Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 13 of 29
Found at i:1801941 original size:13 final size:13
Alignment explanation
Indices: 1801918--1801942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1801908 GCATAAGTGT
1801918 TGTATCGATACAA
1 TGTATCGATACAA
1801931 TGTATCGATACA
1 TGTATCGATACA
1801943 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1801955 original size:19 final size:18
Alignment explanation
Indices: 1801899--1801961 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1801889 ATCGATATAA
*
1801899 TGTATCGATGCATAAGTGT
1 TGTATCGATACATAAGT-T
1801918 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1801931 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1801950 TGTATCGATACA
1 TGTATCGATACA
1801962 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1802032 original size:13 final size:13
Alignment explanation
Indices: 1802014--1802041 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1802004 ACTACTCAAA
1802014 TGTATCGATACAT
1 TGTATCGATACAT
1802027 TGTATCGATACAT
1 TGTATCGATACAT
1802040 TG
1 TG
1802042 ATCTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1808065 original size:2 final size:2
Alignment explanation
Indices: 1808058--1808090 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1808048 CGTCAAAGAA
1808058 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
1808091 AACACGTTAA
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:1809971 original size:118 final size:118
Alignment explanation
Indices: 1809786--1810021 Score: 341
Period size: 118 Copynumber: 2.0 Consensus size: 118
1809776 TATCATTAAA
* * *
1809786 TACTAATAACTTTTAACCCGTATCATCAAGTACTAATTTCGGCATAATTGCATAATTTGAGGATA
1 TACTAATAACTTTTAACCCATATCATCAAGTACTAATTTCGGCATAAGTGCATAATTTCAGGATA
* * *
1809851 ATTAAGGTAAGCTGTTTTATTTTAGTGCTCCTATTATTATTTGGCTATAGGTT
66 ATTAAGGTAAGCTGTTTTATTTTAGTACTCATAATATTATTTGGCTATAGGTT
* * *
1809904 TACTAATTAACTTTTAATCCATGTCATTGAA-TACTAATTTCGGCAT-AGTGCATAATTTCAGGA
1 TACTAA-TAACTTTTAACCCATATCA-TCAAGTACTAATTTCGGCATAAGTGCATAATTTCAGGA
* *
1809967 TAATTAATGTAAGTTGTTTTATTTTAGTACTCATAATATTATTTGGCTATAGGTT
64 TAATTAAGGTAAGCTGTTTTATTTTAGTACTCATAATATTATTTGGCTATAGGTT
1810022 ATAGGTTTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 71 0.68
119 31 0.30
120 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (118 bp):
TACTAATAACTTTTAACCCATATCATCAAGTACTAATTTCGGCATAAGTGCATAATTTCAGGATA
ATTAAGGTAAGCTGTTTTATTTTAGTACTCATAATATTATTTGGCTATAGGTT
Found at i:1810196 original size:17 final size:19
Alignment explanation
Indices: 1810174--1810208 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1810164 AAATCAATGA
1810174 TAATCAG-ATA-AATTAAT
1 TAATCAGAATATAATTAAT
1810191 TAATCAGAATATAATTAA
1 TAATCAGAATATAATTAA
1810209 AAAAATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (19 bp):
TAATCAGAATATAATTAAT
Found at i:1812027 original size:2 final size:2
Alignment explanation
Indices: 1812015--1812051 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1812005 CAATACATGT
*
1812015 TA TA CA 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
1812052 GAATTTCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1816737 original size:16 final size:16
Alignment explanation
Indices: 1816716--1816747 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1816706 ATCATCAAAA
1816716 TAATCCTAAAACTGCC
1 TAATCCTAAAACTGCC
1816732 TAATCCTAAAACTGCC
1 TAATCCTAAAACTGCC
1816748 ACATTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
TAATCCTAAAACTGCC
Found at i:1817628 original size:13 final size:13
Alignment explanation
Indices: 1817612--1817637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1817602 TAGAGTAGTT
1817612 TTGTATCGATACA
1 TTGTATCGATACA
1817625 TTGTATCGATACA
1 TTGTATCGATACA
1817638 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1823600 original size:38 final size:38
Alignment explanation
Indices: 1823533--1823605 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1823523 GCCGTAGTAC
*
1823533 AAAACTATACCTAACGAACTCAGTTTCAATAGAAAGTGA
1 AAAACTATACCTAACGAACTCAATTTCAAT-GAAAGTGA
*
1823572 AAAACTA-ATCCTAATG-ACTCAATTTCAATGAAAG
1 AAAACTATA-CCTAACGAACTCAATTTCAATGAAAG
1823606 GTATGAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 5 0.16
38 13 0.42
39 13 0.42
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.25
Consensus pattern (38 bp):
AAAACTATACCTAACGAACTCAATTTCAATGAAAGTGA
Found at i:1824630 original size:11 final size:11
Alignment explanation
Indices: 1824605--1824655 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
1824595 CATTGGAAGA
1824605 TCTTTCTTTTCT
1 TCTTT-TTTTCT
*
1824617 TCTTTTTTTTT
1 TCTTTTTTTCT
1824628 TCTTTTTTTC-
1 TCTTTTTTTCT
*
1824638 CCTTTTTTTC-
1 TCTTTTTTTCT
1824648 -CTTTTTTT
1 TCTTTTTTT
1824656 TGTTTTTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.22
10 9 0.25
11 14 0.39
12 5 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:1824631 original size:19 final size:19
Alignment explanation
Indices: 1824607--1824652 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1824597 TTGGAAGATC
**
1824607 TTTCTTTTCTTCTTTTTTT
1 TTTCTTTTCTTCCCTTTTT
*
1824626 TTTCTTTTTTTCCCTTTTT
1 TTTCTTTTCTTCCCTTTTT
*
1824645 TTCCTTTT
1 TTTCTTTT
1824653 TTTTGTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTCTTCCCTTTTT
Found at i:1824633 original size:9 final size:9
Alignment explanation
Indices: 1824607--1824662 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
1824597 TTGGAAGATC
1824607 TTTCTTTTCT
1 TTTCTTTT-T
1824617 TCTT-TTTTT
1 T-TTCTTTTT
1824626 TTTCTTTTT
1 TTTCTTTTT
*
1824635 TTCCCTTTTT
1 TT-TCTTTTT
*
1824645 TTCCTTTTT
1 TTTCTTTTT
*
1824654 TTTGTTTTT
1 TTTCTTTTT
1824663 CCTTTTTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
8 2 0.05
9 23 0.57
10 13 0.32
11 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1829981 original size:110 final size:110
Alignment explanation
Indices: 1829849--1830079 Score: 302
Period size: 110 Copynumber: 2.1 Consensus size: 110
1829839 GATTACATAT
* ** * * **
1829849 TTTATTTATTTAAATTATTTTTTTAAAAATATATTTTAAGAGCATGTAGCATGTGATCAATCCCG
1 TTTATTTATTTAAATTAATTTTTTAAAAATATATTTTAAGAGCACATAACAAGTGATCAATCCAA
1829914 TACATGAAATTTATTTATTTTTT-ACGAATTGATGATATAATTTTA
66 TACATGAAATTTATTTATTTTTTGA-GAATTGATGATATAATTTTA
* * * * * *
1829959 TTTATTTATTTGAATTAATTTTTTCAAAATATATTTTAAGAGTACATAACAAGTTATTAATCTAA
1 TTTATTTATTTAAATTAATTTTTTAAAAATATATTTTAAGAGCACATAACAAGTGATCAATCCAA
* * *
1830024 TATATGAAGTTTATTTATTTTTTGAGGATTGATGATATAATTTTA
66 TACATGAAATTTATTTATTTTTTGAGAATTGATGATATAATTTTA
1830069 TTTATTTATTT
1 TTTATTTATTT
1830080 TATTTTGCTC
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 103 0.99
111 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.51
Consensus pattern (110 bp):
TTTATTTATTTAAATTAATTTTTTAAAAATATATTTTAAGAGCACATAACAAGTGATCAATCCAA
TACATGAAATTTATTTATTTTTTGAGAATTGATGATATAATTTTA
Found at i:1831094 original size:26 final size:24
Alignment explanation
Indices: 1831065--1831114 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1831055 AATTAAAAAT
1831065 TTTAAATTAATCTAATATTAAATCAA
1 TTTAAATTAA-CTAA-ATTAAATCAA
* *
1831091 TTTAATTTAACTAAATTCAATCAA
1 TTTAAATTAACTAAATTAAATCAA
1831115 GTCTTCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 4 0.18
26 9 0.41
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTAAATTAACTAAATTAAATCAA
Found at i:1831438 original size:2 final size:2
Alignment explanation
Indices: 1831433--1831462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1831423 ATGTGTGTAC
1831433 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
1831463 GAAAATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1831935 original size:40 final size:40
Alignment explanation
Indices: 1831886--1831965 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
1831876 TAGATGCTTC
* *
1831886 ATTCTTGTATGAAAGATGTAGCACATA-GTGTGTCAAAATA
1 ATTCATGTATCAAAGATGTAGCACATAGGT-TGTCAAAATA
1831926 ATTCATGTATCAAAGATGTAGCACATAGGTTGTCAAAATA
1 ATTCATGTATCAAAGATGTAGCACATAGGTTGTCAAAATA
1831966 TATAGTAGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (40 bp):
ATTCATGTATCAAAGATGTAGCACATAGGTTGTCAAAATA
Found at i:1832599 original size:59 final size:62
Alignment explanation
Indices: 1832536--1832650 Score: 148
Period size: 59 Copynumber: 1.9 Consensus size: 62
1832526 TTTAGTAAGG
* *
1832536 TTTCATTTTTATGGATGAA-ATTTAAAAGTTATA-TTTA-TCATCTATAA-TTTTTACTAATA
1 TTTCATTTTTATCGATGAATA-TTAAAAGTTATATTTTATTCATCCATAACTTTTTACTAATA
* * *
1832595 TTTCATTTTTATCTATGAGTATTAATAGTTATATTTTATTCATCCATAACTTTTTA
1 TTTCATTTTTATCGATGAATATTAAAAGTTATATTTTATTCATCCATAACTTTTTA
1832651 AAATAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 27 0.57
60 5 0.11
61 9 0.19
62 6 0.13
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (62 bp):
TTTCATTTTTATCGATGAATATTAAAAGTTATATTTTATTCATCCATAACTTTTTACTAATA
Found at i:1832661 original size:31 final size:30
Alignment explanation
Indices: 1832625--1832698 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
1832615 ATTAATAGTT
* *
1832625 ATATTTTATTCATCCATAACTTTTTAAAATA
1 ATATTTTATTCATCCATAACCTTTCAAAA-A
*
1832656 ATA-TTTATT-GTCCATAACCTTTCAAAAA
1 ATATTTTATTCATCCATAACCTTTCAAAAA
1832684 AT-TTTATGATTCATC
1 ATATTT-T-ATTCATC
1832699 ATTTTTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
28 5 0.14
29 16 0.46
30 9 0.26
31 5 0.14
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (30 bp):
ATATTTTATTCATCCATAACCTTTCAAAAA
Found at i:1832671 original size:29 final size:27
Alignment explanation
Indices: 1832627--1832690 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
1832617 TAATAGTTAT
* * *
1832627 ATTTTATTCATCCATAACTTTTTAAAATA
1 ATTTTATT-GTCCATAACCTTTCAAAA-A
1832656 ATATTTATTGTCCATAACCTTTCAAAAA
1 AT-TTTATTGTCCATAACCTTTCAAAAA
1832684 ATTTTAT
1 ATTTTAT
1832691 GATTCATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 5 0.16
28 3 0.10
29 17 0.55
30 6 0.19
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTATTGTCCATAACCTTTCAAAAA
Found at i:1834953 original size:79 final size:78
Alignment explanation
Indices: 1834824--1835242 Score: 360
Period size: 79 Copynumber: 5.3 Consensus size: 78
1834814 GGATTGGTGA
* * *
1834824 AAAATC-GATGTTTTAGAAATAAAA-TCGGGGTTAGAGTATTCCCTCAGAAATAACAGGGTTGGA
1 AAAATCAG-TGTTTTAAAAATAAAACT-GAGGTTGGAGTA-TCCCTCAGAAATAACAGGGTTGGA
1834887 GTATCTCCGATGGCGA-
63 GTATCTCCGATGG-GAG
* *
1834903 AAAATCAAT-TATTTAAAAATAAAACT-AGAGTTGGAGTATCTCCTCAGAAATAATAGGGTTGGA
1 AAAATCAGTGT-TTTAAAAATAAAACTGAG-GTTGGAGTATC-CCTCAGAAATAACAGGGTTGGA
*
1834966 GTATC-CTCGATGGCAG
63 GTATCTC-CGATGGGAG
** * * * *
1834982 AAAATTGGTATTTTAGAAATAAAACTGGGGTTAGAGTATCCCCTC-GAAAATAAC-GAGGTTGGA
1 AAAATCAGTGTTTTAAAAATAAAACTGAGGTTGGAGTAT-CCCTCAG-AAATAACAG-GGTTGGA
* *
1835045 GTATCTCTGATGGTAG
63 GTATCTCCGATGGGAG
* * ** * *
1835061 AAAATCAGTGTTTTAGAAATAAAACTGAGGTTGGAGTATCCCTTCAAAAATAATTGAGTTGAAGT
1 AAAATCAGTGTTTTAAAAATAAAACTGAGGTTGGAGTATCCC-TCAGAAATAACAGGGTTGGAGT
