Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 4 of 171
Found at i:1294743 original size:3 final size:3
Alignment explanation
Indices: 1294735--1294766 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1294725 CCCAGGCTGC
1294735 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1294767 ATACCCCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1300831 original size:2 final size:2
Alignment explanation
Indices: 1300824--1300852 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1300814 TTAGCATGCA
1300824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1300853 GGAACCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1305255 original size:17 final size:17
Alignment explanation
Indices: 1305228--1305267 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
1305218 GCCTTACTAT
1305228 TTTTGTAAT-AATTATTAA
1 TTTT-TAATAAATTA-TAA
1305246 TTTTTAATAAATTATAA
1 TTTTTAATAAATTATAA
1305263 TTTTT
1 TTTTT
1305268 TATAGTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTAATAAATTATAA
Found at i:1305267 original size:18 final size:18
Alignment explanation
Indices: 1305226--1305269 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1305216 TTGCCTTACT
1305226 ATTTTTGTAATAATTATTA
1 ATTTTT-TAATAATTATTA
1305245 A-TTTTTAATAAATTA-TA
1 ATTTTTTAAT-AATTATTA
1305262 ATTTTTTA
1 ATTTTTTA
1305270 TAGTTCTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 15 0.65
19 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTTTAATAATTATTA
Found at i:1311814 original size:54 final size:54
Alignment explanation
Indices: 1311716--1311838 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
1311706 GTGTCGAAAT
* * * * * *
1311716 TGATTTAAATATATAAACAATCGATTTAAAAGAAGCAGTATTCTAACATA-ATAA
1 TGATTTAAACATTTAAAAAATCGATTTAAAAAAAACAGTATTCTAACATACA-AC
1311770 TCGATTTAAACATTTAAAAAATCGA-TTAAAAAAAACAGTATTCTAACATACAAC
1 T-GATTTAAACATTTAAAAAATCGATTTAAAAAAAACAGTATTCTAACATACAAC
1311824 TGATTTAAACATTTA
1 TGATTTAAACATTTA
1311839 CTAATTTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
53 14 0.23
54 26 0.43
55 21 0.34
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (54 bp):
TGATTTAAACATTTAAAAAATCGATTTAAAAAAAACAGTATTCTAACATACAAC
Found at i:1312284 original size:2 final size:2
Alignment explanation
Indices: 1312279--1312312 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1312269 AAAACTATTG
* *
1312279 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1312313 GTAAAACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1312645 original size:34 final size:34
Alignment explanation
Indices: 1312576--1312643 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
1312566 ATGAGTAATT
** **
1312576 TAATTTTTTAATATTTTTTTGTTTTTATCAAAAA
1 TAATTTTTTAATATTTTTTTAATACTATCAAAAA
1312610 TAATTTTTTAATATTATTTTTAATACTATACAAA
1 TAATTTTTTAATATT-TTTTTAATACTAT-CAAA
1312644 TATTAATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 15 0.54
35 9 0.32
36 4 0.14
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (34 bp):
TAATTTTTTAATATTTTTTTAATACTATCAAAAA
Found at i:1315765 original size:18 final size:18
Alignment explanation
Indices: 1315718--1315770 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1315708 ATGATTTGTG
*
1315718 ATCAAAATTGAACGTGAA
1 ATCAAAATTGAAAGTGAA
* *
1315736 AGT-GAAAGTGAAAGTGAA
1 A-TCAAAATTGAAAGTGAA
1315754 ATCAAAATTGAAAGTGA
1 ATCAAAATTGAAAGTGA
1315771 TATGAATTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.21
Consensus pattern (18 bp):
ATCAAAATTGAAAGTGAA
Found at i:1315920 original size:41 final size:40
Alignment explanation
Indices: 1315872--1315972 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
1315862 TCGACCTTGA
** *
1315872 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
1315912 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
1315950 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
1315973 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:1317319 original size:70 final size:70
Alignment explanation
Indices: 1317237--1317378 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
1317227 ATTAAAACAT
1317237 TAAATTCCAACAATCTCTCATTTACCCTAATGAAATTAGTGAAATAAGTAAATCATATTTTCTAT
1 TAAATTCCAACAATCTCTCATTTACCCTAATGAAATTAGTGAAATAAGTAAATCATATTTTCTAT
1317302 ACCCA
66 ACCCA
1317307 TAAATTCCAACAATCTCTCATTTACCCTAATGAAATTAGTGAAATAAGTAAATCATATTTTCTAT
1 TAAATTCCAACAATCTCTCATTTACCCTAATGAAATTAGTGAAATAAGTAAATCATATTTTCTAT
1317372 ACCCA
66 ACCCA
1317377 TA
1 TA
1317379 CCATTTTATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.35
Consensus pattern (70 bp):
TAAATTCCAACAATCTCTCATTTACCCTAATGAAATTAGTGAAATAAGTAAATCATATTTTCTAT
ACCCA
Found at i:1320641 original size:12 final size:12
Alignment explanation
Indices: 1320624--1320649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1320614 TTAGAGTACT
1320624 ATCATTTAGCAG
1 ATCATTTAGCAG
1320636 ATCATTTAGCAG
1 ATCATTTAGCAG
1320648 AT
1 AT
1320650 GTCTGAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATCATTTAGCAG
Found at i:1324423 original size:26 final size:28
Alignment explanation
Indices: 1324377--1324433 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1324367 TGATTGGGGT
1324377 AAAAAAGTAAAACAATGATTA-AAGTGA
1 AAAAAAGTAAAACAATGATTATAAGTGA
* *
1324404 AAAAAAG-ATAAA-AATTATTATAATTGA
1 AAAAAAGTA-AAACAATGATTATAAGTGA
1324431 AAA
1 AAA
1324434 TAATTATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.23
Consensus pattern (28 bp):
AAAAAAGTAAAACAATGATTATAAGTGA
Found at i:1325130 original size:13 final size:13
Alignment explanation
Indices: 1325112--1325139 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1325102 AAGATGAAAT
1325112 GGCTTAAAAGTTG
1 GGCTTAAAAGTTG
1325125 GGCTTAAAAGTTG
1 GGCTTAAAAGTTG
1325138 GG
1 GG
1325140 TGACCAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (13 bp):
GGCTTAAAAGTTG
Found at i:1330235 original size:24 final size:24
Alignment explanation
Indices: 1330207--1330263 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1330197 TAGACTAATA
*
1330207 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
*
1330231 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
*
1330255 AGAATTTAA
1 AGAGTTTAA
1330264 CCAACAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:1332917 original size:2 final size:2
Alignment explanation
Indices: 1332912--1332940 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1332902 CACTCGTGTG
1332912 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 T
1332941 GCATGCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1333560 original size:20 final size:20
Alignment explanation
Indices: 1333535--1333576 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1333525 TGCATTTGGA
1333535 ATTTATTCCTTATAATGCAC
1 ATTTATTCCTTATAATGCAC
1333555 ATTTATTCCTTATAATGCAC
1 ATTTATTCCTTATAATGCAC
1333575 AT
1 AT
1333577 GCATTGCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTATTCCTTATAATGCAC
Found at i:1334445 original size:23 final size:23
Alignment explanation
Indices: 1334399--1334443 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1334389 ATGTACTCTC
1334399 TTTTTTTTTAGATTTTATATAAA
1 TTTTTTTTTAGATTTTATATAAA
*
1334422 TTTTTTTTTATATTTT-TATAAA
1 TTTTTTTTTAGATTTTATATAAA
1334444 ATAATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTAGATTTTATATAAA
Found at i:1334455 original size:20 final size:21
Alignment explanation
Indices: 1334430--1334468 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1334420 AATTTTTTTT
1334430 TATATTTTT-ATAAAATAATA
