Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008213.1 Hibiscus syriacus cultivar Beakdansim tig00110839_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: 2348840
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:436101 original size:16 final size:16
Alignment explanation
Indices: 436080--436110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
436070 GCGAAACATA
*
436080 ATTTTTATGATATGAT
1 ATTTTTATAATATGAT
436096 ATTTTTATAATATGA
1 ATTTTTATAATATGA
436111 GTTACCATTT
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:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
ATTTTTATAATATGAT
Found at i:436965 original size:47 final size:47
Alignment explanation
Indices: 436896--436987 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
436886 ATTTGTACAA
436896 TTTATGGTGAATTTTCAAAGTTGACTGACATAATCTGTTTTGATCTC
1 TTTATGGTGAATTTTCAAAGTTGACTGACATAATCTGTTTTGATCTC
436943 TTTATGGTGAATTTTCAAAGTTGACTGACATAATCTGTTTTGATC
1 TTTATGGTGAATTTTCAAAGTTGACTGACATAATCTGTTTTGATC
436988 AGAATCTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (47 bp):
TTTATGGTGAATTTTCAAAGTTGACTGACATAATCTGTTTTGATCTC
Found at i:447620 original size:12 final size:12
Alignment explanation
Indices: 447603--447632 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
447593 ATTGGGATAG
*
447603 TATTTTTATTGT
1 TATTTTTATTAT
447615 TATTTTTATTAT
1 TATTTTTATTAT
447627 TATTTT
1 TATTTT
447633 CAAGCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:454264 original size:2 final size:2
Alignment explanation
Indices: 454257--454287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
454247 ACTATTGATG
454257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
454288 ATTGGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454980 original size:12 final size:12
Alignment explanation
Indices: 454963--454987 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
454953 TGAGTTTGAC
454963 TGACCATTAACT
1 TGACCATTAACT
454975 TGACCATTAACT
1 TGACCATTAACT
454987 T
1 T
454988 TGACTTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (12 bp):
TGACCATTAACT
Found at i:459677 original size:29 final size:29
Alignment explanation
Indices: 459634--459716 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
459624 CTCACCTAAC
459634 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
459664 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
459693 TAAATGATGTAAGCAATGGCATCA
1 TAAATGATGTAAGCAATGACATCA
459717 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:464429 original size:29 final size:29
Alignment explanation
Indices: 464386--464467 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
464376 CTCACCTAAC
464386 TAAATTGATGTAAGCAATGACAT-TATTACT
1 TAAA-TGATGTAAGCAATGACATCT-TTACT
464416 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCTTTACT
*
464445 TAAATTATGTAAGCAATGACATC
1 TAAATGATGTAAGCAATGACATC
464468 AATTTAGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCTTTACT
Found at i:472297 original size:17 final size:17
Alignment explanation
Indices: 472275--472379 Score: 129
Period size: 17 Copynumber: 6.1 Consensus size: 17
472265 AATTACAAGT
*
472275 TAGTTTAATAAATGAAC
1 TAGTTTAATCAATGAAC
* *
472292 TAGTTTTATGAATGAAC
1 TAGTTTAATCAATGAAC
*
472309 TAGTTTAATTAATGAAC
1 TAGTTTAATCAATGAAC
* *
472326 TAACTTTATTCAATGAAC
1 T-AGTTTAATCAATGAAC
* *
472344 TAGTTGAATGAATGAAC
1 TAGTTTAATCAATGAAC
472361 TAGTTTAATCAATGAAC
1 TAGTTTAATCAATGAAC
472378 TA
1 TA
472380 CTTAGTTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
17 60 0.81
18 14 0.19
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Found at i:472391 original size:17 final size:17
Alignment explanation
Indices: 472371--472416 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
472361 TAGTTTAATC
* *
472371 AATGAACTACTTAGTTA
1 AATGAACTACATAGCTA
* *
472388 AATGAAGTGCATAGCTA
1 AATGAACTACATAGCTA
472405 AATGAACTACAT
1 AATGAACTACAT
472417 GTTTAAATGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (17 bp):
AATGAACTACATAGCTA
Found at i:472392 original size:34 final size:34
Alignment explanation
Indices: 472283--472393 Score: 100
Period size: 34 Copynumber: 3.2 Consensus size: 34
472273 GTTAGTTTAA
* * * *
472283 TAAATGAACTAGTTTTATGAATGAACTAGTTTAAT
1 TAAATGAACTAGTTTAATCAATGAACTA-CTTAGT
* * * *
472318 T-AATGAACTAACTTTATTCAATGAACTAGTT-GAA
1 TAAATGAACT-AGTTTAATCAATGAACTACTTAG-T
*
472352 TGAATGAACTAGTTTAATCAATGAACTACTTAGT
1 TAAATGAACTAGTTTAATCAATGAACTACTTAGT
472386 TAAATGAA
1 TAAATGAA
472394 GTGCATAGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
34 36 0.60
35 24 0.40
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (34 bp):
TAAATGAACTAGTTTAATCAATGAACTACTTAGT
Found at i:480396 original size:20 final size:20
Alignment explanation
Indices: 480370--480430 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
480360 GGGTCTCACA
480370 CGCATCACAAGACTCACACC
1 CGCATCACAAGACTCACACC
*
480390 TGCATCACAAGACTCACACC
1 CGCATCACAAGACTCACACC
*
480410 CGCATCACCAGACTCACACC
1 CGCATCACAAGACTCACACC
480430 C
1 C
480431 CTATAGCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.46, G:0.10, T:0.11
Consensus pattern (20 bp):
CGCATCACAAGACTCACACC
Found at i:492309 original size:2 final size:2
Alignment explanation
Indices: 492302--492501 Score: 234
Period size: 2 Copynumber: 101.5 Consensus size: 2
492292 ATGTAGTATT
492302 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
*
492344 TA TA TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* *
492386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TT TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
492429 T- TT TA TA TA TA TA T- TA TG TA -A TG TT TA TA -A TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
492467 GTA TA TA T- TA TA TA GTA TT TA TA T- TA TA TA TA TA T
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T
492502 CTTAGATATT
Statistics
Matches: 173, Mismatches: 14, Indels: 22
0.83 0.07 0.11
Matches are distributed among these distances:
1 7 0.04
2 158 0.91
3 8 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:492531 original size:4 final size:4
Alignment explanation
Indices: 492522--492549 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
492512 ATATTGTATG
492522 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
492550 TATATGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:493386 original size:17 final size:17
Alignment explanation
Indices: 493361--493400 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
493351 GTATGTTCTT
*
493361 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
493378 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
493395 CATTTA
1 CATTTA
493401 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:493501 original size:17 final size:17
Alignment explanation
Indices: 493481--493514 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
493471 AATTAAGTTG
493481 GTTCATTCATCAAACTA
1 GTTCATTCATCAAACTA
* *
493498 GTTCATTTATTAAACTA
1 GTTCATTCATCAAACTA
493515 ACTCTCAATT
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:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
GTTCATTCATCAAACTA
Found at i:497300 original size:14 final size:14
Alignment explanation
Indices: 497281--497308 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
497271 AAATTGATCG
497281 AGTATTTAACAGGT
1 AGTATTTAACAGGT
497295 AGTATTTAACAGGT
1 AGTATTTAACAGGT
497309 GGAACAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
AGTATTTAACAGGT
Found at i:499306 original size:16 final size:18
Alignment explanation
Indices: 499273--499309 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
499263 ATAAAACTAA
*
499273 TATTTTTTTCTTATATTT
1 TATTTTTATCTTATATTT
499291 TATTTTTAT-TTA-ATTT
1 TATTTTTATCTTATATTT
499307 TAT
1 TAT
499310 ACGCTAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTATCTTATATTT
Found at i:504566 original size:9 final size:9
Alignment explanation
Indices: 504552--504583 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
504542 AATGAAGCTA
504552 TGAAAATTT
1 TGAAAATTT
504561 TGAAAATTT
1 TGAAAATTT
504570 TGAAAATTT
1 TGAAAATTT
504579 T-AAAA
1 TGAAAA
504584 CACATGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (9 bp):
TGAAAATTT
Found at i:508807 original size:264 final size:264
Alignment explanation
Indices: 508337--508847 Score: 745
Period size: 264 Copynumber: 1.9 Consensus size: 264
508327 AGAAAGCTCG
* *
508337 TTCTTCTCCAACCTTTGAATCATAACCTCTTTCGACGTAGCGAAAACTACGCCCAATGCCTCACC
1 TTCTTCTCCAACCTTTGAATCACAACCTCTTTCGACGCAGCGAAAACTACGCCCAATGCCTCACC
* * * *
508402 AACGCCCAACGTTTCCACCGCTTCATTTTTTGTCTCCAACCGATCAGCACAAATCTCACCCCCAG
66 AACACCCAACGATTCCACCGCTTCATTTTGTGTCTCCAACCGATCAACACAAATCTCACCCCCAG
* *
508467 AAAGACCTCGAACATCCTCATCCCTTCTGCCATTTTGCAATAAAACTCGCCTTCTCACGCTCTTC
131 AAAGACCTCGAACAGCCTCATCCCTTCTGCCATTTTGCAACAAAACTCGCCTTCTCACGCTCTTC
* * * * *
508532 TTTTTCCTTTTAAGAGTGTTGCTTTTCATACAAAAATTATTCTCAGCCAAAGGCGCCCCCTTAAG
196 TTCTTCCTTTTAAGAGCGTTGATGTTCATACAAAAATTATTCTCAACCAAAGGCGCCCCCTTAAG
508597 GTCA
261 GTCA
* * * * * *
508601 TTCTTCTCCAACCTTTGAATCGCAGCCTCTTTCGACGCAGTGATAACTACGCCTAATGCCTCACT
1 TTCTTCTCCAACCTTTGAATCACAACCTCTTTCGACGCAGCGAAAACTACGCCCAATGCCTCACC
* * * *
508666 GACACCCAACGATTCCACCGCTTCATTTTGTGTCTTCGACCGATCAACGCAGAA-CTCACCCCCA
66 AACACCCAACGATTCCACCGCTTCATTTTGTGTCTCCAACCGATCAACACA-AATCTCACCCCCA
* **
508730 GAAATACCTCGAACAGCCTCATCCCTTCTGCCATTTTGCAACAAAACTCGCCTTCTCGTGCTCTT
130 GAAAGACCTCGAACAGCCTCATCCCTTCTGCCATTTTGCAACAAAACTCGCCTTCTCACGCTCTT
* **
508795 CTTCTTCCTTTTAAGAGCGTTGATGTTCATACCAATTTTATTCTCAACCAAAG
195 CTTCTTCCTTTTAAGAGCGTTGATGTTCATACAAAAATTATTCTCAACCAAAG
508848 ACTCCCCTAA
Statistics
Matches: 217, Mismatches: 29, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
264 215 0.99
265 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (264 bp):
TTCTTCTCCAACCTTTGAATCACAACCTCTTTCGACGCAGCGAAAACTACGCCCAATGCCTCACC
AACACCCAACGATTCCACCGCTTCATTTTGTGTCTCCAACCGATCAACACAAATCTCACCCCCAG
AAAGACCTCGAACAGCCTCATCCCTTCTGCCATTTTGCAACAAAACTCGCCTTCTCACGCTCTTC
TTCTTCCTTTTAAGAGCGTTGATGTTCATACAAAAATTATTCTCAACCAAAGGCGCCCCCTTAAG
GTCA
Found at i:524350 original size:3 final size:3
