Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_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: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1290840 original size:3 final size:3
Alignment explanation
Indices: 1290832--1290861 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1290822 AGTTGTAAAT
1290832 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
1290862 TTTTTATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1308363 original size:27 final size:27
Alignment explanation
Indices: 1308315--1308408 Score: 72
Period size: 27 Copynumber: 3.4 Consensus size: 27
1308305 ATGATAGAAT
*
1308315 AAAAGAAAATAATGTA-ACAAAGAAAAGA
1 AAAAGAAAAAAATG-ACA-AAAGAAAAGA
1308343 AAAAGAAAAAAATGACAAAAG-AAAGTA
1 AAAAGAAAAAAATGACAAAAGAAAAG-A
*
1308370 AAAA-AAAACAAA-AACAAAA-AATAAGA
1 AAAAGAAAA-AAATGACAAAAGAA-AAGA
*
1308396 AAAATAACAAAAA
1 AAAAGAA-AAAAA
1308409 AAATTATAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
26 20 0.35
27 21 0.37
28 16 0.28
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (27 bp):
AAAAGAAAAAAATGACAAAAGAAAAGA
Found at i:1308380 original size:20 final size:20
Alignment explanation
Indices: 1308344--1308382 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1308334 AAGAAAAGAA
*
1308344 AAAGAAAAAAATGACAAAAG
1 AAAGAAAAAAATAACAAAAG
1308364 AAAGTAAAAAAA-AACAAAA
1 AAAG-AAAAAAATAACAAAA
1308383 ACAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAGAAAAAAATAACAAAAG
Found at i:1308409 original size:27 final size:24
Alignment explanation
Indices: 1308330--1308410 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 24
1308320 AAAATAATGT
*
1308330 AACAAAGAAAAGAAAAAGAAAAAAA
1 AACAAAAAAAAGAAAAA-AAAAAAA
* *
1308355 TGACAAAAGAAAGTAAAAAAAAACAAA
1 -AACAAAAAAAAG-AAAAAAAAA-AAA
1308382 AACAAAAAATAAGAAAAATAACAAAAA
1 AACAAAAAA-AAGAAAAA-AA-AAAAA
1308409 AA
1 AA
1308411 ATTATAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
26 25 0.56
27 18 0.40
28 2 0.04
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.05
Consensus pattern (24 bp):
AACAAAAAAAAGAAAAAAAAAAAA
Found at i:1308410 original size:22 final size:21
Alignment explanation
Indices: 1308337--1308411 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
1308327 TGTAACAAAG
* *
1308337 AAAAGAAAAAGAAAAAAATGAC
1 AAAA-AAAAATAAAAAAATAAC
* *
1308359 AAAAGAAAGTAAAAAAA-AAC
1 AAAAAAAAATAAAAAAATAAC
1308379 AAAAACAAAAAATAAGAAAAATAAC
1 --AAA-AAAAAATAA-AAAAATAAC
1308404 AAAAAAAA
1 AAAAAAAA
1308412 TTATAATATG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 2 0.05
21 10 0.24
22 12 0.29
23 10 0.24
24 5 0.12
25 3 0.07
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.05
Consensus pattern (21 bp):
AAAAAAAAATAAAAAAATAAC
Found at i:1310766 original size:285 final size:283
Alignment explanation
Indices: 1310251--1310816 Score: 1030
Period size: 285 Copynumber: 2.0 Consensus size: 283
1310241 TCGTGCTTAC
1310251 ATAATTTCTAATTGAAATTGTTATCCAAAACATGCAATTATTTAATTAATTTAGAGAGAGAATAA
1 ATAATTTCTAATTGAAATTGTTATCCAAAACATGCAATTATTTAATTAATTTAGAGAGAGAATAA
1310316 AGTTAATGATTAATTGTGTAATTTACCCTTTGTACATTTACATAGGAATGAAATTGGTGAAAAAA
66 AGTTAATGATTAATTGTGTAATTTACCCTTTGTACATTTACATAGGAATGAAATTGGTGAAAAAA
1310381 TAGGAGACGCATTGCACTCTATGCGTCTCCCCAAAATTTATGTATAAGTCGCTTGGACTCTAATA
131 TAGGAGACGCATTGCACTCTATGCGTCTCCCCAAAATTTATGTATAAGTCGCTTGGACTCTAATA
*
1310446 CGTCTTTGGATTTACGCATTCACTCTATTTCATGAAATAATTTCCAGAGTGCCCTGTTCAAACAA
196 CGTCTTTGGATTTACGCATTCACTCTATTTCATGAAATAATTTCCAGAGTGCCATGTTCAAACAA
1310511 TTTTTTTTTCAACTGCATTATTGA
261 -TTTTTTTTCAACTGCATTATTGA
*
1310535 ATAATTTCTAATTGAAATTGTTATCCAAAACAGTGCAATTGTATTTAATTAATTTGGAGAGAGAA
1 ATAATTTCTAATTGAAATTGTTATCCAAAACA-TGCAA-T-TATTTAATTAATTTAGAGAGAGAA
1310600 TAAAGTTAATGATT-ATTGTGTAATTTACCCTTTGTACATTTACATAGGAATGAAATTGGTGAAA
63 TAAAGTTAATGATTAATTGTGTAATTTACCCTTTGTACATTTACATAGGAATGAAATTGGTGAAA
*
1310664 AATATGGGAGACGCATTGCACTCTATGCGTCTCCCCAAAA-TT-TGTATAAGTCGCTTGGACTCT
128 AA-ATAGGAGACGCATTGCACTCTATGCGTCTCCCCAAAATTTATGTATAAGTCGCTTGGACTCT
1310727 AATACGTCTTTGGATTTACGCATTCACTCTATTTCATGAAATAATTTCCAGAGTGCCATGTTCAA
192 AATACGTCTTTGGATTTACGCATTCACTCTATTTCATGAAATAATTTCCAGAGTGCCATGTTCAA
*
1310792 ACAATTTTTTTTCAACTGTATTATT
257 ACAATTTTTTTTCAACTGCATTATT
1310817 TGAGAAATCA
Statistics
Matches: 274, Mismatches: 4, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
284 52 0.19
285 94 0.34
286 55 0.20
287 73 0.27
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (283 bp):
ATAATTTCTAATTGAAATTGTTATCCAAAACATGCAATTATTTAATTAATTTAGAGAGAGAATAA
AGTTAATGATTAATTGTGTAATTTACCCTTTGTACATTTACATAGGAATGAAATTGGTGAAAAAA
TAGGAGACGCATTGCACTCTATGCGTCTCCCCAAAATTTATGTATAAGTCGCTTGGACTCTAATA
CGTCTTTGGATTTACGCATTCACTCTATTTCATGAAATAATTTCCAGAGTGCCATGTTCAAACAA
TTTTTTTTCAACTGCATTATTGA
Found at i:1313986 original size:58 final size:60
Alignment explanation
Indices: 1313896--1314013 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 60
1313886 TTAAAGTGAT
1313896 AAGATTAGAATTTTTGCAAAAGTTCAAGGGCAAATATGG-AACTAATAAA-ATTATTTTA
1 AAGATTAGAATTTTTGCAAAAGTTCAAGGGCAAATATGGAAACTAATAAATATTATTTTA
1313954 AAGATTAGAATTTTTGCAAAAGTTCAAGGGCAAATATGGAAACTAATAAATATTATTTTA
1 AAGATTAGAATTTTTGCAAAAGTTCAAGGGCAAATATGGAAACTAATAAATATTATTTTA
1314014 TTAACATGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 39 0.67
59 10 0.17
60 9 0.16
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (60 bp):
AAGATTAGAATTTTTGCAAAAGTTCAAGGGCAAATATGGAAACTAATAAATATTATTTTA
Found at i:1316430 original size:36 final size:36
Alignment explanation
Indices: 1316279--1316438 Score: 148
Period size: 36 Copynumber: 4.5 Consensus size: 36
1316269 TAACATATTT
* *
1316279 AGTGCCATGTGATTGTA-CATAGGTGTGGCACATTC
1 AGTGCCATGTGATTGTACCATAGGTGCGACACATTC
* * * *
1316314 AGTGCCCTATGATTGCACCATAGGTGC-AGCATACTT-
1 AGTGCCATGTGATTGTACCATAGGTGCGA-CACA-TTC
* * * * *
1316350 AGGGCCATATGA-TGTACCGTAGATGCGACACATTT
1 AGTGCCATGTGATTGTACCATAGGTGCGACACATTC
* *
1316385 AGTGTCATGTGATTGAACCATAGGTGCGACACATTC
1 AGTGCCATGTGATTGTACCATAGGTGCGACACATTC
*
1316421 AGTGCCATGTGAATGTAC
1 AGTGCCATGTGATTGTAC
1316439 ATGTATTGTA
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
34 2 0.02
35 37 0.38
36 56 0.58
37 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (36 bp):
AGTGCCATGTGATTGTACCATAGGTGCGACACATTC
Found at i:1317402 original size:223 final size:222
Alignment explanation
Indices: 1316999--1317447 Score: 832
Period size: 223 Copynumber: 2.0 Consensus size: 222
1316989 TGATTTAGCC
*
1316999 CTTACATTCTTACACTTTTCAAATTCAATTATATATCCATAATACCATAATTTTAACCATAGGAT
1 CTTACATTCTTACACCTTTCAAATTCAATTATATATCCATAATACCATAATTTTAACCATAGGAT
1317064 AAATTCTTTAGAATTTCATCTCAACTTTTCTATTTATTCAATAAGTCATTTTTGCCGTTTAATCC
66 AAATTCTTTAGAATTTCATCTCAACTTTTCTATTTATTCAATAAGTCATTTTTGCCGTTTAATCC
1317129 TAAATTCAAGTATCATAAAAAAATCAAACATTCCAACAACATATTCAATTTCTACTCATTAACTT
131 TAAATTCAAGTATCATAAAAAAATCAAACATTCCAACAACATATTCAATTTCTACTCATTAACTT
1317194 ATACAAATTTATATTTCAGACCCACAA
196 ATACAAATTTATATTTCAGACCCACAA
1317221 CTTA-ATTCTTACAACCTTTCAAATTCAATTATATATCCATAATACCATAATTTTAACCATAGGA
1 CTTACATTCTTAC-ACCTTTCAAATTCAATTATATATCCATAATACCATAATTTTAACCATAGGA
1317285 TAAATTCTTTTAGAATTTCATCTCAACTTTTCTATTTTATTCAATAAAGTCATTTTTGCCGTTTA
65 TAAATTC-TTTAGAATTTCATCTCAACTTTTCTA-TTTATTCAAT-AAGTCATTTTTGCCGTTTA
1317350 ATCCTAAA-TCAAGT-TCATAAAAAAATCAAACATTCCAACAACATATTCAATTTCTACTCATTA
127 ATCCTAAATTCAAGTATCATAAAAAAATCAAACATTCCAACAACATATTCAATTTCTACTCATTA
1317413 ACTTATACAAATTTATATTTCAGACCCACAA
192 ACTTATACAAATTTATATTTCAGACCCACAA
1317444 CTTA
1 CTTA
1317448 TACAATTTGT
Statistics
Matches: 222, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
221 8 0.04
222 61 0.27
223 110 0.50
224 16 0.07
225 27 0.12
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.39
Consensus pattern (222 bp):
CTTACATTCTTACACCTTTCAAATTCAATTATATATCCATAATACCATAATTTTAACCATAGGAT
AAATTCTTTAGAATTTCATCTCAACTTTTCTATTTATTCAATAAGTCATTTTTGCCGTTTAATCC
TAAATTCAAGTATCATAAAAAAATCAAACATTCCAACAACATATTCAATTTCTACTCATTAACTT
ATACAAATTTATATTTCAGACCCACAA
Found at i:1320439 original size:24 final size:24
Alignment explanation
Indices: 1320407--1320466 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1320397 TCGATCAATC
1320407 TTGTATTAGTGCATTCGTGCACTA
1 TTGTATTAGTGCATTCGTGCACTA
* *
1320431 TTGTATTAGTGCATTTGTGCACTC
1 TTGTATTAGTGCATTCGTGCACTA
*
1320455 CTGTATTAGTGC
1 TTGTATTAGTGC
1320467 TCTTGTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (24 bp):
TTGTATTAGTGCATTCGTGCACTA
Found at i:1320745 original size:31 final size:31
Alignment explanation
Indices: 1320720--1320780 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1320710 GTTATGATAT
1320720 GTGAATATGTGAAAAATACAGGTTATATGAA
1 GTGAATATGTGAAAAATACAGGTTATATGAA
* * *
1320751 GTGAATATGTGAAAAGTACAAGTGATATGA
1 GTGAATATGTGAAAAATACAGGTTATATGA
1320781 TTTAAATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (31 bp):
GTGAATATGTGAAAAATACAGGTTATATGAA
Found at i:1321553 original size:37 final size:37
