Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold118
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: 1286304
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:535323 original size:21 final size:21
Alignment explanation
Indices: 535297--535372 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
535287 ACATGTTGCA
535297 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
535318 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
535338 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
535359 ATGTATCGATACAT
1 ATGTATCGATACAT
535373 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:535330 original size:41 final size:41
Alignment explanation
Indices: 535279--535372 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
535269 ACAATTCAAA
*
535279 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
535320 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
535361 GTATCGATACAT
1 GTATCGATACAT
535373 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:535429 original size:13 final size:13
Alignment explanation
Indices: 535411--535436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535401 TACAGCAAGT
535411 ATGTATCGATACA
1 ATGTATCGATACA
535424 ATGTATCGATACA
1 ATGTATCGATACA
535437 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:538158 original size:97 final size:96
Alignment explanation
Indices: 538040--538229 Score: 247
Period size: 97 Copynumber: 2.0 Consensus size: 96
538030 AGTGCCCTCG
* * * **
538040 ATGATGACAATTTAGGTAAAAATAAGATTTAAATCTTAACAAATTTAAAAATGAGGTTAGAGTAT
1 ATGACGACAATTTACGCAAAAATAAGAAATAAATCTTAACAAATTTAAAAATGAGGTTAGAGTAT
*
538105 C-CTCTTGGAAGAATAGGGCTGGAGTATCCCCA
66 CTC-CTCGGAAG-ATAGGGCTGGAGTATCCCCA
* * * *
538137 ATGACGACAATTTACGCAAAAATAAGAAATAAATCTTGACGAGTTTAAAAATGGGGTTAGAGTAT
1 ATGACGACAATTTACGCAAAAATAAGAAATAAATCTTAACAAATTTAAAAATGAGGTTAGAGTAT
* *
538202 CTCCTCGGAAGATGGGGTTGGAGTATCC
66 CTCCTCGGAAGATAGGGCTGGAGTATCC
538230 TCGATGAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 15 0.19
97 64 0.80
98 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (96 bp):
ATGACGACAATTTACGCAAAAATAAGAAATAAATCTTAACAAATTTAAAAATGAGGTTAGAGTAT
CTCCTCGGAAGATAGGGCTGGAGTATCCCCA
Found at i:540460 original size:19 final size:19
Alignment explanation
Indices: 540417--540489 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
540407 AACCCTTGTA
*
540417 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
540437 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
540456 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
*
540476 TCTATCGATACATG
1 TGTATCGATACATG
540490 AAACTAGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:546939 original size:20 final size:20
Alignment explanation
Indices: 546913--546967 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
546903 AAAAAGATAG
546913 AATGTATCGATACATTCATAC
1 AATGTATCGATACATT-ATAC
* * *
546934 -ATGTATCGATATATTTTTC
1 AATGTATCGATACATTATAC
546953 AATGTATCGATACAT
1 AATGTATCGATACAT
546968 CTGGGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTATAC
Found at i:550388 original size:13 final size:13
Alignment explanation
Indices: 550370--550396 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
550360 ACAATGTTCT
550370 TTGTATCGATACA
1 TTGTATCGATACA
550383 TTGTATCGATACA
1 TTGTATCGATACA
550396 T
1 T
550397 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:551924 original size:33 final size:33
Alignment explanation
Indices: 551877--551949 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
551867 AGTTGATCAC
* *
551877 TTCACTTTCGCAGCGCATGGATGAGCACTTTAG
1 TTCACTTTCACAGCGCATGGATAAGCACTTTAG
551910 TTCACTTTCACAGCGCATGGATAAGCACTTTAG
1 TTCACTTTCACAGCGCATGGATAAGCACTTTAG
551943 TTCACTT
1 TTCACTT
551950 AATTGACGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (33 bp):
TTCACTTTCACAGCGCATGGATAAGCACTTTAG
Found at i:554080 original size:21 final size:20
Alignment explanation
Indices: 554028--554084 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
554018 AAAAACCCAT
*
554028 AATGTATCGATACAATGAAA
1 AATGTATCGATACATTGAAA
*
554048 AACGTATCGATACATTGCAAA
1 AATGTATCGATACATTG-AAA
* *
554069 CATGTATTGATACATT
1 AATGTATCGATACATT
554085 TACTTATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:554195 original size:20 final size:21
Alignment explanation
Indices: 554172--554210 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
554162 TTTATCGATA
*
554172 CATTCACTTA-TGTATCAACG
1 CATTAACTTATTGTATCAACG
554192 CATTAACTTATTGTATCAA
1 CATTAACTTATTGTATCAA
554211 TACAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (21 bp):
CATTAACTTATTGTATCAACG
Found at i:555479 original size:20 final size:19
Alignment explanation
Indices: 555454--555524 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
555444 ACCCTAAAAA
555454 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
555474 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
555493 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
555514 GTATCGATACA
1 GTATCGATACA
555525 GGATATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:555577 original size:53 final size:53
Alignment explanation
Indices: 555494--555630 Score: 231
Period size: 53 Copynumber: 2.6 Consensus size: 53
555484 AGATTGCATA
555494 GTATCGATACACACAAATATGTATCGATACAGGAT-ATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGG-TCATTGGCAGTAGCCAAATTT
*
555548 GTATCGATACACACAATATGTATCGATACAGGTCGTTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
*
555601 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
555631 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
52 1 0.01
53 65 0.81
54 14 0.17
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
Found at i:555705 original size:21 final size:22
Alignment explanation
Indices: 555675--555726 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
555665 CACTATTCAT
*
555675 ACTGTTCATGTATCGATACGTC
1 ACTGTTCATGTATCGATACATC
555697 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
555718 ACTGTTCAT
1 ACTGTTCAT
555727 AGATCACTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:555726 original size:52 final size:54
Alignment explanation
Indices: 555662--555799 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 54
555652 TTTCACTGTT
*
555662 CATCACTATTCATACTGTTCATGTATCGATAC-GTCACT-TTCATGTATCGATA
1 CATCACTGTTCATACTGTTCATGTATCGATACAGTCACTATTCATGTATCGATA
* * *
555714 CATCACTGTTCATA--GATCACTGT-TC-ACACTATTCACTATTCATGTATCGATA
1 CATCACTGTTCATACTGTTCA-TGTATCGATAC-AGTCACTATTCATGTATCGATA
* *
555766 CATCACTGTTCATCACTATTCATATATCGATACA
1 CATCACTGTTCAT-ACTGTTCATGTATCGATACA
555800 TTGTATCGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
49 3 0.04
50 6 0.09
51 8 0.12
52 40 0.58
53 1 0.01
54 2 0.03
55 6 0.09
56 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (54 bp):
CATCACTGTTCATACTGTTCATGTATCGATACAGTCACTATTCATGTATCGATA
Found at i:555808 original size:13 final size:13
Alignment explanation
Indices: 555790--555826 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
555780 ACTATTCATA
555790 TATCGATACATTG
1 TATCGATACATTG
*
555803 TATCGATACAGTG
1 TATCGATACATTG
555816 TATCGATACAT
1 TATCGATACAT
555827 CATAAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:560272 original size:9 final size:9
Alignment explanation
Indices: 560255--560286 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
560245 ATAAGTTACT
560255 AAAATGATG
1 AAAATGATG
*
560264 AAGATGATG
1 AAAATGATG
560273 AAAATGATG
1 AAAATGATG
560282 AAAAT
1 AAAAT
560287 AGCAAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
AAAATGATG
Found at i:561278 original size:52 final size:52
Alignment explanation
Indices: 561191--561298 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
561181 GATGAGAAGA
* * * **
561191 ATGATAAAGGTGCCAATATGGAGATTCAAGTCCAACGATATTGGGCTTAAAG
1 ATGACAAAGGTGCCAATATGGAGATTCAAGTCCAACAACATTGGAATTAAAG
* **
561243 ATGACAAAGGTGCCAATGTGTTGATTCAAAG-CCAACAACATTGGAATTAAAG
1 ATGACAAAGGTGCCAATATGGAGATTC-AAGTCCAACAACATTGGAATTAAAG
561295 ATGA
1 ATGA
561299 GAAGAATGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 44 0.94
53 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (52 bp):
ATGACAAAGGTGCCAATATGGAGATTCAAGTCCAACAACATTGGAATTAAAG
Found at i:561397 original size:52 final size:52
Alignment explanation
Indices: 561304--561405 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 52
561294 GATGAGAAGA
* * * * * *
561304 ATGATAAAAGTGCTAATATGCTGATTCAAGGTCAGCAATATTGGACTTAAAG
1 ATGACAAAAGTGCCAATATACCGATTCAAGGCCAACAATATTGGACTTAAAG
**
561356 ATGACAAAAGTGCCAATATACCGATTCAAGGCCAATGATATTGGACTTAA
1 ATGACAAAAGTGCCAATATACCGATTCAAGGCCAACAATATTGGACTTAA
561406 GAAAGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (52 bp):
ATGACAAAAGTGCCAATATACCGATTCAAGGCCAACAATATTGGACTTAAAG
Found at i:561400 original size:113 final size:113
Alignment explanation
Indices: 561179--561390 Score: 291
Period size: 113 Copynumber: 1.9 Consensus size: 113
561169 ATCGGGCCTG
* * * *
561179 AAGATGAGAAGAATGATAAAGGTGCCAATATGGAGATTCAAGTCCAACGATATTGGGCTTAAAGA
1 AAGATGAGAAGAATGATAAAAGTGCCAATATGCAGATTCAAGTCCAACAATATTGGACTTAAAGA
* * ***
561244 TGACAAAGGTGCCAATGTGTTGATTCAAAGCCAACAACATTGGAATTA
66 TGACAAAAGTGCCAATATACCGATTCAAAGCCAACAACATTGGAATTA
* * *
561292 AAGATGAGAAGAATGATAAAAGTGCTAATATGCTGATTCAAGGT-CAGCAATATTGGACTTAAAG
1 AAGATGAGAAGAATGATAAAAGTGCCAATATGCAGATTCAA-GTCCAACAATATTGGACTTAAAG
*
561356 ATGACAAAAGTGCCAATATACCGATTCAAGGCCAA
65 ATGACAAAAGTGCCAATATACCGATTCAAAGCCAA
561391 TGATATTGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
113 83 0.98
114 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (113 bp):
AAGATGAGAAGAATGATAAAAGTGCCAATATGCAGATTCAAGTCCAACAATATTGGACTTAAAGA
TGACAAAAGTGCCAATATACCGATTCAAAGCCAACAACATTGGAATTA
Found at i:561592 original size:33 final size:33
Alignment explanation
Indices: 561515--561641 Score: 157
Period size: 33 Copynumber: 3.8 Consensus size: 33
561505 CATTAGGCTT
* * *
561515 AGAAGGAGATGCCACCAACATGCGTGGGCTTTT-
1 AGAAGG-GTTGCCACCAACTTGTGTGGGCTTTTG
* *
561548 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTTG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTTG
* *
561581 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTTG
* *
561614 AGAAGGGTTTCCACCAACTTATGTGGGC
1 AGAAGGGTTGCCACCAACTTGTGTGGGC
