Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 24 of 29
Found at i:10125884 original size:52 final size:53
Alignment explanation
Indices: 10125794--10125918 Score: 130
Period size: 52 Copynumber: 2.4 Consensus size: 53
10125784 AACATGATGT
* * ** *
10125794 ATAATAATTTTTTTTAATCATAACGTGTAATATGTTTTTGGT-A-CATAACGTGTA
1 ATAATAACTTTTTTTAA-CATAACGTGTAACAACTTTTT--TAACCATAACGCGTA
* *
10125848 ATAATAA-TTTTTTTAACATGACGTGTAACAACTTTTTTAACCATAGCGCGTA
1 ATAATAACTTTTTTTAACATAACGTGTAACAACTTTTTTAACCATAACGCGTA
*
10125900 ATAATAACATTTTTTAACA
1 ATAATAACTTTTTTTAACA
10125919 AAGTGTGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
50 1 0.02
51 1 0.02
52 33 0.54
53 19 0.31
54 7 0.11
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (53 bp):
ATAATAACTTTTTTTAACATAACGTGTAACAACTTTTTTAACCATAACGCGTA
Found at i:10126058 original size:21 final size:21
Alignment explanation
Indices: 10126025--10126090 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
10126015 TATTTTTTAA
10126025 CATGATGTGTAACATTATGTG
1 CATGATGTGTAACATTATGTG
* * *
10126046 CATGGTGTATAACATTACGTG
1 CATGATGTGTAACATTATGTG
* *
10126067 CATGACGTGTAACATCATGTG
1 CATGATGTGTAACATTATGTG
10126088 CAT
1 CAT
10126091 TTGATATAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
CATGATGTGTAACATTATGTG
Found at i:10126099 original size:42 final size:44
Alignment explanation
Indices: 10126025--10126110 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 44
10126015 TATTTTTTAA
* *
10126025 CATGATGTGTAACATTATGTGCATGGTGTAT-A-ACATTACGTG
1 CATGACGTGTAACATCATGTGCATGGTGTATAATACATTACGTG
*
10126067 CATGACGTGTAACATCATGTGCAT-TTGATATAATACATTACGTG
1 CATGACGTGTAACATCATGTGCATGGTG-TATAATACATTACGTG
10126111 TAACATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.05
42 25 0.66
43 1 0.03
44 10 0.26
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (44 bp):
CATGACGTGTAACATCATGTGCATGGTGTATAATACATTACGTG
Found at i:10126631 original size:3 final size:3
Alignment explanation
Indices: 10126617--10126650 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
10126607 ATGAGATTTT
*
10126617 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
10126651 GTTAATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:10128489 original size:16 final size:16
Alignment explanation
Indices: 10128468--10128499 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10128458 GGATGCACCT
10128468 AATTTAGAAATTTCTA
1 AATTTAGAAATTTCTA
10128484 AATTTAGAAATTTCTA
1 AATTTAGAAATTTCTA
10128500 CCCTCGCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
AATTTAGAAATTTCTA
Found at i:10143230 original size:2 final size:2
Alignment explanation
Indices: 10143218--10143246 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10143208 TATCTTTAAA
10143218 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10143247 GGAGGAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10145961 original size:189 final size:190
Alignment explanation
Indices: 10145624--10146003 Score: 618
Period size: 189 Copynumber: 2.0 Consensus size: 190
10145614 ATCTCAATCA
* *
10145624 TATGAGTTCAAGTTTAAGTGCTAGCCTTCCTAAGATAAAAATTCCTGTGATGCAAGTTTCCTTCT
1 TATGAGTTCAAGTTTAAGTGCAAGCCTTCCTAAGATAAAAACTCCTGTGATGCAAGTTTCCTTCT
10145689 GTTTTCTTTGCCTAGACTTTGTTCATCACAACCTCGTTAGAGATAATCCTTTCTTGGGTTTGACA
66 GTTTTCTTTGCCTAGACTTTGTTCATCACAACCTCGTTAGAGATAATCCTTTCTTGGGTTTGACA
10145754 GCAGATAAACATTTTTGCCTATGCAAACAATTATTACATGTGGATTATGGGCTGTGCATT
131 GCAGATAAACATTTTTGCCTATGCAAACAATTATTACATGTGGATTATGGGCTGTGCATT
*
10145814 TATGGGTTCAAGTTTAAGTGCAAGCCTTCCTAAGATAAAAACTCCTGTGATGCAAGTTTCCTTCT
1 TATGAGTTCAAGTTTAAGTGCAAGCCTTCCTAAGATAAAAACTCCTGTGATGCAAGTTTCCTTCT
* **********
10145879 GTTTTC-TTGCCTAGTCTTTGTTCATCACAACCTCGTTAGAGATAATCCNNNNNNNNNNTTGACA
66 GTTTTCTTTGCCTAGACTTTGTTCATCACAACCTCGTTAGAGATAATCCTTTCTTGGGTTTGACA
*
10145943 GCAGATAAACATTTTTGCCTATGCAAATAATTATTACATGTGGATTATGGGCTGTGCATT
131 GCAGATAAACATTTTTGCCTATGCAAACAATTATTACATGTGGATTATGGGCTGTGCATT
10146003 T
1 T
10146004 CTTTTTCTTT
Statistics
Matches: 175, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
189 107 0.61
190 68 0.39
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.36
Consensus pattern (190 bp):
TATGAGTTCAAGTTTAAGTGCAAGCCTTCCTAAGATAAAAACTCCTGTGATGCAAGTTTCCTTCT
GTTTTCTTTGCCTAGACTTTGTTCATCACAACCTCGTTAGAGATAATCCTTTCTTGGGTTTGACA
GCAGATAAACATTTTTGCCTATGCAAACAATTATTACATGTGGATTATGGGCTGTGCATT
Found at i:10161246 original size:14 final size:14
Alignment explanation
Indices: 10161223--10161261 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
10161213 TTTAGAAAAA
10161223 AAAAAT-TTTTTGG
1 AAAAATCTTTTTGG
10161236 AAAAATCTTTTTGG
1 AAAAATCTTTTTGG
*
10161250 ATTAAATCTTTT
1 A-AAAATCTTTT
10161262 ATTCAATGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 8 0.35
15 9 0.39
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (14 bp):
AAAAATCTTTTTGG
Found at i:10161869 original size:30 final size:30
Alignment explanation
Indices: 10161797--10161873 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
10161787 TTCTATGCAT
10161797 ATTACATAGTAAATAATCCTACAAACAAAC
1 ATTACATAGTAAATAATCCTACAAACAAAC
** *
10161827 ATTATGTGGTAAATAATCC-AGCAAACAAAC
1 ATTACATAGTAAATAATCCTA-CAAACAAAC
*
10161857 ATTACATTGTAAATAAT
1 ATTACATAGTAAATAAT
10161874 TCAACTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (30 bp):
ATTACATAGTAAATAATCCTACAAACAAAC
Found at i:10168447 original size:56 final size:58
Alignment explanation
Indices: 10168340--10168449 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 58
10168330 AGCTTTGCTG
* * *
10168340 CACTTCTCAGTTTAGTGATGACCTATTGTCCTAATGAATTTTCTCAAGTTTCTTGCAA
1 CACTTCTCAGTTTAGGGAAGACCTATTGTCCTAATCAATTTTCTCAAGTTTCTTGCAA
* * *
10168398 CACTTCTGAGTTTAGGGAAGA-CTA-TGTCTTGATCAATTTTCTTC-AGTTTCTT
1 CACTTCTCAGTTTAGGGAAGACCTATTGTCCTAATCAATTTTC-TCAAGTTTCTT
10168450 CAAATTATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 22 0.49
57 5 0.11
58 18 0.40
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (58 bp):
CACTTCTCAGTTTAGGGAAGACCTATTGTCCTAATCAATTTTCTCAAGTTTCTTGCAA
Found at i:10169978 original size:2 final size:2
Alignment explanation
Indices: 10169971--10170003 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10169961 AAGAAACTGA
10169971 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10170004 AGCGCCAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10174115 original size:2 final size:2
Alignment explanation
Indices: 10174108--10174138 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10174098 ACCTTTTAGA
10174108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10174139 AAGAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10176490 original size:12 final size:12
Alignment explanation
Indices: 10176473--10176497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10176463 TATCCGTTTT
10176473 GGATGGCTTAGG
1 GGATGGCTTAGG
10176485 GGATGGCTTAGG
1 GGATGGCTTAGG
10176497 G
1 G
10176498 TGAGGAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.52, T:0.24
Consensus pattern (12 bp):
GGATGGCTTAGG
Found at i:10182273 original size:12 final size:12
Alignment explanation
Indices: 10182256--10182280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10182246 ATATAAAAAC
10182256 TAATTACATAAT
1 TAATTACATAAT
10182268 TAATTACATAAT
1 TAATTACATAAT
10182280 T
1 T
10182281 TAACCAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTACATAAT
Found at i:10187043 original size:20 final size:22
Alignment explanation
Indices: 10187014--10187054 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10187004 CGTTTTTTTA
*
10187014 GAAAATGAAAA-CTTTTTCCAG
1 GAAAATGAAAAGCATTTTCCAG
10187035 GAAAA-GAAAAGCATTTTCCA
1 GAAAATGAAAAGCATTTTCCA
