Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_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: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1793287 original size:15 final size:16
Alignment explanation
Indices: 1793267--1793300 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1793257 GACACCATCT
1793267 AAAATAT-TTAAAAAC
1 AAAATATATTAAAAAC
*
1793282 AAAATATATTATAAAC
1 AAAATATATTAAAAAC
1793298 AAA
1 AAA
1793301 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATATATTAAAAAC
Found at i:1796073 original size:47 final size:45
Alignment explanation
Indices: 1795996--1796105 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 45
1795986 TGGTATATGG
** *
1795996 TTATGGAAT-AATGACAAGTATATTGATAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
* *
1796040 TTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTATGGAA--TAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
1796087 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
1796106 GGATTTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 8 0.14
45 11 0.19
46 1 0.02
47 37 0.65
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:1796492 original size:30 final size:30
Alignment explanation
Indices: 1796458--1796518 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1796448 TTTGGAAGTT
1796458 ACTGTAGCAGTTACTATAGCGTATCAATGC
1 ACTGTAGCAGTTACTATAGCGTATCAATGC
* *
1796488 ACTGTAGCAGTTACTGTAGCGTATCGATGC
1 ACTGTAGCAGTTACTATAGCGTATCAATGC
1796518 A
1 A
1796519 TAATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (30 bp):
ACTGTAGCAGTTACTATAGCGTATCAATGC
Found at i:1796615 original size:22 final size:22
Alignment explanation
Indices: 1796588--1796640 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1796578 ATGCACTGTT
1796588 CACTGTTCACGGTATTGTTCAA
1 CACTGTTCACGGTATTGTTCAA
*
1796610 CACTGTTCACGGTATTGTTCAT
1 CACTGTTCACGGTATTGTTCAA
*
1796632 CACTATTCA
1 CACTGTTCA
1796641 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (22 bp):
CACTGTTCACGGTATTGTTCAA
Found at i:1805186 original size:13 final size:13
Alignment explanation
Indices: 1805170--1805237 Score: 79
Period size: 13 Copynumber: 5.2 Consensus size: 13
1805160 AATTAATTTT
1805170 TAAATTAAATATA
1 TAAATTAAATATA
1805183 TAAA-TAACATATA
1 TAAATTAA-ATATA
1805196 T-AATTAAATAATA
1 TAAATTAAAT-ATA
*
1805209 AAAATTAAATA-A
1 TAAATTAAATATA
1805221 TAAAATTAAATATA
1 T-AAATTAAATATA
1805235 TAA
1 TAA
1805238 CTTGCGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.17
13 29 0.62
14 10 0.21
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTAAATATA
Found at i:1805216 original size:14 final size:14
Alignment explanation
Indices: 1805197--1805237 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
1805187 TAACATATAT
1805197 AATTAAATAATAAA
1 AATTAAATAATAAA
1805211 AATTAAATAAT-AA
1 AATTAAATAATAAA
1805224 AATTAAATATATAA
1 AATTAAATA-ATAA
1805238 CTTGCGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 13 0.52
15 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTAAATAATAAA
Found at i:1805474 original size:2 final size:2
Alignment explanation
Indices: 1805467--1805502 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1805457 AAATAAATTA
1805467 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
1805503 CAAAATTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1809126 original size:50 final size:50
Alignment explanation
Indices: 1809067--1809182 Score: 223
Period size: 50 Copynumber: 2.3 Consensus size: 50
1809057 AATATCGGTT
*
1809067 ATGAACCGTTAACGGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1809117 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1809167 ATGAACCGTTAACAGT
1 ATGAACCGTTAACAGT
1809183 TAACAAGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (50 bp):
ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
Found at i:1811897 original size:31 final size:31
Alignment explanation
Indices: 1811862--1811923 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1811852 TCAATTTTGC
1811862 CTATTCCGAGGGCTTAAAGAAGAACTGTACT
1 CTATTCCGAGGGCTTAAAGAAGAACTGTACT
1811893 CTATTCCGAGGGCTTAAAGAAGAACTGTACT
1 CTATTCCGAGGGCTTAAAGAAGAACTGTACT
1811924 TGATGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (31 bp):
CTATTCCGAGGGCTTAAAGAAGAACTGTACT
Found at i:1814880 original size:50 final size:50
Alignment explanation
Indices: 1814818--1814929 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
1814808 ATAGAAGTAA
* * * * * *
1814818 AGCGCGCTCCTTAAATCGCGTTATACGCTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCTTAAACCGCGATATACGCTGATTTGACGCCACGTAGGTAT
** * *
1814868 AGCGCGCCCCTTACCCCGTGATATACGGTGATTTGACGCCACGTAGGTAT
1 AGCGCGCCCCTTAAACCGCGATATACGCTGATTTGACGCCACGTAGGTAT
1814918 AGCGCGTCCCCT
1 AGCGCG-CCCCT
1814930 GATCCGCGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 46 0.90
51 5 0.10
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26
Consensus pattern (50 bp):
AGCGCGCCCCTTAAACCGCGATATACGCTGATTTGACGCCACGTAGGTAT
Found at i:1814943 original size:50 final size:48
Alignment explanation
Indices: 1814834--1814943 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 48
1814824 CTCCTTAAAT
* * * *
1814834 CGCGTTATACGCTGATTTGGCGTCACGTGGGTATAGCGCGCCCCTTAC
1 CGCGTTATACGCTGATTTGACGCCACGTAGGTATAGCGCGCCCCTGAC
* *
1814882 CCCGTGATATACGGTGATTTGACGCCACGTAGGTATAGCGCGTCCCCTGATC
1 CGCGT--TATACGCTGATTTGACGCCACGTAGGTATAGCGCG-CCCCTGA-C
1814934 CGCGTTATAC
1 CGCGTTATAC
1814944 ATAGGTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
48 4 0.08
50 36 0.71
51 6 0.12
52 5 0.10
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.26
Consensus pattern (48 bp):
CGCGTTATACGCTGATTTGACGCCACGTAGGTATAGCGCGCCCCTGAC
Found at i:1816986 original size:17 final size:18
Alignment explanation
Indices: 1816957--1816990 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1816947 TATATTTAAT
1816957 TTATTTAAGTATTTTACA
1 TTATTTAAGTATTTTACA
1816975 TTATTTAA-TATTTTAC
1 TTATTTAAGTATTTTAC
1816991 TAATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTTAAGTATTTTACA
Found at i:1817247 original size:111 final size:111
Alignment explanation
Indices: 1817053--1817272 Score: 404
Period size: 111 Copynumber: 2.0 Consensus size: 111
1817043 TGAAAATCAT
* *
1817053 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1817118 TAATTAGTTGATTTATTTAATGCATGATTAGTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTAGTAGATTAAGAATTAA
*
1817164 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
*
1817229 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
66 TAATTAGTTGATTTATTTAATGCATGATTAGTAGATTAAGAATT
1817273 GCCCTTGAAC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACAGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTAGTAGATTAAGAATTAA
Found at i:1822432 original size:16 final size:16
Alignment explanation
Indices: 1822411--1822454 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
1822401 ACCGGACGTG
1822411 ATCATTTCTCTAATCA
1 ATCATTTCTCTAATCA
1822427 ATCATTTCTCTAATCA
1 ATCATTTCTCTAATCA
1822443 ATCATTTCTCTA
1 ATCATTTCTCTA
1822455 TATTAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (16 bp):
ATCATTTCTCTAATCA
Found at i:1824201 original size:22 final size:22
Alignment explanation
Indices: 1824176--1824217 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1824166 ATTTTGAAAG
*
1824176 AAAAAAATAAAAGAAAAAAGAA
1 AAAAAAAGAAAAGAAAAAAGAA
*
1824198 AAAAAAAGGAAAGAAAAAAG
1 AAAAAAAGAAAAGAAAAAAG
1824218 TTGGTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAGAAAAAAGAA
Found at i:1824214 original size:12 final size:12
Alignment explanation
Indices: 1824171--1824217 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1824161 AATCTATTTT
*
1824171 GAAAGAAAAAAAT
1 GAAAG-AAAAAAG
*
1824184 AAAAGAAAAAA-
1 GAAAGAAAAAAG
1824195 GAAA-AAAAAAG
1 GAAAGAAAAAAG
1824206 GAAAGAAAAAAG
1 GAAAGAAAAAAG
1824218 TTGGTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.20
11 7 0.23
12 13 0.43
13 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
GAAAGAAAAAAG
Found at i:1833786 original size:16 final size:16
Alignment explanation
Indices: 1833765--1833795 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1833755 ATAAATAAAT
1833765 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1833781 GAACATAAACGAACA
1 GAACATAAACGAACA
1833796 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1833875 original size:10 final size:10
Alignment explanation
Indices: 1833860--1833918 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
1833850 CATTTAATAA
1833860 ATAAACGAAC
1 ATAAACGAAC
1833870 ATAAACGAAC
1 ATAAACGAAC
** *
1833880 ACGAAC-ATAA
1 ATAAACGA-AC
1833890 ATGAATACGAAC
1 AT-AA-ACGAAC
1833902 ATAAACGAAC
1 ATAAACGAAC
1833912 ATAAACG
1 ATAAACG
1833919 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1833885 original size:16 final size:16
Alignment explanation
Indices: 1833864--1833912 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
1833854 TAATAAATAA
1833864 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1833880 ACGAACATAAATGAAT
1 ACGAACATAAACGAAC
1833896 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1833912 A
1 A
1833913 TAAACGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1834678 original size:14 final size:14