561642 CTTTAACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 22 0.27
33 61 0.73
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCAACTTGTGTGGGCTTTTG
Found at i:561708 original size:32 final size:32
Alignment explanation
Indices: 561650--562117 Score: 460
Period size: 32 Copynumber: 14.5 Consensus size: 32
561640 GCCTTTAACT
*
561650 AACTTGTGTGGGCTTTGA-AAAGGGTTGCCATC
1 AACTTGTGTGGGCTTTGAGAAA-GGTTGCCACC
* * *
561682 AACTTGTGTCGGCTATGAGAAAGGTTGCCACT
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* *
561714 AACTTATGCGGGCTTTAGAGAAAGGCTTGCCACC
1 AACTTGTGTGGGCTTT-GAGAAAGG-TTGCCACC
*
561748 AACTTGTGTGGGCTTTGAGAAGGGTTGCCACC
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* * *
561780 AACTTGTGTAGG-TTTTAGAGAAGGTTTTCCACC
1 AACTTGTGTGGGCTTTGAGA-AAGG-TTGCCACC
*
561813 AGCTTGTGTGGGCTTTGAG-AAGGCTTGCCACC
1 AACTTGTGTGGGCTTTGAGAAAGG-TTGCCACC
*
561845 AACTTGTGTGGGCTTTAGAGAAAAGTTGCCACC
1 AACTTGTGTGGGCTTT-GAGAAAGGTTGCCACC
* * * *
561878 GACTTGTGTGGGATTTGAGAAGGGTTG-CACT
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* * *
561909 GACTTGTGTGGGCTTTAAGAAAGGCTT-CCACT
1 AACTTGTGTGGGCTTTGAGAAAGG-TTGCCACC
* * *
561941 AACTTTTGTGGGCTTCAGAGAAGGGTTGCCACC
1 AACTTGTGTGGGCTT-TGAGAAAGGTTGCCACC
* * ** *
561974 GACTTGTGTGGGCTTTAAGATGGGCTGCCACC
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* * * * *
562006 AACTTATGCGGGCTTTGAGAAGGGTTTCCACT
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* * *
562038 AATTTGTGTGGGCTTTGAGAAGGGTTGCCACT
1 AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
* * *
562070 GATTTGTGTGGGCTTTAGAGAAGGGTTGCCACC
1 AACTTGTGTGGGCTTT-GAGAAAGGTTGCCACC
*
562103 GACTTGTGTGGGCTT
1 AACTTGTGTGGGCTT
562118 AAAAAGGATG
Statistics
Matches: 365, Mismatches: 58, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
31 30 0.08
32 194 0.53
33 112 0.31
34 29 0.08
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
AACTTGTGTGGGCTTTGAGAAAGGTTGCCACC
Found at i:561749 original size:119 final size:119
Alignment explanation
Indices: 561538--561760 Score: 313
Period size: 119 Copynumber: 1.9 Consensus size: 119
561528 ACCAACATGC
* * * * * * *
561538 GTGGGCTTTTAAAAGGGTTGCCACCGACTTGTGTGGGCTTTTGAGAAGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTCGGCTTATGAGAAAGGTTGCCACCAACTTAT
* * *
561603 GTGGGCTTTAGAGAAGGGTTTCCACCAACTTATGTGGGCCTTTAACTAACTTGT
66 GCGGGCTTTAGAGAAGGCTTGCCACCAACTTATGTGGGCCTTTAACTAACTTGT
* *
561657 GTGGGCTTTGAAAAGGGTTGCCATCAACTTGTGTCGGC-TATGAGAAAGGTTGCCACTAACTTAT
1 GTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTCGGCTTATGAGAAAGGTTGCCACCAACTTAT
*
561721 GCGGGCTTTAGAGAAAGGCTTGCCACCAACTTGTGTGGGC
66 GCGGGCTTTAGAG-AAGGCTTGCCACCAACTTATGTGGGC
561761 TTTGAGAAGG
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 33 0.37
119 57 0.63
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (119 bp):
GTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTCGGCTTATGAGAAAGGTTGCCACCAACTTAT
GCGGGCTTTAGAGAAGGCTTGCCACCAACTTATGTGGGCCTTTAACTAACTTGT
Found at i:561834 original size:65 final size:65
Alignment explanation
Indices: 561650--562117 Score: 520
Period size: 65 Copynumber: 7.2 Consensus size: 65
561640 GCCTTTAACT
* * * *
561650 AACTTGTGTGGGCTTT-GA-AAAGGGTTGCCATCAACTTGTGTCGGCTATGAGAAAGGTTGCCAC
1 AACTTGTGTGGGCTTTAGAGAAA-GGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCAC
*
561713 T
65 C
* *
561714 AACTTATGCGGGCTTTAGAGAAAGGCTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCAC
1 AACTTGTGTGGGCTTTAGAGAAAGG-TTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCAC
561779 C
65 C
* * * * *
561780 AACTTGTGTAGGTTTTAGAG-AAGGTTTTCCACCAGCTTGTGTGGGCTTTGAGAAGGCTTGCCAC
1 AACTTGTGTGGGCTTTAGAGAAAGG-TTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCAC
561844 C
65 C
* * * *
561845 AACTTGTGTGGGCTTTAGAGAAAAGTTGCCACCGACTTGTGTGGGATTTGAGAAGGGTTG-CACT
1 AACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCACC
* * * *
561909 GACTTGTGTGGGCTTTA-AGAAAGGCTT-CCACTAACTTTTGTGGGCTTCAGAGAAGGGTTGCCA
1 AACTTGTGTGGGCTTTAGAGAAAGG-TTGCCACCAACTTGTGTGGGCTT-TGAGAAGGGTTGCCA
561972 CC
64 CC
* ** * * * * *
561974 GACTTGTGTGGGCTTTA-AGATGGGCTGCCACCAACTTATGCGGGCTTTGAGAAGGGTTTCCACT
1 AACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCACC
* * ** *
562038 AATTTGTGTGGGCTTT-GAGAAGGGTTGCCACTGATTTGTGTGGGCTTTAGAGAAGGGTTGCCAC
1 AACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTT-GAGAAGGGTTGCCAC
562102 C
65 C
*
562103 GACTTGTGTGGGCTT
1 AACTTGTGTGGGCTT
562118 AAAAAGGATG
Statistics
Matches: 340, Mismatches: 54, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
63 22 0.06
64 99 0.29
65 162 0.48
66 57 0.17
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (65 bp):
AACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCACC
Found at i:561990 original size:129 final size:129
Alignment explanation
Indices: 561647--562117 Score: 533
Period size: 129 Copynumber: 3.6 Consensus size: 129
561637 TGGGCCTTTA
* *
561647 ACTAACTTGTGTGGGCTTTGA-AAAGGGTTGCCA-TCAACTTGTGTCGGC-TATGAGAAAGGTTG
1 ACTAACTTGTGTGGGCTTTGAGAAAGGGTTGCCACT-AACTTGTGTGGGCTTA-GAGAAGGGTTG
* * *
561709 CCACTAACTTATGCGGGCTTTAGAGAAAGGCTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTT
64 CCACCAACTTGTGTGGGCTTTAGAGAAAGG-TTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTT
561774 GCC
128 G-C
* * * * * * * * *
561777 ACCAACTTGTGTAGG-TTTTAGAGAAGGTTTTCCACCAGCTTGTGTGGGCTTTGAGAAGGCTTGC
1 ACTAACTTGTGTGGGCTTTGAGA-AAGGGTTGCCACTAACTTGTGTGGGCTTAGAGAAGGGTTGC
* * *
561841 CACCAACTTGTGTGGGCTTTAGAGAAAAGTTGCCACCGACTTGTGTGGGATTTGAGAAGGGTTGC
65 CACCAACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGC
* * * *
561906 ACTGACTTGTGTGGGCTTTAAGAAAGGCTT-CCACTAACTTTTGTGGGCTTCAGAGAAGGGTTGC
1 ACTAACTTGTGTGGGCTTTGAGAAAGGGTTGCCACTAACTTGTGTGGGCTT-AGAGAAGGGTTGC
* ** * * * *
561970 CACCGACTTGTGTGGGCTTTA-AGATGGGCTGCCACCAACTTATGCGGGCTTTGAGAAGGGTTTC
65 CACCAACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGG-TTG
562034 C
129 C
* * *
562035 ACTAATTTGTGTGGGCTTTGAG-AAGGGTTGCCACTGATTTGTGTGGGCTTTAGAGAAGGGTTGC
1 ACTAACTTGTGTGGGCTTTGAGAAAGGGTTGCCACTAACTTGTGTGGGC-TTAGAGAAGGGTTGC
*
562099 CACCGACTTGTGTGGGCTT
65 CACCAACTTGTGTGGGCTT
562118 AAAAAGGATG
Statistics
Matches: 288, Mismatches: 44, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
128 54 0.19
129 123 0.43
130 55 0.19
131 55 0.19
132 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (129 bp):
ACTAACTTGTGTGGGCTTTGAGAAAGGGTTGCCACTAACTTGTGTGGGCTTAGAGAAGGGTTGCC
ACCAACTTGTGTGGGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGC
Found at i:562210 original size:28 final size:28
Alignment explanation
Indices: 562152--562209 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
562142 ACTTAAAGGG
* *
562152 AAAGGGTGCCATCGAGTTGTGTAGTTTA
1 AAAGGGTGCCAGCGAGTTGTGGAGTTTA
562180 AAAGGGTGCC-GCGGAGTTGTGGA-TTTA
1 AAAGGGTGCCAGC-GAGTTGTGGAGTTTA
562207 AAA
1 AAA
562210 AAAAAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (28 bp):
AAAGGGTGCCAGCGAGTTGTGGAGTTTA
Found at i:562328 original size:90 final size:90
Alignment explanation
Indices: 562219--562420 Score: 228
Period size: 90 Copynumber: 2.2 Consensus size: 90
562209 AAAAAAAAAG
* * * * *
562219 GATGCCACTAAGTCATGGACTTGG-AGATGAGATGCCACTGAGTCATGGACTTTGAAGAAGGATG
1 GATGCCACTAAGTCGTGGACTTGGAAAAAGA-ATACCACTGAGTCATGGACTTTGAAAAAGGATG
* *
562283 CCACTAACTCGTGGAC-TTGGAGAAGA
65 CCACTAACTCGTGAACTTTGAAGAA-A
* ** **
562309 GATGCCACTAAGTCGTGGACTTTGAAAAAGAATACTGCTGAGTTGTGGACTTTGAAAAAGGATGC
1 GATGCCACTAAGTCGTGGACTTGGAAAAAGAATACCACTGAGTCATGGACTTTGAAAAAGGATGC
*
562374 CACTAAGTCGTGAACTTTGAAGAAA
66 CACTAACTCGTGAACTTTGAAGAAA
* * *
562399 GATTCCACTGAGTTGTGGACTT
1 GATGCCACTAAGTCGTGGACTT
562421 TTGAGAAAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
90 83 0.88
91 11 0.12
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (90 bp):
GATGCCACTAAGTCGTGGACTTGGAAAAAGAATACCACTGAGTCATGGACTTTGAAAAAGGATGC
CACTAACTCGTGAACTTTGAAGAAA
Found at i:562357 original size:60 final size:59
Alignment explanation
Indices: 562234--562420 Score: 205
Period size: 60 Copynumber: 3.1 Consensus size: 59
562224 CACTAAGTCA
* * * * * * * *
562234 TGGACTTGGAGATGAGATGCCACTGAGTCATGGACTTTGAAGAAGGATGCCACTAACTCG
1 TGGACTTGGAGAAGAGATGCCACTAAGTCGTGGACTTTGAA-AAAGATACCACTGAGTTG
**
562294 TGGACTTGGAGAAGAGATGCCACTAAGTCGTGGACTTTGAAAAAGAATACTGCTGAGTTG
1 TGGACTTGGAGAAGAGATGCCACTAAGTCGTGGACTTTGAAAAAG-ATACCACTGAGTTG
* * * *
562354 TGGACTTTGA-AAAAGGATGCCACTAAGTCGTGAACTTTGAAGAAAGATTCCACTGAGTTG
1 TGGACTTGGAGAAGA-GATGCCACTAAGTCGTGGACTTTGAA-AAAGATACCACTGAGTTG
562414 TGGACTT
1 TGGACTT
562421 TTGAGAAAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 6 0.06
60 98 0.91
61 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (59 bp):
TGGACTTGGAGAAGAGATGCCACTAAGTCGTGGACTTTGAAAAAGATACCACTGAGTTG
Found at i:562428 original size:30 final size:29
Alignment explanation
Indices: 562219--562428 Score: 186
Period size: 30 Copynumber: 7.0 Consensus size: 29
562209 AAAAAAAAAG
* * *
562219 GATGCCACTAAGTCATGGACTTGGAGATGA
1 GATGCCACTAAGTCGTGGACTTTGAGA-AA
* * *
562249 GATGCCACTGAGTCATGGACTTTGAAGAAG
1 GATGCCACTAAGTCGTGGACTTTG-AGAAA
* *
562279 GATGCCACTAACTCGTGGACTTGGAGAAGA
1 GATGCCACTAAGTCGTGGACTTTGAGAA-A
*
562309 GATGCCACTAAGTCGTGGACTTTGAAAAA
1 GATGCCACTAAGTCGTGGACTTTGAGAAA
* ** * * *
562338 GAATACTGCTGAGTTGTGGACTTTGAAAAA
1 G-ATGCCACTAAGTCGTGGACTTTGAGAAA
*
562368 GGATGCCACTAAGTCGTGAACTTTGAAGAAA
1 -GATGCCACTAAGTCGTGGACTTTG-AGAAA
* * *
562399 GATTCCACTGAGTTGTGGACTTTTGAGAAA
1 GATGCCACTAAGTCGTGGAC-TTTGAGAAA
562429 ATAATTAAAG
Statistics
Matches: 146, Mismatches: 28, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
29 6 0.04
30 128 0.88
31 12 0.08
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (29 bp):
GATGCCACTAAGTCGTGGACTTTGAGAAA
Found at i:563564 original size:20 final size:20
Alignment explanation
Indices: 563534--563592 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
563524 AAATTTCGCA
563534 ATTTGTATCGATACATTGTTC
1 ATTT-TATCGATACATTGTTC
*
563555 ATTTTATCGATACATTATTC
1 ATTTTATCGATACATTGTTC
*
563575 ATTGTATCGATACATTGT
1 ATTTTATCGATACATTGT
563593 ATCGATACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTTATCGATACATTGTTC
Found at i:563592 original size:13 final size:13
Alignment explanation
Indices: 563574--563603 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
563564 ATACATTATT
563574 CATTGTATCGATA
1 CATTGTATCGATA
