Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2159989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1283249 original size:20 final size:20
Alignment explanation
Indices: 1283212--1283249 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1283202 ACAATTAAAC
*
1283212 AATTTATGTTAAACAACATG
1 AATTTATGTAAAACAACATG
1283232 AATTTA-GTAAAACTAACA
1 AATTTATGTAAAAC-AACA
1283250 CCCAAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (20 bp):
AATTTATGTAAAACAACATG
Found at i:1284672 original size:23 final size:23
Alignment explanation
Indices: 1284640--1284685 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1284630 CGCAGAGAAG
* *
1284640 ACTCATAAGTGTCAAGAAGCGTC
1 ACTCAGAAGTGTCAAGAAACGTC
1284663 ACTCAGAAGTGTCAAGAAACGTC
1 ACTCAGAAGTGTCAAGAAACGTC
1284686 TAAGGCCGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
ACTCAGAAGTGTCAAGAAACGTC
Found at i:1285302 original size:21 final size:21
Alignment explanation
Indices: 1285278--1285342 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1285268 AAGGGTTAAG
*
1285278 ACCTTTCGATGAAATGACTTA
1 ACCTTTCGATGAAAGGACTTA
* *
1285299 ACCTTTCGATTAAAGGACGTA
1 ACCTTTCGATGAAAGGACTTA
* * *
1285320 TCCTTTTGATGAAAGGGCTTA
1 ACCTTTCGATGAAAGGACTTA
1285341 AC
1 AC
1285343 ATTTTTCTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
ACCTTTCGATGAAAGGACTTA
Found at i:1296790 original size:58 final size:58
Alignment explanation
Indices: 1296694--1296842 Score: 271
Period size: 58 Copynumber: 2.6 Consensus size: 58
1296684 TTATTGCACA
*
1296694 AAGAAACGCAAAGGATGCCCTTAGGTCACATTCAGCCATTAGGTAACTTTACTAAGAT
1 AAGAATCGCAAAGGATGCCCTTAGGTCACATTCAGCCATTAGGTAACTTTACTAAGAT
**
1296752 AAGAATCGCAAAGGATGCCCTTAGGTCACATTTGGCCATTAGGTAACTTTACTAAGAT
1 AAGAATCGCAAAGGATGCCCTTAGGTCACATTCAGCCATTAGGTAACTTTACTAAGAT
1296810 AAGAATCGCAAAGGATGCCCTTAGGTCACATTC
1 AAGAATCGCAAAGGATGCCCTTAGGTCACATTC
1296843 GTTCATCATA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 87 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (58 bp):
AAGAATCGCAAAGGATGCCCTTAGGTCACATTCAGCCATTAGGTAACTTTACTAAGAT
Found at i:1303194 original size:4 final size:4
Alignment explanation
Indices: 1303155--1303240 Score: 58
Period size: 4 Copynumber: 23.0 Consensus size: 4
1303145 TCGGGCTGGG
* * * * *
1303155 TATA TATA TTTA AAT- TAAA TATA TAAA TAT- TATA TATA TATA TATT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
1303201 TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1303241 AAAAATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
3 12 0.20
4 49 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:1303194 original size:6 final size:6
Alignment explanation
Indices: 1303155--1303240 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
1303145 TCGGGCTGGG
* * * * *
1303155 TATATA TATTTA AAT-TA AATATA TAAATA T-TATA TATATA TATATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
1303201 TAAAT- TAAATT TAT-TA -ATAT- TATATA TATATA TATATA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA
1303241 AAAAATAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
4 2 0.03
5 20 0.31
6 43 0.66
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:1303199 original size:36 final size:36
Alignment explanation
Indices: 1303155--1303235 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
1303145 TCGGGCTGGG
1303155 TATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATATTTAAATTAAATATATAAATATTATATA
* *
1303191 TATATATATTTAAATTAAATTTATTAATATTATATA
1 TATATATATTTAAATTAAATATATAAATATTATATA
1303227 TATATATAT
1 TATATATAT
1303236 ATATAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
TATATATATTTAAATTAAATATATAAATATTATATA
Found at i:1314362 original size:488 final size:482
Alignment explanation
Indices: 1313442--1314414 Score: 1769
Period size: 488 Copynumber: 2.0 Consensus size: 482
1313432 GACAACCAAT
1313442 CCATATCAGAGAACCAATACCAACAGCGTATTTTCCCTATAATCACAGCAATTGATCAGGTAGTC
1 CCATATCAGAGAACCAATACCAACAGCGTATTTTCCCTATAATCACAGCAATTGATCAGGTAGTC
1313507 AGTATTTCATTTGTGAAGAAAAATGATAACAGGTTTTGTTAAGCATGAAAGCTGTGTATAAAACG
66 AGTATTTCATTTGTGAAG-AAAA-GATAACAGGTTTTGTTAAGCATGAAAGCTGTGTATAAAACG
1313572 ATGGATGATACTATAGAACTATTGGCTTTTATGAACATAGGAAACAATAAAGTTAAAACAAACAA
129 ATGGATGATACTATAGAACTATTGGCTTTTATGAACATAGGAAACAATAAAGTTAAAACAAACAA
1313637 ATTTTACAGCATTTGTTCTAGTTAACGAGATGACATGGAATTACGTGCTCCAAGCCACAGTACAT
194 ATTTTACAGCATTTGTTCTAGTTAACGAGATGACATGGAATTACGTGCTCCAAGCCACAGTACAT
1313702 GTCAAAACTCAAGCAAGAACAAGATCATCCTGTTGGTTCTTGCTCAAATGTGGAAGGTGAATCAA
259 GTCAAAACTCAAGCAAGAACAAGATCATCCTGTTGGTTCTTGCTCAAATGTGGAAGGTGAATCAA
1313767 AATAACGGTACTGGAACATGCTTGATTCAATTGCTACCTGGTATATTGCTGGTGGAGGCAATTGA
324 AATAACGGTACTGGAACATGCTTGATTCAATTGCTACCTGGTATATTGCTGGTGGAGGCAATTGA
1313832 GATTATAAATTCATCCAAACAAGGGAAGGGCGACTTTCCTGTTTGGTATGTTGAAGAAACACTCA
389 GATTATAAATTCATCCAAACAAGGGAAGGGCGACTTTCCTGTTTGGTATGTTGAAGAAACA-TCA
1313897 CTGATGCCAATTTTTCTTGAGCTTTGTGATA
453 CT-ATGCCAATTTTTCTTGAGCTTTGTGATA
1313928 CCATATTCAGAGAACCAATACCAACAGCGTATTTTCCCTATAATCACAGCAATTGATCA-GTAGT
1 CCATA-TCAGAGAACCAATACCAACAGCGTATTTTCCCTATAATCACAGCAATTGATCAGGTAGT
*
1313992 CAGTA-TTCATTTGTGAAG-AAA-ATAACAGTTTTTGTTAAGCATTGAAAGCTGTGTATAAAACG
65 CAGTATTTCATTTGTGAAGAAAAGATAACAGGTTTTGTTAAGCA-TGAAAGCTGTGTATAAAACG
1314054 ATGGATGATACTATAGAACTATTGG-TTTTATGAACATAGGAAAACAATAAAGTTAAAACACAAA
129 ATGGATGATACTATAGAACTATTGGCTTTTATGAACATAGG-AAACAATAAAGTT-AAA-ACAAA
1314118 CAAATTTCTACAGCATTTAGTTCTAGTTAACGAGATGACATGGAATTACGTGCTCCAAGCCACAG
191 CAAATTT-TACAGCATTT-GTTCTAGTTAACGAGATGACATGGAATTACGTGCTCCAAGCCACAG
1314183 TACATATGTCAAAACTCAAGCAAGAACAAGATCATCCTGTTGGTTCTTGCTCAAATGTGGAAGGT
254 TAC--ATGTCAAAACTCAAGCAAGAACAAGATCATCCTGTTGGTTCTTGCTCAAATGTGGAAGGT
1314248 GAATCAAAATAACGGTACTGGAACATGCTTGATTCAATTGCTACCTGGTATATTGCTGGTGGAGG
317 GAATCAAAATAACGGTACTGGAACATGCTTGATTCAATTGCTACCTGGTATATTGCTGGTGGAGG
1314313 C-ATTGAGATTATAAATTCATCCAAACAAGGGAAGGGCGACTTTTCCTGTTTGGTATGTTGAAGA
382 CAATTGAGATTATAAATTCATCCAAACAAGGGAAGGGCGAC-TTTCCTGTTTGGTATGTTGAAGA
1314377 AACATCACTATGCCAATTTTTCTTGAGCTTTGTGATA
446 AACATCACTATGCCAATTTTTCTTGAGCTTTGTGATA
1314414 C
1 C
1314415 TTCCAAAGTA
Statistics
Matches: 476, Mismatches: 1, Indels: 20
0.96 0.00 0.04
Matches are distributed among these distances:
481 34 0.07
482 58 0.12
483 6 0.01
484 12 0.03
485 23 0.05
486 93 0.20
487 97 0.20
488 153 0.32
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (482 bp):
CCATATCAGAGAACCAATACCAACAGCGTATTTTCCCTATAATCACAGCAATTGATCAGGTAGTC
AGTATTTCATTTGTGAAGAAAAGATAACAGGTTTTGTTAAGCATGAAAGCTGTGTATAAAACGAT
GGATGATACTATAGAACTATTGGCTTTTATGAACATAGGAAACAATAAAGTTAAAACAAACAAAT
TTTACAGCATTTGTTCTAGTTAACGAGATGACATGGAATTACGTGCTCCAAGCCACAGTACATGT
CAAAACTCAAGCAAGAACAAGATCATCCTGTTGGTTCTTGCTCAAATGTGGAAGGTGAATCAAAA
TAACGGTACTGGAACATGCTTGATTCAATTGCTACCTGGTATATTGCTGGTGGAGGCAATTGAGA
TTATAAATTCATCCAAACAAGGGAAGGGCGACTTTCCTGTTTGGTATGTTGAAGAAACATCACTA
TGCCAATTTTTCTTGAGCTTTGTGATA
Found at i:1314729 original size:82 final size:86
Alignment explanation
Indices: 1314626--1314792 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 86
1314616 AAGTTGTAGC
1314626 AAAAATTATACGATGCAAAAAAAAA-GTAGTTAAGTGATG-AACCC-AA-GCAAAGTTCAAGACT
1 AAAAATTATACGATGCAAAAAAAAATGTAGTTAAGTGATGAAACCCAAAGGCAAAGTTCAAGACT
1314687 ACCTCTGTCTCGAAGTGCGCA
66 ACCTCTGTCTCGAAGTGCGCA
1314708 AAAAATTATACGAATGCAAAAAAAAAATGTAGTTAAGTGATGAAACCCAAAGGCAAAGTTCAAGA
1 AAAAATTATACG-ATGC-AAAAAAAAATGTAGTTAAGTGATGAAACCCAAAGGCAAAGTTCAAGA
1314773 CTACCTCTGTCTCGAAGTGC
64 CTACCTCTGTCTCGAAGTGC
1314793 AGTGTCTTCA
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
82 12 0.15
83 4 0.05
84 9 0.11
85 14 0.18
86 5 0.06
87 2 0.03
88 33 0.42
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (86 bp):
AAAAATTATACGATGCAAAAAAAAATGTAGTTAAGTGATGAAACCCAAAGGCAAAGTTCAAGACT
ACCTCTGTCTCGAAGTGCGCA
Found at i:1322746 original size:50 final size:50
Alignment explanation
Indices: 1322688--1322787 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1322678 GGACGTCGGC
1322688 GGTTGATATACGTACGGGTACGTCACTATAACATCTTTCGGCTGGTCTTT
1 GGTTGATATACGTACGGGTACGTCACTATAACATCTTTCGGCTGGTCTTT
1322738 GGTTGATATACGTACGGGTACGTCACTATAACATCTTTCGGCTGGTCTTT
