAAAAT-A
*
1800896 TTTTTA-TTATTATTTAATTAATAAAAATA
1 TTTTTATTTA-AATTTAATT-ATAAAAATA
1800925 TTTTTATTTAAATTTAATTATAAAAATA
1 TTTTTATTTAAATTTAATTATAAAAATA
1800953 T
1 T
1800954 AAAAATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 6 0.12
28 10 0.21
29 16 0.33
30 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTTATTTAAATTTAATTATAAAAATA
Found at i:1800966 original size:14 final size:14
Alignment explanation
Indices: 1800949--1800976 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1800939 TAATTATAAA
1800949 AATATAAAAATATT
1 AATATAAAAATATT
1800963 AATATAAAAATATT
1 AATATAAAAATATT
1800977 TTTATTCTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:1800968 original size:22 final size:22
Alignment explanation
Indices: 1800934--1800975 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1800924 ATTTTTATTT
1800934 AAATTTAATTATAAAAATATAA
1 AAATTTAATTATAAAAATATAA
1800956 AAATATTAA-TATAAAAATAT
1 AAAT-TTAATTATAAAAATAT
1800976 TTTTATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAA
Found at i:1801009 original size:22 final size:22
Alignment explanation
Indices: 1800958--1801013 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
1800948 AAATATAAAA
* *
1800958 ATATTAATATAAAAATATTTTT
1 ATATTAATTTATAAATATTTTT
1800980 AT-TCTAATTTATAAATATTTTT
1 ATAT-TAATTTATAAATATTTTT
1801002 ATATTAATTTAT
1 ATATTAATTTAT
1801014 CGAGAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTAATTTATAAATATTTTT
Found at i:1801299 original size:11 final size:11
Alignment explanation
Indices: 1801283--1801339 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
1801273 TTACATAATT
1801283 ATATAAATATA
1 ATATAAATATA
*
1801294 ATATAAATAAA
1 ATATAAATATA
1801305 ATAATTAAAATATA
1 AT-A-T-AAATATA
*
1801319 ATAT-AATATT
1 ATATAAATATA
1801329 ATATAAATATA
1 ATATAAATATA
1801340 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.24
11 17 0.45
12 2 0.05
13 2 0.05
14 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1801324 original size:30 final size:31
Alignment explanation
Indices: 1801283--1801395 Score: 106
Period size: 35 Copynumber: 3.5 Consensus size: 31
1801273 TTACATAATT
1801283 ATATAAATATAATATAAATAAAATA-ATTAAA
1 ATAT-AATATAATATAAATAAAATATATTAAA
*
1801314 ATATAATATAATATTATATAAATATATATTTTAAA
1 ATATAATATAATA-TAAATAAA-ATATA--TTAAA
* * *
1801349 ATTTTATATAATATAAATAATTAATATAATAAA
1 ATATAATATAATATAAATAA--AATATATTAAA
1801382 ATAT-ATA-AATATAA
1 ATATAATATAATATAA
1801396 TACTGTTGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
30 9 0.13
31 18 0.26
32 6 0.09
33 8 0.12
34 6 0.09
35 21 0.30
36 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATAATATAATATAAATAAAATATATTAAA
Found at i:1801342 original size:25 final size:25
Alignment explanation
Indices: 1801280--1801397 Score: 92
Period size: 23 Copynumber: 5.0 Consensus size: 25
1801270 AATTTACATA
1801280 ATTATATAAATATAATATAA-ATAA-
1 ATTATATAAATAT-ATATAATATAAT
* *
1801304 AATA-ATTAA-A-ATATAATATAAT
1 ATTATATAAATATATATAATATAAT
** *
1801326 ATTATATAAATATATATTTTAAAAT
1 ATTATATAAATATATATAATATAAT
* *
1801351 TTTATAT-AATATAAATAAT-TAAT
1 ATTATATAAATATATATAATATAAT
*
1801374 ATAATA-AAATATATA-AATATAAT
1 ATTATATAAATATATATAATATAAT
1801397 A
1 A
1801398 CTGTTGTTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
20 6 0.08
21 4 0.06
22 7 0.10
23 27 0.38
24 13 0.18
25 15 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTATATAAATATATATAATATAAT
Found at i:1801373 original size:4 final size:5
Alignment explanation
Indices: 1801283--1801397 Score: 80
Period size: 5 Copynumber: 23.6 Consensus size: 5
1801273 TTACATAATT
* * *
1801283 ATATAA ATATA ATATA A-ATA AAATA ATTAAA ATATA ATATA ATATT ATATA
1 ATAT-A ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA
* * * * * *
1801334 A-ATA TATATT TTAAA ATTTT ATATA ATATA A-ATA AT-TA ATATA ATAAA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1801382 ATAT- ATA-A ATATA ATA
1 ATATA ATATA ATATA ATA
1801398 CTGTTGTTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
4 21 0.25
5 54 0.64
6 9 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1802810 original size:15 final size:14
Alignment explanation
Indices: 1802753--1802813 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
1802743 TATATATTTT
1802753 AAATTTTTAATAT-
1 AAATTTTTAATATA
*
1802766 AAATTATTAATATATTA
1 AAATT-TTTA-ATA-TA
*
1802783 AAATTTATGAATATA
1 AAATTT-TTAATATA
1802798 AAATATTTTAATATA
1 AAAT-TTTTAATATA
1802813 A
1 A
1802814 TTATAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.13
14 3 0.08
15 17 0.44
16 7 0.18
17 7 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AAATTTTTAATATA
Found at i:1802841 original size:31 final size:29
Alignment explanation
Indices: 1802714--1802843 Score: 81
Period size: 31 Copynumber: 4.4 Consensus size: 29
1802704 TAACATAACA
* * *
1802714 TATATAAAATAATAAAAATAT-AATATAAT
1 TATATAATATAATTATAATATAAATAT-AT
* * *
1802743 TATATATTTTAAATTTTTAATATAAAT-TAT
1 TATATAATAT-AA-TTATAATATAAATATAT
* *
1802773 TAATATATTAAAATTTATGAATATAAA-ATAT
1 T-ATATAATATAA-TTAT-AATATAAATATAT
1802804 T-T-TAATATAATTATAATATAATATATAT
1 TATATAATATAATTATAATATAA-ATATAT
1802832 ATATATAATATA
1 -TATATAATATA
1802844 TAAATGATCA
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
26 7 0.09
27 5 0.06
28 10 0.13
29 9 0.11
30 12 0.15
31 33 0.42
32 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TATATAATATAATTATAATATAAATATAT
Done.