10187055 TTCTTCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (22 bp):
GAAAATGAAAAGCATTTTCCAG
Found at i:10201105 original size:57 final size:57
Alignment explanation
Indices: 10201028--10201139 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 57
10201018 TACATATAAT
* * *
10201028 TATAGATTTTGGATGTCTTACCCAATTCATATATATTAATATTTTTATAGTGAATGC
1 TATAGATTTTGGATGCCTTACACAATTCATATATATTAATATTTTTAAAGTGAATGC
* *
10201085 TATAGGTTTTTGATGCCTTACACAATTCATATATATTAATATTTTTAAAGTGAAT
1 TATAGATTTTGGATGCCTTACACAATTCATATATATTAATATTTTTAAAGTGAAT
10201140 ACACATACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (57 bp):
TATAGATTTTGGATGCCTTACACAATTCATATATATTAATATTTTTAAAGTGAATGC
Found at i:10202861 original size:31 final size:28
Alignment explanation
Indices: 10202826--10202898 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
10202816 TATGAAAATT
10202826 TTAAATAAATATTTATTTTTATTACATGTAA
1 TTAAATAAATATTTATTTTTATT--ATG-AA
* *
10202857 TTAAAT---TTTTATATTTTTATTTTGAA
1 TTAAATAAATATT-TATTTTTATTATGAA
10202883 TTAAATAAATATTTAT
1 TTAAATAAATATTTAT
10202899 AATTAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
26 8 0.23
27 2 0.06
28 6 0.17
29 13 0.37
31 6 0.17
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (28 bp):
TTAAATAAATATTTATTTTTATTATGAA
Found at i:10203306 original size:101 final size:101
Alignment explanation
Indices: 10203190--10203374 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
10203180 TCTTTAATAG
*
10203190 TTAAAAATAAATAAAAATGATAAAAAAGCATGTTTCATAGAAATAAATTTAATGACTACATGGCA
1 TTAAAAATAAATAAAAATGATAAAAAAGCATGTTTCATAGAAATAAATTTAATGACTACAAGGCA
10203255 CAATATAGTATTACAAAAAATAAATTAGATGACAAT
66 CAATATAGTATTACAAAAAATAAATTAGATGACAAT
* * * ** * *
10203291 TTAAAAA-AAATTAAAAATTATAAAAATGCATGTTTCGTTTATATAAATTTAGTGACTACAAGGC
1 TTAAAAATAAA-TAAAAATGATAAAAAAGCATGTTTCATAGAAATAAATTTAATGACTACAAGGC
10203355 ACAATATAGTATTACAAAAA
65 ACAATATAGTATTACAAAAA
10203375 TATTTCTAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
100 3 0.04
101 72 0.96
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (101 bp):
TTAAAAATAAATAAAAATGATAAAAAAGCATGTTTCATAGAAATAAATTTAATGACTACAAGGCA
CAATATAGTATTACAAAAAATAAATTAGATGACAAT
Found at i:10203811 original size:2 final size:2
Alignment explanation
Indices: 10203804--10203828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10203794 AAACTCGATA
10203804 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10203829 GATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10207515 original size:30 final size:27
Alignment explanation
Indices: 10207452--10207514 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
10207442 CTCCACGTGA
10207452 GCCACCACCTTATTACTCTACTACCAT
1 GCCACCACCTTATTACTCTACTACCAT
10207479 GCCACCACCTTATTACTCTACTACCAT
1 GCCACCACCTTATTACTCTACTACCAT
10207506 GCCACCACC
1 GCCACCACC
10207515 ATCACCAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.44, G:0.05, T:0.25
Consensus pattern (27 bp):
GCCACCACCTTATTACTCTACTACCAT
Found at i:10213554 original size:6 final size:6
Alignment explanation
Indices: 10213543--10213584 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
10213533 TTCCACAGTT
* *
10213543 TACATA TACATA TACATA TAC--A TACATA TATATA TATATA TA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TA
10213585 TATNNNNNNN
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
4 4 0.12
6 29 0.88
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (6 bp):
TACATA
Found at i:10213569 original size:16 final size:16
Alignment explanation
Indices: 10213548--10213578 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10213538 CAGTTTACAT
10213548 ATACATATACATATAC
1 ATACATATACATATAC
*
10213564 ATACATATATATATA
1 ATACATATACATATA
10213579 TATATATATN
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:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATATACATATAC
Found at i:10216142 original size:8 final size:8
Alignment explanation
Indices: 10216129--10216159 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
10216119 CATTAACCTT
10216129 TCTCTCTG
1 TCTCTCTG
10216137 TCTCTCTG
1 TCTCTCTG
*
10216145 TCTCTCTC
1 TCTCTCTG
10216153 TCTCTCT
1 TCTCTCT
10216160 CCATGTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.52
Consensus pattern (8 bp):
TCTCTCTG
Found at i:10243466 original size:3 final size:3
Alignment explanation
Indices: 10243458--10243483 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10243448 ATAAAATACA
10243458 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10243484 ATTATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10246784 original size:47 final size:47
Alignment explanation
Indices: 10246710--10246854 Score: 218
Period size: 47 Copynumber: 3.1 Consensus size: 47
10246700 TACTAAAAGT
*
10246710 CCAGAAACATGACCCAACTGTACAGCATACAAAAACCGCTTGCAGTA
1 CCAGAAACATGACCCAACTATACAGCATACAAAAACCGCTTGCAGTA
* * * * * *
10246757 CCAGGAACATGAGCCAACTATACAGCATGCAAAACCCGCCTGCTGTA
1 CCAGAAACATGACCCAACTATACAGCATACAAAAACCGCTTGCAGTA
*
10246804 CCAGAAACATGACCCAACTATACAGCATACAAAAACCACTTGCAGTA
1 CCAGAAACATGACCCAACTATACAGCATACAAAAACCGCTTGCAGTA
10246851 CCAG
1 CCAG
10246855 GCTTGAAGCA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.14
Consensus pattern (47 bp):
CCAGAAACATGACCCAACTATACAGCATACAAAAACCGCTTGCAGTA
Found at i:10247498 original size:73 final size:74
Alignment explanation
Indices: 10247379--10247525 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 74
10247369 CCTCTACCTT
*
10247379 CCGAATGAACAGCAGGGTTGCTCTCTGGTAAGGTTTTCTATTGAACCAACCCC-TTGATATTGCT
1 CCGAATGAACAGCAGGGTTGCTCTCTGGCAAGGTTTTCTATTGAACCAACCCCTTTGATATTGCT
*
10247443 GGTGGTAAA
66 AGTGGTAAA
**
10247452 CCGAATGAACATTAGGGTTGCTCTCTGGCAAGGTTTTCTATTGAACCAACCCCTTTGATATTGCT
1 CCGAATGAACAGCAGGGTTGCTCTCTGGCAAGGTTTTCTATTGAACCAACCCCTTTGATATTGCT
10247517 AGTGGTAAA
66 AGTGGTAAA
10247526 AACATGGTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 50 0.72
74 19 0.28
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (74 bp):
CCGAATGAACAGCAGGGTTGCTCTCTGGCAAGGTTTTCTATTGAACCAACCCCTTTGATATTGCT
AGTGGTAAA
Found at i:10265807 original size:20 final size:18
Alignment explanation
Indices: 10265771--10265821 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
10265761 TGAAATCATG
10265771 AAAATTTATTAACTAATC
1 AAAATTTATTAACTAATC
*
10265789 AAAATATTATTTAATTAAT-
1 AAAAT-TTA-TTAACTAATC
10265808 AAATTATTTATTAA
1 AAA--ATTTATTAA
10265822 TTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 10 0.36
20 11 0.39
21 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTATTAACTAATC
Found at i:10265821 original size:19 final size:20
Alignment explanation
Indices: 10265774--10265823 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
10265764 AATCATGAAA
*
10265774 ATTTATTAACTAATCAAAAT
1 ATTTATTAATTAATCAAAAT
*
10265794 A-TTATTTAATTAAT-AAATT
1 ATTTA-TTAATTAATCAAAAT
10265813 ATTTATTAATT
1 ATTTATTAATT
10265824 TATATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATTAATTAATCAAAAT
Found at i:10265863 original size:35 final size:35
Alignment explanation
Indices: 10265792--10265863 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
10265782 ACTAATCAAA
* * * **
10265792 ATATTATTTAATTAATAAATTATTTATTAATTTAT
1 ATATTAATTAATTAAAAAATTATTTATCAAGATAT
10265827 ATATTAATTAA-TAAAAAATTAATTTATCAAGATAT
1 ATATTAATTAATTAAAAAATT-ATTTATCAAGATAT
10265862 AT
1 AT
10265864 TTTTTTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
ATATTAATTAATTAAAAAATTATTTATCAAGATAT
Found at i:10266259 original size:16 final size:17
Alignment explanation
Indices: 10266232--10266265 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10266222 AAGTGAGATT
*
10266232 TATATATATTTTTTAAA
1 TATATATATTTTATAAA