*
1835126 AT-TCCTGATGGTAG
65 ATCTCC-GATGGGAG
*
1835140 AAAATCAGTGTTTTAAAAATAAAA-TCGAGGTTTGAGTATCCCTTC-GAAAATAACAGGGTTGGA
1 AAAATCAGTGTTTTAAAAATAAAACT-GAGGTTGGAGTATCCC-TCAG-AAATAACAGGGTTGGA
1835203 GTATC-CTCGATGGTG-G
63 GTATCTC-CGATGG-GAG
* * *
1835219 AAAATCGGTGTTTGAGAAATAAAA
1 AAAATCAGTGTTTTAAAAATAAAA
1835243 ACATCAATAA
Statistics
Matches: 282, Mismatches: 36, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
78 14 0.05
79 261 0.93
80 7 0.02
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (78 bp):
AAAATCAGTGTTTTAAAAATAAAACTGAGGTTGGAGTATCCCTCAGAAATAACAGGGTTGGAGTA
TCTCCGATGGGAG
Found at i:1835112 original size:158 final size:158
Alignment explanation
Indices: 1834834--1835242 Score: 494
Period size: 158 Copynumber: 2.6 Consensus size: 158
1834824 AAAATCGATG
* *
1834834 TTTTAGAAATAAAATCGGGGTTAGAGTATTCCCTC-AGAAATAACAGGGTTGGAGTATCTCCGAT
1 TTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGA-AAATAACAGGGTTGGAGTATCTCTGAT
* * * * *
1834898 GG-CGAAAAATCAAT-TATTTAAAAATAAAACTAGAGTTGGAGTATCTCCTCAGAAATAATAGGG
65 GGTAG-AAAATCAGTGT-TTTAGAAATAAAACTAGAGTTGGAGTATCTCCTCAAAAATAATAGAG
* **
1834961 TTGGAGTA-TCCTCGATGGCAGAAAATTGGTA
128 TTGAAGTATTCCT-GATGGCAGAAAATCAGTA
1834992 TTTTAGAAATAAAA-CTGGGGTTAGAGTATCCCCTCGAAAATAAC-GAGGTTGGAGTATCTCTGA
1 TTTTAGAAATAAAATC-GGGGTTAGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCTCTGA
*
1835055 TGGTAGAAAATCAGTGTTTTAGAAATAAAACT-GAGGTTGGAGTATC-CCTTCAAAAATAATTGA
64 TGGTAGAAAATCAGTGTTTTAGAAATAAAACTAGA-GTTGGAGTATCTCC-TCAAAAATAATAGA
* *
1835118 GTTGAAGTATTCCTGATGGTAGAAAATCAGTG
127 GTTGAAGTATTCCTGATGGCAGAAAATCAGTA
* * * *
1835150 TTTTAAAAATAAAATCGAGGTTTGAGTATCCCTTCGAAAATAACAGGGTTGGAGTATC-CTCGAT
1 TTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCTCT-GAT
* * *
1835214 GGTGGAAAATCGGTGTTTGAGAAATAAAA
65 GGTAGAAAATCAGTGTTTTAGAAATAAAA
1835243 ACATCAATAA
Statistics
Matches: 220, Mismatches: 20, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
157 8 0.04
158 203 0.92
159 9 0.04
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (158 bp):
TTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCTCTGATG
GTAGAAAATCAGTGTTTTAGAAATAAAACTAGAGTTGGAGTATCTCCTCAAAAATAATAGAGTTG
AAGTATTCCTGATGGCAGAAAATCAGTA
Found at i:1837484 original size:20 final size:20
Alignment explanation
Indices: 1837456--1837493 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1837446 TGCTTGAATG
*
1837456 TATCGATACATTTACTTATA
1 TATCAATACATTTACTTATA
*
1837476 TATCAATACATTTCCTTA
1 TATCAATACATTTACTTA
1837494 GTAATGTGTA
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:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (20 bp):
TATCAATACATTTACTTATA
Found at i:1838397 original size:61 final size:61
Alignment explanation
Indices: 1838098--1838399 Score: 331
Period size: 61 Copynumber: 5.0 Consensus size: 61
1838088 TTAAGATGGA
* * * *
1838098 AAAGGAGAGAGGCGTCCTACTCTTTAAGGACTAAAAGCTGCCACCAACTTGTGTGGGCTTTT
1 AAAGGAGA-AGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTG
** * * * *
1838160 AAAAAAGAAGTGC--CCTGCTCTTCGAGAACTAAAA-AGTGCCACCAACTTGTGTGGCCTTTA
1 AAAGGAGAAG-GCGTCCTGCTCTTTGAGGACTAAAAGA-TGCCACCAACTTGTGTGGGCTTTG
* * * *
1838220 AAAAGAAAATGCGTCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTG
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTG
* * * * * * *
1838281 CAAGGAGAAGGCGTCCTACTCTTCGAAGATTGAAAGATGCTACCAACTTGTGTGGGCTTTG
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTG
** * *
1838342 AAAGGAGAAGGCGTTTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCT
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCT
1838400 CGATGATTAC
Statistics
Matches: 198, Mismatches: 37, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
59 2 0.01
60 46 0.23
61 141 0.71
62 9 0.05
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTG
Found at i:1841322 original size:34 final size:34
Alignment explanation
Indices: 1841284--1841350 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1841274 CTTTTTCATT
*
1841284 TTTTTGTTTTCCCATCGATTCAGACCC-GGGAAAG
1 TTTTTATTTTCCCATCGATTCAG-CCCTGGGAAAG
1841318 TTTTTATTTTCCCATCGATTCAGCCCTGGGAAA
1 TTTTTATTTTCCCATCGATTCAGCCCTGGGAAA
1841351 CAACCTCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (34 bp):
TTTTTATTTTCCCATCGATTCAGCCCTGGGAAAG
Found at i:1841613 original size:42 final size:42
Alignment explanation
Indices: 1841553--1841962 Score: 291
Period size: 42 Copynumber: 9.7 Consensus size: 42
1841543 CCTACCCTTC
*
1841553 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAA
1 AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAA
* ** * *
1841595 AGTCTACCTGTCGACTTTGACTGTAGAGACTTTCC-TATCCCT-C
1 AGTCTGCCTGTCGACTTTGACCCTAGAGAC-TGCCTTAT--CTAA
* *
1841638 AGTCTACCTGTCGATTTTGACCCT-GAAGACTGCCTTATCTAA
1 AGTCTGCCTGTCGACTTTGACCCTAG-AGACTGCCTTATCTAA
* * **
1841680 AGTTTGCCTGTCGGCTTTGACCCT-GAAGACTTTCTTATCTAA
1 AGTCTGCCTGTCGACTTTGACCCTAG-AGACTGCCTTATCTAA
* * * * * *
1841722 AGTCTGCTTGTC-AGTTTTGACACTAGAGACTTTCC-TACCCT-C
1 AGTCTGCCTGTCGA-CTTTGACCCTAGAGAC-TGCCTTA-TCTAA
* * * * *
1841764 AGTTTGTCTGTC-AGCTTTGACCTTAGAGACTATCC-CATCTAA
1 AGTCTGCCTGTCGA-CTTTGACCCTAGAGACT-GCCTTATCTAA
* * * *
1841806 AGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTTATCTAA
1 AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAA
* * * *
1841848 AGTCTGCCTGTCGACTTT-AGCCTTGGACACTGCCTCATCTAA
1 AGTCTGCCTGTCGACTTTGA-CCCTAGAGACTGCCTTATCTAA
** * * * * *
1841890 AGTCTATCTGCCGACTTTGATCGTAGAGAATGCCTCATCTAA
1 AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAA
* *
1841932 AGTCTGCCTATCGACTTTGACCCTGGAGACT
1 AGTCTGCCTGTCGACTTTGACCCTAGAGACT
1841963 TTCCTACCCT
Statistics
Matches: 291, Mismatches: 61, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
41 8 0.03
42 243 0.84
43 38 0.13
44 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (42 bp):
AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAA
Found at i:1841836 original size:126 final size:127
Alignment explanation
Indices: 1841553--1841962 Score: 392
Period size: 126 Copynumber: 3.2 Consensus size: 127
1841543 CCTACCCTTC
* * **
1841553 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTACCTGTCGACTTTGACTG
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGACTTTGACAC
* *
1841618 TAGAGACTTTCCTATCCCTCAGTCTACCTGTCGATTTTGACCCTGAAGACTGCCTTATCTAA
66 TAGAGACTTTCCTATCCCTCAGTCTACCTGTCGACTTTGACCCTGAAGACTGCCTCATCTAA
* * ** * *
1841680 AGTTTGCCTGTCGGCTTTGACCCTGAAGACTTTCTTATCTAAAGTCTGCTTGTC-AGTTTTGACA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGA-CTTTGACA
* ** * *
1841744 CTAGAGACTTTCCTA-CCCTCAGTTTGTCTGTC-AGCTTTGA-CCTTAGAGACTATCC-CATCTA
65 CTAGAGACTTTCCTATCCCTCAGTCTACCTGTCGA-CTTTGACCCTGA-AGACT-GCCTCATCTA
1841805 A
127 A
* *
1841806 AGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGACTTT-AGC-
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGACTTTGA-CA
* * * * * * * * *
1841869 CTTG-GACACTGCCTCAT--CTAAAGTCTATCTGCCGACTTTGATCGT-AGAGAATGCCTCATCT
65 CTAGAGAC-TTTCCT-ATCCCT-CAGTCTACCTGTCGACTTTGACCCTGA-AGACTGCCTCATCT
1841930 AA
126 AA
* *
1841932 AGTCTGCCTATCGACTTTGACCCTGGAGACT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACT
1841963 TTCCTACCCT
Statistics
Matches: 233, Mismatches: 37, Indels: 27
0.78 0.12 0.09
Matches are distributed among these distances:
124 3 0.01
125 17 0.07
126 140 0.60
127 73 0.31
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (127 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGACTTTGACAC
TAGAGACTTTCCTATCCCTCAGTCTACCTGTCGACTTTGACCCTGAAGACTGCCTCATCTAA
Found at i:1841859 original size:84 final size:83
Alignment explanation
Indices: 1841553--1842004 Score: 337
Period size: 84 Copynumber: 5.4 Consensus size: 83
1841543 CCTACCCTTC
*
1841553 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTACCTGTCGACTTTGA-CT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTGTCG-CTTTGACCT
*
1841617 GTAGAGACTTTCCTATCCCT-C
65 -TAGAGACTTTCCTAT--CTAA
* ** *
1841638 AGTCTACCTGTCGATTTTGACCCT-GAAGACTGCCTTATCTAAAGTTTGCCTGTCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTGCCTTATCTAAAGTCTGCCTGTC-GCTTTGACC
* *
1841702 CT-GAAGACTTTCTTATCTAA
64 TTAG-AGACTTTCCTATCTAA
* * * * * * * * *
1841722 AGTCTGCTTGTCAGTTTTGACACTAGAGACTTTCC-TACCCT-CAGTTTGTCTGTCAGCTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTTA-TCTAAAGTCTGCCTGTC-GCTTTGAC
* *
1841785 CTTAGAGACTATCCCATCTAA
63 CTTAGAGACTTTCCTATCTAA
* * *
1841806 AGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTTATCTAAAGTCTGCCTGTCGACTTT-AGCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTGTCG-CTTTGA-CC
* * *
1841870 TTGGACAC-TGCCTCATCTAA
64 TTAGAGACTTTCCT-ATCTAA
** * * * * * * * *
1841890 AGTCTATCTGCCGACTTTGATCGTAGAGAATGCCTCATCTAAAGTCTGCCTATCGACTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTGTCG-CTTTGACCT
* * *
1841955 TGGAGACTTTCCTACCCT-T
65 TAGAGACTTTCCTA-TCTAA
* * *
1841974 AGTCTCCCTGTTGGCTTTGACCTTAGAGACT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT
1842005 ATCCCAGCTT
Statistics
Matches: 287, Mismatches: 63, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
83 11 0.04
84 195 0.68
85 79 0.28
86 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (83 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTGTCGCTTTGACCTT
AGAGACTTTCCTATCTAA
Found at i:1842141 original size:42 final size:41
Alignment explanation
Indices: 1842012--1842467 Score: 210
Period size: 42 Copynumber: 10.8 Consensus size: 41
1842002 ACTATCCCAG
* * * *
1842012 CTTTGACCCTAGAGATTGCCTTATCTAAAGTCTTCTTGTCGG
1 CTTTGACCCTAGAGACTGCC-TATCTAAAGTCTGCCTGTCGA
* * * *
1842054 CTTTGACCCTGGAGACTTTCCTATCCCT-CAGTCTGCCTATCGA
1 CTTTGACCCTAGAGAC-TGCCTAT--CTAAAGTCTGCCTGTCGA
1842097 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTGTCGA
1 CTTTGACCCTAGAGACTGCCT-ATCTAAAGTCTGCCTGTCGA
* * * *
1842139 CTTTGATCCTAGAGACTTTCCTATCCT-CAGTCTGCCTGTCGG
1 CTTTGACCCTAGAGAC-TGCCTAT-CTAAAGTCTGCCTGTCGA
* * * *
1842181 CTTTGACCTTGGAGAGTGCCTTATCTAAAGTCTGCCTGT-TA
1 CTTTGACCCTAGAGACTGCC-TATCTAAAGTCTGCCTGTCGA
* * * *
1842222 GCTTTGACCCTGGAGAGTTTCCTATCCT-CAGTCTGCCTGTC-A
1 -CTTTGACCCTAGAGA-CTGCCTAT-CTAAAGTCTGCCTGTCGA
* * * * * * *
1842264 GCTTTGACCTTGGAGACTACCCGATCCAAAGTCTACCTGT-TA
1 -CTTTGACCCTAGAGACT-GCCTATCTAAAGTCTGCCTGTCGA
* * * * * * *
1842306 GCTTTGACCCTGGAGATTTTCCTATCCCT-CAGTTTGCTTGTCGG
1 -CTTTGACCCTAGAGA-CTGCCTAT--CTAAAGTCTGCCTGTCGA
* * * * *
1842350 CTTTGACCTTGGAAACTGCCTTATCTAAAGTTTGCCTGT-TA
1 CTTTGACCCTAGAGACTGCC-TATCTAAAGTCTGCCTGTCGA
* * * * * * *
1842391 GCTTTGGCCTTGGAGACTTTCCTATCCCTCAA-TCTGCCTATCGG
1 -CTTTGACCCTAGAGAC-TGCCTAT--CTAAAGTCTGCCTGTCGA
* *
1842435 CTTTGACCCTGGAGATTGCCTTATCTAAAGTCT
1 CTTTGACCCTAGAGACTGCC-TATCTAAAGTCT
1842468 ACCCATCGGC
Statistics
Matches: 318, Mismatches: 67, Indels: 58
0.72 0.15 0.13
Matches are distributed among these distances:
41 15 0.05
42 204 0.64
43 92 0.29
44 7 0.02
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.35
