Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 5 of 328
Found at i:1399081 original size:18 final size:18
Alignment explanation
Indices: 1399031--1399081 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1399021 GAAAAAAAAA
* *
1399031 TAGTAATAATAAAAGGGT
1 TAGTAATAATAGAGGGGT
* *
1399049 TAGTTCATCAT-GAGGGGT
1 TAG-TAATAATAGAGGGGT
1399067 TAGTAATAATAGAGG
1 TAGTAATAATAGAGG
1399082 CATTTGGTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.29
Consensus pattern (18 bp):
TAGTAATAATAGAGGGGT
Found at i:1400335 original size:18 final size:18
Alignment explanation
Indices: 1400299--1400337 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1400289 ATTATATCAG
1400299 TAAAATTTAATTCGAATT
1 TAAAATTTAATTCGAATT
*
1400317 TAAATATTTAATTCGATTT
1 TAAA-ATTTAATTCGAATT
1400336 TA
1 TA
1400338 TTATAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAAATTTAATTCGAATT
Found at i:1400536 original size:2 final size:2
Alignment explanation
Indices: 1400525--1400559 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1400515 CTCTCGTGAC
*
1400525 TA TA TCA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1400560 ATGAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1406363 original size:15 final size:16
Alignment explanation
Indices: 1406343--1406379 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1406333 TAATTTTATG
1406343 TTAAAACACATA-A-AT
1 TTAAAAC-CATATATAT
1406358 TTAAAACCATATATAT
1 TTAAAACCATATATAT
1406374 TTAAAA
1 TTAAAA
1406380 AAAATTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAACCATATATAT
Found at i:1406508 original size:21 final size:21
Alignment explanation
Indices: 1406484--1406567 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 21
1406474 TTCACATATA
*
1406484 TTTTAGAAATTTTTTTGAAAT
1 TTTTAAAAATTTTTTTGAAAT
* *
1406505 TTTTATAAATATTTTTG-AA-
1 TTTTAAAAATTTTTTTGAAAT
*
1406524 TTTTAAAAATTATTTT-AAAT
1 TTTTAAAAATTTTTTTGAAAT
* **
1406544 TTTTTAAAATAATTTT-AAAT
1 TTTTAAAAATTTTTTTGAAAT
1406564 TTTT
1 TTTT
1406568 GTTGAAAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
19 15 0.28
20 24 0.44
21 15 0.28
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTAAAAATTTTTTTGAAAT
Found at i:1406565 original size:39 final size:40
Alignment explanation
Indices: 1406483--1406566 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
1406473 CTTCACATAT
* * * *
1406483 ATTTTAGAAATTTTTTTGAAATTTTTATAAATATTTTTGA
1 ATTTTAAAAATTATTTTGAAATTTTTATAAATAATTTTAA
1406523 ATTTTAAAAATTATTTT-AAATTTTT-TAAAATAATTTTAA
1 ATTTTAAAAATTATTTTGAAATTTTTAT-AAATAATTTTAA
1406562 ATTTT
1 ATTTT
1406567 TGTTGAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 1 0.03
39 23 0.59
40 15 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (40 bp):
ATTTTAAAAATTATTTTGAAATTTTTATAAATAATTTTAA
Found at i:1408257 original size:12 final size:13
Alignment explanation
Indices: 1408234--1408273 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
1408224 ATTGAAAGTC
1408234 TTTTTAATAAATA
1 TTTTTAATAAATA
1408247 TTTTTAA-AAATA
1 TTTTTAATAAATA
1408259 TTTTTCAAGTAAATA
1 TTTTT-AA-TAAATA
1408274 AAAATTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
15 5 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (13 bp):
TTTTTAATAAATA
Found at i:1409295 original size:29 final size:28
Alignment explanation
Indices: 1409253--1409362 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 28
1409243 TGTGTATATT
*
1409253 ATATGCGAGCCTATATGTGAACCTTAGA
1 ATATGCAAGCCTATATGTGAACCTTAGA
*
1409281 ATTATGCAAGGCTATATGTGAACCTTAGGA
1 A-TATGCAAGCCTATATGTGAACCTTA-GA
* * *
1409311 ACATGCAAGCCTACATGTGAACCCTAGA
1 ATATGCAAGCCTATATGTGAACCTTAGA
* * *
1409339 TATATGCGAGCCTATGTGCGAACC
1 -ATATGCAAGCCTATATGTGAACC
1409363 CTTGGTGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.04
29 62 0.91
30 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (28 bp):
ATATGCAAGCCTATATGTGAACCTTAGA
Found at i:1409374 original size:58 final size:58
Alignment explanation
Indices: 1409255--1409386 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
1409245 TGTATATTAT
* * * *
1409255 ATGCGAGCCTATATGTGAACCTTAGAATTATGCAAGGCTATATGTGAACCTTAGGAAC
1 ATGCAAGCCTATATGTGAACCCTAGAATTATGCAAGCCTATATGCGAACCTTAGGAAC
* * * **
1409313 ATGCAAGCCTACATGTGAACCCTAG-ATATATGCGAGCCTATGTGCGAACCCTT-GGTGC
1 ATGCAAGCCTATATGTGAACCCTAGAAT-TATGCAAGCCTATATGCGAA-CCTTAGGAAC
*
1409371 ATGCATGCCTATATGT
1 ATGCAAGCCTATATGT
1409387 CAAGAGAACT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
57 2 0.03
58 55 0.90
59 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (58 bp):
ATGCAAGCCTATATGTGAACCCTAGAATTATGCAAGCCTATATGCGAACCTTAGGAAC
Found at i:1414357 original size:39 final size:40
Alignment explanation
Indices: 1414313--1414451 Score: 203
Period size: 39 Copynumber: 3.5 Consensus size: 40
1414303 GGATATTACA
* *
1414313 TATATCCGGGCT-AAGTCCCAAAGGCATTCGTGTTGGTAT
1 TATATCCGGGCTAAAGTCCCGAAGGCATTCGTGCTGGTAT
*
1414352 TATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAAGTCCCGAAGGCATTCGTGCTGGTAT
* *
1414391 TATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAAGTCCCGAAGGCATTCGTGCTGGTAT
1414430 TATATCCGGGCTTAAAGTCCCG
1 TATATCCGGGC-TAAAGTCCCG
1414452 CATGCTTTGT
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 70 0.76
40 22 0.24
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.29
Consensus pattern (40 bp):
TATATCCGGGCTAAAGTCCCGAAGGCATTCGTGCTGGTAT
Found at i:1414459 original size:40 final size:39
Alignment explanation
Indices: 1414313--1414467 Score: 188
Period size: 39 Copynumber: 3.9 Consensus size: 39
1414303 GGATATTACA
** * *
1414313 TATATCCGGGCT-AAGTCCCAAAGGCATTCGTGTTGGTAT
1 TATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTAT
* * *
1414352 TATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTAT
1414391 TATATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGTAT
1 TATATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGTAT
* *
1414430 TATATCCGGGCTTAAAGTCCCGCATGCTTTGTGGTGGT
1 TATATCCGGGC-TAAAGTCCCGCAGGCTTTGTGCTGGT
1414468 GATTGGATTT
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
39 70 0.66
40 36 0.34
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGTAT
Found at i:1417558 original size:30 final size:29
Alignment explanation
Indices: 1417521--1417603 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
1417511 AATAGTTGAA
1417521 ACTAAATTTTGAGATTTAAAAA-ATAGAGAG
1 ACTAAATTTTGAGATTTAAAAATATA-AG-G
* **
1417551 ATTAAATTTCT-AGAAATAAAAATATAAGG
1 ACTAAATTT-TGAGATTTAAAAATATAAGG
* *
1417580 ACTAAATTTTGAAATTTACAAATA
1 ACTAAATTTTGAGATTTAAAAATA
1417604 GTATAGAGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.02
29 18 0.43
30 19 0.45
31 4 0.10
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.33
Consensus pattern (29 bp):
ACTAAATTTTGAGATTTAAAAATATAAGG
Found at i:1417602 original size:29 final size:30
Alignment explanation
Indices: 1417521--1417614 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 30
1417511 AATAGTTGAA
* *
1417521 ACTAAATTTTGAGATTTAAAAAATAGAGAG
1 ACTAAATTTTGAAATTTAAAATATAGAGAG
* *
1417551 ATTAAATTTCTAGAAA-TAAAAATATA-AG-G
1 ACTAAATTT-T-GAAATTTAAAATATAGAGAG
*
1417580 ACTAAATTTTGAAATTTACAAATAGTATAGAG
1 ACTAAATTTTGAAATTTA-AAATA-TAGAGAG
1417612 ACT
1 ACT
1417615 TATAGAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 14 0.27
30 12 0.24
31 11 0.22
32 7 0.14
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (30 bp):
ACTAAATTTTGAAATTTAAAATATAGAGAG
Found at i:1417730 original size:16 final size:16
Alignment explanation
Indices: 1417709--1417740 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1417699 ATTGGTTATC
*
1417709 TTGAAAAACTATTTTT
1 TTGAAAAAATATTTTT
1417725 TTGAAAAAATATTTTT
1 TTGAAAAAATATTTTT
1417741 GAAAAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTGAAAAAATATTTTT
Found at i:1421301 original size:17 final size:18
Alignment explanation
Indices: 1421279--1421318 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1421269 CTCCGTCTTT
*
1421279 GAGTTTAA-GTTAATTTA
1 GAGTTTAAGGTGAATTTA
1421296 GAGTTTAAGGTGAATTTA
1 GAGTTTAAGGTGAATTTA
1421314 -AGTTT
1 GAGTTT
1421319 TGGTTGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (18 bp):
GAGTTTAAGGTGAATTTA
Found at i:1423414 original size:14 final size:15
Alignment explanation
Indices: 1423387--1423417 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1423377 TTATTTTTAC
1423387 AAATTTTCAAAAAAT
1 AAATTTTCAAAAAAT
1423402 AAATTTT-AAAAAAT
1 AAATTTTCAAAAAAT
1423416 AA
1 AA
1423418 TACGAACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTTTCAAAAAAT
Found at i:1430331 original size:3 final size:3
Alignment explanation
Indices: 1430318--1430347 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1430308 TGATGATGAT
*
1430318 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1430348 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1434163 original size:2 final size:2
Alignment explanation
Indices: 1434156--1434189 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1434146 CACTGTCCTT
