Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 17 of 185
Found at i:4568869 original size:14 final size:15
Alignment explanation
Indices: 4568850--4568882 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
4568840 CTTAAACCAG
4568850 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
4568864 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
4568879 AATC
1 AATC
4568883 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:4569373 original size:41 final size:41
Alignment explanation
Indices: 4569316--4569594 Score: 410
Period size: 41 Copynumber: 7.0 Consensus size: 41
4569306 TCAAAAGCGG
* *
4569316 GCATTAGCGGCGCTTTTTCATAAACGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
4569357 GCATTAGCGGCGCTTTTT-AAAAACGCCGCTAAAGGCCTGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
4569397 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
4569437 GCATTAGCGGCGC---TTC-CAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
4569474 GCATTAGCGGCGCTTCTTT-ACAAAGGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGGCCCGA
* *
4569515 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCTGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
4569556 GAATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
4569595 CAAAAACTCA
Statistics
Matches: 216, Mismatches: 14, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
36 15 0.07
37 20 0.09
40 54 0.25
41 127 0.59
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:4569777 original size:41 final size:41
Alignment explanation
Indices: 4569622--4569781 Score: 159
Period size: 40 Copynumber: 4.0 Consensus size: 41
4569612 ACGTCGTTTG
* ** * *
4569622 GCTTAGATTTTTTGCGGCGTTTTTTGGAAAA-TGCCGGTAAT
1 GCTT-GATTTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAT
**
4569663 GCTT-ATTTTTAGCGGCGTTTTCCA-AAAAGCGCCGCTAAT
1 GCTTGATTTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAT
* **
4569702 GCTCGACCTTTAGCGGCG-TTTTTATAAAAGCGCCGCTAAT
1 GCTTGATTTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAT
* *
4569742 GCTTGATTTTTAGTGGCGTTTTTTATCCAAA-CGCCGCTAA
1 GCTTGATTTTTAGCGGCGTTTTTTAT-AAAAGCGCCGCTAA
4569782 AAGCCTGTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.04
39 31 0.32
40 40 0.41
41 20 0.20
42 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
GCTTGATTTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAT
Found at i:4570326 original size:21 final size:23
Alignment explanation
Indices: 4570297--4570345 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
4570287 CATCCACCTA
*
4570297 TTTATAATAACAAAAAAA-T-AT
1 TTTAAAATAACAAAAAAATTAAT
**
4570318 TTTAAAATATTAAAAAAATTAAT
1 TTTAAAATAACAAAAAAATTAAT
4570341 TTTAA
1 TTTAA
4570346 CTTAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAATAACAAAAAAATTAAT
Found at i:4576414 original size:16 final size:16
Alignment explanation
Indices: 4576393--4576424 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4576383 TAAATTATAT
4576393 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
4576409 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
4576425 ATTAAAATAG
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:4579802 original size:21 final size:21
Alignment explanation
Indices: 4579753--4579798 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
4579743 ATCATATGCC
4579753 TATAATTTTAAAAAAGAAAAT
1 TATAATTTTAAAAAAGAAAAT
* *
4579774 TATAATTTT-AGAAAGTAAAT
1 TATAATTTTAAAAAAGAAAAT
4579794 TATAA
1 TATAA
4579799 ATTTCAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
TATAATTTTAAAAAAGAAAAT
Found at i:4581884 original size:13 final size:13
Alignment explanation
Indices: 4581866--4581892 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4581856 CTGAAGTATG
4581866 ATTAGCAGTTACC
1 ATTAGCAGTTACC
4581879 ATTAGCAGTTACC
1 ATTAGCAGTTACC
4581892 A
1 A
4581893 CCGCTGGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTAGCAGTTACC
Found at i:4584818 original size:16 final size:16
Alignment explanation
Indices: 4584797--4584827 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4584787 AAAATTGAAT
4584797 AACAGACGAAGGAGGC
1 AACAGACGAAGGAGGC
4584813 AACAGACGAAGGAGG
1 AACAGACGAAGGAGG
4584828 AACCGAGCGG
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:0.45, C:0.16, G:0.39, T:0.00
Consensus pattern (16 bp):
AACAGACGAAGGAGGC
Found at i:4593286 original size:46 final size:46
Alignment explanation
Indices: 4593218--4593306 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
4593208 AAAAAATTTA
*
4593218 ATATAAAATATTGATTGACGCCTGTCAGATAGGCACCATTAAATAT
1 ATATAAAATATTGATTGACGCCTCTCAGATAGGCACCATTAAATAT
* * *
4593264 ATATATAATATTTATT-AGCGCCTCTCAGATAGGCGCCATTAAA
1 ATATAAAATATTGATTGA-CGCCTCTCAGATAGGCACCATTAAA
4593307 AAAAACAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (46 bp):
ATATAAAATATTGATTGACGCCTCTCAGATAGGCACCATTAAATAT
Found at i:4597905 original size:29 final size:29
Alignment explanation
Indices: 4597863--4597920 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4597853 CAAACTTAAG
4597863 CCCATAGTTAAAACGAGGCTTTGGTTTCC
1 CCCATAGTTAAAACGAGGCTTTGGTTTCC
4597892 CCCATAGTTAAAACGAGGCTTTGGTTTCC
1 CCCATAGTTAAAACGAGGCTTTGGTTTCC
4597921 TTCGCTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (29 bp):
CCCATAGTTAAAACGAGGCTTTGGTTTCC
Found at i:4600211 original size:17 final size:17
Alignment explanation
Indices: 4600183--4600229 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
4600173 ACAATTAGGG
4600183 TTAGGG-TTTTAGGATT
1 TTAGGGTTTTTAGGATT
4600199 TTAGGGTTTTTA-GATT
1 TTAGGGTTTTTAGGATT
* *
4600215 TTAAGGTTTTAAGGA
1 TTAGGGTTTTTAGGA
4600230 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (17 bp):
TTAGGGTTTTTAGGATT
Found at i:4600427 original size:96 final size:96
Alignment explanation
Indices: 4600295--4600523 Score: 363
Period size: 96 Copynumber: 2.4 Consensus size: 96
4600285 TAGAAAATTA
4600295 GTTTATGA-TTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATT
1 GTTTA-GAGTTTTTAA-GAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATT
4600359 AT-AAATTTTAAAGAAATCAAATTAGGGTTTAGT
64 ATAAAATTTTAAA-AAATCAAATTAGGGTTTAGT
* * *
4600392 GTTTAGGGTTTTTAAGAAAAAATTATATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 GTTTAGAGTTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
* *
4600457 AAAATTTTAAAAAATTAGATTAGGGTTTAGT
66 AAAATTTTAAAAAATCAAATTAGGGTTTAGT
*
4600488 GTTTAGAGTTTTTAAGGAAAAATCAAATAAATTAGG
1 GTTTAGAGTTTTTAAGAAAAAATCAAATAAATTAGG
4600524 ATTTGGAGTT
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
96 99 0.82
97 22 0.18
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.38
Consensus pattern (96 bp):
GTTTAGAGTTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
AAAATTTTAAAAAATCAAATTAGGGTTTAGT
Found at i:4600795 original size:126 final size:125
Alignment explanation
Indices: 4600570--4600860 Score: 456
Period size: 126 Copynumber: 2.3 Consensus size: 125
4600560 TAATTTAAAA
* *
4600570 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTAAAAAATAATTTTAAGAAGACGTTTC
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCTAAAAAATAATTTTAAGAAGACGTTTC
* * * *
4600635 TGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCATTGTCAACAAAAGTACTGAAAG
66 TGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGGCAACAAAAGTACTGAAAG
* * * *
4600695 AAGCTCCCACGTGGACGCTCTTTTGCTATAGTAATTTCTGAAAAAATAATTTTGAGAAGATGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCT-AAAAAATAATTTTAAGAAGACGTTT
* *
4600760 CTGAGCAAATAGTGTCAAAAATGCTTCAAGCAGGATGCAATGGCAGCAAAAGTACTGAAAG
65 CTGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGGCAACAAAAGTACTGAAAG
*
4600821 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGTTTCTA
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCTA
4600861 TTTGGCCTGA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 36 0.24
126 114 0.76
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (125 bp):
AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTTCTAAAAAATAATTTTAAGAAGACGTTTC
TGAGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGGCAACAAAAGTACTGAAAG
Found at i:4602538 original size:49 final size:52
Alignment explanation
Indices: 4602477--4602582 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 52
4602467 ATTTAAAAAA
* *
4602477 AAACTCTTTTAC-TATTATTTGTTT-TAAGGTTTTATT-TATCATTTATTCT
1 AAACTCTTTTACTTAATATTTGTTTAAAAGGTTTTATTATATCATTTATTCT
* * * *
4602526 AAACTGTTTTACTTAATATTTGTTTAAAAGTTTTTATTATATTATTTATTTT
1 AAACTCTTTTACTTAATATTTGTTTAAAAGGTTTTATTATATCATTTATTCT
4602578 AAACT
1 AAACT
4602583 ATTATATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 11 0.23
50 11 0.23
51 10 0.21
52 16 0.33
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (52 bp):
AAACTCTTTTACTTAATATTTGTTTAAAAGGTTTTATTATATCATTTATTCT
Found at i:4602585 original size:17 final size:17
Alignment explanation
Indices: 4602565--4602630 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 17
4602555 GTTTTTATTA
4602565 TATTATTTATTTTAAAC
1 TATTATTTATTTTAAAC
* *
4602582 TATTATATATGTTTTTATTA-
1 TATTAT-T-T-ATTTTA-AAC
4602602 TATTATTTATTTTAAAC
1 TATTATTTATTTTAAAC
4602619 TATTATTTATTT
1 TATTATTTATTT
4602631 GTTTTAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 23 0.57
18 2 0.05
19 2 0.05
20 11 0.28
21 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTATTTATTTTAAAC
Found at i:4602625 original size:20 final size:20
Alignment explanation
Indices: 4602565--4602637 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
4602555 GTTTTTATTA
4602565 TATTATTTATTTTAAACTAT
1 TATTATTTATTTTAAACTAT
* *
4602585 TATATATGT-TTTT--ATTA-
1 TAT-TATTTATTTTAAACTAT
4602602 TATTATTTATTTTAAACTAT
1 TATTATTTATTTTAAACTAT
*
4602622 TATTTATTTGTTTTAA
1 TA-TTATTTATTTTAA
4602638 GGAAAACTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
18 3 0.07
19 3 0.07
20 9 0.21
21 16 0.38
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TATTATTTATTTTAAACTAT
Found at i:4607845 original size:33 final size:33
Alignment explanation
Indices: 4607803--4608077 Score: 138
Period size: 33 Copynumber: 7.5 Consensus size: 33
4607793 ATCGATGGAT
*
4607803 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* ** *
4607836 TCAGCACTTAGTAACCCCTTTCACATTCAAAAATACGGTGGAA
1 TCAGCACTTAGCAA---C---CAC---CAATGATTCGG-GGAA
*
4607879 TCAGCACTTAGCAACCACCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * *
4607912 TCAACACTTAGCAACCCCTTTCACATTTAAGATAT-GGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--T--GAT-TCGG-GGAA
4607954 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * * *
4607987 TCAGCACATAGCAACCCCTTTCACATTTAAGATACGGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--T--GATTCGG-GGAA
* * *
4608029 TCAGCACTTAACAACCACCAATGGTTCGAGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
4608062 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
4608078 CCTTGGGGGA
