Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 78 of 97
Found at i:31033238 original size:24 final size:23
Alignment explanation
Indices: 31033211--31033268 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
31033201 TAATTTTTTT
*
31033211 TATTTTAATCTATAGTTTATATTA
1 TATTTTAATCTAT-CTTTATATTA
*
31033235 TATTATTATAT-TATCTTTATTTTA
1 TATT-TTA-ATCTATCTTTATATTA
*
31033259 TATTATAATC
1 TATTTTAATC
31033269 GATTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 16 0.57
25 6 0.21
26 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTTTAATCTATCTTTATATTA
Found at i:31035055 original size:23 final size:23
Alignment explanation
Indices: 31035019--31035073 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
31035009 GTTCAGAGTT
* * *
31035019 TGTGAAACGGCATGTTGGGAATA
1 TGTGACACGACATGGTGGGAATA
31035042 TGTGACACGACATGGTGGGAATA
1 TGTGACACGACATGGTGGGAATA
31035065 TGTGACACG
1 TGTGACACG
31035074 GTTGTGAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.24
Consensus pattern (23 bp):
TGTGACACGACATGGTGGGAATA
Found at i:31035121 original size:81 final size:81
Alignment explanation
Indices: 31034981--31035134 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 81
31034971 ACAGCAGGCC
*** *
31034981 ATATGTGACACGGTTGTGGCACGACAAGGTTCAGAGTTTGTGAAACGGCATGTTGGGAATATGTG
1 ATATGTGACACGGTTGTGGCACGACAAGGTTCAGAGTTTGTGAAACGGCATGGAAGGAATATGTA
31035046 ACACGACATGGTGGGA
66 ACACGACATGGTGGGA
* * *
31035062 ATATGTGACACGGTTGTGAG-ACGACAGGGTTTAGAGTTTGTGACAC-GCTATGGAAGGAATATG
1 ATATGTGACACGGTTGTG-GCACGACAAGGTTCAGAGTTTGTGAAACGGC-ATGGAAGGAATATG
31035125 TAACACGACA
64 TAACACGACA
31035135 GGATGAGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 2 0.03
81 61 0.95
82 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (81 bp):
ATATGTGACACGGTTGTGGCACGACAAGGTTCAGAGTTTGTGAAACGGCATGGAAGGAATATGTA
ACACGACATGGTGGGA
Found at i:31035368 original size:47 final size:47
Alignment explanation
Indices: 31035293--31035470 Score: 160
Period size: 47 Copynumber: 3.8 Consensus size: 47
31035283 GACACGGTTG
* * *
31035293 TGACACGATAGGGTTCAGATTTTATGACACGTCATGGAGGGAATCTT
1 TGACACGATAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTT
* * ** *
31035340 TGACACGGTAGGGTTCAGAGTTTGTGACATGCCATGGAGAAAATCTG
1 TGACACGATAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTT
* * * * * *
31035387 TAACACGACAGGGTTTAAAATTTGTGACACGCCATGAAGGGAAT-TT
1 TGACACGATAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTT
* * * * * *
31035433 GTGACAGGGTAGGGTTTAGCGTGTGTGACACGACATGG
1 -TGACACGATAGGGTTCAGAGTTTGTGACACGCCATGG
31035471 CTTGAACATG
Statistics
Matches: 101, Mismatches: 29, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
46 1 0.01
47 100 0.99
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (47 bp):
TGACACGATAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTT
Found at i:31035485 original size:23 final size:23
Alignment explanation
Indices: 31035456--31035499 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31035446 GTTTAGCGTG
31035456 TGTGACACGACATGGCTTGAACA
1 TGTGACACGACATGGCTTGAACA
* *
31035479 TGTGACATGACATGGTTTGAA
1 TGTGACACGACATGGCTTGAA
31035500 ATATGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (23 bp):
TGTGACACGACATGGCTTGAACA
Found at i:31036109 original size:31 final size:31
Alignment explanation
Indices: 31036068--31036209 Score: 214
Period size: 31 Copynumber: 4.6 Consensus size: 31
31036058 GTGTCAGCGT
*
31036068 TGGCGTGTAACAACATTTGACTTGATACT-CA
1 TGGCGTGTAACAACATTTTACTTGATA-TGCA
* *
31036099 TGACGTGTAACAACATTTTACGTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
31036130 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
31036161 TGGCGTATAACAACATTTTACTTGATATGCG
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
31036192 TGGTGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
31036210 ATTTCTTTCT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 1 0.01
31 100 0.99
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:31037907 original size:145 final size:144
Alignment explanation
Indices: 31037660--31037993 Score: 413
Period size: 145 Copynumber: 2.3 Consensus size: 144
31037650 ACGGTTTTAG
* * * *
31037660 CGATTTGTGTTCAACA--ATCCCATATGTAATTATTGAATAACATATCTGTGTTTGCAGTTTGAC
1 CGATTTGTGTTCAACATTTTCACATATG--ATTATCGAATAACATATCTGTGTTTGCAGTTGGAC
* * * * *
31037723 CATGCGACGGTAGCTCCACAACCACCAAGAAGTCTTCCTCGAACGCACAGTGCTAACGAG-TTGT
64 CATGCGACGATAGCTCCACAACCACCAAGAAGTCCTCCTCAAACGCACAGTGATAACGAGCAT-T
* *
31037787 AGATAAGATCAGTTTTAA
128 AG-TAAAATCAGTTATAA
** *
31037805 CGATTTGTGTTCAATGTTTTCATATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCA
1 CGATTTGTGTTCAACATTTTCACATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCA
**
31037870 TGCGACGATAGCTCCACAACCACTGAGAAGTCCTCCTCAAACGCACAGTGATAACGAGCCATTAG
66 TGCGACGATAGCTCCACAACCACCAAGAAGTCCTCCTCAAACGCACAGTGATAACGAG-CATTAG
**
31037935 TAAAATTGGTTATAA
130 TAAAATCAGTTATAA
* * *
31037950 CGGTTTGTGTTCAACATTTTCACATATGTTTATCGAGTAACATA
1 CGATTTGTGTTCAACATTTTCACATATGATTATCGAATAACATA
31037994 ATAATTTCTG
Statistics
Matches: 161, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
145 150 0.93
146 3 0.02
147 8 0.05
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (144 bp):
CGATTTGTGTTCAACATTTTCACATATGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCA
TGCGACGATAGCTCCACAACCACCAAGAAGTCCTCCTCAAACGCACAGTGATAACGAGCATTAGT
AAAATCAGTTATAA
Found at i:31040373 original size:31 final size:31
Alignment explanation
Indices: 31040335--31040747 Score: 308
Period size: 31 Copynumber: 13.3 Consensus size: 31
31040325 CCAACAAGTT
*
31040335 AGCGTGTCACGTCATAAATCTGCTACCACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* ** * * * *
31040366 AGTGTGTCATACAATAAATCTACAAGCACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * *
31040397 AGCAG-GTCACGTCATGAGTCTGCTACCACTC
1 AGC-GTGTCACGCCATAAATCTGCTACCACTC
* * * **
31040428 AGTGTGTCATGCCATAAATTTGCTAGGACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * *
31040459 AGCGTGTCACACCATAAATTTGCTACCACCC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* ** * *
31040490 AGCGTGTCATGTAATAAATCTGCTACCATTT
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * * * ** **
31040521 AACGTGTTATGCTATAAATCTATTAGGACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * *
31040552 AGCGTGTCATGCCATAAATTTGCTACCACTT
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
*
31040583 AGCGTGTCACG-TAGTAAATCTGCTACCACTC
1 AGCGTGTCACGCCA-TAAATCTGCTACCACTC
* * * * *
31040614 AGCATGTCATGCCATAAATCAGCTAGCATTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * * *
31040645 AACATGTCACGCTATAAATCTGCTACCATTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * **
31040676 AACGTGTCACGCCATAAATCAGCTTGCACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* * *
31040707 AGAGTGTAACCCCATAAATCTGCTACCACTC
1 AGCGTGTCACGCCATAAATCTGCTACCACTC
* *
31040738 AACTTGTCAC
1 AGCGTGTCAC
31040748 CATAAGGTGT
Statistics
Matches: 287, Mismatches: 91, Indels: 8
0.74 0.24 0.02
Matches are distributed among these distances:
30 2 0.01
31 283 0.99
32 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (31 bp):
AGCGTGTCACGCCATAAATCTGCTACCACTC
Found at i:31041727 original size:24 final size:24
Alignment explanation
Indices: 31041700--31041766 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
31041690 GTGTCCCAGT
* * *
31041700 AGCAACTTCAGTAGGTGCAGTAGC
1 AGCAGCTTCAGTTGGTGCAGCAGC
*
31041724 AGCAGCTTTAGTTGGTGCAGCAGC
1 AGCAGCTTCAGTTGGTGCAGCAGC
*
31041748 AGCAGCTTCACTTGGTGCA
1 AGCAGCTTCAGTTGGTGCA
31041767 CCAGTAGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (24 bp):
AGCAGCTTCAGTTGGTGCAGCAGC
Found at i:31044224 original size:42 final size:42
Alignment explanation
Indices: 31044171--31044314 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
31044161 GAAAAGGCCA
* *
31044171 CTAGAAGCTTTAAATTGGCCTTTAGCAAATTCAGATGGGCAG
1 CTAGCAGCTTTAAATTGGCCTCTAGCAAATTCAGATGGGCAG
* * * *
31044213 CTAGCAACTTTAACTTGGCCTCTAGCAATTTCAGATGGGCCG
1 CTAGCAGCTTTAAATTGGCCTCTAGCAAATTCAGATGGGCAG
* * * * *
31044255 TTAGCAGCTTTAAATGGGCCTCCAGCAACTTCAGATGAGCCA-
1 CTAGCAGCTTTAAATTGGCCTCTAGCAAATTCAGATG-GGCAG
*
31044297 CTAGCAGCTTTAAGTTGG
1 CTAGCAGCTTTAAATTGG
31044315 AGTCCAATAC
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
42 82 0.98
43 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (42 bp):
CTAGCAGCTTTAAATTGGCCTCTAGCAAATTCAGATGGGCAG
Found at i:31044253 original size:21 final size:21
Alignment explanation
Indices: 31044187--31044302 Score: 69
Period size: 21 Copynumber: 5.5 Consensus size: 21
31044177 GCTTTAAATT
* *
31044187 GGCCTTTAGCAAATTCAGATG
1 GGCCTCTAGCAATTTCAGATG
** *
31044208 GGCAGCTAGCAACTTT-A-ACTT
1 GGCCTCTAGCAA-TTTCAGA-TG
31044229 GGCCTCTAGCAATTTCAGATG
1 GGCCTCTAGCAATTTCAGATG
* *
31044250 GGCCGT-TAGCAGCTTT-AAATG
1 GGCC-TCTAGCA-ATTTCAGATG
* *
31044271 GGCCTCCAGCAACTTCAGATG
1 GGCCTCTAGCAATTTCAGATG
* *
31044292 AGCCACTAGCA
1 GGCCTCTAGCA
31044303 GCTTTAAGTT
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
20 7 0.10
21 56 0.80
22 7 0.10
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
GGCCTCTAGCAATTTCAGATG
Found at i:31044530 original size:21 final size:21
Alignment explanation
Indices: 31044491--31044531 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31044481 TATCAAAATA
*
31044491 ATCTTCATTTAATCCTTCTTC
1 ATCTTCATTTAAACCTTCTTC
*
31044512 ATCTTCATTTAAACGTTCTT
1 ATCTTCATTTAAACCTTCTT
31044532 AATGTCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (21 bp):
ATCTTCATTTAAACCTTCTTC
Found at i:31049892 original size:22 final size:22
Alignment explanation
Indices: 31049842--31050128 Score: 199
Period size: 22 Copynumber: 12.7 Consensus size: 22
31049832 TCAGTCATGT
** *
31049842 TGTTACACCCCATGTTTAAAATA
1 TGTTACATGCCATGTTCAAAA-A
* *
31049865 TGTTACATGTCATGTTTAAAAA
1 TGTTACATGCCATGTTCAAAAA
* * *
31049887 TGTTACACGCCATCTTAAAAAA
1 TGTTACATGCCATGTTCAAAAA
* * *
31049909 TGTTACACG-CAAGTTCAACACTA
1 TGTTACATGCCATGTTCAA-A-AA
*
31049932 TGTTATCTATACGCATTGTTCAAAAA
1 TGTTA-C-ATGC-CA-TGTTCAAAAA
31049958 TGTTACATG-CATGTTCAAAAA