10266249 TATAT-TATTTTATAAA
1 TATATATATTTTATAAA
10266265 T
1 T
10266266 TTAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATATTTTATAAA
Found at i:10268502 original size:21 final size:21
Alignment explanation
Indices: 10268476--10268517 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10268466 TGCAAAAAGT
10268476 CCTATAAAGCAATTAAGAAGC
1 CCTATAAAGCAATTAAGAAGC
*
10268497 CCTATAAAGCTATTAAGAAGC
1 CCTATAAAGCAATTAAGAAGC
10268518 AATCTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (21 bp):
CCTATAAAGCAATTAAGAAGC
Found at i:10282370 original size:5 final size:5
Alignment explanation
Indices: 10282360--10282389 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
10282350 GTGGTAAAAG
*
10282360 AATAT AATAT AATAT AATAT ATTAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
10282390 CAAATATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:10296681 original size:15 final size:17
Alignment explanation
Indices: 10296650--10296682 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
10296640 ATTAAAATTG
10296650 ATTAAATATATTTGTAT
1 ATTAAATATATTTGTAT
10296667 ATTAAA-ATA-TTGTAT
1 ATTAAATATATTTGTAT
10296682 A
1 A
10296683 AATTTGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTAAATATATTTGTAT
Found at i:10296783 original size:22 final size:22
Alignment explanation
Indices: 10296734--10296783 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
10296724 TTGTTATTAG
* * *
10296734 GTATTATATTATTGATTTTTAC
1 GTATTAAATCATTGATTTTTAA
*
10296756 GCATTAAATCATTGATTTTTAA
1 GTATTAAATCATTGATTTTTAA
10296778 GTATTA
1 GTATTA
10296784 CGAGATTGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (22 bp):
GTATTAAATCATTGATTTTTAA
Found at i:10296907 original size:23 final size:23
Alignment explanation
Indices: 10296881--10296936 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
10296871 TCACACAATT
*
10296881 TCTTACTAACTAATCATATAATG
1 TCTTAATAACTAATCATATAATG
* * *
10296904 TCTTATTAACTAGTCATGTAATG
1 TCTTAATAACTAATCATATAATG
10296927 TCTTAATAAC
1 TCTTAATAAC
10296937 CAGTCACGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (23 bp):
TCTTAATAACTAATCATATAATG
Found at i:10296941 original size:23 final size:23
Alignment explanation
Indices: 10296894--10296942 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
10296884 TACTAACTAA
* *
10296894 TCATATAATGTCTTATTAACTAG
1 TCATATAATGTCTTAATAACCAG
*
10296917 TCATGTAATGTCTTAATAACCAG
1 TCATATAATGTCTTAATAACCAG
10296940 TCA
1 TCA
10296943 CGCAATGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (23 bp):
TCATATAATGTCTTAATAACCAG
Found at i:10296949 original size:23 final size:24
Alignment explanation
Indices: 10296900--10296999 Score: 68
Period size: 23 Copynumber: 4.4 Consensus size: 24
10296890 CTAATCATAT
* * * *
10296900 AATGTCTT-ATTAACTAGTCATGT
1 AATGTCTTAATCAACCAGTCACGC
10296923 AATGTCTTAAT-AACCAGTCACGC
1 AATGTCTTAATCAACCAGTCACGC
* * *
10296946 AATG-CCT-ATCAACCAATCACTC
1 AATGTCTTAATCAACCAGTCACGC
* * *
10296968 AATGTCAT-ATCCACCAGTTACGC
1 AATGTCTTAATCAACCAGTCACGC
10296991 AATGT-TTAA
1 AATGTCTTAA
10297000 AAATTAGTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
21 2 0.03
22 17 0.28
23 40 0.66
24 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (24 bp):
AATGTCTTAATCAACCAGTCACGC
Found at i:10296965 original size:22 final size:23
Alignment explanation
Indices: 10296934--10296995 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
10296924 ATGTCTTAAT
*
10296934 AACCAGTCACGCAATG-CCTATC
1 AACCAGTCACGCAATGTCATATC
* *
10296956 AACCAATCACTCAATGTCATATC
1 AACCAGTCACGCAATGTCATATC
* *
10296979 CACCAGTTACGCAATGT
1 AACCAGTCACGCAATGT
10296996 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23
Consensus pattern (23 bp):
AACCAGTCACGCAATGTCATATC
Found at i:10297074 original size:21 final size:21
Alignment explanation
Indices: 10297021--10297074 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
10297011 ACCATGTCTT
* *
10297021 AAAACTAGTTACGTAATGCCTA
1 AAAACTA-TTACGCAATACCTA
* *
10297043 AAAATCGATTACGCAATACTTA
1 AAAA-CTATTACGCAATACCTA
10297065 AAAACTATTA
1 AAAACTATTA
10297075 AATTTCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAACTATTACGCAATACCTA
Found at i:10317114 original size:2 final size:2
Alignment explanation
Indices: 10317109--10317137 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10317099 GAAAAAAAAA
10317109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10317138 GTCAATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10317950 original size:2 final size:2
Alignment explanation
Indices: 10317943--10317971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10317933 TTAGATAGAA
10317943 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10317972 ATATGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10329434 original size:6 final size:6
Alignment explanation
Indices: 10329423--10329453 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10329413 ACAGTGTAAG
*
10329423 AAGAGA AAGAGA AAGAGA AAGAGA AATAGA A
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA A
10329454 TCTCCAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (6 bp):
AAGAGA
Found at i:10356752 original size:7 final size:7
Alignment explanation
Indices: 10356728--10356762 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
10356718 TTAATAAAAT
10356728 ATTTT-A
1 ATTTTAA
10356734 ATTTTAAA
1 ATTTT-AA
10356742 ATTTTAA
1 ATTTTAA
10356749 ATTTTAA
1 ATTTTAA
10356756 ATTTTAA
1 ATTTTAA
10356763 TATGAGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.19
7 16 0.59
8 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:10378488 original size:85 final size:85
Alignment explanation
Indices: 10378353--10378524 Score: 299
Period size: 85 Copynumber: 2.0 Consensus size: 85
10378343 GTATAAATAT
* *
10378353 TTCATTTAATTATTGCTCTTTAAAATTTCTCGGTGCCAAGTAGAAAATGGCCACAGAGAAAATGA
1 TTCATTTAATTATTACTCTTTAAAATTTCACGGTGCCAAGTAGAAAATGGCCACAGAGAAAATGA
10378418 AGGGAAAAAGAAATAAATGC
66 AGGGAAAAAGAAATAAATGC
*
10378438 TTCATTTAATTATTACTCTTTAAAATTTCAGGGTGCCAAGTAGAAAATGGCCACAGAGAAAATGA
1 TTCATTTAATTATTACTCTTTAAAATTTCACGGTGCCAAGTAGAAAATGGCCACAGAGAAAATGA
**
10378503 AGGGAAGGAGAAATAAATGC
66 AGGGAAAAAGAAATAAATGC
10378523 TT
1 TT
10378525 TTACGAAGCT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (85 bp):
TTCATTTAATTATTACTCTTTAAAATTTCACGGTGCCAAGTAGAAAATGGCCACAGAGAAAATGA
AGGGAAAAAGAAATAAATGC
Found at i:10388201 original size:22 final size:23
Alignment explanation
Indices: 10388171--10388217 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
10388161 GAAAGGAATC
*
10388171 AAACAC-AAAATCGAGAAAAAAA
1 AAACACAAAAATAGAGAAAAAAA
* *
10388193 AAACCCAAAAATATAGAAAAAAA
1 AAACACAAAAATAGAGAAAAAAA
10388216 AA
1 AA
10388218 TTTCAAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.06
Consensus pattern (23 bp):
AAACACAAAAATAGAGAAAAAAA
Found at i:10389426 original size:29 final size:27
Alignment explanation
Indices: 10389361--10389426 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
10389351 TTAAAAAAAT
* * *
10389361 TTAAATAATTTTTTATCTTTTATTATA
1 TTAAATAAATTTTTATATTTTATTAAA
10389388 TT-AATCAAATTTTTATATTTTATTTTAAA
1 TTAAAT-AAATTTTTATATTTTA--TTAAA
10389417 TTAAATAAAT
1 TTAAATAAAT
10389427 AATTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.09
27 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAAATAAATTTTTATATTTTATTAAA
Found at i:10389594 original size:18 final size:19
Alignment explanation
Indices: 10389571--10389613 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
10389561 TAAAATGATA
*
10389571 AATAATATT-TTAATTAAT
1 AATAATATTATAAATTAAT
*
10389589 AATAAT-TTATAAATTGAT
1 AATAATATTATAAATTAAT
10389607 AATAATA
1 AATAATA
