Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:1443393 original size:11 final size:11
Alignment explanation
Indices: 1443358--1443405 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1443348 ATATGATCAG
1443358 ATTATTTTT-T
1 ATTATTTTTAT
*
1443368 A-TATTATTTAA
1 ATTATT-TTTAT
1443379 ATTATTTTTAT
1 ATTATTTTTAT
*
1443390 ATTATATTTAT
1 ATTATTTTTAT
1443401 ATTAT
1 ATTAT
1443406 ATCATCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 20 0.62
12 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:1444905 original size:47 final size:47
Alignment explanation
Indices: 1444852--1444951 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
1444842 ATCAAATACA
*
1444852 ATATAAAAATAAATTAAGATA-TGATGTGATTACATAAACTTATCAAT
1 ATATAAAAATAAATTAAGATACAG-TGTGATTACATAAACTTATCAAT
* * *
1444899 ATATAAAAATAAATTAAGATACAGTGTGATTATATAAATTTATTAAT
1 ATATAAAAATAAATTAAGATACAGTGTGATTACATAAACTTATCAAT
1444946 ATATAA
1 ATATAA
1444952 TATGAATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 47 0.98
48 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (47 bp):
ATATAAAAATAAATTAAGATACAGTGTGATTACATAAACTTATCAAT
Found at i:1445542 original size:5 final size:5
Alignment explanation
Indices: 1445532--1445559 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1445522 AACTCACTTA
1445532 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
1445560 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1445802 original size:24 final size:23
Alignment explanation
Indices: 1445740--1445806 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1445730 TCAAACACAT
*
1445740 TTTTTAATTTTATATAT-ATTTTTA
1 TTTTT-ATTTT-TATATCATATTTA
* *
1445764 TTTTTA-TATTGTATCATATTTA
1 TTTTTATTTTTATATCATATTTA
1445786 TTTATTATTTTTATATCATAT
1 TTT-TTATTTTTATATCATAT
1445807 AATTTATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 4 0.11
24 16 0.46
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (23 bp):
TTTTTATTTTTATATCATATTTA
Found at i:1445968 original size:24 final size:24
Alignment explanation
Indices: 1445908--1445968 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 24
1445898 ACCTAATTGC
1445908 TATA-TCTAAAAAGTTGTACCATA
1 TATAGTCTAAAAAGTTGTACCATA
* *
1445931 CATAGTACTTAAAA-TTGTGA-CATTA
1 TATAGT-CTAAAAAGTTGT-ACCA-TA
1445956 TATAGTCTAAAAA
1 TATAGTCTAAAAA
1445969 CTTGGTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.10
24 13 0.43
25 14 0.47
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (24 bp):
TATAGTCTAAAAAGTTGTACCATA
Found at i:1447173 original size:5 final size:5
Alignment explanation
Indices: 1447166--1447206 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
1447156 AGCTTACATG
*
1447166 TAATG TAATA TAATA TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA T
1447207 GAAATTATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:1447778 original size:63 final size:67
Alignment explanation
Indices: 1447698--1447831 Score: 204
Period size: 63 Copynumber: 2.0 Consensus size: 67
1447688 TTGATATTAA
*
1447698 ATTAAATTTAAATAAATATTTAAATATA-C-T-ACCATATATTAAAATA-TTTTAAAAAATACAA
1 ATTAAATTTAAACAAATATTTAAATATACCTTAACCATATATTAAAATATTTTTAAAAAATACAA
1447759 TT
66 TT
* *
1447761 ATTAAATTTAAACAAATATTTAAATATACCCTTAACCGTATTTTAAAATATTTTTAAAAAATACA
1 ATTAAATTTAAACAAATATTTAAATATA-CCTTAACCATATATTAAAATATTTTTAAAAAATACA
1447826 ATT
65 ATT
1447829 ATT
1 ATT
1447832 TGACTACCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
63 27 0.43
65 1 0.02
66 1 0.02
67 14 0.22
68 20 0.32
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (67 bp):
ATTAAATTTAAACAAATATTTAAATATACCTTAACCATATATTAAAATATTTTTAAAAAATACAA
TT
Found at i:1448767 original size:4 final size:4
Alignment explanation
Indices: 1448758--1448789 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1448748 ACAAGAATTG
1448758 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1448790 CTACCCTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:1453224 original size:3 final size:3
Alignment explanation
Indices: 1453205--1453242 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1453195 TTAACTTTTC
*
1453205 TAA TAA TTAA TTA -AA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1453243 GGGTATCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 27 0.87
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1453491 original size:14 final size:13
Alignment explanation
Indices: 1453465--1453498 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
1453455 TTTATGAAAA
1453465 ATTTAAAAAT-AT
1 ATTTAAAAATAAT
1453477 -TTTAAAAATAAT
1 ATTTAAAAATAAT
1453489 ATTTAAAAAT
1 ATTTAAAAAT
1453499 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 2 0.10
13 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTAAAAATAAT
Found at i:1453976 original size:45 final size:45
Alignment explanation
Indices: 1453927--1454013 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
1453917 AAAATAATTA
* * *
1453927 TAACTTTTAATTGATAA-TTAAATTAATTTTTTTAAGATAAATCTT
1 TAACTTTAAATTGA-AATTTAAATTAATTTTATTAAAATAAATCTT
*
1453972 TAACTTTAAATTTAAATTTAAATTAATTTTATTAAAATAAAT
1 TAACTTTAAATTGAAATTTAAATTAATTTTATTAAAATAAAT
1454014 TAAAGATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (45 bp):
TAACTTTAAATTGAAATTTAAATTAATTTTATTAAAATAAATCTT
Found at i:1455947 original size:17 final size:17
Alignment explanation
Indices: 1455927--1455959 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1455917 AAACTTATTA
1455927 TAATTTT-TTTTATTTTT
1 TAATTTTATTTT-TTTTT
1455944 TAATTTTATTTTTTTT
1 TAATTTTATTTTTTTT
1455960 AAAATTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TAATTTTATTTTTTTTT
Found at i:1456436 original size:16 final size:16
Alignment explanation
Indices: 1456415--1456470 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 16
1456405 TCAATCTTCA
1456415 TAAATTTTAATTTTTT
1 TAAATTTTAATTTTTT
1456431 TAAA-TTT-A---TTT
1 TAAATTTTAATTTTTT
1456442 TAAATTTTAATTATTTT
1 TAAATTTTAATT-TTTT
* *
1456459 TTAATTTAAATT
1 TAAATTTTAATT
1456471 GATTGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 1 0.03
14 1 0.03
15 3 0.09
16 4 0.12
17 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAAATTTTAATTTTTT
Found at i:1456835 original size:21 final size:23
Alignment explanation
Indices: 1456794--1456840 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
1456784 TTGAATTAAA
1456794 TTAATTAAATATTATAATCAAAT
1 TTAATTAAATATTATAATCAAAT
*
1456817 TTAATTCAATA-TA-AATCAAAT
1 TTAATTAAATATTATAATCAAAT
1456838 TTA
1 TTA
1456841 TTTAGTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
23 10 0.43
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATTAAATATTATAATCAAAT
Found at i:1458076 original size:28 final size:28
Alignment explanation
Indices: 1458045--1458116 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
1458035 TTAAGTTAAA
*
1458045 TTTAATAATCTATT-TATATTAT-ATTGTG
1 TTTAAT-AT-TATTATATATTATAATTATG
*
1458073 TTTAGATATTTTTATATATTATAATTATG
1 TTTA-ATATTATTATATATTATAATTATG
1458102 TTTAAAATATTATTA
1 TTT--AATATTATTA
1458117 AGATTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 3 0.08
28 14 0.39
29 10 0.28
30 8 0.22
31 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTAATATTATTATATATTATAATTATG
Found at i:1462717 original size:99 final size:98
Alignment explanation
Indices: 1462588--1462785 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 98
