Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007959.1 Hibiscus syriacus cultivar Beakdansim tig00110386_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: 1044826
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:272410 original size:30 final size:29
Alignment explanation
Indices: 272374--272438 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
272364 GCTGCTGGAA
272374 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
272404 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
272433 ACCGGT
1 ACCGGT
272439 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:272451 original size:5 final size:5
Alignment explanation
Indices: 272441--272510 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
272431 TGACCGGTCT
* *
272441 GACCC GACCC GACCGTT GACCC GACCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
*
272490 GACCGTT GACCC GACCC GACC
1 GACC--C GACCC GACCC GACC
272511 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 41 0.77
7 12 0.23
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:272462 original size:17 final size:17
Alignment explanation
Indices: 272440--272517 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 17
272430 TTGACCGGTC
272440 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
272457 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
272474 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
272496 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
272513 TGACC
1 TGACC
272518 GTTGACTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 39 0.70
22 17 0.30
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:272467 original size:22 final size:22
Alignment explanation
Indices: 272458--272510 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
272448 CCCGACCGTT
272458 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
272480 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
272502 GACCCGACC
1 GACCCGACC
272511 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:272485 original size:39 final size:39
Alignment explanation
Indices: 272441--272517 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
272431 TGACCGGTCT
272441 GACCCGACCCGACCGTTGACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCCGACCCGACCGTTGACCC
272480 GACCCGACCCGACCGTTGACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACCCGACCCGACCGTTGACC
272518 GTTGACTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (39 bp):
GACCCGACCCGACCGTTGACCCGACCCGACCGTTGACCC
Found at i:274089 original size:13 final size:13
Alignment explanation
Indices: 274071--274097 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
274061 TTCAGGTACA
274071 TTTGTTTCTTCAC
1 TTTGTTTCTTCAC
274084 TTTGTTTCTTCAC
1 TTTGTTTCTTCAC
274097 T
1 T
274098 CAATCTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTGTTTCTTCAC
Found at i:275825 original size:6 final size:6
Alignment explanation
Indices: 275814--275848 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
275804 GGAATAATTT
275814 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
275849 TTATGGTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:279580 original size:65 final size:65
Alignment explanation
Indices: 279468--279622 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 65
279458 ACACTAGGGG
* * * * * *
279468 TGCATCGGTACAC-TAATACATTTGATGTTTCAAAAGAGCCAGGAGTGCAAT-TATGCATGATTT
1 TGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGC-ATCGATGCATGACTT
279531 A
65 A
* ** * *
279532 TGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTG
1 TGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGACTTA
279597 TGCATCGGTACACAAAATGCATTCGA
1 TGCATCGGTACACAAAATGCATTCGA
279623 AATGGGTGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 15 0.19
65 63 0.81
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (65 bp):
TGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGACTTA
Found at i:279996 original size:12 final size:13
Alignment explanation
Indices: 279966--279995 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
279956 GATTTTCTTG
*
279966 GAAAATCATTTTT
1 GAAAATAATTTTT
279979 GAAAATAATTTTT
1 GAAAATAATTTTT
279992 GAAA
1 GAAA
279996 TTACTCCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (13 bp):
GAAAATAATTTTT
Found at i:282360 original size:23 final size:22
Alignment explanation
Indices: 282330--282403 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 22
282320 TATAACATAG
282330 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* *
282353 TGCATCGATGCACCTTC-ATGA
1 TGCATCGATGCACATTCAAGGA
*
282374 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
282397 TGCATCG
1 TGCATCG
282404 GTACACTCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
21 16 0.37
22 3 0.07
23 24 0.56
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:282383 original size:44 final size:43
Alignment explanation
Indices: 282328--282428 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
282318 TGTATAACAT
* *
282328 AGTGCATCGATGCACATTCAAGGAATGCATCGATGCAC-CTTC
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATACACTCTTC
* * *
282370 ATGATGTATCGATGCACATTCAAGGGATGCATCGGTACACTCTTT
1 A-G-TGTATCGATGCACATTCAAGGAATGCATCGATACACTCTTC
282415 AGTGTATCGATGCA
1 AGTGTATCGATGCA
282429 TGTTGCACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 13 0.25
44 33 0.65
45 4 0.08
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATACACTCTTC
Found at i:286021 original size:20 final size:21
Alignment explanation
Indices: 285980--286021 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
285970 AAGAAGCTTT
* *
285980 ATGATCATCAATTTTCTTTTG
1 ATGATCATCAATTTACTCTTG
286001 ATGATCATC-ATTTACTCTTG
1 ATGATCATCAATTTACTCTTG
286021 A
1 A
286022 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (21 bp):
ATGATCATCAATTTACTCTTG
Found at i:288174 original size:65 final size:65
Alignment explanation
Indices: 288098--288254 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
288088 TACACTATGG
* * * * * *
288098 GTGCATTGGTACACAAATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGTAT-GATC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-
288162 T
65 T
* **
288163 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
288228 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
288255 AATGGGTGTG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 80 0.98
66 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:291363 original size:42 final size:42
Alignment explanation
Indices: 291299--291378 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
291289 TCTTCATGTT
* *
291299 AAATCATTTTATGAAAAGGTTAAACCCTTTTATCAAAAGGAG
1 AAATCATTTTATCAAAAGGTTAAACCCTTTCATCAAAAGGAG
* *
291341 AAATC-TTTTAATCAAAATGTTAAATCCTTTCATCAAAA
1 AAATCATTTT-ATCAAAAGGTTAAACCCTTTCATCAAAA
291379 TGTCTTAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.34
Consensus pattern (42 bp):
AAATCATTTTATCAAAAGGTTAAACCCTTTCATCAAAAGGAG
Found at i:291379 original size:21 final size:21
Alignment explanation
Indices: 291294--291381 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
291284 AATTCTCTTC
* *
291294 ATGTTAAATCATTTTATGAAA
1 ATGTTAAATCCTTTTATCAAA
* *
291315 AGGTTAAACCCTTTTATCAAA
1 ATGTTAAATCCTTTTATCAAA
* **
291336 AGGAGAAAT-CTTTTAATCAAA
1 ATGTTAAATCCTTTT-ATCAAA
*
291357 ATGTTAAATCCTTTCATCAAA
1 ATGTTAAATCCTTTTATCAAA
291378 ATGT
1 ATGT
291382 CTTAACATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 5 0.09
21 45 0.83
22 4 0.07
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ATGTTAAATCCTTTTATCAAA
Found at i:293461 original size:22 final size:21
Alignment explanation
Indices: 293410--293468 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
293400 ATTTTTGGGT
293410 AAGGGGAATCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
*
293431 AA-GGGAATCGGTACCTATTC
1 AAGGGGAATCGGTACCCATTC
*
293451 AATGGGGAATCGATACCC
1 AA-GGGGAATCGGTACCC
293469 CTCAAGCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.58
21 2 0.06
22 12 0.36
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
AAGGGGAATCGGTACCCATTC
Found at i:293546 original size:23 final size:22
Alignment explanation
Indices: 293502--293546 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
293492 AATCTCATAG
*
293502 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
* *
293524 GGGAATCGATTCCACCTAAAGGA
1 GGGAACCGATTCC-CCCAAAGGA
293547 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:295069 original size:103 final size:103
Alignment explanation
Indices: 294846--295053 Score: 362
Period size: 103 Copynumber: 2.0 Consensus size: 103
294836 TACGCGGTCT
* * * *
294846 TTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTG
1 TTCGGAACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTA
294911 GCATATGTATATGATTCTTAAGGAATGATATGTAGTCC
66 GCATATGTATATGATTCTTAAGGAATGATATGTAGTCC
294949 TTCGGAACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTA
1 TTCGGAACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTA
* *
295014 GTATATGTATATGATTCTTAAGGAATGATATGTGGTCC
66 GCATATGTATATGATTCTTAAGGAATGATATGTAGTCC
295052 TT
1 TT
295054 ATGGACATTA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (103 bp):
TTCGGAACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTA
GCATATGTATATGATTCTTAAGGAATGATATGTAGTCC
Found at i:295103 original size:23 final size:23
Alignment explanation
Indices: 295070--295178 Score: 164
Period size: 23 Copynumber: 4.7 Consensus size: 23
295060 ATTATTATAT
*
295070 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
295093 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
295116 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
295139 GGCACTCCGGTGCAATTCTATGT
1 GGCACTCCGGTGCAATTCTACGC
* *
295162 GCCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
295179 TTACAAGCTG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:298884 original size:22 final size:21
Alignment explanation
Indices: 298833--298891 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
298823 ATTTATGGGT
*
298833 AAGGGGAACCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
298854 AA-GGGAATCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
*
298874 AATGGGGAATCGATACCC
1 AA-GGGGAATCGGTACCC
298892 CTCAAGCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 19 0.56
21 2 0.06
22 13 0.38
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (21 bp):
AAGGGGAATCGGTACCCATTC
Found at i:300441 original size:103 final size:103
Alignment explanation
Indices: 300262--300474 Score: 318
Period size: 103 Copynumber: 2.1 Consensus size: 103
300252 GGGTCTACGC
* * * *
300262 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACAGATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATAAGACACATACTTGAT
** **
300327 CTTTGGCATATGTATATGATTCTCAAGGAATGATATGT
66 CCCTAACATATGTATATGATTCTCAAGGAATGATATGT
* *
300365 GGTCCTTCGAGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGATAAGATACATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATAAGACACATACTTGAT
* *
300430 CCCTAATATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAACATATGTATATGATTCTCAAGGAATGATATGT