Alignment explanation
Indices: 1834661--1834716 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1834651 AATGAACATA
1834661 AACGAACATAATCG
1 AACGAACATAATCG
1834675 AACGAACAT-A---
1 AACGAACATAATCG
* *
1834685 AACGAACATAACCA
1 AACGAACATAATCG
1834699 AACGAACATAATCG
1 AACGAACATAATCG
1834713 AACG
1 AACG
1834717 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:1834681 original size:24 final size:24
Alignment explanation
Indices: 1834641--1834715 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1834631 GATTGGGTTA
*
1834641 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1834665 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1834689 AACATAACCAAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
1834713 AAC
1 AAC
1834716 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1835386 original size:12 final size:12
Alignment explanation
Indices: 1835354--1835393 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1835344 TTCAAAGAAA
1835354 TTAAAA-TTA-T
1 TTAAAATTTATT
*
1835364 TT-AAATCTATT
1 TTAAAATTTATT
1835375 TTAAAATTTATT
1 TTAAAATTTATT
1835387 TTAAAAT
1 TTAAAAT
1835394 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:1835405 original size:22 final size:22
Alignment explanation
Indices: 1835380--1835699 Score: 493
Period size: 22 Copynumber: 14.6 Consensus size: 22
1835370 CTATTTTAAA
1835380 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* **
1835402 ATTTATTTTAAAATGTGGA-AA
1 ATTTATTTTAAAATATGGATTG
1835423 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
**
1835446 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
1835467 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1835489 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1835511 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1835533 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
1835555 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* **
1835577 ATTTATTTTAAAATATAGA-AA
1 ATTTATTTTAAAATATGGATTG
1835598 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
1835621 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1835643 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
1835665 ATTTATTTTAAATTTTGGATTG
1 ATTTATTTTAAAATATGGATTG
1835687 ATTTATTTTAAAA
1 ATTTATTTTAAAA
1835700 AAATTATTAT
Statistics
Matches: 270, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
21 21 0.08
22 247 0.91
23 2 0.01
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1835780 original size:31 final size:31
Alignment explanation
Indices: 1835723--1835781 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1835713 AGTTGTATGG
*
1835723 ATTATTTAAATTTCAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
* *
1835754 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
1835782 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:1843119 original size:32 final size:32
Alignment explanation
Indices: 1843078--1843145 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
1843068 TCGAATTTTC
1843078 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
1 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
1843110 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
1 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
1843142 CTGT
1 CTGT
1843146 CACCGCTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (32 bp):
CTGTTCAAGGACTTCTTTTTCTATCACCAATG
Found at i:1849460 original size:33 final size:32
Alignment explanation
Indices: 1849388--1849462 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
1849378 ACTTGTTGCA
1849388 ATTTTTTGTAAGTAAACTTACATATTGCTACC
1 ATTTTTTGTAAGTAAACTTACATATTGCTACC
* * * *
1849420 ATATTTTGTAAGT-AAGTTCAACTTATTGCTATC
1 ATTTTTTGTAAGTAAACTT--ACATATTGCTACC
1849453 ATTTTTTGTA
1 ATTTTTTGTA
1849463 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.11
32 12 0.33
33 20 0.56
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (32 bp):
ATTTTTTGTAAGTAAACTTACATATTGCTACC
Found at i:1851917 original size:12 final size:12
Alignment explanation
Indices: 1851900--1851930 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1851890 GCATGAATCA
1851900 AACTCAAAATTG
1 AACTCAAAATTG
1851912 AACTCAAAATTG
1 AACTCAAAATTG
*
1851924 AGCTCAA
1 AACTCAA
1851931 GTCTTGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (12 bp):
AACTCAAAATTG
Found at i:1856325 original size:67 final size:67
Alignment explanation
Indices: 1856217--1856351 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
1856207 AGTGATGAAG
1856217 CTGGTTTGTCAAAACATAAAGAGGTGAAAGTGTCATGTACATGGGGGTGTTTAAGTTCTTGGCTT
1 CTGGTTTGTCAAAACATAAAGAGGTGAAAGTGTCATGTACATGGGGGTGTTTAAGTTCTTGGCTT
1856282 GT
66 GT
*
1856284 CTGGTTTGTCAAAACATAAAGAGGTGAAAGTGTCATGTACATGGGGGTGTTTAAGTTCTTGGTTT
1 CTGGTTTGTCAAAACATAAAGAGGTGAAAGTGTCATGTACATGGGGGTGTTTAAGTTCTTGGCTT
1856349 GT
66 GT
1856351 C
1 C
1856352 ATTGTTACTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (67 bp):
CTGGTTTGTCAAAACATAAAGAGGTGAAAGTGTCATGTACATGGGGGTGTTTAAGTTCTTGGCTT
GT
Found at i:1858661 original size:2 final size:2
Alignment explanation
Indices: 1858654--1858686 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1858644 GACAACTCAA
1858654 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 A
1858687 ATTCATTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1861935 original size:46 final size:46
Alignment explanation
Indices: 1861882--1861969 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
1861872 CATCATATTT
1861882 GAATTGGCAAATTTACTGGGATAAAGTAAGGAGAAAATGGATACAC
1 GAATTGGCAAATTTACTGGGATAAAGTAAGGAGAAAATGGATACAC
* *
1861928 GAATTGGCAAATTTATTGGGATAATGTAAGGAGAAAATGGAT
1 GAATTGGCAAATTTACTGGGATAAAGTAAGGAGAAAATGGAT
1861970 TTGTATGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.25
Consensus pattern (46 bp):
GAATTGGCAAATTTACTGGGATAAAGTAAGGAGAAAATGGATACAC
Found at i:1862404 original size:2 final size:2
Alignment explanation
Indices: 1862397--1862438 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1862387 TTTTTATTTG
*
1862397 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AA 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
1862437 AT
1 AT
1862439 TTTTAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1862444 original size:16 final size:16
Alignment explanation
Indices: 1862397--1862446 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1862387 TTTTTATTTG
* *
1862397 ATATATATATATATAT
1 ATATATATATATTTAA
*
1862413 ATATATATATAATTAA
1 ATATATATATATTTAA
*
1862429 ATATATATATTTTTAA
1 ATATATATATATTTAA
1862445 AT
1 AT
1862447 GAATTGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATATATATTTAA
Found at i:1863869 original size:20 final size:21
Alignment explanation
Indices: 1863844--1863883 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1863834 AACATTGGCA
*
1863844 ACTTCGGCA-GCTATTTTTCC
1 ACTTCGGCAGGCAATTTTTCC
*
1863864 ACTTCGTCAGGCAATTTTTC
1 ACTTCGGCAGGCAATTTTTC
1863884 TGGTTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.40
Consensus pattern (21 bp):
ACTTCGGCAGGCAATTTTTCC
Found at i:1874486 original size:20 final size:20
Alignment explanation
Indices: 1874461--1874500 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1874451 TTGCGTAGTC
1874461 TACCTATCA-GTGGTCCTCAA
1 TACCTATCAGGT-GTCCTCAA
1874481 TACCTATCAGGTGTCCTCAA
1 TACCTATCAGGTGTCCTCAA
1874501 ACCCGTCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (20 bp):
TACCTATCAGGTGTCCTCAA
Found at i:1875778 original size:3 final size:3
Alignment explanation
Indices: 1875770--1875831 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
1875760 CTCCATTTTC
1875770 TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT TAT T-T TATT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T
*
1875815 TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1875832 CAAACAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1875794 original size:21 final size:22
Alignment explanation
Indices: 1875770--1875831 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
1875760 CTCCATTTTC
1875770 TATTATTATTATTATT-TTATA
1 TATTATTATTATTATTATTATA
*
1875791 TATTATTATTATTATTATTTTA
1 TATTATTATTATTATTATTATA
*
1875813 T-TTAGTATTATTATTATTA
1 TATTATTATTATTATTATTA
1875832 CAAACAGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTATTATTATTATTATTATA
Found at i:1875797 original size:24 final size:24
Alignment explanation
Indices: 1875770--1875831 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1875760 CTCCATTTTC
*
1875770 TATTATTATTATTATTTTATATAT
1 TATTATTATTATTATTTTATATAG
*
1875794 TATTATTATTATTATTTTATTTAG
1 TATTATTATTATTATTTTATATAG
1875818 TATTATTATTATTA
1 TATTATTATTATTA
1875832 CAAACAGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTATTATTATTATTTTATATAG
Found at i:1877136 original size:13 final size:14
Alignment explanation
Indices: 1877092--1877182 Score: 53
Period size: 14 Copynumber: 6.4 Consensus size: 14
1877082 TTTATTTTTG
1877092 ATTAT-TTTTTTAT
1 ATTATATTTTTTAT
* *
1877105 ATTTTATATTTTAAT
1 ATTATAT-TTTTTAT
1877120 ATTATATTTTTTA-
1 ATTATATTTTTTAT
***
1877133 ATTATTATTTGCAAT
1 ATTA-TATTTTTTAT
*
1877148 ATTAT-TTTATTATT
1 ATTATATTTTTTA-T
*
1877162 ATTATTACTTTTTATT
