Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1338242 original size:19 final size:20
Alignment explanation
Indices: 1338207--1338245 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1338197 CTACCTTAAT
1338207 AATTTATTTAATTAGTACAA
1 AATTTATTTAATTAGTACAA
*
1338227 AATTTA-TTATTTAGTACAA
1 AATTTATTTAATTAGTACAA
1338246 GTATGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
AATTTATTTAATTAGTACAA
Found at i:1338522 original size:21 final size:21
Alignment explanation
Indices: 1338496--1338535 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1338486 TGAGTTGTTG
*
1338496 AAAAAATATAAAG-GCTTAATA
1 AAAAAAAAT-AAGTGCTTAATA
1338517 AAAAAAAATAAGTGCTTAA
1 AAAAAAAATAAGTGCTTAA
1338536 ACTTTACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (21 bp):
AAAAAAAATAAGTGCTTAATA
Found at i:1339188 original size:17 final size:16
Alignment explanation
Indices: 1339162--1339204 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1339152 AACATTTTAG
*
1339162 TGTTCTATTTTATGGGT
1 TGTTCGATTTTAT-GGT
1339179 TGTTCGATTTTATGGT
1 TGTTCGATTTTATGGT
*
1339195 TATTCGATTT
1 TGTTCGATTT
1339205 GTGGGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGATTTTATGGT
Found at i:1339726 original size:44 final size:43
Alignment explanation
Indices: 1339668--1339774 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 43
1339658 TAGATGTGTT
* * * *
1339668 AAGACTAAGAAAAATGTTTGGTTATGTGTTTTGTTTGATATGTG
1 AAGAC-AAGTAAAATGTTTGCTTATGTATTATGTTTGATATGTG
* *
1339712 AAGACCAATTAAAATGTTTACTTATGTATTATGTTTGATATGTG
1 AAGA-CAAGTAAAATGTTTGCTTATGTATTATGTTTGATATGTG
1339756 AAGACAAGTAAAATGTTTG
1 AAGACAAGTAAAATGTTTG
1339775 ATATCTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 13 0.24
44 40 0.74
45 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (43 bp):
AAGACAAGTAAAATGTTTGCTTATGTATTATGTTTGATATGTG
Found at i:1340271 original size:21 final size:21
Alignment explanation
Indices: 1340247--1340305 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1340237 CGGACTGTTA
*
1340247 AGAATATGTTGCAGTAGGGGC
1 AGAATATGTTGCAGCAGGGGC
1340268 AGAATATGTTGCAGCAGGGGC
1 AGAATATGTTGCAGCAGGGGC
*
1340289 AGAAAATGTTGCAGCAG
1 AGAATATGTTGCAGCAG
1340306 AATGAGAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.36, T:0.20
Consensus pattern (21 bp):
AGAATATGTTGCAGCAGGGGC
Found at i:1348244 original size:126 final size:126
Alignment explanation
Indices: 1348019--1348266 Score: 496
Period size: 126 Copynumber: 2.0 Consensus size: 126
1348009 TCATCTTTTC
1348019 TTCCTCCTCTCCACCGTGACTTCATAGCTAAGGTAGGAATCTTTAAGTTAGTTATTTCTTGTAAT
1 TTCCTCCTCTCCACCGTGACTTCATAGCTAAGGTAGGAATCTTTAAGTTAGTTATTTCTTGTAAT
1348084 TTTTCATTAGTTTTGATTCTTGGGGTATTAGAGAAGTTTGAGAACTTAAAGAGAAGTCTTT
66 TTTTCATTAGTTTTGATTCTTGGGGTATTAGAGAAGTTTGAGAACTTAAAGAGAAGTCTTT
1348145 TTCCTCCTCTCCACCGTGACTTCATAGCTAAGGTAGGAATCTTTAAGTTAGTTATTTCTTGTAAT
1 TTCCTCCTCTCCACCGTGACTTCATAGCTAAGGTAGGAATCTTTAAGTTAGTTATTTCTTGTAAT
1348210 TTTTCATTAGTTTTGATTCTTGGGGTATTAGAGAAGTTTGAGAACTTAAAGAGAAGT
66 TTTTCATTAGTTTTGATTCTTGGGGTATTAGAGAAGTTTGAGAACTTAAAGAGAAGT
1348267 AGAAATTAAG
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (126 bp):
TTCCTCCTCTCCACCGTGACTTCATAGCTAAGGTAGGAATCTTTAAGTTAGTTATTTCTTGTAAT
TTTTCATTAGTTTTGATTCTTGGGGTATTAGAGAAGTTTGAGAACTTAAAGAGAAGTCTTT
Found at i:1349427 original size:24 final size:25
Alignment explanation
Indices: 1349386--1349433 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1349376 CAATTCTATA
*
1349386 TGGTTATTCGGGACAAATTTCTACG
1 TGGTCATTCGGGACAAATTTCTACG
1349411 TGGTCATTCGGGA-AAATTTCTAC
1 TGGTCATTCGGGACAAATTTCTAC
1349434 ATGGCACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (25 bp):
TGGTCATTCGGGACAAATTTCTACG
Found at i:1355371 original size:35 final size:35
Alignment explanation
Indices: 1355331--1355409 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
1355321 TGGTTAAGGA
** *
1355331 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATGAAATGGCAATAGAAG
*
1355366 ATGGTGATGATATAGGCGTGAAATGGCAATAGAAG
1 ATGGTGATGATATAGGCATGAAATGGCAATAGAAG
1355401 ATGGTGATG
1 ATGGTGATG
1355410 GACATATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.37, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCATGAAATGGCAATAGAAG
Found at i:1355798 original size:19 final size:20
Alignment explanation
Indices: 1355751--1355801 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1355741 GAAACCCCTT
**
1355751 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1355771 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1355790 TGAAGATACATG
1 TGAAAATACATG
1355802 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1357988 original size:36 final size:36
Alignment explanation
Indices: 1357942--1358013 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1357932 CAACTTCAAA
* *
1357942 AAGCTTTTCTTTATTTGAATTTTCCTCTAAACGTTC
1 AAGCTTTTCTTCATTTGAATTTTCCTCCAAACGTTC
*
1357978 AAGCTTTTCTTCATTTGAATTTTCCTCCAAATGTTC
1 AAGCTTTTCTTCATTTGAATTTTCCTCCAAACGTTC
1358014 TCCTTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.49
Consensus pattern (36 bp):
AAGCTTTTCTTCATTTGAATTTTCCTCCAAACGTTC
Found at i:1359532 original size:35 final size:35
Alignment explanation
Indices: 1359492--1359570 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
1359482 TAGTTAAGGA
*
1359492 ATGGTGATGATATAGGCGTGAAATAGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATAGCGATGGAAG
*
1359527 ATGGTGATGATATAGGCGTGAAATGGCGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATAGCGATGGAAG
1359562 ATGGTGATG
1 ATGGTGATG
1359571 GACAGATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.32, C:0.04, G:0.39, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATAGCGATGGAAG
Found at i:1359953 original size:19 final size:19
Alignment explanation
Indices: 1359913--1359961 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1359903 GAAACCCCTT
* **
1359913 TGAAAATGCATGATTTTTA
1 TGAAAATACATGATTTAAA
1359932 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
1359951 TGAAGATACAT
1 TGAAAATACAT
1359962 ACTCTTGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:1362650 original size:15 final size:17
Alignment explanation
Indices: 1362619--1362651 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1362609 ACGGAAATGT
1362619 TCTACAATCTGCTGAGC
1 TCTACAATCTGCTGAGC
1362636 TCTACAAT-T-CTGAGC
1 TCTACAATCTGCTGAGC
1362651 T
1 T
1362652 TGGTACTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (17 bp):
TCTACAATCTGCTGAGC
Found at i:1369384 original size:21 final size:22
Alignment explanation
Indices: 1369360--1369403 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1369350 TAATTCAAAT
*
1369360 AAATTAAATTATA-AGATAAAA
1 AAATAAAATTATATAGATAAAA
*
1369381 AAATAAAATTATATATATAAAA
1 AAATAAAATTATATAGATAAAA
1369403 A
1 A
1369404 TACTAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAAAATTATATAGATAAAA
Found at i:1369437 original size:19 final size:19
Alignment explanation
Indices: 1369413--1369473 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1369403 ATACTAATTG
*
1369413 TTTTGTAATTTTTCTGATT
1 TTTTGTAATTTTTATGATT
*
1369432 TTTTGT-ATTTTTTTGTATT
1 TTTTGTAATTTTTATG-ATT
*
1369451 TTTATG-ATTTTTTATGATT
1 TTT-TGTAATTTTTATGATT
1369470 TTTT
1 TTTT
1369474 TTTAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.25
19 18 0.50
20 9 0.25
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTGTAATTTTTATGATT
Found at i:1369443 original size:10 final size:9
Alignment explanation
Indices: 1369420--1369474 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
1369410 TTGTTTTGTA
*
1369420 ATTTTTCTG
1 ATTTTTTTG
1369429 A-TTTTTTG
1 ATTTTTTTG
1369437 TATTTTTTTG
1 -ATTTTTTTG
*
1369447 TATTTTTATG
1 -ATTTTTTTG
1369457 ATTTTTTATG
1 ATTTTTT-TG
1369467 ATTTTTTT
1 ATTTTTTT
1369475 TTAAATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.15
9 9 0.22
10 25 0.62
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.75
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:1374138 original size:17 final size:17
Alignment explanation
Indices: 1374116--1374150 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1374106 TTCATTAATA
*
1374116 TTTCATTTTTATTCCTT
1 TTTCATCTTTATTCCTT
*
1374133 TTTCATCTTTATTTCTT
1 TTTCATCTTTATTCCTT
1374150 T
1 T
1374151 ATTTTCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCATCTTTATTCCTT
Found at i:1389482 original size:33 final size:35
Alignment explanation
Indices: 1389440--1389506 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
1389430 TCATTTAGGG
1389440 GGGAATCGATA-CCCCC-AGGGGGAATCTGTTCAC
1 GGGAATCGATACCCCCCTAGGGGGAATCTGTTCAC
*
1389473 GGGAATCGATACCCCCCCTGGGGGGAATCTGTTC
1 GGGAATCGATA-CCCCCCTAGGGGGAATCTGTTC
1389507 CCCCTGCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 11 0.37
35 5 0.17
36 14 0.47
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.19
Consensus pattern (35 bp):
GGGAATCGATACCCCCCTAGGGGGAATCTGTTCAC
Found at i:1393306 original size:31 final size:31
Alignment explanation
Indices: 1393268--1393421 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
1393258 CCCGAAGGAC
* *
1393268 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAT
1393299 CAGTCCATATGTCCCGAAGAACATAGGTAAAT
1 CAGTCCATATGTCCCGAAGAACATAGGT-AAT
*
1393331 -AGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
1393361 CAG-CTCATATGTCCCGAAGAACATAGGTAAG
1 CAGTC-CATATGTCCCGAAGAACATAGGTAAT
* *
1393392 CAATCCATATGTCCCGAATAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1393422 ACCATCGACT
Statistics
Matches: 112, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
30 3 0.03
31 104 0.93
32 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:1397313 original size:29 final size:29
Alignment explanation
Indices: 1397274--1397358 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
1397264 TTATATGGCC
*
1397274 CAATTATTTTTAATACTTATTATTAAAGGTT
1 CAATT-TTTTTAATAATTATTATTAAA-GTT
** * *
1397305 TTATTTTTTTAAT-GTTTTTATTATAAGTT
1 CAATTTTTTTAATAATTATTATTA-AAGTT
1397334 CAATTTTTTTAATAATTATTATTAA
1 CAATTTTTTTAATAATTATTATTAA
1397359 GTGTTACTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 23 0.52
30 18 0.41
31 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.59
Consensus pattern (29 bp):
CAATTTTTTTAATAATTATTATTAAAGTT
Found at i:1397425 original size:99 final size:98
Alignment explanation
Indices: 1397307--1397521 Score: 313
Period size: 99 Copynumber: 2.2 Consensus size: 98
1397297 TAAAGGTTTT
* * * * * *
1397307 ATTTTTTTAATGTTTTTATTATAAGTTCAATTTTTTTAATAATTATTATTAAGTGTTACTCTTAT