Statistics
Matches: 183, Mismatches: 29, Indels: 60
0.67 0.11 0.22
Matches are distributed among these distances:
33 71 0.39
34 16 0.09
36 7 0.04
37 5 0.03
38 2 0.01
39 9 0.05
40 1 0.01
41 10 0.05
42 45 0.25
43 17 0.09
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAA
Found at i:4607983 original size:75 final size:75
Alignment explanation
Indices: 4607803--4608081 Score: 441
Period size: 75 Copynumber: 3.7 Consensus size: 75
4607793 ATCGATGGAT
* * * *
4607803 TCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGTAACCCCTTTCACATTCAAAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT-TAAG
*
4607868 ATACGGTGGAA
65 ATACGGTGGGA
* *
4607879 TCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGA
*
4607944 TATGGTGGGA
66 TACGGTGGGA
*
4607954 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACATAGCAACCCCTTTCACATTTAAGA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGA
4608019 TACGGTGGGA
66 TACGGTGGGA
* * *
4608029 TCAGCACTTAACAACCACCAATGGTTCGAGGAATCAGCACTTAGCAACCCCTT
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
4608082 GGGGGAATCA
Statistics
Matches: 187, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
75 131 0.70
76 56 0.30
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (75 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGA
TACGGTGGGA
Found at i:4609600 original size:7 final size:7
Alignment explanation
Indices: 4609588--4609613 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4609578 TTATATATAT
4609588 AATACTA
1 AATACTA
4609595 AATACTA
1 AATACTA
4609602 AATACTA
1 AATACTA
4609609 AATAC
1 AATAC
4609614 GAATTGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:4609628 original size:20 final size:20
Alignment explanation
Indices: 4609603--4609640 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4609593 TAAATACTAA
4609603 ATACTAAATACGAATTGACT
1 ATACTAAATACGAATTGACT
4609623 ATACTAAATACGAATTGA
1 ATACTAAATACGAATTGA
4609641 TTATCTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (20 bp):
ATACTAAATACGAATTGACT
Found at i:4610781 original size:23 final size:24
Alignment explanation
Indices: 4610742--4610786 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4610732 AAATAAATCC
4610742 AAAAAAATAAAATTAGAGCTTTTT
1 AAAAAAATAAAATTAGAGCTTTTT
*
4610766 AAAAAAATTAAA-TAGAGCTTT
1 AAAAAAATAAAATTAGAGCTTT
4610787 GAGAGGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (24 bp):
AAAAAAATAAAATTAGAGCTTTTT
Found at i:4610825 original size:13 final size:11
Alignment explanation
Indices: 4610784--4610826 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
4610774 TAAATAGAGC
*
4610784 TTTGAGAGGAA
1 TTTGAGAGAAA
4610795 TTTGAGAGAAA
1 TTTGAGAGAAA
4610806 TTTGAGAGAAA
1 TTTGAGAGAAA
*
4610817 TTTGGGAGAA
1 TTTGAGAGAA
4610827 TATTGAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:4611057 original size:21 final size:21
Alignment explanation
Indices: 4611017--4611058 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4611007 CCTAAAGGAT
**
4611017 GCGTTTTCTATCCATGTGGAC
1 GCGTTTTCTATCCACATGGAC
*
4611038 GCGTTTTCTGTCCACATGGAC
1 GCGTTTTCTATCCACATGGAC
4611059 AAAGCGCTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (21 bp):
GCGTTTTCTATCCACATGGAC
Found at i:4613457 original size:18 final size:18
Alignment explanation
Indices: 4613416--4613450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4613406 GCCAGGTGCG
* *
4613416 TATCCTAGCCCTTTTATT
1 TATCCTAACCCTTATATT
4613434 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
4613451 GTTTCCTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.03, T:0.46
Consensus pattern (18 bp):
TATCCTAACCCTTATATT
Found at i:4613760 original size:21 final size:21
Alignment explanation
Indices: 4613697--4613760 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
4613687 CCCAACACCG
* *
4613697 ACAACCATATCCCCTACCGGA
1 ACAACCATAACCCCCACCGGA
** * * * *
4613718 GGAACCAGAATCCCCGCGGGA
1 ACAACCATAACCCCCACCGGA
4613739 ACAACCATAACCCCCACCGGA
1 ACAACCATAACCCCCACCGGA
4613760 A
1 A
4613761 GCTAGACAAA
Statistics
Matches: 29, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.41, G:0.17, T:0.08
Consensus pattern (21 bp):
ACAACCATAACCCCCACCGGA
Found at i:4613919 original size:34 final size:34
Alignment explanation
Indices: 4613881--4613977 Score: 185
Period size: 34 Copynumber: 2.9 Consensus size: 34
4613871 GAATATTTTG
4613881 ATATTATTTAATGTAATAAAATAGAAATTCTTCT
1 ATATTATTTAATGTAATAAAATAGAAATTCTTCT
4613915 ATATTATTTAATGTAATAAAATAGAAATTCTTCT
1 ATATTATTTAATGTAATAAAATAGAAATTCTTCT
*
4613949 ATATTATTTCATGTAATAAAATAGAAATT
1 ATATTATTTAATGTAATAAAATAGAAATT
4613978 TACTTTTACA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (34 bp):
ATATTATTTAATGTAATAAAATAGAAATTCTTCT
Found at i:4614161 original size:58 final size:55
Alignment explanation
Indices: 4613987--4614164 Score: 153
Period size: 58 Copynumber: 3.1 Consensus size: 55
4613977 TTACTTTTAC
* *
4613987 ATTTTTAATATAATAGAAATTCTTTTAAATAACACAATATTTTGAATATTTCTATATT
1 ATTTTTAATAAAATAGAAATTCTTTTAAAT-A-ACAGTA-TTTGAATATTTCTATATT
* * * * * *
4614045 ATTTCATTTAATAAAATAAAACATTGTTTTGAATAA-AGTAATTGTAAT-TTACTTTATT
1 A-TT--TTTAATAAAATAGAA-ATTCTTTTAAATAACAGTATTTG-AATATTTCTATATT
**
4614103 ATTTTTAATAAAATAGATTTTCTTTTAAATAAGTCAGTATTCTGAATATTTCTATATT
1 ATTTTTAATAAAATAGAAATTCTTTTAAATAA--CAGTATT-TGAATATTTCTATATT
4614161 ATTT
1 ATTT
4614165 GATTTAAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 20
0.72 0.12 0.15
Matches are distributed among these distances:
54 11 0.12
55 13 0.14
57 10 0.11
58 27 0.29
59 8 0.09
60 1 0.01
61 14 0.15
62 10 0.11
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (55 bp):
ATTTTTAATAAAATAGAAATTCTTTTAAATAACAGTATTTGAATATTTCTATATT
Found at i:4615698 original size:126 final size:126
Alignment explanation
Indices: 4615467--4615760 Score: 489
Period size: 126 Copynumber: 2.3 Consensus size: 126
4615457 TCAGGCCAAA
* * *
4615467 CAGGAGCTACTGTAGCAAAAGCTCGTCCACGGGGGAGCTTCTTTCAATACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAAAGC
*
4615532 ATCCTACTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCGAAATTATTTTTT
66 ATCCTACTTAAAGCGTTTTTGACACTATTTACTCAAAAACGTCTACTCGAAATTATTTTTT
* *
4615593 CAGGAGCTACTGTAGTAAAAGCGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAATGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAAAGC
* * * *
4615658 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTCCTCGAATTTATTTTTT
66 ATCCTACTTAAAGCGTTTTTGACACTATTTACTCAAAAACGTCTACTCGAAATTATTTTTT
*
4615719 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTT
4615761 CTAAATTAAC
Statistics
Matches: 156, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 156 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAAAGC
ATCCTACTTAAAGCGTTTTTGACACTATTTACTCAAAAACGTCTACTCGAAATTATTTTTT
Found at i:4615942 original size:96 final size:95
Alignment explanation
Indices: 4615795--4616098 Score: 398
Period size: 96 Copynumber: 3.2 Consensus size: 95
4615785 AGTAATCTTA
*
4615795 AACCCCAAACCCTAATTTATTTGAGTTTTTCCTTAAAAA-CCTTAAACACTAAACCCTAATCTAA
1 AACCCTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTT-AACACTAAACCCTAATCTAA
4615859 TTTTTTTAAAATTTATAATTAATTTACTTAAAT
64 -TTTTTTAAAATTTATAATTAATTTACTTAAAT
* *
4615892 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCTTAATCTGA-T
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
* * *
4615956 TTTTAAAATTTTTTTAATTAATTTACTCAAGT
66 TTTTAAAA--TTTATAATTAATTTACTTAAAT
* * * * * *
4615988 AACCCTAAACCCTAATTTAATTGATTTTTCTTTAAAAACCATAAACGCAAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
** *
4616053 TTGAAAAATTTATAATTAATTTAATTAAGA-
66 TTTTAAAATTTATAATTAATTTACTTAA-AT
4616083 AACCCTAAACCCTAAT
1 AACCCTAAACCCTAAT
4616099 CCCTTATTTA
Statistics
Matches: 182, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
94 9 0.05
95 33 0.18
96 106 0.58
97 34 0.19
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
TTTTAAAATTTATAATTAATTTACTTAAAT
Found at i:4616164 original size:7 final size:7
Alignment explanation
Indices: 4616139--4616180 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
4616129 CCTAAACCTA
4616139 AAAACCC
1 AAAACCC
4616146 AAAAACCC
1 -AAAACCC
4616154 -AAACCC
1 AAAACCC
*
4616160 TAAACCC
1 AAAACCC
4616167 AAAACCC
1 AAAACCC
4616174 AAAACCC
1 AAAACCC
4616181 TGACAGCGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.55, C:0.43, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAACCC
Found at i:4616164 original size:21 final size:21
Alignment explanation
Indices: 4616140--4616181 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4616130 CTAAACCTAA
4616140 AAACCCAAAAACCC-AAACCCT
1 AAACCC-AAAACCCAAAACCCT
4616161 AAACCCAAAACCCAAAACCCT
1 AAACCCAAAACCCAAAACCCT
4616182 GACAGCGCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.43, G:0.00, T:0.05
Consensus pattern (21 bp):
AAACCCAAAACCCAAAACCCT
Found at i:4618031 original size:31 final size:31
Alignment explanation
Indices: 4617996--4618056 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4617986 AAACAATTCA
* *
4617996 ACTCTTTTTGAAAGATTGATGGTCAAATTTT
1 ACTCTTTTTAAAAGATTGAAGGTCAAATTTT
*
4618027 ACTCTTTTTAAAAGGTTGAAGGTCAAATTT
1 ACTCTTTTTAAAAGATTGAAGGTCAAATTT
4618057 AGTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (31 bp):
ACTCTTTTTAAAAGATTGAAGGTCAAATTTT
Found at i:4620965 original size:27 final size:27
Alignment explanation
Indices: 4620927--4620980 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4620917 ATCGAGAACA
4620927 TTGTTAGAAGCTTTATTTGAGGGGGGT
1 TTGTTAGAAGCTTTATTTGAGGGGGGT
4620954 TTGTTAGAAGCTTTATTTGAGGGGGGT
1 TTGTTAGAAGCTTTATTTGAGGGGGGT
4620981 ATTGATTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.41
Consensus pattern (27 bp):
TTGTTAGAAGCTTTATTTGAGGGGGGT
Found at i:4623579 original size:33 final size:32
Alignment explanation
Indices: 4623542--4623619 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
4623532 TGGCCCTACC
** * **
4623542 ATGGTCTTACATTCGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATGAG-AATGCCATAACCCAACT
*
4623575 ATGGTCTTATCATGAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATGAGAATGCCATAACCCAACT
4623608 ATGGTCTTACAT
1 ATGGTCTTACAT
4623620 AATAATGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.82
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATGAGAATGCCATAACCCAACT
Found at i:4624904 original size:75 final size:75
Alignment explanation
Indices: 4624780--4624929 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
4624770 TTTTTGACTC
4624780 CAAATTTGTGGTCCTAAAACCACTGTTTCGATTTCACTGTAAATAGGCCGTTACAACTCTCCCCC
1 CAAATTTGTGGTCCTAAAACCACTGTTTCGATTTCACTGTAAATAGGCCGTTACAACTCTCCCCC
4624845 TTAGGACTTT
66 TTAGGACTTT
* *
4624855 CAAATTTGTGGTCCTAAAACCACTGTTTCGATTTCACTGTAAATGGGCCGTTATAACTCTCCCCC
1 CAAATTTGTGGTCCTAAAACCACTGTTTCGATTTCACTGTAAATAGGCCGTTACAACTCTCCCCC
4624920 TTAGGACTTT
