Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold278
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: 1156311
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 38162 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:957776 original size:31 final size:32
Alignment explanation
Indices: 957731--957793 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
957721 ATAGGTTGCT
* *
957731 CCCCCTTTAATAAAAGTCATTTTCAATTTAAG
1 CCCCCTATAATAAAAATCATTTTCAATTTAAG
*
957763 CCCCCTAT-ATAAAAATCCTTTTCAATTTAAG
1 CCCCCTATAATAAAAATCATTTTCAATTTAAG
957794 GTATAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (32 bp):
CCCCCTATAATAAAAATCATTTTCAATTTAAG
Found at i:961254 original size:50 final size:50
Alignment explanation
Indices: 961126--961311 Score: 196
Period size: 50 Copynumber: 3.7 Consensus size: 50
961116 GATAATAACA
* * * **
961126 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGT-AA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATCGG
* * * *
961175 TACCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** * *
961225 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCACATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
961275 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
961312 TCTCTTTACC
Statistics
Matches: 111, Mismatches: 24, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
48 3 0.03
49 36 0.32
50 72 0.65
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:962549 original size:20 final size:20
Alignment explanation
Indices: 962520--962570 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
962510 TTAGAGCAGG
*
962520 AATATTGATACCTT-AGAAA
1 AATATCGATACCTTAAGAAA
*
962539 ATATATCGATACGTTAAGAAA
1 A-ATATCGATACCTTAAGAAA
*
962560 AGTATCGATAC
1 AATATCGATAC
962571 TGGATTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.74
21 6 0.22
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
AATATCGATACCTTAAGAAA
Found at i:966099 original size:10 final size:10
Alignment explanation
Indices: 966060--966106 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
966050 TATTGTTATT
966060 TTTTAATAAAA
1 TTTTAAT-AAA
*
966071 TTTTTATAAA
1 TTTTAATAAA
966081 TTATATAATAAA
1 TT-T-TAATAAA
966093 TTTTAATAAA
1 TTTTAATAAA
966103 TTTT
1 TTTT
966107 GCTTCTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 16 0.50
11 8 0.25
12 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:966508 original size:13 final size:15
Alignment explanation
Indices: 966475--966504 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
966465 TTATTAGCAT
*
966475 ACTATATATTTAGAA
1 ACTATATATATAGAA
966490 ACTATATATATAGAA
1 ACTATATATATAGAA
966505 TATAATGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (15 bp):
ACTATATATATAGAA
Found at i:971460 original size:14 final size:14
Alignment explanation
Indices: 971443--971473 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
971433 CAGTTAATTT
971443 ATAACTGCTAACTA
1 ATAACTGCTAACTA
*
971457 ATAACTGTTAACTA
1 ATAACTGCTAACTA
971471 ATA
1 ATA
971474 CTTAACAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (14 bp):
ATAACTGCTAACTA
Found at i:974079 original size:19 final size:18
Alignment explanation
Indices: 974050--974085 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
974040 TTTTTTAATA
*
974050 ATCAATTTTTATATTTTT
1 ATCAATTTTTAAATTTTT
974068 ATCAATTTTTTAAATTTT
1 ATCAA-TTTTTAAATTTT
974086 ACCGGATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
ATCAATTTTTAAATTTTT
Found at i:979385 original size:29 final size:29
Alignment explanation
Indices: 979353--979408 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
979343 GTGGTGCCCC
* * * *
979353 AACTTTGGTAAAATTGCAGTAACACCCTT
1 AACTTTAGAAAAATTACAATAACACCCTT
979382 AACTTTAGAAAAATTACAATAACACCC
1 AACTTTAGAAAAATTACAATAACACCC
979409 CAAAAGTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (29 bp):
AACTTTAGAAAAATTACAATAACACCCTT
Found at i:982068 original size:5 final size:5
Alignment explanation
Indices: 982058--982086 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
982048 TGTTTTCTAC
982058 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
982087 ATCAGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:982697 original size:16 final size:15
Alignment explanation
Indices: 982673--982706 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
982663 ATTTTTATGT
*
982673 AATTTAATTAAAGTAA
1 AATTAAATTAAAG-AA
982689 AATTAAATTAAAGAA
1 AATTAAATTAAAGAA
982704 AAT
1 AAT
982707 ATCATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AATTAAATTAAAGAA
Found at i:987455 original size:10 final size:10
Alignment explanation
Indices: 987440--987467 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
987430 ACTAATTTTT
987440 GTCCTATTTC
1 GTCCTATTTC
987450 GTCCTATTTC
1 GTCCTATTTC
987460 GTCCTATT
1 GTCCTATT
987468 AGTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.11, T:0.50
Consensus pattern (10 bp):
GTCCTATTTC
Found at i:994955 original size:130 final size:131
Alignment explanation
Indices: 994710--994978 Score: 513
Period size: 130 Copynumber: 2.1 Consensus size: 131
994700 AAAAAAAAAT
994710 ATAATAAAAGTATTTGTATGGTTTCAAATACGCTTTTAATTATTTATTTTTATTAAATTATAAAG
1 ATAATAAAAGTATTTGTATGGTTTCAAATACGCTTTTAATTATTTATTTTTATTAAATTATAAAG
* *
994775 TAAAAATTTCAAAGAAAATATTTGATATCAGTAAAGTTTTTAGACTCCACAAGTAGGATTAAGGT
66 TAAAAATTTCAAAGAAAATATTTGATAACAATAAAGTTTTTAGACTCCACAAGTAGGATTAAGGT
994840 G
131 G
994841 ATAATAAAAGT-TTTGTATGGTTTCAAATACGCTTTTAATTATTTATTTTTATTAAATTATAAAG
1 ATAATAAAAGTATTTGTATGGTTTCAAATACGCTTTTAATTATTTATTTTTATTAAATTATAAAG
994905 TAAAAATTTCAAAGAAAATATTTGATAACAATAAAGTTTTTAGACTCCACAAGTAGGATTAAGGT
66 TAAAAATTTCAAAGAAAATATTTGATAACAATAAAGTTTTTAGACTCCACAAGTAGGATTAAGGT
994970 G
131 G
994971 ATAATAAA
1 ATAATAAA
994979 TATCCTAAAG
Statistics
Matches: 136, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
130 125 0.92
131 11 0.08
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (131 bp):
ATAATAAAAGTATTTGTATGGTTTCAAATACGCTTTTAATTATTTATTTTTATTAAATTATAAAG
TAAAAATTTCAAAGAAAATATTTGATAACAATAAAGTTTTTAGACTCCACAAGTAGGATTAAGGT
G
Found at i:995014 original size:2 final size:2
Alignment explanation
Indices: 995007--995033 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
994997 TAAAATATTA
995007 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 A
995034 AAGGGGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:996022 original size:27 final size:27
Alignment explanation
Indices: 995982--996033 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
995972 AAAAAAAAGG
*
995982 TAATGCATATTTTTTAATTATAAAAATT
1 TAATACATATTTTTTAATT-TAAAAATT
996010 TAATACATA-TTTTTAATTTAAAAA
1 TAATACATATTTTTTAATTTAAAAA
996034 GGTACTACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
TAATACATATTTTTTAATTTAAAAATT
Found at i:996042 original size:26 final size:28
Alignment explanation
Indices: 995975--996042 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
995965 AACAATTAAA
*
995975 AAAAAGGTAATGCATATTTTTTAATTAT
1 AAAAAGGTAATACATATTTTTTAATTAT
**
996003 AAAAATTTAATACATA-TTTTTAATT-T
