Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 51
Found at i:5380556 original size:182 final size:181
Alignment explanation
Indices: 5380071--5380558 Score: 707
Period size: 182 Copynumber: 2.7 Consensus size: 181
5380061 CGTACTTACG
*
5380071 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACC-GTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
5380135 TATCATATTTTTACCTGTTATATCATTGTGGATCGATATATTTTT--TTAAAGTATCGACACATT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTAATT--AGTATCGACACATT
*
5380198 ATAGGTGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
129 ATAGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
5380251 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
5380316 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAA-AAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACA-TTTTTAATTAGTATCGACACATTA
* *
5380380 TAGGAT-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 TAGG-TGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * **
5380433 AAAGTATCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
5380498 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTTTAATTTGGATCGACACA
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTAATTAGTATCGACACA
5380559 AACCGACAAG
Statistics
Matches: 276, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
180 59 0.21
181 107 0.39
182 110 0.40
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTAATTAGTATCGACACATTAT
AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:5384320 original size:6 final size:6
Alignment explanation
Indices: 5384311--5384343 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5384301 CATTACCATT
*
5384311 ACCAGG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5384344 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5384840 original size:6 final size:6
Alignment explanation
Indices: 5384832--5384906 Score: 132
Period size: 6 Copynumber: 12.5 Consensus size: 6
5384822 TCTCGTCTCG
* *
5384832 GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5384880 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
5384907 AATGGTAATG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:5385024 original size:21 final size:21
Alignment explanation
Indices: 5384998--5385140 Score: 109
Period size: 21 Copynumber: 6.9 Consensus size: 21
5384988 TTTTTAATTT
5384998 ACTGTAGACTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
*
5385019 ACTGTAGATTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
5385039 GAAATG--GAAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
5385060 ACTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* ** *
5385080 GA--GATGGAAAATCGCAACGAT
1 -ACTG-TAGACTATCGCAACGAC
* *
5385101 ACTGTACACTATCGCAACGAT
1 ACTGTAGACTATCGCAACGAC
*
5385122 ACTGTACACTATCGCAACG
1 ACTGTAGACTATCGCAACG
5385141 CGATTTTCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
19 4 0.04
20 26 0.27
21 63 0.65
22 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:5385054 original size:20 final size:20
Alignment explanation
Indices: 5385029--5385098 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
5385019 ACTGTAGATT
5385029 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
5385049 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
5385070 ATCGCAACGCGAGATGGAAA
1 ATCGCAACGCGAAATGGAAA
5385090 ATCGCAACG
1 ATCGCAACG
5385099 ATACTGTACA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 18 0.47
21 9 0.24
22 2 0.05
23 3 0.08
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5385065 original size:41 final size:41
Alignment explanation
Indices: 5385008--5385181 Score: 194
Period size: 41 Copynumber: 4.2 Consensus size: 41
5384998 ACTGTAGACT
*
5385008 ATCGCAACGACACTGTAGATTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
5385049 ATCGCAACGACACTGTAGACTATCGCAACGCGAGATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* * * * *
5385090 ATCGCAACGATACTGTACACTATCGCAA--CGATACTGTACACT
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA-AATGGA-A-A
* *
5385132 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGAC-ACTGT-AGACTATCGCAACGCGAAATGGAAA
5385173 ATCGCAACG
1 ATCGCAACG
5385182 CGAAATGGAA
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
39 3 0.03
40 3 0.03
41 75 0.67
42 23 0.21
43 5 0.04
44 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:5385178 original size:20 final size:20
Alignment explanation
Indices: 5385153--5385242 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
5385143 ATTTTCAACT
5385153 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
5385173 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
5385193 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
5385214 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
5385234 ATAGCAACG
1 ATCGCAACG
5385243 ACACTGTAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 37 0.64
21 9 0.16
22 3 0.05
23 3 0.05
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5385218 original size:41 final size:41
Alignment explanation
Indices: 5385173--5385270 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
5385163 GAAATGGAAA
*
5385173 ATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACT
1 ATCGCAACGCGAAATGGAAAATAGCAACGACACTGTAGACT
5385214 ATCGCAACGCGAAATGGAAAATAGCAACGACACTGTAGACT
1 ATCGCAACGCGAAATGGAAAATAGCAACGACACTGTAGACT
5385255 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
5385271 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.14
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATAGCAACGACACTGTAGACT
Found at i:5385219 original size:21 final size:21
Alignment explanation
Indices: 5385193--5385263 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5385183 GAAATGGAAA
5385193 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
5385214 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
5385234 ATAGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
5385255 ATCGCAACG
1 ATCGCAACG
5385264 CGAAATGCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
19 3 0.08
20 11 0.30
21 20 0.54
22 3 0.08
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.15
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:5385528 original size:29 final size:31
Alignment explanation
Indices: 5385466--5385533 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
5385456 AACGGTCTAA
5385466 TAATCAAAATATAATAATTTGATAATATAAG
1 TAATCAAAATATAATAATTTGATAATATAAG
* * * *
5385497 TAATTAAAATATAAT-TTTTTA-AATATCAG
1 TAATCAAAATATAATAATTTGATAATATAAG
5385526 TAATCAAA
1 TAATCAAA
5385534 CTCAGACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.44
30 4 0.12
31 14 0.44
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (31 bp):
TAATCAAAATATAATAATTTGATAATATAAG
Found at i:5393079 original size:11 final size:12
Alignment explanation
Indices: 5393063--5393096 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5393053 TCGAGTATTA
5393063 TTAAATTAAAT-
1 TTAAATTAAATG
5393074 TTAAATTAAATG
1 TTAAATTAAATG
*
5393086 TTTAATTAAAT
1 TTAAATTAAAT
5393097 CGACATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TTAAATTAAATG
Found at i:5404051 original size:2 final size:2
Alignment explanation
Indices: 5404044--5404089 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5404034 TCGAGTAGTC
5404044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5404086 AT AT
1 AT AT
5404090 GGCTTCCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5419170 original size:22 final size:22
Alignment explanation
Indices: 5419134--5419200 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
5419124 AAATAATAAG
* *
5419134 AGGTATCGATTCCCCTATGAAT
1 AGGTATCAATACCCCTATGAAT
*
5419156 GGGTATCAATACCCCTATGAAT
1 AGGTATCAATACCCCTATGAAT
* * * *
5419178 AGGTACCGATAACCCTATCAAT
1 AGGTATCAATACCCCTATGAAT
5419200 A
1 A
5419201 CCTCTATGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (22 bp):
AGGTATCAATACCCCTATGAAT
Found at i:5422406 original size:18 final size:20
Alignment explanation
Indices: 5422368--5422406 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5422358 CAACAATTGG
*
5422368 TAACAATTGGTGTATCTTTT
1 TAACAATTGGTGTATCCTTT
5422388 TAACAATT-G-GTATCCTTT
1 TAACAATTGGTGTATCCTTT
5422406 T
1 T
5422407 GTAAACAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (20 bp):
TAACAATTGGTGTATCCTTT
Found at i:5422415 original size:21 final size:19
Alignment explanation
Indices: 5422368--5422427 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
5422358 CAACAATTGG
5422368 TAACAATTGGTGTAT-CTTTT
1 TAACAATT-G-GTATCCTTTT
5422388 TAACAATTGGTATCCTTTT
1 TAACAATTGGTATCCTTTT
*
5422407 GTAAACAATTGATAT-CTTTT
1 -T-AACAATTGGTATCCTTTT
5422427 T
1 T
5422428 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 14 0.39
21 11 0.31
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (19 bp):
TAACAATTGGTATCCTTTT
Found at i:5422673 original size:22 final size:22