1 ATTTTTTCAATATTTTTATTATAAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTAT
1397372 AATTTATTTTTTCTAATATTTAATAAATACCTA
66 AATTTATTTTTTCTAATATTTAATAAATACCTA
** *
1397405 ATTTTTTCAATATTTATTATTATGGGTTCAAATTTTCTAATAATTATTATTAGGGGCTACTCTTA
1 ATTTTTTCAATATTT-TTATTATAAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTA
**
1397470 TAATTTATTTTTTCTAATATTTAATAAATGTCTA
65 TAATTTATTTTTTCTAATATTTAATAAATACCTA
1397504 ATTTTTTCCAATATTTTT
1 ATTTTTT-CAATATTTTT
1397522 TTTTCTAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
98 13 0.12
99 83 0.80
100 8 0.08
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (98 bp):
ATTTTTTCAATATTTTTATTATAAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTAT
AATTTATTTTTTCTAATATTTAATAAATACCTA
Found at i:1403919 original size:16 final size:16
Alignment explanation
Indices: 1403900--1403942 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1403890 TTTCGGGTTG
1403900 GGTTACTTTCGGTTCA
1 GGTTACTTTCGGTTCA
* *
1403916 GGTTAATTTCTGTTCA
1 GGTTACTTTCGGTTCA
*
1403932 AGTTACTTTCG
1 GGTTACTTTCG
1403943 AGTCGGGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (16 bp):
GGTTACTTTCGGTTCA
Found at i:1403942 original size:32 final size:30
Alignment explanation
Indices: 1403901--1404040 Score: 102
Period size: 32 Copynumber: 4.4 Consensus size: 30
1403891 TTCGGGTTGG
* *
1403901 GTTACTTTCGGTTCAGGTTAATTTCTGTTCAA
1 GTTACTTTCGGTTCGGGTTAAATTC-GTTC-A
*
1403933 GTTACTTTCGAG-TCGGGTTAAATTCAGTTCGG
1 GTTACTTTCG-GTTCGGGTTAAATTC-GTTC-A
* *
1403965 GTTGCTTTCGGATCGGGTTAAAATTCGATTCA
1 GTTACTTTCGGTTCGGGTT-AAATTCG-TTCA
* * * *
1403997 GTTTCTTTCGGTTTGGGTTAATTTGGTTCTA
1 GTTACTTTCGGTTCGGGTTAAATTCGTTC-A
**
1404028 GTTGTTTTCGGTT
1 GTTACTTTCGGTT
1404041 TGGATTAATT
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
30 3 0.03
31 18 0.20
32 58 0.65
33 10 0.11
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.46
Consensus pattern (30 bp):
GTTACTTTCGGTTCGGGTTAAATTCGTTCA
Found at i:1416305 original size:31 final size:31
Alignment explanation
Indices: 1416270--1416345 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
1416260 TTAACTCGGG
** *
1416270 GTGACTACATCTTAATTACGTAAAAATAAAA
1 GTGACTACATCTTAATTAAATAAAAACAAAA
* *
1416301 GTGACCACATTTTAATTAAATAAAAACAAAA
1 GTGACTACATCTTAATTAAATAAAAACAAAA
*
1416332 GTGACTATATCTTA
1 GTGACTACATCTTA
1416346 TATTTTTTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.30
Consensus pattern (31 bp):
GTGACTACATCTTAATTAAATAAAAACAAAA
Found at i:1424860 original size:20 final size:19
Alignment explanation
Indices: 1424815--1424868 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
1424805 AAAAAGCCTA
*
1424815 AAAAGTTTCGATACT-TCT
1 AAAAGTTTCGAAACTATCT
*
1424833 -ATAGTTTCGAAACTATCT
1 AAAAGTTTCGAAACTATCT
1424851 CAAAAGTTTCGAAACTAT
1 -AAAAGTTTCGAAACTAT
1424869 GGGAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.40
18 3 0.10
20 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (19 bp):
AAAAGTTTCGAAACTATCT
Found at i:1427710 original size:13 final size:13
Alignment explanation
Indices: 1427692--1427740 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1427682 TTGACCGGTT
*
1427692 TTGACCTGACCCG
1 TTGACCCGACCCG
1427705 TTGACCCGACCTGATCG
1 TTGACCCGACC----CG
1427722 TTGACCCGACCCG
1 TTGACCCGACCCG
1427735 TTGACC
1 TTGACC
1427741 GTTGATCAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 18 0.58
17 13 0.42
ACGTcount: A:0.16, C:0.39, G:0.22, T:0.22
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:1427717 original size:18 final size:17
Alignment explanation
Indices: 1427694--1427732 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1427684 GACCGGTTTT
1427694 GACCTGACCCGTTGACCC
1 GACCTGA-CCGTTGACCC
*
1427712 GACCTGATCGTTGACCC
1 GACCTGACCGTTGACCC
1427729 GACC
1 GACC
1427733 CGTTGACCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (17 bp):
GACCTGACCGTTGACCC
Found at i:1427788 original size:29 final size:29
Alignment explanation
Indices: 1427749--1427822 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
1427739 CCGTTGATCA
*
1427749 GGTGCTATTTTAGTAATTATTTCTAACAG
1 GGTGCTATTTTAGTAATTATTTCTAAAAG
* *
1427778 GGTGCTATTTTTGTAATTATTTTTAAAAG
1 GGTGCTATTTTAGTAATTATTTCTAAAAG
*
1427807 GGTGCTATTTTCGTAA
1 GGTGCTATTTTAGTAA
1427823 AATGGTTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTATTTCTAAAAG
Found at i:1428552 original size:24 final size:24
Alignment explanation
Indices: 1428524--1428596 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1428514 ATTTTTGACG
1428524 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
1428548 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* *
1428572 GGATTTTGATCTGCTACTTGACCT
1 GGATTTTGATATGATACTTGACCT
1428596 G
1 G
1428597 AATTATGCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:1428620 original size:2 final size:2
Alignment explanation
Indices: 1428613--1428649 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1428603 GCTTTAAATT
1428613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1428650 CCGTTATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1440872 original size:65 final size:65
Alignment explanation
Indices: 1440738--1440898 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
1440728 GTGCACTAAG
* *
1440738 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAACCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCT
* * * *
1440802 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAACCACAGTGCATCGATGCATGGC
1440865 T
65 T
* *
1440866 AAGTGCATCGATACATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
1440899 CAATTTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 29 0.34
65 53 0.62
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCT
Found at i:1441406 original size:2 final size:2
Alignment explanation
Indices: 1441399--1441475 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
1441389 TAGCCAATTG
1441399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1441440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1441476 GCTTAAGCTG
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1449529 original size:18 final size:17
Alignment explanation
Indices: 1449475--1449523 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1449465 TTGGACCCTT
* *
1449475 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1449493 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1449511 AGTGCATTCGATG
1 AGTGCA-TCGATG
1449524 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1450421 original size:5 final size:5
Alignment explanation
Indices: 1450389--1450725 Score: 145
Period size: 5 Copynumber: 68.8 Consensus size: 5
1450379 GACCTAAAAA
* *
1450389 ATAAT ATAA- ATTAAT AT-AT AAGAAT ATAAT ATATGAT ATAAT AATACT
1 ATAAT ATAAT A-TAAT ATAAT -ATAAT ATAAT ATA--AT ATAAT -ATAAT
* *
1450437 ATAAT ATAAT AATAAT A-AAT A-CAT ATACT ATAAT AT-AT A-ATAT ATAAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
* * *
1450485 AT-A- ATACT ATAAT AT-AT ATATAT ATAAT AT-AT AT-AT ATTAT ATTAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
*
1450531 ATACT AT-AT A-AAT ACT-AT ATAAT ATGCAAT ATAA- ATAAT ATAAAT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT AT--AAT ATAAT ATAAT AT-AAT
* * *
1450576 ATTAT ATAAT AT-AT ACT-AT ATAAT ATAAC ATAAT AT-AT AATACT AT-AT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
* * *
1450624 ACT-AT ATAACT AT--T ATAAT AT-AT TTTAT ATAAT ATACCAT GCT-AT
1 A-TAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT -ATAAT
* *
1450669 ATAAT AT-AT AGT-AT ATAAA ATAAT ATAAT AT-AT AT-AT ATAAT ATAGT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1450716 ATATAT ATAA
1 ATA-AT ATAA
1450726 AAAGAAATCC
Statistics
Matches: 261, Mismatches: 28, Indels: 86
0.70 0.07 0.23
Matches are distributed among these distances:
3 5 0.02
4 61 0.23
5 151 0.58
6 31 0.12
7 12 0.05
8 1 0.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:1450422 original size:2 final size:2
Alignment explanation
Indices: 1450412--1450724 Score: 154
Period size: 2 Copynumber: 166.5 Consensus size: 2
1450402 ATATATAAGA
1450412 AT AT A- AT AT AT GAT AT A- AT A- AT ACT AT A- AT AT A- AT A- AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
1450450 A- AT AA AT AC AT AT ACT AT A- AT AT AT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
1450488 AT ACT AT A- AT AT AT AT AT AT AT A- AT AT AT AT AT AT -T AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** *
1450528 -T AT AT ACT AT AT AA AT ACT AT AT A- AT AT GC A- AT AT AA AT A-
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
1450568 AT AT AA AT AT -T AT AT A- AT AT AT ACT AT AT A- AT AT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
1450607 A- AT AT AT A- AT ACT AT AT ACT AT AT A- ACT AT -T AT A- AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT
* * *
1450645 AT -T TT AT AT A- AT AT ACC AT GCT AT AT A- AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT A-T AT AT
*
1450685 A- AA AT A- AT AT A- AT AT AT AT AT AT A- AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1450724 A
1 A
1450725 AAAAGAAATC
Statistics
Matches: 243, Mismatches: 20, Indels: 96
0.68 0.06 0.27
Matches are distributed among these distances:
1 34 0.14
2 184 0.76
3 25 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1450427 original size:7 final size:7
Alignment explanation
Indices: 1450392--1450725 Score: 201
Period size: 7 Copynumber: 45.9 Consensus size: 7
1450382 CTAAAAAATA
1450392 ATATAA-
1 ATATAAT
1450398 AT-TAAT
1 ATATAAT
*
1450404 ATATAAGA
1 ATATAA-T
1450412 ATATAAT
1 ATATAAT
*
1450419 ATATGAT
1 ATATAAT
1450426 ATAATAAT
1 AT-ATAAT
1450434 ACTATAAT
1 A-TATAAT
1450442 ATAATAAT
1 AT-ATAAT
1450450 A-ATAA-
1 ATATAAT
*
1450455 ATACATAT
1 ATATA-AT
1450463 ACTATAAT
1 A-TATAAT
1450471 ATATAAT
1 ATATAAT
1450478 ATAT-A-
1 ATATAAT
1450483 ATATAAT
1 ATATAAT
1450490 ACTATAAT
1 A-TATAAT
1450498 ATATATAT
1 ATATA-AT
1450506 ATATAAT
1 ATATAAT
1450513 ATAT-AT
1 ATATAAT
1450519 ATAT--T
1 ATATAAT
*
1450524 ATATTAT
1 ATATAAT
1450531 ATACTATAT
1 ATA-TA-AT
* *
1450540 AAATACT
1 ATATAAT
1450547 ATATAAT
1 ATATAAT
**
1450554 ATGCAAT
1 ATATAAT
1450561 ATA-AAT
1 ATATAAT
1450567 AATATAA-
1 -ATATAAT
1450574 ATAT--T
1 ATATAAT
1450579 ATATAAT
1 ATATAAT
*
1450586 ATATACT
1 ATATAAT
1450593 ATATAAT
1 ATATAAT
1450600 ATAACATAAT
1 AT---ATAAT
1450610 ATATAAT
1 ATATAAT
1450617 ACTATATACT
1 A-TATA-A-T
1450627 ATATAACT
1 ATATAA-T
1450635 ATTATAAT
1 A-TATAAT
**
1450643 ATATTTT
1 ATATAAT
1450650 ATATAAT
1 ATATAAT