1462578 ATATAGATGG
*
1462588 AAGATGACCCAACTTATAACGTTTTATACGGTGAGATTTCTAGCAATGCTGAGAAATTTTCAGAT
1 AAGATGACCCAACTTATAACGTTTTATACGGTGAGATTTCTAACAATGCTGAGAAATTTTCAGAT
*
1462653 GAATAATAGCAAATATGTGATTACCACAACTGC
66 GAATAATAGCAAACATGTGATTACCACAACTGC
* *
1462686 AAGATGACCCAACCTTTTAACGTTTTATACGGTGATATTTCTAACAATGCTGAGAAATTTTCAGA
1 AAGATGACCCAA-CTTATAACGTTTTATACGGTGAGATTTCTAACAATGCTGAGAAATTTTCAGA
*
1462751 TGAATAATAGTAAACATGTGATTACCACAACTGC
65 TGAATAATAGCAAACATGTGATTACCACAACTGC
1462785 A
1 A
1462786 TGAAAATCAA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 12 0.13
99 82 0.87
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (98 bp):
AAGATGACCCAACTTATAACGTTTTATACGGTGAGATTTCTAACAATGCTGAGAAATTTTCAGAT
GAATAATAGCAAACATGTGATTACCACAACTGC
Found at i:1465230 original size:19 final size:20
Alignment explanation
Indices: 1465187--1465230 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1465177 TTCAAAGTCG
1465187 AAATAGATACGTTAAAATAT
1 AAATAGATACGTTAAAATAT
*
1465207 CAATA-ATAC-TTAAAATTAT
1 AAATAGATACGTTAAAA-TAT
1465226 AAATA
1 AAATA
1465231 CATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATAGATACGTTAAAATAT
Found at i:1465312 original size:6 final size:6
Alignment explanation
Indices: 1465301--1465436 Score: 57
Period size: 6 Copynumber: 21.8 Consensus size: 6
1465291 AAATTTAATT
* * *
1465301 ATATAA ATATAA A-ATAA ATA-AA ATAT-G ATATAA ATATATA TTTTAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A ATATAA
** * * *
1465347 A-ATTT ATATAA A-ATAA ATTATTAAA ATATTA ATATTA ATGTAA ATATAA
1 ATATAA ATATAA ATATAA A-TA-T-AA ATATAA ATATAA ATATAA ATATAA
* *
1465396 CATATTTTAA ATATAA TTATATA ATAAAA ATTATAA ATATA
1 -ATA---TAA ATATAA ATATA-A ATATAA A-TATAA ATATA
1465437 TAAAATCTAG
Statistics
Matches: 97, Mismatches: 18, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
5 21 0.22
6 46 0.47
7 18 0.19
8 3 0.03
9 6 0.06
10 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:1465360 original size:25 final size:24
Alignment explanation
Indices: 1465319--1465375 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
1465309 ATAAAATAAA
1465319 TAAAATATGATATAAATATATATT-T
1 TAAAATATGATATAAATA-A-ATTAT
*
1465344 TAAAAT-TTATATAAAATAAATTAT
1 TAAAATATGATAT-AAATAAATTAT
1465368 TAAAATAT
1 TAAAATAT
1465376 TAATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 3 0.11
24 13 0.46
25 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAAATATGATATAAATAAATTAT
Found at i:1465370 original size:24 final size:26
Alignment explanation
Indices: 1465298--1465415 Score: 99
Period size: 25 Copynumber: 4.8 Consensus size: 26
1465288 TGTAAATTTA
* *
1465298 ATTATATAAATATAAAATAAATAAAAT
1 ATTATATAAATAT-AAATTATTAAAAT
* *
1465325 ATGATATAAATATATATT-TTAAAAT
1 ATTATATAAATATAAATTATTAAAAT
1465350 -TTATATAAA-ATAAATTATTAAAAT
1 ATTATATAAATATAAATTATTAAAAT
* * *
1465374 ATTAATATTAATGTAAA-TA-TAACAT
1 ATT-ATATAAATATAAATTATTAAAAT
1465399 ATT-T-TAAATAT-AATTAT
1 ATTATATAAATATAAATTAT
1465416 ATAATAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.03
22 7 0.09
23 7 0.09
24 15 0.20
25 16 0.22
26 11 0.15
27 16 0.22
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTATATAAATATAAATTATTAAAAT
Found at i:1469036 original size:26 final size:27
Alignment explanation
Indices: 1468986--1469044 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1468976 AATCAATTCG
* *
1468986 ATTAATTTTAATATTAAAATTAATTTA
1 ATTAATTTTAATATTAAAATAAATTAA
*
1469013 ATTAATTTTTA-ATTAAAATAAATTAA
1 ATTAATTTTAATATTAAAATAAATTAA
1469039 ATTAAT
1 ATTAAT
1469045 CGAATCGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTAATTTTAATATTAAAATAAATTAA
Found at i:1474161 original size:7 final size:7
Alignment explanation
Indices: 1474149--1474177 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1474139 TTAAAGTTAC
1474149 ATTTAAA
1 ATTTAAA
1474156 ATTTAAA
1 ATTTAAA
1474163 ATTTAAA
1 ATTTAAA
1474170 ATTTAAA
1 ATTTAAA
1474177 A
1 A
1474178 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:1479720 original size:30 final size:30
Alignment explanation
Indices: 1479681--1479764 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
1479671 GTTGAATATG
*
1479681 TTTTAAATTATTATTTAATAAAAATAGTTAAA
1 TTTT-AATTATTATTTAATAAAAATA-TAAAA
* *
1479713 -TTTAATTATAATATTAATATAAATATAAAA
1 TTTTAATTATTAT-TTAATAAAAATATAAAA
1479743 TTTTAA-TATTATTTTAATAAAA
1 TTTTAATTATTA-TTTAATAAAA
1479765 TAAATTTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 24 0.55
31 20 0.45
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTTTAATTATTATTTAATAAAAATATAAAA
Found at i:1479886 original size:76 final size:76
Alignment explanation
Indices: 1479806--1479964 Score: 255
Period size: 76 Copynumber: 2.1 Consensus size: 76
1479796 GTAAATCTCT
* * * *
1479806 TTAATGTTTTAAATTGGTCAAGAATGTTCAATAATTTTAAATAAAATATAATTAAAAATTTTAAA
1 TTAATGTTTTAAATTAGTCAAAAATATTCAATAATTATAAATAAAATATAATTAAAAATTTTAAA
1479871 AATTAAGAATA
66 AATTAAGAATA
* *
1479882 TTAATATTTTAAATTAGTCAAAAATATTCAATAATTATAAATAAAATATAATTTAAAATTTTAAA
1 TTAATGTTTTAAATTAGTCAAAAATATTCAATAATTATAAATAAAATATAATTAAAAATTTTAAA
1479947 AATTAAGAATA
66 AATTAAGAATA
*
1479958 TAAATGT
1 TTAATGT
1479965 GAATGTGATA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.40
Consensus pattern (76 bp):
TTAATGTTTTAAATTAGTCAAAAATATTCAATAATTATAAATAAAATATAATTAAAAATTTTAAA
AATTAAGAATA
Found at i:1479946 original size:24 final size:24
Alignment explanation
Indices: 1479838--1479946 Score: 71
Period size: 24 Copynumber: 4.4 Consensus size: 24
1479828 AATGTTCAAT
*
1479838 AATTTTAAATAAAATATAATTAAA
1 AATTTTAAATAAAATATAATTTAA
* *
1479862 AATTTT-AA-AAATTAAGAATATTAA
1 AATTTTAAATAAAAT-ATAAT-TTAA
* * *
1479886 TATTTTAAATTAGTCAAAAAT-ATTCAA
1 AATTTTAAA-TA---AAATATAATTTAA
*
1479913 TAATTATAAATAAAATATAATTTAA
1 -AATTTTAAATAAAATATAATTTAA
1479938 AATTTTAAA
1 AATTTTAAA
1479947 AATTAAGAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 20
0.65 0.14 0.21
Matches are distributed among these distances:
22 4 0.06
23 6 0.10
24 27 0.44
25 7 0.11
27 6 0.10
28 9 0.15
29 1 0.02
30 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AATTTTAAATAAAATATAATTTAA
Found at i:1480022 original size:20 final size:19
Alignment explanation
Indices: 1479999--1480036 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1479989 TTTTAATATT
1479999 TATATAAATAAAAATAAAAA
1 TATATAAA-AAAAATAAAAA
*
1480019 TATATAAAAAAAGTAAAA
1 TATATAAAAAAAATAAAA
1480037 GTGAACGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
TATATAAAAAAAATAAAAA
Found at i:1488362 original size:16 final size:15
Alignment explanation
Indices: 1488343--1488381 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1488333 AATTAAATTT
1488343 TTTAATATTTAATATA
1 TTTAATATTTAA-ATA
*
1488359 TTTATTATTTAAATA
1 TTTAATATTTAAATA
1488374 TATTAATA
1 T-TTAATA
1488382 AATCCAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATATTTAAATA
Found at i:1488708 original size:31 final size:29
Alignment explanation
Indices: 1488668--1488756 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 29
1488658 TTTAAATATA
*
1488668 TTAACATATTATTTATATATATTTTGATATT
1 TTAATATATTATTTATATATATTTT-AT-TT
* *
1488699 TTGATATATTTATGTTATATTTATTTTATTT
1 TTAATATA-TTAT-TTATATATATTTTATTT
1488730 TTAATATCA-TATTTATATTATATTTTA
1 TTAATAT-ATTATTTATA-TATATTTTA