Alignment explanation
Indices: 5422648--5422701 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5422638 AGAGGTACTG
*
5422648 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTACCA
*
5422670 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTACCA
5422692 ATACCCCTAT
1 ATACCCCTAT
5422702 TGATACCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTACCA
Found at i:5426915 original size:26 final size:26
Alignment explanation
Indices: 5426856--5426940 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
5426846 GAAGAAGATG
* *
5426856 ATGAAATGAGAGAGAAAAAGTAAAAGTA
1 ATGAAATGAAAGAGAAAAAGT-TAA-TA
*
5426884 A-AAAATGAAAGAGAAAAAGTTAATA
1 ATGAAATGAAAGAGAAAAAGTTAATA
* * *
5426909 ATGAAAT-ATAAAAGAAAAATTTAAAA
1 ATGAAATGA-AAGAGAAAAAGTTAATA
5426935 ATGAAA
1 ATGAAA
5426941 GGGAAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 4 0.08
26 26 0.54
27 17 0.35
28 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (26 bp):
ATGAAATGAAAGAGAAAAAGTTAATA
Found at i:5431491 original size:21 final size:21
Alignment explanation
Indices: 5431450--5431491 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5431440 TGAGCTATGG
* *
5431450 CTTTGAAGTAAGGTGTCTTGA
1 CTTTGAAGTAAAGTCTCTTGA
5431471 CTTTGAAGTAAAG-CTCATTGA
1 CTTTGAAGTAAAGTCTC-TTGA
5431492 TTATTAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (21 bp):
CTTTGAAGTAAAGTCTCTTGA
Found at i:5434642 original size:33 final size:33
Alignment explanation
Indices: 5434600--5434664 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5434590 AATGCAAAAA
*
5434600 GGGTACCGATGCCCCCATGAGTATCAATACCCT
1 GGGTACCGATACCCCCATGAGTATCAATACCCT
* *
5434633 GGGTACCGATACCCCTATGGGTATCAATACCC
1 GGGTACCGATACCCCCATGAGTATCAATACCC
5434665 CTGGCTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (33 bp):
GGGTACCGATACCCCCATGAGTATCAATACCCT
Found at i:5434655 original size:18 final size:18
Alignment explanation
Indices: 5434632--5434666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5434622 ATCAATACCC
*
5434632 TGGGTACCGATACCCCTA
1 TGGGTACCAATACCCCTA
*
5434650 TGGGTATCAATACCCCT
1 TGGGTACCAATACCCCT
5434667 GGCTCCAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (18 bp):
TGGGTACCAATACCCCTA
Found at i:5435581 original size:24 final size:24
Alignment explanation
Indices: 5435536--5435589 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5435526 CACCGAAGTG
* *
5435536 CCACATAG-ATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
* *
5435559 CCGCGTAGAATTTGTCTCAAAGGA
1 CCACGTAGAATTTGTCCCAAAGGA
5435583 CCACGTA
1 CCACGTA
5435590 AAAATTTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCAAAGGA
Found at i:5435601 original size:25 final size:24
Alignment explanation
Indices: 5435554--5435601 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5435544 ATTTGTCCCG
* * *
5435554 AAGGACCGCGTAGAATTTGTCTCA
1 AAGGACCACGTAAAATTTATCTCA
5435578 AAGGACCACGTAAAAATTTATCTC
1 AAGGACCACGT-AAAATTTATCTC
5435602 GAATGACCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (24 bp):
AAGGACCACGTAAAATTTATCTCA
Found at i:5435812 original size:15 final size:15
Alignment explanation
Indices: 5435794--5435833 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5435784 TAGAACATAG
*
5435794 TCACTTAGCACATTT
1 TCACATAGCACATTT
*
5435809 TCACATAGAACATTT
1 TCACATAGCACATTT
*
5435824 TCACGTAGCA
1 TCACATAGCA
5435834 TTATTCAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (15 bp):
TCACATAGCACATTT
Found at i:5438452 original size:36 final size:36
Alignment explanation
Indices: 5438389--5438458 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
5438379 TCGTTCAAGA
* *
5438389 TGGTATCGATACATTCCTTAAGGTATCGGTACCCCT
1 TGGTATCGATACATTCATTAAGGTATCGATACCCCT
* *
5438425 TGGTATCGATACTATT-ATTCAGTTATCGATACCC
1 TGGTATCGATAC-ATTCATTAAGGTATCGATACCC
5438459 TTTGAAGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 26 0.90
37 3 0.10
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (36 bp):
TGGTATCGATACATTCATTAAGGTATCGATACCCCT
Found at i:5438822 original size:26 final size:25
Alignment explanation
Indices: 5438775--5438823 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5438765 TCAAATTTAG
* **
5438775 CTTCAAATTTTACTTATCAACTCTT
1 CTTCAAATTTCACTTAAAAACTCTT
5438800 CTTCAAGATTTCACTTAAAAACTC
1 CTTCAA-ATTTCACTTAAAAACTC
5438824 ATTTTCTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (25 bp):
CTTCAAATTTCACTTAAAAACTCTT
Found at i:5443462 original size:15 final size:15
Alignment explanation
Indices: 5443432--5443474 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5443422 ACTTATCATT
* *
5443432 TATTCTCGTAGAACA
1 TATTCACGTAGCACA
*
5443447 TATTCACTTAGCACA
1 TATTCACGTAGCACA
*
5443462 TTTTCACGTAGCA
1 TATTCACGTAGCA
5443475 TTATTCAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (15 bp):
TATTCACGTAGCACA
Found at i:5446933 original size:14 final size:14
Alignment explanation
Indices: 5446911--5446953 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
5446901 TCAATTATAT
*
5446911 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
5446925 GTTCATTTATGTTC
1 GTTCATTTATGTTC
5446939 GTTCATTTATGTTC
1 GTTCATTTATGTTC
5446953 G
1 G
5446954 AATAGAGGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:5448068 original size:20 final size:20
Alignment explanation
Indices: 5448045--5448082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5448035 TGATATACCA
5448045 GGTA-AAAATATGATAAAATC
1 GGTATAAAA-ATGATAAAATC
*
5448065 GGTATCAAAATGATAAAA
1 GGTATAAAAATGATAAAA
5448083 CTAGTAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (20 bp):
GGTATAAAAATGATAAAATC
Found at i:5448125 original size:182 final size:180
Alignment explanation
Indices: 5447833--5448304 Score: 667
Period size: 180 Copynumber: 2.6 Consensus size: 180
5447823 GATCCAAATT
* * * **
5447833 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
5447898 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACTGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
* *
5447963 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 ATGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTA
* * *
5448015 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
5448080 AAACTAGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTA
66 AAACTGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCA
** *
5448145 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTA
131 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
** *
5448195 AAAAAAATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
5448260 AAA-TCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACT-GGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
5448305 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
179 1 0.00
180 102 0.40
181 60 0.23
182 94 0.37
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACTGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCA
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:5448248 original size:20 final size:19
Alignment explanation
Indices: 5448225--5448271 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5448215 CGATATAACA
5448225 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
5448245 GGTATCAAAATGATAAAATC
1 GGTA-AAAAATGATAAAACC
5448265 GGTAAAA
1 GGTAAAA
5448272 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5450499 original size:21 final size:21
Alignment explanation
Indices: 5450473--5450537 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
5450463 AAGACAATCA
*
5450473 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
5450494 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
5450515 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
5450536 AG
1 AG
5450538 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:5450615 original size:33 final size:33
Alignment explanation
Indices: 5450573--5450636 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5450563 ATAGATGGAA
*
5450573 TGGTGAAAGAAGTAGAGATGTTGAGGGGTGAAG
1 TGGTGAAAGAAGTAGAGATGTTAAGGGGTGAAG
* * *
5450606 TGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 TGGTGAAAGAAGTAGAGATGTTAAGGGGTGA
5450637 TATTAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
TGGTGAAAGAAGTAGAGATGTTAAGGGGTGAAG
Found at i:5452453 original size:19 final size:19
Alignment explanation
Indices: 5452429--5452477 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
5452419 AATGTAGGGT
5452429 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
5452448 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
5452467 TAATTTTGTAT
1 TAATTTTGTAT
5452478 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5458702 original size:21 final size:21
Alignment explanation
Indices: 5458676--5458738 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5458666 TTTTGGTGCA
*
5458676 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
