Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 10 of 39
Found at i:1284456 original size:54 final size:53
Alignment explanation
Indices: 1283933--1284477 Score: 432
Period size: 49 Copynumber: 10.8 Consensus size: 53
1283923 ACATTGGCAC
* * *
1283933 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATGTTGGCA-CCTTTTCCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
** * * * * *
1283985 CTTTAAATCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CC--TT-CAC
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* *
1284034 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTT--AT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* * * ** *
1284083 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGGACATTGGCA-CC-TTT--AT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* * * * * * *
1284132 CTTTAAGTCCAATGTAGCTGGCCTTGACTTAGCACATTGGCA-CC--TT-CAC
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* *
1284181 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTT--AT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* * * * *
1284230 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CC-TTT--AT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* * * * *
1284279 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCATATTGGCA-CC--TT-CAC
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
* *
1284328 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
** * * *
1284380 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCC-TTTTC-CAT
* * *
1284435 CTTT-AGCCCAATATCGTTGGCCATGAATCAACATATTGGCATC
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATC
1284478 TTTATCACTT
Statistics
Matches: 429, Mismatches: 54, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
48 4 0.01
49 294 0.69
50 6 0.01
51 2 0.00
52 78 0.18
53 2 0.00
54 36 0.08
55 7 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (53 bp):
CTTTAAGCCCAATATAGCTGGCCTTGAATCAACATATTGGCATCCTTTTCCAT
Found at i:1284538 original size:67 final size:67
Alignment explanation
Indices: 1284431--1284556 Score: 173
Period size: 67 Copynumber: 1.9 Consensus size: 67
1284421 ATCCTTTTTC
* * *
1284431 TCATCTTTAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCAT
1 TCATCTTTAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCAT
1284495 CA
66 CA
* * * *
1284497 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTT-AGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
1284557 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 8 0.16
67 39 0.76
68 4 0.08
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (67 bp):
TCATCTTTAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCAT
CA
Found at i:1285344 original size:33 final size:33
Alignment explanation
Indices: 1285307--1285373 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1285297 TTCAACGATT
1285307 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1285340 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1285373 T
1 T
1285374 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1285345 original size:13 final size:13
Alignment explanation
Indices: 1285327--1285351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1285317 CATAAAATGT
1285327 TGTATCGATACAA
1 TGTATCGATACAA
1285340 TGTATCGATACA
1 TGTATCGATACA
1285352 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1285503 original size:52 final size:52
Alignment explanation
Indices: 1285447--1285566 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
1285437 CACTGATCTT
*
1285447 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1285499 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1285551 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1285567 AGTAACTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1287581 original size:13 final size:13
Alignment explanation
Indices: 1287563--1287587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287553 ATTTTGCTTA
1287563 GTATCGATACATT
1 GTATCGATACATT
1287576 GTATCGATACAT
1 GTATCGATACAT
1287588 AAACTAACAG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1287748 original size:22 final size:22
Alignment explanation
Indices: 1287680--1287776 Score: 108
Period size: 22 Copynumber: 4.5 Consensus size: 22
1287670 CATTGTTCAC
* *
1287680 CACTGTTTATGTATCGATAAAAT
1 CACTGTTCATGTATCGAT-ACAT
* * * *
1287703 CACGGTTCAT-CA-CTATTCAT
1 CACTGTTCATGTATCGATACAT
*
1287723 CACTGTTCATGTATCGATATAT
1 CACTGTTCATGTATCGATACAT
1287745 CACTGTTCATGTATCGATACAT
1 CACTGTTCATGTATCGATACAT
1287767 CACTGTTCAT
1 CACTGTTCAT
1287777 CATTATACAT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
20 11 0.18
21 4 0.07
22 37 0.62
23 8 0.13
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (22 bp):
CACTGTTCATGTATCGATACAT
Found at i:1287861 original size:22 final size:22
Alignment explanation
Indices: 1287833--1287897 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
1287823 ATTCATCACA
1287833 GTATCGATACATCACTATTCAT
1 GTATCGATACATCACTATTCAT
1287855 GTATCGATACATCACTATTCAT
1 GTATCGATACATCACTATTCAT
*
1287877 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTATTCA
1287898 CACTATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (22 bp):
GTATCGATACATCACTATTCAT
Found at i:1294613 original size:100 final size:100
Alignment explanation
Indices: 1294440--1294660 Score: 261
Period size: 100 Copynumber: 2.2 Consensus size: 100
1294430 AAGTTTGACC
* * **
1294440 TTGCTAGGCTTACCTTTAACCCACTAAGTCAAACTTAAAATCTAAAACACAAACCTTGTTAAGCT
1 TTGCTAGGCTTAACTTTAACCCACTAAGTCAAACCTAAAATCTAAAACACAAACCTTACTAAGCT
*
1294505 TACTTTTAAGC-TGAAAAGCTAAGAACATTAC-AACT
66 TACCTTTAA-CTTGAAAAGCTAAGAACATT-CTAACT
* * * *
1294540 TTGCTAGGCTTAACTTTAA-CTAGCTAAGTCAGACCTAAAATCTAAAACACTAACCTTACTAGGC
1 TTGCTAGGCTTAACTTTAACCCA-CTAAGTCAAACCTAAAATCTAAAACACAAACCTTACTAAGC
* ** *
1294604 TTACCTTTAACTTGTACGGCTAAGAGCATTCTAACT
65 TTACCTTTAACTTGAAAAGCTAAGAACATTCTAACT
1294640 TTGCTAGGCTT-ACTTTTAACC
1 TTGCTAGGCTTAAC-TTTAACC
1294661 AGGCAAATTG
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
99 6 0.06
100 96 0.93
101 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (100 bp):
TTGCTAGGCTTAACTTTAACCCACTAAGTCAAACCTAAAATCTAAAACACAAACCTTACTAAGCT
TACCTTTAACTTGAAAAGCTAAGAACATTCTAACT
Found at i:1294905 original size:56 final size:56
Alignment explanation
Indices: 1294740--1295006 Score: 171
Period size: 56 Copynumber: 4.7 Consensus size: 56
1294730 TTTTCTTTTT
* * ** *
1294740 GGTGCCAATTTCAACTAGAGCTATCCTTACCAACTATTCTAAGGCTTTCTCATTTG
1 GGTGCCAATTTCAACTAGAGCTATCCTTATCAACTACTCTTGGGTTTTCTCATTTG
* * * * * ** *
1294796 GGTACCTATTTCAACTAGAGCTAT-CTT-TGCCATTAACCCTTGTACTATT-TCATTTG
1 GGTGCCAATTTCAACTAGAGCTATCCTTAT-CAACT-ACTCTTG-GGTTTTCTCATTTG
* * *
1294852 GGTGCCAATTTTAACTAGAGCTATCCTTATCAACTACTATTGGGTTTTCTCATTTT
1 GGTGCCAATTTCAACTAGAGCTATCCTTATCAACTACTCTTGGGTTTTCTCATTTG
* * * * * * * * *
1294908 GTTGCCAATTTTAATTAGGGCTATCAGCTTCTTTATGAGCTACTCTTAGGCTTTCTCATTTA
1 GGTGCCAATTTCAACTAGAGCTAT---C--C-TTATCAACTACTCTTGGGTTTTCTCATTTG
* * * *
1294970 GGTGCTAATTTCAACTAAAGCTATCTTTACCAACTAC
1 GGTGCCAATTTCAACTAGAGCTATCCTTATCAACTAC
1295007 CCATGGCCTT
Statistics
Matches: 156, Mismatches: 43, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
55 9 0.06
56 93 0.60
57 8 0.05
58 1 0.01
59 2 0.01
61 1 0.01
62 42 0.27
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (56 bp):
GGTGCCAATTTCAACTAGAGCTATCCTTATCAACTACTCTTGGGTTTTCTCATTTG
Found at i:1300945 original size:26 final size:27
Alignment explanation
Indices: 1300899--1300949 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1300889 AACCAATCTT
1300899 TTTTATTTTCTTTTCCTTACTTTTTAA
1 TTTTATTTTCTTTTCCTTACTTTTTAA
*
1300926 TTTT-TTTTCATTTTTC-TACTTTTT
1 TTTTATTTTC-TTTTCCTTACTTTTT
1300950 TTACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTATTTTCTTTTCCTTACTTTTTAA
Found at i:1300959 original size:9 final size:9
Alignment explanation
Indices: 1300919--1300961 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1300909 TTTTCCTTAC
*
1300919 TTTTTAATT
1 TTTTTACTT
*
1300928 TTTTTTCATT
1 TTTTTAC-TT
*
1300938 TTTCTACTT
1 TTTTTACTT
1300947 TTTTTACTT
1 TTTTTACTT
1300956 TTTTTA
1 TTTTTA
1300962 AAAATCGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTACTT
Found at i:1303057 original size:76 final size:75
Alignment explanation
Indices: 1302838--1303119 Score: 226
Period size: 76 Copynumber: 3.7 Consensus size: 75
1302828 TTGAATATAG
* * * * * * * * *
1302838 TATTTCCTAAATACCCCTAGTGGATATGTATCGACACAAAGGTTCCCACATGGCCCTAGACTTGG
1 TATTACCTAAATACCCTTAATGGACATGTTTTGACTCAAAGGTTCCCACAT-GACCTAGACTTAG
*
1302903 TTTTAAGGTTC
65 TTTTAAGGTAC
* * * * * ** * *
1302914 AATTACCTAAATACCTTTAATGGACATGTTTTGACTCAAAAGTCCCCATAAAAACCTAAACTCAG
1 TATTACCTAAATACCCTTAATGGACATGTTTTGACTCAAAGGTTCCCA-CATGACCTAGACTTAG
1302979 TTTTAAGGTAC
65 TTTTAAGGTAC
* ** * *
1302990 TATTACCTAAATACCCTTAATGGATATGTTTTGACTTGAAGGTTCCCACATGACTGTAGATTTAG
1 TATTACCTAAATACCCTTAATGGACATGTTTTGACTCAAAGGTTCCCACATGAC-CTAGACTTAG
*
1303055 TTTTAAAGTAGC
65 TTTTAAGGTA-C
* * ** **
1303067 -ATTATCTAAATAACCC-TAATAGACATGTTTCAACTCAAAGGTTCTGACATGAC
1 TATTACCTAAAT-ACCCTTAATGGACATGTTTTGACTCAAAGGTTCCCACATGAC
1303120 TTTAGACTCA
Statistics
Matches: 159, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
75 3 0.02
76 150 0.94
77 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (75 bp):
TATTACCTAAATACCCTTAATGGACATGTTTTGACTCAAAGGTTCCCACATGACCTAGACTTAGT
TTTAAGGTAC
Found at i:1304302 original size:26 final size:26
Alignment explanation
Indices: 1304266--1304316 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1304256 AATTGTCCAG
1304266 CCCAAAACTAAGATGTTCCTATTTAA
1 CCCAAAACTAAGATGTTCCTATTTAA
1304292 CCCAAAACTAAGATGTTCCTATTTA
1 CCCAAAACTAAGATGTTCCTATTTA
1304317 CATACTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (26 bp):
CCCAAAACTAAGATGTTCCTATTTAA