1 AAAAAGGTAATACATATTTTTTAATTAT
*
996029 AAAAAGGTACTACA
1 AAAAAGGTAATACA
996043 GACTTTTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 12 0.35
27 9 0.26
28 13 0.38
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (28 bp):
AAAAAGGTAATACATATTTTTTAATTAT
Found at i:996049 original size:27 final size:27
Alignment explanation
Indices: 995975--996049 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
995965 AACAATTAAA
* *
995975 AAAAAGGTAATGCATATTTTTTAATTAT
1 AAAAAGGTAATACAGA-TTTTTAATTAT
** *
996003 AAAAATTTAATACATATTTTTAATT-T
1 AAAAAGGTAATACAGATTTTTAATTAT
* *
996029 AAAAAGGTACTACAGACTTTT
1 AAAAAGGTAATACAGATTTTT
996050 GAAATATTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 17 0.44
27 9 0.23
28 13 0.33
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (27 bp):
AAAAAGGTAATACAGATTTTTAATTAT
Found at i:998573 original size:21 final size:21
Alignment explanation
Indices: 998540--998579 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
998530 ATATATTCTT
* * *
998540 TTTATTCTTTTTTATTTTAAA
1 TTTATTATATTTTAATTTAAA
998561 TTTATTATATTTTAATTTA
1 TTTATTATATTTTAATTTA
998580 TTTTCTTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTATATTTTAATTTAAA
Found at i:998588 original size:15 final size:15
Alignment explanation
Indices: 998549--998588 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
998539 TTTTATTCTT
998549 TTTTATTTTAAATTTA
1 TTTTATTTT-AATTTA
*
998565 TTATATTTTAATTTA
1 TTTTATTTTAATTTA
*
998580 TTTTCTTTT
1 TTTTATTTT
998589 CCCAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTTAATTTA
Found at i:1000159 original size:37 final size:40
Alignment explanation
Indices: 1000080--1000157 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
1000070 TTATAATACA
*
1000080 TAAAATTATATATTATCATTGTATTAAATATTAATTATTT
1 TAAAATTATATATTATCATTGTATGAAATATTAATTATTT
* *
1000120 TAAAATTATTTATT-T-ATTG-ATGACATATTAATATATTT
1 TAAAATTATATATTATCATTGTATGAAATATTAAT-TATTT
1000158 AATACAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 11 0.32
38 9 0.26
39 1 0.03
40 13 0.38
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (40 bp):
TAAAATTATATATTATCATTGTATGAAATATTAATTATTT
Found at i:1001562 original size:19 final size:19
Alignment explanation
Indices: 1001538--1001575 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1001528 AAGTTAACAA
1001538 CAAATTTGATTACGATGGG
1 CAAATTTGATTACGATGGG
*
1001557 CAAATTTGATTACGGTGGG
1 CAAATTTGATTACGATGGG
1001576 TGATAGTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (19 bp):
CAAATTTGATTACGATGGG
Found at i:1002124 original size:7 final size:7
Alignment explanation
Indices: 1002112--1002139 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1002102 ATTATAATAT
1002112 GTCACAA
1 GTCACAA
1002119 GTCACAA
1 GTCACAA
1002126 GTCACAA
1 GTCACAA
1002133 GTCACAA
1 GTCACAA
1002140 CCTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
GTCACAA
Found at i:1003177 original size:18 final size:18
Alignment explanation
Indices: 1003154--1003197 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1003144 TCCGAACAAT
** *
1003154 AACTTCTCCAATGACCCA
1 AACTTCTCCAACAACCAA
*
1003172 AACTTCCCCAACAACCAA
1 AACTTCTCCAACAACCAA
1003190 AACTTCTC
1 AACTTCTC
1003198 TAACTTCCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.41, G:0.02, T:0.20
Consensus pattern (18 bp):
AACTTCTCCAACAACCAA
Found at i:1004077 original size:21 final size:21
Alignment explanation
Indices: 1004051--1004093 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1004041 TACAACAAGT
*
1004051 TGAATCCATCAAAGCATTCAC
1 TGAATCCATCAAAGAATTCAC
1004072 TGAATCCATCAAAGAATTCAC
1 TGAATCCATCAAAGAATTCAC
1004093 T
1 T
1004094 TCTCATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (21 bp):
TGAATCCATCAAAGAATTCAC
Found at i:1006838 original size:220 final size:219
Alignment explanation
Indices: 1006455--1006898 Score: 782
Period size: 220 Copynumber: 2.0 Consensus size: 219
1006445 AAGATATTAT
1006455 CCTTTTTTCAGTGGTTACCTAAAGATCATTATTTGACTAACAGAAAGGGGTTTTATTTTCCTCTT
1 CCTTTTTTCAGTGGTTACCTAAAGATCATTATTTGACTAACAGAAAGGGGTTTTATTTTCCTCTT
*
1006520 TGAAAAGTTTGAAGAGTTATTCTATTCGTTTTTCTTTCGGGTGGATCAAGTAAAGCCTAGGGCGA
66 TGAAAAGTTTGAAGAGTTATTCTATTCATTTTTCTTTCGGGTGGATCAAGTAAAGCCTAGGGCGA
*
1006585 TTTGTTGCCACCGTGGTTTGTGATTTAGATAGAGGCTTCATAATACAATTGGTTAGCTCTTATTA
131 TTTGTTGCCACCGTGGTTTGTGATTTAGATAGAGGCTTCATAATACAATTGGTTAGCTCTTACTA
1006650 GATTTTTTTTAAGGTATATTTTCCAA
196 GA-TTTTTTTAAGGTATATTTT-CAA
*
1006676 CCTTTTTTCAGTGGTTACCTAAAGATCATTATTTGACTAACAGAAA-GGGTTTTCTTTTCCTCTT
1 CCTTTTTTCAGTGGTTACCTAAAGATCATTATTTGACTAACAGAAAGGGGTTTTATTTTCCTCTT
* * *
1006740 TGAAAAGTTTGAAGAGTTATTCTATTCATTTTTCTTTTGGGTGGATCAAGTATAGGCTAGGGCGA
66 TGAAAAGTTTGAAGAGTTATTCTATTCATTTTTCTTTCGGGTGGATCAAGTAAAGCCTAGGGCGA
* *
1006805 TTTGTTGCGACCGTGGTTTGTGATTTAGATAGAGGCTTCATAATATAATTGGTTAGCTCTTACTA
131 TTTGTTGCCACCGTGGTTTGTGATTTAGATAGAGGCTTCATAATACAATTGGTTAGCTCTTACTA
*
1006870 GATTTTTTTAAGGTATCTTTTCAA
196 GATTTTTTTAAGGTATATTTTCAA
1006894 CCTTT
1 CCTTT
1006899 GTCAACCTCG
Statistics
Matches: 214, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
218 8 0.04
219 18 0.08
220 142 0.66
221 46 0.21
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (219 bp):
CCTTTTTTCAGTGGTTACCTAAAGATCATTATTTGACTAACAGAAAGGGGTTTTATTTTCCTCTT
TGAAAAGTTTGAAGAGTTATTCTATTCATTTTTCTTTCGGGTGGATCAAGTAAAGCCTAGGGCGA
TTTGTTGCCACCGTGGTTTGTGATTTAGATAGAGGCTTCATAATACAATTGGTTAGCTCTTACTA
GATTTTTTTAAGGTATATTTTCAA
Found at i:1012825 original size:17 final size:17
Alignment explanation
Indices: 1012799--1012832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1012789 GGGTTGTGTG
*
1012799 AATTATTTAATTGAATT
1 AATTAATTAATTGAATT
*
1012816 AATTAATTAATTTAATT
1 AATTAATTAATTGAATT
1012833 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTAATTAATTGAATT
Found at i:1017588 original size:22 final size:22
Alignment explanation
Indices: 1017546--1017589 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1017536 TTTTTATATA
**
1017546 TTTTAATATTTTAATTTATTTT
1 TTTTAATATTTTAATAAATTTT
1017568 TTTTAAATATTTT-ATAAATTTT
1 TTTT-AATATTTTAATAAATTTT
1017590 AAATCATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTAATATTTTAATAAATTTT
Found at i:1019949 original size:21 final size:21
Alignment explanation
Indices: 1019925--1019972 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
1019915 AAAATACATA
1019925 AATATTTTTAAAAAATATAAT
1 AATATTTTTAAAAAATATAAT
** ** *
1019946 AATAAATTTAAAATTTATATT
1 AATATTTTTAAAAAATATAAT
1019967 AATATT
1 AATATT
1019973 AATATTAATA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTTTTAAAAAATATAAT
Found at i:1019971 original size:6 final size:6
Alignment explanation
Indices: 1019962--1019986 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1019952 TTTAAAATTT
1019962 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
1019987 ATAAAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:1020483 original size:10 final size:10
Alignment explanation
Indices: 1020464--1020496 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1020454 TTTGAAAATA