1 ATTA-TATTTTTTA-T
1877178 ATTAT
1 ATTAT
1877183 TCTTATTATT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
13 12 0.20
14 18 0.31
15 18 0.31
16 11 0.19
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (14 bp):
ATTATATTTTTTAT
Found at i:1877153 original size:3 final size:3
Alignment explanation
Indices: 1877147--1877192 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1877137 TTATTTGCAA
* *
1877147 TAT TAT T-T TAT TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1877192 T
1 T
1877193 TATTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1877176 original size:19 final size:18
Alignment explanation
Indices: 1877092--1877196 Score: 67
Period size: 19 Copynumber: 5.7 Consensus size: 18
1877082 TTTATTTTTG
1877092 ATTATTTTT-TTA-TATT
1 ATTATTTTTATTATTATT
*
1877108 -TTATATTTTAATATTA-T
1 ATTAT-TTTTATTATTATT
*
1877125 ATT-TTTTAATTATTATTT
1 ATTATTTTTATTATTA-TT
*
1877143 GCAATATTATTTTATTATTATT
1 --ATTA-T-TTTTATTATTATT
1877165 ATTACTTTTTATTATTATT
1 ATTA-TTTTTATTATTATT
*
1877184 CTTATTATTTATT
1 ATTATT-TTTATT
1877197 TAAATAAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
15 4 0.06
16 13 0.19
17 4 0.06
18 7 0.10
19 22 0.32
20 6 0.09
22 3 0.04
23 10 0.14
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
ATTATTTTTATTATTATT
Found at i:1877190 original size:39 final size:38
Alignment explanation
Indices: 1877083--1877193 Score: 99
Period size: 39 Copynumber: 2.9 Consensus size: 38
1877073 CATTCAAAAT
*
1877083 TTATTTTTGATTATTTTT-TTA-TATT-TTA-TATTTTA
1 TTATTATT-ATTATTTTTATTATTATTCTTATTATTTTA
* * *
1877118 ATATTA-TATT-TTTTAATTATTATTTGCAATATTATTTTA
1 TTATTATTATTATTTTTATTATTA-TT-C-TTATTATTTTA
1877157 TTATTATTATTACTTTTTATTATTATTCTTATTATTT
1 TTATTATTATTA-TTTTTATTATTATTCTTATTATTT
1877194 ATTTAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
32 4 0.07
33 6 0.10
34 3 0.05
35 6 0.10
38 2 0.03
39 20 0.34
40 5 0.08
41 2 0.03
42 11 0.19
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (38 bp):
TTATTATTATTATTTTTATTATTATTCTTATTATTTTA
Found at i:1877412 original size:20 final size:19
Alignment explanation
Indices: 1877387--1877428 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1877377 TTATTTTATA
1877387 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1877407 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1877426 AAT
1 AAT
1877429 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1877430 original size:119 final size:120
Alignment explanation
Indices: 1877291--1877520 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 120
1877281 TTTTAATATA
* * * * *
1877291 TATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAAC-TGGATGTTCATTTTCT
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTT-AAAGAACGTAGAAG-TCATTTTCT
* *
1877353 GATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAATTGTTTTAAT
64 GATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAATTGTTTTAAT
* * * * *
1877410 TATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACGTAGAAGTCATTTTCTTA
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAGAACGTAGAAGTCATTTTCTGA
*
1877475 TATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
66 TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAAT
1877521 ATATATTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
119 29 0.31
120 50 0.53
121 15 0.16
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (120 bp):
TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAGAACGTAGAAGTCATTTTCTGA
TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAATTGTTTTAAT
Found at i:1878047 original size:16 final size:17
Alignment explanation
Indices: 1878013--1878056 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
1878003 TTTCTTTCAA
1878013 ATTTTTTATTACTTATT
1 ATTTTTTATTACTTATT
*
1878030 ATTTTTATATTATTTTATT
1 ATTTTT-TATTA-CTTATT
1878049 AATTTTTT
1 -ATTTTTT
1878057 TTGCATTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 6 0.26
20 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTACTTATT
Found at i:1882352 original size:14 final size:15
Alignment explanation
Indices: 1882322--1882364 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
1882312 CTCATCCAGT
1882322 AAAGAAAGAAGAAAAAA
1 AAAG-AAGAA-AAAAAA
1882339 AAAGAA-AAAAAAAA
1 AAAGAAGAAAAAAAA
*
1882353 GAAGAAGAAAAA
1 AAAGAAGAAAAA
1882365 GGAAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
15 7 0.29
16 2 0.08
17 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAAAAAAA
Found at i:1884764 original size:115 final size:114
Alignment explanation
Indices: 1884604--1884830 Score: 382
Period size: 115 Copynumber: 2.0 Consensus size: 114
1884594 AGGTGCTATG
1884604 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
1884669 TGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTAAAAGATGAATT
66 TGGTTCGGTAGGAACCAC-AAAACCAATCATTGGAATTAAAAGATGAATT
*
1884719 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
1884784 TGGTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 TGGTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
1884831 CTGCATTATC
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 26 0.25
115 79 0.75
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:1885954 original size:75 final size:74
Alignment explanation
Indices: 1885786--1885960 Score: 192
Period size: 74 Copynumber: 2.4 Consensus size: 74
1885776 AACAAGAAGT
* * * * * * *
1885786 AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCCGAATTAGAAATGTTGAAATATTCTGAATAT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAC
1885851 TTGTCAGCA
66 TTGTCAGCA
* ** *
1885860 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAATTGTTGATGCATTTTGAACAC
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAC
1885925 TTGT-ATTGGC-
66 TTGTCA---GCA
* *
1885935 CAATGTTGGGGCATGCTGAAGGCCCA
1 AAATGTTGGGGCATGCTGAAAGCCCA
1885961 CAACATCCTG
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 58 0.68
75 24 0.28
76 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (74 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAC
TTGTCAGCA
Found at i:1886954 original size:40 final size:40
Alignment explanation
Indices: 1886899--1886978 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1886889 GAGCAGAAGC
1886899 CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCT
1 CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCT
1886939 CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCT
1 CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCT
1886979 GAGCTGAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (40 bp):
CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCT
Found at i:1887021 original size:90 final size:92
Alignment explanation
Indices: 1886845--1887024 Score: 231
Period size: 90 Copynumber: 2.0 Consensus size: 92
1886835 GAGCAGAAAC
*
1886845 CACAGAAAAGGATGAATGTATTGTCAAATGCTTTACGAACATCTGAGCAGAAGCCACAGAAAAGG
1 CACAGAAAAGGATGAATGTATTGTCAAATGCTTTA--AACATCTGAGCAGAAACCACAGAAAAGG
* *
1886910 ATGAATGTGTTGTCAAGTGTTTTACATCT
64 AAGAATGTGTTGTCAAATGTTTTACATCT
* * * * * *
1886939 CACAGAAAAGGATGAATGTGTTGTCAAGTG-TTT-TACATCTGAGCTGAAACCACATG-AGATGA
1 CACAGAAAAGGATGAATGTATTGTCAAATGCTTTAAACATCTGAGCAGAAACCACA-GAAAAGGA
1887001 AGAATGTGTTGTCAAATGTTTTAC
65 AGAATGTGTTGTCAAATGTTTTAC
1887025 GAACATCTGA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
90 44 0.58
91 1 0.01
93 3 0.04
94 28 0.37
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (92 bp):
CACAGAAAAGGATGAATGTATTGTCAAATGCTTTAAACATCTGAGCAGAAACCACAGAAAAGGAA
GAATGTGTTGTCAAATGTTTTACATCT
Found at i:1887060 original size:54 final size:54
Alignment explanation
Indices: 1886939--1887082 Score: 154
Period size: 54 Copynumber: 2.7 Consensus size: 54
1886929 TTTTACATCT
* * *
1886939 CACAGAAAAGGATGAATGTGTTGTCAAGTGTTTT----ACATCTGAGCTGAAAC
1 CACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCTAAAAC
* * * *
1886989 CACATGAGATGAAGAATGTGTTGTCAAATGTTTTACGAACATCTGAGC-AAAAGC
1 CACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCTAAAA-C
***
1887043 CACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1887083 CTACTATTCT
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
50 28 0.37
53 3 0.04
54 44 0.59
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (54 bp):
CACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCTAAAAC
Found at i:1888185 original size:113 final size:112
Alignment explanation
Indices: 1887845--1888732 Score: 834
Period size: 113 Copynumber: 7.8 Consensus size: 112
1887835 GATTCAAATC
* * *
1887845 CATCACTTGATGGATCAGCTTTTTCAAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * ** *
1887910 AAAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
1887958 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
1888020 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
* *
1888068 CATCATTTGATGGATCAGCTTTTCAAGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1888133 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTT-GCTTGAATT
* * * * * **** *
1888181 CATCATTCGATTGATCAACATTACCAGGTCGAGTTCATAATGATAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
1888246 AGAATAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-TTTTGCTTGAATT
* * * * ***
