Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015091.1 Kokia drynarioides strain JFW-HI SEQ_130135, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 803680
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 595 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:9549 original size:97 final size:94
Alignment explanation
Indices: 9367--9690 Score: 312
Period size: 99 Copynumber: 3.3 Consensus size: 94
9357 GGCGGATCTT
* ** *
9367 GTACCATAGAAATAAAGGGAAAGGTTGAGGCTGCAATAACAAACCCTGTACCTTAGAAGATGTGA
1 GTACCAT-GAAATAAAGGGAAAGGTTGAGGTTGCAATGGCGAACCCTGTACCTTAGAAGATGTGA
* *
9432 TAGG-AAGGATCGAGACCGTAACGAC-AGCTCTA
65 T-GGAAAGGAT-TAGACCGTAACGACGA-ATC-A
* *
9464 GTACCATGGAAATAAAGGGAAAGGTTGAGGTTGCAATGGCGAACCCTGCACCTTAGAAGGTGTGA
1 GTACCAT-GAAATAAAGGGAAAGGTTGAGGTTGCAATGGCGAACCCTGTACCTTAGAAGATGTGA
* *
9529 TGGAAAGGATTA-ACGTCGTAACGGCGAATCC
65 TGGAAAGGATTAGAC--CGTAACGACGAATCA
* * *
9560 GATACCATGAAGATATGAAGGGAAAGGTTGAGGTTGCAATGGCGAACTCGGTACCTTAAAAGATG
1 G-TACCATGAA-ATA--AAGGGAAAGGTTGAGGTTGCAATGGCGAACCCTGTACCTTAGAAGATG
* ** *
9625 TGATGGAAAGGATTGAGGCCACAATGACGAATCTA
62 TGATGGAAAGGATT-AGACCGTAACGACGAATC-A
*
9660 GTACCATGAAGATACGAAGGAAAAGGTTGAG
1 GTACCATGAA-ATA--AAGGGAAAGGTTGAG
9691 CCCATAATGG
Statistics
Matches: 192, Mismatches: 24, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
95 2 0.01
96 7 0.04
97 84 0.44
98 1 0.01
99 95 0.49
100 2 0.01
101 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.19
Consensus pattern (94 bp):
GTACCATGAAATAAAGGGAAAGGTTGAGGTTGCAATGGCGAACCCTGTACCTTAGAAGATGTGAT
GGAAAGGATTAGACCGTAACGACGAATCA
Found at i:9634 original size:49 final size:50
Alignment explanation
Indices: 9481--9642 Score: 152
Period size: 49 Copynumber: 3.3 Consensus size: 50
9471 GGAAATAAAG
* * * *
9481 GGAAAGG-TTGAGGTTGCAATGGCGAACCCTGCACCTTAGAAGGTGTGAT
1 GGAAAGGATTGAGGTTGCAATGGCGAACTCGGTACCTTAGAAGATGTGAT
* * * * * * * * *
9530 GGAAAGGATTAACGTCGTAACGGCGAA-TCCGATACCAT-GAAGATATGAAG
1 GGAAAGGATTGAGGTTGCAATGGCGAACT-CGGTACCTTAGAAGATGTG-AT
*
9580 GGAAAGG-TTGAGGTTGCAATGGCGAACTCGGTACCTTAAAAGATGTGAT
1 GGAAAGGATTGAGGTTGCAATGGCGAACTCGGTACCTTAGAAGATGTGAT
9629 GGAAAGGATTGAGG
1 GGAAAGGATTGAGG
9643 CCACAATGAC
Statistics
Matches: 84, Mismatches: 23, Indels: 11
0.71 0.19 0.09
Matches are distributed among these distances:
49 43 0.51
50 41 0.49
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (50 bp):
GGAAAGGATTGAGGTTGCAATGGCGAACTCGGTACCTTAGAAGATGTGAT
Found at i:9650 original size:50 final size:49
Alignment explanation
Indices: 9569--9714 Score: 116
Period size: 50 Copynumber: 3.0 Consensus size: 49
9559 CGATACCATG
* * ****
9569 AAGATATGAAGGGAAAGGTTGAGGTTGCAATGGCGAACTCGGTACCTTAA
1 AAGATACGAAGGAAAAGGTTGAGCCCACAATGGCGAACTCGGTACCTT-A
** * * * * * *
9619 AAGATGTGATGG-AAAGGATTGAGGCCACAATGACGAA-TCTAGTACCATG
1 AAGATACGAAGGAAAAGG-TTGAGCCCACAATGGCGAACTC-GGTACCTTA
*
9668 AAGATACGAAGGAAAAGGTTGAGCCCATAATGGCGAACTCGGTACCT
1 AAGATACGAAGGAAAAGGTTGAGCCCACAATGGCGAACTCGGTACCT
9715 CAACGACAGA
Statistics
Matches: 75, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
49 37 0.49
50 38 0.51
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (49 bp):
AAGATACGAAGGAAAAGGTTGAGCCCACAATGGCGAACTCGGTACCTTA
Found at i:9713 original size:49 final size:48
Alignment explanation
Indices: 9562--9713 Score: 144
Period size: 49 Copynumber: 3.1 Consensus size: 48
9552 GCGAATCCGA
***
9562 TACCATGAAGATATGAAGGGAAAGGTTGAGGTTGCAATGGCGAACTCGG
1 TACCATGAAGATATGAA-GGAAAGGTTGAGGCCACAATGGCGAACTCGG
* * * * * *
9611 TACCTTAAAAGATGTGATGGAAAGGATTGAGGCCACAATGACGAA-TCTAG
1 TACCAT-GAAGATATGAAGGAAAGG-TTGAGGCCACAATGGCGAACTC-GG
* * *
9661 TACCATGAAGATACGAAGGAAAAGGTTGAGCCCATAATGGCGAACTCGG
1 TACCATGAAGATATGAAGG-AAAGGTTGAGGCCACAATGGCGAACTCGG
9710 TACC
1 TACC
9714 TCAACGACAG
Statistics
Matches: 80, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
49 44 0.55
50 36 0.45
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (48 bp):
TACCATGAAGATATGAAGGAAAGGTTGAGGCCACAATGGCGAACTCGG
Found at i:13582 original size:12 final size:12
Alignment explanation
Indices: 13565--13589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13555 TAGAACATTC
13565 AACATCTATCAT
1 AACATCTATCAT
13577 AACATCTATCAT
1 AACATCTATCAT
13589 A
1 A
13590 CTTCATTATT
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
AACATCTATCAT
Found at i:16001 original size:3 final size:3
Alignment explanation
Indices: 15993--16027 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
15983 GGTAGACTTG
15993 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16028 ATACCTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17335 original size:40 final size:40
Alignment explanation
Indices: 17129--17333 Score: 205
Period size: 40 Copynumber: 5.1 Consensus size: 40
17119 TAAAATACTT
* *
17129 GTGATATAATTCAAGTTACGACTTAGCAGGCTTTGAGCTG
1 GTGATATGATTCAAGTTACGGCTTAGCAGGCTTTGAGCTG
* * * * *
17169 GTGATTTAATTCAAGTTACGGCTTAGCAGACTATGAGCTA
1 GTGATATGATTCAAGTTACGGCTTAGCAGGCTTTGAGCTG
* * * * *
17209 GTGATATGATTCAAGCTACGGTTTAGCAGACTATGAGCCG
1 GTGATATGATTCAAGTTACGGCTTAGCAGGCTTTGAGCTG
* * * * * *
17249 GTGATATGATT-AGGGTTATGGCCTAACAGGCTTTTAGCCG
1 GTGATATGATTCA-AGTTACGGCTTAGCAGGCTTTGAGCTG
* * *
17289 GTGATGTGATTCAAGCTACGGCTTAGCAGGCTTTGAACTG
1 GTGATATGATTCAAGTTACGGCTTAGCAGGCTTTGAGCTG
17329 GTGAT
1 GTGAT
17334 GTTGTAAAAT
Statistics
Matches: 134, Mismatches: 29, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
39 1 0.01
40 132 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (40 bp):
GTGATATGATTCAAGTTACGGCTTAGCAGGCTTTGAGCTG
Found at i:27751 original size:14 final size:14
Alignment explanation
Indices: 27729--27823 Score: 59
Period size: 14 Copynumber: 6.8 Consensus size: 14
27719 CTGAAAAAAG
*
27729 TCAATGGTCAACTA
1 TCAACGGTCAACTA
*
27743 TCAACGGTCAACTG
1 TCAACGGTCAACTA
* * * *
27757 TTAACGATCATCTG
1 TCAACGGTCAACTA
*
27771 TCAATGGTCAAC-A
1 TCAACGGTCAACTA
* * *
27784 GCCAATGGACAACTA
1 -TCAACGGTCAACTA
27799 TCAACGGTCAAC-A
1 TCAACGGTCAACTA
*
27812 GTCAACTGTCAA
1 -TCAACGGTCAA
27824 TGGTTAACGG
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
13 1 0.02
14 60 0.97
15 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (14 bp):
TCAACGGTCAACTA
Found at i:27817 original size:21 final size:21
Alignment explanation
Indices: 27793--27837 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27783 AGCCAATGGA
27793 CAACTATCAACGGTCAACAGT
1 CAACTATCAACGGTCAACAGT
* * * *
27814 CAACTGTCAATGGTTAACGGT
1 CAACTATCAACGGTCAACAGT
27835 CAA
1 CAA
27838 TGGGTTCACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
CAACTATCAACGGTCAACAGT
Found at i:30768 original size:43 final size:43
Alignment explanation
Indices: 30683--30768 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
30673 TTGTAAAGAA
*
30683 GAAAAATTTTGTGTTCTTTTAAGAATTTAACTACTTTACTAAT
1 GAAAAATTTTGTGTTCTTTTAAGAATTTAAATACTTTACTAAT
* * *
30726 GAAAAATTTTGTGTTCTTTTAAGATTTTAAATATTTTTCTAAT
1 GAAAAATTTTGTGTTCTTTTAAGAATTTAAATACTTTACTAAT
30769 TGATCTCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (43 bp):
GAAAAATTTTGTGTTCTTTTAAGAATTTAAATACTTTACTAAT
Found at i:31875 original size:18 final size:18
Alignment explanation
Indices: 31868--31934 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
31858 CGCCTCTTGT
*
31868 TGTGAGCTTGCCTCTTGTTA
1 TGTGAGCTTGCCAC-T-TTA
31888 TGT--GCTTGCCACTTTA
1 TGTGAGCTTGCCACTTTA
*
31904 TGTGAGCTTGCCACTTTC
1 TGTGAGCTTGCCACTTTA
*
31922 TGTGAGCTCGCCA
1 TGTGAGCTTGCCA
31935 AATGTGTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.14
17 1 0.02
18 32 0.76
20 3 0.07
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (18 bp):
TGTGAGCTTGCCACTTTA
Found at i:35654 original size:18 final size:18
Alignment explanation
Indices: 35612--35655 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35602 TTATCCCGAA
*
35612 AATTAAAAATCTTAAAAT
1 AATTAAAAATCTTAAAAC
*
35630 AAATAAAAATCTTAAAAC
1 AATTAAAAATCTTAAAAC
*
35648 GATTAAAA
1 AATTAAAA
35656 GTTAAAGTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (18 bp):
AATTAAAAATCTTAAAAC
Found at i:38485 original size:12 final size:12
Alignment explanation
Indices: 38468--38492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38458 CTTCGTAGAT
38468 ATCATCATCATA
1 ATCATCATCATA
38480 ATCATCATCATA
1 ATCATCATCATA
38492 A
1 A
38493 ATGTCATCTA
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCATCATCATA
Found at i:39369 original size:2 final size:2
Alignment explanation
Indices: 39362--39394 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39352 ATAAACACAA
39362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39395 AACATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46531 original size:13 final size:14
Alignment explanation
Indices: 46515--46556 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
46505 TTTCAATTTT
46515 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
46528 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
46543 ATTTTAAATAATAT
1 ATTTT-AATAATAT
46557 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:46541 original size:16 final size:16
Alignment explanation
Indices: 46519--46555 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
46509 AATTTTATTT
46519 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