1 TATATTTTTAATAAAATAATA
1334450 TATATTTTTAATAAAATAA
1 TATATTTTTAATAAAATAA
1334469 CAATTGAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTTTTAATAAAATAATA
Found at i:1339168 original size:59 final size:60
Alignment explanation
Indices: 1339010--1339177 Score: 182
Period size: 59 Copynumber: 2.8 Consensus size: 60
1339000 TTTTTCTAAT
* * * *
1339010 ATTATATATTATAATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTGA
1 ATTATTTATTAT--TTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAA
* * * * *
1339073 ATTAATTATTA--TTTCATTAAATTGTATTTAACAATAATTATGTT-AAAATATAATTAA
1 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAA
*
1339130 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTTTATTAA
1 ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAA
1339178 TATTTAATAA
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
57 20 0.23
58 16 0.19
59 36 0.42
60 5 0.06
63 9 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (60 bp):
ATTATTTATTATTTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAA
Found at i:1339364 original size:16 final size:16
Alignment explanation
Indices: 1339343--1339411 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
1339333 AATTACTGAC
1339343 TACAGTCCTATTCCAT
1 TACAGTCCTATTCCAT
**
1339359 TACAGTTTTATTCCAT
1 TACAGTCCTATTCCAT
* *
1339375 TACA-ACTCTAATCCAT
1 TACAGTC-CTATTCCAT
* *
1339391 TACAGTTCTATTCTAT
1 TACAGTCCTATTCCAT
1339407 TACAG
1 TACAG
1339412 CGAACCAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.41
Consensus pattern (16 bp):
TACAGTCCTATTCCAT
Found at i:1340780 original size:60 final size:59
Alignment explanation
Indices: 1340708--1340870 Score: 170
Period size: 58 Copynumber: 2.7 Consensus size: 59
1340698 AAATATGAAT
* * * *
1340708 AAAAAATTATTTTTTTGGGTGTCTGTCAACTCTTGGCCGACATCCCCTTTTTCAGATACC
1 AAAAAAATATTTTTTTGGGTGTCTGTCAAC-CATGGCCGACATCCCCTTTTCCAAATACC
* * * *
1340768 AAAAAAATA--TTTTTGGGTGTCTG-CTAAGCCATGACTGTCATCTCCTTTTCCAAATACC
1 AAAAAAATATTTTTTTGGGTGTCTGTC-AA-CCATGGCCGACATCCCCTTTTCCAAATACC
* * *
1340826 AAAAATATATTTTTTTGGGTGTTTGTCAACCCATGGTCGACATCC
1 AAAAAAATATTTTTTTGGGTGTCTGTCAA-CCATGGCCGACATCC
1340871 AAAAATAAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
57 1 0.01
58 46 0.56
59 1 0.01
60 33 0.40
61 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (59 bp):
AAAAAAATATTTTTTTGGGTGTCTGTCAACCATGGCCGACATCCCCTTTTCCAAATACC
Found at i:1340977 original size:58 final size:56
Alignment explanation
Indices: 1340879--1341025 Score: 127
Period size: 58 Copynumber: 2.6 Consensus size: 56
1340869 CCAAAAATAA
* * * * * * * *
1340879 AAAAAATTATATTTTGGTGTTTGTCATCTAATGACTGACACCCACAAATAATACG-A-
1 AAAAAATAATTTTTTCGTGTTTGACAACCAATAACCGACACCCA-AAA-AATACGAAT
* *
1340935 AAAAAATAAATTTTTTTCGTGTTTGACAACCAATAACCGACACTCATAAAATACGAATT
1 AAAAAAT-AA-TTTTTTCGTGTTTGACAACCAATAACCGACACCCAAAAAATACGAA-T
* *
1340994 AAAAAATAATTTTTTGGTGTTTGGCAACCAAT
1 AAAAAATAATTTTTTCGTGTTTGACAACCAAT
1341026 GGCTAACACA
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
56 13 0.18
57 25 0.34
58 29 0.39
59 7 0.09
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (56 bp):
AAAAAATAATTTTTTCGTGTTTGACAACCAATAACCGACACCCAAAAAATACGAAT
Found at i:1349694 original size:18 final size:18
Alignment explanation
Indices: 1349671--1349709 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1349661 TATATCTTTT
*
1349671 ATAATTAAATAATTATTA
1 ATAATTAAATAATTATCA
*
1349689 ATAATTAAATGATTATCA
1 ATAATTAAATAATTATCA
1349707 ATA
1 ATA
1349710 TAATTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAATTAAATAATTATCA
Found at i:1355279 original size:6 final size:6
Alignment explanation
Indices: 1355268--1355298 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1355258 TTGTCACATC
1355268 CCCATT CCCATT CCCATT CCCATT CCCATT C
1 CCCATT CCCATT CCCATT CCCATT CCCATT C
1355299 TCATCAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCATT
Found at i:1355653 original size:6 final size:7
Alignment explanation
Indices: 1355636--1355660 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1355626 TTATAATTCT
1355636 TTTTTAA
1 TTTTTAA
1355643 TTTTTAA
1 TTTTTAA
1355650 TTTTTAA
1 TTTTTAA
1355657 TTTT
1 TTTT
1355661 CAATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:1372169 original size:2 final size:2
Alignment explanation
Indices: 1372162--1372187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1372152 TATGTTCATA
1372162 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1372188 CTCGCATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1386630 original size:2 final size:2
Alignment explanation
Indices: 1386623--1386658 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1386613 TTACATTACA
1386623 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
1386659 TGATCTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1404924 original size:2 final size:2
Alignment explanation
Indices: 1404917--1404945 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1404907 ATTGGGTTTT
1404917 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 T
1404946 TATTGGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1409317 original size:54 final size:54
Alignment explanation
Indices: 1409254--1409365 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
1409244 CCCATGTCCT
1409254 CTTCTTACGCTTTCCACATTTGACGGGTTATTTTGTATGTTCACATCTGAACTA
1 CTTCTTACGCTTTCCACATTTGACGGGTTATTTTGTATGTTCACATCTGAACTA
1409308 CTTCTTACGCTTTCCACATTTGACGGGTTATTTTGTATGTTCACATCTGAACTA
1 CTTCTTACGCTTTCCACATTTGACGGGTTATTTTGTATGTTCACATCTGAACTA
1409362 CTTC
1 CTTC
1409366 ATAGTTCATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (54 bp):
CTTCTTACGCTTTCCACATTTGACGGGTTATTTTGTATGTTCACATCTGAACTA
Found at i:1409352 original size:27 final size:27
Alignment explanation
Indices: 1409268--1409353 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1409258 TTACGCTTTC
1409268 CACATTTGACGGGTTATTTTGTATGTT
1 CACATTTGACGGGTTATTTTGTATGTT
* *** * ** *
1409295 CACATCTGAACTACTTCTTACGCT-T-TC
1 CACATTTG-ACGGGTTATTTTG-TATGTT
1409322 CACATTTGACGGGTTATTTTGTATGTT
1 CACATTTGACGGGTTATTTTGTATGTT
1409349 CACAT
1 CACAT
1409354 CTGAACTACT
Statistics
Matches: 39, Mismatches: 16, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
25 1 0.03
26 8 0.21
27 21 0.54
28 8 0.21
29 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (27 bp):
CACATTTGACGGGTTATTTTGTATGTT
Found at i:1431512 original size:3 final size:3
Alignment explanation
Indices: 1431504--1431529 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1431494 TCAGACCAAA
1431504 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1431530 ATAGATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1437182 original size:30 final size:31
Alignment explanation
Indices: 1437146--1437211 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1437136 GTTTACATTT
1437146 CAGTCCCTCAAATT-TGAAAATATGACAAAA
1 CAGTCCCTCAAATTCTGAAAATATGACAAAA
* *
1437176 CAGTCCCTCAACTTCTGAAAATGTGACAAAA
1 CAGTCCCTCAAATTCTGAAAATATGACAAAA
1437207 CAGTC
1 CAGTC
1437212 TTTTTCCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (31 bp):
CAGTCCCTCAAATTCTGAAAATATGACAAAA
Found at i:1438727 original size:30 final size:31
Alignment explanation
Indices: 1438662--1438734 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
1438652 CATAATAAGA
* *
1438662 TGACTATTTTGTCACTTTTCGATAACTTTAG
1 TGACTGTTTTGTCACTTTTCGATAACTTGAG
*
1438693 TGACTGTTTTGTCACATTTTC-A-AAGTTGAG
1 TGACTGTTTTGTCAC-TTTTCGATAACTTGAG
1438723 TGACTGTTTTGT