1 GGTTGATATACGTACGGGTACGTCACTATAACATCTTTCGGCTGGTCTTT
1322788 CTTCGGCTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (50 bp):
GGTTGATATACGTACGGGTACGTCACTATAACATCTTTCGGCTGGTCTTT
Found at i:1323447 original size:14 final size:14
Alignment explanation
Indices: 1323430--1323463 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1323420 GCTCGAATGG
1323430 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
1323444 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
*
1323458 CTTCGG
1 CCTCGG
1323464 ATGCCCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.35, T:0.24
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:1323684 original size:4 final size:4
Alignment explanation
Indices: 1323677--1323701 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1323667 TATATATACC
1323677 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
1323702 TAAATTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1329115 original size:13 final size:13
Alignment explanation
Indices: 1329097--1329121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1329087 GGATTTGGGG
1329097 GCTTGCTTCAGTT
1 GCTTGCTTCAGTT
1329110 GCTTGCTTCAGT
1 GCTTGCTTCAGT
1329122 GTGAATTGAG
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:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (13 bp):
GCTTGCTTCAGTT
Found at i:1329721 original size:2 final size:2
Alignment explanation
Indices: 1329714--1329747 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1329704 ATCGGCTAAC
1329714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1329748 TAGAGGAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1337087 original size:15 final size:17
Alignment explanation
Indices: 1337069--1337102 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1337059 TTATTGTAAA
1337069 ATTTTA-AA-ATAATTC
1 ATTTTATAATATAATTC
1337084 ATTTTATAATATAATTC
1 ATTTTATAATATAATTC
1337101 AT
1 AT
1337103 AATTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTATAATATAATTC
Found at i:1339193 original size:28 final size:28
Alignment explanation
Indices: 1339135--1339193 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1339125 GGAGCTGCAT
* *
1339135 AAAAAATATTAATATCCGATTTTACGTA
1 AAAAAATATTAATATCCGATTTTAAGAA
1339163 AAAAAATATCTGAA-AT-CGATTTTAAGAA
1 AAAAAATAT-T-AATATCCGATTTTAAGAA
1339191 AAA
1 AAA
1339194 TTGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 22 0.81
29 3 0.11
30 2 0.07
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (28 bp):
AAAAAATATTAATATCCGATTTTAAGAA
Found at i:1340721 original size:18 final size:19
Alignment explanation
Indices: 1340690--1340727 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1340680 ATTCTTTTCT
*
1340690 AAAATACGTGGAAAATAAA
1 AAAATACGTAGAAAATAAA
1340709 AAAATA-GTAGAAAATAAA
1 AAAATACGTAGAAAATAAA
1340727 A
1 A
1340728 TAAACAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAATACGTAGAAAATAAA
Found at i:1340988 original size:26 final size:26
Alignment explanation
Indices: 1340937--1340984 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
1340927 TAAAAACTAA
*
1340937 TTAATATAATATCTATATTTATATTT
1 TTAATATAAAATCTATATTTATATTT
1340963 TTAAT-TAAAATCT-TA-TTATATT
1 TTAATATAAAATCTATATTTATATT
1340985 ATTTCATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 7 0.33
26 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAATATAAAATCTATATTTATATTT
Found at i:1342145 original size:17 final size:16
Alignment explanation
Indices: 1342093--1342195 Score: 86
Period size: 17 Copynumber: 6.3 Consensus size: 16
1342083 ACCTTATCAT
*
1342093 ATTTTGTAGGGTTATG
1 ATTTTGTGGGGTTATG
*
1342109 ATTTT-TGGGTGTTTTG
1 ATTTTGTGGG-GTTATG
1342125 ATTTTGTGGAGGTTATG
1 ATTTTGTGG-GGTTATG
*
1342142 ATTTTAAAT-GGGTTATG
1 ATTTT--GTGGGGTTATG
* *
1342159 ATTTT-TGGGTTTTTG
1 ATTTTGTGGGGTTATG
*
1342174 ATTTTGTGGAGGTTATA
1 ATTTTGTGG-GGTTATG
1342191 ATTTT
1 ATTTT
1342196 CAATAGGGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.01
15 14 0.20
16 18 0.26
17 34 0.49
18 2 0.03
19 1 0.01
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.54
Consensus pattern (16 bp):
ATTTTGTGGGGTTATG
Found at i:1342167 original size:50 final size:50
Alignment explanation
Indices: 1342099--1342248 Score: 212
Period size: 50 Copynumber: 3.0 Consensus size: 50
1342089 TCATATTTTG
1342099 TAGGGTTATGATTTTTGGGTGTTTTGATTTTGTGGAGGTTATGATTTTAAA
1 TAGGGTTATGATTTTTGGGT-TTTTGATTTTGTGGAGGTTATGATTTTAAA
* *
1342150 T-GGGTTATGATTTTTGGGTTTTTGATTTTGTGGAGGTTATAATTTTCAA
1 TAGGGTTATGATTTTTGGGTTTTTGATTTTGTGGAGGTTATGATTTTAAA
* * * * *
1342199 TAGGGTTATGATTTTTGAGTCTTTGATTTTTTTGGAGGTTAGGGTTTTAA
1 TAGGGTTATGATTTTTGGGTTTTTGA-TTTTGTGGAGGTTATGATTTTAA
1342249 GGAGGAGAAG
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 29 0.33
50 40 0.45
51 19 0.22
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.52
Consensus pattern (50 bp):
TAGGGTTATGATTTTTGGGTTTTTGATTTTGTGGAGGTTATGATTTTAAA
Found at i:1342732 original size:31 final size:33
Alignment explanation
Indices: 1342686--1342748 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
1342676 TTTTATTTCT
*
1342686 TTTTTATATTATTATATCATAAT-ATTTTTTTA
1 TTTTTATATAATTATATCATAATAATTTTTTTA
* *
1342718 TTTTTA-ATAATTATATCTTTATAATTTTTTT
1 TTTTTATATAATTATATCATAATAATTTTTTT
1342749 CCTTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTTTATATAATTATATCATAATAATTTTTTTA
Found at i:1363224 original size:24 final size:23
Alignment explanation
Indices: 1363191--1363235 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
1363181 TCAAATAACA
*
1363191 GTTTAGTGGTTTAATATAGTCCTT
1 GTTTAATGGTTTAATAT-GTCCTT
1363215 GTTTAATGGTTTAATATGTCC
1 GTTTAATGGTTTAATATGTCC
1363236 ATAGTTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (23 bp):
GTTTAATGGTTTAATATGTCCTT
Found at i:1363243 original size:23 final size:24
Alignment explanation
Indices: 1363190--1363241 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1363180 TTCAAATAAC
*
1363190 AGTTTAGTGGTTTAATATAGTCCT
1 AGTTTAATGGTTTAATATAGTCCT
*
1363214 TGTTTAATGGTTTAATAT-GTCCAT
1 AGTTTAATGGTTTAATATAGTCC-T
1363238 AGTT
1 AGTT
1363242 AAGAAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (24 bp):
AGTTTAATGGTTTAATATAGTCCT
Found at i:1371543 original size:21 final size:21
Alignment explanation
Indices: 1371517--1371561 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1371507 TGATTCTGGG
* *
1371517 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1371538 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1371559 CAA
1 CAA
1371562 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1373301 original size:23 final size:22
Alignment explanation
Indices: 1373242--1373308 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
1373232 TATGAACATC
*
1373242 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
1373264 ATTCTACGGGCACTTCGATGCA
1 ATTCTACGGGCACTTCGGTGCA
1373286 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1373309 TTTATACGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 27 0.66
23 14 0.34
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1376440 original size:21 final size:21
Alignment explanation
Indices: 1376414--1376458 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1376404 GATTTCTGGG
* *
1376414 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1376435 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1376456 CAA
1 CAA
1376459 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1378210 original size:23 final size:22
Alignment explanation
Indices: 1378151--1378217 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1378141 TATGGACATC
*
1378151 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1378173 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1378195 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1378218 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1385166 original size:20 final size:20
Alignment explanation
Indices: 1385141--1385190 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1385131 ATTTGTAATA
*
1385141 ATATTTTTAATAAAATATTT
1 ATATTTTAAATAAAATATTT
1385161 ATATTTTAAATAAAATATTT
1 ATATTTTAAATAAAATATTT
1385181 ATATTTTAAA
1 ATATTTTAAA