1434156 TA TA TA TA TA TA TA T- 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 T
1434190 GTTTTGGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1438358 original size:2 final size:2
Alignment explanation
Indices: 1438351--1438376 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1438341 TTGAAGATAA
1438351 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1438377 GAAAACAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1441369 original size:48 final size:48
Alignment explanation
Indices: 1441308--1441427 Score: 231
Period size: 48 Copynumber: 2.5 Consensus size: 48
1441298 ATTACAAACA
*
1441308 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAAATTCATT
1441356 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAAATTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAAATTCATT
1441404 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
1441428 GTTCGGACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAAATTCATT
Found at i:1443984 original size:30 final size:30
Alignment explanation
Indices: 1443950--1444009 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1443940 CAAATGGTCA
1443950 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
* *
1443980 TTGAACTATTTGAAAGTTTTTATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1444010 ACTAGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (30 bp):
TTGAACTATTTAAAAGTTTTCATTTAAGTC
Found at i:1450480 original size:22 final size:22
Alignment explanation
Indices: 1450455--1450501 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1450445 TTAATATTTC
*
1450455 AAAATT-TTTAAATAAAATTAAA
1 AAAATTATTT-AATAAAATGAAA
*
1450477 AAAATTATTTACTAAAATGAAA
1 AAAATTATTTAATAAAATGAAA
1450499 AAA
1 AAA
1450502 TTGCATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTATTTAATAAAATGAAA
Found at i:1454783 original size:60 final size:58
Alignment explanation
Indices: 1454719--1454845 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 58
1454709 GGAAAAATTA
* * * * *
1454719 AATAGTTAGATGACTATTTTATAATTTTTCATAGTTAGATGACTAAAAAAGAAATTTACT
1 AATAGTT-GATGACTATTTTATAACTTTTCATAATTAAATGAC-AAAAAAGAAATATACC
* * *
1454779 AATAGTTGAGTGACTATTTTGTCACTTTTCATAATTAAATGACCAAAAAGAAATATACC
1 AATAGTTGA-TGACTATTTTATAACTTTTCATAATTAAATGACAAAAAAGAAATATACC
1454838 AATAGTTG
1 AATAGTTG
1454846 GGTGACTACT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 23 0.40
60 35 0.60
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (58 bp):
AATAGTTGATGACTATTTTATAACTTTTCATAATTAAATGACAAAAAAGAAATATACC
Found at i:1460609 original size:12 final size:12
Alignment explanation
Indices: 1460592--1460617 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1460582 TTAGAACTCA
1460592 ATCTAAATGCCT
1 ATCTAAATGCCT
1460604 ATCTAAATGCCT
1 ATCTAAATGCCT
1460616 AT
1 AT
1460618 GAAAGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCTAAATGCCT
Found at i:1464383 original size:11 final size:11
Alignment explanation
Indices: 1464367--1464391 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1464357 AAAAAATCAT
1464367 AATTATAATAA
1 AATTATAATAA
1464378 AATTATAATAA
1 AATTATAATAA
1464389 AAT
1 AAT
1464392 ATGAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATAATAA
Found at i:1464385 original size:17 final size:16
Alignment explanation
Indices: 1464353--1464386 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1464343 GTGATGGTAT
1464353 TTATAAAAAATCATAA
1 TTATAAAAAATCATAA
*
1464369 TTATAATAAAATTATAA
1 TTATAA-AAAATCATAA
1464386 T
1 T
1464387 AAAATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATAAAAAATCATAA
Found at i:1465898 original size:3 final size:3
Alignment explanation
Indices: 1465890--1465931 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1465880 GTGGGGTCTT
1465890 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1465932 CCTGCTAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1465981 original size:27 final size:27
Alignment explanation
Indices: 1465943--1465998 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1465933 CTGCTAAACT
1465943 CATAGCCAAAACTTCCCAACTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
*
1465970 CATAGCCAAAACTTCCCAGCTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
1465997 CA
1 CA
1465999 CATACATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.41, G:0.05, T:0.18
Consensus pattern (27 bp):
CATAGCCAAAACTTCCCAACTTAACCC
Found at i:1469805 original size:17 final size:17
Alignment explanation
Indices: 1469783--1469823 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1469773 GATTTCATCA
*
1469783 ATTTAAATCTT-ATTTTG
1 ATTTAAATCTTGA-ATTG
1469800 ATTTAAA-CTTGAATTG
1 ATTTAAATCTTGAATTG
1469816 ATTTAAAT
1 ATTTAAAT
1469824 TCAAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTTAAATCTTGAATTG
Found at i:1473259 original size:24 final size:25
Alignment explanation
Indices: 1473212--1473259 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1473202 ATTAAAATTG
* *
1473212 TAAGTGGATATTATTTTTTTAAATAA
1 TAAGTGGATA-TATTTATTCAAATAA
1473238 TAAGTGGATA-ATTTATTCAAAT
1 TAAGTGGATATATTTATTCAAAT
1473260 TACTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
26 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TAAGTGGATATATTTATTCAAATAA
Found at i:1475754 original size:21 final size:21
Alignment explanation
Indices: 1475719--1475759 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1475709 TTTGTAATAT
* *
1475719 TATTAATTCATTTATGTTTTA
1 TATTAATTCAATTATATTTTA
*
1475740 TATTAATTTAATTATATTTT
1 TATTAATTCAATTATATTTT
1475760 GTAACTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTAATTCAATTATATTTTA
Found at i:1484726 original size:25 final size:23
Alignment explanation
Indices: 1484698--1484744 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1484688 AATTTAAATT
1484698 ATAATAAAAGTGTAATTTAACATGG
1 ATAA-AAAA-TGTAATTTAACATGG
*
1484723 ATAAAAAATGTCATTTAACATG
1 ATAAAAAATGTAATTTAACATG
1484745 CACGGATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (23 bp):
ATAAAAAATGTAATTTAACATGG
Found at i:1486218 original size:31 final size:31
Alignment explanation
Indices: 1486156--1486220 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1486146 TGTAATAATG
*
1486156 ATATATACACAATATGATATTAAGAATATAT
1 ATATATACACAATATGATATTAAGAAAATAT
1486187 ATATATACACAATAT-AGTATTTAA-AAAATAT
1 ATATATACACAATATGA-TA-TTAAGAAAATAT
1486218 ATA
1 ATA
1486221 CATAGGATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.03
31 26 0.84
32 4 0.13
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (31 bp):
ATATATACACAATATGATATTAAGAAAATAT
Found at i:1486414 original size:3 final size:3
Alignment explanation
Indices: 1486406--1486469 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
1486396 GCATATAAAA
*
1486406 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1486454 AAT AAG AAT AAG AAT A
1 AAT AAT AAT AAT AAT A
1486470 TCTACAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1486586 original size:37 final size:37
Alignment explanation
Indices: 1486515--1486586 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
1486505 AAATATATAC
* *
1486515 ATATAAAATATTTACAATAATGATGTAAATAAACAAT
1 ATATAAAATATTTACAATAATCATATAAATAAACAAT
1486552 ATATAAAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATAAAATATTT-ACAATAATCATATAAAT-AAACA
1486587 TTTAAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (37 bp):
ATATAAAATATTTACAATAATCATATAAATAAACAAT
Found at i:1488360 original size:107 final size:108
Alignment explanation
Indices: 1488170--1488367 Score: 326
Period size: 107 Copynumber: 1.8 Consensus size: 108
1488160 ATGTGACCCG
* *
1488170 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTTAACTC
1 AGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1488235 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAA
66 ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAA
*** **
1488278 AGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTTGAAAC-TTAATTAAAAGGCTCAACTC
1 AGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1488342 ACCTCTCGCAATATGAGTTGATTTTT
66 ACCTCTCGCAATATGAGTTGATTTTT
1488368 TTTTATTTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 43 0.52
108 40 0.48
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (108 bp):
AGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAA
Found at i:1488369 original size:53 final size:54
Alignment explanation
Indices: 1488170--1488367 Score: 317
Period size: 54 Copynumber: 3.7 Consensus size: 54
1488160 ATGTGACCCG
1488170 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
* *
1488224 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
* *** **
1488278 AGGCTCAACCCACCTCTCGCAATATGAGTTGATTTTTTTGAAAC-TTAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1488331 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1488368 TTTTATTTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 43 0.32
54 91 0.68
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:1488533 original size:75 final size:73
Alignment explanation