5458697 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
5458718 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
5458739 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:5458746 original size:21 final size:21
Alignment explanation
Indices: 5458720--5458759 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5458710 CCCCCTTTGA
*
5458720 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5458741 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5458760 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5460709 original size:15 final size:15
Alignment explanation
Indices: 5460689--5460730 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
5460679 TTGTTTCAAC
*
5460689 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
5460704 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
5460721 ATTTTGGATT
1 ATTTTGGATT
5460731 TATGAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:5460715 original size:17 final size:17
Alignment explanation
Indices: 5460693--5460726 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5460683 TTCAACATTT
*
5460693 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
5460710 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
5460727 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:5462651 original size:200 final size:200
Alignment explanation
Indices: 5462308--5464866 Score: 4680
Period size: 200 Copynumber: 12.8 Consensus size: 200
5462298 AATTTACAAT
* *
5462308 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTCTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
5462373 CGAAATCCATAAGTATAATGTAATAGTTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5462438 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCGAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5462503 AATGA
196 AATGA
5462508 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5462573 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
5462638 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5462703 AATGA
196 AATGA
5462708 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5462773 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5462838 TTGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5462903 AATGA
196 AATGA
* *
5462908 ATGTCAAATAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5462973 CGAAACCCATAAGTATAATGTAATAGTTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
5463038 ATGAGATAATAGGTCTAAATAATGTATCAACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5463103 AATGA
196 AATGA
*
5463108 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTCTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5463173 CGAAACCCATAAGTATAATGTAATAGTTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5463238 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCGAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5463303 AATGA
196 AATGA
5463308 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
5463373 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
5463438 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5463503 AATGA
196 AATGA
* *
5463508 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCTATAAATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5463573 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
5463638 ATCAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5463703 AATGA
196 AATGA
*
5463708 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTCTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5463773 CGAAACCCATAAGTATAATGTAATAGTTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
5463838 ATGAGAGAATAGGTCTAAATAATATATTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCGAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5463903 AATGA
196 AATGA
* *
5463908 ATGGCAAACAGGGTGCAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATTCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
5463973 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5464038 ATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5464103 AATGA
196 AATGA
5464108 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
5464173 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5464238 GTGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5464303 AATGA
196 AATGA
*
5464308 ATGTCAAACAGGGTGCAACAATAAAGTGTCG-----TATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5464368 CGAAACCCATAAGTATAATGTAATAGTTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
5464433 ATGAGAGAATAGGTCTAAATAATGTATCAACACTTTTGTAGTTTGTGTCGATATTTTTGGTCGAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5464498 AATGA
196 AATGA
*
5464503 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
***
5464568 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACAAATACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5464633 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCAATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5464698 AATGA
196 AATGA
* *
5464703 ATGGCAAACAGGGTGCAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
5464768 CGAAACCTATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
5464833 ATGAGAGAATAGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
5464867 GTTTAATGTT
Statistics
Matches: 2279, Mismatches: 74, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
195 190 0.08
200 2086 0.92
201 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:5463955 original size:21 final size:23
Alignment explanation
Indices: 5463925--5463967 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
5463915 ACAGGGTGCA
5463925 ATAATAAAGTGTCGA-TCCATAT
1 ATAATAAAGTGTCGATTCCATAT
5463947 ATAA-AAAGTGTCGATTCCATA
1 ATAATAAAGTGTCGATTCCATA
5463968 AACATCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (23 bp):
ATAATAAAGTGTCGATTCCATAT
Found at i:5466375 original size:6 final size:6
Alignment explanation
Indices: 5466364--5466421 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
5466354 CAAGCGGTCA
* * * * *
5466364 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
5466412 ATGATG ATGA
1 ATGAAG ATGA
5466422 TGATCCAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:5466413 original size:3 final size:3
Alignment explanation
Indices: 5466381--5466425 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5466371 TGAAGCTGAC
* * * *
5466381 GAT GAA GAT GAC GAT GAA GAT GAC GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
5466426 CCAAACAAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:5466425 original size:12 final size:12
Alignment explanation
Indices: 5466364--5466421 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
5466354 CAAGCGGTCA
*
5466364 ATGAAGATGAAG
1 ATGACGATGAAG
*
5466376 CTGACGATGAAG
1 ATGACGATGAAG
5466388 ATGACGATGAAG
1 ATGACGATGAAG
*
5466400 ATGACGATGATG
1 ATGACGATGAAG
*
5466412 ATGATGATGA
1 ATGACGATGA
5466422 TGATCCAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:5467755 original size:18 final size:19
Alignment explanation
Indices: 5467732--5467769 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5467722 ATCGGAACCC
*
5467732 ATAA-TTATAATTTAATAG
1 ATAATTTATAATATAATAG
5467750 ATAATTTTATAATATAATAG
1 ATAA-TTTATAATATAATAG
5467770 GTATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATAATTTATAATATAATAG
Found at i:5467940 original size:116 final size:120
Alignment explanation
Indices: 5467734--5467972 Score: 369
Period size: 118 Copynumber: 2.0 Consensus size: 120
5467724 CGGAACCCAT
* * *
5467734 AATTATAATTTAATAGATAATTTTATAATATAATAGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACAGGTATAAATATACCGGTTTTATGAGCAAAT
5467799 AGGTCTACAACCTATATCGACACTTTTT-A-ATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
* * * * *
5467852 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTAT-ACT-TACCGGTTTTATTAGCAAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACAGGTATAAATATACCGGTTTTATGAGCAAAT
*
5467915 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
5467970 AAT
1 AAT
5467973 GGAAGAAAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
116 45 0.41
117 3 0.03
118 62 0.56
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTATAATATAACAGGTATAAATATACCGGTTTTATGAGCAAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
Found at i:5468245 original size:120 final size:120
Alignment explanation
Indices: 5468029--5468275 Score: 413
Period size: 120 Copynumber: 2.1 Consensus size: 120
5468019 ACATCGGAAC
* * *
5468029 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGATATAAATATACCGATTTTATGAGC
* *
5468094 GAATAGGTCTACAACCTATATCGACAATTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACATATATCGACAATTTTTAATATTGTGTCGGTACTTTATGT
* *
5468149 CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGATATAAATATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGATATAAATATACCGATTTTATGAGC
* *
5468214 GAATAGGTCTACAACATATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACATATATCGACAATTTTTAATATTGTGTCGGTACTTTATGT
5468269 CCAGAAT
1 CCAGAAT
5468276 GGAAGAAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGATATAAATATACCGATTTTATGAGC
GAATAGGTCTACAACATATATCGACAATTTTTAATATTGTGTCGGTACTTTATGT
Found at i:5468303 original size:303 final size:303
Alignment explanation
Indices: 5467634--5469046 Score: 2487
Period size: 303 Copynumber: 4.7 Consensus size: 303
5467624 CACAGTTTTC
* *
5467634 ACACTTTTTAATATTGTGTCAGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * * * * *
5467699 CAAAAAGTATC-A-ATTGAAAAAACATCGGAACCCATAATTATAATTTAATAGATAATTTTATAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
**
5467762 TATAATAGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
*
5467827 AA--TTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGT
193 AATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGT
* *
5467890 AT-ACT-TACCGGTTTTATTAGCAAATAGGTCTACAACCTATGTCG
258 ATAAATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
*
5467934 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATATCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
5467999 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTACTAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
5468064 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCGACAATTTTTAAT
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
* *
5468129 TTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTATAATATAACCGATATA
196 TTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATA
*
5468194 AATATACCGGTTTTATTAGCGAATAGGTCTACAACATATGTCG
261 AATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
5468237 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
5468302 CAAAAAGTGTCAACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
5468367 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
*
5468432 TTTGTGTCGGTACTTTATGTCCAGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATA
196 TTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATA
5468497 AATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
261 AATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
5468540 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
5468605 CAAAAAGTGTCGACATTTATACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
5468670 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAAACTTTTTAAT
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
* *
5468735 TTTGTGTCGGTACTTTATGTCCAAAATTATAATCTAATAGATAATTTTGTAATATAACCGGTATA
196 TTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATA
*
5468800 AATATACCAGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
261 AATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
5468843 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
5468908 CAAAAAGTGTCGACATTTACACATCGGAACCCCGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
5468973 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
* *
5469038 ATCGTGTCG
196 TTTGTGTCG
5469047 CTAATTTTAA
Statistics
Matches: 1067, Mismatches: 40, Indels: 9
0.96 0.04 0.01
Matches are distributed among these distances:
299 102 0.10
300 72 0.07
301 61 0.06
302 5 0.00
303 827 0.78
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (303 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
TTTGTGTCGGTACTTTATGTCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATA
AATATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
Found at i:5468545 original size:120 final size:120
Alignment explanation
Indices: 5468332--5468578 Score: 458
Period size: 120 Copynumber: 2.1 Consensus size: 120
5468322 ACATCGGAAC
*
5468332 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
5468397 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
*
5468452 CCAGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATTAGC
1 CCAGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
5468517 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
5468572 CCAGAAT
1 CCAGAAT
5468579 GGAAGAAAAA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:5468852 original size:120 final size:120
Alignment explanation
Indices: 5468639--5468877 Score: 424
Period size: 120 Copynumber: 2.0 Consensus size: 120
5468629 CGGAACCCAG
* *
5468639 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATCTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
*
5468704 AGGTCTACAACCTATATCGAAACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
66 AGGTCTACAACCTATATCGAAACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
*
5468759 AATTATAATCTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATTAGCGAAT
1 AATTATAATCTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
* *
5468824 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
66 AGGTCTACAACCTATATCGAAACTTTTTAATATTGTGTCGGTACTTTATGTCCA
5468878 GAATGGAAGA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 113 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (120 bp):
AATTATAATCTAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGAAACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:5471788 original size:20 final size:22
Alignment explanation
Indices: 5471758--5471817 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 22
5471748 ATAGGTAAAA
*
5471758 ATATGATGTATAGGTAGCG-CT
1 ATATAATGTATAGGTAGCGTCT
*
5471779 -TATAATGTATAGGTAGCGTTT
1 ATATAATGTATAGGTAGCGTCT
5471800 ATATAATGTAATAGGTAG
1 ATATAATGT-ATAGGTAG
5471818 ACAATCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 8 0.24
23 8 0.24
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (22 bp):
ATATAATGTATAGGTAGCGTCT
Found at i:5471949 original size:22 final size:22
Alignment explanation
Indices: 5471917--5471960 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5471907 ATTACATAAC
5471917 TTTAAAAAAGTATCGAC-CTTT
1 TTTAAAAAAGTATCGACACTTT
*
5471938 TTTATAAAAAGTATGGACACTTT
1 TTTA-AAAAAGTATCGACACTTT
5471961 CAATATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
TTTAAAAAAGTATCGACACTTT
Found at i:5471982 original size:216 final size:219
Alignment explanation
Indices: 5471602--5472032 Score: 691
Period size: 216 Copynumber: 2.0 Consensus size: 219
5471592 AAATATCAAA
*
5471602 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAAAAACAC
1 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAAAAACAC
5471667 TATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTATAAAAAG
66 TATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTATAAAAAG
5471732 TATAGACACTTTCAATATAGGTAAAAATATGATGT-ATAGGTAGCGC-T-TATAATGTATAGGTA
131 TATAGACACTTTCAATATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTATAGGTA
*
5471794 GCGTTTATATAATGTAATAGGTAG
196 ACGTTTATATAATGTAATAGGTAG
*
5471818 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACCTGAAA
1 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA---AAAA
5471883 CACTATT-AAAAAAATTG-AACATAAATTACATAACTTT-AAAAAAGTATCGA-CCTTTTTTATA
63 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCC--TTTTATA
* * *
5471944 AAAAGTATGGACACTTTCAATATAATGT-AAAA-ATGATGTAATAGGTATCGCTTATATAATGTA
126 AAAAGTATAGACACTTTCAATAT-AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
5472007 TAGGTAACGTTTATATAATGTAATAG
190 TAGGTAACGTTTATATAATGTAATAG
5472033 TAGTGTTATA
Statistics
Matches: 200, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
215 2 0.01
216 77 0.38
217 63 0.31
218 14 0.07
219 44 0.22
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (219 bp):
ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAAAAACAC
TATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTATAAAAAG
TATAGACACTTTCAATATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTATAGGTA
ACGTTTATATAATGTAATAGGTAG
Found at i:5472010 original size:22 final size:22
Alignment explanation
Indices: 5471979--5472028 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
5471969 TGTAAAAATG
*
5471979 ATGTAATAGGTATCGCTTATATA
1 ATGT-ATAGGTAACGCTTATATA
*
5472002 ATGTATAGGTAACGTTTATATA
1 ATGTATAGGTAACGCTTATATA
5472024 ATGTA
1 ATGTA
5472029 ATAGTAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (22 bp):
ATGTATAGGTAACGCTTATATA
Found at i:5472474 original size:23 final size:23
Alignment explanation
Indices: 5472448--5472497 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
5472438 ATAATGTAAA
5472448 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
5472471 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
5472494 ATAT
1 ATAT
5472498 TGTAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5472793 original size:456 final size:442
Alignment explanation
Indices: 5471997--5472873 Score: 1404
Period size: 456 Copynumber: 2.0 Consensus size: 442
5471987 GGTATCGCTT
* *
5471997 ATATAATGTATAGGTAACGTTTATATAATGTAATAGTAGTGTTATATTGTAAAGTATCTATCCTT
1 ATATAATGTATAGGTAACGCTTATATAATGTAATAGTAGCGTTATATTGTAAAGTATCTATCCTT
