Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1179768 original size:39 final size:38
Alignment explanation
Indices: 1179722--1179824 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 38
1179712 ATACCTAAAT
* *
1179722 TTTAGTTTTTGTTTCATTTAGTACTCTGTCATTAAAGAA
1 TTTAGTTTTTGTTTAATTTAGTA-TCCGTCATTAAAGAA
** * *
1179761 TTTAGTTTTTGTTTTTGTTTAGTATCCGTCGTTAAAGAC
1 TTTAGTTTTTG-TTTAATTTAGTATCCGTCATTAAAGAA
1179800 TTTAGTTTTTGTTTAATTTTAGTAT
1 TTTAGTTTTTGTTTAA-TTTAGTAT
1179825 TTTTGTTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.05
39 42 0.76
40 10 0.18
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (38 bp):
TTTAGTTTTTGTTTAATTTAGTATCCGTCATTAAAGAA
Found at i:1180700 original size:15 final size:15
Alignment explanation
Indices: 1180676--1180706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1180666 ATTCACACGG
*
1180676 TTTCTTTTAATTTTC
1 TTTCTCTTAATTTTC
1180691 TTTCTCTTAATTTTC
1 TTTCTCTTAATTTTC
1180706 T
1 T
1180707 AATTTATTAT
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:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTCTTAATTTTC
Found at i:1187304 original size:14 final size:14
Alignment explanation
Indices: 1187285--1187320 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1187275 GCAAAGAAAC
1187285 AGAAAGAAAAAAAA
1 AGAAAGAAAAAAAA
1187299 AGAAAGAAAAAAAA
1 AGAAAGAAAAAAAA
1187313 AGAAAGAA
1 AGAAAGAA
1187321 GAGAAGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAAAA
Found at i:1187312 original size:18 final size:19
Alignment explanation
Indices: 1187285--1187325 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1187275 GCAAAGAAAC
*
1187285 AGAAAGAAAAAAAAAGAA-
1 AGAAAAAAAAAAAAAGAAG
*
1187303 AGAAAAAAAAAGAAAGAAG
1 AGAAAAAAAAAAAAAGAAG
1187322 AGAA
1 AGAA
1187326 GCTTACCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AGAAAAAAAAAAAAAGAAG
Found at i:1189423 original size:9 final size:9
Alignment explanation
Indices: 1189409--1189433 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1189399 TTACATGTAA
1189409 ATTTAAATT
1 ATTTAAATT
1189418 ATTTAAATT
1 ATTTAAATT
1189427 ATTTAAA
1 ATTTAAA
1189434 AGCATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:1199488 original size:5 final size:5
Alignment explanation
Indices: 1199478--1199524 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
1199468 TAAAAAAAAG
*
1199478 AGAAA AG-AA A-AAA AGAAA AG-AA AG-AA AGAAA AAAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1199524 A
1 A
1199525 AGGAAAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 14 0.38
5 23 0.62
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:1199488 original size:13 final size:12
Alignment explanation
Indices: 1199456--1199533 Score: 74
Period size: 12 Copynumber: 6.6 Consensus size: 12
1199446 TATGCTTAAT
1199456 GAAAA-AAAATAA
1 GAAAAGAAAA-AA
* *
1199468 TAAAA-AAAAGA
1 GAAAAGAAAAAA
1199479 GAAAAGAAAAAAA
1 GAAAAG-AAAAAA
1199492 GAAAAGAAAGAAA
1 GAAAAGAAA-AAA
1199505 G-AAA-AAAAAA
1 GAAAAGAAAAAA
*
1199515 GAAAAGAAAAAG
1 GAAAAGAAAAAA
1199527 GAAAAGA
1 GAAAAGA
1199534 GGGGTCAAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.07
11 11 0.20
12 26 0.46
13 15 0.27
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:1199505 original size:28 final size:25
Alignment explanation
Indices: 1199457--1199525 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
1199447 ATGCTTAATG
*
1199457 AAAAAAAATAATAAAAAAAAGAGAAAA
1 AAAAAAAAGAA-AAAAAAAAGA-AAAA
*
1199484 GAAAAAAAGAAAAGAAAGAAAGAAAAA
1 AAAAAAAAGAAAA-AAA-AAAGAAAAA
1199511 AAAAGAAAAGAAAAA
1 AAAA-AAAAGAAAAA
1199526 GGAAAAGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAAAAGAAAAA
Found at i:1200815 original size:83 final size:83
Alignment explanation
Indices: 1200671--1200976 Score: 495
Period size: 83 Copynumber: 3.7 Consensus size: 83
1200661 ATTAGCTGGA
*
1200671 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1200736 ACTAATCATTGAATTTGG
66 ACTAATCATTGAATTTGG
1200754 AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1200819 ACTAATCATTGAATTTGG
66 ACTAATCATTGAATTTGG
*
1200837 AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
* *
1200902 ACCAATCATTGAATTTGA
66 ACTAATCATTGAATTTGG
** * * * *
1200920 AAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 AAG-AGGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCT
1200977 AATTTGGTTT
Statistics
Matches: 211, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
83 165 0.78
84 5 0.02
85 2 0.01
86 39 0.18
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
AAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
ACTAATCATTGAATTTGG
Found at i:1201905 original size:113 final size:112
Alignment explanation
Indices: 1201707--1202263 Score: 813
Period size: 113 Copynumber: 5.0 Consensus size: 112
1201697 GCAAAGATTT
*
1201707 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTA-G-AGTTCATAATGAGAAGAACTCATCTAAA
*
1201771 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
1201820 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTAAAG
1201885 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
1201933 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTAAAG
*
1201998 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
1202046 AAATCCATCACTTGATGGATCAACTTTTCTAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTAG--AGTTCATAATGAGAAGAACTCATCTAAA
* *
1202110 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
1202159 AAATCCATCACTTGATGGGTCAGTTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATC---AG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTAG-AGTTCATAATGAGAAGAACTCATCTAAAG
* ** *
1202220 GA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1202264 AATGACTCTA
Statistics
Matches: 413, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
108 37 0.09
109 3 0.01
111 1 0.00
112 25 0.06
113 346 0.84
114 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTAAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1202246 original size:17 final size:17
Alignment explanation
Indices: 1202191--1202246 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
1202181 GTTTTTCCAG
1202191 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
1202208 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
1202227 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
1202244 AGA
1 AGA
1202247 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:1202501 original size:3 final size:3
Alignment explanation
Indices: 1202493--1202567 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
1202483 ATGTTATTTA
* * * *
1202493 TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TAT AAT TAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1202539 AAT AAT TAT TAT TAA TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
1202568 TAATATTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:1203070 original size:20 final size:20
Alignment explanation
Indices: 1203045--1203084 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1203035 AAAGAAACAG
1203045 AAAAGAAAAAAAAAAAGAAA
1 AAAAGAAAAAAAAAAAGAAA
* *
1203065 AAAAGAAAAAGAAAGAGAAA
1 AAAAGAAAAAAAAAAAGAAA
1203085 GCTTACCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAAAGAAA
Found at i:1210111 original size:19 final size:19
Alignment explanation
Indices: 1210089--1210133 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1210079 ACCAGTCCAA
1210089 ACCGGTCAGAACCGGATTG
1 ACCGGTCAGAACCGGATTG
* *
1210108 ACCGGTCTGAACCGGGTTG
1 ACCGGTCAGAACCGGATTG
1210127 ACCGGTC
1 ACCGGTC
1210134 GGACCCGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.18
Consensus pattern (19 bp):
ACCGGTCAGAACCGGATTG
Found at i:1210204 original size:29 final size:29
Alignment explanation
Indices: 1210160--1210320 Score: 218
Period size: 29 Copynumber: 5.6 Consensus size: 29
1210150 GACCCGACCC
1210160 GGTGACATTATGGGAAATATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
* *
1210189 GGTGACATTCTAGGAAATATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
*
1210218 GGTAACATTATGGGAAATATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
*
1210247 -GTGACATTATGGGAATTATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
* * * *
1210275 TGTGACATTTTAGGAATTATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAA
* *
1210304 AGTGACATT-TTGGAAAT
1 GGTGACATTATGGGAAAT
1210321 TTTCAAATTT
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.27
29 87 0.73
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (29 bp):
GGTGACATTATGGGAAATATTTTGAAAAA
Found at i:1210304 original size:58 final size:58
Alignment explanation
Indices: 1210160--1210321 Score: 218
Period size: 57 Copynumber: 2.8 Consensus size: 58
1210150 GACCCGACCC
* * * *
1210160 GGTGACATTATGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAAAGTGACATTATGGGAATTATTTTGAAAAA
*
1210218 GGTAACATTATGGGAAATATTTTG-AAAAAGTGACATTATGGGAATTATTTTGAAAAA
1 GGTGACATTATGGGAAATATTTTGAAAAAAGTGACATTATGGGAATTATTTTGAAAAA
* * * * * *
1210275 TGTGACATTTTAGGAATTATTTTGAAAAAAGTGACATTTTGGAAATT
1 GGTGACATTATGGGAAATATTTTGAAAAAAGTGACATTATGGGAATT
1210322 TTCAAATTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 48 0.53
58 43 0.47
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (58 bp):
GGTGACATTATGGGAAATATTTTGAAAAAAGTGACATTATGGGAATTATTTTGAAAAA
Found at i:1210312 original size:86 final size:85
Alignment explanation
Indices: 1210161--1210320 Score: 248
Period size: 86 Copynumber: 1.9 Consensus size: 85
1210151 ACCCGACCCG
*
1210161 GTGACATTATGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAGGTAACAT
1 GTGACATTATGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAAGTAACAT
1210226 TATGGGAAATATTTTGAAAAA
66 T-TGGGAAATATTTTGAAAAA
* * * * *
1210247 GTGACATTATGGGAATTATTTTGAAAAATGTGACATTTTAGGAATTATTTTGAAAAAAGTGACAT
1 GTGACATTATGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAAGTAACAT
*
1210312 TTTGGAAAT
66 TTGGGAAAT
1210321 TTTCAAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
85 7 0.10
86 60 0.90
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (85 bp):
GTGACATTATGGGAAATATTTTGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAAGTAACAT
TTGGGAAATATTTTGAAAAA
Found at i:1211403 original size:26 final size:26
Alignment explanation
Indices: 1211350--1211403 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1211340 AGGGTAACTC
*
1211350 TTTTATGAGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
1211376 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
1211402 TT
1 TT
1211404 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:1217564 original size:12 final size:12
Alignment explanation
Indices: 1217547--1217611 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
1217537 TCGGACCCAA
1217547 ACCGACCCGTTG
1 ACCGACCCGTTG
1217559 ACCGACCCG--G
1 ACCGACCCGTTG
* *
1217569 TCTGACCCGTTG
1 ACCGACCCGTTG
1217581 ACCGACCCG--G
1 ACCGACCCGTTG
* *
1217591 TCTGACCCGTTG
1 ACCGACCCGTTG
1217603 ACCGACCCG
1 ACCGACCCG
1217612 ACCCGGTGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 16 0.39
12 25 0.61
ACGTcount: A:0.15, C:0.43, G:0.26, T:0.15
Consensus pattern (12 bp):
ACCGACCCGTTG
Found at i:1217618 original size:27 final size:22
Alignment explanation