Indices: 1488402--1488561 Score: 205
Period size: 75 Copynumber: 2.2 Consensus size: 73
1488392 TTGAAAAACG
* * *
1488402 GAAATTGAAAATACCTCGGCGTGTGACCTGAGACTCAACTCACTTCTCGTAATATGAGTTAATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAA---
*
1488467 TTTTGATGAACA
62 TTTTGACGAACA
* * * *
1488479 GAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAATTTT
1488543 GACGAACA
66 GACGAACA
1488551 GAAATTGAAAA
1 GAAATTGAAAA
1488562 ACAGAAATTG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 21 0.28
75 31 0.42
77 22 0.30
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (73 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAATTTT
GACGAACA
Found at i:1488564 original size:14 final size:14
Alignment explanation
Indices: 1488547--1488575 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1488537 GATTTTGACG
1488547 AACAGAAATTGAAA
1 AACAGAAATTGAAA
1488561 AACAGAAATTGAAA
1 AACAGAAATTGAAA
1488575 A
1 A
1488576 TACCTCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:1488660 original size:80 final size:78
Alignment explanation
Indices: 1488564--1488709 Score: 238
Period size: 78 Copynumber: 1.8 Consensus size: 78
1488554 ATTGAAAAAC
*
1488564 AGAAATTGAAAATACCTCAGCACGTGAGCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATT
1 AGAAATTGAAAATACCTCAG--CGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATT
1488629 TTTTTTTTTATGAAT
64 TTTTTTTTTATGAAT
* * *
1488644 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTT
1488709 T
66 T
1488710 GAAAAACATA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 43 0.69
80 19 0.31
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (78 bp):
AGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTT
TTTTTTTATGAAT
Found at i:1488697 original size:166 final size:165
Alignment explanation
Indices: 1488386--1489226 Score: 819
Period size: 166 Copynumber: 5.1 Consensus size: 165
1488376 TTTTTTAAGG
* * * * *
1488386 CAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGACTCAACTCACTTCTCG
1 CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTCTCG
* * *
1488451 TAATATGAGTT-AATTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAA
66 CAATATGAGTTGATTTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAA
**
1488515 CTCACCTCTCGCAATATGAGTTGA-TTTTGACGAA
131 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* * *
1488549 CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCACGTGAGCTGAGGCTCAACTCACCTCTCA
1 CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTCTCG
* *
1488614 CAATATGAGTTGATTTTTTTTTTTATGAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
66 CAATATGAGTTGA--TTTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
1488679 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
129 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* *
1488716 CATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGT--CCTGAGGCTCAACTCACCTCT
1 CAGAAATTG-A-AAAACAGAAATTGAAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTCT
* * * *
1488779 CGCAATATGAGTTGA-TTTTTTTGAAGAACAGAAATTAAAACTACCTCAGCATGTCCTGAGGCTC
64 CGCAATATGAGTTGATTTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
1488843 AACTCACCTCTCGCAATATGAGTTGACTTTTTCTGAAAAAA
129 AACTCACCTCTCGCAATATGAGTTGA--TTTT-TG-AAAAA
* * * * *
1488884 CA-AAATTTGAAAAATAGAATTTGAAAATACCTCAACGTGTGAGCC-AAGGCTCAACTCACCTCT
1 CAGAAA-TTGAAAAACAGAAATTGAAAATACCTCAGCATGTGA-CCTGAGGCTCAACTCACCTCT
* * **
1488947 CGCAATATGAGTTGATTTTTTTGAAACACAGAAATTGAAGAACAGAAATAGAAAACACCTCAGAA
64 CGCAATATGAGTTGA-TTTTTT------------TTGATGAACAGAAATTGAAATTACCTCAG--
** * *
1489012 TATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT------
114 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* * * * *
1489058 ------TT-AAACACAAAAATTGAAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTC
1 CAGAAATTGAAAAACAGAAATTG-AAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTCTC
* * * * * *
1489116 GCAATATGAGTTGA--TTTTTTGA-AAAGTATAAATTGAAAATACCTCAACGTGTCTTGAGGCTC
65 GCAATATGAGTTGATTTTTTTTGATGAA-CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
* ** * *
1489178 GACTCATTTCTCGCAATATGAGTTGAGTTTTGACAAA
129 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
1489215 TAGAAATTGAAA
1 CAGAAATTGAAA
1489227 TTACCTCAGC
Statistics
Matches: 571, Mismatches: 61, Indels: 91
0.79 0.08 0.13
Matches are distributed among these distances:
151 37 0.06
152 2 0.00
153 20 0.04
163 69 0.12
164 73 0.13
165 4 0.01
166 101 0.18
167 68 0.12
168 94 0.16
169 30 0.05
170 5 0.01
181 1 0.00
182 29 0.05
184 38 0.07
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (165 bp):
CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
Found at i:1488733 original size:16 final size:16
Alignment explanation
Indices: 1488712--1488742 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1488702 TGATTTTTGA
*
1488712 AAAACATAAATTGAAG
1 AAAACAGAAATTGAAG
1488728 AAAACAGAAATTGAA
1 AAAACAGAAATTGAA
1488743 ATTACCTCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAACAGAAATTGAAG
Found at i:1488801 original size:330 final size:330
Alignment explanation
Indices: 1488389--1489226 Score: 904
Period size: 335 Copynumber: 2.5 Consensus size: 330
1488379 TTTAAGGCAG
* * * *
1488389 AAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGACTCAACTCACTTCTCGTAA
1 AAATTGAAAAAC-GAAATTG-AAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCTCTCGCAA
* *
1488454 TATGAGTTAATTTTTTTGATGAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
63 TATGAGTTGATTTTTTTGA-GAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
*
1488519 CCTCTCGCAATATGAGTTGA-TTTTGACGAACAGAAATTGAAAAACAGAAATTGAAAATACCTCA
127 CCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAAAACAGAAATTGAAAATACCTCA
* ** * * * *
1488583 GCACGTGAGCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTT-TTTTATGAATAGA
192 ACACGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTAATTGAAGAACAGA
* ** * * *
1488647 AATTGAAATTACCTCAG-CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
257 AATAGAAAACACCTCAGACATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
1488710 GAAAAACAT
322 GAAAAACAA
*
1488719 AAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGT-CCTGAGGCTCAACTCACCTCTCGCA
1 AAATTG-A-AAAAC-GAAATTGAAA-TACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCA
* *
1488783 ATATGAGTTGATTTTTTTGAAGAACAGAAATT-AAAACTACCTCAGCATGTCCTGAGGCTCAACT
62 ATATGAGTTGATTTTTTTG-AGAACAGAAATTGAAAA-TACCTCAGCGTGTCTTGAGGCTCAACT
* * *
1488847 CACCTCTCGCAATATGAGTTGACTTTTTCTGAAAAAACA-AAATTTGAAAAATAGAATTTGAAAA
125 CACCTCTCGCAATATGAGTTGA--TTTT-TG-ACAAACAGAAA-TTGAAAAACAGAAATTGAAAA
** *
1488911 TACCTCAACGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACAC
185 TACCTCAACACGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTT-------
*
1488976 AGAAATTGAAGAACAGAAATAGAAAACACCTCAGAATATGACCCGAGGCTCAACTCACCTCTCGC
243 ---AATTGAAGAACAGAAATAGAAAACACCTCAG-ACATGACCCGAGGCTCAACTCACCTCTCGC
* *
1489041 AATATGAGTTGATTTTTTTAAACACAA
304 AATATGAGTTGATTTTTTGAAAAACAA
*
1489068 AAATTGAAAAAC-----------ACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
1 AAATTGAAAAACGAAATTGAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATA
* * * * * **
1489122 TGAGTTGA-TTTTTTGAAAAGTATAAATTGAAAATACCTCAACGTGTCTTGAGGCTCGACTCATT
65 TGAGTTGATTTTTTTGAGAA-CAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACC
* *
1489186 TCTCGCAATATGAGTTGAGTTTTGACAAATAGAAATTGAAA
129 TCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAA
1489227 TTACCTCAGC
Statistics
Matches: 430, Mismatches: 48, Indels: 59
0.80 0.09 0.11
Matches are distributed among these distances:
329 3 0.01
330 104 0.24
331 16 0.04
332 28 0.07
333 6 0.01
334 19 0.04
335 132 0.31
336 39 0.09
346 23 0.05
347 5 0.01
348 38 0.09
349 17 0.04
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (330 bp):
AAATTGAAAAACGAAATTGAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTTGAGAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAAAACAGAAATTGAAAATACCTCAACAC
GTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTAATTGAAGAACAGAAATA
GAAAACACCTCAGACATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
AACAA
Found at i:1488853 original size:75 final size:76
Alignment explanation
Indices: 1488730--1488879 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 76
1488720 AATTGAAGAA
* *
1488730 AACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 AACAGAAATTAAAACTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAC
*
1488794 TTTTTTTGAAG
66 TTTTTCTGAAG
1488805 AACAGAAATTAAAACTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAC
1 AACAGAAATTAAAACTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAC
1488870 TTTTTCTGAA
66 TTTTTCTGAA
1488880 AAAACAAAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 62 0.87
76 9 0.13
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (76 bp):
AACAGAAATTAAAACTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAC
TTTTTCTGAAG
Found at i:1489041 original size:91 final size:88
Alignment explanation
