Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 4 of 126
Found at i:1015401 original size:17 final size:18
Alignment explanation
Indices: 1015372--1015407 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1015362 ATTATATTCA
*
1015372 TATTTAAATTATTCGTAT
1 TATTTAAATTATTCATAT
1015390 TATTTAAA-TATTCATAT
1 TATTTAAATTATTCATAT
1015407 T
1 T
1015408 GTGTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTAAATTATTCATAT
Found at i:1017424 original size:31 final size:31
Alignment explanation
Indices: 1017386--1017448 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1017376 CCATATTAAT
* *
1017386 TCTAAATTCA-TTATAGATAATAAATTTTTTA
1 TCTAAATT-AGTTATAAATAATAAACTTTTTA
1017417 TCTAAATTAGTTATAAATAATAAACTTTTTA
1 TCTAAATTAGTTATAAATAATAAACTTTTTA
1017448 T
1 T
1017449 TTGAATCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (31 bp):
TCTAAATTAGTTATAAATAATAAACTTTTTA
Found at i:1019705 original size:105 final size:105
Alignment explanation
Indices: 1019582--1019794 Score: 426
Period size: 105 Copynumber: 2.0 Consensus size: 105
1019572 AGATCACAAA
1019582 AAAAAAAAGTCCAAACAAAAATTTAAAATATCCTTGAAGATATTATAAAAAGACTCTTTTTTCTT
1 AAAAAAAAGTCCAAACAAAAATTTAAAATATCCTTGAAGATATTATAAAAAGACTCTTTTTTCTT
1019647 ATCTTTATTTGTGGCATATATTATAATTTTTATTGATAAT
66 ATCTTTATTTGTGGCATATATTATAATTTTTATTGATAAT
1019687 AAAAAAAAGTCCAAACAAAAATTTAAAATATCCTTGAAGATATTATAAAAAGACTCTTTTTTCTT
1 AAAAAAAAGTCCAAACAAAAATTTAAAATATCCTTGAAGATATTATAAAAAGACTCTTTTTTCTT
1019752 ATCTTTATTTGTGGCATATATTATAATTTTTATTGATAAT
66 ATCTTTATTTGTGGCATATATTATAATTTTTATTGATAAT
1019792 AAA
1 AAA
1019795 CATTTAAAGA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 108 1.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (105 bp):
AAAAAAAAGTCCAAACAAAAATTTAAAATATCCTTGAAGATATTATAAAAAGACTCTTTTTTCTT
ATCTTTATTTGTGGCATATATTATAATTTTTATTGATAAT
Found at i:1020394 original size:19 final size:20
Alignment explanation
Indices: 1020348--1020388 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1020338 CTAAAAATTC
*
1020348 AATTGATCCAAAATAGAAAAA
1 AATTAATCCAAAATA-AAAAA
1020369 AATTAATCCAAAATAAAAAA
1 AATTAATCCAAAATAAAAAA
1020389 TTTAATGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
AATTAATCCAAAATAAAAAA
Found at i:1022258 original size:21 final size:20
Alignment explanation
Indices: 1022233--1022297 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
1022223 ATGAATATAA
1022233 TTTAATAATTTTGGATAAAAT
1 TTTAATAATTTT-GATAAAAT
* *
1022254 TTTAACAATATTTGATACAAT
1 TTTAATAAT-TTTGATAAAAT
* * *
1022275 TCTAATAATTTTTATATAAT
1 TTTAATAATTTTGATAAAAT
1022295 TTT
1 TTT
1022298 GATTTTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 11 0.31
21 22 0.61
22 3 0.08
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTAATAATTTTGATAAAAT
Found at i:1026419 original size:24 final size:25
Alignment explanation
Indices: 1026356--1026425 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
1026346 AGTGAAATGT
*
1026356 ATTTAATAAT-TGAAAATGAAAATAA
1 ATTTAA-AATATGAAAATAAAAATAA
** *
1026381 ATTTAAAA-ACAAAAATAAAAATAT
1 ATTTAAAATATGAAAATAAAAATAA
1026405 A-TTAAAATATGAAAATAAAAA
1 ATTTAAAATATGAAAATAAAAA
1026426 ATTTATGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
23 6 0.16
24 25 0.68
25 6 0.16
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (25 bp):
ATTTAAAATATGAAAATAAAAATAA
Found at i:1030268 original size:27 final size:27
Alignment explanation
Indices: 1030233--1030284 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1030223 CTCCTAGCTT
*
1030233 TGACCGAAAGTAAGCATCCCGTTCAGC
1 TGACCGAAAGTAAACATCCCGTTCAGC
*
1030260 TGACTGAAAGTAAACATCCCGTTCA
1 TGACCGAAAGTAAACATCCCGTTCA
1030285 TCATCCAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (27 bp):
TGACCGAAAGTAAACATCCCGTTCAGC
Found at i:1031203 original size:17 final size:17
Alignment explanation
Indices: 1031161--1031215 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
1031151 AAGGGAGAAA
* * *
1031161 AAAATTAAAAAGTTCAG
1 AAAATTTAAAAGTACAT
*
1031178 AAAA-ATAAAAGTACAT
1 AAAATTTAAAAGTACAT
1031194 AAAATTT-AAAGTACAT
1 AAAATTTAAAAGTACAT
1031210 AAAATT
1 AAAATT
1031216 GGTCCAAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (17 bp):
AAAATTTAAAAGTACAT
Found at i:1031214 original size:16 final size:16
Alignment explanation
Indices: 1031185--1031215 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1031175 CAGAAAAATA
1031185 AAAGTACATAAAATTT
1 AAAGTACATAAAATTT
1031201 AAAGTACATAAAATT
1 AAAGTACATAAAATT
1031216 GGTCCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAGTACATAAAATTT
Found at i:1033278 original size:27 final size:27
Alignment explanation
Indices: 1033240--1033291 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1033230 CTCCTAGCTT
* *
1033240 TGACCGAAAGTAAGCATTCCGTTCAGG
1 TGACCGAAAGTAAACATCCCGTTCAGG
*
1033267 TGACTGAAAGTAAACATCCCGTTCA
1 TGACCGAAAGTAAACATCCCGTTCA
1033292 TCATCCAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (27 bp):
TGACCGAAAGTAAACATCCCGTTCAGG
Found at i:1034317 original size:15 final size:16
Alignment explanation
Indices: 1034297--1034331 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1034287 ATTGAAAATG
1034297 AAAATAAATTTTTA-A
1 AAAATAAATTTTTAGA
*
1034312 AAAATAAGTTTTTAGA
1 AAAATAAATTTTTAGA
1034328 AAAA
1 AAAA
1034332 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAATAAATTTTTAGA
Found at i:1039857 original size:12 final size:11
Alignment explanation
Indices: 1039840--1039883 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
1039830 ATTCAGAAAA
1039840 TTTT-TTTTTG
1 TTTTCTTTTTG
*
1039850 CTTTTTTTTTTG
1 -TTTTCTTTTTG
1039862 TTTTCTTTTTG
1 TTTTCTTTTTG
1039873 TTTTCTTTTTG
1 TTTTCTTTTTG
1039884 GAAAGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:1039869 original size:16 final size:15
Alignment explanation
Indices: 1039840--1039882 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1039830 ATTCAGAAAA
*
1039840 TTTTTTTTTGCTTTT
1 TTTTTTTTTTCTTTT
1039855 TTTTTTGTTTTCTTTT
1 TTTTTT-TTTTCTTTT
1039871 TGTTTTCTTTTT
1 T-TTTT-TTTTT
1039883 GGAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 9 0.38
17 8 0.33
18 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTCTTTT
Found at i:1040254 original size:8 final size:8
Alignment explanation
Indices: 1040218--1040254 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1040208 ATTCCAAAAC
*
1040218 TTTTTATA
1 TTTTTATT
1040226 TTTTTATT
1 TTTTTATT
*
1040234 TTTTTATG
1 TTTTTATT
1040242 TTTTTATT
1 TTTTTATT
1040250 TTTTT
1 TTTTT
1040255 TTGTTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:1040259 original size:16 final size:16
Alignment explanation
Indices: 1040218--1040260 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1040208 ATTCCAAAAC
*
1040218 TTTTTATATTTTTATT
1 TTTTTATGTTTTTATT
1040234 TTTTTATGTTTTTATT
1 TTTTTATGTTTTTATT
*
1040250 TTTTTTTGTTT
1 TTTTTATGTTT
1040261 GAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTTATGTTTTTATT
Found at i:1040438 original size:203 final size:201
Alignment explanation
Indices: 1040073--1040455 Score: 460
Period size: 203 Copynumber: 1.9 Consensus size: 201
1040063 GAAAGAATAC
* * *
1040073 AATTATTTGTATTGAAATTTCATCTAAACATTCCACCATTTGAGCCAAATTTAGAGAAAATTTCT
1 AATTATTTGTATTGAAATTTCATCTAAACATTCCACAATTTGAGACAAATTTAGACAAAATTTCT
* * **
1040138 CACCTAGAGATTTCTTAGAATTTACCATTTGAAATTTTTAAGAATCTCATCATTGGGTAATTTGT
66 CACCTAGAGATTTCTTAAAATTTACCATTTGAAATTTTTAAGAATCTCATCATTGGATAATTAAT
*
1040203 ATTTAATTCCAAAACTTTTTATATTTTTATTTT-TTTATGTTTTTATTTTTTTTTGTTTGAAAAT
131 ATTTAATTCCAAAACTTTTTATATTTTTATTTTATTT-TATTTTTATTTTTTTTTGTTTGAAAAT
1040267 AAATATT
195 AAATATT
* ** * *
1040274 AATTA-TTGTTATTGAAATTTTATCTATATTATTCCACAATTTGGGATAAATTTAGACAAAATTT
1 AATTATTTG-TATTGAAATTTCATCTA-AACATTCCACAATTTGAGACAAATTTAGACAAAATTT
* *
1040338 CTTACCTAG-GAATTT-TATAAAAATTTACCATTTGAAATCTTTATA-AAT-TCCATCATTGGAT
64 CTCACCTAGAG-ATTTCT-T-AAAATTTACCATTTGAAATTTTTA-AGAATCT-CATCATTGGAT
*
1040399 AATTAATATTT-ATTCCCAAAA-TTTTT-TTTTTACTTATTTTATTTTATTTTTATTTTT
124 AATTAATATTTAATT-CCAAAACTTTTTATATTT--TTATTTTATTTTATTTTTATTTTT
1040456 ATAATAAATA
Statistics
Matches: 155, Mismatches: 16, Indels: 20
0.81 0.08 0.10
Matches are distributed among these distances:
200 3 0.02
201 27 0.17
202 52 0.34
203 69 0.45
204 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (201 bp):
AATTATTTGTATTGAAATTTCATCTAAACATTCCACAATTTGAGACAAATTTAGACAAAATTTCT
CACCTAGAGATTTCTTAAAATTTACCATTTGAAATTTTTAAGAATCTCATCATTGGATAATTAAT
ATTTAATTCCAAAACTTTTTATATTTTTATTTTATTTTATTTTTATTTTTTTTTGTTTGAAAATA