563587 CATTGTATCGATA
1 CATTGTATCGATA
563600 CATT
1 CATT
563604 CTAGGTTTAC
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:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:566028 original size:47 final size:49
Alignment explanation
Indices: 565977--566084 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 49
565967 TCCCGGTTTC
* *
565977 ATTTCCAAAACATCAATTTTTC-TTA-GAGATACTCCAACTCCGATTTT
1 ATTTCCAAAACACCAATTTTCCATTACGAGATACTCCAACTCCGATTTT
* * * *
566024 ATTTCTAAAACACCCATTTTCCATTATCGGGGATACTCCAACTCTGATTTT
1 ATTTCCAAAACACCAATTTTCCATTA-C-GAGATACTCCAACTCCGATTTT
566075 ATTTCCAAAA
1 ATTTCCAAAA
566085 GATCGACTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 18 0.36
48 3 0.06
51 29 0.58
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (49 bp):
ATTTCCAAAACACCAATTTTCCATTACGAGATACTCCAACTCCGATTTT
Found at i:566109 original size:51 final size:50
Alignment explanation
Indices: 566004--566116 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 50
565994 TTTTCTTAGA
* *
566004 GATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATTATCGGG
1 GATACTCCAACTCCGATTTTATTTCCAAAACACCCATTTTCCA-TATCGAG
* * * *
566055 GATACTCCAACTCTGATTTTATTTCCAAAAGATCGACTTTTCACA-ATCGAG
1 GATACTCCAACTCCGATTTTATTTCCAAAACACCCA-TTTTC-CATATCGAG
566106 GATACTCCAAC
1 GATACTCCAAC
566117 CTCGTTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
51 47 0.87
52 5 0.09
53 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.33
Consensus pattern (50 bp):
GATACTCCAACTCCGATTTTATTTCCAAAACACCCATTTTCCATATCGAG
Found at i:566300 original size:79 final size:78
Alignment explanation
Indices: 566052--566326 Score: 358
Period size: 79 Copynumber: 3.5 Consensus size: 78
566042 TTCCATTATC
* * * * * * *
566052 GGGGATACTCCAACTCTGATTTTATTTCCAAAAGATCGACTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCA-AATCGGGGATACTCCAAC
* *
566117 CTCGTTATTTCCGA
65 CCCGTTATTTTCGA
* * *
566131 GGGGACACTCCAACCCCGGTTTTATTTCTAAAACATCAAATTTTC--ATCGGGGATACTCCAA-C
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCAAATCGGGGATACTCCAACC
566193 CCGTTTATTTTCGA
66 CCG-TTATTTTCGA
* *
566207 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCA-AATCGGGGATACTCCAAC
*
566272 CCCGTTATTTTTGA
65 CCCGTTATTTTCGA
*
566286 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATT
566327 CTCCACAATC
Statistics
Matches: 174, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
75 3 0.02
76 67 0.39
79 100 0.57
80 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCAAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:566363 original size:51 final size:51
Alignment explanation
Indices: 566287--566402 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
566277 TATTTTTGAG
* *
566287 GGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCA
1 GGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
* * * * * *
566338 GGGATATTCTAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCG
1 GGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
566389 GGGATACTCTAACC
1 GGGATACTCTAACC
566403 TCGTTATTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCA
Found at i:566417 original size:28 final size:28
Alignment explanation
Indices: 566385--566461 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
566375 ATTTTTCACA
* *
566385 ATCGGGGATACTCTAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
566413 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
566441 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
566462 GCTTTATTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:566446 original size:158 final size:157
Alignment explanation
Indices: 566258--566590 Score: 409
Period size: 157 Copynumber: 2.1 Consensus size: 157
566248 TTTCATAATT
** * *
566258 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACC
* ** *
566323 AATTCTCCACAATCAGGGATA-TTCTAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAAT
66 AATTCT-CACAATCAGGGATACTTC-AACCCCGACCTTATTTCCAAAACACTAATTTCTCACAAT
* * *
566387 CGGGGATACTCTAACCTCGTTA-TTTCATC
129 CGGGGATACTCCAACCCCATTATTTTCA-C
* * **
566416 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACC
* * * * * * * *
566481 GATTCTCACAATCAGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTG
66 AATTCTCACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCG
566546 GGGATACTCCAACCCCATTATTTTCAC
131 GGGATACTCCAACCCCATTATTTTCAC
*
566573 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
566591 ATTTTATTTT
Statistics
Matches: 149, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
157 79 0.53
158 70 0.47
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (157 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACC
AATTCTCACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCG
GGGATACTCCAACCCCATTATTTTCAC
Found at i:566508 original size:50 final size:51
Alignment explanation
Indices: 566445--566561 Score: 173
Period size: 50 Copynumber: 2.3 Consensus size: 51
566435 TATTTCCGAG
*
566445 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTCTCACAATCA
1 GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
* * * **
566495 GGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTG
1 GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
566546 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
566562 ATTATTTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 35 0.59
51 24 0.41
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:566651 original size:287 final size:286
Alignment explanation
Indices: 566208--566725 Score: 661
Period size: 287 Copynumber: 1.8 Consensus size: 286
566198 TATTTTCGAG
** *
566208 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATTGGGGATACTCCAACC
* *
566273 CCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCA
66 CCATTATTTTTCAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCA
* * ** * *
566338 GGGATATTCTAACTCCGATTTTATTTCCAAAACA-CTAATTTTTCACAATCGGGGATACTCTAAC
131 GGGACATTCAAACTCCGACCTTATTTCCAAAACATC-AATTTTTCACAATCGGGGATACCCCAAC
* * *
566402 CTCGTTA-TTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTT
195 CCCATTATTTTCA--GGGGATACTACAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTT
566466 TATTTCCAAAATATTGATTCTCACAATCA
258 TATTTCCAAAATATTGATTCTCACAATCA
* * **
566495 GGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATTGGGGATACTCCAACC
* * * * * * * *
566560 CCATTA-TTTTCACGGGGATACTCCAATCCCGATTTTATTTTTGAAACATCTATTTTCTATAATC
66 CCATTATTTTTCA-GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
* * *
566624 -GTGGACACTTCAAAC-CTTG-CCTTATTTCTAAATCATCAATTTTTCACAATCGGGGATACCCC
130 AG-GGACA-TTCAAACTC-CGACCTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACCCC
566686 AACCCCATTATTTTCGAGGGGATACTACAACCCCGTTATT
192 AACCCCATTATTTTC-AGGGGATACTACAACCCCGTTATT
566726 ATCTCCAAAA
Statistics
Matches: 195, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
286 6 0.03
287 176 0.90
288 12 0.06
289 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (286 bp):
GGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATTGGGGATACTCCAACC
CCATTATTTTTCAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCA
GGGACATTCAAACTCCGACCTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACCCCAACC
CCATTATTTTCAGGGGATACTACAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTAT
TTCCAAAATATTGATTCTCACAATCA
Found at i:566747 original size:130 final size:129
Alignment explanation
Indices: 566413--566748 Score: 358
Period size: 130 Copynumber: 2.6 Consensus size: 129
566403 TCGTTATTTC
* * *
566413 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCC-GTTTTATTTCCAAAAT
* * * ** *
566478 ATTGA-TTCTCACAATCAGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATA
65 ATTAATTTCTCACAATCAGGGACACTTCAAACCCGGCCTTATTTCTAAAATATCAATTTCTCACA
* * ***
566542 ATTGGGGATACTCCAACCCCATTATTTTC-ACGGGGATACTCCAATCCCGATTTTATTTTTGAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGA-GGGGATACTCCAACCCCG-TTTTATTTCCAAAA
* * * ** *
566606 CATCTATTTTCT-ATAATC-GTGGACACTTCAAACCTTGCCTTATTTCT-AAATCATCAATTTTT
64 TAT-TAATTTCTCACAATCAG-GGACACTTCAAACCCGGCCTTATTTCTAAAAT-ATCAATTTCT
566668 CACA
126 CACA
* * *
566672 ATCGGGGATACCCCAACCCCATTATTTTCGAGGGGATACTACAACCCCGTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGTT-TTATTTCCAAAAT
566737 ATTAAATTTCTC
65 ATT-AATTTCTC
566749 GTCGGGAGAT
Statistics
Matches: 167, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
128 2 0.01
129 62 0.37
130 98 0.59
131 5 0.03
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (129 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGTTTTATTTCCAAAATA
TTAATTTCTCACAATCAGGGACACTTCAAACCCGGCCTTATTTCTAAAATATCAATTTCTCACA
Found at i:569341 original size:20 final size:20
Alignment explanation
Indices: 569316--569378 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
569306 CCACCCATCG
*
569316 ATACATTAGTAAGTGTATCA
1 ATACATTAGTAAATGTATCA
* *
569336 ATACATTAGTAAAAGTATCG
1 ATACATTAGTAAATGTATCA
569356 ATACATTAGTAAATGTATCA
1 ATACATTAGTAAATGTATCA
569376 ATA
1 ATA
569379 TATTCTTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
ATACATTAGTAAATGTATCA
Found at i:576859 original size:22 final size:21
Alignment explanation
Indices: 576824--576873 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
576814 TTTGTTGATG
*
576824 ATTTTG-A-TAAAAAATGAAGT
1 ATTTTGAAGTAAAAAAT-AAGA
576844 ATTTTGAAGTAAAAAATAAGA
1 ATTTTGAAGTAAAAAATAAGA
*
576865 AATTTGAAG
1 ATTTTGAAG
576874 AAGATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTAAAAAATAAGA
Found at i:576870 original size:21 final size:22
Alignment explanation
Indices: 576831--576873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
576821 ATGATTTTGA
* *
576831 TAAAAAATGAAGTATTTTGAAG
1 TAAAAAATGAAGAAATTTGAAG
576853 TAAAAAAT-AAGAAATTTGAAG
1 TAAAAAATGAAGAAATTTGAAG
576874 AAGATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (22 bp):
TAAAAAATGAAGAAATTTGAAG
Found at i:577022 original size:20 final size:20
Alignment explanation
Indices: 576997--577058 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
576987 GATATAATGC
576997 ATCGATACAAAGAATATTGT
1 ATCGATACAAAGAATATTGT
*
577017 ATCGAT-------ATAATGT
1 ATCGATACAAAGAATATTGT
577030 ATCGATACAAAGAATATTGT
1 ATCGATACAAAGAATATTGT
577050 ATCGATACA
1 ATCGATACA
577059 TTTGGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 12 0.36
20 21 0.64