1888294 CATCATTCGATGGGTCAGCATTGCCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1888359 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-TTTTGCTTGAATT
* * *
1888407 CATCATTCT-ATGGATCAACATTGCCAG-----G----T-A-GAGAAGAACTCATCT---GAAG-
1 CATCATT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
** *
1888456 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
* * * *
1888504 CTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
1 C-AT--C---AT----TTGAT--GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
* * * *
1888569 TCTGAAGGAGGAAGAAGAAGTTCATAATGAGAA-AATTATGTTCAACCTTTTTCATG-ACT
54 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT-TGTTCAA-CTTTTGCTTGAATT
* * *
1888628 CTATCATAGAAGGAGATAGATCAGCATCAACTTTTCCAG--AAAGTTCATAATGAGAAGAACTCA
1 C-ATCAT---------TTGAT--GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCA
*
1888691 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
54 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1888733 TAACCCTTTT
Statistics
Matches: 680, Mismatches: 52, Indels: 77
0.84 0.06 0.10
Matches are distributed among these distances:
97 5 0.01
98 41 0.06
99 5 0.01
100 1 0.00
102 15 0.02
103 3 0.00
104 1 0.00
107 3 0.00
108 1 0.00
109 13 0.02
110 104 0.15
111 1 0.00
112 6 0.01
113 317 0.47
114 5 0.01
118 1 0.00
119 3 0.00
120 15 0.02
122 61 0.09
123 8 0.01
124 71 0.10
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTGCTTGAATT
Found at i:1888597 original size:124 final size:123
Alignment explanation
Indices: 1888437--1888815 Score: 484
Period size: 122 Copynumber: 3.2 Consensus size: 123
1888427 TTGCCAGGTA
* *
1888437 GAGAAGAACTCATCTG-A-A-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCA
1 GAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCA
* *
1888499 TAATTCTATCACAGAATGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAAT
66 TAATTCTATCATAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAAT
* *
1888557 GAGAAGAACTCATCTGAAGGAGGAAGAAGAAGTTCATAATGAGAA-AATTATGTTCAACCTTTTT
1 GAGAAGAACTCATCTGAA-GAGGAAGAAGAAGTTCATAATGAGAAGAACT-TGTTCAACCTTTTC
* *
1888621 CATGACTCTATCATAGAAGGAGATAGATCAGCATCAACTTTTCC--AGAAAGTTCATAAT
64 CATAATTCTATCATAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAAT
*
1888679 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCCTTTTC
1 GAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CCTTTTC
* * *
1888744 CA-AATTAC-ATCATAGAAGGAGAT--ATTATCATC--C----CCAGCGGAAAGTTCATAAT
64 CATAATT-CTATCATAGAAGGAGATAGATCAGCATCAACTTTTCCAG-AGAAAGTTCATAAT
1888796 GAGAAGAACTCATCTGAAGA
1 GAGAAGAACTCATCTGAAGA
1888816 AAGAGAAGAA
Statistics
Matches: 232, Mismatches: 15, Indels: 28
0.84 0.05 0.10
Matches are distributed among these distances:
114 2 0.01
116 1 0.00
117 32 0.14
118 1 0.00
120 23 0.10
121 2 0.01
122 80 0.34
123 15 0.06
124 76 0.33
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
GAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCA
TAATTCTATCATAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAAT
Found at i:1888972 original size:3 final size:3
Alignment explanation
Indices: 1888966--1889027 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1888956 CTCCATTTTC
*
1888966 TAT TAT TAT TAT TAT T-T TAT ATAT TAT TGT TAT TAT TAT T-T TATT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T
*
1889011 TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1889028 CAAACAGGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1888998 original size:24 final size:24
Alignment explanation
Indices: 1888966--1889027 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1888956 CTCCATTTTC
*
1888966 TATTATTATTATTATTTTATATAT
1 TATTATTATTATTATTTTATATAG
* *
1888990 TATTGTTATTATTATTTTATTTAG
1 TATTATTATTATTATTTTATATAG
1889014 TATTATTATTATTA
1 TATTATTATTATTA
1889028 CAAACAGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TATTATTATTATTATTTTATATAG
Found at i:1889513 original size:3 final size:3
Alignment explanation
Indices: 1889505--1889564 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
1889495 CTCCATTTTC
1889505 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
*
1889548 TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1889565 CAAACAGGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1889530 original size:17 final size:17
Alignment explanation
Indices: 1889499--1889549 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1889489 TTTTTTCTCC
*
1889499 ATTTTCTAT-TATTATT
1 ATTTTATATATATTATT
1889515 ATTTTATATATATTATT
1 ATTTTATATATATTATT
*
1889532 ATTATTAT-TATTTTATT
1 ATT-TTATATATATTATT
1889549 A
1 A
1889550 GTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 8 0.26
17 19 0.61
18 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATATATATTATT
Found at i:1889530 original size:20 final size:20
Alignment explanation
Indices: 1889505--1889564 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1889495 CTCCATTTTC
1889505 TATTATTATTATT-TTATATA
1 TATTATTATTATTATTAT-TA
*
1889525 TATTATTATTATTATTATTT
1 TATTATTATTATTATTATTA
*
1889545 TATTAGTATTATTATTATTA
1 TATTATTATTATTATTATTA
1889565 CAAACAGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 32 0.89
21 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTATTATTATTATTA
Found at i:1889534 original size:26 final size:26
Alignment explanation
Indices: 1889505--1889564 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
1889495 CTCCATTTTC
1889505 TATTATTATTATTTTATATA-TATTAT
1 TATTATTATTATTTTAT-TAGTATTAT
1889531 TATTATTATTATTTTATTAGTATTAT
1 TATTATTATTATTTTATTAGTATTAT
1889557 TATTATTA
1 TATTATTA
1889565 CAAACAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTATTATTATTTTATTAGTATTAT
Found at i:1890482 original size:6 final size:6
Alignment explanation
Indices: 1890462--1890576 Score: 70
Period size: 6 Copynumber: 17.8 Consensus size: 6
1890452 ATCATTCAAA
*
1890462 TTTATT TTTGATT TTT-TT TTTATTT TTTATT TTTATT TTAATT TTATATT
1 TTTATT TTT-ATT TTTATT TTTA-TT TTTATT TTTATT TTTATT TT-TATT
* * * * * *
1890512 TTTAATT ATTATT TGCAATATT ATTTATT ATTATT ATTACT TTTATT ATTATT
1 TTT-ATT TTTATT T---TTATT -TTTATT TTTATT TTTATT TTTATT TTTATT
*
1890565 CTTATT ATTTAT
1 TTTATT -TTTAT
1890577 ATAAATAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
5 5 0.06
6 46 0.53
7 30 0.35
9 4 0.05
10 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTATT
Found at i:1890511 original size:19 final size:19
Alignment explanation
Indices: 1890472--1890515 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1890462 TTTATTTTTG
* *
1890472 ATTTTT-TTTTTATTTTTT
1 ATTTTTATTTTAATTTTAT
1890490 ATTTTTATTTTAATTTTAT
1 ATTTTTATTTTAATTTTAT
1890509 ATTTTTA
1 ATTTTTA
1890516 ATTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
ATTTTTATTTTAATTTTAT
Found at i:1890536 original size:3 final size:3
Alignment explanation
Indices: 1890530--1890573 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1890520 TTATTTGCAA
*
1890530 TAT TATT TAT TAT TAT TAT TACT T-T TAT TAT TAT TCT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
1890574 TATATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1890920 original size:25 final size:25
Alignment explanation
Indices: 1890861--1890921 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
1890851 ATATTTCTAA
1890861 ATAAATAA-ATATTTTATTATAAAT
1 ATAAATAATATATTTTATTATAAAT
*
1890885 ATAAAATTAATATATTTT-TTCATAATT
1 AT-AAA-TAATATATTTTATT-ATAAAT
1890912 ATAAATAATA
1 ATAAATAATA
1890922 GGATTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 8 0.25
26 8 0.25
27 14 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAAATAATATATTTTATTATAAAT
Found at i:1897159 original size:551 final size:551
Alignment explanation
Indices: 1896118--1897221 Score: 2110
Period size: 551 Copynumber: 2.0 Consensus size: 551
1896108 TCTCCTTTGT
1896118 TTCTGGAGCTTATTCTTTCAAATAATGTGAATAATGAAATGTTTTTTTTTCTATTTGTGTAATGT
1 TTCTGGAGCTTATTCTTTCAAATAATGTGAATAATGAAATGTTTTTTTTTCTATTTGTGTAATGT
1896183 AACTTGCCAGGATTAACCCACCATTTGATCGACCCACCATTTATGAATTTGATTAATGGAGGTTC
66 AACTTGCCAGGATTAACCCACCATTTGATCGACCCACCATTTATGAATTTGATTAATGGAGGTTC
1896248 TGAATGCTCATTATTTTTTTAATCCTTTGCTAAGTTCCAAAGGTTGATGGATTTTACCCTATTTC
131 TGAATGCTCATTATTTTTTTAATCCTTTGCTAAGTTCCAAAGGTTGATGGATTTTACCCTATTTC
1896313 ATCCTCAAGGTTTGTTGTGGAAGCTACGCCAGTGTTTTTGAGGATAGAATTTATCCTATTTAGAA
196 ATCCTCAAGGTTTGTTGTGGAAGCTACGCCAGTGTTTTTGAGGATAGAATTTATCCTATTTAGAA
1896378 TTTGGGTTTTTGAAATAGGGGAGAAAGATGTCATTGATGAATTGAGATTTGAGGTTTGAATTTCG
261 TTTGGGTTTTTGAAATAGGGGAGAAAGATGTCATTGATGAATTGAGATTTGAGGTTTGAATTTCG
1896443 GGTTTTTTTTTATCCTTTGTTAAGTGCCAAAGGATGATGGTTTTCTCTATTAGCAATTTCTGCTT
326 GGTTTTTTTTTATCCTTTGTTAAGTGCCAAAGGATGATGGTTTTCTCTATTAGCAATTTCTGCTT
1896508 GAAGGGATTATCTATGATTTATTTGGTTACCTGGGAAAATGGAGAAGAGAAGATGGTGGAGAGAT
391 GAAGGGATTATCTATGATTTATTTGGTTACCTGGGAAAATGGAGAAGAGAAGATGGTGGAGAGAT
1896573 AAAGGTATAAGAGAAGACCGGGTTGGGCATAATAATAAGATATATATATAA-ATATATTAATTGA
456 AAAGGTATAAGAGAAGACCGGGTTGGGCATAATAATAAGATATATATATAATA-ATATTAATTGA
1896637 TTAAGAAATTAAT-AAAAAATGCTAGGTTATGA
520 TTAAG-AATTAATAAAAAAATGCTAGGTTATGA
1896669 TTCTGGAGCTTATTCTTTCAAATAATGTGAATAATGAAATGTTTTTTTTTCTATTTGTGTAATGT
1 TTCTGGAGCTTATTCTTTCAAATAATGTGAATAATGAAATGTTTTTTTTTCTATTTGTGTAATGT