Indices: 1217550--1217611 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
1217540 GACCCAAACC
1217550 GACCCGTTGACCGACCCGGTCT
1 GACCCGTTGACCGACCCGGTCT
1217572 GACCCGTTGACCGACCCGGTCT
1 GACCCGTTGACCGACCCGGTCT
1217594 GACCCGTTGACCGACCCG
1 GACCCGTTGACCGACCCG
1217612 ACCCGGTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.15, C:0.42, G:0.27, T:0.16
Consensus pattern (22 bp):
GACCCGTTGACCGACCCGGTCT
Found at i:1217712 original size:59 final size:57
Alignment explanation
Indices: 1217616--1217817 Score: 262
Period size: 57 Copynumber: 3.5 Consensus size: 57
1217606 GACCCGACCC
* *
1217616 GGTGACATTCTGGGAAATATTTTGAAATAGGTTACATTCTGGGAAATATTTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATA-TTTTGAAA-A
**
1217675 GGTGACATTCTGGGAAATATTTTGAAAAATATGACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTTTG-AAAA
* * * * *
1217733 AGTGACATT-TTGGAAATATTTTGAAAAAGGTGATATTATGGGAATTATTTTGAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTTTGAAAA
** *
1217789 GGTGACATTCTATGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
1217818 AAGTGATATT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
56 12 0.10
57 53 0.42
58 14 0.11
59 47 0.37
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (57 bp):
GGTGACATTCTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTTTGAAAA
Found at i:1217748 original size:28 final size:29
Alignment explanation
Indices: 1217616--1217817 Score: 264
Period size: 29 Copynumber: 7.0 Consensus size: 29
1217606 GACCCGACCC
*
1217616 GGTGACATTCTGGGAAATATTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* *
1217645 GGTTACATTCTGGGAAATATTTTTGAAATA
1 GGTGACATTCTGGGAAATA-TTTTGAAAAA
1217675 GGTGACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
**
1217704 TATGACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* *
1217733 AGTGACATT-TTGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* * *
1217761 GGTGATATTATGGGAATTATTTTG-AAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
** *
1217789 GGTGACATTCTATGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
1217818 AAGTGATATT
Statistics
Matches: 154, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
28 49 0.32
29 77 0.50
30 28 0.18
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (29 bp):
GGTGACATTCTGGGAAATATTTTGAAAAA
Found at i:1217903 original size:12 final size:12
Alignment explanation
Indices: 1217886--1217911 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1217876 GATCGGCTTT
1217886 AAGCGGCCATTA
1 AAGCGGCCATTA
1217898 AAGCGGCCATTA
1 AAGCGGCCATTA
1217910 AA
1 AA
1217912 TGACCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (12 bp):
AAGCGGCCATTA
Found at i:1218927 original size:26 final size:26
Alignment explanation
Indices: 1218874--1218927 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1218864 AGGGTAACTC
*
1218874 TTTTATGAGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
1218900 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
1218926 TT
1 TT
1218928 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:1221742 original size:18 final size:18
Alignment explanation
Indices: 1221719--1221758 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1221709 CCGGTTCGCT
1221719 AACCGGTCCGATTCTAAA
1 AACCGGTCCGATTCTAAA
*
1221737 AACCGGTCCGATTCTGAA
1 AACCGGTCCGATTCTAAA
1221755 AACC
1 AACC
1221759 ATGATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (18 bp):
AACCGGTCCGATTCTAAA
Found at i:1226481 original size:132 final size:132
Alignment explanation
Indices: 1226243--1227407 Score: 1855
Period size: 132 Copynumber: 8.8 Consensus size: 132
1226233 AGGTCTTATG
* * *
1226243 GATGGCCCGAATGACTTACAAATCAAGAAACCCCCGAATGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* * *
1226308 AACATCATGCACTGAAGGTCTTATGGATGGCTCGGAGGACTTACGTATCATGCTCGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1226373 CT
131 CT
* *
1226375 GATGGCCCAGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTCTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* * * * *
1226440 AACATCCTGCACTGAAAGTCTTATAGATGGACTGGAAGACTTACGCATCATGCTCGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1226505 CT
131 CT
* * *
1226507 GATGTCCCGGAGAACTTACAAATCAAGAAACCCCAGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* * * * * *
1226572 AACATCATGCACTGAAGGTCTTATGGAAGGCCCGTAGGACTTATGCATCATGCTCGAAAGACTTG
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1226637 CT
131 CT
* *
1226639 GATGGCCTGGAGGACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* *
1226704 AACATCTTGCACTGAAAGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1226769 CT
131 CT
*
1226771 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGATTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* * * * * *
1226836 AACATCCTGTATTGAAAGTCTTATGTATGGCCCGAAGGACTTACGTATCATGCTCGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1226901 CT
131 CT
* ** *
1226903 GATGGCTCAAAGGACTTACCAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
*
1226968 AACATTCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1227033 CT
131 CT
* * *
1227035 GATGGCCTGGAGGACTTAAAAATCAAGAAACCCCCGAAGGTTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* * * * *
1227100 AACATCTTGCACTGAAAGTCTTATGGATGGCCCGGACGACTTAAGCATCATGCTTGGAAGACTTA
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
1227165 CT
131 CT
1227167 GATGGCCCGGAGGACTTACAAATCAAGTAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
1 GATGGCCCGGAGGACTTACAAATCAAG-AAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
* * *
1227231 AAACATCCTGCACTGAAGGTCTTATGAATGTCCCGGAGGACTTACGCATCATACTCGGAAGACTT
65 AAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTT
1227296 ACT
130 ACT
1227299 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* *
1227364 AACATCCTGCACTGAAGGTCTTATGGATGACCCAGAGGACTTAC
66 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTAC
1227408 AACTCAAGAA
Statistics
Matches: 943, Mismatches: 88, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
131 3 0.00
132 937 0.99
133 3 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (132 bp):
GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTA
CT
Found at i:1226786 original size:20 final size:19
Alignment explanation
Indices: 1226729--1226789 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
1226719 AAGTCTTATG
1226729 GATGGCCCGGAGGACTTAC
1 GATGGCCCGGAGGACTTAC
* * *
1226748 GCATCATGCTCGGAAGACTTAC
1 G-AT--GGCCCGGAGGACTTAC
1226770 TGATGGCCCGGAGGACTTAC
1 -GATGGCCCGGAGGACTTAC
1226790 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
22 15 0.47
23 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.20
Consensus pattern (19 bp):
GATGGCCCGGAGGACTTAC
Found at i:1227461 original size:90 final size:90
Alignment explanation
Indices: 1227299--1227482 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 90
1227289 AAGACTTACT
* * *
1227299 GATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGACCCAGAGGACTTACAAATCAAGAAACCCCCGAAGACTTAGTTTCTAAAATCTCATTTGAA
1227364 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* * *
1227389 GATGACCCAGAGGACTTACAACTCAAGAAAGCCCCGAAGACTTAGTTTCTAAAATCTCGTTTGAA
1 GATGACCCAGAGGACTTACAAATCAAGAAACCCCCGAAGACTTAGTTTCTAAAATCTCATTTGAA
* *
1227454 AATATCCTGTACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
1227479 GATG
1 GATG
1227483 GCCGGAAGAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (90 bp):
GATGACCCAGAGGACTTACAAATCAAGAAACCCCCGAAGACTTAGTTTCTAAAATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:1227646 original size:43 final size:42
Alignment explanation
Indices: 1227576--1227725 Score: 192
Period size: 43 Copynumber: 3.5 Consensus size: 42
1227566 TCAGTTTCTT
* * * *
1227576 AGTTGTAACCAAGGAACCCCTACATATCACGTTGGTCCCTCA
1 AGTTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCA
*
1227618 AGTGTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAA
1 AGT-TGTCATCAAGAAACCCCTACATATCACGATGGTCCCTC-A
* * **
1227662 ACTTGTCCTCAAGAAACCCCTACATATCACGATGGTTTCTCA
1 AGTTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCA
1227704 AGCTTGTCATCAAGAAACCCCT
1 AG-TTGTCATCAAGAAACCCCT
1227726 GAAAATTAGG
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
42 5 0.05
43 87 0.92
44 3 0.03
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (42 bp):
AGTTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCA
Found at i:1229044 original size:28 final size:26
Alignment explanation
Indices: 1229003--1229063 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
1228993 GATAAAAGGC
*
1229003 TCAGGTTGACTTGGGAAGGTAATGTGTT
1 TCAGGTTAACTT-GG-AGGTAATGTGTT
*
1229031 TCAGGTTAATTTGGAGGTAATGTGTT
1 TCAGGTTAACTTGGAGGTAATGTGTT
*
1229057 TGAGGTT
1 TCAGGTT
1229064 GGCTTATTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 18 0.60
27 2 0.07
28 10 0.33
ACGTcount: A:0.21, C:0.05, G:0.34, T:0.39
Consensus pattern (26 bp):
TCAGGTTAACTTGGAGGTAATGTGTT
Found at i:1229706 original size:7 final size:7
Alignment explanation
Indices: 1229694--1229770 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
1229684 ATTTGTATAT
1229694 TTTCTTC
1 TTTCTTC
1229701 TTTCTTC
1 TTTCTTC
1229708 TTT-TT-
1 TTTCTTC
1229713 TTT-TT-
1 TTTCTTC
1229718 TTTCTT-
1 TTTCTTC
*
1229724 TTT-TTT
1 TTTCTTC
*
1229730 TTTCTTT
1 TTTCTTC
1229737 TTTCTTC
1 TTTCTTC
1229744 TGTT-TTC
1 T-TTCTTC
1229751 TTT-TTC
1 TTTCTTC
*
1229757 TCTTTTTC
1 T-TTCTTC
1229765 TTTCTT
1 TTTCTT
1229771 TTTGTGTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
5 10 0.16
6 16 0.26
7 30 0.48
8 6 0.10
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (7 bp):
TTTCTTC
Found at i:1229727 original size:12 final size:12
Alignment explanation
Indices: 1229710--1229773 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
1229700 CTTTCTTCTT
1229710 TTTTTTTTTTTC
1 TTTTTTTTTTTC
1229722 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
1229734 --TTTTTTCTTC
1 TTTTTTTTTTTC
*
1229744 TGTTTTCTTTTTC
1 T-TTTTTTTTTTC
* *
1229757 TCTTTTTCTTTC
1 TTTTTTTTTTTC
1229769 TTTTT
1 TTTTT
1229774 GTGTTTTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 9 0.21
12 24 0.57
13 9 0.21
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:1229741 original size:36 final size:35
Alignment explanation
Indices: 1229693--1229773 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
1229683 GATTTGTATA
* * * *
1229693 TTTTCTTCTTTCTTCTTTTTTTTTTTTTCTTTTTTT
1 TTTTCTTTTTTCTTC-TGTTTTCTTTTTCTCTTTTT
1229729 TTTTCTTTTTTCTTCTGTTTTCTTTTTCTCTTTTT
1 TTTTCTTTTTTCTTCTGTTTTCTTTTTCTCTTTTT
*
1229764 CTTTCTTTTT
1 TTTTCTTTTT
1229774 GTGTTTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 26 0.65
36 14 0.35
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.83
Consensus pattern (35 bp):
TTTTCTTTTTTCTTCTGTTTTCTTTTTCTCTTTTT
Found at i:1229741 original size:43 final size:43
Alignment explanation
Indices: 1229693--1229784 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
1229683 GATTTGTATA
* * * *
1229693 TTTTCTTCT-TTCTTCTTTTTTTTTTTTTCTTTTTTTTTTTCTT
1 TTTTCTTCTGTT-TTCTTTTTCTCTTTTTCTTTCTTTTTGTCTT
*
1229736 TTTTCTTCTGTTTTCTTTTTCTCTTTTTCTTTCTTTTTGTGTT
1 TTTTCTTCTGTTTTCTTTTTCTCTTTTTCTTTCTTTTTGTCTT
1229779 TTTTCT
1 TTTTCT
1229785 ATATCTCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 41 0.95