Alignment explanation
Indices: 1321503--1321578 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1321493 ACTGAATTTC
*
1321503 AAATAGTATATGTTTTAAACTTTGATGTGACATCTCT
1 AAATAGTATATGTTTTAAACTTTGATATGACATCTCT
*
1321540 AAATAGTATATGTTTTAAATTTTGATATGACATCTCT
1 AAATAGTATATGTTTTAAACTTTGATATGACATCTCT
1321577 AA
1 AA
1321579 CTCGTATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (37 bp):
AAATAGTATATGTTTTAAACTTTGATATGACATCTCT
Found at i:1328830 original size:48 final size:48
Alignment explanation
Indices: 1328758--1328873 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
1328748 ACAAAATGCC
* * *
1328758 CATAGCTTGTCCATAAATGGTGGCACTGACATTGAGAAACAAGATGTA
1 CATAGCTCGACCATAAATGATGGCACTGACATTGAGAAACAAGATGTA
* * *
1328806 CATAGCTCGACCATTAATGATGGCACTGACATTGAGGAACAAGATGTG
1 CATAGCTCGACCATAAATGATGGCACTGACATTGAGAAACAAGATGTA
* *
1328854 CATAGCCCGACCGTAAATGA
1 CATAGCTCGACCATAAATGA
1328874 AGACGCTGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (48 bp):
CATAGCTCGACCATAAATGATGGCACTGACATTGAGAAACAAGATGTA
Found at i:1328890 original size:48 final size:48
Alignment explanation
Indices: 1328781--1328890 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
1328771 TAAATGGTGG
* * * * * * *
1328781 CACTGACATTGAGAAACAAGATGTACATAGCTCGACCATTAATGATGG
1 CACTGAAAATGAGGAACAAGATGTACATAGCCCGACCATAAATGAAGA
* * * *
1328829 CACTGACATTGAGGAACAAGATGTGCATAGCCCGACCGTAAATGAAGA
1 CACTGAAAATGAGGAACAAGATGTACATAGCCCGACCATAAATGAAGA
*
1328877 CGCTGAAAATGAGG
1 CACTGAAAATGAGG
1328891 TCGTTTGAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (48 bp):
CACTGAAAATGAGGAACAAGATGTACATAGCCCGACCATAAATGAAGA
Found at i:1332342 original size:45 final size:45
Alignment explanation
Indices: 1332248--1332345 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
1332238 GGGTAGACTT
* * * * * **
1332248 GGGTCACATAGAATCAATATCTCTCAAGTATCTCAGGTGAGGTTT
1 GGGTCACATAGAATCAACACCTCCCAAGTATCTAAAGTGAGGTCC
* * *
1332293 GGGTCACATAGCATCGACACCTCCCAAGTATCTAAAGTTAGGTCC
1 GGGTCACATAGAATCAACACCTCCCAAGTATCTAAAGTGAGGTCC
1332338 GGGTCACA
1 GGGTCACA
1332346 CAACATCAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (45 bp):
GGGTCACATAGAATCAACACCTCCCAAGTATCTAAAGTGAGGTCC
Found at i:1334303 original size:15 final size:15
Alignment explanation
Indices: 1334266--1334326 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
1334256 CTTGAATAAG
1334266 ATGAAAGAAGAAGAA
1 ATGAAAGAAGAAGAA
1334281 ATG-AAGAAGAAG-A
1 ATGAAAGAAGAAGAA
1334294 ATGAAGAGAAG-AGAA
1 ATGAA-AGAAGAAGAA
*
1334309 GTGGAAAGGAA-AAGAA
1 AT-GAAA-GAAGAAGAA
1334325 AT
1 AT
1334327 CCACATCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
13 4 0.11
14 12 0.32
15 11 0.29
16 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (15 bp):
ATGAAAGAAGAAGAA
Found at i:1334308 original size:17 final size:18
Alignment explanation
Indices: 1334259--1334309 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1334249 ATAGTCACTT
1334259 GAAT-AAGATGAA-AGAA
1 GAATGAAGATGAAGAGAA
1334275 GAA-GAA-ATGAAGAAGAA
1 GAATGAAGATGAAG-AGAA
1334292 GAATGAAGA-GAAGAGAA
1 GAATGAAGATGAAGAGAA
1334309 G
1 G
1334310 TGGAAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 12 0.40
18 7 0.23
19 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (18 bp):
GAATGAAGATGAAGAGAA
Found at i:1335466 original size:13 final size:13
Alignment explanation
Indices: 1335448--1335480 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1335438 TACATAGGGA
1335448 AACTCACTTAGCT
1 AACTCACTTAGCT
1335461 AACTCACTTAGCT
1 AACTCACTTAGCT
1335474 AACTCAC
1 AACTCAC
1335481 ATAACACTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (13 bp):
AACTCACTTAGCT
Found at i:1344467 original size:162 final size:162
Alignment explanation
Indices: 1344200--1344524 Score: 641
Period size: 162 Copynumber: 2.0 Consensus size: 162
1344190 TAATTATGTT
1344200 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
1 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
1344265 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
66 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
1344330 ATCTATTACATTCGACATCTCCCTAGTAATTA
131 ATCTATTACATTCGACATCTCCCTAGTAATTA
*
1344362 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACTTATTTATTTGTTT
1 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
1344427 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
66 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
1344492 ATCTATTACATTCGACATCTCCCTAGTAATTA
131 ATCTATTACATTCGACATCTCCCTAGTAATTA
1344524 T
1 T
1344525 TTACCTTCTT
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (162 bp):
TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
ATCTATTACATTCGACATCTCCCTAGTAATTA
Found at i:1347484 original size:25 final size:25
Alignment explanation
Indices: 1347450--1347500 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1347440 CTTTTGTGTT
1347450 TGTTTGTGATACATGTGATTCACCA
1 TGTTTGTGATACATGTGATTCACCA
1347475 TGTTTGTGATACATGTGATTCACCA
1 TGTTTGTGATACATGTGATTCACCA
1347500 T
1 T
1347501 TCCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (25 bp):
TGTTTGTGATACATGTGATTCACCA
Found at i:1348667 original size:16 final size:17
Alignment explanation
Indices: 1348630--1348666 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1348620 AAATCATTTG
*
1348630 AAAATAATAAAAAAGTC
1 AAAATAATAAAAAAATC
*
1348647 AAAATTATAAAAAAATC
1 AAAATAATAAAAAAATC
1348664 AAA
1 AAA
1348667 TATTTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAATAATAAAAAAATC
Found at i:1348792 original size:19 final size:19
Alignment explanation
Indices: 1348765--1348816 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
1348755 TTTAATATTG
* *
1348765 ATTTCTAATTTATTTTATA
1 ATTTTTAATTTATTTTAGA
*
1348784 ATTTTTAA-TTA-TTTCGA
1 ATTTTTAATTTATTTTAGA
*
1348801 ACTTTTAATTTATTTT
1 ATTTTTAATTTATTTT
1348817 TAAATATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 11 0.41
18 6 0.22
19 10 0.37
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTAATTTATTTTAGA
Found at i:1348834 original size:28 final size:29
Alignment explanation
Indices: 1348784--1348840 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1348774 TTATTTTATA
*
1348784 ATTTTTAATTATTTCGAACTTTTA-ATTT
1 ATTTTTAAATATTTCGAACTTTTATATTT
* **
1348812 ATTTTTAAATATTTCTATTTTTTATATTT
1 ATTTTTAAATATTTCGAACTTTTATATTT
1348841 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTAAATATTTCGAACTTTTATATTT
Found at i:1353717 original size:21 final size:21
Alignment explanation
Indices: 1353691--1353730 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1353681 TCTATTGAAA
* *
1353691 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
1353712 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
1353731 CTACTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:1356531 original size:37 final size:37
Alignment explanation
Indices: 1356481--1356551 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1356471 TGCCAACTTA
1356481 CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
1 CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
*
1356518 CCAAATTTGACAATTTGCAAGCCAAATCTAACAA
1 CCAAATTTGACAATTTGCAAGCCAAACCTAACAA
1356552 CGGGTATATA
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:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (37 bp):
CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
Found at i:1356543 original size:21 final size:21
Alignment explanation
Indices: 1356481--1356544 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1356471 TGCCAACTTA
1356481 CCAAATTTGACAATTTGCAAG
1 CCAAATTTGACAATTTGCAAG
** *
1356502 CCAAACCTAACAA-TT----G
1 CCAAATTTGACAATTTGCAAG
1356518 CCAAATTTGACAATTTGCAAG
1 CCAAATTTGACAATTTGCAAG
1356539 CCAAAT
1 CCAAAT
1356545 CTAACAACGG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
20 2 0.06
21 17 0.53
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (21 bp):
CCAAATTTGACAATTTGCAAG
Found at i:1358279 original size:26 final size:26
Alignment explanation
Indices: 1358243--1358292 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1358233 AAGGCCAAGG
1358243 ATGAGGTCATAGTATAAAATAGCGTT
1 ATGAGGTCATAGTATAAAATAGCGTT
1358269 ATGAGGTCATAGTATAAAATAGCG
1 ATGAGGTCATAGTATAAAATAGCG
1358293 GTTGTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (26 bp):
ATGAGGTCATAGTATAAAATAGCGTT
Found at i:1358328 original size:14 final size:14
Alignment explanation
Indices: 1358311--1358345 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1358301 ATCTGTCGTT
1358311 GTTGCGGTGTCGCA
1 GTTGCGGTGTCGCA
*
1358325 GTTGCGGTGTCGCG
1 GTTGCGGTGTCGCA
1358339 GTTGCGG
1 GTTGCGG
1358346 GACGTTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.03, C:0.20, G:0.49, T:0.29
Consensus pattern (14 bp):
GTTGCGGTGTCGCA
Found at i:1360319 original size:23 final size:26
Alignment explanation
Indices: 1360271--1360325 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1360261 ATAAGAAAAA