1385191 AAATGACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTAAATAAAATATTT
Found at i:1385203 original size:21 final size:20
Alignment explanation
Indices: 1385141--1385203 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1385131 ATTTGTAATA
* *
1385141 ATATTTTTAATAAAATATTT
1 ATATTTTAAATAAAACATTT
*
1385161 ATATTTTAAATAAAATATTT
1 ATATTTTAAATAAAACATTT
1385181 ATATTTTAAA-AAATGACATTT
1 ATATTTTAAATAAA--ACATTT
1385202 AT
1 AT
1385204 CACAAAATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 3 0.08
20 29 0.74
21 7 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTTTAAATAAAACATTT
Found at i:1385434 original size:6 final size:6
Alignment explanation
Indices: 1385423--1385448 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1385413 AACACCTCGA
1385423 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
1385449 CTGACCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1386533 original size:17 final size:17
Alignment explanation
Indices: 1386500--1386545 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1386490 AATTAAATCC
1386500 ATATTTTATTGAATAAAA
1 ATATTTT-TTGAATAAAA
* *
1386518 ATATTTTTTTAATAAAT
1 ATATTTTTTGAATAAAA
1386535 ATATTATTTTG
1 ATATT-TTTTG
1386546 GGTCGGATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
ATATTTTTTGAATAAAA
Found at i:1387294 original size:18 final size:18
Alignment explanation
Indices: 1387271--1387308 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1387261 CCCAACATTG
1387271 TCGACCTTTTCTTCAACC
1 TCGACCTTTTCTTCAACC
1387289 TCGACCTTTTCTTCAACC
1 TCGACCTTTTCTTCAACC
1387307 TC
1 TC
1387309 ACCGCCGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.39, G:0.05, T:0.39
Consensus pattern (18 bp):
TCGACCTTTTCTTCAACC
Found at i:1390686 original size:2 final size:2
Alignment explanation
Indices: 1390679--1390708 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1390669 AATATTTGTG
1390679 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1390709 TATCGTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1395971 original size:3 final size:3
Alignment explanation
Indices: 1395965--1395999 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1395955 TCTTCTTCTT
1395965 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1396000 ACACGTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:1397705 original size:17 final size:18
Alignment explanation
Indices: 1397680--1397713 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1397670 AAATTTGGTT
*
1397680 AATTGATTG-ATTAATCG
1 AATTAATTGAATTAATCG
1397697 AATTAATTGAATTAATC
1 AATTAATTGAATTAATC
1397714 AAAATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
AATTAATTGAATTAATCG
Found at i:1397829 original size:2 final size:2
Alignment explanation
Indices: 1397822--1397862 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1397812 AAGCTAAATA
1397822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1397863 ATTTTGGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1398366 original size:27 final size:27
Alignment explanation
Indices: 1398335--1398413 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
1398325 TAACATTTTT
* *
1398335 GGTAAAGTGTCCAATAATAATAAAATC
1 GGTAAAGCGTCCAATAATAACAAAATC
1398362 GGTAAAGCGTCCAATAATAACAAAATC
1 GGTAAAGCGTCCAATAATAACAAAATC
* *
1398389 GATAAAGCGCCCAATAATAACAAAA
1 GGTAAAGCGTCCAATAATAACAAAA
1398414 CCGATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (27 bp):
GGTAAAGCGTCCAATAATAACAAAATC
Found at i:1398418 original size:27 final size:27
Alignment explanation
Indices: 1398345--1398421 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
1398335 GGTAAAGTGT
* * *
1398345 CCAATAATAATAAAATCGGTAAAGCGT
1 CCAATAATAACAAAATCGATAAAGCGC
1398372 CCAATAATAACAAAATCGATAAAGCGC
1 CCAATAATAACAAAATCGATAAAGCGC
*
1398399 CCAATAATAACAAAACCGATAAA
1 CCAATAATAACAAAATCGATAAA
1398422 AATAATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.53, C:0.19, G:0.10, T:0.17
Consensus pattern (27 bp):
CCAATAATAACAAAATCGATAAAGCGC
Found at i:1407832 original size:36 final size:36
Alignment explanation
Indices: 1407774--1407869 Score: 138
Period size: 36 Copynumber: 2.7 Consensus size: 36
1407764 ACCTGCTAAG
* * *
1407774 GAAGAAAAAAAGGAAGAAAAGAAGGAAGAAAAGAAA
1 GAAGAGAAGAAGGAAGAAAAGAAAGAAGAAAAGAAA
* * *
1407810 GAGGAGAAGAAGGAAGAGAAGAAAGAGGAAAAGAAA
1 GAAGAGAAGAAGGAAGAAAAGAAAGAAGAAAAGAAA
1407846 GAAGAGAAGAAGGAAGAAAAGAAA
1 GAAGAGAAGAAGGAAGAAAAGAAA
1407870 TGAATTTTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (36 bp):
GAAGAGAAGAAGGAAGAAAAGAAAGAAGAAAAGAAA
Found at i:1407867 original size:12 final size:12
Alignment explanation
Indices: 1407771--1407868 Score: 115
Period size: 12 Copynumber: 8.2 Consensus size: 12
1407761 CGGACCTGCT
*
1407771 AAGGAAGAAAAA
1 AAGGAAGAAAAG
1407783 AAGGAAGAAAAG
1 AAGGAAGAAAAG
1407795 AAGGAAGAAAAG
1 AAGGAAGAAAAG
* * *
1407807 AAAGAGGAGAAG
1 AAGGAAGAAAAG
*
1407819 AAGGAAGAGAAG
1 AAGGAAGAAAAG
* *
1407831 AAAGAGGAAAAG
1 AAGGAAGAAAAG
* *
1407843 AAAGAAGAGAAG
1 AAGGAAGAAAAG
1407855 AAGGAAGAAAAG
1 AAGGAAGAAAAG
1407867 AA
1 AA
1407869 ATGAATTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 73 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGGAAGAAAAG
Found at i:1416824 original size:34 final size:34
Alignment explanation
Indices: 1416781--1416861 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
1416771 CTTCTATGAT
1416781 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1416815 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1416849 TGTTTCATGAAAC
1 TGTTTCATGAAAC
1416862 GATATTATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (34 bp):
TGTTTCATGAAACTAACATATCACTGTCTAGTTG
Found at i:1422074 original size:19 final size:19
Alignment explanation
Indices: 1422052--1422095 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1422042 TAGAAACGTT
1422052 AAATAACCAAAT-TGACAAA
1 AAATAACCAAATGTGA-AAA
*
1422071 AAATAAACTAAATGTGAAAA
1 AAAT-AACCAAATGTGAAAA
1422091 AAATA
1 AAATA
1422096 TAATTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 14 0.64
21 3 0.14
ACGTcount: A:0.66, C:0.09, G:0.07, T:0.18
Consensus pattern (19 bp):
AAATAACCAAATGTGAAAA
Found at i:1429025 original size:31 final size:31
Alignment explanation
Indices: 1428954--1429026 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1428944 ATTTTTAATA
* * *
1428954 GTTATAAAATAGTCATTAAATTTATCGAATT
1 GTTATAAAATAATCATTAAATTTATCAAACT
*
1428985 ATTATAAAATAATCATTAAATTTATCAAACT
1 GTTATAAAATAATCATTAAATTTATCAAACT
*
1429016 GTTACAAAATA
1 GTTATAAAATA
1429027 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
GTTATAAAATAATCATTAAATTTATCAAACT
Found at i:1429046 original size:28 final size:28
Alignment explanation
Indices: 1428999--1429058 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
1428989 TAAAATAATC
1428999 ATTAAATTTATCAAACTGTTACAAAA-T
1 ATTAAATTTATCAAACTGTTACAAAATT
*
1429026 ATTAAATTTTATTGAAA-TGTTACAAAATT
1 ATTAAA-TTTA-TCAAACTGTTACAAAATT
1429055 ATTA
1 ATTA
1429059 TTATTAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.21
28 14 0.48
29 9 0.31
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (28 bp):
ATTAAATTTATCAAACTGTTACAAAATT
Found at i:1431722 original size:25 final size:25
Alignment explanation
Indices: 1431694--1431771 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
1431684 GTGAAGGTTG
1431694 GAAGGAACAAGTGATTTAATCGATT
1 GAAGGAACAAGTGATTTAATCGATT
1431719 GAAGGAACAAGTGATTTAATCGATT
1 GAAGGAACAAGTGATTTAATCGATT
1431744 GAAGGAACAAGTGATTTAATCGATT
1 GAAGGAACAAGTGATTTAATCGATT
1431769 GAA
1 GAA
1431772 CAAAACAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (25 bp):
GAAGGAACAAGTGATTTAATCGATT
Found at i:1453855 original size:8 final size:8
Alignment explanation
Indices: 1453842--1453891 Score: 100
Period size: 8 Copynumber: 6.2 Consensus size: 8
1453832 CAACACATAT
1453842 TTGTTCAC
1 TTGTTCAC
1453850 TTGTTCAC
1 TTGTTCAC
1453858 TTGTTCAC
1 TTGTTCAC
1453866 TTGTTCAC
1 TTGTTCAC
1453874 TTGTTCAC
1 TTGTTCAC
1453882 TTGTTCAC
1 TTGTTCAC
1453890 TT
1 TT
1453892 TCTTTTACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTTCAC
Found at i:1459790 original size:27 final size:27