1 TGTTACATGCCATGTTCAAAAA
* *
31049979 TTGTTACATGCCTTG-TAAAAAA
1 -TGTTACATGCCATGTTCAAAAA
*
31050001 TGTTACA--CACAAGTTCAAAAA
1 TGTTACATGC-CATGTTCAAAAA
* * *
31050022 TTGTTACACGCCTTGTTCAAAAT
1 -TGTTACATGCCATGTTCAAAAA
* *
31050045 TGTTACACG-CAAGTTCAAAAA
1 TGTTACATGCCATGTTCAAAAA
* *
31050066 TGTTACACGCCATGTTCACAACA
1 TGTTACATGCCATGTTCA-AAAA
*
31050089 TGTTACATGCCATGTTAAATAAAAA
1 TGTTACATGCCATGTT---CAAAAA
31050114 TGTTACATGCCATGT
1 TGTTACATGCCATGT
31050129 GCTAACACAT
Statistics
Matches: 213, Mismatches: 32, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.00
20 2 0.01
21 47 0.22
22 69 0.32
23 54 0.25
24 4 0.02
25 20 0.09
26 7 0.03
27 3 0.01
28 6 0.03
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (22 bp):
TGTTACATGCCATGTTCAAAAA
Found at i:31050017 original size:43 final size:44
Alignment explanation
Indices: 31049857--31050095 Score: 205
Period size: 43 Copynumber: 5.3 Consensus size: 44
31049847 CACCCCATGT
* * * * * * *
31049857 TTAAAATATGTTACATGTCATGTTTAAAAA-TGTTACACGCCATC
1 TTAAAAAATGTTACACG-CAAGTTCAAAAATTGTTACATGCCTTG
* * *
31049901 TTAAAAAATGTTACACGCAAGTTCAACACTATGTTATCTATACGCATTG
1 TTAAAAAATGTTACACGCAAGTTCAAAAAT-TGTTA-C-AT--GCCTTG
* * *
31049950 TTCAAAAATGTTACATGCATGTTCAAAAATTGTTACATGCCTTG
1 TTAAAAAATGTTACACGCAAGTTCAAAAATTGTTACATGCCTTG
* *
31049994 -TAAAAAATGTTACACACAAGTTCAAAAATTGTTACACGCCTTG
1 TTAAAAAATGTTACACGCAAGTTCAAAAATTGTTACATGCCTTG
* * * *
31050037 TTCAAAATTGTTACACGCAAGTTCAAAAA-TGTTACACGCCATG
1 TTAAAAAATGTTACACGCAAGTTCAAAAATTGTTACATGCCTTG
* *
31050080 TTCACAACATGTTACA
1 TT-AAAAAATGTTACA
31050096 TGCCATGTTA
Statistics
Matches: 158, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
43 61 0.39
44 54 0.34
45 5 0.03
46 3 0.02
47 2 0.01
48 5 0.03
49 28 0.18
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (44 bp):
TTAAAAAATGTTACACGCAAGTTCAAAAATTGTTACATGCCTTG
Found at i:31051045 original size:21 final size:21
Alignment explanation
Indices: 31051015--31051054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31051005 GCGTGTGTAT
*
31051015 ATATATATATATGTACTTTAA
1 ATATAAATATATGTACTTTAA
*
31051036 ATATAAATATATTTACTTT
1 ATATAAATATATGTACTTT
31051055 TTATTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATAAATATATGTACTTTAA
Found at i:31052358 original size:20 final size:21
Alignment explanation
Indices: 31052333--31052401 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
31052323 TGTCTGCCAC
31052333 CTCTAT-TTTTGTATATAGAA
1 CTCTATCTTTTGTATATAGAA
* *
31052353 CTCTATCTTTTG-ATGTTTG--
1 CTCTATCTTTTGTAT-ATAGAA
31052372 -T-TAT-TTTTGTATATAGAA
1 CTCTATCTTTTGTATATAGAA
31052390 CTCTATCTTTTG
1 CTCTATCTTTTG
31052402 ATGTTTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 15
0.66 0.07 0.27
Matches are distributed among these distances:
16 7 0.19
17 5 0.14
18 1 0.03
19 1 0.03
20 11 0.30
21 12 0.32
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
CTCTATCTTTTGTATATAGAA
Found at i:31052386 original size:37 final size:37
Alignment explanation
Indices: 31052336--31052409 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
31052326 CTGCCACCTC
31052336 TATTTTTGTATATAGAACTCTATCTTTTGATGTTTGT
1 TATTTTTGTATATAGAACTCTATCTTTTGATGTTTGT
31052373 TATTTTTGTATATAGAACTCTATCTTTTGATGTTTGT
1 TATTTTTGTATATAGAACTCTATCTTTTGATGTTTGT
31052410 GCTTAAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (37 bp):
TATTTTTGTATATAGAACTCTATCTTTTGATGTTTGT
Found at i:31052557 original size:23 final size:23
Alignment explanation
Indices: 31052526--31052572 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31052516 GTTATAAAAT
* *
31052526 ATAATTTGAAAGAATAAATAAAG
1 ATAACTTGAAAGAAGAAATAAAG
*
31052549 ATAACTTGAAAGAAGAACTAAAG
1 ATAACTTGAAAGAAGAAATAAAG
31052572 A
1 A
31052573 AAGAGACGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (23 bp):
ATAACTTGAAAGAAGAAATAAAG
Found at i:31052767 original size:16 final size:17
Alignment explanation
Indices: 31052746--31052782 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
31052736 TGGATTAAAT
31052746 TCTAATCTTA-ATCC-AA
1 TCTAAT-TTACATCCAAA
31052762 TCTAATTTACATCCAAA
1 TCTAATTTACATCCAAA
31052779 TCTA
1 TCTA
31052783 GATATACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 10 0.53
17 6 0.32
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAATTTACATCCAAA
Found at i:31056506 original size:13 final size:13
Alignment explanation
Indices: 31056488--31056517 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31056478 AATATTAAAT
*
31056488 ATATAATTAAAAC
1 ATATAATAAAAAC
31056501 ATATAATAAAAAC
1 ATATAATAAAAAC
31056514 ATAT
1 ATAT
31056518 CATCTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAATAAAAAC
Found at i:31056697 original size:64 final size:64
Alignment explanation
Indices: 31056608--31056730 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
31056598 TTCATTCTTG
** *
31056608 GATATTTTTATTACCAATCAAATGATCAATTCCTCTTTCAAGGTGGACAAGAAAATCAATAATA
1 GATATTTCCATTACCAATCAAATGATCAATTCCTCTTTCAAGGTAGACAAGAAAATCAATAATA
* * * *
31056672 GATATTTCCATTAGCAATCATATGATCAATTCCTTTTTCATGGTAGACAAGAAAATCAA
1 GATATTTCCATTACCAATCAAATGATCAATTCCTCTTTCAAGGTAGACAAGAAAATCAA
31056731 CAACAGATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (64 bp):
GATATTTCCATTACCAATCAAATGATCAATTCCTCTTTCAAGGTAGACAAGAAAATCAATAATA
Found at i:31056972 original size:8 final size:8
Alignment explanation
Indices: 31056959--31056984 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31056949 TATTCACTTC
31056959 TAGTGAGT
1 TAGTGAGT
31056967 TAGTGAGT
1 TAGTGAGT
31056975 TAGTGAGT
1 TAGTGAGT
31056983 TA
1 TA
31056985 AGGTATCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (8 bp):
TAGTGAGT
Found at i:31057039 original size:27 final size:27
Alignment explanation
Indices: 31057009--31057072 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
31056999 TTTTTAGTAA
* *
31057009 GTAAAATTATCCATCCACTTTTGGTGG
1 GTAAAGTTATACATCCACTTTTGGTGG
*
31057036 GTAAAGTTATATATCCACTTTTGGTGG
1 GTAAAGTTATACATCCACTTTTGGTGG
31057063 GTAAAGTTAT
1 GTAAAGTTAT
31057073 TCTTAGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (27 bp):
GTAAAGTTATACATCCACTTTTGGTGG
Found at i:31063063 original size:18 final size:18
Alignment explanation
Indices: 31063014--31063070 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
31063004 TAATTAATCT
31063014 TGTTATCGTGTTTAAACG
1 TGTTATCGTGTTTAAACG
* * * * *
31063032 TATAAACGTATTTAATCG
1 TGTTATCGTGTTTAAACG
31063050 TGTTATCGTGTTTAAACG
1 TGTTATCGTGTTTAAACG
31063068 TGT
1 TGT
31063071 ATACATGATA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTTATCGTGTTTAAACG
Found at i:31063499 original size:17 final size:17
Alignment explanation
Indices: 31063477--31063511 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
31063467 ATTTAATCTT
*
31063477 AACGTATTTCATATTTA
1 AACGTATTTCAGATTTA
31063494 AACGTATTTCAGATTTA
1 AACGTATTTCAGATTTA
31063511 A
1 A
31063512 TTGAAGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (17 bp):
AACGTATTTCAGATTTA
Found at i:31064496 original size:22 final size:22
Alignment explanation
Indices: 31064445--31064504 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
31064435 TATTATTTTC
**
31064445 ATTTTATTTCATATTATCGTAT
1 ATTTTATTTTTTATTATCGTAT
* *
31064467 -TTTCTATTTTTTATTCTCTTAT
1 ATTT-TATTTTTTATTATCGTAT
31064489 ATTTTATTTTTT-TTAT
1 ATTTTATTTTTTATTAT
31064505 ATTCTAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.19
22 22 0.71
23 3 0.10
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTATTTTTTATTATCGTAT
Found at i:31064633 original size:20 final size:19
Alignment explanation
Indices: 31064598--31064638 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
31064588 TCGTCTTAGA
31064598 TTTTTTATTATTTATTTAT
1 TTTTTTATTATTTATTTAT
*
31064617 TTTTTTATTTTTCTATTTAT
1 TTTTTTATTATT-TATTTAT
31064637 TT
1 TT
31064639 AATGTCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTATTATTTATTTAT
Found at i:31064752 original size:17 final size:18
Alignment explanation
Indices: 31064715--31064753 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31064705 TTTATCATCA
*
31064715 TATTTTTTTATCTATTGT
1 TATTTATTTATCTATTGT
*
31064733 TATTTATTTAT-TATTTT
1 TATTTATTTATCTATTGT
31064750 TATT
1 TATT
31064754 GAATAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTTATTTATCTATTGT
Found at i:31066665 original size:84 final size:83
Alignment explanation
Indices: 31066522--31066680 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 83
31066512 CTACCCTGCT
*
31066522 AGACGCGAATTTTTCACATCTGGCAGGGTGAGGGAGGTGCCTGGCAGGGTGCGTCCGCACCCTGC
1 AGACGCGAATTTTTCACATCTGGCAGGGTGAAGGAGGTGCCTGGCAGGGTGCGTCCGCACCCTGC
31066587 CAGTCGTACCCTCTCCCC
66 CAGTCGTACCCTCTCCCC
* * * * * *
31066605 NAGACGCGAATTTTT-AGCGTTTGGTAGGGTGAAGGTGGCT-CCTGGCAGGGTGTGTTCGCACCC
1 -AGACGCGAATTTTTCA-CATCTGGCAGGGTGAAGGAGG-TGCCTGGCAGGGTGCGTCCGCACCC
31066668 TGCCAGTCGTACC
63 TGCCAGTCGTACC
31066681 TCTTTTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 1 0.02
84 64 0.97
85 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (83 bp):
AGACGCGAATTTTTCACATCTGGCAGGGTGAAGGAGGTGCCTGGCAGGGTGCGTCCGCACCCTGC
CAGTCGTACCCTCTCCCC
Found at i:31066914 original size:25 final size:23
Alignment explanation
Indices: 31066876--31066931 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
31066866 TTACCAAGGT
*
31066876 TTTTTTTTTTTTTTGGTTTGTTTGG
1 TTTTTTTTTGTTTTGGTTT-TTT-G
*
31066901 TTTTTTTTTGTTTTTGTTTTTTG
1 TTTTTTTTTGTTTTGGTTTTTTG
31066924 TTTTTTTT
1 TTTTTTTT
31066932 AAATGAGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.31
24 3 0.10
25 17 0.59
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTGTTTTGGTTTTTTG
Found at i:31066923 original size:28 final size:26
Alignment explanation
Indices: 31066873--31066931 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
31066863 CTCTTACCAA
31066873 GGTTTTTTTTTTTTTTTGGTTTGTTT
1 GGTTTTTTTTTTTTTTTGGTTTGTTT
*
31066899 GGTTTTTTTTTGTTTTT-GTTT-TTT
1 GGTTTTTTTTTTTTTTTGGTTTGTTT
31066923 -GTTTTTTTT
1 GGTTTTTTTT
31066932 AAATGAGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 9 0.28
24 3 0.09
25 4 0.12
26 16 0.50