**
1450657 ATACCATGCT
1 AT---ATAAT
1450667 ATATAAT
1 ATATAAT
1450674 ATATAGTAT
1 ATATA--AT
*
1450683 ATAAAAT
1 ATATAAT
1450690 AATATAAT
1 -ATATAAT
1450698 ATAT-AT
1 ATATAAT
1450704 ATATAAT
1 ATATAAT
1450711 ATAGTATAT
1 ATA-TA-AT
1450720 ATATAA
1 ATATAA
1450726 AAAGAAATCC
Statistics
Matches: 263, Mismatches: 26, Indels: 77
0.72 0.07 0.21
Matches are distributed among these distances:
5 17 0.06
6 31 0.12
7 106 0.40
8 66 0.25
9 29 0.11
10 14 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:1464813 original size:21 final size:22
Alignment explanation
Indices: 1464767--1464813 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1464757 TTATGTTTCT
*
1464767 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
1464789 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
1464809 TTGTT
1 TTGTT
1464814 GGTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:1472310 original size:150 final size:150
Alignment explanation
Indices: 1472039--1472337 Score: 559
Period size: 150 Copynumber: 2.0 Consensus size: 150
1472029 AACTCAATTA
1472039 GGGGAAAGACCGGCTGCAAACCAATGCCTCCACCAGGGTGATGGTCGACCTGATGTTTTGAGCAA
1 GGGGAAAGACCGGCTGCAAACCAATGCCTCCACCAGGGTGATGGTCGACCTGATGTTTTGAGCAA
1472104 CAGGCTACCAAGAAAAAGGCAGATATTAGGAAAGTATTGCTTCCTCTTTTCGTTTTTTCCCTT-A
66 CAGGCTACCAAGAAAAAGGCAGATATTAGGAAAGTATTGCTTCCTCTTTTCGTTTTTTCCCTTAA
1472168 AATAACAGA-TAGTGTATCT
131 AATAACAGATTAGTGTATCT
1472187 GGGGAAAGACCGGCTGCAAACCAATGCCCTCCACCAGGGTGATGGTCGACCTTGATGTTTTGAGC
1 GGGGAAAGACCGGCTGCAAACCAATG-CCTCCACCAGGGTGATGGTCGACC-TGATGTTTTGAGC
1472252 AACAGGCTACCAAGAAAAAGGCAGATATTAGGAAAGTA-TGCTTCCTCTTTTCGTTTTTTCCCTT
64 AACAGGCTACCAAGAAAAAGGCAGATATTAGGAAAGTATTGCTTCCTCTTTTCGTTTTTTCCCTT
1472316 AAAATAACAGATTAGTGTATCT
129 AAAATAACAGATTAGTGTATCT
1472338 TTTTGAAAAG
Statistics
Matches: 147, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
148 26 0.18
149 50 0.34
150 61 0.41
151 10 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (150 bp):
GGGGAAAGACCGGCTGCAAACCAATGCCTCCACCAGGGTGATGGTCGACCTGATGTTTTGAGCAA
CAGGCTACCAAGAAAAAGGCAGATATTAGGAAAGTATTGCTTCCTCTTTTCGTTTTTTCCCTTAA
AATAACAGATTAGTGTATCT
Found at i:1477276 original size:19 final size:19
Alignment explanation
Indices: 1477239--1477277 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1477229 TTGTTATTGT
*
1477239 TAATAATATATTAATAATA
1 TAATAATATATTAACAATA
1477258 TAATAATAT-TATAACAATA
1 TAATAATATAT-TAACAATA
1477277 T
1 T
1477278 TATTAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATAATATATTAACAATA
Found at i:1483859 original size:4 final size:4
Alignment explanation
Indices: 1483850--1483892 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
1483840 TGGCTTCTCC
1483850 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1483893 TGTGAATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1486853 original size:17 final size:17
Alignment explanation
Indices: 1486819--1486854 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1486809 ACAACCTGAC
*
1486819 CCGACCCGTTAACTCGA
1 CCGACCCGTTAACCCGA
*
1486836 CCGACCCGTTGACCCGA
1 CCGACCCGTTAACCCGA
1486853 CC
1 CC
1486855 CGTTAATCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.14
Consensus pattern (17 bp):
CCGACCCGTTAACCCGA
Found at i:1491888 original size:13 final size:13
Alignment explanation
Indices: 1491884--1491931 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
1491874 CCGTTGACCC
1491884 GACCCGACCCGTT
1 GACCCGACCCGTT
1491897 GACCCGACCCGATATGTT
1 GACCCGACCC-----GTT
1491915 GACCCGACCCGTT
1 GACCCGACCCGTT
1491928 GACC
1 GACC
1491932 GTTGACCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 17 0.57
18 13 0.43
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1491893 original size:18 final size:18
Alignment explanation
Indices: 1491870--1491925 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
1491860 ACAACCTGAT
1491870 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
1491888 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
***
1491906 CGATATGTTGACCCGACC
1 CGACCCGTTGACCCGACC
1491924 CG
1 CG
1491926 TTGACCGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:1496369 original size:160 final size:155
Alignment explanation
Indices: 1496198--1496503 Score: 526
Period size: 160 Copynumber: 1.9 Consensus size: 155
1496188 TACTGTAATG
1496198 AAAAATATCC-AGATATGTTCGCAAAGTTCCATGATTCCTACAAATATAACTAATTCAAGTTATA
1 AAAAATATCCAAGATATGTTCGCAAAGTTCCATGATTCCTAC-AATATAACT-ATTCAAGTTATA
1496262 GTCCAATTAATTGTTTT-ATAATTTTGAATAAATTTATTGAAAACAATTTGAGATTCTAAATTAA
64 GTCCAATTAATTGTTTTAAT-ATTTTGAATAAATTTATTG--AACAATTTGAGATTCTAAATTAA
1496326 TATAAGTCACGTATTTTCAATTGAAAAAAATC
126 TA-AAGTCACGTA-TTTCAATTGAAAAAAATC
1496358 AAAAATATCCAGAGATATGTTCGCAAAGTTCCATGATTCCTACAATATAACTATTCAAGTTATAG
1 AAAAATATCCA-AGATATGTTCGCAAAGTTCCATGATTCCTACAATATAACTATTCAAGTTATAG
1496423 TCCAATTAATTGTTTTAATATTTTGAATAAATTTATTGAACAATTTGAGATTCTAAATTAATAAA
65 TCCAATTAATTGTTTTAATATTTTGAATAAATTTATTGAACAATTTGAGATTCTAAATTAATAAA
1496488 GTCACGTATTTCAATT
130 GTCACGTATTTCAATT
1496504 AAGCACACAA
Statistics
Matches: 143, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
156 8 0.06
157 10 0.07
158 25 0.17
160 58 0.41
161 11 0.08
162 31 0.22
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (155 bp):
AAAAATATCCAAGATATGTTCGCAAAGTTCCATGATTCCTACAATATAACTATTCAAGTTATAGT
CCAATTAATTGTTTTAATATTTTGAATAAATTTATTGAACAATTTGAGATTCTAAATTAATAAAG
TCACGTATTTCAATTGAAAAAAATC
Found at i:1496845 original size:21 final size:21
Alignment explanation
Indices: 1496817--1496858 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1496807 ATAGTTTACC
1496817 CTTTA-TTTTAAATAATTTAT
1 CTTTATTTTTAAATAATTTAT
*
1496837 CTTTAATTTTTAACTAATTTAT
1 CTTT-ATTTTTAAATAATTTAT
1496859 AGTTATACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 1 0.05
22 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
CTTTATTTTTAAATAATTTAT
Found at i:1498579 original size:38 final size:41
Alignment explanation
Indices: 1498528--1498608 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 41
1498518 ATGAGCATGA
1498528 AGGTACGCATTTTCATAAAT-ACACACTGTAG-AGC-TTAT
1 AGGTACGCATTTTCATAAATAACACACTGTAGAAGCTTTAT
1498566 AGGTACGCATTTTCATAAATAACACACTGTAGAAGCTTTAT
1 AGGTACGCATTTTCATAAATAACACACTGTAGAAGCTTTAT
1498607 AG
1 AG
1498609 AAATCTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 20 0.50
39 11 0.28
40 3 0.08
41 6 0.15
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (41 bp):
AGGTACGCATTTTCATAAATAACACACTGTAGAAGCTTTAT
Found at i:1501909 original size:188 final size:181
Alignment explanation
Indices: 1501556--1501925 Score: 677
Period size: 188 Copynumber: 2.0 Consensus size: 181
1501546 GTTTGCTAGC
1501556 TTCATGATTCACCATAGTTACACAAGTTGACTATGAGCTTGTGTCTATCATAGGAAGCTCTCGAT
1 TTCATGATTCACCATAGTTACACAAGTTGACTATGAGCTTGTGTCTATCATAGGAAGCTCTCGAT
1501621 GATTCATATTTATTTGCTGTTATATGTTGATGACATGTTGATTGCTTCTAAAGAATATTGGAAAT
66 GATTCATATTTATTTGCTGTTATATGTTGATGACATGTTGATTGCTTCTAAAGAATATTGGAAAT
1501686 CAAAAATTTAAAGTCTCAGTTAAGTGGTGAGTTCGAGATGAAGGACCTGGG
131 CAAAAATTTAAAGTCTCAGTTAAGTGGTGAGTTCGAGATGAAGGACCTGGG
1501737 TTCATGATTCACCATAGTTACACAAGTTGTGACTATGATGCTTGTGTCTATCATAGGAAGCTCTC
1 TTCATGATTCACCATAGTTACACAAG-T-TGACTATGA-GCTTGTGTCTATCATAGGAAGCTCTC
1501802 AGATGATTCATACATTTATTTGCTGTTATATGTTGATGACATGTTGATTGCTTCTAAAGACATAT
63 -GATGATTCAT--ATTTATTTGCTGTTATATGTTGATGACATGTTGATTGCTTCTAAAGA-ATAT
1501867 TGGAAATCAAAAATTTAAAGTCTCAGTTAAGTGGTGAGTTCGAGATGAAGGACCTGGG
124 TGGAAATCAAAAATTTAAAGTCTCAGTTAAGTGGTGAGTTCGAGATGAAGGACCTGGG
1501925 T
1 T
1501926 ACTGCCAAGA
Statistics
Matches: 182, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
181 26 0.14
182 1 0.01
183 9 0.05
184 26 0.14
185 10 0.05
187 47 0.26
188 63 0.35
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (181 bp):
TTCATGATTCACCATAGTTACACAAGTTGACTATGAGCTTGTGTCTATCATAGGAAGCTCTCGAT
GATTCATATTTATTTGCTGTTATATGTTGATGACATGTTGATTGCTTCTAAAGAATATTGGAAAT
CAAAAATTTAAAGTCTCAGTTAAGTGGTGAGTTCGAGATGAAGGACCTGGG
Found at i:1503103 original size:16 final size:16
Alignment explanation
Indices: 1503063--1503106 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1503053 ACAAAAAAAC
*
1503063 TCAAGTAGA-AGAGTT
1 TCAAGTTGAGAGAGTT
*
1503078 TGAGAGTTGAGAGAGTT
1 TCA-AGTTGAGAGAGTT
1503095 TCAAGTTGAGAG
1 TCAAGTTGAGAG
1503107 TCGGGTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 8 0.33
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (16 bp):
TCAAGTTGAGAGAGTT
Found at i:1503436 original size:19 final size:17
Alignment explanation
Indices: 1503412--1503446 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1503402 ATTAGGGAAA
1503412 ATTATTTTCTTATAATTAT
1 ATTATTTT-TTA-AATTAT
1503431 ATTATTTTTTAAATTA
1 ATTATTTTTTAAATTA
1503447 GGTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTTTTTAAATTAT
Found at i:1504308 original size:19 final size:19
Alignment explanation
Indices: 1504284--1504355 Score: 135
Period size: 19 Copynumber: 3.8 Consensus size: 19
1504274 AGTGTACAGT
1504284 AGGGGAATCGATTCCTATA
1 AGGGGAATCGATTCCTATA
1504303 AGGGGAATCGATTCCTATA
1 AGGGGAATCGATTCCTATA
1504322 AGGGGAATCGATTCCTATA
1 AGGGGAATCGATTCCTATA
*
1504341 AGGGGAATCGGTTCC
1 AGGGGAATCGATTCC
1504356 CCTTAAGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (19 bp):
AGGGGAATCGATTCCTATA
Found at i:1505095 original size:40 final size:40
Alignment explanation
Indices: 1504970--1505079 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
1504960 ACCATAGTGC
* * *
1504970 TACATATAAGGTCGTGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1505010 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1505050 TACACATAAGGTTGTGCCCACCATGTACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
1505080 TTAGTGTCCT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1515405 original size:19 final size:20
Alignment explanation
Indices: 1515391--1515446 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1515381 TGAAACTTTT
1515391 CTAAAGTTTCAAAACTCTTA
1 CTAAAGTTTCAAAACTCTTA
* *
1515411 ATAAAAGTTTAAAAACTCTTA
1 CT-AAAGTTTCAAAACTCTTA
*
1515432 C-AAAGTTTCCAAACT
1 CTAAAGTTTCAAAACT
1515447 ATGAGCAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 17 0.57
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (20 bp):
CTAAAGTTTCAAAACTCTTA
Found at i:1517611 original size:23 final size:23
Alignment explanation
Indices: 1517585--1517644 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
1517575 GATCAAGCAC
*
1517585 TATAATATATTAGGTAGC-TCTTA
1 TATAATATAATAGGTAGCGT-TTA
*
1517608 TATAATGTAATAGGTAGCGTTTA