Consensus pattern (41 bp):
CTTTGACCCTAGAGACTGCCTATCTAAAGTCTGCCTGTCGA
Found at i:1842213 original size:84 final size:85
Alignment explanation
Indices: 1842011--1842467 Score: 578
Period size: 85 Copynumber: 5.4 Consensus size: 85
1842001 GACTATCCCA
* * * * **
1842011 GCTTTGACCCTAGAGATTGCCTTATCTAAAGTCTTCTTGTCGGCTTTGACCCTGGAGACTTTCCT
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGACTTTCCT
*
1842076 ATCCCTCAGTCTGCCTATCG
66 ATCCCTCAGTCTGCCTGTCG
* * * * * *
1842096 ACTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTG-TCGACTTTGATCCTAGAGACTTTCC
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAG-CTTTGACCCTGGAGACTTTCC
1842160 TAT-CCTCAGTCTGCCTGTCG
65 TATCCCTCAGTCTGCCTGTCG
* * *
1842180 GCTTTGACCTTGGAGAGTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGAGTTTCCT
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGACTTTCCT
*
1842245 AT-CCTCAGTCTGCCTGTCA
66 ATCCCTCAGTCTGCCTGTCG
* * ** * * *
1842264 GCTTTGACCTTGGAGACTACCCGATCCAAAGTCTACCTGTTAGCTTTGACCCTGGAGATTTTCCT
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGACTTTCCT
* *
1842329 ATCCCTCAGTTTGCTTGTCG
66 ATCCCTCAGTCTGCCTGTCG
* * * * *
1842349 GCTTTGACCTTGGAAACTGCCTTATCTAAAGTTTGCCTGTTAGCTTTGGCCTTGGAGACTTTCCT
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGACTTTCCT
* *
1842414 ATCCCTCAATCTGCCTATCG
66 ATCCCTCAGTCTGCCTGTCG
*
1842434 GCTTTGACCCTGGAGATTGCCTTATCTAAAGTCT
1 GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCT
1842468 ACCCATCGGC
Statistics
Matches: 321, Mismatches: 48, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
84 148 0.46
85 173 0.54
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.35
Consensus pattern (85 bp):
GCTTTGACCCTGGAGACTGCCTTATCTAAAGTCTGCCTGTTAGCTTTGACCCTGGAGACTTTCCT
ATCCCTCAGTCTGCCTGTCG
Found at i:1842966 original size:8 final size:8
Alignment explanation
Indices: 1842955--1843004 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1842945 TTATAATAAG
1842955 TAAAAAAA
1 TAAAAAAA
*
1842963 TAAAAATA
1 TAAAAAAA
1842971 TAATAATAAA
1 TAA-AA-AAA
1842981 -AATAAAAA
1 TAA-AAAAA
1842989 T-AAAAAA
1 TAAAAAAA
1842996 TAAAAAAA
1 TAAAAAAA
1843004 T
1 T
1843005 CAAACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 6 0.17
8 21 0.58
9 7 0.19
10 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1842969 original size:6 final size:6
Alignment explanation
Indices: 1842958--1843001 Score: 61
Period size: 6 Copynumber: 6.8 Consensus size: 6
1842948 TAATAAGTAA
1842958 AAAAAT AAAAAT ATAATAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT AAAAAT A-AA-AAT AAAAAT AAAAAT -AAAAAT AAAAA
1843002 AATCAAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 21 0.60
7 10 0.29
8 4 0.11
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:1842971 original size:26 final size:26
Alignment explanation
Indices: 1842939--1842998 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
1842929 TATTTGATAT
* *
1842939 AAAATATTATAATAAGTAA-AAAAATA
1 AAAATATAATAATAA-AAATAAAAATA
1842965 AAAATATAATAATAAAAATAAAAATA
1 AAAATATAATAATAAAAATAAAAATA
1842991 AAAA-ATAA
1 AAAATATAA
1842999 AAAAATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAATATAATAATAAAAATAAAAATA
Found at i:1842973 original size:20 final size:20
Alignment explanation
Indices: 1842947--1843021 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1842937 ATAAAATATT
1842947 ATAATAAGTAAAAAAATAAAA
1 ATAATAA-TAAAAAAATAAAA
1842968 AT-ATAATAATAAAAATAAAA
1 ATAATAATAA-AAAAATAAAA
* *
1842988 ATAAAAAATAAAAAAATCAAA
1 AT-AATAATAAAAAAATAAAA
*
1843009 CTAA-AA-AAAAAAA
1 ATAATAATAAAAAAA
1843022 GGGAGCTGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 7 0.15
19 5 0.10
20 18 0.38
21 12 0.25
22 6 0.12
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.17
Consensus pattern (20 bp):
ATAATAATAAAAAAATAAAA
Found at i:1843249 original size:19 final size:18
Alignment explanation
Indices: 1843218--1843267 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1843208 ACTTAAGAAA
*
1843218 CATTTGATGCATTGCATT
1 CATTTCATGCATTGCATT
*
1843236 CATTTCATTGCATTGCTTT
1 CATTTCA-TGCATTGCATT
1843255 CATTTCATGCATT
1 CATTTCATGCATT
1843268 CATACGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (18 bp):
CATTTCATGCATTGCATT
Found at i:1857060 original size:4 final size:4
Alignment explanation
Indices: 1857044--1857089 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
1857034 AAACAGAACA
*
1857044 AAAT AAAT TAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1857090 GCACCTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1858635 original size:21 final size:20
Alignment explanation
Indices: 1858610--1858663 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
1858600 TTACAAGCCA
1858610 ATGTATCGATACAAT-TTGGT
1 ATGTATCGATACAATCTT-GT
1858630 CATGTATCGATAC-ATCTTGT
1 -ATGTATCGATACAATCTTGT
1858650 ATGTATCGATACAA
1 ATGTATCGATACAA
1858664 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.39
20 5 0.16
21 14 0.45
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATCTTGT
Found at i:1858757 original size:21 final size:20
Alignment explanation
Indices: 1858704--1858779 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 20
1858694 GCCAATCACT
*
1858704 TGTATCGATACATTCT-TTGCA
1 TGTATCGATACATT-TGGT-CA
*
1858725 AGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGGTCA
1858745 TGTATCGATTACATTTGGTCA
1 TGTATCGA-TACATTTGGTCA
1858766 TGTATCGATACATT
1 TGTATCGATACATT
1858780 GTATTGATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.32
21 34 0.68
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTGGTCA
Found at i:1858838 original size:20 final size:20
Alignment explanation
Indices: 1858799--1858839 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1858789 CTGTGCATTA
*
1858799 TGTATCGATACATCTGAAGG
1 TGTATCGATACATCTAAAGG
* *
1858819 TGTATCGATACTTTTAAAGG
1 TGTATCGATACATCTAAAGG
1858839 T
1 T
1858840 TTTGACCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATCTAAAGG
Found at i:1859376 original size:26 final size:27
Alignment explanation
Indices: 1859342--1859396 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1859332 TTTCCTTTTC
*
1859342 TCTCCCCCTTAA-ACAAATAAAA-AATT
1 TCTCCCCCTTAATA-AAACAAAACAATT
1859368 TCTCCCCCTTAATAAAACAAAACAATT
1 TCTCCCCCTTAATAAAACAAAACAATT
1859395 TC
1 TC
1859397 CTTTAATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (27 bp):
TCTCCCCCTTAATAAAACAAAACAATT
Found at i:1861059 original size:13 final size:13
Alignment explanation
Indices: 1861041--1861065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1861031 ATAAACCCTT
1861041 TGTATCGATACAC
1 TGTATCGATACAC
1861054 TGTATCGATACA
1 TGTATCGATACA
1861066 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1867419 original size:20 final size:20
Alignment explanation
Indices: 1867380--1867420 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1867370 CTGTGCATTA
*
1867380 TGTATCGATACATCTGAAGG
1 TGTATCGATACATCTAAAGG
* *
1867400 TGTATCGATACTTTTAAAGG
1 TGTATCGATACATCTAAAGG
1867420 T
1 T
1867421 TTTGACCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATCTAAAGG
Found at i:1869157 original size:117 final size:116
Alignment explanation
Indices: 1868944--1869163 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 116
1868934 GAAAAATTTA
* * *
1868944 ATATTTTAGAGATAAAAATAGGTTTGGAGTATCCCCTTGAAAATAACGGAGTTGGAGTATCCTTG
1 ATATTTTAGAAATAAAAATAGGGTTGGAGTATCCCCTTGAAAATAACGGAGTTGGAGTATCCTCG
* ** *
1869009 ATGGTGAAAAATTTATTTTTTAGAAATAAAATTGGGGTTTGCTGAAAAATCG
66 ATAGTGAAAAATCGATGTTTTAGAAATAAAA-TGGGGTTTGCTGAAAAATCG
* * *
1869061 ATATTTTAGAAAT-AAAATCGGGGTTGGAGTATCCCTTTGGAAATAACAGG-GTTGGAGTAT-CT
1 ATATTTTAGAAATAAAAAT-AGGGTTGGAGTATCCCCTTGAAAATAAC-GGAGTTGGAGTATCCT
* *
1869123 CGATAGTGGAAAATCGGTGTTTTAGAAATAAAAATGGGGTT
64 CGATAGTGAAAAATCGATGTTTTAGAAAT-AAAATGGGGTT
1869164 GGAGTATGCC
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
116 36 0.41
117 50 0.57
118 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.33
Consensus pattern (116 bp):
ATATTTTAGAAATAAAAATAGGGTTGGAGTATCCCCTTGAAAATAACGGAGTTGGAGTATCCTCG
ATAGTGAAAAATCGATGTTTTAGAAATAAAATGGGGTTTGCTGAAAAATCG
Found at i:1869182 original size:78 final size:78
Alignment explanation
Indices: 1869054--1869467 Score: 423
Period size: 78 Copynumber: 5.3 Consensus size: 78
1869044 GGTTTGCTGA
* *
1869054 AAAATCGATATTTTAGAAAT-AAAATCGGGGTTGGAGTATCCCTTTGGAAATAACAGGGTTGGAG
1 AAAATCGATGTTTTAGAAATAAAAAT-GGGGTTGGAGTATCCC-TTAGAAATAACAGGGTTGGAG
*
1869118 TAT-CTCGATAGTGG
64 TATCCTCGATGGTGG
* *
1869132 AAAATCGGTGTTTTAGAAATAAAAATGGGGTTGGAGTATGCCCTTAGAAATAAC-GAGGTTAGAG
1 AAAATCGATGTTTTAGAAATAAAAATGGGGTTGGAGTAT-CCCTTAGAAATAACAG-GGTTGGAG
1869196 TATCCTCGATGGT-G
64 TATCCTCGATGGTGG
* * * * * *
1869210 --AATCGGTGTTTTAAAAATAAAACTAGGGTTGGAGTATCCCCTTAGAAATAACGGGGTTAGAAG
1 AAAATCGATGTTTTAGAAATAAAAATGGGGTTGGAGTAT-CCCTTAGAAATAACAGGGTT-GGAG
*
1869273 -ATCCCCGATGGTGG
64 TATCCTCGATGGTGG
* * * * * * * * *
1869287 AAAATCGATGTTTTAAAAATAAAATTGGGGTTGAAATATCCTCTCAAAAATGATAAGGTTGGAGT
1 AAAATCGATGTTTTAGAAATAAAAATGGGGTTGGAGTATCC-CTTAGAAATAACAGGGTTGGAGT
*
1869352 ATCCTCGATGGTGA
65 ATCCTCGATGGTGG
* * * * *
1869366 AAAATCAATATTTTAGAAATAAAACT-AGGTTGGAGTATCCCTTCAAAAATAACAGGGTTGGAGT
1 AAAATCGATGTTTTAGAAATAAAAATGGGGTTGGAGTATCCCTT-AGAAATAACAGGGTTGGAGT
*
1869430 ATCCCCGATGGTGG
65 ATCCTCGATGGTGG
* *
1869444 AAAATTGGTGTTTTAG-AATAAAAA
1 AAAATCGATGTTTTAGAAATAAAAA
1869468 CATCAATGAA
Statistics
Matches: 280, Mismatches: 44, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
76 63 0.22
77 14 0.05
78 109 0.39
79 94 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (78 bp):
AAAATCGATGTTTTAGAAATAAAAATGGGGTTGGAGTATCCCTTAGAAATAACAGGGTTGGAGTA
TCCTCGATGGTGG
Found at i:1871402 original size:17 final size:17
Alignment explanation
Indices: 1871380--1871412 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1871370 TATCAAGGGT
1871380 TTTTTTGTTGCTGGAAC
1 TTTTTTGTTGCTGGAAC
*
1871397 TTTTTTTTTGCTGGAA
1 TTTTTTGTTGCTGGAA
1871413 AAAATCCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.58
Consensus pattern (17 bp):
TTTTTTGTTGCTGGAAC
Found at i:1871847 original size:51 final size:51
Alignment explanation
Indices: 1871805--1871915 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
1871795 AAAATGCCTG
* * * *
1871805 AATGTAT-GATAT-A-GAGAAATGTCTCGATACATTTGGGTTAAAACACAT
1 AATGTATCGATATAATGAAAAATGTATCGATACATCTGGGTTAAAAAACAT
* * *
1871853 AATGTATCGATATAATGAAAAATGTATCTATACATCTGGGTT-AAAACCTAA
1 AATGTATCGATATAATGAAAAATGTATCGATACATCTGGGTTAAAAAAC-AT
1871904 AATGTATCGATA
1 AATGTATCGATA
1871916 AAAATAGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
48 7 0.13
49 5 0.10
50 5 0.10
51 35 0.67
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (51 bp):
AATGTATCGATATAATGAAAAATGTATCGATACATCTGGGTTAAAAAACAT
Found at i:1877661 original size:19 final size:20
Alignment explanation
Indices: 1877633--1877681 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1877623 CATTTTATGG