10389614 AAAAAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATAATATTATAAATTAAT
Found at i:10389675 original size:26 final size:30
Alignment explanation
Indices: 10389625--10389687 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
10389615 AAAAACTTAA
10389625 AATAAAAGTATATAATTTTAATTAAAA-AT
1 AATAAAAGTATATAATTTTAATTAAAATAT
*
10389654 AATAAAAG-A-ATAATTTT-TTTAAAATAT
1 AATAAAAGTATATAATTTTAATTAAAATAT
*
10389681 ATTAAAA
1 AATAAAA
10389688 AAATTTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 6 0.19
27 16 0.52
28 1 0.03
29 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
AATAAAAGTATATAATTTTAATTAAAATAT
Found at i:10412539 original size:21 final size:20
Alignment explanation
Indices: 10412492--10412539 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
10412482 TGGAAGTGAG
*
10412492 GAGAAAGAGAAAGGGGTATT
1 GAGAAAGAGAAAGGGATATT
* *
10412512 AAGGAAAGAGAATGAGGATATT
1 GA-GAAAGAGAAAG-GGATATT
10412534 GAGAAA
1 GAGAAA
10412540 CTGGAGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (20 bp):
GAGAAAGAGAAAGGGATATT
Found at i:10430603 original size:4 final size:4
Alignment explanation
Indices: 10430596--10430645 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
10430586 TTTTCTTTCA
*
10430596 ATTT ATTTT ATTAT TTTT ATTT ATTT ATTT ATTT A-TT -TTT ATTCT ATTT
1 ATTT A-TTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT
10430645 A
1 A
10430646 CTCATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 4 0.10
4 24 0.62
5 11 0.28
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:10430617 original size:18 final size:19
Alignment explanation
Indices: 10430596--10430643 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
10430586 TTTTCTTTCA
10430596 ATTTATTTTATTATTT-TT
1 ATTTATTTTATTATTTATT
10430614 ATTTA-TTTATTTATTTATT
1 ATTTATTTTA-TTATTTATT
*
10430633 -TTTATTCTATT
1 ATTTATTTTATT
10430644 TACTCATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTATTTTATTATTTATT
Found at i:10430622 original size:22 final size:23
Alignment explanation
Indices: 10430596--10430645 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
10430586 TTTTCTTTCA
10430596 ATTTATTT-TATTATTTTTATT-T
1 ATTTATTTAT-TTATTTTTATTCT
10430618 ATTTATTTATTTATTTTTATTCT
1 ATTTATTTATTTATTTTTATTCT
10430641 ATTTA
1 ATTTA
10430646 CTCATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (23 bp):
ATTTATTTATTTATTTTTATTCT
Found at i:10430655 original size:23 final size:22
Alignment explanation
Indices: 10430607--10430657 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
10430597 TTTATTTTAT
* * *
10430607 TATTTTTATTTATTTATTTATT
1 TATTTTTATTTATTTACTCATA
10430629 TATTTTTATTCTATTTACTCATA
1 TATTTTTATT-TATTTACTCATA
10430652 TATTTT
1 TATTTT
10430658 AAATCTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTTATTTATTTACTCATA
Found at i:10431048 original size:61 final size:61
Alignment explanation
Indices: 10430953--10431080 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 61
10430943 AATAATAATG
* *
10430953 ATATACAAGTGAATTGGTAGAATGAAATAATTGTATTTCTTTCAATACAATTTTATTTATT
1 ATATACAAATGAATTGATAGAATGAAATAATTGTATTTCTTTCAATACAATTTTATTTATT
* *
10431014 ATATACAAATGAATTGATAGAATGAAATAATTGTATTTTTTTCAATATAATTTTATTTATT
1 ATATACAAATGAATTGATAGAATGAAATAATTGTATTTCTTTCAATACAATTTTATTTATT
10431075 ATATAC
1 ATATAC
10431081 TTTTAATGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (61 bp):
ATATACAAATGAATTGATAGAATGAAATAATTGTATTTCTTTCAATACAATTTTATTTATT
Found at i:10434626 original size:17 final size:17
Alignment explanation
Indices: 10434586--10434628 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10434576 GATAGCAAAC
*
10434586 AAGGAAAAAAAAGAAAG
1 AAGGAAAGAAAAGAAAG
* * *
10434603 AAAGAAAGAAAGGAAGG
1 AAGGAAAGAAAAGAAAG
10434620 AAGGAAAGA
1 AAGGAAAGA
10434629 TTGCTGGTCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAGGAAAGAAAAGAAAG
Found at i:10442519 original size:30 final size:30
Alignment explanation
Indices: 10442483--10442543 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
10442473 CTCATTTAAG
10442483 AGCCAGAACTTGGTCTTTATGTAAATTTCC
1 AGCCAGAACTTGGTCTTTATGTAAATTTCC
10442513 AGCCAGAACTTGGTCTTTATGTAAATTTCC
1 AGCCAGAACTTGGTCTTTATGTAAATTTCC
10442543 A
1 A
10442544 TAAACTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (30 bp):
AGCCAGAACTTGGTCTTTATGTAAATTTCC
Found at i:10443994 original size:27 final size:28
Alignment explanation
Indices: 10443963--10444017 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
10443953 GAATATAAGT
*
10443963 TATTTATAGGGTGCTAATTGA-AAAAAA
1 TATTTATAGAGTGCTAATTGAGAAAAAA
*
10443990 TATTTATAGAGTGTTAATTGAGAAAAAA
1 TATTTATAGAGTGCTAATTGAGAAAAAA
10444018 ATTATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (28 bp):
TATTTATAGAGTGCTAATTGAGAAAAAA
Found at i:10464787 original size:22 final size:22
Alignment explanation
Indices: 10464734--10464787 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
10464724 AAATAAATTT
* *
10464734 TATTTTTATTA-TATTTAATTA
1 TATTTTTATTATTATATAAATA
10464755 -ATTTTTA-TATTATATAAATA
1 TATTTTTATTATTATATAAATA
10464775 TATTTTTATTATT
1 TATTTTTATTATT
10464788 TAATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 7 0.25
22 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTTATTATTATATAAATA
Found at i:10467148 original size:16 final size:17
Alignment explanation
Indices: 10467122--10467159 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
10467112 ATATAAAATT
10467122 ATAAATATATACATATA
1 ATAAATATATACATATA
* *
10467139 TTAAAT-TATATATATA
1 ATAAATATATACATATA
10467155 ATAAA
1 ATAAA
10467160 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATATATACATATA
Found at i:10467773 original size:12 final size:13
Alignment explanation
Indices: 10467751--10467780 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10467741 GTTATATTAC
10467751 AATATAATAAATA
1 AATATAATAAATA
10467764 AATA-AATAAATA
1 AATATAATAAATA
10467776 AATAT
1 AATAT
10467781 TGCCCCCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATAATAAATA
Found at i:10470494 original size:2 final size:2
Alignment explanation
Indices: 10470487--10470519 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10470477 GTCTGTAATC
10470487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10470520 GAAATAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10486740 original size:15 final size:17
Alignment explanation
Indices: 10486710--10486744 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10486700 GGTGCATATT
10486710 TTATTTTTTATAATTAA
1 TTATTTTTTATAATTAA
10486727 TTATTTTTT-T-ATTAA
1 TTATTTTTTATAATTAA
10486742 TTA
1 TTA
10486745 AGTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 1 0.06
17 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTTTATAATTAA
Found at i:10487644 original size:25 final size:25
Alignment explanation
Indices: 10487615--10487666 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
10487605 CTTGTACCTA
10487615 AACTGCTAAACAGTTGACTCCTTCC
1 AACTGCTAAACAGTTGACTCCTTCC
10487640 AACTGCTAAACAGTTGACTCCTTCC
1 AACTGCTAAACAGTTGACTCCTTCC
10487665 AA
1 AA
10487667 TTATGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (25 bp):
AACTGCTAAACAGTTGACTCCTTCC
Found at i:10487703 original size:2 final size:2
Alignment explanation
Indices: 10487696--10487728 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10487686 GCTCCTACAT
10487696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10487729 GACATGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10489448 original size:27 final size:27
Alignment explanation
Indices: 10489416--10489582 Score: 142
Period size: 27 Copynumber: 6.2 Consensus size: 27
10489406 GTAAATACTG
*
10489416 AATTTTCAATATGATATATAACAATTA