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
ATCGATACAAAGAATATTGT
Found at i:577022 original size:33 final size:33
Alignment explanation
Indices: 576980--577056 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
576970 ATAGTAACCC
576980 TTGTATCGATATAATGCATCGATACAAAGAATA
1 TTGTATCGATATAATGCATCGATACAAAGAATA
*
577013 TTGTATCGATATAATGTATCGATACAAAGAATA
1 TTGTATCGATATAATGCATCGATACAAAGAATA
577046 TTGTATCGATA
1 TTGTATCGATA
577057 CATTTGGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGTATCGATATAATGCATCGATACAAAGAATA
Found at i:581592 original size:3 final size:3
Alignment explanation
Indices: 581586--581615 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
581576 TCACCACCAC
*
581586 CAT CAT CAT CAT CAT CAT CAT CAT TAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
581616 TTTCATCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:583225 original size:20 final size:20
Alignment explanation
Indices: 583200--583253 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
583190 GTTTGAAGCA
583200 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
583220 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
583240 ATGTATCGATACAA
1 ATGTATCGATACAA
583254 ACAGGGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:583320 original size:13 final size:13
Alignment explanation
Indices: 583302--583328 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
583292 TACAATGAAC
583302 ATGTATCAATACA
1 ATGTATCAATACA
583315 ATGTATCAATACA
1 ATGTATCAATACA
583328 A
1 A
583329 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:585961 original size:20 final size:20
Alignment explanation
Indices: 585936--586000 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
585926 CTGCCAGTTT
585936 CATGTATCGATATAATTGTC
1 CATGTATCGATATAATTGTC
585956 CATGTATCG--AT-A----C
1 CATGTATCGATATAATTGTC
585969 CATGTATCGATATAATTGTC
1 CATGTATCGATATAATTGTC
585989 CATGTATCGATA
1 CATGTATCGATA
586001 CCATGTATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 22 0.58
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (20 bp):
CATGTATCGATATAATTGTC
Found at i:585973 original size:13 final size:13
Alignment explanation
Indices: 585955--586013 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
585945 ATATAATTGT
585955 CCATGTATCGATA
1 CCATGTATCGATA
585968 CCATGTATCGAT-
1 CCATGTATCGATA
* *
585980 --AT-AATTG-T-
1 CCATGTATCGATA
585988 CCATGTATCGATA
1 CCATGTATCGATA
586001 CCATGTATCGATA
1 CCATGTATCGATA
586014 TAAAGCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 4 0.11
11 3 0.08
12 1 0.03
13 25 0.68
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (13 bp):
CCATGTATCGATA
Found at i:585978 original size:33 final size:33
Alignment explanation
Indices: 585936--586016 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
585926 CTGCCAGTTT
585936 CATGTATCGATATAATTGTCCATGTATCGATAC
1 CATGTATCGATATAATTGTCCATGTATCGATAC
585969 CATGTATCGATATAATTGTCCATGTATCGATAC
1 CATGTATCGATATAATTGTCCATGTATCGATAC
586002 CATGTATCGATATAA
1 CATGTATCGATATAA
586017 AGCATAATGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (33 bp):
CATGTATCGATATAATTGTCCATGTATCGATAC
Found at i:586027 original size:33 final size:33
Alignment explanation
Indices: 585936--586034 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
585926 CTGCCAGTTT
* *
585936 CATGTATCGATATAATTGTCCATGTATCGATAC
1 CATGTATCGATATAATAGTCAATGTATCGATAC
* *
585969 CATGTATCGATATAATTGTCCATGTATCGATAC
1 CATGTATCGATATAATAGTCAATGTATCGATAC
586002 CATGTATCGATATAA-AG-CATAATGTATCGATAC
1 CATGTATCGATATAATAGTC--AATGTATCGATAC
586035 ATCTGGGTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 60 0.97
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (33 bp):
CATGTATCGATATAATAGTCAATGTATCGATAC
Found at i:588327 original size:20 final size:21
Alignment explanation
Indices: 588302--588341 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
588292 TTTGTTGGTG
*
588302 ATTTTGATG-AAAAATGAAGT
1 ATTTTGAAGTAAAAATGAAGT
588322 ATTTTGAAGTAAAAATGAAG
1 ATTTTGAAGTAAAAATGAAG
588342 AAATTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTAAAAATGAAGT
Found at i:594015 original size:20 final size:20
Alignment explanation
Indices: 593990--594045 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
593980 TTGCCAGTTT
**
593990 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
594010 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
594029 CATTTATCGATACAATT
1 CATGTATCGATACAATT
594046 TGTTGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:594911 original size:20 final size:21
Alignment explanation
Indices: 594886--594938 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
594876 ATCGATACAT
*
594886 TGTATCAATACATG-ACCA-AA
1 TGTATCAATACATGCA-AAGAA
* *
594906 TGTATCGATACTTGCAAAGAA
1 TGTATCAATACATGCAAAGAA
594927 TGTATCAATACA
1 TGTATCAATACA
594939 GGTGATTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (21 bp):
TGTATCAATACATGCAAAGAA
Found at i:603066 original size:22 final size:22
Alignment explanation
Indices: 603040--603084 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
603030 TGATTAAAGA
603040 AAATTGTTTT-ATTAAGGGCGAG
1 AAATT-TTTTGATTAAGGGCGAG
*
603062 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGATTAAGGGCGAG
603084 A
1 A
603085 GAAAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (22 bp):
AAATTTTTTGATTAAGGGCGAG
Found at i:603789 original size:21 final size:21
Alignment explanation
Indices: 603743--603796 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
603733 CCTTAACTGT
603743 TTGTATCGATACA-CACAAGA
1 TTGTATCGATACATCACAAGA
*
603763 -TGTATCGATACATGACCAA-A
1 TTGTATCGATACATCA-CAAGA
603783 TTGTATCGATACAT
1 TTGTATCGATACAT
603797 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 16 0.53
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACATCACAAGA
Found at i:609569 original size:10 final size:10
Alignment explanation
Indices: 609542--609575 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
609532 TGAGGATCGT
*
609542 TTTAAAAATA
1 TTTAAAAATC
609552 TTTCAAAAATC
1 TTT-AAAAATC
609563 TTTAAAAATC
1 TTTAAAAATC
609573 TTT
1 TTT
609576 TTCCCAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATC
Found at i:612333 original size:28 final size:28
Alignment explanation
Indices: 612221--612714 Score: 562
Period size: 28 Copynumber: 17.1 Consensus size: 28
612211 TTTTTTAAAA
* *
612221 AAAAAGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAGGTGCCACTGAC-T-TGTGGGCTTTG
*
612251 AAAAGAGTTACCACTGACTCGTGTGGGCTTTG
1 AAAAG-G-TGCCACTGACT--TGTGGGCTTTG
* *
612283 AAAAGAGTTACCACTGGCTTGTGGGCTTTG
1 AAAAG-G-TGCCACTGACTTGTGGGCTTTG
* *
612313 AAACGGTGCCACTGACTTGTGGTCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * **
612341 -AAAGGATGCCACTAATTTGTGCACTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
612369 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
612398 AAAAGGTGCCACTGACTTATGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
612426 AAAAGAGCGCCACTAACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
612455 -AAAGAGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAG-GTGCCACTGACTT--GTGGGCTTTG
** * *
612485 AAAAGACGCCACTAACTTGTGGTCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
612513 AAAATAGTGCCACTAACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
*
612542 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
612570 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
612599 AAAGGGTGCCACTGACTTACGTGGGCTTTG
1 AAAAGGTGCCACTGACTT--GTGGGCTTTG
* *
612629 AAAGGGTGCCACTGACTGGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
612657 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
612685 AAAAGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
612713 AA
1 AA
612715 GAGATGAACG
Statistics
Matches: 408, Mismatches: 40, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
27 8 0.02
28 186 0.46
29 103 0.25
30 67 0.16
31 6 0.01
32 38 0.09
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:612397 original size:57 final size:57
Alignment explanation
Indices: 612227--612714 Score: 513
Period size: 57 Copynumber: 8.4 Consensus size: 57
612217 AAAAAAAAAG
* *
612227 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGTGGGCTTTGAAAAGAGT
1 TGCCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-GA
* ** * *
612291 TACCACTGGCTTGTGGGCTTTGAAACG-GTGCCACTGACTTGTGGTCTTTGAAAGGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* ** *
612347 TGCCACTAATTTGTGCACTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGG-
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGA
* * * *
612404 TGCCACTGACTTATGGGCTTTGAAAAGAGCGCCACTAACTTGTGGGCTTTGAAA-GA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * **
612460 GTGCCACTGACTTGCGTGGGCTTTGAAAAGA-CGCCACTAACTTGTGGTCTTTGAAAATA
1 -TGCCACTAACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
612519 GTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 -TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
612576 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTACGTGGGCTTTGAAAGGG
1 -TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGA
* * * *
612635 TGCCACTGACTGGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
612691 TGCCACTGACTTGTGGGCTTTGAA
1 TGCCACTAACTTGTGGGCTTTGAA
612715 GAGATGAACG
Statistics
Matches: 373, Mismatches: 40, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
55 1 0.00
56 65 0.17
57 156 0.42
58 72 0.19
59 45 0.12
60 10 0.03
61 1 0.00
62 15 0.04
63 1 0.00
64 7 0.02
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (57 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:612522 original size:144 final size:142
Alignment explanation
Indices: 612220--612714 Score: 670
Period size: 144 Copynumber: 3.4 Consensus size: 142
612210 TTTTTTTAAA
* *
612220 AAAAAAGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGTGGGCTTTGAA
1 AAAAGAGTGCCACTAAC-T-TGTGGGCTTTGAAAAG-G-TGCCACTGACT--TGTGGGCTTTGAA
* * *
612285 AAGAGTTACCACTGGCTTGTGGGCTTTGAAACGGTGCCACTGACTT-GTGGTCTTTGAAAGGATG
60 AAGAG-TGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTTCGTGGGCTTTGAAAGGATG
* *
612349 CCACTAATTTGTGCACTTTG
123 CCACTAACTTGTGGACTTTG
* *
612369 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGAGC
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * *
612434 GCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAAGACGCCACTA
66 GCCACTGACTTGTGGGCTTTGAAAG-GTGCCACTGACTT-CGTGGGCTTTGAAAGGATGCCACTA
*
612499 ACTTGTGGTCTTTG
129 ACTTGTGGACTTTG
* *
612513 AAAATAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
* *
612578 GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTACGTGGGCTTTGAAAGGGTGCCACTG
66 GCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTT-CGTGGGCTTTGAAAGGATGCCACTA
* *
612643 ACTGGTGGGCTTTG
129 ACTTGTGGACTTTG
* * *
612657 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAA
612715 GAGATGAACG
Statistics
Matches: 312, Mismatches: 30, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
141 1 0.00
142 34 0.11
143 66 0.21
144 166 0.53
145 11 0.04
146 1 0.00
147 16 0.05
148 1 0.00
149 16 0.05
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (142 bp):
AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
GCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTTCGTGGGCTTTGAAAGGATGCCACTAAC
TTGTGGACTTTG
Found at i:627988 original size:20 final size:19
Alignment explanation
Indices: 627965--628005 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
627955 CATCCTCCAT
627965 AAAAAAAAACAACAAACAAA
1 AAAAAAAAACAAC-AACAAA
*
627985 AAAAAAACACAACAACAAA
1 AAAAAAAAACAACAACAAA
628004 AA
1 AA
628006 GGGTCTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAACAACAAA
Found at i:627996 original size:17 final size:17
Alignment explanation
Indices: 627965--628005 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
627955 CATCCTCCAT
627965 AAAAAAAAACAACAAACA
1 AAAAAAAAACAAC-AACA
627983 AAAAAAAAAC-ACAACA
1 AAAAAAAAACAACAACA
627999 ACAAAAA
1 A-AAAAA
628006 GGGTCTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 7 0.32
18 10 0.45
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAACAACA
Found at i:629524 original size:49 final size:49
Alignment explanation
Indices: 629353--630245 Score: 948
Period size: 49 Copynumber: 18.9 Consensus size: 49
629343 ATATTTAAAC
* * * ** *
629353 CCAATGTCGCTGCCCATGAATCAGCATATTGGTGCCTTTGTCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGT
* * * **
629405 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTC-TT-AGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
629452 ACCAATGTCGATGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
1 -CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * **
629502 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTT-AAGT
* * * ** *
629555 CCAACGTTGTTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
629602 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
629645 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
629694 CCAATGTAGCTGGCCTTGAATCAGCACATTGG------CATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
629737 CCAATGTAGCTGGCCTTGAATCAGCACATTAGCA----C-T-TTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * *
629780 CCAATATCGTTGGCCTTGAATCAGCATATTCGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
629829 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * * *
629872 CCAATATCGGTGGCTTTAAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
629921 CTAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
629970 CCAATGTAGCTGGCCTTGAATCAGCTCATTGGCA----C--CTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
630013 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
630062 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
630105 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
630154 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
630203 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
630246 AGCCTTGAAT
Statistics
Matches: 710, Mismatches: 90, Indels: 85
0.80 0.10 0.10
Matches are distributed among these distances:
43 223 0.31
44 5 0.01
45 2 0.00
46 6 0.01
47 36 0.05
48 52 0.07
49 315 0.44
50 5 0.01
52 38 0.05
53 28 0.04
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:629720 original size:92 final size:92
Alignment explanation
Indices: 629565--630466 Score: 933
Period size: 92 Copynumber: 9.8 Consensus size: 92
629555 CCAACGTTGT
** *
629565 TGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* *
629628 CATTGGCACCTCCAAGTCCAATATCGC
66 CATTGGCACCTCTAAGTCCAATGTCGC
*
629655 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* * *
629720 CATTGGCATCTTTAAGTCCAATGTAGC
66 CATTGGCACCTCTAAGTCCAATGTCGC
* * * *
629747 TGGCCTTGAATCAGCACATTAGCA----C-T-TTTAAGTCCAATATCGTTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* * *
629806 TATTCGCACCTTCATCTTTAAGTCCAATGTAGC
66 CATTGGCA-C--C-TC--TAAGTCCAATGTCGC
* * * * *
629839 TGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATATCGGTGGCTTTAAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* *
629898 TATTGGCACCTTTATCTTTAAGTCTAATGTCGC
66 CATTGGCACC----TC--TAAGTCCAATGTCGC
* *
629931 TGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCT
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* * *
629996 CATTGGCACCTTTAAGTCCAATATCAC
66 CATTGGCACCTCTAAGTCCAATGTCGC
*
630023 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* *
630088 CATTGGCACCTCCAAGTCCAATATCGC
66 CATTGGCACCTCTAAGTCCAATGTCGC
* * *
630115 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
630180 CATTGGCACTTTCATCTTTAAGTCCAATGTCGC
66 CATTGGCAC---C-TC--TAAGTCCAATGTCGC
* * *
630213 TGGCCTTGAATCAGCACATTGGCACTTTCATC--T-AG-CCTTGAAT-TAGC--ACATTG-----
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC---AATGTAGCTGGCCTTGAATCA
* * *
630266 GCAC-TT-TCATCTTTAAGTCCAATGTCGC
63 GCACATTGGCACCTCTAAGTCCAATGTCGC
* * *
630294 TGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
630359 CATTGGCACCTTCATCTTTAAGTCCAATGTCGC
66 CATTGGCA-C--C-TC--TAAGTCCAATGTCGC
* * * *
630392 TGGCCTTGAATCAGAACATTGGCACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
630457 TATTGGCACC
66 CATTGGCACC
630467 CTCTTCATCT
Statistics
Matches: 696, Mismatches: 66, Indels: 95
0.81 0.08 0.11
Matches are distributed among these distances:
81 47 0.07
82 3 0.00
83 5 0.01
84 3 0.00
85 6 0.01
86 36 0.05
87 3 0.00
88 3 0.00
89 6 0.01
90 26 0.04
91 3 0.00
92 369 0.53
93 2 0.00
94 7 0.01
95 7 0.01
96 7 0.01
97 4 0.01
98 159 0.23
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
CATTGGCACCTCTAAGTCCAATGTCGC
Found at i:630090 original size:233 final size:232
Alignment explanation
Indices: 629401--630466 Score: 1402
Period size: 233 Copynumber: 4.6 Consensus size: 232
629391 TGTCACCTTT
* * *
629401 AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTC-TT-AGTACCAATGTCGAT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT-CCAATGTCGCT
* *
629464 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCAT
65 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC-T
* * * * * **
629529 -ATTGGCGCCTTCGTCATCTTTAAAACCCAACGTTGTTGGCCTTGTCTCAGCACATTGGCA--TT
129 CATTGGCACCTT--TAATC--CAATA-TC-AC-----TGGCCTTGAATCAGCACATTGGCACCTT
*
629591 CTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
183 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* *
629641 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
* *
629706 GCCTTGAATCAGCACATTGG------CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
66 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCTCA
* * ** * *
629765 TTAGCACTTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTCGCACCTTCATCTTTAAGTC
131 TTGGCACCTTTAA-TCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTC
629830 CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
195 CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* * * *
629868 AAGTCCAATATCGGTGGCTTTAAATCAGCATATTGGCACCTTTATCTTTAAGTCTAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
* *
629933 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCTCA
66 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCTCA
*
629998 TTGGCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
131 TTGGCACCTTTAA-TCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTC
630063 CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
195 CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
630101 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
* *
630166 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
66 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCTCA
* * *
630231 TTGGCA-C-TT--T-C---AT--CTAGCCTTGAATTAGCACATTGGCACTTTCATCTTTAAGTCC
131 TTGGCACCTTTAATCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC
* *
630286 AATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTT
196 AATGTAGCTGGCCTTGAATCAGCACATTGGCAC---C-TC--C
* *
630329 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
* * *
630394 GCCTTGAATCAGAACATTGGCACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCAT-
66 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC-TC
630458 ATTGGCACC
130 ATTGGCACC
630467 CTCTTCATCT
Statistics
Matches: 752, Mismatches: 54, Indels: 51
0.88 0.06 0.06
Matches are distributed among these distances:
222 70 0.09
224 2 0.00
225 21 0.03
226 2 0.00
227 131 0.17
228 129 0.17
229 1 0.00
231 3 0.00
232 4 0.01
233 268 0.36
234 2 0.00
235 41 0.05
240 43 0.06
241 32 0.04
242 3 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (232 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCTCA
TTGGCACCTTTAATCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC
AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:630261 original size:32 final size:32
Alignment explanation
Indices: 630215--630277 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
630205 AATGTCGCTG
630215 GCCTTGAATCAGCACATTGGCACTTTCATCTA
1 GCCTTGAATCAGCACATTGGCACTTTCATCTA
*
630247 GCCTTGAATTAGCACATTGGCACTTTCATCT
1 GCCTTGAATCAGCACATTGGCACTTTCATCT
630278 TTAAGTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
GCCTTGAATCAGCACATTGGCACTTTCATCTA
Found at i:630301 original size:81 final size:81
Alignment explanation
Indices: 630166--630326 Score: 313
Period size: 81 Copynumber: 2.0 Consensus size: 81
630156 AATGTCGCTG
630166 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
630231 TTGGCACTTTCATCTA
66 TTGGCACTTTCATCTA
*
630247 GCCTTGAATTAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
630312 TTGGCACTTTCATCT
66 TTGGCACTTTCATCT
630327 TTAAGTCCAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (81 bp):
GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
TTGGCACTTTCATCTA