300468 GGTCCTT
1 GGTCCTT
300475 ATGGACATTA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATAAGACACATACTTGAT
CCCTAACATATGTATATGATTCTCAAGGAATGATATGT
Found at i:300524 original size:23 final size:23
Alignment explanation
Indices: 300490--300581 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
300480 CATTATTATA
*
300490 TGGCACTACGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
* *
300513 CGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
300536 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
* *
300559 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTCTACG
300582 AGCTGTGGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:305765 original size:173 final size:169
Alignment explanation
Indices: 305441--305780 Score: 476
Period size: 173 Copynumber: 2.0 Consensus size: 169
305431 TTAAATAGAT
**
305441 ATATGAAATTCATCTAATTTCCACTTGTGAGTTTTAAAATCCACCACCATTCTATATTGTAGAAT
1 ATATGAAAACCATCTAATTTCCACTTGTGAGTTTTAAAATCCACCACCATTCTATATTGTAGAAT
* * * *
305506 AAAAAGCCCGTACCTTAAAATAAGCAGTCTCAAAAAAATTTAACAACATTATGTGAATCATGGCA
66 -AAAAGCCCGTAACTTAAAATAAGCAGTCT-AAAAAAATTT-A-AACATTATCTGAACCACGGCA
** *
305571 TGTAGGTTAAAGCCTTTTCTTTATTTCTTTATTCTTTTTTACA
127 TACAGGATAAAGCCTTTTCTTTATTTCTTTATTCTTTTTTACA
305614 ATATGAAAACCATCTAATTTCCACTTGTGAGTTTTAAAATCCACCACCATTCTATATTG-AGGAA
1 ATATGAAAACCATCTAATTTCCACTTGTGAGTTTTAAAATCCACCACCATTCTATATTGTA-GAA
* *
305678 T-AAAGGCCGTAACTTAAGATAAGCAGTCT-AAAAAATTT-AACATTATCTGAACCACGGCATAC
65 TAAAAGCCCGTAACTTAAAATAAGCAGTCTAAAAAAATTTAAACATTATCTGAACCACGGCATAC
* *
305740 A-GATGAAGCCTTTTCTTTCTTTCTTTATT-TTTTTTACA
130 AGGATAAAGCCTTTTCTTTATTTCTTTATTCTTTTTTACA
305778 ATA
1 ATA
305781 CAAACCCTTA
Statistics
Matches: 153, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
164 12 0.08
165 25 0.16
166 20 0.13
169 9 0.06
171 25 0.16
172 1 0.01
173 61 0.40
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (169 bp):
ATATGAAAACCATCTAATTTCCACTTGTGAGTTTTAAAATCCACCACCATTCTATATTGTAGAAT
AAAAGCCCGTAACTTAAAATAAGCAGTCTAAAAAAATTTAAACATTATCTGAACCACGGCATACA
GGATAAAGCCTTTTCTTTATTTCTTTATTCTTTTTTACA
Found at i:324067 original size:95 final size:95
Alignment explanation
Indices: 323891--324081 Score: 312
Period size: 95 Copynumber: 2.0 Consensus size: 95
323881 TATAATCATG
* * *
323891 TCTTAATAAAAATTATAATTTATATATTATGACCATACCCTCAAATGAAAGATAAAACTGATAGC
1 TCTTAATAAAAATTATAATTTATAAATTATGAACATACCCTCAAATAAAAGATAAAACTGATAGC
* *
323956 TTGAAATTTTCGAACACAAAAAATTGAACT
66 TTGAAATCTTCAAACACAAAAAATTGAACT
*
323986 TCTTAATAAAAATTATAATTTATAAATTATGAACATACCCTCAAATAAAAGTTAAAACTGATAGC
1 TCTTAATAAAAATTATAATTTATAAATTATGAACATACCCTCAAATAAAAGATAAAACTGATAGC
324051 TT-AAACTCTTCAAACACAAAAAATTGAACT
66 TTGAAA-TCTTCAAACACAAAAAATTGAACT
324081 T
1 T
324082 TTAGTTTGTG
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 3 0.03
95 86 0.97
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (95 bp):
TCTTAATAAAAATTATAATTTATAAATTATGAACATACCCTCAAATAAAAGATAAAACTGATAGC
TTGAAATCTTCAAACACAAAAAATTGAACT
Found at i:326665 original size:331 final size:331
Alignment explanation
Indices: 326063--327058 Score: 1974
Period size: 331 Copynumber: 3.0 Consensus size: 331
326053 TTGCTCTTGG
*
326063 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAATGTAGTTAAGAGCTTCACTAGTTGGTAGG
1 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
326128 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
66 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
326193 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
131 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
326258 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
196 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
326323 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
261 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
326388 TCTTAC
326 TCTTAC
326394 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
1 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
326459 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
66 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
326524 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
131 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
326589 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
196 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
326654 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
261 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
326719 TCTTAC
326 TCTTAC
326725 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
1 TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
*
326790 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCAGT
66 GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
326855 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
131 TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
326920 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
196 TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
326985 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
261 ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
327050 TCTTAC
326 TCTTAC
327056 TCC
1 TCC
327059 TCTACCCCTT
Statistics
Matches: 663, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
331 663 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (331 bp):
TCCAAGGATTTAATTAGGCACATTTATAAAATGTAAAGTAGTTAAGAGCTTCACTAGTTGGTAGG
GCTGAGCAACGAAACCAAGAAAACCGAAAAACCGACATTACCCGAGTAAAACGGTTCGGTTCGGT
TTCGGGTTGATTTAAAGAATCATTGTAGTTGGTAGTGCACAAATAAGTCCTATCTATAGATAATC
TATCTTTACAATGGAAATTAGGCACATTCTGAAAGCCTCCAAGATAACCTATTCAGTGCTGTCCT
ACCAATATTAACTTCAAATTTCCAGACCATGATCTCCATTTAAATTTCATTTTCTTCCACTATGA
TCTTAC
Found at i:331037 original size:15 final size:15
Alignment explanation
Indices: 331017--331047 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
331007 ATATAAGTCC
*
331017 TTAATTTTAGTTTCT
1 TTAATTATAGTTTCT
331032 TTAATTATAGTTTCT
1 TTAATTATAGTTTCT
331047 T
1 T
331048 ATTCTACTAG
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:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
TTAATTATAGTTTCT
Found at i:338267 original size:23 final size:23
Alignment explanation
Indices: 338219--338323 Score: 99
Period size: 23 Copynumber: 4.7 Consensus size: 23
338209 GTAATTTGCA
338219 CCGAAGTG-CCACATAA--TTGTC
1 CCGAAG-GACCACATAAGTTTGTC
* *
338240 TCGAAGGATCACATAAGTTTGTC
1 CCGAAGGACCACATAAGTTTGTC
* * *
338263 CCGAAGGACTACATAGGTTTGTA
1 CCGAAGGACCACATAAGTTTGTC
* * *
338286 CCGAATGACCACGTAGGTTTGTC
1 CCGAAGGACCACATAAGTTTGTC
*
338309 CCGAATGACCACATA
1 CCGAAGGACCACATA
338324 TAATCCTCGA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.01
21 12 0.17
23 56 0.81
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
CCGAAGGACCACATAAGTTTGTC
Found at i:341569 original size:18 final size:20
Alignment explanation
Indices: 341546--341586 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
341536 ACTTCTTCAA
*
341546 GAAAAT-AAAATG-GATTTT
1 GAAAATCAAAATGAGATATT
341564 GAAAATCAAAATGAGATATT
1 GAAAATCAAAATGAGATATT
341584 GAA
1 GAA
341587 GAAGGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (20 bp):
GAAAATCAAAATGAGATATT
Found at i:345991 original size:12 final size:13
Alignment explanation
Indices: 345974--346002 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
345964 GAGATAAGAT
345974 AAAGTT-AAAGGA
1 AAAGTTAAAAGGA
345986 AAAGTTAAAAGGA
1 AAAGTTAAAAGGA
345999 AAAG
1 AAAG
346003 AAGATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (13 bp):
AAAGTTAAAAGGA
Found at i:356719 original size:21 final size:20
Alignment explanation
Indices: 356695--356752 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 20
356685 ATCCTCGATA
356695 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
* *
356716 TGTACCGATATATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
*
356739 TGTATTGATACACT
1 TGTATCGATACACT
356753 CAGGAGTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.07
21 10 0.34
23 15 0.52
24 2 0.07
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:372240 original size:23 final size:23
Alignment explanation
Indices: 372214--372257 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
372204 TACCATATAA
*
372214 TTGTCCCGAATGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGGT
*
372237 TTGTCCCGTAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
372258 AACCCTCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGT
Found at i:373474 original size:45 final size:45
Alignment explanation
Indices: 373410--373767 Score: 384
Period size: 45 Copynumber: 8.0 Consensus size: 45
373400 TTTCATTTAA
* * * * *
373410 CATCCTTTCATG-CTTATAATGTATCGTTATGCATTTAATTAATGG
1 CATCCTTTCATGTC-GATAATGCACCGTTATGCATTTCATTTATGG
*
373455 CATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATTG
1 CATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGG
* *
373500 CATCCTTTCATGTCGTTAATGCACCAG-TATGCATTTTATTTATGG
1 CATCCTTTCATGTCGATAATGCACC-GTTATGCATTTCATTTATGG
* * * * *
373545 CATCATTTCATG-CTGTTAATGCGCCATTATGCATTTCATTTATGA
1 CATCCTTTCATGTC-GATAATGCACCGTTATGCATTTCATTTATGG
* * * * *
373590 CATCATTTCATGTC-ATTAATGAATCGTTATGTATTTTATTTATGG
1 CATCCTTTCATGTCGA-TAATGCACCGTTATGCATTTCATTTATGG
* * *
373635 CATCCTTTCATGTCGTTAATGCAGCGTTATACATTTCATTTATGG
1 CATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGG
* * * ** *
373680 CATCTTTTCATGTCGTTAATGCACCATTATATATTTCATTTATGA
1 CATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGG
*
373725 CATCCTTTCATGTC-ATTAATGCATCGTTATGCATTTCATTTAT
1 CATCCTTTCATGTCGA-TAATGCACCGTTATGCATTTCATTTAT
373768 TCATTCATTT
Statistics
Matches: 265, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.00
45 261 0.98
46 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (45 bp):
CATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGG
Found at i:373657 original size:135 final size:135
Alignment explanation
Indices: 373436--373767 Score: 472
Period size: 135 Copynumber: 2.5 Consensus size: 135
373426 TAATGTATCG
* * * * *
373436 TTATGCATTTAATTAATGGCATCCTTTCATGTCGA-TAATGCACCGTTATGCATTTCATTTATTG
1 TTATGCATTTCATTTATGACATCCTTTCATGTC-ATTAATGCATCGTTATGCATTTCATTTATGG
* *
373500 CATCCTTTCATGTCGTTAATGCACCAG-TATGCATTTTATTTATGGCATCATTTCATG-CTGTTA
65 CATCCTTTCATGTCGTTAATGCACC-GTTATACATTTCATTTATGGCATCATTTCATGTC-GTTA
*
373563 ATGCGCCA
128 ATGCACCA
* * * *
373571 TTATGCATTTCATTTATGACATCATTTCATGTCATTAATGAATCGTTATGTATTTTATTTATGGC
1 TTATGCATTTCATTTATGACATCCTTTCATGTCATTAATGCATCGTTATGCATTTCATTTATGGC
* *
373636 ATCCTTTCATGTCGTTAATGCAGCGTTATACATTTCATTTATGGCATCTTTTCATGTCGTTAATG
66 ATCCTTTCATGTCGTTAATGCACCGTTATACATTTCATTTATGGCATCATTTCATGTCGTTAATG
373701 CACCA
131 CACCA
**
373706 TTATATATTTCATTTATGACATCCTTTCATGTCATTAATGCATCGTTATGCATTTCATTTAT
1 TTATGCATTTCATTTATGACATCCTTTCATGTCATTAATGCATCGTTATGCATTTCATTTAT
373768 TCATTCATTT
Statistics
Matches: 174, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
134 2 0.01
135 171 0.98
136 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (135 bp):
TTATGCATTTCATTTATGACATCCTTTCATGTCATTAATGCATCGTTATGCATTTCATTTATGGC