*
1020464 TTTATGTATT
1 TTTATATATT
1020474 TTTATATATT
1 TTTATATATT
1020484 TTTATAT-TT
1 TTTATATATT
1020493 TTTA
1 TTTA
1020497 ACTGTCGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTATATATT
Found at i:1025661 original size:44 final size:44
Alignment explanation
Indices: 1025592--1026201 Score: 690
Period size: 44 Copynumber: 13.9 Consensus size: 44
1025582 ATCACAAAGC
* *
1025592 CCTATCTCCCTGACCAGCAGTGGAATAGATTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* * * *
1025636 CCTAGCTCCCTAAACAGTAGCGGAATAGG-TGAAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTG-AAGATTGTAAGT
* * *
1025680 CCTATCCCCCTGACCAGCAGTGGAGTAGG-TGAAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTG-AAGATTGTAAGT
* * * * * *
1025724 CCTATCCCCCTAACCAGTAGCAGAGTAGGTGGAAGATTGTAAG-
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* * *
1025767 CCATATCTCCCTGACCAGTAGTGGAATAGGTTGAAGAATGTAAGT
1 CC-TATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* * *
1025812 CCTAGCTCCCTGAACAGCAGCGGAATATG-TGAAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTG-AAGATTGTAAGT
* *
1025856 CCTATCCCCCTGACCAGCAGCGGAGTAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* *
1025900 CCTAGCTCCCTGAACAGCAGCGGAATAGG-TGAAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTG-AAGATTGTAAGT
* * * * * *
1025944 CCTATCCCCCTAATCAGCAGCGGAGTAGGTGGAAGATTGTAAGC
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* *
1025988 CCTATCTCTCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* * * * *
1026032 CCTAGCTCCTTGAACAGCAGTGGAATAGGTGGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
** * * *
1026076 CCTAGATCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTATGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* * ** *
1026120 CCTATCTCTCTTATTAGCAGCGGAATAGGTGGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
* *
1026164 CCTATCTCCCTGGCCAGCAGCGGAATAGGTGGAAGATT
1 CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATT
1026202 CGAAGTAGAT
Statistics
Matches: 480, Mismatches: 78, Indels: 16
0.84 0.14 0.03
Matches are distributed among these distances:
43 8 0.02
44 466 0.97
45 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGCGGAATAGGTTGAAGATTGTAAGT
Found at i:1040535 original size:63 final size:63
Alignment explanation
Indices: 1040356--1040538 Score: 160
Period size: 63 Copynumber: 2.9 Consensus size: 63
1040346 ATCACACAAC
** * * *
1040356 CGTGTGT-TAGGTTGTGTGACTCACTGTTTAC-CTCTAAGGATCA-ACGAACCAGAGACACGAG
1 CGTGTGTCTAGGCCGTGTGACTCACTGTTTACTATC-AGGGATCACACGAGCCAGAGACACGAG
* * * * * * * * *
1040417 CATG-GATCCAGGCCTTGTGACTTACTGTTTGCTATTAGGAATCACAC-AGGTCAGAGACACGAT
1 CGTGTG-TCTAGGCCGTGTGACTCACTGTTTACTATCAGGGATCACACGA-GCCAGAGACACGAG
* *
1040480 CGTGTGTCTAGGCCGTGTGACTCACTGTTCACTATCAGGGACCACACGAGCCAGAGACA
1 CGTGTGTCTAGGCCGTGTGACTCACTGTTTACTATCAGGGATCACACGAGCCAGAGACA
1040539 TAGGTTGTGT
Statistics
Matches: 91, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
60 1 0.01
61 4 0.04
62 25 0.27
63 59 0.65
64 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (63 bp):
CGTGTGTCTAGGCCGTGTGACTCACTGTTTACTATCAGGGATCACACGAGCCAGAGACACGAG
Found at i:1048983 original size:22 final size:22
Alignment explanation
Indices: 1048955--1048998 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1048945 TAACCTTCTC
1048955 AATCAAAGAGGTTCACAGAAGG
1 AATCAAAGAGGTTCACAGAAGG
1048977 AATCAAAGAGGTTCACAGAAGG
1 AATCAAAGAGGTTCACAGAAGG
1048999 TAAAGCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.27, T:0.14
Consensus pattern (22 bp):
AATCAAAGAGGTTCACAGAAGG
Found at i:1049567 original size:9 final size:9
Alignment explanation
Indices: 1049553--1049583 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1049543 GTTAAACGAA
1049553 TCGAGTTAT
1 TCGAGTTAT
*
1049562 TCGAGTTAA
1 TCGAGTTAT
1049571 TCGAGTTAT
1 TCGAGTTAT
1049580 TCGA
1 TCGA
1049584 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1049653 original size:9 final size:9
Alignment explanation
Indices: 1049636--1049672 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1049626 TGAGTTTTCG
1049636 AATTCGAAT
1 AATTCGAAT
*
1049645 AACTCGAAT
1 AATTCGAAT
*
1049654 AATTCAAAT
1 AATTCGAAT
1049663 AATTCGAAT
1 AATTCGAAT
1049672 A
1 A
1049673 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1049941 original size:30 final size:29
Alignment explanation
Indices: 1049885--1049941 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
1049875 AACCTTTTAT
* *
1049885 TTTTTCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCAC
* *
1049914 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCC-AAAACTTTTACTCCCTTCC
1049942 CATTCCACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCAC
Found at i:1052211 original size:26 final size:25
Alignment explanation
Indices: 1052170--1052221 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
1052160 ACGAACGCCC
1052170 TTCTTTGCTCTCTGCCCTCTGCCGG
1 TTCTTTGCTCTCTGCCCTCTGCCGG
*
1052195 TTCTTTGTTCCTCTGCCCTCTGCCGG
1 TTCTTTGCT-CTCTGCCCTCTGCCGG
1052221 T
1 T
1052222 GAGTTTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (25 bp):
TTCTTTGCTCTCTGCCCTCTGCCGG
Found at i:1055179 original size:13 final size:13
Alignment explanation
Indices: 1055161--1055235 Score: 96
Period size: 13 Copynumber: 5.8 Consensus size: 13
1055151 ACACTCAAAT
1055161 TTCTCAAAAGTAC
1 TTCTCAAAAGTAC
* *
1055174 TTCTCAAAAGCAA
1 TTCTCAAAAGTAC
*
1055187 TTCTCAAAAGCAC
1 TTCTCAAAAGTAC
* *
1055200 TTCTGAAAAATAC
1 TTCTCAAAAGTAC
*
1055213 TTCTCGAAAGTAC
1 TTCTCAAAAGTAC
1055226 TTCTCAAAAG
1 TTCTCAAAAG
1055236 CAATAAAGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (13 bp):
TTCTCAAAAGTAC
Found at i:1055215 original size:39 final size:39
Alignment explanation
Indices: 1055161--1055237 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
1055151 ACACTCAAAT
*
1055161 TTCTCAAAAGTACTTCTCAAAAGCAATTCTCAAAAGCAC
1 TTCTCAAAAATACTTCTCAAAAGCAATTCTCAAAAGCAC
* * * *
1055200 TTCTGAAAAATACTTCTCGAAAGTACTTCTCAAAAGCA
1 TTCTCAAAAATACTTCTCAAAAGCAATTCTCAAAAGCA
1055238 ATAAAGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.27
Consensus pattern (39 bp):
TTCTCAAAAATACTTCTCAAAAGCAATTCTCAAAAGCAC
Found at i:1055247 original size:39 final size:39
Alignment explanation
Indices: 1055166--1055247 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
1055156 CAAATTTCTC
* * ***
1055166 AAAAGTACTTCTCAAAAGCAATTCTCAAAAGCACTTCTG
1 AAAAATACTTCTCAAAAGCAATTCTCAAAAGCAATAAAG
* * *
1055205 AAAAATACTTCTCGAAAGTACTTCTCAAAAGCAATAAAG
1 AAAAATACTTCTCAAAAGCAATTCTCAAAAGCAATAAAG
1055244 AAAA
1 AAAA
1055248 TGTTTCTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (39 bp):
AAAAATACTTCTCAAAAGCAATTCTCAAAAGCAATAAAG
Found at i:1055452 original size:24 final size:24
Alignment explanation
Indices: 1055403--1055454 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1055393 TTTTCATCCT
* * *
1055403 TTTAAAAAATATTAATTTATTTAC
1 TTTAAAAAATATTAAATTAATCAC
1055427 TTTAAAAAATATTAAATTAATCAC
1 TTTAAAAAATATTAAATTAATCAC
1055451 TTTA
1 TTTA
1055455 CCATTAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAAAAATATTAAATTAATCAC
Found at i:1060554 original size:40 final size:41
Alignment explanation
Indices: 1060491--1060572 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
1060481 TAAAATGGGT
*
1060491 ATATATATATATATGTAGATGTACATGAAT-TAAAATATATGA
1 ATATATATATATACGTA-ATGTACATGAATGTAAAA-ATATGA
* *
1060533 ATATATATATATACGT-TTGTACATGTATGTAAAAATATGA
1 ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
1060573 GTCAAGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 16 0.44
41 5 0.14
42 15 0.42
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (41 bp):
ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
Found at i:1060832 original size:3 final size:3
Alignment explanation
Indices: 1060814--1060881 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
1060804 ATAAAGAAGC
* *
1060814 AAT AAT CAT GAAT AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1060860 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
1060882 GCAATAACGT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 58 0.97
4 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1061132 original size:40 final size:41
Alignment explanation
Indices: 1061069--1061150 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
1061059 TAAAATGGGT
*
1061069 ATATATATATATATGTAGATGTACATGAAT-TAAAATATATGA
1 ATATATATATATACGTA-ATGTACATGAATGTAAAA-ATATGA
* *
1061111 ATATATATATATACGT-TTGTACATGTATGTAAAAATATGA
1 ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
1061151 GTCAAGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 16 0.44
41 5 0.14
42 15 0.42
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (41 bp):
ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
Found at i:1063340 original size:44 final size:44
Alignment explanation
Indices: 1063277--1063583 Score: 183
Period size: 44 Copynumber: 7.1 Consensus size: 44
1063267 ATCTGATGCG
*
1063277 ATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGCGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * * * *
1063321 ATCAGCTCCACTGCAACTTCAGGGAGATAGGAT-TGAC--TTCTTCT
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG-CGGTT-TT-A
* * * * *
1063365 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT--GGATGTG
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* ** *
1063406 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTATGATTTTA
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * * *
1063450 ATCCGCTCTACTGCAACTTTAGAGAGATAGGAT-T--GG-TTTC
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * * * ***
1063490 CTCTGTCTACTCCACTACAACTTCAGGGAGATAAGA-CT--GGATACG
1 ATCTG-CT-CT--ACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * *
1063535 ATCTG-TCTACTGCAACTTCAAAGAGATAAGATCTACGATTTTCA
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTT-A
1063579 ATCTG
1 ATCTG
1063584 TTTAATTGTG
Statistics
Matches: 202, Mismatches: 42, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
40 26 0.13
41 34 0.17
42 9 0.04
43 9 0.04
44 119 0.59
45 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
Found at i:1063433 original size:129 final size:129
Alignment explanation
Indices: 1063271--1063581 Score: 444
Period size: 129 Copynumber: 2.4 Consensus size: 129
1063261 AAAAAAATCT
* * *
1063271 GATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGCGGTTTTAATCAGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACGATTTTAATCAGCTCCACTGCA
* * * *
1063336 ACTTCAGGGAGATAGGATTGACTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
66 ACTTCAGAGAGATAGGATTGACTTCCTCTATCTACTCCACTACAACTTCAGGGAGATAAGACTG
* * * * *
1063400 GATGTGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTATGATTTTAATCCGCTCTACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACGATTTTAATCAGCTCCACTGCA
* ** *
1063465 ACTTTAGAGAGATAGGATTGGTTTCCTCTGTCTACTCCACTACAACTTCAGGGAGATAAGACTG
66 ACTTCAGAGAGATAGGATTGACTTCCTCTATCTACTCCACTACAACTTCAGGGAGATAAGACTG
* *
1063529 GATACGATCTG-TCTACTGCAACTTCAAAGAGATAAGATCTACGATTTTCAATC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACGATTTT-AATC
1063582 TGTTTAATTG
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
128 34 0.21
129 126 0.79
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACGATTTTAATCAGCTCCACTGCA
ACTTCAGAGAGATAGGATTGACTTCCTCTATCTACTCCACTACAACTTCAGGGAGATAAGACTG
Found at i:1063805 original size:50 final size:50
Alignment explanation
Indices: 1063750--1063920 Score: 190
Period size: 50 Copynumber: 3.4 Consensus size: 50
1063740 CTGTATCGCT
1063750 GGGAAATAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCG
1 GGGAAATAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCG
* * * * * * *
1063800 GGGAAATGAGATTCACCGTCGT-AGCTTAAATATGTT-CCTTTGC---ATCG
1 GGGAAATAAGATTCGCCGTTGTGA-CTTTAATCTTTTAAC-TTGCAATATCG
1063847 TTGGGAAATAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCG
1 --GGGAAATAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCG
* *
1063899 GGGAAGTGAGATTCGCCGTTGT
1 GGGAAATAAGATTCGCCGTTGT
1063921 AGCTTCAATC
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
47 4 0.04
49 34 0.35
50 54 0.56
52 4 0.04
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (50 bp):
GGGAAATAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCG
Found at i:1063820 original size:99 final size:99
Alignment explanation
Indices: 1063602--1063989 Score: 444
Period size: 99 Copynumber: 3.9 Consensus size: 99
1063592 TGATGTTAGA
* ** * * *
1063602 GAAATTAGATTCACCACCGTAGCTTCAATCTGTT-CTACTGCATCGCCTGAGAAGTAAGATTCGC
1 GAAATGAGATTCACCGTCGTAGCTTCAATATGTTCCT-CTGCATCG-CTGGGAAATAAGATTCGC
* * *
1063666 C-TTCGTGACTTCAATCTATTTTAA-TTGCCATGTCGGG
64 CGTT-GTGACTTTAATC--TTTTAACTTGCAATATCGGG
* *
1063703 GAAGTGAGATTCACCGTCGTAGCTTCAATATGTTCCTCTGTATCGCTGGGAAATAAGATTCGCCG
1 GAAATGAGATTCACCGTCGTAGCTTCAATATGTTCCTCTGCATCGCTGGGAAATAAGATTCGCCG
1063768 TTGTGACTTTAATCTTTTAACTTGCAATATCGGG
66 TTGTGACTTTAATCTTTTAACTTGCAATATCGGG
* * *
1063802 GAAATGAGATTCACCGTCGTAGCTTAAATATGTTCCTTTGCATCGTTGGGAAATAAGATTCGCCG
1 GAAATGAGATTCACCGTCGTAGCTTCAATATGTTCCTCTGCATCGCTGGGAAATAAGATTCGCCG
1063867 TTGTGACTTTAATCTTTTAACTTGCAATATCGGG
66 TTGTGACTTTAATCTTTTAACTTGCAATATCGGG
* * * * * * * *
1063901 GAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACAAT-GCTAGGAAAGTAAGATCCGC
1 GAAATGAGATTCACCGTCGTAGCTTCAATATGTTCCTCTGC-ATCGCTGGGAAA-TAAGATTCGC
* *
1063965 TGTTGT-AGCTTCAATCTTTTTAACT
64 CGTTGTGA-CTTTAATC-TTTTAACT
1063990 GCCAGGGAAG
Statistics
Matches: 251, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
98 6 0.02
99 146 0.58
100 51 0.20
101 46 0.18
102 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (99 bp):
GAAATGAGATTCACCGTCGTAGCTTCAATATGTTCCTCTGCATCGCTGGGAAATAAGATTCGCCG
TTGTGACTTTAATCTTTTAACTTGCAATATCGGG
Found at i:1063931 original size:50 final size:49
Alignment explanation
Indices: 1063656--1063931 Score: 169
Period size: 49 Copynumber: 5.6 Consensus size: 49
1063646 GCCTGAGAAG
* *
1063656 TAAGATTCGCC-TTCGTGACTTCAATCTATTTTAA-TTGCCATGTCGGGGAAG
1 TAAGATTCGCCGTT-GTGACTTCAATC--TTTTAACTTG-CATATCGGGGAAA
* * * * * *
1063707 TGAGATTCACCGTCGT-AGCTTCAATATGTT-CCTCTG--TATCGCTGGGAAA