1360271 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
1360296 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
1360319 AGAAATA
1 AGAAATA
1360326 TCAGAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:1361885 original size:3 final size:3
Alignment explanation
Indices: 1361877--1361941 Score: 82
Period size: 3 Copynumber: 21.7 Consensus size: 3
1361867 TGTAATTTTT
1361877 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
1361922 TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
1361942 TTTAAATGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.11
3 42 0.75
4 8 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1362528 original size:117 final size:116
Alignment explanation
Indices: 1362323--1362653 Score: 465
Period size: 117 Copynumber: 2.9 Consensus size: 116
1362313 TGTGAACTTT
* * * *
1362323 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATG
1 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAACTGATCCATCAAATGATG
* **
1362388 GATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCC
66 AATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCC
*** *
1362439 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCATGGAAATTTTAATCCATCAAATGAT
1 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACC-TGGAAAAACTGATCCATCAAATGAT
* *
1362504 GAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTTTTCTTCC
65 GAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCC
*
1362556 TTCTTC--A-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAACTGATCCATCAAATGAT
1 TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAACTGATCCATCAAATGAT
*
1362617 GAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTA
65 GAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTA
1362654 GATGAGTTCT
Statistics
Matches: 192, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
113 57 0.30
114 25 0.13
115 1 0.01
116 37 0.19
117 69 0.36
118 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (116 bp):
TTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAACTGATCCATCAAATGATG
AATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCC
Found at i:1362685 original size:91 final size:91
Alignment explanation
Indices: 1362562--1362744 Score: 260
Period size: 91 Copynumber: 2.0 Consensus size: 91
1362552 TTCCTTCTTC
* * *
1362562 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAGC
1 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTAATCCATCAAATAATGAATTCAAAC
1362627 AAAAAGTTGAACAAATTCTTCTCATT
66 AAAAAGTTGAACAAATTCTTCTCATT
* * *** *
1362653 AGATGAGTTCTTCTTATTATGAACTCTT-TCTGGCAATGTTAATCCATCAAATAATGAATTTAAA
1 AGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAACTAATCCATCAAATAATGAATTCAAA
*
1362717 CAAAAGGTTGAACAAATTCTTCTCATT
65 CAAAAAGTTGAACAAATTCTTCTCATT
1362744 A
1 A
1362745 TGAACTTCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 79 0.98
92 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (91 bp):
AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTAATCCATCAAATAATGAATTCAAAC
AAAAAGTTGAACAAATTCTTCTCATT
Found at i:1362810 original size:204 final size:205
Alignment explanation
Indices: 1362449--1362821 Score: 577
Period size: 204 Copynumber: 1.8 Consensus size: 205
1362439 TTCTTCAGAT
* *
1362449 GATGAGTTCTTCTCATTATGAACTCTACCATGGAAATTTTAATCCATCAAATGATGAATTCAAAC
1 GATGAGTTCTTCTCATTATGAACTCTACCATGGAAATGTTAATCCATCAAATAATGAATTCAAAC
*
1362514 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
66 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
****
1362579 TATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATT
131 TATGAACTCGAACTGGAAAAACTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATT
1362644 CTTCTCATTA
196 CTTCTCATTA
* ** * *
1362654 GATGAGTTCTTCTTATTATGAACTCTTTC-TGGCAATGTTAATCCATCAAATAATGAATTTAAAC
1 GATGAGTTCTTCTCATTATGAACTCTACCATGGAAATGTTAATCCATCAAATAATGAATTCAAAC
* *
1362718 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
66 AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
1362783 TATGAACTCGAACTGGTAATGCTGATCCATCAATTGATG
131 TATGAACTCGAACTGGAAAAACTGATCCATCAAATGATG
1362822 GATTTGAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
204 124 0.83
205 26 0.17
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (205 bp):
GATGAGTTCTTCTCATTATGAACTCTACCATGGAAATGTTAATCCATCAAATAATGAATTCAAAC
AAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAACTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATT
CTTCTCATTA
Found at i:1363764 original size:93 final size:93
Alignment explanation
Indices: 1363497--1364316 Score: 1491
Period size: 93 Copynumber: 8.8 Consensus size: 93
1363487 TCCATCTTTT
* * *
1363497 AATTCCAATGATTGG-TTCT-GTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACACTTCC
1 AATT-CAATGATTGGTTTTTAG-GGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCC
1363560 AGAAGATGCTATGAGCACATTCATCTTCCA
64 AGAAGATGCTATGAGCACATTCATCTTCCA
* *
1363590 AATTCAATGATTGGTTTTTTGGGGTTCATACTAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 AATTCAATGATTGG-TTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1363655 GAAGATGCTATGAGCACATTCATCTTCCA
65 GAAGATGCTATGAGCACATTCATCTTCCA
*
1363684 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCATATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
1363749 AAGATGCTATGAGCACATTTATCTTCTA
66 AAGATGCTATGAGCACATTCATCTTCCA
1363777 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1363842 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
1363870 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1363935 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
1363963 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1364028 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
1364056 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1364121 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
*
1364149 AATTCAATGATTGGTTTTTAGGATTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
1364214 AAGATACTATGAGCACATTCATCTTCTA
66 AAGATGCTATGAGCACATTCATCTTCCA
*
1364242 AATTCAATTATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1364307 AAGATGCTAT
66 AAGATGCTAT
1364317 TGGGTCTACG
Statistics
Matches: 706, Mismatches: 18, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
92 10 0.01
93 609 0.86
94 86 0.12
95 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (93 bp):
AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATGAGCACATTCATCTTCCA
Found at i:1365328 original size:6 final size:6
Alignment explanation
Indices: 1365313--1365360 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
1365303 TGACCCCCCT
*
1365313 TTTTTCC TTTTTC TTTTTC TTTTTT TTTCTTC TTTTT- TTTTTC TTTTT
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTTTT
1365361 TTCAATCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.14
6 22 0.59
7 10 0.27
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:1365348 original size:24 final size:23
Alignment explanation
Indices: 1365312--1365362 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
1365302 TTGACCCCCC
1365312 TTTTTTCCTTTTTCTTTTTCTTT
1 TTTTTTCCTTTTTCTTTTTCTTT
1365335 TTTTTTCTTCTTTTT-TTTTTCTTT
1 TTTTTTC--CTTTTTCTTTTTCTTT
1365359 TTTT
1 TTTT
1365363 CAATCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTCCTTTTTCTTTTTCTTT
Found at i:1365351 original size:22 final size:22
Alignment explanation
Indices: 1365311--1365363 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1365301 CTTGACCCCC
*
1365311 CTTTTTTCCTTTTTCTTTTTCTT
1 CTTTTTTTCTTTTTCTTTTT-TT
1365334 -TTTTTTTCTTCTTT-TTTTTTT
1 CTTTTTTTCTT-TTTCTTTTTTT
1365355 CTTTTTTTC
1 CTTTTTTTC
1365364 AATCATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
CTTTTTTTCTTTTTCTTTTTTT
Found at i:1372628 original size:15 final size:15
Alignment explanation
Indices: 1372605--1372636 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1372595 AATAATGAAT
1372605 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1372620 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1372635 AA
1 AA
1372637 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1376522 original size:23 final size:26
Alignment explanation
Indices: 1376474--1376528 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1376464 ATGAGAAAAA
1376474 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
1376499 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
1376522 AGAAATA
1 AGAAATA
1376529 TCAGAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:1378088 original size:3 final size:3
Alignment explanation
Indices: 1378080--1378160 Score: 105
Period size: 3 Copynumber: 26.7 Consensus size: 3
1378070 TGTAATTTTT
1378080 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TA-A TAA
1378126 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1378161 TTTAAATGAA
Statistics
Matches: 71, Mismatches: 0, Indels: 14
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.08
3 54 0.76