66 TTAGGACTTT
4624930 TCGTCCTCAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (75 bp):
CAAATTTGTGGTCCTAAAACCACTGTTTCGATTTCACTGTAAATAGGCCGTTACAACTCTCCCCC
TTAGGACTTT
Found at i:4634992 original size:30 final size:30
Alignment explanation
Indices: 4634922--4634992 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
4634912 TAGTTTATAT
* *
4634922 TTTTATAATTTTTAAAAGATTAAATCAAAA
1 TTTTATCATTTTTAAAAGATAAAATCAAAA
*
4634952 TTTTATCATTTTTAAAAAGACTAAAAT-ACAA
1 TTTTATCATTTTT-AAAAGA-TAAAATCAAAA
4634983 TTTTA-CATTT
1 TTTTATCATTT
4634993 ACTATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTATCATTTTTAAAAGATAAAATCAAAA
Found at i:4640280 original size:9 final size:9
Alignment explanation
Indices: 4640268--4640335 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
4640258 AAAATAAAAA
4640268 AATTCGGGT
1 AATTCGGGT
4640277 AATTCGGGT
1 AATTCGGGT
* *
4640286 ATTTTGCGGT
1 AATTCG-GGT
*
4640296 AATTCGGTT
1 AATTCGGGT
*
4640305 AATTCGGTT
1 AATTCGGGT
4640314 AATTCGGGT
1 AATTCGGGT
4640323 AATTCGGGT
1 AATTCGGGT
4640332 AATT
1 AATT
4640336 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
9 45 0.87
10 7 0.13
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:4640512 original size:12 final size:12
Alignment explanation
Indices: 4640495--4640519 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4640485 AATAATTTCG
4640495 GGTCGGTTAACC
1 GGTCGGTTAACC
4640507 GGTCGGTTAACC
1 GGTCGGTTAACC
4640519 G
1 G
4640520 AATGAACACC
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:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:4640706 original size:5 final size:5
Alignment explanation
Indices: 4640696--4640721 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4640686 TACTTTCTTC
4640696 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
4640722 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:4641154 original size:25 final size:25
Alignment explanation
Indices: 4641121--4641169 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4641111 GTTCAGAGTA
4641121 AAAAAATTATCAAAATTATGTGTTT
1 AAAAAATTATCAAAATTATGTGTTT
4641146 AAAAAATTATCAAAATTATGTGTT
1 AAAAAATTATCAAAATTATGTGTT
4641170 AGTGACGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (25 bp):
AAAAAATTATCAAAATTATGTGTTT
Found at i:4644285 original size:10 final size:10
Alignment explanation
Indices: 4644270--4644294 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4644260 CTTTCTTATT
4644270 TTAGTTGTTC
1 TTAGTTGTTC
4644280 TTAGTTGTTC
1 TTAGTTGTTC
4644290 TTAGT
1 TTAGT
4644295 GGTAGTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.20, T:0.60
Consensus pattern (10 bp):
TTAGTTGTTC
Found at i:4653972 original size:26 final size:25
Alignment explanation
Indices: 4653940--4654028 Score: 105
Period size: 26 Copynumber: 3.7 Consensus size: 25
4653930 TGTATTTGTT
4653940 TTTTATATATATGATTAACTTTATA
1 TTTTATATATATGATTAACTTTATA
*
4653965 TATTTATATATATAATTAACTTTATA
1 T-TTTATATATATGATTAACTTTATA
* *
4653991 TTTTATA-AGA-GGTTAA-TTTATA
1 TTTTATATATATGATTAACTTTATA
*
4654013 TTTT-TATATATAATTA
1 TTTTATATATATGATTA
4654029 TATATAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.04
22 12 0.22
23 7 0.13
24 2 0.04
25 7 0.13
26 24 0.44
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TTTTATATATATGATTAACTTTATA
Found at i:4657532 original size:14 final size:14
Alignment explanation
Indices: 4657513--4657558 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4657503 CTAATTATGT
4657513 TAAAAATTTAAAGA
1 TAAAAATTTAAAGA
4657527 TAAAAA-TT-AAGA
1 TAAAAATTTAAAGA
**
4657539 TTTAAATTTAAAGA
1 TAAAAATTTAAAGA
4657553 TAAAAA
1 TAAAAA
4657559 CTAAGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAAAATTTAAAGA
Found at i:4657545 original size:26 final size:26
Alignment explanation
Indices: 4657516--4657569 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
4657506 ATTATGTTAA
*
4657516 AAATTTAAAGATAAAAATTAAGATTT
1 AAATTTAAAGATAAAAACTAAGATTT
4657542 AAATTTAAAGATAAAAACTAAGATTT
1 AAATTTAAAGATAAAAACTAAGATTT
4657568 AA
1 AA
4657570 TTATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (26 bp):
AAATTTAAAGATAAAAACTAAGATTT
Found at i:4659282 original size:3 final size:3
Alignment explanation
Indices: 4659274--4659311 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4659264 ATAACAAACA
4659274 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4659312 GACAAATAGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4659497 original size:3 final size:3
Alignment explanation
Indices: 4659489--4659521 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
4659479 TAAATGGGTA
4659489 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AA
4659522 AGAAATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4660687 original size:4 final size:4
Alignment explanation
Indices: 4660678--4660703 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4660668 TAGGGTTAGG
4660678 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
4660704 TGTTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:4661165 original size:44 final size:44
Alignment explanation
Indices: 4661108--4661309 Score: 198
Period size: 44 Copynumber: 4.7 Consensus size: 44
4661098 AGGATTCATC
* * *
4661108 TTCAATCTTCTCCACTGTAACTTCAGGGAGATAAGATCTGTGGT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * *
4661152 TTCAATCCGCTCCACCGCAACTTCAGAGAGATAGGAT-TG-GATT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTG-GT
** * *
4661195 CTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGA
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
4661237 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
4661281 TTTAATCCGCTCCACTGTAACTTCAGAGA
1 TTCAATCTGCTCCACTGCAACTTCAGAGA
4661310 TATAGGATTG
Statistics
Matches: 124, Mismatches: 27, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
41 31 0.25
42 2 0.02
43 4 0.03
44 87 0.70
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGT
Found at i:4661219 original size:88 final size:83
Alignment explanation
Indices: 4661083--4661269 Score: 214
Period size: 88 Copynumber: 2.2 Consensus size: 83
4661073 TGACCTACTA
* *
4661083 CAACTTCAGAG-GTATAGGATTCATCTTCAATCTTCTCCACTGTAACTTCAGGGAGATAAGATCT
1 CAACTTCAGAGAG-ATAGGATTCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-C-
* *
4661147 GTGGTTTCAATCCGCTCCACCG
63 -TGGATGCAATCCGCTCCACCG
* **
4661169 CAACTTCAGAGAGATAGGATTGGATTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CAACTTCAGAGAGATAGGATT-CA-TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
* * * *
4661234 GGATGCGATCTGCTCTACTG
64 GGATGCAATCCGCTCCACCG
4661254 CAACTTCAGAGAGATA
1 CAACTTCAGAGAGATA
4661270 AGATCTGTGG
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
85 31 0.36
86 19 0.22
87 3 0.03
88 34 0.39
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (83 bp):
CAACTTCAGAGAGATAGGATTCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG
ATGCAATCCGCTCCACCG
Found at i:4661297 original size:85 final size:87
Alignment explanation
Indices: 4661106--4661306 Score: 221
Period size: 85 Copynumber: 2.3 Consensus size: 87
4661096 ATAGGATTCA
** * *
4661106 TCTTCAATCTTCTCCACTGTAACTTCAGGGAGATAAGATCTGTGGTTTCAATCCGCTCCACCGCA
1 TCTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGATC-GTGGATGCAATCCGCTCCACCGCA
*
4661171 ACTTCAGAGAGATAGGATTGGAT
65 ACTTCAGAGAGATAAGATTGGAT
** * * * * * *
4661194 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C-TGGATGCGATCTGCTCTACTGCAA
1 TCTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGATCGTGGATGCAATCCGCTCCACCGCAA
*
4661257 CTTCAGAGAGATAAGATCTGTGGT
66 CTTCAGAGAGATAAGAT-TG-GAT
4661281 T-TT-AATCCGCTCCACTGTAACTTCAG
1 TCTTCAATCCGCTCCACTGTAACTTCAG
4661307 AGATATAGGA
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
85 53 0.56
86 4 0.04
87 4 0.04
88 34 0.36
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
TCTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGATCGTGGATGCAATCCGCTCCACCGCAA
CTTCAGAGAGATAAGATTGGAT
Found at i:4661775 original size:197 final size:197
Alignment explanation
Indices: 4661357--4662327 Score: 1136
Period size: 197 Copynumber: 4.9 Consensus size: 197
4661347 TCAGGGCATT
* * * ** *
4661357 AAGATTCGTCGTTGTAGCTTCAATCTATCCCACTGCACCGCCTAGGAAATAAGATTCACCATTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCCT-GGAAATAAGATTTGCCGTTGT
* * * * * * * * *
4661422 GACTTCAATCTTTAAATTGCAATGTCGGAGAAAACAAGATTTGTCATTGTAGCTTCAATCTATTT
65 GGCCTCAATCTTTTAATTGCAATGTCGGGGAAAAGAAGATTCGCCATTGTAGCTTCAATCTGTTC
* * *
4661487 CGCTGCACTGCCTGAGAAGTAAGATTTGCCGTTGTGGCCTT-AATATTTTAATTGCAATGTC-GA
130 CGCTGCACTGCCTGGGAA-TAAGATTTGCCGTTGTGG-CTTCAATCTTTTAATTGCAATGTCGGG
4661550 GAAAGC
193 GAAA-C
* * * * * *
4661556 AAGATTTGCCGTCGTAGCTTCAATATGTTCTACTGCACTGCCTGGAAATAAGATTCGCCGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCCTGGAAATAAGATTTGCCGTTGTG
* * ** *
4661621 GCATCAATCTTTTAATTGTAATGTCGGGGAAAATGAA-ATTCATCGTTGTAGCTTCAATCTGTTC
66 GCCTCAATCTTTTAATTGCAATGTCGGGGAAAA-GAAGATTCGCCATTGTAGCTTCAATCTGTTC
*
4661685 CGCTGCA-TCGCCTGGGAATAAGATTTGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
130 CGCTGCACT-GCCTGGGAATAAGATTTGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
4661749 AAAC
194 AAAC
* * * * *
4661753 AAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACTGCTTGCGAAGTAAGATTTGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCCTG-GAAATAAGATTTGCCGTTGT
* * * * *
4661818 GGCCTCAATCTTTTAATTGCAATGTCAGGG--AAGCAAGATTCACCGTTGTAGTTTCAATCTATT
65 GGCCTCAATCTTTTAATTGCAATGTCGGGGAAAAG-AAGATTCGCCATTGTAGCTTCAATCTGTT
* *
4661881 CCGCTGCACCGCCTGGGAATAAGATTTGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
129 CCGCTGCACTGCCTGGGAATAAGATTTGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
4661946 AAAC
194 AAAC
* * * * * * *
4661950 AAGATTCACCGTTATAGCTTCAATCTATTTCGCTGCACCGCTTGGGAAGTAAGATTTGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCCT-GGAAATAAGATTTGCCGTTGT
* *
4662015 GGCCTCAATTTTTTAATTGCAATGTCGGGG--AAGCAAGATTCGCCATTGTAGTTTCAATCTGTT
65 GGCCTCAATCTTTTAATTGCAATGTCGGGGAAAAG-AAGATTCGCCATTGTAGCTTCAATCTGTT
* * * *
4662078 CTGCTGTACTGCCTGGGAATAAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGG
129 CCGCTGCACTGCCTGGGAATAAGATTTGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
*
4662143 AATC
194 AAAC
* * * * *
4662147 AAAATTCGCTGTCGTAGCTTCAATCTATTCCACTGCACCT-CCTGGGAATAAGATTTACCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCA-CTGCCTGGAAATAAGATTTGCCGTTGT
* * * * * *
4662211 GGCTTCAATTTTTTAATTGCAATATCGGGG--AAGCAAAATTTGCCATTGTAGCTTCAATATGTT
65 GGCCTCAATCTTTTAATTGCAATGTCGGGGAAAAG-AAGATTCGCCATTGTAGCTTCAATCTGTT
* *
4662274 CCGCTGCACTGCCTGGGAATAAGATTTACCGTTGTGGCCTCAATCTTTTAATTG
129 CCGCTGCACTGCCTGGGAATAAGATTTGCCGTTGTGGCTTCAATCTTTTAATTG
4662328 GAAACTATGG
Statistics
Matches: 684, Mismatches: 78, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
195 1 0.00