1 TATAATATAATAGGTAGCGTTTA
*
1517631 TATAATAAAATAGG
1 TATAATATAATAGG
1517645 CATTTAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (23 bp):
TATAATATAATAGGTAGCGTTTA
Found at i:1517660 original size:87 final size:87
Alignment explanation
Indices: 1517558--1517720 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
1517548 TTAGGTATAT
* * * *
1517558 CATTTAACCAAAAATATGATCAAGCACTATAATATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCAAAAATATGATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAAGT
1517623 AGCGTTTATATAATAAAATAGG
66 AGCGTTTATATAATAAAATAGG
* * * * *
1517645 CATTTAACCAGAAATATTATTAAGTACAATAGCATATTAGGTAGCGCTTATATAATGTAATAAGT
1 CATTTAACCAAAAATATGATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAAGT
1517710 AGCGTTTATAT
66 AGCGTTTATAT
1517721 TGACATATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCAAAAATATGATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAAGT
AGCGTTTATATAATAAAATAGG
Found at i:1518329 original size:182 final size:182
Alignment explanation
Indices: 1518012--1518733 Score: 1015
Period size: 182 Copynumber: 4.0 Consensus size: 182
1518002 CAATTTATAC
* * * *
1518012 GTATCGATACTTTATAGGCGCTATAATTTCTTTTCTTTCAAATTCCAAAAGTGTCGATACTTATA
1 GTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATA
* * *** *
1518077 TTAAAGTATCGACACTTTCAACATATCCGATAGTTCTTTATC-GATTTTGTCATTTTGAGACCGG
66 TTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGA-TTTGTCATTTTGAGACCGG
* **
1518141 TTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAA
130 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
* *
1518194 GTATCGACACTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTAT
1 GTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTAT
* *
1518258 ATTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTTGGGACCGA
65 ATTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTTGAGACCGG
* * *
1518323 TTTTGTCATATTTTTACATGTTATATTATTATGGATCGAT--ATTTTTTTTAA
130 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
* * * *
1518374 GTATCGACACTTTATAGGCGCTATAATTTC-TCTTCTTTTAAATTCCAAAAAATTTCGATATTTA
1 GTATCGACACTTTATAGGCGCTATAACTTCTTC-TCTTTTAAATTCC-AAAAGTGTCGATACTTA
* *** *
1518438 TATTAAATTATCGACACTTTTAACATATCCGGT-ATTTTTTACCGGTTTTGTCATTTTTGAGACC
64 TATTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCA-TTTTGAGACC
*
1518502 TGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
128 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
1518557 GTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATA
1 GTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATA
* * * * *
1518622 TTAAATTATCGACACTTTCAACATATCCGGTATCGTTTTATCGGTTTTGTCATTTCGAGACCGGT
66 TTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTTGAGACCGGT
* * *
1518687 TTTGTCATATTTTTACCTGTAATATTGATATGGAGCGATACATTTTT
131 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1518734 CATTTGTATC
Statistics
Matches: 479, Mismatches: 51, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
179 2 0.00
180 62 0.13
181 95 0.20
182 248 0.52
183 70 0.15
184 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
GTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATA
TTAAATTATCGACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTTGAGACCGGT
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
Found at i:1518524 original size:20 final size:19
Alignment explanation
Indices: 1518471--1518525 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
1518461 CATATCCGGT
*
1518471 ATTTTTTACCGGTTTTGTC
1 ATTTTTTACCTGTTTTGTC
*
1518490 ATTTTTGAGACCTGTTTTGTC
1 ATTTTT--TACCTGTTTTGTC
1518511 ATATTTTTACCTGTT
1 AT-TTTTTACCTGTT
1518526 ATATTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 13 0.43
22 4 0.13
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (19 bp):
ATTTTTTACCTGTTTTGTC
Found at i:1518527 original size:363 final size:362
Alignment explanation
Indices: 1518012--1518726 Score: 1121
Period size: 363 Copynumber: 2.0 Consensus size: 362
1518002 CAATTTATAC
* * *
1518012 GTATCGATACTTTATAGGCGCTATAATTTCTTTTCTTTCAAATTCCAAAAGTGTCGATACTTATA
1 GTATCGACACTTTATAGGCGCTATAATTTCTCTTCTTTCAAATTCCAAAAATGTCGATACTTATA
*
1518077 TTAAAGTATCGACACTTTCAACATATCCGATAGTTCTTTATCGATTTTGTCATTTTGAGACCGGT
66 TTAAAGTATCGACACTTTCAACATATCCGATAGTTCTTTACCGATTTTGTCATTTTGAGACCGGT
*
1518142 TTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTT
131 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTT
* *
1518207 TTAGGCGTTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCGA
196 ATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAATTATCGA
* *
1518271 CACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTTGGGACCGATTTTGTCATATTT
260 CACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTCGAGACCGATTTTGTCATATTT
* *
1518336 TTACATGTTATATT-ATTATGGATCGATATTTTTTTTAA
325 TTACATGTAATATTGA-TATGGAGCGATATTTTTTTTAA
* * *
1518374 GTATCGACACTTTATAGGCGCTATAATTTCTCTTCTTTTAAATTCCAAAAAATTTCGATATTTAT
1 GTATCGACACTTTATAGGCGCTATAATTTCTCTTCTTTCAAATTCC-AAAAATGTCGATACTTAT
* * * * * *
1518439 ATTAAATTATCGACACTTTTAACATATCCGGTA-TTTTTTACCGGTTTTGTCATTTTTGAGACCT
65 ATTAAAGTATCGACACTTTCAACATATCCGATAGTTCTTTACCGATTTTGTCA-TTTTGAGACCG
**
1518503 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
129 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACT
1518568 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
194 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
* * * * *
1518633 ACACTTTCAACATATCCGGTATCGTTTTATCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATT
259 ACACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTCGAGACCGATTTTGTCATATT
*
1518698 TTTACCTGTAATATTGATATGGAGCGATA
324 TTTACATGTAATATTGATATGGAGCGATA
1518727 CATTTTTCAT
Statistics
Matches: 321, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
362 59 0.18
363 259 0.81
364 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (362 bp):
GTATCGACACTTTATAGGCGCTATAATTTCTCTTCTTTCAAATTCCAAAAATGTCGATACTTATA
TTAAAGTATCGACACTTTCAACATATCCGATAGTTCTTTACCGATTTTGTCATTTTGAGACCGGT
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTT
ATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCGAC
ACTTTCAACATATCCGGTAACGCTTTACCGGATTTGTCATTTCGAGACCGATTTTGTCATATTTT
TACATGTAATATTGATATGGAGCGATATTTTTTTTAA
Found at i:1519596 original size:22 final size:22
Alignment explanation
Indices: 1519559--1519602 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1519549 TCATAATTTG
*
1519559 TTATTTATGTAATATTGTGATT
1 TTATTTATGTAATATTATGATT
**
1519581 TTATTTATGTTGTATTATGATT
1 TTATTTATGTAATATTATGATT
1519603 CGTTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (22 bp):
TTATTTATGTAATATTATGATT
Found at i:1521208 original size:14 final size:13
Alignment explanation
Indices: 1521189--1521239 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
1521179 AATAAATGAT
1521189 AAATAAAGTAAAA
1 AAATAAAGTAAAA
* *
1521202 CAAATAAAATAAAG
1 -AAATAAAGTAAAA
* *
1521216 AGATTAAG-AAAA
1 AAATAAAGTAAAA
1521228 AAATAAAGTAAA
1 AAATAAAGTAAA
1521240 TATAAAATGA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
12 9 0.32
13 8 0.29
14 11 0.39
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (13 bp):
AAATAAAGTAAAA
Found at i:1521427 original size:37 final size:36
Alignment explanation
Indices: 1521329--1521459 Score: 92
Period size: 37 Copynumber: 3.6 Consensus size: 36
1521319 ATGATAATAC
* * * *
1521329 AAATAAATAAATAAAACAAGTAAAAGAATATAAAAACAT
1 AAATAAATAAGTAAAATAA-TAAAA-AA-GTAAAATCAT
* *
1521368 AAA-ATATAAG-ATAAA-AAT-AAAAAG-AAAATAGAT
1 AAATAAATAAGTA-AAATAATAAAAAAGTAAAAT-CAT
*
1521401 AAATAAATGAGTAAAATATATAAAAAAGTAAAATCAT
1 AAATAAATAAGTAAAATA-ATAAAAAAGTAAAATCAT
* *
1521438 ATATATATAAGTAAAATAATAA
1 AAATAAATAAGTAAAATAATAA
1521460 TAATAAAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
32 4 0.05
33 5 0.07
34 10 0.14
35 5 0.07
36 7 0.10
37 26 0.36
38 13 0.18
39 3 0.04
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (36 bp):
AAATAAATAAGTAAAATAATAAAAAAGTAAAATCAT
Found at i:1521441 original size:20 final size:20
Alignment explanation
Indices: 1521415--1521469 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1521405 AAATGAGTAA
1521415 AATATATAAAAAAGTAAAAT
1 AATATATAAAAAAGTAAAAT
* * *
1521435 CATATATATATAAGTAAAAT
1 AATATATAAAAAAGTAAAAT
1521455 AATAATAATAAAAAA
1 AAT-AT-ATAAAAAA
1521470 AAATCAAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 19 0.70
21 2 0.07
22 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AATATATAAAAAAGTAAAAT
Found at i:1521984 original size:37 final size:37
Alignment explanation
Indices: 1521943--1522047 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1521933 GTGCTTGTGG
* *
1521943 ATCATATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
1521980 ATCATATTTTTAGGAGTTTAAATCCTAGCAAAATTTT
1 ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
1522017 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCATATTTTTAGGAGTTTAAATCCTAGTAG
1522048 GACGAAAACG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:1522965 original size:106 final size:105
Alignment explanation
Indices: 1522780--1524467 Score: 2422
Period size: 106 Copynumber: 16.0 Consensus size: 105
1522770 ATTGTTCCGG
* * * * * *
1522780 GTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAATCAGGAAATTGTGTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT-TGGAAATTGTTTGTTGACAACC
* * * *
1522845 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1522886 GTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
** *
1522951 AGCGGTCCCTTCGTTTTGAAGTTGAACTTGCGTTGTCTCGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
1522992 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAACTGTTTGTTGTCAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
* *
1523057 AGCGGTCCCTTCATCGTGAAATTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
1523098 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAACC
* **
1523163 AGCGGTCCCTTCGTCGTGAAGTTAAACTTATGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1523204 GTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCTCCGAAATT-GAAATTGTTTGTTGACAACCA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAACCA
*
1523268 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
1523308 GTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
*
1523373 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
** *
1523414 GTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
* *