44 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (43 bp):
TTTTCTTCTGTTTTCTTTTTCTCTTTTTCTTTCTTTTTGTCTT
Found at i:1229754 original size:25 final size:24
Alignment explanation
Indices: 1229695--1229784 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
1229685 TTTGTATATT
1229695 TTCTTCTTTCTTCTTTTT-TTTTTT-
1 TTCTT-TTTCTT-TTTTTCTTTTTTC
1229719 TTC-TTTT-TTTTTTTCTTTTTTC
1 TTCTTTTTCTTTTTTTCTTTTTTC
*
1229741 TTCTGTTTTCTTTTTCTC-TTTTTC
1 TTCT-TTTTCTTTTTTTCTTTTTTC
*
1229765 TTTCTTTTTGTGTTTTTTCT
1 -TTCTTTTTCT-TTTTTTCT
1229785 ATATCTCTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
20 5 0.09
21 8 0.15
22 6 0.11
23 1 0.02
24 18 0.33
25 17 0.31
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (24 bp):
TTCTTTTTCTTTTTTTCTTTTTTC
Found at i:1229781 original size:18 final size:18
Alignment explanation
Indices: 1229694--1229773 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
1229684 ATTTGTATAT
1229694 TTTCTTCTTTCTTCTTTTT-
1 TTTCTT-TTTC-TCTTTTTC
* *
1229713 TTT-TTTTTCTTTTTTTT
1 TTTCTTTTTCTCTTTTTC
*
1229730 TTTCTTTTT-TCTTCTGT-
1 TTTCTTTTTCTCTT-TTTC
1229747 TTTCTTTTTCTCTTTTTC
1 TTTCTTTTTCTCTTTTTC
1229765 TTTCTTTTT
1 TTTCTTTTT
1229774 GTGTTTTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 6 0.12
17 21 0.40
18 22 0.42
19 3 0.06
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.82
Consensus pattern (18 bp):
TTTCTTTTTCTCTTTTTC
Found at i:1232273 original size:6 final size:6
Alignment explanation
Indices: 1232262--1232286 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1232252 AAATAAATAC
1232262 ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA A
1232287 AATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:1237565 original size:12 final size:12
Alignment explanation
Indices: 1237548--1237579 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1237538 ATGTATAACG
1237548 TTTAATTTATAT
1 TTTAATTTATAT
1237560 TTTAATTTATAT
1 TTTAATTTATAT
1237572 TTTAATTT
1 TTTAATTT
1237580 GGTATCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTAATTTATAT
Found at i:1247249 original size:22 final size:22
Alignment explanation
Indices: 1247224--1247272 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1247214 GAACCGGTTT
1247224 GACCCGAACCGTTGACCGACCC
1 GACCCGAACCGTTGACCGACCC
*
1247246 GACCCGACCCGTTGACCGACCC
1 GACCCGAACCGTTGACCGACCC
1247268 GACCC
1 GACCC
1247273 AGTGACATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.08
Consensus pattern (22 bp):
GACCCGAACCGTTGACCGACCC
Found at i:1247343 original size:29 final size:29
Alignment explanation
Indices: 1247296--1247405 Score: 148
Period size: 29 Copynumber: 3.8 Consensus size: 29
1247286 AAATTTTTTA
* *
1247296 TGAAAAATGTGACATTCTGGGAAATATTT
1 TGAAAAAGGTAACATTCTGGGAAATATTT
* *
1247325 TGAGAAAGGTGACATTCTGGGAAATATTT
1 TGAAAAAGGTAACATTCTGGGAAATATTT
* *
1247354 TGAAAAAGGTAACATGCTGGGAATTATTT
1 TGAAAAAGGTAACATTCTGGGAAATATTT
* *
1247383 TGAAAAATGTAACATTTTGGGAA
1 TGAAAAAGGTAACATTCTGGGAA
1247406 TTTTCGAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (29 bp):
TGAAAAAGGTAACATTCTGGGAAATATTT
Found at i:1247406 original size:29 final size:29
Alignment explanation
Indices: 1247277--1247407 Score: 145
Period size: 29 Copynumber: 4.5 Consensus size: 29
1247267 CGACCCAGTG
** * * *
1247277 ACATTCTGAAAATTTTTTATGAAAAATGTG
1 ACATTCTGGGAATTATTT-TGAAAAAGGTA
* * *
1247307 ACATTCTGGGAAATATTTTGAGAAAGGTG
1 ACATTCTGGGAATTATTTTGAAAAAGGTA
*
1247336 ACATTCTGGGAAATATTTTGAAAAAGGTA
1 ACATTCTGGGAATTATTTTGAAAAAGGTA
* *
1247365 ACATGCTGGGAATTATTTTGAAAAATGTA
1 ACATTCTGGGAATTATTTTGAAAAAGGTA
*
1247394 ACATTTTGGGAATT
1 ACATTCTGGGAATT
1247408 TTCGAATATG
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 74 0.84
30 14 0.16
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (29 bp):
ACATTCTGGGAATTATTTTGAAAAAGGTA
Found at i:1251613 original size:23 final size:23
Alignment explanation
Indices: 1251587--1251655 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1251577 CACCACAGCT
* *
1251587 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1251610 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1251633 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1251656 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1256404 original size:15 final size:16
Alignment explanation
Indices: 1256380--1256417 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1256370 TCGAGATCCT
*
1256380 AGATTTTATACTTC-G
1 AGATTGTATACTTCAG
*
1256395 AGATTGTATATTTCAG
1 AGATTGTATACTTCAG
1256411 AGATTGT
1 AGATTGT
1256418 CAGATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (16 bp):
AGATTGTATACTTCAG
Found at i:1258147 original size:29 final size:28
Alignment explanation
Indices: 1258105--1258268 Score: 186
Period size: 29 Copynumber: 5.7 Consensus size: 28
1258095 ACCCGACCCA
1258105 GTGACATTCTGGGAATTTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTT-TGAAAAAG
* * *
1258134 GTGATATTCTGGGAAATATTTTGAAAAAT
1 GTGACATTCTGGG-AATTTTTTGAAAAAG
* *
1258163 GTGACATTCAGGGAAATATTTTGAAAAAG
1 GTGACATTCTGGG-AATTTTTTGAAAAAG
* *
1258192 GTGACATTTTAGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATT-TTTTGAAAAAG
*
1258221 GTGACATGT-TGGGAATTATTTTGAAAAAT
1 GTGACAT-TCTGGGAATT-TTTTGAAAAAG
*
1258250 GTGACATTTTGGGAATTTT
1 GTGACATTCTGGGAATTTT
1258269 CGAATATGGA
Statistics
Matches: 119, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
28 6 0.05
29 106 0.89
30 7 0.06
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (28 bp):
GTGACATTCTGGGAATTTTTTGAAAAAG
Found at i:1258265 original size:58 final size:58
Alignment explanation
Indices: 1258105--1258266 Score: 220
Period size: 58 Copynumber: 2.8 Consensus size: 58
1258095 ACCCGACCCA
* * * *
1258105 GTGACATTCTGGGAATT-TTTGTGAAAAAGGTGATATTCTGGGAAATATTTTGAAAAAT
1 GTGACATTCTGGGAATTATTT-TGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAAG
* * *
1258163 GTGACATTCAGGGAAATATTTTGAAAAAGGTGACATTTTAGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAAG
*
1258221 GTGACATGT-TGGGAATTATTTTGAAAAATGTGACATTTTGGGAATT
1 GTGACAT-TCTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATT
1258267 TTCGAATATG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 87 0.96
59 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (58 bp):
GTGACATTCTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:1266832 original size:16 final size:17
Alignment explanation
Indices: 1266806--1266844 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1266796 AACTTTCATA
*
1266806 TTTCATTTTCATATGCT
1 TTTCATTTTCATATACT
1266823 TTTC-TTTTCATATACT
1 TTTCATTTTCATATACT
1266839 TTTCAT
1 TTTCAT
1266845 AACTTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTCATTTTCATATACT
Found at i:1267150 original size:21 final size:21
Alignment explanation
Indices: 1267110--1267154 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1267100 GGGCTCTCAG
*
1267110 ATCATATCATATCCATTCATTA
1 ATCATATCATATCCAATCA-TA
*
1267132 ATCATA-CATTTCCAATCATA
1 ATCATATCATATCCAATCATA
1267152 ATC
1 ATC
1267155 TTTTTCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCATATCATATCCAATCATA
Found at i:1271084 original size:3 final size:3
Alignment explanation
Indices: 1271078--1271129 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
1271068 TAATATTTAT
1271078 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1271125 TAA TA
1 TAA TA
1271130 TTTAAATGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1271683 original size:229 final size:224
Alignment explanation
Indices: 1271369--1272228 Score: 706
Period size: 229 Copynumber: 3.9 Consensus size: 224
1271359 TTGAATAAGC
* * ** *
1271369 TCTTCTCATTATGAACTTCTTCTCCTCTTTAGATGAGTTCTTCTTATTATGAACTCTTTCTAGCA
1 TCTTCTCATTATGAACTTCTTCTCCTCTTGAGATGAGTTCTTCTCATTATGAACTCTACCTAGAA
* * * * * *
1271434 ATACTGATCCATCGAATGATGAAATCGAGCAAAAATTTGAACAAATTCTTCTCATTATGAA-TTC
66 ATACTAATCCATCAAATGATGAAATCAAACAAAAAGTTAAACAAATTCTTCTCATTATGAACTT-
1271498 CTTCTT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
130 CTTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
1271562 GAGATGGATTTGAGCAAAAGGTTGACCAAAT
194 GAGATGGATTTGAGCAAAAGGTTGACCAAAT
*
1271593 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACC
1 TCTTCTCATTATGAACTTCTTC-TCC-TCTT--GA-GATGAGTTCTTCTCATTATGAACTCTACC
* ** * *
1271658 TGGAAATTTTAATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGA
61 TAGAAATACTAATCCATCAAATGATGAAATCAAACAAAAAGTTAAACAAATTCTTCTCATTATGA
1271723 ACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCAT
126 ACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCAT
* * ** * * *
1271788 TAA-ATGATGAATTCAAGAAAAAAGTTGAACAAAT
191 CAAGA-GATGGATTTGAGCAAAAGGTTGACCAAAT
* * * * ** * *
1271822 TATTCTCTTTA-GATGAGTTCTTCT--TATT---ATGAACTCTT-TC--T-GGCAA-TGT---T-
1 TCTTCTCATTATGA--ACTTCTTCTCCTCTTGAGATGAGTTCTTCTCATTATG-AACTCTACCTA
* * * *** * *
1271872 --AAT-C-CAT-CA-AATAATGAATTTAAA-C--A-AAAGGTTGAAC-AAATTCTTCTCATTATG
63 GAAATACTAATCCATCA-AATG-A-TGAAATCAAACAAAAAGTTAAACAAATTCTTCTCATTATG
* *
1271926 AACTTCTTTTTCCTTCTTCAGATGAGTTC-T-T-ATTATGAACTTTCTCTGGAAAAGCTGATCCA
125 AACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
* ** * *
1271988 TCAA-ATGATGAATTCAAGCAAAAAGTTGAACAAAT
190 TCAAGA-GATGGATTTGAGCAAAAGGTTGACCAAAT
* * * * ** * *
1272023 TCTTCTCATTATGAATTTCTTCTTCTCTTTAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCA
1 TCTTCTCATTATGAACTTCTTCTCCTCTTGAGATGAGTTCTTCTCATTATGAACTCTACCTAGAA
** * * * * *
1272088 ATGTTAATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
66 ATACTAATCCATCAAATGATGAAATCAAACAAAAAGTTAAACAAATTCTTCTCATTATGAACTTC
* * **** * * **
1272153 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGCTGATCCATCAATT
131 TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGA
1272218 GATGGATTTGA
196 GATGGATTTGA
1272229 ATCTTTGCTA
Statistics
Matches: 515, Mismatches: 77, Indels: 88
0.76 0.11 0.13
Matches are distributed among these distances:
200 8 0.02
201 73 0.14
202 6 0.01
203 1 0.00
204 44 0.09
205 15 0.03
206 3 0.01
207 6 0.01
208 7 0.01
209 6 0.01
210 3 0.01
212 1 0.00
213 1 0.00
215 3 0.01
216 6 0.01
217 6 0.01
218 5 0.01
219 4 0.01
220 14 0.03
221 45 0.09
222 1 0.00
223 1 0.00
224 58 0.11
225 3 0.01
226 7 0.01
228 4 0.01
229 174 0.34
230 10 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (224 bp):
TCTTCTCATTATGAACTTCTTCTCCTCTTGAGATGAGTTCTTCTCATTATGAACTCTACCTAGAA
ATACTAATCCATCAAATGATGAAATCAAACAAAAAGTTAAACAAATTCTTCTCATTATGAACTTC
TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGA
GATGGATTTGAGCAAAAGGTTGACCAAAT
Found at i:1271696 original size:116 final size:113
Alignment explanation
Indices: 1271369--1271828 Score: 540
Period size: 113 Copynumber: 4.1 Consensus size: 113
1271359 TTGAATAAGC
* *
1271369 TCTTCTCATTATGAACTTCTTC-TCC-TCTTTAGATGAGTTCTTCTTATTATGAACTCTT-TCTA
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT-
* * * * * * *
1271431 GCAATA-CTGATCCATCGAATGATGAAATCGAGCAAAAATTTGAACAAAT
64 GGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAAT
*
1271480 TCTTCTCATTATGAA-TTCCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TCTTCTCATTATGAACTT-CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* ** * * *
1271544 GAAAAGCTGATCCATCAAGA-GATGGATTTGAGCAAAAGGTTGACCAAAT