* *
5472062 TTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGTTATCTTTTGAGTGAG
66 TTTATAAAAGTGTCAATACTTATTTCACTGTGGAAAACATTAATTTAAGGTATCTTTTGAGTGAG
*
5472127 TTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
131 TTTTAAGATATTAATTTAGTAATTATA-GCATCTAATGATTTATTTTTTACGTTACGATATATAT
* *
5472192 TATTAAATTAAAACAATAAACAATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAA
195 CATTAAATTAAAACAATAAACAATATATTACATATTTATTATTATCTTTGGCTAATATTGTTAAA
5472257 TTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAAT
260 TTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAAT
5472322 TATTAAATTATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACAT
325 TATTAAATTATATTGTAGGTGG-AAACAT--AA-ACTATT--AAAAATTG-AACATAAATTACAT
*
5472387 AACTTTAAAAAAAGTATCTATCCTTTTTATAAAA-GTATGAACACTTTCAATATAATGTAAA
383 AACTTT-AAAAAAGTATCGATCC-TTTTATAAAATGTATGAACACTTTCAATATAATGTAAA
*
5472448 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATTGTAAAGTATCTATC
1 ATATAATGT-ATAGGTAACGCTTATATAATGTAATA-GTAGCG-TTATATTGTAAAGTATCTATC
*
5472513 CTTTTTATAGAAGTGTCAATACTTATTTCACTGTGGAAAACATTAATTTAAGGTATCTTTTGAGT
63 CTTTTTATAAAAGTGTCAATACTTATTTCACTGTGGAAAACATTAATTTAAGGTATCTTTTGAGT
* * *
5472578 GAGTTTTAAGATA-TCATTTAGTAATTAT-GTATCTAATGATTTATTTTTTTATGTTACAGTATA
128 GAGTTTTAAGATATTAATTTAGTAATTATAGCATCTAATGATTTA-TTTTTTACGTTAC-G-ATA
*
5472641 TCTTATCATTAAATTAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGCTAATAT
190 T-ATATCATTAAATTAAAACAATAAACA-ATATATTACATATTTATTATTATCTTTGGCTAATAT
*
5472706 TGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
253 TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-TTTTTGTGCA
5472771 AATG-AATTA-TAAATTAATATTGTAGGTGGAAACATAAACTATTAAAAATTGAACATAAATTAC
317 AATGAAATTATTAAATT-ATATTGTAGGTGGAAACATAAACTATTAAAAATTGAACATAAATTAC
5472834 ATAACTTTAAAAAAGTATCGATCCTTTTATAAAATGTATG
381 ATAACTTTAAAAAAGTATCGATCCTTTTATAAAATGTATG
5472874 GATACTTCAA
Statistics
Matches: 400, Mismatches: 15, Indels: 25
0.91 0.03 0.06
Matches are distributed among these distances:
447 10 0.03
448 20 0.05
449 20 0.05
450 8 0.02
451 22 0.05
452 42 0.10
453 22 0.05
454 100 0.25
455 36 0.09
456 106 0.26
457 14 0.04
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.41
Consensus pattern (442 bp):
ATATAATGTATAGGTAACGCTTATATAATGTAATAGTAGCGTTATATTGTAAAGTATCTATCCTT
TTTATAAAAGTGTCAATACTTATTTCACTGTGGAAAACATTAATTTAAGGTATCTTTTGAGTGAG
TTTTAAGATATTAATTTAGTAATTATAGCATCTAATGATTTATTTTTTACGTTACGATATATATC
ATTAAATTAAAACAATAAACAATATATTACATATTTATTATTATCTTTGGCTAATATTGTTAAAT
TTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAATGAAATT
ATTAAATTATATTGTAGGTGGAAACATAAACTATTAAAAATTGAACATAAATTACATAACTTTAA
AAAAGTATCGATCCTTTTATAAAATGTATGAACACTTTCAATATAATGTAAA
Found at i:5480519 original size:4 final size:4
Alignment explanation
Indices: 5480510--5480536 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5480500 CAATTCATAT
5480510 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
5480537 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:5484162 original size:24 final size:25
Alignment explanation
Indices: 5484117--5484164 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5484107 CACCAATCCC
*
5484117 TAAAAATGATGTCGTAAGTTCCCAA
1 TAAAAATGATGTCGCAAGTTCCCAA
5484142 TAAAAA-GATGTCGC-AGATTCCCA
1 TAAAAATGATGTCGCAAG-TTCCCA
5484165 GAATAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 13 0.62
25 6 0.29
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (25 bp):
TAAAAATGATGTCGCAAGTTCCCAA
Found at i:5485439 original size:21 final size:21
Alignment explanation
Indices: 5485415--5485466 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5485405 GCAAATAGTA
5485415 TACCGATGCATTGCTACAGTG
1 TACCGATGCATTGCTACAGTG
5485436 TACCGATGCATTGCTACAGTG
1 TACCGATGCATTGCTACAGTG
*
5485457 TACTGATGCA
1 TACCGATGCA
5485467 CAAAAACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
TACCGATGCATTGCTACAGTG
Found at i:5486066 original size:23 final size:23
Alignment explanation
Indices: 5486040--5486104 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
5486030 AGCTCGTATA
5486040 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
**
5486063 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
* *
5486086 AATTGTACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
5486105 ATAAAATTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:5486112 original size:23 final size:23
Alignment explanation
Indices: 5486039--5486112 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5486029 CAGCTCGTAT
5486039 AAATTGCACCGAAGTGCCATGTA
1 AAATTGCACCGAAGTGCCATGTA
* **
5486062 GAATTGCACCGAAGTGCCGCGTA
1 AAATTGCACCGAAGTGCCATGTA
* * * *
5486085 GAATTGTACCGTAGTGCCATATA
1 AAATTGCACCGAAGTGCCATGTA
5486108 AAATT
1 AAATT
5486113 TGTCCATAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (23 bp):
AAATTGCACCGAAGTGCCATGTA
Found at i:5486248 original size:23 final size:23
Alignment explanation
Indices: 5486217--5486260 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5486207 AATACATATA
5486217 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
5486240 TGTCTCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
5486261 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:5495465 original size:53 final size:53
Alignment explanation
Indices: 5495407--5495512 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
5495397 ATATAAACTA
* * * *
5495407 TTTAATAAGTCATTTAAGTTCTAGAATAAAATGAAATTGTTTGTAGAAAAGTC
1 TTTAATAAGCCATTTAAGTTATAGAATAAAATGAAATTATTCGTAGAAAAGTC
*
5495460 TTTAATAAGCCTTTTAAGTTATAGAATAAAATGAAATTATTCGTAGAAAAGTC
1 TTTAATAAGCCATTTAAGTTATAGAATAAAATGAAATTATTCGTAGAAAAGTC
5495513 ATGTTCGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (53 bp):
TTTAATAAGCCATTTAAGTTATAGAATAAAATGAAATTATTCGTAGAAAAGTC
Found at i:5499259 original size:21 final size:21
Alignment explanation
Indices: 5499217--5499259 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5499207 TTTTTGGGCT
* * *
5499217 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
5499238 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
5499259 A
1 A
5499260 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:5499332 original size:23 final size:22
Alignment explanation
Indices: 5499288--5499332 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5499278 AATGTCATGG
*
5499288 GGGAACCGAAACCCCCACAGGA
1 GGGAACCGAAACCCCCAAAGGA
**
5499310 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGAAACCCCC-AAAGGA
5499333 AAGTTGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.33, G:0.27, T:0.07
Consensus pattern (22 bp):
GGGAACCGAAACCCCCAAAGGA
Found at i:5500944 original size:23 final size:23
Alignment explanation
Indices: 5500887--5500955 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
5500877 CATTATTATA
5500887 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
** * * *
5500910 CAGTACTCCGGTACAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
5500933 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
5500956 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:5501128 original size:13 final size:13
Alignment explanation
Indices: 5501110--5501134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5501100 GTGATATATG
5501110 TGATATGATGATA
1 TGATATGATGATA
5501123 TGATATGATGAT
1 TGATATGATGAT
5501135 GTGTATATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
TGATATGATGATA
Found at i:5503157 original size:15 final size:15
Alignment explanation
Indices: 5503137--5503166 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5503127 TTAGCTGGGT
*
5503137 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
5503152 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
5503167 AAGTAATGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:5509201 original size:58 final size:58
Alignment explanation
Indices: 5509106--5509277 Score: 179
Period size: 58 Copynumber: 2.9 Consensus size: 58
5509096 AACTATAACT
* * *
5509106 CTCAATTTAAATT-GATCCTTAAATTTTTGAATTTTCTAATTTCATCCCCAAATTATGA-
1 CTCATTTTAAATTAG-T-CTTAAACTTTTGAATATTCTAATTTCATCCCCAAATTATGAC
* ** *
5509164 CTCATTTTAAATTAGTCATTAAACTTTTGAACATTCTAATTTCATCCATAAACTATGATC
1 CTCATTTTAAATTAGTC-TTAAACTTTTGAATATTCTAATTTCATCCCCAAATTATGA-C
* ** *
5509224 CTC-TTTCTAAAGTAGTCCCAAACTTTTGAATATTCCAATTTCATCCCCAAATTA
1 CTCATTT-TAAATTAGTCTTAAACTTTTGAATATTCTAATTTCATCCCCAAATTA
5509278 ATCCAAGTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.50
59 34 0.36
60 12 0.13
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (58 bp):
CTCATTTTAAATTAGTCTTAAACTTTTGAATATTCTAATTTCATCCCCAAATTATGAC
Found at i:5509395 original size:2 final size:2
Alignment explanation
Indices: 5509388--5509424 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5509378 GTGATCAATA
5509388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5509425 GTTTGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5510981 original size:24 final size:24