1 TGACTGTTTTGT
1438735 TACACGTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.48
Consensus pattern (31 bp):
TGACTGTTTTGTCACTTTTCGATAACTTGAG
Found at i:1441394 original size:12 final size:12
Alignment explanation
Indices: 1441377--1441416 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1441367 AGCTTCTCTC
*
1441377 GATGGTGATGGT
1 GATGGTGATGAT
1441389 GATGGTGATGAT
1 GATGGTGATGAT
*
1441401 GATGATGATGAT
1 GATGGTGATGAT
1441413 GATG
1 GATG
1441417 ACAGCTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (12 bp):
GATGGTGATGAT
Found at i:1441402 original size:3 final size:3
Alignment explanation
Indices: 1441377--1441417 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1441367 AGCTTCTCTC
* * *
1441377 GAT GGT GAT GGT GAT GGT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1441418 CAGCTATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1446174 original size:16 final size:16
Alignment explanation
Indices: 1446153--1446183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1446143 GTGTGCTTTT
*
1446153 TGATTGGTTGAAAATA
1 TGATTGATTGAAAATA
1446169 TGATTGATTGAAAAT
1 TGATTGATTGAAAAT
1446184 TCCCCTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (16 bp):
TGATTGATTGAAAATA
Found at i:1446492 original size:31 final size:27
Alignment explanation
Indices: 1446422--1446472 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1446412 ACAATTTAAT
*
1446422 AATTTAGGTATCAATTTTGATAAAAAA
1 AATTTAGGTATCAATTTTGAAAAAAAA
1446449 AATTTAGGTATCAA-TTTGAAAAAA
1 AATTTAGGTATCAATTTTGAAAAAA
1446473 GTAATATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (27 bp):
AATTTAGGTATCAATTTTGAAAAAAAA
Found at i:1447491 original size:33 final size:34
Alignment explanation
Indices: 1447420--1447498 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
1447410 ACTATAATAG
* *
1447420 ATAAAAT-TATTT-AATATTAAAATAAAATAAAT
1 ATAAAATATATTTAAAAATTAAAATAAAACAAAT
*
1447452 AT-AAATATATTTAAAAATTAAAAT-GAACAAAT
1 ATAAAATATATTTAAAAATTAAAATAAAACAAAT
* *
1447484 TTAAAATAAATTTAA
1 ATAAAATATATTTAA
1447499 TTTAATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 4 0.10
32 14 0.36
33 21 0.54
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (34 bp):
ATAAAATATATTTAAAAATTAAAATAAAACAAAT
Found at i:1448152 original size:27 final size:27
Alignment explanation
Indices: 1448111--1448177 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
1448101 AAAATACGAG
* *
1448111 TTGGTGCCACTTGACAGAAAGGCACCA
1 TTGGTGCCGCCTGACAGAAAGGCACCA
**
1448138 TTGGTGCCGCCTGACAGGTAGGCACCA
1 TTGGTGCCGCCTGACAGAAAGGCACCA
*
1448165 CTGGTGCCGCCTG
1 TTGGTGCCGCCTG
1448178 TCAAGTAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.19
Consensus pattern (27 bp):
TTGGTGCCGCCTGACAGAAAGGCACCA
Found at i:1448185 original size:27 final size:27
Alignment explanation
Indices: 1448130--1448192 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
1448120 CTTGACAGAA
* *
1448130 AGGCACCATTGGTGCCGCCTGACAGGT
1 AGGCACCACTGGTGCCGCCTGACAAGT
*
1448157 AGGCACCACTGGTGCCGCCTGTCAAGT
1 AGGCACCACTGGTGCCGCCTGACAAGT
1448184 AGGCACCAC
1 AGGCACCAC
1448193 CCACTTATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.16
Consensus pattern (27 bp):
AGGCACCACTGGTGCCGCCTGACAAGT
Found at i:1448367 original size:2 final size:2
Alignment explanation
Indices: 1448362--1448392 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1448352 ATTATTTTGG
1448362 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 T
1448393 TTGTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1459927 original size:6 final size:6
Alignment explanation
Indices: 1459918--1459946 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1459908 CCCACCACCA
1459918 CCGTCC CCGTCC CCGTCC CCGTCC CCGTC
1 CCGTCC CCGTCC CCGTCC CCGTCC CCGTC
1459947 TTCAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCGTCC
Found at i:1475298 original size:22 final size:24
Alignment explanation
Indices: 1475263--1475310 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1475253 TGAATTATTG
1475263 AAAATCATAATCAAA-TTAAAATA
1 AAAATCATAATCAAACTTAAAATA
* *
1475286 AAAAT-ATACTCAAACTTAAATTA
1 AAAATCATAATCAAACTTAAAATA
1475309 AA
1 AA
1475311 TTAAAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATCATAATCAAACTTAAAATA
Found at i:1477058 original size:15 final size:16
Alignment explanation
Indices: 1477038--1477067 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1477028 GTTTAACCGA
1477038 TTTAATA-ATTTTTAT
1 TTTAATATATTTTTAT
1477053 TTTAATATATTTTTA
1 TTTAATATATTTTTA
1477068 GATTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAATATATTTTTAT
Found at i:1481322 original size:21 final size:19
Alignment explanation
Indices: 1481298--1481346 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1481288 ATACATATGA
1481298 ATCATAATTCAAATTATATAC
1 ATCA-AATTCAAATT-TATAC
* * *
1481319 ATCAAAATAAAATTTATGC
1 ATCAAATTCAAATTTATAC
1481338 ATCAAATTC
1 ATCAAATTC
1481347 TACTTACCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 11 0.48
20 8 0.35
21 4 0.17
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (19 bp):
ATCAAATTCAAATTTATAC
Found at i:1488755 original size:23 final size:23
Alignment explanation
Indices: 1488729--1488826 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
1488719 ACACTAGCGC
1488729 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1488752 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
1488775 GCTCTCTGTTATTAGCACTGTTTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
1488800 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1488823 GCTC
1 GCTC
1488827 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.05
23 42 0.65
25 17 0.26
26 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1488781 original size:25 final size:25
Alignment explanation
Indices: 1488730--1488806 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
1488720 CACTAGCGCG
*
1488730 CTCTCTGATTAGCACTGTGT-GTGCT
1 CTCTCTTATTAGCACTGT-TCGTGCT
*
1488755 CTCT-GT-TTAGCAC-GTCTCGTGCT
1 CTCTCTTATTAGCACTGT-TCGTGCT
* *
1488778 CTCTGTTATTAGCACTGTTTGTGCT
1 CTCTCTTATTAGCACTGTTCGTGCT
1488803 CTCT
1 CTCT
1488807 GATTAGCACT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.07
23 16 0.37
24 1 0.02
25 21 0.49
26 2 0.05
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.43
Consensus pattern (25 bp):
CTCTCTTATTAGCACTGTTCGTGCT
Found at i:1492897 original size:23 final size:22
Alignment explanation
Indices: 1492867--1493012 Score: 161
Period size: 23 Copynumber: 6.4 Consensus size: 22
1492857 ACACTAGCGC
*
1492867 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGT-T-GT
1492890 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGT-TGT
*
1492913 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGT-TGT
*
1492936 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGT-TGT
*
1492959 GCTCTCTGATTAGTACT-TTGT
1 GCTCTCTGATTAGCACTGTTGT
*
1492980 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGATTAGCACTGT-TGT
1493005 GCTCTCTG
1 GCTCTCTG
1493013 TTGTCCAGCA
Statistics
Matches: 112, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
21 4 0.04
22 1 0.01
23 99 0.88
24 4 0.04
25 4 0.04
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTGTTGT
Found at i:1493013 original size:23 final size:23
Alignment explanation
Indices: 1492888--1493058 Score: 213
Period size: 23 Copynumber: 7.4 Consensus size: 23
1492878 AGCACGTCTC
*
1492888 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
