Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 29
Found at i:1197729 original size:26 final size:27
Alignment explanation
Indices: 1197642--1197733 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 27
1197632 TAAATACACA
*
1197642 TCTTAATATTAAAAATATATTCTATTCTTA-
1 TCTTAAT-TTAAAAA-ATA-TATATT-TTAG
*
1197672 TCTTAA-CTAAAAAATATATATTTTAG
1 TCTTAATTTAAAAAATATATATTTTAG
*
1197698 TCTTAACTTTAAAAAA-A-ATATTTTAT
1 TCTTAA-TTTAAAAAATATATATTTTAG
*
1197724 TTTTAATTTA
1 TCTTAATTTA
1197734 TTTTAAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.13
26 24 0.44
27 4 0.07
28 13 0.24
30 6 0.11
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (27 bp):
TCTTAATTTAAAAAATATATATTTTAG
Found at i:1197803 original size:32 final size:30
Alignment explanation
Indices: 1197765--1197864 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 30
1197755 TCTTATAATA
1197765 TTTTAAAATTCAGATAAAAAATAAAATATATT
1 TTTTAAAATT-AGAT-AAAAATAAAATATATT
* * *
1197797 TTTTAAAATTAAAATTAAATTAAAATATATGT
1 TTTTAAAATT-AGATAAAAATAAAATATAT-T
* *
1197829 TTTT-AAGTTAGGATAAAAATAAAATATATA
1 TTTTAAAATTA-GATAAAAATAAAATATATT
1197859 TTTTAA
1 TTTTAA
1197865 GTTAAAACAA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 5 0.09
31 33 0.59
32 18 0.32
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTAAAATTAGATAAAAATAAAATATATT
Found at i:1197865 original size:30 final size:30
Alignment explanation
Indices: 1197781--1197871 Score: 110
Period size: 31 Copynumber: 3.0 Consensus size: 30
1197771 AATTCAGATA
*
1197781 AAAAATAAAATATATTTTTTAAAATTAAAAT
1 AAAAATAAAATATATTTTTT-AAGTTAAAAT
* * **
1197812 TAAATTAAAATATATGTTTTTAAGTTAGGAT
1 AAAAATAAAATATAT-TTTTTAAGTTAAAAT
*
1197843 AAAAATAAAATATATATTTTAAGTTAAAA
1 AAAAATAAAATATATTTTTTAAGTTAAAA
1197872 CAAGATTAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 11 0.22
31 33 0.67
32 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAAATAAAATATATTTTTTAAGTTAAAAT
Found at i:1197920 original size:30 final size:30
Alignment explanation
Indices: 1197832--1198005 Score: 153
Period size: 30 Copynumber: 5.9 Consensus size: 30
1197822 TATATGTTTT
* * * *
1197832 TAAGTTAGGATAAAAATAAAATATATATT-T
1 TAAGTTAAGATAAGAATATAATATAT-TTAA
* * *
1197862 TAAGTTAAAACAAGATTA-AATAATATTTAA
1 TAAGTTAAGATAAGAATATAAT-ATATTTAA
* *
1197892 TAATTTAAGGTAAGAATATAATATATTTAA
1 TAAGTTAAGATAAGAATATAATATATTTAA
* * * *
1197922 TAATTTAAGTTAATAATATAATATATGTAA
1 TAAGTTAAGATAAGAATATAATATATTTAA
1197952 TAAGTTAAGATAA-AA-A-AA-ATATTTATA
1 TAAGTTAAGATAAGAATATAATATATTTA-A
*
1197979 AAAGTTAAGATAAGAATATAATATATT
1 TAAGTTAAGATAAGAATATAATATATT
1198006 ACTTATGTCC
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
26 6 0.05
27 15 0.13
28 3 0.03
29 8 0.07
30 78 0.66
31 8 0.07
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.37
Consensus pattern (30 bp):
TAAGTTAAGATAAGAATATAATATATTTAA
Found at i:1199040 original size:20 final size:20
Alignment explanation
Indices: 1199015--1199062 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1199005 TCCTCAGTAG
* *
1199015 CGATACTGACCTCTGGGTAT
1 CGATACTAACATCTGGGTAT
*
1199035 CGATACTAACATTTGGGTAT
1 CGATACTAACATCTGGGTAT
*
1199055 CAATACTA
1 CGATACTA
1199063 CTGACTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (20 bp):
CGATACTAACATCTGGGTAT
Found at i:1200564 original size:30 final size:30
Alignment explanation
Indices: 1200532--1200755 Score: 125
Period size: 30 Copynumber: 7.3 Consensus size: 30
1200522 AAATAATAAT
*
1200532 AAATAATATTTAATAGTTTAAGGTAAGAATA
1 AAAT-ATATTTAATAATTTAAGGTAAGAATA
*
1200563 AAATATATTTAATAATTTAAGTTAAGAATA
1 AAATATATTTAATAATTTAAGGTAAGAATA
* * * * *
1200593 TAGTATATGTAATAAGTTAA--TACAAAACTAA
1 AAATATATTTAATAATTTAAGGTA-AGAA-T-A
* ** * *
1200624 AATATATATTTAAAAAAATAAGATAAAAATA
1 AA-ATATATTTAATAATTTAAGGTAAGAATA
** * *
1200655 AAATATACTTTTCTAGA-TTAAGATAAGAAAA
1 AAATATA-TTTAATA-ATTTAAGGTAAGAATA
* * * *
1200686 AAATATATATT-TTTAGTTAAGATAAGAATA
1 AAATATAT-TTAATAATTTAAGGTAAGAATA
* * *
1200716 AAATATATTTAAT-ATGTCAAGATAAAAATA
1 AAATATATTTAATAAT-TTAAGGTAAGAATA
1200746 AAATATATTT
1 AAATATATTT
1200756 TTTAATGTTA
Statistics
Matches: 155, Mismatches: 26, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 7 0.05
30 92 0.59
31 33 0.21
32 15 0.10
33 4 0.03
34 2 0.01
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (30 bp):
AAATATATTTAATAATTTAAGGTAAGAATA
Found at i:1200719 original size:61 final size:61
Alignment explanation
Indices: 1200512--1200775 Score: 175
Period size: 60 Copynumber: 4.3 Consensus size: 61
1200502 ATAGAGTATA
* * * * *
1200512 TTTTAA-GTTAAAATAATAAT-AAATAATATTTAATA-GTTTAAGGTAAGAATAAAATATATT
1 TTTTAATGTTAAGATAAGAATAAAAT-ATATTTAATATG-TCAAGATAAAAATAAAATATATT
** * * * * * * * * *
1200572 TAATAAT-TTAAGTTAAGAATATAGTATATGTAATAAGTTAATACAAAACTAAAATATATAT
1 TTTTAATGTTAAGATAAGAATAAAATATATTTAATATGTCAAGATAAAAATAAAATATAT-T
** *** * ** *
1200633 TTAAAAAAATAAGATAAAAATAAAATATACTTTTCTA-GATTAAGATAAGAAA-AAAATATATAT
1 TTTTAATGTTAAGATAAGAATAAAATATA-TTTAATATG-TCAAGATAA-AAATAAAATATAT-T
1200696 TTTT-A-GTTAAGATAAGAATAAAATATATTTAATATGTCAAGATAAAAATAAAATATATT
1 TTTTAATGTTAAGATAAGAATAAAATATATTTAATATGTCAAGATAAAAATAAAATATATT
*
1200755 TTTTAATGTTAAGATGAGAAT
1 TTTTAATGTTAAGATAAGAAT
1200776 TTAATTTAAT
Statistics
Matches: 156, Mismatches: 36, Indels: 23
0.73 0.17 0.11
Matches are distributed among these distances:
59 8 0.05
60 63 0.40
61 41 0.26
62 18 0.12
63 24 0.15
64 2 0.01
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (61 bp):
TTTTAATGTTAAGATAAGAATAAAATATATTTAATATGTCAAGATAAAAATAAAATATATT
Found at i:1200793 original size:18 final size:18
Alignment explanation
Indices: 1200756--1200802 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1200746 AAATATATTT
1200756 TTTAATGTTAAGATGAGAA
1 TTTAAT-TTAAGATGAGAA
* *
1200775 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGAGAA
*
1200793 TTCAATTTAA
1 TTTAATTTAA
1200803 AATTTATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (18 bp):
TTTAATTTAAGATGAGAA
Found at i:1205172 original size:50 final size:50
Alignment explanation
Indices: 1205090--1205186 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
1205080 CATGAAGACA
* * * *
1205090 TTGGCGCCAAGATGAACCAACATGTCATCATTCGGCCAAGGGAGATGACT
1 TTGGCGCCAAGATGAACAAACATATCACCATTCAGCCAAGGGAGATGACT
*
1205140 TTGGCGCCAAGATGAACAAACATATCACCATTCAGCCAAGGGTGATG
1 TTGGCGCCAAGATGAACAAACATATCACCATTCAGCCAAGGGAGATG
1205187 TATCTTCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.20
Consensus pattern (50 bp):
TTGGCGCCAAGATGAACAAACATATCACCATTCAGCCAAGGGAGATGACT
Found at i:1207665 original size:11 final size:10
Alignment explanation
Indices: 1207633--1207658 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1207623 CACTTTTTTT
1207633 AAAAAAACAA
1 AAAAAAACAA
1207643 AAAAAAACAA
1 AAAAAAACAA
1207653 AAAAAA
1 AAAAAA
1207659 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1217514 original size:14 final size:14
Alignment explanation
Indices: 1217476--1217516 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1217466 GTGTTTTGGT
1217476 TTAAGTGTTATGTA
1 TTAAGTGTTATGTA
* *
1217490 ATCAGTGTTATGTA
1 TTAAGTGTTATGTA
*
1217504 TTAAGTATTATGT
1 TTAAGTGTTATGT
1217517 TGTAAGCAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (14 bp):
TTAAGTGTTATGTA
Found at i:1218637 original size:14 final size:14
Alignment explanation
Indices: 1218618--1218657 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1218608 TGTTTTGGTT
1218618 TAAGTGTTATGTAA
1 TAAGTGTTATGTAA
* *
1218632 TCAGTGTTATGTAT
1 TAAGTGTTATGTAA
1218646 TAAGTGTTATGT
1 TAAGTGTTATGT
1218658 TGTAAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (14 bp):
TAAGTGTTATGTAA
Found at i:1223806 original size:33 final size:33
Alignment explanation
Indices: 1223764--1223832 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1223754 TCTCACAAAA
1223764 GATCAAATATTTTATATGAGGACAAAATACATT
1 GATCAAATATTTTATATGAGGACAAAATACATT
1223797 GATCAAATATTTTATATGAGGACAAAATACATT
1 GATCAAATATTTTATATGAGGACAAAATACATT
1223830 GAT
1 GAT
1223833 ATTTGATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (33 bp):
GATCAAATATTTTATATGAGGACAAAATACATT
Found at i:1228609 original size:30 final size:30
Alignment explanation
Indices: 1228575--1228648 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
1228565 AGTCTGCAAG
* * * *
1228575 AAGGTGATAGGCAGCTAGCATGTGATAAGC
1 AAGGTGATAGGCACCAAACATATGATAAGC
*
1228605 AAGGTGATAGGCGACCAAACTTATGATAAGC
1 AAGGTGATAGGC-ACCAAACATATGATAAGC
*
1228636 AAGGTGATGGGCA
1 AAGGTGATAGGCA
1228649 TCATAGTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (30 bp):
AAGGTGATAGGCACCAAACATATGATAAGC
Found at i:1231855 original size:20 final size:21
Alignment explanation
Indices: 1231832--1231874 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 21
1231822 ACCACATGAA
1231832 TAGTACCAATACT-CTTATGG
1 TAGTACCAATACTACTTATGG
1231852 TAGTACCAATACTACCTTATGG
1 TAGTACCAATACTA-CTTATGG
