Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1263389 original size:18 final size:19
Alignment explanation
Indices: 1263345--1263389 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1263335 GGTTTCAAAG
* *
1263345 TATTCGTATTTCTCTTTAG
1 TATTCATATTTCTCTTTAC
1263364 TATTCATATTTCTCTTT-C
1 TATTCATATTTCTCTTTAC
*
1263382 TTTTCATA
1 TATTCATA
1263390 CGATTTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (19 bp):
TATTCATATTTCTCTTTAC
Found at i:1265188 original size:112 final size:116
Alignment explanation
Indices: 1265065--1265308 Score: 336
Period size: 121 Copynumber: 2.1 Consensus size: 116
1265055 AATTAAATTG
*
1265065 TTTTTATTTTGTGATTTGGATTCTCTAAATAA-TTT-TAA-T-TGTTTAGTATAATTTATAAATT
1 TTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTATAATTATGTTTAATATAATTTATAAATT
*
1265126 GTTATTTAAAAATAATTGTAAAAAATAATTTAAATAAAAACTTA-AAACTTA
66 GTTATTTAAAAATAATTGTAAAAAATAATTTAAATAAAAA-TTATAAACTCA
*
1265177 TTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAACGTAATTTTATTTTTAATATAATTTAT
1 TTTTTATTTTGTGATTTGGATTCTCTAAATAATTTT-A--TAA--TTATGTTTAATATAATTTAT
* * *
1265242 ATATTGTTATTTAAAAATATTTGTAAAAAATAATTTAAATAAAAATTATTAAAGTCA
61 AAATTGTTATTTAAAAATAATTGTAAAAAATAATTTAAATAAAAATTA-TAAACTCA
1265299 TTTTTATTTT
1 TTTTTATTTT
1265309 TAAGTCTTAC
Statistics
Matches: 115, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
112 32 0.28
113 3 0.03
117 3 0.03
120 4 0.03
121 58 0.50
122 15 0.13
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (116 bp):
TTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTATAATTATGTTTAATATAATTTATAAATT
GTTATTTAAAAATAATTGTAAAAAATAATTTAAATAAAAATTATAAACTCA
Found at i:1265330 original size:121 final size:122
Alignment explanation
Indices: 1265094--1265332 Score: 308
Period size: 121 Copynumber: 2.0 Consensus size: 122
1265084 ATTCTCTAAA
*
1265094 TAATTTTAATTGTTTAGTATAATTTATAAATTGTTATTTAAAAATAATTGTAAAAAATAATTTAA
1 TAATTTTAATTGTTTAATATAATTTATAAATTGTTATTTAAAAATAATTGTAAAAAATAATTTAA
* * ** **
1265159 ATAAAAACTTAAAACTTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAACG
66 ATAAAAACTTAAAACTCATTTTTATTTTGTAATTTACATTAACT-AATAATTTTAACG
* *
1265217 TAATTTT-ATT-TTTAATATAATTTATATATTGTTATTTAAAAATATTTGTAAAAAATAATTTAA
1 TAATTTTAATTGTTTAATATAATTTATAAATTGTTATTTAAAAATAATTGTAAAAAATAATTTAA
*
1265280 ATAAAAA-TTATTAAAGTCATTTTTATTTT-TAAGTCTTACATTAACT-ATAATTT
66 ATAAAAACTTA--AAACTCATTTTTATTTTGTAA-T-TTACATTAACTAATAATTT
1265333 AATATATATA
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
120 3 0.03
121 66 0.65
122 19 0.19
123 14 0.14
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (122 bp):
TAATTTTAATTGTTTAATATAATTTATAAATTGTTATTTAAAAATAATTGTAAAAAATAATTTAA
ATAAAAACTTAAAACTCATTTTTATTTTGTAATTTACATTAACTAATAATTTTAACG
Found at i:1266309 original size:27 final size:27
Alignment explanation
Indices: 1266273--1266339 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1266263 TATTAGCTTA
* *
1266273 TTAAATATATTTTCTTATTAACTTAATT
1 TTAAA-ATATATTATTATTAACTTAATT
* **
1266301 TTAAAATATATTATTTTTATTTTAATT
1 TTAAAATATATTATTATTAACTTAATT
*
1266328 TAAAAATATATT
1 TTAAAATATATT
1266340 TTAACACCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAAAATATATTATTATTAACTTAATT
Found at i:1267052 original size:31 final size:33
Alignment explanation
Indices: 1267017--1267082 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 33
1267007 TATATAATAA
1267017 ATTATTATCTAAACTTTT-AAA-AATATATTTT
1 ATTATTATCTAAACTTTTCAAAGAATATATTTT
* * *
1267048 ATTATTATTTTAACTTTTCAAAGTATATATTTT
1 ATTATTATCTAAACTTTTCAAAGAATATATTTT
1267081 AT
1 AT
1267083 CTTAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 16 0.53
32 3 0.10
33 11 0.37
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (33 bp):
ATTATTATCTAAACTTTTCAAAGAATATATTTT
Found at i:1267099 original size:57 final size:56
Alignment explanation
Indices: 1267037--1267161 Score: 141
Period size: 57 Copynumber: 2.2 Consensus size: 56
1267027 AAACTTTTAA
* * *
1267037 AAATATATTTTATTATTATTTTAACTT-TTCAAAGTATA-TATT-TTATCTTAATTTAC
1 AAATATATTTTATTACTACTTTAAATTATT-AAA-TATATTATTCTTATCTTAATTT-C
*
1267093 TAAATATATTATATTACTACTTTAAATTATTAAATATATTTATTCTTATCTTAATTTC
1 -AAATATATTTTATTACTACTTTAAATTATTAAATATA-TTATTCTTATCTTAATTTC
1267151 AAA-ATATTTTA
1 AAATATATTTTA
1267162 ACAACAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
56 11 0.19
57 29 0.49
58 7 0.12
59 12 0.20
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (56 bp):
AAATATATTTTATTACTACTTTAAATTATTAAATATATTATTCTTATCTTAATTTC
Found at i:1268525 original size:120 final size:120
Alignment explanation
Indices: 1268312--1268527 Score: 360
Period size: 120 Copynumber: 1.8 Consensus size: 120
1268302 TCGATTCTAT
* *
1268312 CAAATCTTAGATCGGATAAATCAGTTCAAATAATCAGATTCAGATCAAATTTATCAAATTTAATA
1 CAAATCTTAGATCAGATAAATCAGTTCAAATAATCAGATTCAGATCAAATTTACCAAATTTAATA
* *
1268377 AAACATGTATAATTTAAGGGGCAATGGTTCAATAATCGGTTCGAATGATTCAAAA
66 AAACATGTATAATCTAAGGGGAAATGGTTCAATAATCGGTTCGAATGATTCAAAA
* * * *
1268432 CAAATCTTAGATCAGATAAATTAGTTCGAATAATTAGATTCATATCAAATTTACCAAATTTAATA
1 CAAATCTTAGATCAGATAAATCAGTTCAAATAATCAGATTCAGATCAAATTTACCAAATTTAATA
1268497 AAACATGTATAATCTAAGGGGAAATGGTTCA
66 AAACATGTATAATCTAAGGGGAAATGGTTCA
1268528 GTAAGCCTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 88 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (120 bp):
CAAATCTTAGATCAGATAAATCAGTTCAAATAATCAGATTCAGATCAAATTTACCAAATTTAATA
AAACATGTATAATCTAAGGGGAAATGGTTCAATAATCGGTTCGAATGATTCAAAA
Found at i:1273390 original size:23 final size:23
Alignment explanation
Indices: 1273364--1273412 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1273354 TTCTGATACA
*
1273364 TTTATCTCTGTCTTTGTGACACG
1 TTTATCTATGTCTTTGTGACACG
* * *
1273387 TTTATTTATGTTTTTGTGGCACG
1 TTTATCTATGTCTTTGTGACACG
1273410 TTT
1 TTT
1273413 TTTTCTCGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (23 bp):
TTTATCTATGTCTTTGTGACACG
Found at i:1284237 original size:34 final size:35
Alignment explanation
Indices: 1284194--1284265 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
1284184 TCTTCTACAT
1284194 GAATTGGAT-GTCATTCCATTCAACCACTAAATTA
1 GAATTGGATAGTCATTCCATTCAACCACTAAATTA
* **
1284228 GAATTGGATGAGTCATTCCATTCGAGTACTAAATTA
1 GAATTGGAT-AGTCATTCCATTCAACCACTAAATTA
1284264 GA
1 GA
1284266 TTAACGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 9 0.27
36 24 0.73
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (35 bp):
GAATTGGATAGTCATTCCATTCAACCACTAAATTA
Found at i:1290408 original size:22 final size:22
Alignment explanation
Indices: 1290380--1290427 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1290370 CGTTGAATGT
*
1290380 TGAACGGTTCAGAATTCAGTGC
1 TGAACGGTTCAGAATTCAGCGC
*
1290402 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGAATTCAGCGC
1290424 TGAA
1 TGAA
1290428 TGATTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (22 bp):
TGAACGGTTCAGAATTCAGCGC
Found at i:1292960 original size:2 final size:2
Alignment explanation
Indices: 1292953--1293000 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1292943 ACTTATCCAA
1292953 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
1292995 AT AT AT
1 AT AT AT
1293001 TGGTGGTGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1300778 original size:5 final size:6
Alignment explanation
Indices: 1300763--1300787 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1300753 TGGAAAATTA
1300763 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
1300788 GGAGGATCAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1307735 original size:24 final size:22
Alignment explanation
Indices: 1307708--1307763 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
1307698 ATTTGTTTTT
*
1307708 ATTTCTTTTAAATAATGCTTTGGG
1 ATTTCTTTTAAATAAT-CTGT-GG
1307732 ATTT-TTTGTAAATAATCTGTGG
1 ATTTCTTT-TAAATAATCTGTGG
1307754 ATTTTCTTTT
1 A-TTTCTTTT
1307764 TTTGTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 15 0.54
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.55
Consensus pattern (22 bp):
ATTTCTTTTAAATAATCTGTGG
Found at i:1308591 original size:30 final size:30
Alignment explanation
Indices: 1308555--1308654 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
1308545 TAAACGAATA
1308555 AACATGAACAACATCAAAAATAAATAAACG
1 AACATGAACAACATCAAAAATAAATAAACG
*
1308585 AACATGAAC-ACGATACTAAAAAT--TTAAACG
1 AACATGAACAAC-AT-C-AAAAATAAATAAACG
* * * * * *
1308615 AACATGAATATCTTCAAAAACAAACAAATG
1 AACATGAACAACATCAAAAATAAATAAACG
*
1308645 AACACGAACA
1 AACATGAACA
1308655 CAGTTTTATT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 5 0.09
29 3 0.06
30 38 0.70
31 2 0.04
32 6 0.11
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.16
Consensus pattern (30 bp):
AACATGAACAACATCAAAAATAAATAAACG
Found at i:1312031 original size:19 final size:19
Alignment explanation
Indices: 1312009--1312048 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1311999 CACCCTTTGC
*
1312009 AGTAAGGCGCACCCCCTGT
1 AGTAAGACGCACCCCCTGT
* *
1312028 AGTATGACGCGCCCCCTGT
1 AGTAAGACGCACCCCCTGT
1312047 AG
1 AG
1312049 CGAGCTATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (19 bp):
AGTAAGACGCACCCCCTGT
Found at i:1312413 original size:9 final size:9
Alignment explanation
Indices: 1312397--1312433 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1312387 ATTTAGTATT
1312397 TTTA-TTAA
1 TTTATTTAA
1312405 TTTATTTAA
1 TTTATTTAA
1312414 TTTATTTAA
1 TTTATTTAA
1312423 -TTATTTTAA
1 TTTA-TTTAA
1312432 TT
1 TT
1312434 GTTTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 18 0.69
10 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTTAA
Found at i:1312417 original size:17 final size:18
Alignment explanation