1488757 ATTATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
29 5 0.10
30 11 0.22
31 14 0.29
32 7 0.14
33 12 0.24
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (29 bp):
TTAATATATTATTTATATATATTTTATTT
Found at i:1488736 original size:29 final size:32
Alignment explanation
Indices: 1488676--1488756 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 32
1488666 TATTAACATA
*
1488676 TTATTTATATATATTTTGATATTTTGATATAT-
1 TTATTTATATTTATTTT-ATATTTTGATATATC
1488708 TTATGTTATATTTATTTTAT-TTTT-A-ATATC
1 TTAT-TTATATTTATTTTATATTTTGATATATC
*
1488738 ATATTTATATTATATTTTA
1 TTATTTATATT-TATTTTA
1488757 ATTATTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 11 0.25
30 11 0.25
31 4 0.09
32 6 0.14
33 12 0.27
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (32 bp):
TTATTTATATTTATTTTATATTTTGATATATC
Found at i:1488762 original size:34 final size:34
Alignment explanation
Indices: 1488702--1488779 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
1488692 TGATATTTTG
* *
1488702 ATATATTTATGTTATATTTATTTTATT-TTTAAT
1 ATATATTTATATTATATTTATATTATTATTTAAT
*
1488735 ATCATATTTATATTATATTT-TAATTATTATTTTAT
1 AT-ATATTTATATTATATTTAT-ATTATTATTTAAT
1488770 ATAGTATTTA
1 ATA-TATTTA
1488780 AAATTGTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
33 3 0.08
34 22 0.58
35 13 0.34
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (34 bp):
ATATATTTATATTATATTTATATTATTATTTAAT
Found at i:1488765 original size:23 final size:22
Alignment explanation
Indices: 1488714--1488771 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
1488704 ATATTTATGT
*
1488714 TATATTTATTTTATTTTTAATA
1 TATATTTATATTATTTTTAATA
1488736 TCATATTTATATTATATTTTAAT-
1 T-ATATTTATATTAT-TTTTAATA
1488759 TATTATTTTATAT
1 TA-TA-TTTATAT
1488772 AGTATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 2 0.06
23 15 0.48
24 14 0.45
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTATATTATTTTTAATA
Found at i:1488778 original size:12 final size:12
Alignment explanation
Indices: 1488679--1488771 Score: 61
Period size: 11 Copynumber: 7.6 Consensus size: 12
1488669 TAACATATTA
1488679 TTTATA-TATAT
1 TTTATATTATAT
1488690 TTTGATATTTTGATAT
1 TTT-ATA--TT-ATAT
*
1488706 ATTTATGTTATA-
1 -TTTATATTATAT
*
1488718 TTTATTTTAT-T
1 TTTATATTATAT
*
1488729 TTTAATATCATA-
1 TTT-ATATTATAT
1488741 TTTATATTATAT
1 TTTATATTATAT
1488753 TTTA-ATTATTAT
1 TTTATATTA-TAT
1488765 TTTATAT
1 TTTATAT
1488772 AGTATTTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
11 26 0.40
12 22 0.34
13 5 0.08
14 2 0.03
15 1 0.02
16 6 0.09
17 3 0.05
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1488778 original size:24 final size:24
Alignment explanation
Indices: 1488715--1488771 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1488705 TATTTATGTT
*
1488715 ATATTTATTTTAT-TTTTAATATC
1 ATATTTATATTATATTTTAATATC
*
1488738 ATATTTATATTATATTTTAATTATT
1 ATATTTATATTATATTTTAA-TATC
1488763 AT-TTTATAT
1 ATATTTATAT
1488772 AGTATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 12 0.40
24 13 0.43
25 5 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATTTATATTATATTTTAATATC
Found at i:1489434 original size:2 final size:2
Alignment explanation
Indices: 1489427--1489465 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1489417 CTTTTAACGA
1489427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1489466 ATTTTAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1496618 original size:16 final size:16
Alignment explanation
Indices: 1496574--1496630 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1496564 ATTGTTATGA
*
1496574 TTTTTAAATTTAAAAATG
1 TTTTTAAATTT--AAATT
* *
1496592 ATTTT-AATTTAATTT
1 TTTTTAAATTTAAATT
1496607 TTTTTAAATTTAAATT
1 TTTTTAAATTTAAATT
1496623 TTTTTAAA
1 TTTTTAAA
1496631 AAAAATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 7 0.21
16 17 0.52
17 5 0.15
18 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTAAATTTAAATT
Found at i:1496622 original size:17 final size:17
Alignment explanation
Indices: 1496574--1496627 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1496564 ATTGTTATGA
* *
1496574 TTTTTAAATTTAAAAATG
1 TTTTTAAATTT-AAATTT
*
1496592 ATTTT-AATTT-AATTT
1 TTTTTAAATTTAAATTT
1496607 TTTTTAAATTTAAATTT
1 TTTTTAAATTTAAATTT
1496624 TTTT
1 TTTT
1496628 AAAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 14 0.47
18 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTTAAATTT
Found at i:1500587 original size:13 final size:14
Alignment explanation
Indices: 1500555--1500593 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
1500545 AAAATTTTAT
1500555 TTAATATTTAAAAAA
1 TTAA-ATTTAAAAAA
1500570 TTAAATTTAAAAAA
1 TTAAATTTAAAAAA
1500584 -TAAATTTAAA
1 TTAAATTTAAA
1500594 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.42
14 10 0.42
15 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAATTTAAAAAA
Found at i:1505770 original size:2 final size:2
Alignment explanation
Indices: 1505763--1505800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1505753 ATATAAACAC
1505763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1505801 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1509283 original size:17 final size:16
Alignment explanation
Indices: 1509261--1509352 Score: 66
Period size: 17 Copynumber: 5.7 Consensus size: 16
1509251 TGATAATTTA
1509261 TTTATTTATATCATAAT
1 TTTATTTATAT-ATAAT
* *
1509278 TTTATTTA-AAATATT
1 TTTATTTATATATAAT
1509293 TTATATTTATATA-AAT
1 TT-TATTTATATATAAT
*
1509309 TTTA-ATATATTAATAAT
1 TTTATTTATA-T-ATAAT
*
1509326 TTATATATATATATAA-
1 TT-TATTTATATATAAT
*
1509342 TATATTTATAT
1 TTTATTTATAT
1509353 TTTAATTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 4 0.07
15 17 0.28
16 13 0.21
17 19 0.31
18 3 0.05
19 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATTTATATATAAT
Found at i:1509329 original size:33 final size:33
Alignment explanation
Indices: 1509229--1509338 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 33
1509219 ATATATAAAA
*
1509229 ATATAAATTATTAAATTATATTTGATAATTTATTTATTT
1 ATATAAATT-TT-AA-TATA-TTAATAATTTA--TATTT
* * *
1509268 ATATCATAATTTT-ATTTA-AAATATTTTATATTT
1 ATAT-A-AATTTTAATATATTAATAATTTATATTT
*
1509301 ATATAAATTTTAATATATTAATAATTTATATAT
1 ATATAAATTTTAATATATTAATAATTTATATTT
1509334 ATATA
1 ATATA
1509339 TAATATATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
31 6 0.10
32 5 0.08
33 26 0.44
35 7 0.12
37 3 0.05
38 1 0.02
39 4 0.07
40 3 0.05
41 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
ATATAAATTTTAATATATTAATAATTTATATTT
Found at i:1509359 original size:33 final size:34
Alignment explanation
Indices: 1509244--1509380 Score: 99
Period size: 33 Copynumber: 4.1 Consensus size: 34
1509234 AATTATTAAA
* * *
1509244 TTATATTTGATAATTTATTTATTTATATCATA-AT
1 TTATATTT-ATAATTTATATATATATATAATATAT
* * *
1509278 TT-TATTTAAAATATTTTATATTTATATAA-AT-T
1 TTATATTTATAAT-TTATATATATATATAATATAT
1509310 TTAATATATTAATAATTTATATATATATATAATATAT
1 TT-ATAT-TT-ATAATTTATATATATATATAATATAT
* **
1509347 TTATATTT-TAA-TTATAT-TAAATATTTTATAT
1 TTATATTTATAATTTATATATATATATAATATAT
1509378 TTA
1 TTA
1509381 AAAATAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
31 14 0.16
32 14 0.16
33 21 0.25
34 5 0.06
35 18 0.21
36 10 0.12
37 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (34 bp):
TTATATTTATAATTTATATATATATATAATATAT