ATCCTTTCATGTCGTTAATGCACCGTTATACATTTCATTTATGGCATCATTTCATGTCGTTAATG
CACCA
Found at i:379409 original size:45 final size:45
Alignment explanation
Indices: 379345--379713 Score: 358
Period size: 45 Copynumber: 8.2 Consensus size: 45
379335 TATCCTTTAT
* * *
379345 TTTCATTTCTAGCATCCTTTCATGCTTATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTTATAATGCACCGTTATGCA
* * * * *
379390 TTTCATTTATGACATCCTTTCATG-TCGATAATGTACCATTATGTA
1 TTTCATTTATGGCATCCTTTCATGCT-TATAATGCACCGTTATGCA
* * *
379435 TTCCATTTATGGCATCCTTTCAT--TTAGTTAATGCACCGGTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCTTA--TAATGCACCGTTATGCA
* * * *
379480 TTTCATTTAGGGTATCCTTTCATGCCGT-TAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATG-CTTATAATGCACCGTTATGCA
* * * * * *
379525 TTTCATTCATGGCATCATTTAATGCCGT-TAATGCATCGTTATACA
1 TTTCATTTATGGCATCCTTTCATG-CTTATAATGCACCGTTATGCA
* *
379570 TTTCATTTATGGCAT-TTTTCATGCCGT-TAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATG-CTTATAATGCACCGTTATGCA
* ** *
379614 TTTTATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTTATAATGCACCGTTATGCA
* *
379659 TTTCATTTATGGCATCCTTTCATG-TTGTTAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTT-ATAATGCACCGTTATGCA
379704 TTTCATTTAT
1 TTTCATTTAT
379714 TCATTCATTT
Statistics
Matches: 268, Mismatches: 47, Indels: 18
0.80 0.14 0.05
Matches are distributed among these distances:
43 1 0.00
44 42 0.16
45 224 0.84
48 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCTTATAATGCACCGTTATGCA
Found at i:379501 original size:90 final size:90
Alignment explanation
Indices: 379345--379713 Score: 411
Period size: 90 Copynumber: 4.1 Consensus size: 90
379335 TATCCTTTAT
* * * * *
379345 TTTCATTTCTAGCATCCTTTCATG-CTTATAATGCACTGTTATGCATTTCATTTATGACATCCTT
1 TTTCATTTATGGCATCCTTTCATGTCAT-TAATGCACCGTTATGCATTTCATTTATGGCATCCTT
* * * * *
379409 TCATGTCGATAATGTACCATTATGTA
65 TCATGCCGTTAATGCACCGTTATGCA
* * * * * *
379435 TTCCATTTATGGCATCCTTTCAT-TTAGTTAATGCACCGGTGTGCATTTCATTTAGGGTATCCTT
1 TTTCATTTATGGCATCCTTTCATGTCA-TTAATGCACCGTTATGCATTTCATTTATGGCATCCTT
*
379499 TCATGCCGTTAATGCACTGTTATGCA
65 TCATGCCGTTAATGCACCGTTATGCA
* * * * * * * *
379525 TTTCATTCATGGCATCATTTAATGCCGTTAATGCATCGTTATACATTTCATTTATGGCAT-TTTT
1 TTTCATTTATGGCATCCTTTCATGTCATTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
379589 CATGCCGTTAATGCACCGTTATGCA
66 CATGCCGTTAATGCACCGTTATGCA
* * * *
379614 TTTTATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGTCATTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
** *
379679 CATGTTGTTAATGTACCGTTATGCA
66 CATGCCGTTAATGCACCGTTATGCA
379704 TTTCATTTAT
1 TTTCATTTAT
379714 TCATTCATTT
Statistics
Matches: 229, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
89 78 0.34
90 150 0.66
91 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGTCATTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
CATGCCGTTAATGCACCGTTATGCA
Found at i:380198 original size:44 final size:44
Alignment explanation
Indices: 380146--380291 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
380136 TGGTATCAAT
380146 ATTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACC
1 ATTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACC
* *
380190 ATTTCTATATTCTGTAATTCATGGTATCGATA--CCATTCTCTTAGTATCGATA-C
1 ATTTCTATA--C------T-ATGGTACCGATACTCCCTT-TC--AGTATCGATACC
*
380243 --TTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACC
1 ATTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACC
380285 ATTTCTA
1 ATTTCTA
380292 CATTCTGGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 34
0.67 0.04 0.29
Matches are distributed among these distances:
41 10 0.12
42 11 0.14
43 3 0.04
44 18 0.22
46 1 0.01
49 1 0.01
51 11 0.14
52 3 0.04
53 12 0.15
54 10 0.12
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (44 bp):
ATTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACC
Found at i:381209 original size:19 final size:19
Alignment explanation
Indices: 381175--381223 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
381165 TCCCTTCAAT
*
381175 GGTATCGATA-CCCCCTAC
1 GGTACCGATACCCCCCTAC
*
381193 GGTACTGATACCCCCCTAC
1 GGTACCGATACCCCCCTAC
381212 GGTACCGATACC
1 GGTACCGATACC
381224 ATTTTGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.20
Consensus pattern (19 bp):
GGTACCGATACCCCCCTAC
Found at i:381280 original size:20 final size:20
Alignment explanation
Indices: 381255--381307 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
381245 ATCTTGGAAA
*
381255 TGGTATTGATACTATACCCT
1 TGGTATCGATACTATACCCT
381275 TGGTATCGATACTATACCCT
1 TGGTATCGATACTATACCCT
381295 TGGTATCGATACT
1 TGGTATCGATACT
381308 CCCATTTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACTATACCCT
Found at i:382255 original size:59 final size:60
Alignment explanation
Indices: 382150--382273 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 60
382140 TTAAGTATAT
* * ** * *
382150 AAATCATCCCACAATTATAAGATATTGTTTTATTGATTCTCTAAACTATTAAAAGTTACA
1 AAATGATCCCACAACTATAAGATATTACTTTATTGAGTCTCCAAACTATTAAAAGTTACA
* *
382210 AAATGATCCC-CAACTATAAGATGTTACTTTGTTGAGTCTCCAAACTATTAAAAGTTACA
1 AAATGATCCCACAACTATAAGATATTACTTTATTGAGTCTCCAAACTATTAAAAGTTACA
382269 AAATG
1 AAATG
382274 GTCACTTAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 47 0.84
60 9 0.16
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.35
Consensus pattern (60 bp):
AAATGATCCCACAACTATAAGATATTACTTTATTGAGTCTCCAAACTATTAAAAGTTACA
Found at i:385195 original size:17 final size:19
Alignment explanation
Indices: 385173--385213 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
385163 TTAAATTTAG
*
385173 ATTTT-AATAAATGATTA-
1 ATTTTAAATAAATCATTAT
385190 ATTTTAAATAAATCATTAT
1 ATTTTAAATAAATCATTAT
385209 ATTTT
1 ATTTT
385214 TTAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTAAATAAATCATTAT
Found at i:385447 original size:25 final size:25
Alignment explanation
Indices: 385415--385472 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
385405 TTGTTTTTAT
385415 TTTGGATCTACGCCTTATTCCAATA
1 TTTGGATCTACGCCTTATTCCAATA
385440 TTTGGATCTACGCCTTATTCCAATA
1 TTTGGATCTACGCCTTATTCCAATA
385465 TTTGGATC
1 TTTGGATC
385473 AATTGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (25 bp):
TTTGGATCTACGCCTTATTCCAATA
Found at i:386557 original size:2 final size:2
Alignment explanation
Indices: 386552--386596 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
386542 TCTAAATTGT
386552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
386594 TA T
1 TA T
386597 GAAATATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:387115 original size:3 final size:3
Alignment explanation
Indices: 387107--387147 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
387097 TAATGGGTTA
* *
387107 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATA ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
387148 ATATATGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:387337 original size:2 final size:2
Alignment explanation
Indices: 387330--387354 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
387320 TGCGTGCGTT
387330 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 T
387355 CAATGGAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:388121 original size:21 final size:22
Alignment explanation
Indices: 388097--388144 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
388087 TACCCAGTCA
*
388097 TTCGGGATA-TCTATGTGGTC-C
1 TTCGGGACATTCTATGTGG-CAC
388118 TTCGGGACATTCTATGTGGCAC
1 TTCGGGACATTCTATGTGGCAC
388140 TTCGG
1 TTCGG
388145 TGCAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (22 bp):
TTCGGGACATTCTATGTGGCAC
Found at i:388134 original size:22 final size:22
Alignment explanation
Indices: 388046--388144 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 22
388036 GGTTCTAAGC
388046 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTACGT
* * * **
388069 GATCTTTCGAGACATTTCTACCC
1 GGTCCTTCGGGACA-TTCTACGT
* * * *
388092 AGTCATTCGGGATA-TCTATGT
1 GGTCCTTCGGGACATTCTACGT
*
388113 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTACGT
388135 GG-CACTTCGG
1 GGTC-CTTCGG
388145 TGCAATTTAT
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
21 16 0.28
22 16 0.28
23 25 0.44
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTACGT
Found at i:390407 original size:14 final size:14
Alignment explanation
Indices: 390388--390439 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
390378 TCAACCCAAA
*
390388 CTGAGTCAACTCAT
1 CTGAGTCAACTCGT
390402 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
390416 CCT-AGTCAACTCGT
1 -CTGAGTCAACTCGT
*
390430 ATGAGTCAAC
1 CTGAGTCAAC
390440 CCGTTGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 1 0.03
14 31 0.91
15 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:392787 original size:31 final size:31
Alignment explanation
Indices: 392752--392810 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
392742 GGTAGGATGT
*
392752 GAGGCCCCAAGATCTTTCTTGGGTAGGCCCC
1 GAGGCCCCAAGAACTTTCTTGGGTAGGCCCC
**
392783 GAGGCCCTGAGAACTTTCTTGGGTAGGC
1 GAGGCCCCAAGAACTTTCTTGGGTAGGC
392811 TCTCAGGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (31 bp):
GAGGCCCCAAGAACTTTCTTGGGTAGGCCCC
Found at i:393235 original size:32 final size:31
Alignment explanation
Indices: 393091--393245 Score: 154
Period size: 31 Copynumber: 5.0 Consensus size: 31
393081 AAGGTGACCT
* * * *
393091 TTGGGTAGGCTTCGAGGCCTCGAGATCTTTC
1 TTGGGTAGGCCTCGTGGCCCCGAGATCATTC
* *
393122 TTGGTTAGGCC-CTGTGGCCCCAAGATCATTC
1 TTGGGTAGGCCTC-GTGGCCCCGAGATCATTC
* *
393153 TTGGGTAGGCCCCGTGGCCCTGAGATCATTC
1 TTGGGTAGGCCTCGTGGCCCCGAGATCATTC
* * *
393184 TTGGGTAGGCCTTGTGGCCCCGAGTAACTTTC
1 TTGGGTAGGCCTCGTGGCCCCGAG-ATCATTC
*
393216 TTGGGTAGGCTCTCG-GGCCCCAAGA-CATTC
1 TTGGGTAGGC-CTCGTGGCCCCGAGATCATTC
393246 CCTTAGGGTG
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
30 5 0.05
31 71 0.69
32 24 0.23
33 3 0.03
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.28
Consensus pattern (31 bp):
TTGGGTAGGCCTCGTGGCCCCGAGATCATTC
Found at i:393245 original size:62 final size:63
Alignment explanation
Indices: 393091--393245 Score: 174
Period size: 62 Copynumber: 2.5 Consensus size: 63
393081 AAGGTGACCT
* * * *
393091 TTGGGTAGGCT-TCGAGGCCTCGAGATCTTTCTTGGTTAGGCCCTGTGGCCCCAAGATCATTC
1 TTGGGTAGGCTCTCGAGGCCCCGAGATCATTCTTGGGTAGGCCCTGTGGCCCCAAGAACATTC
* * * * * *
393153 TTGGGTAGGC-CCCGTGGCCCTGAGATCATTCTTGGGTAGGCCTTGTGGCCCCGAGTAACTTTC
1 TTGGGTAGGCTCTCGAGGCCCCGAGATCATTCTTGGGTAGGCCCTGTGGCCCCAAG-AACATTC
*
393216 TTGGGTAGGCTCTCG-GGCCCCAAGA-CATTC
1 TTGGGTAGGCTCTCGAGGCCCCGAGATCATTC
393246 CCTTAGGGTG
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 51 0.66
63 23 0.30
64 3 0.04
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.28
Consensus pattern (63 bp):
TTGGGTAGGCTCTCGAGGCCCCGAGATCATTCTTGGGTAGGCCCTGTGGCCCCAAGAACATTC
Found at i:395376 original size:31 final size:31
Alignment explanation
Indices: 395315--395375 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
395305 AATTATATTT
*
395315 TCAAAATATAATTTTTTAAAGATAAGTTGTTG
1 TCAAAATATAATTTTTCAAAGA-AAGTTGTTG
395347 TCAAAA-ATAATTTTTCAAAG-AAGTT-TTG