46536 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
46551 TAATA
1 TAATA
46556 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:50562 original size:20 final size:20
Alignment explanation
Indices: 50495--50563 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
50485 TCTAGATGTG
* *
50495 GTTATTAAGAAATCATAAATT
1 GTTATTAAAAAATTATAAA-T
* * *
50516 ATTATT-TAAAATTA-AAAA
1 GTTATTAAAAAATTATAAAT
*
50534 GTAATTTAAAAAATTATAAAT
1 GTTA-TTAAAAAATTATAAAT
50555 GTTATTAAA
1 GTTATTAAA
50564 GTATTGAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 7
0.67 0.19 0.13
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 17 0.49
21 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (20 bp):
GTTATTAAAAAATTATAAAT
Found at i:50697 original size:46 final size:46
Alignment explanation
Indices: 50597--50714 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 46
50587 ATTATAAACA
*
50597 TATAAAATTATATTAAAAATTTCAAATTCATAAAATTATAATAAAAGC
1 TATAAAA-AATATTAAAAATTT-AAATTCATAAAATTATAATAAAAGC
*
50645 TATAAAAAATATTAAAAATTTAAATT-ATAAAAATTATCAA-AAAA-T
1 TATAAAAAATATTAAAAATTTAAATTCAT-AAAATTAT-AATAAAAGC
*
50690 TATTAAAAAACA-TAACAAATTTAAA
1 TA-TAAAAAATATTAA-AAATTTAAA
50715 AAAATTCTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
45 7 0.11
46 34 0.54
47 15 0.24
48 7 0.11
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (46 bp):
TATAAAAAATATTAAAAATTTAAATTCATAAAATTATAATAAAAGC
Found at i:51036 original size:14 final size:14
Alignment explanation
Indices: 51019--51059 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
51009 ATTTTAAAAT
51019 TTTTTATAATTTAA
1 TTTTTATAATTTAA
*
51033 TTTTTATGATTTTAA
1 TTTTTAT-AATTTAA
51048 TTTTTATAATTT
1 TTTTTATAATTT
51060 CCTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTTATAATTTAA
Found at i:56470 original size:116 final size:115
Alignment explanation
Indices: 56330--56582 Score: 380
Period size: 116 Copynumber: 2.2 Consensus size: 115
56320 AGCTGAGAAG
* * * *
56330 TCCTACCCTGCAACTTCTACCGATACAAATATTTAAACTACCAATACCTCAATGTACAAAACTAC
1 TCCTACCCTG-TACTTCTACCGATACAAACATTTAAACTACCAATACCTCAATGCACAAAACCAC
* * *
56395 TGATACATGTTATACAACTACCGAAACGACTCAAGTCAGAGAACAACCTATC
65 CGATACATGTTATACAACTACCAAAACAACTCAAGTCAGAGAACAA-CTATC
* *
56447 TCCTACCCTGTACTTCTATCGATACAAGCATTTAAACTACCAATACCTCAATGCACAAAACCACC
1 TCCTACCCTGTACTTCTACCGATACAAACATTTAAACTACCAATACCTCAATGCACAAAACCACC
* *
56512 GATACATGTTATACAACTACCAAAACAACTCAAGTTAGAGAACAACTCTC
66 GATACATGTTATACAACTACCAAAACAACTCAAGTCAGAGAACAACTATC
*
56562 TCCTACCCTGTATTTCTACCG
1 TCCTACCCTGTACTTCTACCG
56583 GTAAAAGTAT
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
115 23 0.19
116 90 0.73
117 10 0.08
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (115 bp):
TCCTACCCTGTACTTCTACCGATACAAACATTTAAACTACCAATACCTCAATGCACAAAACCACC
GATACATGTTATACAACTACCAAAACAACTCAAGTCAGAGAACAACTATC
Found at i:57153 original size:36 final size:36
Alignment explanation
Indices: 57082--57185 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
57072 ATCGTTATTT
57082 GTTTTACTCCCTGTTGACCCTAAAGGTCATGATGCTC
1 GTTTTACTCCCTGTTGACCC-AAAGGTCATGATGCTC
* *
57119 GTTTTACTCTCTGTTGACCCAAAGGTCATTATGCTC
1 GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
* * *
57155 ATTTTTCTCCCTATTGACCCAAAGGTCATGA
1 GTTTTACTCCCTGTTGACCCAAAGGTCATGA
57186 CTGTTACCAG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 41 0.68
37 19 0.32
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (36 bp):
GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
Found at i:74520 original size:16 final size:16
Alignment explanation
Indices: 74495--74543 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
74485 TTATCATAAA
74495 TTTC-TTTTCTTTTTT
1 TTTCTTTTTCTTTTTT
74510 TTTCTTTTTCTTCCTTTT
1 TTTCTTTTTCTT--TTTT
*
74528 TCTCATTTTTCTTTTT
1 TTTC-TTTTTCTTTTT
74544 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 3 0.10
18 7 0.24
19 8 0.28
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTT
Found at i:83384 original size:22 final size:23
Alignment explanation
Indices: 83358--83401 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
83348 AAATTGTTAA
*
83358 AATTGTCAATGTAAC-AAAAGTT
1 AATTGTCAATGCAACTAAAAGTT
*
83380 AATTGTCAGTGCAACTAAAAGT
1 AATTGTCAATGCAACTAAAAGT
83402 AAATCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (23 bp):
AATTGTCAATGCAACTAAAAGTT
Found at i:86069 original size:37 final size:36
Alignment explanation
Indices: 86027--86131 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
86017 TGATCATTAT
86027 TCGTTTTACT-CCTAATTGACCCCAAAGGTCATGATGC
1 TCGTTTTACTCCCT-ATTGA-CCCAAAGGTCATGATGC
* * *
86064 TCGTTTTACTCCCTGTTGATCCAAAGGTCATTATGC
1 TCGTTTTACTCCCTATTGACCCAAAGGTCATGATGC
** * * *
86100 TTATTTTTCTCCCTATCGACCAAAAGGTCATG
1 TCGTTTTACTCCCTATTGACCCAAAGGTCATG
86132 CCTATTACCA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
36 39 0.70
37 14 0.25
38 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (36 bp):
TCGTTTTACTCCCTATTGACCCAAAGGTCATGATGC
Found at i:88083 original size:21 final size:20
Alignment explanation
Indices: 88035--88093 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
88025 AATGGTGCAG
88035 ACTTCTACTGATACAAGTGC
1 ACTTCTACTGATACAAGTGC
*
88055 AGTTCTACTGATACAAGTGAC
1 ACTTCTACTGATACAAGTG-C
* * *
88076 TCTTCTACCGAAACAAGT
1 ACTTCTACTGATACAAGT
88094 CTTACTTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (20 bp):
ACTTCTACTGATACAAGTGC
Found at i:95492 original size:35 final size:36
Alignment explanation
Indices: 95446--95551 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
95436 GTGGATAAGT
* *
95446 GGTATGGTATTCATGCCATGTTACAG-AAATATGTG
1 GGTATGATATTCATGCCATGTGACAGTAAATATGTG
* * *
95481 GGTATGTTATTCATGTCATGAGACAGTAAATATGTG
1 GGTATGATATTCATGCCATGTGACAGTAAATATGTG
* * *
95517 GATATGATATTCGTGCCATGTGACAGTGAATATGT
1 GGTATGATATTCATGCCATGTGACAGTAAATATGT
95552 TATGTTAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 22 0.37
36 38 0.63
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (36 bp):
GGTATGATATTCATGCCATGTGACAGTAAATATGTG
Found at i:97175 original size:19 final size:19
Alignment explanation
Indices: 97151--97204 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
97141 ATATTCTGTA
97151 ATTATATTTATTTTATATT
1 ATTATATTTATTTTATATT
* * *
97170 ATTATATTT-TTTGAAAAT
1 ATTATATTTATTTTATATT
97188 ATT-TATTTATTTTATAT
1 ATTATATTTATTTTATAT
97205 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 5 0.18
18 14 0.50
19 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTATATTTATTTTATATT
Found at i:97206 original size:17 final size:17
Alignment explanation
Indices: 97155--97221 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
97145 TCTGTAATTA
97155 TATTTATTTTATATTATT
1 TATTTATTTTATA-TATT
* *
97173 ATATTT-TTTGAAAATATT
1 -TATTTATTT-TATATATT
97191 TATTTATTTTATATATT
1 TATTTATTTTATATATT
*
97208 T-TTAAATTTTATAT
1 TATT-TATTTTATAT
97222 CTTATTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 2 0.05
17 21 0.52
18 10 0.25
19 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (17 bp):
TATTTATTTTATATATT
Found at i:97272 original size:21 final size:21
Alignment explanation
Indices: 97247--97305 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
97237 CATAAATATT
97247 TTTATTTTTATATATTTGAAA
1 TTTATTTTTATATATTTGAAA
* * *
97268 TTTATTATTATATTTTTGAAT
1 TTTATTTTTATATATTTGAAA
97289 TTGTGCATTTTTATATA
1 TT-T--ATTTTTATATA
97306 CTTTTTTGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 20 0.67
22 1 0.03
24 9 0.30
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTATTTTTATATATTTGAAA
Found at i:99213 original size:75 final size:75
Alignment explanation
Indices: 99110--99343 Score: 344
Period size: 74 Copynumber: 3.1 Consensus size: 75
99100 CTGACAAAGG
* * * *
99110 TTGCGCCCAGCGCTAGTCGAATAAACCGACGATATCAATAGTGAGCCCAACTCTAGTTGGTTATA
1 TTGCGCCCAGCGCTAGTCGGAT-AACCGACAATATCAATAGTGAGCCCAGCTCTAGTTGGATATA
99175 CCAACGATGTT
65 CCAACGATGTT
* *
99186 TTGCGCCTAGCGCTAGTCGGATAACCGACAATATCAATAATGAGCCCAGCTCTAGTTGGATATAC
1 TTGCGCCCAGCGCTAGTCGGATAACCGACAATATCAATAGTGAGCCCAGCTCTAGTTGGATATAC
99251 CAACGAT-TT
66 CAACGATGTT
* ** * *
99260 TTGTGCCCAATGCTAGTCGGATAACTGACAATATCAATAGTGAGCGCAGCTCTAGTTGGATATAC
1 TTGCGCCCAGCGCTAGTCGGATAACCGACAATATCAATAGTGAGCCCAGCTCTAGTTGGATATAC
99325 CAACGATGTT
66 CAACGATGTT
*
99335 TTACGCCCA
1 TTGCGCCCA
99344 ATTCTAGTTG
Statistics
Matches: 142, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
74 67 0.47
75 55 0.39
76 20 0.14
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (75 bp):
TTGCGCCCAGCGCTAGTCGGATAACCGACAATATCAATAGTGAGCCCAGCTCTAGTTGGATATAC
CAACGATGTT
Found at i:107639 original size:71 final size:69
Alignment explanation
Indices: 107562--107894 Score: 322
Period size: 75 Copynumber: 4.6 Consensus size: 69
107552 TTATTAAAAT
* * *
107562 ATCAATTTAAATGATTAATTTAAA-TTAAAAATAAAATTTAATTAAAAGAAGACATATTTAAAGA
1 ATCAATTTAAA-CAATAAATTAAATTTAAAAATAAAATTTAATT-AAA-AAGACATATTTAAAGA
107626 ATAATAA
63 ATAATAA
*
107633 ATCAATTTAAAACAATAAATTAAATTTTTAAAAAATATAATTTAAATTAAAAAGACATATTT---
1 ATCAATTT-AAACAATAAATTAAA--TTT-AAAAATAAAATTT-AATTAAAAAGACATATTTAAA
*
107695 GAAGAATAA
61 GAATAATAA
*
107704 ATCAATTTAAAGCAATAAATTAAATTTTAAAAATAGAATTTAATTAAAAA-ACATATTTAAAGAA
1 ATCAATTTAAA-CAATAAATTAAA-TTTAAAAATAAAATTTAATTAAAAAGACATATTTAAAGAA
107768 TAATAA