Alignment explanation
Indices: 524342--524419 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
524332 AATTATTTTT
* *
524342 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
524387 TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
524420 ATAAATAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:525155 original size:113 final size:113
Alignment explanation
Indices: 524787--525341 Score: 713
Period size: 113 Copynumber: 5.0 Consensus size: 113
524777 AAAATTATGT
*
524787 AAAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * *** * * *
524848 TATGAACTTTCTCTAGAAAAGCCAATCCA-TCAAGTGATGGATTTGAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATTGAA-TGATGAATTTAAGC
*
524896 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * **
524957 TATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTT-A--
63 CATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAAGC
*
525005 AAAA-GTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
525069 TATGAACTCGAACTGGAAATGCTGATCCATTGAATCATGAATTCAAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAAGC
* *
525117 AAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** *
525182 TATGAACTCGAACTGGAAATGTTGATCCACCGATTGATGAATTTAAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAAGC
525230 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
525295 TATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGGATTTAAG
66 TATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAAG
525342 TCTTTGCTAA
Statistics
Matches: 393, Mismatches: 40, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
108 24 0.06
109 97 0.25
110 2 0.01
111 6 0.02
112 56 0.14
113 208 0.53
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAAGC
Found at i:534184 original size:15 final size:15
Alignment explanation
Indices: 534161--534192 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
534151 TGAAATGAAT
534161 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
534176 AATGCATGTATGCAA
1 AATGAATGTATGCAA
534191 AA
1 AA
534193 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:537522 original size:20 final size:21
Alignment explanation
Indices: 537478--537527 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
537468 AATACTTGAA
*
537478 AAAATAAAATAAATCATTAAT
1 AAAATAATATAAATCATTAAT
537499 AAAATAATATAAAT-ATT-AT
1 AAAATAATATAAATCATTAAT
537518 GAAAATAATA
1 -AAAATAATA
537528 AATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 13 0.48
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAATATAAATCATTAAT
Found at i:537534 original size:20 final size:21
Alignment explanation
Indices: 537477--537544 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
537467 TAATACTTGA
*
537477 AAAAATAAAATAAATCAT-TA-
1 AAAAATAATATAAAT-ATATAT
537497 ATAAAATAATATAAATAT-TAT
1 A-AAAATAATATAAATATATAT
*
537518 GAAAATAATA-AATATATATAT
1 AAAAATAATATAA-ATATATAT
537539 AAAAAT
1 AAAAAT
537545 TTTGAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.05
20 18 0.44
21 21 0.51
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAAATAATATAAATATATAT
Found at i:537539 original size:30 final size:28
Alignment explanation
Indices: 537495--537552 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
537485 AATAAATCAT
*
537495 TAATAAAATAATATAAATATTATGAAAA
1 TAATAAAATAATATAAAAATTATGAAAA
*
537523 TAATAAATATATATATAAAAATTTTGAAAA
1 TAATAAA-ATA-ATATAAAAATTATGAAAA
537553 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 3 0.12
30 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TAATAAAATAATATAAAAATTATGAAAA
Found at i:539346 original size:23 final size:26
Alignment explanation
Indices: 539320--539373 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
539310 TTGCTGTTGG
*
539320 TCTTTGTTCT-TGTT-TTTTTTTC-T
1 TCTTTGTTCTCTGTTGGTTTTTTCTT
539343 TCTTT-TTCTCTGTTGGTTTTTTCTT
1 TCTTTGTTCTCTGTTGGTTTTTTCTT
539368 TCTTTG
1 TCTTTG
539374 CAGGTTGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 7 0.27
25 6 0.23
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.74
Consensus pattern (26 bp):
TCTTTGTTCTCTGTTGGTTTTTTCTT
Found at i:539779 original size:3 final size:3
Alignment explanation
Indices: 539771--539848 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
539761 AATTATTTTT
* * *
539771 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TTA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
539816 TAA TAA TTA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
539849 ATAAATAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:552437 original size:13 final size:13
Alignment explanation
Indices: 552421--552451 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
552411 AACAGTACTC
552421 GTGAATAGTAATA
1 GTGAATAGTAATA
552434 GTGAATAGTAATA
1 GTGAATAGTAATA
*
552447 ATGAA
1 GTGAA
552452 CAGTGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (13 bp):
GTGAATAGTAATA
Found at i:552551 original size:12 final size:12
Alignment explanation
Indices: 552534--552572 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
552524 ATATTCATTA
552534 CTACAGTAACTG
1 CTACAGTAACTG
552546 CTACAGTAA--G
1 CTACAGTAACTG
*
552556 CTACATTAACTG
1 CTACAGTAACTG
552568 CTACA
1 CTACA
552573 ATATTTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (12 bp):
CTACAGTAACTG
Found at i:564163 original size:8 final size:9
Alignment explanation
Indices: 564142--564167 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
564132 CATACAAAGA
564142 AAAAAATAC
1 AAAAAATAC
564151 AAAAAATAC
1 AAAAAATAC
564160 AAAAAATA
1 AAAAAATA
564168 TTATTGTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAC
Found at i:565105 original size:29 final size:28
Alignment explanation
Indices: 565052--565106 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
565042 GGAGTACTCA
*
565052 GGCCCCCATTTTTTATTCTTGTAATTGG
1 GGCCCCCATTTTTTATTCTTATAATTGG
*
565080 GGCCCTCATTTTTTCA-TCTTTATAATT
1 GGCCCCCATTTTTT-ATTC-TTATAATT
565107 AGGTCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (28 bp):
GGCCCCCATTTTTTATTCTTATAATTGG
Found at i:565186 original size:43 final size:41
Alignment explanation
Indices: 565089--565191 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 41
565079 GGGCCCTCAT
* *
565089 TTTTTCATCTTTATAATT-AGGTCTTTAATTTTAAATCTTA
1 TTTTTCATCTTTATAATTGAGGTCTTAAATTTTAAATCTAA
* * *
565129 TTTTTCACCTTTATAATTGAGGTCTTAATATTATTTATTCTAA
1 TTTTTCATCTTTATAATTGAGGTCTTAA-ATT-TTAAATCTAA
565172 CTTTTT-ATCTTTATAATTGA
1 -TTTTTCATCTTTATAATTGA
565192 AATCTCTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 17 0.32
41 8 0.15
42 3 0.06
43 20 0.38
44 5 0.09
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (41 bp):
TTTTTCATCTTTATAATTGAGGTCTTAAATTTTAAATCTAA
Found at i:565245 original size:44 final size:44
Alignment explanation
Indices: 565129--565438 Score: 226
Period size: 45 Copynumber: 7.1 Consensus size: 44
565119 TTAAATCTTA
* * * * * *
565129 TTTTTCACCTTTATAATTGAGG-TCTTAATATTATTTATTCTAAC
1 TTTTTTACCTTTATAATTGAGGCCCCTAAT-TTTTTTAATCTCAC
* *** *
565173 -TTTTTATCTTTATAATTGAAATCTCTAATTTTTTTTCAATC-C-C
1 TTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTT-AATCTCAC
* *
565216 TTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTGTAATCTAAC
1 TTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTAATCTCAC
* *** *
565259 --TTTTAACTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTCAC
1 TTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTTAATCTCAC
* * * *
565302 -TTTCTACCTTT-TCAATTAAGGCCTCTAAGTTTTTTTCAATCTCAA
1 TTTTTTACCTTTAT-AATTGAGGCCCCTAA-TTTTTTT-AATCTCAC
* * *
565347 TTTCTT-CCTTTATAATTAAGGGCCCTAATTTTTTTTAATCTCAC
1 TTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTTAATCTCAC
* *
565391 TTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCAC
1 TTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTTAATCTCAC
565436 TTT
1 TTT
565439 CTAACTTTCT
Statistics
Matches: 209, Mismatches: 43, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
41 27 0.13
42 5 0.02
43 31 0.15
44 70 0.33
45 72 0.34
46 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (44 bp):
TTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTAATCTCAC
Found at i:565341 original size:45 final size:45
Alignment explanation
Indices: 565195--565458 Score: 237
Period size: 44 Copynumber: 6.0 Consensus size: 45
565185 TAATTGAAAT
* * * *
565195 CTCTAATTTTTTTTCAATC-C-CTTTTTTACCTTTATAATTGAGGC
1 CTCTAAGTTTTTTTCAATCTCAC-TTTCTAACTTTATAATTAAGGC
* * * *
565239 CCCTAA--TTTTGT-AATCTAACTTT-TAACTTTATAATTGAGGC
1 CTCTAAGTTTTTTTCAATCTCACTTTCTAACTTTATAATTAAGGC
* * *
565280 TTTTAAG-TTTTTTCAATCTCACTTTCTACCTTT-TCAATTAAGGC
1 CTCTAAGTTTTTTTCAATCTCACTTTCTAACTTTAT-AATTAAGGC
* **
565324 CTCTAAGTTTTTTTCAATCTCAATTTCTTCCTTTATAATTAAGGGC
1 CTCTAAGTTTTTTTCAATCTCACTTTCTAACTTTATAATTAA-GGC
* * *
565370 C-CTAA-TTTTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGC
1 CTCTAAGTTTTTTTCAATCTCAC-TTTCTAACTTTATAATTAAGGC
*
565414 C-CTTAAGTTTTTTT-AATCTCACTTTCTAACTTTCTAATTAAGGC
1 CTC-TAAGTTTTTTTCAATCTCACTTTCTAACTTTATAATTAAGGC
565458 C
1 C
565459 CTTAAGAATT
Statistics
Matches: 184, Mismatches: 24, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
41 24 0.13
42 13 0.07
43 12 0.07
44 63 0.34
45 60 0.33
46 12 0.07
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (45 bp):
CTCTAAGTTTTTTTCAATCTCACTTTCTAACTTTATAATTAAGGC
Found at i:565422 original size:134 final size:129
Alignment explanation
Indices: 565195--565458 Score: 352
Period size: 134 Copynumber: 2.0 Consensus size: 129
565185 TAATTGAAAT
* * * *
565195 CTCTAATTTTTTTTCAATCCCTTTTTTACCTTTATAATTGAGGCCCCTAATTTTGTAATCTAACT
1 CTCTAAGTTTTTTTCAATCCATTTCTTACCTTTATAATTAAGGCCCCTAATTTTGTAATCTAACT
** *
565260 TTTAACTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTCACTTTCTACCTTT-TCAATTAAGGC
66 TTTAACTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTAACTTTCT-AATTAAGGC
* *
565324 CTCTAAGTTTTTTTCAATCTCAATTTCTT-CCTTTATAATTAAGGGCCCTAATTTTTTTTAATCT
1 CTCTAAGTTTTTTTCAATC-C-ATTTCTTACCTTTATAATTAAGGCCCCTAA--TTTTGTAATCT
* *
565388 CACTTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAACTTTCTAATT
62 AAC--TTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTAACTTTCTAATT
565453 AAGGC
125 AAGGC
565458 C
1 C
565459 CTTAAGAATT
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
129 18 0.15
130 21 0.18
131 5 0.04
132 12 0.10
134 60 0.51
135 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (129 bp):
CTCTAAGTTTTTTTCAATCCATTTCTTACCTTTATAATTAAGGCCCCTAATTTTGTAATCTAACT
TTTAACTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTAACTTTCTAATTAAGGC
Found at i:565444 original size:44 final size:44
Alignment explanation
Indices: 565224--565502 Score: 257
Period size: 44 Copynumber: 6.4 Consensus size: 44
565214 CCTTTTTTAC
* * *
565224 CTTTATAATTGAGGCCCCTAA--TTTTGTAATCTAACTTT-TAA
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
** * *
565265 CTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
* * **
565309 CTTT-TCAATTAAGG-CCTCTAAGTTTTTTTCAATCTCAATTTCTTC
1 CTTTAT-AATTGAGGCCCT-TAAGTTTTTTT-AATCTCACTTTCTAA
* * *
565354 CTTTATAATTAAGGGCCC-TAATTTTTTTTAATCTCACTTTTTTAA
1 CTTTATAATTGA-GGCCCTTAAGTTTTTTTAATCTCAC-TTTCTAA
565399 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
* * ** ** * * *
565443 CTTTCTAATTAAGGCCCTTAAGAATTTTCGATCTCA-ATTATAT
1 CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
565486 CTTTATAATTGAGGCCC
1 CTTTATAATTGAGGCCC
565503 ATATTTTTCA
Statistics
Matches: 195, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
41 18 0.09
43 35 0.18
44 71 0.36
45 66 0.34
46 3 0.02
47 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (44 bp):
CTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAA
Found at i:565477 original size:89 final size:88
Alignment explanation
Indices: 565129--565502 Score: 295
Period size: 89 Copynumber: 4.3 Consensus size: 88
565119 TTAAATCTTA
* * * * * *
565129 TTTTTCACCTTTATAATTGAGG-TCTTAA-TATTATTTATTCTAACTTTTTATCTTTATAATTGA
1 TTTTT-ACCTTTATAATTGAGGCCCTTAAGT-TTTTTTAATCTCACTTTCTAACTTTATAATT-A
** * *
565192 AATCTC-TAATTTTTTTTCAATC-C-C
63 AGGCCCTTAA-GTTTTTTCAATCTCAC
* * * *
565216 TTTTTTACCTTTATAATTGAGGCCCCTAA--TTTTGTAATCTAACTTT-TAACTTTATAATTGAG
1 -TTTTTACCTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAACTTTATAATTAAG
**
565278 GCTTTTAAGTTTTTTCAATCTCAC
65 GCCCTTAAGTTTTTTCAATCTCAC
* * * **
565302 TTTCTACCTTT-TCAATTAAGG-CCTCTAAGTTTTTTTCAATCTCAATTTCTTCCTTTATAATTA
1 TTTTTACCTTTAT-AATTGAGGCCCT-TAAGTTTTTTT-AATCTCACTTTCTAACTTTATAATTA
* *
565365 AGGGCCC-TAATTTTTTTTAATCTCAC
63 A-GGCCCTTAAGTTTTTTCAATCTCAC
* *
565391 TTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAACTTTCTAATTAAG
1 -TTTTTACCTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAACTTTATAATTAAG
** *
565456 GCCCTTAAGAATTTTCGATCTCA-
65 GCCCTTAAGTTTTTTCAATCTCAC
* * *
565479 ATTATATCTTTATAATTGAGGCCC
1 TTTTTACCTTTATAATTGAGGCCC
565503 ATATTTTTCA
Statistics
Matches: 232, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
84 17 0.07
85 36 0.16
86 15 0.06
87 42 0.18
88 23 0.10
89 65 0.28
90 30 0.13
91 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (88 bp):
TTTTTACCTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAACTTTATAATTAAGG
CCCTTAAGTTTTTTCAATCTCAC
Found at i:565517 original size:29 final size:29
Alignment explanation
Indices: 565484--565539 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
565474 TCTCAATTAT
*
565484 ATCTTTATAATTGAGGCC-CATATTTTTCA
1 ATCTTTATAATTAAGGCCTC-TATTTTTCA
565513 ATCTTTATAATTAAGGCCTCTATTTTT
1 ATCTTTATAATTAAGGCCTCTATTTTT
565540 TTTACAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (29 bp):
ATCTTTATAATTAAGGCCTCTATTTTTCA
Found at i:571099 original size:7 final size:7
Alignment explanation
Indices: 571087--571111 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
571077 TTTATTTTAC
571087 TTTTGAA
1 TTTTGAA
571094 TTTTGAA
1 TTTTGAA
571101 TTTTGAA
1 TTTTGAA
571108 TTTT
1 TTTT
571112 AGAAGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:581830 original size:25 final size:26
Alignment explanation
Indices: 581782--581830 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
581772 CACTTCAATA
* *
581782 TAAAAATTATATACATATTTTATTAC
1 TAAAAATTATATACATAATATATTAC
*
581808 TAAAAA-TATATATATAATATATT
1 TAAAAATTATATACATAATATATT
581831 CATAGTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAAAATTATATACATAATATATTAC
Found at i:584015 original size:25 final size:23
Alignment explanation
Indices: 583985--584032 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
583975 CTTGAAGATG
583985 CTATTATTTTCTTTCATCTATTTTT
1 CTATTATTTTCTTTC-T-TATTTTT
*
584010 CTATTATTTTTTTTCTTATTTTT
1 CTATTATTTTCTTTCTTATTTTT
584033 TCACTAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 1 0.05
25 14 0.64
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (23 bp):
CTATTATTTTCTTTCTTATTTTT
Found at i:587080 original size:19 final size:19
Alignment explanation
Indices: 587056--587092 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
587046 ATTCCCATTG
587056 ATAAAATTATAAGATTTTA
1 ATAAAATTATAAGATTTTA
* *
587075 ATAAAATTGTGAGATTTT
1 ATAAAATTATAAGATTTT
587093 GAATTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
ATAAAATTATAAGATTTTA
Found at i:587168 original size:40 final size:40
Alignment explanation
Indices: 587089--587168 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
587079 AATTGTGAGA
* *
587089 TTTTGAATTTATAATAAATCATATTAATTAATATGATTAAT
1 TTTTAAATTTATAATAAA-CATATTAATTAATATAATTAAT
587130 TTTTAAATGTTATAATAAA-ATATTAATT-ATGATAATTAA
1 TTTTAAAT-TTATAATAAACATATTAATTAAT-ATAATTAA
587169 ATTAATTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 2 0.06
40 16 0.46
41 7 0.20
42 10 0.29
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (40 bp):
TTTTAAATTTATAATAAACATATTAATTAATATAATTAAT
Found at i:589971 original size:24 final size:24
Alignment explanation
Indices: 589944--590055 Score: 77
Period size: 24 Copynumber: 4.7 Consensus size: 24
589934 TATATCAAAA
*
589944 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
589968 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
589992 AACAGATCAG-AATCCAAGTC-AGAT
1 ATCAAAACAGAAAT-CAGGTCAAG-T
* * *
590016 ATCAGATCAG-AATCCATGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
*
590040 ATCAAATCAGAAATCA
1 ATCAAAACAGAAATCA
590056 AATCGAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
23 5 0.07
24 65 0.87
25 5 0.07
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:591174 original size:18 final size:18
Alignment explanation
Indices: 591153--591188 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
591143 CTTCCATCCG
*
591153 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
591171 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
591189 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:592526 original size:13 final size:13
Alignment explanation
Indices: 592508--592600 Score: 90
Period size: 13 Copynumber: 7.4 Consensus size: 13
592498 TCCGGTCAAC
592508 GGTCAACGGGTCG
1 GGTCAACGGGTCG
592521 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
592534 GGTAAACGGGTCG
1 GGTCAACGGGTCG
592547 GGT---CGGGTCAACG
1 GGTCAACGGGT---CG
*
592560 GGT---CGGGTCA
1 GGTCAACGGGTCG
592570 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
592583 GGTAAACGGGTCG
1 GGTCAACGGGTCG
592596 GGTCA
1 GGTCA
592601 GGTTGTGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.13
13 60 0.87
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:592580 original size:31 final size:31
Alignment explanation
Indices: 592508--592603 Score: 126
Period size: 31 Copynumber: 3.1 Consensus size: 31
592498 TCCGGTCAAC
*
592508 GGTCAACGGGTCGGGTCAACGGGTCGGGTAAACG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGT---CA
592542 GGT---CGGGTCGGGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCA
*
592570 GGTCAACGGGTCGGGTAAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCA
592601 GGT
1 GGT
592604 TGTGACCGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.07
31 50 0.88
34 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.47, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCA
Found at i:592599 original size:18 final size:18
Alignment explanation
Indices: 592527--592585 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
592517 GTCGGGTCAA
*
592527 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
592545 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
592563 CGGGTCAGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
592581 CGGGT
1 CGGGT
592586 AAACGGGTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:595361 original size:29 final size:29
Alignment explanation
Indices: 595285--595361 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
595275 CGTGTATAAT
*
595285 GTATGTATAACTT-ATTAATATATAATGTA
1 GTATGTATAA-TTAATTAATATATAATATA
595314 GGTATGTATAATTAA-TAATATATAATATA
1 -GTATGTATAATTAATTAATATATAATATA
595343 -TATTGTATTAA-TAATTAAT
1 GTA-TGTA-TAATTAATTAAT
595362 TAACGCATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 2 0.05
28 7 0.17
29 22 0.52
30 11 0.26
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (29 bp):
GTATGTATAATTAATTAATATATAATATA
Found at i:595589 original size:33 final size:33
Alignment explanation
Indices: 595544--595725 Score: 155
Period size: 33 Copynumber: 5.5 Consensus size: 33
595534 TATATAATTT
*
595544 ATATATAGTTTATATATACTAATGAACTATAAA
1 ATATATAGTTTATATATACTAATGAACTATATA
* * *
595577 ATATGTAATTTATATATATTAATGAACTATATA
1 ATATATAGTTTATATATACTAATGAACTATATA
* * * *
595610 CTATATAGTTTATACATACTAATCAACTTTATA
1 ATATATAGTTTATATATACTAATGAACTATATA
595643 ATATATAGTTATATATATA-TATAT-ATA-TATATA
1 ATATATAGTT-TATATATACTA-ATGA-ACTATATA
*
595676 TATATATA-TATATATATA-TATAT-ATA-TATATA
1 -ATATATAGTTTATATATACTA-ATGA-ACTATATA
*
595708 TATATATA-TATATATATA
1 -ATATATAGTTTATATATA
595726 TATATATATA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
32 40 0.31
33 73 0.56
34 17 0.13
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (33 bp):
ATATATAGTTTATATATACTAATGAACTATATA
Found at i:595657 original size:2 final size:2
Alignment explanation
Indices: 595639--595863 Score: 189
Period size: 2 Copynumber: 113.0 Consensus size: 2
595629 TAATCAACTT
595639 TA TA -A TA TA TA GT- 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
595680 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