1896734 AACTTGCCAGGATTAACCCACCATTTGATCGACCCACCATTTATGAATTTGATTAATGGAGGTTC
66 AACTTGCCAGGATTAACCCACCATTTGATCGACCCACCATTTATGAATTTGATTAATGGAGGTTC
1896799 TGAATGCTCATTATTTTTTTAATCCTTTGCTAAGTTCCAAAGGTTGATGGATTTTACCCTATTTC
131 TGAATGCTCATTATTTTTTTAATCCTTTGCTAAGTTCCAAAGGTTGATGGATTTTACCCTATTTC
1896864 ATCCTCAAGGTTTGTTGTGGAAGCTACGCCAGTGTTTTTGAGGATAGAATTTATCCTATTTAG-A
196 ATCCTCAAGGTTTGTTGTGGAAGCTACGCCAGTGTTTTTGAGGATAGAATTTATCCTATTTAGAA
1896928 TTTGGGTTTTTGAAATAGGGGAGAAAGATGTCATTGATGAATTGAGATTTGAGGTTTGAATTTCG
261 TTTGGGTTTTTGAAATAGGGGAGAAAGATGTCATTGATGAATTGAGATTTGAGGTTTGAATTTCG
1896993 GGTTTTTTTTTATCCTTTGTTAAGTGCCAAAGGATGATGGGTTTTCT-TATTAGCAATTTCTGCT
326 GGTTTTTTTTTATCCTTTGTTAAGTGCCAAAGGATGAT-GGTTTTCTCTATTAGCAATTTCTGCT
1897057 TGAAGGGATTATCTATGATTTATTTGGTTA-CTGGGAAAATGGAGAAGAGAAGATGGTGGAGAGA
390 TGAAGGGATTATCTATGATTTATTTGGTTACCTGGGAAAATGGAGAAGAGAAGATGGTGGAGAGA
1897121 TTAGAAGGTATAAGAGAAGACCGGGTTGGGCATAATAATAAGATATATATATAATAATATTAATT
455 -TA-AAGGTATAAGAGAAGACCGGGTTGGGCATAATAATAAGATATATATATAATAATATTAATT
1897186 GATTAAGAATTAATAAAAAAAAATGCTAGGTTATGA
518 GATTAAGAATTAAT--AAAAAAATGCTAGGTTATGA
1897222 CGGTGTTAAG
Statistics
Matches: 546, Mismatches: 0, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
549 34 0.06
550 160 0.29
551 332 0.61
552 1 0.00
553 19 0.03
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (551 bp):
TTCTGGAGCTTATTCTTTCAAATAATGTGAATAATGAAATGTTTTTTTTTCTATTTGTGTAATGT
AACTTGCCAGGATTAACCCACCATTTGATCGACCCACCATTTATGAATTTGATTAATGGAGGTTC
TGAATGCTCATTATTTTTTTAATCCTTTGCTAAGTTCCAAAGGTTGATGGATTTTACCCTATTTC
ATCCTCAAGGTTTGTTGTGGAAGCTACGCCAGTGTTTTTGAGGATAGAATTTATCCTATTTAGAA
TTTGGGTTTTTGAAATAGGGGAGAAAGATGTCATTGATGAATTGAGATTTGAGGTTTGAATTTCG
GGTTTTTTTTTATCCTTTGTTAAGTGCCAAAGGATGATGGTTTTCTCTATTAGCAATTTCTGCTT
GAAGGGATTATCTATGATTTATTTGGTTACCTGGGAAAATGGAGAAGAGAAGATGGTGGAGAGAT
AAAGGTATAAGAGAAGACCGGGTTGGGCATAATAATAAGATATATATATAATAATATTAATTGAT
TAAGAATTAATAAAAAAATGCTAGGTTATGA
Found at i:1897779 original size:18 final size:18
Alignment explanation
Indices: 1897744--1897794 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1897734 ATATCATTGA
*
1897744 TCACATT-TTAT-GATAT
1 TCACATTATTATAAATAT
1897760 TCACATTATTATAAATAT
1 TCACATTATTATAAATAT
1897778 TCACATTATTATAAATA
1 TCACATTATTATAAATA
1897795 ATGTTACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 7 0.22
17 4 0.12
18 21 0.66
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (18 bp):
TCACATTATTATAAATAT
Found at i:1897997 original size:3 final size:3
Alignment explanation
Indices: 1897989--1898060 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
1897979 TTAAACATGA
*
1897989 AAT AAT AAT AAT AGT AA- AAT AAT AAT AAT AAT -AT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1898034 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1898061 GTTACATGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 6 0.09
3 58 0.91
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1898010 original size:17 final size:17
Alignment explanation
Indices: 1897988--1898056 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
1897978 TTTAAACATG
*
1897988 AAATAATAATAATAGTA
1 AAATAATAATAATAATA
1898005 AAATAATAATAATAATA
1 AAATAATAATAATAATA
*
1898022 TAATAAT-ATAATAATA
1 AAATAATAATAATAATA
1898038 ATAATAATAATAATAATA
1 A-AATAATAATAATAATA
1898056 A
1 A
1898057 TAATGTTACA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.19
17 28 0.60
18 10 0.21
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (17 bp):
AAATAATAATAATAATA
Found at i:1898027 original size:28 final size:29
Alignment explanation
Indices: 1897989--1898058 Score: 117
Period size: 28 Copynumber: 2.4 Consensus size: 29
1897979 TTAAACATGA
1897989 AATAATAATAATAGTAA-AATAATAATAAT
1 AATAATAATAATA-TAATAATAATAATAAT
1898018 AAT-ATAATAATATAATAATAATAATAAT
1 AATAATAATAATATAATAATAATAATAAT
1898046 AATAATAATAATA
1 AATAATAATAATA
1898059 ATGTTACATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 3 0.08
28 24 0.62
29 12 0.31
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
AATAATAATAATATAATAATAATAATAAT
Found at i:1903140 original size:24 final size:24
Alignment explanation
Indices: 1903044--1903142 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
1903034 TTCCTATTGG
* * * *
1903044 ATTCTGTTATGATACCTGACATGG
1 ATTCTGATCTGATACTTGACATGA
*
1903068 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGA
* **
1903092 ATTCTGATCCGATGTTTGACATGA
1 ATTCTGATCTGATACTTGACATGA
*
1903116 ATTCTGATCTGATACTTGACCTGA
1 ATTCTGATCTGATACTTGACATGA
1903140 ATT
1 ATT
1903143 ATGTTTTGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGA
Found at i:1914222 original size:18 final size:18
Alignment explanation
Indices: 1914175--1914222 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 18
1914165 CATCTAATAA
* *
1914175 TTAATTAATCAAAATTAT
1 TTAATTAATTAAAACTAT
1914193 TTAATT--TT--AACTAT
1 TTAATTAATTAAAACTAT
1914207 TTAATTAATTAAAACT
1 TTAATTAATTAAAACT
1914223 CATCAAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
14 11 0.46
16 3 0.12
18 10 0.42
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTAATTAAAACTAT
Found at i:1916237 original size:31 final size:27
Alignment explanation
Indices: 1916168--1916240 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
1916158 TTGTTCAAAT
*
1916168 AACCGAATTAATTCGGTTAATTGATCG
1 AACCGAATTAGTTCGGTTAATTGATCG
*
1916195 AACTGAATTAGTTCGGTTAATTCGATTCG
1 AACCGAATTAGTTCGGTTAATT-GA-TCG
1916224 ATTACCGAATTAGTTCG
1 A--ACCGAATTAGTTCG
1916241 ATCGATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 20 0.51
28 2 0.05
29 4 0.10
31 13 0.33
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (27 bp):
AACCGAATTAGTTCGGTTAATTGATCG
Found at i:1923614 original size:29 final size:28
Alignment explanation
Indices: 1923573--1923667 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 28
1923563 TCTCATTTTA
1923573 AATTGATCCTTAAACTTTTAAATATTCT
1 AATTGATCCTTAAACTTTTAAATATTCT
* * **
1923601 AATTGTATTCTTAAA-TTGTGACTTATTCT
1 AATTG-ATCCTTAAACTT-TTAAATATTCT
* *
1923630 AAATTAATCCTTAAACTTTTGAATATTCT
1 -AATTGATCCTTAAACTTTTAAATATTCT
1923659 AATTTGATC
1 AA-TTGATC
1923668 ACTTCTAGTC
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
28 9 0.18
29 36 0.71
30 6 0.12
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (28 bp):
AATTGATCCTTAAACTTTTAAATATTCT
Found at i:1923781 original size:87 final size:86
Alignment explanation
Indices: 1923658--1923817 Score: 257
Period size: 87 Copynumber: 1.8 Consensus size: 86
1923648 TTGAATATTC
* * * *
1923658 TAATTTGATCACTTCTAGTCTATATTTTTAAGAATATGGATATTTAGTCATGATGTCAACTTTTT
1 TAATTTGATCACTTCTAATATATACTTTTAAAAATATGGATATTTAGTCATGATGTCAACTTTTT
1923723 AAATTAATTACGACTCTCATTA
66 -AATTAATTACGACTCTCATTA
* *
1923745 TAATTTGATCACTTCTAATATGTACTTTTAAAAATATGGATATTTAGTCATGGTGTCAACTTTTT
1 TAATTTGATCACTTCTAATATATACTTTTAAAAATATGGATATTTAGTCATGATGTCAACTTTTT
1923810 AATTAATT
66 AATTAATT
1923818 TCTTAGACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 8 0.12
87 59 0.88
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (86 bp):
TAATTTGATCACTTCTAATATATACTTTTAAAAATATGGATATTTAGTCATGATGTCAACTTTTT
AATTAATTACGACTCTCATTA
Found at i:1924335 original size:63 final size:63
Alignment explanation
Indices: 1924268--1924393 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1924258 TTAGAGTAGA
1924268 GGTCGTAGTCTGGGGGATAAGATTGGAATGTTTAAAACTTTGAGGATGAATTAAGAATGATAG
1 GGTCGTAGTCTGGGGGATAAGATTGGAATGTTTAAAACTTTGAGGATGAATTAAGAATGATAG
1924331 GGTCGTAGTCTGGGGGATAAGATTGGAATGTTTAAAACTTTGAGGATGAATTAAGAATGATAG
1 GGTCGTAGTCTGGGGGATAAGATTGGAATGTTTAAAACTTTGAGGATGAATTAAGAATGATAG
1924394 TCACGGTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.30
Consensus pattern (63 bp):
GGTCGTAGTCTGGGGGATAAGATTGGAATGTTTAAAACTTTGAGGATGAATTAAGAATGATAG
Found at i:1942701 original size:40 final size:37
Alignment explanation
Indices: 1942621--1942696 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 37
1942611 CATTAAACCT
*
1942621 TTTTATATTTTTAATTTTGTAAAAACAATTATATAAA
1 TTTTATATTTTAAATTTTGTAAAAACAATTATATAAA
*
1942658 TTTTATGATATTTAAATTTTTTAAAGAA-AA-TATATAAA
1 TTTTAT-AT-TTTAAATTTTGTAAA-AACAATTATATAAA
1942696 T
1 T
1942697 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 6 0.18
38 11 0.32
39 15 0.44
40 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (37 bp):
TTTTATATTTTAAATTTTGTAAAAACAATTATATAAA
Found at i:1942907 original size:20 final size:20
Alignment explanation
Indices: 1942852--1942901 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1942842 TCCTATTCTT
1942852 TGGTAATCTTTTATTCTCAC
1 TGGTAATCTTTTATTCTCAC
1942872 TGGTAATCTTTTATTCTCAC
1 TGGTAATCTTTTATTCTCAC
1942892 TGGTAATCTT
1 TGGTAATCTT
1942902 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (20 bp):
TGGTAATCTTTTATTCTCAC
Found at i:1946608 original size:2 final size:2
Alignment explanation
Indices: 1946601--1946625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1946591 GAACAACTAA
1946601 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 A
1946626 GAAAGAGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1947602 original size:10 final size:10
Alignment explanation
Indices: 1947575--1947622 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1947565 ACGTTCGTGA