1 TAAGATTCGCCGTTGTGA-CTTCAATCTTTTAACT-TGCATATCG--GGGAAA
*
1063756 TAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCGGGGAAA
1 TAAGATTCGCCGTTGTGACTTCAATCTTTTAACTTGC-ATATCGGGGAAA
* * * * * * *
1063806 TGAGATTCACCGTCGT-AGCTTAAATATGTT-CCTTTGC--ATCGTTGGGAAA
1 TAAGATTCGCCGTTGTGA-CTTCAATCTTTTAAC-TTGCATATCG--GGGAAA
* *
1063855 TAAGATTCGCCGTTGTGACTTTAATCTTTTAACTTGCAATATCGGGGAAG
1 TAAGATTCGCCGTTGTGACTTCAATCTTTTAACTTGC-ATATCGGGGAAA
*
1063905 TGAGATTCGCCGTTGT-AGCTTCAATCT
1 TAAGATTCGCCGTTGTGA-CTTCAATCT
1063932 GTTCCACTAC
Statistics
Matches: 172, Mismatches: 32, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
47 8 0.05
49 68 0.40
50 68 0.40
51 18 0.10
52 10 0.06
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (49 bp):
TAAGATTCGCCGTTGTGACTTCAATCTTTTAACTTGCATATCGGGGAAA
Found at i:1064025 original size:95 final size:95
Alignment explanation
Indices: 1063918--1065358 Score: 2149
Period size: 95 Copynumber: 15.1 Consensus size: 95
1063908 GATTCGCCGT
* **
1063918 TGTAGCTTCAATCTGTTCCACTACAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1063983 TTTAACTGCCAGGGAAGCAAGACCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
** *
1064013 TGTAGCTTCAATCTGTTCCACTGCAATGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1064078 TTTAACTGTCAGGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* * * * *
1064108 TGTAGCTTCAATCCGTTCCACTGTAACACTAGGAAAATAAGATCCACTATTGTAGCTTCAATC-T
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
* *
1064172 TTTAACTGCCGGGGAAGCAAGATCCGCTGA
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* **
1064202 TGTAGCTTCAATCTATTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1064267 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* * *
1064297 TGTCGCTTCAATCCGTTCCACTGCAACACTAGAAAAGTAAGATCCGCTGTTGTAGCTTCAATC--
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
* * *
1064360 TTTAACTG-CTGAGGCAGCAAGATCCACTGC
66 TTTAACTGCCAG-GGAAGCAAGATCCGCTGC
* ** *
1064390 TGTAGCTTCAATCTGTTCCAATGCAATGCTAGGAAAGTAAGATCCGCTATTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1064455 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
** *
1064485 TGTAGCTTCAATCTGTTCCACTGCAATGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1064550 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* * *
1064580 TGTAGCTTCAATCTGTTCCACTGCATCACTAGGAAAATAAGATCCGCTATTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
**
1064645 TTTAACTGCTGGGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* * *
1064675 TGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAATAAGATCCGCTATTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1064740 TTTAACTG-CTGAGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAG-GGAAGCAAGATCCGCTGC
* * *
1064770 TGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAATAAGATCCGCTATTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1064835 TTTAACTG-CTGAGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAG-GGAAGCAAGATCCGCTGC
* * *
1064865 TGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAATAAGATCCGCTATTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1064930 TTTAACTG-CTGAGGAAGCAAGATCCGCTGC
66 TTTAACTGCCAG-GGAAGCAAGATCCGCTGC
1064960 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
*
1065025 TTTAACTGCCAGGGAAGCAAGATCTGCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* *
1065055 TGTAGCTTCAATCCGTTCCACTGCAACACTAGGAAAATAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
** *
1065120 TTTAACTGCTGGGGAAGCAAGATCCGCTGT
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
* *
1065150 TTTAGCTTCAATTTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
* ***
1065215 TTTAACTGCCGGGGAAGCAAGATTTTCTGC
66 TTTAACTGCCAGGGAAGCAAGATCCGCTGC
** *
1065245 TGTAGCTTCAATCTGTTCCACTGCAATGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
* * * *
1065310 TTTAATTGCAATGTCAGGGAAGTAAGATACGCTGT
66 TTTAA---C--TGCCAGGGAAGCAAGATCCGCTGC
1065345 TGTAGCTTCAATCT
1 TGTAGCTTCAATCT
1065359 TTTTAACTGC
Statistics
Matches: 1244, Mismatches: 90, Indels: 19
0.92 0.07 0.01
Matches are distributed among these distances:
92 2 0.00
93 80 0.06
94 84 0.07
95 1042 0.84
96 4 0.00
98 1 0.00
100 31 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (95 bp):
TGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
TTTAACTGCCAGGGAAGCAAGATCCGCTGC
Found at i:1065465 original size:50 final size:50
Alignment explanation
Indices: 1064378--1065469 Score: 368
Period size: 50 Copynumber: 22.9 Consensus size: 50
1064368 CTGAGGCAGC
* * ** * *
1064378 AAGATCCACTGCTGTAGCTTCAATCTGTTCCAA-TGCAATGCTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCT-TTTTAATTGTAATGCTAAGAAAGT
* * * * * *
1064428 AAGATCCGCTATTGTAGCTTCAATCTTTTT-A----ACTGCCAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * *
1064473 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAATGCTAAGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * * *
1064523 AAGATCCGCTGTTGTAGCTTCAATCTTTTT-A----ACTGCCAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * * * * *
1064568 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTG-CATCACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAAT-GCTAAGAAAGT
* * ** * *
1064618 AAGATCCGCTATTGTAGCTTCAATCTTTTT-A----ACTGCTGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * * *** * *
1064663 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * * *
1064713 AAGATCCGCTATTGTAGCTTCAATCTTTTT-A----ACTGCTGAGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * * *** * *
1064758 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * * *
1064808 AAGATCCGCTATTGTAGCTTCAATCTTTTT-A----ACTGCTGAGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * * *** * *
1064853 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAGCACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * * *
1064903 AAGATCCGCTATTGTAGCTTCAATCTTTTT-A----ACTGCTGAGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** * * ** *
1064948 AAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * * *
1064998 AAGATCCGCTGTTGTAGCTTCAATCTTTTT-A----ACTGCCAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * ** ** * * ** * *
1065043 AAGATCTGCTGCTGTAGCTTCAATCCGTTCCACTGCAACACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* ** * *
1065093 AAGATCCGCTGTTGTAGCTTCAATCTTTTT-A----ACTGCTGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* ** * * ** *
1065138 AAGATCCGCTGTTTTAGCTTCAAT-TTGTTCCACTGCAACACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTT-TTTAATTGTAATGCTAAGAAAGT
* *** * *
1065188 AAGATCCGCTGTTGTAGCTTCAATCTTTTT-A----ACTGCCGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
*** * * ** * *
1065233 AAGATTTTCTGCTGTAGCTTCAATCTGTTCCACTGCAATGCTAAGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * *
1065283 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATG-TCAGGGAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCT-AAGAAAGT
* * * * *
1065333 AAGATACGCTGTTGTAGCTTCAATCTTTTT-A----ACTGCTAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
* * * ** *