Indices: 1488799--1489139 Score: 318
Period size: 91 Copynumber: 3.9 Consensus size: 88
1488789 GTTGATTTTT
* * * * *
1488799 TTGAAGAACAGAAATTAAAACTACCTCAG-CATGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATGAAAAC-ACCTCAGATATGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
1488863 AGTTGACTTTTTCTGAAAAAACAAAA
65 AGTTGA-TTTTTTTG-AAACACAAAA
* * * * * *
1488889 TTTGAAAAATAGAATTTGAAAATACCTCA-ACGTGTGAGCCAAGGCTCAACTCACCTCTCGCAAT
1 -TTGAAAAACAGAA-ATGAAAACACCTCAGA--TATGACCCGAGGCTCAACTCACCTCTCGCAAT
1488953 ATGAGTTGATTTTTTTGAAACACAGAAA
62 ATGAGTTGATTTTTTTGAAACACA-AAA
*
1488981 TTGAAGAACAGAAATAGAAAACACCTCAGAATATGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAAT-GAAAACACCTCAG-ATATGACCCGAGGCTCAACTCACCTCTCGCAATAT
1489046 GAGTTGATTTTTTT-AAACACAAAAA
64 GAGTTGATTTTTTTGAAACAC-AAAA
* *
1489071 TT--------G--A--AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATGAAAACACCTCAG-ATATGACCCGAGGCTCAACTCACCTCTCGCAATATG
1489124 AGTTGA-TTTTTTGAAA
65 AGTTGATTTTTTTGAAA
1489140 AGTATAAATT
Statistics
Matches: 217, Mismatches: 23, Indels: 34
0.79 0.08 0.12
Matches are distributed among these distances:
76 6 0.03
77 55 0.25
80 1 0.00
82 1 0.00
90 12 0.06
91 91 0.42
92 15 0.07
93 36 0.17
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATGAAAACACCTCAGATATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTGAAACACAAAA
Found at i:1489125 original size:77 final size:74
Alignment explanation
Indices: 1488992--1489286 Score: 321
Period size: 77 Copynumber: 4.0 Consensus size: 74
1488982 TGAAGAACAG
* **
1488992 AAATAGAAAACACCTCAGAATATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAACACCTCAGCGTATG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
1489057 TTTAAACACAA
65 TTGAAA-ATAA
*
1489068 AAATTGAAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAATTG-AAAACACCTCAGCGTATG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
1489133 TTTGAAAAGTAT
64 TTTGAAAA-TAA
* * * ** * ** *
1489145 AAATTGAAAATACCTCAACGTGT-CTTGAGGCTCGACTCATTTCTCGCAATATGAGTTGA-GTTT
1 AAATTGAAAACACCTCAGCGTATGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
1489208 TGACAAATAG
66 TGA-AAATAA
**
1489218 AAATTGAAATTACCTCAGC--ATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
1 AAATTGAAAACACCTCAGCGTATGCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1489280 TTGAAAA
65 TTGAAAA
1489287 CAGAAATAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
71 1 0.01
72 4 0.02
73 61 0.32
74 34 0.18
76 21 0.11
77 68 0.36
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (74 bp):
AAATTGAAAACACCTCAGCGTATGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
TGAAAATAA
Found at i:1489250 original size:73 final size:72
Alignment explanation
Indices: 1489020--1489293 Score: 307
Period size: 73 Copynumber: 3.7 Consensus size: 72
1489010 AATATGACCC
* * * *
1489020 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAACACAAAAATTGAAAAACACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-ATAGAAATTG-AAAATACCTC
* *
1489085 AGCGTGTGACCC-
63 AAC--ATG-CCCT
*
1489097 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTATAAATTGAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA-TAGAAATTGAAAATACCTCA
* * *
1489162 ACGTGTCTT
64 ACATGCCCT
* ** * * *
1489171 GAGGCTCGACTCATTTCTCGCAATATGAGTTGAGTTTTGACAAATAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAATAGAAATTGAAAATACCTCAA
1489236 CATGCCCT
65 CATGCCCT
*
1489244 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAAT
1489294 AAAACATCAA
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
72 9 0.05
73 66 0.38
74 36 0.21
76 12 0.07
77 49 0.28
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (72 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATTGAAAATACCTCAAC
ATGCCCT
Found at i:1490866 original size:10 final size:10
Alignment explanation
Indices: 1490848--1490889 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1490838 GACCTCTCCA
*
1490848 TTTTCTTCTT
1 TTTTTTTCTT
1490858 TTTTTTTCTT
1 TTTTTTTCTT
1490868 TTTTTTT-TT
1 TTTTTTTCTT
1490877 TTTTTTTGCTT
1 TTTTTTT-CTT
1490888 TT
1 TT
1490890 GAATGAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.31
10 16 0.55
11 4 0.14
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1490866 original size:13 final size:12
Alignment explanation
Indices: 1490848--1490883 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1490838 GACCTCTCCA
1490848 TTTTCTTCTTTTT
1 TTTTCTT-TTTTT
1490861 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1490873 TTTT-TTTTTTT
1 TTTTCTTTTTTT
1490884 GCTTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.30
12 9 0.39
13 7 0.30
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1491484 original size:14 final size:14
Alignment explanation
Indices: 1491463--1491500 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1491453 TGGCTTTTGA
1491463 TTTC-TTTTTTTCT
1 TTTCATTTTTTTCT
1491476 TGTT-ATTTTTTTCT
1 T-TTCATTTTTTTCT
1491490 TTTCATTTTTT
1 TTTCATTTTTT
1491501 GTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTCATTTTTTTCT
Found at i:1491505 original size:13 final size:12
Alignment explanation
Indices: 1491463--1491522 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
1491453 TGGCTTTTGA
1491463 TTTCTTTTTTTCT
1 TTTC-TTTTTTCT
*
1491476 TGTTATTTTTTTCT
1 T-TT-CTTTTTTCT
*
1491490 TTTCATTTTTTGT
1 TTTC-TTTTTTCT
1491503 TTTC-TTTTTCTT
1 TTTCTTTTTTC-T
1491515 TTTCTTTT
1 TTTCTTTT
1491523 CATGACTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 17 0.45
14 11 0.29
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:1491506 original size:32 final size:30
Alignment explanation
Indices: 1491456--1491525 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 30
1491446 TTCTTTCTGG
* *
1491456 CTTTTGATTTCTTTTTTTCTTGTTATTTTTTT
1 CTTTTCATTTCTTTTTTTCTT-TT-TCTTTTT
1491488 CTTTTCATTT-TTTGTTTTCTTTTTCTTTTT
1 CTTTTCATTTCTTT-TTTTCTTTTTCTTTTT
1491518 CTTTTCAT
1 CTTTTCAT
1491526 GACTATCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 14 0.40
31 5 0.14
32 16 0.46
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (30 bp):
CTTTTCATTTCTTTTTTTCTTTTTCTTTTT
Found at i:1495799 original size:31 final size:31
Alignment explanation
Indices: 1495737--1495801 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1495727 TGTAATAATG
*
1495737 ATATATACACAATATGATATTAAGAATATAT
1 ATATATACACAATATGATATTAAGAAAATAT
1495768 ATATATACACAATAT-AGTATTTAA-AAAATAT
1 ATATATACACAATATGA-TA-TTAAGAAAATAT
1495799 ATA
1 ATA
1495802 CATAGGATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.03
31 26 0.84
32 4 0.13
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (31 bp):
ATATATACACAATATGATATTAAGAAAATAT
Found at i:1495989 original size:3 final size:3
Alignment explanation
Indices: 1495981--1496028 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1495971 ATATATGCAT
* * *
1495981 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA AGA ATA AGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1496029 TCTACAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1496145 original size:37 final size:37
Alignment explanation
Indices: 1496074--1496145 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
1496064 AAATATATAC
* *
1496074 ATATAAAATATTTACAATAATGATGTAAATAAACAAT
1 ATATAAAATATTTACAATAATCATATAAATAAACAAT
1496111 ATATAAAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATAAAATATTT-ACAATAATCATATAAAT-AAACA
1496146 TTTAAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (37 bp):
ATATAAAATATTTACAATAATCATATAAATAAACAAT
Found at i:1500350 original size:16 final size:16
Alignment explanation
Indices: 1500331--1500362 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1500321 AAAATTTTCT
1500331 ATTCAAATCATTTTAA
1 ATTCAAATCATTTTAA
*
1500347 ATTCACATCATTTTAA
1 ATTCAAATCATTTTAA
1500363 CTTGTTCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCAAATCATTTTAA
Found at i:1502470 original size:16 final size:17
Alignment explanation
Indices: 1502449--1502486 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1502439 TTTTGGATTC
1502449 GAGTTTAAATT-ATTTT
1 GAGTTTAAATTAATTTT
*
1502465 GAGTTTAAGTTAATTTT
1 GAGTTTAAATTAATTTT
*
1502482 TAGTT
1 GAGTT
1502487 CGAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (17 bp):
GAGTTTAAATTAATTTT
Found at i:1502718 original size:17 final size:17
Alignment explanation
Indices: 1502698--1502733 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1502688 TCACTTTGAG
*
1502698 TTCAAATTTACTCAGGT
1 TTCAAATTTACTCAAGT
*
1502715 TTCAAGTTTACTCAAGT
1 TTCAAATTTACTCAAGT
1502732 TT
1 TT
1502734 GTTAGTTGAG
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:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAAATTTACTCAAGT
Found at i:1502821 original size:17 final size:17
Alignment explanation
Indices: 1502795--1502830 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1502785 TGATATTAGG
*
1502795 TTCAAATTTACTCAGGT
1 TTCAAATTTACTCAAGT
*
1502812 TTCAAGTTTACTCAAGT
1 TTCAAATTTACTCAAGT
1502829 TT
1 TT
1502831 GATAGTCGAG
