Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1507
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: 297493
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:171264 original size:13 final size:13
Alignment explanation
Indices: 171246--171270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171236 ATAATGCATA
171246 GTATCGATACATT
1 GTATCGATACATT
171259 GTATCGATACAT
1 GTATCGATACAT
171271 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:171376 original size:19 final size:20
Alignment explanation
Indices: 171352--171403 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
171342 CTTAACTGTT
*
171352 TGTATCGATACAT-ACAAGA
1 TGTATCGATACATCACAAAA
*
171371 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
171391 TGTATCGATACAT
1 TGTATCGATACAT
171404 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:172974 original size:13 final size:13
Alignment explanation
Indices: 172956--172980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172946 AGATTGCACA
172956 GTATCGATACATT
1 GTATCGATACATT
172969 GTATCGATACAT
1 GTATCGATACAT
172981 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:172993 original size:20 final size:21
Alignment explanation
Indices: 172968--173020 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
172958 ATCGATACAT
*
172968 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
172988 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
173009 TGTATCGATACA
1 TGTATCGATACA
173021 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:173143 original size:10 final size:10
Alignment explanation
Indices: 173128--173161 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
173118 TCGATACATT
173128 GGCTTGTAAC
1 GGCTTGTAAC
173138 GGCTTGTAAC
1 GGCTTGTAAC
*
173148 GGCTAGTAAC
1 GGCTTGTAAC
173158 GGCT
1 GGCT
173162 ATATTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (10 bp):
GGCTTGTAAC
Found at i:179303 original size:13 final size:13
Alignment explanation
Indices: 179285--179322 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
179275 CAGCATTCTC
*
179285 TGTATCGATACAT
1 TGTATCGATACAG
179298 TGTATCGATACAG
1 TGTATCGATACAG
179311 TGTATCGATACA
1 TGTATCGATACA
179323 AAGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:181789 original size:13 final size:13
Alignment explanation
Indices: 181771--181795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
181761 AGATTGCACA
181771 GTATCGATACATT
1 GTATCGATACATT
181784 GTATCGATACAT
1 GTATCGATACAT
181796 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:181917 original size:32 final size:33
Alignment explanation
Indices: 181876--181943 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
181866 CCTTAACTGT
**
181876 TTGTATCGATACA-CACATTATGTATCCATACA
1 TTGTATCGATACATCACAAAATGTATCCATACA
* *
181908 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCCATACA
181941 TTG
1 TTG
181944 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCCATACA
Found at i:189780 original size:13 final size:13
Alignment explanation
Indices: 189762--189787 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189752 CAATTTTTTG
189762 TGTATCGATACAT
1 TGTATCGATACAT
189775 TGTATCGATACAT
1 TGTATCGATACAT
189788 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:189873 original size:20 final size:20
Alignment explanation
Indices: 189848--189920 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
189838 ATCTTTTTTT
189848 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
189868 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
189889 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
189909 ATGTATCGATAC
1 ATGTATCGATAC
189921 TTTGAGTTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:189899 original size:41 final size:42
Alignment explanation
Indices: 189826--189920 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
189816 CTGCCAAGAA
*
189826 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
189868 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
189909 ATGTATCGATAC
1 ATGTATCGATAC
189921 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:190557 original size:16 final size:16
Alignment explanation
Indices: 190526--190571 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
190516 CTCTCCTTTG
190526 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
190544 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
190560 TCTCCCCCTTAA
1 TCTCCCCCTTAA
190572 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:192394 original size:13 final size:13
Alignment explanation
Indices: 192376--192414 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
192366 ATAATCACCC
*
192376 TGTATCGATACAG
1 TGTATCGATACAA
192389 TGTATCGATACAA
1 TGTATCGATACAA
192402 TGTATCGATACAA
1 TGTATCGATACAA
192415 CAAAAAATGT
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:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:192425 original size:20 final size:20
Alignment explanation
Indices: 192400--192478 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
192390 GTATCGATAC
192400 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
192420 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
192445 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
192464 ACATGTATCGATACA
1 A-ATGTATCGATACA
192479 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:194507 original size:15 final size:15
Alignment explanation
Indices: 194487--194517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