1231874 T
1 T
1231875 TTCAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (21 bp):
TAGTACCAATACTACTTATGG
Found at i:1232984 original size:66 final size:65
Alignment explanation
Indices: 1232897--1233051 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 65
1232887 ATTGAATTTA
* * * * *
1232897 GAATGCA-TTTAGTGTACCGATGCATAAT-CTATGCATCGATGCACCCCCA-GCTATTTTTAAAA
1 GAATGCATTTTA-TGCATCGATGCA-AATACCATGCATCGATGCA-CCCCAGGCT-TGTATAAAA
1232959 CATC
62 CATC
* * *
1232963 GAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCCAGGCTTGTATGAAACATC
1 GAATGCATTTTATGCATCGATGCAAATACCATGCATCGATGCACCCCAGGCTTGTATAAAACATC
* *
1233028 GAATGTATTATATGCATCGATGCA
1 GAATGCATTTTATGCATCGATGCA
1233052 CCATAAGTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
65 38 0.50
66 34 0.45
67 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (65 bp):
GAATGCATTTTATGCATCGATGCAAATACCATGCATCGATGCACCCCAGGCTTGTATAAAACATC
Found at i:1236432 original size:18 final size:18
Alignment explanation
Indices: 1236409--1236448 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1236399 TTGTTGAGAG
1236409 GAAAATCGAACTTTAGAA
1 GAAAATCGAACTTTAGAA
1236427 GAAAATCGAACTTTAGAA
1 GAAAATCGAACTTTAGAA
1236445 GAAA
1 GAAA
1236449 TGGCTAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
GAAAATCGAACTTTAGAA
Found at i:1241703 original size:65 final size:65
Alignment explanation
Indices: 1241634--1241760 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
1241624 AATGCATAAT
* * *
1241634 CCATGCATCGATGCACCCCA-GCTATTTCT-AAAACATCGAATGCATTTTATGCATCGATGCACA
1 CCATGCATCGATGCACCCCAGGCT-TGTATGAAAA-ATCGAATGCATTATATGCATCGATGCACA
1241697 TA
64 TA
* * *
1241699 CCATGCATTGATGCACTCCAGGCTTGTATGAAAAATCGAATGTATTATATGCATCGATGCAC
1 CCATGCATCGATGCACCCCAGGCTTGTATGAAAAATCGAATGCATTATATGCATCGATGCAC
1241761 CATAAGTGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
65 47 0.87
66 7 0.13
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
CCATGCATCGATGCACCCCAGGCTTGTATGAAAAATCGAATGCATTATATGCATCGATGCACATA
Found at i:1243724 original size:21 final size:21
Alignment explanation
Indices: 1243698--1243737 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1243688 AAGACTTTAT
1243698 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
1243719 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1243738 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:1246851 original size:16 final size:16
Alignment explanation
Indices: 1246830--1246866 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1246820 TGCCTTCTCA
1246830 GATGCGGATTTTAGAG
1 GATGCGGATTTTAGAG
*
1246846 GATGCGGATTTTGGAG
1 GATGCGGATTTTAGAG
1246862 GATGC
1 GATGC
1246867 AAATTAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.41, T:0.30
Consensus pattern (16 bp):
GATGCGGATTTTAGAG
Found at i:1247612 original size:44 final size:40
Alignment explanation
Indices: 1247558--1247680 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 40
1247548 TTTTGCATAA
1247558 TGCATCGATACACTAGAGAGTGCATCGATGCATCCTTTTGAATG
1 TGCATCGATACACTAGA-A-TGCATCGATGCATCC--TTGAATG
* *
1247602 TGCATCGATACATTATGAATATGCATCGATGTACTCCTTGAATG
1 TGCATCGATACACTA-G-A-ATGCATCGATGCA-TCCTTGAATG
* **
1247646 TGCATCGATGCACAATACCATGCATCGATGCATCC
1 TGCATCGAT--ACACTAGAATGCATCGATGCATCC
1247681 GTTGGTTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.04
43 12 0.18
44 30 0.45
45 12 0.18
46 10 0.15
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (40 bp):
TGCATCGATACACTAGAATGCATCGATGCATCCTTGAATG
Found at i:1247649 original size:23 final size:23
Alignment explanation
Indices: 1247577--1247655 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
1247567 ACACTAGAGA
*
1247577 GTGCATCGATGCA-TCCTTTTGAAT
1 GTGCATCGATGTACTCC--TTGAAT
1247601 GTGCATCGA--TACAT--TATGAAT
1 GTGCATCGATGTAC-TCCT-TGAAT
*
1247622 ATGCATCGATGTACTCCTTGAAT
1 GTGCATCGATGTACTCCTTGAAT
1247645 GTGCATCGATG
1 GTGCATCGATG
1247656 CACAATACCA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 2 0.04
23 18 0.40
24 11 0.24
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (23 bp):
GTGCATCGATGTACTCCTTGAAT
Found at i:1248186 original size:13 final size:12
Alignment explanation
Indices: 1248151--1248184 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1248141 CATATTATGA
*
1248151 TTTTTCAAATAT
1 TTTTTCAAATAG
1248163 TATTTTCAAATAG
1 T-TTTTCAAATAG
1248176 TTTTTCAAA
1 TTTTTCAAA
1248185 ATCTTGCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTTCAAATAG
Found at i:1250451 original size:65 final size:65
Alignment explanation
Indices: 1250352--1250478 Score: 184
Period size: 65 Copynumber: 2.0 Consensus size: 65
1250342 GATGCATAAT
* * *
1250352 CCATGCATCGATGCACCCCAGCTATTTTTAAAACATCGAATGCATTTTATGCATCGATGCACATA
1 CCATGCATCGATGCACCCCAGCTATGTATAAAACATCGAATGCATTATATGCATCGATGCACATA
* * *
1250417 CCATGCATCGATGCACTCCAGGCT-TGTATGAAACATCGAATGTATTATATGCATCGATGCAC
1 CCATGCATCGATGCACCCCA-GCTATGTATAAAACATCGAATGCATTATATGCATCGATGCAC
1250479 CATAAGTGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 52 0.95
66 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
CCATGCATCGATGCACCCCAGCTATGTATAAAACATCGAATGCATTATATGCATCGATGCACATA
Found at i:1252440 original size:21 final size:21
Alignment explanation
Indices: 1252414--1252453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1252404 AAGACTTTAT
1252414 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
1252435 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1252454 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:1255934 original size:21 final size:20
Alignment explanation
Indices: 1255901--1255939 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1255891 AGAATTTGTT
* *
1255901 GATACTTTTGAATGTGCATC
1 GATACTTATGAATATGCATC
1255921 GATACATTATGAATATGCA
1 GATAC-TTATGAATATGCA
1255940 CTGATGCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
GATACTTATGAATATGCATC
Found at i:1256501 original size:13 final size:12
Alignment explanation
Indices: 1256466--1256499 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1256456 CGTATTATGA
*
1256466 TTTTTCAAATAT
1 TTTTTCAAATAG
1256478 TATTTTCAAATAG
1 T-TTTTCAAATAG
1256491 TTTTTCAAA
1 TTTTTCAAA
1256500 ATCTTGCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTTCAAATAG
Found at i:1258740 original size:64 final size:65
Alignment explanation
Indices: 1258662--1258787 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 65
1258652 GATGCATAAT
* * * *
1258662 CCATGCATCGATGCACCCCA-GCTATTTTTAAAACATCGAATGCATTTTATGCATCGATGCACAT
1 CCATGCATCGATGCACCCCAGGCT-TGTATAAAACATCAAATGCATTATATGCATCGATGCACAT
1258726 A
65 A
* * *
1258727 CCATGCATC-ATGCACTCCAGGCTTGTATGAAACATCAAATGTATTATATGCATCGATGCAC
1 CCATGCATCGATGCACCCCAGGCTTGTATAAAACATCAAATGCATTATATGCATCGATGCAC
1258788 CATAAGTGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 41 0.77
65 12 0.23
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (65 bp):
CCATGCATCGATGCACCCCAGGCTTGTATAAAACATCAAATGCATTATATGCATCGATGCACATA
Found at i:1260561 original size:21 final size:21
Alignment explanation
Indices: 1260520--1260562 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1260510 AAAATGAAAG
* **
1260520 TAGATGAAGTACCTTGTAAAT
1 TAGATAAAGTACCTTAAAAAT
1260541 TAGATAAAGTACCTTAAAAAT
1 TAGATAAAGTACCTTAAAAAT
1260562 T
1 T
1260563 GTCTGGGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (21 bp):
TAGATAAAGTACCTTAAAAAT
Found at i:1262058 original size:16 final size:18
Alignment explanation
Indices: 1262033--1262071 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1262023 TATGGATTTT
*
1262033 TTTTTGATTTTT-TTGGC
1 TTTTTGATTTTTATTGCC
1262050 TTTTT-ATTTTTATTGCC
1 TTTTTGATTTTTATTGCC
1262067 TTTTT
1 TTTTT
1262072 TCTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.74
Consensus pattern (18 bp):
TTTTTGATTTTTATTGCC
Found at i:1262462 original size:17 final size:17
Alignment explanation
Indices: 1262436--1262471 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1262426 GTTGGTGGAA
*
1262436 ATTAAAACAAATAATAG
1 ATTAAAACAAAGAATAG
*
1262453 ATTAAGACAAAGAATAG
1 ATTAAAACAAAGAATAG
1262470 AT
1 AT
1262472 AAGGATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (17 bp):
ATTAAAACAAAGAATAG
Found at i:1263105 original size:20 final size:20
Alignment explanation
Indices: 1263080--1263123 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1263070 ATAAAAACAA
*
1263080 GTTGAGGACACTTGAAGAGT
1 GTTGAGGACACTTGAAGAAT
1263100 GTTGAGGACACTTGAAGAAT
1 GTTGAGGACACTTGAAGAAT
1263120 GTTG
1 GTTG
1263124 GAACACCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (20 bp):
GTTGAGGACACTTGAAGAAT
Found at i:1265539 original size:13 final size:13
Alignment explanation
Indices: 1265521--1265554 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1265511 ATTTTTCAAA
1265521 TGCATAACATTTT
1 TGCATAACATTTT
1265534 TGCATAACATTTT
1 TGCATAACATTTT
1265547 TGCATAAC
1 TGCATAAC