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (26 bp):
GGTTTTTTTTTTTTTTTGGTTTGTTT
Found at i:31066927 original size:21 final size:19
Alignment explanation
Indices: 31066877--31066930 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
31066867 TACCAAGGTT
31066877 TTTTTTTTTTTTTGGTTTG
1 TTTTTTTTTTTTTGGTTTG
* *
31066896 TTTGGTTTTTTTTTGTTTTTG
1 TTT-TTTTTTTTTTG-GTTTG
31066917 TTTTTTGTTTTTTT
1 TTTTTT-TTTTTTT
31066931 TAAATGAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 12 0.41
21 14 0.48
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTTTTTGGTTTG
Found at i:31067033 original size:41 final size:41
Alignment explanation
Indices: 31066932--31067050 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
31066922 TGTTTTTTTT
* *
31066932 AAATGAGACTCCTCAAAGCTGAGAC-AATGAAACTTT--AAA
1 AAATGAAACTCCTCAAAGCTGAGGCTAA-GAAACTTTAAAAA
** *
31066971 AAA-G-AACTCCTCAAAATTGAGGCTACGAAACTTTAAAAA
1 AAATGAAACTCCTCAAAGCTGAGGCTAAGAAACTTTAAAAA
* *
31067010 AAATGAAACTCCCCAAAGCTGAGG-TAATATAACTTTAAAAA
1 AAATGAAACTCCTCAAAGCTGAGGCTAAGA-AACTTTAAAAA
31067051 TATAGCTCCT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
37 23 0.36
38 2 0.03
39 9 0.14
40 4 0.06
41 26 0.41
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (41 bp):
AAATGAAACTCCTCAAAGCTGAGGCTAAGAAACTTTAAAAA
Found at i:31067232 original size:38 final size:37
Alignment explanation
Indices: 31066939--31067238 Score: 230
Period size: 37 Copynumber: 7.9 Consensus size: 37
31066929 TTTAAATGAG
* *
31066939 ACTCCTCAAAGCTGAGACAATGAAACTTTAAAAA-AGA
1 ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATA-A
** *
31066976 ACTCCTCAAAATTGAGGCTACGAAACTTTAAAAAAAATGAA
1 ACTCCTCAAAGCTGAGGCAACGAAACTTT---AAAAAT-AA
* * *
31067017 ACTCCCCAAAGCTGAGGTAA-TATAACTTTAAAAATATA
1 ACTCCTCAAAGCTGAGGCAACGA-AACTTTAAAAATA-A
* * * * *
31067055 GCTCCTCAATGCTGAGGCAAC-ATGACTTTAGAAATGA
1 ACTCCTCAAAGCTGAGGCAACGA-AACTTTAAAAATAA
* * * *
31067092 ACTCTTTAGAGCTGAGGCAACGAGACTTTAAAAATAA
1 ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATAA
** *
31067129 ACTCCTCAAAATTGAGGCAAC-AAGACTTTAAAAATGA
1 ACTCCTCAAAGCTGAGGCAACGAA-ACTTTAAAAATAA
** * *
31067166 ACTCCTCAAAATTGAGGTAATGAAACTTTAAAAATAAA
1 ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAAT-AA
* * * *
31067204 ACTCCCCAAAGCTGAGTCAACGAGACTTTTAAAAT
1 ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAAT
31067239 CTTGAAACTA
Statistics
Matches: 208, Mismatches: 43, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
36 1 0.00
37 112 0.54
38 66 0.32
40 6 0.03
41 22 0.11
42 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (37 bp):
ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATAA
Found at i:31067484 original size:116 final size:116
Alignment explanation
Indices: 31067280--31067498 Score: 375
Period size: 116 Copynumber: 1.9 Consensus size: 116
31067270 ATACACTCGG
* * *
31067280 AGGATTTAAGAGAATAATGTGCCCAGAGGTTTTCAGAATGTATCCGAAGAATTTAGGAAATGTGG
1 AGGATTTAAGAGAATAATGTGCCAAGAGGTCTTCAGAATGTACCCGAAGAATTTAGGAAATGTGG
31067345 CTCCTCGAAAACTGAGGCAACGTAACTTTAAAAATGAAACTAATTACCCGA
66 CTCCTCGAAAACTGAGGCAACGTAACTTTAAAAATGAAACTAATTACCCGA
* *
31067396 AGGATTTAAGAGAATAATGTGCCAAGAGGTCTTCAGAATGTACCCGGAGGATTTAGGAAATGTGG
1 AGGATTTAAGAGAATAATGTGCCAAGAGGTCTTCAGAATGTACCCGAAGAATTTAGGAAATGTGG
* *
31067461 CTTCTCGAAAATTGAGGCAACGTAACTTTAAAAATGAA
66 CTCCTCGAAAACTGAGGCAACGTAACTTTAAAAATGAA
31067499 CTCCTCAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 96 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (116 bp):
AGGATTTAAGAGAATAATGTGCCAAGAGGTCTTCAGAATGTACCCGAAGAATTTAGGAAATGTGG
CTCCTCGAAAACTGAGGCAACGTAACTTTAAAAATGAAACTAATTACCCGA
Found at i:31079598 original size:22 final size:22
Alignment explanation
Indices: 31079562--31079617 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
31079552 TATTATTTTC
** *
31079562 ATTTTATTTCATATTATCGTAT
1 ATTTTATTTTTTATTATCCTAT
* *
31079584 TTTTTATTTTTTATTCTCCTAT
1 ATTTTATTTTTTATTATCCTAT
31079606 ATTTTATTTTTT
1 ATTTTATTTTTT
31079618 TTCTATTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTATTTTTTATTATCCTAT
Found at i:31079815 original size:3 final size:3
Alignment explanation
Indices: 31079809--31079870 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
31079799 ATATATTCAA
* * * * *
31079809 ATT ATT ATT ATT ATT ATT ATC ATT ATT TTT TTT TTT ATT GTT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
31079855 ATTT ATT ATT TTT ATT
1 A-TT ATT ATT ATT ATT
31079871 GAATAATCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
3 43 0.86
4 7 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:31081758 original size:7 final size:7
Alignment explanation
Indices: 31081748--31081777 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31081738 CTTTTTCTCT
31081748 TTTTTTA
1 TTTTTTA
31081755 TTTTTTA
1 TTTTTTA
31081762 -TTTTTA
1 TTTTTTA
31081768 TTTTTTA
1 TTTTTTA
31081775 TTT
1 TTT
31081778 GTTGTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:31081765 original size:13 final size:13
Alignment explanation
Indices: 31081749--31081777 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31081739 TTTTTCTCTT
31081749 TTTTTATTTTTTA
1 TTTTTATTTTTTA
31081762 TTTTTATTTTTTA
1 TTTTTATTTTTTA
31081775 TTT
1 TTT
31081778 GTTGTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:31081791 original size:20 final size:20
Alignment explanation
Indices: 31081748--31081791 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
31081738 CTTTTTCTCT
* *
31081748 TTTTTTATTTTTTATTTTTA
1 TTTTTTATTTGTTATTTATA
* *
31081768 TTTTTTATTTGTTGTTTATC
1 TTTTTTATTTGTTATTTATA
31081788 TTTT
1 TTTT
31081792 GTTTACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTTATTTGTTATTTATA
Found at i:31081849 original size:11 final size:10
Alignment explanation
Indices: 31081747--31081848 Score: 55
Period size: 11 Copynumber: 9.4 Consensus size: 10
31081737 TCTTTTTCTC
*
31081747 TTTTTTTATT
1 TTTTTTTATA
*
31081757 TTTTATTTTTA
1 TTTT-TTTATA
31081768 -TTTTTTAT-
1 TTTTTTTATA
*
31081776 TTGTTGTTTATC
1 TT-TT-TTTATA
31081788 TTTTGTTTACTA
1 TTTT-TTTA-TA
*
31081800 TTATTTTATTA
1 TTTTTTTA-TA
*
31081811 TTTTATTATA
1 TTTTTTTATA
31081821 TTTTTTATCATA
1 TTTTTT-T-ATA
31081833 TATTTATTTATA
1 T-TTT-TTTATA
31081845 TTTT
1 TTTT
31081849 AAACACCAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.07
10 16 0.22
11 32 0.44
12 14 0.19
13 4 0.05
14 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:31081983 original size:20 final size:20
Alignment explanation
Indices: 31081947--31081985 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31081937 TTTAGTTTTA
31081947 AAAATATTAAATATTAATAT
1 AAAATATTAAATATTAATAT
*
31081967 AAAA-ATTAATATTTTAATA
1 AAAATATTAA-ATATTAATA
31081986 ATAGATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTAAATATTAATAT
Found at i:31085936 original size:30 final size:30
Alignment explanation
Indices: 31085902--31086001 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
31085892 TTATAAAGAT
* * *
31085902 TTATTTGATTCAAAATAAAAGTATAAGGGC
1 TTATTTGAATCAAAATAAAAATATAAGAGC
**
31085932 TTATTTGGCTCAAAATAAAAATATAAGAGC
1 TTATTTGAATCAAAATAAAAATATAAGAGC
* * * *
31085962 TTGA-TTGAACCAAAATAAAAATTTAAAAGG
1 TT-ATTTGAATCAAAATAAAAATATAAGAGC
31085992 TTATTTGAAT
1 TTATTTGAAT
31086002 ATTTCTAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 55 0.96
31 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (30 bp):
TTATTTGAATCAAAATAAAAATATAAGAGC
Found at i:31091306 original size:18 final size:17
Alignment explanation
Indices: 31091281--31091323 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
31091271 ATTCAATAAT
*
31091281 TAAAAAAAGTATAAATAAA
1 TAAAAAAA-TAGAAA-AAA
31091300 TAAAAAAATAGAAAAAA
1 TAAAAAAATAGAAAAAA
31091317 TAAAAAA
1 TAAAAAA
31091324 CTCCTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 5 0.22
19 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
TAAAAAAATAGAAAAAA
Found at i:31091308 original size:8 final size:8
Alignment explanation
Indices: 31091281--31091323 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
31091271 ATTCAATAAT
31091281 TAAAAAAA
1 TAAAAAAA
31091289 GTATAAATAAA
1 -TA-AAA-AAA
31091300 TAAAAAAA
1 TAAAAAAA
31091308 TAGAAAAAA
1 TA-AAAAAA
31091317 TAAAAAA
1 TAAAAAA
31091324 CTCCTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 10 0.32
9 13 0.42
10 5 0.16
11 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:31091317 original size:17 final size:19
Alignment explanation
Indices: 31091275--31091323 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
31091265 TCTTGCATTC
* *
31091275 AATAATTAAAAAAAGTATA
1 AATAAATAAAAAAAGTAGA
31091294 AATAAATAAAAAAA-TAGA
1 AATAAATAAAAAAAGTAGA
31091312 AA-AAATAAAAAA
1 AATAAATAAAAAA
31091324 CTCCTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 13 0.46
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
AATAAATAAAAAAAGTAGA
Found at i:31092092 original size:22 final size:22
Alignment explanation
Indices: 31092064--31092126 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
31092054 GTAGTTTTTG
*
31092064 TAGTTTTTAGGCATTGTGTAAC
1 TAGTTTTTAGGCATTGCGTAAC
* * *
31092086 TAGTTTTTGGGTATTGCGTTAC
1 TAGTTTTTAGGCATTGCGTAAC
* * *
31092108 TAATTTTTAAGAATTGCGT
1 TAGTTTTTAGGCATTGCGT
31092127 GATTGATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.48
Consensus pattern (22 bp):
TAGTTTTTAGGCATTGCGTAAC
Found at i:31092260 original size:21 final size:22
Alignment explanation
Indices: 31092210--31092302 Score: 98
Period size: 22 Copynumber: 4.3 Consensus size: 22
31092200 AGGCATTGCT
* * *
31092210 TAAAAATTAATCACGCAGTATC
1 TAAAAATCAGTCACGCAATATC
*
31092232 TAAAAATCAGTCACGCAATGTC
1 TAAAAATCAGTCACGCAATATC
* *
31092254 T-AAAATCGGTCACGTAATATC
1 TAAAAATCAGTCACGCAATATC
* * *
31092275 TAAAAATCAGTCTCACACTATC
1 TAAAAATCAGTCACGCAATATC
31092297 TAAAAA
1 TAAAAA
31092303 CTAGTGACAC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
21 18 0.31
22 40 0.69
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (22 bp):
TAAAAATCAGTCACGCAATATC
Found at i:31092313 original size:22 final size:22
Alignment explanation