Alignment explanation
Indices: 1459744--1459797 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1459734 AAATTCAAAA
* *
1459744 AGTAATCTCTAATCTTGATAAAGTTTT
1 AGTAATCTCTAATATGGATAAAGTTTT
*
1459771 AGTAATCTCTGATATGGATAAAGTTTT
1 AGTAATCTCTAATATGGATAAAGTTTT
1459798 TTCACTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (27 bp):
AGTAATCTCTAATATGGATAAAGTTTT
Found at i:1460319 original size:114 final size:114
Alignment explanation
Indices: 1460119--1460347 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
1460109 GTACATTTTC
1460119 AAGCTGTTAAAAGAATTCTGCGGTATCTCCAAGGAACACTTCACTATGGCTTGAAGTTTTCTGGT
1 AAGCTGTTAAAAGAATTCTGCGGTATCTCCAAGGAACACTTCACTATGGCTTGAAGTTTTCTGGT
1460184 TCTTCACGACTAGCGATAACCAGTTTTGCTGATGCTGATTGGGATTCTG
66 TCTTCACGACTAGCGATAACCAGTTTTGCTGATGCTGATTGGGATTCTG
1460233 AAGCTGTTAAAAGAATTCTGCGGTATCTCCAAGGAACACTTCACTATGGCTTGAAGTTTTCTGGT
1 AAGCTGTTAAAAGAATTCTGCGGTATCTCCAAGGAACACTTCACTATGGCTTGAAGTTTTCTGGT
1460298 TCTTCACGACTAGCGATAACCAGTTTTGCTGATGCTGATTGGGATTCTG
66 TCTTCACGACTAGCGATAACCAGTTTTGCTGATGCTGATTGGGATTCTG
1460347 A
1 A
1460348 TCTGGTTGAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (114 bp):
AAGCTGTTAAAAGAATTCTGCGGTATCTCCAAGGAACACTTCACTATGGCTTGAAGTTTTCTGGT
TCTTCACGACTAGCGATAACCAGTTTTGCTGATGCTGATTGGGATTCTG
Found at i:1463684 original size:31 final size:32
Alignment explanation
Indices: 1463614--1463684 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1463604 TCCTTATTGC
* **
1463614 GATATATATCATAATATTAAAAATAATAATTT
1 GATATATAACATAATATTAAAAATAATAAGAT
* * *
1463646 GACATATAACAT-ATTTTTAAAATAATAAGAT
1 GATATATAACATAATATTAAAAATAATAAGAT
1463677 GATATATA
1 GATATATA
1463685 TATATCACAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (32 bp):
GATATATAACATAATATTAAAAATAATAAGAT
Found at i:1464878 original size:26 final size:26
Alignment explanation
Indices: 1464831--1464881 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1464821 ATATTATCTT
* * *
1464831 ATAATAATTATAAACTATTTAAAGTA
1 ATAATAATAATAAACAAATTAAAGTA
*
1464857 ATAATAATAATAATCAAATTAAAGT
1 ATAATAATAATAAACAAATTAAAGT
1464882 CAAACATGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAATAATAATAAACAAATTAAAGTA
Found at i:1468286 original size:29 final size:29
Alignment explanation
Indices: 1468253--1468309 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1468243 AGTGTTGGCC
1468253 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
1468282 GTAGGTCGCCATGTACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1468310 ACCCTCGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1468358 original size:33 final size:33
Alignment explanation
Indices: 1468313--1468382 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1468303 GCGACCTACC
* *
1468313 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCAGTTGCCCTCGGATGCCCTCGCATAG
1468346 CTCGCTCAGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCAGTTGCCCTCGGATGCCCTCGCATAG
1468379 CTCG
1 CTCG
1468383 TTCGGATGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.10, C:0.40, G:0.24, T:0.26
Consensus pattern (33 bp):
CTCGCTCAGTTGCCCTCGGATGCCCTCGCATAG
Found at i:1468396 original size:33 final size:33
Alignment explanation
Indices: 1468313--1468397 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
1468303 GCGACCTACC
* * *
1468313 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCAGATGCCCTCGGATGCCCTCGCATAG
*
1468346 CTCGCTCAGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCAGATGCCCTCGGATGCCCTCGCATAG
* * *
1468379 CTCGTTCGGATGGCCTCGG
1 CTCGCTCAGATGCCCTCGG
1468398 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.38, G:0.27, T:0.26
Consensus pattern (33 bp):
CTCGCTCAGATGCCCTCGGATGCCCTCGCATAG
Found at i:1468401 original size:14 final size:14
Alignment explanation
Indices: 1468379--1468411 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1468369 CCTCGCATAG
*
1468379 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1468393 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1468407 CTCGG
1 CTCGG
1468412 ATGCCCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1468647 original size:19 final size:19
Alignment explanation
Indices: 1468623--1468661 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1468613 CCCCACAGGT
1468623 CGCCCGGATGCCATGGCGA
1 CGCCCGGATGCCATGGCGA
1468642 CGCCCGGATGCCATGGCGA
1 CGCCCGGATGCCATGGCGA
1468661 C
1 C
1468662 CTCTAAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.38, G:0.36, T:0.10
Consensus pattern (19 bp):
CGCCCGGATGCCATGGCGA
Found at i:1471723 original size:11 final size:10
Alignment explanation
Indices: 1471703--1471730 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1471693 AGAAAACCAG
1471703 AAAAAGAAAA
1 AAAAAGAAAA
1471713 AAAAAGAAAA
1 AAAAAGAAAA
1471723 AAAAAGAA
1 AAAAAGAA
1471731 GAAGCAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1473316 original size:238 final size:240
Alignment explanation
Indices: 1472894--1473334 Score: 579
Period size: 238 Copynumber: 1.8 Consensus size: 240
1472884 GATTCTTACG
* * * * * *
1472894 TGTAGACATATAACACGTGTTACGAAAATTAAAATGTTCATGTGAAACTATAATCTTAAATATTG
1 TGTAAACAAATAACACGTGTTACGAAAATTAAAATATACATGTGAAACTACAATCATAAATATTG
*
1472959 ATGTCGTTTATTGTGACATCAATAATTCAATTTAGCAATCAAAATAATTCTAAGATGATTGGATC
66 ATGTCGTTTATTGTGACATCAATAATTCAAGTTAGCAATCAAAATAATTCTAAGATGATTGGATC
* * * * *
1473024 TATTAAAATAATTGGGACTTATGCACTTAATAAAGTTCTCATTGTTATTGAGTGAAAAG-GTTAG
131 TATTAAAATAATCGGGACTTACGCACTTAAGAAAGTTATCATTGTTACTGAGTG-AAAGCGTTAG
1473088 ATCATGTTAATAACAAGTCAAGTTAAAACGGTCAATGATTGTTATT
195 ATCATGTTAATAACAAGTCAAGTTAAAACGGTCAATGATTGTTATT
* *
1473134 TGTAAACAAATAACACGTGTTGCGAAAATTAAAATATACATGTG-AA-TGCAATCATAAATATT-
1 TGTAAACAAATAACACGTGTTACGAAAATTAAAATATACATGTGAAACTACAATCATAAATATTG
** ** * *
1473196 ATTGTCGTTTATTGTGACATCAATAATTTGAGTTATTAATCAGAATATTTCTAAGATGATTGGAT
66 A-TGTCGTTTATTGTGACATCAATAATTCAAGTTAGCAATCAAAATAATTCTAAGATGATTGGAT
* * * * *
1473261 CTATTGAAATTATCGAGG-CTTACGCGCTTGAGAAAGTTAT-ATTTGTTGCTGAGTGAAAGCGTT
130 CTATTAAAATAATCG-GGACTTACGCACTTAAGAAAGTTATCA-TTGTTACTGAGTGAAAGCGTT
1473324 AGATCATGTTA
193 AGATCATGTTA
1473335 TCATCAAATC
Statistics
Matches: 172, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
237 6 0.03
238 123 0.72
239 4 0.02
240 39 0.23
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (240 bp):
TGTAAACAAATAACACGTGTTACGAAAATTAAAATATACATGTGAAACTACAATCATAAATATTG
ATGTCGTTTATTGTGACATCAATAATTCAAGTTAGCAATCAAAATAATTCTAAGATGATTGGATC
TATTAAAATAATCGGGACTTACGCACTTAAGAAAGTTATCATTGTTACTGAGTGAAAGCGTTAGA
TCATGTTAATAACAAGTCAAGTTAAAACGGTCAATGATTGTTATT
Found at i:1473651 original size:261 final size:261
Alignment explanation
Indices: 1473187--1473661 Score: 677
Period size: 261 Copynumber: 1.8 Consensus size: 261
1473177 GAATGCAATC
* * * * * *
1473187 ATAAATATTATTGTCGTTTATTGTGACATCAATAATTTGAGTTATTAATCAGAATATTTCTAAGA
1 ATAAATATTATTGTCGTTTACTGTGACATCAATAATTTGAGATATCAATCAGAAGAATTCTAAAA
** * * *
1473252 TGATTGGATCTATTGAAATTATCGAGGCTTACGCGCTTGAGAAAGTTATATTTGTTGCTGAGTGA
66 TGATTGGATCTATTGAAACAATCGAGGCTTACGCGCTTGAAAAAGTTATATTTGTTACCGAGTGA
* * *
1473317 AAGCGTTAGATCATGTTATCATCAAATCAAATTATAATGATCTTATTTATTGTGTTTATTTGACT
131 AAGCGTTAGATCATGTTACCATCAAATCAAATTATAATGATCTTATTTATTGTATTTATTCGACT
1473382 TCAATGATTAATATTTGTATACAACACGTGTTACAAAAATTGAAATGTACATATGATACTATACT
196 TCAATGATTAATATTTGTATACAACACGTGTTACAAAAATTGAAATGTACATATGATACTATACT
1473447 A
261 A
*
1473448 ATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTGAGATATCAATTCA-AAGAATTCTAAA
1 ATAAATATTATTGTCGTTTACTGTGACATCAATAATTTGAGATATCAA-TCAGAAGAATTCTAAA
* * * * * *
1473512 ATTATTGGATCTATTGTAACAACTGGA-GTTTATGCGCTTGAAAAAGTTCTATTTGTTACCGAGT
65 ATGATTGGATCTATTGAAACAA-TCGAGGCTTACGCGCTTGAAAAAGTTATATTTGTTACCGAGT
* *
1473576 GAAAAG-GTTATATCATGTTACCATCAAGTCAAATTATAATGATCTTATTTATTGTATTTATTCG
129 G-AAAGCGTTAGATCATGTTACCATCAAATCAAATTATAATGATCTTATTTATTGTATTTATTCG
* *
1473640 ACTTCAATGATTATTGTTTGTA
193 ACTTCAATGATTAATATTTGTA
1473662 AACATATAAC
Statistics
Matches: 186, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
261 176 0.95
262 10 0.05
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (261 bp):