1492911 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
1492934 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
1492957 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
1492980 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
1493003 GTGCTCTCTGTTGTCCAGCAC-TTAT
1 GTGCTCTCTGAT-T--AGCACTTTGT
*
1493028 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
1493049 GTACTCTCTG
1 GTGCTCTCTG
1493059 TTTGTTCCGT
Statistics
Matches: 132, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.10
22 2 0.02
23 98 0.74
24 2 0.02
25 12 0.09
26 5 0.04
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:1493056 original size:46 final size:44
Alignment explanation
Indices: 1492867--1493061 Score: 205
Period size: 46 Copynumber: 4.2 Consensus size: 44
1492857 ACACTAGCGC
* *
1492867 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCAC-T-TTGTGCTCTCTGATTAGCACTTTGTGT
*
1492913 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-TT-TGTGCTCTCTGATTAGCACTTTGTGT
* * * *
1492959 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTG--CTCTCTGATTAGCACTTTGTGT
*
1493005 GCTCTCTGTTGTCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTT-T--AGCACTT-TGTGCTCTCTGATTAGCACTTTGTGT
*
1493051 ACTCTCTGTTT
1 GCTCTCTGTTT
1493062 GTTCCGTATA
Statistics
Matches: 130, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
44 4 0.03
45 4 0.03
46 95 0.73
47 10 0.08
48 7 0.05
49 6 0.05
50 4 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (44 bp):
GCTCTCTGTTTAGCACTTTGTGCTCTCTGATTAGCACTTTGTGT
Found at i:1493059 original size:69 final size:69
Alignment explanation
Indices: 1492888--1493061 Score: 237
Period size: 69 Copynumber: 2.5 Consensus size: 69
1492878 AGCACGTCTC
* * * * *
1492888 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
*
1492953 TTGT
66 TTAT
*
1492957 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGTCCAGC
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGAT-T--AGC
1493022 AC-TTAT
63 ACTTTAT
1493028 GTGCTCTCTG-TTAGTACTTTG-GTACTCTCTGTTT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTT
1493062 GTTCCGTATA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
69 65 0.68
70 12 0.13
71 13 0.14
72 5 0.05
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (69 bp):
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
TTAT
Found at i:1508098 original size:22 final size:20
Alignment explanation
Indices: 1508058--1508115 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1508048 TACAAAATAA
1508058 TCAAAATAATTATAAAAATT
1 TCAAAATAATTATAAAAATT
*
1508078 TCAAAATATATTTTTAAAAATT
1 TCAAAATA-A-TTATAAAAATT
* * *
1508100 TTAAAAAAATTCTAAA
1 TCAAAATAATTATAAA
1508116 GAATATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 16 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAAAATAATTATAAAAATT
Found at i:1509687 original size:21 final size:23
Alignment explanation
Indices: 1509663--1509714 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1509653 TAAATTAAAA
1509663 TATAAAATA-TATGA-ATTATTT
1 TATAAAATATTATGATATTATTT
** * *
1509684 TATATTATATTATTATATTTTTT
1 TATAAAATATTATGATATTATTT
1509707 TATAAAAT
1 TATAAAAT
1509715 GAATCGAGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 7 0.30
22 4 0.17
23 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATAAAATATTATGATATTATTT
Found at i:1514294 original size:17 final size:17
Alignment explanation
Indices: 1514272--1514305 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1514262 TTTCTTCATA
1514272 TTGGTAAACTGAAAATT
1 TTGGTAAACTGAAAATT
1514289 TTGGTAAACTGAAAATT
1 TTGGTAAACTGAAAATT
1514306 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
TTGGTAAACTGAAAATT
Found at i:1514319 original size:13 final size:13
Alignment explanation
Indices: 1514301--1514325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1514291 GGTAAACTGA
1514301 AAATTAAAAAATT
1 AAATTAAAAAATT
1514314 AAATTAAAAAAT
1 AAATTAAAAAAT
1514326 GCGCCTGTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:1517545 original size:16 final size:15
Alignment explanation
Indices: 1517514--1517543 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1517504 TATTTTTGAA
1517514 ATTTAACTTTTTTTT
1 ATTTAACTTTTTTTT
1517529 ATTTAACTTTTTTTT
1 ATTTAACTTTTTTTT
1517544 TAAAGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTAACTTTTTTTT
Found at i:1528169 original size:7 final size:7
Alignment explanation
Indices: 1528159--1528184 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1528149 TTTTTTTTAT
1528159 TTTAAAA
1 TTTAAAA
1528166 TTTAAAA
1 TTTAAAA
1528173 TTTAAAA
1 TTTAAAA
1528180 TTTAA
1 TTTAA
1528185 TCCATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:1529143 original size:21 final size:22
Alignment explanation
Indices: 1529118--1529159 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1529108 CTCGTATAAT
1529118 TTTATTT-AATAATTGTTCAAA
1 TTTATTTGAATAATTGTTCAAA
* *
1529139 TTTATTTGTATATTTGTTCAA
1 TTTATTTGAATAATTGTTCAA
1529160 TAATACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTATTTGAATAATTGTTCAAA
Found at i:1539016 original size:6 final size:6
Alignment explanation
Indices: 1539005--1539033 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1538995 TATAAAAATA
1539005 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1539034 ATTATAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:1542063 original size:34 final size:34
Alignment explanation
Indices: 1541998--1542063 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1541988 TTTATCTTGT
* * * *
1541998 TAAAAAAATAAATATTAATTATAATCATTAAACA
1 TAAAAAAATAAAAATCAAATATAAACATTAAACA
1542032 TAAAAAAATAAAAATCAAATATGAAAC-TTAAA
1 TAAAAAAATAAAAATCAAATAT-AAACATTAAA
1542064 ATCCACAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (34 bp):
TAAAAAAATAAAAATCAAATATAAACATTAAACA
Found at i:1561747 original size:5 final size:5
Alignment explanation
Indices: 1561739--1561774 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1561729 ACATTTTAAG
* *
1561739 GTTTT GTTTT GTTTT GTTTT GTTTT TTTTT TTTTT G
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT G
1561775 AGAAACTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
GTTTT
Found at i:1563541 original size:22 final size:23
Alignment explanation
Indices: 1563510--1563552 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1563500 TTGTACCTAC
*
1563510 AAATCTCCTTAAAAA-TATTTTG
1 AAATCACCTTAAAAATTATTTTG
1563532 AAATCACCTTAAAAATTATTT
1 AAATCACCTTAAAAATTATTT
1563553 GTTACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATCACCTTAAAAATTATTTTG
Found at i:1564957 original size:23 final size:24
Alignment explanation
Indices: 1564930--1564984 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1564920 ATGGAAGAGC
*
1564930 ATATTTATG-AAATGATT-TTTTTA
1 ATATTTATGAAAAT-ATTATTGTTA
*
1564953 ATATTTAAGAAAATATTATTGTTA
1 ATATTTATGAAAATATTATTGTTA
1564977 ATATTTAT
1 ATATTTAT
1564985 TTTGTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
ATATTTATGAAAATATTATTGTTA
Found at i:1566320 original size:23 final size:23
Alignment explanation
Indices: 1566294--1566337 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1566284 AAGGATTAGC
*
1566294 TTAAATAACGGTTTTTTTGGGAT
1 TTAAACAACGGTTTTTTTGGGAT
*
1566317 TTAAACAAGGGTTTTTTTGGG
1 TTAAACAACGGTTTTTTTGGG
1566338 GTTTGAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (23 bp):
TTAAACAACGGTTTTTTTGGGAT
Found at i:1567463 original size:14 final size:14
Alignment explanation
Indices: 1567444--1567494 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1567434 TATATTTATA