194477 ATTTCGTTTG
*
194487 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
194502 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
194517 G
1 G
194518 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:198597 original size:13 final size:13
Alignment explanation
Indices: 198579--198604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198569 CAATTTTTTG
198579 TGTATCGATACAT
1 TGTATCGATACAT
198592 TGTATCGATACAT
1 TGTATCGATACAT
198605 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:198690 original size:20 final size:20
Alignment explanation
Indices: 198665--198737 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
198655 ATCTTTTTTT
198665 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
198685 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
198706 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
198726 ATGTATCGATAC
1 ATGTATCGATAC
198738 TTTGAGTTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:198716 original size:41 final size:42
Alignment explanation
Indices: 198643--198737 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
198633 CTGCCAAGAA
*
198643 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
198685 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
198726 ATGTATCGATAC
1 ATGTATCGATAC
198738 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:199483 original size:16 final size:16
Alignment explanation
Indices: 199464--199494 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
199454 TGATTAAAAG
*
199464 AAATTGTTAATTTGCA
1 AAATTGTTAAATTGCA
199480 AAATTGTTAAATTGC
1 AAATTGTTAAATTGC
199495 TTTATTAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (16 bp):
AAATTGTTAAATTGCA
Found at i:200095 original size:13 final size:13
Alignment explanation
Indices: 200077--200101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200067 ATAATGCACA
200077 GTATCGATACATT
1 GTATCGATACATT
200090 GTATCGATACAT
1 GTATCGATACAT
200102 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:200114 original size:20 final size:21
Alignment explanation
Indices: 200089--200141 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
200079 ATCGATACAT
**
200089 TGTATCGATACATG-ACCAAA
1 TGTATCGATACATGCAAAAAA
*
200109 TGTATCGATACTTGCAAAAAA
1 TGTATCGATACATGCAAAAAA
200130 TGTATCGATACA
1 TGTATCGATACA
200142 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAAAA
Found at i:200219 original size:13 final size:13
Alignment explanation
Indices: 200201--200226 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200191 TACACACAAG
200201 ATGTATCGATACA
1 ATGTATCGATACA
200214 ATGTATCGATACA
1 ATGTATCGATACA
200227 TCCCAAAATG
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:209367 original size:13 final size:13
Alignment explanation
Indices: 209349--209374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
209339 AATTTTTTGG
209349 TGTATCGATACAT
1 TGTATCGATACAT
209362 TGTATCGATACAT
1 TGTATCGATACAT
209375 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:209469 original size:20 final size:20
Alignment explanation
Indices: 209443--209499 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
209433 TACATCTTTT
209443 TCATGTATCGATACTTTGCAA
1 TCATGTATCGATACTTTG-AA
209464 -CATGTATCGATACTTTGAA
1 TCATGTATCGATACTTTGAA
209483 TTC-TGTATCGATACTTT
1 -TCATGTATCGATACTTT
209500 TAAGGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.06
20 31 0.91
21 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:211474 original size:21 final size:20
Alignment explanation
Indices: 211445--211487 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
211435 GGCTAGTGTG
*
211445 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
211466 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
211486 GG
1 GG
211488 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:211947 original size:13 final size:13
Alignment explanation
Indices: 211929--211966 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
211919 ATAATCCCCC
*
211929 TGTATCGATACAG
1 TGTATCGATACAA
*
211942 TGTATCAATACAA
1 TGTATCGATACAA
211955 TGTATCGATACA
1 TGTATCGATACA
211967 TTGAATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:218174 original size:32 final size:34
Alignment explanation
Indices: 218108--218176 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
218098 CGTTACAAGC
** *
218108 CAATGTATCGATACAATTTTTTGGTGTATTGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
218142 CAATGTATCGATAC-A-TACTTGGTGTATCGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
218174 CAA
1 CAA
218177 GTTTGGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 1 0.03
34 14 0.44
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (34 bp):
CAATGTATCGATACAATTACTTGGTGTATCGATA
Found at i:219291 original size:51 final size:51
Alignment explanation
Indices: 219234--219376 Score: 223
Period size: 51 Copynumber: 2.8 Consensus size: 51
219224 TTTTAACTAG
* * *
219234 ATGTATCAATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
* * *
219285 ATGTATCGATACATTGAAGAATATATCGATACATCTGGGTAAAAGGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
*
219336 ATGTATCGATACATTGAAGAATGTTTCGATACATCTGGGTA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTA
219377 CCTTTCCATA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:221397 original size:13 final size:13
Alignment explanation
Indices: 221379--221403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221369 ATAATGCATA