64 TAATAA
*
107774 ATCACTTTCAAACAATAAATTAAATTTAAAATATATATAATTTAAATTAAATACA-ACATATTTA
1 ATCAATTT-AAACAATAAATTAAATTTAAAA-ATA-A-AATTT-AATTAAA-A-AGACATATTTA
107838 AAGAATAATAA
59 AAGAATAATAA
* * *
107849 ATTATTTTAAA-ATTATAAATTTAATTTTAAAAAATAGAAA-TTAATT
1 ATCAATTTAAACA--ATAAA-TTAAATTT-AAAAATA-AAATTTAATT
107895 GAAAGATGAA
Statistics
Matches: 228, Mismatches: 13, Indels: 40
0.81 0.05 0.14
Matches are distributed among these distances:
67 8 0.04
68 9 0.04
69 19 0.08
70 37 0.16
71 48 0.21
72 8 0.04
73 12 0.05
74 19 0.08
75 49 0.21
76 15 0.07
77 4 0.02
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (69 bp):
ATCAATTTAAACAATAAATTAAATTTAAAAATAAAATTTAATTAAAAAGACATATTTAAAGAATA
ATAA
Found at i:107662 original size:21 final size:22
Alignment explanation
Indices: 107638--107680 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
107628 AATAAATCAA
107638 TTTAAAACAATA-AA-TTAAATT
1 TTTAAAA-AATATAATTTAAATT
107659 TTTAAAAAATATAATTTAAATT
1 TTTAAAAAATATAATTTAAATT
107681 AAAAAGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAAAATATAATTTAAATT
Found at i:107672 original size:22 final size:21
Alignment explanation
Indices: 107638--107680 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
107628 AATAAATCAA
*
107638 TTTAAAACAATAAATTAAATT
1 TTTAAAAAAATAAATTAAATT
*
107659 TTTAAAAAATATAATTTAAATT
1 TTTAAAAAA-ATAAATTAAATT
107681 AAAAAGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAATAAATTAAATT
Found at i:107787 original size:141 final size:143
Alignment explanation
Indices: 107562--107845 Score: 404
Period size: 141 Copynumber: 2.0 Consensus size: 143
107552 TTATTAAAAT
* *
107562 ATCAATTTAAATGATTAATTTAAATTAAAAATAAAATTTAATTAAAAGAAGACATATTTAAAGAA
1 ATCAATTTAAATGAATAAATTAAATTAAAAATAAAATTTAATTAAAAGAAGACATATTTAAAGAA
107627 TAATAAATCAATTTAAAACAATAAATTAAATTTTTAAAA-A-ATATAATTTAAATTAAA-A-AGA
66 TAATAAATCAATTTAAAACAATAAATTAAA--TTTAAAATATATATAATTTAAATTAAATACA-A
*
107688 CATATTTGAAGAATAA
128 CATATTTAAAGAATAA
*
107704 ATCAATTTAAA-GCAATAAATTAAATTTTAAAAATAGAATTTAATT-AAA-AA-ACATATTTAAA
1 ATCAATTTAAATG-AATAAATTAAA--TTAAAAATAAAATTTAATTAAAAGAAGACATATTTAAA
* *
107765 GAATAATAAATCACTTTCAAACAATAAATTAAATTTAAAATATATATAATTTAAATTAAATACAA
63 GAATAATAAATCAATTTAAAACAATAAATTAAATTTAAAATATATATAATTTAAATTAAATACAA
107830 CATATTTAAAGAATAA
128 CATATTTAAAGAATAA
107846 TAAATTATTT
Statistics
Matches: 129, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
139 7 0.05
140 1 0.01
141 60 0.47
142 39 0.30
143 4 0.03
144 18 0.14
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (143 bp):
ATCAATTTAAATGAATAAATTAAATTAAAAATAAAATTTAATTAAAAGAAGACATATTTAAAGAA
TAATAAATCAATTTAAAACAATAAATTAAATTTAAAATATATATAATTTAAATTAAATACAACAT
ATTTAAAGAATAA
Found at i:107881 original size:21 final size:20
Alignment explanation
Indices: 107834--107894 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
107824 ATACAACATA
*
107834 TTTAAAGAATAATAAATT-AT
1 TTTAAA-AATTATAAATTAAT
107854 TTT-AAAATTATAAATTTAAT
1 TTTAAAAATTATAAA-TTAAT
* *
107874 TTTAAAAAATAGAAATTAAT
1 TTTAAAAATTATAAATTAAT
107894 T
1 T
107895 GAAAGATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 8 0.23
19 4 0.11
20 14 0.40
21 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTAAAAATTATAAATTAAT
Found at i:120352 original size:19 final size:20
Alignment explanation
Indices: 120317--120355 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
120307 ACCCAAATCA
120317 TGTGAATAAATAAAAATTAGT
1 TGTGAATAAAT-AAAATTAGT
120338 TGTGAATAAAT-AAATTAG
1 TGTGAATAAATAAAATTAG
120356 ACTTGGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTGAATAAATAAAATTAGT
Found at i:122987 original size:20 final size:21
Alignment explanation
Indices: 122926--122996 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
122916 TGCAGATTTT
*
122926 TACCGATACAAGTTATAG-TTC
1 TACCGATACAAGTCAT-GCTTC
122947 TACCGATACAAGTGTCA--CTTC
1 TACCGATACAA--GTCATGCTTC
122968 TACCGA-ACAAGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
122988 TACCGATAC
1 TACCGATAC
122997 TAAAAACTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
18 4 0.09
20 14 0.33
21 22 0.51
23 3 0.07
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:127016 original size:15 final size:14
Alignment explanation
Indices: 126984--127025 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
126974 TTTGGGTTTT
*
126984 ATAATAATAAAAATC
1 ATAA-AATAAAAAGC
126999 ATAAAATAAAATAGC
1 ATAAAATAAAA-AGC
127014 ATAAAATAAAAA
1 ATAAAATAAAAA
127026 AAGGTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (14 bp):
ATAAAATAAAAAGC
Found at i:129127 original size:145 final size:145
Alignment explanation
Indices: 128856--129170 Score: 380
Period size: 145 Copynumber: 2.2 Consensus size: 145
128846 GTAACAGAGT
* * * * *
128856 TTGTGCCCAACGCTAGTCGGGTAATTGACGATTTGTGTGCCCGGCACTAGTCAGTTAAACTGACA
1 TTGTGCCCAACGCAAGTCGGATAACTGACGATTTGTGTGCCCAGCACTAGTCAATTAAACTGACA
* * * * *
128921 AAGGTTGCGCCCAGAGCTAGTCGGATAAATCGACTATTTCAATAGTGAGCCCATCTCTAGTTGGT
66 AAGGTTGCGCCCAGAGCTAGTCGGATAAACCGACAATATCAATAGTGAGCCCATCTCTAGTTAGA
128986 TATACCAATGATGTC
131 TATACCAATGATGTC
* * * * **
129001 TTGTGCCCAATGCAAGTTGGATAACTGATGATTTGTGTGCCCAGCACTAGTCAATTCAACTGATG
1 TTGTGCCCAACGCAAGTCGGATAACTGACGATTTGTGTGCCCAGCACTAGTCAATTAAACTGACA
* * *
129066 AAGGTTGGGCCCAGTGCTAGTCGGATAAACCGACAATATCAATAGTGAGCCC-TGCTGTAGTTAG
66 AAGGTTGCGCCCAGAGCTAGTCGGATAAACCGACAATATCAATAGTGAGCCCAT-CTCTAGTTAG
** *
129130 ATATACCAACAATGTT
130 ATATACCAATGATGTC
* * * *
129146 TTGGGCTCAACGCTAGTCGAATAAC
1 TTGTGCCCAACGCAAGTCGGATAAC
129171 CGATGATATC
Statistics
Matches: 141, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
144 1 0.01
145 140 0.99
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (145 bp):
TTGTGCCCAACGCAAGTCGGATAACTGACGATTTGTGTGCCCAGCACTAGTCAATTAAACTGACA
AAGGTTGCGCCCAGAGCTAGTCGGATAAACCGACAATATCAATAGTGAGCCCATCTCTAGTTAGA
TATACCAATGATGTC
Found at i:129202 original size:75 final size:76
Alignment explanation
Indices: 129081--129222 Score: 191
Period size: 75 Copynumber: 1.9 Consensus size: 76
129071 TGGGCCCAGT
* * *
129081 GCTAGTCGGATAAACCGACAATATCAATAGTGAGCCCTGCTGTAGTT-AGATATACCAACAATGT
1 GCTAGTCGAATAAACCGACAATATCAATAGTGAGCCATGCTCTAGTTGA-ATATACCAACAATGT
129145 TTTGGGCTCAAC
65 TTTGGGCTCAAC
** *
129157 GCTAGTCGAAT-AACCGATGATATCAATAGTGAG-CATAGCTCTAGTTGAATATACCAACGATGT
1 GCTAGTCGAATAAACCGACAATATCAATAGTGAGCCAT-GCTCTAGTTGAATATACCAACAATGT
129220 TTT
65 TTT
129223 TCACCCAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
74 2 0.03
75 45 0.78
76 11 0.19
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (76 bp):
GCTAGTCGAATAAACCGACAATATCAATAGTGAGCCATGCTCTAGTTGAATATACCAACAATGTT
TTGGGCTCAAC
Found at i:129237 original size:75 final size:75
Alignment explanation
Indices: 129082--129249 Score: 187
Period size: 75 Copynumber: 2.2 Consensus size: 75
129072 GGGCCCAGTG
* * *
129082 CTAGTCGGATAAACCGACAATATCAATAGTGAGCCCTGCTGTAGTTAGATATACCAACAATGTTT
1 CTAGTCGAAT-AACCGACAATATCAATAGTGAGCCATGCTCTAGTTAGATATACCAACAATGTTT
** * *
129147 TGGGCTCAACG
65 TGCACCCAACA
** *
129158 CTAGTCGAATAACCGATGATATCAATAGTGAG-CATAGCTCTAGTT-GAATATACCAACGATGTT
1 CTAGTCGAATAACCGACAATATCAATAGTGAGCCAT-GCTCTAGTTAG-ATATACCAACAATGTT
* *
129221 TTTCACCCAGCA
64 TTGCACCCAACA
129233 CTAGTCGAATAACCGAC
1 CTAGTCGAATAACCGAC
129250 GATTTGTGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
74 3 0.04
75 65 0.84
76 9 0.12
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (75 bp):
CTAGTCGAATAACCGACAATATCAATAGTGAGCCATGCTCTAGTTAGATATACCAACAATGTTTT
GCACCCAACA
Found at i:129921 original size:18 final size:16
Alignment explanation
Indices: 129898--129933 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
129888 GGTTTAAAAT
129898 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
129916 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
129932 TT
1 TT
129934 CTCATTCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:130121 original size:31 final size:29
Alignment explanation
Indices: 130058--130125 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
130048 TACTAACATT
* * *
130058 AGTGACTAAAACGTAATATTTCAAACATA
1 AGTGACTAAAACGTAACATTGCAAACAAA
*
130087 AGTGACTAAAATGTAACATGATGCAAACAAA
1 AGTGACTAAAACGTAACAT--TGCAAACAAA
130118 AGTGACTA
1 AGTGACTA
130126 TTTTTGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAACGTAACATTGCAAACAAA
Found at i:131426 original size:15 final size:15
Alignment explanation
Indices: 131406--131444 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
131396 GCACATCAAA
*
131406 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
131421 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
131435 CAAGAATTAA
1 CAAGAATTAA
131445 GTACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:131843 original size:25 final size:23
Alignment explanation
Indices: 131815--131860 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
131805 GTTGGATCCA
131815 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
131840 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
131861 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:131947 original size:13 final size:13
Alignment explanation
Indices: 131926--131959 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
131916 ACAATATAAT
131926 AATAATAATCCTA
1 AATAATAATCCTA
*