Indices: 1312376--1312433 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1312366 TATTAAGGTA
1312376 TAATTTATTATATTTAGTAT
1 TAATTTATTA-ATTTAGT-T
1312396 T--TTTATTAATTTA-TT
1 TAATTTATTAATTTAGTT
*
1312411 TAATTTATTTAA-TTATTT
1 TAATTTA-TTAATTTAGTT
1312429 TAATT
1 TAATT
1312434 GTTTAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 12 0.35
18 18 0.53
20 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TAATTTATTAATTTAGTT
Found at i:1312422 original size:18 final size:17
Alignment explanation
Indices: 1312397--1312450 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
1312387 ATTTAGTATT
1312397 TTTATTAATT-TATTTAA
1 TTTATTAATTAT-TTTAA
1312414 TTTATTTAATTATTTTAA
1 TTTA-TTAATTATTTTAA
1312432 TTGT-TTAA-TATTTT-A
1 TT-TATTAATTATTTTAA
1312447 TTTA
1 TTTA
1312451 AATAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 6 0.18
17 8 0.24
18 13 0.39
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTAATTATTTTAA
Found at i:1316965 original size:144 final size:145
Alignment explanation
Indices: 1316701--1316991 Score: 566
Period size: 144 Copynumber: 2.0 Consensus size: 145
1316691 TCATCTTCAC
1316701 CATCAGAGTTGAATTGCGGTGATTCTAGGTGAATGAATAGTCCAGTCTCAGCACCATCCATACCA
1 CATCAGAGTTGAATTGCGGTGATTCTAGGTGAATGAATAGTCCAGTCTCAGCACCATCCA-ACCA
1316766 AGCTCACGAAGCAGTTCTTCTGGTGGAGATGATGGTTCCTCCATGCTCTCCACATTTAGGTCGAA
65 AGCTCACGAAGCAGTTCTTCTGGTGGAGATGATGGTTCCTCCATGCTCTCCACATTTAGGTCGAA
1316831 GAACCTACTACTTGCA
130 GAACCTACTACTTGCA
1316847 CATCAGAGTTGAATTGCGGTGATTCTAGGTGAATGAATAGTCCAGTCTCAGCACCATCC-ACCAA
1 CATCAGAGTTGAATTGCGGTGATTCTAGGTGAATGAATAGTCCAGTCTCAGCACCATCCAACCAA
1316911 GCTCACGAAGCAGTTCTTCTGGTGGAGATGATGGTTCCTCCATGCTCTCCACATTTAGGTCGAAG
66 GCTCACGAAGCAGTTCTTCTGGTGGAGATGATGGTTCCTCCATGCTCTCCACATTTAGGTCGAAG
1316976 AACCTACTACTTGCA
131 AACCTACTACTTGCA
1316991 C
1 C
1316992 GCCTTCCCCT
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
144 86 0.59
146 59 0.41
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (145 bp):
CATCAGAGTTGAATTGCGGTGATTCTAGGTGAATGAATAGTCCAGTCTCAGCACCATCCAACCAA
GCTCACGAAGCAGTTCTTCTGGTGGAGATGATGGTTCCTCCATGCTCTCCACATTTAGGTCGAAG
AACCTACTACTTGCA
Found at i:1321949 original size:31 final size:31
Alignment explanation
Indices: 1321873--1321934 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1321863 AGTACACAAA
* *
1321873 TGATCCATCGACTATAAGACATTGTTTTGTT
1 TGATCCCTCGACTATAAGACATTGCTTTGTT
1321904 TGATCCCTCGACTATAAGACATTGCTTTGTT
1 TGATCCCTCGACTATAAGACATTGCTTTGTT
1321935 GAGTCTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (31 bp):
TGATCCCTCGACTATAAGACATTGCTTTGTT
Found at i:1321979 original size:60 final size:60
Alignment explanation
Indices: 1321911--1322038 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 60
1321901 GTTTGATCCC
* * * *
1321911 TCGACTATAAGACATTGCTTTGTTGAG-TCTCTTGACTATTATAAGTTATAAAATGGTCAT
1 TCGACTATAAGACAATGATTTGTTGAGTTCTC-TGACTATTAAAAGTTACAAAATGGTCAT
* *
1321971 TTGACTATAAGACAATGATTTGTTGAGTTCTCTGATTATTAAAAGTTACAAAATGGTCAT
1 TCGACTATAAGACAATGATTTGTTGAGTTCTCTGACTATTAAAAGTTACAAAATGGTCAT
1322031 TCGACTAT
1 TCGACTAT
1322039 TCATATATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 56 0.93
61 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (60 bp):
TCGACTATAAGACAATGATTTGTTGAGTTCTCTGACTATTAAAAGTTACAAAATGGTCAT
Found at i:1331242 original size:23 final size:23
Alignment explanation
Indices: 1331198--1331242 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1331188 ATTATTATAT
*
1331198 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* * *
1331221 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTACAATTATACG
1331243 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:1332177 original size:204 final size:204
Alignment explanation
Indices: 1331815--1332192 Score: 535
Period size: 204 Copynumber: 1.9 Consensus size: 204
1331805 GGGTGTTACA
* * *
1331815 AGCGAACTCGTTTAGCAAACACCTTTGCCGGAAGGATGACTCAAACCTCACCCTCCATCACATTG
1 AGCGAACTCGTTTAGCAAACACCTCTACCGGAAGGATGACTCAAACCTCACCCTACATCACATTG
* * *
1331880 GGAAGAAAGAATTGCAACGAGTGTTCTTCTGAGGAAGAAAAAATGACCTATAATCCAAATTAGGG
66 GGAAGAAAGAACTGCAACGAGTGTTCTTCTGAGGAAGAAAAAACGACCTACAATCCAAATTAGGG
* * * *
1331945 CCCTCCATCCCCGCCTTCACAGCAGCGAAGCACTCAGACCCTCCGACCTTGCACCAATACCGAAT
131 CCATCCATCCCCACCTCCACAGCAGCGAAGCAATCAGACCCTCCGACCTTGCACCAATACCGAAT
1332010 TTCTCCAGT
196 TTCTCCAGT
* * * * * *
1332019 AGCGAGCTCGTTTAGTAAACACCTCTACCGGAGGGATGACTCGAACCTCACCCTACGTCGCA-TG
1 AGCGAACTCGTTTAGCAAACACCTCTACCGGAAGGATGACTCAAACCTCACCCTACATCACATTG
* * * * *
1332083 AGGAGGAAAGAACTGCAACGAGTGTTCTTTTGAGGAAGAAAAAACGGCCTCCAATCCAAATT-TG
66 -GGAAGAAAGAACTGCAACGAGTGTTCTTCTGAGGAAGAAAAAACGACCTACAATCCAAATTAGG
1332147 GCCATCCATCCCCACCTCCACAGCCAGCGAAGCAATCAGACCCTCC
130 GCCATCCATCCCCACCTCCACAG-CAGCGAAGCAATCAGACCCTCC
1332193 AACCCAACCT
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
203 23 0.15
204 128 0.85
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (204 bp):
AGCGAACTCGTTTAGCAAACACCTCTACCGGAAGGATGACTCAAACCTCACCCTACATCACATTG
GGAAGAAAGAACTGCAACGAGTGTTCTTCTGAGGAAGAAAAAACGACCTACAATCCAAATTAGGG
CCATCCATCCCCACCTCCACAGCAGCGAAGCAATCAGACCCTCCGACCTTGCACCAATACCGAAT
TTCTCCAGT
Found at i:1332467 original size:75 final size:75
Alignment explanation
Indices: 1332376--1332560 Score: 203
Period size: 75 Copynumber: 2.5 Consensus size: 75
1332366 CATAAATAAA
* * *
1332376 GTCAAATATCAAGATTCAAACCACAATATTAAGAT-TAGAACAGTAAAATCCATAAACAACCCAT
1 GTCAAATATCAAGATTCAAACCACAATATTAA-ATCAAGAACAATAAAATCCATAAACAAACCAT
1332440 AATATTAAAAT
65 AATATTAAAAT
* * * * * *
1332451 GTCAAATTTCAAGATTCAACCCACAATATTAACTCAAGAATAATAAAATCCATAATCAAATCATA
1 GTCAAATATCAAGATTCAAACCACAATATTAAATCAAGAACAATAAAATCCATAAACAAACCATA
*
1332516 ATATTAAAGT
66 ATATTAAAAT
* * * * *
1332526 GTCCAATCTTAAGACTT-AAACTATAATATTAAATC
1 GTCAAATATCAAGA-TTCAAACCACAATATTAAATC
1332561 CAAACCAAAC
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 1 0.01
75 88 0.97
76 2 0.02
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (75 bp):
GTCAAATATCAAGATTCAAACCACAATATTAAATCAAGAACAATAAAATCCATAAACAAACCATA
ATATTAAAAT
Found at i:1345857 original size:24 final size:25
Alignment explanation
Indices: 1345829--1345875 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1345819 ATTTGAGGAC
1345829 TTATTTA-ATTTAAAAA-ATAAAAAA
1 TTATTTAGA-TTAAAAATATAAAAAA
1345853 TTATTTAGATTAAAAATATAAAA
1 TTATTTAGATTAAAAATATAAAA
1345876 TATAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATTTAGATTAAAAATATAAAAAA
Found at i:1346360 original size:14 final size:15
Alignment explanation
Indices: 1346341--1346373 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1346331 TGGAAGGTTA
1346341 ATTTGGAGTTTAGG-
1 ATTTGGAGTTTAGGT
*
1346355 ATTTGGATTTTAGGT
1 ATTTGGAGTTTAGGT
1346370 ATTT
1 ATTT
1346374 TAATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (15 bp):
ATTTGGAGTTTAGGT
Found at i:1349942 original size:64 final size:63
Alignment explanation
Indices: 1349855--1350013 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1349845 TTAACATGTA
* * * *
1349855 CATCGATACACTACCTATGCATCGATACACAA-AGCACCTTCGATGTTTTAATCTTAAGGGGGTG
1 CATCGATGCACTACCTATGCATCGATACACAATAGCA--TTCGATATTTCAATCTTAAAGGGGTG
* * * * * * *
1349919 TATCGATGCACTCCCTATGCATCGATGCACTAATTGTATTCGATATTTCCATTTTAAAGGGGTG
1 CATCGATGCACTACCTATGCATCGATACAC-AATAGCATTCGATATTTCAATCTTAAAGGGGTG
* *
1349983 CATCAATGCACTTCCTATGCATCGATACACA
1 CATCGATGCACTACCTATGCATCGATACACA
1350014 CTAAACAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 73 0.94
65 2 0.03
66 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (63 bp):
CATCGATGCACTACCTATGCATCGATACACAATAGCATTCGATATTTCAATCTTAAAGGGGTG
Found at i:1353348 original size:23 final size:23
Alignment explanation
Indices: 1353332--1353390 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1353322 CGTATAAATG
1353332 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* *
1353355 CACCGAAGTGCCGCATAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
1353378 CACCGAAGTGCCA
1 CACCGAAGTGCCA
1353391 TATAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:1354993 original size:64 final size:63
Alignment explanation
Indices: 1354909--1355070 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 63
1354899 CCCTTAACAT
* * *
1354909 GTGCATCGATGCACTACCTATGCATCGATTCACAA-AGCACCTTCGATGTTT-TAATCTTAAGGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAATAGCA--TTCGATATTTCT-ATCTTAAAGG
1354972 G
63 G
* * * * *
1354973 GTGTATCGATGCACTCCCTATGCATCGATGCACTAATTGCATTCGATATTTCTATTTTAAAGGG
1 GTGCATCGATGCACTACCTATGCATCGATACAC-AATAGCATTCGATATTTCTATCTTAAAGGG
* * *
1355037 GTGCATCAATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTACCTATGCATCGATACACA
1355071 CTGAACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.01
64 76 0.92
65 3 0.04
66 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTATGCATCGATACACAATAGCATTCGATATTTCTATCTTAAAGGG
Found at i:1360569 original size:10 final size:10
Alignment explanation
Indices: 1360554--1360579 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1360544 CAGTCATAAT
1360554 TTATTTTTGA
1 TTATTTTTGA
1360564 TTATTTTTGA
1 TTATTTTTGA
1360574 TTATTT
1 TTATTT
1360580 GCTTTATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
TTATTTTTGA
Found at i:1361438 original size:45 final size:44
Alignment explanation
Indices: 1361347--1361450 Score: 104
Period size: 45 Copynumber: 2.4 Consensus size: 44
1361337 TCTATCAAAA
* * ** *
1361347 AATTACTAATTTATTAATAGATAATAAAATGATGATAAATGGTT
1 AATTAATAATTTATTAATAAATAATAAAAAAATGATAAATGATT
* * *
1361391 AATCTATTAATTTTTTAATAAATAATAAAAAAAT-ACTAAATTATT
1 AAT-TAATAATTTATTAATAAATAATAAAAAAATGA-TAAATGATT
1361436 AATTAATAA-TTATTA
1 AATTAATAATTTATTA