4 11 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1379876 original size:15 final size:16
Alignment explanation
Indices: 1379835--1379874 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1379825 TTAATTAATT
* *
1379835 AAATATAAAATATTACA
1 AAAT-TAAATTATTAAA
1379852 AAATTAAATTATTAAA
1 AAATTAAATTATTAAA
1379868 AAATTAA
1 AAATTAA
1379875 TTTAAGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAAATTATTAAA
Found at i:1382933 original size:10 final size:10
Alignment explanation
Indices: 1382905--1382947 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1382895 AGCATTTGTT
1382905 TAAAAAGAAAA
1 TAAAAA-AAAA
1382916 T-AAAAAAAA
1 TAAAAAAAAA
**
1382925 TAAGTAAAAA
1 TAAAAAAAAA
1382935 TAAAAAAAAA
1 TAAAAAAAAA
1382945 TAA
1 TAA
1382948 CTTTAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 5 0.19
10 21 0.78
11 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:1384893 original size:114 final size:114
Alignment explanation
Indices: 1384688--1385042 Score: 665
Period size: 114 Copynumber: 3.1 Consensus size: 114
1384678 ATTGTTACCA
1384688 TCAATTATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACA
1 TCAA-TATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACA
1384753 TGATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
65 TGATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
*
1384803 TCAATATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTACATGTGACAT
1 TCAATATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACAT
1384868 GATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
66 GATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
* *
1384917 CCTATTATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACA
1 TC-AATATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACA
1384982 TGATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
65 TGATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
1385032 TCAATATTTAT
1 TCAATATTTAT
1385043 CATATATCTT
Statistics
Matches: 233, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
114 118 0.51
115 115 0.49
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (114 bp):
TCAATATTTATATACCTTCTATTATTCTGTGTTCGATTGACACTCCTATTATTTGCATGTGACAT
GATTAAAATATTCTAAGACTGTCGAACCAGATGAAACATAAACCACACT
Found at i:1387101 original size:19 final size:19
Alignment explanation
Indices: 1387077--1387116 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1387067 TTCAGAAGGG
* *
1387077 AAAAAAGCAGAGGAAAAAT
1 AAAAAAGAAGAAGAAAAAT
1387096 AAAAAAGAAGAAGAAAAAT
1 AAAAAAGAAGAAGAAAAAT
1387115 AA
1 AA
1387117 CAGAGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAGAAGAAAAAT
Found at i:1388874 original size:24 final size:26
Alignment explanation
Indices: 1388828--1388880 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
1388818 AAAATACCAA
1388828 TTTTTCAAAATAAAAATTATAATTAT
1 TTTTTCAAAATAAAAATTATAATTAT
* *
1388854 TTTTTTAAAAT-AATATT-TAATTAT
1 TTTTTCAAAATAAAAATTATAATTAT
1388878 TTT
1 TTT
1388881 CCGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 5 0.20
26 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTCAAAATAAAAATTATAATTAT
Found at i:1389974 original size:24 final size:24
Alignment explanation
Indices: 1389947--1389992 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1389937 CTGTTAAAAA
1389947 TTAAATAATGTT-TAATTTTTTATT
1 TTAAATAAT-TTCTAATTTTTTATT
* *
1389971 TTAATTAATTTCTTATTTTTTA
1 TTAAATAATTTCTAATTTTTTA
1389993 GAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTAAATAATTTCTAATTTTTTATT
Found at i:1390630 original size:35 final size:35
Alignment explanation
Indices: 1390591--1390737 Score: 177
Period size: 35 Copynumber: 4.2 Consensus size: 35
1390581 AAAACAGTCC
* * *
1390591 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
1390626 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
1390661 TTAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
1390696 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1390731 TCAATTT
1 TCAATTT
1390738 AAGGTTTAGA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 99 1.00
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1391491 original size:14 final size:15
Alignment explanation
Indices: 1391451--1391492 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1391441 ATTTTTAATT
1391451 ATGAGATAA-ATTTTG
1 ATGAGA-AATATTTTG
*
1391466 TTGAGAAATATTTTG
1 ATGAGAAATATTTTG
1391481 ATGAG-AATATTT
1 ATGAGAAATATTT
1391493 AAATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (15 bp):
ATGAGAAATATTTTG
Found at i:1397095 original size:13 final size:13
Alignment explanation
Indices: 1397074--1397108 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1397064 TATAGTTTTA
*
1397074 TTTTAAAATATAT
1 TTTTTAAATATAT
1397087 TTTTTAAATATAT
1 TTTTTAAATATAT
*
1397100 TTTATAAAT
1 TTTTTAAAT
1397109 TTTCTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAATATAT
Found at i:1401107 original size:127 final size:127
Alignment explanation
Indices: 1400857--1401487 Score: 998
Period size: 127 Copynumber: 5.0 Consensus size: 127
1400847 GTACTATTCA
* *
1400857 CGTGAAGGCGCATTCTCGAGGGG-G-GCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCC
1 CGTGAAGGCGCGTTCTCG-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
* * *
1400920 CTATTATGTCACTTATGTCCCCCGGGAACTAATCATGTCAATACCTATTATTCCTTAGGGGAT
65 CTATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
1400983 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGCCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
1401048 TATTATGTAACTTATGTCCCCTAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
1401110 CGTGAAGGCGCGTTCCCGGGGGCGCGCGTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *** *
1401175 TATTATGTCATTTATGTCCCTTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGGC
66 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
1401237 CGTGAAGGCGCATTATCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
1401302 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCTTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
1401364 CGTGAAGGCGCGTTCTCGGGGGGGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* * *
1401429 TATTGTGTCACTTATGTCCCCC-GAGAACTATTCATGTCAATACCTACTATTTCTTAGGG
66 TATTATGTCACTTATGTCCCCCAG-GAACTATTCATGTCAATACCTATTATTCCTTAGGG
1401488 AACTTTAAAG
Statistics
Matches: 466, Mismatches: 36, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
125 4 0.01
126 18 0.04
127 444 0.95
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:1401958 original size:34 final size:34
Alignment explanation
Indices: 1401920--1402020 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
1401910 GAATTTAATG
* *
1401920 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
1401954 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
1401988 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1402021 AACATTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:1404429 original size:31 final size:31
Alignment explanation
Indices: 1404362--1404462 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
1404352 TAATTAGCAC
* * *
1404362 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
1404390 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
1404421 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
1404452 TAAAATATAAT
1 -AAAAAATAAT
1404463 AACTATTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:1405754 original size:229 final size:227
Alignment explanation
Indices: 1405349--1405797 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 227
1405339 GTAAATTATC
* * * *
1405349 TATCCTTTTTATAAAAGTGTCCATATTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1405414 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1405479 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1405544 AAACATAAATGACATAACTTTCAAAAAAGTATA
196 AAACATAAATGACATAACTTT-AAAAAAGTATA
*
1405577 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1405642 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1405707 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
1405772 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATGACATAACTTTAAAA
1405798 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 39 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATGACATAACTTTAAAAAAGTATA
Found at i:1405886 original size:20 final size:19
Alignment explanation
Indices: 1405863--1405908 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1405853 CGATATACCA
1405863 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1405883 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1405903 GGTAAA
1 GGTAAA
1405909 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1406053 original size:20 final size:19
Alignment explanation
Indices: 1406030--1406076 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1406020 CGATATAACA
1406030 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1406050 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1406070 GGTAAAA