1265555 TTTATGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (13 bp):
TGCATAACATTTT
Found at i:1265562 original size:12 final size:13
Alignment explanation
Indices: 1265520--1265562 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1265510 AATTTTTCAA
1265520 ATGCATAACATTT
1 ATGCATAACATTT
*
1265533 TTGCATAACATTT
1 ATGCATAACATTT
*
1265546 TTGCATAAC-TTT
1 ATGCATAACATTT
1265558 ATGCA
1 ATGCA
1265563 CATGCACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (13 bp):
ATGCATAACATTT
Found at i:1267482 original size:30 final size:31
Alignment explanation
Indices: 1267446--1267505 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1267436 GGTCTTCTAG
*
1267446 AAGGTGATAGACGG-CTAGCATATGATAAGT
1 AAGGTGATAGACGGTCAAGCATATGATAAGT
* *
1267476 AAGGTGATAGGCGGTCAAGCTTATGATAAG
1 AAGGTGATAGACGGTCAAGCATATGATAAG
1267506 CACGATGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.23
Consensus pattern (31 bp):
AAGGTGATAGACGGTCAAGCATATGATAAGT
Found at i:1268945 original size:19 final size:18
Alignment explanation
Indices: 1268908--1268953 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
1268898 TTGTAATAGC
1268908 GTTTTGGGA-TATATCGG
1 GTTTTGGGATTATATCGG
*
1268925 GTTTTGGGATCTATATTGG
1 GTTTTGGGAT-TATATCGG
1268944 GTTTTGGGAT
1 GTTTTGGGAT
1268954 ACATTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.15, C:0.04, G:0.35, T:0.46
Consensus pattern (18 bp):
GTTTTGGGATTATATCGG
Found at i:1271471 original size:16 final size:16
Alignment explanation
Indices: 1271450--1271484 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1271440 TTCTTTCAAG
1271450 ATCAATGACTATATCC
1 ATCAATGACTATATCC
1271466 ATCAATGACTATATCC
1 ATCAATGACTATATCC
1271482 ATC
1 ATC
1271485 TCGGCAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (16 bp):
ATCAATGACTATATCC
Found at i:1272218 original size:16 final size:17
Alignment explanation
Indices: 1272181--1272218 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1272171 GGATAAAAAA
*
1272181 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
1272198 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
1272214 TTAAA
1 TTAAA
1272219 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:1272263 original size:27 final size:28
Alignment explanation
Indices: 1272228--1272281 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1272218 ATTAATTGTA
* *
1272228 AATTATTTATTTGAATTTA-AAAATATTT
1 AATTATTTATAT-AACTTAGAAAATATTT
1272256 AATT-TTTATATAACTTAGAAAATATT
1 AATTATTTATATAACTTAGAAAATATT
1272282 AAAAAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 14 0.61
28 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
AATTATTTATATAACTTAGAAAATATTT
Found at i:1272424 original size:29 final size:29
Alignment explanation
Indices: 1272392--1272455 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
1272382 AAAAAATCGG
*
1272392 TTAATTCGGTTCGGTTAATAATTTTTAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
1272421 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
*
1272450 TAAATT
1 TTAATT
1272456 TTGATTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (29 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAA
Found at i:1272597 original size:107 final size:109
Alignment explanation
Indices: 1272477--1272724 Score: 358
Period size: 107 Copynumber: 2.3 Consensus size: 109
1272467 AACCGAACTG
* * *
1272477 AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTAGATTAACCGAGC
1 AAAAAAATTGGTTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTAGATTAACCAAAC
1272542 CGAATTAACCAAATTTTTGCTTCGATTAATTC-GATTAATAA-TT
66 CGAATTAACCAAATTTTTGCTTCGATTAATTCTG-TTAATAATTT
* *
1272585 -AAAAAATTGGTTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAAC
1 AAAAAAATTGGTTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTAGATTAACCAAAC
* * *
1272649 CGAATTAATCGAATTTTTGCTTCGATTATTTCTGTTAATAATTTT
66 CGAATTAACCAAATTTTTGCTTCGATTAATTCTGTTAATAA-TTT
*
1272694 CAAAAAAATTTGGTTAATTCGGTTCGATTAA
1 -AAAAAAA-TTGGTTAATTCGGTTCGGTTAA
1272725 CCGAACCGAA
Statistics
Matches: 124, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
107 95 0.77
108 1 0.01
109 2 0.02
111 6 0.05
112 20 0.16
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (109 bp):
AAAAAAATTGGTTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTAGATTAACCAAAC
CGAATTAACCAAATTTTTGCTTCGATTAATTCTGTTAATAATTT
Found at i:1272825 original size:20 final size:20
Alignment explanation
Indices: 1272800--1272838 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1272790 ATTAGTCATG
*
1272800 AATAATTTATTTAATTAAAC
1 AATAATTTATTTAAATAAAC
*
1272820 AATAATTTGTTTAAATAAA
1 AATAATTTATTTAAATAAA
1272839 TAATTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AATAATTTATTTAAATAAAC
Found at i:1273297 original size:30 final size:30
Alignment explanation
Indices: 1273261--1273334 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
1273251 ATTAACGGCG
*
1273261 CGGTGGTCTGATTGAA-TCAATTAAAA-AGTT
1 CGGTGGTCTGATTGAAGACAA--AAAATAGTT
*
1273291 TGGTGGTCTGATT-AAGACAAAAAATAGTT
1 CGGTGGTCTGATTGAAGACAAAAAATAGTT
1273320 CGGTGGTCTGATTGA
1 CGGTGGTCTGATTGA
1273335 TTATTGAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.11
29 18 0.47
30 16 0.42
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.32
Consensus pattern (30 bp):
CGGTGGTCTGATTGAAGACAAAAAATAGTT
Found at i:1274108 original size:28 final size:28
Alignment explanation
Indices: 1274050--1274109 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1274040 CAGAATATGC
*
1274050 TCAACATCCTCCATGCTGCTTCAACTCT
1 TCAACATCCTCCATGCTGCTCCAACTCT
*
1274078 TCAACATCCTTTC-TGCTGCTCCAAGCT-T
1 TCAACATCC-TCCATGCTGCTCCAA-CTCT
1274106 TCAA
1 TCAA
1274110 ATGGCAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.22, C:0.37, G:0.08, T:0.33
Consensus pattern (28 bp):
TCAACATCCTCCATGCTGCTCCAACTCT
Found at i:1287576 original size:29 final size:29
Alignment explanation
Indices: 1287534--1287592 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1287524 ATTTTCACCT
1287534 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1287563 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1287592 A
1 A
1287593 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1290225 original size:13 final size:14
Alignment explanation
Indices: 1290196--1290227 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1290186 TAAATTCATT
1290196 AAATATTTTAGAAA
1 AAATATTTTAGAAA
*
1290210 AAATATTTTAAAAA
1 AAATATTTTAGAAA
1290224 AAAT
1 AAAT
1290228 TACAAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAATATTTTAGAAA
Found at i:1297753 original size:19 final size:18
Alignment explanation
Indices: 1297693--1297778 Score: 59
Period size: 19 Copynumber: 4.6 Consensus size: 18
1297683 AAAAATATAT
*
1297693 ATAAAAAATAAATCAAAGG
1 ATAAAAAATAAAT-AAAAG
* *
1297712 AAAAAAAATACAAATACAA-
1 ATAAAAAAT--AAATAAAAG
1297731 ATAAAAAATGAAATAAAAG
1 ATAAAAAAT-AAATAAAAG
*
1297750 AT-AAAAATAATTAAATAG
1 ATAAAAAATAAATAAA-AG
*
1297768 ACCAAAAAATA
1 A-TAAAAAATA
1297779 TAAGATAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 6 0.11
18 16 0.30
19 18 0.34
20 9 0.17
21 4 0.08
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (18 bp):
ATAAAAAATAAATAAAAG
Found at i:1297827 original size:2 final size:2
Alignment explanation
Indices: 1297820--1297860 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1297810 GAAGTAAATA
1297820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1297861 AATAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1297939 original size:16 final size:17
Alignment explanation
Indices: 1297916--1297964 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
1297906 GAAACTATAT
*
1297916 ACAAAATAAATCAAAGA
1 ACAAAATAAATCAAAAA
1297933 A-AAAAT-AAT-AAAAA
1 ACAAAATAAATCAAAAA
1297947 ACTAAAATAAATCAAAAA
1 AC-AAAATAAATCAAAAA
1297965 GAAAAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 10 0.37
17 4 0.15
18 5 0.19
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (17 bp):
ACAAAATAAATCAAAAA
Found at i:1298016 original size:2 final size:2
Alignment explanation
Indices: 1297978--1298004 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1297968 AAGAAAGAAA
1297978 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 A
1298005 AGTATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1299288 original size:7 final size:6
Alignment explanation
Indices: 1299270--1299322 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
1299260 AAAACAAACA
* * *
1299270 AAAAAT AAAAAT AAGAAAT AAATAAT AATAAT AATAAT AATAAAT AATAAT
1 AAAAAT AAAAAT AA-AAAT AAA-AAT AAAAAT AAAAAT AA-AAAT AAAAAT
1299321 AA
1 AA
1299323 TATATTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 25 0.61
7 16 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:1299298 original size:3 final size:3
Alignment explanation
Indices: 1299290--1299324 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1299280 ATAAGAAATA