1 TCAAAATATAATTTTTCAAAGAAAGTTGTTG
395375 T
1 T
395376 TATATCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 5 0.18
31 13 0.46
32 6 0.21
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (31 bp):
TCAAAATATAATTTTTCAAAGAAAGTTGTTG
Found at i:397705 original size:24 final size:24
Alignment explanation
Indices: 397678--397731 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
397668 CGTTCATTTA
397678 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCGTGAACGTTCGGTTATGTT
** **
397702 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGTGAACGTTCGGTTATGTT
397726 CGTTCG
1 CGTTCG
397732 ATTATGTTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (24 bp):
CGTTCGTGAACGTTCGGTTATGTT
Found at i:397716 original size:14 final size:14
Alignment explanation
Indices: 397699--397743 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
397689 GTTCGGTTAT
*
397699 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
*
397713 GTTCGGTTATGTTC
1 GTTCGATTATGTTC
397727 GTTCGATTATGTTC
1 GTTCGATTATGTTC
397741 GTT
1 GTT
397744 TATGTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.53
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:397740 original size:24 final size:23
Alignment explanation
Indices: 397689--397763 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 23
397679 GTTCGTGAAC
*
397689 GTTCGGTTATGTTCGTTTATGT-T
1 GTTCGGTTATGTTCGTTCAT-TAT
397712 CGTTCGGTTATGTTCGTTCGATTAT
1 -GTTCGGTTATGTTCGTTC-ATTAT
* *
397737 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCGTTCA-TTAT
397761 GTT
1 GTT
397764 TATCCCAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.02
24 41 0.91
25 3 0.07
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGGTTATGTTCGTTCATTAT
Found at i:397761 original size:38 final size:38
Alignment explanation
Indices: 397688--397763 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
397678 CGTTCGTGAA
* * *
397688 CGTTCGGTTATGTTCGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
*
397726 CGTTCGATTATGTTCGTTTATGTTCATTCATTTATGTT
1 CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
397764 TATCCCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.54
Consensus pattern (38 bp):
CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
Found at i:398205 original size:16 final size:16
Alignment explanation
Indices: 398182--398258 Score: 136
Period size: 16 Copynumber: 4.8 Consensus size: 16
398172 GGGTCTCCAA
398182 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
398198 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
398214 CGTTTATATTCGTGTT
1 CGTTTATGTTCGTGTT
398230 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
398246 CGTTTATGTTCGT
1 CGTTTATGTTCGT
398259 TTATTTATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:398353 original size:16 final size:16
Alignment explanation
Indices: 398328--398358 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
398318 AAAAAAAATT
398328 TGTTCATTTATGTTCA
1 TGTTCATTTATGTTCA
*
398344 TGTTCGTTTATGTTC
1 TGTTCATTTATGTTC
398359 GTTTATTTAT
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:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCA
Found at i:399173 original size:3 final size:3
Alignment explanation
Indices: 399160--399225 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
399150 TATAAGATGA
* *
399160 AAT AA- AAT AAT AAT AAT AAG AGGT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT
399206 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
399226 ATATAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 1 0.02
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:400345 original size:19 final size:19
Alignment explanation
Indices: 400310--400372 Score: 78
Period size: 18 Copynumber: 3.4 Consensus size: 19
400300 ACCTAAAACG
*
400310 AGAAAAACAAA-GAAATAA
1 AGAAAAATAAATGAAATAA
*
400328 TA-AATAATAAATGAAATAA
1 -AGAAAAATAAATGAAATAA
400347 AGAAAAATAAAT-AAATAA
1 AGAAAAATAAATGAAATAA
400365 AGAAAAAT
1 AGAAAAAT
400373 GTTTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 22 0.56
19 17 0.44
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (19 bp):
AGAAAAATAAATGAAATAA
Found at i:400369 original size:26 final size:27
Alignment explanation
Indices: 400318--400369 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
400308 CGAGAAAAAC
400318 AAAGAAATAATAAATAATAAATGAAAT
1 AAAGAAATAATAAATAATAAATGAAAT
400345 AAAGAAA-AATAAATAAATAAA-GAAA
1 AAAGAAATAATAAAT-AATAAATGAAA
400370 AATGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (27 bp):
AAAGAAATAATAAATAATAAATGAAAT
Found at i:400461 original size:76 final size:74
Alignment explanation
Indices: 400376--400862 Score: 707
Period size: 76 Copynumber: 6.5 Consensus size: 74
400366 GAAAAATGTT
* * * *
400376 TTTTTAAAACTATATAATATATATGTTTTTAAAAAAATAATTTTAAAAACCATATAATATATATT
1 TTTTCAAAACTATATAATATATAT-TTTTT-AAAAACTAATTTTCAAAACTATATAATATATATT
400441 TTAAAAACTAA
64 TTAAAAACTAA
*
400452 TTTTCAAAACTATATAATATATA--TTTT-AAAACTAATTTTCAAAACTATATAATATATATATT
1 TTTTCAAAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATTTT
400514 AAAAACTAA
66 AAAAACTAA
*
400523 TTTTCAAAAATATATAATATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATT
1 TTTTCAAAACTATAT-A-ATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATA--
400588 TTTTAAAAACTAA
62 TTTTAAAAACTAA
400601 TTTTCAAAACTATATAATATATA-TTTTTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTTTCAAAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATAT-TT
*
400665 TCGAAAACTAA
65 T-AAAAACTAA
400676 TTTTCAAAACTATATAATATATA-TTTTTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTTTCAAAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATAT-A-ATATATA-T
400740 TTTAAAAACTAA
63 TTTAAAAACTAA
400752 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
1 TTTTCAAAACTATATAATATATAT-TTTTTAAAAACTAATTTTCAAAACTATATAATATATAT-T
*
400817 TTCAAAAA-TTA
64 TT-AAAAACTAA
* *
400828 TTTTCAAAACTATATAATGTATATGTTTTCAAAAA
1 TTTTCAAAACTATATAATATATAT-TTTTTAAAAA
400863 TGTTTTTTTA
Statistics
Matches: 381, Mismatches: 14, Indels: 32
0.89 0.03 0.07
Matches are distributed among these distances:
71 54 0.14
72 1 0.00
73 12 0.03
74 3 0.01
75 102 0.27
76 136 0.36
77 17 0.04
78 56 0.15
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.43
Consensus pattern (74 bp):
TTTTCAAAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATTTT
AAAAACTAA
Found at i:400474 original size:38 final size:38
Alignment explanation
Indices: 400376--400862 Score: 724
Period size: 37 Copynumber: 12.9 Consensus size: 38
400366 GAAAAATGTT
* * *
400376 TTTTTAAAACTATATAATATATATGTTTTTAAAAAAATAA
1 TTTTCAAAACTATATAATATATAT-ATTTT-AAAAACTAA
* *
400416 TTTTAAAAACCATAT-A-ATATATATTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
400452 TTTTCAAAACTATAT-A-ATATATATTTT-AAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
400487 TTTTCAAAACTATATAATATATATA--TTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
*
400523 TTTTCAAAAATATATAATATATATATTTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATA--TTTTAAAAACTAA
*
400563 TTTTCAAAACTATATAATATATATTTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
400601 TTTTCAAAACTATATAATATATAT-TTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
**
400638 TTTTCAAAACTATATAATATATATATTTCGAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
400676 TTTTCAAAACTATATAATATATAT-TTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
400713 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATA-TTTTAAAAACTAA
400752 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATA-TTTTAAAAACTAA
* *
400791 TTTTCAAAACTATATAATATATATATTTCAAAAA-TTA
1 TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
* *
400828 TTTTCAAAACTATATAATGTATATGTTTTCAAAAA
1 TTTTCAAAACTATATAATATATATATTTT-AAAAA
400863 TGTTTTTTTA
Statistics
Matches: 418, Mismatches: 18, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
35 25 0.06
36 66 0.16
37 111 0.27
38 91 0.22
39 78 0.19
40 47 0.11
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.43
Consensus pattern (38 bp):
TTTTCAAAACTATATAATATATATATTTTAAAAACTAA
Found at i:400889 original size:38 final size:37
Alignment explanation
Indices: 400367--400890 Score: 418
Period size: 38 Copynumber: 13.8 Consensus size: 37
400357 ATAAATAAAG
* * * * *
400367 AAAAATGTTTTTTTAAAACTATATAATATATATGTTTTTAA
1 AAAAAT-TATTTTCAAAACTATAT-AT-TATATATATTT-C
* * * *
400408 AAAAATAATTTTAAAAACCATATA--ATATATATTTT
1 AAAAATTATTTTCAAAACTATATATTATATATATTTC
* *
400443 AAAAACTAATTTTCAAAACTATATA--ATATATATTTT
1 AAAAA-TTATTTTCAAAACTATATATTATATATATTTC
* * *
400479 AAAACTAATTTTCAAAACTATATAATATATATA-TT-
1 AAAAATTATTTTCAAAACTATATATTATATATATTTC
* * * *
400514 AAAAACTAATTTTCAAAAATATATAATATATATATTTTTT
1 AAAAA-TTATTTTCAAAACTATAT-AT-TATATATATTTC
* * * *
400554 AAAAACTAATTTTCAAAACTATATAATATATATTTTTT
1 AAAAA-TTATTTTCAAAACTATATATTATATATATTTC
* * *
400592 AAAAACTAATTTTCAAAACTATATAATATATAT-TTTT
1 AAAAA-TTATTTTCAAAACTATATATTATATATATTTC
* *
400629 AAAAACTAATTTTCAAAACTATATAATATATATATTTC
1 AAAAA-TTATTTTCAAAACTATATATTATATATATTTC
* * * *
400667 GAAAACTAATTTTCAAAACTATATAATATATAT-TTTT
1 -AAAAATTATTTTCAAAACTATATATTATATATATTTC
* * *
400704 AAAAACTAATTTTCAAAACTATATAATATATATATTTTT
1 AAAAA-TTATTTTCAAAACTATATATTATATATA-TTTC
* * *
400743 AAAAACTAATTTTCAAAACTATATAATATATATATTTTT
1 AAAAA-TTATTTTCAAAACTATATATTATATATA-TTTC
* *
400782 AAAAACTAATTTTCAAAACTATATAATATATATATTTC
1 AAAAA-TTATTTTCAAAACTATATATTATATATATTTC
*
400820 AAAAATTATTTTCAAAACTATATAATGTATATGT-TTTC
1 AAAAATTATTTTCAAAACTATAT-AT-TATATATATTTC
* *
400858 AAAAATGTTTTTTTAAAGACTATATATTATATA
1 AAAAAT-TATTTTCAAA-ACTATATATTATATA
400891 CATATTTTCA
Statistics
Matches: 439, Mismatches: 27, Indels: 37
0.87 0.05 0.07
Matches are distributed among these distances:
35 28 0.06
36 63 0.14
37 92 0.21
38 106 0.24
39 101 0.23
40 43 0.10
41 6 0.01
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (37 bp):
AAAAATTATTTTCAAAACTATATATTATATATATTTC
Found at i:401614 original size:84 final size:84
Alignment explanation
Indices: 401526--402657 Score: 1055
Period size: 84 Copynumber: 13.6 Consensus size: 84
401516 ATTTACCTCT
* * * * * *
401526 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* *
401591 CTGCAAATGATGTGCCTTA
66 CTGTAAATGATGTGCCTTG
* * * * *
401610 GAGCTAAGCGCAGTCGAACTCGCAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
*
401674 CTGTAAATGATGTGCCCTCG
66 CTGTAAATGATGTG-CCTTG
* * * * * ** * *
401694 AAGATGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGGCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* *
401755 CTGCAAATAATGTGCCTTG
66 CTGTAAATGATGTGCCTTG
* * *
401774 CAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * *
401839 TTGCAAATGATATGCCTTG
66 CTGTAAATGATGTGCCTTG
* ** *
401858 GAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGATAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTAT
**
401922 GCTGTAAATGATGTGCCCTCA
65 GCTGTAAATGATGTG-CCTTG
* * * * * * * * *
401943 AAGCTGAGTGTAATCAAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTTGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