1567444 AATTATATATAAAT
1 AATTATATATAAAT
* **
1567458 AATTATATTTATTT
1 AATTATATATAAAT
*
1567472 AATTA-AAATAAA-
1 AATTATATATAAAT
1567484 AATTATATATA
1 AATTATATATA
1567495 TACCAAACTA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
12 5 0.18
13 7 0.25
14 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTATATATAAAT
Found at i:1567482 original size:27 final size:26
Alignment explanation
Indices: 1567433--1567496 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
1567423 CAACATTATT
*
1567433 TTATATTTATAAATTATATATAAATAA
1 TTATATTTATAAATTATAAATAAA-AA
*
1567460 TTATATTTATTTAATTA-AAATAAAAA
1 TTATATTTA-TAAATTATAAATAAAAA
*
1567486 TTATATATATA
1 TTATATTTATA
1567497 CCAAACTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 10 0.31
27 15 0.47
28 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATATTTATAAATTATAAATAAAAA
Found at i:1570167 original size:59 final size:59
Alignment explanation
Indices: 1570087--1570512 Score: 592
Period size: 59 Copynumber: 7.2 Consensus size: 59
1570077 GCGCGGGGGC
* * *
1570087 AAAATGATAATTTTT-AGTGAAATCGGGGTTAAAAATGCAATCTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGA-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
1570146 AAAATGGTAATCTTTGATGAAACCGGGGTTAATAATGGAATTTTGGAAAGTTC-AGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGT
*
1570205 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGT
* * *
1570264 AAAATGGTAATTTTAG-TGAAA-CTGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGATGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
** * *
1570322 AAAATGGTAATTTTTGATGAAATTAGGGTTAAAAATGGAATTTTGGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
1570381 AAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * **
1570440 AAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGT
1 AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
1570499 AAAATGGTAATTTT
1 AAAATGGTAATTTT
1570513 GAATAGTCCA
Statistics
Matches: 332, Mismatches: 28, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.00
58 52 0.16
59 278 0.84
60 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:1570505 original size:235 final size:235
Alignment explanation
Indices: 1570080--1570512 Score: 715
Period size: 235 Copynumber: 1.8 Consensus size: 235
1570070 TTTGGACGCG
*
1570080 CGGGGGCAAAATGATAATTTTTAGTGAAATCGGGGTTAAAAATGCAATCTTGGAAAGTTCGAGGG
1 CGGGGGCAAAATGATAATTTTTAGTGAAATCAGGGTTAAAAATGCAATCTTGGAAAGTTCGAGGG
*
1570145 TAAAATGGTAATCTTTGATGAAACCGGGGTTAATAATGGAATTTTGGAAAGTTCAGGGGTAAAAT
66 TAAAATGGTAATCTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAT
* * *
1570210 GGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
131 GGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAATGGTAAT
1570275 TTTAGTGAAACTGGGGTTAAAAATAGAATTTTGGAAAGTT
196 TTTAGTGAAACTGGGGTTAAAAATAGAATTTTGGAAAGTT
* * * * * * *
1570315 CGGGGGTAAAATGGTAATTTTT-GATGAAATTAGGGTTAAAAATGGAATTTTGGGAAGTTCGGGG
1 CGGGGGCAAAATGATAATTTTTAG-TGAAATCAGGGTTAAAAATGCAATCTTGGAAAGTTCGAGG
* * *
1570379 GTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGGAAGTTCGGGGGTAAAA
65 GTAAAATGGTAATCTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAA
1570444 TGGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAATGGTAA
130 TGGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAATGGTAA
1570509 TTTT
195 TTTT
1570513 GAATAGTCCA
Statistics
Matches: 182, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
234 1 0.01
235 181 0.99
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (235 bp):
CGGGGGCAAAATGATAATTTTTAGTGAAATCAGGGTTAAAAATGCAATCTTGGAAAGTTCGAGGG
TAAAATGGTAATCTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAT
GGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAATGGTAAT
TTTAGTGAAACTGGGGTTAAAAATAGAATTTTGGAAAGTT
Found at i:1571256 original size:18 final size:19
Alignment explanation
Indices: 1571214--1571263 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1571204 AAAGTTATTA
*
1571214 TTATCATTATTAAAATACAT
1 TTATTATTATT-AAATACAT
*
1571234 TTATTATTATTAAA-ACCT
1 TTATTATTATTAAATACAT
1571252 TTATTATTATTA
1 TTATTATTATTA
1571264 TTATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
19 3 0.11
20 10 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTATTAAATACAT
Found at i:1572448 original size:41 final size:40
Alignment explanation
Indices: 1572400--1572500 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
1572390 TCGACCTCGA
** *
1572400 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
1572440 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
1572478 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
1572501 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:1580316 original size:6 final size:6
Alignment explanation
Indices: 1580301--1580376 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
1580291 TTAAATTTGA
* * * *
1580301 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTGAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
1580349 ATAAAT TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1580377 ACCCATTTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
5 12 0.22
6 38 0.70
8 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:1580327 original size:17 final size:17
Alignment explanation
Indices: 1580302--1580376 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
1580292 TAAATTTGAT
* *
1580302 TAAACTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
*
1580319 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
1580333 TGAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
1580350 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
1580367 TAAATTTAAA
1 TAAATTTAAA
1580377 ACCCATTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
14 12 0.24
15 1 0.02
16 1 0.02
17 37 0.73
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1581279 original size:2 final size:2
Alignment explanation
Indices: 1581272--1581317 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1581262 GTGATAAAAG
1581272 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
1581314 AT AT
1 AT AT
1581318 TAAGAGCTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1609867 original size:12 final size:11
Alignment explanation
Indices: 1609840--1609874 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1609830 ATTATATATT
*
1609840 TAAAAATTATA
1 TAAAAATAATA
1609851 TAAAAATAATA
1 TAAAAATAATA
1609862 TAAAAAGTAATA
1 TAAAAA-TAATA
1609874 T
1 T
1609875 GGGCGAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:1610172 original size:22 final size:25
Alignment explanation
Indices: 1610128--1610173 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
1610118 GAAATAACAT
*
1610128 TGAATAATATAATTTATTTTAATTA
1 TGAATAATATAATTTATTGTAATTA
1610153 TGAATAA-AT-ATTT-TTGTAATT
1 TGAATAATATAATTTATTGTAATT
1610174 TTTCTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 2 0.10
25 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (25 bp):
TGAATAATATAATTTATTGTAATTA
Found at i:1614345 original size:149 final size:149
Alignment explanation
Indices: 1614075--1614379 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 149
1614065 CCAAAATAAA
1614075 TGAACTTCGTTGCTGTTAAAGAATCATCCATCTAGGGCTTTGCATGACCATTTATTAAAATTATT
1 TGAACTTCGTTGCTGTTAAAGAATCATCCATCTAGGGCTTTGCATGACCATTTATTAAAATTATT
*
1614140 TCCTTTCCTCTTTATTGCATGAGGAAAGATGTTTTCTGTCTTTCTTTTTGTTTTCAACTTTTATG
66 TCCTTTCCTCTTTATTGCATGAGGAAAGATGTTTTCTGTCTTTCTTTTTATTTTCAACTTTTATG