1523479 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTATCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
1523520 GTCCAATATCCTTTGTAGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAACC
*
1523585 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * **
1523626 GTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTCATTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
* * *
1523691 AGCGGTCCCTTCGTCATAAAGTTGAAC-TGC-----AT-GA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * * *
1523725 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAACT
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
*
1523790 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1523831 GTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAACC
* *
1523896 CGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
1523937 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAACC
* *
1524002 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * * * *
1524043 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTATTTATTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAACC
*
1524108 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * * *
1524149 GTCCAATATCATTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAAAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAACC
1524214 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1524255 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA-TTGTTTGTTGACAACC
* * *
1524320 AGCGATCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* ** * *
1524361 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGAAAATT-ATTGTTGTCAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAACC
** * * *
1524425 AGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
1524466 GT
1 GT
1524468 GGCACGATAT
Statistics
Matches: 1444, Mismatches: 120, Indels: 37
0.90 0.07 0.02
Matches are distributed among these distances:
99 86 0.06
100 4 0.00
104 97 0.07
105 60 0.04
106 1192 0.83
107 5 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
Found at i:1525319 original size:22 final size:22
Alignment explanation
Indices: 1525293--1525348 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1525283 TTTTGTTTGG
*
1525293 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
1525315 TCAAATGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
1525337 TCAAAGGTTTGA
1 TCAAAGGTTTGA
1525349 TGGGGTAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:1525986 original size:18 final size:18
Alignment explanation
Indices: 1525958--1525996 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1525948 TCCCATTTTC
*
1525958 TTTTTGATTTTTGTTCTTT
1 TTTTTGA-TTTTCTTCTTT
1525977 TTTTTG-TTTTCTTCTTT
1 TTTTTGATTTTCTTCTTT
1525994 TTT
1 TTT
1525997 GCTTCTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
19 6 0.32
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.82
Consensus pattern (18 bp):
TTTTTGATTTTCTTCTTT
Found at i:1525994 original size:14 final size:15
Alignment explanation
Indices: 1525971--1526017 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1525961 TTGATTTTTG
1525971 TTCTT-TTTTTTGTT
1 TTCTTCTTTTTTGTT
1525985 TTCTTCTTTTTTGCTT
1 TTCTTCTTTTTTG-TT
1526001 CTT-TTCTTTTTTGTT
1 -TTCTTCTTTTTTGTT
1526016 TT
1 TT
1526018 TGCCCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.23
15 9 0.30
16 12 0.40
17 2 0.07
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (15 bp):
TTCTTCTTTTTTGTT
Found at i:1527228 original size:25 final size:25
Alignment explanation
Indices: 1527191--1527239 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1527181 CATGTTTATG
*
1527191 AAAATGCTTAAAATGAATGTAGATGC
1 AAAATGCTAAAAATGAATG-AGATGC
*
1527217 AAAATGC-AAAAATGCATGAGATG
1 AAAATGCTAAAAATGAATGAGATG
1527240 TTCGAGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.22
Consensus pattern (25 bp):
AAAATGCTAAAAATGAATGAGATGC
Found at i:1527956 original size:5 final size:5
Alignment explanation
Indices: 1527946--1527973 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1527936 GAAAGTGATG
1527946 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1527974 GATGAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1529399 original size:2 final size:2
Alignment explanation
Indices: 1529392--1529422 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1529382 TAAAATAGAA
1529392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1529423 ATAACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1529872 original size:37 final size:37
Alignment explanation
Indices: 1529831--1529935 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1529821 GTGCTTGTGG
* * *
1529831 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
1529868 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
1529905 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
1529936 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:1532043 original size:87 final size:87
Alignment explanation
Indices: 1531893--1532146 Score: 429
Period size: 87 Copynumber: 2.9 Consensus size: 87
1531883 CGGTTATGTT
** *
1531893 ATAT-TATTTAACCAGAAATATTATCAAGTACAATAACTTATTAGGTAACGCTTATATAATGTAA
1 ATATGTATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
1531957 TAGATAGCGCTTATATAATAAA
66 TAGATAGCGCTTATATAATAAA
1531979 ATATGTATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
1 ATATGTATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
1532044 TAGATAGCGCTTATATAATAAA
66 TAGATAGCGCTTATATAATAAA
* * * *
1532066 ATAGGTATTTAACGGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 ATATGTATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
*
1532131 TAGGTAGCGCTTATAT
66 TAGATAGCGCTTATAT
1532147 TGACCTATTT
Statistics
Matches: 159, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
86 4 0.03
87 155 0.97
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
ATATGTATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
TAGATAGCGCTTATATAATAAA
Found at i:1535928 original size:300 final size:302
Alignment explanation
Indices: 1535376--1535967 Score: 1035
Period size: 300 Copynumber: 2.0 Consensus size: 302
1535366 TTAAAATTAG
* *
1535376 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
*
1535441 ATACCGATTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATA-CGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
1535506 CACTATTTGACAAGGTATGGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
130 CACTATTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
1535571 AAAAAGTGTCGACATAGGTTGTAGACATATTCGCTAATAAAACCAATATACTTATACCGGTTATA
195 AAAAAGTGTCGACATAGGTTGTAGACATATTCGCTAATAAAACCAATATACTTATACCGGTTATA
1535636 TTATAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
260 TTATAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
1535679 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC-ATATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
* *
1535743 AT-CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTTCGATGTGTAAATGTCGAC
66 ATACGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
*
1535807 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTA
131 ACTATTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTA
* * * ** *
1535872 AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATAT
196 AAAAGTGTCGACATAGGTTGTAGACATATTCGCTAATAAAACCAATATACTTATACCGGTTATAT
*
1535937 TATAAAATTATCTATTACATTATAATTCTGG
261 TATAAAATTATCTAGTACATTATAATTCTGG
1535968 GTTCCGATGT
Statistics
Matches: 275, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
300 211 0.77
302 9 0.03
303 55 0.20
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (302 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
ATACGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
ACTATTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTA
AAAAGTGTCGACATAGGTTGTAGACATATTCGCTAATAAAACCAATATACTTATACCGGTTATAT
TATAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:1536002 original size:183 final size:182
Alignment explanation
Indices: 1535661--1536244 Score: 980
Period size: 183 Copynumber: 3.2 Consensus size: 182
1535651 GTACATTATA
*
1535661 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1535726 CATAAAACC-ATATATTTAT--CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGATATATTTATACCGGTTATATTA-AAAATTATCTATTACATTATAATTCTGGGTT
*
1535788 TCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
130 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
1535841 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
1535906 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGATATATTTATACCGGTTATATTA-AAAATTATCTATTACATTATAATTCTGGGTT
1535971 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
130 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
1536024 ATTCTGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * *
1536089 CATAAAACCGATATATTTATACCGATTATATTACAAATTATCTATTAC-TTATAATTATGGGTTC
66 CATAAAACCGATATATTTATACCGGTTATATTAAAAATTATCTATTACATTATAATTCTGGGTTC
* *** * *
1536153 CGATGTTTTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CGATGTGTAAAT--GTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
1536207 ATTCTGGACATAAAGTACCGACACAATATT-AAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1536245 GAAAACTTTA
Statistics
Matches: 383, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
180 73 0.19
181 32 0.08
182 22 0.06
183 256 0.67
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (182 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGATATATTTATACCGGTTATATTAAAAATTATCTATTACATTATAATTCTGGGTTC
CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:1537449 original size:3 final size:3
Alignment explanation
Indices: 1537441--1537491 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1537431 ACTTGTTTGG
* * * * *
1537441 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1537489 ATC
1 ATC
1537492 GTCAGCTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:1537492 original size:12 final size:12
Alignment explanation
Indices: 1537445--1537508 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
1537435 GTTTGGATCA
* *
1537445 TCATCATCATCA
1 TCATCTTCATCG
*
1537457 TCATCATCATCG
1 TCATCTTCATCG
*
1537469 TCGTCTTCATCG
1 TCATCTTCATCG
1537481 TCATCTTCATCG
1 TCATCTTCATCG
* *
1537493 TCAGCTTCATCT
1 TCATCTTCATCG
1537505 TCAT
1 TCAT
1537509 TGACCGCTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1537506 original size:6 final size:6
Alignment explanation
Indices: 1537445--1537508 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
1537435 GTTTGGATCA