402004 CTGTAAATGATGTGCCTTG
66 CTGTAAATGATGTGCCTTG
* *
402023 GAGCTAAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
*
402088 CTGTAAATGATATGCCTTG
66 CTGTAAATGATGTGCCTTG
* * * *
402107 GAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGG-TGACAGATAACTCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTAT
** *
402171 ATTGTAAATGATGAGCCCTTG
65 GCTGTAAATGATGTG-CCTTG
* * * * * * * * * *
402192 AAGTTGAGTGTACTTGAACT-TAAGGGC-CT--TTGGCAGATAACCCCACCCTTCTCGACTTAAG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT-A----ACCCTTCTAGCCTTAAG
** * *
402253 CCATGCTGTACACGATGTGCCTTG
61 TTATGCTGTAAATGATGTGCCTTG
* * *
402277 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* *
402342 CTGCAAATGATATGCCTTG
66 CTGTAAATGATGTGCCTTG
** * *
402361 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGATAAATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTAT
*
402425 GCTGTAAATGATGTGTCCTTA
65 GCTGTAAATGATGTG-CCTTG
* * * * * * * *
402446 AAGCTAAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTTGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * * *
402507 CTGCAAACGCTGCGCCTTG
66 CTGTAAATGATGTGCCTTG
* ** * * * * * *
402526 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
*
402591 TTGTAAATGATGTGCCTTG
66 CTGTAAATGATGTGCCTTG
* * * *
402610 GAGCTGAGTGTAGTCGAACTCGAAGGTC-TTGGATGACAGACAACCCTT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
402658 GAGTTATGTT
Statistics
Matches: 842, Mismatches: 175, Indels: 63
0.78 0.16 0.06
Matches are distributed among these distances:
80 76 0.09
81 117 0.14
82 8 0.01
83 53 0.06
84 441 0.52
85 107 0.13
86 30 0.04
87 1 0.00
88 1 0.00
89 8 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
CTGTAAATGATGTGCCTTG
Found at i:401973 original size:249 final size:249
Alignment explanation
Indices: 401526--402657 Score: 1523
Period size: 249 Copynumber: 4.5 Consensus size: 249
401516 ATTTACCTCT
* * * * * *
401526 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * * * * *
401591 CTGCAAATGATGTGCCTTAGAGCTAAGCGCAGTCGAACTCGCAGGTC-TTTGTTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
* *
401655 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCGAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGG
** * **
401720 TCTTTGGCAGATAGGCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCTTG
196 TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAACGATGTGCCTTG
* * *
401774 CAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * *
401839 TTGCAAATGATATGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
*
401904 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCAAACTCGAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGG
* * * *
401969 TCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTG
196 TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAACGATGTGCCTTG
* *
402023 GAGCTAAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * *
402088 CTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACT
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
** * ** * * * **
402153 CTTCTAGCCTTGAGTTATATTGTAAATGATGAGCCCTTGAAGTTGAGTGTACTTGAACTTAAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGG
* * * *
402218 CCTTTGGCAGATAACCCCACCCTTCTCGACTTAAGCCATGCTGTACACGATGTGCCTTG
196 TCTTTGGCAGAT-A----ACCCTTCTCGACTTAAGCTATGCTGCAAACGATGTGCCTTG
* * *
402277 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* *
402342 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAAATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
* * *
402407 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCCTTAAAGCTAAGTGTAATCGAACTCGAGGG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGG
* * *
402472 TCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAACGCTGCGCCTTG
196 TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAACGATGTGCCTTG
* ** * * * * * *
402526 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
* * * * *
402591 TTGTAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC--TTGGATGACAGACAAC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAAC
402654 CCTT
130 CCTT
402658 GAGTTATGTT
Statistics
Matches: 777, Mismatches: 100, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
247 4 0.01
248 108 0.14
249 442 0.57
250 1 0.00
253 1 0.00
254 221 0.28
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (249 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGG
TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAACGATGTGCCTTG
Found at i:402480 original size:503 final size:498
Alignment explanation
Indices: 401478--402657 Score: 1639
Period size: 503 Copynumber: 2.4 Consensus size: 498
401468 ATTTATTGAT
** * * * * *
401478 AGATAGCCCTTCTTCCCTTGAGCTATGCTGTAAATTTGATTTACCTCT-GAGCTGAGTGTAATCG
1 AGATAGCCCTTCTTGACTTAAGCTATGCTGTAAA--TGATGTGCCT-TGGAGCTGAGCGTAGTCG
* * *
401542 AACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
63 AACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCC
* * * * *
401607 TTAGAGCTAAGCGCAGTCGAACTCGCAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTT
128 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
* * * * **
401671 ATGCTGTAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGGC
193 ATACTGTAAATGATGAGCCCTCGAAGATGAGTGTAATCGAACTCAAGGGCCTTTGGCAGATAACC
** *
401736 CTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAAGT
258 CTTCTCGACTTAAGCCATGCTGCAAACAATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAAGT
* * *
401801 CTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTGGAGATGAG
323 CTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGATGAG
*
401866 CGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
388 CGTAGTCGAACTCGAAGGTCTTTTGGTGATAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
*
401931 GATGTGCCCTCAAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGC
453 GATGTGCCCTCAAAGCTAAGTGTAATCAAACTCGAGGGTCTTTGGC
*
401977 AGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAAC
1 AGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * *
402042 TTGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATATGCCTTG
66 TCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTG
* *
402107 GAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATA
131 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATA
* * * * * *
402172 TTGTAAATGATGAGCCCTTGAAGTTGAGTGTACTTGAACTTAAGGGCCTTTGGCAGATAACCCCA
196 CTGTAAATGATGAGCCCTCGAAGATGAGTGTAATCGAACTCAAGGGCCTTTGGCAGAT-A----A
* * * * *
402237 CCCTTCTCGACTTAAGCCATGCTGTACACGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
256 CCCTTCTCGACTTAAGCCATGCTGCAAACAATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAA
* * *
402302 GTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
321 GTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGATG
402367 AGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAAATAACCCTTCTAGCCTTGAGTTATGCTGTAA
386 AGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAAATAACCCTTCTAGCCTTGAGTTATGCTGTAA
* * *
402432 ATGATGTGTCCTTAAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGC
451 ATGATGTGCCCTCAAAGCTAAGTGTAATCAAACTCGAGGGTCTTTGGC
* * * * *
402480 AGATAACCCTTCTTGACTTAAGCTATGCTGCAAACGCTGCGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* ** * * * **
402545 TCAAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGTAAATGATGTGCCTTG
66 TCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTG
* *
402610 GAGCTGAGTGTAGTCGAACTCGAAGGTC--TTGGATGACAGACAACCCTT
131 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTT
402658 GAGTTATGTT
Statistics
Matches: 598, Mismatches: 75, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
496 1 0.00
497 105 0.18
498 82 0.14
499 32 0.05
501 4 0.01
502 13 0.02
503 361 0.60
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (498 bp):
AGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATA
CTGTAAATGATGAGCCCTCGAAGATGAGTGTAATCGAACTCAAGGGCCTTTGGCAGATAACCCTT
CTCGACTTAAGCCATGCTGCAAACAATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAAGTCTT
TGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGATGAGCGT
AGTCGAACTCGAAGGTCTTTTGGTGATAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
GTGCCCTCAAAGCTAAGTGTAATCAAACTCGAGGGTCTTTGGC
Found at i:407799 original size:19 final size:20
Alignment explanation
Indices: 407754--407802 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
407744 ACCTGAAACG
*
407754 AGAAAAACAAA-GAAATAAT
1 AGAAAAATAAATGAAATAAT
*
407773 A-AATAATAAATGAAATAA-
1 AGAAAAATAAATGAAATAAT
407791 AGAAAAATAAAT
1 AGAAAAATAAAT
407803 AAAGAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (20 bp):
AGAAAAATAAATGAAATAAT
Found at i:407802 original size:14 final size:14
Alignment explanation
Indices: 407766--407813 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
407756 AAAAACAAAG
*
407766 AAAT-AATAAATAA
1 AAATAAATAAAGAA
407779 TAAATGAAATAAAGAA
1 -AAAT-AAATAAAGAA
407795 AAATAAATAAAGAA
1 AAATAAATAAAGAA
407809 AAATA
1 AAATA
407814 TTTTTTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 19 0.61
15 4 0.13
16 8 0.26
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAATAAATAAAGAA
Found at i:407922 original size:38 final size:38
Alignment explanation
Indices: 407820--408310 Score: 645
Period size: 38 Copynumber: 12.7 Consensus size: 38
407810 AATATTTTTT
*
407820 AAACTATATAATATATATGTTTTTTTTAAAAA-TAATTTTCA
1 AAACTATATAATATATA----TATTTTAAAAACTAATTTTCA
*
407861 AAACCATAT-A-ATATATATTTTAAAAACTAATTTTCA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
*
407897 GAACTATATAATATATATATTTTAAAAACTAATTTTCA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
*
407935 AAACTATATAATATATATATTTTAAAAACGAATTTTCA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
407973 AAACTATATAATATATATATATTTTAAAAACTAATTTTCA
1 AAACTATAT-A-ATATATATATTTTAAAAACTAATTTTCA
408013 AAACTATATAATATATAT-TTTTAAAAAAACTAATTTTCA
1 AAACTATATAATATATATATTTT--AAAAACTAATTTTCA
* * *
408052 AAACTATAT-A-ATGTATATTTAAAAATAATAATTTTCA
1 AAACTATATAATATATATATTTTAAAA-ACTAATTTTCA
*
408089 AAACTATATAATATATATATTTCAAAAACTAATTTTCA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
*
408127 AAACTAGATAATATATATATATATTTAAAAACTAATTTTCA
1 AAACTATAT-A-ATATATATAT-TTTAAAAACTAATTTTCA
* *
408168 AAACTATATACTATATATTTTTTAAAAACTAATTTTCA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
408206 AAACTATATAATATATATATTTTTAAAAACTAATTTTCA
1 AAACTATATAATATATATA-TTTTAAAAACTAATTTTCA
* ** *
408245 AAACTATATAATATATATATTTCAAAAA-TTGTTTTAA
1 AAACTATATAATATATATATTTTAAAAACTAATTTTCA
* * *
408282 AAACAATATAATGTATATGTTTTTAAAAA
1 AAACTATATAATATATAT-ATTTTAAAAA
408311 AAAAATATAA
Statistics
Matches: 406, Mismatches: 28, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
35 10 0.02
36 20 0.05
37 51 0.13
38 153 0.38
39 91 0.22
40 48 0.12
41 33 0.08
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (38 bp):
AAACTATATAATATATATATTTTAAAAACTAATTTTCA
Found at i:407937 original size:13 final size:13
Alignment explanation
Indices: 407877--408018 Score: 55
Period size: 13 Copynumber: 11.0 Consensus size: 13
407867 TATAATATAT
407877 ATTTTAAAAACTA
1 ATTTTAAAAACTA