1065378 AAGATCTGCTGCTGTAGCTTCAATCTGTTCCACTGTAATGCTAAGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
*
1065428 AAGATCCGCTGTTGTAGTTTCAATCTTTTTAATTGTAA-GCTA
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTA
1065470 TGGTTTCTTC
Statistics
Matches: 768, Mismatches: 220, Indels: 109
0.70 0.20 0.10
Matches are distributed among these distances:
44 2 0.00
45 331 0.43
46 12 0.02
48 1 0.00
49 17 0.02
50 403 0.52
51 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (50 bp):
AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGCTAAGAAAGT
Found at i:1070758 original size:3 final size:3
Alignment explanation
Indices: 1070740--1070807 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
1070730 ATAAAGAAGC
* *
1070740 AAT AAT CAT GAAT AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1070786 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
1070808 GCAATAACGT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 58 0.97
4 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1071058 original size:40 final size:41
Alignment explanation
Indices: 1070995--1071076 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
1070985 TAAAATGGGT
*
1070995 ATATATATATATATGTAGATGTACATGAAT-TAAAATATATGA
1 ATATATATATATACGTA-ATGTACATGAATGTAAAA-ATATGA
* *
1071037 ATATATATATATACGT-TTGTACATGTATGTAAAAATATGA
1 ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
1071077 GTCAAGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 16 0.44
41 5 0.14
42 15 0.42
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (41 bp):
ATATATATATATACGTAATGTACATGAATGTAAAAATATGA
Found at i:1072403 original size:163 final size:164
Alignment explanation
Indices: 1072122--1072439 Score: 595
Period size: 163 Copynumber: 1.9 Consensus size: 164
1072112 GTGTGGTTCT
*
1072122 TTGTTTTGCAGGTGGAGCAGGTGGTGGCAGGCGTGCGGCGCGGTGGCAGGGAGTTGGTGGCTGAA
1 TTGTTTTCCAGGTGGAGCAGGTGGTGGCAGGCGTGCGGCGCGGTGGCAGGGAGTTGGTGGCTGAA
1072187 AACCCTAGGTACGGCGCACCTAGGGTTGCTGCTACTTGCTCTTTTTTCTTTTCTGAACATGGGCT
66 AACCCTAGGTACGGCGCACCTAGGGTTGCTGCTACTTGCTCTTTTTTCTTTTCTGAACATGGGCT
*
1072252 AGGGTTAGGTAGATTGG-GTTTGGGCTTGTTGGGC
131 AGGGTTAGGTAAATTGGTG-TTGGGCTTGTTGGGC
1072286 TTGTTTTCCA-GTGGAGCAGGTGGTGGCAGGCGTGCGGCGCGGTGGCAGGGAGTTGGTGGCTGAA
1 TTGTTTTCCAGGTGGAGCAGGTGGTGGCAGGCGTGCGGCGCGGTGGCAGGGAGTTGGTGGCTGAA
1072350 AACCCTAGGTACGGCGCACCTAGGGTTGCTGCTACTTGCTCTTTTTTCTTTTCTGAACATGGGCT
66 AACCCTAGGTACGGCGCACCTAGGGTTGCTGCTACTTGCTCTTTTTTCTTTTCTGAACATGGGCT
1072415 AGGGTTAGGTAAATTGGTGTTGGGC
131 AGGGTTAGGTAAATTGGTGTTGGGC
1072440 CTGCTGGTTG
Statistics
Matches: 151, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
163 141 0.93
164 10 0.07
ACGTcount: A:0.14, C:0.18, G:0.38, T:0.30
Consensus pattern (164 bp):
TTGTTTTCCAGGTGGAGCAGGTGGTGGCAGGCGTGCGGCGCGGTGGCAGGGAGTTGGTGGCTGAA
AACCCTAGGTACGGCGCACCTAGGGTTGCTGCTACTTGCTCTTTTTTCTTTTCTGAACATGGGCT
AGGGTTAGGTAAATTGGTGTTGGGCTTGTTGGGC
Found at i:1078589 original size:48 final size:48
Alignment explanation
Indices: 1078514--1078609 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
1078504 TAAGGCAATT
** *
1078514 CTGTTGAATCCTTTATCGTTGCGAGTTAAGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
*
1078562 CTGTTGAATCCTTTATCACTGCAAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
1078610 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
Found at i:1080026 original size:13 final size:13
Alignment explanation
Indices: 1080008--1080038 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1079998 TAACTAAAAT
1080008 TAAATTTAAATAA
1 TAAATTTAAATAA
*
1080021 TAAATTTAAATGA
1 TAAATTTAAATAA
1080034 TAAAT
1 TAAAT
1080039 AATTAAAATA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
TAAATTTAAATAA
Found at i:1080118 original size:16 final size:16
Alignment explanation
Indices: 1080097--1080152 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1080087 TAGAGTAGAA
1080097 AGAAAATTAGAAAGAT
1 AGAAAATTAGAAAGAT
*
1080113 AGAAAATT-GAAGCGAT
1 AGAAAATTAGAA-AGAT
* *
1080129 GGAAAAAATAGAAAGAT
1 AG-AAAATTAGAAAGAT
*
1080146 GGAAAAT
1 AGAAAAT
1080153 ATAATAGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 3 0.09
16 16 0.50
17 10 0.31
18 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (16 bp):
AGAAAATTAGAAAGAT
Found at i:1080538 original size:17 final size:16
Alignment explanation
Indices: 1080507--1080542 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1080497 GTACTTAATT
1080507 AGAAAAAAAAAATAAG
1 AGAAAAAAAAAATAAG
*
1080523 AGAAAAGAAAATATAAG
1 AGAAAA-AAAAAATAAG
1080540 AGA
1 AGA
1080543 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (16 bp):
AGAAAAAAAAAATAAG
Found at i:1083108 original size:36 final size:38
Alignment explanation
Indices: 1083029--1083118 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 38
1083019 ACCACTCCGA
* *
1083029 CCACCCTACACACCACAATTGAGCTATGGTAGGCCCAT
1 CCACCCTACACACCACAATAGAGATATGGTAGGCCCAT
* * *
1083067 TCACCCTGCACACCACAA-AGGGATATGGTA-GCCCAT
1 CCACCCTACACACCACAATAGAGATATGGTAGGCCCAT
1083103 CCACCCTACACACCAC
1 CCACCCTACACACCAC
1083119 GGTAGTGGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 20 0.44
37 9 0.20
38 16 0.36
ACGTcount: A:0.30, C:0.40, G:0.14, T:0.16
Consensus pattern (38 bp):
CCACCCTACACACCACAATAGAGATATGGTAGGCCCAT
Found at i:1091392 original size:19 final size:21
Alignment explanation
Indices: 1091317--1091394 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
1091307 TTTTGTTGAG
*
1091317 CTCTTACGAGCTTCTGTTCAA
1 CTCTTACGAGCTTCTATTCAA
* *
1091338 CTCTTATGAGCTTCTTTTCAA
1 CTCTTACGAGCTTCTATTCAA
* *
1091359 CTCTTAAGAGTTTCTATTC-A
1 CTCTTACGAGCTTCTATTCAA
*
1091379 -GCTTACGAGCTTCTAT
1 CTCTTACGAGCTTCTAT
1091395 GAACGATGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.27
20 1 0.02
21 35 0.71
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (21 bp):
CTCTTACGAGCTTCTATTCAA
Found at i:1100153 original size:13 final size:13
Alignment explanation
Indices: 1100135--1100164 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1100125 GTAATACATT
1100135 ATATGAAAAATTA
1 ATATGAAAAATTA
1100148 ATATGAAAAATTA
1 ATATGAAAAATTA
1100161 ATAT
1 ATAT
1100165 AAACATGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (13 bp):
ATATGAAAAATTA
Found at i:1104279 original size:24 final size:24
Alignment explanation
Indices: 1104247--1104292 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1104237 AGAAAATGTT
*
1104247 TTCTTTTTTCCTTTTTCGATTGGG
1 TTCTTTTTTCCTTTTCCGATTGGG
*
1104271 TTCTTTTTTTCTTTTCCGATTG
1 TTCTTTTTTCCTTTTCCGATTG
1104293 CTCTTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.17, G:0.13, T:0.65
Consensus pattern (24 bp):
TTCTTTTTTCCTTTTCCGATTGGG
Found at i:1104299 original size:25 final size:24
Alignment explanation
Indices: 1104247--1104310 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1104237 AGAAAATGTT
* * *
1104247 TTCTTTTTTCCTTTTTCGATTGGG
1 TTCTTTTTTTCTTTTCCGATTGGC
*
1104271 TTCTTTTTTTCTTTTCCGATTGCTC
1 TTCTTTTTTTCTTTTCCGATTG-GC
*
1104296 TTCTTTCTTT-TTTTC
1 TTCTTTTTTTCTTTTC
1104311 TGTTTTGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 25 0.74