131939 AATACTAATCCTA
1 AATAATAATCCTA
*
131952 AAAAATAA
1 AATAATAA
131960 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:135079 original size:21 final size:21
Alignment explanation
Indices: 135053--135110 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
135043 TAAAAGTAAG
135053 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTTTCGGTAGAAGAGTC
* * **
135074 ACTTGTATCGATAGAA-CTTC
1 ACTTGTTTCGGTAGAAGAGTC
135094 ACTTGTATT-GGTAGAAG
1 ACTTGT-TTCGGTAGAAG
135111 TCTGCACTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
ACTTGTTTCGGTAGAAGAGTC
Found at i:137343 original size:26 final size:26
Alignment explanation
Indices: 137305--137362 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
137295 AAAAGGGCAT
*
137305 TATT-ATTGATTTGACCAACTAATTA
1 TATTAATTAATTTGACCAACTAATTA
** * *
137330 TATTAATTAATTTGATTAATTAATTC
1 TATTAATTAATTTGACCAACTAATTA
137356 TATTAAT
1 TATTAAT
137363 GGTTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (26 bp):
TATTAATTAATTTGACCAACTAATTA
Found at i:137360 original size:13 final size:12
Alignment explanation
Indices: 137324--137362 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
137314 TTTGACCAAC
137324 TAATTATATTAAT
1 TAATT-TATTAAT
137337 TAATTTGATTAAT
1 TAATTT-ATTAAT
137350 TAATTCTATTAAT
1 TAATT-TATTAAT
137363 GGTTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (12 bp):
TAATTTATTAAT
Found at i:137481 original size:18 final size:18
Alignment explanation
Indices: 137446--137479 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
137436 CATAATACAT
137446 TTTATTGATAATTATTTA
1 TTTATTGATAATTATTTA
*
137464 TTTATTTATAA-TATTT
1 TTTATTGATAATTATTT
137480 TAGTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTATTGATAATTATTTA
Found at i:145479 original size:14 final size:14
Alignment explanation
Indices: 145460--145489 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
145450 AAACTCGAAT
145460 AATTCGAATAACTC
1 AATTCGAATAACTC
*
145474 AATTCGATTAACTC
1 AATTCGAATAACTC
145488 AA
1 AA
145490 AATTATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (14 bp):
AATTCGAATAACTC
Found at i:147366 original size:30 final size:30
Alignment explanation
Indices: 147300--147366 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
147290 ACTTTTACAA
**
147300 ATTAGAAATTTAGTCTCTATATTTTTATTTC
1 ATTA-AAATTTAGTCTCTATATTTTTAGATC
*
147331 A-TAAAATTTAGTCTCTCTACTTTTTAGAT-
1 ATTAAAATTTAGTCTCTATA-TTTTTAGATC
147360 ATTAAAA
1 ATTAAAA
147367 GTCAGGTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 16 0.52
30 14 0.45
31 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTAAAATTTAGTCTCTATATTTTTAGATC
Found at i:147560 original size:29 final size:28
Alignment explanation
Indices: 147526--147590 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 28
147516 ACAATTAGAT
147526 CTAAATTT-TGAAATATGAAAAGT-AAAGAA
1 CTAAATTTATGAAA-A--AAAAGTAAAAGAA
147555 CTAAATTTCATGAAAAAAAAGTAAAAGAA
1 CTAAATTT-ATGAAAAAAAAGTAAAAGAA
147584 CTAAATT
1 CTAAATT
147591 CCTAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.18
29 21 0.64
30 1 0.03
31 5 0.15
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (28 bp):
CTAAATTTATGAAAAAAAAGTAAAAGAA
Found at i:148400 original size:44 final size:44
Alignment explanation
Indices: 148351--148493 Score: 103
Period size: 44 Copynumber: 3.1 Consensus size: 44
148341 AAATAAATAA
148351 TATAAAAATATTTAATATGGATATCTTTATATTTGTAAAAAAAT
1 TATAAAAATATTTAATATGGATATCTTTATATTTGTAAAAAAAT
* * *** * * * *
148395 TATAAATAGT-TTTAAAAAAAATATCGGAATTACAAATT-AAAAATAAAT
1 TATAAA-AATATTTAATATGGATATC---TTTA-TATTTGTAAAA-AAAT
*
148443 ACTATAAAAATATTTAATATGGATATCTTTATATTTGT-AAAAAGT
1 --TATAAAAATATTTAATATGGATATCTTTATATTTGTAAAAAAAT
148488 TATAAA
1 TATAAA
148494 TAGTTTTAAT
Statistics
Matches: 70, Mismatches: 19, Indels: 21
0.64 0.17 0.19
Matches are distributed among these distances:
43 6 0.09
44 17 0.24
45 5 0.07
46 6 0.09
47 10 0.14
48 7 0.10
49 2 0.03
50 17 0.24
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.38
Consensus pattern (44 bp):
TATAAAAATATTTAATATGGATATCTTTATATTTGTAAAAAAAT
Found at i:150256 original size:24 final size:25
Alignment explanation
Indices: 150225--150289 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 25
150215 ACAGACAACA
*
150225 TTAGCTCTCACGAGCCCGAG-ATGG
1 TTAGCTCTTACGAGCCCGAGAATGG
*
150249 TTAGCTCTTACGAG-CCTAGAATGG
1 TTAGCTCTTACGAGCCCGAGAATGG
*
150273 TTAGCTCTTATGAGCCC
1 TTAGCTCTTACGAGCCC
150290 AAAGTAGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.11
24 30 0.83
25 2 0.06
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (25 bp):
TTAGCTCTTACGAGCCCGAGAATGG
Found at i:150299 original size:24 final size:24
Alignment explanation
Indices: 150225--150299 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
150215 ACAGACAACA
* *
150225 TTAGCTCTCACGAGCCC-GAGATGG
1 TTAGCTCTTACGAGCCCAGA-ATAG
* *
150249 TTAGCTCTTACGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATAG
*
150273 TTAGCTCTTATGAGCCCA-AAGTAG
1 TTAGCTCTTACGAGCCCAGAA-TAG
150297 TTA
1 TTA
150300 ACCAGTATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATAG
Found at i:156814 original size:42 final size:42
Alignment explanation
Indices: 156773--156851 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
156763 ATCGAATTAA
156773 AAATAATTTTAT-AA-TTT-TAAAAAATAAAAATTTTAAAATT
1 AAAT-ATTTTATAAATTTTATAAAAAATAAAAATTTTAAAATT
* *
156813 AAATATTTTATAAATTTTATAAAAAATATAATTTTTAAA
1 AAATATTTTATAAATTTTATAAAAAATAAAAATTTTAAA
156852 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.21
40 6 0.18
41 3 0.09
42 18 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (42 bp):
AAATATTTTATAAATTTTATAAAAAATAAAAATTTTAAAATT
Found at i:156827 original size:16 final size:15
Alignment explanation
Indices: 156785--156828 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
156775 ATAATTTTAT
*
156785 AATTTTAAAAAATAAA
1 AATTTT-AAAATTAAA
156801 AATTTTAAAATTAAA
1 AATTTTAAAATTAAA
*
156816 TATTTTATAAATT
1 AATTTTA-AAATT
156829 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAAAATTAAA
Found at i:165667 original size:59 final size:59
Alignment explanation
Indices: 165585--165859 Score: 206
Period size: 59 Copynumber: 4.6 Consensus size: 59
165575 GATCAAAACA
* *
165585 GAATTTTTGGACA--TCTGAGGGTAAAATAGTAATTTTTGAGAGTTTTAGGGTTAAAGAT-G
1 GAATTTTTGGA-AGTTC-GAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAA-ATAG
* * * ** *
165644 GAATTTTTGGAGGTTCGGGGGTAATATGGTAATTTTCAAAAGTTTCTA-GGTTAAAATTGG
1 GAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTT-TAGGGTTAAAA-TAG
** * ** ** *
165704 GTTTTTTTGGAAGTTTG-GAAATAAAATGGTAATTTTCAAAAGTTTTGGGGTTAAAATCAG
1 GAATTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAT-AG
* ** ** *
165764 G-ATTTTTTGAAGTTTTAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTTAAAAT-C
1 GAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAATAG
*
165821 GAGATTTTTAGAAGTTCGAGGGTAAAAAT-GTAATTTTTG
1 GA-ATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTG
165860 GACAATTTAG
Statistics
Matches: 176, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 117 0.66
60 57 0.32
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (59 bp):
GAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAATAG
Found at i:165759 original size:30 final size:30
Alignment explanation
Indices: 165606--165858 Score: 105
Period size: 30 Copynumber: 8.5 Consensus size: 30
165596 CATCTGAGGG
* * * *
165606 TAAAATAGTAATTTTTGAGAGTTTTAGGGT
1 TAAAATGGTAATTTTTAAAAGTTTTGGGGT
** * * *
165636 TAAAGATGG-AATTTTT-GGAGGTTCGGGGG
1 TAAA-ATGGTAATTTTTAAAAGTTTTGGGGT
* * *
165665 TAATATGGTAATTTTCAAAAGTTTCT-AGGT
1 TAAAATGGTAATTTTTAAAAGTTT-TGGGGT
* ** ***
165695 TAAAATTGGGT-TTTTTTGGAAG-TTTGGAAA
1 TAAAA-T-GGTAATTTTTAAAAGTTTTGGGGT
*
165725 TAAAATGGTAATTTTCAAAAGTTTTGGGGT
1 TAAAATGGTAATTTTTAAAAGTTTTGGGGT
** *
165755 TAAAATCAGG--ATTTTTTGAAGTTTTAGGG-
1 TAAAAT--GGTAATTTTTAAAAGTTTTGGGGT
* *
165784 TAAAATGGTAATTTTTGAAAGTTTCGGGGT
1 TAAAATGGTAATTTTTAAAAGTTTTGGGGT
* * *
165814 TAAAATCG-AGATTTTTAGAAG-TTCGAGGGT
1 TAAAATGGTA-ATTTTTAAAAGTTTTG-GGGT
*
165844 AAAAAT-GTAATTTTT
1 TAAAATGGTAATTTTT
165859 GGACAATTTA
Statistics
Matches: 164, Mismatches: 42, Indels: 35
0.68 0.17 0.15
Matches are distributed among these distances:
27 2 0.01
28 7 0.04
29 59 0.36
30 80 0.49
31 11 0.07
32 5 0.03
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (30 bp):
TAAAATGGTAATTTTTAAAAGTTTTGGGGT
Found at i:166979 original size:3 final size:3
Alignment explanation
Indices: 166971--167043 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
166961 TTCAATTTCT
* * *
166971 TTA TTA TTA TTA TTA TTA TTA ATA CTA TTTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
167017 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
167044 ACCATTTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 62 0.97
4 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:170306 original size:21 final size:21
Alignment explanation
Indices: 170280--170378 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
170270 TATATTGTTA
*
170280 TTTTGGTGTTGTTTTTTATTG
1 TTTTGGTGTTGTTTTTTACTG
*
170301 TTTTGGTTGCTT-TTTTTTGCTG
1 TTTTGG-TG-TTGTTTTTTACTG
*
170323 TTTTTGTGTTGTTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
*
170344 TTTTGGTG--CTTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