* * * * * * *
1537445 TCATCA TCATCA TCATCA TCATCG TCGTCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
1537493 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
1537509 TGACCGCTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1539482 original size:193 final size:198
Alignment explanation
Indices: 1538956--1539701 Score: 1189
Period size: 193 Copynumber: 3.8 Consensus size: 198
1538946 CATTAAACAA
* * *
1538956 TGTCGATACA-TATTATATACCA-ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGA
1 TGTCGATACATTATT-TAGA-CATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
1539019 AAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
64 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACAC-TTTTATATATG
1539084 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
128 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1539149 ACAAAAG
193 AC-AAAG
*
1539156 TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
1539221 AATTACCTATTACATTATACTTAT-GGTTTCGATGTTTATGGGATCGACACTTTT-TATATGGAT
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATGGAT
* *
1539284 CGACACTTTATTGTTGCACCCTGTTTGTCATTCATTCTGGACC-AAAA-ATCGACACAAACTACA
131 CGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACA
1539347 AAG
196 AAG
1539350 TGTCGATACATTATTTAGACATATTCTCTCATAAAACC-GTATACTTGTACCGGTTAGATTG-AA
1 TGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
1539413 AATTACCTATTACATTATACTTATGGGTTTTCGATG-TTATCGGATCGACACTTTT-TATATGGA
66 AATTACCTATTACATTATACTTATGGG-TTTCGATGTTTATGGGATCGACACTTTTATATATGGA
*
1539476 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAT
130 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA-
*
1539541 AAAAG
194 CAAAG
* * *
1539546 TGTTGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATAC-TGTACCGATTAGATTG-AA
1 TGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
* *
1539609 AATT-CCTATTACA-T-TACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTATATATAGAT
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATGGAT
1539671 CGACACTTTATGGTTGCACCCTGTTTGCCAT
131 CGACACTTTATGGTTGCACCCTGTTTGCCAT
1539702 ATTGTAAATT
Statistics
Matches: 517, Mismatches: 19, Indels: 26
0.92 0.03 0.05
Matches are distributed among these distances:
192 34 0.07
193 121 0.23
194 92 0.18
195 38 0.07
196 65 0.13
197 56 0.11
198 4 0.01
199 28 0.05
200 75 0.15
201 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (198 bp):
TGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATGGAT
CGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACA
AAG
Found at i:1539517 original size:390 final size:391
Alignment explanation
Indices: 1538956--1539697 Score: 1214
Period size: 390 Copynumber: 1.9 Consensus size: 391
1538946 CATTAAACAA
*
1538956 TGTCGATACATATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
1 TGTCGATACATATTATAGACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
* *
1539021 AATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTAATACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGA
1539086 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
*
1539151 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
196 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC-TGTACCGATTAGAT
1539216 TGAAAAATTACCTATTACATTATACTTAT-GGTTTCGATGTTTATGGGATCGACACTTTT-TATA
260 TG-AAAATT-CCTATTACA-T-TACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATA
* *
1539279 TGGATCGACACTTTATTGTTGCACCCTGTTTGTCATTCATTCTGGACCAAAAATCGACACAAACT
321 TAGATCGACACTTTATGGTTGCACCCTGTTTGTCATTCATTCTGGACCAAAAATCGACACAAACT
1539344 ACAAAG
386 ACAAAG
* *
1539350 TGTCGATACATTATT-TAGA-CATATTCTCTCATAAAACC-GTATACTTGTACCGGTTAGATTG-
1 TGTCGATACA-TATTATAGACCA-ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGA
*
1539411 AAAATTACCTATTACATTATACTTATGGGTTTTCGATG-TTATCGGATCGACAC-TTTT-TATAT
64 AAAATTACCTAATACATTATACTTATGGG-TTTCGATGTTTATCGGATCGACACTTTTTATATAT
*
1539473 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
128 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
* * * *
1539538 TATAAAAGTGTTGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTGTACCGATTAG
193 TACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTGTACCGATTAG
*
1539603 ATTGAAAATTCCTATTACATTACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTATATATA
258 ATTGAAAATTCCTATTACATTACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATA
1539668 GATCGACACTTTATGGTTGCACCCTGTTTG
323 GATCGACACTTTATGGTTGCACCCTGTTTG
1539698 CCATATTGTA
Statistics
Matches: 328, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
385 6 0.02
386 31 0.09
387 43 0.13
388 6 0.02
389 15 0.05
390 118 0.36
391 4 0.01
392 41 0.12
393 32 0.10
394 28 0.09
395 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (391 bp):
TGTCGATACATATTATAGACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
AATTACCTAATACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGA
TCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTGTACCGATTAGATT
GAAAATTCCTATTACATTACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTATATATAGAT
CGACACTTTATGGTTGCACCCTGTTTGTCATTCATTCTGGACCAAAAATCGACACAAACTACAAA
G
Found at i:1539954 original size:19 final size:19
Alignment explanation
Indices: 1539930--1539978 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1539920 ATATATTCAC
1539930 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
1539949 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
1539968 ATACAAAATTA
1 ATACAAAATTA
1539979 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1541821 original size:32 final size:33
Alignment explanation
Indices: 1541762--1541826 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1541752 CCATCTTATA
*
1541762 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1541795 TCACCCCTCAACA-CTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1541827 CCATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1541921 original size:21 final size:21
Alignment explanation
Indices: 1541872--1541922 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1541862 CAAGTGTACC
*
1541872 TTCGACTCTCTCAAGTTTCTT
1 TTCGACTCTATCAAGTTTCTT
*
1541893 TTCAACTCTATCAAGTTTCTCT
1 TTCGACTCTATCAAGTTTCT-T
1541915 TT-GACTCT
1 TTCGACTCT
1541923 TGATTCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (21 bp):
TTCGACTCTATCAAGTTTCTT
Found at i:1544331 original size:19 final size:18
Alignment explanation
Indices: 1544287--1544344 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
1544277 TCCGGTAACG
1544287 TTTTACCGGTTTTATCAT
1 TTTTACCGGTTTTATCAT
*
1544305 TTGATACCGGTTTTATCAT
1 TT-TTACCGGTTTTATCAT
*
1544324 ATTTTACCTGG-TATATCAT
1 -TTTTACC-GGTTTTATCAT
1544343 TT
1 TT
1544345 GGATCGATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 26 0.76
20 4 0.12
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.52
Consensus pattern (18 bp):
TTTTACCGGTTTTATCAT
Found at i:1544470 original size:176 final size:179
Alignment explanation
Indices: 1544129--1544480 Score: 484
Period size: 176 Copynumber: 2.0 Consensus size: 179
1544119 GGTATCGTTT
* *
1544129 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCATTGTGGATCGATATATTTTTTTAAAGTATCG
1544194 ACACATTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGT
66 ACACATTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAG-
* *
1544259 ATAGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTGA
130 ATAGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTGA
*
1544309 TACCGGTTTTATCATA-TTTTACCTGGTATATCATT-TGGATCGATA-CTTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCATTGTGGATCGATATATTTTTTTAAAGTATCG
* ** *
1544371 ACACTTTATAGGA-TTTAAAACT-ACTTCTCTTTT-AATTCACGAAGTGTCGATCCTTATATTAA
66 ACACATTATA-GACGCTAAAACTGA-TTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAA
* * * * *
1544433 A-ATCCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTGTCAT
128 AGAT-AGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCAT
1544481 AGTTTTACCT
Statistics
Matches: 154, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
175 2 0.01
176 62 0.40
177 45 0.29
178 12 0.08
179 17 0.11
180 16 0.10
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (179 bp):
TACCGGTTTTATCATATTTTTACCTGGTATATCATTGTGGATCGATATATTTTTTTAAAGTATCG
ACACATTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGA
TAGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTGA
Found at i:1547170 original size:260 final size:259
Alignment explanation
Indices: 1546710--1547228 Score: 970
Period size: 260 Copynumber: 2.0 Consensus size: 259
1546700 CAATCCATAG
1546710 AGATCCTTCACCAACTAAAATATTTTAACATCATGAGACACAAGTTTTGTTCCAACCAACCAAAT
1 AGATCCTTCACCAACTAAAATATTTTAACATCATGAGACACAAGTTTTGTTCCAACCAACCAAAT
1546775 TCCTTAACCCCAGACCTCCCTCAGATTTTAGGGAGCAAATCTGATTCCAGCTGACTCTAGCACCT
66 TCCTTAACCCCAGACCTCCCTCAGATTTTAGGGAGCAAATCTGATTCCAGCTGACTCTAGCACCT
1546840 TGAGCCGAGGTATCATTGCCCTTCTAAAAGAATCTTATACAAATCCTTTCAATATCCCAAATGAC
131 TGAGCCGAGGTATCATTGCCCTTCTAAAAGAATCTTATACAAATCCTTTCAATATCCCAAATGAC
1546905 TCTCTTAGGCAGAATAAGCTGCCTACTCCAGTAATTAAAGATGCTAAAAAAATTGTTTTTACAA
196 TCTCTTAGGCAGAATAAGCTGCCTACTCCAGTAATTAAAGATGCTAAAAAAATTGTTTTTACAA
1546969 AGATCCTTCACCAACT-AAATATTTTAACAATCATGAGACAACAAGTTTTTGTTCCAACCAACCA
1 AGATCCTTCACCAACTAAAATATTTTAAC-ATCATGAGAC-ACAAG-TTTTGTTCCAACCAACCA
1547033 AATTCCTTAACCCCAGACCTCCCTCAGATTTTAGGGAGC-AATCTGATTCCAGCTGACTCTAGCA
63 AATTCCTTAACCCCAGACCTCCCTCAGATTTTAGGGAGCAAATCTGATTCCAGCTGACTCTAGCA
1547097 CCTTGAGCCGAGGTATCATTGCCCTTCTAAAAGAATCTTATACAAATCCTTTCAATATCCCAAAT
128 CCTTGAGCCGAGGTATCATTGCCCTTCTAAAAGAATCTTATACAAATCCTTTCAATATCCCAAAT
* * *
1547162 GACTCTCTTAGTCATAATAAGTTGCCTACTCCAGTAATTAAAGATGCTAAAAAAATTGTTTTTAC
193 GACTCTCTTAGGCAGAATAAGCTGCCTACTCCAGTAATTAAAGATGCTAAAAAAATTGTTTTTAC
1547227 AA
258 AA
1547229 GTTGCAGGCT
Statistics
Matches: 254, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
258 12 0.05
259 26 0.10
260 159 0.63
261 57 0.22
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (259 bp):
AGATCCTTCACCAACTAAAATATTTTAACATCATGAGACACAAGTTTTGTTCCAACCAACCAAAT
TCCTTAACCCCAGACCTCCCTCAGATTTTAGGGAGCAAATCTGATTCCAGCTGACTCTAGCACCT
TGAGCCGAGGTATCATTGCCCTTCTAAAAGAATCTTATACAAATCCTTTCAATATCCCAAATGAC
TCTCTTAGGCAGAATAAGCTGCCTACTCCAGTAATTAAAGATGCTAAAAAAATTGTTTTTACAA
Found at i:1550148 original size:22 final size:21
Alignment explanation
Indices: 1550124--1550163 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1550114 GAGAAATTAT
1550124 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