Found at i:1305808 original size:13 final size:13
Alignment explanation
Indices: 1305790--1305814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1305780 CATTATGCTT
1305790 TGTATCGATACAA
1 TGTATCGATACAA
1305803 TGTATCGATACA
1 TGTATCGATACA
1305815 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1305899 original size:13 final size:13
Alignment explanation
Indices: 1305881--1305909 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1305871 AATACATGGC
1305881 ACATTGTATCGAT
1 ACATTGTATCGAT
1305894 ACATTGTATCGAT
1 ACATTGTATCGAT
1305907 ACA
1 ACA
1305910 CGTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1305909 original size:33 final size:32
Alignment explanation
Indices: 1305864--1305930 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
1305854 CTACCACTGT
1305864 TTGTATCAATACA-TGGCACATTGTATCGATACA
1 TTGTATCAATACACTGG-A-ATTGTATCGATACA
* *
1305897 TTGTATCGATACACGTTGAATTGTATCGATACA
1 TTGTATCAATACAC-TGGAATTGTATCGATACA
1305930 T
1 T
1305931 GATGAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 27 0.90
34 1 0.03
35 2 0.07
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (32 bp):
TTGTATCAATACACTGGAATTGTATCGATACA
Found at i:1305950 original size:20 final size:20
Alignment explanation
Indices: 1305896--1305950 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1305886 GTATCGATAC
* *
1305896 ATTGTATCGATACACGTTGA
1 ATTGTATCGATACATGATGA
1305916 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
1305936 ATTGTATCGATACAT
1 ATTGTATCGATACAT
1305951 TGCTTCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:1307548 original size:3 final size:3
Alignment explanation
Indices: 1307533--1307566 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1307523 AACCATCAAA
*
1307533 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1307567 GGGACTCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1314331 original size:13 final size:13
Alignment explanation
Indices: 1314313--1314337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1314303 CATTATGCTT
1314313 TGTATCGATACAA
1 TGTATCGATACAA
1314326 TGTATCGATACA
1 TGTATCGATACA
1314338 TGTTCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1314352 original size:19 final size:20
Alignment explanation
Indices: 1314328--1314378 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1314318 CGATACAATG
**
1314328 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
1314347 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
1314367 TATCGATACATG
1 TATCGATACATG
1314379 AAAGTGGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:1314372 original size:20 final size:20
Alignment explanation
Indices: 1314322--1314378 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
1314312 TTGTATCGAT
*
1314322 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
1314341 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
1314360 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
1314379 AAAGTGGTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:1315560 original size:29 final size:28
Alignment explanation
Indices: 1315527--1315617 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
1315517 ATAAAAAATG
1315527 CTAAATGGTCCTTAAATTATGAAAATAA
1 CTAAATGGTCCTTAAATTATGAAAATAA
** * * *
1315555 CTTAAAT-ACCCTAAAATATATAAAAATTA
1 C-TAAATGGTCCTTAAAT-TATGAAAATAA
*
1315584 CTAAATGGTACC-TAGATTATGAAAATAA
1 CTAAATGGT-CCTTAAATTATGAAAATAA
1315612 CCTAAA
1 -CTAAA
1315618 AGACCCTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
28 22 0.47
29 23 0.49
30 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (28 bp):
CTAAATGGTCCTTAAATTATGAAAATAA
Found at i:1315578 original size:57 final size:58
Alignment explanation
Indices: 1315506--1315629 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 58
1315496 ACCTAAGTCG
* * * *
1315506 CCCTAAAATGCATAAAAAATGCTAAATGGT-CCTTAAATTATGAAAATAA-CTTAAATA
1 CCCTAAAATACATAAAAAATACTAAATGGTACC-TAAATTATGAAAATAACCTAAAAGA
* * *
1315563 CCCTAAAATATATAAAAATTACTAAATGGTACCTAGATTATGAAAATAACCTAAAAGA
1 CCCTAAAATACATAAAAAATACTAAATGGTACCTAAATTATGAAAATAACCTAAAAGA
1315621 CCCTAAAAT
1 CCCTAAAAT
1315630 GCATGAAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 41 0.71
58 17 0.29
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (58 bp):
CCCTAAAATACATAAAAAATACTAAATGGTACCTAAATTATGAAAATAACCTAAAAGA
Found at i:1316213 original size:13 final size:13
Alignment explanation
Indices: 1316195--1316219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1316185 AGATTGCACA
1316195 GTATCGATACATT
1 GTATCGATACATT
1316208 GTATCGATACAT
1 GTATCGATACAT
1316220 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1316338 original size:13 final size:13
Alignment explanation
Indices: 1316320--1316345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1316310 ACACACATTA
1316320 TGTATCGATACAT
1 TGTATCGATACAT
1316333 TGTATCGATACAT
1 TGTATCGATACAT
1316346 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1316358 original size:20 final size:20
Alignment explanation
Indices: 1316333--1316398 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1316323 ATCGATACAT
1316333 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
*
1316353 TGTATCCATACAT-------
1 TGTATCGATACATCCCAAAA
1316366 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
1316386 TGTATCGATACAT
1 TGTATCGATACAT
1316399 TGGCTTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 12 0.32
20 25 0.68
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATCCCAAAA
Found at i:1316364 original size:33 final size:33
Alignment explanation
Indices: 1316300--1316400 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
1316290 CCTTAACTGT
* **
1316300 TTGTATCGATACA-CACATTATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
*
1316332 TTGTATCGATACATCCCAAAATGTATCCATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
1316365 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
1316398 TTG
1 TTG
1316401 GCTTGTAACC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 13 0.21
33 50 0.79
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATCCCAAAATGTATCGATACA
Found at i:1317584 original size:16 final size:16
Alignment explanation
Indices: 1317563--1317600 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1317553 AAAACTCTCT
*
1317563 TTTTTTTTCCTTTTTC
1 TTTTTTCTCCTTTTTC
*
1317579 TTTTTTCTCTTTTTTC
1 TTTTTTCTCCTTTTTC
1317595 TTTTTT
1 TTTTTT
1317601 GGTTATCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTCCTTTTTC
Found at i:1319824 original size:4 final size:4
Alignment explanation
Indices: 1319815--1319841 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1319805 AAGAAGAAGG
1319815 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1319842 AGTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1321150 original size:70 final size:69
Alignment explanation
Indices: 1321063--1321216 Score: 186
Period size: 70 Copynumber: 2.2 Consensus size: 69
1321053 CTCGGAGGAA
* * * *
1321063 TGGGGTTGGAGTGTTCCCAATGATGACAATTT-AGATGAACATAAGATTTAAATCTTGATGA-GT
1 TGGGGTTGGAGTATTCCCAATAATGACAATTTGAGA--AAAATAACATTTAAATCTTGA-GACGT
1321126 TTAAAAG
63 TTAAAAG
* *
1321133 TGGGGTTGGAGTATTCCCGATAATGATAATTTGAGCAAAAATAACATTTAAATCTTGAGACGTTT
1 TGGGGTTGGAGTATTCCCAATAATGACAATTTGAG-AAAAATAACATTTAAATCTTGAGACGTTT
1321198 AAAAG
65 AAAAG
**
1321203 CAGGGTTGGAGTAT
1 TGGGGTTGGAGTAT
1321217 CTCCTTGGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
69 2 0.03
70 68 0.93
71 2 0.03
72 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (69 bp):
TGGGGTTGGAGTATTCCCAATAATGACAATTTGAGAAAAATAACATTTAAATCTTGAGACGTTTA
AAAG
Found at i:1324496 original size:52 final size:51
Alignment explanation
Indices: 1324434--1324722 Score: 249
Period size: 52 Copynumber: 5.5 Consensus size: 51
1324424 ACAATGTGTA
* * *
1324434 GATTCAAGGCCTA-CAACATTGGTCTTAAAGATGACAAGGGTGTCAATATGCT
1 GATTCAAGGCC-AGCAACATTGGACTTAAAGATGAAAAGAGTG-CAATATGCT
* * * * * *
1324486 TATTCAAGGCCAGCGACATTGAACTTGAAGATTATAAGTAGTGCCAATATGCT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAAAG-AGTG-CAATATGCT
* * * * * * *
1324539 AATTCAAGG-CAGCGATATCGGACTTAAAAATGAGAAGAGTGCTAATTTGCT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAAAGAGTGC-AATATGCT
* * * * *
1324590 GATTCAAGGCCAACGACATTGGACTTAAATATGATAAAAAGGTGTCAACATGCT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGA-AAAGA-GTG-CAATATGCT
* * * *
1324644 GATTCAAGGCCAGCAATATTGGACTTAGAGGTAAAAAGAGTGCTAATATGCT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAAAGAGTGC-AATATGCT
*
1324696 GATTCAAGGCCAACAACATTGGACTTA
1 GATTCAAGGCCAGCAACATTGGACTTA
1324723 GAAAGAGATG
Statistics
Matches: 191, Mismatches: 38, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
50 1 0.01
51 21 0.11
52 105 0.55
53 27 0.14
54 36 0.19
55 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAAAGAGTGCAATATGCT
Found at i:1324690 original size:106 final size:104
Alignment explanation
Indices: 1324478--1324722 Score: 292
Period size: 106 Copynumber: 2.3 Consensus size: 104
1324468 CAAGGGTGTC
* * * * * ** *
1324478 AATATGCTTATTCAAGGCCAGCGACATTGAACTTGAAGATTATAAGTAGTGCCAATATGCTAATT
1 AATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAAAGTGCCAACATGCTAATT
* * *
1324543 CAAGGCAGCGATATCGGACTTAAAAATGAGAAGAGTGCT
66 CAAGGCAGCAATATCGGACTTAAAAATAAAAAGAGTGCT
* * * *
1324582 AATTTGCTGATTCAAGGCCAACGACATTGGACTTAAATATGATAAAAAGGTGTCAACATGCTGAT
1 AATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAAA-GTGCCAACATGCTAAT
* * **
1324647 TCAAGGCCAGCAATATTGGACTTAGAGGTAAAAAGAGTGCT
65 TCAAGG-CAGCAATATCGGACTTAAAAATAAAAAGAGTGCT
*
1324688 AATATGCTGATTCAAGGCCAACAACATTGGACTTA
1 AATATGCTGATTCAAGGCCAACGACATTGGACTTA
1324723 GAAAGAGATG
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
104 39 0.33
105 19 0.16
106 60 0.51
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (104 bp):
AATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAAAGTGCCAACATGCTAATT
CAAGGCAGCAATATCGGACTTAAAAATAAAAAGAGTGCT
Found at i:1324870 original size:33 final size:32
Alignment explanation
Indices: 1324774--1324881 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
1324764 CCAACGACAT
* *
1324774 TGGGC-TTAGAAAAAGATACCACTGACTTGTG
1 TGGGCTTTTGAAAAGGATACCACTGACTTGTG
* * *
1324805 TGAGCTTTTGAGAAGGTTACCA-TCGACTTGTG
1 TGGGCTTTTGAAAAGGATACCACT-GACTTGTG
* *
1324837 TGGGCTTTTGGAAAAGGATGCCACTAACTTGTG
1 TGGGCTTTT-GAAAAGGATACCACTGACTTGTG
1324870 TGGGC-TTTGAAA
1 TGGGCTTTTGAAA
1324882 GGGTTGCCAT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
31 9 0.14
32 31 0.49
33 22 0.35
34 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (32 bp):
TGGGCTTTTGAAAAGGATACCACTGACTTGTG
Found at i:1324914 original size:31 final size:31
Alignment explanation
Indices: 1324819--1325139 Score: 265
Period size: 31 Copynumber: 10.3 Consensus size: 31
1324809 CTTTTGAGAA
* * *
1324819 GGTTACCATCGACTTGTGTGGGCTTTTGGAAAA-
1 GGTTGCCACCGACTTGTATGGGC-TTT--AAAAG
* ** * *
1324852 GGATGCCACTAACTTGTGTGGGCTTTGAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
* * *
1324883 GGTTGCCATCGACTTATATGGGATTTAAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
** * *
1324914 GGTTGCCACCGACTTGTGCGGTCTTTGAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
** * *
1324945 GGTTAACACCAACTTGTGTGGGCTTTAAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
1324976 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
*
1325007 GGTTGCCACCGACTTGTTTGGGCTTTAAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
* * * *
1325038 TGCTACCACC-AATT-TATGTAGGCTTTAAAAG
1 GGTTGCCACCGACTTGTATG--GGCTTTAAAAG
* * *
1325069 GGTAGCCACCGACTTGTGTGAGCTTTAAAAG
1 GGTTGCCACCGACTTGTATGGGCTTTAAAAG
* ** *
1325100 GGTTTCCA-TTAGCTTGTGTGGGCTTTGAAAAG
1 GGTTGCCACCGA-CTTGTATGGGCTTT-AAAAG
1325132 GG-TGCCAC
1 GGTTGCCAC
1325140 GAAGTTGTGG
Statistics
Matches: 230, Mismatches: 50, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
29 3 0.01
30 7 0.03
31 186 0.81
32 13 0.06
33 21 0.09
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (31 bp):
GGTTGCCACCGACTTGTATGGGCTTTAAAAG
Found at i:1324940 original size:62 final size:62
Alignment explanation
Indices: 1324792--1325139 Score: 299
Period size: 62 Copynumber: 5.6 Consensus size: 62
1324782 GAAAAAGATA
* * * * * *
1324792 CCACTGACTTGTGTGAGCTTTTGAGAA-GGTTACCATCGACTTGTGTGGGCTTTTGGAAAA-GGA
1 CCACCGACTTGTGTGGGC-TTTGA-AAGGGTTGCCACCGACTTGTATGGGC-TTT--AAAAGGGT
1324855 TG
61 TG
** * * *
1324857 CCACTAACTTGTGTGGGCTTTGAAAGGGTTGCCATCGACTTATATGGGATTTAAAAGGGTTG
1 CCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTG
* * ** * *
1324919 CCACCGACTTGTGCGGTCTTTGAAAGGGTTAACACCAACTTGTGTGGGCTTTAAAAGGGTTG
1 CCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTG
* * * * * *
1324981 CCACCGACTTGTATGGGCTTTAAAAGGGTTGCCACCGACTTGTTTGGGCTTTAAAAGTGCTA
1 CCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTG
* * * * * * * * *
1325043 CCACCAATTTATGTAGGCTTTAAAAGGGTAGCCACCGACTTGTGTGAGCTTTAAAAGGGTTT
1 CCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTG
**
1325105 CCA-TTAGCTTGTGTGGGCTTTGAAAAGGG-TGCCAC
1 CCACCGA-CTTGTGTGGGCTTTG-AAAGGGTTGCCAC
1325140 GAAGTTGTGG
Statistics
Matches: 232, Mismatches: 47, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
61 5 0.02
62 176 0.76
63 11 0.05
64 24 0.10
65 16 0.07
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (62 bp):
CCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTG
Found at i:1324966 original size:93 final size:93
Alignment explanation
Indices: 1324862--1325103 Score: 331
Period size: 93 Copynumber: 2.6 Consensus size: 93
1324852 GGATGCCACT
* * * *
1324862 AACTTGTGTGGGCTTTGAAAGGGTTGCCATCGACTTATATGGGATTTAAAAGGGTTGCCACCGAC
1 AACTTGTGTGGGCTTTAAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTGCCACCGAC
* * *
1324927 TTGTGCGGTCTTTGAAAGGGTTAACACC
66 TTGTGCGGGCTTTAAAAGGGCTAACACC
1324955 AACTTGTGTGGGCTTTAAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTGCCACCGAC
1 AACTTGTGTGGGCTTTAAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTGCCACCGAC
** * *
1325020 TTGTTTGGGCTTTAAAAGTGCTACCACC
66 TTGTGCGGGCTTTAAAAGGGCTAACACC
* * * * * *
1325048 AATTTATGTAGGCTTTAAAAGGGTAGCCACCGACTTGTGTGAGCTTTAAAAGGGTT
1 AACTTGTGTGGGCTTTAAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTT
1325104 TCCATTAGCT
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 132 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (93 bp):
AACTTGTGTGGGCTTTAAAAGGGTTGCCACCGACTTGTATGGGCTTTAAAAGGGTTGCCACCGAC
TTGTGCGGGCTTTAAAAGGGCTAACACC
Found at i:1325116 original size:93 final size:94
Alignment explanation
Indices: 1324829--1325131 Score: 308
Period size: 93 Copynumber: 3.2 Consensus size: 94
1324819 GGTTACCATC
* * * * * * * *
1324829 GACTTGTGTGGGCTTTTGGAAAAG-GATGCCACTAACTTGTGTGGGCTTTGAAAGGGTTGCCATC
1 GACTTGTGTGGGC-TTT-GAAAAGTGCTACCACCAACTTATGTAGGCTTTAAAAGGGTAGCCACC
* * * *
1324893 GACTTATATGGGATTTAAAAGGGTTGCCACC
64 GACTTGTATGAGCTTTAAAAGGGTTGCCACA
* * * * * * * *
1324924 GACTTGTGCGGTCTTTG-AAAGGGTTAACACCAACTTGTGTGGGCTTTAAAAGGGTTGCCACCGA
1 GACTTGTGTGGGCTTTGAAAAGTGCTACCACCAACTTATGTAGGCTTTAAAAGGGTAGCCACCGA
* *
1324988 CTTGTATGGGCTTTAAAAGGGTTGCCACC
66 CTTGTATGAGCTTTAAAAGGGTTGCCACA
* *
1325017 GACTTGTTTGGGCTTT-AAAAGTGCTACCACCAATTTATGTAGGCTTTAAAAGGGTAGCCACCGA
1 GACTTGTGTGGGCTTTGAAAAGTGCTACCACCAACTTATGTAGGCTTTAAAAGGGTAGCCACCGA
* * *
1325081 CTTGTGTGAGCTTTAAAAGGGTTTCCATTA
66 CTTGTATGAGCTTTAAAAGGGTTGCCA-CA
1325111 G-CTTGTGTGGGCTTTGAAAAG
1 GACTTGTGTGGGCTTTGAAAAG
1325132 GGTGCCACGA
Statistics
Matches: 178, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
92 4 0.02
93 154 0.87
94 9 0.05
95 11 0.06
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (94 bp):
GACTTGTGTGGGCTTTGAAAAGTGCTACCACCAACTTATGTAGGCTTTAAAAGGGTAGCCACCGA
CTTGTATGAGCTTTAAAAGGGTTGCCACA
Found at i:1325410 original size:59 final size:60
Alignment explanation
Indices: 1325126--1325885 Score: 462
Period size: 59 Copynumber: 12.6 Consensus size: 60
1325116 TGTGGGCTTT
* * * *
1325126 GAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAAAGGGGTGCCACGAAGTTGTGAACTTT-A
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTG--AAAA-GGGTGCCATGAAGTTGTGGACTTTGA
* ** * ** * *
1325188 TAAAAAGGGGTGCCATAGAGTTATGGACTTAAAAAAGGGTGCCACGGAGTTGTGGACTTT-A
1 GAAAAA--GGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
* * * * * *
1325249 AAAAGAGAGCGAGTGCCACAGAGTTATGGACTTTGAGAAAAGGGTGCCACGAAATTATGGACTTT
1 GAAA-A-A--G-GTGCCACGGAGTTGTGGACTTT--GAAAAGGGTGCCATGAAGTTGTGGACTTT
1325314 -A
59 GA
* ** * *
1325315 AAAAAAGGGTGCCATAGAGTTGTGGACTTT-AAAAGGGTGCCATGGAGTTGTGGGCTTTGA
1 GAAAAA-GGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
* * * *
1325375 GAAAAAGGTACCACGGA-TTGTAGACTTTGAGAAGGGTGCCACGAAGTTGTGGACTTTGA
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
* * ** * * * *
1325434 -AAAGAGGTGTCATAGAGTTATGGACTTTAAAAAGGGTACCATAAAGTTGTGGACTTTG-
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
* * * * *
1325492 G-AAAGGGTGCCACGAAGTTGTGGGCTTTGAGAAAGGGTGCCACGAAATTGTGGACTTT--
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGA-AAAGGGTGCCATGAAGTTGTGGACTTTGA
* * *
1325550 GAAAAAGGTGTCACGGAGTTGTGGGCTTTGAAAAGGGTGCCAAT-AAGTTGTGGTCTTT-A
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCC-ATGAAGTTGTGGACTTTGA
* ** * * *
1325609 G-AAAGGGTGCCACGGAGTTGTAAACTTTAAAAAGAGGCGTCGCA-G-AGTTTTGGACTTT--
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG-GGTG-C-CATGAAGTTGTGGACTTTGA
** * * * *
1325667 GAAAAAGAGTGCCATAGAGTTGTGGACTTT-AAAAGAGGTACCATGGAGTTATAGACTTTGA
1 GAAAAAG-GTGCCACGGAGTTGTGGACTTTGAAAAG-GGTGCCATGAAGTTGTGGACTTTGA
* * * * * * * *
1325728 -AAAGAGGTGCAACGGAGTTGTGAACTTTAAAAAAGGTGCCATAAAATTGTGGACATTGA
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
* * * * * * * *
1325787 -AAAAAGTATTGCCACGGAGTTGTTGACTTTAAAAAAAAAGGTGCCACGGAGTTATGGACTTTAA
1 GAAAAAG--GTGCCACGGAGTTGTGGACTTT---GAAAAGGGTGCCATGAAGTTGTGGACTTT-G
1325851 A
60 A
* * * * *
1325852 AAAAAAGGTGCCACGAAATTATGGATTTTGAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAA
1325886 AAAAAGGTAC
Statistics
Matches: 549, Mismatches: 116, Indels: 67
0.75 0.16 0.09
Matches are distributed among these distances:
57 2 0.00
58 94 0.17
59 220 0.40
60 35 0.06
61 49 0.09
62 29 0.05
63 4 0.01
64 78 0.14
65 2 0.00
66 36 0.07
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (60 bp):
GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGTGCCATGAAGTTGTGGACTTTGA
Found at i:1325613 original size:117 final size:120
Alignment explanation
Indices: 1325128--1325790 Score: 527
Period size: 118 Copynumber: 5.5 Consensus size: 120
1325118 TGGGCTTTGA
* * * *
1325128 AAAGGGTGCCACGAAGTTGTGGACTTTGAAAAAAGGGGTGCCACGAAGTTGTGAACTTTATAAAA
1 AAAGGGTGCCACGAAGTTGTGGACTTTG-AGAAA-GGGTGCCACGAAATTGTGGACTTTAGAAAA
* ***
1325193 AGGGGTGCCATAGAGTTATGGACTTAAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAG
64 A-GGGTGCCATAGAGTTATGGACTTTAAAAAGGGTGCCATAAAGTTGTGGACTTT---AAG
* * * *
1325254 AGAGCGAGTGCCAC-AGAGTTATGGACTTTGAGAAAAGGGTGCCACGAAATTATGGACTTTAAAA
1 AAAG-G-GTGCCACGA-AGTTGTGGACTTTGAG-AAAGGGTGCCACGAAATTGTGGACTTTAGAA
* ** * *
1325318 AAAGGGTGCCATAGAGTTGTGGACTTT-AAAAGGGTGCCATGGAGTTGTGGGCTTTGAG
62 AAAGGGTGCCATAGAGTTATGGACTTTAAAAAGGGTGCCATAAAGTTGTGGACTTTAAG
* * * * *
1325376 AAAAAGGTACCACGGA-TTGTAGACTTTGAG-AAGGGTGCCACGAAGTTGTGGACTTT-G-AAAA
1 -AAAGGGTGCCACGAAGTTGTGGACTTTGAGAAAGGGTGCCACGAAATTGTGGACTTTAGAAAAA
* * *
1325437 GAGGTGTCATAGAGTTATGGACTTTAAAAAGGGTACCATAAAGTTGTGGACTTT-GG
65 G-GGTGCCATAGAGTTATGGACTTTAAAAAGGGTGCCATAAAGTTGTGGACTTTAAG
*
1325493 AAAGGGTGCCACGAAGTTGTGGGCTTTGAGAAAGGGTGCCACGAAATTGTGGACTTT-GAAAAA-
1 AAAGGGTGCCACGAAGTTGTGGACTTTGAGAAAGGGTGCCACGAAATTGTGGACTTTAGAAAAAG
* ** * * * *
1325556 GGTGTCACGGAGTTGTGGGCTTTGAAAAGGGTGCCA-ATAAGTTGTGGTCTTT-AG