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:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAAATTTACTCAAGT
Found at i:1502863 original size:97 final size:97
Alignment explanation
Indices: 1502697--1502899 Score: 388
Period size: 97 Copynumber: 2.1 Consensus size: 97
1502687 TTCACTTTGA
* *
1502697 GTTCAAATTTACTCAGGTTTCAAGTTTACTCAAGTTTGTTAGTTGAGTTTTCAAGTTAAATCATT
1 GTTCAAATTTACTCAGGTTTCAAGTTTACTCAAGTTTGATAGTCGAGTTTTCAAGTTAAATCATT
1502762 TTTAGGTTTTTTTCATTTAAATTTGATATTAG
66 TTTAGGTTTTTTTCATTTAAATTTGATATTAG
1502794 GTTCAAATTTACTCAGGTTTCAAGTTTACTCAAGTTTGATAGTCGAGTTTTCAAGTTAAATCATT
1 GTTCAAATTTACTCAGGTTTCAAGTTTACTCAAGTTTGATAGTCGAGTTTTCAAGTTAAATCATT
1502859 TTTAGGTTTTTTTCATTTAAATTTGATATTAG
66 TTTAGGTTTTTTTCATTTAAATTTGATATTAG
1502891 GTTCAAATT
1 GTTCAAATT
1502900 ACTTTTCATT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 104 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (97 bp):
GTTCAAATTTACTCAGGTTTCAAGTTTACTCAAGTTTGATAGTCGAGTTTTCAAGTTAAATCATT
TTTAGGTTTTTTTCATTTAAATTTGATATTAG
Found at i:1507764 original size:38 final size:39
Alignment explanation
Indices: 1507689--1507764 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
1507679 TGGCATTTAA
* *
1507689 GAGAAAAATAACTATAAATCCTAAAAAAATGATATTATT
1 GAGAAAAATAACCATAAATCCTAAAAAAATGACATTATT
* * **
1507728 GAGAAAATTAACCATAAA-CCTTAAAATTTGACATTAT
1 GAGAAAAATAACCATAAATCCTAAAAAAATGACATTAT
1507765 AAAAAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
38 15 0.48
39 16 0.52
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.29
Consensus pattern (39 bp):
GAGAAAAATAACCATAAATCCTAAAAAAATGACATTATT
Found at i:1507778 original size:23 final size:22
Alignment explanation
Indices: 1507751--1507814 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
1507741 ATAAACCTTA
1507751 AAATTTGACA-TTATAAAAAAAAT
1 AAATTT-ACACTT-TAAAAAAAAT
*
1507774 AAATTTACACTTTGAAAAAAAT
1 AAATTTACACTTTAAAAAAAAT
*
1507796 AAATTTACACTTTGAAAAA
1 AAATTTACACTTTAAAAAA
1507815 TTAATCTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 31 0.79
23 8 0.21
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (22 bp):
AAATTTACACTTTAAAAAAAAT
Found at i:1507794 original size:22 final size:22
Alignment explanation
Indices: 1507766--1507814 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1507756 TGACATTATA
1507766 AAAAAAATAAATTTACACTTTG
1 AAAAAAATAAATTTACACTTTG
1507788 AAAAAAATAAATTTACACTTTG
1 AAAAAAATAAATTTACACTTTG
1507810 AAAAA
1 AAAAA
1507815 TTAATCTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAAAAATAAATTTACACTTTG
Found at i:1510793 original size:33 final size:33
Alignment explanation
Indices: 1510754--1510845 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
1510744 ACTTCCTTCA
* *
1510754 TCATCCTCATCATCGTCATCGTCATCTTCATCT
1 TCATCCTCATCATCCTCATCCTCATCTTCATCT
*
1510787 TCATCCTCATCATCCTCGTCCTCATCTTCATCT
1 TCATCCTCATCATCCTCATCCTCATCTTCATCT
*
1510820 TCATCCTCATCATCCTCGTCCTCATC
1 TCATCCTCATCATCCTCATCCTCATC
1510846 CTCGTCCACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.16, C:0.41, G:0.04, T:0.38
Consensus pattern (33 bp):
TCATCCTCATCATCCTCATCCTCATCTTCATCT
Found at i:1510817 original size:6 final size:6
Alignment explanation
Indices: 1510749--1510830 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 6
1510739 GTCTTACTTC
* * * * *
1510749 CTTCAT CATCCT CATCAT CGTCAT CGTCAT CTTCAT CTTCAT CCTCATCAT
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT -CT--TCAT
* * * *
1510800 CCTCGT CCTCAT CTTCAT CTTCAT CCTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
1510831 ATCCTCGTCC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
6 56 0.89
7 2 0.03
8 1 0.02
9 4 0.06
ACGTcount: A:0.17, C:0.40, G:0.04, T:0.39
Consensus pattern (6 bp):
CTTCAT
Found at i:1510863 original size:33 final size:33
Alignment explanation
Indices: 1510755--1510866 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 33
1510745 CTTCCTTCAT
* * * * **
1510755 CATCCTCATCATCGTCATCGTCATCTTCATCTT
1 CATCCTCATCATCCTCGTCCTCATCCTCATCCA
* **
1510788 CATCCTCATCATCCTCGTCCTCATCTTCATCTT
1 CATCCTCATCATCCTCGTCCTCATCCTCATCCA
*
1510821 CATCCTCATCATCCTCGTCCTCATCCTCGTCCA
1 CATCCTCATCATCCTCGTCCTCATCCTCATCCA
*
1510854 CATCATCATCATC
1 CATCCTCATCATC
1510867 ATCTCCTATC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.18, C:0.42, G:0.04, T:0.36
Consensus pattern (33 bp):
CATCCTCATCATCCTCGTCCTCATCCTCATCCA
Found at i:1510869 original size:12 final size:12
Alignment explanation
Indices: 1510751--1510869 Score: 69
Period size: 12 Copynumber: 9.9 Consensus size: 12
1510741 CTTACTTCCT
*
1510751 TCATCATCCTCA
1 TCATCATCATCA
* *
1510763 TCATCGTCATCG
1 TCATCATCATCA
* *
1510775 TCATCTTCATCT
1 TCATCATCATCA
*
1510787 TCATCCTCATCA
1 TCATCATCATCA
* * *
1510799 TCCTCGTCCTCA
1 TCATCATCATCA
* *
1510811 TCTTCATCTTCA
1 TCATCATCATCA
* *
1510823 TCCTCATCATCC
1 TCATCATCATCA
* * *
1510835 TCGTCCTCATCC
1 TCATCATCATCA
*
1510847 TCGTCCA-CATCA
1 TCAT-CATCATCA
1510859 TCATCATCATC
1 TCATCATCATC
1510870 TCCTATCTCT
Statistics
Matches: 84, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
11 2 0.02
12 81 0.96
13 1 0.01
ACGTcount: A:0.18, C:0.41, G:0.04, T:0.36
Consensus pattern (12 bp):
TCATCATCATCA
Found at i:1513499 original size:15 final size:15
Alignment explanation
Indices: 1513479--1513510 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1513469 GTGCATACAC
1513479 TTTGCTATCTTTTCT
1 TTTGCTATCTTTTCT
1513494 TTTGCTATCTTTTCT
1 TTTGCTATCTTTTCT
1513509 TT
1 TT
1513511 CATCGTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTGCTATCTTTTCT
Found at i:1523800 original size:17 final size:16
Alignment explanation
Indices: 1523768--1523832 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
1523758 ATATCTTGTC
*
1523768 TATAAATAATTTTAAAA
1 TATAAA-AATTATAAAA
1523785 TTATAAAAATTATAAAA
1 -TATAAAAATTATAAAA
*
1523802 AATTAAAAATTATTAAAA
1 TA-TAAAAATTA-TAAAA
*
1523820 -A-AAAAAGTATAAA
1 TATAAAAATTATAAA
1523833 GTACACACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 1 0.02
17 19 0.45
18 11 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
TATAAAAATTATAAAA
Found at i:1523816 original size:10 final size:9
Alignment explanation
Indices: 1523768--1523820 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
1523758 ATATCTTGTC
1523768 TATAAATAAT
1 TATAAA-AAT
*
1523778 T-TTAAAAT
1 TATAAAAAT
1523786 TATAAAAAT
1 TATAAAAAT
*
1523795 TATAAAAAA
1 TATAAAAAT
1523804 T-TAAAAAT
1 TATAAAAAT
1523812 TATTAAAAA
1 TA-TAAAAA
1523821 AAAAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 11 0.31
9 18 0.50
10 7 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TATAAAAAT
Found at i:1532882 original size:54 final size:53
Alignment explanation
Indices: 1532824--1532940 Score: 198
Period size: 54 Copynumber: 2.2 Consensus size: 53
1532814 ATTACAATGA
1532824 TATTTTCCAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTTT
1 TATTTTCCAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATA-TTTT
* * *
1532878 TATTTTCTAATTATGTAAAAAATAGACAAGATAGAAATGGTATTTCATATTTT
1 TATTTTCCAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTT
1532931 TATTTTCCAA
1 TATTTTCCAA
1532941 AATTGAGGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 13 0.22
54 46 0.78
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (53 bp):
TATTTTCCAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTT
Found at i:1533200 original size:47 final size:47
Alignment explanation
Indices: 1533126--1533215 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
1533116 AGTATTTTCT
* * *
1533126 GTCAAAATTTGCCATCAATACAGCTATGCTATCATACTAACTTTAGA
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
* * *
1533173 GTCAAAATTTACCATCAATGCACCTATGCAATGATATTAACTT
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTT
1533216 CCAGAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (47 bp):
GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
Found at i:1540447 original size:31 final size:31
Alignment explanation
Indices: 1540392--1540457 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1540382 TTTTTAACTA
* * *
1540392 AATTTGATCTTCAACCTTTTAAAAAGAATCG
1 AATTTGACCATCAACCTTTCAAAAAGAATCG
* *
1540423 AATTTGACCATCAATCTTTCAAAAAGAGTCG
1 AATTTGACCATCAACCTTTCAAAAAGAATCG
1540454 AATT
1 AATT
1540458 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAAGAATCG
Found at i:1541671 original size:34 final size:31
Alignment explanation
Indices: 1541597--1541707 Score: 95
Period size: 31 Copynumber: 3.5 Consensus size: 31
1541587 AAAATAATTT
* * *
1541597 AATATAATTATACATAAAATAT--AATTTTA
1 AATATAATAATACATAATATTTGAAATTTTA
*
1541626 AATAGT-TTAATACATGACATATTTTGAAATTTTA
1 AATA-TAATAATACAT-A-ATA-TTTGAAATTTTA
* *
1541660 AATATAATAATAAATAATATTTGAACAATTT-
1 AATATAATAATACATAATATTTGAA-ATTTTA
1541691 AATATAATAATACATAA
1 AATATAATAATACATAA
1541708 AATATATTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
29 11 0.17
30 2 0.03
31 24 0.36
32 9 0.14
33 2 0.03
34 18 0.27
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (31 bp):