*
1877633 TGTATTGATATAAAG-AACA
1 TGTATCGATATAAAGCAACA
* *
1877652 TGTATCGATATTAAGCAATA
1 TGTATCGATATAAAGCAACA
*
1877672 CGTATCGATA
1 TGTATCGATA
1877682 CATCTGGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (20 bp):
TGTATCGATATAAAGCAACA
Found at i:1878724 original size:99 final size:101
Alignment explanation
Indices: 1878502--1878775 Score: 371
Period size: 99 Copynumber: 2.7 Consensus size: 101
1878492 TACATGAAAT
* *
1878502 AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACTCT-TTACCTGTAATCTGACATTCATAG
1 AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACT-TGTTACCTGTAATATGACATGCATAG
*
1878566 CTCAAGAAAGTATGTTTATGACCTTACTAATATTTTCA
65 CTCAAGAAAGTA-GTTTATGACCTTACCAATATTTTCA
*
1878604 AGCTTGTGAACAATCAGTGTCTCGGATTTATCAAAACTTGTTACCTGTAAGTATGTA-ATAGCA-
1 AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACTTGTTACCTGTAA-TATG-ACAT-GCAT
* *
1878667 AG-T-ATGCAAGTA-TTTATGACCTTACCAATATTTTCA
63 AGCTCAAGAAAGTAGTTTATGACCTTACCAATATTTTCA
* * * *
1878703 AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACTTGTTACCTATAATCTAACATTCATAGC
1 AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACTTGTTACCTGTAATATGACATGCATAGC
1878768 TCAAGAAA
66 TCAAGAAA
1878776 CACATTAGAA
Statistics
Matches: 151, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
97 3 0.02
98 6 0.04
99 72 0.48
100 4 0.03
101 8 0.05
102 48 0.32
103 7 0.05
104 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (101 bp):
AGCTTGTGAACAATCACTGTCTCGGATTTATCAAAACTTGTTACCTGTAATATGACATGCATAGC
TCAAGAAAGTAGTTTATGACCTTACCAATATTTTCA
Found at i:1883931 original size:51 final size:51
Alignment explanation
Indices: 1883799--1884016 Score: 244
Period size: 51 Copynumber: 4.5 Consensus size: 51
1883789 AAAAGTCACA
* *
1883799 TTTTTACCTAGATGTATCGATACATTCTTCAATGTATCAATACATTTTATC
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATC
* *
1883850 -TTTTACCCAGATGCATCGATACATTCTTCAATGTATCGATACATTCTATC
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATC
* * *
1883900 TTTTTACCCAGATTTATCGATACATTTTTCAATGTATCAATACA-TGTA--
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATC
* * * *
1883948 ----T---GA-ATGTATCGATACATTCTTCAATATATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATC
*
1883991 TTTTTACCCAGATGTATCAATACATT
1 TTTTTACCCAGATGTATCGATACATT
1884017 GATGTATCAA
Statistics
Matches: 137, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
40 29 0.21
41 3 0.02
44 1 0.01
47 1 0.01
50 50 0.36
51 53 0.39
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (51 bp):
TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCAATACATTCTATC
Found at i:1883942 original size:20 final size:20
Alignment explanation
Indices: 1883914--1883985 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1883904 TACCCAGATT
1883914 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * * *
1883934 TATCAATACATGTATGAATG
1 TATCGATACATTTTTCAATG
* *
1883954 TATCGATACATTCTTCAATA
1 TATCGATACATTTTTCAATG
1883974 TATCGATACATT
1 TATCGATACATT
1883986 CTGTCTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:1884022 original size:16 final size:16
Alignment explanation
Indices: 1884001--1884032 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1883991 TTTTTACCCA
1884001 GATGTATCAATACATT
1 GATGTATCAATACATT
1884017 GATGTATCAATACATT
1 GATGTATCAATACATT
1884033 TTTCAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
GATGTATCAATACATT
Found at i:1884947 original size:20 final size:22
Alignment explanation
Indices: 1884907--1884947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1884897 TAGCTTTTGA
*
1884907 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1884929 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
1884948 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1888712 original size:52 final size:52
Alignment explanation
Indices: 1888613--1888720 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
1888603 ATGCATTTGA
* * * * *
1888613 AATTCTAGCCGTTGGGCTCAATGTATTGATACAATTCATAATGTATCGATAC
1 AATTATAGCCGTTGGGCTCAATGTATCGATACAATTCACAATATATCGAAAC
* *
1888665 AATTATAGCCGTTGGGCTCAATGTATCGATACAATTTACCATATATCGAAAC
1 AATTATAGCCGTTGGGCTCAATGTATCGATACAATTCACAATATATCGAAAC
1888717 AATT
1 AATT
1888721 CAATTATGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (52 bp):
AATTATAGCCGTTGGGCTCAATGTATCGATACAATTCACAATATATCGAAAC
Found at i:1888833 original size:33 final size:32
Alignment explanation
Indices: 1888780--1888841 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
1888770 CATTTTATGG
*
1888780 TGTATCGATACAAAGAATATGTATCGATACAA
1 TGTATCAATACAAAGAATATGTATCGATACAA
*
1888812 TGTATCAATACTAAGCAATATGTATCGATA
1 TGTATCAATACAAAG-AATATGTATCGATA
1888842 TATCTGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCAATACAAAGAATATGTATCGATACAA
Found at i:1890033 original size:154 final size:156
Alignment explanation
Indices: 1889762--1890048 Score: 359
Period size: 154 Copynumber: 1.9 Consensus size: 156
1889752 TGCTTTCAAC
** **
1889762 ATGAAAGTATCTCAATAACCTTAAAGGACTTGAAAATTATCATAAAAAGATAAATCTATCCTAAA
1 ATGAAAGTATCTCAATAACCTTAAAGGACTACAAAAAGATCATAAAAAGATAAATCTATCCTAAA
* * * * *
1889827 CGCATACCTTTGACATAAAAGCATCCCGATGACTACCTAAAACTTGATTCTA-GATAAATTACTA
66 CGCATACCTTTGACAGAAAAACATCCAGATGACTACCTAAAACTGGATTCTAGGA-AAATCACTA
1889891 AAATACCCTTAAGGGTCTACTTTTGAT
130 AAATACCCTTAAGGGTCTACTTTTGAT
* * * *
1889918 ATGAAAGTATCT-AATAACCTTAAAGGGC-ACAAAAAGATCATAAAAGGATGAGTCTATCCTAAA
1 ATGAAAGTATCTCAATAACCTTAAAGGACTACAAAAAGATCATAAAAAGATAAATCTATCCTAAA
* * **
1889981 TGCATACCTTTGACAGAAAAACATCTTAG-TGACTACCTAGGACTCGGA-TCTAGGAAAATCACT
66 CGCATACCTTTGACAGAAAAACATC-CAGATGACTACCTAAAACT-GGATTCTAGGAAAATCACT
1890044 AAAAT
129 AAAAT
1890049 GCCTCTAGGT
Statistics
Matches: 111, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
154 79 0.71
155 20 0.18
156 12 0.11
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (156 bp):
ATGAAAGTATCTCAATAACCTTAAAGGACTACAAAAAGATCATAAAAAGATAAATCTATCCTAAA
CGCATACCTTTGACAGAAAAACATCCAGATGACTACCTAAAACTGGATTCTAGGAAAATCACTAA
AATACCCTTAAGGGTCTACTTTTGAT
Found at i:1892950 original size:64 final size:63
Alignment explanation
Indices: 1892752--1892950 Score: 170
Period size: 64 Copynumber: 3.1 Consensus size: 63
1892742 ATGGACCACG
* * *
1892752 GGGAAATTAATACT-GTCAAATGAGGATGACCAAGATGTAACCGAAGTCTAGAGTATTGACCAA
1 GGGAAATTATTA-TAGTCAAACGAGGATGACCAGGATGTAACCGAAGTCTAGAGTATTGACCAA
* ** * * * * * * * * *
1892815 GGGAAAACTATTATAGTCAGGCAAAGATGACCAGGATATAACCTAGGTCTAGAAG-GTTAACTAG
1 GGG-AAATTATTATAGTCAAACGAGGATGACCAGGATGTAACCGAAGTCTAG-AGTATTGACCAA
* *
1892879 GGTGAAATTGA-TATAGTCAAACGAGGATGATCAGGATGTAACCGGAGTCTAGAGTATTGACCAA
1 GG-GAAATT-ATTATAGTCAAACGAGGATGACCAGGATGTAACCGAAGTCTAGAGTATTGACCAA
1892943 GGCGAAAT
1 GG-GAAAT
1892951 CACTATAGCC
Statistics
Matches: 100, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
63 6 0.06
64 90 0.90
65 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (63 bp):
GGGAAATTATTATAGTCAAACGAGGATGACCAGGATGTAACCGAAGTCTAGAGTATTGACCAA
Found at i:1892982 original size:128 final size:130
Alignment explanation
Indices: 1892766--1893051 Score: 328
Period size: 128 Copynumber: 2.2 Consensus size: 130
1892756 AATTAATACT
* * * *
1892766 GTCAAATGAGGATGACCAAGATGTAACCGAAGTCTAGAGTATTGACCAAGGGAAAACTATTATAG
1 GTCAAACGAGGATGATCAGGATGTAACCGAAGTCTAGAGTATTGACCAAGGGAAAACTACTATAG
* * * * * * * *
1892831 TCAGGCAAAGATGACCAGGATATAA-CCTAGGTCTAGAAGG-TTAACTAGGGTGAAATTGATATA
66 CCAAGCAAAGATCACCAGGATATAATCCTAGGTCTAAAAGGATTAACCAGGGCGAAACTAATATA
* *
1892894 GTCAAACGAGGATGATCAGGATGTAACCGGAGTCTAGAGTATTGACCAAGGCGAAATC-ACTATA
1 GTCAAACGAGGATGATCAGGATGTAACCGAAGTCTAGAGTATTGACCAAGG-GAAAACTACTATA
* * ** * *
1892958 GCCAAGCGAAGGTCATTAGGATATAATCCTAGGTCTAAAAGGATTGACCAGGGCGAAACTAATTT
65 GCCAAGCAAAGATCACCAGGATATAATCCTAGGTCTAAAAGGATTAACCAGGGCGAAACTAATAT
1893023 A
130 A
* *
1893024 GTTAAACGAAGG-TGATCAGGGTGTAACC
1 GTCAAACG-AGGATGATCAGGATGTAACC
1893052 TACATTTAGA
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
128 71 0.54
129 19 0.14
130 39 0.30
131 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (130 bp):
GTCAAACGAGGATGATCAGGATGTAACCGAAGTCTAGAGTATTGACCAAGGGAAAACTACTATAG
CCAAGCAAAGATCACCAGGATATAATCCTAGGTCTAAAAGGATTAACCAGGGCGAAACTAATATA
Found at i:1893194 original size:65 final size:64
Alignment explanation
Indices: 1893056--1893194 Score: 145
Period size: 65 Copynumber: 2.2 Consensus size: 64
1893046 GTAACCTACA
* ** * * *
1893056 TTTAGAAGGTTGACTAGGTGAAAATGATGCAATGAAATGAAGGTGACTTGAATATAATCCTAGG
1 TTTAGAAGGTTAACTAGGTGAAAACAATACAATCAAATGAAGGTGACTAGAATATAATCCTAGG
** * * * *
1893120 ACTAAAAGGTTAACTAGGGTGAAACCAATACAATCAAAT-AGAGGTGACTAGGATATAATCTTAG
1 TTTAGAAGGTTAACTA-GGTGAAAACAATACAATCAAATGA-AGGTGACTAGAATATAATCCTAG
1893184 G
64 G
1893185 TTTAGAAGGT
1 TTTAGAAGGT
1893195 AGACCAGAGC
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
64 13 0.22
65 45 0.78
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (64 bp):
TTTAGAAGGTTAACTAGGTGAAAACAATACAATCAAATGAAGGTGACTAGAATATAATCCTAGG
Found at i:1893306 original size:66 final size:66
Alignment explanation
Indices: 1893107--1893357 Score: 206
Period size: 66 Copynumber: 3.8 Consensus size: 66
1893097 GGTGACTTGA
* * * ** * * * * *
1893107 ATATAATCCTAGGACTAAAAG-GTTAACTAGGGTGAAACCAATACAATCAAATAGAGGTGACTAG
1 ATATAATCCTAGGTCTAAAAGAGTTAACCAAGGTGAAACTGATACAGTCAAACAAAGGTGACCAA
1893171 G
66 G
* * * ** * *
1893172 ATATAATCTTAGGTTTAGAAG-G-TAGACC-AGAGCAAAACCGATATAGTCAAACAAAGGTGACC
1 ATATAATCCTAGGTCTAAAAGAGTTA-ACCAAG-GTGAAACTGATACAGTCAAACAAAGGTGACC
1893234 AAG
64 AAG
* * * * *
1893237 ATATAATCTTTA-TTCTAAAAGAGTTAACCAAGGTGAATCTGATACAGTCGAACGAAGGTGACCA
1 ATATAATC-CTAGGTCTAAAAGAGTTAACCAAGGTGAAACTGATACAGTCAAACAAAGGTGACCA
*
1893301 GG
65 AG
* * *
1893303 ATATAATCCTAGGTCTAAAAGGGTTGACCAAGGTGAAACTAATACAGTCAAACAA
1 ATATAATCCTAGGTCTAAAAGAGTTAACCAAGGTGAAACTGATACAGTCAAACAA
1893358 GATAAAAAAG
Statistics
Matches: 145, Mismatches: 34, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
64 3 0.02
65 61 0.42
66 77 0.53
67 4 0.03
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (66 bp):
ATATAATCCTAGGTCTAAAAGAGTTAACCAAGGTGAAACTGATACAGTCAAACAAAGGTGACCAA
G
Found at i:1894070 original size:75 final size:75
Alignment explanation
Indices: 1893806--1894145 Score: 256
Period size: 75 Copynumber: 4.5 Consensus size: 75
1893796 ATCATCTAGG
* * * * * * * *
1893806 AGCTAAAAAAGAAGAACATGATTAGGAATATATGATTTTCTAAAATTTCTATCAACAATTGAAGT
1 AGCTAAAAAA-AAGAACATAATAAGGAATATGTG-GTTTCTAAAATTTCTATTAATAAATGAAAT
* *
1893871 GAACTAATAACA
64 AAATTAATAACA
** * * ** * **
1893883 AGCTGAAGGAGAAGAGCACCAT-GGAGAATATGTGGTTTCTAAAATTT-TCATT-ATAGCTGAAA
1 AGCT-AAAAAAAAGAACATAATAAG-GAATATGTGGTTTCTAAAATTTCT-ATTAATAAATGAAA
**
1893945 TAAATTAATAATG
63 TAAATTAATAACA
* * * * *
1893958 AGCTGAAAAGAAGAGCATGATAAGGAATATGTGGTTTCTAAAATTTCTATTAATAAATGAAATAG