Found at i:630319 original size:49 final size:49
Alignment explanation
Indices: 630247--630517 Score: 389
Period size: 49 Copynumber: 5.4 Consensus size: 49
630237 CTTTCATCTA
*
630247 GCCTTGAATTAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
*
630296 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
*
630345 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
* * * *
630394 GCCTTGAATCAGAACATTGGCACCTTCATCTTTAAGTCCAATATCGCTA
1 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
* ** *
630443 GCCTTGAATCAGCATATTGGCACCCTCTTCATCTTTAAAACCCAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCA--CT-TTCATCTTT-AAGTCCAATGTCGCTG
* *
630496 GCCCTGAATCAGCATATTGGCA
1 GCCTTGAATCAGCACATTGGCA
630518 TCGATACAAG
Statistics
Matches: 202, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
49 160 0.79
51 1 0.00
52 9 0.04
53 32 0.16
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (49 bp):
GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTG
Found at i:630329 original size:179 final size:179
Alignment explanation
Indices: 630101--630424 Score: 578
Period size: 179 Copynumber: 1.8 Consensus size: 179
630091 TGGCACCTCC
* *
630101 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCTG
* *
630166 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
66 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGAACA
*
630231 TTGGCACTTTCATCTAGCCTTGAATTAGCACATTGGCACTTTCATCTTT
131 TTGGCACCTTCATCTAGCCTTGAATTAGCACATTGGCACTTTCATCTTT
*
630280 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAAGTCCAATATCGCT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-ATCTTTAAGTCCAATATCGCT
630344 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGAAC
65 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGAAC
630409 ATTGGCACCTTCATCT
130 ATTGGCACCTTCATCT
630425 TTAAGTCCAA
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
178 4 0.03
179 134 0.97
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (179 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGAACA
TTGGCACCTTCATCTAGCCTTGAATTAGCACATTGGCACTTTCATCTTT
Found at i:630350 original size:130 final size:130
Alignment explanation
Indices: 630117--630375 Score: 466
Period size: 130 Copynumber: 2.0 Consensus size: 130
630107 AATATCGCTG
*
630117 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* *
630182 TTGGCACTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTA
66 TTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTA
*
630247 GCCTTGAATTAGCACATTGGCA-CTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAC
1 GCCTTGAATCAGCACATTGGCACCTTT-ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAC
630311 ATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
65 ATTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
630376 TTAAGTCCAA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
129 4 0.03
130 120 0.97
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (130 bp):
GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
TTGGCACTTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTA
Found at i:630586 original size:19 final size:18
Alignment explanation
Indices: 630560--630643 Score: 79
Period size: 19 Copynumber: 4.8 Consensus size: 18
630550 AATTTCAACG
630560 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
630578 ATGTTGTATCAATAC---A
1 AT-TTGTATCGATACATAA
*
630594 A--TGCATCGATACATAA
1 ATTTGTATCGATACATAA
*
630610 GTGTTGTATCGATACATAA
1 AT-TTGTATCGATACATAA
*
630629 GTTTGTATCGATACA
1 ATTTGTATCGATACA
630644 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 9 0.17
16 3 0.06
18 15 0.28
19 27 0.50
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:630773 original size:52 final size:52
Alignment explanation
Indices: 630690--630794 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
630680 CGATACATTA
***
630690 CCCAAATGTATCGATACACTGATCTTTGTATCGATACATACAGGCAAATTTG
1 CCCAAATGTATCGATACACTGATAAATGTATCGATACATACAGGCAAATTTG
* *
630742 CCCAGATGTATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAATTTG
1 CCCAAATGTATCGATACACTGAT-AAATGTATCGATACATACAGGCAAATTTG
630794 C
1 C
630795 ATATTTTAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.04
52 45 0.96
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (52 bp):
CCCAAATGTATCGATACACTGATAAATGTATCGATACATACAGGCAAATTTG
Found at i:634043 original size:9 final size:9
Alignment explanation
Indices: 634023--634109 Score: 70
Period size: 9 Copynumber: 9.4 Consensus size: 9
634013 TCTAGACCCC
634023 TTTTTGTTT
1 TTTTTGTTT
*
634032 TTTGT-TTT
1 TTTTTGTTT
* *
634040 TTTTTCTTA
1 TTTTTGTTT
* *
634049 GTTTTCTATT
1 TTTTTGT-TT
634059 TTTTTGTTT
1 TTTTTGTTT
634068 TTGTTT-TTT
1 TT-TTTGTTT
*
634077 TTTCTGTTTT
1 TTTTTG-TTT
634087 TTTTCTGTTT
1 TTTT-TGTTT
634097 TTTTTGTTT
1 TTTTTGTTT
634106 TTTT
1 TTTT
634110 CTGTATGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 9 0.14
9 30 0.48
10 22 0.35
11 2 0.03
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:634052 original size:14 final size:13
Alignment explanation
Indices: 634023--634107 Score: 70
Period size: 13 Copynumber: 6.4 Consensus size: 13
634013 TCTAGACCCC
634023 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
634036 TTTTT-TTTTCTTAG
1 TTTTTGTTTT-TT-G
*
634050 TTTTCTATTTTTTTG
1 TTTT-T-GTTTTTTG
634065 TTTTTGTTTTTT-
1 TTTTTGTTTTTTG
*
634077 TTTCTGTTTTTT-
1 TTTTTGTTTTTTG
634089 TTCTGTT-TTTTTTG
1 TT-T-TTGTTTTTTG
634103 TTTTT
1 TTTTT
634108 TTCTGTATGA
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
12 19 0.31
13 21 0.34
14 9 0.15
15 6 0.10
16 2 0.03
17 4 0.07
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:634069 original size:35 final size:31
Alignment explanation
Indices: 634023--634109 Score: 104
Period size: 35 Copynumber: 2.6 Consensus size: 31
634013 TCTAGACCCC
634023 TTTTTGTTTTTTGTTTTTTTTTCTTAGTTTTCTATT
1 TTTTTG-TTTTTGTTTTTTTTTC-T-GTTTT-T-TT
634059 TTTTTGTTTTTGTTTTTTTTTCTGTTTTTTT
1 TTTTTGTTTTTGTTTTTTTTTCTGTTTTTTT
634090 TCTGTTT-TTTTTGTTTTTTT
1 T-T-TTTGTTTTTGTTTTTTT
634110 CTGTATGAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
31 3 0.06
32 15 0.31
33 8 0.16
34 1 0.02
35 16 0.33
36 6 0.12
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (31 bp):
TTTTTGTTTTTGTTTTTTTTTCTGTTTTTTT
Found at i:636207 original size:20 final size:20
Alignment explanation
Indices: 636184--636256 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
636174 ACAATTCAAA
636184 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
636204 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
636225 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
636245 GTATCGATACAT
1 GTATCGATACAT
636257 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:636228 original size:21 final size:21
Alignment explanation
Indices: 636202--636277 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
636192 ACATGTTGCA
636202 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
636223 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
636243 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
636264 ATGTATCGATACAT
1 ATGTATCGATACAT
636278 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:636235 original size:41 final size:41
Alignment explanation
Indices: 636184--636277 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
636174 ACAATTCAAA
*
636184 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
636225 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
636266 GTATCGATACAT
1 GTATCGATACAT
636278 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:640423 original size:15 final size:15
Alignment explanation
Indices: 640403--640433 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
640393 TAAAAATGTC
*
640403 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
640418 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
640433 C
1 C
640434 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:642318 original size:13 final size:13
Alignment explanation
Indices: 642300--642338 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
642290 ACATTTTTCC
642300 TTGTATCGATACA
1 TTGTATCGATACA
642313 TTGTATCGATACA
1 TTGTATCGATACA
*
642326 CTGTATCGATACA
1 TTGTATCGATACA
642339 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:644169 original size:34 final size:34
Alignment explanation
Indices: 644131--644226 Score: 178
Period size: 32 Copynumber: 2.9 Consensus size: 34
644121 AATTTTGATA
644131 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
644165 TGAATTACTTGATTAAGGGGGAGA--TTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
644197 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
644227 AATAAACGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
32 32 0.53
34 28 0.47
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (34 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
Found at i:644870 original size:20 final size:20
Alignment explanation
Indices: 644847--644919 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
644837 ACAATTCAAA
644847 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
644867 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
644888 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
644908 GTATCGATACAT
1 GTATCGATACAT
644920 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:644891 original size:21 final size:21
Alignment explanation
Indices: 644865--644940 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
644855 ACATGTTGCA
644865 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
644886 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
644906 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
644927 ATGTATCGATACAT
1 ATGTATCGATACAT
644941 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:644898 original size:41 final size:41
Alignment explanation
Indices: 644847--644940 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
644837 ACAATTCAAA
*
644847 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
644888 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
644929 GTATCGATACAT
1 GTATCGATACAT
644941 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:653699 original size:22 final size:23
Alignment explanation
Indices: 653671--653715 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
653661 AAAAATAATG
*
653671 AGAATGAATAGCAA-CAAAAAAA