* * *
595722 TA TA TA TA TA TA TA AA CTA TA TGG TT TA T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * * * * *
595764 CTA CA TA GTT TG TA TA CA GTA TA TA -A AA T- TA TA AA TA TA AA
1 -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
595805 CTA TA TA T- TT TA AA TT TA T- TA TA AA TA TA TA CTA 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
595847 TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
595864 ATTGATTTAA
Statistics
Matches: 182, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
1 9 0.05
2 163 0.90
3 10 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:596877 original size:13 final size:13
Alignment explanation
Indices: 596871--596895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
596861 ATAAAAATCT
596871 TAAATAAAATATA
1 TAAATAAAATATA
596884 TAAATAAAATAT
1 TAAATAAAATAT
596896 CGATAAACTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATAAAATATA
Found at i:598597 original size:21 final size:23
Alignment explanation
Indices: 598573--598615 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
598563 CAATGAGTGT
*
598573 TGGAAAAA-ATT-TGGGTTAAAG
1 TGGAAAAATATTATGGATTAAAG
598594 TGGAAAAATATTATGGATTAAA
1 TGGAAAAATATTATGGATTAAA
598616 CTTAAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGAAAAATATTATGGATTAAAG
Found at i:602534 original size:20 final size:20
Alignment explanation
Indices: 602506--602545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
602496 TACCATAGTA
*
602506 TAGAAGTATTGATACCATGG
1 TAGAAGTATGGATACCATGG
* *
602526 TAGAGGTATGGATACTATGG
1 TAGAAGTATGGATACCATGG
602546 AGCCTGAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (20 bp):
TAGAAGTATGGATACCATGG
Found at i:602975 original size:111 final size:110
Alignment explanation
Indices: 602761--603535 Score: 1052
Period size: 111 Copynumber: 7.0 Consensus size: 110
602751 ATTACCAAAT
* * *
602761 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATATTGAATTTAGGAATTTTCGTATGGGCACTTTG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTG
*
602826 TGTGCAAAACTAAGAAATTCATAGTGAGTTTATGAATTTTCGTATG
65 TGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
** * * * *
602872 GAAACTTTGTGTGCAAAACCAAGAAATTCATAACGAGTTTATGAA-TTTCTGTATGGGCACTGTA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATGGGCACTTTG
* * * *
602936 TGTGCAAAAGCTAAGAAATTCATAATAAGTTTATAAATTTCCGTACG
65 TGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
* * * * *
602983 AGTACTTTGTGTGTAAAACTAAGAAATTCATAATGAGTTTACGAATTTTCGTATGGGCACTTTAT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
* * *
603048 GTGTAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
66 GTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
* *
603094 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGTGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
*
603159 GTGCAAAACTAAGAAATTCATAATGAGTTTATTAA-TTTCTGTATG
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATG
* *
603204 GGCACTTTATGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTG
*
603269 TGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAA-TTTCTATATG
65 TGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATG
* * * * ** *
603316 GGTACTTTGTGTACAAAACTAAGAAATGCATAATAAGTTTATGAATTTTCGTATATGTACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
* * *
603381 GTGGAAAAGCTAAAAAATTCATAATGAGTTTATGAATTTCCGTATG
66 GTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
* * *
603427 GGCACTCTGTGTACAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
* * *
603492 GTGCAAAACTAAGAAATTAATAATAAGTTTATGAATTTTTGTAT
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTAT
603536 TGGTAGTGGG
Statistics
Matches: 589, Mismatches: 67, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
109 7 0.01
110 125 0.21
111 396 0.67
112 61 0.10
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (110 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTGT
GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATG
Found at i:603118 original size:166 final size:166
Alignment explanation
Indices: 602761--603535 Score: 1113
Period size: 166 Copynumber: 4.7 Consensus size: 166
602751 ATTACCAAAT
* * * *
602761 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATATTGAATTTAGGAATTTTCGTATGGGCACTTTG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTG
* ** *
602826 TGTGCAAAACTAAGAAATTCATAGTGAGTTTATGAATTTTCGTATGGAAACTTTGTGTGCAAAA-
65 TGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTATGTGCAAAAG
* ** *
602890 CCAAGAAATTCATAACGAGTTTATGAATTTCTGTATG
130 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * * * *
602927 GGCACTGTATGTGCAAAAGCTAAGAAATTCATAATAAGTTTATAAATTTCCGTACGAGTACTTTG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTG
* * *
602992 TGTGTAAAACTAAGAAATTCATAATGAGTTTACGAATTTTCGTATGGGCACTTTATGTGTAAAAG
65 TGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTATGTGCAAAAG
603057 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
130 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
603094 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGTGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
*
603159 GTGCAAAACTAAGAAATTCATAATGAGTTTATTAA-TTTCTGTATGGGCACTTTATGTGCAAAAG
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATGGGCACTTTATGTGCAAAAG
*
603223 CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
130 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
** *
603260 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGGTACTTTG
1 GGCACTTTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTG
* * * ** * * *
603325 TGTACAAAACTAAGAAATGCATAATAAGTTTATGAATTTTCGTATATGTACTTTGTGTGGAAAAG
65 TGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTATGTGCAAAAG
* *
603390 CTAAAAAATTCATAATGAGTTTATGAATTTCCGTATG
130 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
603427 GGCACTCTGTGTACAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * *
603492 GTGCAAAACTAAGAAATTAATAATAAGTTTATGAATTTTTGTAT
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTAT
603536 TGGTAGTGGG
Statistics
Matches: 546, Mismatches: 59, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
165 4 0.01
166 346 0.63
167 192 0.35
168 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (166 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTATGTGCAAAAGC
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:603552 original size:55 final size:55
Alignment explanation
Indices: 602761--603529 Score: 1070
Period size: 55 Copynumber: 13.9 Consensus size: 55
602751 ATTACCAAAT
* * * *
602761 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATATTGAATTTAGGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* *
602817 GGCACTTTGTGTGCAAAACTAAGAAATTCATAGTGAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
** * * *
602872 GAAACTTTGTGTGCAAAACCAAGAAATTCATAACGAGTTTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * *
602927 GGCACTGTATGTGCAAAAGCTAAGAAATTCATAATAAGTTTATAAATTTCCGTACG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * *
602983 AGTACTTTGTGTGTAAAACTAAGAAATTCATAATGAGTTTACGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
603038 GGCACTTTATGTGTAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
603094 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
603149 TGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATTAATTTCTGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
603204 GGCACTTTATGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
**
603260 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATG
1 GGCACTTTGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * * * *
603316 GGTACTTTGTGTACAAAACTAAGAAATGCATAATAAGTTTATGAATTTTCGTATA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * * *
603371 TGTACTTTGTGTGGAAAAGCTAAAAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* *
603427 GGCACTCTGTGTACAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* *
603482 GGCACTTTGTGTGCAAAACTAAGAAATTAATAATAAGTTTATGAATTT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTT
603530 TTGTATTGGT
Statistics
Matches: 629, Mismatches: 79, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
55 377 0.60
56 248 0.39
57 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
Found at i:608620 original size:22 final size:22
Alignment explanation
Indices: 608543--608620 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
608533 ACCAAAAGGG
* * *
608543 AGTATCGATACTATAGTGTAGT
1 AGTATCGATACCATAGTATAGA
* *
608565 AGTATCGATACTA-AG-AGA-A
1 AGTATCGATACCATAGTATAGA
*
608584 AGGTATC-AGTGCCATAGTATAGA
1 A-GTATCGA-TACCATAGTATAGA
608607 AGTATCGATACCAT
1 AGTATCGATACCAT
608621 GGTAGATGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 4 0.09
22 25 0.58
23 3 0.07
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:609027 original size:55 final size:55
Alignment explanation
Indices: 608961--609510 Score: 787
Period size: 55 Copynumber: 9.9 Consensus size: 55
608951 TATAGAATGA
*
608961 CACTTTGTGTGCAAAAGCTAAGAAA-TCATACTGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
609016 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * * * * *
609071 CACTTTGTGTACAAAATTAAGAAAATCATAATGAGTTTATAAATTTCCTTATCGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * * * *
609126 CACTTTATGTGCAAAAGATAAGAAATTCATAATAAGTTTATGAATTTTCGTATAGG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * *
609182 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAATTTATTAATTTCTGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * **
609237 CACTTTATGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
*
609293 CACTTTATGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * * *
609348 CACTTAGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* * * *
609403 CATTTTGTGTACAAAAGCTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
* *
609459 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
609511 TGGTAGTGGG
Statistics
Matches: 444, Mismatches: 47, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
54 8 0.02
55 286 0.64
56 150 0.34
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (55 bp):
CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