AATATT
Found at i:1041285 original size:6 final size:6
Alignment explanation
Indices: 1041274--1041367 Score: 77
Period size: 6 Copynumber: 15.7 Consensus size: 6
1041264 AGAGACTAGA
* * *
1041274 AAAAAT AAAAAT AAAAAT AAAAAT AAATAT GAAAAT AAAAA- AAATAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
1041321 AATAAAT AAAAA- ATATAAT AAAAA- ATACAAT AAAATT AAAACT AAAA
1 AA-AAAT AAAAAT A-AAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAA
1041368 TTGAGCCCTT
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
5 6 0.09
6 57 0.81
7 7 0.10
ACGTcount: A:0.77, C:0.02, G:0.01, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:1041333 original size:16 final size:16
Alignment explanation
Indices: 1041312--1041342 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1041302 ATGAAAATAA
1041312 AAAAAATATAATAAAT
1 AAAAAATATAATAAAT
1041328 AAAAAATATAATAAA
1 AAAAAATATAATAAA
1041343 AAATACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATATAATAAAT
Found at i:1041341 original size:30 final size:29
Alignment explanation
Indices: 1041275--1041361 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
1041265 GAGACTAGAA
*
1041275 AAAATAAAAATAAAAATAAAAATAAATATG
1 AAAATAAAAA-AAAAATAAAAATAAAAATG
*
1041305 AAAATAAAAAAAATATAATAAATAAAAAAT-
1 AAAATAAAAAAAAAATAA-AAAT-AAAAATG
* * *
1041335 ATAATAAAAAATACAATAAAATTAAAA
1 AAAATAAAAAA-AAAATAAAAATAAAA
1041362 CTAAAATTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 11 0.23
30 27 0.56
31 10 0.21
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.21
Consensus pattern (29 bp):
AAAATAAAAAAAAAATAAAAATAAAAATG
Found at i:1041361 original size:28 final size:27
Alignment explanation
Indices: 1041273--1041354 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
1041263 AAGAGACTAG
* *
1041273 AAAAAATAAAAATAAAAATAAAAATAAAT
1 AAAAAATATAAA-AAAAAT-ACAATAAAT
** *
1041302 ATGAAA-ATAAAAAAAATATAATAAAT
1 AAAAAATATAAAAAAAATACAATAAAT
1041328 AAAAAATATAATAAAAAATACAATAAA
1 AAAAAATATAA-AAAAAATACAATAAA
1041355 ATTAAAACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 12 0.27
27 10 0.23
28 18 0.41
29 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.01, T:0.20
Consensus pattern (27 bp):
AAAAAATATAAAAAAAATACAATAAAT
Found at i:1043487 original size:21 final size:20
Alignment explanation
Indices: 1043458--1043503 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 20
1043448 AATTAAAAAT
1043458 AAAAATAAGCTAAAATATGA
1 AAAAATAAGCTAAAATATGA
1043478 AAAAATTAAGCTAAAATATGA
1 AAAAA-TAAGCTAAAATATGA
1043499 AAAAA
1 AAAAA
1043504 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAATAAGCTAAAATATGA
Found at i:1044578 original size:21 final size:21
Alignment explanation
Indices: 1044546--1044586 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1044536 TATAAGTTGA
1044546 TAATTTTGGATAAAATTTTAC
1 TAATTTTGGATAAAATTTTAC
*
1044567 TAATATTT-GATACAATTTTA
1 TAAT-TTTGGATAAAATTTTA
1044587 ATAGTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
TAATTTTGGATAAAATTTTAC
Found at i:1044616 original size:27 final size:26
Alignment explanation
Indices: 1044581--1044631 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1044571 ATTTGATACA
** *
1044581 ATTTTAATAGTTTTCATATAATTTTC
1 ATTTTAATACCTTTAATATAATTTTC
1044607 ATTTTAAATACCTTTAATATAATTT
1 ATTTT-AATACCTTTAATATAATTT
1044632 ATAACCAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTAATACCTTTAATATAATTTTC
Found at i:1056395 original size:27 final size:27
Alignment explanation
Indices: 1056360--1056411 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1056350 CTCCTAGCTT
* *
1056360 TGACCGAAAGTAAGCATCCCGTTCAGC
1 TGACCGAAAATAAACATCCCGTTCAGC
*
1056387 TGACTGAAAATAAACATCCCGTTCA
1 TGACCGAAAATAAACATCCCGTTCA
1056412 TCATTCAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (27 bp):
TGACCGAAAATAAACATCCCGTTCAGC
Found at i:1057439 original size:17 final size:18
Alignment explanation
Indices: 1057419--1057461 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1057409 ATTGAAAATG
1057419 AAAATAAATTTTGA-AAA
1 AAAATAAATTTTGAGAAA
* *
1057436 AAAATAAGTTTTTAGAAA
1 AAAATAAATTTTGAGAAA
1057454 AAAATAAA
1 AAAATAAA
1057462 AATAGATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAATAAATTTTGAGAAA
Found at i:1059877 original size:284 final size:284
Alignment explanation
Indices: 1059367--1059885 Score: 736
Period size: 284 Copynumber: 1.8 Consensus size: 284
1059357 TGTGGTACTA
* *
1059367 TTGTCACGGGTCGAGACTTAAGCTCCGAACCCACGCGACTCCGAGATCCGGGCATTCACCCTTCT
1 TTGTCACGGGTCGAGACTTAAGCTCCGAACCCACGCGACTCCGAGACCCGGGCATTCACCCTTCC
* ** * * *
1059432 GGCATCCCAGATCAGTCTACCTGTCACGGTTTACACCCTTGTGAGGTATTGTCCGCTCTGGCCCC
66 GACATCCCAGATCAACCTACCTGACACGGTTCACACCCTTATGAGGTATTGTCCGCTCTGGCCCC
* * * *
1059497 TTTGGCCTCACGGTTTTGTCCTACAAAAGGTGTCTCACAAGGAAGAGATGGTGTGAACCCTTTTA
131 TCTGGCCTCACAGTTTTGTCCTACAAAAGGTGCCTCACAAGGAAGAGATGGTGTGAACACTTTTA
*** * *
1059562 TACCCCAGTGACTTTCCTATTATGTTCGATGTGGGATTCAAGACTCTAACCTCGTGGATCAAACG
196 TACCCCAGTGACCCCCCTATTATATTCGATGTAGGATTCAAGACTCTAACCTCGTGGATCAAACG
1059627 GTTTAGGGCTGACTCTGATACCAC
261 GTTTAGGGCTGACTCTGATACCAC
* * ** * * *
1059651 TTGTCACGGGTTGAGACTTAAGCTCTGAACCTGCGCGGCTCTGGGACCCGGGCATTCACCCTTCC
1 TTGTCACGGGTCGAGACTTAAGCTCCGAACCCACGCGACTCCGAGACCCGGGCATTCACCCTTCC
* * *
1059716 GACATCCCAGATCAACCTATCT-ACAACGGTTCACATCCTTATGAGGTATTGTCTGCTCTGGCCT
66 GACATCCCAGATCAACCTACCTGAC-ACGGTTCACACCCTTATGAGGTATTGTCCGCTCTGGCC-
* * *
1059780 CC-CTGGTCTCACAGTTTTGTCCTACAAAATGTGCCTCACAAGGAAGAGGTGGTGTGAACACTTT
129 CCTCTGGCCTCACAGTTTTGTCCTACAAAAGGTGCCTCACAAGGAAGAGATGGTGTGAACACTTT
1059844 TATACCCCAGTGACCCCCCTATTATATTCGATGTAGGATTCA
194 TATACCCCAGTGACCCCCCTATTATATTCGATGTAGGATTCA
1059886 GGATTCTTTC
Statistics
Matches: 203, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
283 1 0.00
284 200 0.99
285 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (284 bp):
TTGTCACGGGTCGAGACTTAAGCTCCGAACCCACGCGACTCCGAGACCCGGGCATTCACCCTTCC
GACATCCCAGATCAACCTACCTGACACGGTTCACACCCTTATGAGGTATTGTCCGCTCTGGCCCC
TCTGGCCTCACAGTTTTGTCCTACAAAAGGTGCCTCACAAGGAAGAGATGGTGTGAACACTTTTA
TACCCCAGTGACCCCCCTATTATATTCGATGTAGGATTCAAGACTCTAACCTCGTGGATCAAACG
GTTTAGGGCTGACTCTGATACCAC
Found at i:1067631 original size:27 final size:27
Alignment explanation
Indices: 1067593--1067644 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1067583 CTCCTAGCAT
*
1067593 TGACCGAAAGTAAGCATCCCATTCAGC
1 TGACCGAAAGTAACCATCCCATTCAGC
*
1067620 TGACTGAAAGTAACCATCCCATTCA
1 TGACCGAAAGTAACCATCCCATTCA
1067645 TCATCCAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (27 bp):
TGACCGAAAGTAACCATCCCATTCAGC
Found at i:1068843 original size:19 final size:20
Alignment explanation
Indices: 1068811--1068850 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1068801 GTTTGGTTTT
*
1068811 AAAAAATAAAATATCCTTAA
1 AAAAAATAAAATATACTTAA
*
1068831 AAAAAAT-AGATATACTTAA
1 AAAAAATAAAATATACTTAA
1068850 A
1 A
1068851 TAATCAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAATAAAATATACTTAA
Found at i:1069758 original size:23 final size:23
Alignment explanation
Indices: 1069731--1069782 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1069721 ATCTGAAATA
1069731 GAAAAAGTCAATTAATCCAAAAC
1 GAAAAAGTCAATTAATCCAAAAC
1069754 GAAAAAGTCAATTAATCCAAAAC
1 GAAAAAGTCAATTAATCCAAAAC
*
1069777 AAAAAA
1 GAAAAA
1069783 TTTAATGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (23 bp):
GAAAAAGTCAATTAATCCAAAAC
Found at i:1070527 original size:59 final size:58
Alignment explanation
Indices: 1070391--1070845 Score: 463
Period size: 59 Copynumber: 7.7 Consensus size: 58
1070381 TTTTGTGTAG
* * *
1070391 GGAAAATTGATACTTTTAACTTTTTCTCAAAAATATTCTTTT-AAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTGAAAACTTTATTTTCGA
*
1070449 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTT-ATTTTCGA
* * * * **
1070508 GGAAAATTGATATTTTCAACTTTTCCTTAAAAAAAATTTTTTTTGAAAA-TTTTTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCC-T--CAAAAATATTTTTTGAAAACTTTATTTTCGA
* * *
1070568 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTGATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTT-ATTTTCGA
* * ** **
1070627 AGAAAATTAATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTATTTTCGA
* * * **
1070684 AGAAAATTGATACTTTCAACTTTT-CTCCAAAAATTTTTTTTTTTGGATTCTTTGATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCT-CAAAAA---TATTTTTTGAAAACTTT-ATTTTCGA
* * **
1070746 GGAAAATTGATACTTTCAACTTTTCTTCAAAAACTTTTTTTTTGAAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAACTTTATTTTCGA
* * *
1070805 GAAAAATTG-TAATTTCAACTTTTCCCCAAAAATATTATTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTT
1070846 TTAGGTTTTA
Statistics
Matches: 332, Mismatches: 50, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
56 5 0.02
57 59 0.18
58 68 0.20
59 91 0.27
60 39 0.12
61 17 0.05
62 52 0.16
63 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTATTTTCGA
Found at i:1070562 original size:12 final size:13
Alignment explanation
Indices: 1070540--1070564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1070530 TTCCTTAAAA
1070540 AAAATTTTTTTTG
1 AAAATTTTTTTTG
1070553 AAAATTTTTTTT
1 AAAATTTTTTTT
1070565 TAAGAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AAAATTTTTTTTG
Found at i:1070571 original size:16 final size:16
Alignment explanation
Indices: 1070534--1070575 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
1070524 CAACTTTTCC
*
1070534 TTAAAAAAAATTTTTT
1 TTAAGAAAAATTTTTT
*
1070550 TT--GAAAATTTTTTT
1 TTAAGAAAAATTTTTT
1070564 TTAAGAAAAATT
1 TTAAGAAAAATT
1070576 GATACTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAGAAAAATTTTTT
Found at i:1070591 original size:177 final size:176
Alignment explanation
Indices: 1070393--1070845 Score: 526
Period size: 178 Copynumber: 2.6 Consensus size: 176
1070383 TTGTGTAGGG
* *
1070393 AAAATTGATACTTTTAACTTTTTCTCAAAAATATTCTTTT-AAAACTTTAATTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATT-TTTTGAAAACTTTATTTTCGAGGAAAATT
* * *
1070457 GATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAGGAAAATTGATATT
65 GATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTT-ATTTTCAAAGAAAATTGATACT
*
1070522 TTCAACTTTTC-CTTAAAAAAAATTTTTTTTGAAAATT-TTT-TTTT-AAGA
128 TTCAACTTTTCTC-CAAAAAAAATTTTTTTTG--AATTCTTTATTTTCAAGA
* *
1070570 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTGATTTTCGAAGAAAATT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTT-ATTTTCGAGGAAAATT
* * ** *
1070635 AATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAAAGAAAATTGATACTTT
65 GATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTCAAAGAAAATTGATACTTT
*** * * *
1070700 CAACTTTTCTCCAAAAATTTTTTTTTTTGGATTCTTTGATTTTCGAGG
130 CAACTTTTCTCCAAAAAAAATTTTTTTTGAATTCTTT-ATTTTCAAGA
* ** *
1070748 AAAATTGATACTTTCAAC-TTTTCTTCAAAAACTTTTTTTTTGAAAA-TTTATTTTTAAGAAAAA
1 AAAATTGATACTTTCAACTTTTTC-TCAAAAA--TATTTTTTGAAAACTTTATTTTCGAGGAAAA
*
1070811 TTG-TAATTTCAACTTTTCCCCAAAAATATTATTTT
63 TTGATACTTTCAACTTTTCCCCAAAAATATT-TTTT
1070846 TTAGGTTTTA
Statistics
Matches: 235, Mismatches: 30, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
174 3 0.01
175 3 0.01
176 47 0.20
177 77 0.33
178 91 0.39
179 3 0.01
180 11 0.05
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (176 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTATTTTCGAGGAAAATTG
ATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTCAAAGAAAATTGATACTTTC
AACTTTTCTCCAAAAAAAATTTTTTTTGAATTCTTTATTTTCAAGA
Found at i:1070846 original size:119 final size:118
Alignment explanation
Indices: 1070391--1070845 Score: 573
Period size: 119 Copynumber: 3.8 Consensus size: 118
1070381 TTTTGTGTAG
* * * * ** *
1070391 GGAAAATTGATACTTTTAACTTTT-TCTCAAAAA-TATTCTTTT-AAAACTTTAATTTCGAGGAA
1 GGAAAATTGATACTTTCAACTTTTCT-TCAAAAACTTTTTTTTTGAAAA-TTTATTTTTAAGAAA
*
1070453 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
64 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTGATTTTCGA
* * ** *
1070508 GGAAAATTGATATTTTCAACTTTTCCTTAAAAAAAATTTTTTTTGAAAATTTTTTTTTAAGAAAA
1 GGAAAATTGATACTTTCAACTTTT-CTTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAA
* *
1070573 ATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACTTTGATTTTCGA
65 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTGATTTTCGA
* * * *
1070627 AGAAAATTAATACTTTCAACTTTTCCTCAAAAAC--CTTTTTTGAAAATTTATTTTTAA-AGAAA
1 GGAAAATTGATACTTTCAACTTTTCTTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGA-AAA
* * **
1070689 ATTGATACTTTCAACTTTTCTCCAAAAATTTTTTTTTTTGGATTCTTTGATTTTCGA
65 ATTGATACTTTCAACTTTTCCCCAAAAA---TATTTTTTGGAAACTTTGATTTTCGA
1070746 GGAAAATTGATACTTTCAACTTTTCTTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCTTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAA
*
1070811 TTG-TAATTTCAACTTTTCCCCAAAAATATTATTTT
66 TTGATACTTTCAACTTTTCCCCAAAAATATT-TTTT
1070846 TTAGGTTTTA
Statistics
Matches: 291, Mismatches: 35, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
115 1 0.00
116 49 0.17
117 25 0.09
118 17 0.06
119 144 0.49
120 25 0.09
121 29 0.10
122 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCTTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTGATTTTCGA
Found at i:1070896 original size:17 final size:16
Alignment explanation
Indices: 1070875--1070942 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
1070865 AATAAAATAA
1070875 TAAAACAAAATAAAAG
1 TAAAACAAAATAAAAG
* *
1070891 TGAAAATAAAAAAAAAAG
1 T-AAAA-CAAAATAAAAG
*
1070909 TAAAACAAAAATAAAAA
1 TAAAAC-AAAATAAAAG
*
1070926 TAAAATAAAGATAAAAG
1 TAAAACAAA-ATAAAAG
1070943 AACATTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 4 0.10
17 27 0.66
18 10 0.24
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.13
Consensus pattern (16 bp):
TAAAACAAAATAAAAG
Found at i:1070939 original size:6 final size:5
Alignment explanation
Indices: 1070863--1070941 Score: 54
Period size: 5 Copynumber: 14.8 Consensus size: 5
1070853 TTATTTAAAG
* *
1070863 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAAAA AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT AAAA-T
*
1070910 AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAA
1 AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAA
1070942 GAACATTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 3 0.05
5 28 0.47
6 24 0.41
7 4 0.07
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:1070939 original size:11 final size:11
Alignment explanation
Indices: 1070863--1070941 Score: 70
Period size: 11 Copynumber: 6.8 Consensus size: 11
1070853 TTATTTAAAG
1070863 AAAATAAAATAA
1 AAAATAAAAT-A
*
1070875 TAAAACAAAATA
1 -AAAATAAAATA
*
1070887 AAAGTGAAAATA
1 AAAAT-AAAATA
*
1070899 AAAAAAAAAGTA
1 AAAATAAAA-TA
1070911 AAACA-AAAATA
1 AAA-ATAAAATA
1070922 AAAATAAAATA
1 AAAATAAAATA
*
1070933 AAGATAAAA
1 AAAATAAAA
1070942 GAACATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
10 1 0.02
11 26 0.46
12 19 0.34
13 10 0.18
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1070985 original size:16 final size:16
Alignment explanation
Indices: 1070964--1071009 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1070954 ATTCTAATTT
1070964 AATAAATAAAAAAACA
1 AATAAATAAAAAAACA
* *
1070980 AATAAATAAATAAATA
1 AATAAATAAAAAAACA
*
1070996 TATAAA-AAAAAAAC
1 AATAAATAAAAAAAC
1071010 CTGGAGCGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (16 bp):
AATAAATAAAAAAACA
Found at i:1071952 original size:16 final size:16
Alignment explanation
Indices: 1071928--1071961 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1071918 ATAAATACCT
*
1071928 AAGATAAAAAAAATAA
1 AAGAAAAAAAAAATAA
*
1071944 AAGAAAAAAAATATAA
1 AAGAAAAAAAAAATAA
1071960 AA
1 AA
1071962 TCATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGAAAAAAAAAATAA
Found at i:1071970 original size:3 final size:3
Alignment explanation
Indices: 1071964--1072019 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
1071954 ATATAAAATC
*
1071964 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA A-A ATA GA-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
1072011 ATA A-A ATA A
1 ATA ATA ATA A
1072020 GAATGTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 5 0.11
3 41 0.87
4 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1072012 original size:11 final size:11
Alignment explanation
Indices: 1071936--1072063 Score: 91
Period size: 11 Copynumber: 11.0 Consensus size: 11
1071926 CTAAGATAAA
*
1071936 AAAAATAAAAG
1 AAAAATAAAAT
1071947 AAAAA-AAATAT
1 AAAAATAAA-AT
1071958 AAAATCATAATAAT
1 AAAA--ATAA-AAT
*
1071972 AATAATAATAAT
1 AAAAATAA-AAT
*
1071984 AATAATAATAAT
1 AAAAATAA-AAT
1071996 AAAAATAAAAT
1 AAAAATAAAAT
*
1072007 AGAAATAAAAT
1 AAAAATAAAAT
*
1072018 AAGAATGTAAAAT
1 AA-AA-ATAAAAT
1072031 ACAAAAATAAAA-
1 --AAAAATAAAAT
*
1072043 AATAA-AAAAT
1 AAAAATAAAAT
1072053 AAAAATAAAAT
1 AAAAATAAAAT
1072064 GAAGAAAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.04
10 11 0.11
11 29 0.30
12 29 0.30
13 12 0.12
14 9 0.09
15 3 0.03