1 AATTTTCAATATGATATATAATAATTA
*
10489443 AGTTTTCAACT-TGATATATAATAATTA
1 AATTTTCAA-TATGATATATAATAATTA
* * **
10489470 AATTTTTAACATGACGTATAATAATTA
1 AATTTTCAATATGATATATAATAATTA
* ** *
10489497 TATTTTTCAATATGACGTGTAATAATTA
1 -AATTTTCAATATGATATATAATAATTA
* * * *
10489525 TATTTTTAACATGATATGTAATAA-T-
1 AATTTTCAATATGATATATAATAATTA
* * *
10489550 AATTTTTAACATGATATGTAATAATTA
1 AATTTTCAATATGATATATAATAATTA
10489577 AATTTT
1 AATTTT
10489583 AAAATATAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
25 23 0.20
26 2 0.02
27 68 0.58
28 24 0.21
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (27 bp):
AATTTTCAATATGATATATAATAATTA
Found at i:10489510 original size:82 final size:80
Alignment explanation
Indices: 10489418--10489582 Score: 197
Period size: 82 Copynumber: 2.0 Consensus size: 80
10489408 AAATACTGAA
* *
10489418 TTTTCAATATGATATATAACAATTA-AGTTTTCAACTTGATATATAATAATTAAATTTTTAACAT
1 TTTTCAATATGACATATAACAATTATA-TTTTCAACATGATATATAATAA-T-AATTTTTAACAT
* *
10489482 GACGTATAATAATTATAT
63 GACATATAATAATTAAAT
* * * * * *
10489500 TTTTCAATATGACGTGTAATAATTATATTTTTAACATGATATGTAATAATAATTTTTAACATGAT
1 TTTTCAATATGACATATAACAATTATATTTTCAACATGATATATAATAATAATTTTTAACATGAC
*
10489565 ATGTAATAATTAAAT
66 ATATAATAATTAAAT
10489580 TTT
1 TTT
10489583 AAAATATAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
80 29 0.41
81 1 0.01
82 40 0.56
83 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (80 bp):
TTTTCAATATGACATATAACAATTATATTTTCAACATGATATATAATAATAATTTTTAACATGAC
ATATAATAATTAAAT
Found at i:10489524 original size:55 final size:52
Alignment explanation
Indices: 10489416--10489582 Score: 154
Period size: 55 Copynumber: 3.1 Consensus size: 52
10489406 GTAAATACTG
* * * * * * * *
10489416 AATTTTCAATATGATATATAACAATTAAGTTTTCAACTTGATATATAATAATTA
1 AATTTTTAACATGACATATAATAA-TAA-TTTTTAACATGACATGTAATAATTA
* * *
10489470 AATTTTTAACATGACGTATAATAATTATATTTTTCAATATGACGTGTAATAATTA
1 AATTTTTAACATGACATATAATAA-TA-ATTTTT-AACATGACATGTAATAATTA
* * * *
10489525 TATTTTTAACATGATATGTAATAATAATTTTTAACATGATATGTAATAATTA
1 AATTTTTAACATGACATATAATAATAATTTTTAACATGACATGTAATAATTA
10489577 AATTTT
1 AATTTT
10489583 AAAATATAAT
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
52 22 0.24
53 6 0.07
54 28 0.30
55 36 0.39
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (52 bp):
AATTTTTAACATGACATATAATAATAATTTTTAACATGACATGTAATAATTA
Found at i:10489574 original size:22 final size:23
Alignment explanation
Indices: 10489526--10489575 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
10489516 TAATAATTAT
10489526 ATTTTTAACATGATATGTAATAATA
1 ATTTTTAACATGATATG--ATAATA
10489551 ATTTTTAACATGATATG-TAATA
1 ATTTTTAACATGATATGATAATA
10489573 ATT
1 ATT
10489576 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.32
25 17 0.68
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTTTAACATGATATGATAATA
Found at i:10489589 original size:80 final size:82
Alignment explanation
Indices: 10489445--10489598 Score: 195
Period size: 80 Copynumber: 1.9 Consensus size: 82
10489435 AACAATTAAG
* * * **
10489445 TTTTCAACTTGATATATAATAATTAAATTTTTAACATGACGTATAATAATTATATTTTTCAATAT
1 TTTTCAACATGATATATAATAATTAAATTTTTAACATGACATATAATAATTAAATTTTAAAATAT
*
10489510 GACGTGTAATAATTATA
66 AACGTGTAATAATTATA
* * * *
10489527 TTTTTAACATGATATGTAATAA-T-AATTTTTAACATGATATGTAATAATTAAATTTTAAAATAT
1 TTTTCAACATGATATATAATAATTAAATTTTTAACATGACATATAATAATTAAATTTTAAAATAT
*
10489590 AATGTGTAA
66 AACGTGTAA
10489599 GATTACATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 41 0.67
81 1 0.02
82 19 0.31
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (82 bp):
TTTTCAACATGATATATAATAATTAAATTTTTAACATGACATATAATAATTAAATTTTAAAATAT
AACGTGTAATAATTATA
Found at i:10494299 original size:28 final size:29
Alignment explanation
Indices: 10494263--10494328 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
10494253 TAGTTTTAGA
*
10494263 AATTATTTATAA-ATAATACA-AAATTATT
1 AATTTTTTATAATATAA-ACACAAATTATT
* *
10494291 AATTTTTTA-AATATAAAGACAAATTTTT
1 AATTTTTTATAATATAAACACAAATTATT
10494319 AATTTTTTAT
1 AATTTTTTAT
10494329 GAGTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTTTTTATAATATAAACACAAATTATT
Found at i:10519281 original size:30 final size:30
Alignment explanation
Indices: 10519219--10519289 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
10519209 TTTTAATATA
* ***
10519219 TTATAAGAAAATATTACATAATATAGTGATT
1 TTATAA-AAAAGATTACATAATATAACAATT
10519250 TTCA-AAAAAAGATTACATAATATAACAATT
1 TT-ATAAAAAAGATTACATAATATAACAATT
10519280 TTATAAAAAA
1 TTATAAAAAA
10519290 TCCTTAAGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 1 0.03
30 28 0.82
31 4 0.12
32 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (30 bp):
TTATAAAAAAGATTACATAATATAACAATT
Found at i:10520875 original size:142 final size:143
Alignment explanation
Indices: 10520703--10520989 Score: 391
Period size: 142 Copynumber: 2.0 Consensus size: 143
10520693 CTTTAACCTT
* * *
10520703 TTAAATATTATTTTAAGTACATTTTCAAAAA-TTTTCATGTGATTTTATTAATTTAAAGTCATTA
1 TTAAATACTATTTTAAGTACATTTTCAAAAACTTTT-ATGTGATTTTAGTAACTTAAAGTCATTA
* ** * *
10520767 AAATTTTCGATA-ACATTTGGAAGGTATAATGCTTTGAGAAAGCC-TTAAACTATTTAGAAAACT
65 AAATTTTAGATATACATTTCAAAGGTATAATGCTTTGA-AAAGCCTTTAAACTATTTAAAAAAAT
*
10520830 TTAAATAAACTCTTA
129 TCAAATAAACTCTTA
*
10520845 TTAAATACTATTTTAAGTATATTTTCAAAAACTTTTATGTGATTTTAGTAACTTAAAGTCATTAA
1 TTAAATACTATTTTAAGTACATTTTCAAAAACTTTTATGTGATTTTAGTAACTTAAAGTCATTAA
* * * * *
10520910 AATTTTATATATTATATTTCAAAGGTATAATGTTTTTAAAAGCCTTTAAATTATTTAAAAAAATT
66 AATTTTAGATA-TACATTTCAAAGGTATAATGCTTTGAAAAGCCTTTAAACTATTTAAAAAAATT
10520975 CAAATAAACTCTTA
130 CAAATAAACTCTTA
10520989 T
1 T
10520990 ATTATTGCAT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
142 65 0.52
143 10 0.08
144 51 0.40
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (143 bp):
TTAAATACTATTTTAAGTACATTTTCAAAAACTTTTATGTGATTTTAGTAACTTAAAGTCATTAA
AATTTTAGATATACATTTCAAAGGTATAATGCTTTGAAAAGCCTTTAAACTATTTAAAAAAATTC
AAATAAACTCTTA
Found at i:10522169 original size:20 final size:20
Alignment explanation
Indices: 10522130--10522176 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
10522120 GCCAAAAACG
10522130 AGGAAGAGAAAGAGAAGGAA
1 AGGAAGAGAAAGAGAAGGAA
*
10522150 AGGAGAGAGAAAGA-AGGGAA
1 AGGA-AGAGAAAGAGAAGGAA
10522170 AGGAAGA
1 AGGAAGA
10522177 AAGGCCCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 13 0.52
21 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (20 bp):
AGGAAGAGAAAGAGAAGGAA
Found at i:10524436 original size:64 final size:64
Alignment explanation
Indices: 10524340--10524502 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
10524330 TGACGATGAG
* *
10524340 AGCAAGGA-GAAAG-GAGAAAAAGAAAAAAAAAGAG-AGAAAAAAAGAAGAGCCCATCAACAAAA
1 AGCAAGGAGGAAGGAGAGAAAAAGAAAAAAAAAGAGAAGAAAAAAAG-AGAGCCAATCAACAAAA
* * * * * *
10524402 AGCAAGGAGGAAGGAGAGAAAAAGAAAAAGAAAGAGAAGAAAAGAAGAGGGCCAATCACCACAG
1 AGCAAGGAGGAAGGAGAGAAAAAGAAAAAAAAAGAGAAGAAAAAAAGAGAGCCAATCAACAAAA
** *
10524466 AGCAACAAGGAAGGAGAGAAAAAAGGAAATAAAAAGA
1 AGCAAGGAGGAAGGAGAG-AAAAA-GAAAAAAAAAGA
10524503 AGAGCCCACC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 8 0.10
63 4 0.05
64 48 0.57
65 14 0.17
66 10 0.12
ACGTcount: A:0.62, C:0.09, G:0.27, T:0.02
Consensus pattern (64 bp):
AGCAAGGAGGAAGGAGAGAAAAAGAAAAAAAAAGAGAAGAAAAAAAGAGAGCCAATCAACAAAA
Found at i:10524663 original size:33 final size:33
Alignment explanation
Indices: 10524597--10524657 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
10524587 GTGAAACAAC
*
10524597 TTAACTAATTAATTAATATTTTTATAAAATAAT
1 TTAACTAAGTAATTAATATTTTTATAAAATAAT
*
10524630 TTAACTAAGTAATTTA-ATTTTT-TAAAAT
1 TTAACTAAGTAATTAATATTTTTATAAAAT