AATATAATAATACATAATATTTGAAATTTTA
Found at i:1541683 original size:31 final size:31
Alignment explanation
Indices: 1541648--1541745 Score: 90
Period size: 37 Copynumber: 3.0 Consensus size: 31
1541638 CATGACATAT
1541648 TTTGAAATTTTAAATATAATAATAAATAATA
1 TTTGAAATTTTAAATATAATAATAAATAATA
* *
1541679 TTTGAACAATTTAATATAATAATACATAAAATATATT
1 TTTGAA-ATTTTAA-AT-ATAATA-AT-AAATA-ATA
* *
1541716 TTTAAAATTTTTAAATATAAT-TTAAATAAT
1 TTTGAAA-TTTTAAATATAATAATAAATAAT
1541746 TAATGTAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
31 8 0.15
32 11 0.20
33 3 0.05
34 6 0.11
35 7 0.13
36 8 0.15
37 12 0.22
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
TTTGAAATTTTAAATATAATAATAAATAATA
Found at i:1541736 original size:35 final size:32
Alignment explanation
Indices: 1541644--1541745 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 32
1541634 AATACATGAC
*
1541644 ATATTTTGAAATTTTAAATATAATAATAAATA
1 ATATTTTAAAATTTTAAATATAATAATAAATA
*
1541676 ATATTTGAACAA-TTTAATATAATAATACATAAA-A
1 ATATTTTAA-AATTTTAA-AT-ATAATA-ATAAATA
*
1541710 TATATTTTTAAAATTTTTAAATATAAT-TTAAATA
1 -ATA-TTTTAAAA-TTTTAAATATAATAATAAATA
1541744 AT
1 AT
1541746 TAATGTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
32 12 0.21
33 10 0.18
34 8 0.14
35 15 0.26
36 7 0.12
37 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
ATATTTTAAAATTTTAAATATAATAATAAATA
Found at i:1543738 original size:25 final size:25
Alignment explanation
Indices: 1543704--1543756 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1543694 ATATCGATAA
1543704 ATTTTATGTACAATTCATGAAAAAC
1 ATTTTATGTACAATTCATGAAAAAC
1543729 ATTTTATGTACAATTCATGAAAAAC
1 ATTTTATGTACAATTCATGAAAAAC
1543754 ATT
1 ATT
1543757 AACTTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (25 bp):
ATTTTATGTACAATTCATGAAAAAC
Found at i:1544489 original size:4 final size:5
Alignment explanation
Indices: 1544464--1544496 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1544454 TACTGTGAAA
1544464 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
1544497 GAACACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1548938 original size:9 final size:9
Alignment explanation
Indices: 1548924--1548954 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1548914 AATTTGTGAA
1548924 AAATAAAAT
1 AAATAAAAT
1548933 AAATAAAAT
1 AAATAAAAT
1548942 AAATAAAAAT
1 AAAT-AAAAT
1548952 AAA
1 AAA
1548955 GAACACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1550706 original size:204 final size:206
Alignment explanation
Indices: 1550304--1550717 Score: 805
Period size: 204 Copynumber: 2.0 Consensus size: 206
1550294 TTATATTTTT
1550304 AAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAATGC
1 AAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAATGC
1550369 TCATTTTATCAAAATAAATTTAAAAAATTTAAAAAAAAAATTTAACCAACCCAACCTAATCCAGT
66 TCATTTTATCAAAATAAATTTAAAAAATTTAAAAAAAAAATTTAACCAACCCAACCTAATCCAGT
*
1550434 CAGCAAAAAAGGCAAAAGTCCACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAG
131 CAGCAAAAAAGGCAAAAGTCAACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAG
1550499 AAAAGAGATTA
196 AAAAGAGATTA
1550510 AAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAATGC
1 AAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAATGC
1550575 TCATTTTATCAAAATAAATTTAAAAAA-TT-AAAAAAAAATTTAACCAACCCAACCTAATCCAGT
66 TCATTTTATCAAAATAAATTTAAAAAATTTAAAAAAAAAATTTAACCAACCCAACCTAATCCAGT
1550638 CAGCAAAAAAGGCAAAAGTCAACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAG
131 CAGCAAAAAAGGCAAAAGTCAACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAG
1550703 AAAAGAGATTA
196 AAAAGAGATTA
1550714 AAAA
1 AAAA
1550718 AAAATTTTAA
Statistics
Matches: 207, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
204 113 0.55
205 2 0.01
206 92 0.44
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.22
Consensus pattern (206 bp):
AAAATATTAATGAAAAAATTCATAAAAAATTACCAGACAATATTAAATAAATTATAAAATAATGC
TCATTTTATCAAAATAAATTTAAAAAATTTAAAAAAAAAATTTAACCAACCCAACCTAATCCAGT
CAGCAAAAAAGGCAAAAGTCAACTCAGAAGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAG
AAAAGAGATTA
Found at i:1550802 original size:106 final size:106
Alignment explanation
Indices: 1550601--1550816 Score: 389
Period size: 106 Copynumber: 2.0 Consensus size: 106
1550591 AATTTAAAAA
1550601 ATTAAAAAAAAATTTAACCAACCCAACCTAATCCAGTCAGCAAAAAAGGCAAAAGTCAACTCAGA
1 ATTAAAAAAAAATTTAACCAACCCAACCTAATCCAGTCAGCAAAAAAGGCAAAAGT--A-TCAGA
1550666 AGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAGAAAAGAG
63 AGCCATAAAAACAAAACGGTGCCGTATAAGTAACAAGAAAAGAG
1550710 ATTAAAAAAAAATTTTAACCAACCCAACCTAATCCAGTCAGCAAAAAAGGCAAAAGT-TCAGAAG
1 ATTAAAAAAAAA-TTTAACCAACCCAACCTAATCCAGTCAGCAAAAAAGGCAAAAGTATCAGAAG
1550774 CCATAAAAACAAAACGGTGCCGTATAAGTAACAAGAAAAGAG
65 CCATAAAAACAAAACGGTGCCGTATAAGTAACAAGAAAAGAG
1550816 A
1 A
1550817 GGCAAATTTT
Statistics
Matches: 106, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
106 50 0.47
109 12 0.11
110 44 0.42
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.14
Consensus pattern (106 bp):
ATTAAAAAAAAATTTAACCAACCCAACCTAATCCAGTCAGCAAAAAAGGCAAAAGTATCAGAAGC
CATAAAAACAAAACGGTGCCGTATAAGTAACAAGAAAAGAG
Found at i:1550936 original size:15 final size:16
Alignment explanation
Indices: 1550907--1550949 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1550897 TATAGAAAAG
* *
1550907 AAAAGAAAAACTAA-T
1 AAAAAAAAAAATAATT
*
1550922 AACAAAAAAAATAATT
1 AAAAAAAAAAATAATT
1550938 AAAAAAAAAAAT
1 AAAAAAAAAAAT
1550950 CCTTTGCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAAAAAAAAATAATT
Found at i:1551226 original size:10 final size:10
Alignment explanation
Indices: 1551211--1551246 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1551201 CCCTCTCTAG
1551211 TATTTTTATT
1 TATTTTTATT
1551221 TATTTTT-TT
1 TATTTTTATT
*
1551230 AATTTTTATT
1 TATTTTTATT
1551240 TATTTTT
1 TATTTTT
1551247 CGTCGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1552527 original size:41 final size:42
Alignment explanation
Indices: 1552438--1552536 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
1552428 TGAATGAACC
*
1552438 ATACATCTTATTATTGATGATAAGATTGAACTTTGAGAAACT
1 ATACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACT
1552480 ATACATCTTGTTATTGATGATAAGATTGAAC-TTGAGAAACT
1 ATACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACT
*
1552521 ATACATCTCGTTATTG
1 ATACATCTTGTTATTG
1552537 GTTTAAAGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 25 0.45
42 30 0.55
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (42 bp):
ATACATCTTGTTATTGATGATAAGATTGAACTTTGAGAAACT
Found at i:1556996 original size:28 final size:27
Alignment explanation
Indices: 1556943--1556997 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1556933 CAACTTCATG
* * **
1556943 ACCTAACTTAGACAAAAAAATTTCAAA
1 ACCTAACTTAAAAAAAAAAAAATCAAA
1556970 ACCTAACTTAAATAAAAAAAAAATCAAA
1 ACCTAACTTAAA-AAAAAAAAAATCAAA
1556998 CACCAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.62, C:0.16, G:0.02, T:0.20
Consensus pattern (27 bp):
ACCTAACTTAAAAAAAAAAAAATCAAA
Found at i:1558993 original size:37 final size:37
Alignment explanation
Indices: 1558952--1559026 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1558942 ATAACATCGA
1558952 AGGTTAATTTTAAAAGAACGAGAAAAAAATAAAAATT
1 AGGTTAATTTTAAAAGAACGAGAAAAAAATAAAAATT
1558989 AGGTTAATTTTAAAAGAACGAGAAAAAAATAAAAATT
1 AGGTTAATTTTAAAAGAACGAGAAAAAAATAAAAATT
1559026 A
1 A
1559027 TTATCTTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.24
Consensus pattern (37 bp):
AGGTTAATTTTAAAAGAACGAGAAAAAAATAAAAATT
Found at i:1560841 original size:31 final size:31
Alignment explanation
Indices: 1560767--1560839 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
1560757 TGAGAATTAA
1560767 ATTAAATTAAAAATTTATATATAAAATTACAC
1 ATTAAA-TAAAAATTTATATATAAAATTACAC
* * *
1560799 A--AAATCAAAATTTATATATAAAATTATAT
1 ATTAAATAAAAATTTATATATAAAATTACAC
1560828 ATTAAACTAAAA
1 ATTAAA-TAAAA
1560840 TTCATGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 23 0.68
30 3 0.09
31 3 0.09
32 5 0.15
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTAAATAAAAATTTATATATAAAATTACAC
Found at i:1561159 original size:24 final size:23
Alignment explanation
Indices: 1561114--1561161 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
1561104 GTTTACACAT
1561114 ATTAATTTAATCTTAATTTTTTA
1 ATTAATTTAATCTTAATTTTTTA
1561137 ATTAATTTAATAAC-TAATTTTTTA
1 ATTAATTTAAT--CTTAATTTTTTA
1561161 A
1 A
1561162 AGAGTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.48
24 11 0.48
25 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTAATTTAATCTTAATTTTTTA
Found at i:1564001 original size:21 final size:21
Alignment explanation
Indices: 1563966--1564061 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1563956 AGGCACTTTA
1563966 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1563989 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
1564010 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
1564031 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