65 GAAAAGCTGATCCATCAA-ATGATGAATTCAAACAAAAAGTTGAACAAAT
* *
1271593 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTAC-
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACT-TTCT
*** * * *
1271657 CTGGAAATTTTAATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAAT
62 CTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAAT
*
1271709 TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
1271774 AAAAGCTGATCCATTAAATGATGAATTCAAGA-AAAAAGTTGAACAAAT
66 AAAAGCTGATCCATCAAATGATGAATTCAA-ACAAAAAGTTGAACAAAT
*
1271822 TATTCTC
1 TCTTCTC
1271829 TTTAGATGAG
Statistics
Matches: 300, Mismatches: 35, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
110 2 0.01
111 19 0.06
112 10 0.03
113 166 0.55
114 5 0.02
115 2 0.01
116 94 0.31
117 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAAT
Found at i:1271864 original size:91 final size:91
Alignment explanation
Indices: 1271736--1271919 Score: 237
Period size: 91 Copynumber: 2.0 Consensus size: 91
1271726 TCTTCTTCTT
* * *
1271736 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGAATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAATAATGAATT
1271801 CAAGA-AAAAAGTTGAACAAATTATTC
66 CAA-ACAAAAAGTTGAACAAATTATTC
* * * * *
1271827 TCTTTAGATGAGTTCTTCTTATTATGAACTCTT-TCTGGCAATGTTAATCCATCAAATAATGAAT
1 TCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTAATCCATCAAATAATGAAT
* * *
1271891 TTAAACAAAAGGTTGAACAAATTCTTC
65 TCAAACAAAAAGTTGAACAAATTATTC
1271918 TC
1 TC
1271920 ATTATGAACT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
90 1 0.01
91 77 0.96
92 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (91 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAATAATGAATT
CAAACAAAAAGTTGAACAAATTATTC
Found at i:1272111 original size:111 final size:113
Alignment explanation
Indices: 1271827--1272191 Score: 571
Period size: 111 Copynumber: 3.3 Consensus size: 113
1271817 CAAATTATTC
*
1271827 TCTTTAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATT
1 TCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATT
*
1271892 TAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCT
66 TAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
* * * * *
1271940 TCTTCAGATGAG---TTCTTATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAAT
1 TCTTCAGATGAGTTCTTCTTATTATGAACTCTT-TCTGGCAATGTTAATCCATCAAATAATGAAT
* * * *
1272001 TCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C-
65 TTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
*
1272048 TCTTTAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATT
1 TCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATT
1272113 TAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
66 TAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
1272161 TCTTCAGATGAGTTCTTCTTATTATGAACTC
1 TCTTCAGATGAGTTCTTCTTATTATGAACTC
1272192 GAACTGGTAA
Statistics
Matches: 223, Mismatches: 22, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
108 11 0.05
109 3 0.01
110 82 0.37
111 83 0.37
112 3 0.01
113 41 0.18
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (113 bp):
TCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATT
TAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
Found at i:1273192 original size:94 final size:94
Alignment explanation
Indices: 1273016--1273590 Score: 1037
Period size: 94 Copynumber: 6.1 Consensus size: 94
1273006 CTTATTTCTA
* * * *
1273016 CTATGATCGCATTCATCTTTCAAATTCAATGATTGG--TTCTGTGGTTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGG-TTCATACCAAACCAGATC
1273079 AGATAACTCAAAGAACACTTCCAGAAGATG
65 AGATAACTCAAAGAACACTTCCAGAAGATG
1273109 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
* *
1273174 AATTACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
* *
1273203 CTATGAGCACATTCATCTTTTAAATCCAATGATTGGTTTTTTATGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1273268 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1273297 CTATGAGCACATTCATCTTTCAAATCTAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1273362 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1273391 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTATGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1273456 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1273485 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
1273550 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1273579 CTATGAGCACAT
1 CTATGAGCACAT
1273591 GGCACTTGTT
Statistics
Matches: 464, Mismatches: 16, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 33 0.07
94 424 0.91
95 7 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (94 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTTGTGGTTCATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1284590 original size:472 final size:471
Alignment explanation
Indices: 1283706--1284657 Score: 1868
Period size: 472 Copynumber: 2.0 Consensus size: 471
1283696 CAATGAGTCT
1283706 ATTTCCAATATTTGGATTTCATGATTTATGAATACTAGTATGTTGTGATATGATTTCTATGTGTA
1 ATTTCCAATATTTGGATTTCATGATTTATGAATACTAGTATGTTGTGATATGATTTCTATGTGTA
1283771 TTGGATTATAAGCATATGTCTATGTGTTATATGTACTATTTTATTTGGTTTATGTGATTACATGA
66 TTGGATTATAAGCATATGTCTATGTGTTATATGTACTATTTTATTTGGTTTATGTGATTACATGA
1283836 AAAGGTAAAATAAGCTAGGTGACATTTACTTATGTGATACCTGAAAATGTGATATATGCTATGTG
131 AAAGGTAAAATAAGCTAGGTGACATTTACTTATGTGATACCTGAAAATGTGATATATGCTATGTG
1283901 ACCATAATCTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAACTATGTGCTAT
196 ACCATAATCTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAACTATGTGCTAT
1283966 TGACCTAAGTGATTATATGAACATGTGCTATAAGTTATGTGATAAGGATCGATGTGCTTATATGT
261 TGACCTAAGTGATTATATGAACATGTGCTATAAGTTATGTGATAAGGATCGATGTGCTTATATGT
1284031 ATATGTTATATTGAACTACATGATTATATGAATATGTGAAATAAGAAAATGGTATATGTGAATAC
326 ATATGTTATATTGAACTACATGATTATATGAATATGTGAAATAAGAAAATGGTATATGTGAATAC
*
1284096 ATGCCTATGTGATAAGCTATATGAAATGGTTTAAAAAGTAAAGCCCATAAGTATGTGATATGAGA
391 ATGCCTATGTGATAAGCTATATGAAATGGTATAAAAAGTAAAGCCCATAAGTATGTGATATGAGA
1284161 GCTAAGGGTATAATTTG
456 GCTAAGGGTATAA-TTG
1284178 ATTTCCAATATTTGGATTTCATGATTTATGAATACTAGTATGTTGTGATATGATTTCTATGTGTA
1 ATTTCCAATATTTGGATTTCATGATTTATGAATACTAGTATGTTGTGATATGATTTCTATGTGTA
1284243 TTGGATTATAAGCATATGTCTATGTGTTATATGTACTATTTTATTTGGTTTATGTGATTACATGA
66 TTGGATTATAAGCATATGTCTATGTGTTATATGTACTATTTTATTTGGTTTATGTGATTACATGA
1284308 AAAGGTAAAATAAGCTAGGTGACATTTACTTATGTGATACCTGAAAATGTGATATATGCTATGTG
131 AAAGGTAAAATAAGCTAGGTGACATTTACTTATGTGATACCTGAAAATGTGATATATGCTATGTG
*
1284373 ACCATAATCTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAGCTATGTGCTAT
196 ACCATAATCTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAACTATGTGCTAT
1284438 TGACCTAAGTGATTATATGAACATGTGCTATAAGTTATGTGATAAGGATCGATGTGCTTATATGT
261 TGACCTAAGTGATTATATGAACATGTGCTATAAGTTATGTGATAAGGATCGATGTGCTTATATGT
1284503 ATATGTTATATTGAACTACATGATTATATGAATATGTGAAATAAGAAAATGGTATATGTGAATAC
326 ATATGTTATATTGAACTACATGATTATATGAATATGTGAAATAAGAAAATGGTATATGTGAATAC
1284568 ATGCCTATGTGATAAGCTATATGAAATGGTATAAAAAGTAAAGCCCATAAGTATGTGATATGAGA
391 ATGCCTATGTGATAAGCTATATGAAATGGTATAAAAAGTAAAGCCCATAAGTATGTGATATGAGA
1284633 GCTAAGGGTATAATTG
456 GCTAAGGGTATAATTG
1284649 ATATTCCAA
1 AT-TTCCAA
1284658 GAGTCGAGGG
Statistics
Matches: 477, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
471 5 0.01
472 472 0.99
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (471 bp):
ATTTCCAATATTTGGATTTCATGATTTATGAATACTAGTATGTTGTGATATGATTTCTATGTGTA
TTGGATTATAAGCATATGTCTATGTGTTATATGTACTATTTTATTTGGTTTATGTGATTACATGA
AAAGGTAAAATAAGCTAGGTGACATTTACTTATGTGATACCTGAAAATGTGATATATGCTATGTG
ACCATAATCTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAACTATGTGCTAT
TGACCTAAGTGATTATATGAACATGTGCTATAAGTTATGTGATAAGGATCGATGTGCTTATATGT
ATATGTTATATTGAACTACATGATTATATGAATATGTGAAATAAGAAAATGGTATATGTGAATAC
ATGCCTATGTGATAAGCTATATGAAATGGTATAAAAAGTAAAGCCCATAAGTATGTGATATGAGA
GCTAAGGGTATAATTG
Found at i:1284730 original size:23 final size:22
Alignment explanation
Indices: 1284668--1284741 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
1284658 GAGTCGAGGG
* *
1284668 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTC-AGACAT
* *
1284691 TTCTACGTGGACCTTCAAGACAT
1 TTCTACGCGGTCCTTC-AGACAT
*
1284714 TTCTACGCGGTCTTTCAGAACAT
1 TTCTACGCGGTCCTTCAG-ACAT
1284737 TTCTA
1 TTCTA
1284742 TGTGGCACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (22 bp):
TTCTACGCGGTCCTTCAGACAT
Found at i:1290979 original size:23 final size:21
Alignment explanation
Indices: 1290928--1290988 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
1290918 TTTTGGTGCA
*
1290928 GAGGGAATCGA-TCCCCCATT
1 GAGGGAACCGATTCCCCCATT
*
1290948 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCATT
1290969 GAAAGGGAACCGATTCCCCC
1 G--AGGGAACCGATTCCCCC
1290989 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
23 17 0.47
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCATT
Found at i:1312122 original size:19 final size:19
Alignment explanation
Indices: 1312098--1312136 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1312088 AACTTATACA
1312098 ATTTCATAAAAAATTTAAT
1 ATTTCATAAAAAATTTAAT
1312117 ATTTCATAAAAAATTTAAT
1 ATTTCATAAAAAATTTAAT
1312136 A
1 A
1312137 CATACCTGTA
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:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTCATAAAAAATTTAAT
Found at i:1312256 original size:25 final size:25
Alignment explanation
Indices: 1312228--1312278 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1312218 TCTAAACATT
1312228 CTGATATATTCCTCTTATTCATTAA
1 CTGATATATTCCTCTTATTCATTAA
1312253 CTGATATATTCCTCTTATTCATTAA
1 CTGATATATTCCTCTTATTCATTAA
1312278 C
1 C
1312279 CTCATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (25 bp):
CTGATATATTCCTCTTATTCATTAA
Found at i:1321609 original size:21 final size:21
Alignment explanation
Indices: 1321585--1321639 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1321575 TGCAACTCAG
1321585 TTTCCAAATTCGCATTGT-AGT
1 TTTCCAAATTCGCATTGTGA-T
*
1321606 TTTCCAAATTCGCGTTGTGAT
1 TTTCCAAATTCGCATTGTGAT
1321627 TTT-CAAATTCGCA
1 TTTCCAAATTCGCA
1321640 ACTAGATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 9 0.29
21 21 0.68
22 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGTGAT
Found at i:1321678 original size:40 final size:40
Alignment explanation
Indices: 1321625--1321717 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
1321615 TCGCGTTGTG
* *
1321625 ATTTTCAAATTCGCAACTAGA-TTTCTGAATTCGCAACGCGA
1 ATTTT-AATTTCGCAACTAGATTTTC-GAATTCGCAACACGA
* *
1321666 ATTTTATTTTCGCAACTCGATTTTCGAATTCGCAACACGA
1 ATTTTAATTTCGCAACTAGATTTTCGAATTCGCAACACGA
1321706 ATTTTAATTTCG
1 ATTTTAATTTCG
1321718 TAACATGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 37 0.80
41 9 0.20
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (40 bp):
ATTTTAATTTCGCAACTAGATTTTCGAATTCGCAACACGA
Found at i:1321717 original size:20 final size:19
Alignment explanation
Indices: 1321624--1321741 Score: 73
Period size: 20 Copynumber: 6.0 Consensus size: 19
1321614 TTCGCGTTGT
*
1321624 GATTTTCAAATTCGCAACTA-
1 GATTTT-AATTTCGCAAC-AC
*
1321644 GATTTCTGAA-TTCGCAACGC
1 GATTT-T-AATTTCGCAACAC
* *
1321664 GAATTTTATTTTCGCAACTC
1 G-ATTTTAATTTCGCAACAC