10524658 TTAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 6 0.23
33 14 0.54
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (33 bp):
TTAACTAAGTAATTAATATTTTTATAAAATAAT
Found at i:10524700 original size:17 final size:16
Alignment explanation
Indices: 10524680--10524740 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 16
10524670 TTAAAAATAA
10524680 ATAT-TTATTAATTTT
1 ATATATTATTAATTTT
10524695 ATATATT-TTAATATTT
1 ATATATTATTAAT-TTT
* *
10524711 AAATAATATATTATTTTT
1 ATAT-AT-TATTAATTTT
10524729 ATCATATTATTA
1 AT-ATATTATTA
10524741 TTTATTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
15 9 0.24
16 8 0.22
17 7 0.19
18 7 0.19
19 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTATTAATTTT
Found at i:10524727 original size:33 final size:33
Alignment explanation
Indices: 10524677--10524744 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
10524667 TCATTAAAAA
* *
10524677 TAAATATTTATTAATTTTATAT-ATTTTAATATT
1 TAAATATATATTAATTTT-TATCATATTAATATT
*
10524710 TAAATAATATATT-ATTTTTATCATATTATTATT
1 TAAAT-ATATATTAATTTTTATCATATTAATATT
10524743 TA
1 TA
10524745 TTATTTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.10
33 21 0.70
34 6 0.20
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
TAAATATATATTAATTTTTATCATATTAATATT
Found at i:10529520 original size:25 final size:25
Alignment explanation
Indices: 10529464--10529521 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
10529454 ATTTAGTATA
*
10529464 ATATCTAAAAAATATATTTTGAATT
1 ATATTTAAAAAATATATTTTGAATT
* * *
10529489 TTTTTTAAAAAAT-TATTTTTTAATT
1 ATATTTAAAAAATATA-TTTTGAATT
10529514 ATATTTAA
1 ATATTTAA
10529522 TTAAATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATTTAAAAAATATATTTTGAATT
Found at i:10529797 original size:18 final size:18
Alignment explanation
Indices: 10529774--10529808 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10529764 TTAGCAACTA
10529774 TTAATTATAAAA-AAATTT
1 TTAATT-TAAAATAAATTT
10529792 TTAATTTAAAATAAATT
1 TTAATTTAAAATAAATT
10529809 ATAAGGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTTAAAATAAATTT
Found at i:10537299 original size:62 final size:62
Alignment explanation
Indices: 10537201--10537323 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
10537191 TGGATATTTC
**
10537201 CACTTTTAAGGGGTTTTTAGTTTACCATGCTGTACATGTCTATTTTCTCTTCTGGTTTTGGT
1 CACTTTTAAGGGGTTTTTAGTTTACCATGCCATACATGTCTATTTTCTCTTCTGGTTTTGGT
10537263 CACTTTTAAGGGGTTTGTT-GTTTACCATGCCATACATGTCTATTTTCTCTTCTGGTTTTGG
1 CACTTTTAAGGGGTTT-TTAGTTTACCATGCCATACATGTCTATTTTCTCTTCTGGTTTTGG
10537324 CAAAGAAAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 56 0.97
63 2 0.03
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (62 bp):
CACTTTTAAGGGGTTTTTAGTTTACCATGCCATACATGTCTATTTTCTCTTCTGGTTTTGGT
Found at i:10569713 original size:2 final size:2
Alignment explanation
Indices: 10569706--10569735 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10569696 GTATTTTTCC
*
10569706 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10569736 CGCAGGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10573552 original size:2 final size:2
Alignment explanation
Indices: 10573545--10573571 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10573535 TCTCAATCAA
10573545 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10573572 AAATTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10582657 original size:3 final size:3
Alignment explanation
Indices: 10582649--10582683 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10582639 TAATTTTGAT
10582649 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
10582684 TGTTACGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:10584418 original size:14 final size:14
Alignment explanation
Indices: 10584399--10584453 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
10584389 AGAAAGCTTG
10584399 TTCCTTTTTCTTTT
1 TTCCTTTTTCTTTT
10584413 TTCCTTTTAT-TTTCT
1 TTCCTTTT-TCTTT-T
*
10584428 TTTC-TTTTCTTTT
1 TTCCTTTTTCTTTT
*
10584441 TTATCTTTTTCTT
1 TT-CCTTTTTCTT
10584454 CTTCTTACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 4 0.11
14 19 0.54
15 12 0.34
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCCTTTTTCTTTT
Found at i:10594042 original size:2 final size:2
Alignment explanation
Indices: 10594035--10594072 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
10594025 TATAGAGCTA
10594035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
10594073 AATCTAACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10599133 original size:32 final size:33
Alignment explanation
Indices: 10599082--10599166 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
10599072 TTTTAATATC
*
10599082 ATATATTTTATTTTTATTTCTTATTATAATCCT
1 ATATATTTTATTTTTATTTCTTAATATAATCCT
* **
10599115 ATATGTTTTA-TTTTATTTCTTAATATAATTTT
1 ATATATTTTATTTTTATTTCTTAATATAATCCT
* *
10599147 TTATATTGTATATTTTATTT
1 ATATATTTTAT-TTTTATTT
10599167 TAAGTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 26 0.60
33 9 0.21
34 8 0.19
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTCTTAATATAATCCT
Found at i:10599153 original size:27 final size:27
Alignment explanation
Indices: 10599069--10599153 Score: 66
Period size: 32 Copynumber: 3.0 Consensus size: 27
10599059 CTCTTAAATA
*
10599069 TATTT-TTAATATCATATATTTTAT-TTT
1 TATTTCTTAATAT-A-ATTTTTTATATTT
* *
10599096 TATTTCTTATTATAATCCTATATGTTTTATTT
1 TATTTCTTAATATAAT--T-T-T-TTATATTT
10599128 TATTTCTTAATATAATTTTTTATATT
1 TATTTCTTAATATAATTTTTTATATT
10599154 GTATATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
26 2 0.04
27 12 0.26
28 7 0.15
29 2 0.04
30 2 0.04
31 3 0.07
32 18 0.39
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (27 bp):
TATTTCTTAATATAATTTTTTATATTT
Found at i:10608847 original size:3 final size:3
Alignment explanation
Indices: 10608839--10608873 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
10608829 TGAGATGACG
* *
10608839 GCT GCT GCT GCT GCT GCT GCT GTT GCT GTT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
10608874 AACTTTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.29, G:0.34, T:0.37
Consensus pattern (3 bp):
GCT
Found at i:10609022 original size:21 final size:21
Alignment explanation
Indices: 10608996--10609044 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
10608986 GCAGCGGTGA
*
10608996 CTGCTGCAACTGCGTTTGTTG
1 CTGCTGCAACTGCGTCTGTTG
*
10609017 CTGCTGCAACTGTGTCTGTTG
1 CTGCTGCAACTGCGTCTGTTG
10609038 CTGCTGC
1 CTGCTGC
10609045 CTCTGTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.08, C:0.27, G:0.29, T:0.37
Consensus pattern (21 bp):
CTGCTGCAACTGCGTCTGTTG
Found at i:10609343 original size:18 final size:18
Alignment explanation
Indices: 10609320--10609355 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10609310 GCTGTTGTCT
*
10609320 TTGTTGTTGTTTTTGCTG
1 TTGTTGTTGTTGTTGCTG
10609338 TTGTTGTTGTTGTTGCTG
1 TTGTTGTTGTTGTTGCTG
10609356 CTGCTGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.64
Consensus pattern (18 bp):
TTGTTGTTGTTGTTGCTG
Found at i:10609426 original size:9 final size:9
Alignment explanation
Indices: 10609414--10609443 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10609404 TGGCTGCTGC
10609414 TGTGGTTGT
1 TGTGGTTGT
10609423 TGTGGTTGT
1 TGTGGTTGT
*
10609432 TGTGGCTGT
1 TGTGGTTGT
10609441 TGT
1 TGT
10609444 CGCTGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.43, T:0.53
Consensus pattern (9 bp):
TGTGGTTGT
Found at i:10626139 original size:26 final size:27
Alignment explanation
Indices: 10626106--10626172 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
10626096 AGAAACATTC
10626106 AAATAAATTTTATTTTTATTAT-ATTT
1 AAATAAATTTTATTTTTATTATAATTT
* *
10626132 AATTAAATTTTTATATTTTTATTTTAATTT