25 9 0.26
ACGTcount: A:0.03, C:0.20, G:0.09, T:0.67
Consensus pattern (24 bp):
TTCTTTTTTTCTTTTCCGATTGGC
Found at i:1105059 original size:22 final size:22
Alignment explanation
Indices: 1105022--1105063 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1105012 TCTTTTATTT
1105022 TTTTAATCTTATTATATAGATCC
1 TTTTAATCTTATTATA-AGATCC
*
1105045 TTTTATTC-TATTATAAGAT
1 TTTTAATCTTATTATAAGAT
1105064 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTAATCTTATTATAAGATCC
Found at i:1109645 original size:26 final size:26
Alignment explanation
Indices: 1109616--1109684 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
1109606 AAGGGGGAAG
*
1109616 AAAAATCAAAATCAAAAGCAAAAG-CA
1 AAAAATAAAAATCAAAAGC-AAAGTCA
** *
1109642 AAAAGGAAAAATCAAAATCAAAGTCA
1 AAAAATAAAAATCAAAAGCAAAGTCA
* *
1109668 AAAAATGAAAATGAAAA
1 AAAAATAAAAATCAAAA
1109685 AGAGGGGGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.70, C:0.10, G:0.10, T:0.10
Consensus pattern (26 bp):
AAAAATAAAAATCAAAAGCAAAGTCA
Found at i:1112128 original size:128 final size:128
Alignment explanation
Indices: 1111990--1112494 Score: 839
Period size: 128 Copynumber: 3.9 Consensus size: 128
1111980 CCCTTGGTTA
1111990 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
1 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
1112055 GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAG
66 GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAG
*
1112118 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACG
1 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
* *
1112183 GCGAATCTTATCTTCAAGAGTAGGGAAGTAGATTTAAGCCACAAGTCCTATCTCCTTGGTCAG
66 GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAG
* * * *
1112246 AAGTGGAATAGGTTGGAAATTACAGATTTTGTCTCCCTAAGCAGTAGCGGAGCATATCGAATACG
1 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
* * * *
1112311 GTGAATCTTATCTTCAAGAGTAAGGTAGCAGATTTAAGCCACAAGTCTTATCTCCCTGGTCAG
66 GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAG
* * * *
1112374 CAGTGGAATAGGTTGGAAATCACAGATCTTATCTCCCTAAGCAGTAGCGGAGGAGATCGGAGACG
1 CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
* * * *
1112439 GTGAATCTTATCTTCAAGAGTAGGGAAACATATTTAAGCCACAAATCCTATCTCCC
66 GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCC
1112495 CGACGTTGCG
Statistics
Matches: 349, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 349 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (128 bp):
CAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACG
GCGAATCTTATCTTCAAGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAG
Found at i:1113228 original size:24 final size:24
Alignment explanation
Indices: 1113198--1113243 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1113188 AGAAAAGGTT
*
1113198 TTCTTTTTTCCTTTTTCGATTGGG
1 TTCTTTTTTCCTTTTCCGATTGGG
*
1113222 TTCTTTTTTTCTTTTCCGATTG
1 TTCTTTTTTCCTTTTCCGATTG
1113244 CTCTTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.17, G:0.13, T:0.65
Consensus pattern (24 bp):
TTCTTTTTTCCTTTTCCGATTGGG
Found at i:1113250 original size:25 final size:24
Alignment explanation
Indices: 1113198--1113261 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1113188 AGAAAAGGTT
* * *
1113198 TTCTTTTTTCCTTTTTCGATTGGG
1 TTCTTTTTTTCTTTTCCGATTGGC
*
1113222 TTCTTTTTTTCTTTTCCGATTGCTC
1 TTCTTTTTTTCTTTTCCGATTG-GC
*
1113247 TTCTTTCTTT-TTTTC
1 TTCTTTTTTTCTTTTC
1113262 TGTTTTGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 25 0.74
25 9 0.26
ACGTcount: A:0.03, C:0.20, G:0.09, T:0.67
Consensus pattern (24 bp):
TTCTTTTTTTCTTTTCCGATTGGC
Found at i:1114025 original size:23 final size:23
Alignment explanation
Indices: 1113999--1114052 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1113989 ATATAGATCC
1113999 TTTTATTTTATTATAAG-A-TATTA
1 TTTTATTTT-TT-TAAGTATTATTA
* *
1114022 TTTTATGTTTTTAGGTATTATTA
1 TTTTATTTTTTTAAGTATTATTA
1114045 TTTTATTT
1 TTTTATTT
1114053 CTATATTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 3 0.12
23 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTATTTTTTTAAGTATTATTA
Found at i:1116271 original size:15 final size:15
Alignment explanation
Indices: 1116243--1116292 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1116233 TTCCACTTTC
1116243 TTATCATTTCTTTTA
1 TTATCATTTCTTTTA
1116258 TTAT-ATTTCATTTTA
1 TTATCATTTC-TTTTA
1116273 TT-TC--TTCTTCTTA
1 TTATCATTTCTT-TTA
1116286 TTATCAT
1 TTATCAT
1116293 ATACATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
12 2 0.07
13 8 0.28
14 8 0.28
15 11 0.38
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATCATTTCTTTTA
Found at i:1119687 original size:9 final size:9
Alignment explanation
Indices: 1119673--1119703 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1119663 GTTAAACGAA
1119673 TCGAGTTAT
1 TCGAGTTAT
*
1119682 TCGAGTTAA
1 TCGAGTTAT
1119691 TCGAGTTAT
1 TCGAGTTAT
1119700 TCGA
1 TCGA
1119704 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1120856 original size:24 final size:23
Alignment explanation
Indices: 1120812--1120863 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1120802 TTTATTATAT
* *
1120812 TAAATCAAAATTTTAAATAAAAAG
1 TAAAACAAAATTTAAAAT-AAAAG
1120836 TAAAACAAAA-TTAAAAGTAAAAG
1 TAAAACAAAATTTAAAA-TAAAAG
1120859 TAAAA
1 TAAAA
1120864 GGGTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (23 bp):
TAAAACAAAATTTAAAATAAAAG
Found at i:1121421 original size:15 final size:15
Alignment explanation
Indices: 1121397--1121435 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1121387 ACCAAAATTT
**
1121397 TATTTATTATTTATA
1 TATTTATTATAAATA
*
1121412 TATTTTTTATAAATA
1 TATTTATTATAAATA
1121427 TATTTATTA
1 TATTTATTA
1121436 AATAGTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTATTATAAATA
Found at i:1135732 original size:72 final size:72
Alignment explanation
Indices: 1135611--1135785 Score: 266
Period size: 72 Copynumber: 2.5 Consensus size: 72
1135601 AAAATCATAT
* * * *
1135611 ATAAACAACTATTGATAAAATTA-ATTTAGTATAAATAAGTATAACATAAATTCAATATCCAAAG
1 ATAAACAACTATTGATAAAACTAGATTTAGCATAAATAAGTAGAACATAAATTCAATATCCAAAA
1135675 ACCAAAC
66 ACCAAAC
*
1135682 ATAAACAACTATTAATAAAACTAGATTATA-CATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATT-TAGCATAAATAAGTAGAACATAAATTCAATATCCAAA
1135746 AACCAAAC
65 AACCAAAC
*
1135754 ATAAATAACTATTGATAAAACTAG-TTTAGCAT
1 ATAAACAACTATTGATAAAACTAGATTTAGCAT
1135786 TGTTGTTTAG
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
70 2 0.02
71 26 0.28
72 64 0.68
73 2 0.02
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTTAGCATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:1136046 original size:18 final size:18
Alignment explanation
Indices: 1136025--1136072 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1136015 TCCATCAATT
* *
1136025 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATA
1136043 TGAACATCATTTAAAATA
1 TGAACATCATTTAAAATA
1136061 TGAACATCATTT
1 TGAACATCATTT
1136073 CTCAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATA
Found at i:1139532 original size:11 final size:11
Alignment explanation