1564052 TGTGTCGTAT
1 TGTGTCGTAT
1564062 ACTGATCAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 58 0.87
23 9 0.13
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1564036 original size:42 final size:42
Alignment explanation
Indices: 1563953--1564061 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
1563943 GGCTTTATCG
* *
1563953 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTA--TCAGGCACCTCGTGTGTCGT
*
1563997 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
* * * *
1564039 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
1564062 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 38 0.67
44 19 0.33
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.36
Consensus pattern (42 bp):
ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
Found at i:1567071 original size:2 final size:2
Alignment explanation
Indices: 1567064--1567088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1567054 TTTCTCTGTT
1567064 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1567089 TTTGAATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1569465 original size:51 final size:51
Alignment explanation
Indices: 1569387--1569490 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
1569377 AAATGTTGGG
*
1569387 TACATTTTAATTTGCATTAGAACCAGAAGGGAAATGCAGGGAGGTTTAGAA
1 TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
*
1569438 TACATTTTAATTTGCATTAGAATCAGAAGGGAAAGGCAGGGAGGTTTAGAA
1 TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
1569489 TA
1 TA
1569491 ATAGCAGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (51 bp):
TACATTTTAATTTGCATTAGAACCAGAAGGGAAAGGCAGGGAGGTTTAGAA
Found at i:1572967 original size:21 final size:21
Alignment explanation
Indices: 1572941--1572982 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1572931 ATGAATCGCA
*
1572941 AAGGATCAGCAGATTAAAAAC
1 AAGGATCAGCAGATCAAAAAC
1572962 AAGGATCAGCAGATCAAAAAC
1 AAGGATCAGCAGATCAAAAAC
1572983 TTACTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (21 bp):
AAGGATCAGCAGATCAAAAAC
Found at i:1573193 original size:1 final size:1
Alignment explanation
Indices: 1573189--1573213 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1573179 AGAAAAATGC
1573189 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1573214 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1582336 original size:15 final size:15
Alignment explanation
Indices: 1582316--1582346 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1582306 ATCTAAATGC
1582316 GAAGAAGAAAGAAAA
1 GAAGAAGAAAGAAAA
*
1582331 GAAGAAGAAGGAAAA
1 GAAGAAGAAAGAAAA
1582346 G
1 G
1582347 TAGCTACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAGAAAA
Found at i:1585548 original size:46 final size:44
Alignment explanation
Indices: 1585489--1585603 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1585479 ACAGGACAGA
* *
1585489 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1585535 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1585579 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1585604 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:1585584 original size:44 final size:45
Alignment explanation
Indices: 1585489--1585622 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1585479 ACAGGACAGA
* *
1585489 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1585535 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1585579 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1585623 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1591490 original size:46 final size:44
Alignment explanation
Indices: 1591431--1591545 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
1591421 ACAGGACAGA
* *
1591431 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
1591477 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
1591521 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
1591546 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:1591526 original size:44 final size:45
Alignment explanation
Indices: 1591431--1591564 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
1591421 ACAGGACAGA
* *
1591431 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1591477 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
1591521 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1591565 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1599779 original size:46 final size:46
Alignment explanation
Indices: 1599727--1600083 Score: 382
Period size: 46 Copynumber: 7.8 Consensus size: 46
1599717 TTCTGAAATG
* * *
1599727 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
* * * * * *
1599773 AAATGTGTAAGGCCATGGTTGAAAGACACCATGGCAACATGATATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
* *
1599819 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
1599865 AAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAAC-GTGACATGA
1 AAATGA-GTAAGACCATGGTTGAAAGATACCATGGCAACAG-GACAT-A
* * * * **
1599912 AAA-GAATAAGACAATGGTTGAAAGATACCATGACAACATGAC-GG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
* * * * *
1599956 AAATGAATAAGACCATGGTTGAAATATACCATGGCAA-TGTAACATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAG-GACATA
* ** *
1600002 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
* * *
1600048 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
1600084 TCATGTTGAA
Statistics
Matches: 268, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
44 3 0.01
45 33 0.12
46 227 0.85
47 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACAGGACATA
Found at i:1599881 original size:92 final size:92
Alignment explanation
Indices: 1599724--1600088 Score: 437
Period size: 92 Copynumber: 4.0 Consensus size: 92
1599714 GCTTTCTGAA
** * * * *
1599724 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGATATAAAATGTGTAAGGCCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATAGAAAATGAGTAAGACCAT
*
1599789 GGTTGAAAGACACCATGGCAACATGAT
66 GGTTGAAAGACACCATGGCAACATGAC
** *
1599816 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAAT-ATGTAAGACCA
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATAGAAAATGA-GTAAGACCA
* *
1599880 TGGTTGAAAGATACCATGGCAACGTGAC
65 TGGTTGAAAGACACCATGGCAACATGAC
* * * * * * *
1599908 ATGAAAAGAATAAGACAATGGTTGAAAGATACCATGACAACATGA-CGGAAATGAATAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATAGAAAATGAGTAAGACCAT
* * ** *
1599972 GGTTGAAATATACCATGGCAATGTAAC
66 GGTTGAAAGACACCATGGCAACATGAC
** *
1599999 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATAGAAAATGAGTAAGACCAT
* * *
1600064 AGTTGAAAGACACTATGGCATCATG
66 GGTTGAAAGACACCATGGCAACATG
1600089 TTGAAGATAA
Statistics
Matches: 236, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
91 78 0.33
92 158 0.67
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (92 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGATAGAAAATGAGTAAGACCAT
GGTTGAAAGACACCATGGCAACATGAC
Found at i:1600060 original size:183 final size:184
Alignment explanation
Indices: 1599734--1600083 Score: 452
Period size: 183 Copynumber: 1.9 Consensus size: 184
1599724 ATGAAATGTG
* * * * ** *
1599734 TAAGACCATGGTTGAAAGATACCATGGCAATAGGATATAAAATGTGTAAGGCCATGGTTGAAAGA
1 TAAGACAATGGTTGAAAGATACCATGACAACAGGATAGAAAATGAATAAGACCATGGTTGAAAGA
* * ** * *
1599799 CACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATAT
66 CACCATGGCAACATAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGACAG
* *
1599864 AAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
131 AAAATATGTAAGACCATAGTTGAAAGACACCATGGCAACGTGACATGAAAAGAA
* * * *
1599918 TAAGACAATGGTTGAAAGATACCATGACAACATGA-CGGAAATGAATAAGACCATGGTTGAAATA
1 TAAGACAATGGTTGAAAGATACCATGACAACAGGATAGAAAATGAATAAGACCATGGTTGAAAGA
* ** **
1599982 TACCATGGCAATGTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACAG
66 CACCATGGCAACATAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGACAG
*
1600047 AAAATGA-GTAAGACCATAGTTGAAAGACACTATGGCA
131 AAAAT-ATGTAAGACCATAGTTGAAAGACACCATGGCA
1600084 TCATGTTGAA
Statistics
Matches: 140, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
183 108 0.77
184 32 0.23
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (184 bp):
TAAGACAATGGTTGAAAGATACCATGACAACAGGATAGAAAATGAATAAGACCATGGTTGAAAGA
CACCATGGCAACATAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACAGGACAG
AAAATATGTAAGACCATAGTTGAAAGACACCATGGCAACGTGACATGAAAAGAA
Found at i:1600102 original size:137 final size:137
Alignment explanation
Indices: 1599724--1600106 Score: 450
Period size: 137 Copynumber: 2.8 Consensus size: 137
1599714 GCTTTCTGAA
* * * * * * *
1599724 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGATATAAAATGTGTAAGGCCAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCAT
**
1599789 GGTTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
66 GGTTGAAAGACACCATGGCAACATGAT-TGAAATGAATAAGACCATGGTTGAAAGATACCATGGC
* *
1599854 AACAGGAT
130 AACAGAAC
* * * *
1599862 ATAAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA-GAATAAGACA