1550145 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1550164 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:1553986 original size:20 final size:20
Alignment explanation
Indices: 1553961--1553998 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1553951 TTTTGGTGCA
*
1553961 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
1553981 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
1553999 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1559041 original size:23 final size:23
Alignment explanation
Indices: 1559015--1559061 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1559005 AATAATTATC
* *
1559015 TTTTTGTGAAACGTTTATCTTTA
1 TTTTTATGAAACATTTATCTTTA
**
1559038 TTTTTATGCCACATTTATCTTTA
1 TTTTTATGAAACATTTATCTTTA
1559061 T
1 T
1559062 CATTATGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTTTATGAAACATTTATCTTTA
Found at i:1559075 original size:23 final size:23
Alignment explanation
Indices: 1559028--1559076 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1559018 TTGTGAAACG
** *
1559028 TTTATCTTTATTTTTATGCCACA
1 TTTATCTTTATCATTATGACACA
*
1559051 TTTATCTTTATCATTATGACTCA
1 TTTATCTTTATCATTATGACACA
1559074 TTT
1 TTT
1559077 TTCGATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTATCTTTATCATTATGACACA
Found at i:1564172 original size:45 final size:46
Alignment explanation
Indices: 1564104--1564196 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
1564094 CGGTGGGGTT
1564104 AAAAAAAACATAGAACCTGAGAAAAAACTGAGGGAATCCAACTAAA
1 AAAAAAAACATAGAACCTGAGAAAAAACTGAGGGAATCCAACTAAA
1564150 AAAAAAAACATAGAACCT-AGAAAAAACTGAGGGAATCCAACTAAA
1 AAAAAAAACATAGAACCTGAGAAAAAACTGAGGGAATCCAACTAAA
1564195 AA
1 AA
1564197 CCCTTAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 29 0.62
46 18 0.38
ACGTcount: A:0.60, C:0.15, G:0.14, T:0.11
Consensus pattern (46 bp):
AAAAAAAACATAGAACCTGAGAAAAAACTGAGGGAATCCAACTAAA
Found at i:1564254 original size:15 final size:14
Alignment explanation
Indices: 1564218--1564244 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1564208 ATTAGAACCA
1564218 AACACAAAAAAGAG
1 AACACAAAAAAGAG
1564232 AACACAAAAAAGA
1 AACACAAAAAAGA
1564245 AAGAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (14 bp):
AACACAAAAAAGAG
Found at i:1570569 original size:4 final size:4
Alignment explanation
Indices: 1570560--1570598 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
1570550 ATTGAGAAAA
1570560 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1570599 TATGATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 31 0.94
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:1571235 original size:106 final size:104
Alignment explanation
Indices: 1570973--1571274 Score: 308
Period size: 102 Copynumber: 3.0 Consensus size: 104
1570963 GCTTGAGACA
* *
1570973 ATTTCTTTCAAAACAAATTT-GTCTCACTTGAGACA-TTTTCCTTTGAGATACAAAATTTGAATT
1 ATTT-TTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATT
* * * *
1571036 TGTTTCACATTAAACAAGTTGATCTCATTTGAGATCGCTT
65 TGATTCACATTAAACAAATTAATCTCACTTGAGATCGCTT
* * * * *
1571076 -TCTCTT-AAAACAACTTATC--CTTGCTTGAGACATTTTTTCCTTTGATATACAAATTTTGAAT
1 ATTTTTTCAAAACAAATT-TCGTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAATTTTGAAT
*
1571137 TTGATTCAC-TTGAAACAAAAATTAATCTCACTTGAGATTG-TT
64 TTGATTCACATT-AAAC--AAATTAATCTCACTTGAGATCGCTT
*
1571179 ATTTTTTCAAAACAAATTTCGTCTCGTTTGAGACATTTTTCCTTTGAGAATACAAA-TTTG---T
1 ATTTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAG-ATACAAATTTTGAATT
* *
1571240 T--TTCACATTAAACAAGTTGATCTCACTTGAGATCG
65 TGATTCACATTAAACAAATTAATCTCACTTGAGATCG
1571275 TTTTCTCAAA
Statistics
Matches: 165, Mismatches: 21, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
98 19 0.12
100 29 0.18
101 7 0.04
102 41 0.25
103 2 0.01
104 24 0.15
105 25 0.15
106 18 0.11
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (104 bp):
ATTTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
GATTCACATTAAACAAATTAATCTCACTTGAGATCGCTT
Found at i:1571321 original size:35 final size:35
Alignment explanation
Indices: 1571277--1571381 Score: 135
Period size: 34 Copynumber: 3.1 Consensus size: 35
1571267 TGAGATCGTT
* *
1571277 TTCTC-AAAAACAAACGTTGTCTCGCTTCAGACAA
1 TTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
* *
1571311 TTCTCTAAAAA-ACATTTTTGTCTCG-TTGAGACAA
1 TTCTCTAAAAACA-AATGTTGTCTCGCTTGAGACAA
*
1571345 TTCTCTAAAAACAAATGTTGTCTCACTTGAGACAA
1 TTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
1571380 TT
1 TT
1571382 TTCCAAATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
34 34 0.57
35 26 0.43
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (35 bp):
TTCTCTAAAAACAAATGTTGTCTCGCTTGAGACAA
Found at i:1571446 original size:31 final size:30
Alignment explanation
Indices: 1571408--1571478 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
1571398 TGTTTCACTG
1571408 GAAACAAACATCATCTTTGAGTCGT-TTCTT-T
1 GAAACAAACATC-T-TTTGAGTC-TATTCTTAT
*
1571439 GAAACAAAGGATCTTTTGAGTCTATTCTTAT
1 GAAACAAA-CATCTTTTGAGTCTATTCTTAT
1571470 GAAACAAAC
1 GAAACAAAC
1571479 TTGTCTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 1 0.03
30 13 0.37
31 18 0.51
32 3 0.09
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (30 bp):
GAAACAAACATCTTTTGAGTCTATTCTTAT
Found at i:1571686 original size:63 final size:64
Alignment explanation
Indices: 1571541--1571711 Score: 183
Period size: 63 Copynumber: 2.7 Consensus size: 64
1571531 AAACAAAATG
*
1571541 AAAAATCTTTGAGTATGTTTCTTT-GATAAC-AAATTTTGTCTCTTTTGAGAAAGTTTCTTTTGA
1 AAAAATCTTTGAGTATGTTTCTTTGGA-AACAAAATTTTGTCTCTTTTGAGAAAGTTTCCTTTGA
* * * *
1571604 AAGAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCACTTTT-TGACAG-TTCCTTTGA
1 AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGAAAGTTTCCTTTGA
* * * * **
1571666 AGAAAATCTTTAAATCTG-TT-TTTGAAAACAAAGGTTTGTCTCTTTT
1 A-AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTT
1571712 AAGACAATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 22 0.24
62 11 0.12
63 42 0.46
64 17 0.18
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (64 bp):
AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGAAAGTTTCCTTTGA
Found at i:1571772 original size:30 final size:29
Alignment explanation
Indices: 1571719--1571810 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
1571709 TTTAAGACAA
* *
1571719 TTTCTCTTAAAACAAACATCTTGAGATTG
1 TTTCCCTTGAAACAAACATCTTGAGATTG
*
1571748 TTTCCCTTG-AACAAACCTATCTTGAGTTTG
1 TTTCCCTTGAAACAAA-C-ATCTTGAGATTG
*
1571778 TTTCTCTTGAAACAAA-AGTCTGTGAG-TTG
1 TTTCCCTTGAAACAAACA-TCT-TGAGATTG
1571807 TTTC
1 TTTC
1571811 TTTGAAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
28 7 0.13
29 18 0.33
30 23 0.43
31 6 0.11
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (29 bp):
TTTCCCTTGAAACAAACATCTTGAGATTG
Found at i:1571822 original size:28 final size:29
Alignment explanation
Indices: 1571766--1571906 Score: 127
Period size: 28 Copynumber: 5.0 Consensus size: 29
1571756 GAACAAACCT
* *
1571766 ATCT-TGAGTTTGTTTCTCTTGAAACAAA
1 ATCTGTGAGTTTGTTTCTTTTGAAATAAA
1571794 AGTCTGTGAG-TTGTTTC-TTTGAAATAAA
1 A-TCTGTGAGTTTGTTTCTTTTGAAATAAA
*
1571822 ATCTGCGAGTTTGTTTCTTTTTTG-AATAGAA
1 ATCTGTGAGTTTGTTTC--TTTTGAAATA-AA
*
1571853 ATCTTTGAG-TTGTTTCTTTTG-AA-AAA
1 ATCTGTGAGTTTGTTTCTTTTGAAATAAA
* * *
1571879 AT-TCTGAGTCTGTTTCTTTTGAACTAAA
1 ATCTGTGAGTTTGTTTCTTTTGAAATAAA
1571907 GTTTTTTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
25 5 0.05
26 15 0.16
27 9 0.09
28 28 0.29
29 10 0.11
30 15 0.16
31 13 0.14
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (29 bp):
ATCTGTGAGTTTGTTTCTTTTGAAATAAA
Found at i:1571892 original size:26 final size:26
Alignment explanation
Indices: 1571800--1571901 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 26
1571790 CAAAAGTCTG
* *
1571800 TGAGTTGTTTC-TTTGAAATAAAATC
1 TGAGTTGTTTCTTTTGAAAGAAATTC
*
1571825 TGCGAGTTTGTTTCTTTTTTGAATAGAAATCTT
1 T--GAG-TTGTTTC--TTTTGAA-AGAAAT-TC
1571858 TGAGTTGTTTCTTTTGAAA-AAATTC
1 TGAGTTGTTTCTTTTGAAAGAAATTC
1571883 TGAGTCTGTTTCTTTTGAA
1 TGAGT-TGTTTCTTTTGAA
1571902 CTAAAGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
25 7 0.11
26 17 0.27
27 4 0.06
28 14 0.22
30 7 0.11
31 9 0.14
32 4 0.06
33 2 0.03
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.49
Consensus pattern (26 bp):
TGAGTTGTTTCTTTTGAAAGAAATTC
Found at i:1572059 original size:90 final size:88
Alignment explanation
Indices: 1571851--1572071 Score: 240
Period size: 90 Copynumber: 2.5 Consensus size: 88
1571841 TTTTGAATAG
* * *
1571851 AAATCTTTGAGT-TGTTTCTTTTGAAAAAAT-TCTGAGTCTGTTTCTTTTGAACTAAAGTTTTTT
1 AAATCTTTGAGTCTG-TTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAACTAAAGTTTTGT
*
1571914 TTCTCTTAAGACAATTTCGTGAAA
65 CTCTCTTAAGACAATTTCGTGAAA
1571938 AAATC-TTGAGTCAT-TTCTTTTGAAACTAAAATCTTTGAGTTTGTTTCTTTTGAAAC-AAAGTT
1 AAATCTTTGAGTC-TGTTCTTTTG-AA--AAAATCTTTGAGTTTGTTTCTTTTG-AACTAAAGTT
* *
1572000 TTGTCTCTC-TGAGACAATTTTTCTTGAGAA
61 TTGTCTCTCTTAAGACAA--TTTCGTGA-AA
*
1572030 AAATCTTTGAGTCTGTTCCTTTTG-AAAAATCTTTGAGATTGT
1 AAATCTTTGAGTCTGTT-CTTTTGAAAAAATCTTTGAGTTTGT
1572072 GTCTCTTAAC
Statistics
Matches: 114, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
86 14 0.12
87 7 0.06
88 1 0.01
89 12 0.11
90 46 0.40
91 10 0.09
92 9 0.08
93 9 0.08
94 6 0.05
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (88 bp):
AAATCTTTGAGTCTGTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAACTAAAGTTTTGTC
TCTCTTAAGACAATTTCGTGAAA
Found at i:1572220 original size:29 final size:29
Alignment explanation
Indices: 1572180--1572259 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
1572170 AAAAAAAATC
*
1572180 TTTGAGTTTGTTTCTTTTGAAACATCATA
1 TTTGAGTCTGTTTCTTTTGAAACATCATA
*
1572209 TTTGAGTCTGTTTCTTTTGAAACATCATC
1 TTTGAGTCTGTTTCTTTTGAAACATCATA
*
1572238 TTTGAGTCAGTTTCTTTTGAAA
1 TTTGAGTCTGTTTCTTTTGAAA
1572260 TCATTATCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (29 bp):
TTTGAGTCTGTTTCTTTTGAAACATCATA
Found at i:1572334 original size:40 final size:39
Alignment explanation
Indices: 1572279--1572354 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
1572269 CTATAGATGG
1572279 CCAGAGCTCTTCATCACGTATGAGCCGTGTCATCCCCCGA
1 CCAGAGCTCTTCATCACGTATGAGCCGTGTCA-CCCCCGA
*
1572319 CCAGATCTCTTCATCACGTATGAGCCGTGTCACCCC
1 CCAGAGCTCTTCATCACGTATGAGCCGTGTCACCCC
1572355 TAGATAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (39 bp):
CCAGAGCTCTTCATCACGTATGAGCCGTGTCACCCCCGA
Found at i:1572468 original size:40 final size:39
Alignment explanation
Indices: 1572413--1572488 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