66 GGTGCCATAGAGTTATGGACTTTAAAAAGGGTGCCATA-AAGTTGTGGACTTTAAG
* ** * * * *
1325610 AAAGGGTGCCACGGAGTTGTAAACTTT-AAAAAGAGGCGTCGCA-G-AGTTTTGGACTTT-GAAA
1 AAAGGGTGCCACGAAGTTGTGGACTTTGAGAAAG-GGTG-C-CACGAAATTGTGGACTTTAGAAA
* * * ** * * *
1325671 AAGAGTGCCATAGAGTTGTGGACTTT-AAAAGAGGTACCATGGAGTTATAGACTTTGA-
63 AAGGGTGCCATAGAGTTATGGACTTTAAAAAG-GGTGCCATAAAGTTGTGGACTTTAAG
* * * * * ** *
1325728 AAAGAGGTGCAACGGAGTTGTGAACTTT-AAAAAAGGTGCCATAAAATTGTGGACATT-GAAAAA
1 AAAG-GGTGCCACGAAGTTGTGGACTTTGAGAAAGGGTGCCACGAAATTGTGGACTTTAGAAAAA
1325791 AGTATTGCCA
Statistics
Matches: 446, Mismatches: 69, Indels: 52
0.79 0.12 0.09
Matches are distributed among these distances:
116 25 0.06
117 127 0.28
118 133 0.30
119 33 0.07
120 12 0.03
121 7 0.02
122 3 0.01
123 2 0.00
125 26 0.06
126 25 0.06
127 30 0.07
128 23 0.05
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (120 bp):
AAAGGGTGCCACGAAGTTGTGGACTTTGAGAAAGGGTGCCACGAAATTGTGGACTTTAGAAAAAG
GGTGCCATAGAGTTATGGACTTTAAAAAGGGTGCCATAAAGTTGTGGACTTTAAG
Found at i:1325755 original size:30 final size:30
Alignment explanation
Indices: 1325116--1325913 Score: 478
Period size: 29 Copynumber: 26.3 Consensus size: 30
1325106 CATTAGCTTG
* *
1325116 TGTGGGCTTTGAAAAG-GGTGCCACGAAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* *
1325145 TGTGGACTTTGAAAAAAGGGGTGCCACGAAGT
1 TGTGGACTTTG--AAAAGAGGTGCCACGGAGT
* * * **
1325177 TGTGAACTTTATAAAAAGGGGTGCCATAGAGT
1 TGTGGAC-TT-TGAAAAGAGGTGCCACGGAGT
* **
1325209 TATGGACTTAAAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* *
1325238 TGTGGACTTTAAAAAGAGAGCGAGTGCCACAGAGT
1 TGTGGACTTT-GAAA-AGA--G-GTGCCACGGAGT
* * *
1325273 TATGGACTTTGAGAAA-AGGGTGCCACGAAAT
1 TGTGGACTTTGA-AAAGA-GGTGCCACGGAGT
* * * **
1325304 TATGGACTTTAAAAAAAGGGTGCCATAGAGT
1 TGTGGACTTTGAAAAGA-GGTGCCACGGAGT
*
1325335 TGTGGACTTT-AAAAG-GGTGCCATGGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * *
1325363 TGTGGGCTTTGAGAAAAAGGTACCACGGA-T
1 TGTGGACTTTGA-AAAGAGGTGCCACGGAGT
* * *
1325393 TGTAGACTTTGAGAAG-GGTGCCACGAAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* **
1325422 TGTGGACTTTGAAAAGAGGTGTCATAGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * * ***
1325452 TATGGACTTTAAAAAG-GGTACCATAAAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* *
1325481 TGTGGACTTTGGAAAG-GGTGCCACGAAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * *
1325510 TGTGGGCTTTGAGAAAG-GGTGCCACGAAAT
1 TGTGGACTTTGA-AAAGAGGTGCCACGGAGT
*
1325540 TGTGGACTTTGAAAA-AGGTGTCACGGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* ***
1325569 TGTGGGCTTTGAAAAG-GGTGCCAATAAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
*
1325598 TGTGGTCTTT-AGAAAG-GGTGCCACGGAGT
1 TGTGGACTTTGA-AAAGAGGTGCCACGGAGT
** * * * * *
1325627 TGTAAACTTTAAAAAGAGGCGTCGCAGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* **
1325657 TTTGGACTTTGAAAA-AGAGTGCCATAGAGT
1 TGTGGACTTTGAAAAGAG-GTGCCACGGAGT
* *
1325687 TGTGGACTTT-AAAAGAGGTACCATGGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * *
1325716 TATAGACTTTGAAAAGAGGTGCAACGGAGT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * *** *
1325746 TGTGAACTTT-AAAAAAGGTGCCATAAAAT
1 TGTGGACTTTGAAAAGAGGTGCCACGGAGT
* * *
1325775 TGTGGACATTGAAAAAAGTATTGCCACGGAGT
1 TGTGGACTTTGAAAAGAG--GTGCCACGGAGT
* * *
1325807 TGTTGACTTTAAAAAAAAAGGTGCCACGGAGT
1 TGTGGACTTT--GAAAAGAGGTGCCACGGAGT
* * * * *
1325839 TATGGACTTTAAAAAAAAAGGTGCCACGAAAT
1 TGTGGACTTT--GAAAAGAGGTGCCACGGAGT
* * * *
1325871 TATGGATTTTGAAAAAAAAAGGTACCACGGAGT
1 TGTGGACTTTG---AAAAGAGGTGCCACGGAGT
*
1325904 TGTGAACTTT
1 TGTGGACTTT
1325914 TTTTAAAAAA
Statistics
Matches: 608, Mismatches: 126, Indels: 66
0.76 0.16 0.08
Matches are distributed among these distances:
28 31 0.05
29 205 0.34
30 151 0.25
31 58 0.10
32 104 0.17
33 26 0.04
34 11 0.02
35 22 0.04
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (30 bp):
TGTGGACTTTGAAAAGAGGTGCCACGGAGT
Found at i:1325854 original size:33 final size:32
Alignment explanation
Indices: 1325796--1325913 Score: 155
Period size: 32 Copynumber: 3.7 Consensus size: 32
1325786 AAAAAAGTAT
* *
1325796 TGCCACGGAGTTGTTGACTTTAAAAAAAAAGG
1 TGCCACGGAGTTATGGACTTTAAAAAAAAAGG
1325828 TGCCACGGAGTTATGGACTTTAAAAAAAAAGG
1 TGCCACGGAGTTATGGACTTTAAAAAAAAAGG
* * *
1325860 TGCCACGAAATTATGGATTTTGAAAAAAAAAGG
1 TGCCACGGAGTTATGGACTTT-AAAAAAAAAGG
* * *
1325893 TACCACGGAGTTGTGAACTTT
1 TGCCACGGAGTTATGGACTTT
1325914 TTTTAAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
32 48 0.65
33 26 0.35
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (32 bp):
TGCCACGGAGTTATGGACTTTAAAAAAAAAGG
Found at i:1328419 original size:20 final size:20
Alignment explanation
Indices: 1328390--1328427 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1328380 TCAAAAACTT
* *
1328390 AGAATGTATCGATACAATGA
1 AGAATATATCAATACAATGA
1328410 AGAATATATCAATACAAT
1 AGAATATATCAATACAAT
1328428 TGGGTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (20 bp):
AGAATATATCAATACAATGA
Found at i:1328450 original size:51 final size:52
Alignment explanation
Indices: 1328364--1328470 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 52
1328354 TAACTGTATG
* * * * *
1328364 TATCGATACATTTGGGTCAAAAACTTAGAATGTATCGATACAATGAAGAATA
1 TATCAATACAATTGGGTCAAAAACCTAGAATGTATCAATACAATGAAAAATA
* *
1328416 TATCAATACAATTGGGTC-AAAACCTAGAATGTATCAATATAATGAAAAATG
1 TATCAATACAATTGGGTCAAAAACCTAGAATGTATCAATACAATGAAAAATA
1328467 TATC
1 TATC
1328471 GATGCATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 32 0.67
52 16 0.33
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (52 bp):
TATCAATACAATTGGGTCAAAAACCTAGAATGTATCAATACAATGAAAAATA
Found at i:1328562 original size:20 final size:21
Alignment explanation
Indices: 1328539--1328587 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1328529 TCAAGCATGC
1328539 ATCGATACATT-CACTT-CTGT
1 ATCGATACATTAC-CTTACTGT
*
1328559 ATCGATACATTACCTTATTGT
1 ATCGATACATTACCTTACTGT
1328580 ATCGATAC
1 ATCGATAC
1328588 TAATTGCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
ATCGATACATTACCTTACTGT
Found at i:1333491 original size:58 final size:58
Alignment explanation
Indices: 1333362--1333492 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
1333352 ATGCAATTTT
* *
1333362 ATGTTGATGTCATTTAGATCATTTATTATGATCTAAGGATTTTGATGCAATTTTATAA
1 ATGTTGATGTCATTTAGATCATTTATTATGATCTAAGGACTTTGATACAATTTTATAA
* * * * * *
1333420 ACT-TTAATATCATTTAGGTCATTT-TCTATGA-CTTAGGAACTTTGATATAATTTTATGA
1 A-TGTTGATGTCATTTAGATCATTTAT-TATGATCTAAGG-ACTTTGATACAATTTTATAA
1333478 ATGTTGATGTCATTT
1 ATGTTGATGTCATTT
1333493 TGATGATCTA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
57 7 0.12
58 51 0.86
59 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (58 bp):
ATGTTGATGTCATTTAGATCATTTATTATGATCTAAGGACTTTGATACAATTTTATAA
Found at i:1333526 original size:106 final size:107
Alignment explanation
Indices: 1333380--1333599 Score: 264
Period size: 106 Copynumber: 2.1 Consensus size: 107
1333370 GTCATTTAGA
* * * * *
1333380 TCATTTATTATGATCTAAGGATTTTGATGCAATTTTATAAACTTTAATATCATTTAGGTCATTTT
1 TCATTTATGATGATCTAAGGACTTTGACGCAATTTTATAAACTTTAATATCATTTAGATCAATTT
* *
1333445 CTATGACTT-AGGAACTTTGATATAATTTTATGAATGTTGATG
66 CCATGACTTAAGG-ACTTGGATATAATTTTATGAATGTTGATG
* * * * *
1333487 TCATTT-TGATGATCTAAGGACTTTGACGTAATTTTATAAATTTTGATGTCATTTAGATTAATTT
1 TCATTTATGATGATCTAAGGACTTTGACGCAATTTTATAAACTTTAATATCATTTAGATCAATTT
* * * *
1333551 CCATTATTTAAGGACTTGGATGTAATTTTATGAATTTTGATG
66 CCATGACTTAAGGACTTGGATATAATTTTATGAATGTTGATG
*
1333593 TAATTTA
1 TCATTTA
1333600 GGCTATTTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
106 85 0.90
107 9 0.10
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (107 bp):
TCATTTATGATGATCTAAGGACTTTGACGCAATTTTATAAACTTTAATATCATTTAGATCAATTT
CCATGACTTAAGGACTTGGATATAATTTTATGAATGTTGATG
Found at i:1333625 original size:58 final size:58
Alignment explanation
Indices: 1333498--1333646 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 58
1333488 CATTTTGATG
* * * *
1333498 ATCTAAGGACTTTGACGTAATTTTATAAATTTTGATGTCATTTAGATTAATTTCCATT
1 ATCTAAGGACTTTGATGTAATTTTATAAATTTTGATGTAATTTAGACTAATTTCCATA
* * * * * *
1333556 ATTTAAGGACTTGGATGTAATTTTATGAATTTTGATGTAATTTAGGCTATTTTTCATA
1 ATCTAAGGACTTTGATGTAATTTTATAAATTTTGATGTAATTTAGACTAATTTCCATA
* * *
1333614 ATCTATA-GACTTTAATGCAATTTTATACATTTT
1 ATCTA-AGGACTTTGATGTAATTTTATAAATTTT
1333647 AGAAATATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
58 73 0.99
59 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.48
Consensus pattern (58 bp):
ATCTAAGGACTTTGATGTAATTTTATAAATTTTGATGTAATTTAGACTAATTTCCATA
Found at i:1336734 original size:20 final size:20
Alignment explanation
Indices: 1336711--1336755 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1336701 CCAATAATTC
*
1336711 AAATTTTAATCAAAT-ATTAA
1 AAATATTAA-CAAATGATTAA
*
1336731 AAATATTAAGAAATGATTAA
1 AAATATTAACAAATGATTAA
1336751 AAATA
1 AAATA
1336756 ATCATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATTAACAAATGATTAA
Found at i:1336749 original size:11 final size:9
Alignment explanation
Indices: 1336722--1336780 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
1336712 AATTTTAATC
1336722 AAATATTAA
1 AAATATTAA
1336731 AAATATTAA
1 AAATATTAA
1336740 GAAATGATTAA
1 -AAAT-ATTAA
* *
1336751 AAATAATCA
1 AAATATTAA
* *
1336760 TATTATTAA
1 AAATATTAA
1336769 AAATTATTAA
1 AAA-TATTAA
1336779 AA
1 AA
1336781 TAATAATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 18 0.46
10 16 0.41
11 5 0.13
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATATTAA
Found at i:1336789 original size:27 final size:28
Alignment explanation
Indices: 1336734--1336800 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
1336724 ATATTAAAAA
* *
1336734 TATTAAGAAATGATTAAAAATAATCATAT
1 TATTAA-AAATTATTAAAAATAATAATAT
1336763 TATTAAAAATTATT-AAAATAATAATAT
1 TATTAAAAATTATTAAAAATAATAATAT
*
1336790 TATTATAAATT