ATAAATATTATTGTCGTTTACTGTGACATCAATAATTTGAGATATCAATCAGAAGAATTCTAAAA
TGATTGGATCTATTGAAACAATCGAGGCTTACGCGCTTGAAAAAGTTATATTTGTTACCGAGTGA
AAGCGTTAGATCATGTTACCATCAAATCAAATTATAATGATCTTATTTATTGTATTTATTCGACT
TCAATGATTAATATTTGTATACAACACGTGTTACAAAAATTGAAATGTACATATGATACTATACT
A
Found at i:1475134 original size:41 final size:41
Alignment explanation
Indices: 1475089--1475170 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1475079 ATAATTTCGT
* *
1475089 CTCCACACTTTTATAATATTTACATATATATATTAGTATTA
1 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1475130 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1475171 ATTTCATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (41 bp):
CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
Found at i:1487430 original size:50 final size:52
Alignment explanation
Indices: 1487351--1487448 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 52
1487341 AATACTTCGC
* **
1487351 TTAGGATGAAAACCCGAGAGGGCGTCCT-AAGT-AAAAAAAAAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAAGTGAAAAAAAAAAAAGAACGT
* * *
1487401 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAAGTGAAAAAAAAAAAAGA
1487449 GAAGAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 24 0.60
51 3 0.08
52 13 0.32
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.13
Consensus pattern (52 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAAGTGAAAAAAAAAAAAGAACGT
Found at i:1488356 original size:105 final size:105
Alignment explanation
Indices: 1488174--1488874 Score: 1222
Period size: 105 Copynumber: 6.7 Consensus size: 105
1488164 AGGTTTTACC
*
1488174 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1488239 ACGAAAGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1488279 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1488344 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1488384 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1488449 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1488489 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1488554 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1488594 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1488659 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1488699 CAGAGCCAATTTCAACTGCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
1488764 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTT
* * **** *
1488805 CAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAGTATAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1488870 ACGAA
66 ACGAA
1488875 TGAGCTATAT
Statistics
Matches: 573, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 503 0.88
106 70 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1489307 original size:41 final size:41
Alignment explanation
Indices: 1489250--1489331 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1489240 ATAATTTCGT
* *
1489250 CTCCACACTTTTATAATATTTACATATATATATTAGTATTA
1 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1489291 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1 CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
1489332 ATTTCATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (41 bp):
CTCCACACTCTTATAATATTCACATATATATATTAGTATTA
Found at i:1498663 original size:103 final size:103
Alignment explanation
Indices: 1498483--1498796 Score: 565
Period size: 103 Copynumber: 3.0 Consensus size: 103
1498473 GTTTCGATTT
*
1498483 GACCTAACCTTATAGGGATGGATTTTTTTTTAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGG
1 GACCTGACCTTATAGGGATGGA-TTTTTTTTAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGG
* *
1498548 CGAGATCGGGTTTAAGGTGAAAAATCACCAACCCGACTC
65 CGGGATCGGGTTTAAGGTGAAAAATCACCAACCCGACCC
*
1498587 GACCTGACCTTATAGGGATGGATTTTTTTAAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGGC
1 GACCTGACCTTATAGGGATGGATTTTTTTTAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGGC
1498652 GGGATCGGGTTTAAGGTGAAAAATCACCAACCCGACCC
66 GGGATCGGGTTTAAGGTGAAAAATCACCAACCCGACCC
*
1498690 GACCTGACCTTATAGGGATGGATTTTTTTTTAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGGC
1 GACCTGACCTTATAGGGATGGATTTTTTTTAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGGC
*
1498755 GGGATCGAGTTTAAGGTGAAAAATCACCAACCCGACCC
66 GGGATCGGGTTTAAGGTGAAAAATCACCAACCCGACCC
1498793 GACC
1 GACC
1498797 AGATTAATTT
Statistics
Matches: 203, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
103 182 0.90
104 21 0.10
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (103 bp):
GACCTGACCTTATAGGGATGGATTTTTTTTAAAATTTGAGGACTCAGGGCAGGGCAGGGCAGGGC
GGGATCGGGTTTAAGGTGAAAAATCACCAACCCGACCC
Found at i:1498894 original size:24 final size:24
Alignment explanation
Indices: 1498848--1498894 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1498838 TTAAAATTTA
* *
1498848 TATTATTAAAATATGTTCTTTAAT
1 TATTATTAAAATATATTATTTAAT
1498872 TATTA-TAAAATATATTATCTTAA
1 TATTATTAAAATATATTAT-TTAA
1498895 CCTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTATTAAAATATATTATTTAAT
Found at i:1500894 original size:28 final size:28
Alignment explanation
Indices: 1500859--1500913 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1500849 CTTTGTATTC
*
1500859 ATTATATTATCGAGTCAGTTCTTGAAAT
1 ATTATATTATCGAGTCAGTGCTTGAAAT
* *
1500887 ATTATATTGTTGAGTCAGTGCTTGAAA
1 ATTATATTATCGAGTCAGTGCTTGAAA
1500914 GCAACGGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (28 bp):
ATTATATTATCGAGTCAGTGCTTGAAAT
Found at i:1501564 original size:18 final size:17
Alignment explanation
Indices: 1501540--1501576 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1501530 ATAAAATTAT
*
1501540 GTTTTTCCGGATACCTA
1 GTTTTTTCGGATACCTA
1501557 GTTTTTTCGGATACCTA
1 GTTTTTTCGGATACCTA
1501574 GTT
1 GTT
1501577 ACTCGAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (17 bp):
GTTTTTTCGGATACCTA
Found at i:1505115 original size:18 final size:19
Alignment explanation
Indices: 1505084--1505121 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1505074 TTTGATGTTA
1505084 TAAAAAATAAATAA-ATTT
1 TAAAAAATAAATAATATTT
**
1505102 TAAAAAATTCATAATATTT
1 TAAAAAATAAATAATATTT
1505121 T
1 T
1505122 TATAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAAATAAATAATATTT
Found at i:1505190 original size:23 final size:23
Alignment explanation
Indices: 1505163--1505221 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1505153 AAAAATATTT
1505163 TAAAAATATTATAATTTCAAA-A
1 TAAAAATATTATAATTTCAAAGA
* *
1505185 TGAAAATAATTTATAATTTTAAAGA
1 TAAAAAT-A-TTATAATTTCAAAGA
*
1505210 TAAATATATTAT
1 TAAAAATATTAT
1505222 TGAACTCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 6 0.20
23 5 0.17
24 13 0.43
25 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (23 bp):
TAAAAATATTATAATTTCAAAGA
Found at i:1507995 original size:2 final size:2
Alignment explanation
Indices: 1507990--1508019 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1507980 TATATATGGT
1507990 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1508020 AACGTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1514418 original size:21 final size:21
Alignment explanation
Indices: 1514394--1514436 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1514384 ACAAAAGAAA
1514394 ACCTAATTTTGAAACCAACTC
1 ACCTAATTTTGAAACCAACTC
1514415 ACCTAATTTTGAAACCAACTC
1 ACCTAATTTTGAAACCAACTC
1514436 A
1 A
1514437 TTAGACCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.28
Consensus pattern (21 bp):
ACCTAATTTTGAAACCAACTC
Found at i:1516131 original size:19 final size:20
Alignment explanation
Indices: 1516107--1516145 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1516097 TAATAAATTG
*
1516107 ACTTGT-TTGTGAAAAAAAC
1 ACTTGTATTCTGAAAAAAAC
1516126 ACTTGTACTTCTGAAAAAAA
1 ACTTGTA-TTCTGAAAAAAA
1516146 TCAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
ACTTGTATTCTGAAAAAAAC
Found at i:1526099 original size:3 final size:3
Alignment explanation
Indices: 1526091--1526116 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1526081 ACAATACCAA
1526091 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
1526117 ATCAGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1526828 original size:61 final size:61