1 AGCTAAAAAAAAGAACATAATAAGGAATATGTGGTTTCTAAAATTTCTATTAATAAATGAAATAA
*
1894023 ATTGATAACA
66 ATTAATAACA
* *** *
1894033 AGCTAAAAAAAAGAACATAATAGGGAATATGTGGTTTCTAAAATTTCTATTAATAACCAAAACAA
1 AGCTAAAAAAAAGAACATAATAAGGAATATGTGGTTTCTAAAATTTCTATTAATAAATGAAATAA
* *
1894098 ACTAATAACG
66 ATTAATAACA
* * *
1894108 AGTTAAAGAAAAAGAACATGAT-GGGAAATATGTGGTTT
1 AGCTAAA-AAAAAGAACATAATAAGG-AATATGTGGTTT
1894146 GTACAATGTC
Statistics
Matches: 210, Mismatches: 45, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
74 37 0.18
75 110 0.52
76 40 0.19
77 20 0.10
78 3 0.01
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (75 bp):
AGCTAAAAAAAAGAACATAATAAGGAATATGTGGTTTCTAAAATTTCTATTAATAAATGAAATAA
ATTAATAACA
Found at i:1894179 original size:77 final size:75
Alignment explanation
Indices: 1893908--1894184 Score: 189
Period size: 75 Copynumber: 3.7 Consensus size: 75
1893898 GCACCATGGA
** * * ** * * ** * *
1893908 GAATATGTGGTTTCTAAAATTTTCATT-ATAGCTGAAATAAATTAATAATGAGCTGAAAAGAAGA
1 GAATATGTGGTTTCTAAAATTCCCATTAACAACCAAAACAAACTAATAACAAGCTAAAAAAAAGA
* * *
1893972 GCATGATAAG
66 ACATAATAGG
* * * *** * * * *
1893982 GAATATGTGGTTTCTAAAATTTCTATTAATAAATGAAATAGATTGATAACAAGCTAAAAAAAAGA
1 GAATATGTGGTTTCTAAAATTCCCATTAACAACCAAAACAAACTAATAACAAGCTAAAAAAAAGA
1894047 ACATAATAGG
66 ACATAATAGG
* * * * *
1894057 GAATATGTGGTTTCTAAAATTTCTATTAATAACCAAAACAAACTAATAACGAGTTAAAGAAAAAG
1 GAATATGTGGTTTCTAAAATTCCCATTAACAACCAAAACAAACTAATAACAAGCTAAA-AAAAAG
*
1894122 AACATGAT-GG
65 AACATAATAGG
* * * * *
1894132 GAAATATGTGGTTTGTACAATGTCCCATTAACAGCCAAAATAAACTAAAAACA
1 G-AATATGTGGTTTCTAAAAT-TCCCATTAACAACCAAAACAAACTAATAACA
1894185 TAATGTTATT
Statistics
Matches: 167, Mismatches: 32, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
74 25 0.15
75 88 0.53
76 30 0.18
77 24 0.14
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (75 bp):
GAATATGTGGTTTCTAAAATTCCCATTAACAACCAAAACAAACTAATAACAAGCTAAAAAAAAGA
ACATAATAGG
Found at i:1904030 original size:13 final size:13
Alignment explanation
Indices: 1904012--1904038 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1904002 ACAATATTCT
1904012 TTGTATCGATACA
1 TTGTATCGATACA
1904025 TTGTATCGATACA
1 TTGTATCGATACA
1904038 T
1 T
1904039 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1905563 original size:33 final size:33
Alignment explanation
Indices: 1905521--1905587 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1905511 TGAGAGTTGA
*
1905521 TCACTTCACT-TTCGTAGCACATGAATGAGCACT
1 TCACTTCACTCTT-GCAGCACATGAATGAGCACT
* *
1905554 TCACTTCACTCTTGCAGCGCATGGATGAGCACT
1 TCACTTCACTCTTGCAGCACATGAATGAGCACT
1905587 T
1 T
1905588 TAGTTCTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (33 bp):
TCACTTCACTCTTGCAGCACATGAATGAGCACT
Found at i:1913096 original size:47 final size:44
Alignment explanation
Indices: 1913043--1913135 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 44
1913033 CTAGAAGCTA
* * *
1913043 CTGCTTGCTAGAGTGGATGCTACTAGAAGTTGTCTGTGGGCTGGGAG
1 CTGCTTGCTAGAGTAGATG---CTAGAAGCTGTCCGTGGGCTGGGAG
* *
1913090 CTGCTTGCTGGAGTAGATGCTGGAAGCTGTCCGTGGGCTGGGAG
1 CTGCTTGCTAGAGTAGATGCTAGAAGCTGTCCGTGGGCTGGGAG
1913134 CT
1 CT
1913136 ACTGCTTGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 24 0.59
47 17 0.41
ACGTcount: A:0.15, C:0.17, G:0.40, T:0.28
Consensus pattern (44 bp):
CTGCTTGCTAGAGTAGATGCTAGAAGCTGTCCGTGGGCTGGGAG
Found at i:1913141 original size:47 final size:48
Alignment explanation
Indices: 1913038--1913146 Score: 127
Period size: 47 Copynumber: 2.3 Consensus size: 48
1913028 GGATGCTAGA
* * *
1913038 AGCTACTGCTTGCTAGAGTGGATGCTACTAGAAGTTGTCTGTGGGCTGGG
1 AGCTACTGCTTGCTAGAGTAGATG--ACTAGAAGCTGTCCGTGGGCTGGG
* *
1913088 AG---CTGCTTGCTGGAGTAGATG-CTGGAAGCTGTCCGTGGGCTGGG
1 AGCTACTGCTTGCTAGAGTAGATGACTAGAAGCTGTCCGTGGGCTGGG
1913132 AGCTACTGCTTGCTA
1 AGCTACTGCTTGCTA
1913147 TCTTTTGATC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
44 22 0.44
47 26 0.52
50 2 0.04
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (48 bp):
AGCTACTGCTTGCTAGAGTAGATGACTAGAAGCTGTCCGTGGGCTGGG
Found at i:1914500 original size:44 final size:43
Alignment explanation
Indices: 1914440--1914535 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
1914430 TAACCCTAGT
*
1914440 GGTAA-AAAGCCTACCGAGGACAAAGTCGACAGGTAAACAAAG
1 GGTAAGAAAGCCTACCGAGGACAAAGCCGACAGGTAAACAAAG
* * *
1914482 GGTAAGAAAGGCTAACCGAGGACAAAGCCGATAGGTCAACAAAG
1 GGTAAGAAAGCCT-ACCGAGGACAAAGCCGACAGGTAAACAAAG
* *
1914526 TGCAAGAAAG
1 GGTAAGAAAG
1914536 TCTCTAAGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 5 0.11
43 6 0.13
44 35 0.76
ACGTcount: A:0.45, C:0.18, G:0.28, T:0.09
Consensus pattern (43 bp):
GGTAAGAAAGCCTACCGAGGACAAAGCCGACAGGTAAACAAAG
Found at i:1914589 original size:42 final size:42
Alignment explanation
Indices: 1914533--1914943 Score: 314
Period size: 42 Copynumber: 9.8 Consensus size: 42
1914523 AAGTGCAAGA
* * * **
1914533 AAGTCTCTAAGGTCAAAGTCGACAAGCAGACTTTAGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGATGAGG
* * * *
1914575 TAGTCTACAGGGTCAAAGCCGACAGGCAGACTGAAGGATG-GA
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAA-GATGAGG
* * * ** *
1914617 AAGTCTCCAAGGTTAAAGCCGACAAGCAAACTTTAGATAAGG
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGATGAGG
** * * *
1914659 TGGTCTCCAGGGTCAAAGCCGACTAGCAGACTAAAAGATGA-A
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACT-GAAGATGAGG
* * * * *
1914701 AAGTCTCCAAGGTCAAAGTCGA-TAGTTAGAC-GAAGATAAGG
1 AAGTCTCCAGGGTCAAAGCCGACAAG-CAGACTGAAGATGAGG
* * * * *
1914742 CAGTCTCCAGGGTCAAAGCTGACATGTAGACTGAAGGATG-GA
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAA-GATGAGG
* * * *
1914784 AAGTCTCTAGGGTCAAAGTCGACAGGCAGACTGAAGGATG-GA
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAA-GATGAGG
* *
1914826 AAGTCTCCA-GGTCAAAGCCGACAAGTAGACTAAAGGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAA-GATGAGG
* * * * *
1914868 CAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTAAGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGATGAGG
* * * *
1914910 TAGACTCCAGGGTCAAAACCGACAGGCAGACTGA
1 AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGA
1914944 GGGAAGGAAA
Statistics
Matches: 291, Mismatches: 68, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
40 6 0.02
41 55 0.19
42 197 0.68
43 33 0.11
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (42 bp):
AAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGATGAGG
Found at i:1914629 original size:84 final size:84
Alignment explanation
Indices: 1914531--1914953 Score: 433
Period size: 84 Copynumber: 5.0 Consensus size: 84
1914521 CAAAGTGCAA
* * *
1914531 GAAAGTCTCTAAGGTCAAAGTCGACAAGCAGACTTTAGATGAGGTAGTCTACAGGGTCAAAGCCG
1 GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTTAAGATGAGGTAGTCTCCAGGGTCAAAGCCG
1914596 ACAGGCAGACTGAAGGATG
66 ACAGGCAGACTGAAGGATG
* * * * * *
1914615 GAAAGTCTCCAAGGTTAAAGCCGACAAGCAAACTTTAGATAAGGTGGTCTCCAGGGTCAAAGCCG
1 GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTTAAGATGAGGTAGTCTCCAGGGTCAAAGCCG
* *
1914680 ACTA-GCAGACTAAAAGATG
66 AC-AGGCAGACTGAAGGATG
* * * * * * *
1914699 AAAAGTCTCCAAGGTCAAAGTCGA-TAGTTAGAC-GAAGATAAGGCAGTCTCCAGGGTCAAAGCT
1 GAAAGTCTCCAAGGTCAAAGTCGACAAG-CAGACTTAAGATGAGGTAGTCTCCAGGGTCAAAGCC
* *
1914762 GACATGTAGACTGAAGGATG
65 GACAGGCAGACTGAAGGATG
* * * * **
1914782 GAAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTGAAGGATG-GAAAGTCTCCA-GGTCAAAGCC
1 GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTTAA-GATGAGGTAGTCTCCAGGGTCAAAGCC
* * *
1914845 GACAAGTAGACTAAAGGATG
65 GACAGGCAGACTGAAGGATG
** * * * * *
1914865 AGGCAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTAAGATGAGGTAGACTCCAGGGTCAAAACC
1 -GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTTAAGATGAGGTAGTCTCCAGGGTCAAAGCC
* *
1914930 GACAGGCAGACTGAGGGAAG
65 GACAGGCAGACTGAAGGATG
1914950 GAAA
1 GAAA
1914954 AAAGATGAAG
Statistics
Matches: 277, Mismatches: 53, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
82 1 0.00
83 98 0.35
84 150 0.54
85 28 0.10
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.17
Consensus pattern (84 bp):
GAAAGTCTCCAAGGTCAAAGTCGACAAGCAGACTTAAGATGAGGTAGTCTCCAGGGTCAAAGCCG
ACAGGCAGACTGAAGGATG
Found at i:1925661 original size:21 final size:21
Alignment explanation
Indices: 1925635--1925689 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1925625 GTTACAAGTA
*
1925635 ATGTATCGATACAATT-TCCTT
1 ATGTATCGATACAATTGTCC-C
1925656 ATGTATCGATAC-ATTGTCCC
1 ATGTATCGATACAATTGTCCC
1925676 ATGTATCGATACAA
1 ATGTATCGATACAA
1925690 ATAGGGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACAATTGTCCC
Found at i:1925681 original size:20 final size:20
Alignment explanation
Indices: 1925635--1925688 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1925625 GTTACAAGTA
*
1925635 ATGTATCGATACAATTTCCTT
1 ATGTATCGATAC-ATTTCCTC
1925656 ATGTATCGATACATTGTCC-C
1 ATGTATCGATACATT-TCCTC
1925676 ATGTATCGATACA
1 ATGTATCGATACA
1925689 AATAGGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTCCTC
Found at i:1925762 original size:19 final size:19
Alignment explanation
Indices: 1925718--1925773 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1925708 CTGCCAGTTT
*
1925718 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
1925738 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
1925757 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1925774 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:1925776 original size:13 final size:13
Alignment explanation
Indices: 1925758--1925784 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1925748 TACAATGAGC
1925758 ATGTATCGATACA
1 ATGTATCGATACA
1925771 ATGTATCGATACA
1 ATGTATCGATACA
1925784 A
1 A
1925785 AGCAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1925800 original size:33 final size:32
Alignment explanation
Indices: 1925739--1925803 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1925729 ACAATTGTCC
*
1925739 ATGTATCGATACAATGAGCATGTATCGATACA
1 ATGTATCGATACAAAGAGCATGTATCGATACA
*
1925771 ATGTATCGATACAAAGCAGTATGTATCGATACA
1 ATGTATCGATACAAAG-AGCATGTATCGATACA
1925804 TCTGGGAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAGCATGTATCGATACA
Found at i:1926401 original size:15 final size:15
Alignment explanation
Indices: 1926381--1926410 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1926371 AATAATAAAA
1926381 AATTTATTTATCTTC
1 AATTTATTTATCTTC
1926396 AATTTATTTATCTTC
1 AATTTATTTATCTTC
1926411 CATATCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTATTTATCTTC
Found at i:1928262 original size:13 final size:13
Alignment explanation
Indices: 1928244--1928285 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1928234 AAATAGTACC
*
1928244 CAATGTATCTATA
1 CAATGTATCGATA
1928257 CAATGTATCGATA
1 CAATGTATCGATA
1928270 CAATGTATCGATA
1 CAATGTATCGATA
1928283 CAA
1 CAA
1928286 GCACTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1934472 original size:13 final size:13