196 133 0.19
197 376 0.55
198 137 0.20
199 37 0.05
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (197 bp):
AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCCTGGAAATAAGATTTGCCGTTGTG
GCCTCAATCTTTTAATTGCAATGTCGGGGAAAAGAAGATTCGCCATTGTAGCTTCAATCTGTTCC
GCTGCACTGCCTGGGAATAAGATTTGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAA
AC
Found at i:4661947 original size:98 final size:98
Alignment explanation
Indices: 4661357--4662327 Score: 1129
Period size: 98 Copynumber: 9.8 Consensus size: 98
4661347 TCAGGGCATT
* * * * ** *
4661357 AAGATTCGTCGTTGTAGCTTCAATCTATCCCACTGCACCGCCTAGGAAATAAGATTCACCATTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCT-GGGAATAAGATTTGCCGTTGT
* * * *
4661422 GACTTCAATCTTTAAATTGCAATGTCGGAGAAAAC
65 GGCTTCAATCTTTTAATTGCAATGTCGG-GGAAGC
* * * * * *
4661457 AAGATTTGTCATTGTAGCTTCAATCTATTTCGCTGCACTGCCTGAGAAGTAAGATTTGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAA-TAAGATTTGCCGTTGT
* * *
4661522 GGCCTT-AATATTTTAATTGCAATGTCGAGAAAGC
65 GG-CTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * * ** * * *
4661556 AAGATTTGCCGTCGTAGCTTCAATATGTTCTACTGCACTGCCTGGAAATAAGATTCGCCGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
* *
4661621 GCATCAATCTTTTAATTGTAATGTCGGGGAA--
66 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
** * * *
4661652 AATGAAATTCATCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAATAAGATTTGCTGTT
1 AA-G--ATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTT
*
4661717 GTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAAC
63 GTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * * *
4661753 AAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACTGCTTGCGAAGTAAGATTTGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAA-TAAGATTTGCCGTTGT
* *
4661818 GGCCTCAATCTTTTAATTGCAATGTCAGGGAAGC
65 GGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * *
4661852 AAGATTCACCGTTGTAGTTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCTGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
*
4661917 GCTTCAATCTTTTAATTGCAATGTCGGGGAAAC
66 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * *
4661950 AAGATTCACCGTTATAGCTTCAATCTATTTCGCTGCACCGCTTGGGAAGTAAGATTTGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAA-TAAGATTTGCCGTTGT
* *
4662015 GGCCTCAATTTTTTAATTGCAATGTCGGGGAAGC
65 GGCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * * * *
4662049 AAGATTCGCCATTGTAGTTTCAATCTGTTCTGCTGTACTGCCTGGGAATAAGATTTGCCGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
* * *
4662114 GCCTCAATCTTTTAATTGCAATGTCAGGGAATC
66 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * * * *
4662147 AAAATTCGCTGTCGTAGCTTCAATCTATTCCACTGCACCTCCTGGGAATAAGATTTACCGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
* *
4662212 GCTTCAATTTTTTAATTGCAATATCGGGGAAGC
66 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
* * * * * * *
4662245 AAAATTTGCCATTGTAGCTTCAATATGTTCCGCTGCACTGCCTGGGAATAAGATTTACCGTTGTG
1 AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
*
4662310 GCCTCAATCTTTTAATTG
66 GCTTCAATCTTTTAATTG
4662328 GAAACTATGG
Statistics
Matches: 748, Mismatches: 113, Indels: 22
0.85 0.13 0.02
Matches are distributed among these distances:
96 2 0.00
97 3 0.00
98 369 0.49
99 298 0.40
100 71 0.09
101 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (98 bp):
AAGATTCGCCGTTGTAGCTTCAATCTATTCCGCTGCACCGCCTGGGAATAAGATTTGCCGTTGTG
GCTTCAATCTTTTAATTGCAATGTCGGGGAAGC
Found at i:4662121 original size:49 final size:48
Alignment explanation
Indices: 4661457--4662324 Score: 411
Period size: 49 Copynumber: 17.6 Consensus size: 48
4661447 CGGAGAAAAC
* * ** * *
4661457 AAGATTTGTCATTGTAGCTTCAATCTATTTCGCTGCACTGCCTGAGAAGT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCAATGCCTGGGAA-T
* * * * * *
4661507 AAGATTTGCCGTTGTGGCCTT-AATATTTTAATTGCAATGTC-GAGAAAGC
1 AAGATTTGCCGTTGTAG-CTTCAATCTTTTAACTGCAATGCCTG-GGAA-T
* * * *
4661556 AAGATTTGCCGTCGTAGCTTCAATATGTTCT-ACTGCACTGCCTGGAAAT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TT-TAACTGCAATGCCTGGGAAT
* * * * * * *
4661605 AAGATTCGCCGTTGTGGCATCAATCTTTTAATTGTAATGTCGGGGAA-
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAAT
* ***
4661652 AATGAAATT-CATCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGGGAAT
1 AA-G-ATTTGC--CGTTGTAGCTTCAATCT-TTTAACTGCAAT-GCCTGGGAAT
* * * * * *
4661704 AAGATTTGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAAC
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGG-AAT
** *** * * *
4661753 AAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACTGCTTGCGAAGT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCAATGCCTGGGAA-T
* * * * * *
4661803 AAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGC
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAA-T
** * *** **
4661852 AAGATTCACCGTTGTAGTTTCAATCTATTCCGCTGCACCGCCTGGGAAT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCAATGCCTGGGAAT
* * * * * *
4661901 AAGATTTGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAAC
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGG-AAT
** * ** ** *
4661950 AAGATTCACCGTTATAGCTTCAATCTATTTCGCTGCACCGCTTGGGAAGT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCAATGCCTGGGAA-T
* * * * * * *
4662000 AAGATTTGCCGTTGTGGCCTCAATTTTTTAATTGCAATGTCGGGGAAGC
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAA-T
* * * * * *
4662049 AAGATTCGCCATTGTAGTTTCAATCTGTTCT-GCTGTACTGCCTGGGAAT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TT-TAACTGCAATGCCTGGGAAT
* * * * *
4662098 AAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAT
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAAT
* * * * ** *
4662146 CAAAATTCGCTGTCGTAGCTTCAATCTATTCCACTGCACCT-CCTGGGAAT
1 -AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCA-ATGCCTGGGAAT
* * * * ** * *
4662196 AAGATTTACCGTTGTGGCTTCAATTTTTTAATTGCAATATCGGGGAAGC
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAA-T
* * * *** *
4662245 AAAATTTGCCATTGTAGCTTCAATATGTTCCGCTGCACTGCCTGGGAAT
1 AAGATTTGCCGTTGTAGCTTCAATCT-TTTAACTGCAATGCCTGGGAAT
* * *
4662294 AAGATTTACCGTTGTGGCCTCAATCTTTTAA
1 AAGATTTGCCGTTGTAGCTTCAATCTTTTAA
4662325 TTGGAAACTA
Statistics
Matches: 578, Mismatches: 208, Indels: 66
0.68 0.24 0.08
Matches are distributed among these distances:
47 5 0.01
48 69 0.12
49 314 0.54
50 168 0.29
51 20 0.03
52 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (48 bp):
AAGATTTGCCGTTGTAGCTTCAATCTTTTAACTGCAATGCCTGGGAAT
Found at i:4669723 original size:23 final size:22
Alignment explanation
Indices: 4669678--4669724 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4669668 CGAAAATATA
*
4669678 TTAAATATATATATTTTTATTT
1 TTAAATATATATAGTTTTATTT
*
4669700 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TAGTTTTATTT
4669722 TTA
1 TTA
4669725 TTTTAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAAATATATATAGTTTTATTT
Found at i:4669865 original size:40 final size:40
Alignment explanation
Indices: 4669819--4669928 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
4669809 AACAATTAAT
4669819 ACAATTAACAATTAATAATTTTACTAACAAAATGTTAGTA
1 ACAATTAACAATTAATAATTTTACTAACAAAATGTTAGTA
* * *
4669859 ACAATTAATAATTAATAATTTGA-T-----AATTTTAGTA
1 ACAATTAACAATTAATAATTTTACTAACAAAATGTTAGTA
4669893 ACAATTAATACAATTAATAATTTTACTAACAAAATG
1 ACAATT-A-ACAATTAATAATTTTACTAACAAAATG
4669929 ATAGATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
34 15 0.27
35 1 0.02
36 14 0.25
37 1 0.02
39 1 0.02
40 21 0.38
42 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (40 bp):
ACAATTAACAATTAATAATTTTACTAACAAAATGTTAGTA
Found at i:4669916 original size:28 final size:27
Alignment explanation
Indices: 4669868--4669924 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
4669858 AACAATTAAT
* * *
4669868 AATTAATAATTTGATAATTTTAGTAAC
1 AATTAATAAATTAATAATTTTACTAAC
4669895 AATTAATACAATTAATAATTTTACTAAC
1 AATTAATA-AATTAATAATTTTACTAAC
4669923 AA
1 AA
4669925 AATGATAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (27 bp):
AATTAATAAATTAATAATTTTACTAAC
Found at i:4669997 original size:16 final size:16
Alignment explanation
Indices: 4669978--4670034 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
4669968 AATTTGATAC
*
4669978 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
4669994 AATTTTGATAACAATT
1 AATTTTAATAACAATT
4670010 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
4670026 AGTTTTAAT
1 AATTTTAAT
4670035 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:4670018 original size:22 final size:23
Alignment explanation
Indices: 4670008--4670069 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
4669998 TTGATAACAA
* *
4670008 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
4670030 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
4670053 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
4670070 ACGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:4671852 original size:31 final size:31
Alignment explanation
Indices: 4671814--4671885 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
4671804 ATAAAAAAAA
* * *
4671814 TTCATTTTGGGTATTGCCATTGAAACCCATT
1 TTCATTTTGGGCATTGCCATTAAAAACCATT
* * * *
4671845 TTTATTTTAGGCATTGCCGTTAAAAATCATT
1 TTCATTTTGGGCATTGCCATTAAAAACCATT
4671876 TTCATTTTGG
1 TTCATTTTGG
4671886 TCACTCGCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (31 bp):
TTCATTTTGGGCATTGCCATTAAAAACCATT
Found at i:4672865 original size:3 final size:3
Alignment explanation
Indices: 4672857--4672886 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4672847 TGTAGAATCC
4672857 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4672887 TTGTTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4674316 original size:30 final size:30
Alignment explanation
Indices: 4674282--4674346 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
4674272 AAAAAAATTG
* *
4674282 ATTTTAGGTATTGCCATT-AAAACCATTTTC
1 ATTTTAGGCATTGCCATTAAAAACTA-TTTC
*
4674312 ATTTTAGGCATTGTCATTAAAAACTATTTC
1 ATTTTAGGCATTGCCATTAAAAACTATTTC
4674342 ATTTT
1 ATTTT
4674347 GGTCACCCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (30 bp):
ATTTTAGGCATTGCCATTAAAAACTATTTC
Found at i:4681393 original size:16 final size:16
Alignment explanation
Indices: 4681372--4681402 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4681362 AAAATTGAAT
4681372 AACAGACGAAGGAGGC
1 AACAGACGAAGGAGGC
4681388 AACAGACGAAGGAGG
1 AACAGACGAAGGAGG
4681403 AACCGAGCGG
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:0.45, C:0.16, G:0.39, T:0.00
Consensus pattern (16 bp):
AACAGACGAAGGAGGC
Found at i:4685829 original size:25 final size:28
Alignment explanation
Indices: 4685782--4685835 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
4685772 ATCGCTTGCT
*
4685782 AATAATATTTATCAGATTTTTTAATAAA
1 AATAATATTTATCAGATTATTTAATAAA
*
4685810 AATAATATTT-T-A-ATTATTTATTAAA