221379 GTATCGATACATT
1 GTATCGATACATT
221392 GTATCGATACAT
1 GTATCGATACAT
221404 GACCACTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:221535 original size:33 final size:32
Alignment explanation
Indices: 221474--221539 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
221464 TTAACTGTTC
*
221474 GTATCGATACATACAAGATGTATCGATACATT
1 GTATAGATACATACAAGATGTATCGATACATT
*
221506 GTATAGATACATGACCAA-ATGTATTGATACATT
1 GTATAGATACAT-A-CAAGATGTATCGATACATT
221539 G
1 G
221540 GCTTGTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 11 0.37
33 16 0.53
34 3 0.10
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
GTATAGATACATACAAGATGTATCGATACATT
Found at i:227752 original size:13 final size:13
Alignment explanation
Indices: 227730--227760 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
227720 CTCTGCATCA
*
227730 ATACATTGTATCG
1 ATACAGTGTATCG
227743 ATACAGTGTATCG
1 ATACAGTGTATCG
227756 ATACA
1 ATACA
227761 AAAGGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATACAGTGTATCG
Found at i:230261 original size:13 final size:13
Alignment explanation
Indices: 230243--230267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230233 ATAATGCATA
230243 GTATCGATACATT
1 GTATCGATACATT
230256 GTATCGATACAT
1 GTATCGATACAT
230268 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:230400 original size:33 final size:32
Alignment explanation
Indices: 230339--230402 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
230329 TAACTATTTG
230339 TATCGATACATACAAGATGTATCAATACATTA
1 TATCGATACATACAAGATGTATCAATACATTA
*
230371 TATCGATACATGACCAA-ATGTATCGATACATT
1 TATCGATACAT-A-CAAGATGTATCAATACATT
230403 GGCTTGTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.38
33 15 0.52
34 3 0.10
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (32 bp):
TATCGATACATACAAGATGTATCAATACATTA
Found at i:232464 original size:20 final size:20
Alignment explanation
Indices: 232441--232513 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
232431 ACAATTCAAA
232441 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
232461 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
232482 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
232502 GTATCGATACAT
1 GTATCGATACAT
232514 AAAAAAAGAT
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:232492 original size:41 final size:42
Alignment explanation
Indices: 232441--232535 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
232431 ACAATTCAAA
*
232441 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
232482 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
232524 GTATCGATACAT
1 GTATCGATACAT
232536 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:232592 original size:13 final size:13
Alignment explanation
Indices: 232574--232599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232564 TACAGCAAGT
232574 ATGTATCGATACA
1 ATGTATCGATACA
232587 ATGTATCGATACA
1 ATGTATCGATACA
232600 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:232927 original size:23 final size:22
Alignment explanation
Indices: 232901--232943 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
232891 TTTGTTTATA
232901 TTGTCATTATT-TTTCTAAGCTCT
1 TTGT-ATTATTATTTC-AAGCTCT
*
232924 TTGTATTCTTATTTCAAGCT
1 TTGTATTATTATTTCAAGCT
232944 TAAATTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGTATTATTATTTCAAGCTCT
Found at i:236682 original size:15 final size:15
Alignment explanation
Indices: 236662--236692 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
236652 TAAAAATGTC
*
236662 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
236677 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
236692 C
1 C
236693 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:238777 original size:20 final size:21
Alignment explanation
Indices: 238707--238784 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
238697 ATGTCCAAAA
*
238707 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
238727 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
238751 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
*
238772 TGTATCAATACAT
1 TGTATCGATACAT
238785 TGTATCGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 26 0.58
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.29
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:238789 original size:13 final size:13
Alignment explanation
Indices: 238771--238809 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
238761 ACATTTTTTG
*
238771 TTGTATCAATACA
1 TTGTATCGATACA
238784 TTGTATCGATACA
1 TTGTATCGATACA
*
238797 CTGTATCGATACA
1 TTGTATCGATACA
238810 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:240505 original size:36 final size:36
Alignment explanation
Indices: 240458--240530 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
240448 GGGGAGATTT
240458 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
1 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
240494 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
1 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
240530 A
1 A
240531 ATTACCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.36, T:0.16
Consensus pattern (36 bp):
ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
Found at i:241139 original size:20 final size:20
Alignment explanation
Indices: 241116--241188 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
241106 ACAATTCAAA
241116 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