1299290 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
1299325 TATTATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1299323 original size:13 final size:13
Alignment explanation
Indices: 1299272--1299324 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
1299262 AACAAACAAA
* *
1299272 AAATAAAAATAAG
1 AAATAATAATAAT
1299285 AAATAAATAATAAT
1 AAAT-AATAATAAT
1299299 -AATAATAATAAT
1 AAATAATAATAAT
1299311 AAATAATAATAAT
1 AAATAATAATAAT
1299324 A
1 A
1299325 TATTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 9 0.25
13 20 0.56
14 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:1299406 original size:39 final size:37
Alignment explanation
Indices: 1299319--1299634 Score: 234
Period size: 37 Copynumber: 8.6 Consensus size: 37
1299309 ATAAATAATA
*
1299319 ATAATATATTATATATAT-AAAAATATTTTTAAAAAACTAT
1 ATAATATATTAT-T-T-TCAAAAAT-GTTTTAAAAAACTAT
* *
1299359 TTATTATATGTATTTTCTAAAAATGTTTTAAAAAACTAT
1 ATAATATAT-TATTTTC-AAAAATGTTTTAAAAAACTAT
*
1299398 AAAATATA-TATTTTCAAAAATGTTTTAAAAAAACTAT
1 ATAATATATTATTTTCAAAAATGTTTT-AAAAAACTAT
*
1299435 AAAATATA-TATTTTCAAAAATGTTTTAAAAAAACTAT
1 ATAATATATTATTTTCAAAAATGTTTT-AAAAAACTAT
* ***
1299472 ATATTATATATATTTTCAAAAAAAATTTAAAAAACTAT
1 ATAATATAT-TATTTTCAAAAATGTTTTAAAAAACTAT
* *
1299510 ATAATATATAAATGTTTTC-AAAATGTTTT-TAAAAC---
1 ATAATATAT---TATTTTCAAAAATGTTTTAAAAAACTAT
* *
1299545 ----TATA-TATTTTCTAAAAT-TTTTTAAAAACTAT
1 ATAATATATTATTTTCAAAAATGTTTTAAAAAACTAT
*
1299576 ATAGTATA-TAGTTTTCAAAAATG-TTT-AAAAACTAT
1 ATAATATATTA-TTTTCAAAAATGTTTTAAAAAACTAT
*
1299611 ATATTATATACGTATTTTCAAAAA
1 ATA--ATATA-TTATTTTCAAAAA
1299635 CCGTTTGGAA
Statistics
Matches: 232, Mismatches: 21, Indels: 48
0.77 0.07 0.16
Matches are distributed among these distances:
27 10 0.04
28 10 0.04
31 4 0.02
35 18 0.08
36 24 0.10
37 64 0.28
38 34 0.15
39 44 0.19
40 21 0.09
41 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (37 bp):
ATAATATATTATTTTCAAAAATGTTTTAAAAAACTAT
Found at i:1299408 original size:74 final size:73
Alignment explanation
Indices: 1299328--1299606 Score: 201
Period size: 76 Copynumber: 3.9 Consensus size: 73
1299318 AATAATATAT
* ** *
1299328 TATATATAT-AAAAATATTTTTAAAAAACTATTTATTATATGTATTTTCTAAAAATGTTTT-AAA
1 TATATATATCAAAAATATTTTAAAAAAACTA--TAAAATATATATTTTC-AAAAATGTTTTAAAA
1299391 AAACTATAAAA
63 AAACTATAAAA
* *
1299402 TATATATTTTCAAAAATGTTTTAAAAAAACTATAAAATATATATTTTCAAAAATGTTTTAAAAAA
1 TATATA-TATCAAAAATATTTTAAAAAAACTATAAAATATATATTTTCAAAAATGTTTTAAAAAA
*
1299467 ACTATATATTA
65 ACTATA-A-AA
* * * *
1299478 TATATATTTTCAAAAAAAATTT-AAAAAACTATATAATATATAAATGTTTTC-AAAATGTTTT--
1 TATATA-TATCAAAAATATTTTAAAAAAACTATA-AA-ATAT--ATATTTTCAAAAATGTTTTAA
*
1299539 TAAAACTAT---A
61 AAAAACTATAAAA
* * * *
1299549 TAT-T-T-TCTAAAAT-TTTT-TAAAAACTATATAGTATATAGTTTTCAAAAATG-TTTAAAAA
1 TATATATATCAAAAATATTTTAAAAAAACTATAAAATATATA-TTTTCAAAAATGTTTTAAAAA
1299607 CTATATATTA
Statistics
Matches: 172, Mismatches: 20, Indels: 35
0.76 0.09 0.15
Matches are distributed among these distances:
62 2 0.01
63 8 0.05
64 9 0.05
65 3 0.02
66 13 0.08
67 6 0.03
68 1 0.01
70 1 0.01
71 4 0.02
73 11 0.06
74 30 0.17
75 14 0.08
76 49 0.28
77 4 0.02
78 10 0.06
79 7 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (73 bp):
TATATATATCAAAAATATTTTAAAAAAACTATAAAATATATATTTTCAAAAATGTTTTAAAAAAA
CTATAAAA
Found at i:1299571 original size:28 final size:27
Alignment explanation
Indices: 1299524--1299578 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
1299514 TATATAAATG
1299524 TTTTCAAAATGTTTTTAAAACTATATA
1 TTTTCAAAATGTTTTTAAAACTATATA
1299551 TTTTCTAAAAT-TTTTTAAAAACTATATA
1 TTTTC-AAAATGTTTTT-AAAACTATATA
1299579 GTATATAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTCAAAATGTTTTTAAAACTATATA
Found at i:1299657 original size:37 final size:35
Alignment explanation
Indices: 1299564--1299659 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 35
1299554 TCTAAAATTT
* *
1299564 TTTAAAAACTATATAGTATATAGTTTTCAAAAATG
1 TTTAAAAACTATATAATATATAGTTTTCAAAAACG
*
1299599 TTTAAAAACTATATATTATATACGTATTTTCAAAAACCG
1 TTTAAAAACTATATAATATATA-G--TTTTCAAAAA-CG
**
1299638 TTTGGAAACTATATAATATATA
1 TTTAAAAACTATATAATATATA
1299660 TATATATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 21 0.40
36 1 0.02
38 10 0.19
39 20 0.38
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (35 bp):
TTTAAAAACTATATAATATATAGTTTTCAAAAACG
Found at i:1300395 original size:83 final size:83
Alignment explanation
Indices: 1300226--1301380 Score: 1365
Period size: 84 Copynumber: 13.9 Consensus size: 83
1300216 ACTCGGTAAT
* * * * * *
1300226 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAGTTTGATTTGCCTCTGAGTTGAA
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAA--ATGATGTGCCTTTGAGCTGAG
*
1300291 TGTAATCGAACTCGAAAGTC
64 TGTAATCGAACTCGAAGGTC
* * * * * * *
1300311 TTTGATGACAGATAACCCTTATTGCCTTGAGTTATGCTACAAATAATGTGCCTTTGAGTTGAGTG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
1300376 TAATTGAACTCGAATGTC
66 TAATCGAACTCGAAGGTC
* *
1300394 TTTTGTTGGA-AGATAGCCCTTCTTGCCTTCAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAG
1 -TTTGTT-GACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
*
1300458 TGTAATCAAACTCGAAGGTC
64 TGTAATCGAACTCGAAGGTC
* * * * *
1300478 TTTGATGACAAATAACCCTTCTTGTCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
1300543 TAATCAAACTCGAAGGTA
66 TAATCGAACTCGAAGGTC
* * * * * *
1300561 TTTGATGACAAATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
*
1300626 TAATCGAACTCAAAGGTC
66 TAATCGAACTCGAAGGTC
* * *
1300644 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGAGCCTTTGAGCTGAGT
1 -TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
1300709 GTAATCAAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * * * * *
1300728 TTTGATGACATATAACCCTTCTCGTCTTGAGTTATGCTGCAAATAATGTGCCTTTGAGCTGACTG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
1300793 TAATCAAACTCGAAGGTTT
66 TAATCGAACTCGAAGG-TC
* * *
1300812 TTTGTTGGA-AGATAACCATTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGTTGAGT
1 TTTGTT-GACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
1300876 GTAATCAAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * *
1300895 TTTTTTTGGCAGATAGTCCTTCTTGCCTTGTGCTATACTGCAAATGATGTGCCTTTGAGCTGAGT
1 -TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
1300960 GTAATCAAACTCAAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * *
1300979 TTTG--G-CAGATAGCCCTTATTGCCTTAAGTTATGCTGTAAATAATGTGCCTTTGAGCTGAGTG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
*
1301041 TAATC-AACTCGAAGATC
66 TAATCGAACTCGAAGGTC
* * * ** * *
1301058 TTTTGTTGGCAAATAGCTCTTCTTGCCTTGAGCTATATTGCAAATGATATGCCTTTGATCTGAGT
1 -TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
1301123 GTAATCGAACTCGAAGGCC
65 GTAATCGAACTCGAAGGTC
** * * *
1301142 TTTTGTTGGTAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGT
1 -TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
1301207 GTAATTGAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * *
1301226 TTTG--G-CAGATAGCCCTTCTTGCCTTGAACTATGCTGCAAATGATATGCCTTTGAGCTTAGTG
1 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
1301288 TAATCGAACTCGAAGGTC
66 TAATCGAACTCGAAGGTC
* * * ** *
1301306 TTTTGTTGGCAAATAGCCCTTCTTACCTTGAGCTATATTGCAAATGATGTGCCTTTGAGCCGAGT
1 -TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
1301371 GTAATCGAAC
65 GTAATCGAAC
1301381 GCCCTTCTTG
Statistics
Matches: 922, Mismatches: 131, Indels: 35
0.85 0.12 0.03
Matches are distributed among these distances:
79 10 0.01
80 125 0.14
81 6 0.01
82 3 0.00
83 312 0.34
84 426 0.46
85 40 0.04
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (83 bp):
TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTC
Found at i:1300495 original size:167 final size:167
Alignment explanation
Indices: 1300225--1301376 Score: 1344
Period size: 167 Copynumber: 6.9 Consensus size: 167
1300215 AACTCGGTAA
* * * * *
1300225 TTTTGTT-GACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAGTTTGATTTGCCTCTGAGTTG
1 TTTTGTTGGA-AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAA--ATGATGTGCCTTTGAGCTG
* * * * * *
1300289 AATGTAATCGAACTCGAAAGTCTTTGATGACAGATAACCCTTATTGCCTTGAGTTATGCTACAAA
63 AGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA
* * ** *
1300354 TAATGTGCCTTTGAGTTGAGTGTAATTGAACTCGAATGTC
128 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* *
1300394 TTTTGTTGGAAGATAGCCCTTCTTGCCTTCAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGT
1 TTTTGTTGGAAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * * * *
1300459 GTAATCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTTGTCTTGAGCTATGCTACAAATGA
66 GTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGA
1300524 TGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGT-
131 TGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* * * * * *