1 AATAATATTTATCAGATTATTTAATAAA
4685835 A
1 A
4685836 GTTTATTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 1 0.04
27 1 0.04
28 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
AATAATATTTATCAGATTATTTAATAAA
Found at i:4690114 original size:2 final size:2
Alignment explanation
Indices: 4690107--4690131 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4690097 CGCCATTTCT
4690107 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 T
4690132 TGTGAGACCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4691528 original size:21 final size:20
Alignment explanation
Indices: 4691481--4691529 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4691471 TATATACATG
4691481 TACATATTATTTATTTATTT
1 TACATATTATTTATTTATTT
* *
4691501 TAAATATATATTTTTTTATATT
1 TACATAT-TATTTATTTAT-TT
4691523 T-CATATT
1 TACATATT
4691530 CCCTACATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TACATATTATTTATTTATTT
Found at i:4693760 original size:31 final size:31
Alignment explanation
Indices: 4693725--4693790 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
4693715 ATTAAAAAAC
* * *
4693725 AATTC-AACTCTTTTTGAAATATTGATGGTCA
1 AATTCTAA-TCTTTTTAAAAGATTGAAGGTCA
*
4693756 AATTCTAATCTTTTTAAAAGGTTGAAGGTCA
1 AATTCTAATCTTTTTAAAAGATTGAAGGTCA
4693787 AATT
1 AATT
4693791 TAGTTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (31 bp):
AATTCTAATCTTTTTAAAAGATTGAAGGTCA
Found at i:4693989 original size:31 final size:31
Alignment explanation
Indices: 4693948--4694045 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 31
4693938 TATCATTCGG
*
4693948 TACCTAAGTTTGACTTTAATATTTAATTTGA
1 TACCTGAGTTTGACTTTAATATTTAATTTGA
* * *
4693979 TACTTGAGTTT---TTT--T-TTCAATTTGG
1 TACCTGAGTTTGACTTTAATATTTAATTTGA
*
4694004 TACCTAAGTTTGACTTTAATATTTAATTTGA
1 TACCTGAGTTTGACTTTAATATTTAATTTGA
*
4694035 TGCCTGAGTTT
1 TACCTGAGTTT
4694046 TCTTATTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
25 17 0.33
26 1 0.02
28 6 0.12
30 1 0.02
31 26 0.51
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (31 bp):
TACCTGAGTTTGACTTTAATATTTAATTTGA
Found at i:4697209 original size:21 final size:21
Alignment explanation
Indices: 4697185--4697270 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
4697175 CGAACTTCTG
*
4697185 TTTAACT-TATATGAGTTTCCA
1 TTTAACTCT-TATGAGCTTCCA
* *
4697206 TTTAGCTCTTTTGAGCTTCCA
1 TTTAACTCTTATGAGCTTCCA
* * * *
4697227 TTTAACCCTTATGGGTTTCCG
1 TTTAACTCTTATGAGCTTCCA
* *
4697248 TTCAGCTCTTATGAGCTTCCA
1 TTTAACTCTTATGAGCTTCCA
4697269 TT
1 TT
4697271 CAGCCCTTAT
Statistics
Matches: 49, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 48 0.98
22 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (21 bp):
TTTAACTCTTATGAGCTTCCA
Found at i:4697231 original size:42 final size:42
Alignment explanation
Indices: 4697194--4697287 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
4697184 GTTTAACTTA
* *
4697194 TATGAGTTTCCATTTAGCTCTTTTGAGCTTCCATTTAACCCT
1 TATGAGTTTCCATTCAGCTCTTATGAGCTTCCATTTAACCCT
* * * *
4697236 TATGGGTTTCCGTTCAGCTCTTATGAGCTTCCATTCAGCCCT
1 TATGAGTTTCCATTCAGCTCTTATGAGCTTCCATTTAACCCT
*
4697278 TATGGGTTTC
1 TATGAGTTTC
4697288 TGTTTAGCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (42 bp):
TATGAGTTTCCATTCAGCTCTTATGAGCTTCCATTTAACCCT
Found at i:4697272 original size:21 final size:21
Alignment explanation
Indices: 4697194--4697281 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
4697184 GTTTAACTTA
* * *
4697194 TATGAGTTTCCATTTAGCTCT
1 TATGAGCTTCCATTCAGCCCT
* * *
4697215 TTTGAGCTTCCATTTAACCCT
1 TATGAGCTTCCATTCAGCCCT
* * * *
4697236 TATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCCATTCAGCCCT
4697257 TATGAGCTTCCATTCAGCCCT
1 TATGAGCTTCCATTCAGCCCT
4697278 TATG
1 TATG
4697282 GGTTTCTGTT
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (21 bp):
TATGAGCTTCCATTCAGCCCT
Found at i:4697297 original size:42 final size:42
Alignment explanation
Indices: 4697206--4697329 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
4697196 TGAGTTTCCA
* * * *
4697206 TTTAGCTCTTTTGAGCTTCCATTTAACCCTTATGGGTTTCCG
1 TTTAGCTCTTATGAGCTTCCATTCAGCCCTTATGGGTTTCTG
*
4697248 TTCAGCTCTTATGAGCTTCCATTCAGCCCTTATGGGTTTCTG
1 TTTAGCTCTTATGAGCTTCCATTCAGCCCTTATGGGTTTCTG
* * ** *
4697290 TTTAGCTCTCATGATCTTCTGTTCAG-CCTT-TGGGCTTCTG
1 TTTAGCTCTTATGAGCTTCCATTCAGCCCTTATGGGTTTCTG
4697330 AAAATGATGT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 9 0.13
41 4 0.06
42 58 0.82
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (42 bp):
TTTAGCTCTTATGAGCTTCCATTCAGCCCTTATGGGTTTCTG
Found at i:4703110 original size:13 final size:13
Alignment explanation
Indices: 4703092--4703116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4703082 CCTTAAAGAC
4703092 TTATATTTTATTA
1 TTATATTTTATTA
4703105 TTATATTTTATT
1 TTATATTTTATT
4703117 CAACTTATCT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATATTTTATTA
Found at i:4703148 original size:17 final size:17
Alignment explanation
Indices: 4703126--4703163 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4703116 TCAACTTATC
4703126 TACCAACAGTTCTTGTT
1 TACCAACAGTTCTTGTT
4703143 TACCAACAGTTCTTGTT
1 TACCAACAGTTCTTGTT
4703160 TACC
1 TACC
4703164 TTGTTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (17 bp):
TACCAACAGTTCTTGTT
Found at i:4709491 original size:5 final size:5
Alignment explanation
Indices: 4709481--4709511 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4709471 TATCTTCTTC
4709481 AAATT AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT AAATT A
4709512 TTTAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:4710844 original size:18 final size:18
Alignment explanation
Indices: 4710802--4710844 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4710792 TCACTGTGTT
*
4710802 TTTTTTTCATTATTTTTA
1 TTTTTTTCATTATTATTA
***
4710820 AAATTTTCATTATTATTA
1 TTTTTTTCATTATTATTA
4710838 TTTTTTT
1 TTTTTTT
4710845 TGTAATTCCA
Statistics
Matches: 18, Mismatches: 7, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTCATTATTATTA
Found at i:4717314 original size:51 final size:52
Alignment explanation
Indices: 4717223--4717321 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 52
4717213 GAAGAAGGAA
* * * * * *
4717223 CCAAGGTGAAAGCCCGCAAATGGCGCTTTGATTTCTAAAAAA-AAAAAGGGG
1 CCAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAAAGGGG
* *
4717274 CCAAGGTGAAAACTCACAAAGGGTGCTTTGAGTCCAAAAAAATAAAAA
1 CCAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAAA
4717322 TCAAAATCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 34 0.87
52 5 0.13
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (52 bp):
CCAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAAAGGGG
Found at i:4718683 original size:44 final size:44
Alignment explanation
Indices: 4718618--4719636 Score: 1046
Period size: 44 Copynumber: 23.0 Consensus size: 44
4718608 TAGAAAGGAT
* *
4718618 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGGTCCAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * *
4718662 AACAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * * *
4718706 AGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
* * *
4718751 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * * * *
4718795 AGCAAATTTTGTCTTCCTATACTGGTG-GCAAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGAA
* * * *
4718840 AACAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
4718884 AGCAGATCTTGTCTTCCCATACTAGT-G-GTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCGAAGAA
* * * *
4718929 AACGGATCTTGTCTTCATGTATTGGCGTGAAGTGGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * * *
4718973 AGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATAC
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*** * * *
4719017 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
** *
4719062 AATAGATCTTGTCTTCATGGATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
4719106 AGCTGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAG
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * * *
4719150 AGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*** * * * *
4719194 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
* * * *
4719239 AACAAATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
4719283 AGC-GAATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGAA
1 AGCAG-ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
4719327 AGCGGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
4719371 AGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
4719415 AGCAGATCTTGTCTTCATGTATTGGCGTGAGGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
4719459 AGCAGATCTTGTTTTCCCATACTAGTGGC--GAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCGAAGAA
* * * * *
4719504 AGTAGATCTTATATTCATGTATTGGCGTGAAGTAGAT-AAAAAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *** * *
4719547 TAGCAGATCTTATCTTCCCATACTGGTG-GCAAAGTAGATCGAAGAA
1 -AGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGAA
* * **
4719593 AGCAGATATTGTCTTCCTGTATCAGCAGTGAAGTAGATCGAAGA
1 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGA
4719637 TACAAGTCTT
Statistics
Matches: 797, Mismatches: 154, Indels: 47
0.80 0.15 0.05
Matches are distributed among these distances:
42 9 0.01
43 13 0.02
44 524 0.66
45 228 0.29
46 13 0.02
47 10 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
Found at i:4718765 original size:89 final size:88
Alignment explanation
Indices: 4718618--4719636 Score: 1055
Period size: 89 Copynumber: 11.5 Consensus size: 88
4718608 TAGAAAGGAT
* * *
4718618 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGGTCCAAGAAAACAGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* *
4718683 TTGGCGTGAAATAGATCAAAGAT
66 TTGGCGTGAAGTAGATCAAAGAA
* * * * * *
4718706 AGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
4718771 ATTGGCGTGAAGTAGATCAAAGAT
65 ATTGGCGTGAAGTAGATCAAAGAA
* * * * * * * *
4718795 AGCAAATTTTGTCTTCCTATACTGGTG-GCAAAGTAGATCGAAGAAAACAGATCTTATCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATG
*
4718859 TATTGGCGTGAAGTAGATCAAAGAT
64 TATTGGCGTGAAGTAGATCAAAGAA
* * * *
4718884 AGCAGATCTTGTCTTCCCATACTAGT-G-GTGAAGTAGATCGAAGAAAACGGATCTTGTCTTCAT
1 AGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCAT
*
4718947 GTATTGGCGTGAAGTGGATCAAAGAA
63 GTATTGGCGTGAAGTAGATCAAAGAA
* * * * * ***
4718973 AGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATACAGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* * **
4719038 CTGGTGGTGAAGTAGATTGAAGAA
66 TTGG-CGTGAAGTAGATCAAAGAA
** * *
4719062 AATAGATCTTGTCTTCATGGATTGGCGTGAAGTAGATCGAAGAAAGCTGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
*
4719127 TTGGCGTGAAGTAGATCAAAGAG
66 TTGGCGTGAAGTAGATCAAAGAA
* * * * * ***
4719150 AGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATATAGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* * *