1 AGAATGAACAGCAATCAAAAAAA
*
653693 AGAATGAACATCAATCAAAAAAA
1 AGAATGAACAGCAATCAAAAAAA
653716 GAGTGGCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (23 bp):
AGAATGAACAGCAATCAAAAAAA
Found at i:657971 original size:20 final size:20
Alignment explanation
Indices: 657945--657999 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
657935 AAAAAGACAG
*
657945 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
657965 CATGTATCGATGCATTGAAA
1 AATGTATCGATACATTCAAA
*
657985 AACGTATCGATACAT
1 AATGTATCGATACAT
658000 CTGGGTAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:658395 original size:72 final size:72
Alignment explanation
Indices: 658255--658395 Score: 239
Period size: 72 Copynumber: 2.0 Consensus size: 72
658245 GCCAATTTTT
* *
658255 GACAACTTGAAGCCTAGCTAGTAGGTGGAGGATTGGACATATGTGGAGACGAATTCGCCGGGCGC
1 GACAACTTAAAGCCTAGCTAGTAGGTGGAGGATTGGACATATGTGGAGACGAATTCGCCGGGCAC
658320 CGTTATC
66 CGTTATC
*
658327 GACAACTTAAAGCCTAGCTAGTAGGTGGAGGATTGGACATATGTGGGGACGAATTCGCCAGGG-A
1 GACAACTTAAAGCCTAGCTAGTAGGTGGAGGATTGGACATATGTGGAGACGAATTCGCC-GGGCA
658391 CCGTT
65 CCGTT
658396 GGCGCCCGGC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 62 0.95
73 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.22
Consensus pattern (72 bp):
GACAACTTAAAGCCTAGCTAGTAGGTGGAGGATTGGACATATGTGGAGACGAATTCGCCGGGCAC
CGTTATC
Found at i:658653 original size:13 final size:13
Alignment explanation
Indices: 658635--658692 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
658625 TACATAAGTG
658635 TGTATCGATACAA
1 TGTATCGATACAA
658648 TGTATCGATACATAA
1 TGTATCGATAC--AA
658663 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
658680 TGTATCGCTACAA
1 TGTATCGATACAA
658693 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:658653 original size:31 final size:32
Alignment explanation
Indices: 658615--658691 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
658605 ACAAACAGTA
658615 AATGTATCGATACATAAG-TGTGTATCGATAC
1 AATGTATCGATACATAAGTTGTGTATCGATAC
*
658646 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTGTGTATCGATAC
*
658678 AATGTATCGCTACA
1 AATGTATCGATACA
658692 AAGCTACTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
AATGTATCGATACATAAGTTGTGTATCGATAC
Found at i:661168 original size:51 final size:49
Alignment explanation
Indices: 661112--661349 Score: 219
Period size: 51 Copynumber: 4.6 Consensus size: 49
661102 TTAAGTTTCT
* * *
661112 CAATTTTGCATAATCTGGGGTATTCCAACCCCGGTTTTATTTCTAG-AACAC
1 CAATTTT-CACAATC-GGGGTACTCCAACCCCGATTTTATTT-TAGAAACAC
* * *
661163 TAATTTTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTTGAAACAC
1 CAATTTTC-ACAATCGGGG-TACTCCAACCCCGATTTTATTTTAGAAACAC
* *
661214 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTTCA-AAGCAC
1 CAA-TTTTCACAATCG-GGGTACTCCAACCCCGATTTTATTTT-AGAAACAC
* * * * *
661265 CAATTTTCTATAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTC-ACAATCG-GGGTACTCCAACCCCGATTTTATTT-TAGAAACAC
*
661317 CAATTTTTCACAATCGAGGATACTCCAACCCCG
1 CAA-TTTTCACAATCG-GGGTACTCCAACCCCG
661350 TTAATCATTG
Statistics
Matches: 160, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
50 12 0.08
51 106 0.66
52 37 0.23
53 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (49 bp):
CAATTTTCACAATCGGGGTACTCCAACCCCGATTTTATTTTAGAAACAC
Found at i:661288 original size:102 final size:103
Alignment explanation
Indices: 661135--661349 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 103
661125 TCTGGGGTAT
* * *
661135 TCCAACCCCGGTTTTATTTCTAGAACACTAATTTTCTACAATCGGGGATACTCCAACTCCGATTT
1 TCCAACCCCGATTTTATTTCTAGAACACCAATTTTCTACAATCGAGGATACTCCAACTCCGATTT
***
661200 TATTT-TTGAAACACCAATTTTTCACAATCGAGGATAC
66 TATTTCCAAAAACACCAATTTTTCACAATCGAGGATAC
*
661237 TCCAACCCCGATTTTATTT-TCA-AAGCACCAATTTTCTATAATCGAGGATACTCCAACTCCGAT
1 TCCAACCCCGATTTTATTTCT-AGAA-CACCAATTTTCTACAATCGAGGATACTCCAACTCCGAT
661300 TTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATAC
64 TTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATAC
661340 TCCAACCCCG
1 TCCAACCCCG
661350 TTAATCATTG
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
101 3 0.03
102 61 0.59
103 39 0.38
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (103 bp):
TCCAACCCCGATTTTATTTCTAGAACACCAATTTTCTACAATCGAGGATACTCCAACTCCGATTT
TATTTCCAAAAACACCAATTTTTCACAATCGAGGATAC
Found at i:661399 original size:28 final size:26
Alignment explanation
Indices: 661334--661401 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
661324 TCACAATCGA
661334 GGATACTCCAACCCCGTTAATCATTGG
1 GGATACTCCAACCCCGTTAATCA-TGG
*
661361 GGATACTCCAACCCCGTTATTTTCGA-GG
1 GGATACTCCAACCCCGTTA--ATC-ATGG
661389 GGATACTCCAACC
1 GGATACTCCAACC
661402 TCGGCTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 19 0.51
28 15 0.41
29 2 0.05
30 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (26 bp):
GGATACTCCAACCCCGTTAATCATGG
Found at i:661442 original size:79 final size:79
Alignment explanation
Indices: 661359--661562 Score: 318
Period size: 79 Copynumber: 2.6 Consensus size: 79
661349 GTTAATCATT
* *
661359 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAATATT
*
661424 GATTTCTCATAATC
66 GATTTCTCACAATC
* * * *
661438 GGGGATACTCCAACCTCGTTATTTACGAGGGGATACTCAAACCCCGATTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAATATT
661503 GATTTCTCACAATC
66 GATTTCTCACAATC
* * *
661517 AGGGATACTCCAACCCCGTTTTTTTCGCGGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
661563 TTATTTTTGA
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 112 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAATATT
GATTTCTCACAATC
Found at i:661558 original size:28 final size:28
Alignment explanation
Indices: 661518--661588 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
661508 CTCACAATCA
*
661518 GGGATACTCCAACCCCGTT-TTTTTCGCG
1 GGGATACTCCAACCCCGTTATTTTT-GAG
661546 GGGATACTCCAACCCCGTTATTTTTGAG
1 GGGATACTCCAACCCCGTTATTTTTGAG
661574 GGGATACTCCAACCC
1 GGGATACTCCAACCC
661589 TGATTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 36 0.88
29 5 0.12
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.28
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTTTGAG
Found at i:661628 original size:107 final size:107
Alignment explanation
Indices: 661437--661669 Score: 274
Period size: 107 Copynumber: 2.2 Consensus size: 107
661427 TTCTCATAAT
* * *
661437 CGGGGATACTCCAACCTCGTTATTTACGAGGGGATACTCAAACCCCGATTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTACGAGGGGATACTCAAACCCCGATTTTATTCCTAAAACAC
** * *
661502 TGATTTCTCACAATCAGGGATACTCCAACCCCGTT-TTTTTCG
66 CAATTTCTCACAATCAGGGATACTCCAACCCCGTTATTTCT-A
** * * *
661544 CGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATT-TTCAAAACA
1 CGGGGATACTCCAACCCCGTTATTTACGAGGGGATACTCAAACCCCGATTTTATTCCT-AAAACA
* * *
661608 CCAATTT-TCTATAATTAGGGATACTCCAACCCTGTTATTTCTA
65 CCAATTTCTC-ACAATCAGGGATACTCCAACCCCGTTATTTCTA
*
661651 AGGGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCG
661670 ATTTTATTTC
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
106 3 0.03
107 100 0.93
108 4 0.04
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (107 bp):
CGGGGATACTCCAACCCCGTTATTTACGAGGGGATACTCAAACCCCGATTTTATTCCTAAAACAC
CAATTTCTCACAATCAGGGATACTCCAACCCCGTTATTTCTA
Found at i:661629 original size:79 final size:79
Alignment explanation
Indices: 661546--661721 Score: 235
Period size: 79 Copynumber: 2.2 Consensus size: 79
661536 TTTTTTCGCG
* * * *
661546 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTTCAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* *
661611 ATTTTCTATAATTA
66 ATTTTCCATAATCA
* * * *
661625 GGGATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAGAACATCG
1 GGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
661690 ATTTTCCATAATCA
66 ATTTTCCATAATCA
* * *
661704 GGGGTACTGCAGCCCCGT
1 GGGATACTCCAACCCCGT
661722 CGTCATCTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
ATTTTCCATAATCA
Found at i:661705 original size:186 final size:185
Alignment explanation
Indices: 661282--661721 Score: 477
Period size: 186 Copynumber: 2.4 Consensus size: 185
661272 CTATAATCGA
* * * *
661282 GGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATC-GAGGATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACATCGATTTTCCACAATCAG-GGATACTCCAAC
*
661346 CCCGTTAATCATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGCTTTA
65 CCCGTT-ATCATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTA
* *** * *
661411 TTCCTAAAATATTGATTTCTCATAATCGGGGATACTCCAACCTCGTTATTTACGAGG
129 TTCCTAAAACACCAATTTCTCATAATCAGGGATACTCCAACCTCGTTATTTACAAGG
* * * *
661468 GGATACTCAAACCCCGATTTTA-TTCCTAAAATATTGA-TTTCTCACAATCAGGGATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACATCGATTTTC-CACAATCAGGGATACTCCAAC
** * *
661531 CCCGTT-TTTTTCGCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACC-CTGATT
65 CCCGTTATCATT---GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTC-GACT
* *
661594 TTATT-TTCAAAACACCAATTT-TCTATAATTAGGGATACTCCAACC-CTGTTATTT-CTAAGG
126 TTATTCCT-AAAACACCAATTTCTC-ATAATCAGGGATACTCCAACCTC-GTTATTTAC-AAGG
* * * * *
661654 GGATACTCCAACCCCGATTTTATTTCC-AGAACATCGATTTTCCATAATCAGGGGTACTGCAGCC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACATCGATTTTCCACAATCAGGGATACTCCAACC
661718 CCGT
66 CCGT
661722 CGTCATCTCC
Statistics
Matches: 213, Mismatches: 29, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
183 3 0.01
184 3 0.01
185 41 0.19
186 158 0.74
187 8 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (185 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAAACATCGATTTTCCACAATCAGGGATACTCCAACC
CCGTTATCATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATT
CCTAAAACACCAATTTCTCATAATCAGGGATACTCCAACCTCGTTATTTACAAGG
Found at i:663486 original size:13 final size:13
Alignment explanation
Indices: 663468--663494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
663458 TATAATGATC
663468 ATGTATCGATACA
1 ATGTATCGATACA
663481 ATGTATCGATACA
1 ATGTATCGATACA
663494 A
1 A
663495 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:663830 original size:2 final size:2
Alignment explanation
Indices: 663823--663851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
663813 GCATATAAAC
663823 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 A
663852 AATAAGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:664196 original size:24 final size:23