1300560 ATTTGAT-GACAAATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
1 TTTTGTTGGA-AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * * * *
1300624 CGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAAT
65 TGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAT
*
1300689 GATGAGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
129 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* * * * * * * *
1300728 -TTTGAT-GACATATAACCCTTCTCGTCTTGAGTTATGCTGCAAATAATGTGCCTTTGAGCTGAC
1 TTTTGTTGGA-AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * *
1300791 TGTAATCAAACTCGAAGGTTTTTTGTTGGA-AGATAACCATTCTTGCCTTGAGCTATGCTGCAAA
65 TGTAATCGAACTCGAAGG-TCTTTGTT-GACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA
*
1300855 TGATGTGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTC
128 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* * * * *
1300895 TTTTTTTGGCAGATAGTCCTTCTTGCCTTGTGCTATACTGCAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGAAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * * * * * * *
1300960 GTAATCAAACTCAAAGGTCTTTG--G-CAGATAGCCCTTATTGCCTTAAGTTATGCTGTAAATAA
66 GTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGA
*
1301022 TGTGCCTTTGAGCTGAGTGTAATC-AACTCGAAGATC
131 TGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* ** * *
1301058 TTTTGTTGGCAA-ATAGCTCTTCTTGCCTTGAGCTATATTGCAAATGATATGCCTTTGATCTGAG
1 TTTTGTTGG-AAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* ** * *
1301122 TGTAATCGAACTCGAAGGCCTTTTGTTGGTAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAAT
65 TGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAT
**
1301187 GATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC
129 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
* * * *
1301226 ---T-TTGGCAGATAGCCCTTCTTGCCTTGAACTATGCTGCAAATGATATGCCTTTGAGCTTAGT
1 TTTTGTTGGAAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * * * **
1301287 GTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTACCTTGAGCTATATTGCAAATG
66 GTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATG
*
1301352 ATGTGCCTTTGAGCCGAGTGTAATC
130 ATGTGCCTTTGAGCTGAGTGTAATC
1301377 GAACGCCCTT
Statistics
Matches: 855, Mismatches: 112, Indels: 37
0.85 0.11 0.04
Matches are distributed among these distances:
163 83 0.10
164 193 0.23
165 3 0.00
166 71 0.08
167 386 0.45
168 78 0.09
169 39 0.05
170 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (167 bp):
TTTTGTTGGAAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGA
TGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
Found at i:1301414 original size:60 final size:60
Alignment explanation
Indices: 1301321--1301436 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
1301311 TTGGCAAATA
*
1301321 GCCCTTCTTACCTTGAGCTATATTGCAAATGATGTGCCTTTGAGCCGAGTGTAATCGAAC
1 GCCCTTCTTACCTTAAGCTATATTGCAAATGATGTGCCTTTGAGCCGAGTGTAATCGAAC
* * ** *
1301381 GCCCTTCTTGCCTTAAGCTATGTTGCAAATGATGTTTCTTTGAGCTGAGTGTAATC
1 GCCCTTCTTACCTTAAGCTATATTGCAAATGATGTGCCTTTGAGCCGAGTGTAATC
1301437 AAACTCGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (60 bp):
GCCCTTCTTACCTTAAGCTATATTGCAAATGATGTGCCTTTGAGCCGAGTGTAATCGAAC
Found at i:1301523 original size:143 final size:144
Alignment explanation
Indices: 1301237--1301523 Score: 407
Period size: 143 Copynumber: 2.0 Consensus size: 144
1301227 TTGGCAGATA
* *
1301237 GCCCTTCTTGCCTTGAACTATGCTGCAAATGATATGCCTTTGAGCTTAGTGTAATCGAACTCGAA
1 GCCCTTCTTGCCTTGAACTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAA
* * *
1301302 GGTCTTTTGTTGGCAAATAGCCCTTCTTACCTTGAGCTATATTGCAAATGATGTGCCTTTGAGCC
66 GGTCTTTTGTTGGCAAATAGACCTTCTTACCTTGAGCTATATTACAAATGATGTGCCTTGGAGCC
*
1301367 GAGTGTAATCGAAC
131 GAGCGTAATCGAAC
* * **
1301381 GCCCTTCTTGCCTT-AAGCTATGTTGCAAATGATGTTTCTTTGAGCTGAGTGTAATCAAACTCGA
1 GCCCTTCTTGCCTTGAA-CTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGA
** * *
1301445 A-GTCTTTTGTTGGGGAATAGACCTTCTTTCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGC
65 AGGTCTTTTGTTGGCAAATAGACCTTCTTACCTTGAGCTATATTACAAATGATGTGCCTTGGAGC
* *
1301509 TGAGCGTAGTCGAAC
130 CGAGCGTAATCGAAC
1301524 TCGAAGGTCT
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
143 70 0.56
144 56 0.44
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (144 bp):
GCCCTTCTTGCCTTGAACTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAA
GGTCTTTTGTTGGCAAATAGACCTTCTTACCTTGAGCTATATTACAAATGATGTGCCTTGGAGCC
GAGCGTAATCGAAC
Found at i:1301577 original size:84 final size:84
Alignment explanation
Indices: 1301382--1302161 Score: 994
Period size: 84 Copynumber: 9.3 Consensus size: 84
1301372 TAATCGAACG
* * * * ** * * * *
1301382 CCCTTCTTGCCTTAAGCTATGTTGCAAATGATGTTTCTTTGAGCTGAGTGTAATCAAACTCGAA-
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1301446 GTCTTTTGTTGG-GGAATAGA
66 GTCTTTTGTTGGCAG-ATA-A
** * * *
1301466 -CCTTCTTTCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1301530 GTCTTTTGTTGGCAGATAA
66 GTCTTTTGTTGGCAGATAA
* * *
1301549 CCCTTCTAGACTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
1301614 GTCTTTTATTGGCAAATAA
66 GTCTTTTGTTGGCAGATAA
** * * * *
1301633 CCCTTCTTTCCTTGAACTT-TGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACAT-GA
1 CCCTTCTAGCCTTG-AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC-TCGA
1301696 AGGTCTTTTGTTGGCAGATAA
64 AGGTCTTTTGTTGGCAGATAA
* * * *
1301717 CCCTTCTAGCCTTGAGTTAAGTTACAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1301782 GTCTTTGGTTGGCAGATAA
66 GTCTTTTGTTGGCAGATAA
*
1301801 CCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
1301866 GTCTTTTGGTGGCAAATAA
66 GTCTTTTGTTGGCAGATAA
* * * * *
1301885 CACTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1301950 GTCTTTGGTTGGCAGATAA
66 GTCTTTTGTTGGCAGATAA
*
1301969 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * *
1302034 GTCTTTTGGTGACAAATAT
66 GTCTTTTGTTGGCAGATAA
** * *
1302053 CCCTTCTTCCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * *
1302118 GTCTTTGGCTGACAGATAA
66 GTCTTTTGTTGGCAGATAA
* *
1302137 CCTTTCTCGCCTTGAGTTATGCTGC
1 CCCTTCTAGCCTTGAGTTATGCTGC
1302162 CGATAGTTTC
Statistics
Matches: 613, Mismatches: 76, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
83 59 0.10
84 549 0.90
85 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTTGTTGGCAGATAA
Found at i:1303496 original size:95 final size:94
Alignment explanation
Indices: 1303294--1303557 Score: 325
Period size: 95 Copynumber: 2.7 Consensus size: 94
1303284 AGCTAGCTGA
* * *
1303294 ATCCATAAAGCCGAGGCATTTAACCAATTTCTCTAGAGGGAC-AGTTCAATGTCATTGTATAG-A
1 ATCCATAAAGCCG-GGCATTTAACCAATTACTCTAGAGGGACAACTT-AA-G-C-TT-TATTGTA
1303357 TATTATAATAACCTTTATCAGGCTAGCTGAATATT
60 TATTATAATAACCTTTATCAGGCTAGCTGAATATT
* *
1303392 ATCCATAAAGCCGGGACATTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTGTATATTG
1 ATCCATAAAGCCGGG-CATTTAACCAATTACTCTAGAGGGACAACTTAAGCTTTATTGTATATTA
* *
1303457 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATAACCTTTATCAGGCTAGCTGAATATT
* * * * *
1303487 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTGGAGGGACAACTCAAGCTATATTGTATATAT
1 ATCCATAAAG-CCGGGCATTTAACCAATTACTCTAGAGGGACAACTTAAGCTTTATTGTATAT-T
1303552 ATAATA
64 ATAATA
1303558 TTATAATCTG
Statistics
Matches: 147, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
94 4 0.03
95 87 0.59
96 10 0.07
97 3 0.02
98 40 0.27
99 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (94 bp):
ATCCATAAAGCCGGGCATTTAACCAATTACTCTAGAGGGACAACTTAAGCTTTATTGTATATTAT
AATAACCTTTATCAGGCTAGCTGAATATT
Found at i:1306140 original size:2 final size:2
Alignment explanation
Indices: 1306133--1306183 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1306123 AAGGAAAGGA
1306133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1306175 AT AT AT AT A
1 AT AT AT AT A
1306184 AATAAATCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1306230 original size:12 final size:13
Alignment explanation
Indices: 1306200--1306239 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1306190 TCAAAGGAAA
1306200 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1306213 AAAAATAAAAAAT
1 AAAAATAAAAAAT
* *
1306226 -GAAATAAAAGAT
1 AAAAATAAAAAAT
1306238 AA
1 AA
1306240 TAAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1306319 original size:24 final size:23
Alignment explanation
Indices: 1306292--1306344 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1306282 AAAGAAAAAA
1306292 ATATAATA-AGAAGTAAATAATAAT
1 ATATAATATAGAA-T-AATAATAAT
*
1306316 ATATATATATATAATAATAATAAT
1 ATATA-ATATAGAATAATAATAAT
1306340 A-ATAA
1 ATATAA
1306345 AAAAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 15 0.58
25 4 0.15
26 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAATATAGAATAATAATAAT
Found at i:1306410 original size:16 final size:17
Alignment explanation
Indices: 1306389--1306437 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
1306379 TAAACTATAT
*
1306389 ACAAAATAAATCAAAGA