1 GGTAAAA
1406077 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1406078 original size:17 final size:19
Alignment explanation
Indices: 1406039--1406081 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1406029 AGGTAAAAAT
1406039 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1406059 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1406076 ATGATA
1 ATGATA
1406082 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1407343 original size:23 final size:23
Alignment explanation
Indices: 1407312--1407384 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1407302 ATAGGTAAAA
*
1407312 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1407335 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1407358 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1407381 ATAT
1 ATAT
1407385 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1407774 original size:23 final size:23
Alignment explanation
Indices: 1407743--1407815 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1407733 ATAGGTAAAA
*
1407743 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
1407766 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1407789 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1407812 ATAT
1 ATAT
1407816 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1408029 original size:430 final size:431
Alignment explanation
Indices: 1407182--1408164 Score: 1934
Period size: 431 Copynumber: 2.3 Consensus size: 431
1407172 GTATCGATCC
1407182 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
1 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
1407247 AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
66 AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
1407312 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
131 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
1407377 GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACA
196 GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACA
1407442 TTAATTTAAGGTTATCTTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAAT
261 TTAATTTAAGGTTATCTTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAAT
1407507 GATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAA
326 GATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAA
1407572 AATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTA
391 AATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTA
1407613 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
1 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
1407678 AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
66 AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
*
1407743 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGT
131 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
1407808 GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACA
196 GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACA
1407873 TTAATTTAAGGTTATC-TTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAAT
261 TTAATTTAAGGTTATCTTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAAT
1407937 GATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAA
326 GATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAA
1408002 AATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTA
391 AATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTA
1408043 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACAT
1 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
*
1408107 AACTTTAAAAGAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATA
66 AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
1408165 TAATGTAATA
Statistics
Matches: 550, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
429 82 0.15
430 193 0.35
431 275 0.50
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
AACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACA
TTAATTTAAGGTTATCTTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAAT
GATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAA
AATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTA
Found at i:1411292 original size:24 final size:25
Alignment explanation
Indices: 1411265--1411311 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1411255 CTATTCTTTC
1411265 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
1411289 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
1411312 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:1415229 original size:24 final size:26
Alignment explanation
Indices: 1415202--1415260 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
1415192 TCCTACATGG
*
1415202 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
1415226 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
1415255 TTAATT
1 TTAATT
1415261 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:1415418 original size:20 final size:20
Alignment explanation
Indices: 1415358--1415420 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
1415348 ACTTGTTATT
1415358 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
1415379 TTGTTTATCTATAATATGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
1415402 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
1415421 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 5 0.15
23 14 0.42
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:1418974 original size:26 final size:25
Alignment explanation
Indices: 1418942--1419034 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 25
1418932 ACTTTTTTTA
*
1418942 ATTAAATACAAACATTACATTAGAAC
1 ATTAAAT-CATACATTACATTAGAAC
*
1418968 ATTAAATCCTACATTACATTAGAAAC
1 ATTAAATCATACATTACATTAG-AAC
* *
1418994 ATTAACTCCTACATTACATT--AA-
1 ATTAAATCATACATTACATTAGAAC
1419016 ATTAAAT--TACATTACATTA
1 ATTAAATCATACATTACATTA
1419035 CATTACATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
20 11 0.18
22 6 0.10
23 2 0.03
25 13 0.21
26 29 0.48
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTAAATCATACATTACATTAGAAC
Found at i:1418984 original size:25 final size:25
Alignment explanation
Indices: 1418953--1419034 Score: 111
Period size: 26 Copynumber: 3.4 Consensus size: 25
1418943 TTAAATACAA
1418953 ACATTACATTAGAACATTAAATCCT
1 ACATTACATTAGAACATTAAATCCT
*
1418978 ACATTACATTAGAAACATTAACTCCT
1 ACATTACATTAG-AACATTAAATCCT
1419004 ACATTACATT--AA-ATTAAAT--T
1 ACATTACATTAGAACATTAAATCCT
1419024 ACATTACATTA
1 ACATTACATTA
1419035 CATTACATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
20 11 0.21
22 6 0.11
23 2 0.04
25 12 0.23
26 22 0.42
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (25 bp):
ACATTACATTAGAACATTAAATCCT
Found at i:1419013 original size:5 final size:5
Alignment explanation
Indices: 1419003--1419051 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
1418993 CATTAACTCC
* *
1419003 TACAT TACAT TAAAT TAAAT TACAT TACAT TACAT TACAT TACAT TACA
1 TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACA
1419052 ATAGAAGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (5 bp):
TACAT
Found at i:1422223 original size:29 final size:26
Alignment explanation
Indices: 1422164--1422223 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
1422154 GTCATACTTA
*
1422164 TTTT-TCTTCTCAATTTTCATCTCCT
1 TTTTATCTTCTCAAGTTTCATCTCCT
*
1422189 TATTATCTTCTTCAAGTTTCATTCTCTCT
1 TTTTATCTTC-TCAAGTTTCA-TCTC-CT
1422218 TTTTAT
1 TTTTAT
1422224 TGATAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 3 0.11
26 5 0.18
27 9 0.32
28 4 0.14
29 7 0.25
ACGTcount: A:0.15, C:0.23, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTATCTTCTCAAGTTTCATCTCCT
Found at i:1423075 original size:29 final size:30
Alignment explanation
Indices: 1423011--1423067 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1423001 AGAGTAAATT
1423011 AATATTTTATTTCAAATTTATGGGTTAAAAC
1 AATATTTTATTTCAAATTTA-GGGTTAAAAC
1423042 AATATTTTATTT-AAACTTTA-GGTTAA
1 AATATTTTATTTCAAA-TTTAGGGTTAA
1423068 TATCATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 6 0.24
30 3 0.12
31 16 0.64
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (30 bp):
AATATTTTATTTCAAATTTAGGGTTAAAAC
Found at i:1426402 original size:2 final size:2
Alignment explanation
Indices: 1426395--1426427 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1426385 TAATGTATGT
*
1426395 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1426428 TAATCTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1428526 original size:254 final size:254
Alignment explanation
Indices: 1428055--1428654 Score: 882
Period size: 254 Copynumber: 2.3 Consensus size: 254
1428045 TATAAGATAA
* * *
1428055 AATTATATATTTTTTTCGGGTCGGTTTGGTTTTTTTCACCCTAAATCCGAACCCGACTCGACCTG
1 AATTATATA-TATTTTCGGGTCGGTTCGGTTTTTTTCACCCT--A----AACCCGA--C-ACCCG
* * *
1428120 ACCCGAATTTCACATTTAAAAAAATCTGACCCGACTCGACCCGAATATCACACTTAAAAAGCCAA