1 AAATAAA--TTT-TATTTTTATTATAATTT
10626162 AAATAAATTTT
1 AAATAAATTTT
10626173 TATATTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 6 0.18
27 1 0.03
28 6 0.18
29 11 0.32
30 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
AAATAAATTTTATTTTTATTATAATTT
Found at i:10626147 original size:18 final size:18
Alignment explanation
Indices: 10626124--10626178 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
10626114 TTTATTTTTA
10626124 TTATATTTAATTAAATTT
1 TTATATTTAATTAAATTT
10626142 TTATATTT--TT--A-TT
1 TTATATTTAATTAAATTT
*
10626155 TTA-ATTTAAATAAATTT
1 TTATATTTAATTAAATTT
10626172 TTATATT
1 TTATATT
10626179 AATAGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
12 4 0.13
13 5 0.17
14 2 0.07
16 3 0.10
17 5 0.17
18 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATTTAATTAAATTT
Found at i:10626152 original size:29 final size:30
Alignment explanation
Indices: 10626116--10626178 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
10626106 AAATAAATTT
*
10626116 TATTTTTATTAT-ATTTAATTAAATTTTTA
1 TATTTTTATTATAATTTAAATAAATTTTTA
*
10626145 TATTTTTATTTTAATTTAAATAAATTTTTA
1 TATTTTTATTATAATTTAAATAAATTTTTA
10626175 TATT
1 TATT
10626179 AATAGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TATTTTTATTATAATTTAAATAAATTTTTA
Found at i:10626358 original size:14 final size:13
Alignment explanation
Indices: 10626325--10626362 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10626315 TATAAAATAA
10626325 TAATTAA-AATTT
1 TAATTAATAATTT
*
10626337 TAAGTAATAATATT
1 TAATTAATAAT-TT
10626351 TAATTAATAATT
1 TAATTAATAATT
10626363 AATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATTAATAATTT
Found at i:10626383 original size:21 final size:20
Alignment explanation
Indices: 10626322--10626393 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
10626312 AAGTATAAAA
* *
10626322 TAATAATTAAAATT-TTAAG
1 TAATAATAAAAATTATTAAT
** *
10626341 TAATAATATTTAATTAATAAT
1 TAATAATA-AAAATTATTAAT
10626362 TAATAATAAAAATTATTAAATT
1 TAATAATAAAAATTATT-AA-T
10626384 TAA-AATAAAA
1 TAATAATAAAA
10626394 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 7 0.17
20 10 0.24
21 20 0.49
22 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
TAATAATAAAAATTATTAAT
Found at i:10626398 original size:28 final size:29
Alignment explanation
Indices: 10626345--10626439 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 29
10626335 TTTAAGTAAT
* * *
10626345 AATATTTAA-TTAATA-ATTAATAATAAA
1 AATATTAAATTTAATAGATAAAAAATAAA
*
10626372 AATTATTAAATTTAA-A-ATAAAATATAAA
1 AA-TATTAAATTTAATAGATAAAAAATAAA
10626400 AA-ATT-AATTTAATATGATAAAAAATAAAA
1 AATATTAAATTTAATA-GATAAAAAAT-AAA
10626429 AATATTTAAAT
1 AATA-TTAAAT
10626440 ATTTTTAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.13
26 4 0.07
27 2 0.04
28 26 0.48
29 9 0.17
30 1 0.02
31 2 0.04
32 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AATATTAAATTTAATAGATAAAAAATAAA
Found at i:10626406 original size:20 final size:21
Alignment explanation
Indices: 10626383--10626429 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
10626373 ATTATTAAAT
10626383 TTAAAATAAAAT-ATAAAAAA
1 TTAAAATAAAATGATAAAAAA
** *
10626403 TTAATTTAATATGATAAAAAA
1 TTAAAATAAAATGATAAAAAA
*
10626424 TAAAAA
1 TTAAAA
10626430 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAAATAAAATGATAAAAAA
Found at i:10633977 original size:16 final size:16
Alignment explanation
Indices: 10633956--10633994 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10633946 TAATTAGTAA
10633956 TTATTTCATTGAAATT
1 TTATTTCATTGAAATT
* *
10633972 TTATTTTATTGCAATT
1 TTATTTCATTGAAATT
10633988 TTCATTT
1 TT-ATTT
10633995 AGTTCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (16 bp):
TTATTTCATTGAAATT
Found at i:10635023 original size:42 final size:45
Alignment explanation
Indices: 10634976--10635084 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 45
10634966 TATCTTACTC
* *
10634976 CCCGCTGGAAG-TT-TC-TCTTCAATGTGAGATTTTGTGACTCTA
1 CCCGCTGGAAGATTATCTTATTCAATGTGAGATTTTGTAACTCTA
*
10635018 CCCGCTGGGAGCATTATCTTATTCAATGTGAGATTTTGTAACTCTA
1 CCCGCTGGAAG-ATTATCTTATTCAATGTGAGATTTTGTAACTCTA
*
10635064 CCCTCT-GAGAGCATTATCTTA
1 CCCGCTGGA-AG-ATTATCTTA
10635085 CTCCCTGCTG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 10 0.18
44 2 0.04
45 3 0.05
46 42 0.74
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (45 bp):
CCCGCTGGAAGATTATCTTATTCAATGTGAGATTTTGTAACTCTA
Found at i:10635046 original size:46 final size:46
Alignment explanation
Indices: 10634993--10635084 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
10634983 GAAGTTTCTC
* *
10634993 TTCAATGTGAGATTTTGTGACTCTACCCGCTGGGAGCATTATCTTA
1 TTCAATGTGAGATTTTGTAACTCTACCCGCTGAGAGCATTATCTTA
*
10635039 TTCAATGTGAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTA
1 TTCAATGTGAGATTTTGTAACTCTACCCGCTGAGAGCATTATCTTA
10635085 CTCCCTGCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (46 bp):
TTCAATGTGAGATTTTGTAACTCTACCCGCTGAGAGCATTATCTTA
Found at i:10635124 original size:112 final size:112
Alignment explanation
Indices: 10634927--10635164 Score: 415
Period size: 112 Copynumber: 2.1 Consensus size: 112
10634917 AGGCTTTTTC
* *
10634927 TTCAAAGTAAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTACTCCCCGCTGGAAGTTTCT
1 TTCAATGTGAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTACTCCCCGCTGGAAGTTTCT
*
10634992 CTTCAATGTGAGATTTTGTGACTCTACCCGCTGGGAGCATTATCTTA
66 CTTCAATGTGAGATTTTGTGACTCTACCCGCTAGGAGCATTATCTTA
*
10635039 TTCAATGTGAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTACTCCCTGCTGGAAGTTTCT
1 TTCAATGTGAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTACTCCCCGCTGGAAGTTTCT
10635104 CTTCAATGTGAGATTTTGTGACTCTACCCGCTAGGAGCATTATCTTA
66 CTTCAATGTGAGATTTTGTGACTCTACCCGCTAGGAGCATTATCTTA
* *
10635151 AT-GATGTGAGATTT
1 TTCAATGTGAGATTT
10635165 ACGTCGAGTA
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 11 0.09
112 109 0.91
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (112 bp):
TTCAATGTGAGATTTTGTAACTCTACCCTCTGAGAGCATTATCTTACTCCCCGCTGGAAGTTTCT
CTTCAATGTGAGATTTTGTGACTCTACCCGCTAGGAGCATTATCTTA
Found at i:10636024 original size:41 final size:41
Alignment explanation
Indices: 10635967--10636051 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
10635957 ATCTAAAGAG
*
10635967 AGTTAGATGATAGGTGTCATGATCCACACCAATCTTTATGA
1 AGTTAGATGATAGGTGTCATGACCCACACCAATCTTTATGA
*
10636008 AGTTAGATGATAGGTGTCATGGCCCACACCAATCTTTATGA
1 AGTTAGATGATAGGTGTCATGACCCACACCAATCTTTATGA
10636049 AGT
1 AGT
10636052 ATTGTTTGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (41 bp):
AGTTAGATGATAGGTGTCATGACCCACACCAATCTTTATGA
Found at i:10636303 original size:66 final size:66
Alignment explanation
Indices: 10636206--10636339 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 66
10636196 GACATCTACC
* * * *
10636206 CTTACTCCCCACTAAGAGTTTCTCTTCAATGTTAGATTTTGCGACTCTACTTGCT-GAGAGCATT
1 CTTACTCCCCACTAAGAGTTTCTCTTCAATGTGAGACTTTACGACTCTACTCGCTGGA-AGCATT
10636270 AT
65 AT
* * * * *
10636272 CTTACTCCCCGCT-AGAAGTTTTTCTTTAATGTGAGACTTTATGACTCTAGTCGCTGGAAGCATT
1 CTTACTCCCCACTAAG-AGTTTCTCTTCAATGTGAGACTTTACGACTCTACTCGCTGGAAGCATT
10636336 AT
65 AT
10636338 CT
1 CT
10636340 CAATGATGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.04
66 53 0.93
67 2 0.04
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (66 bp):
CTTACTCCCCACTAAGAGTTTCTCTTCAATGTGAGACTTTACGACTCTACTCGCTGGAAGCATTA
T
Found at i:10637046 original size:54 final size:54
Alignment explanation
Indices: 10636964--10637073 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
10636954 TAAAAAGTAT
* * *
10636964 GAATCCAAAAAGCATACCTAATAAATGATGGAAGGTCGATGTTTATATATTTAA