1321684 GATTTTCGAA-TTCGCAACAC
1 GATTTT--AATTTCGCAACAC
* *
1321704 GAATTTTAATTTCGTAACAT
1 G-ATTTTAATTTCGCAACAC
*
1321724 G-TTTTATTTTCGCAACAC
1 GATTTTAATTTCGCAACAC
1321742 AAATGTTGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
18 14 0.18
19 8 0.10
20 44 0.56
21 13 0.16
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (19 bp):
GATTTTAATTTCGCAACAC
Found at i:1322522 original size:12 final size:12
Alignment explanation
Indices: 1322501--1322534 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1322491 ACCATATTTC
*
1322501 CAATACCAAACA
1 CAATATCAAACA
1322513 CAATATCAAACA
1 CAATATCAAACA
*
1322525 CAATCTCAAA
1 CAATATCAAA
1322535 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1322682 original size:24 final size:24
Alignment explanation
Indices: 1322655--1322701 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1322645 AGTCAGTATT
*
1322655 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTCGATCTTGGTCAATACC
* *
1322679 CGAACTTCGATCTTGGTTAATAC
1 CGAAATTCGATCTTGGTCAATAC
1322702 TCGGATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTCGATCTTGGTCAATACC
Found at i:1325300 original size:29 final size:29
Alignment explanation
Indices: 1325258--1325314 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1325248 GCGAGTTTTT
1325258 GTTGCGATTGTTGCAAAAGTCAAATTCGC
1 GTTGCGATTGTTGCAAAAGTCAAATTCGC
*
1325287 GTTGCGATTGTTGCGAAAGTCAAATTCG
1 GTTGCGATTGTTGCAAAAGTCAAATTCG
1325315 AAATGCGAAA
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:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (29 bp):
GTTGCGATTGTTGCAAAAGTCAAATTCGC
Found at i:1325321 original size:29 final size:29
Alignment explanation
Indices: 1325260--1325322 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
1325250 GAGTTTTTGT
***
1325260 TGCGATTGTTGCAAAAGTCAAATTCGCGT
1 TGCGATTGTTGCAAAAGTCAAATTCGAAA
*
1325289 TGCGATTGTTGCGAAAGTCAAATTCGAAA
1 TGCGATTGTTGCAAAAGTCAAATTCGAAA
1325318 TGCGA
1 TGCGA
1325323 AAGTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (29 bp):
TGCGATTGTTGCAAAAGTCAAATTCGAAA
Found at i:1325323 original size:20 final size:20
Alignment explanation
Indices: 1325299--1325364 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
1325289 TGCGATTGTT
* *
1325299 GCGAAAGTCAAATTCGAAAT
1 GCGAAAGTAAAATTCGAAAC
*
1325319 GCGAAAGTAAAATTTGAAAC
1 GCGAAAGTAAAATTCGAAAC
* *
1325339 GCGAAAGAAAAATTCGCAAC
1 GCGAAAGTAAAATTCGAAAC
1325359 GCGAAA
1 GCGAAA
1325365 ATCGCAACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (20 bp):
GCGAAAGTAAAATTCGAAAC
Found at i:1325397 original size:20 final size:20
Alignment explanation
Indices: 1325374--1325436 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
1325364 AATCGCAACA
*
1325374 CGAATTTGGCTTTCGCATTG
1 CGAATTTGACTTTCGCATTG
* **
1325394 CGAATTTAACTTTCGTGTTG
1 CGAATTTGACTTTCGCATTG
* *
1325414 CCAATTTGAC-TTCGCAATG
1 CGAATTTGACTTTCGCATTG
1325433 CGAA
1 CGAA
1325437 AATTGCAACG
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
CGAATTTGACTTTCGCATTG
Found at i:1327482 original size:21 final size:21
Alignment explanation
Indices: 1327452--1327498 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1327442 ACCATTGTCG
* * *
1327452 TCACGTAAAGTACCGACCTCC
1 TCACGCAAAGCACCGACCTCA
*
1327473 TCACGCAAAGCACTGACCTCA
1 TCACGCAAAGCACCGACCTCA
1327494 TCACG
1 TCACG
1327499 TAACTCCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.38, G:0.15, T:0.17
Consensus pattern (21 bp):
TCACGCAAAGCACCGACCTCA
Found at i:1329672 original size:20 final size:20
Alignment explanation
Indices: 1329644--1329722 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
1329634 GTGTTGTGAA
**
1329644 TTACAAATTCGTATTGCGAT
1 TTACAAATTCGCGTTGCGAT
*
1329664 TTTCAAATTCGCGTTGCGAT
1 TTACAAATTCGCGTTGCGAT
*
1329684 TTACATATTCGCGTTGCGAT
1 TTACAAATTCGCGTTGCGAT
*
1329704 TTACATATTCGCGTTGCGA
1 TTACAAATTCGCGTTGCGA
1329723 ATTTGAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
TTACAAATTCGCGTTGCGAT
Found at i:1335607 original size:256 final size:256
Alignment explanation
Indices: 1335145--1336049 Score: 1251
Period size: 256 Copynumber: 3.5 Consensus size: 256
1335135 GTCTCAAGTT
* * * * * *
1335145 AGACCGACAGATAACCCAAAGGATTTAATCATCATGCTCGAATGACTTACTGATGACCCGAAGGA
1 AGACTGACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGA
* * * *
1335210 CTTACTAATTTTGGAAATAATTTACTGGGTAATAAACTTTGGAAATCGCTTTCTTACTTTTCAAA
66 CTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
* * *
1335275 AGTTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTAAAATTCA
131 AATTTCATTTTCTGAAAATTCTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCA
** * * * *
1335340 TACGAAAACATCCTACCCAAAGATCTTATAGATGGCCCGAAGAACTTATCATCTTGCTCGAA
196 TGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAG-ACTTATCATCTTGCTCGAA
* * * * *
1335402 AGATTGACAGATGACCCGAAGGATTTAATCATCATCCTCGAAAGACTTACTGATGGCGAGAAGGA
1 AGACTGACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGA
* *
1335467 CTTACTAATTTTGGAAATAGTTTACT-GGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAAA
66 CTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
* * * *
1335531 AATTTCAATTTCTGAAAATTCTAAATAAGAAACTTTGGATATCACTTTCTCATTTTTCAAATTCA
131 AATTTCATTTTCTGAAAATTCTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCA
** * *
1335596 TGTGGAAACATCCTGCTTGAAGGTCTTATAGATGCCCCGAATGACTTATCATCTTGCTCAAA
196 TGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAA-GACTTATCATCTTGCTCGAA
* * *
1335658 AGACTGAAAGATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCTA-AAGG
1 AGACTGACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC-AGAAGG
* * * *
1335722 GCTTACAAATTTCGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTATTTTTCAA
65 ACTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAA
*
1335787 AAATTTCATTTTCTGAAAACAT-TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAA
130 AAATTTCATTTTCTGAAAA-TTCTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTC---AA
* *
1335851 ATT-ATGTGGAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTTG
191 ATTCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAA-GACTTATCATCTTGCTCG
1335915 AA
255 AA
* * * * *
1335917 AGACTGACAGATGAGCCGAAGGATTTAAGCATCAGGCTCGAAAGACTTACTGATGGCCCGAATGA
1 AGACTGACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGA
* *
1335982 CTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTCATTTTTCAAA
66 CTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
1336047 AAT
131 AAT
1336050 CATGTGGAAA
Statistics
Matches: 572, Mismatches: 68, Indels: 14
0.87 0.10 0.02
Matches are distributed among these distances:
256 220 0.38
257 170 0.30
258 1 0.00
259 176 0.31
260 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (256 bp):
AGACTGACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGA
CTTACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
AATTTCATTTTCTGAAAATTCTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCA
TGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGACTTATCATCTTGCTCGAA
Found at i:1335978 original size:42 final size:41
Alignment explanation
Indices: 1335884--1335985 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
1335874 AAGGTCTTAT
* ** *
1335884 AGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAC
1 AGATGGCCCGAAGGACTTAGCATCAGGCTCGAAAGACTGAC
* *
1335925 AGATGAG-CCGAAGGATTTAAGCATCAGGCTCGAAAGACTTAC
1 AGATG-GCCCGAAGGACTT-AGCATCAGGCTCGAAAGACTGAC
* *
1335967 TGATGGCCCGAATGACTTA
1 AGATGGCCCGAAGGACTTA
1335986 CAAATTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
41 17 0.35
42 32 0.65
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTAGCATCAGGCTCGAAAGACTGAC
Found at i:1336555 original size:41 final size:42
Alignment explanation
Indices: 1336494--1336601 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
1336484 ATCATTCCCG
* * * **
1336494 AAGGTCTTATAGATGGCCCGAAGGAGTT-ATCATCTTGCTCGA
1 AAGG-CTTACAGATGACCCGAAGGAGTTAAGCATCAGGCTCGA
* *
1336536 AAGGCTTACAGATGACCCGAAAGATTTAAGCATCAGGCTCGA
1 AAGGCTTACAGATGACCCGAAGGAGTTAAGCATCAGGCTCGA
* *
1336578 AAGACTTACTGAT-AGCCCGAAGGA
1 AAGGCTTACAGATGA-CCCGAAGGA
1336602 CTTACAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (42 bp):
AAGGCTTACAGATGACCCGAAGGAGTTAAGCATCAGGCTCGA
Found at i:1336580 original size:254 final size:255
Alignment explanation
Indices: 1336088--1336730 Score: 929
Period size: 254 Copynumber: 2.5 Consensus size: 255
1336078 ATAGATGGTT
*
1336088 CGAATGACTTACAAATTTTGGAAATAATTTACT-GGTAAGAAACTTTGGAAATCACTTTCTTACT
1 CGAAGGACTTACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCAC-TTCTTACT
* * *
1336152 TTTCAAAAATTTGATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCAC-TTTTTC
65 TTTCAAAAATTTCATTTTCTGAAAAAATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTC
* *
1336216 -AAAATCATGTGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGACTTATCACCTTGCT
130 AAAAATCATGTGAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGACTTATCACCTTGCT
* * * *
1336280 CGAAAGACTGACAGATGACCGAAGGATTTAAGCATCATGCTCGAAAGACTTAGTGATGGCC
195 CGAAAGACTGACAGATGACCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCC
* * * * *
1336341 TGAAGGACTTACCAATTTTGGAAATAGTCTATTGGGTAAGAAACTTTGGAAATCAC-T-TTA-TT
1 CGAAGGACTTACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTCTTACTT
* * *
1336403 TTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCA
66 TTCAAAAATTTCATTTTCTGAAAAAATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCA
* * * * * *
1336468 AAAATTATGTGAAAATATCATTCCCGAAGGTCTTATAGATGGCCCGAAGGAGTTATCATCTTGCT
131 AAAATCATGTGAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAA-GACTTATCACCTTGCT
* *
1336533 CGAAAGGCTTACAGATGACCCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCC
195 CGAAAGACTGACAGATGA-CCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCC
* *
1336595 CGAAGGACTTACAAATTTTGAAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACT
1 CGAAGGACTTACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCAC-TTCTTACT
*
1336660 TTTCAAAAATTTCATTTTCTGAAAACAATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTT
65 TTTCAAAAATTTCATTTTCTGAAAA-AA-TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTT
1336725 TCAAAA
128 TCAAAA
1336731 TAACTTAATG
Statistics
Matches: 343, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
250 54 0.16
251 9 0.03
252 43 0.13
253 57 0.17
254 110 0.32
256 1 0.00
257 3 0.01
258 26 0.08
259 1 0.00
260 39 0.11
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (255 bp):
CGAAGGACTTACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTCTTACTT
TTCAAAAATTTCATTTTCTGAAAAAATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCA
AAAATCATGTGAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGACTTATCACCTTGCTC
GAAAGACTGACAGATGACCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCC
Found at i:1336665 original size:620 final size:627
Alignment explanation
Indices: 1335465--1336669 Score: 1904
Period size: 620 Copynumber: 1.9 Consensus size: 627
1335455 TGGCGAGAAG
* *
1335465 GACTTACTAATTTTGGAAATAGTTTACTGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAA
1 GACTTACAAATTTTGGAAATAATTTACTGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAA
* * * *
1335530 AAATTTCAATTTCTGAAAATTCTAAATAAGAAACTTTGGATATCACTTTCTCATTTTTCAAATTC