*
1947575 ATGTTCGGTT
1 ATGTTCGTTT
1947585 ATGTTCGTTT
1 ATGTTCGTTT
1947595 ATGTTCGTTCGATT
1 ATGTTCG-T---TT
1947609 ATGTTCGTTT
1 ATGTTCGTTT
1947619 ATGT
1 ATGT
1947623 GTGCTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.12, C:0.10, G:0.23, T:0.54
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:1947604 original size:24 final size:24
Alignment explanation
Indices: 1947577--1947622 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1947567 GTTCGTGAAT
*
1947577 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTTC
1947601 GTTCGATTATGTTCGTTTATGT
1 GTTCGATTATGTTCGTTTATGT
1947623 GTGCTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.24, T:0.54
Consensus pattern (24 bp):
GTTCGATTATGTTCGTTTATGTTC
Found at i:1947604 original size:34 final size:34
Alignment explanation
Indices: 1947552--1947622 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
1947542 ACATAGGTCT
1947552 TGTTCGTTCATTTACGTTCG-TGAATGTTCGGTTA
1 TGTTCGTTCATTTACGTTCGAT-AATGTTCGGTTA
* * *
1947586 TGTTCGTTTATGTT-CGTTCGATTATGTTCGTTTA
1 TGTTCGTTCAT-TTACGTTCGATAATGTTCGGTTA
1947620 TGT
1 TGT
1947623 GTGCTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 29 0.91
35 3 0.09
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (34 bp):
TGTTCGTTCATTTACGTTCGATAATGTTCGGTTA
Found at i:1947610 original size:14 final size:14
Alignment explanation
Indices: 1947587--1947617 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1947577 GTTCGGTTAT
*
1947587 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
1947601 GTTCGATTATGTTC
1 GTTCGATTATGTTC
1947615 GTT
1 GTT
1947618 TATGTGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:1949198 original size:16 final size:16
Alignment explanation
Indices: 1949177--1949227 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1949167 GTCTCCAACG
1949177 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1949193 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1949209 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1949223 TTTAT
1 TTTAT
1949228 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1956256 original size:15 final size:15
Alignment explanation
Indices: 1956236--1956265 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1956226 TATCACAATC
*
1956236 GCGCAGGATTTCGGG
1 GCGCAGGATTCCGGG
1956251 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1956266 AGCACCGTGG
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:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:1972045 original size:2 final size:2
Alignment explanation
Indices: 1972038--1972068 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1972028 ATAAACAACT
1972038 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
1972069 GAGAAGTATT
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:1973211 original size:2 final size:2
Alignment explanation
Indices: 1973206--1973233 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1973196 GCTTTTTTAA
1973206 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
1973234 GTATTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1974855 original size:24 final size:24
Alignment explanation
Indices: 1974828--1974917 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 24
1974818 TTTATGAATT
1974828 TAATATTAATAAAATATTTTAATA
1 TAATATTAATAAAATATTTTAATA
* *
1974852 TAATTTTAATCAAAATATTAATTATTA
1 TAATATTAAT-AAAATATT--TTAATA
* * *
1974879 AAATATTTA-AAAATATATTAATA
1 TAATATTAATAAAATATTTTAATA
**
1974902 TTTTTATTAATAAAAT
1 -TAATATTAATAAAAT
1974918 TATAGAAATA
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
23 5 0.10
24 14 0.28
25 20 0.40
27 11 0.22
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATATTAATAAAATATTTTAATA
Found at i:1974913 original size:20 final size:20
Alignment explanation
Indices: 1974867--1974913 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1974857 TTAATCAAAA
1974867 TATTAAT-TATTAAAATATT
1 TATTAATATATTAAAATATT
** * *
1974886 TAAAAATATATTAATATTTT
1 TATTAATATATTAAAATATT
1974906 TATTAATA
1 TATTAATA
1974914 AAATTATAGA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATATATTAAAATATT
Found at i:1975538 original size:14 final size:15
Alignment explanation
Indices: 1975513--1975541 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1975503 CGTGTTACGT
1975513 AAATATTTTTTAAAA
1 AAATATTTTTTAAAA
1975528 AAATA-TTTTTAAAA
1 AAATATTTTTTAAAA
1975542 TATTTAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTTTTAAAA
Found at i:1976068 original size:45 final size:45
Alignment explanation
Indices: 1976004--1976098 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
1975994 ATTTTATTAA
1976004 TATTAAATCACCAAAATCCAATGCTCATAAATTTTAATATGTTTC
1 TATTAAATCACCAAAATCCAATGCTCATAAATTTTAATATGTTTC
1976049 TATTAAATCACCAAAATCCAATGCTCATAAATTTTAATATGTTTC
1 TATTAAATCACCAAAATCCAATGCTCATAAATTTTAATATGTTTC
1976094 TATTA
1 TATTA
1976099 TATATTTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (45 bp):
TATTAAATCACCAAAATCCAATGCTCATAAATTTTAATATGTTTC
Found at i:1976316 original size:20 final size:20
Alignment explanation
Indices: 1976291--1976354 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
1976281 ATAAATACCA
1976291 AATAATATTATTTATTAAAT
1 AATAATATTATTTATTAAAT
1976311 AATAATAATAATATTT-TTAAATT
1 AATAAT-AT--TATTTATTAAA-T
* * *
1976334 ATTAAAATAATTTATTAAAT
1 AATAATATTATTTATTAAAT
1976354 A
1 A
1976355 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
20 12 0.33
21 7 0.19
22 7 0.19
23 10 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATATTATTTATTAAAT
Found at i:1976386 original size:14 final size:14
Alignment explanation
Indices: 1976331--1976387 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1976321 ATATTTTTAA
*
1976331 ATTATTAAAATAAT
1 ATTATTAAAATATT
1976345 -TTATT-AAATATTT
1 ATTATTAAAATA-TT
* **
1976358 TTTATTTCAATATT
1 ATTATTAAAATATT
1976372 ATTATTAAAATATT
1 ATTATTAAAATATT
1976386 AT
1 AT
1976388 ATCTATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 20 0.57
15 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATTAAAATATT
Found at i:1976552 original size:25 final size:27
Alignment explanation
Indices: 1976505--1976554 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1976495 TAATTATATT
*
1976505 AAATACTTAATAAATAATGATATTATA
1 AAATACTTAATAAATAATAATATTATA
*
1976532 AAATA-TTAA-AAATTATAATATTA
1 AAATACTTAATAAATAATAATATTA
1976555 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 4 0.19
27 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATACTTAATAAATAATAATATTATA
Found at i:1976665 original size:27 final size:27
Alignment explanation
Indices: 1976594--1976667 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
1976584 TTTTAAATAT
* *
1976594 TTAATAATTTAATA-ATATTATTTTTA
1 TTAATAATTTATTATATATTAATTTTA
* *
1976620 -TAA-AATTAATAAATAATATTAATTTTA
1 TTAATAATTTAT-TAT-ATATTAATTTTA
1976647 TTAATAATTTATTATATATTA
1 TTAATAATTTATTATATATTA
1976668 TTAACATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
24 5 0.14
25 4 0.11
27 17 0.46
28 5 0.14
29 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATAATTTATTATATATTAATTTTA
Found at i:1976697 original size:15 final size:15
Alignment explanation
Indices: 1976533--1976713 Score: 58
Period size: 14 Copynumber: 12.1 Consensus size: 15
1976523 GATATTATAA
* *
1976533 AATATTAAAAATTAT
1 AATATTATATATTAT
* *
1976548 AATATTA-A-AATAA
1 AATATTATATATTAT
*
1976561 AATATTATATTTTA-
1 AATATTATATATTAT
* * *
1976575 AATAATATGTTTTA-
1 AATATTATATATTAT
1976589 AATATT-TAATAATTTAAT
1 AATATTAT-AT-A-TT-AT
*
1976607 AATATTAT-TTTTAT
1 AATATTATATATTAT
* *
1976621 AAAATTA-ATA-AAT
1 AATATTATATATTAT
*
1976634 AATATTAATTTTATTAAT
1 AATATT-A-TATATT-AT
1976652 AATTTATTATATATTATT
1 AA--TATTATATATTA-T
* * *
1976670 AACA-TAAAAATTAT
1 AATATTATATATTAT
1976684 AATATTATATATTAT
1 AATATTATATATTAT
*
1976699 AATAATATA-ATTAT
1 AATATTATATATTAT
1976713 A
1 A
1976714 CCATACATTT
Statistics
Matches: 124, Mismatches: 24, Indels: 37
0.67 0.13 0.20
Matches are distributed among these distances:
13 18 0.15
14 40 0.32
15 34 0.27
16 5 0.04
17 3 0.02
18 18 0.15
19 2 0.02
20 4 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AATATTATATATTAT
Found at i:1976942 original size:20 final size:20
Alignment explanation
Indices: 1976919--1976982 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
1976909 AAATATATTA
1976919 AATAATATTATTTATTAAAT
1 AATAATATTATTTATTAAAT
1976939 AATAATAATAATATTT-TTAAATT
1 AATAAT-AT--TATTTATTAAA-T
* * *
1976962 ATTAAAATAATTTATTAAAT
1 AATAATATTATTTATTAAAT
1976982 A
1 A
1976983 TTATTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
20 12 0.33
21 7 0.19
22 7 0.19
23 10 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATATTATTTATTAAAT
Found at i:1976990 original size:14 final size:14
Alignment explanation
Indices: 1976960--1977015 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
1976950 TATTTTTAAA
*
1976960 TTATTAAA-ATAAT
1 TTATTAAATATTAT
1976973 TTATTAAATATTAT
1 TTATTAAATATTAT
*
1976987 TTATTTCAATATTA-
1 TTA-TTAAATATTAT
1977001 TTATTAAAATATTAT
1 TTATT-AAATATTAT
1977016 ATCTATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.28
14 17 0.47
15 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTAAATATTAT
Found at i:1977068 original size:30 final size:34
Alignment explanation
Indices: 1977025--1977095 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
1977015 TATCTATAAT
*
1977025 TTTA-TAAATAT-AAA-TATTA-AGATTAT-TGTA
1 TTTATTAAATATAAAATTATTACAAATTATAT-TA
1977055 TTTATTAAA-ATAAAATTATTACAAATTATATTA
1 TTTATTAAATATAAAATTATTACAAATTATATTA
1977088 TTTATTAA
1 TTTATTAA
1977096 TTGAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
30 6 0.17
31 7 0.20
32 5 0.14
33 16 0.46
34 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTATTAAATATAAAATTATTACAAATTATATTA
Found at i:1977129 original size:25 final size:25
Alignment explanation
Indices: 1977082--1977131 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1977072 ATTACAAATT
*
1977082 ATATTATTTATTAATTGAAATTAAA
1 ATATTATTTAGTAATTGAAATTAAA
*
1977107 ATATTATATTAGTAATT-ATATTAAA
1 ATATTAT-TTAGTAATTGAAATTAAA
1977132 TACTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
ATATTATTTAGTAATTGAAATTAAA
Found at i:1977176 original size:25 final size:27
Alignment explanation
Indices: 1977129--1977178 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1977119 TAATTATATT
*
1977129 AAATACTTAATAAATAATGATATTATA
1 AAATACTTAATAAATAATAATATTATA
*
1977156 AAATA-TTAA-AAATTATAATATTA
1 AAATACTTAATAAATAATAATATTA
1977179 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 4 0.19
27 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATACTTAATAAATAATAATATTATA
Found at i:1977201 original size:14 final size:14
Alignment explanation
Indices: 1977184--1977218 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1977174 TATTAAAATA
1977184 AAATATTATATTTT
1 AAATATTATATTTT
* *
1977198 AAATAATATGTTTT
1 AAATATTATATTTT
1977212 AAATATT
1 AAATATT
1977219 TAATAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AAATATTATATTTT
Found at i:1977287 original size:624 final size:614
Alignment explanation
Indices: 1976101--1977333 Score: 2256
Period size: 624 Copynumber: 2.0 Consensus size: 614
1976091 TTCTATTATA
1976101 TATTTCAATTTAATTGTCAACTTTGATATTAAATATTAGTTTAAATTGAACCAATTTATTTTTTC
1 TATTTCAATTTAATTGTCAACTTTGATATTAAATATTAGTTTAAATTGAACCAATTTATTTTTTC
1976166 ATTGATTAAATCTTTTAAAAAAAAAGTTAATTTAAGCCACAATTTAGGGCATGCTTGTTTGGATA
66 ATTGATTAAATCTTTT--AAAAAAAGTTAATTTAAGCCACAATTTAGGGCATGCTTGTTTGGATA
1976231 AGGTTACGTAAATAATATTTTATTAGTTGATATATTTTAAAAAATTTATTATAAATACCAAATAA
129 AGGTTACGTAAATAATATTTTATTAGTTGATATATTTTAAAAAATTTATTATAAATACCAAATAA
*
1976296 TATTATTTATTAAATAATAATAATAATATTTTTAAATTATTAAAATAATTTATTAAATATTTTTT
194 TATTATTTATTAAATAATAATAATAATATTTTTAAATTATTAAAATAATTTATTAAATATTATTT
1976361 ATTTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATATAAATATTAAGATTATTGT
259 ATTTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATATAAATATTAAGATTATTGT
1976426 ATTTATTAAAATAAAATTATTACAAATTATATTATTTATTTATTTATTAAAATTAAAATATTATA
324 ATTTATTAAAATAAAATTATTACAAATTATATTATTTATTTA--TATTAAAATTAAAATATTATA
1976491 TTAGTAATTATATTAAATACTTAATAAATAATGATATTATAAAATATTAAAAATTATAATATTAA
387 TTAGTAATTATATTAAATACTTAATAAATAATGATATTATAAAATATTAAAAATTATAATATTAA
1976556 AATAAAATATTATATTTTAAATAATATGTTTTAAATATTTAATAATTTAATAATATTATTTTTAT
452 AATAAAATATTATATTTTAAATAATATGTTTTAAATATTTAATAATTTAATAATATTATTTTTAT
*
1976621 AAAATTAATAAATAATATTAATTTTATTAATAATTTATTATATATTATTAACATAAAAATTATAA
517 AAAATTAATAAATAAAATTAATTTTATTAATAATTTA-T-TATA-TATTAACATAAAAATTATAA
1976686 TATTATATATTATAATAATATAATTATACCATACATT
579 TATTATATA-TATAATAATATAATTATACCATACATT
1976723 TATTTCAATTTAATTGTCAACTTTGATATTAAATATTAGTTTAAATTGAACCAATTTATTTTTTC
1 TATTTCAATTTAATTGTCAACTTTGATATTAAATATTAGTTTAAATTGAACCAATTTATTTTTTC
1976788 ATTGATTAAATCTTTT-AAAAAAGTTAATTTAAGCCACAATTTAGGGCATGCTTGTTTGGATAAG
66 ATTGATTAAATCTTTTAAAAAAAGTTAATTTAAGCCACAATTTAGGGCATGCTTGTTTGGATAAG
*
1976852 GTTACGTAAATAATTTTTTATTAGTTGATATATTTTAAAAAATTTATTATAAATACCAAATATAT
131 GTTACGTAAATAATATTTTATTAGTTGATATATTTTAAAAAATTTATTATAAATACC--------
1976917 TAAATAATATTATTTATTAAATAATAATAATAATATTTTTAAATTATTAAAATAATTTATTAAAT
188 -AAATAATATTATTTATTAAATAATAATAATAATATTTTTAAATTATTAAAATAATTTATTAAAT
1976982 ATTATTTATTTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATATAAATATTAAGA
252 ATTATTTATTTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATATAAATATTAAGA
*
1977047 TTATTGTATTTATTAAAATAAAATTATTACAAATTATATTATTTA-TTA-ATTGAAATTAAAATA
317 TTATTGTATTTATTAAAATAAAATTATTACAAATTATATTATTTATTTATATTAAAATTAAAATA
1977110 TTATATTAGTAATTATATTAAATACTTAATAAATAATGATATTATAAAATATTAAAAATTATAAT
382 TTATATTAGTAATTATATTAAATACTTAATAAATAATGATATTATAAAATATTAAAAATTATAAT
1977175 ATTAAAATAAAATATTATATTTTAAATAATATGTTTTAAATATTTAATAATTTAATAATATTATT
447 ATTAAAATAAAATATTATATTTTAAATAATATGTTTTAAATATTTAATAATTTAATAATATTATT
1977240 TTTATAAAATTAATAAATAAAATTAATTTTATTAATAATTTATTATATATTAACATAAAAATTAT
512 TTTATAAAATTAATAAATAAAATTAATTTTATTAATAATTTATTATATATTAACATAAAAATTAT
1977305 AATATTATATATATAATAATATAATTATA
577 AATATTATATATATAATAATATAATTATA
1977334 TATTAAAAAT
Statistics
Matches: 598, Mismatches: 4, Indels: 20
0.96 0.01 0.03
Matches are distributed among these distances:
619 104 0.17
620 18 0.03
621 29 0.05
622 85 0.14
623 1 0.00
624 185 0.31
627 3 0.01
628 173 0.29
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (614 bp):
TATTTCAATTTAATTGTCAACTTTGATATTAAATATTAGTTTAAATTGAACCAATTTATTTTTTC
ATTGATTAAATCTTTTAAAAAAAGTTAATTTAAGCCACAATTTAGGGCATGCTTGTTTGGATAAG
GTTACGTAAATAATATTTTATTAGTTGATATATTTTAAAAAATTTATTATAAATACCAAATAATA
TTATTTATTAAATAATAATAATAATATTTTTAAATTATTAAAATAATTTATTAAATATTATTTAT
TTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATATAAATATTAAGATTATTGTAT
TTATTAAAATAAAATTATTACAAATTATATTATTTATTTATATTAAAATTAAAATATTATATTAG
TAATTATATTAAATACTTAATAAATAATGATATTATAAAATATTAAAAATTATAATATTAAAATA
AAATATTATATTTTAAATAATATGTTTTAAATATTTAATAATTTAATAATATTATTTTTATAAAA
TTAATAAATAAAATTAATTTTATTAATAATTTATTATATATTAACATAAAAATTATAATATTATA
TATATAATAATATAATTATACCATACATT
Found at i:1977291 original size:27 final size:27
Alignment explanation
Indices: 1977218--1977292 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
1977208 TTTTAAATAT
* *
1977218 TTAATAATTTAATA-ATATTATTTTTA
1 TTAATAATTTATTATATATTAATTTTA
* * *
1977244 -TAA-AATTAATAAATAAAATTAATTTTA
1 TTAATAATTTAT-TAT-ATATTAATTTTA
1977271 TTAATAATTTATTATATATTAA
1 TTAATAATTTATTATATATTAA
1977293 CATAAAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
24 5 0.14
25 4 0.11
27 16 0.44
28 5 0.14
29 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAATAATTTATTATATATTAATTTTA
Found at i:1977327 original size:22 final size:21
Alignment explanation
Indices: 1977295--1977368 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
1977285 TATATTAACA
1977295 TAAAAATTATAATATTATATAT
1 TAAAAATTATAA-ATTATATAT
*
1977317 ATAATAA-TAT-AATTATATAT
1 -TAAAAATTATAAATTATATAT
*
1977337 TAAAAATTATAACATTACATTAT
1 TAAAAATTATAA-ATTATA-TAT
1977360 T-AAAATTAT
1 TAAAAATTAT
1977369 CAATAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 5 0.11
20 12 0.27
21 2 0.05
22 16 0.36
23 9 0.20
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAATTATAAATTATATAT
Found at i:1977347 original size:20 final size:21
Alignment explanation
Indices: 1977294--1977348 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
1977284 ATATATTAAC
1977294 ATAAAAATTATAATATTATATAT
1 ATAAAAATTAT-A-ATTATATAT
*
1977317 ATAATAA-TATAATTATATAT
1 ATAAAAATTATAATTATATAT
1977337 -TAAAAATTATAA
1 ATAAAAATTATAA
1977349 CATTACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 5 0.17
20 14 0.48
21 1 0.03
22 3 0.10
23 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAAATTATAATTATATAT
Found at i:1977425 original size:30 final size:28
Alignment explanation
Indices: 1977384--1977458 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
1977374 AATATAATTT
*
1977384 AATAATTAATATTTTTATTAAAGTGATATTAA
1 AATAA-TAATATTTTAATTAAA-T-ATA-TAA
*
1977416 AATAA-AATATTATAATTAAATATATAA
1 AATAATAATATTTTAATTAAATATATAA
1977443 AATAATAATATTTTAA
1 AATAATAATATTTTAA
1977459 ATATTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 8 0.21
28 12 0.31
29 1 0.03
30 13 0.33
32 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AATAATAATATTTTAATTAAATATATAA
Found at i:1977427 original size:13 final size:13
Alignment explanation
Indices: 1977409--1977454 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1977399 TATTAAAGTG
1977409 ATATTAAAATAAA
1 ATATTAAAATAAA
* *
1977422 ATATTATAATTAA
1 ATATTAAAATAAA
1977435 ATATATAAAATAATA
1 ATAT-TAAAATAA-A
1977450 ATATT
1 ATATT
1977455 TTAAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 15 0.56
14 7 0.26
15 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTAAAATAAA
Found at i:1977462 original size:22 final size:21
Alignment explanation
Indices: 1977412--1977462 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
1977402 TAAAGTGATA
*
1977412 TTAAA-ATAAAATATTATAAT
1 TTAAATATAAAATATAATAAT
* *
1977432 TAAATATATAAAATAATAATATT
1 TTAA-ATATAAAAT-ATAATAAT
1977455 TTAAATAT
1 TTAAATAT
1977463 TTATATCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 1 0.04
22 11 0.46
23 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAATATAAAATATAATAAT
Found at i:1977468 original size:28 final size:27
Alignment explanation