Indices: 1139516--1139553 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1139506 AATTTTGTAT
1139516 TAAAATTTCTA
1 TAAAATTTCTA
*
1139527 TAAAATTTCTG
1 TAAAATTTCTA
1139538 TAAAATTTCTA
1 TAAAATTTCTA
1139549 TAAAA
1 TAAAA
1139554 ATCAAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (11 bp):
TAAAATTTCTA
Found at i:1141456 original size:23 final size:23
Alignment explanation
Indices: 1141425--1141546 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
1141415 TGTGTTATTG
1141425 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
1141448 TTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1141471 ATCAGTGGTAGCTTCAGCAACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
1141494 TTTAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1141517 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1141540 ATCAGTG
1 ATCAGTG
1141547 TGGCACTTAT
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1143444 original size:19 final size:20
Alignment explanation
Indices: 1143416--1143457 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1143406 ATTTGATCCT
* *
1143416 AATTTTAAAAAT-ACATAAA
1 AATTTCAAAAATAAAATAAA
1143435 AATTTCAAAAATAAAATAAA
1 AATTTCAAAAATAAAATAAA
1143455 AAT
1 AAT
1143458 ACATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTTCAAAAATAAAATAAA
Found at i:1147567 original size:7 final size:7
Alignment explanation
Indices: 1147555--1147579 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1147545 AGTCGATTGA
1147555 TATTTAG
1 TATTTAG
1147562 TATTTAG
1 TATTTAG
1147569 TATTTAG
1 TATTTAG
1147576 TATT
1 TATT
1147580 ATTTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:1148256 original size:18 final size:18
Alignment explanation
Indices: 1148229--1148266 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1148219 TAGGTGCATT
*
1148229 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
1148247 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
1148265 TC
1 TC
1148267 ATTTTCCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1148725 original size:25 final size:25
Alignment explanation
Indices: 1148697--1148814 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
1148687 TATTTTAATA
1148697 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
1148722 TTATTTGATGTAATAAAATAGAACT
1 TTATTTGATGTAATAAAATAGAAGT
* * ** *
1148747 TT-TTT--T-TAGTTATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
1148766 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
1148792 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
1148815 ATTTTTGAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 9 0.12
22 1 0.01
23 1 0.01
24 9 0.12
25 50 0.67
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:1148800 original size:70 final size:70
Alignment explanation
Indices: 1148687--1148820 Score: 250
Period size: 70 Copynumber: 1.9 Consensus size: 70
1148677 ATATTTTGAA
*
1148687 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAACTTTTTT
1 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
1148752 TTAGT
66 TTAGT
*
1148757 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTT
1 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTT
1148821 GAATAAACCC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.48
Consensus pattern (70 bp):
TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
TTAGT
Found at i:1148863 original size:23 final size:22
Alignment explanation
Indices: 1148833--1149006 Score: 167
Period size: 23 Copynumber: 7.7 Consensus size: 22
1148823 ATAAACCCTA
1148833 AATTAAAAACCCTAACCCT-TTT
1 AATTAAAAACCCTAA-CCTATTT
* *
1148855 AACTTAAAAACCCTAACTTAATT
1 AA-TTAAAAACCCTAACCTATTT
*
1148878 AACTTAAAAA-CCTAACCTAATTA
1 AA-TTAAAAACCCTAACCT-ATTT
*
1148901 AATTAAAAACTCTAACCTAATTT
1 AATTAAAAACCCTAACCT-ATTT
* * *
1148924 AATTAAAAACCTTAAACC--CTG
1 AATTAAAAACCCT-AACCTATTT
1148945 AACTTAAAAACCCTAACCTAATTT
1 AA-TTAAAAACCCTAACCT-ATTT
*
1148969 AATTAAAAACTCTAACCTAATTT
1 AATTAAAAACCCTAACCT-ATTT
1148992 AATTAAAAACCCTAA
1 AATTAAAAACCCTAA
1149007 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
21 7 0.06
22 28 0.22
23 85 0.67
24 7 0.06
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.29
Consensus pattern (22 bp):
AATTAAAAACCCTAACCTATTT
Found at i:1148907 original size:45 final size:44
Alignment explanation
Indices: 1148833--1149006 Score: 190
Period size: 45 Copynumber: 3.8 Consensus size: 44
1148823 ATAAACCCTA
* * *
1148833 AATTAAAAACCCTAACCCTTTTAACTTAAAAACCCTAACTTAA-TT
1 AATTAAAAA-CCTAA-CCTATTAAATTAAAAACCCTAACCTAATTT
*
1148878 AACTTAAAAACCTAACCTAATTAAATTAAAAACTCTAACCTAATTT
1 AA-TTAAAAACCTAACCT-ATTAAATTAAAAACCCTAACCTAATTT
* * *
1148924 AATTAAAAACCTTAAACC-CTGAACTTAAAAACCCTAACCTAATTT
1 AATTAAAAACC-T-AACCTATTAAATTAAAAACCCTAACCTAATTT
*
1148969 AATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAA
1 AATTAAAAAC-CTAACCT-ATTAAATTAAAAACCCTAA
1149007 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
44 7 0.06
45 70 0.64
46 28 0.26
47 4 0.04
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.29
Consensus pattern (44 bp):
AATTAAAAACCTAACCTATTAAATTAAAAACCCTAACCTAATTT
Found at i:1153133 original size:123 final size:123
Alignment explanation
Indices: 1152910--1153280 Score: 589
Period size: 123 Copynumber: 3.0 Consensus size: 123
1152900 CAAACATGCT
*
1152910 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCATAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTGCT
1152975 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCG
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCG
* * *
1153034 ACTGTAGTAAAAACGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTACTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
* *
1153099 GAAGCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAATTATTTCTTCCATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCG
* * *
1153157 ACTGTAGCAAAAGCGCGTCCACAAGGGCGCGGTTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
* * ** *
1153222 GAAGCGATTTTATATTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCCATGACC
1153281 TAAAACCCCT
Statistics
Matches: 227, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
123 174 0.77
124 34 0.15
125 19 0.08
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (123 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCG
Found at i:1156115 original size:43 final size:41
Alignment explanation
Indices: 1156060--1156201 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 41
1156050 AGATCAGGGG
*
1156060 TCTTTAGCGGCGCCTCGACAGCAAACGCCACTAAAGAACCTAA
1 TCTTTAGCGGCGCCTC-ACA-CAAACGCCGCTAAAGAACCTAA
* * *
1156103 TCTTTAGCGGCGCTTTCATTACAAACGCCGCTAAAG-ACCATGA
1 TCTTTAGCGGCGC-CTCA-CACAAACGCCGCTAAAGAACC-TAA
* * *
1156146 TCTTTAGTGGCGCCTTTTC-CACAAACGCCGCAAAAGACCCTAA
1 TCTTTAGCGGCGCC---TCACACAAACGCCGCTAAAGAACCTAA
1156189 TCTTTAGCGGCGC
1 TCTTTAGCGGCGC
1156202 TTTGACCAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
42 3 0.04
43 71 0.88
44 5 0.06
45 2 0.02
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (41 bp):
TCTTTAGCGGCGCCTCACACAAACGCCGCTAAAGAACCTAA
Done.