Found at i:1509362 original size:17 final size:17
Alignment explanation
Indices: 1509242--1509374 Score: 52
Period size: 16 Copynumber: 8.1 Consensus size: 17
1509232 TAAATTATTA
*
1509242 AATTATATTTGATAATTT
1 AATTATATTT-ATATTTT
**
1509260 -ATT-TATTTATATCAT
1 AATTATATTTATATTTT
*
1509275 AATTTTATTTAAAATATTTT
1 AATTATATTT---ATATTTT
* *
1509295 ATATT-TATATAAATTTT
1 A-ATTATATTTATATTTT
* *
1509312 AA-TATATTAATAATTT
1 AATTATATTTATATTTT
*
1509328 -A-TATA--TATA-TAT
1 AATTATATTTATATTTT
1509340 AA-TATATTTATATTTT
1 AATTATATTTATATTTT
*
1509356 AATTATATTAAATATTTT
1 AATTATATT-TATATTTT
1509374 A
1 A
1509375 TATTTAAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
12 2 0.02
13 8 0.09
15 14 0.16
16 21 0.24
17 21 0.24
18 8 0.09
20 10 0.11
21 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (17 bp):
AATTATATTTATATTTT
Found at i:1509417 original size:21 final size:21
Alignment explanation
Indices: 1509309--1509422 Score: 63
Period size: 21 Copynumber: 5.2 Consensus size: 21
1509299 TTATATAAAT
1509309 TTTAATA-TATTAATAATTTATA
1 TTTAATATTATT-A-AATTTATA
* * *
1509331 TAT-ATATATAATATATTTATA
1 TTTAATAT-TATTAAATTTATA
1509352 TTTTAAT-TATATTAAATATTTTATA
1 -TTTAATAT-TATT-AA-A-TTTATA
* * ** *
1509377 TTTAAAAATAAAAAACTTATA
1 TTTAATATTATTAAATTTATA
1509398 TTTAATATTATTAAATTTATA
1 TTTAATATTATTAAATTTATA
1509419 TTTA
1 TTTA
1509423 CAACCTCGCT
Statistics
Matches: 68, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
21 35 0.51
22 11 0.16
23 8 0.12
24 8 0.12
25 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATATTATTAAATTTATA
Found at i:1514786 original size:19 final size:19
Alignment explanation
Indices: 1514764--1514803 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1514754 ATAAATGACA
1514764 TAAACCAAGATAACATTAC
1 TAAACCAAGATAACATTAC
1514783 TAAACCAAGATAACATTAC
1 TAAACCAAGATAACATTAC
1514802 TA
1 TA
1514804 TGACATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.20, G:0.05, T:0.23
Consensus pattern (19 bp):
TAAACCAAGATAACATTAC
Found at i:1515121 original size:2 final size:2
Alignment explanation
Indices: 1515114--1515141 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1515104 ATATCTGAAT
1515114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1515142 GACGTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1521302 original size:16 final size:17
Alignment explanation
Indices: 1521281--1521313 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1521271 AACTTTTAAA
1521281 TATTTTAAATTT-AATT
1 TATTTTAAATTTGAATT
*
1521297 TATTTTGAATTTGAATT
1 TATTTTAAATTTGAATT
1521314 ATTCTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TATTTTAAATTTGAATT
Found at i:1521817 original size:27 final size:26
Alignment explanation
Indices: 1521770--1521820 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1521760 AACTAGTAAT
*
1521770 ATTAAAAACAATTATATTAATATAAC
1 ATTAAAAACAATTAAATTAATATAAC
1521796 ATTAAAAA-AATTAAAATATAATATA
1 ATTAAAAACAATT-AAAT-TAATATA
1521821 GTAAGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTAAAAACAATTAAATTAATATAAC
Found at i:1521913 original size:17 final size:16
Alignment explanation
Indices: 1521874--1521929 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
1521864 TTAACATATA
*
1521874 AAAATTTAT-ATAAAT
1 AAAATATATCATAAAT
*
1521889 ATAATATATCATAAAT
1 AAAATATATCATAAAT
*
1521905 AAAAATATAACAT-AAT
1 -AAAATATATCATAAAT
1521921 AAAATATAT
1 AAAATATAT
1521930 AAATATGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 15 0.44
16 9 0.26
17 10 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATATATCATAAAT
Found at i:1521924 original size:15 final size:16
Alignment explanation
Indices: 1521883--1521928 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1521873 AAAAATTTAT
* *
1521883 ATAAATATAATATATC
1 ATAAATAAAATATAAC
1521899 ATAAATAAAAATATAAC
1 ATAAAT-AAAATATAAC
1521916 AT-AATAAAATATA
1 ATAAATAAAATATA
1521929 TAAATATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATAAAATATAAC
Found at i:1522313 original size:2 final size:2
Alignment explanation
Indices: 1522306--1522341 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1522296 ATTTATTGAT
*
1522306 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1522342 CAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1522348 original size:10 final size:10
Alignment explanation
Indices: 1522306--1522348 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
1522296 ATTTATTGAT
*
1522306 TATATATATA
1 TATATACATA
1522316 TATATACATA
1 TATATACATA
*
1522326 TATATATATA
1 TATATACATA
*
1522336 TATATACAAA
1 TATATACATA
1522346 TAT
1 TAT
1522349 TTTTATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATACATA
Found at i:1523054 original size:2 final size:2
Alignment explanation
Indices: 1523043--1523075 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1523033 TTCCTCCCTT
1523043 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1523076 AGAATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1523393 original size:3 final size:3
Alignment explanation
Indices: 1523387--1523417 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1523377 CAACAACAAC
1523387 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1523418 CGGTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1524672 original size:2 final size:2
Alignment explanation
Indices: 1524665--1524699 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1524655 TAAATTAATT
1524665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1524700 GGAACCATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1524959 original size:2 final size:2
Alignment explanation
Indices: 1524952--1524983 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1524942 ATTATTATCT
*
1524952 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1524984 AACATAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1525930 original size:37 final size:35
Alignment explanation
Indices: 1525856--1525931 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
1525846 ATAATTTAAT
* *
1525856 AAAATATTATTTTATTTTTATTTAATTTATATATA
1 AAAATATTATTTTATTATTATTTAATTTAAATATA
1525891 AAAATA-TATTTATATTATTATTTTATATTTAAA-ATTA
1 AAAATATTATTT-TATTATTA-TTTA-ATTTAAATA-TA
1525928 AAAA
1 AAAA
1525932 AATAATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 5 0.14
35 13 0.37
36 5 0.14
37 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
AAAATATTATTTTATTATTATTTAATTTAAATATA
Found at i:1536088 original size:36 final size:36
Alignment explanation
Indices: 1536010--1536088 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1536000 CGTTACGTTA
* * *
1536010 AAATATATCACTTTTTTTTAATTTATATTACGTTAC
1 AAATATATCACTTTTTTTTAATTTAAATAACGTAAC
1536046 ATAATATATCAC-TTTTTTTAGA-TTAAATAACGTAATC
1 A-AATATATCACTTTTTTTTA-ATTTAAATAACGTAA-C
1536083 AAATAT
1 AAATAT
1536089 TTAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 24 0.65
37 13 0.35
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATATATCACTTTTTTTTAATTTAAATAACGTAAC
Found at i:1538718 original size:2 final size:2
Alignment explanation
Indices: 1538711--1538747 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1538701 CCATCTATGC
1538711 AT AT 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 AT AT A
1538748 ATCACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1539392 original size:11 final size:12