1 ACAAAATAAATCAAAAA
1306406 A-AAAAT-AAT-AAAAA
1 ACAAAATAAATCAAAAA
1306420 ACTAAAATAAATCAAAAA
1 AC-AAAATAAATCAAAAA
1306438 GGAAAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 10 0.37
17 4 0.15
18 5 0.19
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (17 bp):
ACAAAATAAATCAAAAA
Found at i:1306452 original size:32 final size:30
Alignment explanation
Indices: 1306391--1306464 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 30
1306381 AACTATATAC
*
1306391 AAAATAAATCAAAGAAAAAATAATAAAAAA
1 AAAATAAATCAAAGAAAAAAGAATAAAAAA
*
1306421 CTAAAATAAATCAAA-AAGGAAAGAA-AGAAAAA
1 --AAAATAAATCAAAGAA-AAAAGAATA-AAAAA
1306453 AAAATAAA-CAAA
1 AAAATAAATCAAA
1306465 TATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 4 0.11
30 8 0.21
31 3 0.08
32 23 0.61
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (30 bp):
AAAATAAATCAAAGAAAAAAGAATAAAAAA
Found at i:1306538 original size:19 final size:18
Alignment explanation
Indices: 1306504--1306577 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 18
1306494 AAATCCAAGG
*
1306504 AAAAAAT-ATTAAATAAA
1 AAAAAATAATAAAATAAA
1306521 AAAACAATAATAAAATAATA
1 AAAA-AATAATAAAATAA-A
*
1306541 AAGAAAA-AATGAAATAGGAA
1 AA-AAAATAATAAAATA--AA
1306561 AAAAAATAATAAAATAA
1 AAAAAATAATAAAATAA
1306578 TAATAGTCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 20 0.43
20 16 0.34
21 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAAATAATAAAATAAA
Found at i:1306548 original size:39 final size:38
Alignment explanation
Indices: 1306505--1306580 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 38
1306495 AATCCAAGGA
*
1306505 AAAAATATTAAATA-AAAAAACAATAATAAAATAATAAAG
1 AAAAA-ATGAAATAGAAAAAA-AATAATAAAATAATAAAG
1306544 AAAAAATGAAATAGGAAAAAAAATAATAAAATAATAA
1 AAAAAATGAAATA-GAAAAAAAATAATAAAATAATAA
1306581 TAGTCATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 7 0.21
39 21 0.62
40 6 0.18
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (38 bp):
AAAAAATGAAATAGAAAAAAAATAATAAAATAATAAAG
Found at i:1307916 original size:29 final size:29
Alignment explanation
Indices: 1307870--1308053 Score: 169
Period size: 29 Copynumber: 6.4 Consensus size: 29
1307860 ATCGCGACAC
*
1307870 CCAATATATCACCGTTTTAAAAATAATTA
1 CCAAAATATCACCGTTTTAAAAATAATTA
*
1307899 CTAAAATATCACCGTTTTAAAAATAATTA
1 CCAAAATATCACCGTTTTAAAAATAATTA
* * * * *
1307928 CCAAAATGTCACTGGTTTACAAAA-AAATC
1 CCAAAATATCACCGTTTTA-AAAATAATTA
* *
1307957 CCAAAATGTCACTGTTTTAAAAATAATTA
1 CCAAAATATCACCGTTTTAAAAATAATTA
* ** * *
1307986 -CAAGAATGTCACTATTTTTAAAA-AA-TC
1 CCAA-AATATCACCGTTTTAAAAATAATTA
* * *
1308013 CCAAAATATCACCTTTTTCAAAATAATTC
1 CCAAAATATCACCGTTTTAAAAATAATTA
1308042 CCAAAATATCAC
1 CCAAAATATCAC
1308054 TGGATCGGGT
Statistics
Matches: 131, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.12
28 14 0.11
29 97 0.74
30 4 0.03
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (29 bp):
CCAAAATATCACCGTTTTAAAAATAATTA
Found at i:1308036 original size:56 final size:58
Alignment explanation
Indices: 1307901--1308055 Score: 192
Period size: 56 Copynumber: 2.7 Consensus size: 58
1307891 AATAATTACT
* *
1307901 AAAATATCACCGTTTTAAAAATAATTACCAAAATGTCACTGGTTTACAAAAAAATCCC
1 AAAATATCACCTTTTTAAAAATAATTACCAAAATGTCACTGATTTACAAAAAAATCCC
* **
1307959 AAAATGTCA-CTGTTTTAAAAATAATTA-CAAGAATGTCACT-ATTT-TTAAAAAATCCC
1 AAAATATCACCT-TTTTAAAAATAATTACCAA-AATGTCACTGATTTACAAAAAAATCCC
* * *
1308015 AAAATATCACCTTTTTCAAAATAATTCCCAAAATATCACTG
1 AAAATATCACCTTTTTAAAAATAATTACCAAAATGTCACTG
1308056 GATCGGGTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
56 39 0.47
57 12 0.14
58 32 0.39
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (58 bp):
AAAATATCACCTTTTTAAAAATAATTACCAAAATGTCACTGATTTACAAAAAAATCCC
Found at i:1308089 original size:17 final size:17
Alignment explanation
Indices: 1308067--1308118 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1308057 ATCGGGTCGA
1308067 GTCAACGGGTCGGGTTG
1 GTCAACGGGTCGGGTTG
* **
1308084 GTCAACGAGTCGGGTCA
1 GTCAACGGGTCGGGTTG
*
1308101 GTCAACGGGTCGAGTTG
1 GTCAACGGGTCGGGTTG
1308118 G
1 G
1308119 GTCAGATCGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.21
Consensus pattern (17 bp):
GTCAACGGGTCGGGTTG
Found at i:1308142 original size:19 final size:19
Alignment explanation
Indices: 1308118--1308175 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1308108 GGTCGAGTTG
*
1308118 GGTCAGATCGGTTCGGACC
1 GGTCAGACCGGTTCGGACC
*
1308137 GGTCAGACCGGTTTGGACC
1 GGTCAGACCGGTTCGGACC
* * * *
1308156 GATCATACCGATTTGGACC
1 GGTCAGACCGGTTCGGACC
1308175 G
1 G
1308176 ATCAAGCCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (19 bp):
GGTCAGACCGGTTCGGACC
Found at i:1308176 original size:19 final size:19
Alignment explanation
Indices: 1308132--1308179 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1308122 AGATCGGTTC
* *
1308132 GGACCGGTCAGACCGGTTT
1 GGACCGATCAGACCGATTT
*
1308151 GGACCGATCATACCGATTT
1 GGACCGATCAGACCGATTT
1308170 GGACCGATCA
1 GGACCGATCA
1308180 AGCCGGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (19 bp):
GGACCGATCAGACCGATTT
Found at i:1310494 original size:15 final size:15
Alignment explanation
Indices: 1310470--1310545 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
1310460 GAACAAAACG
1310470 ATAT-TGGTGACATT
1 ATATATGGTGACATT
1310484 ATATATGGTGACAATT
1 ATATATGGTGAC-ATT
** * *
1310500 -T-TGAGTTTTGCCACT
1 ATAT-A-TGGTGACATT
1310515 ATAT-TGGTGACATT
1 ATATATGGTGACATT
*
1310529 ATATATGGTGACGTT
1 ATATATGGTGACATT
1310544 AT
1 AT
1310546 GCATAATCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
14 15 0.33
15 22 0.48
16 8 0.17
17 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (15 bp):
ATATATGGTGACATT
Found at i:1312297 original size:37 final size:36
Alignment explanation
Indices: 1312221--1312586 Score: 309
Period size: 36 Copynumber: 9.8 Consensus size: 36
1312211 ATATATATAT
* * *
1312221 AAATATTTTCAAAAAC-ATATAATATATA-AATTTCCA
1 AAATGTTTT-AAAAACTATAT-ATATATATATTTTCAA
1312257 AAATGTTTTTAAAAAACTATATA-ATATATATTTTCAA
1 AAATG-TTTT-AAAAACTATATATATATATATTTTCAA
*
1312294 AAATGTTTAAAAAAACTATATATTATATATATTTTC-A
1 AAATGTTT-TAAAAACTATATA-TATATATATTTTCAA
* *
1312331 AAATGTTTTTAAAACTATATATTATATAAATTTTCAA
1 AAATGTTTTAAAAACTATATA-TATATATATTTTCAA
* *
1312368 AAATGTTTTCAAAATTATATAT-TATATAAGTTTTC-A
1 AAATGTTTTAAAAACTATATATATATAT-A-TTTTCAA
* *
1312404 AAATGATTTAAAAAAAACTATATATTATATATATTTTCTA
1 AAATG-TTT--TAAAAACTATATA-TATATATATTTTCAA
* *
1312444 AAATGTTTTAAAAACTATATAGTATATA-GTTGTCAA
1 AAATGTTTTAAAAACTATATA-TATATATATTTTCAA
*
1312480 AAATGTTTT-AAAACTATATATTATATACATTTTC-A
1 AAATGTTTTAAAAACTATATA-TATATATATTTTCAA
1312515 AAATGTTTTTTTAAAAACTATATATTATATACCTATTTTCAA
1 AAATG---TTTTAAAAACTATATA-TATATA--TATTTTCAA
*** ** *
1312557 AAACCATTTGCAAACTAAATATATATATAT
1 AAATGTTTTAAAAACTATATATATATATAT
1312587 ATATATATAT
Statistics
Matches: 278, Mismatches: 29, Indels: 46
0.79 0.08 0.13
Matches are distributed among these distances:
35 27 0.10
36 77 0.28
37 77 0.28
38 26 0.09
39 48 0.17
40 8 0.03
41 11 0.04
42 4 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATATATATATATTTTCAA
Found at i:1312336 original size:74 final size:71
Alignment explanation
Indices: 1312221--1312545 Score: 343
Period size: 74 Copynumber: 4.4 Consensus size: 71
1312211 ATATATATAT
* * *
1312221 AAATATTTTCAAAAAC-ATATAATATATAAATTTCCAAAATGTTTTTAAAAAACTATATA-ATAT
1 AAATGTTTT-AAAAACTATATATTATAT-AATTTTCAAAATGTTTTT--AAAACTATATATATAT
1312284 ATATTTTCAA
62 ATATTTTCAA
*
1312294 AAATGTTTAAAAAAACTATATATTATATATATTTTCAAAATGTTTTTAAAACTATATATTATATA
1 AAATGTTT-TAAAAACTATATATTATATA-ATTTTCAAAATGTTTTTAAAACTATATA-TATATA
*
1312359 AATTTTCAA
63 TATTTTCAA
* * **
1312368 AAATGTTTTCAAAATTATATATTATATAAGTTTTCAAAATGATTTAAAAAAAACTATATATTATA
1 AAATGTTTTAAAAACTATATATTATATAA-TTTTCAAAATG-TTT--TTAAAACTATATA-TATA
*
1312433 TATATTTTCTA
61 TATATTTTCAA
* * * *
1312444 AAATGTTTTAAAAACTATATAGTATATAGTTGTCAAAAATG-TTTTAAAACTATATATTATATAC
1 AAATGTTTTAAAAACTATATATTATATAATTTTC-AAAATGTTTTTAAAACTATATA-TATATAT
1312508 ATTTTC-A
64 ATTTTCAA
1312515 AAATGTTTTTTTAAAAACTATATATTATATA
1 AAATG---TTTTAAAAACTATATATTATATA
1312546 CCTATTTTCA
Statistics
Matches: 218, Mismatches: 21, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
71 6 0.03
72 36 0.17
73 42 0.19
74 74 0.34
75 4 0.02
76 56 0.26
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (71 bp):
AAATGTTTTAAAAACTATATATTATATAATTTTCAAAATGTTTTTAAAACTATATATATATATAT
TTTCAA
Found at i:1312395 original size:111 final size:108
Alignment explanation
Indices: 1312204--1312558 Score: 409
Period size: 111 Copynumber: 3.2 Consensus size: 108
1312194 ATAATAAATA
* * *
1312204 ATATATTATATATA-TAT-AAATAT-TTTCAAAAAC-ATATAATATATAAA-TTTCCAAAATGTT
1 ATATATTATATATATTTTCAAA-ATGTTTTAAAAACTATATAATATATAAATTTTCAAAAATG-T
* *
1312264 TTTAAAAAACTATATAATATATATTTTCAAAAATG-TTTAAAAAAACT
64 TTTAAAATA-TATATTATATA-ATTTTC-AAAATGTTTTAAAAAAACT
* *