Alignment explanation
Indices: 5510949--5511000 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5510939 TTTTTAATAT
*
5510949 ATTATTCATATTTCCCTTTTTGAA
1 ATTATTCATATTCCCCTTTTTGAA
*
5510973 ATTATTCATATTCCCCTTTTTGGA
1 ATTATTCATATTCCCCTTTTTGAA
5510997 ATTA
1 ATTA
5511001 GGGCTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTATTCATATTCCCCTTTTTGAA
Found at i:5511212 original size:15 final size:15
Alignment explanation
Indices: 5511188--5511230 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5511178 GCACCATTAA
*
5511188 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
5511203 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
*
5511218 ACTAAACTTATAA
1 ATTAAA-TTATAA
5511231 TTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:5511252 original size:23 final size:22
Alignment explanation
Indices: 5511226--5511282 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
5511216 GTACTAAACT
*
5511226 TATAATTATAAATTAGTTAAAA
1 TATAATTATAAATTAATTAAAA
* *
5511248 -ATATATATGTAATTTAATTAAAA
1 TATA-AT-TATAAATTAATTAAAA
*
5511271 TAAAATTATAAA
1 TATAATTATAAA
5511283 AACTAGGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 15 0.58
24 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
TATAATTATAAATTAATTAAAA
Found at i:5511851 original size:8 final size:8
Alignment explanation
Indices: 5511838--5511863 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5511828 GAACTCCGAC
5511838 ATTGAATA
1 ATTGAATA
5511846 ATTGAATA
1 ATTGAATA
5511854 ATTGAATA
1 ATTGAATA
5511862 AT
1 AT
5511864 ATGATATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
ATTGAATA
Found at i:5513861 original size:57 final size:57
Alignment explanation
Indices: 5513773--5513887 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
5513763 TATCGGATGT
5513773 AAAATCTGATTATCAGTGACTTTTTAAACATATAAAGAATTTAACAGGTGAATCAGC
1 AAAATCTGATTATCAGTGACTTTTTAAACATATAAAGAATTTAACAGGTGAATCAGC
5513830 AAAATCTGATTATCAGTGACTTTTTAAACATATAAAGAATTTAACAGGTGAATCAGC
1 AAAATCTGATTATCAGTGACTTTTTAAACATATAAAGAATTTAACAGGTGAATCAGC
5513887 A
1 A
5513888 GTTTATCGGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (57 bp):
AAAATCTGATTATCAGTGACTTTTTAAACATATAAAGAATTTAACAGGTGAATCAGC
Found at i:5516728 original size:20 final size:20
Alignment explanation
Indices: 5516705--5516742 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5516695 GAGGGATTAT
*
5516705 CAGTGGTCATTTGGGACAAA
1 CAGTGGTCATTCGGGACAAA
*
5516725 CAGTGGTCCTTCGGGACA
1 CAGTGGTCATTCGGGACA
5516743 TAGTGGTTCT
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:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (20 bp):
CAGTGGTCATTCGGGACAAA
Found at i:5516749 original size:18 final size:18
Alignment explanation
Indices: 5516726--5516798 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
5516716 TGGGACAAAC
5516726 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *** *
5516744 AGTGGTTCTTCATAATAAT
1 AGTGGTCCTTCGGGA-CAT
*
5516763 CAGTGTTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
* *
5516782 AGTGGTCATTTGGGACA
1 AGTGGTCCTTCGGGACA
5516799 AATATTCAGT
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
18 25 0.64
19 4 0.10
20 10 0.26
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5517171 original size:4 final size:4
Alignment explanation
Indices: 5517164--5517206 Score: 77
Period size: 4 Copynumber: 10.5 Consensus size: 4
5517154 TGATAATGAC
5517164 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AGTGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT AT
5517207 TTGTTACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 34 0.89
5 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:5518889 original size:47 final size:47
Alignment explanation
Indices: 5518835--5518933 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
5518825 TTGTCTTGTT
5518835 TATATCCGGTTGGAGTAAGAATTTTATATTTTATTATTTATTCATTA
1 TATATCCGGTTGGAGTAAGAATTTTATATTTTATTATTTATTCATTA
5518882 TATATCCGGTTGGAGTAAGAATTTTATATTTTATTATTTATTCATTA
1 TATATCCGGTTGGAGTAAGAATTTTATATTTTATTATTTATTCATTA
5518929 TATAT
1 TATAT
5518934 TTGAAGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (47 bp):
TATATCCGGTTGGAGTAAGAATTTTATATTTTATTATTTATTCATTA
Found at i:5520451 original size:18 final size:18
Alignment explanation
Indices: 5520428--5520462 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5520418 TATATTTTAA
5520428 TTAACTATATTT-TAATTT
1 TTAACTA-ATTTATAATTT
5520446 TTAACTAATTTATAATT
1 TTAACTAATTTATAATT
5520463 ATACATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAACTAATTTATAATTT
Found at i:5526025 original size:22 final size:23
Alignment explanation
Indices: 5525986--5526036 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
5525976 GGAGTTACAT
* * *
5525986 GAGTTATATTGATTTAATTTCAG
1 GAGTTACATTGATATAATATCAG
5526009 GAGTTACA-TGATATAATATCAG
1 GAGTTACATTGATATAATATCAG
5526031 GAGTTA
1 GAGTTA
5526037 TAACAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (23 bp):
GAGTTACATTGATATAATATCAG
Found at i:5531878 original size:22 final size:23
Alignment explanation
Indices: 5531836--5531889 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
5531826 TCAGGAGTTA
* *
5531836 CAGGAGTTACATTGATTTAATTT
1 CAGGAGTTACATTGATATAATAT
5531859 CAGGAGTTACA-TGATATAATAT
1 CAGGAGTTACATTGATATAATAT
5531881 CAGGAGTTA
1 CAGGAGTTA
5531890 TAACAGCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (23 bp):
CAGGAGTTACATTGATATAATAT
Found at i:5538438 original size:15 final size:15
Alignment explanation
Indices: 5538420--5538449 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5538410 CCACGGTGCT
5538420 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
*
5538435 CCCGGAATCCTGCGC
1 CCCGAAATCCTGCGC
5538450 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:5540471 original size:21 final size:21
Alignment explanation
Indices: 5540445--5540494 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5540435 CTACAGTTAC
5540445 TATTATTATCATTAATAATAT
1 TATTATTATCATTAATAATAT
5540466 TATTATTATCATTAATAATAT
1 TATTATTATCATTAATAATAT
5540487 TATTATTA
1 TATTATTA
5540495 GATCCTTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTATCATTAATAATAT
Found at i:5540989 original size:16 final size:16
Alignment explanation
Indices: 5540968--5540999 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5540958 ATAATCTATT
*
5540968 TATTTATTTATTTTTA
1 TATTTATTTATGTTTA
5540984 TATTTATTTATGTTTA
1 TATTTATTTATGTTTA
5541000 GTGTTTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TATTTATTTATGTTTA
Found at i:5541665 original size:2 final size:2
Alignment explanation
Indices: 5541658--5541687 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5541648 TAACTATAAC
*
5541658 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5541688 TTCTTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5549442 original size:293 final size:293
Alignment explanation
Indices: 5548906--5549472 Score: 778
Period size: 293 Copynumber: 1.9 Consensus size: 293
5548896 TTTAAGACTA
*
5548906 TTAAAATAGAAGTTATCACATCCATCTCACAAAGGCTGATATGTTGAGGTGTGATATTTTCAAAG
1 TTAAAATAAAAGTTATCACATCCATCTCACAAAGGCTGATATGTTGAGGTGTGATATTTTCAAAG
*
5548971 CATGGTGATAAGCAGTAAGTTTAGTTGAGGAATTTATAATTTGGCACATTTATATACTATGTTGA
66 CATGGTGATAAGCAGTAAGTTTAGTTCAGGAATTTATAATTTGGCACATTTATATACTATGTTGA
* *
5549036 GAATGATCATTTTCTGTTTTGGGGGTTAATTAGACGTGTACAACATTATATTCTCGTTTCGCTAT
131 GAATGATCATTTTCTGTTTTGGGGGCTAATTAGACGTGTACAACATTATATTCTCGTTTCGATAT
* * * * *
5549101 CCTAATTTTGTTGTACTCTTTTCTTTCAAATAATTGAAGGATGTTTTTAATGAGACATACAACCT
196 CCAAATTGTGTTGTACTCTTTTCTTCCAAATAATTGAAGGACGTTTTTAATGAGACACACAACCT
5549166 AAATTTAATTATAAGCAAATTATTCTTGTCCTT
261 AAATTTAATTATAAGCAAATTATTCTTGTCCTT
** * ** * * *
5549199 TTAAAATAAAAGTTATTGCATCTATCTCGTAAAGGTTGGTATGTTGAGGTGTGATCTTTTCAAAG
1 TTAAAATAAAAGTTATCACATCCATCTCACAAAGGCTGATATGTTGAGGTGTGATATTTTCAAAG
* * * * * * *
5549264 CATGGTGGTAAGCAGTAGGTTTAGTTCAGGAATTTGTAATTTGGCACATTTATATATTGTTTTTA
66 CATGGTGATAAGCAGTAAGTTTAGTTCAGGAATTTATAATTTGGCACATTTATATACTATGTTGA
* * * *** *
5549329 GAATGGTCATTTTCTGTTTTTGGGGCTAGTTAGACGTGTACAGTGTTATATTCTCGTTTTGATAT
131 GAATGATCATTTTCTGTTTTGGGGGCTAATTAGACGTGTACAACATTATATTCTCGTTTCGATAT
* * *
5549394 CCAAATTGTGTTGTACTCTTTT-TCTCCAAATAGGTT-ATGGACGTTTTTAATGAGGCACACAAC
196 CCAAATTGTGTTGTACTCTTTTCT-TCCAAATA-ATTGAAGGACGTTTTTAATGAGACACACAAC
**
5549457 CTAGGTTTAATTATAA
259 CTAAATTTAATTATAA
5549473 ATAAAAATTT
Statistics
Matches: 236, Mismatches: 36, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
292 1 0.00
293 233 0.99
294 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (293 bp):
TTAAAATAAAAGTTATCACATCCATCTCACAAAGGCTGATATGTTGAGGTGTGATATTTTCAAAG
CATGGTGATAAGCAGTAAGTTTAGTTCAGGAATTTATAATTTGGCACATTTATATACTATGTTGA
GAATGATCATTTTCTGTTTTGGGGGCTAATTAGACGTGTACAACATTATATTCTCGTTTCGATAT