Indices: 31092210--31092329 Score: 66
Period size: 22 Copynumber: 5.5 Consensus size: 22
31092200 AGGCATTGCT
* * * *
31092210 TAAAAATTAATCACGCAGTATC
1 TAAAAACTAGTCACACAATATC
* *
31092232 TAAAAA-TCAGTCACGCAATGTC
1 TAAAAACT-AGTCACACAATATC
* * **
31092254 TAAAATC-GGTCACGTAATATC
1 TAAAAACTAGTCACACAATATC
* *
31092275 TAAAAA-TCAGTCTCACACTATC
1 TAAAAACT-AGTCACACAATATC
* **
31092297 TAAAAACTAGTGACACAATGCC
1 TAAAAACTAGTCACACAATATC
31092319 TAAAAACTAGT
1 TAAAAACTAGT
31092330 AATGCAACAC
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
21 17 0.23
22 57 0.76
23 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (22 bp):
TAAAAACTAGTCACACAATATC
Found at i:31094339 original size:15 final size:16
Alignment explanation
Indices: 31094309--31094343 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31094299 GTTAATGAAT
*
31094309 TTATTAATTTTTTTAA
1 TTATTAATTATTTTAA
31094325 TTATT-ATTATTTTAA
1 TTATTAATTATTTTAA
31094340 TTAT
1 TTAT
31094344 AACACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTAATTATTTTAA
Found at i:31103928 original size:5 final size:5
Alignment explanation
Indices: 31103920--31103950 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
31103910 AATTTACAGC
*
31103920 CCTAA CCTAA TCTAA CCTAA CCTAA CCTAA C
1 CCTAA CCTAA CCTAA CCTAA CCTAA CCTAA C
31103951 AAACAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (5 bp):
CCTAA
Found at i:31105649 original size:49 final size:48
Alignment explanation
Indices: 31105563--31105661 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 48
31105553 TTAGGCACCC
31105563 TATCGTTCTGTTGAAGGTTTTGTTAATGACACGTAGGTAAGGTTGAGT
1 TATCGTTCTGTTGAAGGTTTTGTTAATGACACGTAGGTAAGGTTGAGT
*
31105611 TATCGTTCTGTTGAAGGTTTTTGTTAATGACACGTAGGTAGGGTTGAGT
1 TATCGTTCTGTTGAAGG-TTTTGTTAATGACACGTAGGTAAGGTTGAGT
31105660 TA
1 TA
31105662 GTCATTTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 17 0.35
49 32 0.65
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.40
Consensus pattern (48 bp):
TATCGTTCTGTTGAAGGTTTTGTTAATGACACGTAGGTAAGGTTGAGT
Found at i:31129837 original size:50 final size:50
Alignment explanation
Indices: 31129763--31129862 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
31129753 AATCAGCATG
31129763 TAGATAGAGTTTGAGACTGATTCAATTAGTATGAGTCAAAGGCTAAGAAA
1 TAGATAGAGTTTGAGACTGATTCAATTAGTATGAGTCAAAGGCTAAGAAA
31129813 TAGATAGAGTTTGAGACTGATTCAATTAGTATGAGTCAAAGGCTAAGAAA
1 TAGATAGAGTTTGAGACTGATTCAATTAGTATGAGTCAAAGGCTAAGAAA
31129863 GTTGAGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (50 bp):
TAGATAGAGTTTGAGACTGATTCAATTAGTATGAGTCAAAGGCTAAGAAA
Found at i:31146677 original size:12 final size:12
Alignment explanation
Indices: 31146660--31146685 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31146650 GAAGAGGGAT
31146660 AACACCGACGCC
1 AACACCGACGCC
31146672 AACACCGACGCC
1 AACACCGACGCC
31146684 AA
1 AA
31146686 GTGCCGTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.46, G:0.15, T:0.00
Consensus pattern (12 bp):
AACACCGACGCC
Found at i:31147847 original size:4 final size:4
Alignment explanation
Indices: 31147833--31147867 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
31147823 CATCTTCTTC
*
31147833 TTCT CTTCT TTCT TTCT TTCC TTCT TTCT TTCT TT
1 TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
31147868 TATCTCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:31147856 original size:16 final size:16
Alignment explanation
Indices: 31147837--31147867 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31147827 TTCTTCTTCT
31147837 CTTCTTTCTTTCTTTC
1 CTTCTTTCTTTCTTTC
31147853 CTTCTTTCTTTCTTT
1 CTTCTTTCTTTCTTT
31147868 TATCTCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
CTTCTTTCTTTCTTTC
Found at i:31151414 original size:2 final size:2
Alignment explanation
Indices: 31151407--31151432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31151397 TTTTATTATG
31151407 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
31151433 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31152598 original size:33 final size:33
Alignment explanation
Indices: 31152556--31152620 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
31152546 TCCCTTATCT
31152556 AGTTATGTACAATTTAATTTAAAAATAAGGGAC
1 AGTTATGTACAATTTAATTTAAAAATAAGGGAC
31152589 AGTTATGTACAATTTAATTTAAAAATAAGGGA
1 AGTTATGTACAATTTAATTTAAAAATAAGGGA
31152621 TATAATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (33 bp):
AGTTATGTACAATTTAATTTAAAAATAAGGGAC
Found at i:31158317 original size:2 final size:2
Alignment explanation
Indices: 31158310--31158339 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31158300 AGGCAAGCAA
31158310 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
31158340 GAGGTGGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31158476 original size:3 final size:3
Alignment explanation
Indices: 31158470--31158507 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31158460 TTACCGAGGC
31158470 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
31158508 GGAAGTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:31180722 original size:2 final size:2
Alignment explanation
Indices: 31180717--31180741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31180707 AAGCACAAGT
31180717 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
31180742 ATTACTGCAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31186389 original size:4 final size:4
Alignment explanation
Indices: 31186382--31186417 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
31186372 CACACACACA
*
31186382 TATG TATG TATG TACG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
31186418 CATATTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:31186438 original size:23 final size:23
Alignment explanation
Indices: 31186408--31186464 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
31186398 TATGTATGTA
31186408 TGTATGTATGCATATTCTATTCT
1 TGTATGTATGCATATTCTATTCT
31186431 TGTATGTATGCATATTCTATTCT
1 TGTATGTATGCATATTCTATTCT
31186454 TAGTCATGTAT
1 T-GT-ATGTAT
31186465 TTGTGCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 24 0.75
24 2 0.06
25 6 0.19
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (23 bp):
TGTATGTATGCATATTCTATTCT
Found at i:31198104 original size:18 final size:17
Alignment explanation
Indices: 31198069--31198113 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
31198059 GAAATTAATT
31198069 ATTAATTGATAATTGATA
1 ATTAATT-ATAATTGATA
*
31198087 CATTAATTATATTTGATA
1 -ATTAATTATAATTGATA
31198105 ATTAGATTA
1 ATTA-ATTA
31198114 AAAGTCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (17 bp):
ATTAATTATAATTGATA
Found at i:31205854 original size:22 final size:22
Alignment explanation
Indices: 31205808--31205855 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
31205798 AGAATGTTTT
*
31205808 AATTTCTTTCAATTGAGCCTTC
1 AATTTCTTTCAATTGAGCCTCC
* * *
31205830 AATTTCTTTTAATTGGGTCTCC
1 AATTTCTTTCAATTGAGCCTCC
31205852 AATT
1 AATT
31205856 GAATGATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (22 bp):
AATTTCTTTCAATTGAGCCTCC
Found at i:31205983 original size:26 final size:26
Alignment explanation
Indices: 31205954--31206026 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
31205944 TACATTCCTG
31205954 TTTGACTCTTCCTTATTTCTCTGGCA
1 TTTGACTCTTCCTTATTTCTCTGGCA
*
31205980 TTTGACTCTTCCTTATTTCTCTGGCG
1 TTTGACTCTTCCTTATTTCTCTGGCA
31206006 TTTGACTCTTCCTTATTTCTC
1 TTTGACTCTTCCTTATTTCTC
31206027 CGAGTTGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.10, C:0.27, G:0.11, T:0.52
Consensus pattern (26 bp):
TTTGACTCTTCCTTATTTCTCTGGCA
Found at i:31232045 original size:124 final size:124
Alignment explanation
Indices: 31231825--31232073 Score: 471
Period size: 124 Copynumber: 2.0 Consensus size: 124
31231815 AGTGCATCCT
**
31231825 TAACTACTCCTTGACTAAAGTCTGGAAATAAAACTAAAGTCGAAAAATCATCATACCCTGGTCAA
1 TAACTACTCCTTGACTAAAGTCCCGAAATAAAACTAAAGTCGAAAAATCATCATACCCTGGTCAA
31231890 GCTGCTAGAAAAAGGGCTCACCAGAAACTCATTTATATCATGTCTGCTATATATATATA
66 GCTGCTAGAAAAAGGGCTCACCAGAAACTCATTTATATCATGTCTGCTATATATATATA
*
31231949 TAACTACTCCTTGACTAAAGTCCCGAAATAAAACTAAAGTCGAAAAGTCATCATACCCTGGTCAA
1 TAACTACTCCTTGACTAAAGTCCCGAAATAAAACTAAAGTCGAAAAATCATCATACCCTGGTCAA
31232014 GCTGCTAGAAAAAGGGCTCACCAGAAACTCATTTATATCATGTCTGCTATATATATATA
66 GCTGCTAGAAAAAGGGCTCACCAGAAACTCATTTATATCATGTCTGCTATATATATATA
31232073 T
1 T
31232074 TAAAAATTTG
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (124 bp):
TAACTACTCCTTGACTAAAGTCCCGAAATAAAACTAAAGTCGAAAAATCATCATACCCTGGTCAA
GCTGCTAGAAAAAGGGCTCACCAGAAACTCATTTATATCATGTCTGCTATATATATATA
Found at i:31236683 original size:74 final size:73
Alignment explanation
Indices: 31236593--31236729 Score: 220
Period size: 74 Copynumber: 1.9 Consensus size: 73
31236583 TTATATAGAG
* *
31236593 TAAATCTTACTAATAATTATAATAAAACATATTTCAATGATCATCATTTGATGAACACACATTTC
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCA-TTAATGAACACACATTTC
31236658 TAATTGGTT
65 TAATTGGTT
* * *
31236667 TAAATCTTATTAATAATTATAATAAAAAATATTTTAATGATCATCATTAATGAACACATATTT
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTAATGAACACACATTT
31236730 ATAAATATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
73 15 0.26
74 43 0.74
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (73 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTAATGAACACACATTTCT
AATTGGTT
Found at i:31238123 original size:3 final size:3
Alignment explanation
Indices: 31238115--31238143 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31238105 ATGGTTTCAT
31238115 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
31238144 CGTATGGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31240978 original size:15 final size:14
Alignment explanation
Indices: 31240952--31240986 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
31240942 AACATAAAAT
31240952 TAATATTATATATA
1 TAATATTATATATA
31240966 TAATATATATATATA
1 TAATAT-TATATATA
31240981 TAATAT
1 TAATAT
31240987 GACACGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATATTATATATA
Found at i:31241058 original size:12 final size:12
Alignment explanation
Indices: 31241041--31241083 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
31241031 TTAACCTTAC
31241041 TTAAATAATTTT
1 TTAAATAATTTT
31241053 TTAAATAATTATT
1 TTAAATAATT-TT
31241066 TT-AATAAGTTTT
1 TTAAATAA-TTTT
31241078 TTAAAT
1 TTAAAT
31241084 TTTGTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTAAATAATTTT
Found at i:31241191 original size:30 final size:30
Alignment explanation
Indices: 31241135--31241197 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
31241125 AATTTTGAAC
31241135 TTTTGTTTTGTTATATTTGATGTTAT-ATTA
1 TTTTGTTTTGTTATATTT-ATGTTATAATTA
*
31241165 TTTTGTTTTGTTAT-TATTATTTTTATAATTA
1 TTTTGTTTTGTTATAT-TTA-TGTTATAATTA
31241196 TT
1 TT
31241198 GATTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 21 0.72
31 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.70
Consensus pattern (30 bp):
TTTTGTTTTGTTATATTTATGTTATAATTA
Found at i:31245243 original size:31 final size:30
Alignment explanation
Indices: 31245203--31245316 Score: 138
Period size: 31 Copynumber: 3.7 Consensus size: 30
31245193 GGTTAAACGT
*
31245203 TGGATGAATTCTTAAGATATTTAAATCTCGG
1 TGGAGGAATTCTTAAGATATTTAAA-CTCGG
* *
31245234 TAGAGGAATTCTTAAGATATTTGAACTTCGG
1 TGGAGGAATTCTTAAGATATTTAAAC-TCGG
* ** *
31245265 TGGAGGAATTTTTAAGATATCAAAACCTCGA
1 TGGAGGAATTCTTAAGATATTTAAA-CTCGG
31245296 TGGAGGAATTCTTAAGATATT
1 TGGAGGAATTCTTAAGATATT
31245317 GAAGTTTCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.01
31 68 0.97
32 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (30 bp):
TGGAGGAATTCTTAAGATATTTAAACTCGG
Found at i:31245331 original size:62 final size:62
Alignment explanation
Indices: 31245203--31245337 Score: 164
Period size: 62 Copynumber: 2.2 Consensus size: 62
31245193 GGTTAAACGT
* * ** * * **
31245203 TGGATGAATTCTTAAGATATTTAAATCTCGGTAGAGGAATTCTTAAGATATTTGAACTTCGG
1 TGGAGGAATTTTTAAGATATCAAAACCTCGATAGAGGAATTCTTAAGATATTTGAACTTCAA
* *
31245265 TGGAGGAATTTTTAAGATATCAAAACCTCGATGGAGGAATTCTTAAGATA-TTGAAGTTTCAA
1 TGGAGGAATTTTTAAGATATCAAAACCTCGATAGAGGAATTCTTAAGATATTTGAA-CTTCAA
31245327 TGGAGGAATTT
1 TGGAGGAATTT
31245338 AGAGTCTCGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
61 5 0.08
62 57 0.92
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (62 bp):
TGGAGGAATTTTTAAGATATCAAAACCTCGATAGAGGAATTCTTAAGATATTTGAACTTCAA
Found at i:31245525 original size:111 final size:110
Alignment explanation
Indices: 31245379--31245621 Score: 301
Period size: 111 Copynumber: 2.2 Consensus size: 110
31245369 GAAGCCTTGG
* *
31245379 TGGAAAAGTTATAAAAAGTTTTAAAGACTCGATGGAAGAATTCTCATTTCCTTTTAAAGTTTAAA
1 TGGAGAAGTT-TAAAAAGTTTTAAAGACTCAATGGAAGAATTCTCATTTCCTTTTAAAGTTTAAA
* *
31245444 G-CTTCGATGAAGGAGTTTTTATTTCACTTTTT-ATTTGGAGTCTTAA
65 GCCTT-GAAGAAGGAGTTTTTATTTCA-TTTTTAATTTGGAGTCTCAA
* * * * *
31245490 TGGAGAAGTTGTAAAAAGTTTTAAAGCCTTAATGGAGGAATTGTCATTTCCTTTTAAAGTTTGAA
1 TGGAGAAGTT-TAAAAAGTTTTAAAGACTCAATGGAAGAATTCTCATTTCCTTTTAAAGTTTAAA
* *
31245555 GCCTTGAAGGAGGAGTTTTTATTTTATTTTTAAATTTGGAGTCTCAA
65 GCCTTGAAGAAGGAGTTTTTATTTCATTTTT-AATTTGGAGTCTCAA
* * *
31245602 TGTAGGAGATTAAAAAGTTT
1 TGGAGAAGTTTAAAAAGTTT
31245622 CATAACCTTG
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
110 5 0.04
111 86 0.75
112 23 0.20
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (110 bp):
TGGAGAAGTTTAAAAAGTTTTAAAGACTCAATGGAAGAATTCTCATTTCCTTTTAAAGTTTAAAG
CCTTGAAGAAGGAGTTTTTATTTCATTTTTAATTTGGAGTCTCAA
Found at i:31245703 original size:40 final size:41
Alignment explanation
Indices: 31245668--31245750 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 41
31245658 GCCTTGGTAG
31245668 AGGAATTTTCATTTC-CTTTTAAAGTTTGAAGCCTTGATGA
1 AGGAATTTTCATTTCACTTTTAAAGTTTGAAGCCTTGATGA
* * * *
31245708 ATGAGTTTTCATTTCATTTTTAAA-TTTGAAGCCTCGATAGA
1 AGGAATTTTCATTTCACTTTTAAAGTTTGAAGCCTTGAT-GA
31245749 AG
1 AG
31245751 AGATTGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 26 0.72
41 10 0.28
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (41 bp):
AGGAATTTTCATTTCACTTTTAAAGTTTGAAGCCTTGATGA
Found at i:31245793 original size:32 final size:32
Alignment explanation
Indices: 31245757--31245817 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
31245747 GAAGAGATTG
* * *
31245757 AAAAGTTTTGAGGCCTTGTTGGAGGAGTTGTA
1 AAAAGTTTTAAAGCCTTGATGGAGGAGTTGTA
31245789 AAAAGTTTTAAAGCCTTGATGGAGGAGTT
1 AAAAGTTTTAAAGCCTTGATGGAGGAGTT
31245818 CTCATTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.31, T:0.33
Consensus pattern (32 bp):
AAAAGTTTTAAAGCCTTGATGGAGGAGTTGTA
Found at i:31245849 original size:143 final size:142
Alignment explanation
Indices: 31245490--31245833 Score: 440
Period size: 143 Copynumber: 2.4 Consensus size: 142
31245480 GGAGTCTTAA
* * *
31245490 TGGAGAAGTTGTAAAAAGTTTTAAAGCCTTAATGGAGGAATTGTCATTTCCTTTTAAAGTTTGAA
1 TGGAGGAGTTGTAAAAAGTTTTAAAGCCTTGATGGAGGAATTCTCATTTCCTTTTAAAGTTTGAA
* * * * * * *
31245555 GCCTTGAAGGAGGAGTTTTTATTTTATTTTTAAATTTGGAGTCTCAATGTAGGAGATTAAAAAGT
66 GCCTTGATGAAGGAGTTTTCATTTCATTTTTAAATTTGAAGCCTCAATGTAAGAGATTAAAAAGT
31245620 TTCATAACCTTGG
131 TT-ATAACCTTGG
* * * * * *
31245633 TGAAAGAGTTGTAAAAAGTTATAAAGCCTTGGTAGAGGAATTTTCATTTCCTTTTAAAGTTTGAA
1 TGGAGGAGTTGTAAAAAGTTTTAAAGCCTTGATGGAGGAATTCTCATTTCCTTTTAAAGTTTGAA
* * *
31245698 GCCTTGATGAATGAGTTTTCATTTCATTTTTAAATTTGAAGCCTCGATAG-AAGAGATTGAAAAG
66 GCCTTGATGAAGGAGTTTTCATTTCATTTTTAAATTTGAAGCCTCAAT-GTAAGAGATTAAAAAG
* *
31245762 TTT-TGAGGCCTTGT
130 TTTAT-A-ACCTTGG
*
31245776 TGGAGGAGTTGTAAAAAGTTTTAAAGCCTTGATGGAGGAGTTCTCATTTCCTTTTAAA
1 TGGAGGAGTTGTAAAAAGTTTTAAAGCCTTGATGGAGGAATTCTCATTTCCTTTTAAA
31245834 TTGTGGAGCT
Statistics
Matches: 171, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
141 1 0.01
142 1 0.01
143 168 0.98
144 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (142 bp):
TGGAGGAGTTGTAAAAAGTTTTAAAGCCTTGATGGAGGAATTCTCATTTCCTTTTAAAGTTTGAA
GCCTTGATGAAGGAGTTTTCATTTCATTTTTAAATTTGAAGCCTCAATGTAAGAGATTAAAAAGT
TTATAACCTTGG
Found at i:31251740 original size:46 final size:46
Alignment explanation
Indices: 31251688--31251777 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
31251678 AAAAAAAAGA
*
31251688 AAAAAAAGAGAGTTCAATGTGAAAACCCAAAAAGGCAATTTGAATTTC
1 AAAAAAA-A-AGTTCAAGGTGAAAACCCAAAAAGGCAATTTGAATTTC
* * *
31251736 AAAAAAAAAGTTCACGGTGAAAACTCGAAAAGGCAATTTGAA
1 AAAAAAAAAGTTCAAGGTGAAAACCCAAAAAGGCAATTTGAA
31251778 CCCAAAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 30 0.79
47 1 0.03
48 7 0.18
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.19
Consensus pattern (46 bp):
AAAAAAAAAGTTCAAGGTGAAAACCCAAAAAGGCAATTTGAATTTC
Found at i:31252553 original size:31 final size:30
Alignment explanation
Indices: 31252495--31252746 Score: 164
Period size: 31 Copynumber: 8.1 Consensus size: 30
31252485 TTTAAAAAAG
* * *
31252495 TATTGGAACCT-TGTTGGAGGAGATCTTAAAA
1 TATTGGAACCTCAG-TGGAGGA-TTCTTAAGA
*
31252526 TATTGGATCCTCAGTGGACGGATTCTTAAGA
1 TATTGGAACCTCAGTGGA-GGATTCTTAAGA
* * *
31252557 TGTTGGATCCTCAGTAGAGAGATTCTTAAGA
1 TATTGGAACCTCAGTGGAG-GATTCTTAAGA
* * * *
31252588 TATTGGAACCTTAATGGAGGAATTTTTTAGA
1 TATTGGAACCTCAGTGGAGG-ATTCTTAAGA
* * *
31252619 TATTGGAACCTCGGTGGACGAATTTTTAAGA
1 TATTGGAACCTCAGTGGA-GGATTCTTAAGA
* ** **
31252650 TATTGGAACCTCAATCAAAAAATTCTTAAGA
1 TATTGGAACCTCAGT-GGAGGATTCTTAAGA
*** *
31252681 TATCAAAACCTCGGTGGAGGAATTCTTAAGA
1 TATTGGAACCTCAGTGGAGG-ATTCTTAAGA
* ** * *
31252712 TTTTAAAACCTCGGTGGAAGAATTCTTAAGA
1 TATTGGAACCTCAGTGG-AGGATTCTTAAGA
31252743 TATT
1 TATT
31252747 AAAGCTTCGG
Statistics
Matches: 176, Mismatches: 37, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
30 3 0.02
31 165 0.94
32 8 0.05
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (30 bp):
TATTGGAACCTCAGTGGAGGATTCTTAAGA
Found at i:31252656 original size:93 final size:93
Alignment explanation
Indices: 31252509--31252746 Score: 246
Period size: 93 Copynumber: 2.6 Consensus size: 93
31252499 GGAACCTTGT
* * * * * * *
31252509 TGGAGGAGA-TCTTAAAATATTGGATCCTCAGTGGACGGATTCTTAAGATGTTGGATCCTCAGT-
1 TGGAGGA-ATTCTTAAGATATTGGAACCTCGGTGGACGAATTCTTAAGATATTGGAACCTCAATC
* * *** *
31252572 AGAGAGATTCTTAAGATATTGGAACCTTAA
65 A-AAAAATTCTTAAGATATCAAAACCTCAA
* * *
31252602 TGGAGGAATTTTTTAGATATTGGAACCTCGGTGGACGAATTTTTAAGATATTGGAACCTCAATCA
1 TGGAGGAATTCTTAAGATATTGGAACCTCGGTGGACGAATTCTTAAGATATTGGAACCTCAATCA
**
31252667 AAAAATTCTTAAGATATCAAAACCTCGG
66 AAAAATTCTTAAGATATCAAAACCTCAA
* ** *
31252695 TGGAGGAATTCTTAAGATTTTAAAACCTCGGTGGAAGAATTCTTAAGATATT
1 TGGAGGAATTCTTAAGATATTGGAACCTCGGTGGACGAATTCTTAAGATATT
31252747 AAAGCTTCGG
Statistics
Matches: 118, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
92 1 0.01
93 116 0.98
94 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (93 bp):
TGGAGGAATTCTTAAGATATTGGAACCTCGGTGGACGAATTCTTAAGATATTGGAACCTCAATCA
AAAAATTCTTAAGATATCAAAACCTCAA
Found at i:31252749 original size:31 final size:31
Alignment explanation
Indices: 31252578--31252766 Score: 162
Period size: 31 Copynumber: 6.1 Consensus size: 31
31252568 CAGTAGAGAG
** ***
31252578 ATTCTTAAGATATTGGAACCTTAATGGAGGA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
* * ** *
31252609 ATTTTTTAGATATTGGAACCTCGGTGGACGA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
* ** ** ** **
31252640 ATTTTTAAGATATTGGAACCTCAATCAAAAA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
*
31252671 ATTCTTAAGATATCAAAACCTCGGTGGAGGA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
* *
31252702 ATTCTTAAGATTTTAAAACCTCGGTGGAAGA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
* *
31252733 ATTCTTAAGATATTAAAGCTTCGGTGGAGGA
1 ATTCTTAAGATATTAAAACCTCGGTGGAGGA
31252764 ATT
1 ATT
31252767 TAGAGTCTTG
Statistics
Matches: 128, Mismatches: 30, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 128 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (31 bp):
ATTCTTAAGATATTAAAACCTCGGTGGAGGA
Found at i:31253320 original size:143 final size:143
Alignment explanation
Indices: 31252778--31253322 Score: 594
Period size: 143 Copynumber: 3.8 Consensus size: 143
31252768 AGAGTCTTGG
* * * *
31252778 TGGAGGAGATTAGAAAGTTTCAAGAGCCTCAATGAAGGAGTTGTAAAAAGTTTTAAAACCTTGGT