66 AAATTTCAATTTCTGAAAAATCTAAATAAGAAACTTTGGAAATCACTTTCACATTTTTCAAAATC
* * ** * *
1335595 ATGTGGAAACATCCTGCTTGAAGGTCTTATAGATGCCCCGAATGACTTATCATCTTGCTCAAAAG
131 ATGTGAAAACATCCTACCCGAAGGTCTTACAGATGCCCCGAATGACTTATCACCTTGCTCAAAAG
* *
1335660 ACTGAAAGATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCTAAAGGGCT
196 ACTGAAAGATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTAGTGATGGCCTAAAGGACT
*
1335725 TACAAATTTCGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTATTTTTCAAAAA
261 TACAAATTTCGGAAATAGTCTATTGGGTAAGAAACTTTGGAAATCAC-TTCTTATTTTTCAAAAA
* *
1335790 TTTCATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAAATTA
325 TTTCATTTTCTGAAAACACTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAAATTA
* *
1335855 TGTGGAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGA
390 TGTGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * *
1335920 CTGACAGATGAGCCGAAGGATTTAAGCATCAGGCTCGAAAGACTTACTGATGGCCCGAATGACTT
455 CTGACAGATGACCCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCCCGAAGGACTT
* * *
1335985 ACAAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAAT
520 ACAAATTTTGAAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTCACTTTTCAAAAAT
1336050 CATGTGGAAATATCCTGCCCAAGGTCTTATAGATGGTTCGAAT
585 CATGTGGAAATATCCTGCCCAAGGTCTTATAGATGGTTCGAAT
*
1336093 GACTTACAAATTTTGGAAATAATTTACTGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAA
1 GACTTACAAATTTTGGAAATAATTTACTGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAA
* * * *
1336158 AAATTTGATTTTCTGAAAACAT-TAAATGAGAAACTTTGGAAATCGCTTTCAC-TTTTTCAAAAT
66 AAATTTCAATTTCTGAAAA-ATCTAAATAAGAAACTTTGGAAATCACTTTCACATTTTTCAAAAT
* * *
1336221 CATGTGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAA-GACTTATCACCTTGCTCGAAA
130 CATGTGAAAACATCCTACCCGAAGGTCTTACAGATGCCCCGAATGACTTATCACCTTGCTCAAAA
* * * *
1336285 GACTGACAGATGA-CCGAAGGATTTAAGCATCATGCTCGAAAGACTTAGTGATGGCCTGAAGGAC
195 GACTGAAAGATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTAGTGATGGCCTAAAGGAC
* *
1336349 TTACCAATTTTGGAAATAGTCTATTGGGTAAGAAACTTTGGAAATCAC-T-TTA-TTTTCAAAAA
260 TTACAAATTTCGGAAATAGTCTATTGGGTAAGAAACTTTGGAAATCACTTCTTATTTTTCAAAAA
*
1336411 TTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTC-AAAAATTA
325 TTTCATTTTCTGAAAACACTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAAATTA
* * * *
1336475 TGTGAAAATATCATTCCCGAAGGTCTTATAGATGGCCCGAAGGAGTTATCATCTTGCTCGAAAGG
390 TGTGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
*
1336540 CTTACAGATGACCCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCCCGAAGGACTT
455 CTGACAGATGACCCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCCCGAAGGACTT
* *
1336605 ACAAATTTTGAAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
520 ACAAATTTTGAAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTCACTTTTCAAAAAT
1336670 TTCATTTTCT
Statistics
Matches: 528, Mismatches: 48, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
620 187 0.35
621 63 0.12
622 3 0.01
623 1 0.00
625 91 0.17
626 31 0.06
627 46 0.09
628 105 0.20
629 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (627 bp):
GACTTACAAATTTTGGAAATAATTTACTGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAA
AAATTTCAATTTCTGAAAAATCTAAATAAGAAACTTTGGAAATCACTTTCACATTTTTCAAAATC
ATGTGAAAACATCCTACCCGAAGGTCTTACAGATGCCCCGAATGACTTATCACCTTGCTCAAAAG
ACTGAAAGATGACCCAAAGAATTTAAGCATCATGCTCGAAAGACTTAGTGATGGCCTAAAGGACT
TACAAATTTCGGAAATAGTCTATTGGGTAAGAAACTTTGGAAATCACTTCTTATTTTTCAAAAAT
TTCATTTTCTGAAAACACTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAAATTAT
GTGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
TGACAGATGACCCGAAAGATTTAAGCATCAGGCTCGAAAGACTTACTGATAGCCCGAAGGACTTA
CAAATTTTGAAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTCACTTTTCAAAAATC
ATGTGGAAATATCCTGCCCAAGGTCTTATAGATGGTTCGAAT
Found at i:1339327 original size:22 final size:20
Alignment explanation
Indices: 1339281--1339330 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1339271 GAACGTAACG
* *
1339281 ATGCAAAAATGCACAAAAGA
1 ATGCAAAAATACAAAAAAGA
1339301 ATGCAAAAATACAAAAATAGGA
1 ATGCAAAAATACAAAAA-A-GA
1339323 ATGCAAAA
1 ATGCAAAA
1339331 TGTGTGATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 1 0.04
22 10 0.38
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (20 bp):
ATGCAAAAATACAAAAAAGA
Found at i:1340691 original size:17 final size:17
Alignment explanation
Indices: 1340669--1340701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1340659 GGTCTACTTG
*
1340669 ATCATGAAACCCTTTTC
1 ATCATGAAAACCTTTTC
1340686 ATCATGAAAACCTTTT
1 ATCATGAAAACCTTTT
1340702 ACTTGGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (17 bp):
ATCATGAAAACCTTTTC
Found at i:1344459 original size:54 final size:55
Alignment explanation
Indices: 1344348--1344589 Score: 265
Period size: 57 Copynumber: 4.3 Consensus size: 55
1344338 AAATTCACCT
* * * * * * * *
1344348 ACTTATTATGAATTTCTTA-TGTTTACAGATATAGTTCCCATACGGAAATTCACAC
1 ACTTAGTATGAATTTCTTAGT-TTTGCACACAAAGTGCCCATACAGAAATTCATAC
*
1344403 ACTTAGTATGAATTTCTTAG-TTTGCACACATAGTGCCCATACAGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* *
1344457 ACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATAC-GAAAATTCATGC
1 ACTTAGTATGAATTTCTTAG--TTTTGCACACAAAGTGCCCATACAG-AAATTCATAC
* * *
1344514 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCTATAGAGAAATTCATAA
1 ACTTAGTATGAATTTCTTAG--TTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* *
1344571 ACTAATTATGAATTTCTTA
1 ACTTAGTATGAATTTCTTA
1344590 ACTTTTTGTA
Statistics
Matches: 164, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
54 47 0.29
55 18 0.11
56 1 0.01
57 97 0.59
58 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (55 bp):
ACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
Found at i:1344508 original size:57 final size:58
Alignment explanation
Indices: 1344384--1344597 Score: 291
Period size: 57 Copynumber: 3.8 Consensus size: 58
1344374 AGATATAGTT
* * *
1344384 CCCATACG-GAAATTCACACACTTAGTATGAATTTCTTAG---TTTGCACACATAGTG
1 CCCATACGAGAAATTCATACACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTG
1344438 CCCATAC-AGAAATTCATACACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTG
1 CCCATACGAGAAATTCATACACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTG
* *
1344495 CCCATACGA-AAATTCATGCACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTG
1 CCCATACGAGAAATTCATACACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTG
* * *
1344552 CCTATA-GAGAAATTCATAAAC-TAATTATGAATTTCTTAACTTTTTG
1 CCCATACGAGAAATTCATACACTTAA-TATGAATTTCTTAGCTTTTTG
1344598 TACGCTCAAT
Statistics
Matches: 143, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
54 36 0.25
56 4 0.03
57 102 0.71
58 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (58 bp):
CCCATACGAGAAATTCATACACTTAATATGAATTTCTTAGCTTTTTGCACACAAAGTG
Found at i:1346627 original size:3 final size:3
Alignment explanation
Indices: 1346557--1346614 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
1346547 ATTGGCCTGC
*
1346557 AAT AAA AAT AA- ATAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1346601 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
1346615 ATATTGATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 46 0.92
4 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1351582 original size:5 final size:5
Alignment explanation
Indices: 1351572--1351598 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1351562 AAAGATATGT
1351572 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
1351599 GAAAGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1360029 original size:14 final size:14
Alignment explanation
Indices: 1359989--1360038 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1359979 ATGTTTTCAT
1359989 TATTTAATTGTTTG
1 TATTTAATTGTTTG
* *
1360003 AATTGTAA-CGTTTG
1 TATT-TAATTGTTTG
1360017 TATTTAATTGTTT-
1 TATTTAATTGTTTG
*
1360030 TAATTAATT
1 TATTTAATT
1360039 AATTTGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 11 0.38
14 15 0.52
15 3 0.10
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (14 bp):
TATTTAATTGTTTG
Found at i:1363595 original size:83 final size:83
Alignment explanation
Indices: 1363441--1363646 Score: 220
Period size: 83 Copynumber: 2.6 Consensus size: 83
1363431 TGATTTTGTC
* * * *
1363441 AAGATCCAAACTTACTCAACAAATATTTTCAGAAAGTTAGAGAAATTACATAGGGCCCATTAAGA
1 AAGATCCAAACTTACCCAACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGACCCATCAAGA
1363506 AAAAGAAGAAGTTTTACG
66 AAAAGAAGAAGTTTTACG
* * * * *
1363524 AAGATTCAATCTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACA-AAGACTCCATCATG
1 AAGATCCAAACTTACCCAACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGAC-CCATCAAG
1363588 ---AAGAAG-A-----A-G
65 AAAAAGAAGAAGTTTTACG
*
1363597 AAGATTCAAACTTACCCAACAAATATTTTCAGAAAGTT-GAAGAAATTACA
1 AAGATCCAAACTTACCCAACAAATATTTTCAGAAAGTTAG-AGAAATTACA
1363647 GAGGGTCCAT
Statistics
Matches: 110, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
72 1 0.01
73 47 0.43
74 1 0.01
79 1 0.01
80 6 0.05
82 3 0.03
83 51 0.46
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.25
Consensus pattern (83 bp):
AAGATCCAAACTTACCCAACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGACCCATCAAGA
AAAAGAAGAAGTTTTACG
Found at i:1372986 original size:24 final size:24
Alignment explanation
Indices: 1372954--1373010 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1372944 ACAAACAACA
*
1372954 TGCCCTCAAACCTAAGATGTGAAT
1 TGCCCTCAAACCTAAGATGCGAAT
*
1372978 TGCCCTCAAACCTAAGATGCGCAT
1 TGCCCTCAAACCTAAGATGCGAAT
1373002 TGCCCTCAA
1 TGCCCTCAA
1373011 TGCATGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (24 bp):
TGCCCTCAAACCTAAGATGCGAAT
Found at i:1383392 original size:39 final size:37
Alignment explanation
Indices: 1383288--1383397 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 37
1383278 TATAAAAAGT
*
1383288 AATTTAGAATTTAATGCGAAATAATTTAAGAAATTAAG
1 AATTTAGAATTTAA-GTGAAATAATTTAAGAAATTAAG
* * *
1383326 AATTTAGAATATTATAATGGCAA-AATTTAAGAAATTAGG
1 AATTTAGAAT-TTA-AGT-GAAATAATTTAAGAAATTAAG
*
1383365 AATTTAGAATGTTAGAGTGAAATAATTTGAGAA
1 AATTTAGAAT-TTA-AGTGAAATAATTTAAGAA
1383398 GTCTGAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 13 0.22
39 42 0.71
40 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (37 bp):
AATTTAGAATTTAAGTGAAATAATTTAAGAAATTAAG
Found at i:1386600 original size:41 final size:41
Alignment explanation
Indices: 1386507--1386695 Score: 185
Period size: 41 Copynumber: 4.8 Consensus size: 41
1386497 CCGAGAAAGT
* * *
1386507 TCAATGGATTCACCATTCGGGATGAATTTCACATT-AAAACA
1 TCAATGGATTCACCCTTCGGGATGAATTTCAC-TTCGAAATA
* ** * *
1386548 CCGGTGTATTCACCCTTCGAGATGAATTTCACTTCGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
*
1386589 TCAATGGATTCACCCTTTGGGATGAATTTCACTTCGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
* * *
1386630 TCAATGGA-T----CTTCAGGATGAATTTCAATTTGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
* * *
1386666 TCAACGGGTTCA-CCTTTGGGATGAATTTCA
1 TCAATGGATTCACCCTTCGGGATGAATTTCA
1386696 TTTTTGATTA
Statistics
Matches: 121, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
36 29 0.24
37 1 0.01
40 18 0.15
41 73 0.60
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