Found at i:609197 original size:111 final size:110
Alignment explanation
Indices: 608961--609510 Score: 816
Period size: 111 Copynumber: 5.0 Consensus size: 110
608951 TATAGAATGA
* *
608961 CACTTTGTGTGCAAAAGCTAAGAAA-TCATACTGAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTATG
* *
609025 TGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGG
65 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * * * * *
609071 CACTTTGTGTACAAAATTAAGAAAATCATAATGAGTTTATAAATTTCCTTATCGGCACTTTATGT
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTATGT
* *
609136 GCAAAAGATAAGAAATTCATAATAAGTTTATGAATTTTCGTATAGG
66 GCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * *
609182 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAATTTATTAATTTCTGTATGGGCACTTTATGT
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTATGT
*
609247 GCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGG
66 GCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
*
609293 CACTTTATGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCAC-TTAGTG
1 CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTA-TG
* * *
609357 TGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGG
65 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * * * *
609403 CATTTTGTGTACAAAAGCTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGGCACTTTGTG
1 CACTTTGTGTGCAAAA-CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTATG
609468 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
65 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
609511 TGGTAGTGGG
Statistics
Matches: 396, Mismatches: 39, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
109 7 0.02
110 108 0.27
111 279 0.70
112 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (110 bp):
CACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTATGT
GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
Found at i:609241 original size:166 final size:166
Alignment explanation
Indices: 608961--609510 Score: 802
Period size: 166 Copynumber: 3.3 Consensus size: 166
608951 TATAGAATGA
* * *
608961 CACTTTGTGTGCAAAAGCTAAGAAA-TCATACTGAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 CACTTTATGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
609025 TGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTACAAAA-TT
65 TGCAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGCT
* * * *
609089 AAGAAAATCATAATGAGTTTATAAATTTCCTTATCGG
130 AAGAAATTCATAATAAGTTTATGAATTTCCTTATGGG
* * *
609126 CACTTTATGTGCAAAAGATAAGAAATTCATAATAAGTTTATGAATTTTCGTATAGGCACTTTGTG
1 CACTTTATGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
609191 TGCAAAACTAAGAAATTCATAATGAATTTATTAATTTCTGTATGGGCACTTTATGTGCAAAAGCT
65 TGCAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGCT
*
609256 AAGAAATTCATAATAAGTTTATGAATTT-TTGTATGGG
130 AAGAAATTCATAATAAGTTTATGAATTTCCT-TATGGG
* *
609293 CACTTTATGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTAGTGT
1 CACTTTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGT
* * *
609358 GTAAAACTAAGAAATTCATAAT-AAGTTTATGAATTTCCATATGGGCATTTTGTGTACAAAAGCT
66 GCAAAACTAAGAAATTCATAATGAA-TTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGCT
* *
609422 AAGAAATTCATAATTAGTTTATGAATTTCCATATGGG
130 AAGAAATTCATAATAAGTTTATGAATTTCCTTATGGG
* *
609459 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
1 CACTTTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
609511 TGGTAGTGGG
Statistics
Matches: 345, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
165 25 0.07
166 273 0.79
167 47 0.14
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (166 bp):
CACTTTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGT
GCAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGCTA
AGAAATTCATAATAAGTTTATGAATTTCCTTATGGG
Found at i:614923 original size:20 final size:20
Alignment explanation
Indices: 614900--614992 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
614890 CTCTACTTGT
*
614900 AGTATCGATACTCTAGGGTC
1 AGTATCGATACCCTAGGGTC
614920 AGTATCGATACCCTAGGGTC
1 AGTATCGATACCCTAGGGTC
614940 AGTATCGATACCCTAGGGTC
1 AGTATCGATACCCTAGGGTC
*
614960 AGTATCGATACCTTAGGGTC
1 AGTATCGATACCCTAGGGTC
*
614980 AGGATCGATACCC
1 AGTATCGATACCC
614993 CATGACACCA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (20 bp):
AGTATCGATACCCTAGGGTC
Found at i:618048 original size:2 final size:2
Alignment explanation
Indices: 618035--618129 Score: 50
Period size: 2 Copynumber: 52.5 Consensus size: 2
618025 ACGCCCCGAT
* * *
618035 TA TA TA TG TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
618073 TA -A T- TA TA TA TA TA -A TA CTT TA TA TT TT TA TA T- TA -A T-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
618110 TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA T
618130 TTTCGGGTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
1 11 0.15
2 61 0.84
3 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (2 bp):
TA
Found at i:618082 original size:34 final size:33
Alignment explanation
Indices: 618043--618132 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
618033 ATTATATATG
618043 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTTATATTAAT
*
618077 TATATATATAATACTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
* *
618110 TATATATAT-ATATATAATATTTT
1 TATATATATAATATTTTATATTTT
618133 CGGGTTTGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 11 0.21
33 21 0.40
34 20 0.38
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:618102 original size:33 final size:34
Alignment explanation
Indices: 618043--618119 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 34
618033 ATTATATATG
*
618043 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATACTTTATATATTTTATATTAAT
618077 TATATATATAATACTTTATAT-TTTTATATTAAT
1 TATATATATAATACTTTATATATTTTATATTAAT
618110 TATATATATA
1 TATATATATA
618120 TATATAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 22 0.52
34 20 0.48
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATATATAATACTTTATATATTTTATATTAAT
Found at i:620146 original size:18 final size:18
Alignment explanation
Indices: 620123--620171 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
620113 TTGACCGGTT
620123 TTGACCCGACCCGACCCG
1 TTGACCCGACCCGACCCG
620141 TTGACCCGACCCGACCCG
1 TTGACCCGACCCGACCCG
620159 TTGACCCGACCCG
1 TTGACCCGACCCG
620172 TTGACCGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
TTGACCCGACCCGACCCG
Found at i:620148 original size:13 final size:13
Alignment explanation
Indices: 620148--620177 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
620138 CCGTTGACCC
620148 GACCCGACCCGTT
1 GACCCGACCCGTT
620161 GACCCGACCCGTT
1 GACCCGACCCGTT
620174 GACC
1 GACC
620178 GAGTGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:620364 original size:29 final size:29
Alignment explanation
Indices: 620310--620365 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
620300 TAGTAAATAT
* *
620310 TTTTAAAATGGTGCTATATTGGTAATTAA
1 TTTTAAAATGATGCTATATTCGTAATTAA
* *
620339 TTTTAAAATGATGCTATTTTCTTAATT
1 TTTTAAAATGATGCTATATTCGTAATT
620366 TTGTAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTTAAAATGATGCTATATTCGTAATTAA
Found at i:620378 original size:2 final size:2
Alignment explanation
Indices: 620371--620408 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
620361 TAATTTTGTA
620371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
620409 TAATTTTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:625047 original size:2 final size:2
Alignment explanation
Indices: 625040--625075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
625030 ATTCAGAGGT
625040 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
625076 CAATACATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:625622 original size:14 final size:15
Alignment explanation
Indices: 625587--625619 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
625577 CCGAAATAGA
625587 GAAATCAGATATCAG
1 GAAATCAGATATCAG
625602 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
625617 GAA
1 GAA
625620 TCATGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:625631 original size:7 final size:7
Alignment explanation
Indices: 625619--625646 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
625609 ATATTCAGGA
625619 ATCATGT
1 ATCATGT
625626 ATCATGT
1 ATCATGT
625633 ATCATGT
1 ATCATGT
625640 ATCATGT
1 ATCATGT
625647 CATAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
ATCATGT
Found at i:626416 original size:29 final size:29
Alignment explanation
Indices: 626380--626452 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
626370 CATTTTACAG
626380 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * *
626409 AAATAGCACCCTTTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
*
626438 AAATATCA-CCTTTTT
1 AAATAGCACCCTTTTT
626453 CGAATTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:626457 original size:29 final size:29
Alignment explanation
Indices: 626400--626564 Score: 149
Period size: 29 Copynumber: 5.7 Consensus size: 29
626390 CTTTTTAAAA
* *
626400 TAATTACCAAAATAGCACCCTTTTT-GAAT
1 TAATTCCCAAAATATCA-CCTTTTTCGAAT
626429 TAATTCCCAAAATATCACCTTTTTCGAAT
1 TAATTCCCAAAATATCACCTTTTTCGAAT
* **
626458 TAAATTCCCAAAATACCACCCATTTCGAAT
1 T-AATTCCCAAAATATCACCTTTTTCGAAT
** * * *
626488 TAATTCCTGAAATAGT-ACCTATTTCAAAA
1 TAATTCCCAAAATA-TCACCTTTTTCGAAT
*
626517 TAATTCCCAAAATAACA-CTAATTTT-GAAT
1 TAATTCCCAAAATATCACCT--TTTTCGAAT
*
626546 TAATTCCCAAAATGTCACC
1 TAATTCCCAAAATATCACC
626565 CGATCAACGG
Statistics
Matches: 110, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
28 9 0.08
29 71 0.65
30 30 0.27
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (29 bp):
TAATTCCCAAAATATCACCTTTTTCGAAT
Found at i:626471 original size:59 final size:58
Alignment explanation
Indices: 626396--626564 Score: 196
Period size: 59 Copynumber: 2.9 Consensus size: 58
626386 CACCCTTTTT
* * * *
626396 AAAATAATTACCAAAATAGCACCCTTTTTGAATTAATTCCCAAAATATCACCTTTTTC
1 AAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCCAAAATATCACCTATTTC
* * * * **
626454 GAATTAAATTCCCAAAATACCACCCATTTCGAATTAATTCCTGAAATAGT-ACCTATTTC