1 TGGAGGAGATTAAAAAGTTT-TAGAGCCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACCTTGGT
* * * * * * *
31252843 GGAGGAACTCTAATTTCCCTTTAAAGTTTGAAGCCTAGATGGAGGCGTTTTTATTTCATTTTTAA
65 GGAGGAATTCTCATTTCCTTTTAAAGTTTGAAGGCTCGATGAAGGAGTTTTTATTTCATTTTTAA
31252908 ATTTGAAGTCTTAA
130 ATTTGAAGTCTTAA
* * * * **
31252922 TGGAGGAGATTAAAAAGTTTTGGAGCCTCGATGAAGGAGTTGTACAAAGTTTCAAAGTCTTGGTG
1 TGGAGGAGATTAAAAAGTTTTAGAGCCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACCTTGGTG
* * * * * **
31252987 GAGCAATTCTCATTTCTTTTTAAAGTTTGCA-GCATTGACGGGGGAGTTTTTATTTCATTTTTAA
66 GAGGAATTCTCATTTCCTTTTAAAGTTTGAAGGC-TCGATGAAGGAGTTTTTATTTCATTTTTAA
* *
31253051 ATTT-ACAGTCTCAG
130 ATTTGA-AGTCTTAA
* * * * * * * *
31253065 TGGAGGAAATTAAAAAGTTTCAGAGCTTCGATGGAAGAGTTATAGAAAGTTTTAAAGCCTTGATG
1 TGGAGGAGATTAAAAAGTTTTAGAGCCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACCTTGGTG
* * *
31253130 AAGGAATT-TCCATTTCCTTTTAAAGTTTGAAGTCTCGATGAAGGAGTTTTTATTTTATTTTTAA
66 GAGGAATTCT-CATTTCCTTTTAAAGTTTGAAGGCTCGATGAAGGAGTTTTTATTTCATTTTTAA
* *
31253194 ATTTGGAGCCTTAA
130 ATTTGAAGTCTTAA
* * * *
31253208 TGAAGGAGATTAAAAAGTTTTAGAACCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACTTTGGTA
1 TGGAGGAGATTAAAAAGTTTTAGAGCCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACCTTGGTG
* * * *
31253273 GAGGAATTATCATTTCCTTTT-AAGTTATGGAGGCTCGTTGAAAGAGTTTT
66 GAGGAATTCTCATTTCCTTTTAAAGTT-TGAAGGCTCGATGAAGGAGTTTT
31253323 CAATTCTTTT
Statistics
Matches: 331, Mismatches: 63, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
142 8 0.02
143 302 0.91
144 21 0.06
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.36
Consensus pattern (143 bp):
TGGAGGAGATTAAAAAGTTTTAGAGCCTCGATGAAAGAGTTGTAAAAAGTTTTAAAACCTTGGTG
GAGGAATTCTCATTTCCTTTTAAAGTTTGAAGGCTCGATGAAGGAGTTTTTATTTCATTTTTAAA
TTTGAAGTCTTAA
Found at i:31253561 original size:17 final size:17
Alignment explanation
Indices: 31253539--31253576 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31253529 CTTAGGAATG
*
31253539 ATGGGTTTATAACCCAA
1 ATGGGTTCATAACCCAA
*
31253556 ATGGGTTCATAACCTAA
1 ATGGGTTCATAACCCAA
31253573 ATGG
1 ATGG
31253577 TGTTGGGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (17 bp):
ATGGGTTCATAACCCAA
Found at i:31253742 original size:22 final size:21
Alignment explanation
Indices: 31253711--31253755 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
31253701 AAGGAAGATT
*
31253711 AAAAGGAAAAAAGATCAATCGA
1 AAAAGAAAAAAAGATCAA-CGA
31253733 AAAAGAAAAAAAGATCAACGA
1 AAAAGAAAAAAAGATCAACGA
31253754 AA
1 AA
31253756 TCCCTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.69, C:0.09, G:0.16, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAAAAGATCAACGA
Found at i:31254601 original size:19 final size:19
Alignment explanation
Indices: 31254554--31254589 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31254544 TTCATGTTAC
31254554 TTTAT-TTTTTTATTTATG
1 TTTATGTTTTTTATTTATG
31254572 TTTATGTTTTTTATTTAT
1 TTTATGTTTTTTATTTAT
31254590 TTATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTATGTTTTTTATTTATG
Found at i:31262924 original size:15 final size:15
Alignment explanation
Indices: 31262904--31262933 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31262894 AGTTATATAA
31262904 AACTTTAAATATTCT
1 AACTTTAAATATTCT
*
31262919 AACTTTAAATGTTCT
1 AACTTTAAATATTCT
31262934 TTTTGCTTTG
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:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (15 bp):
AACTTTAAATATTCT
Found at i:31279509 original size:105 final size:106
Alignment explanation
Indices: 31279318--31279518 Score: 296
Period size: 105 Copynumber: 1.9 Consensus size: 106
31279308 TTGAGTTGTG
* * * *
31279318 TAGCGCATTAGAGGGTCATTTCTGACTTTTTGTGGTTCTCATTTCGAATTGTGAATTCAACAATC
1 TAGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCTCATTTCAAATTGTGAATTCAACAAAC
31279383 TCTAAAGCATATTCAAGTCATG-CCTTTTTTCTGGGTTCTT
66 TCTAAAGCATATTCAAGTCATGCCCTTTTTTCTGGGTTCTT
* * * **
31279423 TAGCACATTAGAGTGTCATTTCTGACTTTTTGTAGTTCTTATTTCAAATTTTGAATTGGACAAAC
1 TAGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCTCATTTCAAATTGTGAATTCAACAAAC
* *
31279488 TCTAATGCATATTCAATTCATGCCCTTTTTT
66 TCTAAAGCATATTCAAGTCATGCCCTTTTTT
31279519 TCTTGGTGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 76 0.90
106 8 0.10
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (106 bp):
TAGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCTCATTTCAAATTGTGAATTCAACAAAC
TCTAAAGCATATTCAAGTCATGCCCTTTTTTCTGGGTTCTT
Found at i:31298113 original size:16 final size:16
Alignment explanation
Indices: 31298092--31298122 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31298082 AATAATAATA
*
31298092 TTATTTTTATTTTTAT
1 TTATTTTTAATTTTAT
31298108 TTATTTTTAATTTTA
1 TTATTTTTAATTTTA
31298123 AAATATTAAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTAATTTTAT
Found at i:31299990 original size:251 final size:250
Alignment explanation
Indices: 31299345--31300905 Score: 1799
Period size: 251 Copynumber: 6.3 Consensus size: 250
31299335 AAGATTAACA
* * * * *
31299345 TAAAAACTCATAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGTGTAAGAATTAACGT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
* * * * *
31299410 AATAAGTCAATTAAAG-AAAAAAATCTAATTTTAATGAAAAATAAATATTTAAATTTATATTCTT
66 AACAAGTCAATT-AAGTAAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTC
* *
31299474 AGACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAATAATAAT-A--AT-AAAAT
130 AGAATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT
* * * ** *
31299535 AATTGTAGTTCAAAATTGATATATATAAGTCTTGACACAAAACTATAACAATTGACG
195 AATTATAGTTCAAAATTGATATAAAAAAGT-TTGACGTAAAACTGTAACAATTGACG
* *
31299592 TAAAAACTTATAAAGGTGGAATAACTAAACTTTAAATC-T----T-AATGTATGAGAGTTAACGT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
* * * *
31299651 AACAAGTCAATTAAGTAAAAAAATCTAATTTTAGTGAAAAATAAAAATTTAAATTTATATTTTCA
66 AACAAGTCAATTAAGTAAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCA
*
31299716 -AACTAAAAGTGTTTAATGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT
131 GAA-TAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT
* * *
31299780 AATTATAGTTTAAAATTGATATAAAAAAGTTTAACGTAAAACTGTAACAATTGATG
195 AATTATAGTTCAAAATTGATATAAAAAAGTTTGACGTAAAACTGTAACAATTGACG
* * * * * *
31299836 TGAAAATTTATAAATGTGGAATAATTAAATTTTAAATCTTAAAGTAAATGTGTGAGAGTTAACAT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
* * * * *
31299901 AACAAGTCCATTAAATAAAAAAAATATAATTTTAGTAAAAAAAAAACATTTATATTTATATTCT-
66 AACAAGTCAATTAAGT-AAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTC
31299965 AGGAATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT-AGGATAAAAA
130 A-GAATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAA
* * *
31300029 TAATTATAGTTCAAAATTGACATAGAAAAACG-TTAACGTAAAACTGTAAGAATTGACG
194 TAATTATAGTTCAAAATTGATATA-AAAAA-GTTTGACGTAAAACTGTAACAATTGACG
* * * * * *
31300087 TAAAAACTTATAAAGGTAGAATAATTAAATTTTAAATCTTAACGTAAATGCGTGAAAATTAATGT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
* *
31300152 AACAAGTCAATTAAGTAAAAAAAATATAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTC
66 AACAAGTCAATTAAGT-AAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTC
31300217 A-AACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAA
130 AGAA-TAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAA
* * * * * * *
31300281 TAATTATAGTTTAAAATTGACATAGATAAGTCTTGACGTAAAACTGTAAGAATTAACA
194 TAATTATAGTTCAAAATTGATATAAAAAAGT-TTGACGTAAAACTGTAACAATTGACG
* * * * * * **
31300339 TAAAACCTTATAAAGGTAGAATAACTAAAGTTTAAATCTTAATGTAAATGTGTAATAGTTAATAT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
*
31300404 AACAAGTCAATTAAGTTAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCA
66 AACAAGTCAATTAAGTAAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCA
* *
31300469 -AGCTAAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAA-AA-AATAA--A-AAAAAT
131 GA-ATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT
* * * *
31300528 AATTATAGTTCAAAATTAATATAAATAAGCCTTGACGTAAAACTGCAACAATTGACG
195 AATTATAGTTCAAAATTGATATAAAAAAG-TTTGACGTAAAACTGTAACAATTGACG
* * * * *
31300585 TAAAAACTTATAAAGGTGGAATAATTATATTTTAAATTTTAACGTAAATGTGTTAGAGTTAATGT
1 TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
* * * * * * * *
31300650 AATAAGTTAATCAAGTAAAAAAATCTAATTTTAAT-AAAAATAAACATTTATATTTATATTATCA
66 AACAAGTCAATTAAGTAAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCA
** * * * * * * **
31300714 GGCTAAAAGTATATAACGATATTCAAATTTTTA-TTTTAAATAAAAAATAATAAAGATAACGATA
131 GAATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
* * * * * ** * *
31300778 ATTGTAGTT-AAAAGTT-ACTATTGAAAATGCTTGACATAAAGTTGTAAGAATTGACT
196 ATTATAGTTCAAAA-TTGA-TA-TAAAAAAGTTTGACGTAAAACTGTAACAATTGACG
* * * ** *
31300834 TAAAATCTTATAAAAGTGGAATAAGC-AAATTTAAAATCTTAACGTAAACATATGAGAGTTAACG
1 TAAAAACTTATAAAGGTGGAATAA-CTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACG
31300898 TAACAAGT
65 TAACAAGT
31300906 AATAATAATA
Statistics
Matches: 1142, Mismatches: 138, Indels: 66
0.85 0.10 0.05
Matches are distributed among these distances:
240 4 0.00
241 119 0.10
242 2 0.00
244 67 0.06
245 86 0.08
246 143 0.13
247 35 0.03
248 6 0.01
249 103 0.09
250 74 0.06
251 371 0.32
252 132 0.12
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (250 bp):
TAAAAACTTATAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGT
AACAAGTCAATTAAGTAAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCA
GAATAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
ATTATAGTTCAAAATTGATATAAAAAAGTTTGACGTAAAACTGTAACAATTGACG
Found at i:31300826 original size:747 final size:741
Alignment explanation
Indices: 31299345--31300881 Score: 2058
Period size: 747 Copynumber: 2.1 Consensus size: 741
31299335 AAGATTAACA
* *
31299345 TAAAAACTCATAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGTGTAAGAATTAACGT
1 TAAAAACTTATAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGCGTAAGAATTAACGT
* * * *
31299410 AATAAGTCAATTAAAGAAAAAAATCTAATTTTAATGAAAAATAAATATTTAAATTTATATTCTTA