170363 TTTTGGTTGTTGTTTT
1 TTTTGG-TGTTGTTTT
170379 CGTGTTGTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
19 16 0.25
20 4 0.06
21 24 0.37
22 19 0.29
23 2 0.03
ACGTcount: A:0.03, C:0.05, G:0.22, T:0.70
Consensus pattern (21 bp):
TTTTGGTGTTGTTTTTTACTG
Found at i:170314 original size:19 final size:20
Alignment explanation
Indices: 170287--170371 Score: 95
Period size: 19 Copynumber: 4.2 Consensus size: 20
170277 TTATTTTGGT
*
170287 GTTG-TTTTTTATTGTTTTG
1 GTTGCTTTTTTACTGTTTTG
*
170306 GTTGCTTTTTTTTGCTGTTTTTG
1 GTTGC--TTTTTTACTG-TTTTG
170329 TGTTG-TTTTTTACTGTTTTG
1 -GTTGCTTTTTTACTGTTTTG
170349 G-TGCTTTTTTACTGTTTTG
1 GTTGCTTTTTTACTGTTTTG
170368 GTTG
1 GTTG
170372 TTGTTTTCGT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
18 2 0.04
19 21 0.38
20 7 0.12
21 9 0.16
22 8 0.14
23 5 0.09
24 4 0.07
ACGTcount: A:0.04, C:0.06, G:0.22, T:0.68
Consensus pattern (20 bp):
GTTGCTTTTTTACTGTTTTG
Found at i:170408 original size:12 final size:12
Alignment explanation
Indices: 170393--170488 Score: 58
Period size: 12 Copynumber: 8.3 Consensus size: 12
170383 TTGTTCTCAC
170393 TGTTATTTTTGT
1 TGTTATTTTTGT
*
170405 TGTTGTTTTTGT
1 TGTTATTTTTGT
* *
170417 TGCTATTTTTAT
1 TGTTATTTTTGT
*
170429 TGTT-TTTAATGT
1 TGTTATTT-TTGT
*
170441 TG----TTTTGC
1 TGTTATTTTTGT
*
170449 TGTTATTTTTGC
1 TGTTATTTTTGT
* * *
170461 TGCTGTTTTGGT
1 TGTTATTTTTGT
*
170473 TTTTATTTTTGT
1 TGTTATTTTTGT
170485 TGTT
1 TGTT
170489 TGGATGTTAT
Statistics
Matches: 61, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
8 4 0.07
9 2 0.03
11 3 0.05
12 52 0.85
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:170432 original size:56 final size:55
Alignment explanation
Indices: 170372--170489 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
170362 GTTTTGGTTG
** * * *
170372 TTGTTTTCGTGTTGTTCTCACTGTTATTTTTGTTGTTGTTTTTGTTGCTATTTTTA
1 TTGTTTTAATGTTGTT-TCACTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTA
** ** *
170428 TTGTTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTGTTTTGGTTTTTATTTTTG
1 TTG-TTTTAATGTTGTTTCACTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTA
170484 TTGTTT
1 TTGTTT
170490 GGATGTTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
55 3 0.06
56 37 0.73
57 11 0.22
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.68
Consensus pattern (55 bp):
TTGTTTTAATGTTGTTTCACTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTA
Found at i:170498 original size:20 final size:20
Alignment explanation
Indices: 170438--170502 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
170428 TTGTTTTTAA
* *
170438 TGTTGTTTTGCTGTTATTTT
1 TGTTGTTTGGATGTTATTTT
* *
170458 TGCTGCTGTTTTGGTTTTTATTTT
1 TG-T--TG-TTTGGATGTTATTTT
170482 TGTTGTTTGGATGTTATTTT
1 TGTTGTTTGGATGTTATTTT
170502 T
1 T
170503 TATGCGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 16 0.44
21 3 0.08
23 3 0.08
24 14 0.39
ACGTcount: A:0.06, C:0.05, G:0.22, T:0.68
Consensus pattern (20 bp):
TGTTGTTTGGATGTTATTTT
Found at i:172545 original size:20 final size:20
Alignment explanation
Indices: 172487--172551 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
172477 AAAAATATTA
172487 ATTTTGAAAATTTTATAAA-T
1 ATTTTG-AAATTTTATAAATT
* *
172507 ATTTTG-TATTTTAAAAATT
1 ATTTTGAAATTTTATAAATT
172526 ATTTTGAAATTTTATAAATT
1 ATTTTGAAATTTTATAAATT
*
172546 AATTTG
1 ATTTTG
172552 CTTATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 9 0.24
19 7 0.18
20 22 0.58
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTTTGAAATTTTATAAATT
Found at i:178181 original size:24 final size:26
Alignment explanation
Indices: 178145--178192 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
178135 AGAGAAATGT
178145 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
178169 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
178193 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:178300 original size:23 final size:23
Alignment explanation
Indices: 178274--178331 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
178264 TCAACATTGT
*
178274 GTGTGCTTACTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACCTC
*
178297 GTGTGCTTACTATTTCGCACCTC
1 GTGTGCTTACTGTTTCGCACCTC
*
178320 GTGTGCCTACTG
1 GTGTGCTTACTG
178332 ATTTGCGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.28, G:0.22, T:0.40
Consensus pattern (23 bp):
GTGTGCTTACTGTTTCGCACCTC
Found at i:178372 original size:22 final size:23
Alignment explanation
Indices: 178320--178373 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
178310 TTCGCACCTC
*
178320 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGATTTACGCTAT
* * *
178343 GAGCGCCTACTGA-TTACGCTGT
1 GTGTGCCTACTGATTTACGCTAT
178365 GTGTGCCTA
1 GTGTGCCTA
178374 TTGGATTGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (23 bp):
GTGTGCCTACTGATTTACGCTAT
Found at i:187042 original size:23 final size:22
Alignment explanation
Indices: 186998--187046 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
186988 GAATTCTTGT
* *
186998 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
187021 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
187043 TAAA
1 TAAA
187047 CTATACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:193357 original size:25 final size:25
Alignment explanation
Indices: 193329--193379 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
193319 AACTTGACAC
*
193329 TTTT-TCCTAATTTGATACTTAAACT
1 TTTTGTCC-AATTTGATACTCAAACT
*
193354 TTTTGTCCAATTTGGTACTCAAACT
1 TTTTGTCCAATTTGATACTCAAACT
193379 T
1 T
193380 GACATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (25 bp):
TTTTGTCCAATTTGATACTCAAACT
Found at i:193421 original size:33 final size:32
Alignment explanation
Indices: 193351--193442 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
193341 TGATACTTAA
* *
193351 ACTTTTTGTCCAATTTGGTACTCAAACTTGAC
1 ACTTTTTTTCCAATTTGGTACTCAAACTCGAC
193383 A-TTTTTTTCCTAATTTGGTAC-CTAAACTCGAC
1 ACTTTTTTTCC-AATTTGGTACTC-AAACTCGAC
** * *
193415 ACTTTTTTTTAAAGTTGGTACTTAAACT
1 ACTTTTTTTCCAATTTGGTACTCAAACT
193443 TTTTGGGGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
31 9 0.18
32 34 0.68
33 7 0.14
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (32 bp):
ACTTTTTTTCCAATTTGGTACTCAAACTCGAC
Found at i:193772 original size:59 final size:61
Alignment explanation
Indices: 193700--193836 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 61
193690 AAAAAATGCC
* ** * * *
193700 AAGTTCAGGTACCAAATTGGGTTCAAAAA-AGTTTAGGTACCAAATT-AGAAAAAAGTGTA
1 AAGTTCAGATACCAAATTAAGTTAAAAAAGAGTTTAGATACCAAATTAAGAAAAAAGTATA
* * *
193759 AAGTTCAGATACCAAATTAAGTTAAAAAAGAGTTTTGATACCAAATTAATAAAAAAGTATC
1 AAGTTCAGATACCAAATTAAGTTAAAAAAGAGTTTAGATACCAAATTAAGAAAAAAGTATA
*
193820 AAGTTCAGACACCAAAT
1 AAGTTCAGATACCAAAT
193837 ACTATATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 25 0.38
60 15 0.23
61 26 0.39
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (61 bp):
AAGTTCAGATACCAAATTAAGTTAAAAAAGAGTTTAGATACCAAATTAAGAAAAAAGTATA
Found at i:193788 original size:27 final size:26
Alignment explanation
Indices: 193758--193814 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 26
193748 AAAAAAGTGT
193758 AAAGTTCAGATACCAAATTAAGTTAAAA
1 AAAGTTCAGATACCAAATTAA--TAAAA
**
193786 AAGAGTTTTGATACCAAATTAATAAAA
1 AA-AGTTCAGATACCAAATTAATAAAA
193813 AA
1 AA
193815 GTATCAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 2 0.08
29 17 0.65
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (26 bp):
AAAGTTCAGATACCAAATTAATAAAA
Found at i:196472 original size:21 final size:20
Alignment explanation
Indices: 196434--196472 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
196424 GTTATCCTCA
*
196434 TAGGATATCTTTGATCTCTT
1 TAGGATATATTTGATCTCTT
*
196454 TAGGATAATATTTGTTCTC
1 TAGGAT-ATATTTGATCTC
196473 CCAATATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (20 bp):
TAGGATATATTTGATCTCTT
Found at i:200588 original size:29 final size:29
Alignment explanation
Indices: 200509--200596 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 29
200499 GATTAAATCA
* *
200509 AAATTAAAATTTCAAATATATATTTAAACT
1 AAATTAAAA-TTCAAATATATAATTACACT
**
200539 ACAATTAAAATATCACGTATATAATTACACT
1 A-AATTAAAAT-TCAAATATATAATTACACT
* *
200570 AAATTAAAATTCATATATACAATTACA
1 AAATTAAAATTCAAATATATAATTACA
200597 AATTAAATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 14 0.29
30 11 0.22
31 24 0.49
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.35
Consensus pattern (29 bp):
AAATTAAAATTCAAATATATAATTACACT
Found at i:211460 original size:30 final size:31
Alignment explanation
Indices: 211397--211461 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
211387 TACATATGAC
*
211397 CATGCTTGCTCAAAAATTACTCTTTTTGCCA
1 CATGCTTGCTCAAAAATTACTCTATTTGCCA
* *
211428 CATGCTTG-TTAAAAATTACT-TCATTTGTCA
1 CATGCTTGCTCAAAAATTACTCT-ATTTGCCA
211458 CATG
1 CATG
211462 TATATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.70
31 8 0.27
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (31 bp):
CATGCTTGCTCAAAAATTACTCTATTTGCCA
Found at i:212074 original size:13 final size:13
Alignment explanation
Indices: 212056--212082 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
212046 AAGATTCCTC
212056 GATTCTTACTCAA
1 GATTCTTACTCAA
212069 GATTCTTACTCAA