241136 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
241157 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
241177 GTATCGATACAT
1 GTATCGATACAT
241189 AAAAAAAGAT
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:241167 original size:41 final size:42
Alignment explanation
Indices: 241116--241210 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
241106 ACAATTCAAA
*
241116 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
241157 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
241199 GTATCGATACAT
1 GTATCGATACAT
241211 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:241267 original size:13 final size:13
Alignment explanation
Indices: 241249--241274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
241239 TACAGCAAGT
241249 ATGTATCGATACA
1 ATGTATCGATACA
241262 ATGTATCGATACA
1 ATGTATCGATACA
241275 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:241602 original size:23 final size:22
Alignment explanation
Indices: 241576--241618 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
241566 TTTGTTTATA
241576 TTGTCATTATT-TTTCTAAGCTCT
1 TTGT-ATTATTATTTC-AAGCTCT
*
241599 TTGTATTCTTATTTCAAGCT
1 TTGTATTATTATTTCAAGCT
241619 TAAATTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGTATTATTATTTCAAGCTCT
Found at i:246209 original size:47 final size:47
Alignment explanation
Indices: 246156--246266 Score: 161
Period size: 47 Copynumber: 2.3 Consensus size: 47
246146 TTGAGTGTAT
246156 CTGGTCAAACTTTTTCTACCCTTGTTTGACTATATTGGCATTAGAAC
1 CTGGTCAAACTTTTTCTACCCTTGTTTGACTATATTGGCATTAGAAC
* * * *
246203 TTGGTCAAACTCTTTT-TACTCTTGTTTGATTATATTGGCATTAGGAC
1 CTGGTCAAACT-TTTTCTACCCTTGTTTGACTATATTGGCATTAGAAC
246250 CTGGTCAAACTTATTTC
1 CTGGTCAAACTT-TTTC
246267 CATCATCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
46 1 0.02
47 51 0.91
48 4 0.07
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (47 bp):
CTGGTCAAACTTTTTCTACCCTTGTTTGACTATATTGGCATTAGAAC
Found at i:246359 original size:130 final size:130
Alignment explanation
Indices: 246120--246815 Score: 733
Period size: 130 Copynumber: 5.3 Consensus size: 130
246110 TTGACTGTGT
* * * * * *
246120 CTAGTGAAACTTGTTTCCATCATCATTTGAGTGTATCTGGTCAAACTTTTTCTACCCTTGTTTGA
1 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
* * * * **
246185 CTATATTGGCATTAGAACTTGGTCAAACTCTTTTTA-CTCTTGTTTGATTATATTGGCATTAGGA
66 CTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTACCT-TTGTTTGATTGTATTGGTGTTAGGA
246249 C
130 C
* * * * *
246250 CTGGTCAAACTTATTTCCATCATCATTTGACTGTATTTGGTTAAACTCTTTCCACCTTTGTTTGA
1 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
* *
246315 CTATATTGGCGTTAGGACCTGGTCAAATTCTTTTTACCCTTGTTT-ATTGTATTGGTGTTAGGAC
66 CTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTACCTTTGTTTGATTGTATTGGTGTTAGGAC
*
246379 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCATTGTTTGA
1 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
* * * * * *
246444 TTGTATTAGTGTTAGGACCTGGTCAAACTCTTTTTATCTTTGTTTGACTGTATTGGTGTTAGGAC
66 CTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTACCTTTGTTTGATTGTATTGGTGTTAGGAC
* * *
246509 CTAGTCAAACTCT-TTT-CACTC-TTGTTTAACTATATTGACGTGAGGACCTAGTCAAACTCTTT
1 CTAGTCAAACT-TATTTCCA-TCATCGTTTGACTGTA-T--C-T---G-----GTCAAACTCTTT
* * * * * * *
246571 GCACCCTTGTTTGACTACATTGGGGATAGGAACTAGTCAAACTCTTTTTTACCTTTGTTTGATTA
52 CCACCCTTGTTTGACTATATTGGCGTTAGGACCTGGTCAAACTC-TTTTTACCTTTGTTTGATTG
246636 TATTGGTGTTAGGAC
116 TATTGGTGTTAGGAC
* * * * *
246651 CT-GTTCAAACTTATTTCCATCATTGTTTGATTGTATCTGGTCAAACTGTTTCCCCCCTTATTTG
1 CTAG-TCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTG
* * * * *
246715 ACTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTACCTTTGTTTGATTGCATTGGTATTAGGA
65 ACTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTACCTTTGTTTGATTGTATTGGTGTTAGGA
246780 C
130 C
* * *
246781 ATAGTCAAAC-TCTTTCCA-CTATCGTTTGATTGTAT
1 CTAGTCAAACTTATTTCCATC-ATCGTTTGACTGTAT
246816 TAACGTTTGG
Statistics
Matches: 476, Mismatches: 67, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
128 1 0.00
129 147 0.31
130 168 0.35
131 47 0.10
132 1 0.00
133 1 0.00
136 2 0.00
139 1 0.00
140 1 0.00
141 48 0.10
142 47 0.10
143 12 0.03
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (130 bp):
CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
CTATATTGGCGTTAGGACCTGGTCAAACTCTTTTTACCTTTGTTTGATTGTATTGGTGTTAGGAC
Found at i:246442 original size:35 final size:36
Alignment explanation
Indices: 246382--246449 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
246372 TTAGGACCTA
*
246382 GTCAAACTTATTTCCATCATCGTTTGACTGTATCTG
1 GTCAAACTTATTTCCACCATCGTTTGACTGTATCTG
* * *
246418 GTCAAAC-TCTTTCCACCATTGTTTGATTGTAT
1 GTCAAACTTATTTCCACCATCGTTTGACTGTAT
246450 TAGTGTTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 21 0.75
36 7 0.25
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (36 bp):
GTCAAACTTATTTCCACCATCGTTTGACTGTATCTG
Found at i:246487 original size:47 final size:47
Alignment explanation
Indices: 246418--246661 Score: 258
Period size: 47 Copynumber: 5.2 Consensus size: 47
246408 ACTGTATCTG
* * * * * *
246418 GTCAAACTCTTTCCACCATTGTTTGATTGTATTAGTGTTAGGACCTG
1 GTCAAACTCTTTTCACCTTTGTTTGACTATATTGGTGTTAGGACCTA
* * *
246465 GTCAAACTCTTTTTATCTTTGTTTGACTGTATTGGTGTTAGGACCTA
1 GTCAAACTCTTTTCACCTTTGTTTGACTATATTGGTGTTAGGACCTA
* ** *
246512 GTCAAACTCTTTTCA-CTCTTGTTTAACTATATTGACGTGAGGACCTA
1 GTCAAACTCTTTTCACCT-TTGTTTGACTATATTGGTGTTAGGACCTA
* * * * * *
246559 GTCAAACTCTTTGCACCCTTGTTTGACTACATTGGGGATAGGAACTA