56 ACCCGAATATCACACTTAAAAAAATCTGACCCGACTCGACCCGAATATCACACTTAAAAAACCAA
*
1428185 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCTAACT
121 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCTAACC
* *
1428250 CGACCTGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
186 CGACCCGACCCGAAATAATAAAAAAATA-TTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
1428315 ACCCG
250 ACCCG
1428320 AATTATATATATTTTCGGGTCGGTTCGGTTTTTTTCACCCTAAACCCGA-ACCCGACCCGAATAT
1 AATTATATATATTTTCGGGTCGGTTCGGTTTTTTTCACCCTAAACCCGACACCCGACCCGAATAT
* *
1428384 CACACTTAAAAAAA-CTCGACCCGACTCGATCCGAATATCACACTTAAAAAA-CACGACCCGACC
66 CACACTTAAAAAAATCT-GACCCGACTCGACCCGAATATCACACTTAAAAAACCA-AACCCGACC
*
1428447 CGAACAAAATAAAGTTTCATCCGACCTGACCCGAATATATGAATTAGAAATCTAACCCGACCCGA
129 CGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCTAACCCGACCCGA
* *
1428512 CCCGAAATAATAAAAAAATATTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCTG
194 CCCGAAATAATAAAAAAATATTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
* *
1428573 AATTATATATATTTTCGGGTGGGTCCGGTTTTTTTCACCCTAAACCCGAACCCTACCCGACCCGA
1 AATTATATATATTTTCGGGTCGGTTCGGTTTTTTTCACCCTAAACCCG-A--C-ACCCGACCCGA
1428638 ATATCACACTTAAAAAA
62 ATATCACACTTAAAAAA
1428655 CCCGATCCGA
Statistics
Matches: 312, Mismatches: 16, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
253 89 0.29
254 148 0.47
258 35 0.11
262 1 0.00
264 30 0.10
265 9 0.03
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (254 bp):
AATTATATATATTTTCGGGTCGGTTCGGTTTTTTTCACCCTAAACCCGACACCCGACCCGAATAT
CACACTTAAAAAAATCTGACCCGACTCGACCCGAATATCACACTTAAAAAACCAAACCCGACCCG
AACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCTAACCCGACCCGACC
CGAAATAATAAAAAAATATTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
Found at i:1446085 original size:17 final size:17
Alignment explanation
Indices: 1446053--1446086 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1446043 AGCATGTTTA
* *
1446053 AAAATAAAACTTAAAAC
1 AAAATAAAAATGAAAAC
1446070 AAAATAAAAATGAAAAC
1 AAAATAAAAATGAAAAC
1446087 TTGAAAAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATGAAAAC
Found at i:1449895 original size:76 final size:75
Alignment explanation
Indices: 1449804--1449968 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
1449794 TTAAACTCAA
* *
1449804 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTATATTTTAGTTTAAATAGG-TTTTAGT
1449868 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
1449880 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
*
1449945 TTTAATTAGG
66 TTTAATTAAG
*
1449955 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1449969 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:1449954 original size:19 final size:19
Alignment explanation
Indices: 1449926--1449988 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1449916 TATATTTTAG
*
1449926 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
1449945 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
1449964 ATTATATTATTTTTTTAGTAT
1 TTTA-ATTA-GGTTTTAGTAT
1449985 TTTA
1 TTTA
1449989 GTTTAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 4 0.12
21 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1450051 original size:64 final size:64
Alignment explanation
Indices: 1449919--1450051 Score: 155
Period size: 64 Copynumber: 2.1 Consensus size: 64
1449909 TTATCTTTAT
* * *
1449919 ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTTAGT
1 ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATACTATGTTTTTAGG
* * * *
1449983 ATTTTAGTTTAAATA-TTTTTAAGTGTTTTAATTAGGATTTA-AGATGTTTTAGCT-TGTTTTTA
1 ATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGA-ATATTATA-CTATGTTTTTA
1450045 GG
63 GG
1450047 ATTTT
1 ATTTT
1450052 GAAGGCTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 5 0.08
64 53 0.90
65 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (64 bp):
ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATACTATGTTTTTAGG
Found at i:1450642 original size:21 final size:22
Alignment explanation
Indices: 1450616--1450656 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1450606 CTTTAATTTA
1450616 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
1450637 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
1450657 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:1450729 original size:16 final size:17
Alignment explanation
Indices: 1450693--1450729 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1450683 ATCCCCCTTT
1450693 TATATTTATTACTATCA
1 TATATTTATTACTATCA
*
1450710 -ATATTTATTATTAT-A
1 TATATTTATTACTATCA
1450725 TATAT
1 TATAT
1450730 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTATTACTATCA
Found at i:1450746 original size:17 final size:19
Alignment explanation
Indices: 1450713--1450751 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
1450703 ACTATCAATA
1450713 TTTATTATTATATATATAT
1 TTTATTATTATATATATAT
1450732 TTTATT-TTA-ATATATAT
1 TTTATTATTATATATATAT
1450749 TTT
1 TTT
1450752 CAACTTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 3 0.15
19 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTATTATATATATAT
Found at i:1452416 original size:15 final size:15
Alignment explanation
Indices: 1452396--1452429 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1452386 CCAGCAAAAA
1452396 AAGACGCACATCAGG
1 AAGACGCACATCAGG
* *
1452411 AAGACGTACATTAGG
1 AAGACGCACATCAGG
1452426 AAGA
1 AAGA
1452430 ACAAGAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.26, T:0.12
Consensus pattern (15 bp):
AAGACGCACATCAGG
Found at i:1456299 original size:11 final size:10
Alignment explanation
Indices: 1456279--1456313 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1456269 GTTATATATA
1456279 TTTTTTATTT
1 TTTTTTATTT
1456289 TTTTTTCATTT
1 TTTTTT-ATTT
*
1456300 TTTTTAATTT
1 TTTTTTATTT
1456310 TTTT
1 TTTT
1456314 AGCGAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1458302 original size:76 final size:76
Alignment explanation
Indices: 1458145--1458310 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1458135 TTAAACTCAA
*
1458145 ATTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1458210 TTTTAATTAAG
66 TTTTAATTAAG
* ** * *
1458221 TTTTAGGATATTATTTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
**
1458285 ATTTTAATTTGG
65 ATTTTAATTAAG
*
1458297 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1458311 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
76 51 0.65
77 28 0.35
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (76 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
TTTTAATTAAG
Found at i:1458984 original size:21 final size:22
Alignment explanation
Indices: 1458959--1458999 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1458949 CTTTAATTTG
1458959 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
1458980 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
1459000 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:1462705 original size:18 final size:18
Alignment explanation
Indices: 1462684--1462718 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1462674 TGTTTTTGCA
*
1462684 TAATTCATAATATTTATT
1 TAATTCAAAATATTTATT
*
1462702 TAATTTAAAATATTTAT
1 TAATTCAAAATATTTAT
1462719 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTCAAAATATTTATT
Found at i:1466072 original size:13 final size:13
Alignment explanation
Indices: 1466054--1466081 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1466044 TCATCTTTGT
1466054 TCACTCCAATTTC
1 TCACTCCAATTTC
1466067 TCACTCCAATTTC
1 TCACTCCAATTTC
1466080 TC
1 TC
1466082 GGTTATACAA
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:0.39, G:0.00, T:0.39
Consensus pattern (13 bp):
TCACTCCAATTTC
Found at i:1468028 original size:16 final size:16
Alignment explanation
Indices: 1468004--1468045 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1467994 ACCAAAGATG
*
1468004 TCAACTTTGCCAACTT
1 TCAAATTTGCCAACTT
*
1468020 TCAATTTTGCCAACTT
1 TCAAATTTGCCAACTT
1468036 TCAAATTTGC
1 TCAAATTTGC
1468046 TAATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.40
Consensus pattern (16 bp):
TCAAATTTGCCAACTT
Found at i:1472320 original size:16 final size:16
Alignment explanation
Indices: 1472296--1472369 Score: 112
Period size: 16 Copynumber: 4.6 Consensus size: 16
1472286 ACCAAAGATG
1472296 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
* *
1472312 TCAATTTTGCCAACAT
1 TCAACTTTGCCAACTT
*
1472328 TCAAATTTGCCAACTT
1 TCAACTTTGCCAACTT
*
1472344 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
1472360 TCAACTTTGC
1 TCAACTTTGC
1472370 TAATTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:1472342 original size:32 final size:32
Alignment explanation
Indices: 1472296--1472369 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
1472286 ACCAAAGATG
1472296 TCAACTTTGCCAACTTTCAATTTTGCCAACAT
1 TCAACTTTGCCAACTTTCAATTTTGCCAACAT
* *
1472328 TCAAATTTGCCAACTTTCAATTTTGCCAACTT
1 TCAACTTTGCCAACTTTCAATTTTGCCAACAT