1 GATTCTTACTCAA
212082 G
1 G
212083 CTGCCTCAAA
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:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (13 bp):
GATTCTTACTCAA
Found at i:213546 original size:6 final size:6
Alignment explanation
Indices: 213535--213561 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
213525 AATACATACC
213535 TGACCT TGACCT TGACCT TGACCT TGA
1 TGACCT TGACCT TGACCT TGACCT TGA
213562 AGAGGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (6 bp):
TGACCT
Found at i:225458 original size:30 final size:31
Alignment explanation
Indices: 225392--225462 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
225382 TTTAAATCTC
*
225392 AATTTTGATTTAATATACAATTTAATATATA
1 AATTTTAATTTAATATACAATTTAATATATA
*
225423 AATTTTAATTT-A-ATACAATTATACATTTA-A
1 AATTTTAATTTAATATACAATT-TA-ATATATA
225453 AATTTTAATT
1 AATTTTAATT
225463 GTACTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 14 0.39
31 14 0.39
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (31 bp):
AATTTTAATTTAATATACAATTTAATATATA
Found at i:227563 original size:18 final size:19
Alignment explanation
Indices: 227513--227563 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
227503 CAATTGATGG
227513 AAATAATAAAATATGCATAAT
1 AAAT-ATAAAA-ATGCATAAT
** *
227534 AAATATTGAAATGTATAA-
1 AAATATAAAAATGCATAAT
227552 AAATATAAAAAT
1 AAATATAAAAAT
227564 AAAACTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 4 0.16
21 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (19 bp):
AAATATAAAAATGCATAAT
Found at i:238164 original size:8 final size:8
Alignment explanation
Indices: 238146--238224 Score: 54
Period size: 8 Copynumber: 9.5 Consensus size: 8
238136 TTTTAAAAAA
238146 TTTAGTATT
1 TTTA-TATT
238155 TTTATATT
1 TTTATATT
238163 TTTA-ATT
1 TTTATATT
* *
238170 TCATATTTT
1 T-TTATATT
*
238179 TTTCTATT
1 TTTATATT
*
238187 TTTAATAAT
1 TTT-ATATT
238196 TTTA-ATAT
1 TTTATAT-T
238204 TTTATATT
1 TTTATATT
*
238212 TTTTTCATT
1 TTTAT-ATT
238221 TTTA
1 TTTA
238225 AAGATTTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
7 5 0.09
8 28 0.52
9 21 0.39
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTATATT
Found at i:238242 original size:35 final size:35
Alignment explanation
Indices: 238151--238234 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 35
238141 AAAAATTTAG
* *
238151 TATTTTT-AT-ATTTTTA-ATTTCATATTTTTTTC
1 TATTTTTAATAATTTTAATATTTTATATTTTTTTC
238183 TATTTTTAATAATTTTAATATTTTATATTTTTTTC
1 TATTTTTAATAATTTTAATATTTTATATTTTTTTC
238218 -ATTTTTAA-AGATTTTAA
1 TATTTTTAATA-ATTTTAA
238235 GTTTTTTAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 7 0.15
33 3 0.07
34 21 0.46
35 15 0.33
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.67
Consensus pattern (35 bp):
TATTTTTAATAATTTTAATATTTTATATTTTTTTC
Found at i:239882 original size:20 final size:20
Alignment explanation
Indices: 239857--239895 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
239847 GATTTGTTAA
*
239857 TTATTTACAATTTTTAATAT
1 TTATTTAAAATTTTTAATAT
239877 TTATTTAAAATTTTTAATA
1 TTATTTAAAATTTTTAATA
239896 AATTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTAAAATTTTTAATAT
Found at i:239906 original size:20 final size:20
Alignment explanation
Indices: 239854--239906 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
239844 TTTGATTTGT
* *
239854 TAATTATTTACAATTTTTAA
1 TAATTATTCAAAATTTTTAA
* *
239874 TATTTATTTAAAATTTTTAA
1 TAATTATTCAAAATTTTTAA
239894 TAAATT-TTCAAAA
1 T-AATTATTCAAAA
239907 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTCAAAATTTTTAA
Found at i:239979 original size:20 final size:19
Alignment explanation
Indices: 239951--239999 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
239941 TTTTAAAATG
239951 TTTAATTATTATATACAATA
1 TTTAATTATT-TATACAATA
* * *
239971 TTTATTTATTTTTACAATT
1 TTTAATTATTTATACAATA
239990 TTTAA-TATTT
1 TTTAATTATTT
240000 TAGCAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.20
19 11 0.44
20 9 0.36
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATTATTTATACAATA
Found at i:240000 original size:18 final size:19
Alignment explanation
Indices: 239964--240020 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
239954 AATTATTATA
* *
239964 TACAATATTTATTTATTTT
1 TACAATTTTTATATATTTT
239983 TACAATTTTTA-ATA-TTT
1 TACAATTTTTATATATTTT
240000 TAGCAA-TTTTATATATTTT
1 TA-CAATTTTTATATATTTT
240019 TA
1 TA
240021 AATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 15 0.45
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TACAATTTTTATATATTTT
Found at i:248210 original size:6 final size:6
Alignment explanation
Indices: 248199--248257 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
248189 TTGAATTTAT
* * *
248199 TTTAAA TTTAAA TTTAAG TTTAAA TTTATA TTTAAA TTTAAA ATT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
248245 TTATAAA TTTAAA
1 TT-TAAA TTTAAA
248258 AGTCCAGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 2 0.05
5 1 0.02
6 38 0.86
7 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:248212 original size:17 final size:17
Alignment explanation
Indices: 248171--248257 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
248161 TTAAACCCAT
248171 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
248189 -TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
248205 TTT-AA---A-TTTAAG
1 TTTAAATTTATTTTAAA
248217 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
248235 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
248252 TTTAAA
1 TTTAAA
248258 AGTCCAGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
12 8 0.14
13 3 0.05
16 4 0.07
17 27 0.47
18 15 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:250112 original size:29 final size:29
Alignment explanation
Indices: 250080--250244 Score: 129
Period size: 29 Copynumber: 5.6 Consensus size: 29
250070 AAACAGTCCA
* *
250080 AAAATTATATTTTTACCCTCAAACTTTCC
1 AAAATTACATTTTTACCCTCGAACTTTCC
* * **
250109 AAAATTTCATTTTTTACCCT-AAACTTTTTT
1 AAAATTACA-TTTTTACCCTCGAAC-TTTCC
* * *
250139 AAAATTACATTTTTGCCCTCGAATTTTCT
1 AAAATTACATTTTTACCCTCGAACTTTCC
* * *
250168 AAAATTCCATTTTTGA-CCTTGATCTTTCC
1 AAAATTACATTTTT-ACCCTCGAACTTTCC
*
250197 AAAAATTACATTTTTA-TCTCTGAACTTTCC
1 -AAAATTACATTTTTACCCTC-GAACTTTCC
* *
250227 AAAATTCCATTTTGACCC
1 AAAATTACATTTTTACCC
250245 AAAAATTACC
Statistics
Matches: 107, Mismatches: 22, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
29 62 0.58
30 45 0.42
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCGAACTTTCC
Found at i:250158 original size:59 final size:58
Alignment explanation
Indices: 250066--250383 Score: 180
Period size: 59 Copynumber: 5.6 Consensus size: 58
250056 CCATAAAGGT
** * * * *
250066 CCCTAAACAGTCCAAAAATTATATTTTTACCCTCAAACTTTCCAAAATTTCATTTTTTA
1 CCCTAAACTTTCCAAAAATTACATTTTT-CCCTCGAACTTTCCAAAATTCCATTTTTGA
*** * *
250125 CCCTAAACTTTTTTAAAATTACATTTTTGCCCTCGAATTTTCTAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAAATTACATTTTT-CCCTCGAACTTTCCAAAATTCCATTTTTGA
* * * **
250184 CCTTGATCTTTCCAAAAATTACATTTTTATCTCTGAACTTTCCAAAATTCCA-TTTTG-
1 CCCTAAACTTTCCAAAAATTACATTTTTCCCTC-GAACTTTCCAAAATTCCATTTTTGA
* * * *
250241 ------AC---CCAAAAATTACCATTTTACCCCCAAAC-TTCTAAAACTTCCA-TTTT-A
1 CCCTAAACTTTCCAAAAATTA-CATTTTTCCCTCGAACTTTCCAAAA-TTCCATTTTTGA
* * * * * *
250289 ACCTCAATTTCTCCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATTTCATTTTTAA
1 CCCTAAACTT-TCCAAAAATTA-CATTTTTCCCTCGAACTTTCC-AAAATTCCATTTTTGA
** * *
250349 CCCCGATCTTTCCAAAAATTACCATTTTACCCTCG
1 CCCTAAACTTTCCAAAAATTA-CATTTTTCCCTCG
250384 GGTATCCAAA
Statistics
Matches: 203, Mismatches: 39, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
47 7 0.03
48 22 0.11
49 8 0.04
51 1 0.00
54 1 0.00
58 40 0.20
59 118 0.58
60 6 0.03
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAAATTACATTTTTCCCTCGAACTTTCCAAAATTCCATTTTTGA
Found at i:250251 original size:19 final size:19
Alignment explanation
Indices: 250227--250263 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
250217 TGAACTTTCC
250227 AAAATT-CCATTTTGACCCA
1 AAAATTACCATTTT-ACCCA
250246 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
250264 CCAAACTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATTACCATTTTACCCA
Found at i:250308 original size:58 final size:59
Alignment explanation
Indices: 250243--250380 Score: 190
Period size: 58 Copynumber: 2.4 Consensus size: 59
250233 CCATTTTGAC
* * *
250243 CCAAAAATTACCATTTTACCCCCAAACTTCTAAAACTTCCA-TTTTAACCTCAAT-TTCT
1 CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAATCTT-T
* * * *
250301 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTTCATTTTTAACCCCGATCTTT
1 CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAATCTTT
250360 CCAAAAATTACCATTTTACCC
1 CCAAAAATTACCATTTTACCC
250381 TCGGGTATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
58 36 0.51
59 33 0.46
60 2 0.03
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAATCTTT
Found at i:250396 original size:29 final size:29
Alignment explanation
Indices: 250243--250383 Score: 137
Period size: 29 Copynumber: 4.8 Consensus size: 29
250233 CCATTTTGAC
* *
250243 CCAAAAATTACCATTTTACCCCCAAACTT
1 CCAAAAATTACCATTTTACCCTCGAACTT
* * * *
250272 CTAAAACTT-CCATTTTAACCTC-AATTTCT
1 CCAAAAATTACCATTTTACCCTCGAA-CT-T
250301 CCAAAAATTACCATTTTACCCTCGAACTT