1 GTCAAACTCTTTTCACCTTTGTTTGACTATATTGGTGTTAGGACCTA
* *
246606 GTCAAACTCTTTTTTACCTTTGTTTGATTATATTGGTGTTAGGACCT-
1 GTCAAACTC-TTTTCACCTTTGTTTGACTATATTGGTGTTAGGACCTA
246653 GTTCAAACT
1 G-TCAAACT
246662 TATTTCCATC
Statistics
Matches: 163, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
46 2 0.01
47 124 0.76
48 37 0.23
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (47 bp):
GTCAAACTCTTTTCACCTTTGTTTGACTATATTGGTGTTAGGACCTA
Found at i:246852 original size:272 final size:268
Alignment explanation
Indices: 246120--246866 Score: 881
Period size: 272 Copynumber: 2.8 Consensus size: 268
246110 TTGACTGTGT
* * * * * *
246120 CTAGTGAAACTTGTTTCCATCATCATTTGAGTGTATCTGGTCAAACTTTTTCTACCCTTGTTTGA
1 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
* * * *
246185 CTATATTGGCATTAGAACTTGGTCAAACTCTTTTTACTCTTGTTTGATTATATTGGCATTAGGAC
66 CTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTACT-TTGTTTGATTGTATTGGTATTAGGAC
* * *
246250 CTGGTCAAACTTATTTCCA-TCATCATTTGACTG---TA--TTTGG---T--T-AAACTCTTTCC
130 CTAGTCAAAC-TCTTTCCACT-ATCGTTTGACTGTATTACGTTTGGACCTAGTCAAACTCTTTCC
* * * * * * *
246303 ACCTTTGTTTGACTATATTGGCGTTAGGACCTGGTCAAATTCTTTTTACCCTTGTTTATTGTATT
193 ACCCTTGTTTGACTACATTGGCGATAGGAACTAGTCAAACTCTTTTTACCCTTGTTTATTATATT
246368 GGTGTTAGGAC
258 GGTGTTAGGAC
*
246379 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCATTGTTTGA
1 CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
* * * * * * *
246444 TTGTATTAGTGTTAGGACCTGGTCAAACTCTTTTTATCTTTGTTTGACTGTATTGGTGTTAGGAC
66 CTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTA-CTTTGTTTGATTGTATTGGTATTAGGAC
* * * * * ** *
246509 CTAGTCAAACTCTTTTCACTCTTGTTTAACTATATTGACGTGAGGACCTAGTCAAACTCTTTGCA
130 CTAGTCAAACTCTTTCCACTATCGTTTGACTGTATT-ACGTTTGGACCTAGTCAAACTCTTTCCA
* *
246574 CCCTTGTTTGACTACATTGGGGATAGGAACTAGTCAAACTCTTTTTTACCTTTGTTTGATTATAT
194 CCCTTGTTTGACTACATTGGCGATAGGAACTAGTCAAACTC-TTTTTACCCTTGTTT-ATTATAT
246639 TGGTGTTAGGAC
257 TGGTGTTAGGAC
* * * * *
246651 CT-GTTCAAACTTATTTCCATCATTGTTTGATTGTATCTGGTCAAACTGTTTCCCCCCTTATTTG
1 CTAG-TCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTG
*
246715 ACTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTACCTTTGTTTGATTGCATTGGTATTAGGA
65 ACTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTA-CTTTGTTTGATTGTATTGGTATTAGGA
* *
246780 CATAGTCAAACTCTTTCCACTATCGTTTGATTGTATTAACGTTTGGACCTAGTCAAACTCTTTCC
129 CCTAGTCAAACTCTTTCCACTATCGTTTGACTGTATT-ACGTTTGGACCTAGTCAAACTCTTTCC
* *
246845 TCCCTTGTTTGACTGCATTGGC
193 ACCCTTGTTTGACTACATTGGC
246867 ATTGGGGTTT
Statistics
Matches: 404, Mismatches: 67, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
258 13 0.03
259 119 0.29
260 2 0.00
261 1 0.00
262 1 0.00
264 3 0.01
267 1 0.00
269 1 0.00
270 45 0.11
271 15 0.04
272 203 0.50
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (268 bp):
CTAGTCAAACTTATTTCCATCATCGTTTGACTGTATCTGGTCAAACTCTTTCCACCCTTGTTTGA
CTATATTAGCGTTAGAACTTGGTCAAACTCTTTTTACTTTGTTTGATTGTATTGGTATTAGGACC
TAGTCAAACTCTTTCCACTATCGTTTGACTGTATTACGTTTGGACCTAGTCAAACTCTTTCCACC
CTTGTTTGACTACATTGGCGATAGGAACTAGTCAAACTCTTTTTACCCTTGTTTATTATATTGGT
GTTAGGAC
Found at i:246855 original size:47 final size:46
Alignment explanation
Indices: 246690--246856 Score: 113
Period size: 47 Copynumber: 3.6 Consensus size: 46
246680 ATTGTATCTG
* * * * * * * * *
246690 GTCAAACTGTTTCCCCCCTTATTTGACTATATTAGCGTTAGAACTTG
1 GTCAAACTCTTTCCTCCCTTGTTTGATTGTATTA-CGTTTGGACATA
* * * *
246737 GTCAAACTCTTT-TTACCTTTGTTTGATTGCATT-GGTATTAGGACATA
1 GTCAAACTCTTTCCT-CCCTTGTTTGATTGTATTACGT-TT-GGACATA
* ** * *
246784 GTCAAACTCTTTCCACTATCGTTTGATTGTATTAACGTTTGGACCTA
1 GTCAAACTCTTTCCTCCCTTGTTTGATTGTATT-ACGTTTGGACATA
246831 GTCAAACTCTTTCCTCCCTTGTTTGA
1 GTCAAACTCTTTCCTCCCTTGTTTGA
246857 CTGCATTGGC
Statistics
Matches: 89, Mismatches: 25, Indels: 12
0.71 0.20 0.10
Matches are distributed among these distances:
45 2 0.02
46 1 0.01
47 82 0.92
48 2 0.02
49 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (46 bp):
GTCAAACTCTTTCCTCCCTTGTTTGATTGTATTACGTTTGGACATA
Found at i:247160 original size:85 final size:84
Alignment explanation
Indices: 247013--247771 Score: 625
Period size: 85 Copynumber: 9.0 Consensus size: 84
247003 GCATTTCATC
* * * * * *
247013 CCTTGTTTACCCGTCGACTCAGTCC-CTGATAAACCCATTACCCCTATGGTGACTTGTTAGCTCA
1 CCTTGTTTACCTGTCGGCTCAGTCCTC-GGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCA
*
247077 ATCTTCGATCAACCTTTATCT
65 GTC-TCGATCAACCTTTATCT
* * * * * * *
247098 CCTTGTTTACTTGTTGGCTTAATCC-CTAGTAAACCCCTTACCCCTATGGTAACCTATCAGCTCA
1 CCTTGTTTACCTGTCGGCTCAGTCCTC-GGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCA
* *
247162 GTCTCTAGTCAACTTTTATCT
65 GTCTCGA-TCAACCTTTATCT
* *** * * * * * *
247183 CCTCGTTTACCTGTCAATTTAGTCCCCGATAAACCCTTTACACTTATGGTGACCTGTCAGCTCAG
1 CCTTGTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCAG
* *
247248 TCTCTGGTCAACCTTCATCT
66 TCTC-GATCAACCTTTATCT
* * * * * * * *
247268 CATTGTTTACTTGTCGGCTCATTCC-CTGGTAAACCCCTTACACCTATAGTGACCTATTAGCTTA
1 CCTTGTTTACCTGTCGGCTCAGTCCTC-GGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCA
*
247332 GTCTCTAGTCAACCTTTATCT
65 GTCTCGA-TCAACCTTTATCT
* * * * **
247353 CATTGGTAACCTGTCGGCTCAGTCTTCGGTAAACCTATTACCCCTATGGTGACCTGTCAGCTCAG
1 CCTTGTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCAG
*
247418 TCTTCGATCAACCTTCATCT
66 TC-TCGATCAACCTTTATCT
* * * * * * *
247438 CCTTATTTACCTGTCGGCTTAGTCCTCGGCAAACCCCTCACCCCTATGGTAACCTGTCAGTTTAG