1 AAAAT-AATTCCCAAAATAACACCCATTTTGAATTAATTCCCAAAATA-TCACCTATTTC
** *
626513 AAAATAATTCCCAAAATAACACTAATTTTGAATTAATTCCCAAAATGTCACC
1 AAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCCAAAATATCACC
626565 CGATCAACGG
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
57 1 0.01
58 41 0.46
59 47 0.52
60 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCCAAAATATCACCTATTTC
Found at i:626546 original size:58 final size:57
Alignment explanation
Indices: 626379--626558 Score: 182
Period size: 58 Copynumber: 3.1 Consensus size: 57
626369 CCATTTTACA
* * * * *
626379 GAAATAGCACCCTTTTTAAAATAATTACCAAAATAGCACCCTTTTTGAATTAATTCCC
1 GAAATAGTA-CCTTTTCAAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCC
* * * * * *
626437 AAAATA-TCACCTTTTTCGAATTAAATTCCCAAAATACCACCCATTTCGAATTAATTCCT
1 GAAATAGT-ACC-TTTTCAAAAT-AATTCCCAAAATAACACCCATTTTGAATTAATTCCC
**
626496 GAAATAGTACCTATTTCAAAATAATTCCCAAAATAACACTAATTTTGAATTAATTCCC
1 GAAATAGTACCT-TTTCAAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCC
*
626554 AAAAT
1 GAAAT
626559 GTCACCCGAT
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
57 2 0.02
58 49 0.50
59 46 0.47
60 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.33
Consensus pattern (57 bp):
GAAATAGTACCTTTTCAAAATAATTCCCAAAATAACACCCATTTTGAATTAATTCCC
Found at i:633023 original size:27 final size:27
Alignment explanation
Indices: 632992--633060 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
632982 GTTTTTAACT
632992 GGTTTGACCCGTTGACCCGACCCGACC
1 GGTTTGACCCGTTGACCCGACCCGACC
*
633019 GGTTTGACCCGTTGACCCTACCCGACC
1 GGTTTGACCCGTTGACCCGACCCGACC
*
633046 CG-TTGACCC-TTGACC
1 GGTTTGACCCGTTGACC
633061 GTTGACCAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 6 0.15
26 7 0.17
27 27 0.68
ACGTcount: A:0.14, C:0.41, G:0.23, T:0.22
Consensus pattern (27 bp):
GGTTTGACCCGTTGACCCGACCCGACC
Found at i:633117 original size:29 final size:29
Alignment explanation
Indices: 633075--633231 Score: 212
Period size: 29 Copynumber: 5.4 Consensus size: 29
633065 ACCAGGTGAC
*
633075 ATTTTGGGAATTAATTCGAAATGGGTTCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
633104 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
633133 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
* ** *
633162 ATTTTGGGATTTTAAATT--AAA-AAGTGAT
1 ATTTTGGGA-ATT-AATTCGAAATGGGTGCT
*
633190 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
*
633219 ATTTTGGTAATTA
1 ATTTTGGGAATTA
633232 TTTTAAAAAG
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.04
27 2 0.02
28 16 0.14
29 85 0.75
30 2 0.02
31 4 0.04
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAATGGGTGCT
Found at i:633240 original size:29 final size:29
Alignment explanation
Indices: 633075--633251 Score: 207
Period size: 29 Copynumber: 6.1 Consensus size: 29
633065 ACCAGGTGAC
* *
633075 ATTTTGGGAATTAATTCGAAATGGGTTCT
1 ATTTTGGGAATTAATTCGAAAAGGGTGCT
*
633104 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAAAGGGTGCT
*
633133 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAAAGGGTGCT
* * *
633162 ATTTTGGGATTTTAAATT--AAAA-AGTGAT
1 ATTTTGGGA-ATT-AATTCGAAAAGGGTGCT
633190 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAAAGGGTGCT
* * ** *
633219 ATTTTGGTAATTATTTTAAAAAGGGTACT
1 ATTTTGGGAATTAATTCGAAAAGGGTGCT
633248 ATTT
1 ATTT
633252 CTGTAAAATG
Statistics
Matches: 130, Mismatches: 13, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
26 4 0.03
27 2 0.02
28 17 0.13
29 101 0.78
30 2 0.02
31 4 0.03
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAAAGGGTGCT
Found at i:639702 original size:13 final size:13
Alignment explanation
Indices: 639684--639715 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
639674 TTGACCGGTT
639684 TTGACCCGACCCG
1 TTGACCCGACCCG
639697 TTGACCCGACCCG
1 TTGACCCGACCCG
639710 TTGACC
1 TTGACC
639716 TGGTGACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.19
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:639761 original size:29 final size:29
Alignment explanation
Indices: 639729--639792 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
639719 TGACATTTTA
639729 GTAATT-ATTTTGAAAATGGTGCTATATTG
1 GTAATTAATTTT-AAAATGGTGCTATATTG
* *
639758 GTAATTAATTTTAAAATGGTGCTATTTTT
1 GTAATTAATTTTAAAATGGTGCTATATTG
639787 GTAATT
1 GTAATT
639793 TTGTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (29 bp):
GTAATTAATTTTAAAATGGTGCTATATTG
Found at i:640364 original size:24 final size:24
Alignment explanation
Indices: 640337--640421 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
640327 TAGTTATCTG
*
640337 ATATGATATTTGACCTGAATTTTT
1 ATATGATACTTGACCTGAATTTTT
* * * *
640361 ATATGATACTTGACATGGATTCTG
1 ATATGATACTTGACCTGAATTTTT
* * *
640385 ATCTGTTACCTGACCTGAATTTTT
1 ATATGATACTTGACCTGAATTTTT
640409 ATATGATACTTGA
1 ATATGATACTTGA
640422 TATGGATTTT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (24 bp):
ATATGATACTTGACCTGAATTTTT
Found at i:640404 original size:48 final size:48
Alignment explanation
Indices: 640347--640450 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
640337 ATATGATATT
640347 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
* *
640395 TGACCTGAATTTTTATATGATACTTGATATGGATTTTGATCTGTTACC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
640443 TGACCTGA
1 TGACCTGA
640451 TTTATGTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (48 bp):
TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
Found at i:642350 original size:16 final size:16
Alignment explanation
Indices: 642288--642358 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 16
642278 AATTTAGCGA
* *
642288 AACCGAAATCAACCAG
1 AACCAAAATCAACCCG
* *
642304 AACCGAAATTAACCCG
1 AACCAAAATCAACCCG
* *
642320 AA-CTAAAGCAACCCG
1 AACCAAAATCAACCCG
*
642335 AACCAAAATTAACCCG
1 AACCAAAATCAACCCG
*
642351 ATCCAAAA
1 AACCAAAA
642359 GAAACCCAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 12 0.27
16 33 0.73
ACGTcount: A:0.49, C:0.31, G:0.10, T:0.10
Consensus pattern (16 bp):
AACCAAAATCAACCCG
Found at i:642364 original size:16 final size:16
Alignment explanation
Indices: 642314--642365 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
642304 AACCGAAATT
* *
642314 AACCCGAA-CTAAAGC
1 AACCCGAACCAAAAGA
**
642329 AACCCGAACCAAAATT
1 AACCCGAACCAAAAGA
*
642345 AACCCGATCCAAAAGA
1 AACCCGAACCAAAAGA
642361 AACCC
1 AACCC
642366 AATCTGAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.48, C:0.35, G:0.10, T:0.08
Consensus pattern (16 bp):
AACCCGAACCAAAAGA
Found at i:642523 original size:19 final size:19
Alignment explanation
Indices: 642471--642525 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
642461 TCAATAATAA
642471 ATTA-ATTTA-AATAAAAT
1 ATTATATTTATAATAAAAT
* *
642488 -TGATATTT-TATTAAAAAT
1 ATTATATTTATAAT-AAAAT
642506 ATTATATTTATAATAAAAT
1 ATTATATTTATAATAAAAT
642525 A
1 A
642526 ATAGAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 5 0.17
19 13 0.45
20 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTATATTTATAATAAAAT
Found at i:656705 original size:2 final size:2
Alignment explanation
Indices: 656700--656732 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
656690 AAATACGTGA
656700 AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
656733 AAATAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:658224 original size:3 final size:3
Alignment explanation
Indices: 658210--658296 Score: 149
Period size: 3 Copynumber: 29.0 Consensus size: 3
658200 CAAAATGTAT
*
658210 TAA TAA -AA TAA TAA TAA TAA TAC TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
658255 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
658297 AATTTAAATT
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.03
3 75 0.94
4 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:658702 original size:40 final size:40
Alignment explanation
Indices: 658636--658752 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
658626 TTGATTATCT
* * * * *
658636 AGGGG-TGACACAACTCCTACGCGATGAGGAGATCTGGTCG
1 AGGGGATGACACAGCTCATACGTGATGAAGAGTTCTGGT-G
658676 -GGGGATGACACAGCTCATACGTGATGAAGAGTTCTGGTG
1 AGGGGATGACACAGCTCATACGTGATGAAGAGTTCTGGTG
* *
658715 AGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 AGGGGATGACACAGCTCATACGTGATGAAGAGTTCTGG
658753 CCATCTTTAG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 5 0.07
40 63 0.93
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (40 bp):
AGGGGATGACACAGCTCATACGTGATGAAGAGTTCTGGTG
Found at i:659080 original size:29 final size:29
Alignment explanation
Indices: 659048--659104 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
659038 ACAAAACTTT
659048 GTTT-AAAAAAAACAAACTCAAAGATTTTG
1 GTTTCAAAAAAAA-AAACTCAAAGATTTTG
* **
659077 GTTTCAAAAGAAATGACTCAAAGATTTT
1 GTTTCAAAAAAAAAAACTCAAAGATTTT
659105 TTCACGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (29 bp):
GTTTCAAAAAAAAAAACTCAAAGATTTTG
Found at i:659187 original size:89 final size:89
Alignment explanation
Indices: 659031--659194 Score: 240
Period size: 89 Copynumber: 1.8 Consensus size: 89
659021 AAACTATCTC
* * * **
659031 AAGAGAGACAAAACTTTGTTTAAAAAAAACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTC
1 AAGAGAAACAAAACTTTGTTCAAAAAAAACAAACTCAAAGAATTT-GTTTCAAAAGAAACAACTC
659096 AAAGATTTTTTCACGAAATTGTCTT
65 AAAGATTTTTTCACGAAATTGTCTT
* *
659121 AAGAGAAACAAAACTTTGGTTCAAAAGAAACAGACTCAAAGAATTT-TTTCAAAAGAAACAACTC
1 AAGAGAAACAAAACTTT-GTTCAAAAAAAACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTC
659185 AAAGATTTTT
65 AAAGATTTTT
659195 ATTTCAAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
89 26 0.39
90 16 0.24
91 24 0.36
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (89 bp):
AAGAGAAACAAAACTTTGTTCAAAAAAAACAAACTCAAAGAATTTGTTTCAAAAGAAACAACTCA
AAGATTTTTTCACGAAATTGTCTT
Found at i:659208 original size:29 final size:29
Alignment explanation
Indices: 659140--659311 Score: 179
Period size: 29 Copynumber: 5.8 Consensus size: 29
659130 AAAACTTTGG
*
659140 TTCAAAAGAAACAGACTCAAAGA-ATTT-T
1 TTCAAAAGAAACA-ACTCAAAGATTTTTAT
659168 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGATTTTTAT
659197 TTCAAAAGAAACAACTCACAA-ATTTTTAT
1 TTCAAAAGAAACAACTCA-AAGATTTTTAT
* * *