Alignment explanation
Indices: 1539372--1539409 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1539362 TACTTACCTC
1539372 TTTATATTAT-T
1 TTTATATTATAT
*
1539383 TTTATTTTATATT
1 TTTATATTATA-T
1539396 TTTATATTATAT
1 TTTATATTATAT
1539408 TT
1 TT
1539410 AGAGTAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 9 0.39
12 3 0.13
13 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1539397 original size:13 final size:13
Alignment explanation
Indices: 1539379--1539409 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1539369 CTCTTTATAT
*
1539379 TATTTTTATTTTA
1 TATTTTTATATTA
1539392 TATTTTTATATTA
1 TATTTTTATATTA
1539405 TATTT
1 TATTT
1539410 AGAGTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTATATTA
Found at i:1539812 original size:15 final size:16
Alignment explanation
Indices: 1539780--1539829 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
1539770 ATATAATTAT
*
1539780 TTTAATAAA-ATAATA
1 TTTAATAAATTTAATA
1539795 TTTAATAAATTTAA-A
1 TTTAATAAATTTAATA
1539810 TTT--TAAATTTTAATA
1 TTTAATAAA-TTTAATA
1539825 TTTAA
1 TTTAA
1539830 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.14
14 5 0.17
15 17 0.59
16 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATAAATTTAATA
Found at i:1539821 original size:14 final size:14
Alignment explanation
Indices: 1539800--1539834 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1539790 TAATATTTAA
*
1539800 TAAATTTAAAT-TT
1 TAAATTTTAATATT
1539813 TAAATTTTAATATT
1 TAAATTTTAATATT
1539827 TAAATTTT
1 TAAATTTT
1539835 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:1540628 original size:5 final size:5
Alignment explanation
Indices: 1540618--1540689 Score: 52
Period size: 5 Copynumber: 16.0 Consensus size: 5
1540608 AAATAATTAA
*
1540618 AATAT AATAT AATAT AA-A- AA-AT AATAT AA-AT AA-AT TATA- AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * *
1540662 -AT-T AATAT ATTAA AATTT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
1540690 TAATTATCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
3 4 0.08
4 17 0.32
5 32 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:1540638 original size:28 final size:29
Alignment explanation
Indices: 1540607--1540689 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
1540597 AGGATGATAG
1540607 AAAATAATTAAAATATAATATAATATA-A
1 AAAATAATTAAAATATAATATAATATATA
1540635 AAAATAA-TATAAATA-AATTATAA-ATATA
1 AAAATAATTA-AAATATAA-TATAATATATA
** *
1540663 TTAATATATTAAAATTTAATATAATAT
1 AAAATA-ATTAAAATATAATATAATAT
1540690 TAATTATCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 7 0.16
28 22 0.49
29 10 0.22
30 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATAATTAAAATATAATATAATATATA
Found at i:1540643 original size:12 final size:13
Alignment explanation
Indices: 1540621--1540670 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1540611 TAATTAAAAT
1540621 ATAATATAATATAA
1 ATAA-ATAATATAA
1540635 A-AAATAATATAA
1 ATAAATAATATAA
1540647 ATAAAT--TATAA
1 ATAAATAATATAA
*
1540658 ATATATTAATATA
1 ATA-AATAATATA
1540671 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.26
12 12 0.39
13 6 0.19
14 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAATAATATAA
Found at i:1540660 original size:17 final size:16
Alignment explanation
Indices: 1540610--1540662 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
1540600 ATGATAGAAA
*
1540610 ATAATTAAAATATAAT
1 ATAAATAAAATATAAT
*
1540626 ATAATATAAAAAATAAT
1 ATAA-ATAAAATATAAT
*
1540643 ATAAATAAATTATAAAT
1 ATAAATAAAATAT-AAT
1540660 ATA
1 ATA
1540663 TTAATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 11 0.35
17 20 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATAAAATATAAT
Found at i:1540683 original size:57 final size:58
Alignment explanation
Indices: 1540609--1540722 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 58
1540599 GATGATAGAA
*
1540609 AATAATTAAAATATAATATAATATAAAAAAT-AATATAAATAAA-TTATAAATATATT
1 AATAATTAAAATATAATATAATATAAAAAATCAATATAAAAAAATTTATAAATATATT
* * ** *
1540665 AATATATTAAAATTTAATATAATATTAATTATCATTATAAAAAAATTTATAAATATAT
1 AATA-ATTAAAATATAATATAATATAAAAAATCAATATAAAAAAATTTATAAATATAT
1540723 AACGTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
56 4 0.08
57 23 0.47
58 10 0.20
59 12 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (58 bp):
AATAATTAAAATATAATATAATATAAAAAATCAATATAAAAAAATTTATAAATATATT
Found at i:1540973 original size:10 final size:11
Alignment explanation
Indices: 1540948--1541011 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 11
1540938 ATTTTTTTAC
1540948 ATAAATATTAAT
1 ATAAA-ATTAAT
1540960 ATAAAATT-AT
1 ATAAAATTAAT
*
1540970 ATAAAAATAAT
1 ATAAAATTAAT
*
1540981 ATCAAATCTCAAT
1 ATAAAAT-T-AAT
1540994 ACATAAAA-TAAT
1 --ATAAAATTAAT
1541006 ATAAAA
1 ATAAAA
1541012 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 15 0.35
11 10 0.23
12 9 0.21
13 4 0.09
15 5 0.12
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAATTAAT
Found at i:1542683 original size:2 final size:2
Alignment explanation
Indices: 1542676--1542708 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1542666 ATGAAAAGTA
1542676 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
1542709 CATTGACTTT
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:1556930 original size:2 final size:2
Alignment explanation
Indices: 1556923--1556955 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1556913 TGAAATATTT
1556923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1556956 TTGCAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1560022 original size:22 final size:21
Alignment explanation
Indices: 1559997--1560039 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1559987 AAATTATATA
*
1559997 AAATTATAATATATTTTAAAAT
1 AAATAATAAT-TATTTTAAAAT
*
1560019 AAATAATTATTATTTTAAAAT
1 AAATAATAATTATTTTAAAAT
1560040 TAAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATAATAATTATTTTAAAAT
Found at i:1560034 original size:21 final size:20
Alignment explanation
Indices: 1560008--1560055 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
1559998 AATTATAATA
1560008 TATTTTAAAA-TAAATAATTAT
1 TATTTTAAAATTAAA-AATT-T
1560029 TATTTTAAAATTAAAAATTT
1 TATTTTAAAATTAAAAATTT
1560049 TAATTTT
1 T-ATTTT
1560056 GATTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTTAAAATTAAAAATTT
Found at i:1570860 original size:14 final size:14
Alignment explanation
Indices: 1570819--1570861 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1570809 ATCGATGAAA
1570819 AAAATTATAAATATT
1 AAAATTATAAAT-TT
1570834 AAAATT-TAAAATTT
1 AAAATTAT-AAATTT
*
1570848 AAAATTATTAATTT
1 AAAATTATAAATTT
1570862 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTATAAATTT
Found at i:1575165 original size:2 final size:2
Alignment explanation
Indices: 1575160--1575201 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1575150 GCAAATCATA
1575160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1575202 GCAACCAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1575960 original size:15 final size:13
Alignment explanation
Indices: 1575922--1575969 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
1575912 ATAAAAAAAC
1575922 ATATTTAATATATA
1 ATATTT-ATATATA
1575936 ATATTTATATATA
1 ATATTTATATATA
1575949 ATATTT-TGATATA
1 ATATTTAT-ATATA
*
1575962 ATTTTTAT