66 AACAAGTCAATTAAAGAAAAAAATATAATTTTAATGAAAAACAAATATTTAAATTTATATTCTCA
* * *
31299475 GACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAATAATAATAATAAAATAATTG
131 AACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAATAAAATAATTA
* * * *
31299540 TAGTTCAAAATTGATATATATAAGTCTTGACACAAAACTATAACAATTGACGTAAAAACTTATAA
196 TAGTTCAAAATTGACATAGATAAGTCTTGACACAAAACTATAACAATTAACATAAAAACTTATAA
* *
31299605 AGGTGGAATAACTAAACTTTAAATCTTAATGTATGAGAGTTAACGTAACAAGTCAATTAAGTAAA
261 AGGTAGAATAACTAAACTTTAAATCTTAATGTATGAGAGTTAACATAACAAGTCAATTAAGTAAA
* * * *
31299670 AAAATCTAATTTTAGTGAAAAATAAAAATTTAAATTTATATTTTCAAACTAAAAGTGTTTAATGA
326 AAAATATAATTTTAGTAAAAAATAAAAATTTAAATTTATATTCTCAAACTAAAAGTGTTTAACGA
* *
31299735 TATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTTAAAATTGAT
391 TATACAAATTTTAATTTTTAAATAAAGAATAATAA-GATAAAAATAATTATAGTTCAAAATTAAT
* * * * * *
31299800 ATAAAAAAGTTTAACGTAAAACTGTAACAATTGATGTGAAAATTTATAAATGTGGAATAATTAAA
455 ATAAAAAAGCTTAACGTAAAACTGCAACAATTGACGTAAAAACTTATAAAGGTGGAATAATTAAA
* *
31299865 TTTTAAATCTTAAAGTAAATGTGTGAGAGTTAACATAACAAGTCCATTAAATAAAAAAAATATAA
520 TTTTAAATCTTAAAGTAAATGTGTGAGAGTTAACATAACAAGTCAATCAAATAAAAAAAATATAA
* * * *
31299930 TTTTAGTAAAAAAAAAACATTTATATTTATATTCTAGGAATAAAAGTGTTTAACGATATACAAAT
585 TTTTAATAAAAAAAAAACATTTATATTTATATTATAGGAATAAAAGTATATAACGATATACAAAT
* *
31299995 TTTAATTTTTAAATAAAGAATAATAGGATAAAAATAATTATAGTTCAAAATTGACATAGAAAAAC
650 TTTAATTTTTAAATAAAAAATAATAAGATAAAAATAATTATAGTTCAAAATTGACATAGAAAAAC
*
31300060 GTTAACGTAAAACTGTAAGAATTGACG
715 GTTAACATAAAACTGTAAGAATTGACG
* * *
31300087 TAAAAACTTATAAAGGTAGAATAATTAAATTTTAAATCTTAACGTAAATGCGTGAA-AATTAATG
1 TAAAAACTTATAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGCGT-AAGAATTAACG
*
31300151 TAACAAGTCAATT-AAGTAAAAAAAATATAATTTTAGTGAAAAACAAATATTTAAATTTATATTC
65 TAACAAGTCAATTAAAG--AAAAAAATATAATTTTAATGAAAAACAAATATTTAAATTTATATTC
31300215 TCAAACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
128 TCAAACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT-A--AT-AAA
* ** * * *
31300280 ATAATTATAGTTTAAAATTGACATAGATAAGTCTTGACGTAAAACTGTAAGAATTAACATAAAAC
189 ATAATTATAGTTCAAAATTGACATAGATAAGTCTTGACACAAAACTATAACAATTAACATAAAAA
* * *
31300345 CTTATAAAGGTAGAATAACTAAAGTTTAAATCTTAATGTAAATGTGTAATAGTTAATATAACAAG
254 CTTATAAAGGTAGAATAACTAAACTTTAAATCTTAATGT--A--TG--AGAGTTAACATAACAAG
* * *
31300410 TCAATTAAGTTAAAAAATATAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTCAAGCTAA
313 TCAATTAAGTAAAAAAATATAATTTTAGTAAAAAATAAAAATTTAAATTTATATTCTCAAACTAA
*
31300475 AAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAA-AA-AATAA-A-AAAAATAATTATAG
378 AAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGATAAAAATAATTATAG
* *
31300536 TTCAAAATTAATATAAATAAGCCTTGACGTAAAACTGCAACAATTGACGTAAAAACTTATAAAGG
443 TTCAAAATTAATATAAAAAAG-CTTAACGTAAAACTGCAACAATTGACGTAAAAACTTATAAAGG
* * * * ** * * *
31300601 TGGAATAATTATATTTTAAATTTTAACGTAAATGTGTTAGAGTTAATGTAATAAGTTAATCAAGT
507 TGGAATAATTAAATTTTAAATCTTAAAGTAAATGTGTGAGAGTTAACATAACAAGTCAATCAAAT
* * *
31300666 -AAAAAAATCTAATTTTAAT-AAAAATAAACATTTATATTTATATTATCAGG-CTAAAAGTATAT
572 AAAAAAAATATAATTTTAATAAAAAAAAAACATTTATATTTATATTAT-AGGAATAAAAGTATAT
* * ** *
31300728 AACGATATTCAAATTTTTA-TTTTAAATAAAAAATAATAAAGATAACGATAATTGTAGTT-AAAA
636 AACGATATACAAATTTTAATTTTTAAATAAAAAATAAT-AAGATAAAAATAATTATAGTTCAAAA
* * * ** *
31300791 GTT-ACTATTG-AAAATGCTTGACATAAAGTTGTAAGAATTGACT
700 -TTGAC-ATAGAAAAACG-TTAACATAAAACTGTAAGAATTGACG
* * *
31300834 TAAAATCTTATAAAAGTGGAATAAGC-AAATTTAAAATCTTAACGTAAA
1 TAAAAACTTATAAAGGTAGAATAA-CTAAATTTAAAATCTTAACGTAAA
31300882 CATATGAGAG
Statistics
Matches: 692, Mismatches: 83, Indels: 35
0.85 0.10 0.04
Matches are distributed among these distances:
741 3 0.00
742 68 0.10
743 97 0.14
744 1 0.00
746 30 0.04
747 230 0.33
748 52 0.08
749 92 0.13
751 7 0.01
752 2 0.00
753 110 0.16
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (741 bp):
TAAAAACTTATAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGCGTAAGAATTAACGT
AACAAGTCAATTAAAGAAAAAAATATAATTTTAATGAAAAACAAATATTTAAATTTATATTCTCA
AACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAATAAAATAATTA
TAGTTCAAAATTGACATAGATAAGTCTTGACACAAAACTATAACAATTAACATAAAAACTTATAA
AGGTAGAATAACTAAACTTTAAATCTTAATGTATGAGAGTTAACATAACAAGTCAATTAAGTAAA
AAAATATAATTTTAGTAAAAAATAAAAATTTAAATTTATATTCTCAAACTAAAAGTGTTTAACGA
TATACAAATTTTAATTTTTAAATAAAGAATAATAAGATAAAAATAATTATAGTTCAAAATTAATA
TAAAAAAGCTTAACGTAAAACTGCAACAATTGACGTAAAAACTTATAAAGGTGGAATAATTAAAT
TTTAAATCTTAAAGTAAATGTGTGAGAGTTAACATAACAAGTCAATCAAATAAAAAAAATATAAT
TTTAATAAAAAAAAAACATTTATATTTATATTATAGGAATAAAAGTATATAACGATATACAAATT
TTAATTTTTAAATAAAAAATAATAAGATAAAAATAATTATAGTTCAAAATTGACATAGAAAAACG
TTAACATAAAACTGTAAGAATTGACG
Found at i:31301754 original size:26 final size:25
Alignment explanation
Indices: 31301704--31301754 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
31301694 ATGTTCCCTA
*
31301704 GGGAGCACAAATCCAATGCTCCTTG
1 GGGAGCACAAATCCAAAGCTCCTTG
* *
31301729 GGGAGCACCAGATCTAAAGCTCCTTG
1 GGGAGCA-CAAATCCAAAGCTCCTTG
31301755 AGAAATTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (25 bp):
GGGAGCACAAATCCAAAGCTCCTTG
Found at i:31314873 original size:18 final size:17
Alignment explanation
Indices: 31314847--31314881 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31314837 ACCTGCAATT
31314847 GGGGAAGCAATTGGATTA
1 GGGGAAGCAATT-GATTA
*
31314865 GGGGCAGCAATTGATTA
1 GGGGAAGCAATTGATTA
31314882 CTTGTCTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.09, G:0.37, T:0.23
Consensus pattern (17 bp):
GGGGAAGCAATTGATTA
Found at i:31316112 original size:20 final size:20
Alignment explanation
Indices: 31316074--31316112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31316064 TTTACACTAT
***
31316074 TATCTTGTGTAAGTGTTCGG
1 TATCTTGTGTAACAATTCGG
31316094 TATCTTGTGTAACAATTCG
1 TATCTTGTGTAACAATTCG
31316113 ACGGACACAC
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:0.21, C:0.13, G:0.23, T:0.44
Consensus pattern (20 bp):
TATCTTGTGTAACAATTCGG
Found at i:31328387 original size:2 final size:2
Alignment explanation
Indices: 31328368--31328432 Score: 75
Period size: 2 Copynumber: 34.0 Consensus size: 2
31328358 CTTTAAGTAC
31328368 TA TA T- TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
31328406 TA GA TA TA TA TA TA TGC TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA
31328433 GTGATAGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
1 4 0.07
2 49 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31328407 original size:19 final size:19
Alignment explanation
Indices: 31328368--31328432 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
31328358 CTTTAAGTAC
31328368 TATAT-TATATA-ATA-AT
1 TATATATATATATATATAT
31328384 ATATATATATATATATATAT
1 -TATATATATATATATATAT
* **
31328404 TATAGATATATATATATGC
1 TATATATATATATATATAT
31328423 TATATATATA
1 TATATATATA
31328433 GTGATAGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.12
18 6 0.15
19 28 0.68
20 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:31333330 original size:20 final size:22
Alignment explanation
Indices: 31333286--31333331 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
31333276 AATATTTAGT
31333286 ATATAAATAAAGTAATAATTAA
1 ATATAAATAAAGTAATAATTAA
31333308 ATATAAA-AAA-TAAT-ATTATA
1 ATATAAATAAAGTAATAATTA-A
31333328 ATAT
1 ATAT
31333332 TTAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 3 0.13
22 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAATAAAGTAATAATTAA
Found at i:31333542 original size:32 final size:32
Alignment explanation
Indices: 31333473--31333557 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
31333463 TTTAATGTCA
* *
31333473 TATATTTTATTTTCATTTCTTATTATAATCTTC
1 TATATTTTATTTT-ATTTTTTAATATAATCTTC
* *
31333506 TATATTTTATTTTATTTTTTAATATAATTTTT
1 TATATTTTATTTTATTTTTTAATATAATCTTC
*
31333538 TATATTATATAATTTATTTT
1 TATATT-T-TATTTTATTTT
31333558 AATTTTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 21 0.47
33 14 0.31
34 10 0.22
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (32 bp):
TATATTTTATTTTATTTTTTAATATAATCTTC
Found at i:31340593 original size:49 final size:49
Alignment explanation
Indices: 31340521--31340617 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
31340511 CGGCTCCTAT
31340521 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGTACCACACTAC
1 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGTACCACACTAC
* *
31340570 AAAGCATTAAATGATTCTATGTAAGGATTCAGTCCAAGTACCACACTA
1 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGTACCACACTA
31340618 AATAGAACAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (49 bp):
AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGTACCACACTAC
Found at i:31344611 original size:20 final size:21
Alignment explanation
Indices: 31344586--31344627 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31344576 CGTTTCTTTC
*
31344586 AATTTTCTT-TTTATTTAAAA
1 AATTTTCTTCTTTATTGAAAA
31344606 AATTTTCTTCTTTATTGAAAA
1 AATTTTCTTCTTTATTGAAAA
31344627 A
1 A
31344628 GAATGTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AATTTTCTTCTTTATTGAAAA
Found at i:31351203 original size:16 final size:15
Alignment explanation
Indices: 31351182--31351211 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
31351172 ATTAAGTTAC
31351182 AAGATAAAGATAAAAT
1 AAGAT-AAGATAAAAT
31351198 AAGATAAGATAAAA
1 AAGATAAGATAAAA
31351212 GATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
AAGATAAGATAAAAT
Found at i:31353414 original size:2 final size:2
Alignment explanation
Indices: 31353407--31353445 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
31353397 ATGCAATTAA
*
31353407 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31353446 CTTATGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31353949 original size:27 final size:27
Alignment explanation
Indices: 31353892--31353951 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
31353882 TATTTTAATT
* *
31353892 ATAAATTATTACTATTTTAAATGAAAT
1 ATAAATTATTAATATTTTAAATGAAAG
* *
31353919 ATAAATTATTAATTTTTGTAAAT-TAAG
1 ATAAATTATTAATATTT-TAAATGAAAG