1614205 AGGGTAAAGAAATAGGAAC
131 AGGGTAAAGAAATAGGAAC
*
1614224 TGAACTTCGTTGCTGTTAAAGAATCATTCATCTAGGGCTTTGCATGACCATTTATTAAAATTATT
1 TGAACTTCGTTGCTGTTAAAGAATCATCCATCTAGGGCTTTGCATGACCATTTATTAAAATTATT
1614289 TCCTTTCCTCTTTATTGCATGAGGAAAGATGTTTTCTGTCTTTCTTTTTATTTTCAACTTTTATG
66 TCCTTTCCTCTTTATTGCATGAGGAAAGATGTTTTCTGTCTTTCTTTTTATTTTCAACTTTTATG
*
1614354 CGGGTAAAGAAATAGGAAC
131 AGGGTAAAGAAATAGGAAC
*
1614373 TGGACTT
1 TGAACTT
1614380 GCTGTAGTTT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (149 bp):
TGAACTTCGTTGCTGTTAAAGAATCATCCATCTAGGGCTTTGCATGACCATTTATTAAAATTATT
TCCTTTCCTCTTTATTGCATGAGGAAAGATGTTTTCTGTCTTTCTTTTTATTTTCAACTTTTATG
AGGGTAAAGAAATAGGAAC
Found at i:1622172 original size:2 final size:2
Alignment explanation
Indices: 1622165--1622196 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1622155 GGAACTATAA
1622165 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1622197 GGAGGATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1624754 original size:32 final size:32
Alignment explanation
Indices: 1624692--1624758 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1624682 AATGTAAAAG
*
1624692 AACATTCTTCCTTTTTCTTTTTTCTTTTTTTCT
1 AACATTCTTCCCTTTTCTTTTTTC-TTTTTTCT
1624725 AACATTC-TCCCTTTTCTTTCATTTC-TTTTTCT
1 AACATTCTTCCCTTTTCTTT--TTTCTTTTTTCT
1624757 AA
1 AA
1624759 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 20 0.65
33 7 0.23
34 4 0.13
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (32 bp):
AACATTCTTCCCTTTTCTTTTTTCTTTTTTCT
Found at i:1630342 original size:3 final size:3
Alignment explanation
Indices: 1630334--1630363 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1630324 GCGATGGGGA
1630334 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1630364 CGAGTACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:1630771 original size:39 final size:39
Alignment explanation
Indices: 1630707--1630837 Score: 190
Period size: 39 Copynumber: 3.4 Consensus size: 39
1630697 TGGCGCAGGT
* * * * *
1630707 GGTGGGGGTGAAGGGGGCGGTGGTGACGGATAAGTAGGC
1 GGTGGGGGTGAAGGTGGTGGAGGTGACGGATATGTAGGG
*
1630746 GGTGGGGGTGAAGGTGGTGGCGGTGACGGATATGTAGGG
1 GGTGGGGGTGAAGGTGGTGGAGGTGACGGATATGTAGGG
* *
1630785 GGTGGGGGTGATGGTGGTGGAGGTGATGGATATGTAGGG
1 GGTGGGGGTGAAGGTGGTGGAGGTGACGGATATGTAGGG
1630824 GGTGGGGGTGAAGG
1 GGTGGGGGTGAAGG
1630838 AGGGGGTGGT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.16, C:0.04, G:0.60, T:0.20
Consensus pattern (39 bp):
GGTGGGGGTGAAGGTGGTGGAGGTGACGGATATGTAGGG
Found at i:1630962 original size:24 final size:24
Alignment explanation
Indices: 1630935--1630993 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1630925 AGGCGAGGGC
* *
1630935 GGTGGTGG-GGGAGGTGAATAAACT
1 GGTGGTGGAGGG-GGAGAATAAACG
*
1630959 GGTGGTGGAGGGGGAGAGTAAACG
1 GGTGGTGGAGGGGGAGAATAAACG
1630983 GGTGGTGGAGG
1 GGTGGTGGAGG
1630994 TGAAGGAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.03, G:0.58, T:0.17
Consensus pattern (24 bp):
GGTGGTGGAGGGGGAGAATAAACG
Found at i:1635138 original size:16 final size:18
Alignment explanation
Indices: 1635100--1635137 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1635090 ATTTTTTTAG
1635100 TTTTT-TTTCAAAAATAT
1 TTTTTATTTCAAAAATAT
1635117 TTTTTATTT-AAAAATAT
1 TTTTTATTTCAAAAATAT
1635134 TTTT
1 TTTT
1635138 AAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATTTCAAAAATAT
Found at i:1648159 original size:2 final size:2
Alignment explanation
Indices: 1648152--1648185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1648142 GATAAGACTC
1648152 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1648186 TTGGTTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1648572 original size:31 final size:31
Alignment explanation
Indices: 1648515--1648581 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1648505 TAATTTTTTT
* *
1648515 AGTTAAATTTGGATTTTCACACTTTAAAAAA
1 AGTTGAATTTGGATTATCACACTTTAAAAAA
* *
1648546 AGTTGAATTT-GATTATCAACATTTTAAAAAG
1 AGTTGAATTTGGATTATC-ACACTTTAAAAAA
1648577 AGTTG
1 AGTTG
1648582 GATTGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (31 bp):
AGTTGAATTTGGATTATCACACTTTAAAAAA
Found at i:1648701 original size:22 final size:23
Alignment explanation
Indices: 1648670--1648729 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1648660 TTATGTTTTT
1648670 TTTTTG-AATATTTATATT-TAA
1 TTTTTGAAATATTTATATTATAA
* *
1648691 TTTTTGAAATATTTTTTTTATAA
1 TTTTTGAAATATTTATATTATAA
*
1648714 TTTTTAAAATATTTAT
1 TTTTTGAAATATTTAT
1648730 CGACGTGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.18
22 10 0.30
23 17 0.52
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (23 bp):
TTTTTGAAATATTTATATTATAA
Found at i:1649851 original size:96 final size:96
Alignment explanation
Indices: 1649687--1649879 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
1649677 AAAAAATAAA
*
1649687 AATTCCATTTTAAGGGGGACCGAGGCCCTTGCGAGCCCCCATAAATCCGTCCCTGTCAAACACGT
1 AATTCCATTTTAAGGGGGACCGAGGCCCTTGCGAGCCCCCATAAATCCGTCCCTATCAAACACGT
1649752 CTAGGGAATTACAATTCTTTGTAATTACAAG
66 CTAGGGAATTACAATTCTTTGTAATTACAAG
*
1649783 AATTCCATTTTAAGGGGGACCGAGGCCCTTGCGAGCCCCCATAAATCCGTCTCTATCAAACACGT
1 AATTCCATTTTAAGGGGGACCGAGGCCCTTGCGAGCCCCCATAAATCCGTCCCTATCAAACACGT
1649848 CTAGGGAATTACAATTCTTTGTAATTACAAG
66 CTAGGGAATTACAATTCTTTGTAATTACAAG
1649879 A
1 A
1649880 GACTGTAATT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (96 bp):
AATTCCATTTTAAGGGGGACCGAGGCCCTTGCGAGCCCCCATAAATCCGTCCCTATCAAACACGT
CTAGGGAATTACAATTCTTTGTAATTACAAG
Found at i:1659603 original size:71 final size:71
Alignment explanation
Indices: 1659528--1659671 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
1659518 GTATTTTGCT
** * *
1659528 ACATTTATGTATTTATAAATTGCTATATTTTTTAAATTTTAAAATTTAAATTT-TGACACAAAAT
1 ACATTTACATATTTATAAATTACTATATTTTTCAAATTTTAAAATTTAAATTTAT-ACACAAAAT
1659592 TTTATTA
65 TTTATTA
* *
1659599 ACATTTACATATTTATAAATTATTATATTTTTCAAATTTTGAAATTTAAATTTATACACAAAATT
1 ACATTTACATATTTATAAATTACTATATTTTTCAAATTTTAAAATTTAAATTTATACACAAAATT
1659664 TTATTA
66 TTATTA
1659670 AC
1 AC
1659672 TTAATTTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 65 0.98
72 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (71 bp):
ACATTTACATATTTATAAATTACTATATTTTTCAAATTTTAAAATTTAAATTTATACACAAAATT
TTATTA
Found at i:1667696 original size:30 final size:30
Alignment explanation
Indices: 1667633--1667696 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1667623 AGTTTATATC
* * *
1667633 TTTATAATTTTTAAATAATTAAATCATATT
1 TTTATAATTTTTAAAAAATAAAATCATAAT
*
1667663 TTTATAATTTTTAAAAAATCAAAAT-GTAAT
1 TTTATAATTTTTAAAAAAT-AAAATCATAAT
1667693 TTTA
1 TTTA
1667697 CTTCTACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATAAAATCATAAT
Found at i:1669207 original size:22 final size:21
Alignment explanation
Indices: 1669172--1669222 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1669162 AATATTTAAA
*
1669172 TAAAACAAATAAATTTCTACT
1 TAAAACAAATAAATGTCTACT
*
1669193 TAAAATAAAGTAAATGTCTACAT
1 TAAAACAAA-TAAATGTCTAC-T
1669216 ATAAAAC
1 -TAAAAC
1669223 TCAAAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
22 10 0.42
23 1 0.04
24 5 0.21
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAACAAATAAATGTCTACT
Found at i:1670584 original size:15 final size:16
Alignment explanation
Indices: 1670550--1670588 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1670540 TGACTTAGTC
1670550 AATAAAAATACAATAA
1 AATAAAAATACAATAA
* *
1670566 AATAAAAATA-TATAT
1 AATAAAAATACAATAA
1670581 AATAAAAA