1 CCTTGTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCAG
* *
247503 TCTCCAGTCAATCTTTATCT
66 TCTCGA-TCAACCTTTATCT
* * ** * *
247523 -CTTCGTTGACCTATCGATTCAGTCCTCGGTAAACCCCTTACACCTATAGTGACCTGTCAGCTCA
1 CCTT-GTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCA
* * *
247587 ATCTCCGGTCAA-GTTTCATCT
65 GTCT-CGATCAACCTTT-ATCT
** * * * *
247608 TATTGTTTACCTGT-GGACTCAATCCCCGATAAACCCATTACCCCTATGGTGACCTGTCAGCTCA
1 CCTTGTTTACCTGTCGG-CTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCA
* *
247672 GTTTCCGGTCAACCTTTATCT
65 GTCT-CGATCAACCTTTATCT
* * * * * * * *
247693 CTTTATTTACTTGTCGGCTCAATCCTCGGTAAACCCCTTATCCCT-TGGTGACTTGTCGGTTCA-
1 CCTTGTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCAG
247756 TGCTCGATCAACCTTT
66 T-CTCGATCAACCTTT
247772 TTTATCTTAT
Statistics
Matches: 532, Mismatches: 126, Indels: 34
0.77 0.18 0.05
Matches are distributed among these distances:
83 12 0.02
84 30 0.06
85 477 0.90
86 13 0.02
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (84 bp):
CCTTGTTTACCTGTCGGCTCAGTCCTCGGTAAACCCCTTACCCCTATGGTGACCTGTCAGCTCAG
TCTCGATCAACCTTTATCT
Found at i:247694 original size:170 final size:170
Alignment explanation
Indices: 247017--247770 Score: 696
Period size: 170 Copynumber: 4.4 Consensus size: 170
247007 TTCATCCCTT
* * * * *
247017 GTTTACCCGTCGACTCAGTCC-CTGATAAACCCATTACCCCTATGGTGACTTGTTAGCTCAATCT
1 GTTTACCTGTCGACTCAGTCCTC-GGTAAACCCATTACACCTATGGTGACCTGTCAGCTCAATCT
* * * * * * *
247081 TCGATCAACCTTTATCTCCTTGTTTACTTGTTGGCTTAAT-CCCTAGTAAACCCCTTACCCCTAT
65 CCGATCAACCTTCATCTCATTGTTTACCTGTCGGCTCAATCCCCGA-TAAACCCCTTACCCCTAT
* * *
247145 GGTAACCTATCAGCTCAGTCTCTAGTCAACTTTTATCTCCTC
129 GGTAACCTATCAGCTCAGTCTCCAGTCAACCTTTATCTCTTC
* * * * * * * *
247187 GTTTACCTGTCAATTTAGTCCCCGATAAACCCTTTACACTTATGGTGACCTGTCAGCTCAGTCTC
1 GTTTACCTGTCGACTCAGTCCTCGGTAAACCCATTACACCTATGGTGACCTGTCAGCTCAATCTC
* * * * * * * *
247252 TGGTCAACCTTCATCTCATTGTTTACTTGTCGGCTCATTCCCTGGTAAACCCCTTACACCTATAG
66 CGATCAACCTTCATCTCATTGTTTACCTGTCGGCTCAATCCCCGATAAACCCCTTACCCCTATGG
* * * *
247317 TGACCTATTAGCTTAGTCTCTAGTCAACCTTTATCTCATT-
131 TAACCTATCAGCTCAGTCTCCAGTCAACCTTTATCTC-TTC
* * * * * * * *
247357 GGTAACCTGTCGGCTCAGTCTTCGGTAAACCTATTACCCCTATGGTGACCTGTCAGCTCAGTCTT
1 GTTTACCTGTCGACTCAGTCCTCGGTAAACCCATTACACCTATGGTGACCTGTCAGCTCAATCTC
* * * * * ** *
247422 CGATCAACCTTCATCTCCTTATTTACCTGTCGGCTTAGTCCTCGGCAAACCCCTCACCCCTATGG
66 CGATCAACCTTCATCTCATTGTTTACCTGTCGGCTCAATCCCCGATAAACCCCTTACCCCTATGG
* * * *
247487 TAACCTGTCAGTTTAGTCTCCAGTCAATCTTTATCTCTTC
131 TAACCTATCAGCTCAGTCTCCAGTCAACCTTTATCTCTTC
* * * * *
247527 GTTGACCTATCGATTCAGTCCTCGGTAAACCCCTTACACCTATAGTGACCTGTCAGCTCAATCTC
1 GTTTACCTGTCGACTCAGTCCTCGGTAAACCCATTACACCTATGGTGACCTGTCAGCTCAATCTC
* ** * *
247592 CGGTCAAGTTTCATCTTATTGTTTACCTGT-GGACTCAATCCCCGATAAACCCATTACCCCTATG
66 CGATCAACCTTCATCTCATTGTTTACCTGTCGG-CTCAATCCCCGATAAACCCCTTACCCCTATG
* * * * *
247656 GTGACCTGTCAGCTCAGTTTCCGGTCAACCTTTATCTCTTT
130 GTAACCTATCAGCTCAGTCTCCAGTCAACCTTTATCTCTTC
* * * * * * * *
247697 ATTTACTTGTCGGCTCAATCCTCGGTAAACCCCTTATC-CCT-TGGTGACTTGTCGGTTC-ATGC
1 GTTTACCTGTCGACTCAGTCCTCGGTAAACCCATTA-CACCTATGGTGACCTGTCAGCTCAAT-C
247759 T-CGATCAACCTT
64 TCCGATCAACCTT
247771 TTTTATCTTA
Statistics
Matches: 470, Mismatches: 107, Indels: 16
0.79 0.18 0.03
Matches are distributed among these distances:
168 10 0.02
169 19 0.04
170 436 0.93
171 5 0.01
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (170 bp):
GTTTACCTGTCGACTCAGTCCTCGGTAAACCCATTACACCTATGGTGACCTGTCAGCTCAATCTC
CGATCAACCTTCATCTCATTGTTTACCTGTCGGCTCAATCCCCGATAAACCCCTTACCCCTATGG
TAACCTATCAGCTCAGTCTCCAGTCAACCTTTATCTCTTC
Found at i:247933 original size:175 final size:172
Alignment explanation
Indices: 247741--248121 Score: 462
Period size: 172 Copynumber: 2.2 Consensus size: 172
247731 TATCCCTTGG
* *
247741 TGACTTGTCGGTTCATGCTC-GATCAACCTTTTTTATCTTATGTTTACCTT-TCGGCTTAGTCCC
1 TGACTTGTCGGTTCATGCCCAG-TCAACCTTTTTTATCTTATGTTTA-CTTATCGACTTAGTCCC
* * * ** *
247804 TGGTGGTTAATGCTCTTTATCCTTCGTTGACTTATCGGTTCATGCCCGGTTAACCTTTTTATCCT
64 --G-AGTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCT
*
247869 TTGTTTACCTGTCGGCTTAGTCCGAAGTAAATCCTTTCATCCTTCAT
126 TTGTTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTCATCCTTCAT
* * *
247916 TGACTTGTTGGTTCATGCCCAGTCAACCTTTTTTATCTTGTGTTTACTTATTGACTTAGTCCCGA
1 TGACTTGTCGGTTCATGCCCAGTCAACCTTTTTTATCTTATGTTTACTTATCGACTTAGTCCCGA
* * * *
247981 GTAAATCCTCTTTATCTTTTGTCAACTTGTCGGTTCATGCTCGGTCAACCTTTTTATCCTTTGTT
66 GTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCTTTGTT
* * **
248046 TAGCTGTCGGCTTAGTCCCAAGTAAATCCTTTTA-CCTTTTGT
131 TACCTGTCGGCTTAGTCCCAAGTAAATCCTTTCATCC-TTCAT
* **
248088 TGACTTGTCGATTCAAACCCTAGTCAACTCTTTT
1 TGACTTGTCGGTTCATGCCC-AGTCAAC-CTTTT
248122 ATCCTTTATT
Statistics
Matches: 177, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
171 2 0.01
172 106 0.60
173 8 0.05
174 8 0.05
175 52 0.29
176 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.44
Consensus pattern (172 bp):
TGACTTGTCGGTTCATGCCCAGTCAACCTTTTTTATCTTATGTTTACTTATCGACTTAGTCCCGA
GTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCTTTGTT
TACCTGTCGGCTTAGTCCCAAGTAAATCCTTTCATCCTTCAT
Found at i:247974 original size:86 final size:86
Alignment explanation
Indices: 247676--248137 Score: 355
Period size: 86 Copynumber: 5.3 Consensus size: 86
247666 AGCTCAGTTT
* * * * *
247676 CCGGTCAACC--TTTATCTCTTTATTTA-CTTGTCGGCTCAATCCTCG--GTAAACCCCTTATCC
1 CCGGTCAACCTTTTTATC-CTTTGTTTACCTTGTCGGCTTAGTCC-CGAAGTAAATCCTTTAT-C