Alignment explanation
Indices: 664160--664205 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
664150 AAGTATATTA
*
664160 ATTTTTTTATTATTTAATTAAAT
1 ATTTTTTTATTATATAATTAAAT
* *
664183 ATTTTTATTTTTATATATTTAAA
1 ATTTTT-TTATTATATAATTAAA
664206 GTTAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTTATTATATAATTAAAT
Found at i:664309 original size:12 final size:12
Alignment explanation
Indices: 664292--664316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
664282 TATGTAAATT
664292 TAAATTTTTAAA
1 TAAATTTTTAAA
664304 TAAATTTTTAAA
1 TAAATTTTTAAA
664316 T
1 T
664317 TTTAAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATTTTTAAA
Found at i:664979 original size:6 final size:6
Alignment explanation
Indices: 664968--664995 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
664958 ATTGTGGCAA
664968 ATGGCG ATGGCG ATGGCG ATGGCG ATGG
1 ATGGCG ATGGCG ATGGCG ATGGCG ATGG
664996 AAATGGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.50, T:0.18
Consensus pattern (6 bp):
ATGGCG
Found at i:665001 original size:18 final size:17
Alignment explanation
Indices: 664968--665006 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
664958 ATTGTGGCAA
**
664968 ATGGCGATGGCGATGGC
1 ATGGCGATGGAAATGGC
664985 GATGGCGATGGAAATGGC
1 -ATGGCGATGGAAATGGC
665003 ATGG
1 ATGG
665007 GCATAGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.23, C:0.13, G:0.46, T:0.18
Consensus pattern (17 bp):
ATGGCGATGGAAATGGC
Found at i:669292 original size:24 final size:25
Alignment explanation
Indices: 669265--669311 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
669255 ATTTCAATCA
669265 AGAAAATT-ACAAAAGATA-AAATAT
1 AGAAAATTGACAAAA-ATATAAATAT
*
669289 AGAACATTGACAAAAATATAAAT
1 AGAAAATTGACAAAAATATAAAT
669312 TAAGAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (25 bp):
AGAAAATTGACAAAAATATAAATAT
Found at i:669317 original size:25 final size:23
Alignment explanation
Indices: 669264--669317 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
669254 CATTTCAATC
669264 AAGAAAATTACAAAAGATAAAAT
1 AAGAAAATTACAAAAGATAAAAT
*
669287 ATAGAACATTGACAAAA-ATATAAATT
1 A-AGAAAATT-ACAAAAGATA-AAA-T
669313 AAGAA
1 AAGAA
669318 TATTTATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 10 0.38
25 13 0.50
26 2 0.08
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (23 bp):
AAGAAAATTACAAAAGATAAAAT
Found at i:670086 original size:20 final size:20
Alignment explanation
Indices: 670063--670135 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
670053 ACAATTCAAA
670063 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
670083 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
670104 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
670124 GTATCGATACAT
1 GTATCGATACAT
670136 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:670107 original size:21 final size:21
Alignment explanation
Indices: 670081--670156 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
670071 ACATGTTGCA
670081 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
670102 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
670122 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
670143 ATGTATCGATACAT
1 ATGTATCGATACAT
670157 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:670114 original size:41 final size:41
Alignment explanation
Indices: 670063--670156 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
670053 ACAATTCAAA
*
670063 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
670104 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
670145 GTATCGATACAT
1 GTATCGATACAT
670157 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:670213 original size:13 final size:13
Alignment explanation
Indices: 670195--670220 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
670185 TACAGCAAGT
670195 ATGTATCGATACA
1 ATGTATCGATACA
670208 ATGTATCGATACA
1 ATGTATCGATACA
670221 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:674294 original size:15 final size:15
Alignment explanation
Indices: 674274--674312 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
674264 TAAAAATGTC
*
674274 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
674289 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
674304 CCAAATGAA
1 CAAAATGAA
674313 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:676397 original size:20 final size:21
Alignment explanation
Indices: 676318--676396 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
676308 AATGTCCAAA
*
676318 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
676338 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
676363 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
676383 TTGTATCGATACAT
1 ATGTATCGATACAT
676397 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:676401 original size:13 final size:13
Alignment explanation
Indices: 676383--676421 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
676373 ACATTTTTCT
676383 TTGTATCGATACA
1 TTGTATCGATACA
676396 TTGTATCGATACA
1 TTGTATCGATACA
*
676409 CTGTATCGATACA
1 TTGTATCGATACA
676422 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:678896 original size:20 final size:20
Alignment explanation
Indices: 678873--678945 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
678863 ACAATTCAAA
678873 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
678893 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
678914 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
678934 GTATCGATACAT
1 GTATCGATACAT
678946 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:678917 original size:21 final size:21
Alignment explanation
Indices: 678891--678966 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
678881 ACATGTTGCA
678891 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
678912 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
678932 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
678953 ATGTATCGATACAT
1 ATGTATCGATACAT
678967 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:678924 original size:41 final size:41
Alignment explanation
Indices: 678873--678966 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
678863 ACAATTCAAA
*
678873 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
678914 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
678955 GTATCGATACAT
1 GTATCGATACAT
678967 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:679023 original size:13 final size:13
Alignment explanation
Indices: 679005--679030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
678995 TACAGCAAGT
679005 ATGTATCGATACA
1 ATGTATCGATACA
679018 ATGTATCGATACA
1 ATGTATCGATACA
679031 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:680013 original size:16 final size:16
Alignment explanation
Indices: 679994--680030 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
679984 TCGAATTTAG
679994 GTTATTTTAGGTTCAA
1 GTTATTTTAGGTTCAA
680010 GTTATTTTAGGTTCAA
1 GTTATTTTAGGTTCAA
*
680026 TTTAT
1 GTTAT
680031 CATAGATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.54
Consensus pattern (16 bp):
GTTATTTTAGGTTCAA
Found at i:681572 original size:14 final size:16
Alignment explanation
Indices: 681541--681587 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
681531 TGGAAAAGTC
681541 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
681557 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
681571 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
681587 A
1 A
681588 TAAAAAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:683121 original size:28 final size:28
Alignment explanation
Indices: 682985--683598 Score: 759
Period size: 28 Copynumber: 22.0 Consensus size: 28
682975 CCACGATTTA
*
682985 GTGGCATTCCTTTTTAAGTCCACAACTCC
1 GTGGCA-TCCTTTTAAAGTCCACAACTCC
* * * * *
683014 GTGGTAACCCTTT-AAGTCCATAACTCT
1 GTGGCATCCTTTTAAAGTCCACAACTCC
* * *
683041 GTGGCACCCTTTT-AAGTCCACAGCTCT
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683068 GTGGCAACCTTTT-AAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
683095 GTGGCATCCTTTTAAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683123 ATGGCATCCTTTT-AAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683150 TGTGGCAACCTTTTAAAGTCCACAACTCC
1 -GTGGCATCCTTTTAAAGTCCACAACTCC
*
683179 GTGGCATCCTTTTAAAGTACACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683207 GTGACATCCTTTT-AAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683234 GTGGCATCCTTTTAAAGTCTACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
683262 GTGGCATCCTTTTAAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
683290 GTGGCAACCTGGCATCCTTTT-AAGTCCACAACTCC
1 ---G-----TGGCATCCTTTTAAAGTCCACAACTCC
683325 GTGGCATCCTTTTAAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
* * *
683353 ATGGAATCCTTTTAAAGTCCACAACTCT
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683381 GTGGCAACCTTTT-AAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
683408 GTGGGCATCCTTTTAAAGTCCACAACTCC
1 GT-GGCATCCTTTTAAAGTCCACAACTCC
* * *
683437 GTGGGCATCCTTTTAAAGTCCATAATTTC
1 GT-GGCATCCTTTTAAAGTCCACAACTCC
*
683466 GTGGCATCCTTTTAAAGTCTACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
683494 GTGGCATCCTTTTAAAGT---C--C-CC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
* * *
683516 ATGGCAACCATTTAAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
683544 GTAGCATCCTTTTAAAGTCCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
* * *
683572 GTGGTATCCTTTTTAAGTCCATAACTC
1 GTGGCATCCTTTTAAAGTCCACAACTC
683599 TCTAGTCTGG
Statistics
Matches: 514, Mismatches: 50, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
22 17 0.03
23 1 0.00
25 2 0.00
27 137 0.27
28 268 0.52
29 61 0.12
31 1 0.00
32 1 0.00
35 14 0.03
36 12 0.02
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (28 bp):
GTGGCATCCTTTTAAAGTCCACAACTCC
Found at i:683322 original size:35 final size:36
Alignment explanation
Indices: 683263--683330 Score: 129
Period size: 35 Copynumber: 1.9 Consensus size: 36
683253 TACAACTCCG
683263 TGGCATCCTTTTAAAGTCCACAACTCCGTGGCAACC
1 TGGCATCCTTTTAAAGTCCACAACTCCGTGGCAACC
683299 TGGCATCCTTTT-AAGTCCACAACTCCGTGGCA
1 TGGCATCCTTTTAAAGTCCACAACTCCGTGGCA
683331 TCCTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (36 bp):
TGGCATCCTTTTAAAGTCCACAACTCCGTGGCAACC
Done.