1361451 TTCTATTACA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 5 0.10
44 9 0.18
45 35 0.71
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (44 bp):
AATTAATAATTTATTAATAAATAATAAAAAAATGATAAATGATT
Found at i:1364820 original size:71 final size:71
Alignment explanation
Indices: 1364698--1364838 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
1364688 GCGTTTCTAG
*
1364698 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAATCGAACGAAAGGAAGCATCGGCACTTCCG
1 TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAATCGAACGAAAGGAAGCATC-GCACTTCCG
1364763 ATTCAAA
65 ATTCAAA
*
1364770 TCGAACGGAAAGAAGCATC-GCACTTCCGATTCAAGTCGAACGGAAA-GAAGCATCGCACTTCCG
1 TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAATCGAAC-GAAAGGAAGCATCGCACTTCCG
1364833 ATTCAA
65 ATTCAA
1364839 CTAGAACGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
70 15 0.23
71 29 0.44
72 22 0.33
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.17
Consensus pattern (71 bp):
TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAATCGAACGAAAGGAAGCATCGCACTTCCGA
TTCAAA
Found at i:1364846 original size:35 final size:36
Alignment explanation
Indices: 1364698--1364838 Score: 234
Period size: 35 Copynumber: 4.0 Consensus size: 36
1364688 GCGTTTCTAG
*
1364698 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
1 TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAA
1364734 TCGAAC-GAAAGGAAGCATCGGCACTTCCGATTCAAA
1 TCGAACGGAAA-GAAGCATCGGCACTTCCGATTCAAA
*
1364770 TCGAACGGAAAGAAGCATC-GCACTTCCGATTCAAG
1 TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAA
1364805 TCGAACGGAAAGAAGCATC-GCACTTCCGATTCAA
1 TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAA
1364839 CTAGAACGAA
Statistics
Matches: 101, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
35 52 0.51
36 45 0.45
37 4 0.04
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.17
Consensus pattern (36 bp):
TCGAACGGAAAGAAGCATCGGCACTTCCGATTCAAA
Found at i:1373615 original size:45 final size:45
Alignment explanation
Indices: 1373551--1373641 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1373541 AAGTTGAATC
* *
1373551 GAAAAAGAACAGACCGTCGATATTCAGACACTAATGTAGATAAAT
1 GAAAAAGAACAAACCGTCGATATTCAGACACTAATGGAGATAAAT
* *
1373596 GAAAAAGATCAAACCGTCGATATTCAGACATTAATGGAGATAAAT
1 GAAAAAGAACAAACCGTCGATATTCAGACACTAATGGAGATAAAT
1373641 G
1 G
1373642 GTTCGAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (45 bp):
GAAAAAGAACAAACCGTCGATATTCAGACACTAATGGAGATAAAT
Found at i:1375531 original size:20 final size:20
Alignment explanation
Indices: 1375502--1375540 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1375492 TCTAAATTCG
*
1375502 CAACGTGAATCTGTAAATCA
1 CAACGCGAATCTGTAAATCA
1375522 CAACGCGAATCTGTAAATC
1 CAACGCGAATCTGTAAATC
1375541 GCAATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATCA
Found at i:1375549 original size:30 final size:30
Alignment explanation
Indices: 1375515--1375574 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1375505 CGTGAATCTG
1375515 TAAATCACAACGCGAATCTGTAAATCGCAA
1 TAAATCACAACGCGAATCTGTAAATCGCAA
*
1375545 TAAATCGCAACGCGAATCTGTAAATCGCAA
1 TAAATCACAACGCGAATCTGTAAATCGCAA
1375575 CACATAAGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (30 bp):
TAAATCACAACGCGAATCTGTAAATCGCAA
Found at i:1375592 original size:20 final size:20
Alignment explanation
Indices: 1375569--1375692 Score: 128
Period size: 20 Copynumber: 6.1 Consensus size: 20
1375559 AATCTGTAAA
1375569 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1375589 TCGCAACACAGAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1375609 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
1375629 TCGCAACAC-TGAATTTCAAAT
1 TCGCAACACAT-AA-GTCAAAT
* *
1375650 TCGCAACGC-TAAATTTCAAAT
1 TCGCAACACAT-AA-GTCAAAT
*
1375671 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
1375691 TC
1 TC
1375693 TCAAAGCGTG
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.01
20 52 0.58
21 36 0.40
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:1375593 original size:50 final size:50
Alignment explanation
Indices: 1375494--1375594 Score: 116
Period size: 50 Copynumber: 2.0 Consensus size: 50
1375484 TCCCAGTTTC
* * **
1375494 TAAATTCGCAACGTGAATCTGTAAATCACAACGCGAATCTGTAAATCGCAA
1 TAAATTCGCAACGCGAATCTGTAAATCACAACAC-AATAAGTAAATCGCAA
*
1375545 TAAA-TCGCAACGCGAATCTGTAAATCGCAACAC-ATAAGTCAAATTCGCAA
1 TAAATTCGCAACGCGAATCTGTAAATCACAACACAATAAGT-AAA-TCGCAA
1375595 CACAGAAGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
48 4 0.09
49 3 0.07
50 32 0.74
51 4 0.09
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (50 bp):
TAAATTCGCAACGCGAATCTGTAAATCACAACACAATAAGTAAATCGCAA
Found at i:1375881 original size:22 final size:22
Alignment explanation
Indices: 1375856--1375906 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1375846 CTACGGCAAC
1375856 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
1375878 ATCCATCCCCATTTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1375900 ATCCGTC
1 ATCCGTC
1375907 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1378273 original size:4 final size:4
Alignment explanation
Indices: 1378264--1378305 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
1378254 TTTTTCGGTA
* *
1378264 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1378306 TCAGCAGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1380108 original size:20 final size:20
Alignment explanation
Indices: 1380083--1380128 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1380073 AAGGTACACT
1380083 TTCGCAACGCAAAAATCAAA
1 TTCGCAACGCAAAAATCAAA
** *
1380103 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCAAAAATCAAA
1380123 TTCGCA
1 TTCGCA
1380129 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCAAAAATCAAA
Found at i:1380173 original size:20 final size:20
Alignment explanation
Indices: 1380144--1380188 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1380134 ATTTTCTTAT
*
1380144 TGCGATAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
*
1380164 TGCGAAAGTCAAATTCGCAT
1 TGCGAAAGTCAAATTCGCAA
1380184 TGCGA
1 TGCGA
1380189 TTTTTGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCAA
Found at i:1380244 original size:20 final size:20
Alignment explanation
Indices: 1380197--1380253 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1380187 GATTTTTGGT
* * *
1380197 TTGCGATTTTGATTTTCGCG
1 TTGCGAATTTGACTTTCACG
**
1380217 TTATGAATTTGACTTTCACG
1 TTGCGAATTTGACTTTCACG
*
1380237 TTGCGAATTTAACTTTC
1 TTGCGAATTTGACTTTC
1380254 GCAACAATCG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCACG
Found at i:1382611 original size:3 final size:3
Alignment explanation
Indices: 1382603--1382639 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1382593 TCTTCAGGGA
* *
1382603 CTT CTT CTT ATT CTT CTT CTT ATT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1382640 AGGGTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1382618 original size:12 final size:12
Alignment explanation
Indices: 1382603--1382635 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1382593 TCTTCAGGGA
1382603 CTTCTTCTTATT
1 CTTCTTCTTATT
1382615 CTTCTTCTTATT
1 CTTCTTCTTATT
1382627 CTTCTTCTT
1 CTTCTTCTT
1382636 CTTCAGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTCTTCTTATT
Found at i:1382848 original size:24 final size:24
Alignment explanation
Indices: 1382814--1382867 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1382804 CTAAAACATC
1382814 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1382838 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1382862 ATCAAA
1 ATCAAA
1382868 TATCAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1383617 original size:22 final size:23
Alignment explanation
Indices: 1383576--1383618 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1383566 AAGTTGATAG
*
1383576 TTGATAATTTGTGATAGAAATCT
1 TTGAAAATTTGTGATAGAAATCT
1383599 TTGAAAATTTGT-ATAGAAAT
1 TTGAAAATTTGTGATAGAAAT
1383619 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (23 bp):
TTGAAAATTTGTGATAGAAATCT
Found at i:1383847 original size:39 final size:39
Alignment explanation
Indices: 1383801--1383908 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 39
1383791 ACTAAAACCT
*
1383801 ATTGCGAAATT-AAATTCGTATTGCGAATTCGAAAATCA
1 ATTGCGAATTTGAAATTCGTATTGCGAATTCGAAAATCA
* *
1383839 AGTTGCGAATTTGAAATTC--AGTTGCGAATTTGAAATTCA
1 A-TTGCGAATTTGAAATTCGTA-TTGCGAATTCGAAAATCA
*
1383878 ATTGCGAATTTGAAATTCAGTGTTGCGAATT
1 ATTGCGAATTTGAAATTC-GTATTGCGAATT
1383909 TGACTTCTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
38 19 0.32
39 26 0.43
40 15 0.25
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (39 bp):
ATTGCGAATTTGAAATTCGTATTGCGAATTCGAAAATCA
Found at i:1383861 original size:19 final size:19
Alignment explanation
Indices: 1383821--1383911 Score: 128
Period size: 19 Copynumber: 4.6 Consensus size: 19
1383811 TAAATTCGTA
* *
1383821 TTGCGAATTCGAAAATCAAG
1 TTGCGAATTTGAAATTC-AG
1383841 TTGCGAATTTGAAATTCAG
1 TTGCGAATTTGAAATTCAG
*
1383860 TTGCGAATTTGAAATTCAA
1 TTGCGAATTTGAAATTCAG
1383879 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCA--G
1383900 TTGCGAATTTGA
1 TTGCGAATTTGA
1383912 CTTCTGTGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
19 38 0.58
20 15 0.23
21 12 0.18
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (19 bp):
TTGCGAATTTGAAATTCAG
Found at i:1383887 original size:38 final size:40
Alignment explanation
Indices: 1383821--1383911 Score: 141
Period size: 38 Copynumber: 2.3 Consensus size: 40
1383811 TAAATTCGTA
*
1383821 TTGCGAATTCGAAAATCAAGTTGCGAATTTGAAATTCA-G
1 TTGCGAATTTGAAAATCAAGTTGCGAATTTGAAATTCAGG
*