Alignment explanation
Indices: 1934454--1934479 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1934444 CAATTTTTTG
1934454 TGTATCGATACAT
1 TGTATCGATACAT
1934467 TGTATCGATACAT
1 TGTATCGATACAT
1934480 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1934564 original size:20 final size:20
Alignment explanation
Indices: 1934539--1934590 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1934529 CATCTTTTTT
1934539 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1934559 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1934579 ATGTATCGATAC
1 ATGTATCGATAC
1934591 TTTGAATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1935034 original size:33 final size:33
Alignment explanation
Indices: 1934994--1935058 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1934984 CCCGTTTATT
1934994 AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
1935027 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
1935059 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
Found at i:1936867 original size:13 final size:13
Alignment explanation
Indices: 1936849--1936887 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1936839 ATAATCACCC
*
1936849 TGTATCGATACAG
1 TGTATCGATACAA
1936862 TGTATCGATACAA
1 TGTATCGATACAA
1936875 TGTATCGATACAA
1 TGTATCGATACAA
1936888 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1936898 original size:20 final size:20
Alignment explanation
Indices: 1936873--1936951 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1936863 GTATCGATAC
1936873 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1936893 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1936918 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1936938 CATGTATCGATACA
1 AATGTATCGATACA
1936952 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1938986 original size:15 final size:15
Alignment explanation
Indices: 1938966--1938996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1938956 ATTTCGTTTG
*
1938966 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1938981 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1938996 G
1 G
1938997 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1940828 original size:21 final size:21
Alignment explanation
Indices: 1940799--1940843 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1940789 AAGTTTTCAT
*
1940799 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1940819 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1940841 TTT
1 TTT
1940844 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1943076 original size:13 final size:13
Alignment explanation
Indices: 1943058--1943083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1943048 AATTTTTTTG
1943058 TGTATCGATACAT
1 TGTATCGATACAT
1943071 TGTATCGATACAT
1 TGTATCGATACAT
1943084 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1943148 original size:21 final size:21
Alignment explanation
Indices: 1943122--1943197 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1943112 CTGCCAAGAA
*
1943122 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1943143 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1943163 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1943184 ATGTATCGATACAT
1 ATGTATCGATACAT
1943198 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1943168 original size:20 final size:20
Alignment explanation
Indices: 1943143--1943215 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1943133 CATCTTTTTT
1943143 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1943163 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1943184 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1943204 ATGTATCGATAC
1 ATGTATCGATAC
1943216 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1943179 original size:41 final size:41
Alignment explanation
Indices: 1943122--1943215 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1943112 CTGCCAAGAA
*
1943122 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1943163 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1943204 ATGTATCGATAC
1 ATGTATCGATAC
1943216 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1947337 original size:32 final size:29
Alignment explanation
Indices: 1947270--1947327 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1947260 TCATGGGCTA
* *
1947270 AAAGCTGCTGCTTGTTGGAGTGGATGCTG
1 AAAGCTGCTACTTGCTGGAGTGGATGCTG
1947299 AAAGCTGCTACTTGCTGGAGTGGATGCTG
1 AAAGCTGCTACTTGCTGGAGTGGATGCTG
1947328 CTGGAAGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.29
Consensus pattern (29 bp):
AAAGCTGCTACTTGCTGGAGTGGATGCTG
Found at i:1947606 original size:76 final size:76
Alignment explanation
Indices: 1947504--1947670 Score: 268
Period size: 76 Copynumber: 2.2 Consensus size: 76
1947494 GGTTGGGAGT
*
1947504 TGCTTGCTGGAGT-G--GATGCTGAAAGCTATCCGTGGGCTGGGAGCTGCTTCCTGGAGTGGATG
1 TGCTTGCTGGAGTGGATGATGCTGAAAGCTATCCATGGGCTGGGAGCTGCTTCCTGGAGTGGATG
*
1947566 CTGGAAGCTGC
66 CTGGAAGCTAC
* * *
1947577 TGCTTGCTGGAGTGGATGATGCTGGAAGCTGTCCATGGGCTGGGAGCTGCTTGCTGGAGTGGATG
1 TGCTTGCTGGAGTGGATGATGCTGAAAGCTATCCATGGGCTGGGAGCTGCTTCCTGGAGTGGATG
1947642 CTGGAAGCTAC
66 CTGGAAGCTAC
1947653 TGCTTGCTGGAGTGGATG
1 TGCTTGCTGGAGTGGATG
1947671 CTATAGCTAC
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
73 13 0.15
74 1 0.01
76 72 0.84
ACGTcount: A:0.15, C:0.17, G:0.41, T:0.27
Consensus pattern (76 bp):
TGCTTGCTGGAGTGGATGATGCTGAAAGCTATCCATGGGCTGGGAGCTGCTTCCTGGAGTGGATG
CTGGAAGCTAC
Found at i:1947607 original size:29 final size:26
Alignment explanation
Indices: 1947539--1947672 Score: 86
Period size: 29 Copynumber: 5.1 Consensus size: 26
1947529 CTATCCGTGG
*
1947539 GCTGGGAGCTGCTTCCTGGAGTGGAT
1 GCTGGAAGCTGCTTCCTGGAGTGGAT
*
1947565 GCTGGAAGCTGCTGCTTGCTGGAGTGGATGAT
1 GCTGGAA---GCTGCTTCCTGGAGT-G--GAT
1947597 GCTGGAAGCTG--TCC---A-TGG--
1 GCTGGAAGCTGCTTCCTGGAGTGGAT
* *
1947615 GCTGGGAGCTGCTTGCTGGAGTGGAT
1 GCTGGAAGCTGCTTCCTGGAGTGGAT
*
1947641 GCTGGAAGCTACTGCTTGCTGGAGTGGAT
1 GCTGGAAG---CTGCTTCCTGGAGTGGAT
1947670 GCT
1 GCT
1947673 ATAGCTACTA
Statistics
Matches: 85, Mismatches: 6, Indels: 31
0.70 0.05 0.25
Matches are distributed among these distances:
18 10 0.12
20 3 0.04
22 1 0.01
23 2 0.02
24 4 0.05
26 13 0.15
27 2 0.02
29 39 0.46
30 1 0.01
32 10 0.12
ACGTcount: A:0.14, C:0.18, G:0.41, T:0.27
Consensus pattern (26 bp):
GCTGGAAGCTGCTTCCTGGAGTGGAT
Found at i:1947901 original size:76 final size:75
Alignment explanation
Indices: 1947721--1947909 Score: 209
Period size: 76 Copynumber: 2.5 Consensus size: 75
1947711 CCGGTGTTCG
* * * * *
1947721 TGGGCTGGTAGCTGCTTGCTGGAGTGGACGCTAGAAGCTGCTGCTTGCTCGAGTGGATGCTGCTA
1 TGGGCTGGGAGCTGCTT-CTGGAGTGGATGCTGGAAGCTACTGCTTGCTCGAGTGGATGCTGCAA
*
1947786 GAAACTGTCCG
65 GAAACTGTCCA
* * * * * * *
1947797 TGAGCTGAGAGCTACTTGTTGGAATGGATGCTGGAAGCTACTGCTTGGTGGAGTGGATGCTGCAA
1 TGGGCTGGGAGCTGCTT-CTGGAGTGGATGCTGGAAGCTACTGCTTGCTCGAGTGGATGCTGCAA
*
1947862 GAAGCTGTCCA
65 GAAACTGTCCA
1947873 TGGGCTGGGAGCTGCTTACTAGG-GTGGATGCTGGAAG
1 TGGGCTGGGAGCTGCTT-CT-GGAGTGGATGCTGGAAG
1947910 TTGGTTTTTT
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
76 90 0.98
77 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.26
Consensus pattern (75 bp):
TGGGCTGGGAGCTGCTTCTGGAGTGGATGCTGGAAGCTACTGCTTGCTCGAGTGGATGCTGCAAG
AAACTGTCCA
Found at i:1948707 original size:18 final size:18
Alignment explanation
Indices: 1948686--1948735 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1948676 TTTTTTCACG
**
1948686 TTTTTTTTATTTTTTGGA
1 TTTTTTTTATTTTTTAAA
**
1948704 TTTTTTGAATTTTTTAAA
1 TTTTTTTTATTTTTTAAA
*
1948722 TTATTTTTATTTTT
1 TTTTTTTTATTTTT
1948736 AATTTTTGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTTTTTATTTTTTAAA
Found at i:1952458 original size:22 final size:22
Alignment explanation
Indices: 1952433--1952479 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1952423 TTTTTGAAAC
*
1952433 AATGAA-AATCACAAATTATTCA
1 AATGAAGAATCA-AAATTAATCA
*
1952455 AATGAAGTATCAAAATTAATCA
1 AATGAAGAATCAAAATTAATCA
1952477 AAT
1 AAT
1952480 AAATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (22 bp):
AATGAAGAATCAAAATTAATCA
Found at i:1955201 original size:20 final size:20
Alignment explanation
Indices: 1955159--1955211 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1955149 CTACCACTAT
* *
1955159 TTGTATCGATACATGGTACA
1 TTGTATCGATACACGATACA
1955179 TTGTATCGATACACGATGA-A
1 TTGTATCGATACACGAT-ACA
*
1955199 TTGTATCAATACA
1 TTGTATCGATACA
1955212 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACACGATACA
Found at i:1956817 original size:9 final size:9
Alignment explanation
Indices: 1956800--1956833 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1956790 GTCAACCATC
1956800 AATGATGAT
1 AATGATGAT
1956809 GAA-GATGAT
1 -AATGATGAT
1956818 AATGATGAT
1 AATGATGAT
1956827 AATGATG
1 AATGATG
1956834 GTTACTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:1961029 original size:20 final size:20
Alignment explanation
Indices: 1961004--1961041 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1960994 AATATTTTTC
1961004 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
1961024 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
1961042 TGGAAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:1961098 original size:13 final size:13
Alignment explanation
Indices: 1961077--1961113 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1961067 ATATTCCTTG
1961077 TATCGATACATTA
1 TATCGATACATTA
*
1961090 TATCTATACATTA
1 TATCGATACATTA
1961103 TATCGATACAT
1 TATCGATACAT
1961114 GGGTTACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:1963617 original size:20 final size:19
Alignment explanation
Indices: 1963594--1963666 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1963584 CACACCCAAA
*
1963594 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
1963614 TGTATCAATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1963633 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1963653 TGTATCGATACATG
1 TGTATCGATACATG
1963667 AAACTGCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.35
20 29 0.63
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1965646 original size:16 final size:16
Alignment explanation
Indices: 1965625--1965657 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1965615 AAAAATTCAC
1965625 AATTAAAATAAAATTA
1 AATTAAAATAAAATTA
*
1965641 AATTAAATTAAAATTA
1 AATTAAAATAAAATTA
1965657 A
1 A
1965658 CAATCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAAATAAAATTA
Found at i:1965655 original size:11 final size:11
Alignment explanation
Indices: 1965625--1965657 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1965615 AAAAATTCAC
*
1965625 AATTAAAATAA
1 AATTAAAATTA
1965636 AATT-AAATTA
1 AATTAAAATTA
1965646 AATTAAAATTA
1 AATTAAAATTA
1965657 A
1 A
1965658 CAATCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAAAATTA
Found at i:1970385 original size:23 final size:23
Alignment explanation
Indices: 1970343--1970386 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1970333 TAAATAATTT
*
1970343 TTAATTATTATTGAATATAAATA
1 TTAATTATTATTGAAGATAAATA
*
1970366 TTAATTATTATTTAAGATAAA
1 TTAATTATTATTGAAGATAAA
1970387 CTTAATTTTA
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:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAATTATTATTGAAGATAAATA
Found at i:1972788 original size:7 final size:7
Alignment explanation
Indices: 1972768--1972816 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
1972758 CGAGTTACTT
1972768 TAAAAAA
1 TAAAAAA
1972775 -AATAAAA
1 TAA-AAAA
1972782 TAAAAAA
1 TAAAAAA
*
1972789 TAAATAA
1 TAAAAAA
*
1972796 T--TAAA
1 TAAAAAA
1972801 TAAAAAA
1 TAAAAAA
1972808 TAAAAAA
1 TAAAAAA
1972815 TA
1 TA
1972817 TATACATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 27 0.79
8 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAAAAA
Found at i:1989299 original size:33 final size:32
Alignment explanation
Indices: 1989257--1989321 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1989247 CACACCCAGA
* *
1989257 TGTATCGATACATTATGCTTTATATCGATACAT
1 TGTATCGATACATGAT-CATTATATCGATACAT
*
1989290 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTATATCGATACAT
1989322 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTATATCGATACAT
Found at i:1989332 original size:20 final size:20
Alignment explanation
Indices: 1989288--1989381 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
1989278 ATATCGATAC
1989288 ATTGTATCGATACATGATC-
1 ATTGTATCGATACATGATCA
1989307 ATTGTATCGATACATGGA-CA
1 ATTGTATCGATACAT-GATCA
*
1989327 ATTGTATCGATACGTGGA-CA
1 ATTGTATCGATACAT-GATCA
*
1989347 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATCA
*
1989367 ATTGTATCGAAACAT
1 ATTGTATCGATACAT
1989382 TGCTTGTAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
19 18 0.26
20 50 0.74
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
ATTGTATCGATACATGATCA
Found at i:1995560 original size:13 final size:13
Alignment explanation
Indices: 1995542--1995569 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1995532 ACAACATTCC
1995542 TTGTATCGATACA
1 TTGTATCGATACA
1995555 TTGTATCGATACA
1 TTGTATCGATACA
1995568 TT
1 TT
1995570 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1997532 original size:38 final size:38
Alignment explanation
Indices: 1997476--1997577 Score: 168
Period size: 38 Copynumber: 2.7 Consensus size: 38
1997466 AAAGGAAGAG
* *
1997476 AATTGCTTTAATTGAGGGGGAGAAAATTTTTCTTTTAGA
1 AATT-CTTTAATTAAGGGGGAGAAAATTTTTCTTTTAAA
1997515 AATTCTTTAATTAAGGGGGAGAAAATTTTTCTTTTAAA
1 AATTCTTTAATTAAGGGGGAGAAAATTTTTCTTTTAAA
*
1997553 AATTCTTTGATTAAGGGGGAGAAAA
1 AATTCTTTAATTAAGGGGGAGAAAA
1997578 ATGAAAACTT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
38 56 0.93
39 4 0.07
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (38 bp):
AATTCTTTAATTAAGGGGGAGAAAATTTTTCTTTTAAA
Found at i:1998138 original size:13 final size:13
Alignment explanation
Indices: 1998120--1998146 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1998110 ACATTATGCT
1998120 TTGTATCGATACA
1 TTGTATCGATACA
1998133 TTGTATCGATACA
1 TTGTATCGATACA
1998146 T
1 T
1998147 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1998143 original size:33 final size:32
Alignment explanation
Indices: 1998101--1998165 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1998091 CACACCCAAG
* *
1998101 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
1998134 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTGTATCGATACAT
1998166 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:1998155 original size:19 final size:18
Alignment explanation
Indices: 1998130--1998187 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
1998120 TTGTATCGAT
1998130 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
1998148 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
1998168 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1998187 A
1 A
1998188 GATTAGCAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1998176 original size:20 final size:20
Alignment explanation
Indices: 1998131--1998186 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1998121 TGTATCGATA
1998131 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
1998150 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
1998169 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1998187 AGATTAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:1998345 original size:72 final size:72
Alignment explanation
Indices: 1998216--1998389 Score: 276
Period size: 72 Copynumber: 2.4 Consensus size: 72
1998206 TACTACTGTT
* * * * * *
1998216 TGTATCGATACATGATGAATTATATCGATACATTGCTTGTAATGGCTCTAAATGGCTATAATTTC
1 TGTATCGATACATTATGAATTGTATCGATACATTACTTGTAACGGCTATAAACGGCTATAATTTC
1998281 AAATCAA
66 AAATCAA
1998288 TGTATCGATACATTATGAATTGTATCGATACATTACTTGTAACGGCTATAAACGGCTATAATTTC
1 TGTATCGATACATTATGAATTGTATCGATACATTACTTGTAACGGCTATAAACGGCTATAATTTC
1998353 AAATCAA
66 AAATCAA
* *
1998360 CGTATCGATACATTATGAATAGTATCGATA
1 TGTATCGATACATTATGAATTGTATCGATA
1998390 GATGGCTACG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (72 bp):
TGTATCGATACATTATGAATTGTATCGATACATTACTTGTAACGGCTATAAACGGCTATAATTTC
AAATCAA
Found at i:2006681 original size:35 final size:34
Alignment explanation
Indices: 2006641--2006739 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 34
2006631 AAATTTTAAT
*
2006641 ATAAATATAAGTTTAATATTTTTTTAGTATTCAAC
1 ATAAATATAA-TTTAATATTTTTTTATTATTCAAC
* * *
2006676 ATAAATATAATTT--TATTTTTATTTTTATTTAAT
1 ATAAATATAATTTAATATTTTT-TTATTATTCAAC
* *
2006709 ATAAAGATAATTTTAATAATTTTTTATTATT
1 ATAAATATAA-TTTAATATTTTTTTATTATT
2006740 TATTATACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 7 0.13
33 17 0.32
34 6 0.11
35 17 0.32
36 6 0.11
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (34 bp):
ATAAATATAATTTAATATTTTTTTATTATTCAAC
Found at i:2006719 original size:33 final size:32
Alignment explanation
Indices: 2006635--2006752 Score: 101
Period size: 35 Copynumber: 3.5 Consensus size: 32
2006625 AAATTAAAAT
2006635 TTTAATATAAATATAAGTTTAATATTTTTTTAGTA
1 TTTAATATAAATATAA-TTT--TATTTTTTTAGTA
* * **
2006670 TTCAACATAAATATAATTTTATTTTTATTTTTA
1 TTTAATATAAATATAATTTTATTTTT-TTAGTA
* *
2006703 TTTAATATAAAGATAATTTTAATAATTTTTTATTA
1 TTTAATATAAATATAATTTT-AT--TTTTTTAGTA
* *
2006738 TTTATTATACATATA
1 TTTAATATAAATATA
2006753 CATATTTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
32 7 0.10
33 21 0.31
34 5 0.07
35 31 0.46
36 4 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTAATATAAATATAATTTTATTTTTTTAGTA
Found at i:2009880 original size:14 final size:14
Alignment explanation
Indices: 2009871--2009897 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2009861 ATATGAATTT
2009871 ATTTGAATGAATGC
1 ATTTGAATGAATGC
2009885 ATTTGAATGAATG
1 ATTTGAATGAATG
2009898 AACGTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (14 bp):
ATTTGAATGAATGC
Found at i:2019196 original size:24 final size:24
Alignment explanation
Indices: 2019164--2019212 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2019154 GTAGCAAGTA
2019164 TGAGATACATTACGACTATTACGC
1 TGAGATACATTACGACTATTACGC
2019188 TGAGATACATTACGACTATTACGC
1 TGAGATACATTACGACTATTACGC
2019212 T
1 T
2019213 TTCTTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (24 bp):
TGAGATACATTACGACTATTACGC
Found at i:2020674 original size:15 final size:16
Alignment explanation
Indices: 2020654--2020683 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2020644 ACAGTTTTTA
2020654 TTTTATTTTT-TAAGT
1 TTTTATTTTTATAAGT
2020669 TTTTATTTTTATAAG
1 TTTTATTTTTATAAG
2020684 ATCTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTATTTTTATAAGT
Found at i:2021729 original size:3 final size:3
Alignment explanation
Indices: 2021723--2021770 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2021713 AAAAAAACTA
2021723 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2021771 CCCTTAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2029096 original size:155 final size:153
Alignment explanation
Indices: 2028800--2030088 Score: 729
Period size: 155 Copynumber: 8.3 Consensus size: 153
2028790 TACGTCTAAG
* * * * *
2028800 AAAAATTACGAAAATGCC-CCAAGATGATACCTTCGATGTAAAAGTACTTGATA-CACTTAAAGG
1 AAAAATTAC-AAAATGCCTCTAAG-GGATACCTTCGACGTAAAAGTA-TCGATATC-CCTAAAGG
* * * * * *
2028863 GCTTAAAAAGGATTATAGAT--GATACGAACCTATCCTAAATA-CCTACCTTCAGTATAAAAGCT
62 ACTTAAAAAGGATTTTAAATAGGAT--GAACCTATCCTAAATATCC-ACCTTCGGCATAAAAGCG
* * *
2028925 GACCCGATGACAACCTAGGACTCGGTTCTA
124 GACCTGGTGACAACCTAGGACTCGATTCTA
* * *
2028955 GAAAATTATCAAAATGCCTCTAAGGGATATCTTCGACGTAGAAGTGATCGATATCCCTAAAGGAC
1 AAAAATTA-CAAAATGCCTCTAAGGGATACCTTCGACGTAAAAGT-ATCGATATCCCTAAAGGAC
* * **
2029020 TTAAAAAGGATTTTAAAAAGGATAAACCTATCCTAAATATTTACCTTCGGCATAAAAGCGGACCT
64 TTAAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGACCT
* * * * *
2029085 GGTGGCGACCTAGGAGTTGGTTCTA
129 GGTGACAACCTAGGACTCGATTCTA
* * * * * * *
2029110 AAAAATTACGAAAATACC-CTTAGGGGATACCTTTGACGTAAAAGTACCCAATACCCCTAAAAGA
1 AAAAATTAC-AAAATGCCTC-TAAGGGATACCTTCGACGTAAAAGTA-TCGATATCCCTAAAGGA
** * * * *
2029174 CTTAAAAAGGATAATAGATAGGCGTGAACCTATCCTAAATGTCCACCTTCGGCATAAAAGTGGA-
63 CTTAAAAAGGATTTTAAATAGG-ATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGAC
* * ** *
2029238 CTCAGTGATAATTTAAGACTCGATTCTA
127 CT-GGTGACAACCTAGGACTCGATTCTA
** * * * ** *
2029266 TGAAATTACGAAAATACCCCTATGGGTATACCTTCGACGTAAAAAGTATGCCGGCAACCCTAAAG
1 AAAAATTAC-AAAATGCCTCTAAGGG-ATACCTTCGACGT-AAAAGTAT--CGATATCCCTAAAG
* * * * * * * * * * *
2029331 GACTTAAAAAGAATTTTAACTGGGATGAGCCTACCCTAAAAATCAATCTTTGACATAAAAGCGAA
61 GACTTAAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGA
* ** **
2029396 CCCGGTGATGACCTATCACT---TT-TA
126 CCTGGTGACAACCTAGGACTCGATTCTA
* * *
2029420 AAAAATTATCAAAATGCC-CTTAGGGGATACATTCGACGTAAATA-TACCCGATA-CCGCTAAAG
1 AAAAATTA-CAAAATGCCTC-TAAGGGATACCTTCGACGTAAA-AGTA-TCGATATCC-CTAAAG
* * * * * * * * * *
2029482 GACATAAAAATGATTATAGATAAGACGAACCTATCCTAAATACCCATCTTTGGCATAAAAGTGGA
61 GACTTAAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGA
* *
2029547 -CTCGGTGACAACCTAAGACTC-ATTTTGA
126 CCT-GGTGACAACCTAGGACTCGATTCT-A
* * * * *
2029575 AAAAATTACCAAAATG-CTCCT-AGGAGATATCTTCGACGTAGAAGTACCTGATATTCCTAAAAG
1 AAAAATTA-CAAAATGCCT-CTAAGG-GATACCTTCGACGTAAAAGTATC-GATATCCCTAAAGG
* * * * * * *
2029638 ACTTAAAAAGAATTTTAAAAAGTATGAACTTATCCTAAATATCTACCTTCGGTATAAAAGCAGAT
62 ACTTAAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGA-
* * *
2029703 CC-GGTGACGACCTAAGGAGT-TAGTTCTA
126 CCTGGTGACAACCT-AGGACTCGA-TTCTA
* * * * * ** * *
2029731 AAAAATTACAAAAATGCCTTTAAAGGACACCTTTGATGTAAAAGTGCCTA-ATACCCTTAAAAGA
1 AAAAATTAC-AAAATGCCTCTAAGGGATACCTTCGACGTAAAAGTATCGATAT-CCC-TAAAGGA
** * * * * *
2029795 CTTAAAAAGGATAATAGATTAGGGTGAACCTATCCTAAAT-GCTCATCTTCGGCATAAAAGCGTA