Found at i:1387609 original size:63 final size:67
Alignment explanation
Indices: 1387533--1387660 Score: 192
Period size: 68 Copynumber: 2.0 Consensus size: 67
1387523 TAAATATAAT
*
1387533 TATATATTTTGAATATTTCAAATT-AAAG-TA-A-TATCTATTTAATTTTGAATACTAAAAGATG
1 TATATATTTTGAATATTTCAAATTAAAAGATATAGTATCTATTTAAATTTGAATACTAAAAGATG
1387594 TC
66 TC
* *
1387596 TATATCTTTTGAATATTTCAAATTAAAAGATATTAGTATCTGTTTAAATTTGAATACTAAAAGAT
1 TATATATTTTGAATATTTCAAATTAAAAGATA-TAGTATCTATTTAAATTTGAATACTAAAAGAT
1387661 ATCTGATTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 23 0.40
64 4 0.07
65 2 0.04
67 1 0.02
68 27 0.47
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (67 bp):
TATATATTTTGAATATTTCAAATTAAAAGATATAGTATCTATTTAAATTTGAATACTAAAAGATG
TC
Found at i:1387623 original size:34 final size:33
Alignment explanation
Indices: 1387532--1387636 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 33
1387522 GTAAATATAA
*
1387532 TTATATATTTTGAATATTTCAAATT--AA-A-G
1 TTATATCTTTTGAATATTTCAAATTAAAAGATG
* * *
1387561 TAATATCTATTT-AAT-TTTGAATACTAAAAGATG
1 TTATATCT-TTTGAATATTTCAA-ATTAAAAGATG
*
1387594 TCTATATCTTTTGAATATTTCAAATTAAAAGATA
1 T-TATATCTTTTGAATATTTCAAATTAAAAGATG
1387628 TTAGTATCT
1 TTA-TATCT
1387637 GTTTAAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
28 5 0.09
29 11 0.19
30 3 0.05
31 2 0.03
32 1 0.02
33 7 0.12
34 24 0.41
35 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (33 bp):
TTATATCTTTTGAATATTTCAAATTAAAAGATG
Found at i:1387657 original size:34 final size:33
Alignment explanation
Indices: 1387563--1387664 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 33
1387553 AATTAAAGTA
* *
1387563 ATATCTATTTAATTTTGAATACTAAAAGATGTCT
1 ATATCT-TTTAAATTTGAATACTAAAAGATATCT
* *
1387597 ATATCTTTTGAATATTTCAA-ATTAAAAGATAT-T
1 ATATCTTTT-AA-ATTTGAATACTAAAAGATATCT
1387630 AGTATCTGTTTAAATTTGAATACTAAAAGATATCT
1 A-TATCT-TTTAAATTTGAATACTAAAAGATATCT
1387665 GATTGGACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
33 11 0.20
34 36 0.64
35 9 0.16
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (33 bp):
ATATCTTTTAAATTTGAATACTAAAAGATATCT
Found at i:1388171 original size:15 final size:15
Alignment explanation
Indices: 1388151--1388183 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1388141 AATGATGATG
1388151 ATTATTTT-TATAATT
1 ATTATTTTCTAT-ATT
1388166 ATTATTTTCTATATT
1 ATTATTTTCTATATT
1388181 ATT
1 ATT
1388184 CTCTTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATTTTCTATATT
Found at i:1398993 original size:50 final size:51
Alignment explanation
Indices: 1398938--1399040 Score: 145
Period size: 50 Copynumber: 2.0 Consensus size: 51
1398928 TTGATAGATT
* * *
1398938 TATATTCAATATTTTAATTCTATTCGTCATTTAT-ACAAAAATATTGTTTG
1 TATATTCAACATCTTAATTCTATTCGTCATTTATAAAAAAAATATTGTTTG
* **
1398988 TATATTCAACATCTTAATTCTATTCTTTTTTTATAAAAAAAATATTGTTTG
1 TATATTCAACATCTTAATTCTATTCGTCATTTATAAAAAAAATATTGTTTG
1399039 TA
1 TA
1399041 AAATCATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 29 0.63
51 17 0.37
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (51 bp):
TATATTCAACATCTTAATTCTATTCGTCATTTATAAAAAAAATATTGTTTG
Found at i:1400059 original size:46 final size:48
Alignment explanation
Indices: 1399992--1400086 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
1399982 TAAGCCTTAC
* * *
1399992 ATTATTAGTTATGTCTTT-A-ATATTCAACGGTCAGTGCTTTTCTTGA
1 ATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTTCCTTGA
1400038 ATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTTCCTTGA
1 ATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTTCCTTGA
1400086 A
1 A
1400087 GATTCAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 17 0.39
47 1 0.02
48 26 0.59
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (48 bp):
ATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTTCCTTGA
Found at i:1406636 original size:15 final size:14
Alignment explanation
Indices: 1406605--1406655 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1406595 AAGTCAATGG
*
1406605 GTTGACTCGGACGA
1 GTTGACTCAGACGA
1406619 GTTGACTCAGACCGA
1 GTTGACTCAGA-CGA
* *
1406634 GTTGACTCAAACGG
1 GTTGACTCAGACGA
1406648 GTTGACTC
1 GTTGACTC
1406656 GTCAACCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1408607 original size:15 final size:16
Alignment explanation
Indices: 1408584--1408616 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1408574 ATAATTACCA
1408584 TTTGCCATTAAAATAT
1 TTTGCCATTAAAATAT
1408600 TTTG-CATTAAAATAT
1 TTTGCCATTAAAATAT
1408615 TT
1 TT
1408617 CATAGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTGCCATTAAAATAT
Found at i:1413805 original size:18 final size:19
Alignment explanation
Indices: 1413782--1413825 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1413772 CCAGTAATCC
*
1413782 TATTCC-CTGGCAATCTTT
1 TATTCCACTGGCAATCTTA
*
1413800 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGCAATCTTA
1413820 TATTCC
1 TATTCC
1413826 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (19 bp):
TATTCCACTGGCAATCTTA
Found at i:1413816 original size:20 final size:20
Alignment explanation
Indices: 1413788--1413825 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1413778 ATCCTATTCC
*
1413788 CTGGCAATCTTTTATTCCCA
1 CTGGCAATCTTATATTCCCA
*
1413808 CTGGTAATCTTATATTCC
1 CTGGCAATCTTATATTCC
1413826 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGCAATCTTATATTCCCA
Found at i:1419007 original size:22 final size:22
Alignment explanation
Indices: 1418979--1419024 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1418969 ATCATCATCA
1418979 TCATCAAAATCATAATATGCAC
1 TCATCAAAATCATAATATGCAC
1419001 TCATCAAAATCATAATATGCAC
1 TCATCAAAATCATAATATGCAC
1419023 TC
1 TC
1419025 CAAGTGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (22 bp):
TCATCAAAATCATAATATGCAC
Found at i:1422317 original size:19 final size:19
Alignment explanation
Indices: 1422293--1422374 Score: 92
Period size: 19 Copynumber: 4.1 Consensus size: 19
1422283 TAGAAGTTCG
1422293 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
1422312 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
1422331 CACGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
*
1422354 CGTTGCGATTTTCCAAGTT
1 CGTTGCGATTTTCCAAATT
1422373 CG
1 CG
1422375 CGTTGCAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 26 0.50
20 2 0.04
21 16 0.31
22 1 0.02
23 7 0.13
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:1422350 original size:42 final size:40
Alignment explanation
Indices: 1422274--1422380 Score: 151
Period size: 42 Copynumber: 2.6 Consensus size: 40
1422264 CATATTCGCA
**
1422274 TTGCGATAGTAGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
1422314 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
**
1422356 TTGCGATTTTCCAAGTTCGCGTTGC
1 TTGCGATAGTCCAAGTTCGCGTTGC
1422381 AATAGTTGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 24 0.41
41 2 0.03
42 33 0.56
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:1422405 original size:42 final size:40
Alignment explanation
Indices: 1422354--1422459 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 40
1422344 ATTCCAAATT
* *
1422354 CGTTGCGATTTTCCAAGTTCGCGTTGCAATAGTTGAAGTTCG
1 CGTTGCGATTTTCCAAATT--CGTTGCAATAGTCGAAGTTCG
* *
1422396 CGTTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TT-TTCCAAATTCGTTGCAATAGTCGAAGTTCG
1422438 CGTTGCGATTTATTCCAAATTC
1 CGTTGCGA-TT-TTCCAAATTC
1422460 TTAAGAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 47 0.82
43 2 0.04
44 8 0.14
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTTCCAAATTCGTTGCAATAGTCGAAGTTCG
Found at i:1422405 original size:63 final size:63
Alignment explanation
Indices: 1422293--1422443 Score: 207
Period size: 63 Copynumber: 2.4 Consensus size: 63
1422283 TAGAAGTTCG
* * *
1422293 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTTCCAAGTTCGCGTTGCAATAGTCCAAGTTCACGTTACGATTTATTCCAAATT
** *
1422354 CGTTGCGATTTTCCAAGTTCGCGTTGCAATAGTTGAAGTTCGCGTTACGATTTATTCCAAATT
1 CGTTGCGATTTTCCAAGTTCGCGTTGCAATAGTCCAAGTTCACGTTACGATTTATTCCAAATT
** *
1422417 CGTTGCGATAGTCGAAGTTCGCGTTGC
1 CGTTGCGATTTTCCAAGTTCGCGTTGC
1422444 GATTTATTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 18 0.23
63 61 0.77
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (63 bp):
CGTTGCGATTTTCCAAGTTCGCGTTGCAATAGTCCAAGTTCACGTTACGATTTATTCCAAATT
Found at i:1422527 original size:6 final size:6
Alignment explanation
Indices: 1422516--1422542 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1422506 GACACGTATT
1422516 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
1422543 CAAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1423055 original size:6 final size:6
Alignment explanation
Indices: 1423044--1423074 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1423034 CCGTCTCGTC
*
1423044 TCGTGG TCGTGG TCGTGA TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1423075 AATACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.16, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1423216 original size:21 final size:21
Alignment explanation
Indices: 1423192--1423376 Score: 184
Period size: 21 Copynumber: 8.8 Consensus size: 21
1423182 AACTTCGACT
*
1423192 ATCGCAATGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1423213 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1423234 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1423255 ATCGCAACTAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
1423276 ATCGTAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1423297 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1423318 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
1423339 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAA
1423358 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1423377 CTATCGCAAT
Statistics
Matches: 134, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
19 24 0.18
21 92 0.69
23 18 0.13
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1423391 original size:21 final size:19
Alignment explanation
Indices: 1423180--1423385 Score: 142
Period size: 21 Copynumber: 10.0 Consensus size: 19
1423170 TAGCGCAACG
* *
1423180 CGAACTTCGACTATCGCAA
1 CGAACTTGGAATATCGCAA
*
1423199 TGAACTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
*
1423220 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
1423241 CGAACTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
* * *
1423262 CTAATTTGGAATAAATCGTAA
1 CGAACTTGGAAT--ATCGCAA
* *
1423283 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
1423304 CGAACTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
* *
1423325 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
* *
1423346 CGAATTTGGAAAATCGCAA
1 CGAACTTGGAATATCGCAA
*
1423365 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
1423386 TGCGAATATG
Statistics
Matches: 152, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
19 34 0.22
21 100 0.66
23 18 0.12
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
CGAACTTGGAATATCGCAA
Found at i:1423392 original size:42 final size:42
Alignment explanation
Indices: 1423213--1423385 Score: 246
Period size: 42 Copynumber: 4.2 Consensus size: 42
1423203 CTTGGAATAA