1 AATAAAAA
1670589 CGAATCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAAATACAATAA
Found at i:1670675 original size:395 final size:391
Alignment explanation
Indices: 1669909--1670675 Score: 1145
Period size: 395 Copynumber: 2.0 Consensus size: 391
1669899 CCAACATTAA
1669909 TTTAATTGAAATTTTAAAATTTATTATATGATTATATAAAATTATACTTAAAATAAATTCATAAA
1 TTTAATTGAAATTTTAAAATTTATTATATGATTATATAAAATTATACTTAAAATAAATTCATAAA
* * *
1669974 TTAAAAACTTTCGAGTTTAAACATCAAAATATCAACTAAAATTTTATCTATTTTTATATAATTTT
66 TTAAAAACTTTCGAGTTAAAACATCAAAATATCAACCAAAACTTTATCTATTTTTATATAATTTT
* * *
1670039 TAATAAATAATTATTTACATGAAAAGTTTCACTCATATGTAGGCAATAAATTAACTTAATATAAT
131 TAATAAATAATTATTTACATAAAAAGTTTCACTCATATATAGGCAATAAATTAACTCAATATAAT
*
1670104 AATATTATTGATTGAGTTTGGTACGATAATTTAATGATTTTGATTAAGTTAATAAAAATACAATA
196 AATATTATTGATTGAGTTTGGTACGATAATTTAATGATTTTGATTAAGTCAATAAAAATACAATA
* * * * *
1670169 AAATAAAAAATATATATAATAAAAATGAATCCAACGAGTAGTTCTAATGGTAAAGAGGATGTTAT
261 AAATAAAAAATATATATAATAAAAACGAATCAAACGAGTAGCTCTAATGCTAAAGAGAATGTTAT
* * * * *
1670234 TCATCTTAAGAGCTCCAAGTTTGAGTACTTGTGTGTGCAAAATATGTATATGCGTGCGTTATCAA
326 TCATCTTAAAAGATCCAAGTTCGAGTACTTATGTGTACAAAATATGTATATGCGTGCGTTATCAA
1670299 T
391 T
* *
1670300 TTTAGTTGAAATTTTAAAATATTATTATATGATTATATAAATTTATACTTAAAATAAATTCATAA
1 TTTAATTGAAATTTTAAAAT-TTATTATATGATTATATAAAATTATACTTAAAATAAATTCATAA
*
1670365 ATTAAAAACTTT-GAAGTTAAAACATCAAAATATCAACCGAAACTTTATCTATTTTTTATATAAT
65 ATTAAAAACTTTCG-AGTTAAAACATCAAAATATCAACCAAAACTTTATCTA-TTTTTATATAA-
1670429 TTTTTAATAAATAATTATTTACATAAAAAGTTTCACTCATATTATTATAGGCAATAAATTAAC-C
127 TTTTTAATAAATAATTATTTACATAAAAAGTTTCACTC--A-TA-TATAGGCAATAAATTAACTC
1670493 AA-AT-ATAATATTATTGATTGAGTTTGGTACGATAATATTAATGATTTTGACTT-AGTCAATAA
188 AATATAATAATATTATTGATTGAGTTTGGTACGATAAT-TTAATGATTTTGA-TTAAGTCAATAA
* *
1670555 AAATACAATAAAAT-AAAAATATATATAATAAAAACGAATCAAACGAGTGGC-CTCAGTGCTAAA
251 AAATACAATAAAATAAAAAATATATATAATAAAAACGAATCAAACGAGTAGCTCT-AATGCTAAA
* * *
1670618 GAGAATGTTGTTCATCTTAAAAGATCC-GGATTCGAGTATTTATGTGTACAAAATATGT
315 GAGAATGTTATTCATCTTAAAAGATCCAAG-TTCGAGTACTTATGTGTACAAAATATGT
1670676 GTGCGCGCAT
Statistics
Matches: 339, Mismatches: 25, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
391 20 0.06
392 88 0.26
393 11 0.03
394 40 0.12
395 119 0.35
396 38 0.11
397 6 0.02
398 17 0.05
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (391 bp):
TTTAATTGAAATTTTAAAATTTATTATATGATTATATAAAATTATACTTAAAATAAATTCATAAA
TTAAAAACTTTCGAGTTAAAACATCAAAATATCAACCAAAACTTTATCTATTTTTATATAATTTT
TAATAAATAATTATTTACATAAAAAGTTTCACTCATATATAGGCAATAAATTAACTCAATATAAT
AATATTATTGATTGAGTTTGGTACGATAATTTAATGATTTTGATTAAGTCAATAAAAATACAATA
AAATAAAAAATATATATAATAAAAACGAATCAAACGAGTAGCTCTAATGCTAAAGAGAATGTTAT
TCATCTTAAAAGATCCAAGTTCGAGTACTTATGTGTACAAAATATGTATATGCGTGCGTTATCAA
T
Found at i:1671496 original size:11 final size:11
Alignment explanation
Indices: 1671482--1671508 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1671472 GACTAGTACA
1671482 TATATATGACC
1 TATATATGACC
1671493 TATATATGACC
1 TATATATGACC
1671504 TATAT
1 TATAT
1671509 CTATGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (11 bp):
TATATATGACC
Found at i:1673631 original size:6 final size:6
Alignment explanation
Indices: 1673620--1673660 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1673610 ACACATGTCT
1673620 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1673661 TTCCCTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:1675629 original size:12 final size:12
Alignment explanation
Indices: 1675612--1675637 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1675602 TTTCAATTAT
1675612 ATGTTCGTGAAC
1 ATGTTCGTGAAC
1675624 ATGTTCGTGAAC
1 ATGTTCGTGAAC
1675636 AT
1 AT
1675638 TAAACAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:1677252 original size:7 final size:7
Alignment explanation
Indices: 1677240--1677268 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1677230 GAAACTGAAA
1677240 AGCTGAG
1 AGCTGAG
1677247 AGCTGAG
1 AGCTGAG
1677254 AGCTGAG
1 AGCTGAG
1677261 AGCTGAG
1 AGCTGAG
1677268 A
1 A
1677269 ACCAGTTAGT
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:0.31, C:0.14, G:0.41, T:0.14
Consensus pattern (7 bp):
AGCTGAG
Found at i:1686428 original size:23 final size:25
Alignment explanation
Indices: 1686385--1686434 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
1686375 CTTTGAATCA
1686385 AAATTATATATAAATGACATAAAAT
1 AAATTATATATAAATGACATAAAAT
1686410 AAATTAT-TA-AAAT-ATCATAAAAT
1 AAATTATATATAAATGA-CATAAAAT
1686433 AA
1 AA
1686435 TTGAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.04
23 14 0.58
24 2 0.08
25 7 0.29
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATTATATATAAATGACATAAAAT
Found at i:1686556 original size:28 final size:26
Alignment explanation
Indices: 1686505--1686557 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
1686495 AAATACTAAA
* *
1686505 ATTAAATATAAAAATATTGAAATGAT
1 ATTAAATAAAAAAATATTCAAATGAT
1686531 ATTAAATTAAAAAAATGATTCAAATGA
1 ATTAAA-TAAAAAAAT-ATTCAAATGA
1686558 CTCTATAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 8 0.35
28 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (26 bp):
ATTAAATAAAAAAATATTCAAATGAT
Found at i:1697644 original size:29 final size:28
Alignment explanation
Indices: 1697582--1697644 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1697572 TACAAATTTT
1697582 AAATTTAATTTTTATATTTTTATTTTAA
1 AAATTTAATTTTTATATTTTTATTTTAA
*
1697610 AGAATTTAATTTTCTAT-TTTTTATATTTCA
1 A-AATTTAATTTT-TATATTTTTAT-TTTAA
1697640 AAATT
1 AAATT
1697645 GAGATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 1 0.03
29 22 0.71
30 8 0.26
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
AAATTTAATTTTTATATTTTTATTTTAA
Found at i:1704002 original size:21 final size:19
Alignment explanation
Indices: 1703963--1704003 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1703953 TTAGACCTGC
*
1703963 CTTTGATTTGTGGTTTCTT
1 CTTTGATCTGTGGTTTCTT
1703982 CTTTGATGCTGTGGCTTTCTT
1 CTTTGAT-CTGTGG-TTTCTT
1704003 C
1 C
1704004 CTCCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.05, C:0.17, G:0.22, T:0.56
Consensus pattern (19 bp):
CTTTGATCTGTGGTTTCTT
Found at i:1706703 original size:21 final size:21
Alignment explanation
Indices: 1706648--1706705 Score: 57
Period size: 25 Copynumber: 2.6 Consensus size: 21
1706638 AAGTATATAT
1706648 TTTTTAAA-ATTTATTTTCAA
1 TTTTTAAATATTTATTTTCAA
1706668 TTTGTTAGGACATATTTATTTT-AA
1 TTT-TTA--A-ATATTTATTTTCAA
1706692 TGTTTTAAATATTT
1 T-TTTTAAATATTT
1706706 TTAATACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 3 0.09
21 9 0.28
22 1 0.03
23 1 0.03
24 7 0.22
25 11 0.34
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTTAAATATTTATTTTCAA
Found at i:1708601 original size:14 final size:15
Alignment explanation
Indices: 1708571--1708604 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1708561 AGACAAGTCA
1708571 TAATAAACTTAAATT
1 TAATAAACTTAAATT
*
1708586 TAATAAA-TTAATTT
1 TAATAAACTTAAATT
1708600 TAATA
1 TAATA
1708605 TTGACAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAAACTTAAATT
Found at i:1723670 original size:74 final size:74
Alignment explanation
Indices: 1723549--1723690 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
1723539 CAGTGCGTAA
* *
1723549 TTATTTGTCAAGTATCAGTCACTCTTTGAATACGAATTCATGCTTCTTATCATTTGGCATCCACC
1 TTATTTGTCAAGTATCAGTCACTCTTTGAATACGAATTCATGCTTCTTACCATTTGCCATCCACC
1723614 CATGTGTAG
66 CATGTGTAG
* ** * * *