31353946 ATAAAT
1 ATAAAT
31353952 AATCATGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (27 bp):
ATAAATTATTAATATTTTAAATGAAAG
Found at i:31354015 original size:20 final size:20
Alignment explanation
Indices: 31353963--31354015 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
31353953 ATCATGTTAA
*
31353963 TATT-AAATAA-TAATAACT
1 TATTAAAATAATTAATAAAT
* **
31353981 TATTAATATTTTTAATAAAT
1 TATTAAAATAATTAATAAAT
31354001 TATTAAAATAATTAA
1 TATTAAAATAATTAA
31354016 CTATTATAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 4 0.15
19 3 0.12
20 19 0.73
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAAATAATTAATAAAT
Found at i:31361323 original size:34 final size:34
Alignment explanation
Indices: 31361280--31361358 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
31361270 AAGGAGTTGC
*
31361280 AATATTCCTAACATTAGGAAGCTAATAATATTGA
1 AATATTCCTAACATTAGGAAGCCAATAATATTGA
31361314 AATATTCCTAACATTAGGAAGCCAATAATATTGA
1 AATATTCCTAACATTAGGAAGCCAATAATATTGA
31361348 AATATTCCTAA
1 AATATTCCTAA
31361359 TTCAAAATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (34 bp):
AATATTCCTAACATTAGGAAGCCAATAATATTGA
Found at i:31361546 original size:2 final size:2
Alignment explanation
Indices: 31361541--31361576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31361531 ACATACATAC
31361541 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
31361577 GTATGTATGT
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:31361813 original size:20 final size:17
Alignment explanation
Indices: 31361787--31361834 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
31361777 AATGATATAT
31361787 TTTAAAAATATTATTTAAA
1 TTTAAAAATA--ATTTAAA
*
31361806 TATTAAAAATAATTTATA
1 T-TTAAAAATAATTTAAA
31361824 TTTAAAAATAA
1 TTTAAAAATAA
31361835 ATAACAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 1 0.04
20 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAAATAATTTAAA
Found at i:31363054 original size:11 final size:12
Alignment explanation
Indices: 31363028--31363061 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31363018 GAAGATAGGG
*
31363028 AAAGGAAAGAGA
1 AAAGGAAAAAGA
*
31363040 AAAAGAAAAAGA
1 AAAGGAAAAAGA
31363052 AAAGGAAAAA
1 AAAGGAAAAA
31363062 TATTTTTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGGAAAAAGA
Found at i:31363387 original size:16 final size:15
Alignment explanation
Indices: 31363359--31363396 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
31363349 AAAATAAAAA
31363359 TATTATGTTATT-TT
1 TATTATGTTATTATT
*
31363373 T-TAATGTTATTATT
1 TATTATGTTATTATT
31363387 TATTATGTTA
1 TATTATGTTA
31363397 ATTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.45
14 4 0.20
15 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (15 bp):
TATTATGTTATTATT
Found at i:31363624 original size:15 final size:15
Alignment explanation
Indices: 31363604--31363681 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
31363594 CTGTAAAATT
* *
31363604 ATATTCTTAATAATC
1 ATATTCTCAACAATC
*
31363619 ATATTCTTAACAATC
1 ATATTCTCAACAATC
* *
31363634 ATATACCCAACAATC
1 ATATTCTCAACAATC
* *
31363649 ACATTCTCAATAATC
1 ATATTCTCAACAATC
31363664 ATATTC-CTAACAAT-
1 ATATTCTC-AACAATC
31363678 ATAT
1 ATAT
31363682 CAAACGCAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
14 5 0.10
15 47 0.90
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATTCTCAACAATC
Found at i:31363655 original size:30 final size:30
Alignment explanation
Indices: 31363615--31363677 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
31363605 TATTCTTAAT
* *
31363615 AATCATATTCTTAACAATCATATACCCAAC
1 AATCACATTCTCAACAATCATATACCCAAC
* * *
31363645 AATCACATTCTCAATAATCATATTCCTAAC
1 AATCACATTCTCAACAATCATATACCCAAC
31363675 AAT
1 AAT
31363678 ATATCAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (30 bp):
AATCACATTCTCAACAATCATATACCCAAC
Found at i:31364292 original size:27 final size:26
Alignment explanation
Indices: 31364253--31364305 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
31364243 GATTACTTTT
31364253 TTAAATTATTATTTTTATTAATATAAA
1 TTAAATTATTA-TTTTATTAATATAAA
*
31364280 TTAAATT-TATATTTTATTTATATAAA
1 TTAAATTAT-TATTTTATTAATATAAA
31364306 AAAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAAATTATTATTTTATTAATATAAA
Found at i:31364312 original size:27 final size:26
Alignment explanation
Indices: 31364261--31364318 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
31364251 TTTTAAATTA
**
31364261 TTAT-TTTTATTAATATAAATTAAAT
1 TTATATTTTATTAATATAAAAAAAAT
*
31364286 TTATATTTTATTTATATAAAAAAAAAT
1 TTATATTTTATTAATAT-AAAAAAAAT
31364313 TTATAT
1 TTATAT
31364319 CCAAACGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.14
26 11 0.39
27 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATATTTTATTAATATAAAAAAAAT
Found at i:31368259 original size:171 final size:171
Alignment explanation
Indices: 31367974--31368316 Score: 659
Period size: 171 Copynumber: 2.0 Consensus size: 171
31367964 ATCAAACCTT
31367974 TTCCTTTTGATTGAATTGATTGCATTATTTGTATGAGGTGAGTTTATACAGTTAAATTTCATGTA
1 TTCCTTTTGATTGAATTGATTGCATTATTTGTATGAGGTGAGTTTATACAGTTAAATTTCATGTA
*
31368039 TAATTATACTTAACTCAAAATTTATTAGAATACAAAAGAACGTATTTTGTTCTTGATATATATGA
66 TAATTATACTTAACTCAAAATTTATTAGAATACAAAAGAACATATTTTGTTCTTGATATATATGA
31368104 TTTGACAACAAAATAATACCTACTAGATTAATTGTCAAAAG
131 TTTGACAACAAAATAATACCTACTAGATTAATTGTCAAAAG
*
31368145 TTCCTTTTGATTGAATTGATTGCATTATTTGTATGAGGTGAGTTTATACAGTTAAATTTCATGTT
1 TTCCTTTTGATTGAATTGATTGCATTATTTGTATGAGGTGAGTTTATACAGTTAAATTTCATGTA
31368210 TAATTATACTTAACTCAAAATTTATTAGAATACAAAAGAACATATTTTGTTCTTGATATATATGA
66 TAATTATACTTAACTCAAAATTTATTAGAATACAAAAGAACATATTTTGTTCTTGATATATATGA
*
31368275 TTTGACAACAAAATAATACCTACTAGATTAATTGTCGAAAG
131 TTTGACAACAAAATAATACCTACTAGATTAATTGTCAAAAG
31368316 T
1 T
31368317 CCATGCAATG
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 169 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (171 bp):
TTCCTTTTGATTGAATTGATTGCATTATTTGTATGAGGTGAGTTTATACAGTTAAATTTCATGTA
TAATTATACTTAACTCAAAATTTATTAGAATACAAAAGAACATATTTTGTTCTTGATATATATGA
TTTGACAACAAAATAATACCTACTAGATTAATTGTCAAAAG
Found at i:31370806 original size:30 final size:29
Alignment explanation
Indices: 31370767--31370828 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
31370757 GAGTCATGAT
31370767 TTTAAATTTGAAA-AAGTGAAAATAAAAAA
1 TTTAAATTTGAAAGAA-TGAAAATAAAAAA
* *
31370796 TTTAATATTTGAAAGAATGAAATTATAAAA
1 TTTAA-ATTTGAAAGAATGAAAATAAAAAA
31370826 TTT
1 TTT
31370829 TTAACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 22 0.76
31 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (29 bp):
TTTAAATTTGAAAGAATGAAAATAAAAAA
Found at i:31378847 original size:28 final size:27
Alignment explanation
Indices: 31378806--31378947 Score: 83
Period size: 27 Copynumber: 5.1 Consensus size: 27
31378796 TAGGTAAAAG
* * * *
31378806 AAATTAAAATAAAATATATAATATAAA
1 AAATTATATTAAAAAATATAAAATAAA
* *
31378833 AAATTATATTAAAAAATTAAAAAATATA
1 AAATTATATTAAAAAA-TATAAAATAAA
* *
31378861 ATATTATAATAAAAAATA-AAAATAAA
1 AAATTATATTAAAAAATATAAAATAAA
* ** *
31378887 ATATATGATATT-AAAAATAT-ATTTAAG
1 A-A-ATTATATTAAAAAATATAAAATAAA
* *
31378914 AAATGATATTAAATAAAAATTAATAATAAA
1 AAATTATATTAAA-AAATA-TAA-AATAAA
31378944 AAAT
1 AAAT
31378948 ATAAGTATAT
Statistics
Matches: 87, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
25 8 0.09
26 11 0.13
27 31 0.36
28 29 0.33
29 1 0.01
30 7 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATTATATTAAAAAATATAAAATAAA
Found at i:31378854 original size:50 final size:50
Alignment explanation
Indices: 31378757--31378854 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
31378747 GTAACGTTAT
* * * *
31378757 AATTAAAATAAAATATAAGAAATTAAAATTTATATAATATAGGTAAAAGA
1 AATTAAAATAAAATATAAGAAATAAAAAATTATATAATAAAAGTAAAAGA
* *
31378807 AATTAAAATAAAATATATA-ATATAAAAAATTATATTAA-AAAATTAAAA
1 AATTAAAATAAAATATA-AGAAATAAAAAATTATA-TAATAAAAGTAAAA
31378855 AATATAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
50 36 0.90
51 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (50 bp):
AATTAAAATAAAATATAAGAAATAAAAAATTATATAATAAAAGTAAAAGA
Found at i:31378873 original size:20 final size:20
Alignment explanation
Indices: 31378811--31378878 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
31378801 AAAAGAAATT
*
31378811 AAAATAAAATA-TATAATATA
1 AAAATATAATATTATAATA-A
* *
31378831 AAAA-ATTATATTAAAAAATTAA
1 AAAATATAATATT--ATAA-TAA
31378853 AAAATATAATATTATAATAA
1 AAAATATAATATTATAATAA
31378873 AAAATA
1 AAAATA
31378879 AAAATAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.11
20 14 0.37
21 3 0.08
22 8 0.21
23 9 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATAATATTATAATAA
Found at i:31384270 original size:41 final size:40
Alignment explanation
Indices: 31384223--31384432 Score: 146
Period size: 41 Copynumber: 5.1 Consensus size: 40
31384213 ATAAGAATAT
31384223 TTAAATTAAATAAATTATTAATATTTTAAATAAATTAATGA
1 TTAAATTAAATAAATTATTAATATTTTAAAT-AATTAATGA
* * *
31384264 TTAAATTGGAAATAAATTATTAATA-TTTAAATTATCAATTA
1 TTAAATT--AAATAAATTATTAATATTTTAAATAATTAATGA
* **
31384305 TTAATATTTTAAA-AAATATAATAA-AAATTAATTATAA-TAAT-A
1 TTAA-A--TTAAATAAAT-TATTAATATTTTAA--ATAATTAATGA
* *
31384347 TTTAAATTAAATAAAATATGAATATTTTAACAT-ATTAATGA
1 -TTAAATTAAATAAATTATTAATATTTTAA-ATAATTAATGA
* * * *
31384388 TTAAATTATAAATAAAATATTAAT-GTTTAAATTATTAATTA
1 TTAAA-T-TAAATAAATTATTAATATTTTAAATAATTAATGA
31384429 TTAA
1 TTAA
31384433 TATTTTAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
39 1 0.01
40 22 0.16
41 48 0.35
42 37 0.27
43 23 0.17
44 5 0.04
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (40 bp):
TTAAATTAAATAAATTATTAATATTTTAAATAATTAATGA
Found at i:31384342 original size:16 final size:17
Alignment explanation
Indices: 31384321--31384362 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
31384311 TTTTAAAAAA
31384321 TATAATAAAAATT-AAT
1 TATAATAAAAATTAAAT
* *
31384337 TATAATAATATTTAAAT
1 TATAATAAAAATTAAAT
31384354 TA-AATAAAA
1 TATAATAAAA
31384363 TATGAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATAAAAATTAAAT
Done.