63 CTTAAAAAGGATTTTA-AATAGGATGAACCTATCCTAAATATC-CACCTTCGGCATAAAAGCGGA
* * * * *
2029859 CCTAGTAATAACCTAGGACTCAATTTTA
126 CCTGGTGACAACCTAGGACTCGATTCTA
* * * * * * *
2029887 AGAAATTATAAAAATGCCCCTATAGGTATACCTTCGACGTAAAAAGTATCTTAACAACCCTAAAG
1 AAAAATTA-CAAAATGCCTCTA-AGGGATACCTTCGACGT-AAAAGTATC--GATATCCCTAAAG
* * * * * ** **
2029952 GACTTAAAAAGAATTTTAACTAGGATAAACCTACCCTAAATATCAACCTTTAGCATAAAAGCATA
61 GACTTAAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGC-GG
* ** *
2030017 ACC-GATGATGACCTAAGACTCGATTC-A
125 ACCTGGTGACAACCTAGGACTCGATTCTA
* *
2030044 AAAAATTACTAAAATACCT-TGAGGGATACCTTCGACGTAAAAGTA
1 AAAAATTAC-AAAATGCCTCTAAGGGATACCTTCGACGTAAAAGTA
2030089 CCCGATACCT
Statistics
Matches: 859, Mismatches: 218, Indels: 115
0.72 0.18 0.10
Matches are distributed among these distances:
150 3 0.00
151 70 0.08
152 5 0.01
153 16 0.02
154 39 0.05
155 305 0.36
156 168 0.20
157 93 0.11
158 104 0.12
159 51 0.06
160 4 0.00
161 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (153 bp):
AAAAATTACAAAATGCCTCTAAGGGATACCTTCGACGTAAAAGTATCGATATCCCTAAAGGACTT
AAAAAGGATTTTAAATAGGATGAACCTATCCTAAATATCCACCTTCGGCATAAAAGCGGACCTGG
TGACAACCTAGGACTCGATTCTA
Found at i:2029987 original size:621 final size:620
Alignment explanation
Indices: 2028825--2030097 Score: 1590
Period size: 621 Copynumber: 2.0 Consensus size: 620
2028815 GCCCCAAGAT
* * ** * * * * *
2028825 GATACCTTCGATGTAAAAGTACTTGATACAC-TTAAAGGGCTTAAAAAGGATTATAGATGATACG
1 GATACATTCGACGTAAAAGTACCCGATAC-CGCTAAAGGACATAAAAAGGATTATAGATAAGACG
* * * *
2028889 AACCTATCCTAAATACCTACCTTCAGTATAAAAGCTGACCCGATGACAACCTAGGACTCGGTTCT
65 AACCTATCCTAAATACCCACCTTCAGCATAAAAGCTGACCCGATGACAACCTAAGACTCGATTCT
* * * *
2028954 AGAAAATTATCAAAATGCCTCTAAGGGATATCTTCGACGTAGAAGTGATCGATATCCCTAAAGGA
130 AAAAAATTACCAAAATGCCTCTAAGGGATATCTTCGACGTAGAAGTGACCGATATCCCTAAAAGA
* * *
2029019 CTTAAAAAGGATTTTAAAAAGGATAAACCTATCCTAAATATTTACCTTCGGCATAAAAGCGGACC
195 CTTAAAAAGAATTTTAAAAAGGATAAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACC
* * * ** *
2029084 TGGTGGCGACCTAGGAGTTGGTTCTAAAAAATTACGAAAATACCCTTAGGGGATACCTTTGACGT
260 TGGTGACGACCTAGGAGTTAGTTCTAAAAAATTACAAAAATACCCTTAAAGGACACCTTTGACGT
2029149 AAAAGTACCCAATACCCCTAAAAGACTTAAAAAGGATAATAGATAGGCGTGAACCTATCCTAAAT
325 AAAAGTACCCAATACCCCTAAAAGACTTAAAAAGGATAATAGATAGGCGTGAACCTATCCTAAAT
* * ** * * *
2029214 GTCCACCTTCGGCATAAAAGTGGACTCAGTGATAATTTAAGACTCGATTCTATGAAATTACGAAA
390 GTCCACCTTCGGCATAAAAGCGGACTCAGTAATAACCTAAGACTCAATTCTAAGAAATTACAAAA
* **
2029279 ATACCCCTATGGGTATACCTTCGACGTAAAAAGTATGCCGGCAACCCTAAAGGACTTAAAAAGAA
455 ATACCCCTATAGGTATACCTTCGACGTAAAAAGTATGCCAACAACCCTAAAGGACTTAAAAAGAA
* * * * * *
2029344 TTTTAACTGGGATGAGCCTACCCTAAAAATCAATCTTT-GACATAAAAGCGA-ACCCGGTGATGA
520 TTTTAACTAGGATAAACCTACCCTAAAAATCAACCTTTAG-CATAAAAGC-ATAACCGATGATGA
* * *
2029407 CCTATCACT-TTTAAAAAATTA-TCAAAATGCCCTT-AGGG
583 CCTAACACTATTCAAAAAATTACT-AAAAT-ACCTTGA-GG
*
2029445 GATACATTCGACGTAAATA-TACCCGATACCGCTAAAGGACATAAAAATGATTATAGATAAGACG
1 GATACATTCGACGTAAA-AGTACCCGATACCGCTAAAGGACATAAAAAGGATTATAGATAAGACG
* ** * * *
2029509 AACCTATCCTAAATACCCATCTTTGGCATAAAAG-TGGACTCGGTGACAACCTAAGACTC-ATTT
65 AACCTATCCTAAATACCCACCTTCAGCATAAAAGCT-GACCCGATGACAACCTAAGACTCGATTC
*
2029572 TGAAAAAATTACCAAAATG-CTCCT-AGGAGATATCTTCGACGTAGAAGT-ACCTGATATTCCTA
129 T-AAAAAATTACCAAAATGCCT-CTAAGG-GATATCTTCGACGTAGAAGTGACC-GATATCCCTA
* * * *
2029634 AAAGACTTAAAAAGAATTTTAAAAAGTATGAACTTATCCTAAATATCTACCTTCGGTATAAAAGC
190 AAAGACTTAAAAAGAATTTTAAAAAGGATAAACCTATCCTAAATATCTACCTTCGGCATAAAAGC
* *
2029699 AGATCC-GGTGACGACCTAAGGAGTTAGTTCTAAAAAATTACAAAAATGCCTTTAAAGGACACCT
255 AGA-CCTGGTGACGACCT-AGGAGTTAGTTCTAAAAAATTACAAAAATACCCTTAAAGGACACCT
* * * *
2029763 TTGATGTAAAAGTGCCTAATACCCTTAAAAGACTTAAAAAGGATAATAGATTAGG-GTGAACCTA
318 TTGACGTAAAAGTACCCAATACCCCTAAAAGACTTAAAAAGGATAATAGA-TAGGCGTGAACCTA
* * * *
2029827 TCCTAAATG-CTCATCTTCGGCATAAAAGCGTAC-CTAGTAATAACCTAGGACTCAATTTTAAGA
382 TCCTAAATGTC-CACCTTCGGCATAAAAGCGGACTC-AGTAATAACCTAAGACTCAATTCTAAGA
* * *
2029890 AATTATAAAAATGCCCCTATAGGTATACCTTCGACGTAAAAAGTAT-CTTAACAACCCTAAAGGA
445 AATTACAAAAATACCCCTATAGGTATACCTTCGACGTAAAAAGTATGC-CAACAACCCTAAAGGA
*
2029954 CTTAAAAAGAATTTTAACTAGGATAAACCTACCCTAAATATCAACCTTTAGCATAAAAGCATAAC
509 CTTAAAAAGAATTTTAACTAGGATAAACCTACCCTAAAAATCAACCTTTAGCATAAAAGCATAAC
*
2030019 CGATGATGACCTAAGACTCGATTCAAAAAATTACTAAAATACCTTGAGG
574 CGATGATGACCTAACACT--ATTCAAAAAATTACTAAAATACCTTGAGG
*
2030068 GATACCTTCGACGTAAAAGTACCCGATACC
1 GATACATTCGACGTAAAAGTACCCGATACC
2030098 TCTAGTGGGC
Statistics
Matches: 559, Mismatches: 73, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
619 12 0.02
620 219 0.39
621 271 0.48
622 6 0.01
623 33 0.06
624 17 0.03
625 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (620 bp):
GATACATTCGACGTAAAAGTACCCGATACCGCTAAAGGACATAAAAAGGATTATAGATAAGACGA
ACCTATCCTAAATACCCACCTTCAGCATAAAAGCTGACCCGATGACAACCTAAGACTCGATTCTA
AAAAATTACCAAAATGCCTCTAAGGGATATCTTCGACGTAGAAGTGACCGATATCCCTAAAAGAC
TTAAAAAGAATTTTAAAAAGGATAAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACCT
GGTGACGACCTAGGAGTTAGTTCTAAAAAATTACAAAAATACCCTTAAAGGACACCTTTGACGTA
AAAGTACCCAATACCCCTAAAAGACTTAAAAAGGATAATAGATAGGCGTGAACCTATCCTAAATG
TCCACCTTCGGCATAAAAGCGGACTCAGTAATAACCTAAGACTCAATTCTAAGAAATTACAAAAA
TACCCCTATAGGTATACCTTCGACGTAAAAAGTATGCCAACAACCCTAAAGGACTTAAAAAGAAT
TTTAACTAGGATAAACCTACCCTAAAAATCAACCTTTAGCATAAAAGCATAACCGATGATGACCT
AACACTATTCAAAAAATTACTAAAATACCTTGAGG
Found at i:2032671 original size:164 final size:163
Alignment explanation
Indices: 2032386--2033191 Score: 882
Period size: 164 Copynumber: 4.9 Consensus size: 163
2032376 TAGACCAAAG
* * * *
2032386 AAAAT-CCCTCCGAAAATATTTATGGAATAGAAAACT-TGATTTTTC-AAAGAAAGGGAATTTCA
1 AAAATCCCCT-CGAAAAAATTTACGGAGTAGAAAACTCTG-TTTTTCGAAA-AAAGGAAATTTCA
* * * * * *
2032448 AGGAAAAACTTTAAAATTCATGGAAATGAATGAACTTTTGATAACTGAATTACTATGAAATCAAT
63 A-GAAAAA-TTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAAT
** *
2032513 AATAATATTTTTTGAATTTTAAAAATCAAAAAATAAGA
126 AATAATATTTGATGAATTTTAAAAATCAAAAAACAAGA
*
2032551 AAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCTGTTTTTTGGAAAAAAGGAAATTTCAAG
1 AAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCTG-TTTTTCGAAAAAAGGAAATTTCAAG
* *
2032616 AAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTGATATGAAATAAATTATA
65 AAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATA
2032681 ATATTTGATGAA-TTTAAAAGATCAAAAAACAAGA
130 ATATTTGATGAATTTTAAAA-ATCAAAAAACAAGA
* * * * * * *
2032715 AAAATCCCC-CTAAAAATTTTACAGAGTAGAAAACTCCGTATTTCAAAAAAAGGGAATTTCAAGG
1 AAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCTGTTTTTCGAAAAAAGGAAATTTCAA-G
* * * * *
2032779 AAAAATTCAATATTCATGGAAATGAATGATTTTTTTTAAAACTGAATTAATGTGAAATAAATAAT
65 AAAAATTCAAAATTTATGGAAATGAATGA-ATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* *
2032844 AATATTTGATAAATTTT-AGAATCAAAAAACAAGA
129 AATATTTGATGAATTTTAAAAATCAAAAAACAAGA
* * * *
2032878 AAAATCCCC-CTAAAAAAATTTACGGAGTAGAAAACTTTGTATTTCG-AAAAATGAGAATTTCAA
1 AAAATCCCCTC-GAAAAAATTTACGGAGTAGAAAACTCTGTTTTTCGAAAAAAGGA-AATTTC-A
* * * *
2032941 AGAAAAAATTTAAAACTTATGGAAATGAATGAATTTTTTAAAACTGAATTAATATGGAATAAATA
63 AG-AAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATA
* * *
2033006 ATAATATTTGGTGAATTTTAAAAAT-AAAATAAAAATA
127 ATAATATTTGATGAATTTTAAAAATCAAAA-AACAAGA
* * *
2033043 AAAATCTCCTC-AAAAAAGTTTACGGAGTAGAAAACTCCG-TATT-GAAGAAAATGGGAAATTTC
1 AAAATCCCCTCGAAAAAA-TTTACGGAGTAGAAAACTCTGTTTTTCGAA-AAAA--GGAAATTTC
* * * *
2033105 AAAGAAAAAATTCAAAAATTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATAGGAAATAA
62 -AAG-AAAAATTC-AAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAA
*
2033170 ATGATAATATTTGA-GAAATTTT
124 ATAATAATATTTGATG-AATTTT
2033192 GATGTTTAAA
Statistics
Matches: 550, Mismatches: 70, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
162 20 0.04
163 91 0.17
164 224 0.41
165 104 0.19
166 44 0.08
167 67 0.12
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (163 bp):
AAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCTGTTTTTCGAAAAAAGGAAATTTCAAGA
AAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAA
TATTTGATGAATTTTAAAAATCAAAAAACAAGA
Found at i:2032950 original size:328 final size:328
Alignment explanation
Indices: 2032427--2033191 Score: 972
Period size: 328 Copynumber: 2.3 Consensus size: 328
2032417 AAACTTGATT
* * * *
2032427 TTTCAAAGAAAGGGAATTTCAAGGAAAAACTTTAAAATTCATGGAAATGAATGAACTTTTGATAA
1 TTTCAAAAAAAGGGAATTTCAAGGAAAAA-TTCAAAATTCATGGAAATGAATGAATTTTTGAAAA
* * * ** * *
2032492 CTGAATTACTATGAAATCAATAATAATATTTTTTGAATTTTAAAAATCAAAAAATAAGAAAAATC
65 CTGAATTAATGTGAAATAAATAATAATATTTGATAAATTTTAAAAATCAAAAAACAAGAAAAATC
* * *
2032557 CCCTCGAAAAAATTTACGGAGTAGAAAACTCTGTTTTTTGGAAAAAAGGAAATTTCAAGAAAAAT
130 CCCTCAAAAAAATTTACGGAGTAGAAAACTCTGTTATTTCGAAAAAAGGAAATTTCAAGAAAAAT
* * *
2032622 TCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTGATATGAAATAAATTATAATATTT
195 TCAAAACTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAATATTT
* * *
2032687 GATGAA-TTTAAAAGATCAAAA-AACAAGAAAAATC-CCCCTAAAAATTTTACAGAGTAGAAAAC
260 GATGAATTTTAAAA-AT-AAAATAAAAAGAAAAATCTCCCCAAAAAAGTTTACAGAGTAGAAAAC
2032749 TCCGTA
323 TCCGTA
* * *
2032755 TTTCAAAAAAAGGGAATTTCAAGGAAAAATTCAATATTCATGGAAATGAATGATTTTTTTTAAAA
1 TTTCAAAAAAAGGGAATTTCAAGGAAAAATTCAAAATTCATGGAAATGAATGA-ATTTTTGAAAA
*
2032820 CTGAATTAATGTGAAATAAATAATAATATTTGATAAATTTT-AGAATCAAAAAACAAGAAAAATC
65 CTGAATTAATGTGAAATAAATAATAATATTTGATAAATTTTAAAAATCAAAAAACAAGAAAAATC
* *
2032884 CCC-CTAAAAAAATTTACGGAGTAGAAAACTTTG-TATTTCG-AAAAATGAGAATTTCAAAGAAA
130 CCCTC-AAAAAAATTTACGGAGTAGAAAACTCTGTTATTTCGAAAAAAGGA-AATTTC-AAG-AA
* * *
2032946 AAATTTAAAACTTATGGAAATGAATGAATTTTTTAAAACTGAATTAATATGGAATAAATAATAAT
191 AAATTCAAAACTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAAT
* * * *
2033011 ATTTGGTGAATTTTAAAAATAAAATAAAAATAAAAATCTCCTCAAAAAAGTTTACGGAGTAGAAA
256 ATTTGATGAATTTTAAAAATAAAATAAAAAGAAAAATCTCCCCAAAAAAGTTTACAGAGTAGAAA
2033076 ACTCCGTA
321 ACTCCGTA
* * * * *
2033084 -TTGAAGAAAATGGGAAATTTCAAAGAAAAAATTCAAAAATTTATGAAAATGAATGAATTTTTGA
1 TTTCAA-AAAAAGGG-AATTTC-AAGGAAAAATTC-AAAATTCATGGAAATGAATGAATTTTTGA
* * * *
2033148 GAACTGATTTAATAG-GAAATAAATGATAATATTTGAGAAATTTT
62 AAACTGAATTAAT-GTGAAATAAATAATAATATTTGATAAATTTT
2033192 GATGTTTAAA
Statistics
Matches: 379, Mismatches: 45, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
325 7 0.02
326 12 0.03
327 79 0.21
328 157 0.41
329 44 0.12
330 6 0.02
331 55 0.15
332 19 0.05
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (328 bp):
TTTCAAAAAAAGGGAATTTCAAGGAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAAC
TGAATTAATGTGAAATAAATAATAATATTTGATAAATTTTAAAAATCAAAAAACAAGAAAAATCC
CCTCAAAAAAATTTACGGAGTAGAAAACTCTGTTATTTCGAAAAAAGGAAATTTCAAGAAAAATT
CAAAACTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAATATTTG
ATGAATTTTAAAAATAAAATAAAAAGAAAAATCTCCCCAAAAAAGTTTACAGAGTAGAAAACTCC
GTA
Done.