1 TATTAAAAATT
1336801 TTTATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 22 0.63
28 7 0.20
29 6 0.17
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
TATTAAAAATTATTAAAAATAATAATAT
Found at i:1337472 original size:21 final size:22
Alignment explanation
Indices: 1337421--1337472 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1337411 AATTTTAATA
*
1337421 ATATAAATATATTCAATATTTT
1 ATATTAATATATTCAATATTTT
*
1337443 ACTAATAATAT-TTCTAATA-TTT
1 A-TATTAATATATTC-AATATTTT
1337465 ATATTAAT
1 ATATTAAT
1337473 GAAATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 6 0.24
22 8 0.32
23 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATATATTCAATATTTT
Found at i:1337780 original size:24 final size:25
Alignment explanation
Indices: 1337724--1337781 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
1337714 TTCAAAATCA
*
1337724 TTATATAATGACTAAATTCTTATTT
1 TTATATAATAACTAAATTCTTATTT
**
1337749 TTGCATAA-AACTAAATT-TGTATTT
1 TTATATAATAACTAAATTCT-TATTT
1337773 TTATATAAT
1 TTATATAAT
1337782 TATAAGACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
23 1 0.04
24 19 0.73
25 6 0.23
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (25 bp):
TTATATAATAACTAAATTCTTATTT
Found at i:1339244 original size:19 final size:21
Alignment explanation
Indices: 1339217--1339255 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1339207 CTGTATAAAA
1339217 TTAAAA-TTTAAAAA-TTTAC
1 TTAAAATTTTAAAAAGTTTAC
*
1339236 TTAATATTTTAAAAAGTTTA
1 TTAAAATTTTAAAAAGTTTA
1339256 AATCTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAAAATTTTAAAAAGTTTAC
Found at i:1339461 original size:14 final size:15
Alignment explanation
Indices: 1339433--1339462 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1339423 TTAAAAAATT
1339433 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
1339448 ATTAAATT-TTAAAA
1 ATTAAATTATTAAAA
1339462 A
1 A
1339463 AACTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:1339464 original size:34 final size:34
Alignment explanation
Indices: 1339382--1339469 Score: 97
Period size: 35 Copynumber: 2.6 Consensus size: 34
1339372 TATTATAATA
* * * **
1339382 TAAATATTAAAAAAATATTAAATTTTTTATATTT
1 TAAATTTTAAAAAAATATTAAATTTATTAAAAAT
*
1339416 TAAAATTTTAAAAAATTATTAAA-TTATTAAAAAT
1 T-AAATTTTAAAAAAATATTAAATTTATTAAAAAT
1339450 TAAATTTTAAAAAAACTATT
1 TAAATTTTAAAAAAA-TATT
1339470 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
33 13 0.29
34 13 0.29
35 19 0.42
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTTTAAAAAAATATTAAATTTATTAAAAAT
Found at i:1339509 original size:14 final size:14
Alignment explanation
Indices: 1339490--1339518 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1339480 ATATAACATA
1339490 GGTTATCATTAAAT
1 GGTTATCATTAAAT
1339504 GGTTATCATTAAAT
1 GGTTATCATTAAAT
1339518 G
1 G
1339519 AATTTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (14 bp):
GGTTATCATTAAAT
Found at i:1340151 original size:28 final size:26
Alignment explanation
Indices: 1340087--1340160 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 26
1340077 TTTAATATGG
*
1340087 TTATATAATATAAAAA-AATATAAAT
1 TTATATAATATAAAAATATTATAAAT
* *
1340112 TTGATGTGAATATAAAAATATTTTAAAAT
1 TT-ATAT-AATATAAAAATATTAT-AAAT
*
1340141 TTATATAAATATATAAATAT
1 TTATAT-AATATAAAAATAT
1340161 GATTATAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 10 0.26
28 18 0.46
29 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
TTATATAATATAAAAATATTATAAAT
Found at i:1340847 original size:15 final size:15
Alignment explanation
Indices: 1340825--1340868 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 15
1340815 AAACTGTTAT
1340825 TAAATTATAT-TTTA
1 TAAATTATATATTTA
1340839 TAAATTTATATATTTA
1 TAAA-TTATATATTTA
1340855 T---TTATATATTTA
1 TAAATTATATATTTA
1340867 TA
1 TA
1340869 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.44
14 4 0.15
15 6 0.22
16 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTATATATTTA
Found at i:1340859 original size:12 final size:12
Alignment explanation
Indices: 1340842--1340872 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1340832 TATTTTATAA
1340842 ATTTATATATTT
1 ATTTATATATTT
1340854 ATTTATATATTT
1 ATTTATATATTT
1340866 ATATTAT
1 AT-TTAT
1340873 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:1340860 original size:20 final size:20
Alignment explanation
Indices: 1340828--1340878 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1340818 CTGTTATTAA
*
1340828 ATTATATTTTATAAATTTAT
1 ATTATTTTTTATAAATTTAT
*
1340848 A-TATTTATTTATATATTTAT
1 ATTATTT-TTTATAAATTTAT
1340868 ATTATTTTTTA
1 ATTATTTTTTA
1340879 ATATTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTATTTTTTATAAATTTAT
Found at i:1340900 original size:10 final size:11
Alignment explanation
Indices: 1340844--1340903 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 11
1340834 TTTTATAAAT
*
1340844 TTATATATTTAT
1 TTATAT-TTTAA
1340856 TTATATATTTATA
1 TTATAT-TTTA-A
*
1340869 TTATTTTTTAATA
1 TTATATTTT-A-A
1340882 TTATATTTTAA
1 TTATATTTTAA
1340893 TTAT-TTTTAA
1 TTATATTTTAA
1340903 T
1 T
1340904 ACTTTATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
10 7 0.16
11 5 0.12
12 15 0.35
13 16 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:1340903 original size:23 final size:26
Alignment explanation
Indices: 1340856--1340904 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
1340846 ATATATTTAT
1340856 TTATATATTTATATTATTTTTTAATA
1 TTATATATTTATATTATTTTTTAATA
1340882 TTATAT-TTTA-ATTA-TTTTTAATA
1 TTATATATTTATATTATTTTTTAATA
1340905 CTTTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 4 0.17
25 4 0.17
26 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATATATTTATATTATTTTTTAATA
Found at i:1343019 original size:16 final size:15
Alignment explanation
Indices: 1343000--1343053 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
1342990 AATAATTTTT
1343000 TATTTTTTAAATTATA
1 TATTTTTTAAA-TATA
** *
1343016 TATTTTTTTGATAAA
1 TATTTTTTAAATATA
*
1343031 TATTTTTAAAAATATA
1 TATTTTT-TAAATATA
1343047 TATTTTT
1 TATTTTT
1343054 ACATTAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTTTTTAAATATA
Found at i:1343209 original size:18 final size:18
Alignment explanation
Indices: 1343186--1343234 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1343176 TATATATAAA
1343186 AAAATTATATTAAAAAA-T
1 AAAATTA-ATTAAAAAATT
1343204 AAAATTAA-TAAAAAATT
1 AAAATTAATTAAAAAATT
*
1343221 TAAATTAAATTAAA
1 AAAATT-AATTAAA
1343235 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 9 0.33
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTAATTAAAAAATT
Found at i:1343215 original size:16 final size:18
Alignment explanation
Indices: 1343186--1343234 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1343176 TATATATAAA
1343186 AAAATTATATTAAAAAAT
1 AAAATTATATTAAAAAAT
1343204 AAAATTA-A-TAAAAAATT
1 AAAATTATATTAAAAAA-T
* *
1343221 TAAATTAAATTAAA
1 AAAATTATATTAAA
1343235 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 8 0.30
18 8 0.30
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATATTAAAAAAT
Found at i:1343228 original size:17 final size:16
Alignment explanation
Indices: 1343186--1343219 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
1343176 TATATATAAA
1343186 AAAATTATATTAAAAAAT
1 AAAATTA-A-TAAAAAAT
1343204 AAAATTAATAAAAAAT
1 AAAATTAATAAAAAAT
1343220 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTAATAAAAAAT
Found at i:1343560 original size:25 final size:28
Alignment explanation
Indices: 1343532--1343587 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 28
1343522 ACAAATTTAA
*
1343532 ATTTTAT-AAGATAT-AATTTA-TTTTT
1 ATTTTATAAAAATATAAATTTATTTTTT
1343557 A-TTTATAAAAATATAAATTTATTTTTT
1 ATTTTATAAAAATATAAATTTATTTTTT
1343584 ATTT
1 ATTT
1343588 GATTATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 5 0.19
25 7 0.27
26 6 0.23
27 6 0.23
28 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTTTATAAAAATATAAATTTATTTTTT
Found at i:1343582 original size:26 final size:25
Alignment explanation
Indices: 1343534--1343587 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
1343524 AAATTTAAAT
*
1343534 TTTATAAGATATAATTTA-TTTTTA
1 TTTATAAAATATAATTTATTTTTTA
1343558 TTTATAAAAATATAAATTTATTTTTTA
1 TTTAT-AAAATAT-AATTTATTTTTTA
1343585 TTT
1 TTT
1343588 GATTATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 6 0.23
27 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTATAAAATATAATTTATTTTTTA
Found at i:1343603 original size:72 final size:72
Alignment explanation
Indices: 1343517--1343654 Score: 172
Period size: 72 Copynumber: 1.9 Consensus size: 72
1343507 TTTGAATATA
*
1343517 ATTATACAAATTTAAATTTTATA-AGATATAATTTATTTTTATTTATAAAAA-TATAAATTTATT
1 ATTATACAAATTTAAATTTTATATAG-CATAATTTATTTTTATTTATAAAAATTATAAATTT-TT
1343580 TTTTATTTG
64 TTTTATTTG
** * * * * *
1343589 ATTATACATTTTTAAATTTTTTATTGCATGATTTATTTTTATTTGTAAAAATTTTAAATTTTTTT
1 ATTATACAAATTTAAATTTTATATAGCATAATTTATTTTTATTTATAAAAATTATAAATTTTTTT
1343654 T
66 T
1343655 GGTTGATTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
72 47 0.84
73 9 0.16
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (72 bp):
ATTATACAAATTTAAATTTTATATAGCATAATTTATTTTTATTTATAAAAATTATAAATTTTTTT
TTATTTG
Found at i:1343952 original size:68 final size:70
Alignment explanation
Indices: 1343856--1344078 Score: 210
Period size: 67 Copynumber: 3.2 Consensus size: 70
1343846 ATTATATAAT
* *
1343856 TTTAAATTTTTTAA-AGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTTGGTTTGA
1 TTTAAA-TTTTTAATAG-ATGATTTATTTTTATTTGTAGAAGTTTAAATTTAT-TTTTGG-TTGA
1343920 TAATAAGAG
62 TAATAAGAG
* * * * *
1343929 TTTATATTTTT-A-AGGT-A-TTATTTTT-TTTGTAGTAGCTTAAATTTATTTTTTGGAT-ATAC
1 TTTAAATTTTTAATAGATGATTTATTTTTATTTGTAGAAGTTTAAATTTA-TTTTTGGTTGATA-
1343988 CTATAAGAG
64 --ATAAGAG
* * *
1343997 TTTAAATTTTTTAATATATGATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTAGGTTGATT
1 TTTAAA-TTTTTAATAGATGATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTT-GGTTGATA
1344062 ATAAGAG
64 ATAAGAG
1344069 -TTAAATTTTT
1 TTTAAATTTTT
1344079 TTTAAGCTAT
Statistics
Matches: 124, Mismatches: 14, Indels: 27
0.75 0.08 0.16
Matches are distributed among these distances:
65 3 0.02
66 1 0.01
67 23 0.19
68 21 0.17
69 6 0.05
70 7 0.06
71 10 0.08
72 13 0.10
73 18 0.15
74 20 0.16
75 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.55
Consensus pattern (70 bp):
TTTAAATTTTTAATAGATGATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTGGTTGATAAT
AAGAG
Found at i:1344094 original size:73 final size:71
Alignment explanation
Indices: 1343857--1344099 Score: 234
Period size: 73 Copynumber: 3.4 Consensus size: 71
1343847 TTATATAATT
* * * *
1343857 TTAAATTTTTTAAAGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTTGGTTTGATA
1 TTAAATTTTTTTAAGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTAT-TTTTGGATTGATT
1343922 ATAAGAG
65 ATAAGAG
* * * * *
1343929 TT-TATATTTTTAAG-GT-A-TTATTTTT-TTTGTAGTAGCTTAAATTTATTTTTTGGATAT-AC
1 TTAAATTTTTTTAAGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTA-TTTTTGGAT-TGA-
*
1343988 CTATAAGAG
63 TTATAAGAG
*
1343997 TTTAAA-TTTTTTAA-TATATGATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTAGG-TTG
1 -TTAAATTTTTTTAAGTATA--ATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTT-GGATTG
1344059 ATTATAAGAG
62 ATTATAAGAG
1344069 TTAAATTTTTTTTAAGCTATAATTTATTTTT
1 TTAAA-TTTTTTTAAG-TATAATTTATTTTT
1344100 GTTTATAATA
Statistics
Matches: 137, Mismatches: 17, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
67 25 0.18
68 17 0.12
69 11 0.08
70 2 0.01
71 14 0.10
72 12 0.09
73 33 0.24
74 19 0.14
75 4 0.03
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (71 bp):
TTAAATTTTTTTAAGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTGGATTGATTA
TAAGAG
Found at i:1344125 original size:71 final size:71
Alignment explanation
Indices: 1343856--1344126 Score: 197
Period size: 73 Copynumber: 3.8 Consensus size: 71
1343846 ATTATATAAT
* * *
1343856 TTTAAATTTTTTAA-AGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTT-GGTTTG
1 TTTAAATTTTTTAAGA-TATAATTTATTTTTATTTATAAAAG-TTAAATTTAT-TTTTAGG-TTG
*
1343919 ATAATAAGAG
62 ATTATAAGAG
* * * ** *
1343929 TTTATA-TTTTTAAG--GT-A-TTATTTTT-TTTGTAGTAGCTTAAATTTATTTTTTGGATAT-A
1 TTTAAATTTTTTAAGATATAATTTATTTTTATTTATAAAAG-TTAAATTTATTTTTAGG-T-TGA
*
1343987 CCTATAAGAG
63 -TTATAAGAG
* * *
1343997 TTTAAATTTTTTAATATATGATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTAGGTTGATT
1 TTTAAATTTTTTAAGATATAATTTATTTTTATTTATAAAAG-TTAAATTTATTTTTAGGTTGATT
1344062 ATAAGAG
65 ATAAGAG
* * *
1344069 -TTAAATTTTTTTTAAGCTATAATTTATTTTTGTTTATAATA-TT-AATTTGATTTTTAGG
1 TTTAAA--TTTTTTAAGATATAATTTATTTTTATTTATAAAAGTTAAATTT-ATTTTTAGG
1344127 ATGTTTTATC
Statistics
Matches: 162, Mismatches: 22, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
66 4 0.02
67 22 0.14
68 21 0.13
69 8 0.05
70 6 0.04
71 17 0.10
72 17 0.10
73 43 0.27
74 24 0.15
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (71 bp):
TTTAAATTTTTTAAGATATAATTTATTTTTATTTATAAAAGTTAAATTTATTTTTAGGTTGATTA
TAAGAG
Found at i:1344301 original size:413 final size:400
Alignment explanation
Indices: 1343747--1344524 Score: 915
Period size: 400 Copynumber: 1.9 Consensus size: 400
1343737 TAAATATGAT
** * * *
1343747 AAAATTAGTTTGATTCAATTAGTGTATTTTTTTTTGAAATGTAAAGATACTTGGTATTTTAAATG
1 AAAATTAGTTTGATTCAATTAGTGTATTTTTAGTTGAAATATAAAGATAATTGATATTTTAAATG
* * * * *
1343812 AATTTTTTTATTTGTAAAAGCGTTATTAGGAATGATTATATAATTTTAAATTTTTTAAAGTATAA
66 AATATTTTTATTTATAAAAGCATTATTAGGAATGATCATATAAGTTTAAATTTTTTAAAGTATAA
*
1343877 TTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTTGGTTTGATAATAAGAGTT-TATATTTTTA
131 TTTATTTTTATTTGTAGAAGTTTAAA-TT-TA-TTT--TTTGAT--TAA-A-TTATATA-GTTTA
* ** * *
1343941 AGGTATTATTTTTTTTGTAGTAGCTTAAATTTATTTTTTGGATATACCTATAAGAGTTTAAATTT
186 A---A-T-TTTTATTTGTAAAAGCTTAAATTTATTTTTTAG-TATAACTATAAGAGTTTAAATTT
* *
1344006 TTTAATATATGATTTATTTTTATTTGTAAAAGTTTAAATTTATTTT-TAGGTTGATTATAAGAG-
245 TTTAATATATGATTTATTTTTATTTATAAAACTTTAAATTTATTTTCTAGGTTGATTATAAGAGT
* * * *
1344069 TTAAATTTTTTTTAAGCTATAATTTATTTTTGTTTATAATATTAATTTGATTTTTAGGATGTTTT
310 TTAAATTTTTTTAAAG-TATAATTTATATTTATTTATAAAATTAATTTGATTTTTAGGATGTTTT
1344134 ATCTAAATAGGACTTAAATTTAGGCTG
374 ATCTAAATAGGACTTAAATTTAGGCTG
* * *
1344161 AAAATTAGTTTGATT-ACGTTAGTGTA-TTTTAGTTGAAATAT-TAGGTAATTGATATTTTAAAT
1 AAAATTAGTTTGATTCA-ATTAGTGTATTTTTAGTTGAAATATAAAGATAATTGATATTTTAAAT
* * * *
1344223 GAAAATATTTTTATTTATAGAAGTATT-TTAGGTAA-GATCATATGAGTTTAAATTTTTTAAGGT
65 G--AATATTTTTATTTATAAAAGCATTATTAGG-AATGATCATATAAGTTTAAATTTTTTAAAGT
*
1344286 ATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGATTTAATTATATGAGTTTAAATTT
127 ATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGATTAAATTATAT-AGTTTAAATTT
* * * * *
1344351 TTATTTGTAAAAGTTTAGATTTATTTTTTAGTTTAATTATATGAGTTTAAATTTTTTAATATATG
191 TTATTTGTAAAAGCTTAAATTTATTTTTTAGTATAACTATAAGAGTTTAAATTTTTTAATATATG
** * * *
1344416 ATTTATTTTTATTTATTTAACTTTAAATTTGTTTTCTAGTTTGATTATATGAGTTTAAATTTTTT
256 ATTTATTTTTATTTATAAAACTTTAAATTTATTTTCTAGGTTGATTATAAGAGTTTAAATTTTTT
* * *
1344481 TAAAGTATGATTTATATTTATTTGTAAAATTAGTTTGATTTTTA
321 TAAAGTATAATTTATATTTATTTATAAAATTAATTTGATTTTTA
1344525 TTTTGATTGC
Statistics
Matches: 313, Mismatches: 43, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
399 60 0.19
400 75 0.24
401 16 0.05
402 1 0.00
404 2 0.01
405 9 0.03
406 3 0.01
408 6 0.02
410 3 0.01
411 2 0.01
412 20 0.06
413 72 0.23
414 44 0.14
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.53
Consensus pattern (400 bp):
AAAATTAGTTTGATTCAATTAGTGTATTTTTAGTTGAAATATAAAGATAATTGATATTTTAAATG
AATATTTTTATTTATAAAAGCATTATTAGGAATGATCATATAAGTTTAAATTTTTTAAAGTATAA
TTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGATTAAATTATATAGTTTAAATTTTTATT
TGTAAAAGCTTAAATTTATTTTTTAGTATAACTATAAGAGTTTAAATTTTTTAATATATGATTTA
TTTTTATTTATAAAACTTTAAATTTATTTTCTAGGTTGATTATAAGAGTTTAAATTTTTTTAAAG
TATAATTTATATTTATTTATAAAATTAATTTGATTTTTAGGATGTTTTATCTAAATAGGACTTAA
ATTTAGGCTG
Found at i:1344344 original size:32 final size:31
Alignment explanation
Indices: 1344308--1344404 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 31
1344298 TATTTGTAGA
1344308 AGTTTAAATTTATTTTTTGATTTAATTATATG
1 AGTTTAAATTTATTTTTTG-TTTAATTATATG
*
1344340 AGTTTAAATTT-TTATTTG--T-A--A-A--
1 AGTTTAAATTTATTTTTTGTTTAATTATATG
*
1344362 AGTTTAGATTTATTTTTTAGTTTAATTATATG
1 AGTTTAAATTTATTTTTT-GTTTAATTATATG
1344394 AGTTTAAATTT
1 AGTTTAAATTT
1344405 TTTAATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
22 10 0.20
23 5 0.10
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 1 0.02
29 1 0.02
30 1 0.02
31 6 0.12
32 21 0.41
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (31 bp):
AGTTTAAATTTATTTTTTGTTTAATTATATG
Found at i:1344356 original size:54 final size:54
Alignment explanation
Indices: 1344293--1344406 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 54
1344283 GGTATAATTT
*
1344293 ATTTTTATTTGTAGAAGTTTAAATTTATTTTTT-GATTTAATTATATGAGTTTAA
1 ATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAG-TTTAATTATATGAGTTTAA
*
1344347 ATTTTTATTTGTAAAAGTTTAGATTTATTTTTTAGTTTAATTATATGAGTTTAA
1 ATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTTTAATTATATGAGTTTAA
1344401 ATTTTT
1 ATTTTT
1344407 TAATATATGA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 56 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.59
Consensus pattern (54 bp):
ATTTTTATTTGTAAAAGTTTAAATTTATTTTTTAGTTTAATTATATGAGTTTAA
Found at i:1344408 original size:28 final size:28
Alignment explanation
Indices: 1344319--1344408 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 28
1344309 GTTTAAATTT
1344319 ATTTTTT-GATTTAATTATATGAGTTTAA
1 ATTTTTTAG-TTTAATTATATGAGTTTAA
*
1344347 A-TTTTTATTTGTAAAAGTT-TA-GA-TTT--
1 ATTTTTTAGTT-T--AA-TTATATGAGTTTAA
1344373 ATTTTTTAGTTTAATTATATGAGTTTAA
1 ATTTTTTAGTTTAATTATATGAGTTTAA
1344401 ATTTTTTA
1 ATTTTTTA
1344409 ATATATGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 22
0.67 0.03 0.30
Matches are distributed among these distances:
23 2 0.04
24 4 0.08
25 2 0.04
26 5 0.10
27 15 0.31
28 13 0.27
29 2 0.04
30 4 0.08
31 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (28 bp):
ATTTTTTAGTTTAATTATATGAGTTTAA
Found at i:1344424 original size:73 final size:74
Alignment explanation
Indices: 1344328--1344509 Score: 224
Period size: 73 Copynumber: 2.4 Consensus size: 74
1344318 TATTTTTTGA
* * *
1344328 TTTAATTATATGAGTTTAAATTTTTATTTGTAAAAGTTTAGATTTATTTTTTAGTTTAATTATAT
1 TTTAA-TATATGA-TTT--ATTTTTATTTGTAAAACTTTAAATTTATTTTCTAGTTTAATTATAT
1344393 GAGTTTAAA-TTT
62 GAGTTTAAATTTT
* ** * *
1344405 TTTAATATATGATTTATTTTTATTTATTTAACTTTAAATTTGTTTTCTAGTTTGATTATATGAGT
1 TTTAATATATGATTTATTTTTATTTGTAAAACTTTAAATTTATTTTCTAGTTTAATTATATGAGT
1344470 TTAAATTTT
66 TTAAATTTT
*
1344479 TTTAA-AGTATGATTTATATTTATTTGTAAAA
1 TTTAATA-TATGATTTATTTTTATTTGTAAAA
1344510 TTAGTTTGAT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
73 48 0.53
74 28 0.31
75 3 0.03
76 7 0.08
77 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.58
Consensus pattern (74 bp):
TTTAATATATGATTTATTTTTATTTGTAAAACTTTAAATTTATTTTCTAGTTTAATTATATGAGT
TTAAATTTT
Found at i:1344430 original size:22 final size:23
Alignment explanation
Indices: 1344368--1344430 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1344358 TAAAAGTTTA
1344368 GATTTATTTTTTAGTTTAATTATAT
1 GATTTA-TTTTTA-TTTAATTATAT
**
1344393 GAGTTTAAATTT-TTTAA-TATAT
1 GA-TTTATTTTTATTTAATTATAT
1344415 GATTTATTTTTATTTA
1 GATTTATTTTTATTTA
1344431 TTTAACTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 7 0.22
22 11 0.34
23 5 0.16
25 5 0.16
26 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (23 bp):
GATTTATTTTTATTTAATTATAT