Alignment explanation
Indices: 1526734--1526868 Score: 245
Period size: 61 Copynumber: 2.2 Consensus size: 61
1526724 AATCCGTCGG
*
1526734 ATTTGGATA-TTTTAATCATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
1 ATTTGGGTATTTTTAATCATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
*
1526794 ATTTGGGTATTTTTAATTATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
1 ATTTGGGTATTTTTAATCATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
1526855 ATTTGGGTATTTTT
1 ATTTGGGTATTTTT
1526869 TGGTTTACAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
60 8 0.11
61 64 0.89
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (61 bp):
ATTTGGGTATTTTTAATCATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
Found at i:1528964 original size:40 final size:41
Alignment explanation
Indices: 1528871--1529144 Score: 254
Period size: 41 Copynumber: 6.6 Consensus size: 41
1528861 GGTTCATCGA
* * *
1528871 TAGTGGCGTTTTT-TCAACAAACGCCGCAAAAGAGTAGTAC-T
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTCGTACTT
* *
1528912 TAGTGGCG-TTTTATACAAACGTCGCTAAAGACTCGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
1528952 TAGTGGC-ATTTTATACAAACGCCGCTATAGAATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
1528992 TAGTGGCGTTTTTATACAAACGTCGTTATACATA-T-GTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTA-A-AGACTCGTACTT
*
1529033 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * * *
1529076 TAGTGGCGTTTTTATTCAAACGCCGCTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
*
1529117 TAGTGGCGTTTGTGTTTACAAACGCCGC
1 TAGTGGCGTTT-T-TATACAAACGCCGC
1529145 AAGATTACAA
Statistics
Matches: 192, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
39 19 0.10
40 46 0.24
41 78 0.41
42 6 0.03
43 43 0.22
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:1529078 original size:84 final size:82
Alignment explanation
Indices: 1528870--1529144 Score: 301
Period size: 84 Copynumber: 3.3 Consensus size: 82
1528860 AGGTTCATCG
* * *
1528870 ATAGTGGCGTTTTTTCAACAAACGCCGCAAAAGAGTAGTAC-TTAGTGGCG-TTTTATACAAACG
1 ATAGTGGCGTTTTTT-TACAAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATACAAACG
* *
1528933 TCGCTA-A-AGACTCGTAAT
65 TCGCTATACATA-T-GTACT
* * * * *
1528951 TTAGTGGC-ATTTTATACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTATACAAACGT
1 ATAGTGGCGTTTTTTTACAAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATACAAACGT
*
1529015 CGTTATACATATGTACT
66 CGCTATACATATGTACT
* * *
1529032 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAAC
1 ATAGTGGCGTTT-T-TTTACAAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATACAAAC
*
1529097 GCCGCTATACACT-TGTACT
64 GTCGCTATACA-TATGTACT
1529116 ATAGTGGCGTTTGTGTTTACAAACGCCGC
1 ATAGTGGCGTTT-T-TTTACAAACGCCGC
1529145 AAGATTACAA
Statistics
Matches: 166, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
79 20 0.12
80 13 0.08
81 36 0.22
82 4 0.02
83 3 0.02
84 89 0.54
85 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (82 bp):
ATAGTGGCGTTTTTTTACAAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATACAAACGT
CGCTATACATATGTACT
Found at i:1530972 original size:21 final size:21
Alignment explanation
Indices: 1530948--1531006 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1530938 TGATTTATTA
**
1530948 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
1530969 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
1530990 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
1531007 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:1531028 original size:131 final size:130
Alignment explanation
Indices: 1530760--1531016 Score: 442
Period size: 131 Copynumber: 1.9 Consensus size: 130
1530750 TATATTTATT
1530760 ATAGTTAATAATGTTGACTACATTATATTTTACGTTAATGTAAACTTTGATTTATTATTATGGAT
1 ATAGTTAATAATGTTGACTACATTATATTTTACGTTAATGTAAACTTTGATTTATTATTATGGAT
** *
1530825 TTCATTTTCTTGTTATGGATTTTAAGTTGTTGTTGGATGTCAAGTTTATTGGAAAATTATTTATT
66 TTCATTTTCTTGTTATGGATTTTAAGTTGTTGTTGGATGTCAAGTTTATTGGAAAATTAGCTATC
1530890 ATAGTTAATAATGTTGAACTACATTATATTTTACGTTAATGTAAACTTTGATTTATTATTATGGA
1 ATAGTTAATAATGTTG-ACTACATTATATTTTACGTTAATGTAAACTTTGATTTATTATTATGGA
1530955 TTTCATTTTTCTTGTTATGGATTTTAAGTTTGTTGTTATGGATGTCAAGTTTATTGGAAAAT
65 TTTCA-TTTTCTTGTTATGGATTTTAAG-TTGTTG-T-TGGATGTCAAGTTTATTGGAAAAT
1531017 GCTACAGGTT
Statistics
Matches: 122, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
130 16 0.13
131 53 0.43
132 22 0.18
133 6 0.05
134 1 0.01
135 24 0.20
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (130 bp):
ATAGTTAATAATGTTGACTACATTATATTTTACGTTAATGTAAACTTTGATTTATTATTATGGAT
TTCATTTTCTTGTTATGGATTTTAAGTTGTTGTTGGATGTCAAGTTTATTGGAAAATTAGCTATC
Found at i:1531203 original size:42 final size:42
Alignment explanation
Indices: 1531118--1531228 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1531108 GAGGTAATTA
* *
1531118 GCGGCGTTTGTATCTTAAAACGCCGCTATAGATATGACATTTT
1 GCGGCGTTTGT-TCTAAAAACGCCGCTATAGACATGACATTTT
*
1531161 GCGGCGTTTGTTCTAAAAACGCCGCTATATACCA-GATC-TTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGA-CATGA-CATTTT
* ***
1531203 GCGGTGTTTGTGGGAAAAACGCCGCT
1 GCGGCGTTTGTTCTAAAAACGCCGCT
1531229 CAATCTCAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 46 0.78
43 13 0.22
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCTAAAAACGCCGCTATAGACATGACATTTT
Found at i:1531277 original size:43 final size:43
Alignment explanation
Indices: 1531175--1531385 Score: 219
Period size: 43 Copynumber: 4.9 Consensus size: 43
1531165 CGTTTGTTCT
* * * * * * *
1531175 AAAAACGCCGCTATATA-CCAGATCTTTTGCGGTGTTTGTGGG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTGGG
* * *
1531217 AAAAACGCCGCTCAATCTCAACACCTATTACGGCGTTTTTGGG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTGGG
* * * *
1531260 GAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTAGG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTGGG
*
1531303 AAAAACGCCGCCAAATATCAACACCTATTGCGGCGTTTGTT-GG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTGGG
* * ***
1531346 ACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTTTT
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
1531386 TGTTACCAAA
Statistics
Matches: 142, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 16 0.11
43 125 0.88
44 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTGGG
Found at i:1537296 original size:23 final size:23
Alignment explanation
Indices: 1537270--1537317 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1537260 ATAAAGTACA
*
1537270 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1537293 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1537316 AT
1 AT
1537318 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1537673 original size:20 final size:20
Alignment explanation
Indices: 1537648--1537686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1537638 TCCACAGTGA
* *
1537648 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
1537668 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
1537687 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:1538053 original size:18 final size:18
Alignment explanation
Indices: 1538030--1538066 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1538020 CGAAATATAT
1538030 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1538048 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1538066 A
1 A
1538067 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1538334 original size:23 final size:23
Alignment explanation
Indices: 1538270--1538313 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1538260 ATTCGAGATA
1538270 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
1538293 GATACCTATTACATTATATAA
1 GATACCTATTACATTATATAA
1538314 GGGCTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:1538718 original size:21 final size:22
Alignment explanation
Indices: 1538693--1538744 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1538683 ACACTTTACA
*
1538693 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1538716 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1538739 ATATAA
1 ATATAA