* *
1423213 ATCGCAACGAATTTGGAATAAATCGCAA--CGAACTTGGAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* *
1423253 AAATCGCAACTAATTTGGAATAAATCGTAACGCGAACTTCGACT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1423297 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1423339 ATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1423379 ATCGCAA
1 ATCGCAA
1423386 TGCGAATATG
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
40 29 0.24
41 1 0.01
42 80 0.67
44 10 0.08
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1424156 original size:25 final size:23
Alignment explanation
Indices: 1424123--1424174 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
1424113 TTTATTTAAT
*
1424123 ATTAATATATTTTAAATTTTAAATA
1 ATTAATATATATTAAA-TTTAAA-A
*
1424148 ATTAATATATATTACATTTAAAA
1 ATTAATATATATTAAATTTAAAA
1424171 ATTA
1 ATTA
1424175 TAGATGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTAATATATATTAAATTTAAAA
Found at i:1426790 original size:21 final size:21
Alignment explanation
Indices: 1426764--1426844 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
1426754 AGTCAAGGGT
1426764 TTATGTGGTC-CTTCGGGATAA
1 TTATGTGG-CACTTCGGGATAA
1426785 TTATGTGGCACTTCGGTG-TAAA
1 TTATGTGGCACTTCGG-GAT-AA
** *
1426807 TCTATGTGGTC-CTTTAGGACAA
1 T-TATGTGG-CACTTCGGGATAA
1426829 TTATGTGGCACTTCGG
1 TTATGTGGCACTTCGG
1426845 TCCAAATTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 2 0.04
21 26 0.54
22 8 0.17
23 11 0.23
24 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (21 bp):
TTATGTGGCACTTCGGGATAA
Found at i:1428963 original size:13 final size:13
Alignment explanation
Indices: 1428945--1428970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1428935 TGTGTAAGTT
1428945 TTGTCGAGGCAAG
1 TTGTCGAGGCAAG
1428958 TTGTCGAGGCAAG
1 TTGTCGAGGCAAG
1428971 CTTTATTTGG
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:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (13 bp):
TTGTCGAGGCAAG
Found at i:1431839 original size:16 final size:16
Alignment explanation
Indices: 1431818--1431858 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1431808 ACCGTTGGCT
1431818 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
1431834 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
1431850 GAGGCGGCT
1 GAGGCGGCT
1431859 AGGGTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.56, T:0.07
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:1431960 original size:2 final size:2
Alignment explanation
Indices: 1431955--1431985 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1431945 ATTATTTATG
1431955 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 T
1431986 TTAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1431995 original size:3 final size:3
Alignment explanation
Indices: 1431987--1432098 Score: 161
Period size: 3 Copynumber: 37.0 Consensus size: 3
1431977 TATATATATT
* *
1431987 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1432035 TAT TTA TAA TAA TAA TAA TAA TATA TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
1432081 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1432099 ATAAATCAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 94 0.98
4 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1432633 original size:113 final size:113
Alignment explanation
Indices: 1432430--1432859 Score: 797
Period size: 113 Copynumber: 3.8 Consensus size: 113
1432420 AGAATTATGC
* * * *
1432430 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1432495 TATGAACTTTCTCTGGGAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1432543 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1432608 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1432656 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1432721 TATGAACTTTTTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
1432769 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1432834 TATGAACTTTCTCTGGAAAAGTTGAT
66 TATGAACTTTCTCTGGAAAAGATGAT
1432860 GAGTTCTTCT
Statistics
Matches: 309, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 309 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:1432875 original size:39 final size:38
Alignment explanation
Indices: 1432818--1432891 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
1432808 TCCTTCTTCA
1432818 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTT
1 GATGAGTTCTTCTCATTATGAACTTTCTCT-GAAAAGTT
*
1432857 GATGAGTTCTTCTGATTATGAACTTTCTCTGAAAA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGAAAA
1432892 TATTGATCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (38 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAGTT
Found at i:1433204 original size:73 final size:73
Alignment explanation
Indices: 1433080--1433605 Score: 592
Period size: 73 Copynumber: 7.4 Consensus size: 73
1433070 GAGGTCTTAT
* * * * *
1433080 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
*
1433145 TTTGAAAA
66 TTTGGAAA
* * * *
1433153 CATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTATAAGATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
*
1433218 TTTGAAAA
66 TTTGGAAA
* * * * *
1433226 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTATAAGATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
1433291 TTTGGAAA
66 TTTGGAAA
*
1433299 CATCATGCACTGTAGGACTTACAGATG----TG-GG----AACATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
1433355 TTTGGAAA
66 TTTGGAAA
* *
1433363 CATCATGCACTGTAGGACTTACAGATG----TG-GG----AACCTCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
*
1433419 TTTGAAAA
66 TTTGGAAA
* *
1433427 CATCATGCACTGA-AAGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACT-ATAGGACTTACAGATGACCCTGAGGC--T-ATAACATCAAAAAGCTCCCGAAG
1433491 GCTTTTTGGAAA
62 GCTTTTTGGAAA
*
1433503 CATCATGCACTGA-AGGACTTACAGATGACCC-GAAGGCTTTAAAAACATCAAAAAGCTCCCGAA
1 CATCATGCACT-ATAGGACTTACAGATGACCCTG-AGGC--T-ATAACATCAAAAAGCTCCCGAA
1433566 GGCTTTTTGGAAA
61 GGCTTTTTGGAAA
*
1433579 CATCATGCAGTGA-AGGACTTACAGATG
1 CATCATGCACT-ATAGGACTTACAGATG
1433606 TGGGAAATAG
Statistics
Matches: 418, Mismatches: 21, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
64 116 0.28
68 4 0.01
69 4 0.01
73 164 0.39
75 1 0.00
76 129 0.31
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (73 bp):
CATCATGCACTATAGGACTTACAGATGACCCTGAGGCTATAACATCAAAAAGCTCCCGAAGGCTT
TTTGGAAA
Found at i:1433370 original size:64 final size:64
Alignment explanation
Indices: 1433269--1433611 Score: 389
Period size: 76 Copynumber: 5.0 Consensus size: 64
1433259 AGGCTATAAG
* * *
1433269 ATCAAAAAGCTTCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGAAC
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAC
*
1433333 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGAAC
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAC
* * *
1433397 CTCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG----T--G
1433462 GCTTTGAAAAC
60 G----G--AAC
*
1433473 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG---TG--G
1433538 GCTTTAAAAAC
61 G-------AAC
*
1433549 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAGTGAAGGACTTACAGATGTGGGAA
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAA
1433612 ATAGTTTACT
Statistics
Matches: 247, Mismatches: 13, Indels: 38
0.83 0.04 0.13
Matches are distributed among these distances:
64 117 0.47
68 1 0.00
70 2 0.01
71 3 0.01
73 2 0.01
74 1 0.00
75 3 0.01
76 118 0.48
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (64 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAC
Found at i:1433852 original size:162 final size:165
Alignment explanation
Indices: 1433619--1433916 Score: 469
Period size: 163 Copynumber: 1.8 Consensus size: 165
1433609 GAAATAGTTT
* * **
1433619 ACTAATAAAATCGTTTTCTTACTTTTCAACAATTTCATTGATAGAAAAGATTGAATGAGAAACTA
1 ACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATT-ATAGAAAAGATAAAATGAGAAACTA
1433684 TGGAAATCATTTTCTCATTAT-TTTTCAAAATAACATGTTGATTGGGTAACATGCCCCAATCTTC
65 TGGAAATCATTTTCTCATTATGTTTTCAAAATAACATGTTGATTGGGTAACATGCCCCAATC-TC
1433748 -AGATAAGGTTATTGGAAATAGTTTAATAAGTAAAAA
129 AAGATAAGGTTATTGGAAATAGTTTAATAAGTAAAAA
*
1433784 ACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATT-T-TAAAAGATAAAATGAGAAACTAT
1 ACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATTATAGAAAAGATAAAATGAGAAACTAT
* ** *
1433847 GGAAATCGTTTTCTCATTATGTTTTTGAAATAACATGTTGATTGGGTAACATGTCCCAATCTCAA
66 GGAAATCATTTTCTCATTATGTTTTCAAAATAACATGTTGATTGGGTAACATGCCCCAATCTCAA
1433912 GATAA
131 GATAA
1433917 TTTTCATTCT
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
162 41 0.34
163 44 0.36
165 37 0.30
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (165 bp):
ACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATTATAGAAAAGATAAAATGAGAAACTAT
GGAAATCATTTTCTCATTATGTTTTCAAAATAACATGTTGATTGGGTAACATGCCCCAATCTCAA
GATAAGGTTATTGGAAATAGTTTAATAAGTAAAAA
Found at i:1434479 original size:22 final size:22
Alignment explanation
Indices: 1434432--1434510 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
1434422 AATAAAGCTT
* * *
1434432 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTAAAAAGAAAATCTA
* *
1434454 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAAAATCTA
* * **
1434476 TCATCTCTGAAGTGAAAATCTA
1 TCATCTTTAAAAAGAAAATCTA
1434498 TCATCTTTAAAAA
1 TCATCTTTAAAAA
1434511 ATGTAGATGT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAAAATCTA
Found at i:1437126 original size:114 final size:114
Alignment explanation
Indices: 1436926--1437151 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
1436916 GATCATGCAG
* * * * * *
1436926 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
*
1436991 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
1437040 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAAATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
1437105 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
1437152 CATGGCACTT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1439229 original size:7 final size:7
Alignment explanation
Indices: 1439212--1439281 Score: 58
Period size: 7 Copynumber: 10.4 Consensus size: 7
1439202 TGATTCAATT
1439212 TTTTTTC
1 TTTTTTC
1439219 -TTTTTC
1 TTTTTTC
1439225 TTTTTTC
1 TTTTTTC
*
1439232 TTTTTTG
1 TTTTTTC
*
1439239 TTTTGTTG
1 TTTT-TTC
1439247 TTTTTT-
1 TTTTTTC
**
1439253 TGGTTT-
1 TTTTTTC
1439259 TTTTTTC
1 TTTTTTC
1439266 -TTTTTC
1 TTTTTTC
*
1439272 TTCTTTC
1 TTTTTTC
1439279 TTT
1 TTT
1439282 GCTAGATGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
6 20 0.38
7 25 0.48
8 7 0.13
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:1439230 original size:13 final size:13
Alignment explanation
Indices: 1439212--1439281 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
1439202 TGATTCAATT
1439212 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
*
1439225 TTTTTTCTTTTTTG
1 TTTTTTC-TTTTTC
*
1439239 TTTTGTTGTTTTT-
1 TTTT-TTCTTTTTC
1439252 TTGGTTTT-TTTTTC
1 TT--TTTTCTTTTTC
1439266 -TTTTTCTTCTTTC
1 TTTTTTCTT-TTTC
1439279 TTT
1 TTT
1439282 GCTAGATGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
11 4 0.09
12 2 0.04
13 19 0.40
14 18 0.38
15 4 0.09
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Done.