1312311 ATATATTATATATATTTTCAAAATGTTTTTAAAACTATATATTATATAAATTTTCAAAAATGTTT
1 ATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATTTTCAAAAATGTTT
*
1312376 TCAAAATTATATATTATATAAGTTTTCAAAATGATTTAAAAAAAACT
66 T-AAAA-TATATATTATATAA-TTTTCAAAATG-TTTTAAAAAAACT
* * *
1312423 ATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATAGTATAT-AGTTGTCAAAAATGTT
1 ATATATTATATATATTTTC-AAAATGTTTTAAAAACTATATAATATATAAATTTTCAAAAATGTT
**
1312487 TTAAAACTATATATTATATACATTTTCAAAATGTTTTTTTAAAAACT
65 TTAAAA-TATATATTATATA-ATTTTCAAAATG-TTTTAAAAAAACT
1312534 ATATATTATATACCTATTTTCAAAA
1 ATATATTATATA--TATTTTCAAAA
1312559 ACCATTTGCA
Statistics
Matches: 217, Mismatches: 17, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
107 14 0.06
108 4 0.02
109 11 0.05
110 24 0.11
111 79 0.36
112 52 0.24
113 33 0.15
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (108 bp):
ATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATTTTCAAAAATGTTT
TAAAATATATATTATATAATTTTCAAAATGTTTTAAAAAAACT
Found at i:1312582 original size:2 final size:2
Alignment explanation
Indices: 1312575--1312603 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1312565 TGCAAACTAA
1312575 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 A
1312604 ACAAAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1313037 original size:44 final size:42
Alignment explanation
Indices: 1312980--1313076 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 42
1312970 TACTTTTATA
1312980 AATTAATAAATTTATGTTATATAAATTCCAAAAACTGTATCTCAC
1 AATTAAT-AATTTATGTTATATAAATTCCAAAAAC--TATCTCAC
* **
1313025 AATTATTAATTTATGTTATATAAATTTTAAAAACTATCTCAC
1 AATTAATAATTTATGTTATATAAATTCCAAAAACTATCTCAC
1313067 AATTAATAAT
1 AATTAATAAT
1313077 ATATATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
42 17 0.35
44 25 0.52
45 6 0.12
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (42 bp):
AATTAATAATTTATGTTATATAAATTCCAAAAACTATCTCAC
Found at i:1319935 original size:3 final size:3
Alignment explanation
Indices: 1319927--1320018 Score: 74
Period size: 3 Copynumber: 33.0 Consensus size: 3
1319917 TTCATTTGTT
* * *
1319927 TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1319971 TTA TTT TTA TTA TT- TT- TTA TTA TTT TTA TTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
1320014 -TA TTA
1 TTA TTA
1320019 CAGGCCCAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
2 16 0.22
3 55 0.74
4 3 0.04
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1319940 original size:16 final size:16
Alignment explanation
Indices: 1319925--1320014 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 16
1319915 ATTTCATTTG
*
1319925 TTTTATTATTATTTTG
1 TTTTATTATTATTTTA
*
1319941 TTTTAATATTATTATTA
1 TTTTATTATTATT-TTA
* *
1319958 TATTA-TAATATTATTA
1 TTTTATTATTATT-TTA
1319974 TTTTTATTATT-TTTTA
1 -TTTTATTATTATTTTA
* *
1319990 TTATTTTTATTA-TTAA
1 TT-TTATTATTATTTTA
1320006 TTTTATTAT
1 TTTTATTAT
1320015 ATTACAGGCC
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
15 8 0.13
16 37 0.62
17 12 0.20
18 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (16 bp):
TTTTATTATTATTTTA
Found at i:1319952 original size:19 final size:19
Alignment explanation
Indices: 1319928--1320014 Score: 86
Period size: 19 Copynumber: 4.5 Consensus size: 19
1319918 TCATTTGTTT
* *
1319928 TATTATTATTTTGTTTTAA
1 TATTATTATTTTATTATAA
*
1319947 TATTATTATTATATTATAA
1 TATTATTATTTTATTATAA
*
1319966 TATTATTATTTTTATTAT-T
1 TATTATTA-TTTTATTATAA
*
1319985 TTTTATTATTTTTATTATTAA
1 TATTATTA-TTTTATTA-TAA
*
1320006 TTTTATTAT
1 TATTATTAT
1320015 ATTACAGGCC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
19 40 0.69
20 10 0.17
21 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (19 bp):
TATTATTATTTTATTATAA
Found at i:1319955 original size:22 final size:21
Alignment explanation
Indices: 1319927--1320018 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 21
1319917 TTCATTTGTT
*
1319927 TTATTATTATTTTGTTTTAATA
1 TTATTATTATTTT-TTTTATTA
* **
1319949 TTATTATTATATTATAATATTA
1 TTATTATTAT-TTTTTTTATTA
*
1319971 TTATTTTTATTATTTTTTATTA
1 TTATTATTATT-TTTTTTATTA
* **
1319993 TTTTTATTATTAATTTTATTA
1 TTATTATTATTTTTTTTATTA
1320014 -TATTA
1 TTATTA
1320019 CAGGCCCAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 4 0.07
21 9 0.16
22 40 0.73
23 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
TTATTATTATTTTTTTTATTA
Found at i:1321713 original size:126 final size:121
Alignment explanation
Indices: 1321583--1321956 Score: 333
Period size: 126 Copynumber: 3.0 Consensus size: 121
1321573 TTTCCTATTT
1321583 ATAAATTTAATTTTATAAATTACTTTTAAGAAAAATAAGCATATTTTGATATTTATTTATTTTTA
1 ATAAA-TTAATTTTATAAATTACTTTTAA-AAAAA-AAG-ATATTTTGATATTTATTTATTTTTA
* *
1321648 ATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAAAAGTCCTTTTCTGATATTTTTAAATAA
62 ATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAG-CCTTTTCTGATATTTTTAAATAA
* * * ** * *
1321709 ATAAA-T-ATCTTATTAAAATAAATTTTTATTTTAAGAAA-ATATTTTGGTTATTTATTTATTTT
1 ATAAATTAATTTTA-T-AAAT-TACTTTTA--AAAAAAAAGATATTTT-GATATTTATTTATTTT
* * *
1321771 TCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCTCTTTTATGATATTTTTGAAT--
60 T-AATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC-CTTTTCTGATATTTTTAAATAA
** *
1321833 A-AAA-TAA----ATATCTTACTGTATTAAAATAAAATG-T-TTTTGATATTTATTTATTTTTTA
1 ATAAATTAATTTTATAAATTACT-T-TTAAAA-AAAAAGATATTTTGATATTTATTTA-TTTTTA
* *
1321890 ATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCTAAATAA
62 ATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAG-CCTTTTCTGATATTTTTAAATAA
*
1321951 GTAAAT
1 ATAAAT
1321957 ATCTTATTTA
Statistics
Matches: 202, Mismatches: 27, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
116 64 0.32
117 13 0.06
118 7 0.03
119 7 0.03
120 1 0.00
123 9 0.04
124 11 0.05
125 21 0.10
126 66 0.33
127 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (121 bp):
ATAAATTAATTTTATAAATTACTTTTAAAAAAAAAGATATTTTGATATTTATTTATTTTTAATAT
CAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCCTTTTCTGATATTTTTAAATAA
Found at i:1321996 original size:116 final size:116
Alignment explanation
Indices: 1321760--1321997 Score: 300
Period size: 116 Copynumber: 2.1 Consensus size: 116
1321750 TTTTGGTTAT
* * *
1321760 TTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCTCTTTTATGATAT
1 TTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTATGATAT
* * * * *
1321825 TTTTGAATAAAATAAATATCTTACTGTATTAAAATAAAATGTTTTTGATAT
66 TTCTAAATAAAATAAATATCTTACTGTATTAAAATAAAATATTTTTGAAAA
* *
1321876 TTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATAT
1 TTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTATGATAT
* * * * * *
1321941 TTCTAAAT-AAGTAAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAA
66 TTCTAAATAAAATAAATATCTTACTGTAT-TAAAATAAAATATTTT-TGAAAA
1321992 TTATTT
1 TTATTT
1321998 GAAATAATAG
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
114 4 0.04
115 25 0.24
116 75 0.72
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (116 bp):
TTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTATGATAT
TTCTAAATAAAATAAATATCTTACTGTATTAAAATAAAATATTTTTGAAAA
Found at i:1325069 original size:10 final size:11
Alignment explanation
Indices: 1325039--1325067 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1325029 AAATTTATTT
1325039 ATATTTTTAAA
1 ATATTTTTAAA
1325050 ATATTTTTAAA
1 ATATTTTTAAA
1325061 ATATTTT
1 ATATTTT
1325068 AATATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:1325071 original size:19 final size:19
Alignment explanation
Indices: 1325049--1325095 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1325039 ATATTTTTAA
1325049 AATATTTTTAA-AATATTTT
1 AATATTTTTAATAATA-TTT
*
1325068 AATA-TTATAATAATATTT
1 AATATTTTTAATAATATTT
*
1325086 AATTTTTTTA
1 AATATTTTTA
1325096 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTTTTAATAATATTT
Found at i:1326191 original size:2 final size:2
Alignment explanation
Indices: 1326184--1326212 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1326174 ACATATGTTC
1326184 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 A
1326213 ATCATACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1327445 original size:29 final size:29
Alignment explanation
Indices: 1327390--1327556 Score: 158
Period size: 29 Copynumber: 5.7 Consensus size: 29
1327380 AAGTTTTTTC
*
1327390 TTTGATTGTAATTTATATAAAAACAATTGG-A
1 TTTG-TTGTAA-TT-TATAAAAACATTTGGCA
* *
1327421 GTTTGTTGTAATTTATAAAAACAATTGGAA
1 -TTTGTTGTAATTTATAAAAACATTTGGCA
* ****
1327451 TTTGTTGTAATTTTTAAATTTTTTTGGCA
1 TTTGTTGTAATTTATAAAAACATTTGGCA
** *
1327480 TTTGTTGTAATTTATAAAAAGTTTTGGTA
1 TTTGTTGTAATTTATAAAAACATTTGGCA
* *
1327509 TTTTTTGTAATTTATAAAAA-GTTTGGCA
1 TTTGTTGTAATTTATAAAAACATTTGGCA
1327537 TTTGTTTGTAATTTATAAAA
1 TTTG-TTGTAATTTATAAAA
1327557 GTTTTGGTCT
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
28 9 0.08
29 95 0.81
30 3 0.03
31 6 0.05