* *
407890 ATTTTCAGAACT-
1 ATTTTAAAAACTA
* *
407902 A-TATAATATA-TA
1 ATTTTAA-AAACTA
407914 TATTTTAAAAACTA
1 -ATTTTAAAAACTA
*
407928 ATTTTCAAAACT-
1 ATTTTAAAAACTA
* *
407940 A-TATAATATA-TA
1 ATTTTAA-AAACTA
*
407952 TATTTTAAAAACGA
1 -ATTTTAAAAACTA
*
407966 ATTTTCAAAACTA
1 ATTTTAAAAACTA
** * *
407979 TATAATATATA-TA
1 -ATTTTAAAAACTA
407992 TATTTTAAAAACTA
1 -ATTTTAAAAACTA
*
408006 ATTTTCAAAACTA
1 ATTTTAAAAACTA
408019 TATAATATAT
Statistics
Matches: 90, Mismatches: 27, Indels: 24
0.64 0.19 0.17
Matches are distributed among these distances:
11 8 0.09
12 5 0.06
13 59 0.66
14 18 0.20
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.41
Consensus pattern (13 bp):
ATTTTAAAAACTA
Found at i:408011 original size:116 final size:115
Alignment explanation
Indices: 407820--408310 Score: 651
Period size: 116 Copynumber: 4.2 Consensus size: 115
407810 AATATTTTTT
*
407820 AAACTATATAATATATATGTTTTTTTTAAAAA-TAATTTTCAAAAC--CATATA-ATATATATTT
1 AAACTATATAATATATA----TTTTTTAAAAACTAATTTTCAAAACTATATATATATATATATTT
*
407881 TAAAAACTAATTTTCAGAACTATATAATATATATATTTTAAAAACTAATTTTCA
62 TAAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCA
* *
407935 AAACTATATAATATATATATTTTAAAAACGAATTTTCAAAACTATATAATATATATATATTTTAA
1 AAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATAT-ATATATATATATTTTAA
408000 AAACTAATTTTCAAAACTATATAATATATAT-TTTTAAAAAAACTAATTTTCA
65 AAACTAATTTTCAAAACTATATAATATATATATTTT--AAAAACTAATTTTCA
* * * *
408052 AAACTATATAATGTATA--TTTAAAAATAATAATTTTCAAAACTATATA-ATATATATATTTCAA
1 AAACTATATAATATATATTTTTTAAAA-ACTAATTTTCAAAACTATATATATATATATATTTTAA
*
408114 AAACTAATTTTCAAAACTAGATAATATATATATATATTTAAAAACTAATTTTCA
65 AAACTAATTTTCAAAACTATAT-A-ATATATATAT-TTTAAAAACTAATTTTCA
*
408168 AAACTATATACTATATATTTTTTAAAAACTAATTTTCAAAACTATATA-ATATATATATTTTTAA
1 AAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATATATATATATA-TTTTAA
* ** *
408232 AAACTAATTTTCAAAACTATATAATATATATATTTCAAAAA-TTGTTTTAA
65 AAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCA
* *
408282 AAACAATATAATGTATATGTTTTTAAAAA
1 AAACTATATAATATATAT-TTTTTAAAAA
408311 AAAAATATAA
Statistics
Matches: 337, Mismatches: 23, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
111 10 0.03
112 12 0.04
114 58 0.17
115 50 0.15
116 109 0.32
117 62 0.18
118 36 0.11
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (115 bp):
AAACTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATATATATATATATTTTAAA
AACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCA
Found at i:408099 original size:17 final size:17
Alignment explanation
Indices: 408043--408100 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
408033 TTAAAAAAAC
408043 TAATTTTCAAAACTATA
1 TAATTTTCAAAACTATA
* *
408060 TAATGTATATTTAAAAATA-A
1 TAA--T-T-TTCAAAACTATA
408080 TAATTTTCAAAACTATA
1 TAATTTTCAAAACTATA
408097 TAAT
1 TAAT
408101 ATATATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 8 0.25
17 9 0.28
18 1 0.03
19 1 0.03
20 5 0.16
21 8 0.25
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATTTTCAAAACTATA
Found at i:409936 original size:21 final size:22
Alignment explanation
Indices: 409898--409938 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
409888 CTTAATATTA
409898 AAAAATAAATAAACATTTATCT
1 AAAAATAAATAAACATTTATCT
*
409920 AAAAATAAATATA-ATTTAT
1 AAAAATAAATAAACATTTAT
409939 AAAAGTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATAAATAAACATTTATCT
Found at i:411594 original size:3 final size:3
Alignment explanation
Indices: 411586--411626 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
411576 ATATAAAAAT
*
411586 TAA TAA TAA TAAA TAA TAA T-A TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
411627 CACAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:411611 original size:33 final size:33
Alignment explanation
Indices: 411574--411642 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
411564 AATGGACCTG
*
411574 TAATA-TAAAAATTAATAATA-ATAAATAATAATA
1 TAATAGTAAAAA-TAATAATACACAAATAA-AATA
*
411607 TAATAGTAATAATAATAATACACAAATAAAATA
1 TAATAGTAAAAATAATAATACACAAATAAAATA
411640 TAA
1 TAA
411643 AAAAAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (33 bp):
TAATAGTAAAAATAATAATACACAAATAAAATA
Found at i:412229 original size:112 final size:111
Alignment explanation
Indices: 412094--412438 Score: 399
Period size: 112 Copynumber: 3.0 Consensus size: 111
412084 CTGTGATAGC
*
412094 ATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCT
1 ATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
*
412159 TCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGA
66 TCTCATTATGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGA
*
412205 ATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTT
1 A-TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTT
* * *
412270 CTTCTCATTATGAA--TACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTTAAG-GATAGA
64 CTTCTCATTATGAACTTAC-TCTGGAAA----AGT--TGATCCA--T-C---GAGTGAT-GA
* * * * * *
412329 ATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTCTGAACTTCTCCTTCCTCTACAGATGAGTTAT
1 ATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
* *
412394 TCTCATTATGAACTTCCTCTGGAAAAGTTGGTCCATCGAGTGATG
66 TCTCATTATGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATG
412439 GAAATTTTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 38
0.78 0.07 0.15
Matches are distributed among these distances:
111 6 0.03
112 58 0.29
113 27 0.14
114 1 0.01
115 1 0.01
116 2 0.01
117 5 0.03
118 6 0.03
119 2 0.01
120 1 0.01
121 1 0.01
122 26 0.13
123 54 0.27
124 7 0.04
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (111 bp):
ATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
TCTCATTATGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGA
Found at i:412278 original size:235 final size:233
Alignment explanation
Indices: 412011--412438 Score: 696
Period size: 235 Copynumber: 1.8 Consensus size: 233
412001 CTTCTCATTC
*
412011 TTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATTTTGATGCTGATCT
1 TTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCT
* *
412076 ATCTCCTTCT-GTGATAGCATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
66 ATCTCCTT-TAG-GATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCT
* * *
412140 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGA
129 TCCTCTACAGATAAGTTATTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGA
412205 ATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
194 ATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* *
412245 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATACTTCTGGAAATGTTGGTGCTGATC
1 TTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATC
* * *
412310 TATCTCCTTTAAGGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTCTGAACTTCTCCT
65 TATCTCCTTT-AGGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCT
* *
412375 TCCTCTACAGATGAGTTATTCTCATTATGAACTTCCTCTGGAAAAGTTGGTCCATCGAGTGATG
129 TCCTCTACAGATAAGTTATTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATG
412439 GAAATTTTTT
Statistics
Matches: 178, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
234 6 0.03
235 171 0.96
236 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (233 bp):
TTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCT
ATCTCCTTTAGGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTC
CTCTACAGATAAGTTATTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAAT
TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
Found at i:412590 original size:36 final size:36
Alignment explanation
Indices: 412464--412590 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
412454 AGTGAAACTG
*
412464 TCTCAAGCGAGACAAATCTTGTTTTAAGAGAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAGAAACAA
* * * *** * **
412500 TCTCAAGTGAGATACATTGTTGTTTCGGGTGAAACTG
1 TCTCAAGCGAGACAAATT-TTGTTTTAAGAGAAACAA
*
412537 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAGAAACAA
* *
412573 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
412591 ACTATTTGAA
Statistics
Matches: 68, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
36 41 0.60
37 27 0.40
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAGAAACAA
Found at i:412726 original size:73 final size:73
Alignment explanation
Indices: 412595--412848 Score: 429
Period size: 73 Copynumber: 3.5 Consensus size: 73
412585 TAAATTACTA
* * *
412595 TTTGAAAACATCCTGCACTGTAGGTCTTACAGATGA-CCTAGAGGATTTTAGATCAAAAAGCTCC
1 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCT-GAGGCTTTAAGATCAAAAAGCTCC
412659 CGAAGGCTT
65 CGAAGGCTT
* *
412668 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATAAAAAAGCTCCC
1 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
412733 GAAGGCTT
66 GAAGGCTT
* *
412741 TTTGAAAACATCATGCATTGTAGGTCTTACAGATGACCTTGAGGCTTTAAGATCAAAAAGCTCCC
1 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
412806 GAAGGCTT
66 GAAGGCTT
412814 TTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1 TTTGAAAACATCATGCACTGTAGGTCTTACAGATG
412849 TTGGAAATAG
Statistics
Matches: 170, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
73 167 0.98
74 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (73 bp):
TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCC
GAAGGCTT
Found at i:414923 original size:35 final size:35
Alignment explanation
Indices: 414860--414927 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
414850 TTCTTGCTGA
*
414860 TATGAGCCTCCAAGAGTGCCCAAATATTCATATTAC
1 TATGAGCCTCCAAGAATGCCCAAATATTC-TATTAC
* * *
414896 TATGAGCCTTCAA-AATGCCCCACTATTCTATT
1 TATGAGCCTCCAAGAATGCCCAAATATTCTATT
414928 TCTGGTTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 4 0.14
35 12 0.43
36 12 0.43
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (35 bp):
TATGAGCCTCCAAGAATGCCCAAATATTCTATTAC
Found at i:417657 original size:8 final size:8
Alignment explanation
Indices: 417644--417691 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
417634 CTTGGTTCAA
417644 TTTTTCCT
1 TTTTTCCT
417652 TTTTTCCT
1 TTTTTCCT
*
417660 CTTTTCCTCT
1 -TTTTTC-CT
417670 TTTTTCCT
1 TTTTTCCT
417678 TTTTTCCT
1 TTTTTCCT
417686 CTTTTT
1 -TTTTT
417692 TTTCCTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 18 0.51
9 15 0.43
10 2 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCCT
Found at i:417673 original size:18 final size:18
Alignment explanation
Indices: 417650--417692 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
417640 TCAATTTTTC
417650 CTTTTTTCCTCTTTTCCT
1 CTTTTTTCCTCTTTTCCT
*
417668 CTTTTTTCCTTTTTTCCT
1 CTTTTTTCCTCTTTTCCT
417686 CTTTTTT
1 CTTTTTT
417693 TTCCTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTTCCTCTTTTCCT
Found at i:417708 original size:18 final size:17
Alignment explanation
Indices: 417663--417716 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
417653 TTTTCCTCTT
*
417663 TTCCTCTTTTTTCCTTT-T
1 TTCCTCTTTTTT--TTTCC
417681 TTCCTC-TTTTTTTTCC
1 TTCCTCTTTTTTTTTCC
417697 TTCCTCTTTTTTTTTCC
1 TTCCTCTTTTTTTTTCC
417714 TTC
1 TTC
417717 TTCAAGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 18 0.55
18 6 0.18