1723623 TTATTTTTCAAGTATCAGTCACTCTTTGTGTACGTATTGATGTTTCTTACCATTTGCCATCCACC
1 TTATTTGTCAAGTATCAGTCACTCTTTGAATACGAATTCATGCTTCTTACCATTTGCCATCCACC
1723688 CAT
66 CAT
1723691 TTCGCCGCCG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (74 bp):
TTATTTGTCAAGTATCAGTCACTCTTTGAATACGAATTCATGCTTCTTACCATTTGCCATCCACC
CATGTGTAG
Found at i:1728159 original size:24 final size:24
Alignment explanation
Indices: 1728113--1728159 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1728103 TGTGATAGTT
*
1728113 ATAAAATATTATTATTTAAATATG
1 ATAAAATATTATTATATAAATATG
*
1728137 ATAAAGATATT-TTATATATATAT
1 ATAAA-ATATTATTATATAAATAT
1728160 ATATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
ATAAAATATTATTATATAAATATG
Found at i:1740774 original size:16 final size:16
Alignment explanation
Indices: 1740753--1740783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1740743 AGAGATGATA
1740753 TGTCACAATATTAAAG
1 TGTCACAATATTAAAG
*
1740769 TGTCACATTATTAAA
1 TGTCACAATATTAAA
1740784 CTTTTATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (16 bp):
TGTCACAATATTAAAG
Found at i:1743160 original size:36 final size:36
Alignment explanation
Indices: 1743071--1743163 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
1743061 CTCATCAACA
* * *
1743071 CCATCTCCGCCTCCGCCACCGAGGAGTTCCGGTACT
1 CCATCTCCACCTCCGCCTCCGAGGAGTTCCGGGACT
* *
1743107 GCATCTCCACCACCGCCTCCGAGGAGTTCCGGGACT
1 CCATCTCCACCTCCGCCTCCGAGGAGTTCCGGGACT
*
1743143 CCATCTCCTCCTCCGCCTCCG
1 CCATCTCCACCTCCGCCTCCG
1743164 TCTGATTCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.13, C:0.47, G:0.20, T:0.19
Consensus pattern (36 bp):
CCATCTCCACCTCCGCCTCCGAGGAGTTCCGGGACT
Found at i:1747237 original size:17 final size:17
Alignment explanation
Indices: 1747199--1747237 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1747189 TGCTTATTTT
* *
1747199 AAAAATTATCAGTTGAA
1 AAAAATTATAAGTTAAA
1747216 AAAAATTATAAGTTAAA
1 AAAAATTATAAGTTAAA
1747233 AAAAA
1 AAAAA
1747238 AATTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (17 bp):
AAAAATTATAAGTTAAA
Found at i:1747846 original size:2 final size:2
Alignment explanation
Indices: 1747839--1747875 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1747829 CAAAAATGCT
1747839 TA 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 TA T
1747876 GACATTCACA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1752494 original size:6 final size:6
Alignment explanation
Indices: 1752485--1752515 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1752475 TTGAAATGGA
*
1752485 AAAGGG AAAGGG AAAGGG AAAGGT AAAGGG A
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG A
1752516 GAGAAGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (6 bp):
AAAGGG
Found at i:1766079 original size:16 final size:15
Alignment explanation
Indices: 1766055--1766083 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1766045 TAAATAAAAT
1766055 ATTTTAAAAATTTTG
1 ATTTTAAAAATTTTG
1766070 ATTTTAAAAATTTT
1 ATTTTAAAAATTTT
1766084 AAAACTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTTAAAAATTTTG
Found at i:1766082 original size:9 final size:9
Alignment explanation
Indices: 1766049--1766098 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
1766039 AATTGTTAAA
1766049 TAAAATATTT
1 TAAAA-ATTT
1766059 TAAAAATTT
1 TAAAAATTT
*
1766068 T---GATTT
1 TAAAAATTT
1766074 TAAAAATTT
1 TAAAAATTT
*
1766083 TAAAACTTT
1 TAAAAATTT
1766092 TAAAAAT
1 TAAAAAT
1766099 GTTTTATCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
6 5 0.15
9 23 0.70
10 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (9 bp):
TAAAAATTT
Found at i:1775359 original size:29 final size:27
Alignment explanation
Indices: 1775292--1775360 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 27
1775282 AGATTATATT
*
1775292 TTATTTTTTTATTAAAAAATAAATTAG
1 TTATTTTATTATTAAAAAATAAATTAG
1775319 TTCATGTTTATTATATAAAAAATAAATT-G
1 TT-AT-TTTATTAT-TAAAAAATAAATTAG
1775348 ATTATTTCTATTA
1 -TTATTT-TATTA
1775361 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 15 0.42
30 15 0.42
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (27 bp):
TTATTTTATTATTAAAAAATAAATTAG
Found at i:1783159 original size:20 final size:20
Alignment explanation
Indices: 1783134--1783171 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1783124 AAAACTTTGA
1783134 TCAATTCAATTAATAATAGT
1 TCAATTCAATTAATAATAGT
1783154 TCAATTCAATTAATAATA
1 TCAATTCAATTAATAATA
1783172 AATAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (20 bp):
TCAATTCAATTAATAATAGT
Found at i:1785782 original size:12 final size:12
Alignment explanation
Indices: 1785765--1785789 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1785755 GCTGAGGGTC
1785765 TCTGCATAGCTA
1 TCTGCATAGCTA
1785777 TCTGCATAGCTA
1 TCTGCATAGCTA
1785789 T
1 T
1785790 GTTTGTGGAG
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:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TCTGCATAGCTA
Found at i:1801656 original size:5 final size:5
Alignment explanation
Indices: 1801646--1801672 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1801636 ACCCAAATTA
1801646 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1801673 CCTTGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:1815760 original size:3 final size:3
Alignment explanation
Indices: 1815748--1815792 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
1815738 GAAGGAACGG
* * *
1815748 GAA G-A GAA GAA GAT GAA GAT GAA GAA GAC GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1815793 TGGGTGTGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.58, C:0.02, G:0.36, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:1820269 original size:4 final size:4
Alignment explanation
Indices: 1820260--1820284 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1820250 TTATAATAAA
1820260 TGCC TGCC TGCC TGCC TGCC TGCC T
1 TGCC TGCC TGCC TGCC TGCC TGCC T
1820285 ACCCTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.24, T:0.28
Consensus pattern (4 bp):
TGCC
Found at i:1821103 original size:13 final size:13
Alignment explanation
Indices: 1821085--1821111 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1821075 GCACATTATA
1821085 TATTAATCGAGAT
1 TATTAATCGAGAT
1821098 TATTAATCGAGAT
1 TATTAATCGAGAT
1821111 T
1 T
1821112 TTTCTTAGGT
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:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TATTAATCGAGAT
Found at i:1825576 original size:6 final size:6
Alignment explanation
Indices: 1825565--1825603 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1825555 TGATCAAAAT
* * *
1825565 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
1825604 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:1831302 original size:28 final size:28
Alignment explanation
Indices: 1831262--1831318 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1831252 CATATAGCCA
*
1831262 CATTGATCCTACTCTCAAAGTCTATCAC
1 CATTGATACTACTCTCAAAGTCTATCAC
1831290 CATTGATACTACTCTCAAAGTCTATCAC
1 CATTGATACTACTCTCAAAGTCTATCAC
1831318 C
1 C
1831319 CGTGGCCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (28 bp):
CATTGATACTACTCTCAAAGTCTATCAC
Found at i:1832775 original size:16 final size:17
Alignment explanation
Indices: 1832745--1832777 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1832735 TTCTTGTTCC
1832745 TGTTATTTATATTTTTT
1 TGTTATTTATATTTTTT
1832762 TGTTATTT-TATTTTTT
1 TGTTATTTATATTTTTT
1832778 AATTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TGTTATTTATATTTTTT
Done.