1538745 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1538729 original size:23 final size:23
Alignment explanation
Indices: 1538703--1538765 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1538693 ATATAACCAC
1538703 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1538726 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1538749 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1538766 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1540480 original size:3 final size:3
Alignment explanation
Indices: 1540472--1540497 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1540462 ACAATACCAA
1540472 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
1540498 ATCAGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1541209 original size:61 final size:60
Alignment explanation
Indices: 1541115--1541238 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 60
1541105 AATCCGTCGG
*
1541115 ATTTGGATATTTTAATCATCCTTAATTTCTAGTTCTAATAAAATCATTTAATATTAATTT
1 ATTTGGATATTTTAATCATCCTTAATTCCTAGTTCTAATAAAATCATTTAATATTAATTT
* *
1541175 ATTTGGGTATTTTTAATTATCCTTAATTCCTAGTTCTAATAAAATCATTTAATATTAATTT
1 ATTTGGATA-TTTTAATCATCCTTAATTCCTAGTTCTAATAAAATCATTTAATATTAATTT
1541236 ATT
1 ATT
1541239 ATAGAAAACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
60 8 0.13
61 52 0.87
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.51
Consensus pattern (60 bp):
ATTTGGATATTTTAATCATCCTTAATTCCTAGTTCTAATAAAATCATTTAATATTAATTT
Found at i:1541533 original size:18 final size:19
Alignment explanation
Indices: 1541510--1541545 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1541500 TATCAATAAT
1541510 ATATATATATTTT-AAAAA
1 ATATATATATTTTGAAAAA
*
1541528 ATATATATTTTTTGAAAA
1 ATATATATATTTTGAAAA
1541546 TTTCAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATATATATATTTTGAAAAA
Found at i:1543499 original size:33 final size:32
Alignment explanation
Indices: 1543452--1543567 Score: 108
Period size: 33 Copynumber: 3.6 Consensus size: 32
1543442 AATGAATTTC
** * *
1543452 TTGATTGGCATATTATCTCTAGTTACTTTGATT
1 TTGATTGAAATATAATCTCTAGTTA-TTTAATT
* * * *
1543485 TTAATTGAAATATTATCTTTAATTATTTTAATT
1 TTGATTGAAATATAATCTCTAGTTA-TTTAATT
*
1543518 TTGATT-AATATATAATCTCTAGTTATTTTATT
1 TTGATTGAA-ATATAATCTCTAGTTATTTAATT
*
1543550 TTGATTGACATATAATCT
1 TTGATTGAAATATAATCT
1543568 TGAATTTAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
32 23 0.34
33 45 0.66
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (32 bp):
TTGATTGAAATATAATCTCTAGTTATTTAATT
Found at i:1560267 original size:29 final size:29
Alignment explanation
Indices: 1560231--1560289 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1560221 CATAAATTAA
1560231 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1560260 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1560289 T
1 T
1560290 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1564700 original size:29 final size:29
Alignment explanation
Indices: 1564666--1564724 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1564656 CCTAAATTAA
1564666 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1564695 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1564724 T
1 T
1564725 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1566568 original size:6 final size:6
Alignment explanation
Indices: 1566557--1566597 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1566547 ATCGGTTATA
* * *
1566557 TATATG TATATG TATATG TAAATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
1566598 ATCCACATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:1572076 original size:37 final size:37
Alignment explanation
Indices: 1572026--1572100 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1572016 ATAGCCACGA
1572026 AAGACAATGATTAAACTACTATTCTAACGCCATTTGC
1 AAGACAATGATTAAACTACTATTCTAACGCCATTTGC
*
1572063 AAGACAATGATTAAACTACTATTCTAATGCCATTTGC
1 AAGACAATGATTAAACTACTATTCTAACGCCATTTGC
1572100 A
1 A
1572101 TGCACCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (37 bp):
AAGACAATGATTAAACTACTATTCTAACGCCATTTGC
Found at i:1574689 original size:25 final size:25
Alignment explanation
Indices: 1574655--1574714 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
1574645 GAACTTCATT
1574655 TGAAATTTTGTTCGAGTCAAGCCGA
1 TGAAATTTTGTTCGAGTCAAGCCGA
1574680 TGAAATTTTGTTCGAGTCAAGCCGA
1 TGAAATTTTGTTCGAGTCAAGCCGA
1574705 TGAAATTTTG
1 TGAAATTTTG
1574715 AGTCGATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.35
Consensus pattern (25 bp):
TGAAATTTTGTTCGAGTCAAGCCGA
Found at i:1585055 original size:15 final size:15
Alignment explanation
Indices: 1585035--1585071 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1585025 TGAGACATTA
*
1585035 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
1585050 CCCGCCCCATATCCG
1 CCCGCCCCACATCCG
1585065 CCCGCCC
1 CCCGCCC
1585072 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1586542 original size:16 final size:16
Alignment explanation
Indices: 1586523--1586579 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
1586513 TAAATTTATT
*
1586523 AAAAATAAAATAGAAG
1 AAAAATAAAATAAAAG
*
1586539 AAAAAATAAAGATACAA-
1 -AAAAATAAA-ATAAAAG
* *
1586556 AATAATAAAACAAAAG
1 AAAAATAAAATAAAAG
1586572 AAAAATAA
1 AAAAATAA
1586580 TAAATACCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.12
16 15 0.45
17 9 0.27
18 5 0.15
ACGTcount: A:0.77, C:0.04, G:0.07, T:0.12
Consensus pattern (16 bp):
AAAAATAAAATAAAAG
Found at i:1594707 original size:3 final size:3
Alignment explanation
Indices: 1594699--1594735 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1594689 ACAAGTATAT
*
1594699 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1594736 GAAGAAGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1607774 original size:148 final size:148
Alignment explanation
Indices: 1607501--1607793 Score: 482
Period size: 148 Copynumber: 2.0 Consensus size: 148
1607491 AAACTATTTA
* * *
1607501 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
* ***
1607566 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATTGAAAAAATTTCGAGTCAACT
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAACAAAAAAAATTTCGAGTCAACT
1607631 ATGTTATAAACTGAACTG
131 ATGTTATAAACTGAACTG
1607649 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTC-AG
1 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGA-
1607713 AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAAACAAAAAAAATTT-GAGTCAA
65 AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTC-AAACAAAAAAAATTTCGAGTCAA
*
1607777 CTATTTTATAAACTGAA
129 CTATGTTATAAACTGAA
1607794 TTGAGTATTT
Statistics
Matches: 135, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
147 1 0.01
148 122 0.90
149 12 0.09
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAACAAAAAAAATTTCGAGTCAACT
ATGTTATAAACTGAACTG
Found at i:1608008 original size:35 final size:35
Alignment explanation
Indices: 1607960--1608045 Score: 118
Period size: 35 Copynumber: 2.4 Consensus size: 35
1607950 GAATTTGGAG
*
1607960 TTGGACATGTAATTGAAGTATTTTGGAATTTGAGGT
1 TTGGA-ATGTAATTGAAGAATTTTGGAATTTGAGGT
* * *
1607996 TTGGAATATAATTGAAGAATTTTGGATTTTGGGGT
1 TTGGAATGTAATTGAAGAATTTTGGAATTTGAGGT
*
1608031 TTAGAATGTAATTGA
1 TTGGAATGTAATTGA
1608046 TGACTATGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 39 0.89
36 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.42
Consensus pattern (35 bp):
TTGGAATGTAATTGAAGAATTTTGGAATTTGAGGT
Found at i:1615051 original size:19 final size:19
Alignment explanation
Indices: 1615027--1615065 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1615017 TAACCATCAC
1615027 ATGAATTACA-ATTCTTTAA
1 ATGAATTACATATT-TTTAA
1615046 ATGAATTACATATTTTTAA
1 ATGAATTACATATTTTTAA
1615065 A
1 A
1615066 AAAATGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (19 bp):
ATGAATTACATATTTTTAA
Found at i:1626342 original size:82 final size:82
Alignment explanation
Indices: 1626205--1626370 Score: 332
Period size: 82 Copynumber: 2.0 Consensus size: 82
1626195 AAATGTCAAG
1626205 GGTCCCTAAATCTTGATTATGATTTTCTCCATTTTTTTAAGAATACATATATATGTTCAATGAAA
1 GGTCCCTAAATCTTGATTATGATTTTCTCCATTTTTTTAAGAATACATATATATGTTCAATGAAA
1626270 AGGATACGAAAAGGTAT