659226 TTCAAAAGAAACAACTCACAGACTTTTGT
1 TTCAAAAGAAACAACTCAAAGATTTTTAT
* * *
659255 TTCAAGAGAAATAAACTCAAAGATAAGTTTTGT
1 TTCAAAAGAAA-CAACTCAAAGAT---TTTTAT
**
659288 TTCAAGGGAAACAATCTCAAAGAT
1 TTCAAAAGAAACAA-CTCAAAGAT
659312 GTTTGTTTTA
Statistics
Matches: 125, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.07
28 17 0.14
29 61 0.49
30 11 0.09
32 2 0.02
33 25 0.20
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (29 bp):
TTCAAAAGAAACAACTCAAAGATTTTTAT
Found at i:659288 original size:33 final size:31
Alignment explanation
Indices: 659167--659329 Score: 117
Period size: 29 Copynumber: 5.4 Consensus size: 31
659157 CAAAGAATTT
* * *
659167 TTTCAAAAGAAA-CAACTCAAAGAT-TTTTA
1 TTTCAAGAGAAATAAACTCAAAGATGTTTTG
* * *
659196 TTTCAAAAGAAA-CAACTCACAA-AT-TTTTA
1 TTTCAAGAGAAATAAACTCA-AAGATGTTTTG
* * * *
659225 TTTCAAAAGAAA-CAACTCACAGA-CTTTTG
1 TTTCAAGAGAAATAAACTCAAAGATGTTTTG
659254 TTTCAAGAGAAATAAACTCAAAGATAAGTTTTG
1 TTTCAAGAGAAATAAACTCAAAGAT--GTTTTG
* * *
659287 TTTCAAGGGAAACAATCTCAAAGATG-TTTG
1 TTTCAAGAGAAATAAACTCAAAGATGTTTTG
*
659317 TTTTAAGAGAAAT
1 TTTCAAGAGAAAT
659330 TGTCTCAAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.01
29 61 0.53
30 25 0.22
31 1 0.01
33 27 0.23
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTCAAGAGAAATAAACTCAAAGATGTTTTG
Found at i:659443 original size:66 final size:64
Alignment explanation
Indices: 659282--659513 Score: 236
Period size: 64 Copynumber: 3.5 Consensus size: 64
659272 CAAAGATAAG
* * * *
659282 TTTTGTTTCAAGGGAAACA-ATCTCAAAGATGTTTGTTTTAAGAGAAATTGTCTCAAAAGAGACA
1 TTTTGTTTCAA-AGAAACATA-CTCAAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACA
*
659346 AAC
62 AAA
* * * * *
659349 CTTTGTTTTCATAA-AAATAGACTTAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAA
1 TTTTG-TTTCA-AAGAAACATACTCAAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAA
659413 AA
63 AA
* * * *
659415 TTTTGTTTCCAAAGAAACATACTCAAAGA-TTCTTTCAAATGAAACTTTCTCAAAATAGACAAAA
1 TTTTGTTT-CAAAGAAACATACTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAA
659479 TTTTGTTATCAAAGAAACATACTCAAAGATTTTTT
1 TTTTGTT-TCAAAGAAACATACTCAAAGATTTTTT
659514 CATTTTGTTT
Statistics
Matches: 138, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
64 54 0.39
65 14 0.10
66 47 0.34
67 16 0.12
68 6 0.04
69 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (64 bp):
TTTTGTTTCAAAGAAACATACTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAA
Found at i:659519 original size:37 final size:37
Alignment explanation
Indices: 659478--659549 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
659468 AATAGACAAA
659478 ATTTTGTTATCAA-AGAAACATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAAGAGAAACATACTCAAAGATTTTTTC
* * *
659515 ATTTTGTTTTAAGTGAAACATATTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTT
659550 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACATACTCAAAGATTTTTTC
Found at i:659593 original size:100 final size:100
Alignment explanation
Indices: 659428--659608 Score: 242
Period size: 100 Copynumber: 1.8 Consensus size: 100
659418 TGTTTCCAAA
* *
659428 GAAACATACTCAAAGATTCTTTCAAATGAAACTTTCTCAAAATAGACAAAATTTTGTTATCAAAG
1 GAAACATACTCAAAGATTCTTTCAAA-GAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAG
*
659493 AAACATACTCAAAGATTTTTTCATTTTGTTTTAAGT
65 AAACAGACTCAAAGATTTTTTCATTTTGTTTTAAGT
* * *
659529 GAAACATATTCAAAGATT-TTTC-AAGAAAATCTGTCTCAAGAGAGACAAAGTTTTGTT-TCAAA
1 GAAACATACTCAAAGATTCTTTCAAAG-AAA-CTGTCTCAAAAGAGACAAAATTTTGTTATC-AA
*
659591 AGAAATAGACTCAAAGAT
63 AGAAACAGACTCAAAGAT
659609 CCTTTGTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
98 1 0.01
99 7 0.10
100 45 0.64
101 17 0.24
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (100 bp):
GAAACATACTCAAAGATTCTTTCAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAGA
AACAGACTCAAAGATTTTTTCATTTTGTTTTAAGT
Found at i:659635 original size:30 final size:31
Alignment explanation
Indices: 659580--659638 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
659570 GAGACAAAGT
659580 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
659611 TTTGTTTCAAAAGAAATA-ACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
659639 GATGTATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:659720 original size:36 final size:36
Alignment explanation
Indices: 659680--659813 Score: 148
Period size: 36 Copynumber: 3.7 Consensus size: 36
659670 TTTGGAAAAT
* *
659680 TGTCTCAAGTGAGACAACATTTGTTTTTAGAGGAAC
1 TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
* * * *
659716 TGTCTCAAACGAGACAAAAATTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
*
659752 TGTCTCAAGCGAGACAACGTTTGTTTTT-GAGAAAAC
1 TGTCTCAAGCGAGACAACATTTGTTTTTAGAG-AAAC
*
659788 -GATCTCAAGTGAGATCAAC-TTTGTTT
1 TG-TCTCAAGCGAGA-CAACATTTGTTT
659814 AATGTGAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.05
36 75 0.90
37 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
Found at i:659943 original size:107 final size:105
Alignment explanation
Indices: 659789--660102 Score: 373
Period size: 107 Copynumber: 3.0 Consensus size: 105
659779 TGAGAAAACG
*
659789 ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAAAGGAAA
1 ATCTCAAGTGAGATCAACTTTGTTTAATGTG-AAACAAATTCAAAATTTGTA-TCTCAAAGGAAA
* *
659854 AATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAAATAACA
64 AATGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAAATAACA
* ** * *
659896 ATCTCAAGTGAGATTATTTTTTGTTTCAA-GTGAATCAAATTCAAAATTTGTATATCAAAGGAAA
1 ATCTCAAGTGAGATCA-ACTTTGTTT-AATGTGAAACAAATTCAAAATTTGTATCTCAAAGG--A
* * * * * *
659960 AAAATGTCTCAAGCAAGATGAAGTTTGCTTT-AAGAGAA-AACG
62 AAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAAATAACA
* * *
660002 ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAAGAAAAA
1 ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
* * *
660067 TGTCTCAAGTGAGATGAAATTTATTTTGAAAGAAAT
66 TGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAAAT
660103 TGTCTCAAGC
Statistics
Matches: 170, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
103 27 0.16
104 6 0.04
105 35 0.21
106 25 0.15
107 38 0.22
108 37 0.22
109 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (105 bp):
ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
TGTCTCAAGCGAGATGAAATTTGTTTTGAAAAAAATAACA
Found at i:660123 original size:36 final size:37
Alignment explanation
Indices: 660058--660129 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
660048 TTGTATCTCA
* **
660058 AAAGAAAAATGTCTCAAGTGAGATGAAATTTATTTTG
1 AAAGAAAAATGTCTCAAGCGAGACAAAATTTATTTTG
* *
660095 AAAG-AAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 AAAGAAAAATGTCTCAAGCGAGACAAAATTTATTTT
660130 TAAAATTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (37 bp):
AAAGAAAAATGTCTCAAGCGAGACAAAATTTATTTTG
Found at i:667627 original size:3 final size:3
Alignment explanation
Indices: 667613--667681 Score: 113
Period size: 3 Copynumber: 23.0 Consensus size: 3
667603 CAAAATGTAT
*
667613 TAA TAA -AA TAA TAA TAA TAC TAA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
667658 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
667682 AATTTAAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:684905 original size:89 final size:89
Alignment explanation
Indices: 684773--685019 Score: 273
Period size: 89 Copynumber: 2.8 Consensus size: 89
684763 GGTAAGACCT
* * ** * * *
684773 TACGGACCTAAGGATGCCCTTGGATAGGCCCATAGGTCCCAAGGCATATTCTTAGGTTGGTTCCT
1 TACGGAGCTAAGGATACATTTGGATAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGATTCC-
*
684838 TTTTGTTGTGTGCTTAGGGTAACCC
65 TTTTATTGTGTGCTTAGGGTAACCC
* *
684863 TATGGAGCTAAGGATACATTTGGGTAGG-CCATAGGCCCCAAGGCATATCCTTAGGTTGATTCCT
1 TACGGAGCTAAGGATACATTTGGATAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGATTCCT
684927 TTTATTGTGTGCTTAGGGTAACCC
66 TTTATTGTGTGCTTAGGGTAACCC
* * * * ** * ** *
684951 TACGGATCTAATGATAGC-CTTGGGTAAACCCATGGGCCCCAAGAAATATCCTTAGGTTGACTCC
1 TACGGAGCTAAGGATA-CATTTGGATAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGA-TTC
685015 CTTTT
64 CTTTT
685020 GCTATATACT
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
88 44 0.33
89 61 0.46
90 29 0.22
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (89 bp):
TACGGAGCTAAGGATACATTTGGATAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGATTCCT
TTTATTGTGTGCTTAGGGTAACCC
Found at i:690518 original size:89 final size:89
Alignment explanation
Indices: 690351--690591 Score: 340
Period size: 89 Copynumber: 2.7 Consensus size: 89
690341 CCTTACGGAC
* *
690351 CTAAGGATACCCTTGGGTAGGCCCATAGGCCACAAGGCATATCTTTAGGTTGGTTCCCTTTTGAT
1 CTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGAT
* **
690416 GTGTGCTCAGGTAACCCTATGGAT
66 GTGTACTCAGGTAACCCTACAGAT
*
690440 CTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCC-TTTGCT
1 CTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGAT
* * *
690504 GTGTACTTATGGTAACCTTACATAT
66 GTGTACTCA-GGTAACCCTACAGAT
* * * * *
690529 CTAAGGATACCCTTGGGTAGGCCCATGGGCCCCAAAGAATATCCTTAGGTTGGCTCTCTTTTG
1 CTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTG
690592 CTATGTGTTT
Statistics
Matches: 136, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
88 12 0.09
89 120 0.88
90 4 0.03
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (89 bp):
CTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGAT
GTGTACTCAGGTAACCCTACAGAT
Found at i:695762 original size:492 final size:486
Alignment explanation
Indices: 694543--695878 Score: 1468
Period size: 492 Copynumber: 2.7 Consensus size: 486
694533 ACGTTTTCTT
* * *
694543 TTTTACCTATTAGTTTTAAAATCATACAATTTAATTAAGTTAGATACACATGGATCATCCAACAA
1 TTTTACCT-TTAGTTTT-AAACCATACAATTTAAATAAGTTAGATGCACATGGATCATCCAACAA
* * * *
694608 AGGTTTCTTGTTTTTCACAAAACCATACACT-AGAGTTCT-AATAAACAACGTTTATATTTACCT
64 A-GTTT-TCGTTTTTCATAAAACCATACACTGA-AATT-TGAATAAA-AAAGTTTATATTTACCT
* * * *
694671 TTCATTATTTATTTCTATTTGTTATA-TAGATTATTTTTTTATTTGGTCTAATTCATTTGTTTAT
124 TTCATTGTTTATTTTTATTTGTTA-AGTA-ATTATTTATTTATTTGATCTAATTCATTTGTTTAT
* *
694735 GAAAAATTACAAGTTTCGTTCG-ATTGATTTTACTACATTTCCTGAAGTAAATATGATATCTCAT
187 GAAAAATCACAAGTTTCG-TCGTATTGATTTTACTACATTTCCTGAAGTAAATATGATATCTTAT
* * * * *