4719215 CTGGTGGCGAAGTAGATCAAAGAA
66 TTGG-CGTGAAGTAGATCAAAGAA
* * * *
4719239 AACAAATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAAAGC-GAATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAG-ATCTTGTCTTCATGT
* * *
4719303 ACTGGCATGAAGTAGATCGAAGAA
65 ATTGGCGTGAAGTAGATCAAAGAA
* * *
4719327 AGCGGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
*
4719392 TTGGCGTGAAGTAGATCGAAGAA
66 TTGGCGTGAAGTAGATCAAAGAA
* * *
4719415 AGCAGATCTTGTCTTCATGTATTGGCGTGAGGTAGATCGAAGATAGCAGATCTTGTTTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT--CAT-
* * *
4719480 CTAGTGGC--GAAGTAGATCGAAGAA
63 GTATTGGCGTGAAGTAGATCAAAGAA
* * * * * * ***
4719504 AGTAGATCTTATATTCATGTATTGGCGTGAAGTAGAT-AAAAAATAGCAGATCTTATCTTCCCAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGT
* * *
4719568 ACTGGTG-GCAAAGTAGATCGAAGAA
65 ATTGGCGTG--AAGTAGATCAAAGAA
* * **
4719593 AGCAGATATTGTCTTCCTGTATCAGCAGTGAAGTAGATCGAAGA
1 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGA
4719637 TACAAGTCTT
Statistics
Matches: 786, Mismatches: 123, Indels: 41
0.83 0.13 0.04
Matches are distributed among these distances:
86 8 0.01
87 7 0.01
88 280 0.36
89 461 0.59
90 14 0.02
91 13 0.02
92 3 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
TTGGCGTGAAGTAGATCAAAGAA
Found at i:4718779 original size:133 final size:132
Alignment explanation
Indices: 4718618--4719636 Score: 1037
Period size: 133 Copynumber: 7.7 Consensus size: 132
4718608 TAGAAAGGAT
* * *
4718618 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGGTCCAAGAAAACAGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* * * * * * * *
4718683 TTGGCGTGAAATAGATCAAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCGAA
66 TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAA
4718748 GAA
130 GAA
* * * * * * *
4718751 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAAATTTTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* * * * *
4718816 CTGGTG-GCAAAGTAGATCGAAGAAAACAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAA
66 TTGGCGTG--AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAA
*
4718880 AGAT
129 AGAA
* * * *
4718884 AGCAGATCTTGTCTTCCCATACTAGT-G-GTGAAGTAGATCGAAGAAAACGGATCTTGTCTTCAT
1 AGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCAT
* * *
4718947 GTATTGGCGTGAAGTGGATCAAAGAAAGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCA
63 GTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
* *
4719012 AATAC
128 AAGAA
*** * * * ** *
4719017 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGAAAATAGATCTTGTCTTCATGG
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* *
4719082 ATTGGCGTGAAGTAGATCGAAGAAAGCTGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAA
65 ATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAA
*
4719147 GAG
130 GAA
* * * * * ***
4719150 AGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAATATAGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
* * * * * * * *
4719215 CTGGTGGCGAAGTAGATCAAAGAAAACAAATATTGTCTTCATGTATTGGCATGAAGTAGATCGAA
66 TTGG-CGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAA
4719280 GAA
130 GAA
* * * *
4719283 AGC-GAATCTTGTCTTCATGTACTGGCATGAAGTAGATCGAAGAAAGCGGATCTTATCTTCATGT
1 AGCAG-ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* * *
4719347 ATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAA
65 ATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAA
4719412 GAA
130 GAA
* * *
4719415 AGCAGATCTTGTCTTCATGTATTGGCGTGAGGTAGATCGAAGATAGCAGATCTTGTTTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT--CAT-
* * * * * *
4719480 CTAGTGGC--GAAGTAGATCGAAGAAAGTAGATCTTATATTCATGTATTGGCGTGAAGTAGAT-A
63 GTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
*
4719542 AAAAA
128 AAGAA
* *** * * * *
4719547 TAGCAGATCTTATCTTCCCATACTGGTG-GCAAAGTAGATCGAAGAAAGCAGATATTGTCTTCCT
1 -AGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGAAAGCAGATCTTGTCTTCAT
** *
4719611 GTATCAGCAGTGAAGTAGATCGAAGA
63 GTATTGGC-GTGAAGTAGATCAAAGA
4719637 TACAAGTCTT
Statistics
Matches: 729, Mismatches: 136, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
130 3 0.00
131 6 0.01
132 146 0.20
133 449 0.62
134 111 0.15
135 11 0.02
136 3 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (132 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAG
AA
Found at i:4720309 original size:21 final size:23
Alignment explanation
Indices: 4720284--4720328 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
4720274 GCGCCGTACA
4720284 TCGTG-CAACCGCTCC-CGCACG
1 TCGTGCCAACCGCTCCGCGCACG
**
4720305 TCGTGCCTGCCGCTCCGCGCACG
1 TCGTGCCAACCGCTCCGCGCACG
4720328 T
1 T
4720329 TCTCCTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.09, C:0.47, G:0.27, T:0.18
Consensus pattern (23 bp):
TCGTGCCAACCGCTCCGCGCACG
Found at i:4724985 original size:3 final size:3
Alignment explanation
Indices: 4724977--4725056 Score: 106
Period size: 3 Copynumber: 26.3 Consensus size: 3
4724967 AAAATAAAGC
* * * * *
4724977 TAA TAA TAA TTAA TAA TAG TAG TAA TAA TTA TAA TAG TAA TGA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4725023 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4725057 TAATTAAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4728236 original size:16 final size:16
Alignment explanation
Indices: 4728217--4728264 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
4728207 CTATTACATT
4728217 TCTATTTCATTACAGC
1 TCTATTTCATTACAGC
*
4728233 TCTA-TTCAATTAAAGC
1 TCTATTTC-ATTACAGC
*
4728249 TCTATTCCATTACAGC
1 TCTATTTCATTACAGC
4728265 GAACCAGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.11
16 22 0.81
17 2 0.07
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (16 bp):
TCTATTTCATTACAGC
Found at i:4729343 original size:43 final size:43
Alignment explanation
Indices: 4729296--4729386 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
4729286 ACTAAAAGTA
*
4729296 TTTTTGAGAGAAGAAAAACTAAAAATTTTAGTTTCTCCTTTTT
1 TTTTTGAGAGAAGAAAAACTAAAAATTTTAGTTTCTCCTCTTT
4729339 TTTTTGAGAGAAGAAAAACTAAAAATTTTAGTTTCTCCTCTTT
1 TTTTTGAGAGAAGAAAAACTAAAAATTTTAGTTTCTCCTCTTT
4729382 TTTTT
1 TTTTT
4729387 CAAAAGTACT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (43 bp):
TTTTTGAGAGAAGAAAAACTAAAAATTTTAGTTTCTCCTCTTT
Found at i:4730952 original size:43 final size:44
Alignment explanation
Indices: 4730868--4731025 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 44
4730858 GATGTGATCT
* * * *
4730868 CGTGTAAGACCACGTCTAGGACATTGG-TTCGATTTGA-GATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-ATGATTTA
*
4730911 CGTGTAAGACCATGTCTGAGACATTGGCATCG-TATATGATTT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTA
* * * *
4730953 CGCGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA-TTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTA
* * * *
4730996 CATGTAAGTCCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
4731026 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 31 0.33
43 60 0.64
44 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTA
Found at i:4730969 original size:42 final size:44
Alignment explanation
Indices: 4730905--4730994 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 44
4730895 TTCGATTTGA
* *
4730905 GATTTACGTGTAAGACCATGTCTGAGACATTGGCATCG-TATAT
1 GATTTACGCGTAAGACCATGTCTGAGACAGTGGCATCGATATAT
* * *
4730948 GATTT-CGCGTAAGACCCTGTCTGGGACAGTGGCATCGATATTT
1 GATTTACGCGTAAGACCATGTCTGAGACAGTGGCATCGATATAT
4730991 GATT
1 GATT
4730995 ACATGTAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 28 0.68
43 13 0.32
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (44 bp):
GATTTACGCGTAAGACCATGTCTGAGACAGTGGCATCGATATAT
Found at i:4735011 original size:23 final size:23
Alignment explanation
Indices: 4734977--4735458 Score: 339
Period size: 23 Copynumber: 20.6 Consensus size: 23
4734967 TTCACACCAA
4734977 AAATTGGACAGCATATATACAAC
1 AAATTGGACAGCATATATACAAC
* *
4735000 AATTTGGGCAGCATATAT-CAATC
1 AAATTGGACAGCATATATACAA-C
* * *
4735023 AAATTGAACAGCAT-TTTAGCATAA
1 AAATTGGACAGCATATATA-CA-AC
4735047 AAATTGGACAGCATATATACAAC
1 AAATTGGACAGCATATATACAAC
* * * *
4735070 AATTTGGGCAGCCTATATATATACC
1 AAATTGGACAG-C-ATATATACAAC
* * *
4735095 AAATT-GAGCAGCATTTTTACATC
1 AAATTGGA-CAGCATATATACAAC
4735118 AAAATTGGACAGCATATATACAAC
1 -AAATTGGACAGCATATATACAAC
** ** *
4735142 AGTTTGGGTAGCATAAATACAAC
1 AAATTGGACAGCATATATACAAC
* * *
4735165 AAATTGGGCAGCATTTA-AGCATAA
1 AAATTGGACAGCATATATA-CA-AC
*
4735189 AAATTGGACAGCATATATGCAAC
1 AAATTGGACAGCATATATACAAC
* * * *
4735212 AATTTGGGCAGCATAAATATAAC
1 AAATTGGACAGCATATATACAAC
* *
4735235 AAATTGGACAGCAT-TTTAGCATAA
1 AAATTGGACAGCATATATA-CA-AC
* * *
4735259 AAATTTGACAGCATATATGCACC
1 AAATTGGACAGCATATATACAAC
* * *
4735282 AATTTGGGCAGCATAAATACAAC
1 AAATTGGACAGCATATATACAAC
* *
4735305 AAATTGGACAGCAT-TTTAGCATAA
1 AAATTGGACAGCATATATA-CA-AC
* * *
4735329 AAATTTGACAGCATATGTGCAAC
1 AAATTGGACAGCATATATACAAC
* * * *
4735352 AATTTGGGCAGCATATATATACC
1 AAATTGGACAGCATATATACAAC
* * *
4735375 AAATT-GAGCAGCATTTTTACATC
1 AAATTGGA-CAGCATATATACAAC
*
4735398 AAAATTGGACAGCATATATGCAAC
1 -AAATTGGACAGCATATATACAAC
* * *
4735422 AATTTGGGCAGCATAAATACAAC
1 AAATTGGACAGCATATATACAAC
4735445 AAATTGGACAGCAT
1 AAATTGGACAGCAT
4735459 TTAAGCATAA
Statistics
Matches: 345, Mismatches: 92, Indels: 44
0.72 0.19 0.09
Matches are distributed among these distances:
22 11 0.03
23 203 0.59
24 103 0.30
25 28 0.08
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
AAATTGGACAGCATATATACAAC
Found at i:4735067 original size:70 final size:69
Alignment explanation
Indices: 4734958--4735473 Score: 643
Period size: 70 Copynumber: 7.3 Consensus size: 69
4734948 TACCAAACTA
* *
4734958 GACAGCATTTTCA-CACCAAAAATTGGACAGCATATATACAACAATTTGGGCAGCATATATCAAT
1 GACAGCATTTT-AGCA-TAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATCAA-
4735022 CAAATTG
63 CAAATTG
* *
4735029 AACAGCATTTTAGCATAAAAATTGGACAGCATATATACAACAATTTGGGCAGCCTATATAT-ATA
1 GACAGCATTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAG-C-ATATATCA-A
4735093 CCAAATT-
63 -CAAATTG
* * * * *
4735100 GAGCAGCATTTTTA-CATCAAAATTGGACAGCATATATACAACAGTTTGGGTAGCATAAATACAA
1 GA-CAGCA-TTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATAT-CAA
4735164 CAAATTG
63 CAAATTG
* *
4735171 GGCAGCATTTAAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATAT-AAC
1 GACAGCATTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCAT--ATATCAAC
4735235 AAATTG
64 AAATTG
* * *
4735241 GACAGCATTTTAGCATAAAAATTTGACAGCATATATGCACCAATTTGGGCAGCATAAATACAACA
1 GACAGCATTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATAT-CAACA
4735306 AATTG
65 AATTG
* *
4735311 GACAGCATTTTAGCATAAAAATTTGACAGCATATGTGCAACAATTTGGGCAGCATATAT-ATACC
1 GACAGCATTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATCA-A-C
4735375 AAATT-
64 AAATTG
* *