66 AGGATACGAAAAGGTAT
1626287 GGTCCCTAAATCTTGATTATGATTTTCTCCATTTTTTTAAGAATACATATATATGTTCAATGAAA
1 GGTCCCTAAATCTTGATTATGATTTTCTCCATTTTTTTAAGAATACATATATATGTTCAATGAAA
1626352 AGGATACGAAAAGGTAT
66 AGGATACGAAAAGGTAT
1626369 GG
1 GG
1626371 CTAATATTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (82 bp):
GGTCCCTAAATCTTGATTATGATTTTCTCCATTTTTTTAAGAATACATATATATGTTCAATGAAA
AGGATACGAAAAGGTAT
Found at i:1626564 original size:2 final size:2
Alignment explanation
Indices: 1626557--1626598 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1626547 ATAGATTTAA
1626557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1626599 TGATTATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1626822 original size:20 final size:21
Alignment explanation
Indices: 1626785--1626823 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1626775 TTATCCTATT
* *
1626785 TTAGAATTTTTTTTAATTCTC
1 TTAGAATTTTTATAAATTCTC
1626806 TTAGAA-TTTTATAAATTC
1 TTAGAATTTTTATAAATTC
1626824 AAGTTCACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (21 bp):
TTAGAATTTTTATAAATTCTC
Found at i:1634931 original size:26 final size:26
Alignment explanation
Indices: 1634902--1634956 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1634892 TTGAACATTA
*
1634902 AATAGAAACATTCATAATTCTTTAAT
1 AATAGAAACACTCATAATTCTTTAAT
1634928 AATAGAAACACTCATAATTCTTTAAT
1 AATAGAAACACTCATAATTCTTTAAT
1634954 AAT
1 AAT
1634957 GACTTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (26 bp):
AATAGAAACACTCATAATTCTTTAAT
Found at i:1638235 original size:14 final size:16
Alignment explanation
Indices: 1638203--1638248 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1638193 CTTATCTTAA
1638203 TTTTTTATATCAAACT
1 TTTTTTATATCAAACT
*
1638219 TTTTTTATA-GAAA--
1 TTTTTTATATCAAACT
1638232 -TTTTTATATCAAACT
1 TTTTTTATATCAAACT
1638247 TT
1 TT
1638249 AAATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
12 8 0.33
13 3 0.12
15 3 0.12
16 10 0.42
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTTTTATATCAAACT
Found at i:1639157 original size:6 final size:6
Alignment explanation
Indices: 1639142--1639177 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1639132 AATAAACCTT
*
1639142 TATAAC TATAAA TATAAA TATAAA TATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
1639178 ATGGATGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (6 bp):
TATAAA
Found at i:1648416 original size:30 final size:30
Alignment explanation
Indices: 1648376--1648432 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1648366 TTACGGCACG
*
1648376 ATACATGATTTTCTGAATATTGTTTATCTA
1 ATACATGATTTACTGAATATTGTTTATCTA
* * *
1648406 ATACTTGATTTACTGTATATTTTTTAT
1 ATACATGATTTACTGAATATTGTTTAT
1648433 ATGATCTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (30 bp):
ATACATGATTTACTGAATATTGTTTATCTA
Found at i:1648746 original size:17 final size:17
Alignment explanation
Indices: 1648724--1648757 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1648714 ACATATTATG
1648724 GTGTTCAGATGGGGGTA
1 GTGTTCAGATGGGGGTA
*
1648741 GTGTTCAGTTGGGGGTA
1 GTGTTCAGATGGGGGTA
1648758 AAACATGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.47, T:0.32
Consensus pattern (17 bp):
GTGTTCAGATGGGGGTA
Found at i:1649064 original size:2 final size:2
Alignment explanation
Indices: 1649057--1649093 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1649047 CTAATTTATG
1649057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1649094 GCGTGTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1653214 original size:2 final size:2
Alignment explanation
Indices: 1653207--1653265 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1653197 AAATATTTAA
1653207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1653249 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1653266 AAAGTTCTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1653683 original size:2 final size:2
Alignment explanation
Indices: 1653676--1653717 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1653666 TAGAGATAAT
1653676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1653718 AAGATATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1659812 original size:2 final size:2
Alignment explanation
Indices: 1659805--1659842 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1659795 TATAATTTGA
1659805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1659843 TTGTTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1665994 original size:14 final size:13
Alignment explanation
Indices: 1665980--1666031 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
1665970 CATTTATTTA
1665980 ATTAAAATATATT
1 ATTAAAATATATT
*
1665993 AATTAAATATAAATT
1 -ATTAAA-ATATATT
1666008 A-TAAAAT-TATT
1 ATTAAAATATATT
*
1666019 ATTAAAAAATATT
1 ATTAAAATATATT
1666032 TATAACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 8 0.25
14 7 0.22
15 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAAAATATATT
Found at i:1668261 original size:24 final size:23
Alignment explanation
Indices: 1668207--1668262 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1668197 TGTCAAACTT
*
1668207 ATAAATTTTATTTTTAAATAAAA
1 ATAAAATTTATTTTTAAATAAAA
*
1668230 ATATAATTTATTTATTAAA-AAAA
1 ATAAAATTTATTT-TTAAATAAAA
*
1668253 CTCAAAATTT
1 AT-AAAATTT
1668263 TCTTAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAAATTTATTTTTAAATAAAA
Found at i:1672576 original size:2 final size:2
Alignment explanation
Indices: 1672571--1672618 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1672561 AAATATATCC
1672571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1672613 AT AT AT
1 AT AT AT
1672619 GAAAGAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1675386 original size:15 final size:15
Alignment explanation
Indices: 1675368--1675401 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1675358 TCCAAAAGAA
1675368 GAAAATCAAGAACGG
1 GAAAATCAAGAACGG
1675383 GAAAATCAAGAACGG
1 GAAAATCAAGAACGG
1675398 GAAA
1 GAAA
1675402 GAAAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.26, T:0.06
Consensus pattern (15 bp):
GAAAATCAAGAACGG
Found at i:1687202 original size:6 final size:6
Alignment explanation
Indices: 1687191--1687253 Score: 72
Period size: 6 Copynumber: 9.8 Consensus size: 6
1687181 ATTTCATTAC
*
1687191 AAAAAT AAAAAT AAAAAC AAAAAT AAAAAT AAATAAAT AAAAAT AAATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AA-AAAT AAAAAT -AA-AAAT
*
1687243 AAAAAG AAAAA
1 AAAAAT AAAAA
1687254 GAGTTTAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
6 34 0.68
7 8 0.16
8 8 0.16
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1687212 original size:18 final size:18
Alignment explanation
Indices: 1687189--1687253 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 18
1687179 CCATTTCATT
1687189 ACAAAAATAAAAATAAAA
1 ACAAAAATAAAAATAAAA
1687207 ACAAAAATAAAAATAAATAA
1 ACAAAAATAAAAAT-AA-AA
*
1687227 ATAAAAATAAATAAATAAAA
1 ACAAAAAT-AA-AAATAAAA
*
1687247 AGAAAAA
1 ACAAAAA
1687254 GAGTTTAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.34
19 2 0.05
20 17 0.41
21 4 0.10
22 4 0.10
ACGTcount: A:0.82, C:0.03, G:0.02, T:0.14
Consensus pattern (18 bp):
ACAAAAATAAAAATAAAA
Found at i:1687230 original size:14 final size:13
Alignment explanation
Indices: 1687191--1687253 Score: 76
Period size: 14 Copynumber: 4.8 Consensus size: 13
1687181 ATTTCATTAC
1687191 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
*
1687203 AAAAA-CAAAAAT
1 AAAAATAAAAAAT
1687215 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
1687229 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
*
1687243 AAAAAGAAAAA
1 AAAAATAAAAA
1687254 GAGTTTAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
12 16 0.35
13 4 0.09
14 26 0.57
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1689449 original size:9 final size:9
Alignment explanation
Indices: 1689435--1689468 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1689425 TAAAAGGGAA
1689435 AAATAAAAT
1 AAATAAAAT
1689444 AAATAAAAT
1 AAATAAAAT
1689453 AAAT-AAAT
1 AAATAAAAT
1689461 AAGATAAA
1 AA-ATAAA
1689469 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Done.