*
247736 CTT-GGTGACTTGTCGGTTCATGC
63 CTTCGTTGACTTGTCGGTTCATGC
* * ** *
247759 TCGATCAACCTTTTTTAT-CTTATGTTTACCTT-TCGGCTTAGTCCCTGGTGGTTAATGCTCTTT
1 CCGGTCAACC-TTTTTATCCTT-TGTTTACCTTGTCGGCTTAGTCCC--GAAGTAAAT-C-CTTT
*
247822 ATCCTTCGTTGACTTATCGGTTCATGC
60 ATCCTTCGTTGACTTGTCGGTTCATGC
*
247849 CCGGTTAACCTTTTTATCCTTTGTTTACC-TGTCGGCTTAGT-CCGAAGTAAATCCTTTCATCCT
1 CCGGTCAACCTTTTTATCCTTTGTTTACCTTGTCGGCTTAGTCCCGAAGTAAATCCTTT-ATCCT
* *
247912 TCATTGACTTGTTGGTTCATGC
65 TCGTTGACTTGTCGGTTCATGC
* * * *
247934 CCAGTCAACCTTTTTTAT-CTTGTGTTTA-CTTATTGACTTAGTCCCG-AGTAAATCCTCTTTAT
1 CCGGTCAACC-TTTTTATCCTT-TGTTTACCTTGTCGGCTTAGTCCCGAAGTAAAT-C-CTTTAT
* * **
247996 CTTTTGTCAACTTGTCGGTTCATGC
62 CCTTCGTTGACTTGTCGGTTCATGC
* *
248021 TCGGTCAACCTTTTTATCCTTTGTTTAGC-TGTCGGCTTAGTCCC-AAGTAAATCCTTT-TACCT
1 CCGGTCAACCTTTTTATCCTTTGTTTACCTTGTCGGCTTAGTCCCGAAGTAAATCCTTTAT-CC-
* * **
248083 TTTGTTGACTTGTCGATTCAAAC
64 TTCGTTGACTTGTCGGTTCATGC
* *
248106 CCTAGTCAA-CTCTTTTATCCTTTATTTTACCT
1 CC-GGTCAACCT-TTTTATCCTTT-GTTTACCT
248138 ATCAGCTCAG
Statistics
Matches: 304, Mismatches: 45, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
83 9 0.03
84 13 0.04
85 74 0.24
86 92 0.30
87 42 0.14
88 11 0.04
89 30 0.10
90 33 0.11
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (86 bp):
CCGGTCAACCTTTTTATCCTTTGTTTACCTTGTCGGCTTAGTCCCGAAGTAAATCCTTTATCCTT
CGTTGACTTGTCGGTTCATGC
Found at i:248095 original size:172 final size:174
Alignment explanation
Indices: 247741--248077 Score: 466
Period size: 172 Copynumber: 1.9 Consensus size: 174
247731 TATCCCTTGG
* *
247741 TGACTTGTCGGTTCATGCTCGATCAACCTTTTTTATCTTATGTTTACCTTTCGGCTTAGTCCCTG
1 TGACTTGTCGGTTCATGCCCGATCAACCTTTTTTATCTTATGTTTACCTTTCGACTTAGTCCC-G
* * * ** *
247806 GTGGTTAATGCTCTTTATCCTTCGTTGACTTATCGGTTCATGCCCGGTTAACCTTTTTATCCTTT
65 GTAGTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCTTT
*
247871 GTTTACCTGTCGGCTTAGTCCGAAGTAAATCCTTTCATCCTTCAT
130 GTTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTCATCCTTCAT
* * *
247916 TGACTTGTTGGTTCATGCCC-AGTCAACCTTTTTTATCTTGTGTTTA-CTTATTGACTTAGTCCC
1 TGACTTGTCGGTTCATGCCCGA-TCAACCTTTTTTATCTTATGTTTACCTT-TCGACTTAGTCCC
* * * *
247979 -G-AGTAAATCCTCTTTATCTTTTGTCAACTTGTCGGTTCATGCTCGGTCAACCTTTTTATCCTT
64 GGTAGTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCTT
*
248042 TGTTTAGCTGTCGGCTTAGTCCCAAGTAAATCCTTT
129 TGTTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTT
248078 TACCTTTTGT
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
172 86 0.60
173 1 0.01
174 4 0.03
175 52 0.36
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (174 bp):
TGACTTGTCGGTTCATGCCCGATCAACCTTTTTTATCTTATGTTTACCTTTCGACTTAGTCCCGG
TAGTAAATCCTCTTTATCCTTCGTCAACTTATCGGTTCATGCCCGGTCAACCTTTTTATCCTTTG
TTTACCTGTCGGCTTAGTCCCAAGTAAATCCTTTCATCCTTCAT
Found at i:249762 original size:165 final size:166
Alignment explanation
Indices: 249401--249787 Score: 396
Period size: 165 Copynumber: 2.4 Consensus size: 166
249391 CTTGGTTTTT
*
249401 AATTTTTAAAATTCATCAA-A-TATTATTTAA-TTCATATTAAATCAGTTTTCAAAAATTTATTT
1 AATTTTTAAAATTCATCAATATTATTATTTAACTTCATATTAAATCAGTTTTCAAAAATTCATTT
* * ** ** * *
249463 ATTTTCATTAGTTTTTTATTTTTTTCTTAAAATTTCTTTTTTTTCGAAAAATCGAGTTTTCTATT
66 ATTTTCATGAGTTTTTTATTTTTCTCTTAAAATAACCCTGTTTTCAAAAAATCGAGTTTTCTATT
* * *
249528 CCATAAAGGTTTTCGAGGGGGTTTTTCTCGACCTGA
131 CCATAAAGATTTTCGAGGGGATTTTTCTCGACCTAA
* * * * *
249564 AATTTTTAATATTCATCAAATATCATCATTTAACTT-ATATTAAATCAGTTTTGAAAACTTCATT
1 AATTTTTAAAATTCATC-AATATTATTATTTAACTTCATATTAAATCAGTTTTCAAAAATTCATT
* * *
249628 TATTTTCATGAG-TTTTTATTTTTCTCTTGAAATAACCCTGTTTTCAAAAAATTGAGTTTTTTAC
65 TATTTTCATGAGTTTTTTATTTTTCTCTTAAAATAACCCTGTTTTCAAAAAATCGAGTTTTCTA-
** ** * **
249692 TTTGA-AATTATTTT-TAGGGAGATTTTTCTCGATTTAA
129 TTCCATAAAGATTTTCGAGGG-GATTTTTCTCGACCTAA
* * * *
249729 AATTTTTAAAATTCATCTAATATTGTTATTTAACTTTA-ACTAAATTAGTTTT-AAAAATT
1 AATTTTTAAAATTCATC-AATATTATTATTTAACTTCATATTAAATCAGTTTTCAAAAATT
249788 TTAATTTATT
Statistics
Matches: 182, Mismatches: 35, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
163 16 0.09
164 12 0.07
165 104 0.57
166 48 0.26
167 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (166 bp):
AATTTTTAAAATTCATCAATATTATTATTTAACTTCATATTAAATCAGTTTTCAAAAATTCATTT
ATTTTCATGAGTTTTTTATTTTTCTCTTAAAATAACCCTGTTTTCAAAAAATCGAGTTTTCTATT
CCATAAAGATTTTCGAGGGGATTTTTCTCGACCTAA
Found at i:250174 original size:20 final size:20
Alignment explanation
Indices: 250151--250189 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
250141 GAAAAAAAGG
250151 GAGAAAAAAGA-AAGAAAAAA
1 GAGAAAAAA-ACAAGAAAAAA
250171 GAGAAAAAAACAAGAAAAA
1 GAGAAAAAAACAAGAAAAA
250190 TAGAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (20 bp):
GAGAAAAAAACAAGAAAAAA
Found at i:254138 original size:20 final size:20
Alignment explanation
Indices: 254115--254165 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
254105 CATTTGGTCA
*
254115 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * * *
254135 TGTATTGATACATTTAAATG
1 TGTATCGATACAATGAAATC
254155 TGTATCGATAC
1 TGTATCGATAC
254166 TTTTCAGGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:254617 original size:13 final size:13
Alignment explanation
Indices: 254599--254624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
254589 TACAGCAAGT
254599 ATGTATCGATACA
1 ATGTATCGATACA
254612 ATGTATCGATACA
1 ATGTATCGATACA
254625 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:256873 original size:21 final size:22
Alignment explanation