1 GAATCCAAAAAGCATACCTAATAAATGATGAAAGGTCGATATTTATATACTTAA
10637018 GAATCCAAAAAGCATACCTAATAAATGATGAAAGGTCGATATTTATATACTTAA
1 GAATCCAAAAAGCATACCTAATAAATGATGAAAGGTCGATATTTATATACTTAA
10637072 GA
1 GA
10637074 CTCATCTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (54 bp):
GAATCCAAAAAGCATACCTAATAAATGATGAAAGGTCGATATTTATATACTTAA
Found at i:10638165 original size:15 final size:15
Alignment explanation
Indices: 10638148--10638176 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10638138 ATACCCCATT
10638148 TTTTA-AAAAAGAAA
1 TTTTAGAAAAAGAAA
10638162 TTTTAGAAAAAGAAA
1 TTTTAGAAAAAGAAA
10638177 AATCCAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
TTTTAGAAAAAGAAA
Found at i:10659348 original size:3 final size:3
Alignment explanation
Indices: 10659329--10659362 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
10659319 AGTACATTAA
*
10659329 ATT AGTT ATT ATC ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10659363 GACATCTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:10678926 original size:6 final size:6
Alignment explanation
Indices: 10678915--10678955 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
10678905 CCACAACAGC
* *
10678915 TAAAAA TAAAAA TAAAAA TTAAAA TAAAAA TTAAAGA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA -TAAAAA TAAA
10678956 TGTAACAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:10698237 original size:2 final size:2
Alignment explanation
Indices: 10698232--10698263 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10698222 ATTTTTTAAA
10698232 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10698264 GTTTATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10709429 original size:29 final size:29
Alignment explanation
Indices: 10709396--10709452 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
10709386 ATTTAATTTA
*
10709396 AAATAAAAATATAA-AAACTTAAATGAATG
1 AAATAAAAAAATAATAAA-TTAAATGAATG
*
10709425 AAATAAAAAAATAATAAATTATATGAAT
1 AAATAAAAAAATAATAAATTAAATGAAT
10709453 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (29 bp):
AAATAAAAAAATAATAAATTAAATGAATG
Found at i:10711550 original size:15 final size:15
Alignment explanation
Indices: 10711517--10711557 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
10711507 CAGAGATTTT
10711517 TTCTTTTTTCTT-TTC
1 TTCTTTTTT-TTGTTC
10711532 -TCTTTTTTTTGTTC
1 TTCTTTTTTTTGTTC
*
10711546 TTCTTCTTTTTG
1 TTCTTTTTTTTG
10711558 GCCATGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 10 0.43
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (15 bp):
TTCTTTTTTTTGTTC
Found at i:10717543 original size:17 final size:17
Alignment explanation
Indices: 10717517--10717562 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
10717507 AGAAGGAAAA
*
10717517 AAAAAAGAAAAAAAAGT
1 AAAAAAGAAAAAAAAGG
* *
10717534 AAAAATGAAAATAAAGG
1 AAAAAAGAAAAAAAAGG
*
10717551 AAAAAATAAAAA
1 AAAAAAGAAAAA
10717563 TTATATTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGG
Found at i:10717557 original size:18 final size:18
Alignment explanation
Indices: 10717513--10717563 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
10717503 CAGAAGAAGG
10717513 AAAA-AAAAAA-GAAAA-
1 AAAAGAAAAAATGAAAAT
*
10717528 AAAAGTAAAAATGAAAAT
1 AAAAGAAAAAATGAAAAT
* *
10717546 AAAGGAAAAAATAAAAAT
1 AAAAGAAAAAATGAAAAT
10717564 TATATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 4 0.14
16 5 0.17
17 5 0.17
18 15 0.52
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAATGAAAAT
Found at i:10732560 original size:13 final size:13
Alignment explanation
Indices: 10732542--10732566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10732532 TCTTTGAACT
10732542 GAAAAACAGAGCA
1 GAAAAACAGAGCA
10732555 GAAAAACAGAGC
1 GAAAAACAGAGC
10732567 CAAAACAGAG
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:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAAAACAGAGCA
Found at i:10741811 original size:2 final size:2
Alignment explanation
Indices: 10741798--10741833 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10741788 TTTAACCTTC
*
10741798 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10741834 TGCCACATTG
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:10785422 original size:6 final size:6
Alignment explanation
Indices: 10785411--10785441 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
10785401 AGGAAAGATG
10785411 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
10785442 AATTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:10791762 original size:3 final size:3
Alignment explanation
Indices: 10791754--10791794 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
10791744 AACTCCAACT
* *
10791754 GCA GCA GCA GCA GCA GTA GCA GTA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
10791795 TTGCCTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.34, T:0.05
Consensus pattern (3 bp):
GCA
Found at i:10807170 original size:22 final size:22
Alignment explanation
Indices: 10807131--10807172 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10807121 TTCTGCAGAG
10807131 AAACTCAAAAAAAGTCTAAAAC
1 AAACTCAAAAAAAGTCTAAAAC
*
10807153 AAACTTCAAATAAA-TCTAAA
1 AAAC-TCAAAAAAAGTCTAAA
10807173 CACCGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (22 bp):
AAACTCAAAAAAAGTCTAAAAC
Found at i:10826842 original size:5 final size:5
Alignment explanation
Indices: 10826796--10826823 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10826786 TAACAGGGAC
10826796 AGGAA AGGAA AGGAA AGGAA AGGAA AGG
1 AGGAA AGGAA AGGAA AGGAA AGGAA AGG
10826824 GATGGTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:10829173 original size:210 final size:207
Alignment explanation
Indices: 10828946--10829537 Score: 776
Period size: 209 Copynumber: 2.8 Consensus size: 207
10828936 ATGATATAAT
* * *
10828946 TTATATGTTATAATGTTTTATATCAAAGTTTGTATAAAAAATAACTAATTATAAACAATATGTTA
1 TTATATGTTATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATATTA
* *
10829011 TAAAATCTAAAGAGATAGCTAATAAATTTATTAAGTGTAATCATATAAATAAAGTTTATTATAAG
66 TAAAATCTAAAGTGATAACTAATAAATTTATTAAGTGTAATCATATAAATAAAGTTTATTATAAG
* * * *
10829076 TTGTCATAATACTTATGTATAAATTAAATATATGCATATATAA-TTTATTATTTTATTATATATA
131 TTAT-ATAATGCTTATGTATAAATTAAATATATGAATATATAACTTT-TTTTTTTA-TATATATA
*
10829140 TAATTAATAATACAAA
193 -AATTAATAACACAAA
* * *
10829156 TTATATGCTAAAATGTTTTATATCAAAGTTTGTATAAATAGTAACTAATTATAAATAATATATTA
1 TTATATGTTATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATATTA
* * * * * *
10829221 TAAAATTTAAGGTGATAACTAATAAAGTTATTAAATGTAATCATAT-AATAAAGTCTATTACAAG
66 TAAAATCTAAAGTGATAACTAATAAATTTATTAAGTGTAATCATATAAATAAAGTTTATTATAAG
* *
10829285 TTATAATAATGCTTATGTATAAATTAAATATATATAATATATGACTTTTTTTTTTATATATATGA
131 TTAT-ATAATGCTTATGTATAAATTAAATATAT-GAATATATAACTTTTTTTTTTATATATAT-A
* * *
10829350 AATTAATGACATAAC
193 AATTAATAACACAAA
* * * *
10829365 TTATATGTTATAATATTTTATATCAAAGTTTATATAAATAATAATTAAGTATAAATAATATATTA
1 TTATATGTTATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATATTA
* *
10829430 TAAAATCTAAAGTGATAACTAATAAAGTTT-TTAAGTGTAATTATATAAACAAAGTTTATTATAA
66 TAAAATCTAAAGTGATAACTAATAAA-TTTATTAAGTGTAATCATATAAATAAAGTTTATTATAA
* * * *
10829494 ATTATAGTAATGTTTATGTATAAGTTAAATATATGTATATATAA
130 GTTATA-TAATGCTTATGTATAAATTAAATATATGAATATATAA
10829538 AATATTTATA
Statistics
Matches: 330, Mismatches: 46, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
209 168 0.51
210 159 0.48
211 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (207 bp):
TTATATGTTATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATATTA
TAAAATCTAAAGTGATAACTAATAAATTTATTAAGTGTAATCATATAAATAAAGTTTATTATAAG
TTATATAATGCTTATGTATAAATTAAATATATGAATATATAACTTTTTTTTTTATATATATAAAT
TAATAACACAAA
Done.