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1072049 original size:6 final size:6
Alignment explanation
Indices: 1071936--1072062 Score: 73
Period size: 6 Copynumber: 20.7 Consensus size: 6
1071926 CTAAGATAAA
* * * * *
1071936 AAAAAT -AAAAG AAAAA- AAATAT AAAATCAT AATAAT AATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA--AT AAAAAT AAAAAT AAAAAT
* * * * *
1071984 AATAAT AATAAT AAAAAT -AAAAT AGAAAT -AAAAT AAGAATGT AAAATAC
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AA-AT AAAA-AT
1072033 AAAAAT AAAAAAT AAAAAAT AAAAAT AAAA
1 AAAAAT -AAAAAT -AAAAAT AAAAAT AAAA
1072063 TGAAGAAAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
5 17 0.17
6 54 0.53
7 22 0.22
8 8 0.08
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:1072076 original size:7 final size:7
Alignment explanation
Indices: 1071935--1072062 Score: 61
Period size: 7 Copynumber: 17.6 Consensus size: 7
1071925 CCTAAGATAA
1071935 AAAAAAT
1 AAAAAAT
1071942 AAAAGAA-
1 AAAA-AAT
1071949 AAAAAAT
1 AAAAAAT
*
1071956 ATAAAAT
1 AAAAAAT
*
1071963 CATAATAAT
1 -A-AAAAAT
1071972 AATAATAAT
1 AA-AA-AAT
1071981 AATAATAAT
1 AA-AA-AAT
*
1071990 -AATAAT
1 AAAAAAT
1071996 -AAAAAT
1 AAAAAAT
1072002 AAAATAGA-
1 AAAA-A-AT
1072010 AATAAAAT
1 AA-AAAAT
*
1072018 -AAGAAT
1 AAAAAAT
**
1072024 GTAAAAT
1 AAAAAAT
1072031 ACAAAAAT
1 A-AAAAAT
1072039 AAAAAAT
1 AAAAAAT
1072046 AAAAAAT
1 AAAAAAT
1072053 -AAAAAT
1 AAAAAAT
1072059 AAAA
1 AAAA
1072063 TGAAGAAAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
6 20 0.21
7 41 0.43
8 16 0.17
9 19 0.20
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (7 bp):
AAAAAAT
Found at i:1078070 original size:21 final size:21
Alignment explanation
Indices: 1078038--1078078 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1078028 TATAAGTTGA
1078038 TAATTTTGGATAAAATTTTAC
1 TAATTTTGGATAAAATTTTAC
*
1078059 TAATATTT-GATACAATTTTA
1 TAAT-TTTGGATAAAATTTTA
1078079 ATAGTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
TAATTTTGGATAAAATTTTAC
Found at i:1078108 original size:27 final size:26
Alignment explanation
Indices: 1078073--1078123 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1078063 ATTTGATACA
** *
1078073 ATTTTAATAGTTTTCATATAATTTTG
1 ATTTTAATACCTTTAATATAATTTTG
1078099 ATTTTAAATACCTTTAATATAATTT
1 ATTTT-AATACCTTTAATATAATTT
1078124 ATAACCAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
ATTTTAATACCTTTAATATAATTTTG
Found at i:1081561 original size:27 final size:27
Alignment explanation
Indices: 1081526--1081577 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1081516 CTCCTAGCTT
*
1081526 TGACAGAAAGTAAGCATCCCGTTCAGC
1 TGACAGAAAGTAAACATCCCGTTCAGC
*
1081553 TGACTGAAAGTAAACATCCCGTTCA
1 TGACAGAAAGTAAACATCCCGTTCA
1081578 TCATCCAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (27 bp):
TGACAGAAAGTAAACATCCCGTTCAGC
Found at i:1095157 original size:27 final size:27
Alignment explanation
Indices: 1095127--1095178 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1095117 AACTGGATGA
*
1095127 TGAATGGGATGGTTACTTTCAGTCAGC
1 TGAATGGGATGCTTACTTTCAGTCAGC
*
1095154 TGAATGGGATGCTTACTTTCGGTCA
1 TGAATGGGATGCTTACTTTCAGTCA
1095179 AAGCTAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (27 bp):
TGAATGGGATGCTTACTTTCAGTCAGC
Found at i:1105052 original size:15 final size:16
Alignment explanation
Indices: 1105028--1105062 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1105018 TATTTTTATT
1105028 TTTTTCTAAAAACTTA
1 TTTTTCTAAAAACTTA
*
1105044 TTTTT-TAAAAATTTA
1 TTTTTCTAAAAACTTA
1105059 TTTT
1 TTTT
1105063 CATTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTCTAAAAACTTA
Found at i:1105062 original size:14 final size:15
Alignment explanation
Indices: 1105025--1105063 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1105015 ATCTATTTTT
1105025 ATTT-TTTTCTAAAA
1 ATTTATTTTCTAAAA
* *
1105039 ACTTATTTTTTAAAA
1 ATTTATTTTCTAAAA
1105054 ATTTATTTTC
1 ATTTATTTTC
1105064 ATTTTCAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTATTTTCTAAAA
Found at i:1109503 original size:21 final size:21
Alignment explanation
Indices: 1109474--1109523 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1109464 AAATTATATA
*
1109474 AAAATTATTATAATTGTAT-C
1 AAAATTATTAAAATTGTATCC
*
1109494 AAATATTATTAAAATTTTATCC
1 AAA-ATTATTAAAATTGTATCC
1109516 AAAATTAT
1 AAAATTAT
1109524 CAAATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 4 0.15
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATTATTAAAATTGTATCC
Found at i:1110898 original size:27 final size:27
Alignment explanation
Indices: 1110856--1110907 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1110846 AACTGGATGA
* *
1110856 TGAACGGGATGTTTACTTTCAGTCACC
1 TGAACGGAATGCTTACTTTCAGTCACC
*
1110883 TGAACGGAATGCTTACTTTCGGTCA
1 TGAACGGAATGCTTACTTTCAGTCA
1110908 AAGCTAGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (27 bp):
TGAACGGAATGCTTACTTTCAGTCACC
Found at i:1118047 original size:27 final size:26
Alignment explanation
Indices: 1118002--1118052 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1117992 CATTGGTTAT
* **
1118002 AAATTATATTAAAGGTATTTAAAATCA
1 AAATTATATGAAAACTA-TTAAAATCA
1118029 AAATTATATGAAAACTATTAAAAT
1 AAATTATATGAAAACTATTAAAAT
1118053 TGTATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
AAATTATATGAAAACTATTAAAATCA
Found at i:1118073 original size:21 final size:21
Alignment explanation
Indices: 1118047--1118087 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1118037 TGAAAACTAT
1118047 TAAAATTGTAT-CAAATATTAG
1 TAAAATTGTATCCAAA-ATTAG
*
1118068 TAAAATTTTATCCAAAATTA
1 TAAAATTGTATCCAAAATTA
1118088 TCAACTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAAATTGTATCCAAAATTAG
Found at i:1124081 original size:6 final size:6
Alignment explanation
Indices: 1124070--1124204 Score: 85
Period size: 6 Copynumber: 21.7 Consensus size: 6
1124060 TTTTTCTTCA
* *
1124070 TTTTAT TTTTATT TTTTAT TTTTATT TTTGTAT TTTACAT TCTTA- TTTTAT
1 TTTTAT TTTTA-T TTTTAT TTTTA-T TTT-TAT TTT-TAT TTTTAT TTTTAT
* * * * * *
1124121 TTCTA- TTTTAT TTTTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * *
1124168 TATTAT TATGAT TTTATATT TTTTTT CTTTTAT TTTT
1 TTTTAT TTTTAT TTT-TA-T TTTTAT -TTTTAT TTTT
1124205 TTTATCTTAG
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.07
6 69 0.64
7 25 0.23
8 6 0.06
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:1124091 original size:12 final size:12
Alignment explanation
Indices: 1124070--1124205 Score: 78
Period size: 13 Copynumber: 10.3 Consensus size: 12
1124060 TTTTTCTTCA
1124070 TTTTATTTTTATT
1 TTTTA-TTTTATT
1124083 TTTTATTTTTATT
1 TTTTA-TTTTATT
*
1124096 TTTGTATTTTACAT
1 TTT-TATTTTA-TT
*
1124110 TCTTATTTTA-T
1 TTTTATTTTATT
*
1124121 TTCTATTTTATTT
1 TTTTATTTTA-TT
1124134 TTATTATTATTATT
1 TT-TTATT-TTATT
1124148 ATTATTATTATTATT
1 -TT-TTATT-TTATT
*
1124163 ATTATTATTATTATGA
1 -TT-TTATT-TTAT-T
*
1124179 TTTTATATT-TT
1 TTTTATTTTATT
*
1124190 TTTTCTTTTATT
1 TTTTATTTTATT
1124202 TTTT
1 TTTT
1124206 TTATCTTAGG
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
11 16 0.15
12 7 0.07
13 33 0.32
14 15 0.14
15 33 0.32
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:1124142 original size:3 final size:3
Alignment explanation
Indices: 1124112--1124176 Score: 91
Period size: 3 Copynumber: 22.3 Consensus size: 3
1124102 TTTTACATTC
*
1124112 TTA TT- TTA TT- TCTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1124155 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
1124177 GATTTTATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 5 0.09
3 50 0.89
4 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1124198 original size:16 final size:16
Alignment explanation
Indices: 1124179--1124212 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1124169 ATTATTATGA
1124179 TTTTATATTTTTTT-TC
1 TTTTAT-TTTTTTTATC
1124195 TTTTATTTTTTTTATC
1 TTTTATTTTTTTTATC
1124211 TT
1 TT
1124213 AGGTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTTTTTTATC
Found at i:1124313 original size:63 final size:66
Alignment explanation
Indices: 1124166--1124314 Score: 148
Period size: 63 Copynumber: 2.3 Consensus size: 66
1124156 TATTATTATT
* * *
1124166 ATTAT-TATTATGATTTTA-TATTTTTTTTCTTTTATTTTTTTTATCTTAGGTATTTATGTATTT
1 ATTATGTATTAT--TTTTATTATTTTTTTTCTTTTATTTTTTCTATCTTAGATATTTATGTATAT
**
1124229 ATT
64 AAG
* * *
1124232 AATATGTATATATATTTATTA-TTTTTTTCTTTT-TTTTTTCT-TGTTA-ATATTTATGTATATA
1 ATTATGTAT-TATTTTTATTATTTTTTTTCTTTTATTTTTTCTATCTTAGATATTTATGTATATA
1124293 AG
65 AG