1472360 TCAACTTTGC
1 TCAACTTTGC
1472370 TAATTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (32 bp):
TCAACTTTGCCAACTTTCAATTTTGCCAACAT
Found at i:1478329 original size:25 final size:24
Alignment explanation
Indices: 1478300--1478358 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1478290 AATTTTGAAA
*
1478300 AAAAAATGATTGATGAAAGAATTTT-
1 AAAAAATGATTAATG-AAG-ATTTTG
* *
1478325 AAAAAATGTTTAATGAAGTTTTTG
1 AAAAAATGATTAATGAAGATTTTG
1478349 AAAAAATGAT
1 AAAAAATGAT
1478359 GTCCCTTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 13 0.45
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (24 bp):
AAAAAATGATTAATGAAGATTTTG
Found at i:1482363 original size:19 final size:19
Alignment explanation
Indices: 1482339--1482379 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1482329 TTACAGTTTC
*
1482339 AATTTTTATAATATTTT-AT
1 AATTTTT-TAAAATTTTAAT
1482358 AATTTTTTAAAATTTTAAT
1 AATTTTTTAAAATTTTAAT
1482377 AAT
1 AAT
1482380 AGGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTTAAAATTTTAAT
Found at i:1488014 original size:2 final size:2
Alignment explanation
Indices: 1488007--1488082 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1487997 TCCTAACTCG
1488007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1488049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1488083 AGACTTAAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1488877 original size:22 final size:24
Alignment explanation
Indices: 1488827--1488877 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1488817 TTCTAATATG
1488827 AATTTATTTGCTCTTGTGGCACAT
1 AATTTATTTGCTCTTGTGGCACAT
* * *
1488851 GATTTCTTTGTTCTTGT-G-ACAT
1 AATTTATTTGCTCTTGTGGCACAT
1488873 AATTT
1 AATTT
1488878 TTATTACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.35
23 1 0.04
24 14 0.61
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (24 bp):
AATTTATTTGCTCTTGTGGCACAT
Found at i:1492004 original size:21 final size:21
Alignment explanation
Indices: 1491980--1492020 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1491970 TGAAGTAGAA
1491980 GTAAATAAAGTAACTTGGTAT
1 GTAAATAAAGTAACTTGGTAT
* *
1492001 GTAAATGAAGTACCTTGGTA
1 GTAAATAAAGTAACTTGGTA
1492021 AGTGTCTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (21 bp):
GTAAATAAAGTAACTTGGTAT
Found at i:1493966 original size:16 final size:16
Alignment explanation
Indices: 1493942--1493982 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1493932 AAAGGGGGAG
*
1493942 AAGTGTTAACTGTTAA
1 AAGTATTAACTGTTAA
*
1493958 AAGTATTAAGTGTTAA
1 AAGTATTAACTGTTAA
*
1493974 AAGTTTTAA
1 AAGTATTAA
1493983 AGGGGAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (16 bp):
AAGTATTAACTGTTAA
Found at i:1494366 original size:20 final size:20
Alignment explanation
Indices: 1494328--1494366 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1494318 TTTTCAAGGG
*
1494328 CATGCACCGATGCACCAATC
1 CATGCACCGATGAACCAATC
* *
1494348 CATGCATCGATGAATCAAT
1 CATGCACCGATGAACCAAT
1494367 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGAACCAATC
Found at i:1494446 original size:26 final size:26
Alignment explanation
Indices: 1494413--1494477 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
1494403 TGCACATACC
1494413 ATGCATCGATGCATTCAGTGCATTTT
1 ATGCATCGATGCATTCAGTGCATTTT
1494439 ATGCATCGATGCATTCAGTGCATTTT
1 ATGCATCGATGCATTCAGTGCATTTT
1494465 ATGCATCGATGCA
1 ATGCATCGATGCA
1494478 CAAGACCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (26 bp):
ATGCATCGATGCATTCAGTGCATTTT
Found at i:1494558 original size:19 final size:19
Alignment explanation
Indices: 1494531--1494582 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1494521 ATGCATTTTA
*
1494531 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1494550 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1494569 TGCACCGATGCACT
1 TGCACCGATGCACT
1494583 GAGAGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:1503695 original size:16 final size:17
Alignment explanation
Indices: 1503668--1503700 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1503658 TTTTTGAATC
1503668 TTTTTCTCTTTTCTCTT
1 TTTTTCTCTTTTCTCTT
*
1503685 TTTTTCT-TTTTTTCTT
1 TTTTTCTCTTTTCTCTT
1503701 CATTCGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTCTTTTCTCTT
Found at i:1505247 original size:16 final size:16
Alignment explanation
Indices: 1505226--1505257 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1505216 AAATTACTCC
1505226 CCCTTACTATAACACA
1 CCCTTACTATAACACA
1505242 CCCTTACTATAACACA
1 CCCTTACTATAACACA
1505258 TCTTTCCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
CCCTTACTATAACACA
Found at i:1505302 original size:27 final size:28
Alignment explanation
Indices: 1505272--1505324 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
1505262 TCCCCCTTTT
1505272 TTTAAAT-AAAA-AAGACTCTATAAAACG
1 TTTAAATCAAAACAAGACTCTA-AAAACG
**
1505299 TTTAGTTCAAAACAAGACTCTAAAAA
1 TTTAAATCAAAACAAGACTCTAAAAA
1505325 TTTAGCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 5 0.23
28 8 0.36
29 9 0.41
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (28 bp):
TTTAAATCAAAACAAGACTCTAAAAACG
Found at i:1506447 original size:19 final size:19
Alignment explanation
Indices: 1506423--1506476 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1506413 ATAAGACTTA
*
1506423 GTGCATTGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
1506442 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
*
1506461 GTGCATCGGTGCACTA
1 GTGCATCGGTACACTA
1506477 ATTACATTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.24
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:1506550 original size:65 final size:63
Alignment explanation
Indices: 1506461--1506615 Score: 159
Period size: 63 Copynumber: 2.4 Consensus size: 63
1506451 TACACTAGGG
* * * * * * ** * *
1506461 GTGCATCGGTGCACTAATTACATTCGATCTTTCAGAAGAGCCTGGAGTGCATCGATGTATGGTC-
1 GTGCATCGGTACACAAAATGCATTCGAT-GTTCAAAAGAGCC-AAAGTGCATAGATGCATGG-CA
1506525 T
63 T
* **
1506526 GTGCATCGGTACACAAAATGCATTCGATGTTCAAAATATTCAAAGTGCATAGATGCATGGCAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTCAAAAGAGCCAAAGTGCATAGATGCATGGCAT
1506589 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
1506616 AATGGGTGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 1 0.01
63 43 0.57
64 8 0.11
65 24 0.32
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTCAAAAGAGCCAAAGTGCATAGATGCATGGCAT
Found at i:1507518 original size:35 final size:35
Alignment explanation
Indices: 1507477--1507552 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1507467 AAAACAGTCC
* * *
1507477 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
1507512 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1507547 TCAATT
1 TCAATT
1507553 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1508102 original size:130 final size:130
Alignment explanation
Indices: 1507949--1508196 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
1507939 TATTTATATA
* **
1507949 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
1508014 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1508079 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
1508144 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
1508197 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1508227 original size:130 final size:129
Alignment explanation
Indices: 1507963--1508227 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
1507953 ATTTGGTCCT
* ** *
1507963 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1508028 TGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1508093 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
1508158 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1508222 -A
128 CA
1508223 AAATT
1 AAATT
1508228 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1508553 original size:28 final size:27
Alignment explanation
Indices: 1508522--1508584 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1508512 AGTTGATACA
*
1508522 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1508550 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1508578 ATATTTT
1 ATATTTT
1508585 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1508685 original size:16 final size:18
Alignment explanation
Indices: 1508664--1508697 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1508654 ATTTCTTATT
1508664 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1508680 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1508698 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1515041 original size:20 final size:19
Alignment explanation
Indices: 1514975--1515202 Score: 148
Period size: 20 Copynumber: 11.6 Consensus size: 19
1514965 AAATGACCAA
* *
1514975 CAAATTCACAACGCG-ATCT
1 CAAATTCGCAAC-CGAATTT
1514994 CAAATTCGCAACACGAACTCTT
1 CAAATTCGCAAC-CGAA-T-TT
* *
1515016 --ATTTCGCAACCCAATTT
1 CAAATTCGCAACCGAATTT