694799 AATAAGAAAAAATAAGTACCATTCTAGCAATCATGGTCATGATAATGAACAAGACCATAGTCATT
251 AAAAAGAAAAAATAAATATCATTCTAGCAATCATGGTCATGATAATGAACATGACCATAGTCATA
* * * * *
694864 ATCACGATCAAAGATGTGGATGAGGTGGTTGTTTTAAGAATACACACATCCACTAAAGGCAGGAT
316 ATCACGATCAAAGATGTGGATGA---GGTTATTTTAAAAATACACACAACCACGAAAGGCAGAAT
* * *
694929 TATAAAAAATGACATAAGTTACGGAAGTCACGACATCATATGTATGAAATATAATTCATATGTAT
378 TATAAAAAATGACATAAGTGACAGAAGTCACGACATCATATGTATGAAATAAAATTCATATGTAT
* * * * *
694994 TTCACGTTGTTTTGATTGATGCCACTGTGAGCAAAGTTTTTATC
443 TTCACGTTATTTAGATTGATGCCACTATGAGAAAAGTTTTTATA
* ** * * * * *
695038 TTTTACCCTTTAGGCTTTAAACCATATGATTTAAATTAGTTAGACGAACATGAATCAGCCCAACA
1 TTTTA-CCTTTA-GTTTTAAACCATACAATTTAAATAAGTTAGATGCACATGGATCA-TCCAACA
** * * * * *
695103 AAGGTTCTT-GTTTTTTTTCACAACCATACATTTG-AATTTGAATAGATAATGTTTATATTTACT
63 AA-GTT-TTCGTTTTTCAT-AAAACCATACA-CTGAAATTTGAATA-AAAAAGTTTATATTTACC
695166 TTTCATTGTTTATTTTTATTTGTT-AGATAAATTATTTATTTATTTGATCTAATTCATTTGTTTA
123 TTTCATTGTTTATTTTTATTTGTTAAG-T-AATTATTTATTTATTTGATCTAATTCATTTGTTTA
* * * **
695230 TGAAAAATCACAAGTTTTGTCCTATT-AGTTTTATTACATTTTTTTGAAGTAAATATGATATCTT
186 TGAAAAATCACAAGTTTCGTCGTATTGA-TTTTACTACA-TTTCCTGAAGTAAATATGATATCTT
* * * * * * * * *
695294 GTAACAAGAAAATATAAATGTCATTCTAGTAGTCATGGTTATGATAATGAACATGACCATAATTA
249 ATAAAAAGAAAAAATAAATATCATTCTAGCAATCATGGTCATGATAATGAACATGACCATAGTCA
* ***
695359 TAATCACGATCAAGGATGTGGATGAGGTTATTTTAAAAATATTTACAACCACGAAA-GCAGAATT
314 TAATCACGATCAAAGATGTGGATGAGGTTATTTTAAAAATACACACAACCACGAAAGGCAGAATT
* * * * *
695423 ATAATAAATGTCATGAGTGACAGAAGTCATGACATCATATGTATGAAATAAAATTTATATGTATT
379 ATAAAAAATGACATAAGTGACAGAAGTCACGACATCATATGTATGAAATAAAATTCATATGTATT
*
695488 TCAGGTTATTTAGATTGATGCCACTATGAGAAAAGTGTTTT-TA
444 TCACGTTATTTAGATTGATGCCACTATGAGAAAAGT-TTTTATA
* * * * *
695531 TTTTATCCTTTAGTTTTCAAAGCATGCAATTTAAAAAAGTGAGATGCACATGGATCATTCAACAA
1 TTTTA-CCTTTAGTTTT-AAACCATACAATTTAAATAAGTTAGATGCACATGGATCATCCAAC-A
*
695596 AAGATTTTCGGTTTTTCATAAAATCATACACTGAAATTTGAATAAAAAAGTTTATATTTACCTTT
63 AAG-TTTTC-GTTTTTCATAAAACCATACACTGAAATTTGAATAAAAAAGTTTATATTTACCTTT
* * ** * *
695661 CATTGTTTATTTTTATTTTTTAAGTGAATTATTTGTCCACTTGATCTAATTCATTTGTTTATGAG
126 CATTGTTTATTTTTATTTGTTAAGT-AATTATTTATTTATTTGATCTAATTCATTTGTTTATGAA
* *
695726 AAATCGCAAGTTTCGTCGTATTGATTTTACTACATTTCCTGAAGTAAATGTGATATCTTATAAAA
190 AAATCACAAGTTTCGTCGTATTGATTTTACTACATTTCCTGAAGTAAATATGATATCTTATAAAA
** * * * * *
695791 AGAAAAGAATAAATATTTTTCTAACAATAATGATCATGATAATAAACATGAACATAGTCATAATC
255 AGAAAA-AATAAATATCATTCTAGCAATCATGGTCATGATAATGAACATGACCATAGTCATAATC
* *
695856 ACGATTAAAGATGTGGGTGAGGT
319 ACGATCAAAGATGTGGATGAGGT
695879 GGTTAATTCA
Statistics
Matches: 694, Mismatches: 122, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
491 32 0.05
492 178 0.26
493 163 0.23
494 36 0.05
495 48 0.07
496 135 0.19
497 102 0.15
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (486 bp):
TTTTACCTTTAGTTTTAAACCATACAATTTAAATAAGTTAGATGCACATGGATCATCCAACAAAG
TTTTCGTTTTTCATAAAACCATACACTGAAATTTGAATAAAAAAGTTTATATTTACCTTTCATTG
TTTATTTTTATTTGTTAAGTAATTATTTATTTATTTGATCTAATTCATTTGTTTATGAAAAATCA
CAAGTTTCGTCGTATTGATTTTACTACATTTCCTGAAGTAAATATGATATCTTATAAAAAGAAAA
AATAAATATCATTCTAGCAATCATGGTCATGATAATGAACATGACCATAGTCATAATCACGATCA
AAGATGTGGATGAGGTTATTTTAAAAATACACACAACCACGAAAGGCAGAATTATAAAAAATGAC
ATAAGTGACAGAAGTCACGACATCATATGTATGAAATAAAATTCATATGTATTTCACGTTATTTA
GATTGATGCCACTATGAGAAAAGTTTTTATA
Found at i:704222 original size:63 final size:63
Alignment explanation
Indices: 704060--704226 Score: 178
Period size: 63 Copynumber: 2.7 Consensus size: 63
704050 GTGATAACAT
* * * *
704060 TGACTATGGTAGTTTACCAAGGCCCCCTAAAGGTGTTGAGTCCTTAATAGTAGGACAACACTT
1 TGACTATGGTAGTTTACCAAGGCCCCCTAAAAGTGTTGAGTCCTCAATAGAAGGACAACACTA
* * * * * * * *
704123 TGACTATGGCAGTTTTCCATGGCCCCTTGAATGTGTTGAGTTCC-CAGTAGCAAGG-TAACACTA
1 TGACTATGGTAGTTTACCAAGGCCCCCTAAAAGTGTTGAG-TCCTCAATAG-AAGGACAACACTA
*
704186 TGACTATGATAGTTTACCAAGGCCCCCTAAAAGTGTT-AGTC
1 TGACTATGGTAGTTTACCAAGGCCCCCTAAAAGTGTTGAGTC
704227 ATGGGCAACA
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
61 2 0.02
62 2 0.02
63 74 0.88
64 6 0.07
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (63 bp):
TGACTATGGTAGTTTACCAAGGCCCCCTAAAAGTGTTGAGTCCTCAATAGAAGGACAACACTA
Found at i:704498 original size:31 final size:32
Alignment explanation
Indices: 704445--704507 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
704435 CTCATATTCA
**
704445 TTTTTTATTACATATTTATTGTCGTTGCATTT
1 TTTTTTATTACATATTTATTGTCACTGCATTT
*
704477 TTTTTCTATT-CAT-TTTTTTGTCACTGCATTT
1 TTTTT-TATTACATATTTATTGTCACTGCATTT
704508 ATATAACTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 15 0.56
32 8 0.30
33 4 0.15
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (32 bp):
TTTTTTATTACATATTTATTGTCACTGCATTT
Found at i:704616 original size:17 final size:17
Alignment explanation
Indices: 704594--704633 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
704584 ATGTGTGGGG
704594 GAATATAAATGGAAATT
1 GAATATAAATGGAAATT
704611 GAATATAAATGGAAATT
1 GAATATAAATGGAAATT
704628 GAATAT
1 GAATAT
704634 TAACATGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (17 bp):
GAATATAAATGGAAATT
Found at i:721445 original size:21 final size:21
Alignment explanation
Indices: 721394--721450 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
721384 GCGTAGCAGG
* *
721394 CTTCTTCTTTTTCTTCATCATT
1 CTTCTTCTTATT-TTCAGCATT
*
721416 CTT-TGTCTTATTTTCGGCATT
1 CTTCT-TCTTATTTTCAGCATT
721437 CTTCTTCTTCATTT
1 CTTCTTCTT-ATTT
721451 CCTCTCTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.09, C:0.25, G:0.05, T:0.61
Consensus pattern (21 bp):
CTTCTTCTTATTTTCAGCATT
Found at i:724303 original size:2 final size:2
Alignment explanation
Indices: 724296--724343 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
724286 ATTTAACTCA
724296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
724338 AT AT AT
1 AT AT AT
724344 GATTATGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:724580 original size:2 final size:2
Alignment explanation
Indices: 724573--724663 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
724563 CCACCGTAGA
724573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
724615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
724657 AT AT AT A
1 AT AT AT A
724664 ACCTTAATTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:737328 original size:18 final size:19
Alignment explanation
Indices: 737290--737329 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
737280 ACCTTAAAAT
*
737290 TATAAATAATTAAATTTAAA
1 TATAAATAA-TAAATTCAAA
737310 TATAAATAA-AAATTCAAA
1 TATAAATAATAAATTCAAA
737328 TA
1 TA
737330 AATATATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAATAATAAATTCAAA
Found at i:747892 original size:19 final size:20
Alignment explanation
Indices: 747862--747907 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
747852 AATTAATCCT
747862 ACTAAGTATTAA-AGCTAAAA
1 ACTAA-TATTAAGAGCTAAAA
747882 ACTAATATTAAGGAGCTAAAA
1 ACTAATATTAA-GAGCTAAAA
747903 A-TAAT
1 ACTAAT
747908 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (20 bp):
ACTAATATTAAGAGCTAAAA
Found at i:754039 original size:22 final size:22
Alignment explanation
Indices: 754011--754055 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
754001 TAAGGTCACC
*
754011 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGATCGGGTCGGGTCG
754033 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGATCGGGTCGGGTCG
754055 G
1 G
754056 TCGGGTCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGATCGGGTCGGGTCG
Found at i:754059 original size:4 final size:5
Alignment explanation
Indices: 754018--754067 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
754008 ACCGGTCAAC
* *
754018 GGTCG GGTCG GGTCG GGTCAAC GATCG GGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
754068 AGACCGGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 4 0.11
5 31 0.82
7 3 0.08
ACGTcount: A:0.06, C:0.22, G:0.52, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:761044 original size:27 final size:27
Alignment explanation
Indices: 761013--761071 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
761003 TAAGGTCAAT
* *
761013 GGTCAATGGTCGGGTCGAGTCGAGTTG
1 GGTCAACGGTCGGGTCGAGTCGAGTCG
* *
761040 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGAGTCGAGTCG
761067 GGTCA
1 GGTCA
761072 GACCGGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.22
Consensus pattern (27 bp):
GGTCAACGGTCGGGTCGAGTCGAGTCG
Found at i:765161 original size:15 final size:16
Alignment explanation
Indices: 765141--765181 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
765131 GACCAAAATC
765141 AACCCGAATTGAAA-A
1 AACCCGAATTGAAAGA
* *
765156 AACCCGAACTGAAAGC
1 AACCCGAATTGAAAGA
765172 AACCCGAATT
1 AACCCGAATT
765182 TAGTTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (16 bp):
AACCCGAATTGAAAGA
Found at i:765273 original size:3 final size:3
Alignment explanation
Indices: 765267--765317 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
765257 ATTTTTTTAT
765267 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
765316 TT
1 TT
765318 TTTAGCATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:768747 original size:2 final size:2
Alignment explanation
Indices: 768740--768772 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
768730 CGGGTTTAAA
768740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
768773 TTTATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:770265 original size:16 final size:16
Alignment explanation
Indices: 770236--770273 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
770226 TAATTCATTA
770236 TCTTATTTTATTTTTTT
1 TCTT-TTTTATTTTTTT
*
770253 TCTTTTTTCTTTTTTT
1 TCTTTTTTATTTTTTT
770269 TCTTT
1 TCTTT
770274 GATTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TCTTTTTTATTTTTTT
Found at i:770375 original size:12 final size:12
Alignment explanation
Indices: 770358--770384 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
770348 GAATTGAGTT
770358 TTTAAATTTCAA
1 TTTAAATTTCAA
770370 TTTAAATTTCAA
1 TTTAAATTTCAA
770382 TTT
1 TTT
770385 TTCGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Done.