1 ATATTTAT
1575970 TTTATTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 1 0.03
13 23 0.74
14 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTATATATA
Found at i:1576788 original size:21 final size:19
Alignment explanation
Indices: 1576760--1576799 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
1576750 TATAAATTTA
1576760 AATTTAAATTAATAATTATAT
1 AATTTAAATT-AT-ATTATAT
1576781 AATTTAAATTATATTATAT
1 AATTTAAATTATATTATAT
1576800 TAAATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTAAATTATATTATAT
Found at i:1577512 original size:24 final size:24
Alignment explanation
Indices: 1577485--1577544 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 24
1577475 AATTCGAGTC
1577485 AAATATAATATAAAAAAATAAT-T
1 AAATATAATATAAAAAAATAATAT
1577508 AAAATATAATAT--AAAAATAATAT
1 -AAATATAATATAAAAAAATAATAT
1577531 AAATATAATA-AAAA
1 AAATATAATATAAAA
1577545 TATACATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
22 19 0.58
23 3 0.09
24 11 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATATAATATAAAAAAATAATAT
Found at i:1577513 original size:9 final size:11
Alignment explanation
Indices: 1577489--1577554 Score: 64
Period size: 11 Copynumber: 5.7 Consensus size: 11
1577479 CGAGTCAAAT
1577489 ATAATATAAAA
1 ATAATATAAAA
1577500 A-AATAATTAAAA
1 ATAAT-A-TAAAA
1577512 TATAATATAAAA
1 -ATAATATAAAA
*
1577524 ATAATATAAAT
1 ATAATATAAAA
1577535 ATAATA-AAAA
1 ATAATATAAAA
1577545 TATACATATA
1 -ATA-ATATA
1577555 TGTTAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 6 0.13
11 21 0.46
12 13 0.28
13 3 0.07
14 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1577526 original size:22 final size:22
Alignment explanation
Indices: 1577485--1577554 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 22
1577475 AATTCGAGTC
1577485 AAATATAATATAAAAA-AATAATT
1 AAATATAATATAAAAATAAT-A-T
1577508 AAAATATAATATAAAAATAATAT
1 -AAATATAATATAAAAATAATAT
1577531 AAATATAATA-AAAATATACATAT
1 AAATATAATATAAAA-ATA-ATAT
1577554 A
1 A
1577555 TGTTAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 6 0.14
24 17 0.40
25 3 0.07
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATATAATATAAAAATAATAT
Found at i:1577537 original size:17 final size:17
Alignment explanation
Indices: 1577502--1577554 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1577492 ATATAAAAAA
*
1577502 ATAATTAAAATAT-AAT
1 ATAATAAAAATATAAAT
1577518 ATAA-AAATAATATAAAT
1 ATAATAAA-AATATAAAT
*
1577535 ATAATAAAAATATACAT
1 ATAATAAAAATATAAAT
1577552 ATA
1 ATA
1577555 TGTTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 9 0.28
17 18 0.56
18 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAAAAATATAAAT
Found at i:1577657 original size:14 final size:14
Alignment explanation
Indices: 1577638--1577678 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1577628 CTAAATTTTT
1577638 TTTTTTCTTTCTTC
1 TTTTTTCTTTCTTC
* *
1577652 TTTTTTTTTTCCTC
1 TTTTTTCTTTCTTC
1577666 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
1577679 TTCATACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTCTTC
Found at i:1577659 original size:21 final size:21
Alignment explanation
Indices: 1577633--1577680 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1577623 AAGTACTAAA
1577633 TTTTTTTTTT--TCTTTCTTC
1 TTTTTTTTTTCCTCTTTCTTC
*
1577652 TTTTTTTTTTCCTCTTTTTTC
1 TTTTTTTTTTCCTCTTTCTTC
*
1577673 TTTCTTTT
1 TTTTTTTT
1577681 CATACCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
21 15 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTTCCTCTTTCTTC
Found at i:1578002 original size:42 final size:42
Alignment explanation
Indices: 1577938--1578041 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
1577928 ATAATATAAA
*
1577938 AAATAATATTAATATA-TAAATTTTA-ATAAATTTATATAATAT
1 AAAT-ATATTAATATATTAAAATTTATATAAATTTAT-TAATAT
* *
1577980 AAAT-TATTAATATATTAAAATTTATATAAATTTATTATTTT
1 AAATATATTAATATATTAAAATTTATATAAATTTATTAATAT
*
1578021 AAATATATAAATATATATAAA
1 AAATATATTAATATAT-TAAA
1578042 TAAATAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 10 0.19
41 16 0.30
42 24 0.44
43 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (42 bp):
AAATATATTAATATATTAAAATTTATATAAATTTATTAATAT
Found at i:1580202 original size:2 final size:2
Alignment explanation
Indices: 1580197--1580226 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1580187 CTCAAAAATA
1580197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1580227 TCAATTTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1580845 original size:17 final size:16
Alignment explanation
Indices: 1580823--1580857 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1580813 GGTAGGTATA
1580823 AAATATAAATATATATT
1 AAATATAAATATAT-TT
*
1580840 AAATATGAATATATTT
1 AAATATAAATATATTT
1580856 AA
1 AA
1580858 TTTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AAATATAAATATATTT
Found at i:1584189 original size:15 final size:15
Alignment explanation
Indices: 1584151--1584191 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
1584141 TCATAAGTAA
*
1584151 ATGTTAAATATAGAT
1 ATGTTTAATATAGAT
1584166 ATGTTTTTAATATAGAT
1 ATG--TTTAATATAGAT
1584183 ATGTTTAAT
1 ATGTTTAAT
1584192 TTTTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
ATGTTTAATATAGAT
Found at i:1589785 original size:19 final size:19
Alignment explanation
Indices: 1589761--1589799 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1589751 AATAAATAAT
1589761 ACAAAA-AAAACTTTCTAAA
1 ACAAAATAAAACTTT-TAAA
1589780 ACAAAATAAAACTTTTAAA
1 ACAAAATAAAACTTTTAAA
1589799 A
1 A
1589800 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (19 bp):
ACAAAATAAAACTTTTAAA
Found at i:1591315 original size:15 final size:14
Alignment explanation
Indices: 1591297--1591346 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
1591287 TTTGTCAAAT
1591297 TTTTTAAATTTTAAA
1 TTTTT-AATTTTAAA
*
1591312 TTTTTTATTTTAAA
1 TTTTTAATTTTAAA
1591326 TATTTTAATTAATTAAA
1 T-TTTTAATT--TTAAA
1591343 TTTT
1 TTTT
1591347 ATAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.30
15 12 0.40
16 3 0.10
17 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAATTTTAAA
Found at i:1602084 original size:18 final size:18
Alignment explanation
Indices: 1602061--1602095 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1602051 TTCCTGGAAT
*
1602061 CCATTAATATATGTATAC
1 CCATTAATATATATATAC
1602079 CCATTAATATATATATA
1 CCATTAATATATATATA
1602096 TATATATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (18 bp):
CCATTAATATATATATAC
Found at i:1604676 original size:4 final size:4
Alignment explanation
Indices: 1604667--1604697 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1604657 AGAATGACCA
1604667 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1604698 ATGGTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1606103 original size:2 final size:2
Alignment explanation
Indices: 1606096--1606143 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1606086 TAATCATCAA
1606096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1606138 AT AT AT
1 AT AT AT
1606144 CTAACTCCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606286 original size:76 final size:75
Alignment explanation
Indices: 1606205--1606424 Score: 235
Period size: 76 Copynumber: 2.9 Consensus size: 75
1606195 ATGGTTCGAA
* *