1383860 TTGCGAATTTGAAATTCAA-TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATCAAGTTGCGAATTTGAAATTCAG-G
1383900 TTGCGAATTTGA
1 TTGCGAATTTGA
1383912 CTTCTGTGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
38 18 0.38
39 17 0.35
40 13 0.27
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (40 bp):
TTGCGAATTTGAAAATCAAGTTGCGAATTTGAAATTCAGG
Found at i:1383922 original size:20 final size:20
Alignment explanation
Indices: 1383879--1383950 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
1383869 TGAAATTCAA
* *
1383879 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTG-ACTTCTGTG
1383900 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
1383920 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
*
1383940 CTGCGAATTTG
1 TTGCGAATTTG
1383951 GAAACTCGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 36 0.77
21 11 0.23
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:1390804 original size:30 final size:31
Alignment explanation
Indices: 1390769--1390887 Score: 152
Period size: 31 Copynumber: 3.9 Consensus size: 31
1390759 GAAATACTTA
* *
1390769 TCCATATGTTCCGAAGAACATAGGT-AACTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
*
1390799 TCCATATGTCCCGAAGGACATAGGTAAACTA
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
* *
1390830 TCCATATATCTCGGAA-GACATAGGTAAACTG
1 TCCATATGTC-CCGAAGGACATAGGTAAACTG
* *
1390861 TCCATATGCCCCAAAGGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
1390888 CCCTTGACTC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
30 26 0.34
31 46 0.61
32 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAACTG
Found at i:1390878 original size:62 final size:61
Alignment explanation
Indices: 1390767--1390887 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 61
1390757 CTGAAATACT
* * *
1390767 TATCCATATGTTCCGAAGAACATAGGTAACTGTCCATATGTCCCGAAGGACATAGGTAAAC
1 TATCCATATATTCCGAAGAACATAGGTAACTGTCCATATGCCCCAAAGGACATAGGTAAAC
*
1390828 TATCCATATATCTCGGAAG-ACATAGGTAAACTGTCCATATGCCCCAAAGGACATAGGTAA
1 TATCCATATAT-TCCGAAGAACATAGGT-AACTGTCCATATGCCCCAAAGGACATAGGTAA
1390888 CCCTTGACTC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
61 18 0.33
62 36 0.67
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (61 bp):
TATCCATATATTCCGAAGAACATAGGTAACTGTCCATATGCCCCAAAGGACATAGGTAAAC
Found at i:1392616 original size:20 final size:20
Alignment explanation
Indices: 1392587--1392625 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1392577 ATTTCACCAC
*
1392587 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1392607 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
1392626 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1399272 original size:32 final size:31
Alignment explanation
Indices: 1399198--1399282 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
1399188 CTAATGTGAC
* *
1399198 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
1399229 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
*
1399261 TCTTAGGTAGGCCCCACGGCCC
1 TCTTAGGTAGGCCCTACGGCCC
1399283 CAAAATCTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.55
32 19 0.45
ACGTcount: A:0.15, C:0.31, G:0.29, T:0.25
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:1413151 original size:75 final size:74
Alignment explanation
Indices: 1413085--1413297 Score: 197
Period size: 75 Copynumber: 2.9 Consensus size: 74
1413075 TATATTAACT
* *
1413085 TAAAATAT-TTTATTATTATACAAATA-TATAT-ATATATATATATTTAAAATATATTAACTTAA
1 TAAAATATATTT-TT-TAATACAAATACAATATGA-ATATATAT-TTTAAAATATATTAACTTAA
1413147 AAATACAAATTATA
62 AAATA-AAATTATA
* **
1413161 TAAAATATATTTTTTAATACGAATACAATATGAATATATATTTTAAAATATATTAACTTAATTAT
1 TAAAATATATTTTTTAATACAAATACAATATGAATATATATTTTAAAATATATTAACTTAAAAAT
* *
1413226 ACAAACTATG
66 A-AAATTATA
** * *
1413236 T-AAA-ATA-TTTTTAATACAAAT-CTAATACAAATAAATTTTTTTAAAAATATATTAACTTAAA
1 TAAAATATATTTTTTAATACAAATAC-AATATGAATATA-TATTTT-AAAATATATTAACTTAAA
1413297 A
63 A
1413298 TATTTTATTA
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
71 1 0.01
72 22 0.19
73 8 0.07
74 20 0.17
75 40 0.34
76 22 0.19
77 4 0.03
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (74 bp):
TAAAATATATTTTTTAATACAAATACAATATGAATATATATTTTAAAATATATTAACTTAAAAAT
AAAATTATA
Found at i:1413159 original size:59 final size:56
Alignment explanation
Indices: 1413059--1413170 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 56
1413049 ATAATACGAG
* ***
1413059 TATATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATATATA
1 TATATATATTTTAAAATATATTAACTTAAAATATCAAATTA-TATA-AAATATATATA
1413117 TATATATATATTTAAAATATATTAACTTAAAA-ATACAAATTATATAAAATATAT
1 TATATATAT-TTTAAAATATATTAACTTAAAATAT-CAAATTATATAAAATATAT
1413171 TTTTTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 8 0.17
58 15 0.31
59 25 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (56 bp):
TATATATATTTTAAAATATATTAACTTAAAATATCAAATTATATAAAATATATATA
Found at i:1418377 original size:157 final size:158
Alignment explanation
Indices: 1417720--1418387 Score: 966
Period size: 157 Copynumber: 4.3 Consensus size: 158
1417710 ATTTGGTATA
** * *
1417720 AAAAAACAAACTTAAAATAAATGACAAATTGAAGGAATAAGGAGATTATGAAAAATTGAAGGACT
1 AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACT
* * *
1417785 AAATTGAAATATAAAAAAATTGTTATCAAAAAGAGGAACTGAAAGTACACATGTATTCTACTATG
66 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
*
1417850 GTTTAGGAGCATGTGGCTC-AATTTGGT
131 GTTTAGGAGCATGTGACTCAAATTTGGT
* * *
1417877 TAAAAACGGACTTAAAATAAATGACTAATTGAAGAAATAAGGAGATTATGAAAAATCGAAGGACT
1 AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACT
* * *
1417942 AAATTGAAAAGTAAAAATTTTCTT-TCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
66 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
1418006 GTTTAGGAGCATGTGACTCAAATTTGGT
131 GTTTAGGAGCATGTGACTCAAATTTGGT
* * * *
1418034 AAAAAACGGACTAAAAATAAATTACGAATTGCAGAAATAAGGATATTATGAAAAATTGAAGGACT
1 AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACT
* * * *
1418099 AAATTGAAAAGTAAAAAACTTGTTATCAAATAGAGGAATTGAAAGTACACATGCATTCTACTATG
66 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
1418164 GTTTAGGAGCATGTGACTCAAATTT-GT
131 GTTTAGGAGCATGTGACTCAAATTTGGT
* * * * *
1418191 GAAAAAGGGACTTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTAAAGGAAT
1 AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACT
* * * *
1418256 AAATTGAAAAAT-AAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAATATGAATTATACTATG
66 AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
**
1418320 GTTTAGGAGCATGTGGTTCAAATTTGGT
131 GTTTAGGAGCATGTGACTCAAATTTGGT
* ** * *
1418348 AAAAAATGGACTTAAAATGGAGGAGGAATTGAAGAAATAA
1 AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAA
1418388 TGAAATCAGG
Statistics
Matches: 459, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
156 126 0.27
157 270 0.59
158 63 0.14
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (158 bp):
AAAAAACGGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACT
AAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
GTTTAGGAGCATGTGACTCAAATTTGGT
Found at i:1426133 original size:3 final size:3
Alignment explanation
Indices: 1426125--1426165 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1426115 TCTAGATGTG
1426125 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1426166 GATATATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1426487 original size:22 final size:23
Alignment explanation
Indices: 1426461--1426503 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1426451 AATTATAATA
* *
1426461 TTCAATTTTAGTAATA-AAATTT
1 TTCAAATTTAATAATATAAATTT
1426483 TTCAAATTTAATAATATAAAT
1 TTCAAATTTAATAATATAAAT
1426504 ATAAGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATTTAATAATATAAATTT
Found at i:1435088 original size:110 final size:111
Alignment explanation
Indices: 1434894--1435115 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 111
1434884 CGGGTGGAAG
* *
1434894 ATGATAGGACGAAAAAAAATGGAAGTACGAAGAAACTGGAAAGCAATGGAGAAGATAAACAGTCG
1 ATGATAGGACGAAAAAAAATGGAAGTACAAAGAAAATGGAAAGCAATGGAGAAGATAAACAGTCG
1434959 AAGAAAATGGGAAGCAATGGAAATGGAAAAGATAAACAGTAGAGTA
66 AAGAAAATGGGAAGCAATGGAAATGGAAAAGATAAACAGTAGAGTA
* *
1435005 ATGATAGGACG-AAAAAAATGGAAGTACAAAGAAAATGGAAAGTAATGGAGAGGATAAACAGTCG
1 ATGATAGGACGAAAAAAAATGGAAGTACAAAGAAAATGGAAAGCAATGGAGAAGATAAACAGTCG
*
1435069 AAGAAAATGGGAAGTAATGGAAATGGAAAAGATAAACAGTAGAGTA
66 AAGAAAATGGGAAGCAATGGAAATGGAAAAGATAAACAGTAGAGTA
1435115 A
1 A
1435116 ATTGGAACTT
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 95 0.90
111 11 0.10
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.14
Consensus pattern (111 bp):
ATGATAGGACGAAAAAAAATGGAAGTACAAAGAAAATGGAAAGCAATGGAGAAGATAAACAGTCG
AAGAAAATGGGAAGCAATGGAAATGGAAAAGATAAACAGTAGAGTA
Found at i:1435260 original size:14 final size:14
Alignment explanation
Indices: 1435241--1435269 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1435231 ACGGTCATAT
1435241 AAGTAGTCTTATCA
1 AAGTAGTCTTATCA
1435255 AAGTAGTCTTATCA
1 AAGTAGTCTTATCA
1435269 A
1 A
1435270 GGGATTGTAA
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:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
AAGTAGTCTTATCA
Found at i:1435311 original size:32 final size:33
Alignment explanation
Indices: 1435252--1435318 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
1435242 AGTAGTCTTA
1435252 TCAAAGTAGTCTTATCAAGGGATTGTAATTAGT
1 TCAAAGTAGTCTTATCAAGGGATTGTAATTAGT
*
1435285 TCAAAGTAGTCTTATC-GGGGATTGTAATTAGT
1 TCAAAGTAGTCTTATCAAGGGATTGTAATTAGT
1435317 TC
1 TC
1435319 GAGGATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
TCAAAGTAGTCTTATCAAGGGATTGTAATTAGT