1 ATGAAATGA-GTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACC
* * ** *
1599925 ATGGTTGAAAGATACCATGACAACATGACGGAAATGAATAAGACCATGGTTGAAATATACCATGG
64 ATGGTTGAAAGACACCATGGCAACATGATTGAAATGAATAAGACCATGGTTGAAAGATACCATGG
*
1599990 CAA-TGTAAC
129 CAACAG-AAC
* *
1599999 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCAT
* * * *
1600064 AGTTGAAAGACACTATGGCATCATG-TTGAAGATAAATAAGACC
66 GGTTGAAAGACACCATGGCAACATGATTGAA-ATGAATAAGACC
1600107 GTGGATGGGA
Statistics
Matches: 205, Mismatches: 34, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
136 9 0.04
137 119 0.58
138 73 0.36
139 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (137 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCAT
GGTTGAAAGACACCATGGCAACATGATTGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
ACAGAAC
Found at i:1601512 original size:15 final size:15
Alignment explanation
Indices: 1601464--1601515 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1601454 ACTATAAAAC
*
1601464 ATTTAATATTAATAT
1 ATTTATTATTAATAT
*
1601479 ATTTATATTTGTTATATAT
1 A-TT-TA-TTATTA-ATAT
1601498 ATTTATTATTAATAT
1 ATTTATTATTAATAT
1601513 ATT
1 ATT
1601516 AATATATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 4 0.13
18 6 0.20
19 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1601574 original size:18 final size:18
Alignment explanation
Indices: 1601551--1601605 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1601541 TTATTACTTT
1601551 TAAAATTTATTATTAAAA
1 TAAAATTTATTATTAAAA
*
1601569 TAAAATTATAATATT-AAA
1 TAAAATT-TATTATTAAAA
*
1601587 T--AATTTATTA-AAAAA
1 TAAAATTTATTATTAAAA
1601602 TAAA
1 TAAA
1601606 TTATATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
17 1 0.03
18 11 0.37
19 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTATTATTAAAA
Found at i:1601583 original size:19 final size:18
Alignment explanation
Indices: 1601551--1601586 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1601541 TTATTACTTT
*
1601551 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
1601569 TAAAATTATAATATTAAA
1 TAAAATT-TAATATTAAA
1601587 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:1601604 original size:15 final size:17
Alignment explanation
Indices: 1601561--1601614 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
1601551 TAAAATTTAT
*
1601561 TATTAAAATA-AAATTA
1 TATTAAAAAATAAATTA
* **
1601577 TAATATTAAAT-AATT-
1 TATTAAAAAATAAATTA
1601592 TATTAAAAAATAAATTA
1 TATTAAAAAATAAATTA
1601609 TATTAA
1 TATTAA
1601615 TCATTTATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAAAAAATAAATTA
Found at i:1601625 original size:27 final size:28
Alignment explanation
Indices: 1601560--1601640 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
1601550 TTAAAATTTA
* *
1601560 TTATTAAAATAAAATTATAATATTAAATAAT
1 TTATT-AAAT-AAATAATTATATT-AATAAT
*
1601591 TTATTAAA-AAATAAATTATATTAATCAT
1 TTATTAAATAAAT-AATTATATTAATAAT
*
1601619 TTA-TAAATAAATTATTATATTA
1 TTATTAAATAAATAATTATATTA
1601641 TTAAATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 13 0.30
28 16 0.36
29 7 0.16
30 3 0.07
31 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
TTATTAAATAAATAATTATATTAATAAT
Found at i:1601699 original size:22 final size:21
Alignment explanation
Indices: 1601674--1601716 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1601664 ATGTTTAGTA
1601674 ATATTGAAAAG-TATAATATTTT
1 ATATT-AAAAGTTAT-ATATTTT
*
1601696 ATATTAATAGTTATATATTTT
1 ATATTAAAAGTTATATATTTT
1601717 TAGAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
ATATTAAAAGTTATATATTTT
Found at i:1628846 original size:13 final size:13
Alignment explanation
Indices: 1628828--1628852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1628818 AATTTGATTT
1628828 AGTTTTTGAGTCG
1 AGTTTTTGAGTCG
1628841 AGTTTTTGAGTC
1 AGTTTTTGAGTC
1628853 AAATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
AGTTTTTGAGTCG
Found at i:1629559 original size:3 final size:3
Alignment explanation
Indices: 1629551--1629619 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
1629541 ATTAAGTTGG
1629551 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1629599 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
1629620 CACATCGACT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1629802 original size:4 final size:4
Alignment explanation
Indices: 1629793--1629821 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1629783 TACACGACAA
1629793 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1629822 CAGATCCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:1633004 original size:31 final size:29
Alignment explanation
Indices: 1632935--1633008 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1632925 ACAAAATAAT
**
1632935 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGACA
*
1632964 AACATAAGTGACTAAAATGTAACATGAGACA
1 AACATAAGTGACTAAAACGTAACAT--GACA
*
1632995 AACAAAAGTGACTA
1 AACATAAGTGACTA
1633009 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGACA
Found at i:1636019 original size:44 final size:43
Alignment explanation
Indices: 1635951--1636042 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 43
1635941 AAGTATAAAC
* *
1635951 TTAAAAAATAATATTATTTTCTTCAATA-TAAAAATAAAATAA
1 TTAAAAAATAATATTATTTGCTTCAAGATTAAAAATAAAATAA
* *
1635993 TTAAAAAAGTTAATTTTATTTGCTTCAAGATTAAATATAAAATAA
1 TTAAAAAA--TAATATTATTTGCTTCAAGATTAAAAATAAAATAA
1636038 TTAAA
1 TTAAA
1636043 TTAAATATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 8 0.19
44 17 0.40
45 18 0.42
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (43 bp):
TTAAAAAATAATATTATTTGCTTCAAGATTAAAAATAAAATAA
Found at i:1636945 original size:60 final size:59
Alignment explanation
Indices: 1636890--1637010 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 59
1636880 TAAAAAAGAC
* *
1636890 AAAATA-GAATAGTTGAGTAATTATTTTTGTAATTTTTCATAATTGAGTGCTAAAAATAA
1 AAAATATGAATAGTTGAGTAATCA-TTTTATAATTTTTCATAATTGAGTGCTAAAAATAA
* * * * * *
1636949 AGATTATTAATTGTTGAGTAATCATTTTATAATTTTTCATAATT-AGGTACCAAAAATAA
1 AAAATATGAATAGTTGAGTAATCATTTTATAATTTTTCATAATTGA-GTGCTAAAAATAA
1637008 AAA
1 AAA
1637011 TAAAATCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.02
59 36 0.71
60 14 0.27
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (59 bp):
AAAATATGAATAGTTGAGTAATCATTTTATAATTTTTCATAATTGAGTGCTAAAAATAA
Found at i:1637286 original size:71 final size:71
Alignment explanation
Indices: 1637201--1637338 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 71
1637191 TAATTTGGTA
** *
1637201 AAAATTGTTTTTTAATCTCTTAAAATTTGTAAAATTATAACTAACAAAATGGTAAAATTTGAGTT
1 AAAATTGCCTTTTAATATCTTAAAATTTGTAAAATTATAACTAACAAAATGGTAAAATTTGAGTT
1637266 TTTAGT
66 TTTAGT
* * *
1637272 AAAATTGCCTTTTAATATCTTAAAATTTGTAAAATTATAACTAATAAAATGGTAAAGTTTGTGTT
1 AAAATTGCCTTTTAATATCTTAAAATTTGTAAAATTATAACTAACAAAATGGTAAAATTTGAGTT
1637337 TT
66 TT
1637339 AGCCCCCCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (71 bp):
AAAATTGCCTTTTAATATCTTAAAATTTGTAAAATTATAACTAACAAAATGGTAAAATTTGAGTT
TTTAGT
Found at i:1637564 original size:30 final size:28
Alignment explanation
Indices: 1637513--1637616 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 28
1637503 AGATCTCCTC
*
1637513 AAAATTTTTATAAACTCTAATTGAGCCTTCA
1 AAAATTTTTA-AAATTCTAATT-A-CCTTCA
* *
1637544 AAAATTTTTAAAATTTTAATTACTCTCCA
1 AAAATTTTTAAAATTCTAATTAC-CTTCA
* * *
1637573 AAAAATTTGAAAATTCTCATTAACCCTCTCA
1 AAAATTTTTAAAATTCTAATT-A-CCT-TCA
*
1637604 AAATTTTTTAAAA
1 AAAATTTTTAAAA
1637617 AAAAAACTCC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 22 0.38
30 12 0.21
31 23 0.40
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTTTTAAAATTCTAATTACCTTCA
Found at i:1637575 original size:29 final size:31
Alignment explanation
Indices: 1637513--1637616 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 31
1637503 AGATCTCCTC
* * *
1637513 AAAATTTTTATAAACTCTAATTGAGCCT-TCA
1 AAAATTTTTA-AAATTCTAATTAACCCTCTCA
* *
1637544 AAAATTTTTAAAATTTTAATT-ACTCTC-CA
1 AAAATTTTTAAAATTCTAATTAACCCTCTCA
* * *
1637573 AAAAATTTGAAAATTCTCATTAACCCTCTCA
1 AAAATTTTTAAAATTCTAATTAACCCTCTCA
*
1637604 AAATTTTTTAAAA
1 AAAATTTTTAAAA
1637617 AAAAAACTCC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 22 0.38
30 14 0.24
31 22 0.38
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAATTTTTAAAATTCTAATTAACCCTCTCA
Found at i:1643243 original size:22 final size:22
Alignment explanation
Indices: 1643201--1643243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1643191 AAATATTAAA
* *
1643201 ATATATTTTTATTTGATATTTG
1 ATATATTTTTAATTGAAATTTG
1643223 ATATATTTTATAATT-AAATTT
1 ATATATTTT-TAATTGAAATTT
1643244 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATATATTTTTAATTGAAATTTG
Found at i:1645281 original size:19 final size:18
Alignment explanation
Indices: 1645257--1645292 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1645247 ATTTTCAAAG
1645257 TATTATTTAAATATTTTTA
1 TATTATTT-AATATTTTTA
*
1645276 TATTATTTTATATTTTT
1 TATTATTTAATATTTTT
1645293 CATTCACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTATTTAATATTTTTA
Done.