1124295 ATTATGTATTATCTTTTATT
1 ATTATGTATTAT-TTTTATT
1124315 TAATTTTAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
62 3 0.04
63 27 0.39
64 4 0.06
65 7 0.10
66 20 0.29
67 5 0.07
68 3 0.04
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.66
Consensus pattern (66 bp):
ATTATGTATTATTTTTATTATTTTTTTTCTTTTATTTTTTCTATCTTAGATATTTATGTATATAA
G
Found at i:1125227 original size:16 final size:16
Alignment explanation
Indices: 1125187--1125233 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1125177 GCCGCTCCAG
* *
1125187 GTTTTTTTTTTTATAT
1 GTTTTTTTATTTATTT
* *
1125203 ATTTATTTATTTATTT
1 GTTTTTTTATTTATTT
1125219 GTTTTTTTATTTATT
1 GTTTTTTTATTTATT
1125234 AAATTAGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (16 bp):
GTTTTTTTATTTATTT
Found at i:1125273 original size:5 final size:5
Alignment explanation
Indices: 1125256--1125334 Score: 54
Period size: 5 Copynumber: 14.8 Consensus size: 5
1125246 TTTAATGTTC
* *
1125256 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTTTT TTTTA TTTTCA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA --TTTTA TTTTA TTTT-A
*
1125307 CTTTTA TTTTG TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1125335 CTTTAAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
3 3 0.05
5 32 0.53
6 17 0.28
7 8 0.13
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1125276 original size:17 final size:17
Alignment explanation
Indices: 1125256--1125334 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 17
1125246 TTTAATGTTC
*
1125256 TTTTATCTTTATTTTAT
1 TTTTATTTTTATTTTAT
*
1125273 TTTTATTTTTGTTTTACT
1 TTTTATTTTTATTTTA-T
*
1125291 TTTT-TTTTTATTTTCAC
1 TTTTATTTTTATTTT-AT
*
1125308 TTTTA-TTTTGTTTTATT
1 TTTTATTTTTATTTTA-T
1125325 ATTTTATTTT
1 -TTTTATTTT
1125335 CTTTAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 35 0.70
18 11 0.22
19 3 0.06
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:1125413 original size:58 final size:58
Alignment explanation
Indices: 1125351--1125806 Score: 422
Period size: 58 Copynumber: 7.7 Consensus size: 58
1125341 ATAAAACCTA
* * *
1125351 AAAAATAATATTTTTGGGGAAAAGTTGAAATTA-CAATTTTTCTTAAAAATAAATTTTC
1 AAAAA-AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTC
* * * * ** *
1125409 AAAAAAAAAGTTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGAATCC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAA-TTTTC
* *
1125470 AAAAAAAAAAATTTTTG-GAGAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAAATAAATTTTC
1 --AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTC-TT-GAAAATAAATTTTC
** * *
1125531 -AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTAATTAA-TTTTCTTCGAAAATCAAAGTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGT-ATCAATTTTTCTT-GAAAAT-AAATTTTC
* * * *
1125590 CAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTC
* * * * *
1125648 AAAAAAATTTTTTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTCGAAAATCAAAGTTTTC
1 AAAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAA-TTTTC
* * * *
1125710 AAAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTT-
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-TTTTC
* * *
1125767 AAAAGAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1125807 CCCTACACAA
Statistics
Matches: 331, Mismatches: 48, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
57 11 0.03
58 106 0.32
59 75 0.23
60 73 0.22
61 11 0.03
62 41 0.12
63 14 0.04
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTC
Found at i:1125484 original size:120 final size:119
Alignment explanation
Indices: 1125351--1125808 Score: 547
Period size: 119 Copynumber: 3.8 Consensus size: 119
1125341 ATAAAACCTA
*
1125351 AAAAATAATATTTTTGGGGAAAAGTTGAAATTA-CAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 AAAAA-AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
**
1125415 AAAGTTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGAATCC
65 AAAGTTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
* *
1125470 AAAAAAAAAAATTTTTGGAGAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAAATAAATTTTC--A
1 --AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC-TT-AAAAATAAATTTTCAAA
* * * *
1125532 AAAAAGGTTTTTGAGGAAAAGTTGAAAGTAATTAATTTTCTTCGAAAATCAAAGTTTCC
62 AAAAAAGTTTTTGAAGAAAAGTTGAAAGT-ATCAATTTTCCTCGAAAATCAAAGTTTCC
* * *
1125591 -AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAAAATTTTCAAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
*** * * *
1125655 TTTTTTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTCGAAAATCAAAGTTTTC
66 AAGTTTTTGAA-GAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
* ** * *
1125710 AAAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTT-AAAAGA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTCAAAAAA
* *
1125773 ATA-TTTTTG-AGAAAAAGTTAAAAGTATCAATTTTCC
65 AAAGTTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCC
1125809 CTACACAAAA
Statistics
Matches: 291, Mismatches: 35, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
116 1 0.00
117 36 0.12
118 38 0.13
119 85 0.29
120 82 0.28
121 35 0.12
122 14 0.05
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (119 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
AAGTTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCC
Found at i:1126444 original size:21 final size:21
Alignment explanation
Indices: 1126420--1126459 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1126410 AATTTTTTGT
1126420 TTTGGATTAATTGACTTTTCG
1 TTTGGATTAATTGACTTTTCG
1126441 TTTGGATTAATTGACTTTT
1 TTTGGATTAATTGACTTTT
1126460 TCTATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.55
Consensus pattern (21 bp):
TTTGGATTAATTGACTTTTCG
Found at i:1141985 original size:25 final size:25
Alignment explanation
Indices: 1141956--1142005 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1141946 TATGTACGTA
1141956 ATTTATGACAGGTAAAACTTTAATT
1 ATTTATGACAGGTAAAACTTTAATT
1141981 ATTTATGACAGGTAAAACTTTAATT
1 ATTTATGACAGGTAAAACTTTAATT
1142006 TGGTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
ATTTATGACAGGTAAAACTTTAATT
Found at i:1148932 original size:24 final size:24
Alignment explanation
Indices: 1148899--1148950 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1148889 ATGAATGTTT
* *
1148899 AAAAGTTTAATTAATCCAAAATAG
1 AAAAGGTTAATTAATCCAAAATAA
1148923 AAAAGGTTAATTAATCCAAAATAA
1 AAAAGGTTAATTAATCCAAAATAA
1148947 AAAA
1 AAAA
1148951 AAATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
AAAAGGTTAATTAATCCAAAATAA
Found at i:1153636 original size:24 final size:24
Alignment explanation
Indices: 1153579--1153637 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1153569 ATGAATGTTT
*
1153579 AAAAGTTTAATTAATCCAAAATAG
1 AAAAGTTTAATTAATCCAAAATAA
*
1153603 AAAAGGTTAATTAATCCAAAATAA
1 AAAAGTTTAATTAATCCAAAATAA
*
1153627 AAAATTTTAAT
1 AAAAGTTTAAT
1153638 ATTTCATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAGTTTAATTAATCCAAAATAA
Found at i:1156200 original size:26 final size:26
Alignment explanation
Indices: 1156171--1156225 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1156161 TTTTTATTGA
1156171 TTTTTTT-AATCACAAT-TACAATAAT
1 TTTTTTTCAATCAC-ATCTACAATAAT
*
1156196 TTTTTTTCAATCTCATCTACAATAAT
1 TTTTTTTCAATCACATCTACAATAAT
1156222 TTTT
1 TTTT
1156226 ATTATTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTTTTCAATCACATCTACAATAAT
Found at i:1156224 original size:25 final size:24
Alignment explanation
Indices: 1156170--1156225 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
1156160 TTTTTTATTG
1156170 ATTTTTTTAATCACAATTACAATA
1 ATTTTTTTAATCACAATTACAATA
*
1156194 ATTTTTTTTCAATCTC-ATCTACAATA
1 A-TTTTTTT-AATCACAAT-TACAATA
1156220 ATTTTT
1 ATTTTT
1156226 ATTATTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 14 0.50
26 13 0.46
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTTTTAATCACAATTACAATA
Found at i:1157254 original size:20 final size:19
Alignment explanation
Indices: 1157205--1157255 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
1157195 TTACTTTACT
*
1157205 ATTTTTATAAA-A-AGAAA
1 ATTTTTATAAATATTGAAA
*
1157222 ATTTTTAT-TATATTGAAA
1 ATTTTTATAAATATTGAAA
1157240 ACTTTTTATAAATATT
1 A-TTTTTATAAATATT
1157256 TCAATCCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.04
17 9 0.33
18 5 0.19
19 7 0.26
20 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
ATTTTTATAAATATTGAAA
Found at i:1166343 original size:29 final size:29
Alignment explanation