CCAAATTGTGTTGTACTCTTTTCTTCCAAATAATTGAAGGACGTTTTTAATGAGACACACAACCT
AAATTTAATTATAAGCAAATTATTCTTGTCCTT
Found at i:5552680 original size:2 final size:2
Alignment explanation
Indices: 5552673--5552723 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5552663 GTTCATTATC
5552673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5552715 AT AT AT AT A
1 AT AT AT AT A
5552724 CATACACACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5552810 original size:52 final size:52
Alignment explanation
Indices: 5552732--5552835 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
5552722 TACATACACA
5552732 CTTCAATTTTCTCTAATTATCTTGCATGTTTTTCCTTTTTGGTAAAATGAAG
1 CTTCAATTTTCTCTAATTATCTTGCATGTTTTTCCTTTTTGGTAAAATGAAG
* *
5552784 CTTCAATTTTCTCTAATTATCTTGCATGTTTTTCTTTTTTTGTAAAATGAAG
1 CTTCAATTTTCTCTAATTATCTTGCATGTTTTTCCTTTTTGGTAAAATGAAG
5552836 TTGAGATTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (52 bp):
CTTCAATTTTCTCTAATTATCTTGCATGTTTTTCCTTTTTGGTAAAATGAAG
Found at i:5557914 original size:13 final size:13
Alignment explanation
Indices: 5557895--5557970 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
5557885 AACCCGACCC
5557895 GACCCGACCCGTT
1 GACCCGACCCGTT
*
5557908 TACCCGACCCGTT
1 GACCCGACCCGTT
5557921 GACCCGACCCGAACTGTT
1 GACCCGA-CC---C-GTT
* *
5557939 AACCCAACCCGTT
1 GACCCGACCCGTT
*
5557952 GACCCGACTCGTT
1 GACCCGACCCGTT
5557965 GACCCG
1 GACCCG
5557971 TTGACCGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 37 0.73
14 3 0.06
17 3 0.06
18 8 0.16
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5557925 original size:31 final size:31
Alignment explanation
Indices: 5557890--5557959 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
5557880 GTCATAACCC
* * *
5557890 GACCCGACCCGACCCGTTTACCCGACCCGTT
1 GACCCGACCCGAACCGTTAACCCAACCCGTT
*
5557921 GACCCGACCCGAACTGTTAACCCAACCCGTT
1 GACCCGACCCGAACCGTTAACCCAACCCGTT
5557952 GACCCGAC
1 GACCCGAC
5557960 TCGTTGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.21, C:0.46, G:0.19, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGAACCGTTAACCCAACCCGTT
Found at i:5559359 original size:36 final size:37
Alignment explanation
Indices: 5559319--5559394 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
5559309 TGATAAATTG
*
5559319 GAATTAATTAATAAGACCGGATGG-AGGAAAAAGATT
1 GAATTAAATAATAAGACCGGATGGAAGGAAAAAGATT
*
5559355 GAATTAAATAATAAGACCGGATGGAAGGAAAATGATT
1 GAATTAAATAATAAGACCGGATGGAAGGAAAAAGATT
5559392 GAA
1 GAA
5559395 ATACCGTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 23 0.62
37 14 0.38
ACGTcount: A:0.49, C:0.05, G:0.25, T:0.21
Consensus pattern (37 bp):
GAATTAAATAATAAGACCGGATGGAAGGAAAAAGATT
Found at i:5560568 original size:12 final size:11
Alignment explanation
Indices: 5560528--5560588 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
5560518 CGTTACCTAA
5560528 ATTCTGTTCTG
1 ATTCTGTTCTG
* *
5560539 ATTTTGATCTGG
1 ATTCTGTTCT-G
5560551 ATTCTGTTCTG
1 ATTCTGTTCTG
* *
5560562 ATATCTGATATG
1 AT-TCTGTTCTG
*
5560574 AATTCTGTTTTG
1 -ATTCTGTTCTG
5560586 ATT
1 ATT
5560589 TCTGATATCT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 14 0.36
12 23 0.59
13 2 0.05
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:5560578 original size:24 final size:24
Alignment explanation
Indices: 5560501--5560596 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
5560491 ATTTCCGAAT
*
5560501 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
* * *
5560523 CCTAAATTCTGTTCTGAT-TTTGATC
1 --TGAATTCTGTTCTGATATCTGATA
*
5560548 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
5560572 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
5560596 T
1 T
5560597 CTCCGTTTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 14 0.24
24 42 0.72
25 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:5562756 original size:18 final size:18
Alignment explanation
Indices: 5562733--5562779 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5562723 GTCATAACCC
5562733 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
5562751 GACCCGACCCGACCTGTT
1 GACCCGACCCGACCCGTT
* *
5562769 AACCCAACCCG
1 GACCCGACCCG
5562780 TTGACCCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.49, G:0.19, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:5562773 original size:13 final size:13
Alignment explanation
Indices: 5562756--5562800 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5562746 CCGTTGACCC
5562756 GACCCGACCTGTT
1 GACCCGACCTGTT
* * *
5562769 AACCCAACCCGTT
1 GACCCGACCTGTT
*
5562782 GACCCGACATGTT
1 GACCCGACCTGTT
5562795 GACCCG
1 GACCCG
5562801 TTGATCGTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCTGTT
Found at i:5562812 original size:15 final size:15
Alignment explanation
Indices: 5562792--5562838 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
5562782 GACCCGACAT
*
5562792 GTTGACCCGTTGATC
1 GTTGACCCGTTGACC
5562807 GTTGACCCGTTGACC
1 GTTGACCCGTTGACC
5562822 GTTGACCGACGTTGACC
1 GTTGACC--CGTTGACC
5562839 ACTGTTGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.28
Consensus pattern (15 bp):
GTTGACCCGTTGACC
Found at i:5564208 original size:36 final size:36
Alignment explanation
Indices: 5564168--5564242 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
5564158 TGATAAATTG
*
5564168 GAATTAATTAATAAGACCGGATGG-AGGAAAAAGATT
1 GAATTAAATAATAAGACCGGATGGAAGG-AAAAGATT
*
5564204 GAATTAAATAATAAGACCGGATGGAAGGAAATGATT
1 GAATTAAATAATAAGACCGGATGGAAGGAAAAGATT
5564240 GAA
1 GAA
5564243 ATACCGTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 33 0.92
37 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.25, T:0.21
Consensus pattern (36 bp):
GAATTAAATAATAAGACCGGATGGAAGGAAAAGATT
Found at i:5565393 original size:12 final size:12
Alignment explanation
Indices: 5565357--5565446 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 12
5565347 TTCCGAATTA
5565357 AATTCTGTTCTG
1 AATTCTGTTCTG
*
5565369 -ATAC-GTTACCTG
1 AATTCTGTT--CTG
5565381 AATTCTGTTCTG
1 AATTCTGTTCTG
*
5565393 -ATTCTGATCTG
1 AATTCTGTTCTG
* *
5565404 GATTCTTTTCTG
1 AATTCTGTTCTG
* *
5565416 -ATATCTGATATG
1 AAT-TCTGTTCTG
*
5565428 AATTCTGTTTTG
1 AATTCTGTTCTG
*
5565440 ATTTCTG
1 AATTCTG
5565447 ATATCTCCGT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.25
12 34 0.57
13 5 0.08
14 3 0.05
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.49
Consensus pattern (12 bp):
AATTCTGTTCTG
Found at i:5565409 original size:47 final size:48
Alignment explanation
Indices: 5565358--5565448 Score: 116
Period size: 47 Copynumber: 1.9 Consensus size: 48
5565348 TCCGAATTAA
*
5565358 ATTCTGTTCTGATA-C-GTTACCTGAATTCTGTTCTGA-TTCTGATCTGG
1 ATTCTGTTCTGATATCTGATA--TGAATTCTGTTCTGATTTCTGATCTGG
* *
5565405 ATTCTTTTCTGATATCTGATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGAT
5565449 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 27 0.71
48 8 0.21
49 3 0.08
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGATCTGG
Found at i:5565432 original size:24 final size:23
Alignment explanation
Indices: 5565379--5565450 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
5565369 ATACGTTACC
* *
5565379 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTTTTCTGATTCTGATA
*
5565402 TGGATTCTTTTCTGATATCTGATA
1 TGAATTCTTTTCTGAT-TCTGATA
5565426 TGAATTCTGTTT-TGATTTCTGATA
1 TGAATTCT-TTTCTGA-TTCTGATA
5565450 T
1 T
5565451 CTCCGTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.33
24 24 0.57
25 4 0.10
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.51
Consensus pattern (23 bp):
TGAATTCTTTTCTGATTCTGATA
Found at i:5565637 original size:2 final size:2
Alignment explanation
Indices: 5565632--5565675 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5565622 ATGCTTTAAA
5565632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5565674 AT
1 AT
5565676 TACTGGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5567936 original size:4 final size:4
Alignment explanation
Indices: 5567907--5567995 Score: 142
Period size: 4 Copynumber: 22.2 Consensus size: 4
5567897 AAATATATAT
* * *
5567907 ATAC AAAC ATAT ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
5567955 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
5567996 CACACTTCAA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:5570123 original size:3 final size:3
Alignment explanation
Indices: 5570115--5570167 Score: 56
Period size: 3 Copynumber: 17.0 Consensus size: 3
5570105 ACGCAACAAT
5570115 TAA TAA TAA -ACA TAA TTAA -AA TAA TTAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TA-A TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA
5570162 TAA TAA
1 TAA TAA
5570168 AACAGTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 3 0.07
3 31 0.70
4 10 0.23
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5570165 original size:22 final size:22
Alignment explanation
Indices: 5570116--5570168 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