Indices: 256827--256871 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
256817 TTGCAAGTTG
256827 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
256849 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
256869 AAA
1 AAA
256872 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:258695 original size:15 final size:15
Alignment explanation
Indices: 258675--258705 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
258665 TAAAAATGTC
*
258675 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
258690 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
258705 C
1 C
258706 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:260799 original size:13 final size:13
Alignment explanation
Indices: 260781--260806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
260771 ACATTTTTCC
260781 TTGTATCGATACA
1 TTGTATCGATACA
260794 TTGTATCGATACA
1 TTGTATCGATACA
260807 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:260970 original size:20 final size:20
Alignment explanation
Indices: 260927--260972 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
260917 AAATCTTTTG
260927 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
260948 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
260968 CAAAA
1 CAAAA
260973 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:263312 original size:21 final size:21
Alignment explanation
Indices: 263286--263341 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
263276 ACATGTTGCA
263286 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
263307 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
263328 ATGTATCGATACAT
1 ATGTATCGATACAT
263342 TTCTTGGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:263380 original size:13 final size:13
Alignment explanation
Indices: 263362--263386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
263352 TAGCCAAACT
263362 TGTATCGATACAA
1 TGTATCGATACAA
263375 TGTATCGATACA
1 TGTATCGATACA
263387 CAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:266078 original size:20 final size:21
Alignment explanation
Indices: 266049--266090 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
266039 TGGGGGCTAC
*
266049 CCGGTTGCGACCTGG-GGGTG
1 CCGGTCGCGACCTGGTGGGTG
266069 CCGGTCGCGACCTGGTGGGTG
1 CCGGTCGCGACCTGGTGGGTG
266090 C
1 C
266091 TGCCTAGCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.05, C:0.29, G:0.48, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTGGGTG
Found at i:266381 original size:20 final size:21
Alignment explanation
Indices: 266352--266392 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
266342 TGTTTTTGTT
266352 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
266371 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
266393 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:277795 original size:13 final size:13
Alignment explanation
Indices: 277777--277802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
277767 AATTTTTTGG
277777 TGTATCGATACAT
1 TGTATCGATACAT
277790 TGTATCGATACAT
1 TGTATCGATACAT
277803 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:279901 original size:21 final size:20
Alignment explanation
Indices: 279872--279914 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
279862 GGCTAGTGTG
*
279872 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
279893 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
279913 GG
1 GG
279915 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:280374 original size:13 final size:13
Alignment explanation
Indices: 280356--280393 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
280346 ATAATCCCCC
*
280356 TGTATCGATACAG
1 TGTATCGATACAA
*
280369 TGTATCAATACAA
1 TGTATCGATACAA
280382 TGTATCGATACA
1 TGTATCGATACA
280394 TTGAATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:286601 original size:32 final size:34
Alignment explanation
Indices: 286535--286603 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
286525 CGTTACAAGC
** *
286535 CAATGTATCGATACAATTTTTTGGTGTATTGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
286569 CAATGTATCGATAC-A-TACTTGGTGTATCGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
286601 CAA
1 CAA
286604 GTTTGGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 1 0.03
34 14 0.44
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (34 bp):
CAATGTATCGATACAATTACTTGGTGTATCGATA
Found at i:287717 original size:51 final size:51
Alignment explanation
Indices: 287660--287802 Score: 223
Period size: 51 Copynumber: 2.8 Consensus size: 51
287650 TTTTAACTAG
* * *
287660 ATGTATCAATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
* * *
287711 ATGTATCGATACATTGAAGAATATATCGATACATCTGGGTAAAAGGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
*
287762 ATGTATCGATACATTGAAGAATGTTTCGATACATCTGGGTA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTA
287803 CCTTTCCATA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:289947 original size:33 final size:32
Alignment explanation
Indices: 289884--289951 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
289874 CCTTAACTGT
*
289884 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATAGATACATACAAGATGTATCGATACA
*
289916 TTGTATAGATACATGACCAA-ATGTATTGATACA
1 TTGTATAGATACAT-A-CAAGATGTATCGATACA
289949 TTG
1 TTG
289952 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 16 0.50
34 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATAGATACATACAAGATGTATCGATACA
Done.