Found at i:1435739 original size:8 final size:8
Alignment explanation
Indices: 1435712--1435784 Score: 55
Period size: 8 Copynumber: 9.6 Consensus size: 8
1435702 ACAGTGCCTC
*
1435712 GTTAGTAG
1 GTTAGTAA
*
1435720 GTTAGCAA
1 GTTAGTAA
*
1435728 -TTAGTAT
1 GTTAGTAA
1435735 GTTAGTAA
1 GTTAGTAA
1435743 GTTAG-AA
1 GTTAGTAA
*
1435750 GTTAG-GA
1 GTTAGTAA
*
1435757 GTTATTAA
1 GTTAGTAA
* *
1435765 ATTAATAA
1 GTTAGTAA
1435773 GTTAG-AA
1 GTTAGTAA
1435780 GTTAG
1 GTTAG
1435785 GGTTACTAAC
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
7 24 0.47
8 27 0.53
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (8 bp):
GTTAGTAA
Found at i:1435754 original size:30 final size:30
Alignment explanation
Indices: 1435720--1435784 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1435710 TCGTTAGTAG
** *
1435720 GTTAGCAATTAGTATGTTAGTAAGTTAGAA
1 GTTAGCAATTAGTAAATTAATAAGTTAGAA
* * *
1435750 GTTAGGAGTTATTAAATTAATAAGTTAGAA
1 GTTAGCAATTAGTAAATTAATAAGTTAGAA
1435780 GTTAG
1 GTTAG
1435785 GGTTACTAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
GTTAGCAATTAGTAAATTAATAAGTTAGAA
Found at i:1436166 original size:89 final size:90
Alignment explanation
Indices: 1435981--1436209 Score: 289
Period size: 89 Copynumber: 2.6 Consensus size: 90
1435971 TTCGATTTTA
* * * * * * * *
1435981 CATTTTCGTTATTTATATTTACGCATTTTATATTTCAGTTATATACATTTCTGCCCTTTTTATTT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTGTTATTTACATTTATGCACTTTTTATAT
*
1436046 TTATTTTATTTTATTTATATTCTTC
66 ATATTTTATTTTATTTATATTCTTC
* * * * *
1436071 CATTTTTGTTATTTACATTTAAGCACTTTGTTTTTCTGTTATTTACATTTATGTATTTTTTATAT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTGTTATTTACATTTATGCACTTTTTATAT
* *
1436136 AT-TTTTATTTTATTTATGTTCTTT
66 ATATTTTATTTTATTTATATTCTTC
* *
1436160 CATTTTTGTTATTTATATTTATGCTTTTTATTTTTCTGTTATTTACATTT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTGTTATTTACATTT
1436210 CATTCTTTTA
Statistics
Matches: 118, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 65 0.55
90 53 0.45
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (90 bp):
CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTGTTATTTACATTTATGCACTTTTTATAT
ATATTTTATTTTATTTATATTCTTC
Found at i:1436202 original size:30 final size:30
Alignment explanation
Indices: 1435983--1436224 Score: 119
Period size: 30 Copynumber: 8.1 Consensus size: 30
1435973 CGATTTTACA
* * *
1435983 TTTTC-GTTATTTATATTTACGCATTTTAT
1 TTTTCTGTTATTTACATTTATGCTTTTTAT
* * * *
1436012 ATTTCAGTTATATACATTTCTGCCCTTTTTAT
1 TTTTCTGTTATTTACATTTATG--CTTTTTAT
* * * * *
1436044 TTTTATTTTATTT-TATTTAT-ATTCTTCCA-
1 TTTTCTGTTATTTACATTTATGCTT-TT-TAT
* ** *
1436073 TTTT-TGTTATTTACATTTAAGCACTTTGT
1 TTTTCTGTTATTTACATTTATGCTTTTTAT
*
1436102 TTTTCTGTTATTTACATTTATGTATTTTTTAT
1 TTTTCTGTTATTTACATTTATG--CTTTTTAT
* *
1436134 ATATT-T-TTATTT-TATTTATG-TTCTTTCA-
1 -TTTTCTGTTATTTACATTTATGCTT-TTT-AT
*
1436162 TTTT-TGTTATTTATATTTATGCTTTTTAT
1 TTTTCTGTTATTTACATTTATGCTTTTTAT
* *
1436191 TTTTCTGTTATTTACATTTCATTCTTTTAAT
1 TTTTCTGTTATTTACATTT-ATGCTTTTTAT
1436222 TTT
1 TTT
1436225 ATGTACTTTA
Statistics
Matches: 159, Mismatches: 34, Indels: 38
0.69 0.15 0.16
Matches are distributed among these distances:
27 6 0.04
28 19 0.12
29 37 0.23
30 51 0.32
31 23 0.14
32 20 0.13
33 3 0.02
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (30 bp):
TTTTCTGTTATTTACATTTATGCTTTTTAT
Found at i:1436210 original size:15 final size:15
Alignment explanation
Indices: 1436107--1436209 Score: 65
Period size: 15 Copynumber: 6.9 Consensus size: 15
1436097 TTTGTTTTTC
*
1436107 TGTTATTTACATTTA
1 TGTTATTTATATTTA
*
1436122 TGTATTTTTTATATATT-
1 TG--TTATTTATAT-TTA
1436139 T-TTATTT-TATTTA
1 TGTTATTTATATTTA
*
1436152 TGTTCTTTCAT-TTT-
1 TGTTATTT-ATATTTA
1436166 TGTTATTTATATTTA
1 TGTTATTTATATTTA
* *
1436181 TGCTT-TTTATTTTTC
1 TG-TTATTTATATTTA
*
1436196 TGTTATTTACATTT
1 TGTTATTTATATTT
1436210 CATTCTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
12 2 0.03
13 6 0.09
14 22 0.32
15 24 0.35
16 3 0.04
17 9 0.13
18 2 0.03
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TGTTATTTATATTTA
Found at i:1436234 original size:15 final size:15
Alignment explanation
Indices: 1436216--1436253 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1436206 ATTTCATTCT
1436216 TTTAATTTTATGTAC
1 TTTAATTTTATGTAC
*
1436231 TTTAA-TTTATGTTC
1 TTTAATTTTATGTAC
1436245 TTTCAATTT
1 TTT-AATTT
1436254 CCAGCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 7 0.35
16 2 0.10
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTAATTTTATGTAC
Found at i:1436246 original size:30 final size:30
Alignment explanation
Indices: 1436072--1436253 Score: 123
Period size: 30 Copynumber: 6.1 Consensus size: 30
1436062 ATATTCTTCC
* **
1436072 ATTTTTGTTATTTACATTTAAGCACTTTGT-
1 ATTTTTGTTATTTACATTTATGTTCTTT-TA
*
1436102 -TTTTCTGTTATTTACATTTATGTATTTTTTA
1 ATTTT-TGTTATTTACATTTATGT-TCTTTTA
* * *
1436133 TATATTT-TTATTT-TATTTATGTTC-TTTC
1 -ATTTTTGTTATTTACATTTATGTTCTTTTA
* *
1436161 ATTTTTGTTATTTATATTTATGCT-TTTTA
1 ATTTTTGTTATTTACATTTATGTTCTTTTA
*
1436190 TTTTTCTGTTATTTACATTTCA--TTCTTTTA
1 ATTTT-TGTTATTTACATTT-ATGTTCTTTTA
*
1436220 ATTTTATG-TACTTTA-ATTTATGTTCTTTCA
1 ATTTT-TGTTA-TTTACATTTATGTTCTTTTA
1436250 ATTT
1 ATTT
1436254 CCAGCATTTA
Statistics
Matches: 121, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.04
28 10 0.08
29 28 0.23
30 64 0.53
31 10 0.08
32 1 0.01
33 3 0.02
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.65
Consensus pattern (30 bp):
ATTTTTGTTATTTACATTTATGTTCTTTTA
Found at i:1437839 original size:17 final size:17
Alignment explanation
Indices: 1437817--1437849 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1437807 TTCTTTCTTG
1437817 CATTTACATCATTATGC
1 CATTTACATCATTATGC
1437834 CATTTACATCATTATG
1 CATTTACATCATTATG
1437850 ATGAAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (17 bp):
CATTTACATCATTATGC
Found at i:1443985 original size:32 final size:32
Alignment explanation
Indices: 1443944--1444004 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
1443934 CCTGATTAAC
1443944 ATGATATTTTCAAAAGAATTTTTAAATAATCT
1 ATGATATTTTCAAAAGAATTTTTAAATAATCT
1443976 ATGATATTTTCAAAAGAATTTTTAAATAA
1 ATGATATTTTCAAAAGAATTTTTAAATAA
1444005 GCTAAGTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (32 bp):
ATGATATTTTCAAAAGAATTTTTAAATAATCT
Found at i:1444054 original size:106 final size:105
Alignment explanation
Indices: 1443870--1444078 Score: 274
Period size: 106 Copynumber: 2.0 Consensus size: 105
1443860 GCCTAAGATA
* * * * * * *
1443870 TATGATGTTTTCAAATGAGTTTTAAAGAAGTTAAGCCTGATTTTTAGGGGTTTCTTGATGATTAC
1 TATGATATTTTCAAAAGAGTTTTAAAGAAGCTAAGCCTGATGTTCAGAGATTTCTTGATGATTAC
*
1443935 CTGATTAACATGATATTTTCAAAAGAATTTTTAAATAATC
66 CTGATTAACATGATATCTTCAAAAGAATTTTTAAATAATC
* * *
1443975 TATGATATTTTCAAAAGAATTTTTAAATAAGCTAAGTCTGATGTTCAGAGATTTCTTGATGATTA
1 TATGATATTTTCAAAAG-AGTTTTAAAGAAGCTAAGCCTGATGTTCAGAGATTTCTTGATGATTA
* * * *
1444040 CTTGATTAATATGATATCTTCAAATGATTTTTTAAATAA
65 CCTGATTAACATGATATCTTCAAAAGAATTTTTAAATAA
1444079 GCTAAACCTG
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
105 15 0.17
106 73 0.83
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (105 bp):
TATGATATTTTCAAAAGAGTTTTAAAGAAGCTAAGCCTGATGTTCAGAGATTTCTTGATGATTAC
CTGATTAACATGATATCTTCAAAAGAATTTTTAAATAATC
Found at i:1444096 original size:74 final size:74
Alignment explanation
Indices: 1443975--1444113 Score: 215
Period size: 74 Copynumber: 1.9 Consensus size: 74
1443965 TTAAATAATC
* **
1443975 TATGATATTTTCAAAAGAATTTTTAAATAAGCTAAGTCTGATGTTCAGAGATTTCTTGATGATTA
1 TATGATATCTTCAAAAGAATTTTTAAATAAGCTAAACCTGATGTTCAGAGATTTCTTGATGATTA
1444040 CTTGATTAA
66 CTTGATTAA
* * * *
1444049 TATGATATCTTCAAATGATTTTTTAAATAAGCTAAACCTGATTTTCAGAGGTTTCTTGATGATTA
1 TATGATATCTTCAAAAGAATTTTTAAATAAGCTAAACCTGATGTTCAGAGATTTCTTGATGATTA
1444114 AGTCATTCGG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (74 bp):
TATGATATCTTCAAAAGAATTTTTAAATAAGCTAAACCTGATGTTCAGAGATTTCTTGATGATTA
CTTGATTAA
Found at i:1444939 original size:116 final size:116
Alignment explanation
Indices: 1444819--1445038 Score: 325
Period size: 116 Copynumber: 1.9 Consensus size: 116
1444809 CTATTGAAAG
*
1444819 GGTTCATAATGAGAAAAACTCATCTGATAAAGGATAAGAAG-TTCCTAATAAGAAGAACTTATTC
1 GGTTCATAATGAGAAAAACTCATCTGATAAAGGAGAAGAAGCTT-CTAATAAGAAGAACTTATTC
** *
1444883 AACATTGACTCATCCATCACATAAGAAGTTGGATCGACATTTTTAGGGGAAT
65 AACATCAACTCATCCATCACATAAGAAGTTGGATCAACATTTTTAGGGGAAT
* * * * *
1444935 GGTTCATAATGAGAAAAACTCGTCTGATGAGGGAGAAGAAGCTTCTAATGAGAAGAATTTATTCA
1 GGTTCATAATGAGAAAAACTCATCTGATAAAGGAGAAGAAGCTTCTAATAAGAAGAACTTATTCA
* *
1445000 ACCTCAACTCATCCATCACATAAGGAGTTGGATCAACAT
66 ACATCAACTCATCCATCACATAAGAAGTTGGATCAACAT
1445039 CAACATTTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 90 0.98
117 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (116 bp):
GGTTCATAATGAGAAAAACTCATCTGATAAAGGAGAAGAAGCTTCTAATAAGAAGAACTTATTCA
ACATCAACTCATCCATCACATAAGAAGTTGGATCAACATTTTTAGGGGAAT
Found at i:1445287 original size:20 final size:20
Alignment explanation
Indices: 1445225--1445287 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1445215 AATAAAAGGG
* *
1445225 GTTCATAATGAGAAGAACTC
1 GTTCCTAATGAGAAGAACTA
**
1445245 GTT-C-AATGAGAGAGAAGAA
1 GTTCCTAATGAGA-AGAACTA
*
1445264 GTTCCTAATGAGAAGAACTT
1 GTTCCTAATGAGAAGAACTA
1445284 GTTC
1 GTTC
1445288 AACCTTAGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 12 0.36
21 7 0.21
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (20 bp):
GTTCCTAATGAGAAGAACTA
Found at i:1445390 original size:116 final size:115
Alignment explanation
Indices: 1445186--1445399 Score: 288
Period size: 116 Copynumber: 1.8 Consensus size: 115