1606205 ACAAAAACTACTATTCTAAATCGGTGGTACGGTTCGAA-ACAAAAACCATTATTCTAAACTAGTA
1 ACAAAAACTACTATTCT-AATCGGTGGTACGGTTC-AATACAAAAACCATTATTCTTAACTAGTG
* *
1606269 GCACGGTTCAAT
64 GCACGATCCAAT
* * * ** * * **
1606281 GCAAAAATTACTATTCTTATCCGGTGCCACAGTTCAATACAAAAACCATTATTCTTATCCGGTGG
1 ACAAAAACTACTATTCTAAT-CGGTGGTACGGTTCAATACAAAAACCATTATTCTTAACTAGTGG
1606346 CACGATCCAAT
65 CACGATCCAAT
* ** * *
1606357 ACAAAAACTACTATTCTTATTTAGTGGTACGGTTCAATACAAAAACAACTATTCTTAACTAGTGG
1 ACAAAAACTACTATTC-TAATCGGTGGTACGGTTCAATACAAAAACCATTATTCTTAACTAGTGG
1606422 CAC
65 CAC
1606425 ATGTTGAAAC
Statistics
Matches: 114, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
75 4 0.04
76 108 0.95
77 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (75 bp):
ACAAAAACTACTATTCTAATCGGTGGTACGGTTCAATACAAAAACCATTATTCTTAACTAGTGGC
ACGATCCAAT
Found at i:1606420 original size:38 final size:38
Alignment explanation
Indices: 1606190--1606424 Score: 188
Period size: 38 Copynumber: 6.2 Consensus size: 38
1606180 TTTTAAACCG
* * *
1606190 GTGGCATGGTTCGAA-ACAAAAACTACTATTC-TAAATCG
1 GTGGCACGGTTC-AATACAAAAACTACTATTCTTAACT-A
* * * *
1606228 GTGGTACGGTTCGAA-ACAAAAACCATTATTCTAAACTA
1 GTGGCACGGTTC-AATACAAAAACTACTATTCTTAACTA
* * * * **
1606266 GTAGCACGGTTCAATGCAAAAATTACTATTCTTATCCG
1 GTGGCACGGTTCAATACAAAAACTACTATTCTTAACTA
* * * * * **
1606304 GTGCCACAGTTCAATACAAAAACCATTATTCTTATCCG
1 GTGGCACGGTTCAATACAAAAACTACTATTCTTAACTA
* * **
1606342 GTGGCACGATCCAATACAAAAACTACTATTCTTATTTA
1 GTGGCACGGTTCAATACAAAAACTACTATTCTTAACTA
* *
1606380 GTGGTACGGTTCAATACAAAAACAACTATTCTTAACTA
1 GTGGCACGGTTCAATACAAAAACTACTATTCTTAACTA
1606418 GTGGCAC
1 GTGGCAC
1606425 ATGTTGAAAC
Statistics
Matches: 155, Mismatches: 40, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
37 2 0.01
38 150 0.97
39 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (38 bp):
GTGGCACGGTTCAATACAAAAACTACTATTCTTAACTA
Found at i:1610260 original size:2 final size:2
Alignment explanation
Indices: 1610243--1610290 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1610233 AACCTGGAAA
* *
1610243 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1610285 AT AT AT
1 AT AT AT
1610291 GTTTTTGGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1611772 original size:3 final size:3
Alignment explanation
Indices: 1611764--1611804 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1611754 CTGCATTGTC
1611764 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1611805 ATTAATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1619784 original size:12 final size:11
Alignment explanation
Indices: 1619758--1619800 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
1619748 GTCATTGGTA
1619758 ATATA-ATATT
1 ATATATATATT
1619768 ATATATATATAT
1 ATATATATAT-T
*
1619780 GTATATATAATT
1 ATATATAT-ATT
1619792 ATATATATA
1 ATATATATA
1619801 ATTTTTGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 5 0.18
11 5 0.18
12 16 0.57
13 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
ATATATATATT
Found at i:1619801 original size:12 final size:12
Alignment explanation
Indices: 1619765--1619803 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1619755 GTAATATAAT
1619765 ATTATATATAT-
1 ATTATATATATA
*
1619776 ATATGTATATATA
1 AT-TATATATATA
1619789 ATTATATATATA
1 ATTATATATATA
1619801 ATT
1 ATT
1619804 TTTGCCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
ATTATATATATA
Found at i:1623766 original size:2 final size:2
Alignment explanation
Indices: 1623753--1623784 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1623743 AACCTGGAAA
*
1623753 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1623785 GTTTTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1624274 original size:54 final size:53
Alignment explanation
Indices: 1624206--1624344 Score: 197
Period size: 54 Copynumber: 2.6 Consensus size: 53
1624196 AAAATATACA
*
1624206 AAAATAATAAAATAAATATAATACTTTATGTTTAAATACGATTAATAAGACACG
1 AAAATAAT-AAATAAATATAATATTTTATGTTTAAATACGATTAATAAGACACG
* * * *
1624260 AAAATAATACAATAAATATAATATTTTATATTTAAATATGGTTAATAAGATACG
1 AAAATAATA-AATAAATATAATATTTTATGTTTAAATACGATTAATAAGACACG
*
1624314 TAAATAATAACATAAATATAATATTTTATGT
1 AAAATAATAA-ATAAATATAATATTTTATGT
1624345 CCAAAATAGG
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.03
54 74 0.97
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (53 bp):
AAAATAATAAATAAATATAATATTTTATGTTTAAATACGATTAATAAGACACG
Found at i:1625126 original size:3 final size:3
Alignment explanation
Indices: 1625118--1625146 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1625108 CTGCATTGTC
1625118 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1625147 ATTAAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1631214 original size:14 final size:14
Alignment explanation
Indices: 1631182--1631219 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1631172 ATCATCAGTA
1631182 ATATAATATTATAAT
1 ATATAAT-TTATAAT
1631197 ATATACATTTAT-AT
1 ATATA-ATTTATAAT
1631211 ATATAATTT
1 ATATAATTT
1631220 TTTCTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 7 0.32
15 9 0.41
16 2 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATAATTTATAAT
Found at i:1631646 original size:9 final size:9
Alignment explanation
Indices: 1631614--1631667 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
1631604 AATATTTTAA
1631614 TATTTAATT
1 TATTTAATT
**
1631623 TAAGTAATT
1 TATTTAATT
* *
1631632 T-GTTAACT
1 TATTTAATT
1631640 TATTTAATT
1 TATTTAATT
1631649 TATTTAATT
1 TATTTAATT
1631658 TATTTTAATT
1 TA-TTTAATT
1631668 AACATTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
8 5 0.14
9 24 0.67
10 7 0.19
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TATTTAATT
Found at i:1633955 original size:27 final size:28
Alignment explanation
Indices: 1633924--1634015 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 28
1633914 GTCACCTATT
* *
1633924 TATTTGTAAAAAATGGT-GGTTATTTTG
1 TATTTGTCAAAAATGGTAGGTTATTTTA
* *
1633951 TATTTGTCAAAAATGGTAGTTTCTTTTA
1 TATTTGTCAAAAATGGTAGGTTATTTTA
* * *
1633979 TATTTGTCAAATATGG-AGGCT-TGTT-
1 TATTTGTCAAAAATGGTAGGTTATTTTA
1634004 TATTTGTCAAAA
1 TATTTGTCAAAA
1634016 TTTGTGGCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.35
28 22 0.40
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTAGGTTATTTTA
Found at i:1638552 original size:28 final size:27
Alignment explanation
Indices: 1638497--1638588 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 27
1638487 GCCACCCATT
1638497 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
1638524 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
* *
1638552 TATTTGTCAAATATGGAGGCTTA--TT-
1 TATTTGTCAAAAATGGTGG-TTATTTTG
1638577 TATTTGTCAAAA
1 TATTTGTCAAAA
1638589 TTTGTGACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 20 0.36
28 20 0.36
29 2 0.04
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:1639698 original size:21 final size:21
Alignment explanation
Indices: 1639672--1639715 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1639662 AAGCCAGGAA
1639672 AACCATTTGCAGTTTTAGCTT
1 AACCATTTGCAGTTTTAGCTT
1639693 AACCATTTGCAGTTTTAGCTT
1 AACCATTTGCAGTTTTAGCTT
1639714 AA
1 AA
1639716 TCTTCAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
AACCATTTGCAGTTTTAGCTT
Found at i:1640003 original size:44 final size:44
Alignment explanation