Indices: 1166310--1166366 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1166300 GTTTAAGTAC
*
1166310 AAATTAAAATTTATGGATTTATTTGAATA
1 AAATTAAAATTTAAGGATTTATTTGAATA
*
1166339 AAATTAAAGTTTAAGGATTTATTTGAAT
1 AAATTAAAATTTAAGGATTTATTTGAAT
1166367 GCAAACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (29 bp):
AAATTAAAATTTAAGGATTTATTTGAATA
Found at i:1166381 original size:29 final size:29
Alignment explanation
Indices: 1166314--1166391 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1166304 AAGTACAAAT
* * *
1166314 TAAAATTTATGGATTTATTTGAATAAAAT
1 TAAAGTTTAAGGATTTATTTGAATAAAAC
*
1166343 TAAAGTTTAAGGATTTATTTGAATGCAAAC
1 TAAAGTTTAAGGATTTATTTGAAT-AAAAC
* *
1166373 TAATG-TTAAGGGTTTATTT
1 TAAAGTTTAAGGATTTATTT
1166392 TGATACAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (29 bp):
TAAAGTTTAAGGATTTATTTGAATAAAAC
Found at i:1168026 original size:5 final size:6
Alignment explanation
Indices: 1168006--1168080 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
1167996 TTTTGAATCG
* * * *
1168006 AATTTA AATTTA AATTT- AA-TTA AATTTT AA-TAA AATTTTA TACTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA AATTTA
* *
1168052 AATTTA AAATTA AATTTA AATTCA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTT
1168081 TTATTGAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 41 0.77
7 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:1173223 original size:16 final size:16
Alignment explanation
Indices: 1173188--1173222 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1173178 CAAGAAGGAT
1173188 AAAGCAAGAAACTTGA
1 AAAGCAAGAAACTTGA
*
1173204 AAAGACAAGAAGCTTGA
1 AAAG-CAAGAAACTTGA
1173221 AA
1 AA
1173223 GGTACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (16 bp):
AAAGCAAGAAACTTGA
Found at i:1176082 original size:32 final size:34
Alignment explanation
Indices: 1176044--1176129 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 34
1176034 GTTTAATTTG
1176044 AATTAAATTTAAATTTAATTTAATT-A-TTATCA
1 AATTAAATTTAAATTTAATTTAATTGATTTATCA
* * * *
1176076 AATTAAATTTAAGTTTAAATTATTTGATTTATTA
1 AATTAAATTTAAATTTAATTTAATTGATTTATCA
1176110 AA-TAAA-TTAAATTTTAATTT
1 AATTAAATTTAAA-TTTAATTT
1176130 GAATATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 26 0.58
33 12 0.27
34 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (34 bp):
AATTAAATTTAAATTTAATTTAATTGATTTATCA
Found at i:1179696 original size:17 final size:18
Alignment explanation
Indices: 1179662--1179697 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1179652 TGCATTAGAG
1179662 ATAAGTTGAGCATCAGAA
1 ATAAGTTGAGCATCAGAA
*
1179680 ATAAGTTTAGC-TCAGAA
1 ATAAGTTGAGCATCAGAA
1179697 A
1 A
1179698 AGCCAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (18 bp):
ATAAGTTGAGCATCAGAA
Found at i:1180712 original size:3 final size:3
Alignment explanation
Indices: 1180704--1180732 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1180694 ACGAGAAAGC
1180704 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1180733 CAAATCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1181990 original size:19 final size:18
Alignment explanation
Indices: 1181937--1181990 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1181927 ATACGAAATT
*
1181937 TTTTTAAAATGATTTTAAA
1 TTTTTAAAAT-ATTTTTAA
* * *
1181956 ATTTTAAATTAATTTTAA
1 TTTTTAAAATATTTTTAA
1181974 TTTTTGAAAATATTTTT
1 TTTTT-AAAATATTTTT
1181991 TGTAAAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTTTAAAATATTTTTAA
Found at i:1183263 original size:10 final size:10
Alignment explanation
Indices: 1183230--1183263 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1183220 TTGTCAAGGG
1183230 TTTTTTTTAT
1 TTTTTTTTAT
*
1183240 TTATTTTTAAT
1 TT-TTTTTTAT
1183251 TTTTTTTTAT
1 TTTTTTTTAT
1183261 TTT
1 TTT
1183264 GACCTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:1183297 original size:11 final size:11
Alignment explanation
Indices: 1183281--1183305 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1183271 TATGTAATTT
1183281 TATTTTTTAAA
1 TATTTTTTAAA
1183292 TATTTTTTAAA
1 TATTTTTTAAA
1183303 TAT
1 TAT
1183306 CAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:1183461 original size:33 final size:34
Alignment explanation
Indices: 1183418--1183487 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
1183408 ATGAATGATG
*
1183418 AAATTAATTATGA-TAAAATTAAAAATAA-TAATA
1 AAATTAATTATAATTAAAATTAAAAA-AATTAATA
* **
1183451 AAATTTATTATAATTATGATTAAAAAAATTAATA
1 AAATTAATTATAATTAAAATTAAAAAAATTAATA
1183485 AAA
1 AAA
1183488 AATATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (34 bp):
AAATTAATTATAATTAAAATTAAAAAAATTAATA
Found at i:1183884 original size:19 final size:19
Alignment explanation
Indices: 1183860--1183909 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1183850 TTTAAAATTA
1183860 AAATTTAAATATATTAAAT
1 AAATTTAAATATATTAAAT
* * *
1183879 AAATTTAGATAAATTTAAT
1 AAATTTAAATATATTAAAT
1183898 -AATTTAAA-ATAT
1 AAATTTAAATATAT
1183910 GATAAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 3 0.12
18 7 0.27
19 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTTAAATATATTAAAT
Found at i:1183950 original size:27 final size:26
Alignment explanation
Indices: 1183896--1183958 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
1183886 GATAAATTTA
*
1183896 ATAATTTAAAATATGATAAAAATAAT
1 ATAATTTAAAATATAATAAAAATAAT
* * *
1183922 ATAATTTAAAATTTTAATAATAATTAT
1 ATAATTTAAAA-TATAATAAAAATAAT
1183949 ATAAATTTAA
1 AT-AATTTAA
1183959 TAAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 11 0.35
27 13 0.42
28 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATAATTTAAAATATAATAAAAATAAT
Found at i:1183954 original size:21 final size:19
Alignment explanation
Indices: 1183898--1183971 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
1183888 TAAATTTAAT
*
1183898 AATTTAA-AAT-ATGATAA
1 AATTTAATAATAATTATAA
*
1183915 AA-ATAAT-ATAATT-TAA
1 AATTTAATAATAATTATAA
1183931 AATTTTAATAATAATTATATA
1 AA-TTTAATAATAATTATA-A
1183952 AATTTAATAA-AATTA-AA
1 AATTTAATAATAATTATAA
1183969 AAT
1 AAT
1183972 CAATATTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 10 0.21
17 8 0.17
18 5 0.11
19 11 0.23
20 10 0.21
21 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
AATTTAATAATAATTATAA
Found at i:1183961 original size:9 final size:9
Alignment explanation
Indices: 1183860--1183971 Score: 63
Period size: 9 Copynumber: 12.4 Consensus size: 9
1183850 TTTAAAATTA
1183860 AAATTTAAAT
1 AAATTT-AAT
* *
1183870 ATATTAAAT
1 AAATTTAAT
1183879 AAATTTAGAT
1 AAATTTA-AT
1183889 AAATTTAAT
1 AAATTTAAT
1183898 -AATTT-A-
1 AAATTTAAT
* *
1183904 AAATATGAT
1 AAATTTAAT
**
1183913 AAAAATAAT
1 AAATTTAAT
1183922 ATAATTTAA-
1 A-AATTTAAT
*
1183931 AATTTTAAT
1 AAATTTAAT
*
1183940 AATAATTATAT
1 AA-ATTTA-AT
1183951 AAATTTAAT
1 AAATTTAAT
*
1183960 AAAATTAA-
1 AAATTTAAT
1183968 AAAT
1 AAAT
1183972 CAATATTATA
Statistics
Matches: 79, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
7 5 0.06
8 15 0.19
9 30 0.38
10 25 0.32
11 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATTTAAT
Found at i:1184423 original size:2 final size:2
Alignment explanation
Indices: 1184416--1184465 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1184406 ATTCATTACT
* *
1184416 TA TA TA TA TC TA TA TA TA TC 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
1184458 TA TA TA TA
1 TA TA TA TA
1184466 ACAATATAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1188466 original size:22 final size:23
Alignment explanation
Indices: 1188430--1188472 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1188420 ATAATATTAT
1188430 TTTATAATTAAATATT-AAATAA
1 TTTATAATTAAATATTCAAATAA
**
1188452 TTTATAATTTTATATTCAAAT
1 TTTATAATTAAATATTCAAAT
1188473 TCTATTCCTT
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:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTATAATTAAATATTCAAATAA
Found at i:1189544 original size:3 final size:3
Alignment explanation
Indices: 1189536--1189575 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1189526 TAGCTGAAAT
1189536 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1189576 AAGAAACAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1190522 original size:30 final size:29
Alignment explanation
Indices: 1190487--1190575 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 29
1190477 CAATTAGATA
1190487 AAAATAAATATTTAAGAATTTAATTGATTT
1 AAAATAAATATTTAAG-ATTTAATTGATTT
* *
1190517 AAAATAAAAATTTTAAGATTTGATTGATTGT
1 AAAATAAATA-TTTAAGATTTAATTGATT-T
* *
1190548 AATA-AAATA-TTAGTGATTTAATTGATTT