1445176 TTAACTCGTC
* **
1445186 CATCACAAAAGGAGGTGGTTTAACGTTTCAATAAAAGGGGTTCATAATGAGAAGAACTCGTTCAA
1 CATCACAAAAGGAGGTGGATTAACGTTTCAATAAAA-GGGTTCATAATGAGAAGAACTCGACCAA
* *
1445251 TGAGAGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAACCTTAGCTCATT
65 TAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATT
* * *
1445302 CATCACATAAGGAGTTGGATTAATGTTTTCAATAGAAA-GGTTCATAATGAGAAGAACTCGACCA
1 CATCACAAAAGGAGGTGGATTAACG-TTTCAATA-AAAGGGTTCATAATGAGAAGAACTCGACCA
* *
1445366 ATAAGGAGCGAA-AATTTCATAATGAGAAGAACTT
64 ATAA-GAGAGAAGAAGTTCATAATGAGAAGAACTT
1445400 ATAGCTCAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 68 0.80
117 14 0.16
118 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (115 bp):
CATCACAAAAGGAGGTGGATTAACGTTTCAATAAAAGGGTTCATAATGAGAAGAACTCGACCAAT
AAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATT
Found at i:1445884 original size:22 final size:23
Alignment explanation
Indices: 1445859--1445917 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
1445849 CTCTATGCAT
* * *
1445859 CTCGGT-ATCAACTCAATAGTGC
1 CTCGGTCAGCAACCCAACAGTGC
1445881 CTC-GTCAGCAACCCAACAGTGC
1 CTCGGTCAGCAACCCAACAGTGC
1445903 CTC-GTCAGCAACCCA
1 CTCGGTCAGCAACCCA
1445918 CTCGTCTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (23 bp):
CTCGGTCAGCAACCCAACAGTGC
Found at i:1446719 original size:18 final size:18
Alignment explanation
Indices: 1446693--1446735 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1446683 TGAGTTCGTT
*
1446693 TTTTA-TTTAGTGGTTTA
1 TTTTATTTTAGTAGTTTA
* *
1446710 TTTTATTTTATTATTTTA
1 TTTTATTTTAGTAGTTTA
1446728 TTTTATTT
1 TTTTATTT
1446736 AATTTGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTATTTTAGTAGTTTA
Found at i:1446723 original size:13 final size:13
Alignment explanation
Indices: 1446707--1446734 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1446697 ATTTAGTGGT
1446707 TTATTTTATTTTA
1 TTATTTTATTTTA
1446720 TTATTTTATTTTA
1 TTATTTTATTTTA
1446733 TT
1 TT
1446735 TAATTTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1447150 original size:30 final size:28
Alignment explanation
Indices: 1447079--1447230 Score: 89
Period size: 30 Copynumber: 5.2 Consensus size: 28
1447069 TCATTCCTTC
* *
1447079 ATTTTTGTTATTTACATTTAAGCACTTTGTT
1 ATTTTT-TTATTTACATTTATG-TCTTT-TT
*
1447110 -TTTCTGTTATTTACATTTATGTCTTTTTT
1 ATTT-TTTTATTTACATTTATGTC-TTTTT
* *
1447139 ATTTATTTTATTT-TATTTCCAT-TC-TTTC
1 ATTT-TTTTATTTACATTT--ATGTCTTTTT
*
1447167 ATTTTTATTATTTATATTTATG-CTTTTT
1 ATTTTT-TTATTTACATTTATGTCTTTTT
* *
1447195 ATTTTTCTTCTATTTACATTTATTTCTTTTA
1 A-TTTT-TT-TATTTACATTTATGTCTTTTT
1447226 ATTTT
1 ATTTT
1447231 ATGCATTTCA
Statistics
Matches: 97, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
27 5 0.05
28 17 0.18
29 17 0.18
30 49 0.51
31 9 0.09
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (28 bp):
ATTTTTTTATTTACATTTATGTCTTTTT
Found at i:1447172 original size:88 final size:88
Alignment explanation
Indices: 1446989--1447232 Score: 294
Period size: 88 Copynumber: 2.8 Consensus size: 88
1446979 TTCTAGTTTA
* * * * *
1446989 CATTTTTGTTATTTATATTTACGCATTTTATTTGTCTATTATTTATATTTTTGTCCTTTTAATTT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCT-TTATTTACATTTATGTCTTTTTAATTT
* * *
1447054 TGTTTTGTTTTATTTTCATTCCTT
65 TATTTTATTTTATTTCCATTCCTT
* * * *
1447078 CATTTTTGTTATTTACATTTAAGCACTTTGTTTTTCTGTTATTTACATTTATGTCTTTTTTA-TT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCT-TTATTTACATTTATGTCTTTTTAATTT
*
1447142 TATTTTATTTTATTTCCATTCTTT
65 TATTTTATTTTATTTCCATTCCTT
* * * *
1447166 CATTTTTATTATTTATATTTATGCTTTTTATTTTTCTTCTATTTACATTTATTTC-TTTTAATTT
1 CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTT-TATTTACATTTATGTCTTTTTAATTT
1447230 TAT
65 TAT
1447233 GCATTTCAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
87 6 0.05
88 73 0.56
89 52 0.40
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.66
Consensus pattern (88 bp):
CATTTTTGTTATTTATATTTAAGCATTTTATTTTTCTTTATTTACATTTATGTCTTTTTAATTTT
ATTTTATTTTATTTCCATTCCTT
Found at i:1450313 original size:24 final size:24
Alignment explanation
Indices: 1450282--1450340 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1450272 GGAATAAAGG
*
1450282 AAAT-AATATAAGA-TAAAGAAAA
1 AAATGAATATAAAAGTAAAGAAAA
* **
1450304 TAAATGAATAAAAAAGTAAAGGTAA
1 -AAATGAATATAAAAGTAAAGAAAA
1450329 AAATGAATATAA
1 AAATGAATATAA
1450341 TTAATGTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.14
24 18 0.62
25 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATGAATATAAAAGTAAAGAAAA
Found at i:1450486 original size:35 final size:33
Alignment explanation
Indices: 1450386--1450487 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 33
1450376 AAGTAAAAAC
*
1450386 AATAAAA-AAATATATACATATAA-AATACTAGAT
1 AATAAAATAAATATATACATATAATAA-A-TAAAT
* * *
1450419 AATATATATATATATATATATATAAT-AA-AAAT
1 AATA-AAATAAATATATACATATAATAAATAAAT
1450451 AATAAAATAAATATATACATACTAACTAAATAAAT
1 AATAAAATAAATATATACATA-TAA-TAAATAAAT
1450486 AA
1 AA
1450488 GAGTACAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
31 14 0.25
32 10 0.18
33 5 0.09
34 5 0.09
35 21 0.38
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (33 bp):
AATAAAATAAATATATACATATAATAAATAAAT
Found at i:1450630 original size:22 final size:22
Alignment explanation
Indices: 1450599--1450658 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
1450589 GAATTAATAC
1450599 ATATG-ATAATAATATAGA-AAA
1 ATATGTATAATAATATA-ATAAA
1450620 ATATGTATAATTAAATATAATAAA
1 ATATGTATAA-T-AATATAATAAA
1450644 ATAT-T-TAATAA-ATAA
1 ATATGTATAATAATATAA
1450659 AAGGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 6 0.17
22 7 0.20
23 3 0.09
24 13 0.37
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATGTATAATAATATAATAAA
Found at i:1450685 original size:28 final size:29
Alignment explanation
Indices: 1450644--1450710 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
1450634 ATATAATAAA
1450644 ATAT-TTAATAAATAAAAG-GAAAAAAAT
1 ATATATTAATAAATAAAAGAGAAAAAAAT
* *
1450671 ATATATTAATTAATAAGAGTAGAAAAAAAT
1 ATATATTAATAAATAAAAG-AGAAAAAAAT
*
1450701 A-ATAATAATA
1 ATATATTAATA
1450711 TAAATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 12 0.36
29 7 0.21
30 10 0.30
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (29 bp):
ATATATTAATAAATAAAAGAGAAAAAAAT
Found at i:1452517 original size:105 final size:105
Alignment explanation
Indices: 1452320--1453516 Score: 2162
Period size: 105 Copynumber: 11.4 Consensus size: 105
1452310 GTACTGTTCC
* * *
1452320 GAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTCTGAAATTG-GAAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA--TGTTTGTTGACA
*
1452384 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1452426 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1452491 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1452531 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1452596 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1452636 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1452701 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1452741 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1452806 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1452846 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
* *
1452911 CTAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1452952 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1453017 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1453057 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1453122 CAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1453162 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1453227 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1453267 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1453332 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1453372 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1453437 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1453477 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1453517 GGTAAAACCT
Statistics
Matches: 1058, Mismatches: 31, Indels: 5
0.97 0.03 0.00
Matches are distributed among these distances:
105 910 0.86
106 144 0.14
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1453318 original size:526 final size:526
Alignment explanation
Indices: 1452320--1453516 Score: 2216
Period size: 526 Copynumber: 2.3 Consensus size: 526
1452310 GTACTGTTCC
* * * *
1452320 GAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGAAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1452385 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
1452450 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1452515 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGA
196 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGA
1452580 AATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
261 AATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
1452645 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
326 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
1452710 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
391 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
*
1452775 GCTCTGAAATCGAGAAATGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGT
456 GCTCTGAAATCGAGAAATATTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1452840 TGTCTG
521 TGTCTG
*
1452846 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1452911 CTAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
1452976 GTTAAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1453041 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGA
196 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGA
* *
1453106 AATGTTTGTTGACAACCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
261 AATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
1453171 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
326 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
1453236 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
391 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* * *
1453301 GCTCTGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
456 GCTCTGAAATCGAGAAATATTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGT
1453366 TGTCTG
521 TGTCTG
* *
1453372 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1453436 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
1453501 GTTGAAATTGACTCTG
131 GTTGAAATTGGCTCTG
1453517 GGTAAAACCT
Statistics
Matches: 648, Mismatches: 23, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
525 89 0.14
526 559 0.86
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (526 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGA
AATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
GCTCTGAAATCGAGAAATATTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGT
TGTCTG
Found at i:1454374 original size:80 final size:80
Alignment explanation
Indices: 1454241--1454409 Score: 313
Period size: 80 Copynumber: 2.1 Consensus size: 80
1454231 CACCCTTTGT
1454241 GGGTTTTCATCTTGAACCCACCTTATTTTCTCTTCTTTTGTTTGTTTTTCTATTTTTTTTTCAAT
1 GGGTTTTCATCTTGAACCCACCTTATTTTCTCTTCTTTTGTTTGTTTTTCTATTTTTTTTTCAAT
1454306 TTAGGGC-GCCCTTTC
66 TTAGGGCTG-CCTTTC
1454321 GGGTTTTCATCTTGAACCCACCTTATTTTCTCTTCTTTTGTTTGTTTTTCTATTTTTTTTTCAAT
1 GGGTTTTCATCTTGAACCCACCTTATTTTCTCTTCTTTTGTTTGTTTTTCTATTTTTTTTTCAAT
*
1454386 TTAGGGCTGTCTTTC
66 TTAGGGCTGCCTTTC
1454401 GGGTTTTCA
1 GGGTTTTCA
1454410 CCCTAAACGT
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
80 86 0.99
81 1 0.01
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.56
Consensus pattern (80 bp):
GGGTTTTCATCTTGAACCCACCTTATTTTCTCTTCTTTTGTTTGTTTTTCTATTTTTTTTTCAAT
TTAGGGCTGCCTTTC
Found at i:1457314 original size:27 final size:28
Alignment explanation
Indices: 1457284--1457349 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 28
1457274 ATTCACCATT
1457284 TTCAT-TT-CTGCAACGATTCGACAGAGC
1 TTCATCTTACTGCAACGATTCGAC-GAGC
1457311 TTCAAGTCTTCAACTGCAACGATTCGACGAGC
1 TTC-A-TCTT--ACTGCAACGATTCGACGAGC
1457343 TTCATCT
1 TTCATCT
1457350 CTTTCCCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 1 0.03
30 5 0.15
31 1 0.03
32 7 0.21
33 15 0.45
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (28 bp):
TTCATCTTACTGCAACGATTCGACGAGC
Found at i:1458347 original size:19 final size:19
Alignment explanation
Indices: 1458302--1458347 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1458292 ATGAACATAA
*
1458302 TTCACGTTTTGATTCAACT
1 TTCACTTTTTGATTCAACT
* * *
1458321 TCCTCTTTTTGCTTCAACT
1 TTCACTTTTTGATTCAACT
1458340 TTCACTTT
1 TTCACTTT
1458348 CTTCAATCTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (19 bp):
TTCACTTTTTGATTCAACT
Found at i:1469466 original size:24 final size:24
Alignment explanation
Indices: 1469435--1469493 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1469425 GGAATAAAGG
*
1469435 AAAT-AATATAAGA-TAAAGAAAA
1 AAATGAATATAAAAGTAAAGAAAA
* **
1469457 TAAATGAATAAAAAAGTAAAGGTAA
1 -AAATGAATATAAAAGTAAAGAAAA
1469482 AAATGAATATAA
1 AAATGAATATAA
1469494 TTAATGTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.14
24 18 0.62
25 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATGAATATAAAAGTAAAGAAAA
Found at i:1469575 original size:27 final size:28
Alignment explanation
Indices: 1469545--1469625 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 28
1469535 AAACAATAAA
*
1469545 AATATATATACATATAAAATACTAGATAAT
1 AATATATATACATATAAAATAATA-A-AAT
1469575 -ATATATATA-ATA-AAAATAATAAAAT
1 AATATATATACATATAAAATAATAAAAT
1469600 AA-ATATATACATACT-AAATAAATAAA
1 AATATATATACATA-TAAAAT-AATAAA
1469626 TAAGAGTACA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
25 10 0.22
26 5 0.11
27 12 0.27
28 9 0.20
29 9 0.20
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (28 bp):
AATATATATACATATAAAATAATAAAAT
Found at i:1469596 original size:23 final size:24
Alignment explanation
Indices: 1469539--1469608 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
1469529 AAGTAAAAAC
* *
1469539 AATAAAAATATATATACATATAAA
1 AATAATAATATATATATATATAAA
1469563 ATACTAGATAATATATATATA-ATAAA
1 A-A-TA-ATAATATATATATATATAAA
* *
1469589 AATAATAAAATAAATATATA
1 AATAATAATATATATATATA
1469609 CATACTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 12 0.32
24 4 0.11
25 2 0.05
26 8 0.21
27 12 0.32
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (24 bp):
AATAATAATATATATATATATAAA
Found at i:1469600 original size:25 final size:26
Alignment explanation
Indices: 1469532--1469612 Score: 94
Period size: 25 Copynumber: 3.1 Consensus size: 26
1469522 TGCAATAAAG
*
1469532 TAAAAACAATAAAA-ATATATATACA
1 TAAAAATAATAAAATATATATATACA
*
1469557 TATAAAATACTAGATAATATATATATA-A
1 TA-AAAATAATA-A-AATATATATATACA
*
1469585 TAAAAATAATAAAATAAATATATACA
1 TAAAAATAATAAAATATATATATACA
1469611 TA
1 TA
1469613 CTAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
25 13 0.28
26 11 0.23
27 9 0.19
28 5 0.11
29 9 0.19
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (26 bp):
TAAAAATAATAAAATATATATATACA
Found at i:1469626 original size:27 final size:26
Alignment explanation
Indices: 1469534--1469628 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 26
1469524 CAATAAAGTA
*
1469534 AAAACAATAAA-AATATATATACATAT
1 AAAATAATAAATAA-ATATATACATAT
* * *
1469560 AAAATACTAGAT-AATATATATATAAT
1 AAAATAATAAATAAATATATACAT-AT
1469586 AAAAATAATAAAATAAATATATACATACT
1 -AAAATAAT-AAATAAATATATACATA-T
1469615 -AAATAAATAAATAA
1 AAAAT-AATAAATAA
1469629 GAGTACAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
25 9 0.16
26 11 0.20
27 17 0.31
28 7 0.13
29 11 0.20
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (26 bp):
AAAATAATAAATAAATATATACATAT
Found at i:1469772 original size:22 final size:22
Alignment explanation
Indices: 1469741--1469800 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
1469731 GAATTAATAC
1469741 ATATG-ATAATAATATAGA-AAA
1 ATATGTATAATAATATA-ATAAA
1469762 ATATGTATAATTAAATATAATAAA
1 ATATGTATAA-T-AATATAATAAA
1469786 ATAT-T-TAATAA-ATAA
1 ATATGTATAATAATATAA
1469801 AAGGAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 6 0.17
22 7 0.20
23 3 0.09
24 13 0.37
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATGTATAATAATATAATAAA
Found at i:1469815 original size:35 final size:37
Alignment explanation
Indices: 1469776--1469867 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 37
1469766 GTATAATTAA
1469776 ATATAATAAAATAT-TTAATAAATAAAAGGA-AAAAT
1 ATATAATAAAATATATTAATAAATAAAAGGAGAAAAT
* * * *
1469811 ATAT-AT-ATATATATTAATTAATAAGAGTAGAAAAT
1 ATATAATAAAATATATTAATAAATAAAAGGAGAAAAT
*
1469846 A-ATAATAATAATAATATAAATA
1 ATATAATAA-AAT-ATATTAATA
1469868 TATATATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
33 5 0.11
34 17 0.39
35 12 0.27
36 1 0.02
37 2 0.05
38 7 0.16
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (37 bp):
ATATAATAAAATATATTAATAAATAAAAGGAGAAAAT
Found at i:1469867 original size:12 final size:11
Alignment explanation
Indices: 1469856--1469909 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
1469846 AATAATAATA
1469856 ATAATATAAAT
1 ATAATATAAAT
*
1469867 ATATATATATAT
1 ATA-ATATAAAT
*
1469879 ATATATATATAT
1 ATA-ATATAAAT
*
1469891 ATAGT-TAAAT
1 ATAATATAAAT
1469901 ATAATATAA
1 ATAATATAA
1469910 TATTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.22
11 7 0.19
12 22 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1469870 original size:8 final size:8
Alignment explanation
Indices: 1469859--1469919 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
1469849 AATAATAATA
1469859 ATATAAAT
1 ATATAAAT
*
1469867 ATATATAT
1 ATATAAAT
*
1469875 ATATATAT
1 ATATAAAT
*
1469883 ATATATAT
1 ATATAAAT
1469891 ATAGTTAAAT
1 ATA--TAAAT
1469901 ATAATATAAT
1 AT-ATA-AAT
*
1469911 ATTTAAAT
1 ATATAAAT
1469919 A
1 A
1469920 AAAAGAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 30 0.65
9 4 0.09
10 11 0.24
11 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (8 bp):
ATATAAAT
Found at i:1469872 original size:2 final size:2
Alignment explanation
Indices: 1469859--1469893 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1469849 AATAATAATA
*
1469859 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1469894 GTTAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1476390 original size:17 final size:18
Alignment explanation
Indices: 1476355--1476393 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1476345 ATATGAACAA
1476355 GATAATAGAAATATGAAT
1 GATAATAGAAATATGAAT
1476373 GATAATA-AAATGAT-AAT
1 GATAATAGAAAT-ATGAAT
1476390 GATA
1 GATA
1476394 GGAATGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (18 bp):
GATAATAGAAATATGAAT
Found at i:1478550 original size:20 final size:20
Alignment explanation
Indices: 1478525--1478565 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1478515 TGGATTTTCA
*
1478525 AAATTTATTTTTGAAATTAT
1 AAATTTATTTTTAAAATTAT
1478545 AAATTTATTTTTAAAATTAT
1 AAATTTATTTTTAAAATTAT
1478565 A
1 A
1478566 TTTAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATTTATTTTTAAAATTAT
Found at i:1479489 original size:21 final size:21
Alignment explanation
Indices: 1479465--1479522 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1479455 TATCTCAAAA
*
1479465 AAATAAAAAATAATATAATTT
1 AAATAAAAAATAATATAAATT
*
1479486 AAAT-AAAAATATGTATAAATT