Indices: 1977409--1977461 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1977399 TATTAAAGTG
*
1977409 ATAT-TAAAATAAAATATTATAATTAA
1 ATATATAAAATAAAATATTATAAATAA
*
1977435 ATATATAAAATAATAATATTTTAAATA
1 ATATATAAAATAA-AATATTATAAATA
1977462 TTTATATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 8 0.35
28 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATATAAAATAAAATATTATAAATAA
Found at i:1977781 original size:20 final size:20
Alignment explanation
Indices: 1977756--1978015 Score: 135
Period size: 20 Copynumber: 12.6 Consensus size: 20
1977746 AATGACCAAT
1977756 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1977776 AAAATCGCAACGTAAAAAAG
1 AAAATCGCAACGCGATTTAG
***
1977796 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
1977816 ACAAATCGCAACACGAGCTTCC
1 A-AAATCGCAACGCGA-TTTAG
**
1977838 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1977861 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
1977881 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1977901 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1977921 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
1977941 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * *
1977964 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1977984 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1978004 AAAATCGCAACG
1 AAAATCGCAACG
1978016 TTAAAAAGAA
Statistics
Matches: 188, Mismatches: 43, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 133 0.71
21 22 0.12
22 4 0.02
23 28 0.15
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1977944 original size:83 final size:83
Alignment explanation
Indices: 1977842--1978015 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
1977832 GCTTCCAAGT
* ** * *
1977842 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* * *
1977907 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
*
1977925 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
*
1977990 GCAACGCGATTTAGAAAA
66 GCAACGCGATTGAGAAAA
1978008 TCGCAACG
1 TCGCAACG
1978016 TTAAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:1977949 original size:63 final size:63
Alignment explanation
Indices: 1977882--1978005 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
1977872 GCGATTGATT
* * * *
1977882 GAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGA
1977945 GAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1978006 AATCGCAACG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.20
Consensus pattern (63 bp):
GAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGA
Found at i:1978025 original size:20 final size:21
Alignment explanation
Indices: 1978002--1978042 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1977992 AACGCGATTT
1978002 AGAAAATCGCAAC-GTTAAAA
1 AGAAAATCGCAACGGTTAAAA
1978022 AGAAAATCGCAACGGTTAAAA
1 AGAAAATCGCAACGGTTAAAA
1978043 GAATAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (21 bp):
AGAAAATCGCAACGGTTAAAA
Found at i:1978134 original size:6 final size:6
Alignment explanation
Indices: 1978123--1978255 Score: 210
Period size: 6 Copynumber: 23.5 Consensus size: 6
1978113 GACACGTATT
1978123 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1978171 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1978218 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1978256 CGAGACGAGA
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 40 0.31
6 87 0.69
ACGTcount: A:0.29, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1978971 original size:6 final size:6
Alignment explanation
Indices: 1978945--1979077 Score: 227
Period size: 6 Copynumber: 22.5 Consensus size: 6
1978935 TCTCGTCTCG
1978945 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1978990 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
1979038 GGTCGT GGGTGGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT -GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1979078 AATACGTGTC
Statistics
Matches: 124, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
5 15 0.12
6 104 0.84
7 5 0.04
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1979180 original size:20 final size:20
Alignment explanation
Indices: 1979155--1979196 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1979145 TTTTTAACTA
*
1979155 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1979175 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1979195 TT
1 TT
1979197 ATAAATCGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1979208 original size:20 final size:20
Alignment explanation
Indices: 1979185--1979482 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
1979175 TTCTTTTTAA
*
1979185 CGTTGCGATTTTATAAATCG
1 CGTTGCGATTTTCTAAATCG
*
1979205 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1979225 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1979245 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1979265 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * * *
1979288 CGTTGCAACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1979308 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
1979328 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1979348 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1979371 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1979392 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1979410 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1979432 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1979452 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1979471 CGTTGCGATTTT
1 CGTTGCGATTTT
1979483 ATTGGTCATT
Statistics
Matches: 222, Mismatches: 45, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.71
21 15 0.07
22 5 0.02
23 26 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1979231 original size:40 final size:40
Alignment explanation
Indices: 1979187--1979378 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
1979177 CTTTTTAACG
* *
1979187 TTGCGATTTTATAAATCGCGTTGCGATTCTCTAAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
1979227 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
1979267 TTGCGATTCTCTTCTAAATCGCGTTGCAACTCTCTCAATCGCA
1 TTGCGA-T-T-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * **
1979310 TTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1979350 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
1979379 ACTTGGAAGC
Statistics
Matches: 122, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
40 70 0.57
41 2 0.02
42 4 0.03
43 46 0.38
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:1979307 original size:83 final size:83
Alignment explanation
Indices: 1979198--1979381 Score: 269
Period size: 83 Copynumber: 2.2 Consensus size: 83
1979188 TGCGATTTTA
* * * * * ** *
1979198 TAAATCGCGTTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGT
1 TAAATCGCGTTGCAACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAAT
1979263 CGCATTGCGATTCTCTTC
66 CGCATTGCGATTCTCTTC
*
1979281 TAAATCGCGTTGCAACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAAT
1 TAAATCGCGTTGCAACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAAT
*
1979346 CGCATTGCGATTTTCTTC
66 CGCATTGCGATTCTCTTC
1979364 TAAATCGCGTTGCGAACT
1 TAAATCGCGTTGC-AACT
1979382 TGGAAGCTCG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 86 0.96
84 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (83 bp):
TAAATCGCGTTGCAACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAAT
CGCATTGCGATTCTCTTC
Found at i:1979309 original size:63 final size:63
Alignment explanation
Indices: 1979187--1979338 Score: 202
Period size: 63 Copynumber: 2.5 Consensus size: 63
1979177 CTTTTTAACG
* * * * *
1979187 TTGCGATTTTATAAATCGCGTTGCGA-T-TC-TCTAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTTCTAAATCGCATTGCAACTCTCTCAATCGCA
* * * *
1979247 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCGTTGCAACTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTTCTAAATCGCATTGCAACTCTCTCAATCGCA
1979310 TTGCGATTCTATAAATCGCATTGCGATTC
1 TTGCGATTCTATAAATCGCATTGCGATTC
1979339 AATCAATCGC
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
60 21 0.27
61 1 0.01
62 2 0.03
63 53 0.69
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (63 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTTCTAAATCGCATTGCAACTCTCTCAATCGCA
Found at i:1979472 original size:19 final size:20
Alignment explanation
Indices: 1979432--1979482 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1979422 TTCTTTTTAA
*
1979432 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1979452 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1979471 CGTTGCGATTTT
1 CGTTGCGATTTT
1979483 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1985882 original size:29 final size:28
Alignment explanation
Indices: 1985832--1985895 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
1985822 TTTAAGGTTA
* * *
1985832 TTTTAAATTTTTTATTTCTTAAATATAT
1 TTTTTAATTTTTAAATTCTTAAATATAT
1985860 AGTTTTTAATTTTTAAATT-TTAAATATAT
1 --TTTTTAATTTTTAAATTCTTAAATATAT
1985889 TTTTTAA
1 TTTTTAA
1985896 ATTTATCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
29 10 0.32
30 14 0.45
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTAATTTTTAAATTCTTAAATATAT
Done.