Found at i:1344489 original size:23 final size:24
Alignment explanation
Indices: 1344463--1344508 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1344453 AGTTTGATTA
1344463 TATGAGTTTAAATTT-TTT-TAAAG
1 TATGA-TTTAAATTTATTTGTAAAG
*
1344486 TATGATTTATATTTATTTGTAAA
1 TATGATTTAAATTTATTTGTAAA
1344509 ATTAGTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (24 bp):
TATGATTTAAATTTATTTGTAAAG
Found at i:1344496 original size:32 final size:32
Alignment explanation
Indices: 1344437--1344497 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1344427 TTTATTTAAC
** *
1344437 TTTAAATTTGTTTTCTAGTTTGATTATATGAG
1 TTTAAATTTGTTTTAAAGTATGATTATATGAG
1344469 TTTAAATTT-TTTTAAAGTATGATTTATAT
1 TTTAAATTTGTTTTAAAGTATGA-TTATAT
1344498 TTATTTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (32 bp):
TTTAAATTTGTTTTAAAGTATGATTATATGAG
Found at i:1345614 original size:33 final size:33
Alignment explanation
Indices: 1345577--1345641 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1345567 TTTGAAGCAA
* *
1345577 TGTATCGATACAATTCATCATATATCGATACAT
1 TGTATCGATACAATGCACCATATATCGATACAT
* *
1345610 TGTATCGATACAATGCGCCATGTATCGATACA
1 TGTATCGATACAATGCACCATATATCGATACA
1345642 AACAATGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGCACCATATATCGATACAT
Found at i:1353209 original size:20 final size:20
Alignment explanation
Indices: 1353181--1353234 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1353171 GTTTGAAGCA
* *
1353181 ATGTATCGATAGAATTCATC
1 ATGTATCGATACAATGCATC
* *
1353201 ATGTGTCGATACAATGCGTC
1 ATGTATCGATACAATGCATC
1353221 ATGTATCGATACAA
1 ATGTATCGATACAA
1353235 ATAGTGGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGCATC
Found at i:1353307 original size:19 final size:19
Alignment explanation
Indices: 1353267--1353335 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
1353257 CAGTTTCATA
**
1353267 TATCGATACAATTGTCCATG
1 TATCGATACAA-TGAACATG
1353287 TATCGATACAATGAACATG
1 TATCGATACAATGAACATG
*
1353306 TATCGATACAAAGCATA-ATG
1 TATCGATACAATG-A-ACATG
1353326 TATCGATACA
1 TATCGATACA
1353336 TCTAGGTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.41
20 25 0.57
21 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:1362449 original size:24 final size:22
Alignment explanation
Indices: 1362410--1362477 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1362400 AAATGCTTAA
1362410 ATAATTTTTTTCTTTTTTTTCC
1 ATAATTTTTTTCTTTTTTTTCC
*
1362432 ATAATATTTTTTCATTTTTTTTCA
1 ATAAT-TTTTTTC-TTTTTTTTCC
*
1362456 AT-TTTTTTCTTCCTTTTTTTTC
1 ATAATTTTT-TT-CTTTTTTTTC
1362478 TTCTCATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.22
23 19 0.47
24 12 0.30
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (22 bp):
ATAATTTTTTTCTTTTTTTTCC
Found at i:1362459 original size:11 final size:10
Alignment explanation
Indices: 1362414--1362464 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
1362404 GCTTAAATAA
1362414 TTTTTTTC-T
1 TTTTTTTCAT
1362423 TTTTTTTCCAT
1 TTTTTTT-CAT
1362434 AATATTTTTTCAT
1 --T-TTTTTTCAT
*
1362447 TTTTTTTCAA
1 TTTTTTTCAT
1362457 TTTTTTTC
1 TTTTTTTC
1362465 TTCCTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 7 0.19
10 17 0.47
11 2 0.06
13 4 0.11
14 6 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:1365435 original size:3 final size:3
Alignment explanation
Indices: 1365427--1365485 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1365417 TAAAAAATCT
1365427 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1365475 TTA TTA TTA TT
1 TTA TTA TTA TT
1365486 TTAGAATAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1374320 original size:2 final size:2
Alignment explanation
Indices: 1374313--1374355 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1374303 CAGCCTACAA
1374313 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
1374355 A
1 A
1374356 AAGATTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1374415 original size:7 final size:7
Alignment explanation
Indices: 1374403--1374436 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1374393 GGTAAATTTT
1374403 TTTATTG
1 TTTATTG
1374410 TTTATTG
1 TTTATTG
1374417 TTTATTG
1 TTTATTG
1374424 TTTATTG
1 TTTATTG
1374431 TTTATT
1 TTTATT
1374437 TTCAAGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (7 bp):
TTTATTG
Found at i:1380378 original size:17 final size:17
Alignment explanation
Indices: 1380358--1380429 Score: 71
Period size: 16 Copynumber: 4.4 Consensus size: 17
1380348 ATTTTTTTTT
1380358 TTTAAAGATT-TTTTAAA
1 TTTAAA-ATTATTTTAAA
*
1380375 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
1380392 TTT-AAATTATTTTAAA
1 TTTAAAATTATTTTAAA
* *
1380408 -CTAAGA-TATTTTTAAA
1 TTTAAAATTA-TTTTAAA
1380424 TTTAAA
1 TTTAAA
1380430 TTTTTTTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.07
16 23 0.51
17 19 0.42
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:1380436 original size:16 final size:16
Alignment explanation
Indices: 1380366--1380436 Score: 90
Period size: 16 Copynumber: 4.4 Consensus size: 16
1380356 TTTTTAAAGA
1380366 TTTTTTAAATTTAAAT
1 TTTTTTAAATTTAAAT
1380382 TTATTTTAAATTTAAAT
1 TT-TTTTAAATTTAAAT
* *
1380399 TATTTTAAA-CTAAGAT
1 TTTTTTAAATTTAA-AT
*
1380415 ATTTTTAAATTTAAAT
1 TTTTTTAAATTTAAAT
1380431 TTTTTT
1 TTTTTT
1380437 TTGAGTTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.07
16 25 0.54
17 18 0.39
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (16 bp):
TTTTTTAAATTTAAAT
Found at i:1380548 original size:17 final size:17
Alignment explanation
Indices: 1380527--1380585 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1380517 TGAGTTTAAG
*
1380527 TAAAATTAGATAATTTT
1 TAAAATTAAATAATTTT
* **
1380544 AAAAATTTTATAATTTT
1 TAAAATTAAATAATTTT
*
1380561 TAAATTATAAATAATTTT
1 TAAAAT-TAAATAATTTT
1380579 TAAAATT
1 TAAAATT
1380586 TTATTATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TAAAATTAAATAATTTT
Found at i:1380563 original size:18 final size:17
Alignment explanation
Indices: 1380536--1380589 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1380526 GTAAAATTAG
*
1380536 ATAATTTTAAAAATTTT
1 ATAATTTTTAAAATTTT
*
1380553 ATAATTTTT-AAATTATAA
1 ATAATTTTTAAAATT-T-T
1380571 ATAATTTTTAAAATTTT
1 ATAATTTTTAAAATTTT
1380588 AT
1 AT
1380590 TATAATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
18 10 0.32
19 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATTTTTAAAATTTT
Found at i:1380587 original size:26 final size:24
Alignment explanation
Indices: 1380549--1380599 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 24
1380539 ATTTTAAAAA
*
1380549 TTTTATAATTTTTAAATTATAAATAAT
1 TTTTATAAATTTT--ATTAT-AATAAT
1380576 TTTTA-AAATTTTATTATAATAAT
1 TTTTATAAATTTTATTATAATAAT
1380599 T
1 T
1380600 AATTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
24 5 0.22
26 6 0.26
27 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAAATTTTATTATAATAAT
Found at i:1384273 original size:18 final size:18
Alignment explanation
Indices: 1384221--1384273 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1384211 TATATACTAG
*
1384221 ATACTAAATCTCTTACTC
1 ATACTAAATCTCTTATTC
*
1384239 ATACTAAATTTCTTATTC
1 ATACTAAATCTCTTATTC
* *
1384257 ATACGAAATCTCCTATT
1 ATACTAAATCTCTTATT
1384274 AAAAATCTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (18 bp):
ATACTAAATCTCTTATTC
Found at i:1386805 original size:15 final size:15
Alignment explanation
Indices: 1386785--1386827 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1386775 TATATATAAA
1386785 TATAAATTTTAAAAT
1 TATAAATTTTAAAAT
*
1386800 TATAAATATTTAATAT
1 TATAAAT-TTTAAAAT
*
1386816 TAAAAAATTTTA
1 T-ATAAATTTTA
1386828 TATATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
17 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:1386817 original size:16 final size:16
Alignment explanation
Indices: 1386785--1386830 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
1386775 TATATATAAA
*
1386785 TATAAAT-TTTAAAAT
1 TATAAATATTTAATAT
1386800 TATAAATATTTAATAT
1 TATAAATATTTAATAT
* *
1386816 TA-AAAAATTTTATAT
1 TATAAATATTTAATAT
1386831 ATCAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATATTTAATAT
Found at i:1386823 original size:17 final size:19
Alignment explanation
Indices: 1386801--1386842 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1386791 TTTTAAAATT
*
1386801 ATAAATATTTA-ATATTAA
1 ATAAATATTTATATATCAA
1386819 A-AAAT-TTTATATATCAA
1 ATAAATATTTATATATCAA
1386836 ATAAATA
1 ATAAATA
1386843 AGTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATATTTATATATCAA
Found at i:1386945 original size:8 final size:8
Alignment explanation
Indices: 1386932--1386968 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
1386922 TGTAATTATA
1386932 AAAAAATT
1 AAAAAATT
1386940 AAAAAATT
1 AAAAAATT
*
1386948 AAAATATT
1 AAAAAATT
1386956 AAAAATATT
1 AAAAA-ATT
1386965 AAAA
1 AAAA
1386969 TTTAGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAAAATT
Found at i:1387008 original size:9 final size:9
Alignment explanation
Indices: 1386930--1387010 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
1386920 AATGTAATTA
*
1386930 TAAAAAAAT
1 TAAAATAAT
1386939 TAAAA-AAT
1 TAAAATAAT
1386947 TAAAAT-AT
1 TAAAATAAT
1386955 TAAAA-ATAT
1 TAAAATA-AT
*
1386964 TAAAATTTAGT
1 TAAAA--TAAT
*
1386975 TAAAACTCAAA
1 TAAAA-T-AAT
*
1386986 TAAATTATAT
1 TAAAATA-AT
1386996 TAAAATAAT
1 TAAAATAAT
1387005 TAAAAT
1 TAAAAT
1387011 CAACTAGTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
8 15 0.26
9 21 0.37
10 9 0.16
11 11 0.19
12 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
TAAAATAAT
Found at i:1387318 original size:21 final size:21
Alignment explanation
Indices: 1387294--1387334 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1387284 GTTTGAAGAT
1387294 TTCATGTCTTCAATAGGTTGA
1 TTCATGTCTTCAATAGGTTGA
*
1387315 TTCATGTCTTCCATAGGTTG
1 TTCATGTCTTCAATAGGTTG