1572403 CTAAAGATGG
* * *
1572413 CCAGAACTTTTCATCACGTATGAGTCGTGTCATCCCCCGA
1 CCAGAACTATTCATCACATATGAGCCGTGTCA-CCCCCGA
* *
1572453 CCAGATCTATTCATCATATATGAGCCGTGTCACCCC
1 CCAGAACTATTCATCACATATGAGCCGTGTCACCCC
1572489 TAGATAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (39 bp):
CCAGAACTATTCATCACATATGAGCCGTGTCACCCCCGA
Found at i:1572649 original size:134 final size:134
Alignment explanation
Indices: 1572268--1572626 Score: 529
Period size: 134 Copynumber: 2.7 Consensus size: 134
1572258 AATCATTATC
* * *
1572268 CCTATAGATGGCCAGAGCTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCAT
* * *
1572333 CACGTATGAGCCGTGTCACCCCTAGATAACCAGTCATCCTCATCGTGTAGGAACCGAGTTATCAC
66 CACATATGAGCCGTGTCACCCCTAGATAACCAGACATCCTCATCGCGTAGGAACCGAGTTATCAC
1572398 CATT
131 CATT
* *
1572402 CCTAAAGATGGCCAGAACTTTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTATTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCAT
* * *
1572467 CATATATGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAC
66 CACATATGAGCCGTGTCACCCCTAGATAACCAGACATCCTCATCGCGTAGGAACCGAGTTATCAC
1572532 CATT
131 CATT
* * * * * *
1572536 CCTAAAGATGGCCAGAACTCTTCATCACGTATAAGTCGTGTCATACCCTGACTAGATTTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCAT
* ** *
1572601 CACATAGGAATCGTGTCACCCTTAGA
66 CACATATGAGCCGTGTCACCCCTAGA
1572627 CGACCCGAAC
Statistics
Matches: 202, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 202 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCTTCAT
CACATATGAGCCGTGTCACCCCTAGATAACCAGACATCCTCATCGCGTAGGAACCGAGTTATCAC
CATT
Found at i:1579469 original size:20 final size:21
Alignment explanation
Indices: 1579444--1579495 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1579434 TTTTTCCAAT
*
1579444 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1579464 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1579485 TCGCAATGCGA
1 TCGCAATGCGA
1579496 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1579508 original size:41 final size:41
Alignment explanation
Indices: 1579463--1579557 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
1579453 GAATAAGTAA
* * * *
1579463 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-AGAAAATCGCAACGAGATACTGACT
* * *
1579504 ATCGCAATGCGATAATATAAAATCGCAACGAGATATTGACT
1 ATCGCAACGCGATAATAGAAAATCGCAACGAGATACTGACT
*
1579545 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1579558 TCTGACTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATAATAGAAAATCGCAACGAGATACTGACT
Found at i:1579509 original size:20 final size:20
Alignment explanation
Indices: 1579484--1579577 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1579474 AATTGGGAAA
*
1579484 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1579504 ATCGCAATGCGATAATATAAA
1 ATCGCAACGCGATACT-GACT
* *
1579525 ATCGCAACGAGATATTGACT
1 ATCGCAACGCGATACTGACT
* *
1579545 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1579565 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1579578 TTACATAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1579578 original size:20 final size:19
Alignment explanation
Indices: 1579526--1579579 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
1579516 TAATATAAAA
*
1579526 TCGCAACGAGATATTGACTT
1 TCGCAACGCGAT-TTGACTT
1579546 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATT-TGACTT
1579566 TCGCAACGCGATTT
1 TCGCAACGCGATTT
1579580 ACATAGCGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (19 bp):
TCGCAACGCGATTTGACTT
Found at i:1580126 original size:19 final size:19
Alignment explanation
Indices: 1580088--1580143 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1580078 TTCGAGAATG
1580088 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1580108 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
1580127 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
1580144 CCAAATCGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1580176 original size:19 final size:19
Alignment explanation
Indices: 1580149--1580214 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1580139 CGAAACCAAA
*
1580149 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1580168 TCGCGTTGCGA-TTTC---
1 TCGCGTTGCGATTTTCATT
* **
1580183 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1580202 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1580215 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 10 0.27
16 2 0.05
18 4 0.11
19 21 0.57
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1580222 original size:33 final size:34
Alignment explanation
Indices: 1580154--1580236 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 34
1580144 CCAAATCGCA
**
1580154 TTGCGATTTTCATTTCGCGTTGCGATTTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTTCTCTCG
1580188 TTGCGATAGTCATTTCGCGTTGCGA-TTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTTCTCTCG
1580221 TTGCGATAGTCATTTC
1 TTGCGATAGTCATTTC
1580237 CGAACCAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 24 0.51
34 23 0.49
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (34 bp):
TTGCGATAGTCATTTCGCGTTGCGATTTCTCTCG
Found at i:1580224 original size:14 final size:14
Alignment explanation
Indices: 1580171--1580227 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
1580161 TTTCATTTCG
1580171 CGTTGCGATTTCTCT
1 CGTTGCGA-TTCTCT
*
1580186 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
1580205 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1580219 CGTTGCGAT
1 CGTTGCGAT
1580228 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.34
15 8 0.23
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1582363 original size:42 final size:42
Alignment explanation
Indices: 1582287--1582458 Score: 193
Period size: 42 Copynumber: 4.1 Consensus size: 42
1582277 GACTCACCTG
* * *
1582287 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1582329 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
1582371 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGG-CCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1582412 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1582454 TCATC
1 TCATC
1582459 GTTGAAGAGG
Statistics
Matches: 104, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 33 0.32
42 71 0.68
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1582461 original size:21 final size:21
Alignment explanation
Indices: 1582354--1582468 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 21
1582344 CCCCTCCCAC
1582354 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
1582375 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* *
1582396 CGTTGAAGAGGCC-CTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
1582417 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
1582437 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
1582458 CGTTGAAGAGG
1 CGTTCAAGAGG
1582469 TCCCTCCCAC
Statistics
Matches: 65, Mismatches: 24, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
20 12 0.18
21 53 0.82
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:1582467 original size:83 final size:84
Alignment explanation
Indices: 1582284--1582458 Score: 343
Period size: 83 Copynumber: 2.1 Consensus size: 84
1582274 CCCGACTCAC
1582284 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1582349 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1582368 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGG-CCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1582432 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1582451 CTGTCATC
1 CTGTCATC
1582459 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 52 0.57
84 39 0.43
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1583846 original size:14 final size:14
Alignment explanation
Indices: 1583827--1583860 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1583817 TGTTTAATTA
1583827 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
1583841 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
1583855 ATTTGT
1 ATTTGT
1583861 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:1584002 original size:14 final size:14
Alignment explanation
Indices: 1583983--1584039 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1583973 GCGAAATGAA
1583983 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1583997 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1584016 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1584030 AATCGCAACG
1 AATCGCAACG
1584040 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1584010 original size:33 final size:33
Alignment explanation
Indices: 1583965--1584054 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
1583955 AAAAAGTACT
*
1583965 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1583998 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1584031 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1584055 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1584024 original size:19 final size:19
Alignment explanation
Indices: 1583965--1584025 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1583955 AAAAAGTACT
*
1583965 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1583984 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1583998 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1584017 ATCGCAACG
1 ATCGCAACG
1584026 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1584112 original size:19 final size:19
Alignment explanation
Indices: 1584088--1584144 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1584078 GAAATTAGCG
1584088 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1584107 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
1584119 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1584138 TTGCGAT
1 TTGCGAT
1584145 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
12 6 0.19
14 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1584124 original size:31 final size:31
Alignment explanation
Indices: 1584049--1584144 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
1584039 GCGAAATTAA
1584049 ATTCGCGTTGCGA-TTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
1584079 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
1584112 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1584143 AT
1 AT
1584145 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
31 31 0.52
32 12 0.20
33 17 0.28
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (31 bp):
ATTCGCGTTGCGATTTTCATTTCGCATTGCG
Done.