1515033 CCAAATTCGCAACGCG-ATTAT
1 -CAAATTCGCAAC-CGAATT-T
*
1515054 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAAC-CGAATTT
* *
1515074 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAAC-C-GAATTT
* *
1515094 CAAATTCACAACACAGAA-GT
1 CAAATTCGCAAC-C-GAATTT
1515114 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAAC-C-GAATTT
*
1515135 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACCGAATTT
*
1515154 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACCGAATTT
*
1515173 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACCGAATTT
1515192 CAAATTCGCAA
1 CAAATTCGCAA
1515203 AATTCGCAAC
Statistics
Matches: 180, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.01
18 1 0.01
19 74 0.41
20 77 0.43
21 25 0.14
22 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (19 bp):
CAAATTCGCAACCGAATTT
Found at i:1515150 original size:19 final size:19
Alignment explanation
Indices: 1515113--1515202 Score: 162
Period size: 19 Copynumber: 4.6 Consensus size: 19
1515103 AACACAGAAG
1515113 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
1515134 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1515153 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1515172 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1515191 TCAAATTCGCAA
1 TCAAATTCGCAA
1515203 AATTCGCAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
19 58 0.84
20 1 0.01
21 10 0.14
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1515206 original size:28 final size:29
Alignment explanation
Indices: 1515174--1515231 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1515164 ACTGAATTTC
1515174 AAATTCGCAACT-GAATTTCAAATTCGCA
1 AAATTCGCAACTCGAATTTCAAATTCGCA
* *
1515202 AAATTCGCAACTCGATTTTCGAATTCGCA
1 AAATTCGCAACTCGAATTTCAAATTCGCA
1515231 A
1 A
1515232 CACGAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (29 bp):
AAATTCGCAACTCGAATTTCAAATTCGCA
Found at i:1515248 original size:48 final size:47
Alignment explanation
Indices: 1515155--1515250 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 47
1515145 ACTGAATTTC
*
1515155 AAATTCGCAACTGAATTTCAAATTCGCAACTGAATTTCAAATTCGCA
1 AAATTCGCAACTGAATTTCAAATTCGCAACCGAATTTCAAATTCGCA
* * *
1515202 AAATTCGCAACTCGATTTTCGAATTCGCAACACGAATTT-AATTTCGCA
1 AAATTCGCAACT-GAATTTCAAATTCGCAAC-CGAATTTCAAATTCGCA
1515250 A
1 A
1515251 CAGGTTTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 12 0.28
48 25 0.58
49 6 0.14
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.30
Consensus pattern (47 bp):
AAATTCGCAACTGAATTTCAAATTCGCAACCGAATTTCAAATTCGCA
Found at i:1515249 original size:19 final size:19
Alignment explanation
Indices: 1515225--1515271 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1515215 GATTTTCGAA
1515225 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
1515244 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
1515262 TTCGCAACAC
1 TTCGCAACAC
1515272 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:1516231 original size:24 final size:24
Alignment explanation
Indices: 1516171--1516238 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1516161 GTGAGTACTA
* *
1516171 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* *
1516195 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
1516219 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
1516239 GATGTTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:1518436 original size:18 final size:18
Alignment explanation
Indices: 1518413--1518448 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1518403 AAGCAAAAGG
*
1518413 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1518431 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1518449 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1518729 original size:20 final size:20
Alignment explanation
Indices: 1518704--1518753 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1518694 CGATTATTGT
*
1518704 GAAAGTTAAATTTGCAACGC
1 GAAAGTCAAATTTGCAACGC
1518724 GAAAGTCAAATTTGCAACGC
1 GAAAGTCAAATTTGCAACGC
*
1518744 GAAAATCAAA
1 GAAAGTCAAA
1518754 ATCGCAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (20 bp):
GAAAGTCAAATTTGCAACGC
Found at i:1518760 original size:20 final size:20
Alignment explanation
Indices: 1518717--1518760 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1518707 AGTTAAATTT
* * *
1518717 GCAACGCGAAAGTCAAATTT
1 GCAACGCGAAAATCAAAATC
1518737 GCAACGCGAAAATCAAAATC
1 GCAACGCGAAAATCAAAATC
1518757 GCAA
1 GCAA
1518761 ACCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATCAAAATC
Found at i:1518801 original size:20 final size:20
Alignment explanation
Indices: 1518776--1518901 Score: 126
Period size: 20 Copynumber: 6.2 Consensus size: 20
1518766 AAATCACAAC
1518776 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* **
1518796 GCGAATTTAACTTTAAACGTT
1 GCGAATTTGACTTT-CGCGTT
* * **
1518817 GCAAATTTGACTATCGCAAT
1 GCGAATTTGACTTTCGCGTT
*
1518837 ACGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* ***
1518857 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCGCGTT
*
1518877 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCGCGTT
1518897 GCGAA
1 GCGAA
1518902 AGTGTACCTT
Statistics
Matches: 80, Mismatches: 25, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
20 65 0.81
21 15 0.19
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:1518868 original size:40 final size:40
Alignment explanation
Indices: 1518776--1518901 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
1518766 AAATCACAAC
* ** * **
1518776 GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTAAACGTT
1 GCGAATTTGACTATCGCAATGCGAATTTGACTTT-CGCGTT
* *
1518817 GCAAATTTGACTATCGCAATACGAATTTGACTTTCGCGTT
1 GCGAATTTGACTATCGCAATGCGAATTTGACTTTCGCGTT
* *
1518857 GCGAATTTGACTATCGCAACGCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTATCGCAATGCGAATTTGACTTTCGCGTT
1518897 GCGAA
1 GCGAA
1518902 AGTGTACCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 45 0.62
41 28 0.38
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (40 bp):
GCGAATTTGACTATCGCAATGCGAATTTGACTTTCGCGTT
Found at i:1519024 original size:14 final size:14
Alignment explanation
Indices: 1519005--1519042 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1518995 CATCAATTAA
1519005 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1519019 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1519033 ACAAATCAAC
1 ACAAATCAAC
1519043 AAGCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1520492 original size:21 final size:20
Alignment explanation
Indices: 1520468--1520545 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
1520458 GTAGGCGGGA
1520468 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGA-AGGGG
* * *
1520489 CCTCTTAAATGGTGGAAGGGG
1 CCTCTTGAACGAT-GAAGGGG
* *
1520510 CCTCTTGAACGATAGGAGGCG
1 CCTCTTGAACGAT-GAAGGGG
*
1520531 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1520546 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (20 bp):
CCTCTTGAACGATGAAGGGG
Found at i:1520945 original size:63 final size:63
Alignment explanation
Indices: 1520878--1520997 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 63
1520868 ACCACGTAGC
* * *
1520878 GCACCATTATCATCGCGTAAAAAATCAACCTCACCACGTAAAG-ACCGAACCTCATCACGCCAT
1 GCACCATTATCATCACGTAAAAAACCAACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* * ** **
1520941 GCACCATTGTCTTCACGTAAAGTACCAACCTCATGACGCAAAGCACCGACCTCATCA
1 GCACCATTATCATCACGTAAAAAACCAACCTCACCACGCAAAGCACCGACCTCATCA
1520998 TGTAACTCCC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 43 0.91
64 4 0.09
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.18
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAAAACCAACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:1522679 original size:20 final size:20
Alignment explanation
Indices: 1522656--1522746 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1522646 AATTCTCAAT
*
1522656 GCGAAAATGAAAATCACAAC
1 GCGAAAATGAAAATCGCAAC
* *
1522676 GCGAAACTGGAAAATCGCAAT
1 GCGAAAAT-GAAAATCGCAAC
1522697 GC--AAAT----ATCGCAAC
1 GCGAAAATGAAAATCGCAAC
*
1522711 GCGAACATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAAC
*
1522731 GCGAAACT-AAAATCGC
1 GCGAAAATGAAAATCGC
1522747 GTTGCGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.16
16 3 0.05
19 11 0.20
20 21 0.38
21 12 0.21
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
GCGAAAATGAAAATCGCAAC
Found at i:1522770 original size:20 final size:20
Alignment explanation
Indices: 1522745--1522813 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1522735 AACTAAAATC
1522745 GCGTTGCGATTTTCATTTTT
1 GCGTTGCGATTTTCATTTTT
* *
1522765 GCGTTGCGATTTTCATGTTC
1 GCGTTGCGATTTTCATTTTT
1522785 GCGTTGCGATTTTCATTTTT
1 GCGTTGCGATTTTCATTTTT
*
1522805 GTGTTGCGA
1 GCGTTGCGA
1522814 ATTTAAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.49
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTT
Done.