1387335 TCGCCTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (21 bp):
TTCATGTCTTCAATAGGTTGA
Found at i:1389063 original size:5 final size:5
Alignment explanation
Indices: 1389053--1389078 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1389043 TCATTAAATT
1389053 CCCTG CCCTG CCCTG CCCTG CCCTG C
1 CCCTG CCCTG CCCTG CCCTG CCCTG C
1389079 TGTCAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.19, T:0.19
Consensus pattern (5 bp):
CCCTG
Found at i:1389221 original size:40 final size:40
Alignment explanation
Indices: 1389179--1389255 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
1389169 AGTAATATTA
* *
1389179 AAAAATTATTTTA-TA-TTAATTTTATAATTAAAATTAAAT
1 AAAAATAATTTTATTATTTAA-TTAATAATTAAAATTAAAT
1389218 AAAAATAATTTTATTATTTAATTAATAATTAAAATTAA
1 AAAAATAATTTTATTATTTAATTAATAATTAAAATTAA
1389256 TTTGATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 12 0.35
40 18 0.53
41 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (40 bp):
AAAAATAATTTTATTATTTAATTAATAATTAAAATTAAAT
Found at i:1389478 original size:13 final size:13
Alignment explanation
Indices: 1389439--1389481 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 13
1389429 ATAATAATTT
1389439 TTAATTTTTAAAA
1 TTAATTTTTAAAA
1389452 TTATATTATTTTAAAA
1 TTA-A-T-TTTTAAAA
1389468 TTAATTTTTAAAA
1 TTAATTTTTAAAA
1389481 T
1 T
1389482 ATGTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.44
14 2 0.07
15 2 0.07
16 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTTTAAAA
Found at i:1389593 original size:9 final size:9
Alignment explanation
Indices: 1389579--1389634 Score: 67
Period size: 9 Copynumber: 5.9 Consensus size: 9
1389569 ATACTAGTTT
*
1389579 TTTTTTTCA
1 TTTTTTTAA
1389588 TTTTTTTAA
1 TTTTTTTAA
1389597 TTTTTTATAA
1 TTTTTT-TAA
*
1389607 TTTATTTAAA
1 TTT-TTTTAA
1389617 TTTTTTTTAA
1 -TTTTTTTAA
1389627 TTTTTTTA
1 TTTTTTTA
1389635 TAATTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 22 0.54
10 13 0.32
11 6 0.15
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:1389593 original size:10 final size:10
Alignment explanation
Indices: 1389578--1389640 Score: 74
Period size: 10 Copynumber: 6.3 Consensus size: 10
1389568 CATACTAGTT
*
1389578 TTTTTTTTCA
1 TTTTTTTTAA
1389588 -TTTTTTTAA
1 TTTTTTTTAA
*
1389597 TTTTTTATAA
1 TTTTTTTTAA
* *
1389607 TTTATTTAAA
1 TTTTTTTTAA
1389617 TTTTTTTTAA
1 TTTTTTTTAA
1389627 TTTTTTTATAA
1 TTTTTTT-TAA
1389638 TTT
1 TTT
1389641 ATTTAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
9 8 0.18
10 30 0.68
11 6 0.14
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:1389632 original size:31 final size:30
Alignment explanation
Indices: 1389588--1389690 Score: 124
Period size: 31 Copynumber: 3.5 Consensus size: 30
1389578 TTTTTTTTCA
1389588 TTTTTTTAATTTTTTATAATTTATTTAAAT
1 TTTTTTTAATTTTTTATAATTTATTTAAAT
1389618 TTTTTTTAATTTTTTTATAATTTATTTAAA-
1 TTTTTTTAA-TTTTTTATAATTTATTTAAAT
**
1389648 AATTTTTAA---TTTATAATTTATTTAAAGCT
1 TTTTTTTAATTTTTTATAATTTATTTAAA--T
*
1389677 TTTTTTCAATTTTT
1 TTTTTTTAATTTTT
1389691 ATCATTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
26 17 0.28
29 6 0.10
30 16 0.26
31 20 0.33
32 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTTTTTAATTTTTTATAATTTATTTAAAT
Found at i:1389645 original size:11 final size:11
Alignment explanation
Indices: 1389594--1389671 Score: 72
Period size: 11 Copynumber: 7.0 Consensus size: 11
1389584 TTCATTTTTT
1389594 TAATTT-TTTA
1 TAATTTATTTA
1389604 TAATTTATTTA
1 TAATTTATTTA
*
1389615 -AATTT-TTTT
1 TAATTTATTTA
*
1389624 TAATTTTTTTA
1 TAATTTATTTA
1389635 TAATTTATTTAA
1 TAATTTATTT-A
*
1389647 AAATTTTTAATTTA
1 TAA--TTT-ATTTA
1389661 TAATTTATTTA
1 TAATTTATTTA
1389672 AAGCTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
9 3 0.05
10 16 0.29
11 21 0.38
12 6 0.11
14 6 0.11
15 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TAATTTATTTA
Found at i:1389954 original size:19 final size:19
Alignment explanation
Indices: 1389917--1389955 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1389907 AAATATCAAA
* **
1389917 TTTATTTTTTTATTTTTTT
1 TTTAATTTTTTATAGTTTT
1389936 TTTAATTTTTTATAGTTTT
1 TTTAATTTTTTATAGTTTT
1389955 T
1 T
1389956 AGTTTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTAATTTTTTATAGTTTT
Found at i:1390032 original size:15 final size:16
Alignment explanation
Indices: 1390012--1390050 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1390002 TATATTATTA
**
1390012 ATTTTTTTG-GACTTT
1 ATTTTTTTGAGAAGTT
1390027 ATTTTTTTGAGAAGTT
1 ATTTTTTTGAGAAGTT
1390043 ATTTTTTT
1 ATTTTTTT
1390051 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (16 bp):
ATTTTTTTGAGAAGTT
Found at i:1390127 original size:18 final size:20
Alignment explanation
Indices: 1390104--1390149 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
1390094 TCTTCTAATA
1390104 TTTTTTTCT-GTTTTAC-TT
1 TTTTTTTCTAGTTTTACATT
1390122 TTTTTTT-TAGTTTTACATT
1 TTTTTTTCTAGTTTTACATT
*
1390141 ATTTTTTCT
1 TTTTTTTCT
1390150 TTAAGTAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 8 0.33
20 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTTTTTCTAGTTTTACATT
Found at i:1391251 original size:50 final size:51
Alignment explanation
Indices: 1391142--1391270 Score: 138
Period size: 50 Copynumber: 2.5 Consensus size: 51
1391132 ATTTAATAAC
* * * *
1391142 TTGGAGATAAAAATGGGGTTAGAGTATCCTTGATGGTGAAAAATTGATATT
1 TTGGAAATAAAAATGCGGTTAGAGTATCCTTGATAGTGAAAAATCGATATT
** * * *
1391193 TTAAAAATAAAAATGCTGTTGGAGTATCC-TGATAGTGAAAAGTCGATATT
1 TTGGAAATAAAAATGCGGTTAGAGTATCCTTGATAGTGAAAAATCGATATT
1391243 TTGGAAAT-AAAAT-CAGGGTTAGAGTATC
1 TTGGAAATAAAAATGC--GGTTAGAGTATC
1391271 TCCTCAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.02
49 5 0.08
50 34 0.54
51 23 0.37
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (51 bp):
TTGGAAATAAAAATGCGGTTAGAGTATCCTTGATAGTGAAAAATCGATATT
Found at i:1391394 original size:29 final size:28
Alignment explanation
Indices: 1391334--1391407 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1391324 GAAATAAAAT
* *
1391334 CGGG-TTAGAGTATCCCTTCAAAAATAA
1 CGGGATTAGAGTATCCCCTAAAAAATAA
*
1391361 CGGGATTAGAGTTTCCCCTAAAAAATAA
1 CGGGATTAGAGTATCCCCTAAAAAATAA
*
1391389 CAGGGATTAGAGCATCCCC
1 C-GGGATTAGAGTATCCCC
1391408 AATGGTGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.10
28 21 0.52
29 15 0.38
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (28 bp):
CGGGATTAGAGTATCCCCTAAAAAATAA
Found at i:1391456 original size:108 final size:106
Alignment explanation
Indices: 1391320--1391588 Score: 342
Period size: 107 Copynumber: 2.5 Consensus size: 106
1391310 AAAATTGGTA
* *
1391320 TTTAGAAATAAAATC-GGGTTAGAGTATCCCTTCAAAAATAACGGGATTAGAGTTTCCCCTAAAA
1 TTTAGAAATAAAATCAGGGTTAGAGTATCCC-TCAAAAATAACGGGGTTAGAGTATCCCCTAAAA
*
1391384 AATAACAGGGATTAGAGCATCCCCAATGGTGAAAAATCGATGT
65 AATAAC-GGGATTAGAGCATCCCCAATGATGAAAAATCGATGT
* * * ***
1391427 TTTAGAAATAAAATCAGGGTTAGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCTTCGGA
1 TTTAGAAATAAAATCAGGGTTAGAGTAT-CCCTCAAAAATAACGGGGTTAGAGTATCCCCTAAAA
* ** * *
1391492 AATAACGGGATTAGAGTATCCCTGATGATGGAAAATCGGTGT
65 AATAACGGGATTAGAGCATCCCCAATGATGAAAAATCGATGT
* * *
1391534 TTTAAAAATAAAATCAGGGTTAGAATATCTCCTCGAAAATAACGGGGTTAGAGTA
1 TTTAGAAATAAAATCAGGGTTAGAGTATC-CCTCAAAAATAACGGGGTTAGAGTA
1391589 ACTCCGATAA
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
106 1 0.01
107 93 0.66
108 43 0.31
109 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (106 bp):
TTTAGAAATAAAATCAGGGTTAGAGTATCCCTCAAAAATAACGGGGTTAGAGTATCCCCTAAAAA
ATAACGGGATTAGAGCATCCCCAATGATGAAAAATCGATGT
Found at i:1391480 original size:28 final size:28
Alignment explanation
Indices: 1391443--1391513 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1391433 AATAAAATCA
*
1391443 GGGTTAGAGTATCCCCTCAAAAATAATG
1 GGGTTAGAGTATCCCCTCAAAAATAACG
* * **
1391471 GGGTTGGAGTATCCCTTCGGAAATAACG
1 GGGTTAGAGTATCCCCTCAAAAATAACG
*
1391499 GGATTAGAGTATCCC
1 GGGTTAGAGTATCCC
1391514 TGATGATGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (28 bp):
GGGTTAGAGTATCCCCTCAAAAATAACG
Found at i:1395392 original size:26 final size:26
Alignment explanation
Indices: 1395363--1395423 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1395353 GCTAGGTTCG
*
1395363 TTATCATATATCCATAGCGTCTTCCT
1 TTATCATATATCCATAGCATCTTCCT
1395389 TTATCATATATCCATAGCATCTTCCT
1 TTATCATATATCCATAGCATCTTCCT
1395415 TTATCATAT
1 TTATCATAT
1395424 GATTGAGTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.05, T:0.44
Consensus pattern (26 bp):
TTATCATATATCCATAGCATCTTCCT
Found at i:1396217 original size:34 final size:35
Alignment explanation
Indices: 1396179--1396245 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1396169 CCTTACAACA
1396179 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1396213 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1396246 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1396721 original size:13 final size:13
Alignment explanation
Indices: 1396703--1396728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1396693 CAATTTTTTG
1396703 TGTATCGATACAT
1 TGTATCGATACAT
1396716 TGTATCGATACAT
1 TGTATCGATACAT
1396729 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1398538 original size:13 final size:13
Alignment explanation
Indices: 1398520--1398544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1398510 ACTGAAGTAA
1398520 TGTATCGATACAT
1 TGTATCGATACAT
1398533 TGTATCGATACA
1 TGTATCGATACA
1398545 ATCTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1401517 original size:34 final size:35
Alignment explanation
Indices: 1401479--1401545 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1401469 CCTTACAACA
1401479 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1401513 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1401546 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Done.