4735380 GAGCAGCATTTTTA-CATCAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAA
1 GA-CAGCA-TTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATAT-CAA
4735444 CAAATTG
63 CAAATTG
*
4735451 GACAGCATTTAAGCATAAAAATT
1 GACAGCATTTTAGCATAAAAATT
4735474 ACATGAACAT
Statistics
Matches: 394, Mismatches: 29, Indels: 45
0.84 0.06 0.10
Matches are distributed among these distances:
68 4 0.01
69 11 0.03
70 289 0.73
71 26 0.07
72 59 0.15
73 5 0.01
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (69 bp):
GACAGCATTTTAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATCAACAA
ATTG
Found at i:4735220 original size:47 final size:47
Alignment explanation
Indices: 4734977--4735473 Score: 295
Period size: 47 Copynumber: 10.6 Consensus size: 47
4734967 TTCACACCAA
* * *
4734977 AAATTGGACAGCATATATA-CA-ACAATTTGGGCAGCATATAT-CAATC
1 AAATTGGACAGCATATA-AGCATAAAAATTGGACAGCATATATACAA-C
* * *
4735023 AAATTGAACAGCATTTTAGCATAAAAATTGGACAGCATATATACAAC
1 AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
* * * * * * * *
4735070 AATTTGGGCAGCCTATATA-TATACCAAATT-GAGCAGCATTTTTACATC
1 AAATTGGACAGCATATA-AGCATA-AAAATTGGA-CAGCATATATACAAC
* ** ** *
4735118 AAAATTGGACAGCATATATA-CA-ACAGTTTGGGTAGCATAAATACAAC
1 -AAATTGGACAGCATATA-AGCATAAAAATTGGACAGCATATATACAAC
* * *
4735165 AAATTGGGCAGCATTTAAGCATAAAAATTGGACAGCATATATGCAAC
1 AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
* * * * *
4735212 AATTTGGGCAGCATA-AA-TATAACAAATTGGACAGCAT-TTTAGCATAA
1 AAATTGGACAGCATATAAGCATAA-AAATTGGACAGCATATATA-CA-AC
* * ** * * *
4735259 AAATTTGACAGCATATATGCA-CCAATTTGGGCAGCATAAATACAAC
1 AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
* * * * *
4735305 AAATTGGACAGCATTTTAGCATAAAAATTTGACAGCATATGTGCAAC
1 AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
* * * * * * *
4735352 AATTTGGGCAGCATAT-A-TATACCAAATT-GAGCAGCATTTTTACATC
1 AAATTGGACAGCATATAAGCATA-AAAATTGGA-CAGCATATATACAAC
* * * * *
4735398 AAAATTGGACAGCATATATGCA-ACAATTTGGGCAGCATAAATACAAC
1 -AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
*
4735445 AAATTGGACAGCATTTAAGCATAAAAATT
1 AAATTGGACAGCATATAAGCATAAAAATT
4735474 ACATGAACAT
Statistics
Matches: 336, Mismatches: 91, Indels: 47
0.71 0.19 0.10
Matches are distributed among these distances:
45 13 0.04
46 105 0.31
47 171 0.51
48 28 0.08
49 19 0.06
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (47 bp):
AAATTGGACAGCATATAAGCATAAAAATTGGACAGCATATATACAAC
Found at i:4735301 original size:140 final size:140
Alignment explanation
Indices: 4734928--4735473 Score: 778
Period size: 140 Copynumber: 3.9 Consensus size: 140
4734918 CTTTTTACAT
** * * *
4734928 CAATTTGGATAGCAT-TCATATACCAAACT-AGACAGCATTTTCACACCAAAAATTGGACAGCAT
1 CAATTTGGGCAGCATAT-ATATACCAAATTGAG-CAGCATTTTTACA-TAAAAATTGGACAGCAT
* * *
4734991 ATATACAACAATTTGGGCAGCATATAT-CAATCAAATTGAACAGCATTTTAGCATAAAAATTGGA
63 ATATACAACAATTTGGGCAGCATAAATACAA-CAAATTGGACAGCATTTAAGCATAAAAATTGGA
*
4735055 CAGCATATATACAA
127 CAGCATATATGCAA
*
4735069 CAATTTGGGCAGCCTATATATATACCAAATTGAGCAGCATTTTTACATCAAAATTGGACAGCATA
1 CAATTTGGGCAG-C-ATATATATACCAAATTGAGCAGCATTTTTACATAAAAATTGGACAGCATA
* * *
4735134 TATACAACAGTTTGGGTAGCATAAATACAACAAATTGGGCAGCATTTAAGCATAAAAATTGGACA
64 TATACAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGCATAAAAATTGGACA
4735199 GCATATATGCAA
129 GCATATATGCAA
* * *
4735211 CAATTTGGGCAGCATAAATATAACAAATTG-GACAGCA-TTTTAGCATAAAAATTTGACAGCATA
1 CAATTTGGGCAGCATATATATACCAAATTGAG-CAGCATTTTTA-CATAAAAATTGGACAGCATA
* * * *
4735274 TATGCACCAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTTAGCATAAAAATTTGACA
64 TATACAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGCATAAAAATTGGACA
*
4735339 GCATATGTGCAA
129 GCATATATGCAA
*
4735351 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAATTGGACAGCATATA
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATAAAAATTGGACAGCATATA
*
4735416 TGCAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGCATAAAAATT
66 TACAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGCATAAAAATT
4735474 ACATGAACAT
Statistics
Matches: 365, Mismatches: 31, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
139 6 0.02
140 216 0.59
141 17 0.05
142 95 0.26
143 28 0.08
144 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (140 bp):
CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATAAAAATTGGACAGCATATA
TACAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGCATAAAAATTGGACAGC
ATATATGCAA
Found at i:4749906 original size:16 final size:16
Alignment explanation
Indices: 4749885--4749921 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
4749875 TAGCATCATT
*
4749885 TATTTATATTTATAAA
1 TATTTATATATATAAA
4749901 TATTTATATATATAAA
1 TATTTATATATATAAA
4749917 TATTT
1 TATTT
4749922 TTAAAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTATATATATAAA
Found at i:4750785 original size:21 final size:21
Alignment explanation
Indices: 4750770--4750857 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 21
4750760 GTTATATTAC
4750770 TTTTTTT-TATTTTTATTTGA
1 TTTTTTTCTATTTTTATTTGA
4750790 TTTTTTTCTA-TTTTA-TT-A
1 TTTTTTTCTATTTTTATTTGA
* * *
4750808 ATTTTTTATGTTTTTATGTTGA
1 TTTTTTTCTATTTTTAT-TTGA
* *
4750830 TGTAATTTT-TATTTTT-TTTTA
1 T-T-TTTTTCTATTTTTATTTGA
4750851 TTTTTTT
1 TTTTTTT
4750858 ATTTTTCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
18 8 0.15
19 11 0.21
20 13 0.25
21 8 0.15
22 2 0.04
23 7 0.13
24 4 0.08
ACGTcount: A:0.16, C:0.01, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTATTTTTATTTGA
Found at i:4750794 original size:11 final size:9
Alignment explanation
Indices: 4750770--4750863 Score: 55
Period size: 9 Copynumber: 9.6 Consensus size: 9
4750760 GTTATATTAC
4750770 TTTTTTTTA
1 TTTTTTTTA
4750779 TTTTTATTTGA
1 TTTTT-TTT-A
4750790 TTTTTTTCTA
1 TTTTTTT-TA
* *
4750800 TTTTATTAA
1 TTTTTTTTA
* *
4750809 TTTTTTATG
1 TTTTTTTTA
4750818 TTTTTATGTTGA
1 TTTTT-T-TT-A
*
4750830 TGTAATTTTTA
1 T-T-TTTTTTA
4750841 TTTTTTTT-
1 TTTTTTTTA
4750849 TATTTTTTTA
1 T-TTTTTTTA
4750859 TTTTT
1 TTTTT
4750864 CTTTTTATGG
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
8 1 0.02
9 32 0.49
10 15 0.23
11 10 0.15
12 3 0.05
13 2 0.03
14 2 0.03
ACGTcount: A:0.16, C:0.01, G:0.05, T:0.78
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4761457 original size:42 final size:43
Alignment explanation
Indices: 4761397--4761510 Score: 153
Period size: 42 Copynumber: 2.7 Consensus size: 43
4761387 AATTGATTTG
* * *
4761397 GGCTTGTCCGATGATGCACTGTGTGTGCCAATATAATTGCTTC
1 GGCTTATCCGATGATGCACTATGTGTGCCAATATAATTCCTTC
*
4761440 GGCTT-TCCGATGATGCACTATGTGTG-CAATATATTTCCTTC
1 GGCTTATCCGATGATGCACTATGTGTGCCAATATAATTCCTTC
* *
4761481 AGTTTATCCGATGATGCACTATG-GTGCCAA
1 GGCTTATCCGATGATGCACTATGTGTGCCAA
4761511 AATTGGGATA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 19 0.30
42 40 0.62
43 5 0.08
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (43 bp):
GGCTTATCCGATGATGCACTATGTGTGCCAATATAATTCCTTC
Found at i:4766456 original size:50 final size:50
Alignment explanation
Indices: 4766332--4766580 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
4766322 GATAATAACA
* * ** * *
4766332 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
4766383 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4766433 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
4766483 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
4766538 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4766581 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:4766510 original size:100 final size:104
Alignment explanation
Indices: 4766331--4766580 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
4766321 TGATAATAAC
**
4766331 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
4766396 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
4766433 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
4766496 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
4766538 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4766581 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:4766695 original size:13 final size:13
Alignment explanation
Indices: 4766674--4766705 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4766664 GCTTGGATCA
*
4766674 TCATCAAATAAAT
1 TCATAAAATAAAT
4766687 TCATAAAATAAAT
1 TCATAAAATAAAT
4766700 TCATAA
1 TCATAA
4766706 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4774043 original size:50 final size:50
Alignment explanation
Indices: 4773919--4774167 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
4773909 GATAATAACA
* * ** * *
4773919 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
4773970 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4774020 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4774070 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATTTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---A-TCT-CGG
* *
4774125 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4774168 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.20
54 2 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:4774097 original size:100 final size:104
Alignment explanation
Indices: 4773918--4774167 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
4773908 TGATAATAAC
**
4773918 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
4773983 TCCCAGACATGGTCTTATAGGGGACCTCTC-A-TCT-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATTCTAAGG
* *
4774020 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
4774083 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATTTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATTCTAAGG
* *
4774125 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4774168 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 1 0.01
104 2 0.02
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATTCTAAGG
Found at i:4774283 original size:13 final size:13
Alignment explanation
Indices: 4774262--4774293 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4774252 GCTTGGATCA
*
4774262 TCATCAAATAAAT
1 TCATAAAATAAAT
4774275 TCATAAAATAAAT
1 TCATAAAATAAAT
4774288 TCATAA
1 TCATAA
4774294 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4797015 original size:16 final size:16
Alignment explanation
Indices: 4796994--4797026 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4796984 GTAAGACTAC
4796994 ATACATAAGCAAAATT
1 ATACATAAGCAAAATT
4797010 ATACATAAGCAAAATT
1 ATACATAAGCAAAATT
4797026 A
1 A
4797027 AAAAGTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
ATACATAAGCAAAATT
Found at i:4799461 original size:97 final size:99
Alignment explanation
Indices: 4799340--4799530 Score: 323
Period size: 97 Copynumber: 1.9 Consensus size: 99
4799330 AGTTTATAGA
* * *
4799340 TTTATTTTTAGGGGTTTTAAGTGAAAGGATCACAAAGAAAAGAAAAATTGCAAAAAA-ATCCAAT
1 TTTATTTTTAGGGATTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAAT
4799404 TACACAAATTTTGAATGTTGAAGGTTAGAATAAT
66 TACACAAATTTTGAATGTTGAAGGTTAGAATAAT
* *
4799438 TTTATTTTT-GGGATTTTAAGTGAAAAGATCACAAAGAAAAGAAGAATTGCAAAAAAGATTAAAT
1 TTTATTTTTAGGGATTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAAT
4799502 TACACAAATTTTGAATGTTGAAGGTTAGA
66 TACACAAATTTTGAATGTTGAAGGTTAGA
4799531 TTTTTATAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 44 0.51
98 43 0.49
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (99 bp):
TTTATTTTTAGGGATTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAAT
TACACAAATTTTGAATGTTGAAGGTTAGAATAAT
Found at i:4810172 original size:21 final size:18
Alignment explanation
Indices: 4810141--4810199 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
4810131 GAAATTTAAA
4810141 AAAAATCAAAATAATA-TAT
1 AAAAAT-AAAA-AATATTAT
*
4810160 GAAAAATAAAAAATGTTAT
1 -AAAAATAAAAAATATTAT
4810179 AAAAATAAAAAAGTATT-T
1 AAAAATAAAAAA-TATTAT
4810197 AAA
1 AAA
4810200 TTTCAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 19 0.54
19 10 0.29
20 6 0.17
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAATAAAAAATATTAT
Found at i:4819610 original size:90 final size:90
Alignment explanation
Indices: 4819457--4819643 Score: 320
Period size: 90 Copynumber: 2.1 Consensus size: 90
4819447 TACCAGAATA
*
4819457 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTCAGTCAATGTG
1 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTCAGTCAATGTA
* *
4819522 CTAATTTAATTATTTTTGATATTTG
66 CTAATTTAATTACTTTTAATATTTG
* * *
4819547 TACATTTATTAATGGTTAAATTCTATCTTTAATATTATGAGCAAGTTGTTGATTTAGTCAATGTA
1 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTCAGTCAATGTA
4819612 CTAATTTAATTACTTTTAATATTTG
66 CTAATTTAATTACTTTTAATATTTG
4819637 TACATTT
1 TACATTT
4819644 TTTATTTTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (90 bp):
TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTCAGTCAATGTA
CTAATTTAATTACTTTTAATATTTG
Found at i:4824150 original size:42 final size:43
Alignment explanation
Indices: 4824103--4824187 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
4824093 TTAAATCTAT
4824103 AATAACTTATAATACTATAATGTAAACATT-AAAAAAAACTAA
1 AATAACTTATAATACTATAATGTAAACATTAAAAAAAAACTAA
4824145 AATAACTTATAATACTATAATGTAAACATTAAAAAAAAACTAA
1 AATAACTTATAATACTATAATGTAAACATTAAAAAAAAACTAA
4824188 GATGTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 30 0.71
43 12 0.29
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (43 bp):
AATAACTTATAATACTATAATGTAAACATTAAAAAAAAACTAA
Found at i:4841188 original size:97 final size:97
Alignment explanation
Indices: 4841022--4841216 Score: 277
Period size: 97 Copynumber: 2.0 Consensus size: 97
4841012 TATTTTATTT
* * *
4841022 TAATAAAAATTAGGGTCACACAATTTCTAACATCACCGAAGAGAAACTGCTCCATCAACTATATT
1 TAATAAAAATTAGAGTCACACAACTTCTAACATCACCCAAGAGAAACTGCTCCATCAACTATATT
*
4841087 GCATGAATTAGATAATAGAGTTGTTGTTAACA
66 GCATGAATTAGATAATAGAGTTGCTGTTAACA
* * *
4841119 TAATAAAAATTTA-AGTCACAGAACTTCTAACGTCACCCAAGAGAAACTG-TCTCATCAATTATA
1 TAATAAAAA-TTAGAGTCACACAACTTCTAACATCACCCAAGAGAAACTGCTC-CATCAACTATA
* *
4841182 TTGCATGAATTAGATGATGGAGTTGCTGTTAACA
64 TTGCATGAATTAGATAATAGAGTTGCTGTTAACA
4841216 T
1 T
4841217 TTGTATATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 2 0.02
97 82 0.94
98 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (97 bp):
TAATAAAAATTAGAGTCACACAACTTCTAACATCACCCAAGAGAAACTGCTCCATCAACTATATT
GCATGAATTAGATAATAGAGTTGCTGTTAACA
Found at i:4843010 original size:26 final size:26
Alignment explanation
Indices: 4842955--4843011 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4842945 TTTAATTCTT
*
4842955 TTAAATAATTTTATATTTAAAAAATA
1 TTAAATAATTTTATATTAAAAAAATA
* * *
4842981 TTAAATGATTTTCTA-TAAAAAGAATC
1 TTAAATAATTTTATATTAAAAA-AATA
4843007 TTAAA
1 TTAAA
4843012 CAATCAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
TTAAATAATTTTATATTAAAAAAATA
Found at i:4854192 original size:67 final size:65
Alignment explanation
Indices: 4854055--4854228 Score: 149
Period size: 65 Copynumber: 2.6 Consensus size: 65
4854045 ATTACCTTTC
** *
4854055 GCTC-TCATGTTATTTTTGGATGCAACTACCATGTTGATTGTGGGTCTCATATATATGGAGCTTC
1 GCTCTTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCA-ATATATGAAGCTTC
4854119 G
65 G
* * * * *
4854120 GCTCTTTTCATGTTATTTTTCAAT-TAACTACTATGTTGATTTTGGGTCTC-ATATGTGAATCTT
1 GCTC--TTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCAATATATGAAGCTT
4854183 CG
64 CG
* * * * *
4854185 ACTCTCTTCATGTTGTTTTTGGAA-GCAACTATCATGTTAATTGT
1 --GCTCTTCATGTTATTTTT-CAATGCAACTACCATGTTGATTGT
4854229 AAGTATTGTT
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
65 29 0.34
66 16 0.19
67 26 0.30
68 15 0.17
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (65 bp):
GCTCTTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCAATATATGAAGCTTCG
Found at i:4858450 original size:23 final size:22
Alignment explanation
Indices: 4858401--4858451 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
4858391 GTGAAAAGAG
*
4858401 TAAAAAAAATCGAAAACTATTC
1 TAAAAAAAATCGAAAACTATGC
4858423 TAAAAAAAATCGAAAACTATGC
1 TAAAAAAAATCGAAAACTATGC
*
4858445 TCAAAAA
1 TAAAAAA
4858452 TAGAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.20
Consensus pattern (22 bp):
TAAAAAAAATCGAAAACTATGC
Found at i:4862640 original size:16 final size:16
Alignment explanation
Indices: 4862619--4862652 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4862609 AAGCTCAAAT
4862619 TTGAAAGTTATGGCAA
1 TTGAAAGTTATGGCAA
*
4862635 TTGAAAGTTATTGCAA
1 TTGAAAGTTATGGCAA
4862651 TT
1 TT
4862653 TCGATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (16 bp):
TTGAAAGTTATGGCAA
Found at i:4866106 original size:21 final size:21
Alignment explanation
Indices: 4866082--4866126 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4866072 TTCACATTCG
*
4866082 TTTT-TACTAATTCAATATGGT
1 TTTTCTACTAATTAAATAT-GT
*
4866103 TTTTCTACTAGTTAAATATGT
1 TTTTCTACTAATTAAATATGT
4866124 TTT
1 TTT
4866127 AGACCAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTTCTACTAATTAAATATGT
Found at i:4868306 original size:16 final size:18
Alignment explanation
Indices: 4868264--4868306 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
4868254 ACTCGATGGA
4868264 AAATATTAACTTATTTTT
1 AAATATTAACTTATTTTT
* *
4868282 ATATTTTAA-TTA-TTTT
1 AAATATTAACTTATTTTT
4868298 AAATATTAA
1 AAATATTAA
4868307 ATGGACTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATTAACTTATTTTT
Found at i:4868599 original size:44 final size:46
Alignment explanation
Indices: 4868517--4868605 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
4868507 TATTTAATGA
*
4868517 AATAGAGTTGTAATTAGTAATTTAATTGTTTGGTTGAATACAATAC
1 AATAGAATTGTAATTAGTAATTTAATTGTTTGGTTGAATACAATAC
* *
4868563 AATAGAATTGTAA-TAGT-ATTCTTA-TGTTTGGTTGAATAGAATA
1 AATAGAATTGTAATTAGTAATT-TAATTGTTTGGTTGAATACAATA
4868606 AAAGTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 21 0.54
45 6 0.15
46 12 0.31
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (46 bp):
AATAGAATTGTAATTAGTAATTTAATTGTTTGGTTGAATACAATAC
Found at i:4868833 original size:21 final size:23
Alignment explanation
Indices: 4868784--4868833 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
4868774 ATTTAATAAC
* * *
4868784 ATTTTTAATATAATTATGTTTTT
1 ATTTTTAATATAATCATGTTGTA
4868807 ATTTTTAATAT-ATCAT-TTGTA
1 ATTTTTAATATAATCATGTTGTA
4868828 ATTTTT
1 ATTTTT
4868834 TTGAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTTAATATAATCATGTTGTA
Found at i:4876011 original size:7 final size:7
Alignment explanation
Indices: 4875999--4876025 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4875989 AAATTTTTGA
4875999 AAGAATC
1 AAGAATC
4876006 AAGAATC
1 AAGAATC
4876013 AAGAATC
1 AAGAATC
4876020 AAGAAT
1 AAGAAT
4876026 TAAAATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (7 bp):
AAGAATC
Found at i:4876564 original size:70 final size:69
Alignment explanation
Indices: 4876484--4876617 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 69
4876474 TCCGAATAAG
* *
4876484 AAAAGTCAAAACTATGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAG-CAAAACCATT
4876549 TAGTT
65 TAGTT
* * * *
4876554 AAAAGGCAAAACTACGTCGTTTTTATAAATGTTTAACTTTTCTAAAGTTAAAAGGAAAACCATT
1 AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGCAAAACCATT
4876618 ATATTGTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 9 0.16
70 49 0.84
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (69 bp):
AAAAGGCAAAACTACGCCGTTTTGATAAATATTTAACTTTTCTAAAGTTAAAAGCAAAACCATTT
AGTT
Found at i:4878837 original size:24 final size:24
Alignment explanation
Indices: 4878809--4878860 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4878799 TTAGTAAGTC
*
4878809 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
* *
4878833 AAATATATTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
4878857 AAAT
1 AAAT
4878861 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATGCT
Found at i:4883964 original size:12 final size:12
Alignment explanation
Indices: 4883914--4883965 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
4883904 GCATTTCAAA
4883914 GATGAAAG-CTT
1 GATGAAAGACTT
4883925 GATTGAAA-ACTT
1 GA-TGAAAGACTT
* *
4883937 GATTAAAAACTT
1 GATGAAAGACTT
4883949 GATGAAAGACTT
1 GATGAAAGACTT
4883961 GATGA
1 GATGA
4883966 TTAAATGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 6 0.17
12 29 0.83
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (12 bp):
GATGAAAGACTT
Found at i:4885172 original size:18 final size:18
Alignment explanation
Indices: 4885149--4885191 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4885139 ACCCAATCTA
**
4885149 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
4885167 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
4885185 AACCCAA
1 AACCCAA
4885192 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:4885380 original size:9 final size:9
Alignment explanation
Indices: 4885295--4885379 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
4885285 GTAGTGATTC
*
4885295 AATTTGGTT
1 AATTCGGTT
*
4885304 AATTCGGAT
1 AATTCGGTT
*
4885313 AATTCGGGT
1 AATTCGGTT
*
4885322 AATTCAGTT
1 AATTCGGTT
4885331 AATTCGGTT
1 AATTCGGTT
*
4885340 AATTCGGGT
1 AATTCGGTT
4885349 AATTCGGTT
1 AATTCGGTT
*
4885358 AATTCAGTT
1 AATTCGGTT
*
4885367 AATTTGGTT
1 AATTCGGTT
4885376 AATT
1 AATT
4885380 TTTAATCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 65 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4893741 original size:20 final size:20
Alignment explanation
Indices: 4893716--4893760 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4893706 CCTTAAATTG
*
4893716 TTTTATGTATAAGATTATTA
1 TTTTATGTATAAAATTATTA
*
4893736 TTTTATTTATAAAATTATTA
1 TTTTATGTATAAAATTATTA
4893756 TTTTA
1 TTTTA
4893761 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTATGTATAAAATTATTA
Done.