1 AAAATAAATATTTA-AGATTTAATTGATTT
1190576 TTTAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 4 0.08
29 12 0.24
30 24 0.48
31 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (29 bp):
AAAATAAATATTTAAGATTTAATTGATTT
Found at i:1191498 original size:13 final size:13
Alignment explanation
Indices: 1191480--1191505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1191470 TTTAATTAAA
1191480 ATTAAATTCGAAT
1 ATTAAATTCGAAT
1191493 ATTAAATTCGAAT
1 ATTAAATTCGAAT
1191506 GAAATTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTAAATTCGAAT
Found at i:1191619 original size:21 final size:21
Alignment explanation
Indices: 1191589--1191655 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
1191579 ATAATTATTT
1191589 TATA-TAAAATTTTATTTAAA
1 TATATTAAAATTTTATTTAAA
*
1191609 TATATTAAAATTTTTATTAAAA
1 TATATTAAAA-TTTTATTTAAA
* *
1191631 TAATATAAAAAATTTAAATTTAAA
1 T-ATAT-TAAAATTT-TATTTAAA
1191655 T
1 T
1191656 TGGTAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 4 0.11
21 5 0.13
22 11 0.29
23 7 0.18
24 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATTAAAATTTTATTTAAA
Found at i:1191626 original size:22 final size:22
Alignment explanation
Indices: 1191589--1191655 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
1191579 ATAATTATTT
1191589 TATA-TAAAA-TTTTATTTAAA
1 TATATTAAAATTTTTATTTAAA
*
1191609 TATATTAAAATTTTTATTAAAA
1 TATATTAAAATTTTTATTTAAA
* **
1191631 TAATATAAAAAATTTAAATTTAAA
1 T-ATAT-TAAAATTTTTATTTAAA
1191655 T
1 T
1191656 TGGTAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 4 0.11
21 5 0.13
22 11 0.29
23 4 0.11
24 14 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTAAAATTTTTATTTAAA
Found at i:1191797 original size:107 final size:109
Alignment explanation
Indices: 1191681--1191883 Score: 311
Period size: 107 Copynumber: 1.9 Consensus size: 109
1191671 GGATTGAATG
* * * *
1191681 ATTTTAAGAAAAAATAATTTAAATTTGGATTGAATTTAAAAAATTTATAATATTATATATTATAA
1 ATTTCAAGAAAAAATAATTTAAATTTAGATTAAATTTAAAAAATTTATAATATTATACATTATAA
1191746 AAAAAA-CAAATCAAA-CTAATAAAATTCAATTAAGATGAATTA
66 AAAAAATCAAATCAAATCTAATAAAATTCAATTAAGATGAATTA
** *
1191788 ATTTCAAGAAAATTTAATTTAAATTTAGATTAAATTTTAAAAATTTATAATATTATACATTATAA
1 ATTTCAAGAAAAAATAATTTAAATTTAGATTAAATTTAAAAAATTTATAATATTATACATTATAA
**
1191853 AAAAAATCAAATCAAATCTAATTCAATTCAA
66 AAAAAATCAAATCAAATCTAATAAAATTCAA
1191884 ATCATTATCA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 64 0.75
108 9 0.11
109 12 0.14
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (109 bp):
ATTTCAAGAAAAAATAATTTAAATTTAGATTAAATTTAAAAAATTTATAATATTATACATTATAA
AAAAAATCAAATCAAATCTAATAAAATTCAATTAAGATGAATTA
Found at i:1198518 original size:6 final size:6
Alignment explanation
Indices: 1198504--1198533 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1198494 GAATTTTATG
*
1198504 GCTGAA GCTGCA GCTGCA GCTGCA GCTGCA
1 GCTGCA GCTGCA GCTGCA GCTGCA GCTGCA
1198534 ACTCAGGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (6 bp):
GCTGCA
Found at i:1204858 original size:45 final size:45
Alignment explanation
Indices: 1204794--1204927 Score: 223
Period size: 45 Copynumber: 3.0 Consensus size: 45
1204784 TGTCTGAGGG
1204794 GGATCCAAATGCCAGCAAATCTACTGAAGTTATCATCTATCCACA
1 GGATCCAAATGCCAGCAAATCTACTGAAGTTATCATCTATCCACA
* * *
1204839 GGATCCAAATGCCAACAAATCTAATGAAGTTATCATCTATCCACG
1 GGATCCAAATGCCAGCAAATCTACTGAAGTTATCATCTATCCACA
* *
1204884 GGATCCAAATGCCAGCAAAGCTACTGAAGTTATCATCTACCCAC
1 GGATCCAAATGCCAGCAAATCTACTGAAGTTATCATCTATCCAC
1204928 CAAAATCACT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (45 bp):
GGATCCAAATGCCAGCAAATCTACTGAAGTTATCATCTATCCACA
Found at i:1207778 original size:23 final size:25
Alignment explanation
Indices: 1207729--1207788 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
1207719 CAGTAATTTA
*
1207729 AAATTTAATTTAATTAATTTATGTAAT
1 AAATTTAA-ATAA-TAATTTATGTAAT
*
1207756 TAATTTAAATAATAATTT-T-TAAT
1 AAATTTAAATAATAATTTATGTAAT
1207779 AAATTTAAAT
1 AAATTTAAAT
1207789 TAAAAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 13 0.43
24 1 0.03
25 6 0.20
26 3 0.10
27 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATTTAAATAATAATTTATGTAAT
Found at i:1207863 original size:15 final size:14
Alignment explanation
Indices: 1207845--1207886 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
1207835 ATTAATTTCG
1207845 AATTAAATTATTTAA
1 AATTAAATTATTT-A
*
1207860 AATTAAATTAATTA
1 AATTAAATTATTTA
1207874 AATTAAATTATTT
1 AATTAAATTATTT
1207887 TATTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTAAATTATTTA
Found at i:1210841 original size:69 final size:69
Alignment explanation
Indices: 1210712--1210841 Score: 188
Period size: 69 Copynumber: 1.9 Consensus size: 69
1210702 ATTTATTTTT
* * * *
1210712 TTTTATGAAATTTAATTTGATTCAATTTTAGATTAATTTAAATTTAAAATAATTATTAAAATTTA
1 TTTTATGAAATTTAATTTAATTCAATTTTAAATTAATTAAAATTTAAAATAATTACTAAAATTTA
1210777 TCTC
66 TCTC
* * * *
1210781 TTTTATGAAATTTGATTTAATTTAATTTTAAATTAATTAAAATTTAAAGTGATTACTAAAA
1 TTTTATGAAATTTAATTTAATTCAATTTTAAATTAATTAAAATTTAAAATAATTACTAAAA
1210842 CTGAAGGTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (69 bp):
TTTTATGAAATTTAATTTAATTCAATTTTAAATTAATTAAAATTTAAAATAATTACTAAAATTTA
TCTC
Found at i:1214823 original size:13 final size:15
Alignment explanation
Indices: 1214805--1214842 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1214795 CTTACCAATC
1214805 TTTTCTCTCTT-C-T
1 TTTTCTCTCTTCCAT
*
1214818 TTTTCTCTTTTCCAT
1 TTTTCTCTCTTCCAT
1214833 TTTTCTCTCT
1 TTTTCTCTCT
1214843 CTCATCAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.48
14 1 0.05
15 10 0.48
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCTCTCTTCCAT
Found at i:1229316 original size:6 final size:6
Alignment explanation
Indices: 1229305--1229338 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1229295 ATTATAAAAT
*
1229305 TTTAAA TTTAAA TTTAAA ATTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1229339 TATTATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:1229570 original size:13 final size:13
Alignment explanation
Indices: 1229541--1229578 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1229531 TTTATTTATC
*
1229541 AAATAAAATTTTT
1 AAATAAATTTTTT
1229554 -AATAAATTTTTT
1 AAATAAATTTTTT
1229566 AAATAAATATTTT
1 AAATAAAT-TTTT
1229579 GGATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATAAATTTTTT
Found at i:1229586 original size:25 final size:25
Alignment explanation
Indices: 1229541--1229594 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1229531 TTTATTTATC
* *
1229541 AAATAAAATTTTTAATAAATTTTTT
1 AAATAAAATTTTGAATAAATTATTT
*
1229566 AAATAAATATTTTGGAT-AATTATTT
1 AAATAAA-ATTTTGAATAAATTATTT
1229591 AAAT
1 AAAT
1229595 TGAAATCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
AAATAAAATTTTGAATAAATTATTT
Found at i:1231037 original size:17 final size:18
Alignment explanation
Indices: 1231002--1231041 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1230992 ATTTTTATTT
1231002 TATAAAATTTAAAATAAA
1 TATAAAATTTAAAATAAA
1231020 TATAAAA-TTAATAA-AAA
1 TATAAAATTTAA-AATAAA
1231037 TATAA
1 TATAA
1231042 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAATTTAAAATAAA
Found at i:1236231 original size:3 final size:3
Alignment explanation
Indices: 1236223--1236252 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1236213 AGGTATTAGC
1236223 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1236253 TGATTTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1245481 original size:15 final size:15
Alignment explanation
Indices: 1245463--1245493 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1245453 CAGTCAATGC
1245463 TAATAGAAATCTTAA
1 TAATAGAAATCTTAA
1245478 TAATAGAAATCTTAA
1 TAATAGAAATCTTAA
1245493 T
1 T
1245494 TTTCTTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TAATAGAAATCTTAA
Found at i:1248423 original size:142 final size:142
Alignment explanation
Indices: 1248179--1248451 Score: 368
Period size: 142 Copynumber: 1.9 Consensus size: 142
1248169 AACGCATGAA
* * * * *
1248179 GTTGTGTGCTTAACTTTTTCTCATAATTGGACTATTGATGTTTTTCTTTGTGTTTGTTCAAACTT
1 GTTGTGTGCTTAACATTTTCTCAAAATTGGACCATTGATGTTTTTCATTGTGTTTCTTCAAACTT
** ** ** * * *
1248244 GTAAGAGAAACAAATGAAGTACATGAATTTCTGCAATCAAATAATG-TTTGAAAATGTAGATGAC
66 GTAAGAGAAACAAATGAAACACACCAATGGCTACAATCAAATAATGTTTTAAAAATCTAGATGAC
1248308 ATTCATTATTAT
131 ATTCATTATTAT
* *
1248320 GTTGTGTGCTTAACATTTTCTCAAAATTTGACCATTTATGCTTTTTCATTGTGTTTCTTCAAACT