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTCTTTTTTTTTCC
Found at i:417719 original size:20 final size:19
Alignment explanation
Indices: 417651--417719 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 19
417641 CAATTTTTCC
*
417651 TTTTTTCCTCTTTTCCTC--
1 TTTTTTCCT-TCTTCCTCTT
*
417669 TTTTTTCCTTTTTTCCTCTT
1 TTTTTTCC-TTCTTCCTCTT
*
417689 TTTTTTCCTTCCT-CT-TT
1 TTTTTTCCTTCTTCCTCTT
417706 TTTTTTCCTTCTTC
1 TTTTTTCCTTCTTC
417720 AAGTATAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 14 0.32
18 18 0.41
19 4 0.09
20 8 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTCCTTCTTCCTCTT
Found at i:418217 original size:19 final size:19
Alignment explanation
Indices: 418193--418240 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
418183 TCTCGTGCCA
418193 ATCCTTGTAAGTTTCAATG
1 ATCCTTGTAAGTTTCAATG
418212 ATCCTTGTAAGTTTCAATG
1 ATCCTTGTAAGTTTCAATG
*
418231 ATCTTTGTAA
1 ATCCTTGTAA
418241 TGATATTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (19 bp):
ATCCTTGTAAGTTTCAATG
Found at i:422707 original size:21 final size:22
Alignment explanation
Indices: 422669--422709 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
422659 CTTAATATTA
422669 AAAAATAAATAAACATTTATCT
1 AAAAATAAATAAACATTTATCT
*
422691 AAAAATAAATATA-ATTTAT
1 AAAAATAAATAAACATTTAT
422710 AAAAGTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATAAATAAACATTTATCT
Found at i:422973 original size:14 final size:13
Alignment explanation
Indices: 422907--422975 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 13
422897 ATGACTAAGT
422907 AATAATAATAAT-
1 AATAATAATAATA
422919 AAT-ATAATAATGA
1 AATAATAATAAT-A
*
422932 ACATAATAAT-TTA
1 A-ATAATAATAATA
*
422945 AA-CAT-AT-ATA
1 AATAATAATAATA
422955 AATAATAATAATGA
1 AATAATAATAAT-A
422969 AATAATA
1 AATAATA
422976 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
10 6 0.13
11 12 0.27
12 6 0.13
13 5 0.11
14 11 0.24
15 5 0.11
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:423870 original size:15 final size:15
Alignment explanation
Indices: 423850--423887 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
423840 TGCTACTATG
423850 GGTGTTGTTTGGCTT
1 GGTGTTGTTTGGCTT
423865 GGTGTTGTTTGGCTT
1 GGTGTTGTTTGGCTT
*
423880 GCTGTTGT
1 GGTGTTGT
423888 GGTATGTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.08, G:0.39, T:0.53
Consensus pattern (15 bp):
GGTGTTGTTTGGCTT
Found at i:424381 original size:13 final size:13
Alignment explanation
Indices: 424365--424390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
424355 TATAAAAATT
424365 TAATAATAATAAA
1 TAATAATAATAAA
424378 TAATAATAATAAA
1 TAATAATAATAAA
424391 CAAATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:426714 original size:22 final size:22
Alignment explanation
Indices: 426675--426716 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
426665 TGATATTTTG
*
426675 TTTATTAATTTTTATGTTTATT
1 TTTATTAATTATTATGTTTATT
426697 TTTATTAAATTATT-TGTTTA
1 TTTATT-AATTATTATGTTTA
426717 AAACTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTATTAATTATTATGTTTATT
Found at i:426822 original size:16 final size:16
Alignment explanation
Indices: 426801--426831 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
426791 TCACTTTAAA
426801 TTTGAGAACTCAACTC
1 TTTGAGAACTCAACTC
426817 TTTGAGAACTCAACT
1 TTTGAGAACTCAACT
426832 TGTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (16 bp):
TTTGAGAACTCAACTC
Found at i:427837 original size:3 final size:3
Alignment explanation
Indices: 427831--427871 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
427821 CACAACAAAT
*
427831 ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
427872 CATCATCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:427876 original size:3 final size:3
Alignment explanation
Indices: 427870--427905 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
427860 AATAATAATA
427870 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
427906 TATACCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:441887 original size:42 final size:42
Alignment explanation
Indices: 441794--441901 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
441784 ACCCGAAGGT
* * * * *
441794 CTTATAGATGGCCCGAAGGACTT-ATCATCTTGTTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
441835 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
**
441877 CTTACT-GATGACCTAAAGGATTTAA
1 CTTA-TAGATGACCCGAAGGATTTAA
441902 AAATCAAGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 21 0.36
42 36 0.62
43 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
Found at i:442051 original size:90 final size:90
Alignment explanation
Indices: 441892--442349 Score: 706
Period size: 90 Copynumber: 5.1 Consensus size: 90
441882 TGATGACCTA
* * * *
441892 AAGGATTTAAAAATCAAGAAACCCCTGAAGGCCTAGTTT-TTAAAATCTCATTTGAAAACATCCT
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTT-AAATCTCATTTGAAAACATTCT
*
441956 GCACTGAAGGTCTTATGGATGGCTCG
65 GCACTGAAGGTCTTATGGATGGCCCG
* *
441982 AATGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTCTA
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTCTG
** * *
442047 CACTGAATTTCTTATGCATGGCCTG
66 CACTGAAGGTCTTATGGATGGCCCG
*
442072 AAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACA-TCAT
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTC-T
*
442136 GCACTGAA-GTCTTATAGATGGCCCG
65 GCACTGAAGGTCTTATGGATGGCCCG
* * * *
442161 TAGCACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATTCTG
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTCTG
442226 CACTGAAGGTCTTATGGATGGCCCG
66 CACTGAAGGTCTTATGGATGGCCCG
*
442251 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCCTG
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTCTG
*
442316 CACTGAAGGTCTTATGGATGGCCCA
66 CACTGAAGGTCTTATGGATGGCCCG
442341 AAGGACTTA
1 AAGGACTTA
442350 TCATCTTGCT
Statistics
Matches: 336, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
89 81 0.24
90 253 0.75
91 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (90 bp):
AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATTCTG
CACTGAAGGTCTTATGGATGGCCCG
Found at i:442209 original size:179 final size:180
Alignment explanation
Indices: 441892--442349 Score: 724
Period size: 179 Copynumber: 2.5 Consensus size: 180
441882 TGATGACCTA
* * *
441892 AAGGATTTAAAAATCAAGAAACCCCTGAAGGCCTAGTTT-TTAAAATCTCATTTGAAAACATCCT
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTT-AAATCTCATTTGAAAACATCCT
*
441956 GCACTGAAGGTCTTATGGATGGCTCGAATGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTT
65 GCACTGAAGGTCTTATGGATGGCCCGAATGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTT
* ** *
442021 CTTAAATCTCATTTGAAAACATTCTACACTGAATTTCTTATGCATGGCCTG
130 CTAAAATCTCATTTGAAAACATTCTACACTGAAGGTCTTATGCATGGCCCG
* *
442072 AAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCATG
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCCTG
* * *
442137 CACTGAA-GTCTTATAGATGGCCCGTA-GCACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTT
66 CACTGAAGGTCTTATGGATGGCCCGAATG-ACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTT
* *
442200 CTAAAATCTCATTTGAAAACATTCTGCACTGAAGGTCTTATGGATGGCCCG
130 CTAAAATCTCATTTGAAAACATTCTACACTGAAGGTCTTATGCATGGCCCG
442251 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCCTG
1 AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCCTG
* *
442316 CACTGAAGGTCTTATGGATGGCCCAAAGGACTTA
66 CACTGAAGGTCTTATGGATGGCCCGAATGACTTA
442350 TCATCTTGCT
Statistics
Matches: 254, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
178 1 0.00
179 165 0.65
180 85 0.33
181 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (180 bp):
AAGGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCCTG
CACTGAAGGTCTTATGGATGGCCCGAATGACTTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTC
TAAAATCTCATTTGAAAACATTCTACACTGAAGGTCTTATGCATGGCCCG
Found at i:442407 original size:42 final size:42
Alignment explanation
Indices: 442351--442481 Score: 192
Period size: 42 Copynumber: 3.1 Consensus size: 42
442341 AAGGACTTAT
* *
442351 CATCTTGCTCGAAAGACTTA-TAGATGACCCGAAGGATTTACG
1 CATCATGCTCGAAAGACTTACT-GATGACCCGAAGGATTTACA
442393 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACA
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACA
* * * *
442435 CATCATGCTCGAAAGACTCACTGATGGCCCGAAGGACTTACT
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACA
442477 CATCA
1 CATCA
442482 AGAAACTCCT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 81 0.99
43 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACA
Found at i:442413 original size:22 final size:21
Alignment explanation
Indices: 442344--442452 Score: 55
Period size: 20 Copynumber: 5.2 Consensus size: 21
442334 TGGCCCAAAG
* *
442344 GACTTATCATCTTGCTCGAAA
1 GACTTACCATCATGCTCGAAA
* * * *
442365 GACTTA-TA-GATGACCCGAAG
1 GACTTACCATCATG-CTCGAAA
*
442385 GATTTACGCATCATGCTCGAAA
1 GACTTAC-CATCATGCTCGAAA
* * *
442407 GACTTA-C-TGATGACCCGAAG
1 GACTTACCATCATG-CTCGAAA
*
442427 GATTTACACATCATGCTCGAAA
1 GACTTAC-CATCATGCTCGAAA
442449 GACT
1 GACT
442453 CACTGATGGC
Statistics
Matches: 61, Mismatches: 19, Indels: 15
0.64 0.20 0.16
Matches are distributed among these distances:
19 6 0.10
20 22 0.36
21 6 0.10
22 20 0.33
23 7 0.11
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
GACTTACCATCATGCTCGAAA
Found at i:442584 original size:35 final size:36
Alignment explanation
Indices: 442538--442608 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
442528 ACCCCTATAT
*
442538 ATCACGTTGGTCCCTCAAG--TGTTCATCAAGGAACC
1 ATCACATTGGTCCCTCAAGCTTG-TCATCAAGGAACC
442573 ATCACATTGGTCCCTCAAGCTTGTCATCAAGGAACC
1 ATCACATTGGTCCCTCAAGCTTGTCATCAAGGAACC
442609 CCTACATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 18 0.55
36 13 0.39
37 2 0.06
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (36 bp):
ATCACATTGGTCCCTCAAGCTTGTCATCAAGGAACC
Found at i:442627 original size:43 final size:43
Alignment explanation
Indices: 442580--442848 Score: 412
Period size: 43 Copynumber: 6.3 Consensus size: 43
442570 ACCATCACAT
* *
442580 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCATGT
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
* * * *
442623 TGGTCCCTCAAACTTGTCATAAAAGAACCCCTATATATCACGA
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
* * **
442666 TGGTTCCTTAAGCTTGTCATCAAGGAACCCCTACATATCACTT
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
442709 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
* *
442752 TGGTTCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGA
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
* *
442795 TGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATAACGA
1 TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
442838 TGGTCCCTCAA
1 TGGTCCCTCAA
442849 TCTTAGTTTC
Statistics
Matches: 204, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 204 1.00
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (43 bp):
TGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGA
Found at i:442737 original size:129 final size:129
Alignment explanation
Indices: 442526--442848 Score: 423