1 CCAAAAATTACCATTTTACCCTCGAACTT
* *
250330 CCAAAAATT-TCATTTTTAACCC-CGATCTTT
1 CCAAAAATTACCA-TTTT-ACCCTCGAAC-TT
250360 CCAAAAATTACCATTTTACCCTCG
1 CCAAAAATTACCATTTTACCCTCG
250384 GGTATCCAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.02
28 14 0.15
29 37 0.41
30 34 0.37
31 4 0.04
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCTCGAACTT
Found at i:250414 original size:59 final size:59
Alignment explanation
Indices: 250243--250414 Score: 172
Period size: 59 Copynumber: 2.9 Consensus size: 59
250233 CCATTTTGAC
* * * * * * *
250243 CCAAAAATTACCATTTTACCCCCAAACTTCTAAAACT-TCCATT-TTAACCTCAAT-TTCT
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCT-CATTCTCAACCCCGATCTT-T
* * *
250301 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTTCATTTTTAACCCCGATCTTT
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTCTCAACCCCGATCTTT
** *
250360 CCAAAAATTACCATTTTACCCTCG-GGTATCCAAAAATCTCATTCTCAACTCCGAT
1 CCAAAAATTACCATTTTACCCTCGAACT-TCCAAAAATCTCATTCTCAACCCCGAT
250415 TGTTTTATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 38 0.39
59 58 0.59
60 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTCTCAACCCCGATCTTT
Found at i:257211 original size:18 final size:19
Alignment explanation
Indices: 257187--257229 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
257177 AGATGTGAAG
257187 GAAAAGAAGAAAGAGATGA
1 GAAAAGAAGAAAGAGATGA
**
257206 -AAAAGAAGCGAGAGATGA
1 GAAAAGAAGAAAGAGATGA
257224 GAAAAG
1 GAAAAG
257230 CACGACTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAAAGAGATGA
Found at i:261965 original size:49 final size:49
Alignment explanation
Indices: 261911--262293 Score: 277
Period size: 49 Copynumber: 7.8 Consensus size: 49
261901 ACGATGGATT
* * *
261911 CAGTACCATGAAGACATGAAAAGAAAAG-TTTAAGTCGCAATGGCGAAC
1 CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAAC
* * *
261959 CTAGTACCTTAGATG-CAT-AAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 C-AGTACCAT-GAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAA-C
* * * *
262009 CAGTACCACGAAGACATG-AAGGGAAAGATTTAAGCCACAACGGCGGATC
1 CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGC-GAAC
* * * * * *
262058 CGGTACCATGAAGACAT-AAAGGGAAAGGTTTAAGTCACAATGGCGAAC
1 CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAAC
* *
262106 CTAGTACC-TCAGAAG-CACG-AAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 C-AGTACCAT--GAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAA-C
* * * * *
262156 CAGTACCACGAAGACAT-AAAGG-AAAGATCTAAGCCGCAGCAGCGGATC
1 CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGC-GAAC
** * * * * * *
262204 CAGTACCACAAAGACACG-AAGGGAAAGGTTTAAGTCGTAACGGCAAAC
1 CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAAC
* * *
262252 CTAGTACC-TCGGAGACATGAAAGGAAAAGATTAAAGCAGCAA
1 C-AGTACCAT-GAAGACATGAAAGGAAAAGATTTAAGCCGCAA
262294 TACCGAATCT
Statistics
Matches: 264, Mismatches: 49, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
48 62 0.23
49 173 0.66
50 29 0.11
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (49 bp):
CAGTACCATGAAGACATGAAAGGAAAAGATTTAAGCCGCAACGGCGAAC
Found at i:262064 original size:98 final size:98
Alignment explanation
Indices: 261875--262282 Score: 339
Period size: 98 Copynumber: 4.2 Consensus size: 98
261865 GTATCGCGAA
* * ** * * * * **
261875 ACATGAAGGGAAAGATCTAAGTCGCAACGATGGATTCAGTACCATGAAGACATGAAAAGAAA-AG
1 ACATAAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGA-
* * * *
261939 TTTAAGTCGCAATGGC-GAACCTAGTACCTTAGATG
65 TTTAAGCCGCAACGGCGGATCC-AGTACC-TAGAAG
* *
261974 -CATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGAT
1 ACATAAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGAT
* *
262038 TTAAGCCACAACGGCGGATCCGGTACC-ATGAAG
66 TTAAGCCGCAACGGCGGATCCAGTACCTA-GAAG
* * * * * *
262071 ACATAAAGGGAAAGGTTTAAGTCACAATGGCGAA-CCTAGTACCTCAGAAG-CACGAAGGGAAAG
1 ACATAAAGGGAAAGATCTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGACACGAAGGGAAAG
*
262134 ATTTAAGCCGCAACGGCGAATCCAGTACC-ACGAAG
64 ATTTAAGCCGCAACGGCGGATCCAGTACCTA-GAAG
* * * * *
262169 ACATAAA-GGAAAGATCTAAGCCGCAGCAGCGGATCCAGTACCACAAAGACACGAAGGGAAAGGT
1 ACATAAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGAT
* * * * * *
262233 TTAAGTCGTAACGGC-AAACCTAGTACCTCGGAG
66 TTAAGCCGCAACGGCGGATCC-AGTACCTAGAAG
*
262266 ACATGAAAGGAAAAGAT
1 ACAT-AAAGGGAAAGAT
262283 TAAAGCAGCA
Statistics
Matches: 254, Mismatches: 43, Indels: 24
0.79 0.13 0.07
Matches are distributed among these distances:
96 8 0.03
97 70 0.28
98 160 0.63
99 16 0.06
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (98 bp):
ACATAAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGAT
TTAAGCCGCAACGGCGGATCCAGTACCTAGAAG
Found at i:262142 original size:147 final size:147
Alignment explanation
Indices: 261871--262261 Score: 536
Period size: 147 Copynumber: 2.7 Consensus size: 147
261861 CTCAGTATCG
* ** * *
261871 CGAA-ACATGAAGGGAAAGATCTAAGTCGCAACGATGGATTCAGTACCATGAAGACATGAAA-AG
1 CGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACAT-AAAGGG
* * * *
261934 AAAAGTTTAAGTCGCAATGGCGAACCTAGTACCTTAGATGCATAAAGGGAAAGATTTAAGCCGCA
65 AAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGCACAAAGGGAAAGATTTAAGCCGCA
261999 ACGGCGAATCCAGTACCA
130 ACGGCGAATCCAGTACCA
* * *
262017 CGAAGACATGAAGGGAAAGATTTAAGCCACAACGGCGGATCCGGTACCATGAAGACATAAAGGGA
1 CGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGA
* *
262082 AAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAAGCACGAAGGGAAAGATTTAAGCCGCAA
66 AAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGCACAAAGGGAAAGATTTAAGCCGCAA
262147 CGGCGAATCCAGTACCA
131 CGGCGAATCCAGTACCA
* * * ** **
262164 CGAAGACAT-AAAGGAAAGATCTAAGCCGCAGCAGCGGATCCAGTACCACAAAGACACGAAGGGA
1 CGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGA
* * *
262228 AAGGTTTAAGTCGTAACGGCAAACCTAGTACCTC
66 AAGGTTTAAGTCGCAATGGCGAACCTAGTACCTC
262262 GGAGACATGA
Statistics
Matches: 215, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
146 82 0.38
147 133 0.62
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (147 bp):
CGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGA
AAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGCACAAAGGGAAAGATTTAAGCCGCAA
CGGCGAATCCAGTACCA
Found at i:262666 original size:6 final size:6
Alignment explanation
Indices: 262655--262716 Score: 65
Period size: 6 Copynumber: 10.0 Consensus size: 6
262645 TTGAATTTAT
*
262655 TTTAAA TTTAAA TTTCACAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATAA
1 TTTAAA TTTAAA TTT---AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
262706 -TTAAA TTTAAA
1 TTTAAA TTTAAA
262717 AGTCCAGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
5 7 0.15
6 33 0.69
7 2 0.04
9 6 0.12
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:262668 original size:17 final size:17
Alignment explanation
Indices: 262627--262716 Score: 80
Period size: 17 Copynumber: 5.4 Consensus size: 17
262617 CTAAACCCAT
262627 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
262645 -TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
262661 TTTAAATTTCA---CAAA
1 TTTAAATTT-ATTTTAAA
* *
262676 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
262693 TTTAAATTTATAATTAAA
1 TTTAAATTTAT-TTTAAA
262711 TTTAAA
1 TTTAAA
262717 AGTCCAGAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.21
16 1 0.02
17 33 0.57
18 11 0.19
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:262702 original size:12 final size:11
Alignment explanation
Indices: 262627--262716 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
262617 CTAAACCCAT
*
262627 TTTAAATTTAT
1 TTTAAATTTAA
*
262638 TTTAAGATTGAA
1 TTTAA-ATTTAA
*
262650 TTT-ATTTTAAA
1 TTTAAATTT-AA
262661 TTTAAATTTCACAAA
1 TTTAAATTT----AA
262676 TTTAAATTTAA
1 TTTAAATTTAA
*
262687 TTTAAGTTTAAA
1 TTTAAATTT-AA
*
262699 TTTATAATTAAA
1 TTTA-AATTTAA
262711 TTTAAA
1 TTTAAA
262717 AGTCCAGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
10 2 0.03
11 23 0.37
12 23 0.37
13 3 0.05
15 12 0.19
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:264580 original size:29 final size:30
Alignment explanation
Indices: 264530--264762 Score: 164
Period size: 29 Copynumber: 7.9 Consensus size: 30
264520 AAGGTCCCTA
* **
264530 AACTATCCAAAAATTACA-TTTT-ACCCTTA
1 AACTTTCC-AAAATTACATTTTTGACCCTCG
*
264559 AACTTTCCAAAATTCCATTTTTGA-CCTCG
1 AACTTTCCAAAATTACATTTTTGACCCTCG
** *
264588 AACTTTTTGAAAATTGCA-TTTT-ACCCTCG
1 AAC-TTTCCAAAATTACATTTTTGACCCTCG
* *
264617 AATTTTCCAAAATTTA-ATTTTTGA-CCT-T
1 AACTTTCCAAAA-TTACATTTTTGACCCTCG
*
264645 AATCTTTCAAGAAATTACATTTTT-ACCCTCG
1 AA-CTTTCCA-AAATTACATTTTTGACCCTCG
* * *
264676 AATTTTCTAAAATTCCATTTTTGACCC-CG
1 AACTTTCCAAAATTACATTTTTGACCCTCG
* *
264705 ATCTTTCCAAAAAATTATATTTTT-ACCCTCG
1 AACTTTCC--AAAATTACATTTTTGACCCTCG
* * *
264736 AACTTTCTAAAGTTCCATTTTTGACCC
1 AACTTTCCAAAATTACATTTTTGACCC
264763 AAAAATTATC
Statistics
Matches: 159, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
28 19 0.12
29 76 0.48
30 42 0.26
31 22 0.14
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.41
Consensus pattern (30 bp):
AACTTTCCAAAATTACATTTTTGACCCTCG
Found at i:264629 original size:58 final size:59
Alignment explanation
Indices: 264538--264761 Score: 238
Period size: 58 Copynumber: 3.8 Consensus size: 59