Indices: 1639940--1640027 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1639930 TTGCTTGACC
1639940 AGCTGGACAACCCGGAGAATATACATATATATATATATATATAT
1 AGCTGGACAACCCGGAGAATATACATATATATATATATATATAT
1639984 AGCTGGACAACCCGGAGAATATACATATATATATATATATATAT
1 AGCTGGACAACCCGGAGAATATACATATATATATATATATATAT
1640028 GTTTTTGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (44 bp):
AGCTGGACAACCCGGAGAATATACATATATATATATATATATAT
Found at i:1642053 original size:2 final size:2
Alignment explanation
Indices: 1642046--1642071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1642036 TAATGAATAC
1642046 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1642072 CAACTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1647228 original size:22 final size:22
Alignment explanation
Indices: 1647203--1647247 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1647193 TTTAAAGATA
1647203 GACTGTTATATTGAAGACTAAG
1 GACTGTTATATTGAAGACTAAG
1647225 GACTGTTATATTGAAGACTAAG
1 GACTGTTATATTGAAGACTAAG
1647247 G
1 G
1647248 TATCGGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (22 bp):
GACTGTTATATTGAAGACTAAG
Found at i:1649125 original size:14 final size:16
Alignment explanation
Indices: 1649101--1649133 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1649091 TTAAAAGTTA
1649101 TTTTATAATTTTA-AT
1 TTTTATAATTTTATAT
1649116 TTTTAT-ATTTTATAT
1 TTTTATAATTTTATAT
1649131 TTT
1 TTT
1649134 AATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATAATTTTATAT
Found at i:1649134 original size:21 final size:21
Alignment explanation
Indices: 1649099--1649150 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1649089 TTTTAAAAGT
*
1649099 TATTTTATAATTTTAATTTTTA
1 TATTTTAT-ATTTTAATTATTA
1649121 TATTTTATATTTTAATTATTA
1 TATTTTATATTTTAATTATTA
1649142 T-TTATTATA
1 TATT-TTATA
1649151 ATAATAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 18 0.64
22 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTATATTTTAATTATTA
Found at i:1649937 original size:22 final size:23
Alignment explanation
Indices: 1649903--1649946 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1649893 TTTTTTAAAA
* * *
1649903 TATTTATATTTAATATTTAAATT
1 TATTCATATTTAAAATATAAATT
1649926 TATTCATA-TTAAAATATAAAT
1 TATTCATATTTAAAATATAAAT
1649947 ATAAATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTCATATTTAAAATATAAATT
Found at i:1649946 original size:6 final size:6
Alignment explanation
Indices: 1649937--1649961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1649927 ATTCATATTA
1649937 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
1649962 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:1650324 original size:13 final size:13
Alignment explanation
Indices: 1650306--1650360 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1650296 GTCATTTTTT
1650306 ATTAATTTTATAA
1 ATTAATTTTATAA
1650319 ATTAA-TTTATATA
1 ATTAATTTTATA-A
*
1650332 ATTATTTTTA-AA
1 ATTAATTTTATAA
* *
1650344 ATAAAATTTAATAA
1 AT-TAATTTTATAA
1650358 ATT
1 ATT
1650361 TAAAGATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 9 0.27
13 16 0.48
14 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTAATTTTATAA
Found at i:1650512 original size:29 final size:28
Alignment explanation
Indices: 1650480--1650535 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1650470 ATTTAGTATG
1650480 TTATATTTAT-ATAGTTTATTATATTATAA
1 TTATATTTATAATAGTTTA-TAT-TTATAA
*
1650509 TTATATTTATAATATTTTATATTTATA
1 TTATATTTATAATAGTTTATATTTATA
1650536 TAATTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 13 0.52
30 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTATATTTATAATAGTTTATATTTATAA
Found at i:1650529 original size:45 final size:48
Alignment explanation
Indices: 1650480--1650576 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 48
1650470 ATTTAGTATG
*
1650480 TTATATTTATATAGTTTATT-ATA-TT-ATAA-TTATATT-TATAATATT
1 TTATATTTATATAATTT-TTGATAGTTAATAATTTATATTATATAA-ATT
1650525 TTATATTTATATAATTTTTGATATGTTAATAATTTATATTATATAAATT
1 TTATATTTATATAATTTTTGATA-GTTAATAATTTATATTATATAAATT
1650574 TTA
1 TTA
1650577 AAAATATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
44 2 0.04
45 19 0.42
47 2 0.04
48 4 0.09
49 13 0.29
50 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (48 bp):
TTATATTTATATAATTTTTGATAGTTAATAATTTATATTATATAAATT
Found at i:1650539 original size:18 final size:17
Alignment explanation
Indices: 1650509--1650576 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
1650499 TATATTATAA
*
1650509 TTATATTTATA-ATATT
1 TTATATTTATATAAATT
*
1650525 TTATATTTATATAATTT
1 TTATATTTATATAAATT
1650542 TTGATATGTTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
1650558 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
1650574 TTA
1 TTA
1650577 AAAATATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.12
16 18 0.42
17 6 0.14
18 6 0.14
19 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:1660619 original size:32 final size:32
Alignment explanation
Indices: 1660529--1660620 Score: 175
Period size: 32 Copynumber: 2.9 Consensus size: 32
1660519 ATGACTTTGC
*
1660529 TTTCATATATTTCTAAGCTTCTTTGTGTCAAA
1 TTTCATATATTTCTAAGCTTCTTTGTTTCAAA
1660561 TTTCATATATTTCTAAGCTTCTTTGTTTCAAA
1 TTTCATATATTTCTAAGCTTCTTTGTTTCAAA
1660593 TTTCATATATTTCTAAGCTTCTTTGTTT
1 TTTCATATATTTCTAAGCTTCTTTGTTT
1660621 AGATACCAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (32 bp):
TTTCATATATTTCTAAGCTTCTTTGTTTCAAA
Found at i:1661803 original size:23 final size:24
Alignment explanation
Indices: 1661772--1661838 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 24
1661762 ACATTCGTAT
1661772 ATTTATATATTC-TATT-TATATTA
1 ATTTATATA-TCATATTATATATTA
* *
1661795 ATTTTTATATCATATTATATTTTA
1 ATTTATATATCATATTATATATTA
* * *
1661819 A-TTATTTTTTATATTATATA
1 ATTTATATATCATATTATATA
1661839 CATATTTCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.06
23 26 0.74
24 7 0.20
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTATATATCATATTATATATTA
Found at i:1661815 original size:28 final size:28
Alignment explanation
Indices: 1661778--1661837 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1661768 GTATATTTAT
*
1661778 ATATTCTA-TTTATATTAATTTTTATATC
1 ATATTATATTTTA-ATTAATTTTTATATC
* *
1661806 ATATTATATTTTAATTATTTTTTATATT
1 ATATTATATTTTAATTAATTTTTATATC
1661834 ATAT
1 ATAT
1661838 ACATATTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATTATATTTTAATTAATTTTTATATC
Found at i:1663955 original size:96 final size:97
Alignment explanation
Indices: 1663785--1663968 Score: 237
Period size: 96 Copynumber: 1.9 Consensus size: 97
1663775 CAATAAGCAA
* * *
1663785 ATGGGCGGTGGAAGCAGAACTTGTAAACAAGTCAATCACTGACCGACTTAATAGGAAGCAATGAG
1 ATGGGCGGTGGAAGCAGAACATGTAAACAAGTCAATCACTGACAGACTTAACAGGAAGCAATGAG
*
1663850 CACCAAGTAATGAATTTTTTGCTGGTTCAACC
66 CACCAAGTAACGAATTTTTTGCTGGTTCAACC
** * ** *
1663882 ATGGG-GGTGGAAGCAGAACATGTAAGTAAGTCAATCATTTTCAGACTTAGCA-GAGAGCAATGA
1 ATGGGCGGTGGAAGCAGAACATGTAAACAAGTCAATCACTGACAGACTTAACAGGA-AGCAATGA
* *
1663945 GCAGCAAGTAACGGATTTTTTGCT
65 GCACCAAGTAACGAATTTTTTGCT
1663969 CTTTCAACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
95 2 0.03
96 67 0.91
97 5 0.07
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (97 bp):
ATGGGCGGTGGAAGCAGAACATGTAAACAAGTCAATCACTGACAGACTTAACAGGAAGCAATGAG
CACCAAGTAACGAATTTTTTGCTGGTTCAACC
Done.