1 AAATAAAAAATA-ATATAAATT
* *
1479507 ATATAAAAAATTATAT
1 AAATAAAAAATAATAT
1479523 TGGGTTAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.23
21 17 0.57
22 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATAAAAAATAATATAAATT
Found at i:1482603 original size:17 final size:17
Alignment explanation
Indices: 1482581--1482614 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1482571 AGATTTCATT
1482581 TTCCGAAAAATGTTTTC
1 TTCCGAAAAATGTTTTC
1482598 TTCCGAAAAATGTTTTC
1 TTCCGAAAAATGTTTTC
1482615 AGTGATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
TTCCGAAAAATGTTTTC
Found at i:1482645 original size:37 final size:37
Alignment explanation
Indices: 1482604--1482674 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1482594 TTTCTTCCGA
*
1482604 AAAATGTTTTCAGTGATTTCATTTTCCGAAAAATTCG
1 AAAATATTTTCAGTGATTTCATTTTCCGAAAAATTCG
1482641 AAAATATTTTCAGTGATTTCATTTTCCGAAAAAT
1 AAAATATTTTCAGTGATTTCATTTTCCGAAAAAT
1482675 GTTTTCAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (37 bp):
AAAATATTTTCAGTGATTTCATTTTCCGAAAAATTCG
Found at i:1487053 original size:20 final size:20
Alignment explanation
Indices: 1486986--1487042 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1486976 TTCTGGAGAT
1486986 GTGTGGAACCTTATGGAGTA
1 GTGTGGAACCTTATGGAGTA
*
1487006 GTGTGGAACCTTATAGAGTA
1 GTGTGGAACCTTATGGAGTA
1487026 GTGTGGAACCTTATGGA
1 GTGTGGAACCTTATGGA
1487043 AGAGTATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.33, T:0.30
Consensus pattern (20 bp):
GTGTGGAACCTTATGGAGTA
Found at i:1487069 original size:40 final size:40
Alignment explanation
Indices: 1486986--1487073 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
1486976 TTCTGGAGAT
* **
1486986 GTGTGGAACCTTATGGAGTAGTGTGGAACCTTATAGAGTA
1 GTGTGGAACCTTATGGAGTAGTATGGAACAATATAGAGTA
* *
1487026 GTGTGGAACCTTATGGAAG-AGTATGGAAGAATATGGAAG-A
1 GTGTGGAACCTTATGG-AGTAGTATGGAACAATATAG-AGTA
1487066 GTGTGGAA
1 GTGTGGAA
1487074 GAGTGTAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.32, C:0.07, G:0.35, T:0.26
Consensus pattern (40 bp):
GTGTGGAACCTTATGGAGTAGTATGGAACAATATAGAGTA
Found at i:1487079 original size:10 final size:10
Alignment explanation
Indices: 1487037--1487077 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
1487027 TGTGGAACCT
1487037 TATGGAAGAG
1 TATGGAAGAG
*
1487047 TATGGAAGAA
1 TATGGAAGAG
1487057 TATGGAAGAG
1 TATGGAAGAG
*
1487067 TGTGGAAGAG
1 TATGGAAGAG
1487077 T
1 T
1487078 GTAGAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (10 bp):
TATGGAAGAG
Found at i:1487179 original size:7 final size:7
Alignment explanation
Indices: 1487167--1487349 Score: 324
Period size: 7 Copynumber: 27.0 Consensus size: 7
1487157 TGTGGAGGTG
1487167 CCTAAAC
1 CCTAAAC
1487174 CCTAAA-
1 CCTAAAC
1487180 CCTAAAC
1 CCTAAAC
1487187 CCTAAAC
1 CCTAAAC
1487194 CCT-AAC
1 CCTAAAC
1487200 CCTAAAC
1 CCTAAAC
1487207 CCTAAAC
1 CCTAAAC
1487214 CCTAAAC
1 CCTAAAC
1487221 CCTAAAC
1 CCTAAAC
1487228 CCTAAAC
1 CCTAAAC
1487235 CCT-AAC
1 CCTAAAC
1487241 CCTAAAC
1 CCTAAAC
1487248 CCT-AAC
1 CCTAAAC
1487254 CCTAAAC
1 CCTAAAC
1487261 CCT-AAC
1 CCTAAAC
1487267 CCTAAAC
1 CCTAAAC
1487274 CCTAAAC
1 CCTAAAC
1487281 CCTAAA-
1 CCTAAAC
1487287 CCTAAAC
1 CCTAAAC
1487294 CCTAAAC
1 CCTAAAC
1487301 CCTAAAC
1 CCTAAAC
1487308 CCTAAAC
1 CCTAAAC
1487315 CCTAAAC
1 CCTAAAC
1487322 CCTAAAC
1 CCTAAAC
1487329 CCTAAAC
1 CCTAAAC
1487336 CCTAAAC
1 CCTAAAC
1487343 CCTAAAC
1 CCTAAAC
1487350 ACTTAAATTA
Statistics
Matches: 170, Mismatches: 0, Indels: 12
0.93 0.00 0.07
Matches are distributed among these distances:
6 36 0.21
7 134 0.79
ACGTcount: A:0.42, C:0.43, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:1487192 original size:20 final size:21
Alignment explanation
Indices: 1487167--1487349 Score: 324
Period size: 20 Copynumber: 9.0 Consensus size: 21
1487157 TGTGGAGGTG
1487167 CCTAAACCCTAAA-CCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487187 CCTAAACCCT-AACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487207 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487228 CCTAAACCCT-AACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487248 CCT-AACCCTAAACCCT-AAC
1 CCTAAACCCTAAACCCTAAAC
1487267 CCTAAACCCTAAACCCTAAA-
1 CCTAAACCCTAAACCCTAAAC
1487287 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487308 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487329 CCTAAACCCTAAACCCTAAAC
1 CCTAAACCCTAAACCCTAAAC
1487350 ACTTAAATTA
Statistics
Matches: 157, Mismatches: 0, Indels: 11
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.09
20 79 0.50
21 64 0.41
ACGTcount: A:0.42, C:0.43, G:0.00, T:0.15
Consensus pattern (21 bp):
CCTAAACCCTAAACCCTAAAC
Found at i:1489115 original size:23 final size:23
Alignment explanation
Indices: 1489089--1489141 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1489079 CACCACAGCT
*
1489089 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
1489112 CGTAGAATTACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
1489135 CGTAGAA
1 CGTAGAA
1489142 TTGTACCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:1489155 original size:23 final size:23
Alignment explanation
Indices: 1489097--1489143 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1489087 CTCGTATAAA
1489097 TACACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
1489120 TACACCGAAGTGCCGCGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
1489143 T
1 T
1489144 GTACCGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:1493955 original size:20 final size:20
Alignment explanation
Indices: 1493932--1493983 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1493922 GAGATGCGTT
* *
1493932 GAACCTTTTGGAGTAGTTTG
1 GAACCTTATGGAGTAGTGTG
*
1493952 GAACCTTATAGAGTAGTGTG
1 GAACCTTATGGAGTAGTGTG
1493972 GAACCTTATGGA
1 GAACCTTATGGA
1493984 AGTATGGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (20 bp):
GAACCTTATGGAGTAGTGTG
Found at i:1494879 original size:23 final size:23
Alignment explanation
Indices: 1494837--1494886 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1494827 CATTTTGATA
*
1494837 TTTTCAATATATCTAAGTAATAT
1 TTTTCAATATATCTAAGTAATAG
* **
1494860 TTTTCAATATTTCTTGGTAATAG
1 TTTTCAATATATCTAAGTAATAG
1494883 TTTT
1 TTTT
1494887 AAAAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (23 bp):
TTTTCAATATATCTAAGTAATAG
Found at i:1495406 original size:21 final size:21
Alignment explanation
Indices: 1495382--1495421 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1495372 CTCTAAACTC
*
1495382 TAAACCCTAATCCCTAAATAT
1 TAAACCCTAAACCCTAAATAT
* *
1495403 TAAATCTTAAACCCTAAAT
1 TAAACCCTAAACCCTAAAT
1495422 CCTAACTCTA
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:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATAT
Found at i:1495837 original size:43 final size:43
Alignment explanation
Indices: 1495728--1495851 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 43
1495718 TATTGATATA
* *
1495728 CACAAACGCCACAATAGATGTTGATATTTAGCGGCGTTTTT-T
1 CACAAACGCCACAATAGGTGTTGATGTTTAGCGGCGTTTTTCT
*
1495770 -ACAAACGCCATAATAGGT-TATGATGTTTAGCGGCGTTTTTCT
1 CACAAACGCCACAATAGGTGT-TGATGTTTAGCGGCGTTTTTCT
* * *
1495812 CACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTT
1 CACAAACGCCACAATAGGTGTTGATGTTTAGCGGCGTTTT
1495852 CCCATAAATG
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.01
41 35 0.49
42 1 0.01
43 33 0.46
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (43 bp):
CACAAACGCCACAATAGGTGTTGATGTTTAGCGGCGTTTTTCT
Found at i:1495883 original size:44 final size:42
Alignment explanation
Indices: 1495728--1495895 Score: 131
Period size: 41 Copynumber: 4.0 Consensus size: 42
1495718 TATTGATATA
* * * * * * *
1495728 CACAAACGCCACAATAGATGTTGATATTTAGCGGCGTTTT-T
1 CACAAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCC
* ** * * * *
1495769 TACAAACGCCATAATAGGTTATGATGTTTAGCGGCGTTTTTCT
1 CACAAACGCCGCAGTAGGTTTTGATGTTTTGCGGCG-TTTTCC
*
1495812 CACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCC
1 CACAAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCC
* * * *
1495854 CATAAATGTCGCAGTGTAGGTTTTGATGTTTTGCGGCATTTT
1 CACAAACGCCGCA--GTAGGTTTTGATGTTTTGCGGCGTTTT
1495896 GCTAAAAATG
Statistics
Matches: 104, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
41 30 0.29
42 19 0.18
43 30 0.29
44 25 0.24
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
CACAAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCC
Found at i:1496384 original size:20 final size:21
Alignment explanation
Indices: 1496304--1496393 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 21
1496294 GCTGATATGT
* * *
1496304 TGCTTCTCTCTGTGCTGCCAC
1 TGCTTCTCTCTATGTTGCCGC
* * *
1496325 AGCTTCTCTCTGTGTTGTCGC
1 TGCTTCTCTCTATGTTGCCGC
*
1496346 TGCTTCTCTCTATGCTGCCG-
1 TGCTTCTCTCTATGTTGCCGC
*
1496366 TGCTTCTCTCTTTGTTGCCGC
1 TGCTTCTCTCTATGTTGCCGC
*
1496387 TACTTCT
1 TGCTTCT
1496394 TTCCCTACTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 18 0.32
21 39 0.68
ACGTcount: A:0.04, C:0.33, G:0.19, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTATGTTGCCGC
Found at i:1496393 original size:41 final size:42
Alignment explanation
Indices: 1496306--1496393 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
1496296 TGATATGTTG
* * *
1496306 CTTCTCTCTGTGCTGCCACAGCTTCTCTCTGTGTTGTCGCTG
1 CTTCTCTCTATGCTGCCACAGCTTCTCTCTGTGTTGCCGCTA
** *
1496348 CTTCTCTCTATGCTGCC-GTGCTTCTCTCTTTGTTGCCGCTA
1 CTTCTCTCTATGCTGCCACAGCTTCTCTCTGTGTTGCCGCTA
1496389 CTTCT
1 CTTCT
1496394 TTCCCTACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 24 0.60
42 16 0.40
ACGTcount: A:0.05, C:0.34, G:0.18, T:0.43
Consensus pattern (42 bp):
CTTCTCTCTATGCTGCCACAGCTTCTCTCTGTGTTGCCGCTA
Done.