1 GTTGTGTGCTTAACATTTTCTCAAAATTGGACCATTGATG-TTTTTCATTGTGTTTCTTCAAACT
* *
1248385 TGTAAGAGAAACGAATGAAACACACCAATGGCTACAATCAAATTATGTTTTAAAAATCTAGATGA
65 TGTAAGAGAAACAAATGAAACACACCAATGGCTACAATCAAATAATGTTTTAAAAATCTAGATGA
1248450 CA
130 CA
1248452 ATGCAATGAG
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
141 35 0.31
142 60 0.54
143 17 0.15
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (142 bp):
GTTGTGTGCTTAACATTTTCTCAAAATTGGACCATTGATGTTTTTCATTGTGTTTCTTCAAACTT
GTAAGAGAAACAAATGAAACACACCAATGGCTACAATCAAATAATGTTTTAAAAATCTAGATGAC
ATTCATTATTAT
Found at i:1249946 original size:19 final size:19
Alignment explanation
Indices: 1249922--1249959 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1249912 TAACAATTTC
1249922 CCTTATTCCCTCTTCAAAG
1 CCTTATTCCCTCTTCAAAG
1249941 CCTTATTCCCTCTTCAAAG
1 CCTTATTCCCTCTTCAAAG
1249960 TATTATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.05, T:0.37
Consensus pattern (19 bp):
CCTTATTCCCTCTTCAAAG
Found at i:1249965 original size:19 final size:19
Alignment explanation
Indices: 1249924--1249965 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1249914 ACAATTTCCC
*
1249924 TTATTCCCTCTTCAAAGCC
1 TTATTCCCTCTTCAAAGCA
*
1249943 TTATTCCCTCTTCAAAGTA
1 TTATTCCCTCTTCAAAGCA
1249962 TTAT
1 TTAT
1249966 AGTTGATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (19 bp):
TTATTCCCTCTTCAAAGCA
Found at i:1254150 original size:3 final size:3
Alignment explanation
Indices: 1254142--1254198 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
1254132 TGCACGTCTC
*
1254142 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1254189 TAT TAA TAA T
1 TAA TAA TAA T
1254199 TTAATTTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1254716 original size:22 final size:22
Alignment explanation
Indices: 1254691--1254743 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1254681 TTGATTTACA
* *
1254691 ACTAAGTTATCAATGATATATT
1 ACTAAATTATAAATGATATATT
*
1254713 ACTAAATTATAAATGATTTATT
1 ACTAAATTATAAATGATATATT
1254735 ACTAAATTA
1 ACTAAATTA
1254744 GCTTTGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (22 bp):
ACTAAATTATAAATGATATATT
Found at i:1254833 original size:22 final size:22
Alignment explanation
Indices: 1254760--1254833 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1254750 ATTTATTGTT
*
1254760 AAGTTATTGATAATTTATTACA
1 AAGTTATCGATAATTTATTACA
* * **
1254782 GAGTTAT-AATTAATTTATTATT
1 AAGTTATCGA-TAATTTATTACA
* *
1254804 AATTTATCGATAATTTACTACA
1 AAGTTATCGATAATTTATTACA
1254826 AAGTTATC
1 AAGTTATC
1254834 AATGATTAAC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
21 1 0.03
22 37 0.95
23 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (22 bp):
AAGTTATCGATAATTTATTACA
Found at i:1254850 original size:30 final size:30
Alignment explanation
Indices: 1254814--1254870 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1254804 AATTTATCGA
1254814 TAATTTACTAC-AAAGTTATCAATGATTAAC
1 TAATTTACTACTAAA-TTATCAATGATTAAC
* *
1254844 TAATTTATTACTAAATTATCATTGATT
1 TAATTTACTACTAAATTATCAATGATT
1254871 TATAACTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATTTACTACTAAATTATCAATGATTAAC
Found at i:1254871 original size:22 final size:22
Alignment explanation
Indices: 1254846--1254917 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
1254836 TGATTAACTA
* *
1254846 ATTTATTACTAAATTATCATTG
1 ATTTATTACTAAGTTATCAATG
* * * *
1254868 ATTTATAACTAAGTCATTAGTG
1 ATTTATTACTAAGTTATCAATG
* *
1254890 ATTTACTACTAAGTTATCAATA
1 ATTTATTACTAAGTTATCAATG
1254912 ATTTAT
1 ATTTAT
1254918 AAAGAAATTA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (22 bp):
ATTTATTACTAAGTTATCAATG
Found at i:1254949 original size:22 final size:22
Alignment explanation
Indices: 1254924--1254985 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1254914 TTATAAAGAA
1254924 ATTATAAATGATTTACTATTAT
1 ATTATAAATGATTTACTATTAT
*
1254946 ATTAT-TATGCATTTACTATTAT
1 ATTATAAATG-ATTTACTATTAT
* * * *
1254968 GTGATAATTAATTTACTA
1 ATTATAAATGATTTACTA
1254986 CTTAATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.09
22 28 0.88
23 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
ATTATAAATGATTTACTATTAT
Found at i:1255111 original size:16 final size:15
Alignment explanation
Indices: 1255086--1255119 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1255076 ATTATACAAA
*
1255086 ATTTACTATTAAGTT
1 ATTTACTATTAAATT
1255101 ATTTAACTATTAAATT
1 ATTT-ACTATTAAATT
1255117 ATT
1 ATT
1255120 GATGATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTACTATTAAATT
Found at i:1255188 original size:44 final size:44
Alignment explanation
Indices: 1255140--1255250 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 44
1255130 TACTACTAAG
* *
1255140 TTATTGATTTCCTT-TCAAGTTTTCAATAATTAACTATTAAATTA
1 TTATTGATTT-ATTGTCAAGTTATCAATAATTAACTATTAAATTA
* * *
1255184 TTATTGATTTATTGTTAAGTTATCACTAATTTACTATTAAATTA
1 TTATTGATTTATTGTCAAGTTATCAATAATTAACTATTAAATTA
* * * *
1255228 TCATTAATTTATTATTAAGTTAT
1 TTATTGATTTATTGTCAAGTTAT
1255251 TAATGATTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (44 bp):
TTATTGATTTATTGTCAAGTTATCAATAATTAACTATTAAATTA
Found at i:1255201 original size:22 final size:22
Alignment explanation
Indices: 1255174--1255250 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
1255164 AATAATTAAC
* *
1255174 TATTAAATTATTATTGATTTAT
1 TATTAAATTATCATTAATTTAT
* * * *
1255196 TGTTAAGTTATCACTAATTTAC
1 TATTAAATTATCATTAATTTAT
1255218 TATTAAATTATCATTAATTTAT
1 TATTAAATTATCATTAATTTAT
*
1255240 TATTAAGTTAT
1 TATTAAATTAT
1255251 TAATGATTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (22 bp):
TATTAAATTATCATTAATTTAT
Found at i:1255251 original size:11 final size:11
Alignment explanation
Indices: 1255174--1255252 Score: 68
Period size: 11 Copynumber: 7.2 Consensus size: 11
1255164 AATAATTAAC
*
1255174 TATTAAATTAT
1 TATTAATTTAT
*
1255185 TATTGATTTAT
1 TATTAATTTAT
* *
1255196 TGTTAAGTTAT
1 TATTAATTTAT
* * *
1255207 CACTAATTTAC
1 TATTAATTTAT
*
1255218 TATTAAATTAT
1 TATTAATTTAT
*
1255229 CATTAATTTAT
1 TATTAATTTAT
*
1255240 TATTAAGTTAT
1 TATTAATTTAT
1255251 TA
1 TA
1255253 ATGATTCATA
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (11 bp):
TATTAATTTAT
Found at i:1257284 original size:125 final size:124
Alignment explanation
Indices: 1257124--1257607 Score: 422
Period size: 125 Copynumber: 3.9 Consensus size: 124
1257114 TTGTTTTGAG
* * *
1257124 GGATTATTGAAGGCATTTTTT-ACAAGAAATACCTTGAATAACCCCATTCAATTTTTTGTAAGAG
1 GGATTATT-AAAGCATTTTTTGTCAA-AAATGCCTTGAATAACCCCATTCAATTTTTTGTAAGAG
* * *
1257188 ATTATTCAAGGTATTTTCTGGCAAAAAACACATTGAATAATCCCTCTGAAATAATAGGAGA
64 ATTATTCAAGGTATTTTCTGGCAAAAAACACATTAAATAATCCCTCCGAAACAATAGGAGA
* * * * * *
1257249 AGATTATTAAAAGCATTTTTTGTCAGAAACGCCTTGAATAACCCTATTCAATTTTTTCTTAGTA-
1 GGATTATT-AAAGCATTTTTTGTCAAAAATGCCTTGAATAACCCCATTCAATTTTTTGTAAG-AG
* * * * * *
1257313 ATTATTCAA-GTAATTTTTTGGTAAAAAATA-ACTTCAATAATCCCCCCAAAACAAT-GGAAGA
64 ATTATTCAAGGT-ATTTTCTGGCAAAAAACACA-TTAAATAATCCCTCCGAAACAATAGG-AGA
* * * * * * ** *
1257374 GGATTATTGAAGGAGTTTTTGGCTAAAAATACATTGAATAATACCATTCAATTTTTTGTAAGGGA
1 GGATTATTAAAGCATTTTTTGTC-AAAAATGCCTTGAATAACCCCATTCAATTTTTTGTAAGAGA
* * * * * * *
1257439 TTATTCAAGATGTTTTCTGGTAAAAAACTCTTTAAATAATCCCTCCGAAACACTAGAAGA
65 TTATTCAAGGTATTTTCTGGCAAAAAACACATTAAATAATCCCTCCGAAACAATAGGAGA
** * * * * *
1257499 GGATTATTGATGGTATTTTTTTGTCAAAAATGCTTTGAATAATCCTATTCAATTTTTTGTAAGGG
1 GGATTATT-AAAGCA-TTTTTTGTCAAAAATGCCTTGAATAACCCCATTCAATTTTTTGTAAGAG
* * * *
1257564 ATTATTCAATGTATTTTTTGG-ACAAAAACGCCTTAAATAATCCC
64 ATTATTCAAGGTATTTTCTGGCA-AAAAACACATTAAATAATCCC
1257608 CTCAAAACAA
Statistics
Matches: 286, Mismatches: 60, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
124 16 0.06
125 184 0.64
126 79 0.28
127 7 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (124 bp):
GGATTATTAAAGCATTTTTTGTCAAAAATGCCTTGAATAACCCCATTCAATTTTTTGTAAGAGAT
TATTCAAGGTATTTTCTGGCAAAAAACACATTAAATAATCCCTCCGAAACAATAGGAGA
Found at i:1258934 original size:48 final size:48
Alignment explanation
Indices: 1258862--1258961 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
1258852 TCCAGTTACA
* *
1258862 AAATTCTTTAACCTCATCTTGACCAATGTAAGAAATTGATGGTTGATT
1 AAATTCTTTAACCACATCTCGACCAATGTAAGAAATTGATGGTTGATT
1258910 AAATTCTTTAACCACATCTCGACCAATGTAAGAAATTGATGGTTGATT
1 AAATTCTTTAACCACATCTCGACCAATGTAAGAAATTGATGGTTGATT
1258958 AAAT
1 AAAT
1258962 AACGCAGCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (48 bp):
AAATTCTTTAACCACATCTCGACCAATGTAAGAAATTGATGGTTGATT
Done.