264528 TAAACTATCC
** *
264538 AAAAATTACA-TTTTACCCTTAAACTTTCCAAAATTCCATTTTTGACCTCGAACTTTTT
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAACTTTTA
* * * ** * *
264596 GAAAATTGCA-TTTTACCCTCGAATTTTCCAAAATTTAATTTTTGACCT-TAATCTTTCA
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAA-CTTTTA
* * * * * *
264654 AGAAATTACATTTTTACCCTCGAATTTTCTAAAATTCCATTTTTGACCCCGATCTTTCCA
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAACTTT-TA
* * *
264714 AAAAATTATATTTTTACCCTCGAACTTTCTAAAGTTCCATTTTTGACC
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACC
264762 CAAAAATTAT
Statistics
Matches: 139, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
57 2 0.01
58 52 0.37
59 38 0.27
60 47 0.34
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAACTTTTA
Found at i:264894 original size:29 final size:30
Alignment explanation
Indices: 264787--264893 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
264777 ACCCCCAAAC
*
264787 TTCCAAAATTTCCATTTTTGACCCCGAT-T
1 TTCCAAAATTACCATTTTTGACCCCGATCT
*
264816 TCTCCAAAAATTACCA-TTTT-ACCCCCGAACT
1 T-TCC-AAAATTACCATTTTTGA-CCCCGATCT
* * *
264847 TT-CAAAAATCCCATTTTTGACCCTGATCT
1 TTCCAAAATTACCATTTTTGACCCCGATCT
264876 TTCCAAAATTACCATTTT
1 TTCCAAAATTACCATTTT
264894 GCCCTCGGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
28 8 0.13
29 16 0.25
30 28 0.44
31 11 0.17
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (30 bp):
TTCCAAAATTACCATTTTTGACCCCGATCT
Found at i:264914 original size:58 final size:59
Alignment explanation
Indices: 264761--264893 Score: 182
Period size: 59 Copynumber: 2.3 Consensus size: 59
264751 CATTTTTGAC
* * * *
264761 CCAAAAATTATCA-TTTACCCCCAAACTTCCAAAATTTCCATTTTTGACCCCGATTTCT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGATTTCT
* *
264819 CCAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGATCTT-T
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAT-TTCT
264878 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
264894 GCCCTCGGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 26 0.39
59 39 0.58
60 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGATTTCT
Found at i:268042 original size:31 final size:30
Alignment explanation
Indices: 267977--268043 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
267967 TATTATTATT
* * *
267977 ATTAAATATTAATTTTTACATTGATAATAC
1 ATTAAATATTAATTTTTACATTAAAAATAA
*
268007 ATTAAATATTAATTTTT-TATTAAAATATAAA
1 ATTAAATATTAATTTTTACATTAAAA-AT-AA
268038 ATTAAA
1 ATTAAA
268044 AATATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.16
30 19 0.61
31 7 0.23
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTAAATATTAATTTTTACATTAAAAATAA
Found at i:285558 original size:30 final size:29
Alignment explanation
Indices: 285524--285601 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
285514 CTTAACTAAA
* *
285524 AAAAGTTATAATTTAGTCACTGAATTATTC
1 AAAAGTT-TTATTTAGTCACTGAACTATTC
*
285554 AAAAGATTTTCTTTAAGTCACTGAACTATTC
1 AAAAG-TTTTATTT-AGTCACTGAACTATTC
285585 AAAAGTTTTTATTTAGT
1 AAAAG-TTTTATTTAGT
285602 TCACCGAGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.29
31 29 0.71
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (29 bp):
AAAAGTTTTATTTAGTCACTGAACTATTC
Found at i:285573 original size:31 final size:31
Alignment explanation
Indices: 285534--285599 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
285524 AAAAGTTATA
*
285534 ATTT-AGTCACTGAATTATTCAAAAGATTTT
1 ATTTAAGTCACTGAACTATTCAAAAGATTTT
* *
285564 CTTTAAGTCACTGAACTATTCAAAAGTTTTT
1 ATTTAAGTCACTGAACTATTCAAAAGATTTT
285595 ATTTA
1 ATTTA
285600 GTTCACCGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (31 bp):
ATTTAAGTCACTGAACTATTCAAAAGATTTT
Found at i:291004 original size:17 final size:16
Alignment explanation
Indices: 290973--291020 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
290963 TTATCCAAAA
*
290973 AAATTA-TTATTTTTT
1 AAATTATTTATATTTT
290988 AAATTAATTTATATTTT
1 AAATT-ATTTATATTTT
* *
291005 TAATTATTTTTATTTT
1 AAATTATTTATATTTT
291021 GTCCGTCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AAATTATTTATATTTT
Found at i:291006 original size:18 final size:16
Alignment explanation
Indices: 290974--291020 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
290964 TATCCAAAAA
290974 AATTA-TTAT-TTTTT
1 AATTATTTATATTTTT
290988 AAATTAATTTATATTTTT
1 -AATT-ATTTATATTTTT
*
291006 AATTATTTTTATTTT
1 AATTATTTATATTTT
291021 GTCCGTCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 11 0.39
17 8 0.29
18 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTATTTATATTTTT
Found at i:296868 original size:11 final size:11
Alignment explanation
Indices: 296852--296917 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
296842 CCAAACAATC
*
296852 AAAATAACAGA
1 AAAATAACACA
296863 AAAATAACAGC-
1 AAAATAACA-CA
*
296874 AAAACAACAACA
1 AAAATAAC-ACA
*
296886 AAAATAAAAACA
1 AAAAT-AACACA
*
296898 AAAATAACACC
1 AAAATAACACA
*
296909 AAAACAACA
1 AAAATAACA
296918 ATTAAAACAG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
11 29 0.66
12 13 0.30
13 2 0.05
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.06
Consensus pattern (11 bp):
AAAATAACACA
Found at i:296877 original size:12 final size:12
Alignment explanation
Indices: 296852--296912 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
296842 CCAAACAATC
*
296852 AAAATAAC-AGA
1 AAAATAACAACA
*
296863 AAAATAACAGC-
1 AAAATAACAACA
*
296874 AAAACAACAACA
1 AAAATAACAACA
*
296886 AAAATAAAAACA
1 AAAATAACAACA
*
296898 AAAATAACACCA
1 AAAATAACAACA
296910 AAA
1 AAA
296913 CAACAATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
11 17 0.43
12 23 0.57
ACGTcount: A:0.74, C:0.16, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:296966 original size:21 final size:20
Alignment explanation
Indices: 296921--296992 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
296911 AACAACAATT
* * *
296921 AAAACAGTAAAAA-ATCACG
1 AAAACAATAAAAACAGCACC
*
296940 AAAACAATAAAAATAGCAACC
1 AAAACAATAAAAACAGC-ACC
296961 AAAACAATAATAAAACAGCACC
1 AAAACAAT-A-AAAACAGCACC
296983 AAAACAATAA
1 AAAACAATAA
296993 TATAATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
19 12 0.27
20 3 0.07
21 11 0.24
22 12 0.27
23 7 0.16
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.10
Consensus pattern (20 bp):
AAAACAATAAAAACAGCACC
Found at i:296986 original size:22 final size:23
Alignment explanation
Indices: 296940--296994 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
296930 AAAAATCACG
*
296940 AAAACAAT-A-AAAATAGCAACC
1 AAAACAATAATAAAACAGCAACC
296961 AAAACAATAATAAAACAGC-ACC
1 AAAACAATAATAAAACAGCAACC
296983 AAAACAATAATA
1 AAAACAATAATA
296995 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 8 0.26
22 16 0.52
23 7 0.23
ACGTcount: A:0.67, C:0.18, G:0.04, T:0.11
Consensus pattern (23 bp):
AAAACAATAATAAAACAGCAACC
Found at i:298933 original size:23 final size:23
Alignment explanation
Indices: 298831--298934 Score: 138
Period size: 23 Copynumber: 4.4 Consensus size: 23
298821 ACACTAGCGC
*
298831 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
298854 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTCT-GT-TTAGCACTGTGTGT
* *
298879 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
298902 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
298925 GCTCTCTGTT
1 GCTCTCTGTT
298935 GCCCAACACT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 51 0.72
24 1 0.01
25 16 0.23
26 3 0.04
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:306959 original size:21 final size:20
Alignment explanation
Indices: 306934--306976 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
306924 TATAAATATG
306934 TATCACTAAATTTGTATAATA
1 TATCA-TAAATTTGTATAATA
* * *
306955 TATCATTATTTTTTATAATA
1 TATCATAAATTTGTATAATA
306975 TA
1 TA
306977 AAATATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
TATCATAAATTTGTATAATA
Found at i:313959 original size:5 final size:5
Alignment explanation
Indices: 313951--313975 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
313941 AAATAAGTAA
313951 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
313976 TTTATGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:320339 original size:113 final size:113
Alignment explanation
Indices: 320196--320426 Score: 392
Period size: 113 Copynumber: 2.1 Consensus size: 113
320186 TCCATTAACC
* * * *
320196 CAAAA-AAACTTAATAGGAAGAAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGGTT
1 CAAAAGAAACTTAACAGGAAGAAGATATTGGAACCAAAGATATCGAATCTTTTGGTTAATAGATT
320260 TTAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAGATATTGGAAT
66 TTAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAGATATTGGAAT
*
320308 CAAAAGAAACTTAACGGGAAGAAGATATTGGAACCAAAGATATCGAATCTTTTGGTTAATAGATT
1 CAAAAGAAACTTAACAGGAAGAAGATATTGGAACCAAAGATATCGAATCTTTTGGTTAATAGATT
* *
320373 TTAAATATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGGAAT
66 TTAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAGATATTGGAAT
320421 CAAAAG
1 CAAAAG
320427 GGAAGAAGAT
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
112 5 0.05
113 106 0.95
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (113 bp):
CAAAAGAAACTTAACAGGAAGAAGATATTGGAACCAAAGATATCGAATCTTTTGGTTAATAGATT
TTAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAGATATTGGAAT
Done.