Period size: 129 Copynumber: 2.6 Consensus size: 129
442516 TGTCACCAAG
* *
442526 GAACCCCTATATATCACGTTGGTCCCTCAAG-TGT-TCATCAAGGAA---C--C--ATCACATTG
1 GAACCCCTACATATCACGATGGTCCCTCAAGCT-TATCATCAAGGAACCCCTACATATCACATTG
* * *
442582 GTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCATGTTGGTCCCTCAAACTTGTCATAAAA
65 GTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTATCATAAAA
* * * * *
442647 GAACCCCTATATATCACGATGGTTCCTTAAGCTTGTCATCAAGGAACCCCTACATATCACTTTGG
1 GAACCCCTACATATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACATTGG
* * * *
442712 TCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGATGGTTCCTCAAGCTTATCATCAAG
66 TCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTATCATAAAA
*
442776 GAACCCCTACATATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATAACGA-TG
1 GAACCCCTACATATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCAC-ATTG
442840 GTCCCTCAA
65 GTCCCTCAA
442849 TCTTAGTTTC
Statistics
Matches: 175, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
121 29 0.17
122 12 0.07
125 1 0.01
127 1 0.01
129 132 0.75
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (129 bp):
GAACCCCTACATATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACATTGG
TCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTATCATAAAA
Found at i:442812 original size:22 final size:22
Alignment explanation
Indices: 442744--442813 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
442734 AACCCCTACA
*
442744 TATCACGATGGTTCCTCAAGCT
1 TATCACGATGGTCCCTCAAGCT
* * * *
442766 TATCATC-AAGGAACCC-CTA-CA
1 TATCA-CGATGG-TCCCTCAAGCT
442787 TATCACGATGGTCCCTCAAGCT
1 TATCACGATGGTCCCTCAAGCT
442809 TATCA
1 TATCA
442814 TCAAGGAACC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 16 0.47
23 3 0.09
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (22 bp):
TATCACGATGGTCCCTCAAGCT
Found at i:444501 original size:52 final size:51
Alignment explanation
Indices: 444374--444568 Score: 216
Period size: 52 Copynumber: 3.8 Consensus size: 51
444364 ATCCCAACCT
* * * * * *
444374 TTTTCATGCTGGTGTGAGACTTTAAAATG-CCCACCATGAATTACTTTTGTC
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCA-CATGGATTACTTCTGTC
* * * *
444425 TCTTCATGTTGATGTGA-CTTTTCAAGATGCCCCAAATGGATTACTTCTGTC
1 TTTTCATGCTGATGTGAGC-CTTCAAGATGCCCCACATGGATTACTTCTGTC
* *
444476 TTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCCACATAGATTACTTCTATC
1 -TTTTCATGCTGATGTGAGCCTTCAAGATG-CCCCACATGGATTACTTCTGTC
*
444529 TTTTCATGCTGATGTGAGCCTTCAAGAT-ACCCACATGGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGAT
444569 AATATGGACC
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
50 10 0.08
51 35 0.29
52 56 0.46
53 20 0.17
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (51 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTGTC
Found at i:444567 original size:103 final size:103
Alignment explanation
Indices: 444372--444568 Score: 238
Period size: 103 Copynumber: 1.9 Consensus size: 103
444362 ATATCCCAAC
* * * * *
444372 CTTTTTCATGCTGGTGTGAGACTTTAAAATGCCCACCATGAATTACTTTTGTCTCTTCATGTTGA
1 CTTTTTCATGCTGATGTGAGACTTCAAAATGCCCACCATGAATTACTTCTATCTCTTCATGCTGA
* *
444437 TGTGACTTTTCAAGATGCCCCAAATGGATTACTTCTGT
66 TGTGACTCTTCAAGATGACCCAAATGGATTACTTCTGT
* * * *
444475 CTTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCCACAT-AGATTACTTCTATCTTTTCATGCT
1 CTTTTTCATGCTGATGTGAGACTTCAAAATGCCCAC-CATGA-ATTACTTCTATCTCTTCATGCT
*
444539 GATGTGAGC-CTTCAAGAT-ACCCACATGGAT
64 GATGTGA-CTCTTCAAGATGACCCAAATGGAT
444569 AATATGGACC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
103 42 0.53
104 36 0.46
105 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (103 bp):
CTTTTTCATGCTGATGTGAGACTTCAAAATGCCCACCATGAATTACTTCTATCTCTTCATGCTGA
TGTGACTCTTCAAGATGACCCAAATGGATTACTTCTGT
Found at i:445755 original size:11 final size:11
Alignment explanation
Indices: 445739--445798 Score: 68
Period size: 11 Copynumber: 5.3 Consensus size: 11
445729 TTGTTACTTA
445739 TTCTTTCTTTT
1 TTCTTTCTTTT
*
445750 TTCTTTTTTTT
1 TTCTTTCTTTT
445761 CTTCTTT-TTTT
1 -TTCTTTCTTTT
445772 TTCTTTTCCTTTT
1 TTC-TTT-CTTTT
*
445785 TTCTCTCTTTT
1 TTCTTTCTTTT
445796 TTC
1 TTC
445799 CCTTCCTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 3 0.07
11 25 0.58
12 8 0.19
13 7 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:445760 original size:9 final size:9
Alignment explanation
Indices: 445746--445798 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
445736 TTATTCTTTC
445746 TTTTTTCTT
1 TTTTTTCTT
445755 TTTTTTCTT
1 TTTTTTCTT
445764 CTTTTTT-TT
1 -TTTTTTCTT
*
445773 TCTTTTCCTT
1 T-TTTTTCTT
* *
445783 TTTTCTCTC
1 TTTTTTCTT
445792 TTTTTTC
1 TTTTTTC
445799 CCTTCCTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 1 0.03
9 26 0.72
10 9 0.25
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:445778 original size:28 final size:28
Alignment explanation
Indices: 445742--445797 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
445732 TTACTTATTC
* *
445742 TTTCTTTTTTCTTTTTTTTCTTCTTTTTT
1 TTTCTTTTTCCTTTTTTCTC-TCTTTTTT
445771 TTTC-TTTTCCTTTTTTCTCTCTTTTTT
1 TTTCTTTTTCCTTTTTTCTCTCTTTTTT
445798 CCCTTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 13 0.52
29 4 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTCTTTTTCCTTTTTTCTCTCTTTTTT
Found at i:453170 original size:29 final size:31
Alignment explanation
Indices: 453117--453174 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
453107 AATTTAAGGT
453117 AAATGGTTTGTGGACTTGAATTGAATTTACA
1 AAATGGTTTGTGGACTTGAATTGAATTTACA
*
453148 AAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAATGGTTTGTGGACTTGAATTGAATTTA
453175 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 11 0.42
31 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (31 bp):
AAATGGTTTGTGGACTTGAATTGAATTTACA
Found at i:453422 original size:21 final size:21
Alignment explanation
Indices: 453389--453428 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
453379 ATTTGAATTT
* *
453389 TATGAAGTAGTACTGATACTG
1 TATGAAGGAGTACCGATACTG
*
453410 TATGAAGGGGTACCGATAC
1 TATGAAGGAGTACCGATAC
453429 CCCTTATCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACTG
Found at i:456449 original size:19 final size:19
Alignment explanation
Indices: 456424--456469 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
456414 AACATTTGGT
456424 TATCTTTT-TAACAATTAG
1 TATCTTTTGTAACAATTAG
*
456442 TATCCTTTTGTAACAATTGG
1 TAT-CTTTTGTAACAATTAG
456462 TATCTTTT
1 TATCTTTT
456470 CATTAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 12 0.48
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (19 bp):
TATCTTTTGTAACAATTAG
Found at i:456647 original size:29 final size:30
Alignment explanation
Indices: 456577--456636 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
456567 CAATTTAAGG
*
456577 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
456608 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
456637 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:456947 original size:20 final size:22
Alignment explanation
Indices: 456909--456948 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
456899 TTTGAGCAGA
456909 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
456931 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
456949 ATATACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:465575 original size:13 final size:13
Alignment explanation
Indices: 465557--465581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465547 AAATAGTGTC
465557 TGATATCCGAATT
1 TGATATCCGAATT
465570 TGATATCCGAAT
1 TGATATCCGAAT
465582 CCAGTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGATATCCGAATT
Found at i:468091 original size:22 final size:23
Alignment explanation
Indices: 468029--468100 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
468019 AAACATGACA
* *
468029 AAAGACAGAAGAAAATGTGTCAT
1 AAAGACATAAGAAAACGTGTCAT
*
468052 AAATACATAAGAAAACGTGTCAT
1 AAAGACATAAGAAAACGTGTCAT
468075 AAAGACATAA-AAAACGTGTCAT
1 AAAGACATAAGAAAACGTGTCAT
468097 AAAG
1 AAAG
468101 GTAAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 16 0.36
23 29 0.64
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (23 bp):
AAAGACATAAGAAAACGTGTCAT
Found at i:469182 original size:20 final size:20
Alignment explanation
Indices: 469157--469205 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
469147 GTTTCTGCAA
469157 TCGCAACGCGATTT-TCAAAT
1 TCGCAACGCGATTTCT-AAAT
* *
469177 TCGCAACTCGATTTCTGAAT
1 TCGCAACGCGATTTCTAAAT
469197 TCGCAACGC
1 TCGCAACGC
469206 AAATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTCTAAAT
Found at i:469219 original size:20 final size:19
Alignment explanation
Indices: 469196--469263 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
469186 GATTTCTGAA
*
469196 TTCGCAACGCAAATTTATTT
1 TTCGCAACACAAATTT-TTT
* *
469216 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAATTT-TTT
*
469236 TTCGCAACACGAATTTTGTT
1 TTCGCAACACAAATTTT-TT
469256 TTCGCAAC
1 TTCGCAAC
469264 TCGATTTTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (19 bp):
TTCGCAACACAAATTTTTT
Found at i:469220 original size:40 final size:40
Alignment explanation
Indices: 469176--469303 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
469166 GATTTTCAAA
*
469176 TTCGCAACTCGATTTCTGAATTCGCAACGCAAATTTAT-TT
1 TTCGCAACTCGATTTCTGAATTCGCAACACAAATTT-TGTT
* * * *
469216 TTCGCAACACAAGTTTCCT--TTTCGCAACACGAATTTTGTT
1 TTCGCAACTCGA-TTT-CTGAATTCGCAACACAAATTTTGTT
* **
469256 TTCGCAACTCGATTT-TCGAATTCGCAACACGAATTTTAAT
1 TTCGCAACTCGATTTCT-GAATTCGCAACACAAATTTTGTT
469296 TTCGCAAC
1 TTCGCAAC
469304 ACTTTTATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
37 1 0.01
39 4 0.06
40 62 0.86
41 3 0.04
42 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTCTGAATTCGCAACACAAATTTTGTT
Found at i:469299 original size:20 final size:20
Alignment explanation
Indices: 469235--469305 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
469225 CAAGTTTCCT
**
469235 TTTCGCAACACGAATTTTGT
1 TTTCGCAACACGAATTTTAA
*
469255 TTTCGCAACTCG-ATTTTCGAA
1 TTTCGCAACACGAATTTT--AA
469276 -TTCGCAACACGAATTTTAA
1 TTTCGCAACACGAATTTTAA
469295 TTTCGCAACAC
1 TTTCGCAACAC
469306 TTTTATTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 7 0.16
20 31 0.72
21 5 0.12
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (20 bp):
TTTCGCAACACGAATTTTAA
Found at i:469315 original size:17 final size:17
Alignment explanation
Indices: 469289--469322 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
469279 GCAACACGAA
469289 TTTTAATTTCGCAACAC
1 TTTTAATTTCGCAACAC
* *
469306 TTTTATTTTCGTAACAC
1 TTTTAATTTCGCAACAC
469323 AAATATTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTTAATTTCGCAACAC
Found at i:469479 original size:14 final size:15
Alignment explanation
Indices: 469460--469497 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
469450 TCCCAATCTC
469460 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
469474 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
469490 TAATTTTT
1 TAATTTTT
469498 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Done.