5570106 CGCAACAATT
5570116 AATAATAAACATAATTAAAATA
1 AATAATAAACATAATTAAAATA
*
5570138 ATTAATAATA-ATAA-TAATAATA
1 AATAATAA-ACATAATTAA-AATA
5570160 AATAATAAA
1 AATAATAAA
5570169 ACAGTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 22 0.81
23 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAATAAACATAATTAAAATA
Found at i:5570362 original size:23 final size:22
Alignment explanation
Indices: 5570323--5570369 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
5570313 TGCAAAAATT
5570323 AAAATAACAGTAGCTAAATAAA
1 AAAATAACAGTAGCTAAATAAA
*
5570345 AAAACTAACAGT-GACTAAATTAA
1 AAAA-TAACAGTAG-CTAAATAAA
5570368 AA
1 AA
5570370 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.19
Consensus pattern (22 bp):
AAAATAACAGTAGCTAAATAAA
Found at i:5570589 original size:11 final size:11
Alignment explanation
Indices: 5570575--5570695 Score: 71
Period size: 11 Copynumber: 10.5 Consensus size: 11
5570565 GGTTATGTTT
5570575 TGGTTAGGGTA
1 TGGTTAGGGTA
5570586 TGGTTGTTAGGGTA
1 T-G--GTTAGGGTA
* * *
5570600 TGATTTGGTTTA
1 TGGTTAGG-GTA
*
5570612 GGGTTTAGGGTA
1 TGG-TTAGGGTA
* *
5570624 TGGTTATGGTTT
1 TGGTTA-GGGTA
5570636 TGGTTAGGGTA
1 TGGTTAGGGTA
* * * *
5570647 GGGTTATGTTT
1 TGGTTAGGGTA
5570658 TGGTTAGGGTA
1 TGGTTAGGGTA
* * *
5570669 TGGTTATGTTT
1 TGGTTAGGGTA
5570680 TGGTTAGGGTA
1 TGGTTAGGGTA
5570691 TGGTT
1 TGGTT
5570696 TGGTTTGGGT
Statistics
Matches: 78, Mismatches: 26, Indels: 12
0.67 0.22 0.10
Matches are distributed among these distances:
11 46 0.59
12 17 0.22
13 5 0.06
14 10 0.13
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (11 bp):
TGGTTAGGGTA
Found at i:5570633 original size:6 final size:6
Alignment explanation
Indices: 5570622--5570700 Score: 53
Period size: 6 Copynumber: 14.2 Consensus size: 6
5570612 GGGTTTAGGG
* * * * *
5570622 TATGGT TATGGT TTTGGT TA-GGG TAGGGT TAT-GT TTTGGT TA-GGG
1 TATGGT TATGGT TATGGT TATGGT TATGGT TATGGT TATGGT TATGGT
* *
5570667 TATGGT TAT-GT TTTGGT TA-GGG TATGGT T-TGGT T
1 TATGGT TATGGT TATGGT TATGGT TATGGT TATGGT T
5570701 TGGGTAATGG
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
5 25 0.45
6 30 0.55
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (6 bp):
TATGGT
Found at i:5570660 original size:22 final size:22
Alignment explanation
Indices: 5570616--5570703 Score: 142
Period size: 22 Copynumber: 4.0 Consensus size: 22
5570606 GGTTTAGGGT
5570616 TTAGGGTATGGTTATGGTTTTGG
1 TTAGGGTATGGTTAT-GTTTTGG
*
5570639 TTAGGGTAGGGTTATGTTTTGG
1 TTAGGGTATGGTTATGTTTTGG
5570661 TTAGGGTATGGTTATGTTTTGG
1 TTAGGGTATGGTTATGTTTTGG
*
5570683 TTAGGGTATGGTT-TGGTTTGG
1 TTAGGGTATGGTTATGTTTTGG
5570704 GTAATGGGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
21 7 0.11
22 41 0.66
23 14 0.23
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (22 bp):
TTAGGGTATGGTTATGTTTTGG
Found at i:5571595 original size:9 final size:10
Alignment explanation
Indices: 5571558--5571597 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
5571548 ACACAACAAT
*
5571558 TAATAATAAA
1 TAATAATTAA
5571568 T-ATAATTAA
1 TAATAATTAA
5571577 -AATAATTAA
1 TAATAATTAA
5571586 TAATAA-TAA
1 TAATAATTAA
5571595 TAA
1 TAA
5571598 AACAGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAATAATTAA
Found at i:5571792 original size:23 final size:22
Alignment explanation
Indices: 5571753--5571799 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
5571743 TGCAAAAATT
5571753 AAAATAACAGTAGCTAAATCAA
1 AAAATAACAGTAGCTAAATCAA
*
5571775 AAAATTAACAGT-GACTAAATTAA
1 AAAA-TAACAGTAG-CTAAATCAA
5571798 AA
1 AA
5571800 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAATAACAGTAGCTAAATCAA
Found at i:5572022 original size:22 final size:22
Alignment explanation
Indices: 5571995--5572111 Score: 182
Period size: 22 Copynumber: 5.2 Consensus size: 22
5571985 TTAGGATCAA
5571995 GGTTATGTTTTGGTTAGGGTAT
1 GGTTATGTTTTGGTTAGGGTAT
5572017 GGTTATGTTTTGGTTAGGGTAT
1 GGTTATGTTTTGGTTAGGGTAT
*
5572039 GGTT-TGGTTTAGGGTTTAGGGTAT
1 GGTTAT-GTTT-TGG-TTAGGGTAT
5572063 GGTTATGGTTTTGGTTAGGGTAT
1 GGTTAT-GTTTTGGTTAGGGTAT
5572086 GGTTATGTTTTGGTTAGGGTAT
1 GGTTATGTTTTGGTTAGGGTAT
5572108 GGTT
1 GGTT
5572112 TGGTTAGGGT
Statistics
Matches: 89, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
21 1 0.01
22 50 0.56
23 17 0.19
24 15 0.17
25 6 0.07
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (22 bp):
GGTTATGTTTTGGTTAGGGTAT
Found at i:5572096 original size:69 final size:67
Alignment explanation
Indices: 5571995--5572121 Score: 236
Period size: 69 Copynumber: 1.9 Consensus size: 67
5571985 TTAGGATCAA
5571995 GGTTATGTTTTGGTTAGGGTATGGTTATGTTTTGGTTAGGGTATGGTTTGGTTTAGGGTTTAGGG
1 GGTTATGTTTTGGTTAGGGTATGGTTATGTTTTGGTTAGGGTATGGTTTGG-TTAGGGTTTAGGG
5572060 TAT
65 TAT
5572063 GGTTATGGTTTTGGTTAGGGTATGGTTATGTTTTGGTTAGGGTATGGTTTGGTTAGGGT
1 GGTTAT-GTTTTGGTTAGGGTATGGTTATGTTTTGGTTAGGGTATGGTTTGGTTAGGGT
5572122 AATGGGCTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 13 0.22
69 45 0.78
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (67 bp):
GGTTATGTTTTGGTTAGGGTATGGTTATGTTTTGGTTAGGGTATGGTTTGGTTAGGGTTTAGGGT
AT
Found at i:5573677 original size:2 final size:2
Alignment explanation
Indices: 5573670--5573714 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5573660 TTTCCATGTA
*
5573670 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5573712 TC T
1 TC T
5573715 TTTTCTCTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5576267 original size:24 final size:24
Alignment explanation
Indices: 5576215--5576271 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
5576205 AATAATAATA
5576215 ATAAAATAAAACAATAAAAACAAC
1 ATAAAATAAAACAATAAAAACAAC
* *
5576239 CTAAAATAAAA-AATGAAAATA-AAT
1 ATAAAATAAAACAAT-AAAA-ACAAC
5576263 ATAAAATAA
1 ATAAAATAA
5576272 GTACAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.11
24 24 0.86
25 1 0.04
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.18
Consensus pattern (24 bp):
ATAAAATAAAACAATAAAAACAAC
Found at i:5577968 original size:4 final size:5
Alignment explanation
Indices: 5577943--5577971 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5577933 GCCAAATCAT
5577943 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
5577972 GATTCAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5583947 original size:6 final size:6
Alignment explanation
Indices: 5583936--5583996 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
5583926 GACACGTATT
* ** * *
5583936 ACCACG ACCACG ACCTCG ACCTTG ACCTCG ACTACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5583984 ACCACG ACCACG A
1 ACCACG ACCACG A
5583997 GCCGAGCCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.30, C:0.46, G:0.16, T:0.08
Consensus pattern (6 bp):
ACCACG
Found at i:5584004 original size:5 final size:5
Alignment explanation
Indices: 5583994--5584067 Score: 94
Period size: 5 Copynumber: 14.8 Consensus size: 5
5583984 ACCACGACCA
* * *
5583994 CGAGC CGAGC CGAAC CGAGC CGAAC CGAGC CGAGC CGAGC CGAGC CGAAC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* * *
5584044 CGAGC CAAGC CGTGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAG
5584068 ACGGACGGAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.26, C:0.38, G:0.35, T:0.01
Consensus pattern (5 bp):
CGAGC
Found at i:5592468 original size:14 final size:14
Alignment explanation
Indices: 5592449--5592484 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
5592439 GTAGAGTCGG
5592449 ATAACAGCAAAGCA
1 ATAACAGCAAAGCA
5592463 ATAACAGCAAAGCA
1 ATAACAGCAAAGCA
5592477 ATAACAGC
1 ATAACAGC
5592485 GTTGAAAGGG
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:0.56, C:0.22, G:0.14, T:0.08
Consensus pattern (14 bp):
ATAACAGCAAAGCA
Found at i:5607644 original size:2 final size:2
Alignment explanation
Indices: 5607639--5607718 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
5607629 AAATGAAATG
5607639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5607681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5607719 GTTTGAATCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5608286 original size:26 final size:26
Alignment explanation
Indices: 5608250--5608312 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
5608240 TAAGCACTGT
5608250 AATAACTAAATACTCTCCAGCTCTGA
1 AATAACTAAATACTCTCCAGCTCTGA
5608276 AATAACTAAATACTCTCCAGCTCTGA
1 AATAACTAAATACTCTCCAGCTCTGA
5608302 AATGAA-TAAAT
1 AAT-AACTAAAT
5608313 TAACCTCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 34 0.94
27 2 0.06
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (26 bp):
AATAACTAAATACTCTCCAGCTCTGA
Found at i:5608458 original size:2 final size:2
Alignment explanation
Indices: 5608451--5608487 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5608441 ATGGAAGAAT
5608451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5608488 CCAAATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.