32 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTGTTGTAATTTATAAAAACATTTGGCA
Found at i:1327562 original size:29 final size:29
Alignment explanation
Indices: 1327422--1327585 Score: 172
Period size: 29 Copynumber: 5.7 Consensus size: 29
1327412 ACAATTGGAG
*** *
1327422 TTTGTTGTAATTTATAAAAACAATTGGAA
1 TTTGTTGTAATTTATAAAAAGTTTTGGCA
* ***
1327451 TTTGTTGTAATTTTTAAATTTTTTTGGCA
1 TTTGTTGTAATTTATAAAAAGTTTTGGCA
*
1327480 TTTGTTGTAATTTATAAAAAGTTTTGGTA
1 TTTGTTGTAATTTATAAAAAGTTTTGGCA
*
1327509 TTTTTTGTAATTTATAAAAAG-TTTGGCA
1 TTTGTTGTAATTTATAAAAAGTTTTGGCA
1327537 TTTGTTTGTAATTTAT-AAAAGTTTTGGTC-
1 TTTG-TTGTAATTTATAAAAAGTTTTGG-CA
* * *
1327566 TTTATTGTAATATATCAAAA
1 TTTGTTGTAATTTATAAAAA
1327586 TATTATTTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.21
29 89 0.78
30 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGTTGTAATTTATAAAAAGTTTTGGCA
Found at i:1347829 original size:12 final size:12
Alignment explanation
Indices: 1347808--1347837 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1347798 TAATCCCGAG
1347808 TTTG-TTTTTCA
1 TTTGATTTTTCA
1347819 TTTGATTTTTCA
1 TTTGATTTTTCA
1347831 TTTGATT
1 TTTGATT
1347838 ATCAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:1349294 original size:85 final size:84
Alignment explanation
Indices: 1349143--1349331 Score: 247
Period size: 85 Copynumber: 2.2 Consensus size: 84
1349133 AATGATGTGT
* * *
1349143 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAAATTTTGT
1 GCTTCAATGACGCGCAATGTAACTCATACATGCGTGTCATAAATTTATGACACACAAAATTGTGT
*
1349208 CAAGC-AGATTTATGACGGGG
66 C-AGCTA-ATTTATAACGGGG
* * *
1349228 GCTTCAATGACGCTCAATGTAACTCATACATGCTTGTCATAAATTTATGACATAC-AAATGTGTG
1 GCTTCAATGACGCGCAATGTAACTCATACATGCGTGTCATAAATTTATGACACACAAAAT-TGTG
* *
1349292 TCATCTTAATTTATAATGGGG
65 TCAGC-TAATTTATAACGGGG
1349313 GCTTCAATGACGCGCAATG
1 GCTTCAATGACGCGCAATG
1349332 AGCGTAATAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
84 6 0.07
85 84 0.92
86 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (84 bp):
GCTTCAATGACGCGCAATGTAACTCATACATGCGTGTCATAAATTTATGACACACAAAATTGTGT
CAGCTAATTTATAACGGGG
Found at i:1349353 original size:85 final size:85
Alignment explanation
Indices: 1349143--1349356 Score: 233
Period size: 85 Copynumber: 2.5 Consensus size: 85
1349133 AATGATGTGT
* * * *
1349143 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAAATTTTGT
1 GCTTCAATGACGCGCAATGTACGTCATACATGCGTTTCATAAATTTATGACACACAAAATTGTGT
*
1349208 CAAGCAGATTTATGACGGGG
66 CAAGCAGATTTATAACGGGG
* *
1349228 GCTTCAATGACGCTCAATGTAAC-TCATACATGC-TTGTCATAAATTTATGACATAC-AAATGTG
1 GCTTCAATGACGCGCAATGT-ACGTCATACATGCGTT-TCATAAATTTATGACACACAAAAT-TG
* *
1349290 TGTC-ATCTTA-ATTTATAATGGGG
63 TGTCAAGC--AGATTTATAACGGGG
* *
1349313 GCTTCAATGACGCGCAATG-AGCGTAATAAATGCGTTTCATAAAT
1 GCTTCAATGACGCGCAATGTA-CGTCATACATGCGTTTCATAAAT
1349357 GCGCGTCATA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
83 1 0.01
84 8 0.07
85 96 0.88
86 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTACGTCATACATGCGTTTCATAAATTTATGACACACAAAATTGTGT
CAAGCAGATTTATAACGGGG
Found at i:1373341 original size:34 final size:34
Alignment explanation
Indices: 1373293--1373367 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
1373283 TAATTATCCC
1373293 AGATATAGTAAGTAAGCATTAAAAGAATGTAATTT
1 AGAT-TAGTAAGTAAGCATTAAAAGAATGTAATTT
* *
1373328 ATATTAGTAAGTAAGCATTAAAATAATGTAATTT
1 AGATTAGTAAGTAAGCATTAAAAGAATGTAATTT
1373362 AGATTA
1 AGATTA
1373368 CAACTCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 34 0.92
35 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.35
Consensus pattern (34 bp):
AGATTAGTAAGTAAGCATTAAAAGAATGTAATTT
Found at i:1374653 original size:24 final size:24
Alignment explanation
Indices: 1374618--1374663 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1374608 TTCATTTCTT
1374618 GAGGATTGGGAGGAGGGTTTGGAA
1 GAGGATTGGGAGGAGGGTTTGGAA
* *
1374642 GAGGATTTGGAGGTGGGTTTGG
1 GAGGATTGGGAGGAGGGTTTGG
1374664 TGGTTGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.54, T:0.26
Consensus pattern (24 bp):
GAGGATTGGGAGGAGGGTTTGGAA
Found at i:1374887 original size:2 final size:2
Alignment explanation
Indices: 1374880--1374906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1374870 ATTTTTATGA
1374880 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 A
1374907 ATCAAAACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1375478 original size:22 final size:21
Alignment explanation
Indices: 1375452--1375508 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
1375442 ATAGTAGGCT
1375452 AGTAGTATCAATACCTA-GTAAG
1 AGTAGTATCAATACCTATGT--G
1375474 AGTAGTATCAATA-CTATGTG
1 AGTAGTATCAATACCTATGTG
*
1375494 AGTAGTATCGATACC
1 AGTAGTATCAATACC
1375509 AGGTGCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.41
21 4 0.12
22 15 0.47
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (21 bp):
AGTAGTATCAATACCTATGTG
Found at i:1384044 original size:27 final size:27
Alignment explanation
Indices: 1383966--1384038 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
1383956 TTTTGACTCT
*
1383966 ATATTTTAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
* *
1383993 ATATTTGAATTAATTTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
1384020 ATATTTGAATGAATGTGAT
1 ATATTTGAATGAATGTGAT
1384039 GGATATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:1394178 original size:13 final size:13
Alignment explanation
Indices: 1394160--1394189 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1394150 TTGCGAAAAT
*
1394160 AAAATAATGAAAG
1 AAAATAAAGAAAG
1394173 AAAATAAAGAAAG
1 AAAATAAAGAAAG
1394186 AAAA
1 AAAA
1394190 GTAGGGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAATAAAGAAAG
Found at i:1408665 original size:26 final size:26
Alignment explanation
Indices: 1408625--1408690 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
1408615 TTCTAAAATA
*
1408625 AGGATAATAATGTGTTAGATGATGTAG
1 AGGA-AATAAAGTGTTAGATGATGTAG
1408652 AGGAAATAAAGTGTTAGATGATGTAG
1 AGGAAATAAAGTGTTAGATGATGTAG
1408678 AGGAAATAAAGTG
1 AGGAAATAAAGTG
1408691 GTAAGACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 34 0.89
27 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (26 bp):
AGGAAATAAAGTGTTAGATGATGTAG
Found at i:1411331 original size:18 final size:18
Alignment explanation
Indices: 1411308--1411350 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1411298 GTTGGTTATT
1411308 GAAGCTTTGAGTATGATA
1 GAAGCTTTGAGTATGATA
*
1411326 GAAGCTTTGAGTATGTTA
1 GAAGCTTTGAGTATGATA
1411344 GAAGCTT
1 GAAGCTT
1411351 ACAGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (18 bp):
GAAGCTTTGAGTATGATA
Found at i:1411903 original size:22 final size:19
Alignment explanation
Indices: 1411853--1411923 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 19
1411843 GAAAAATATT
1411853 GTATCGATACCATAGTAGG
1 GTATCGATACCATAGTAGG
*
1411872 GTTTCGATACCATAGTAAGG
1 GTATCGATACCATAGT-AGG
*
1411892 TAGTATCGATACCATGGTAGGG
1 --GTATCGATACCATAGTA-GG
1411914 GTATCGATAC
1 GTATCGATAC
1411924 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.33
20 13 0.29
21 1 0.02
22 16 0.36
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (19 bp):
GTATCGATACCATAGTAGG
Found at i:1412412 original size:55 final size:55
Alignment explanation
Indices: 1412261--1412412 Score: 187
Period size: 56 Copynumber: 2.7 Consensus size: 55
1412251 TAAGTATGAA
* * *
1412261 AAAACATAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCCATTATATGTTC
1 AAAAC-TAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGCCACTATATGTGC
* * *
1412317 AAAATTTAAAAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGCCACTATATGTGC
* * * * *
1412373 AAAACTAGGAAATTTATACTAAGTGTATAAATTTTTGTAT
1 AAAACTAAGAAATTCATACTAAGTGGATGAATTTCTGTAT
1412413 TGGTAGTAGG
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
55 29 0.35
56 53 0.65
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGCCACTATATGTGC
Found at i:1418522 original size:20 final size:19
Alignment explanation
Indices: 1418475--1418523 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1418465 ATTGAATCAT
* *
1418475 TATCAATACCGAGGGGGAG
1 TATCAATACCGAAGGGAAG
*
1418494 TATCGATACCGAAGGGAATG
1 TATCAATACCGAAGGGAA-G
*
1418514 TTTCAATACC
1 TATCAATACC
1418524 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (19 bp):
TATCAATACCGAAGGGAAG
Found at i:1419008 original size:56 final size:56
Alignment explanation
Indices: 1418933--1419090 Score: 228
Period size: 56 Copynumber: 2.8 Consensus size: 56
1418923 TATCTGTGCA
*
1418933 AAAACTTAAGAAAGTCATACTCAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAAACTTAAGAAAGTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** *
1418989 AAAACTTAAGAACA-TCATACTAAGTCAATGATTTTCCGTATGGGCACTATATGTGT
1 AAAACTTAAGAA-AGTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
1419045 AAAACTTAAGAAATTAATACTAAGTGGACGAATTTCCGCATGGGCA
1 AAAACTTAAGAAAGTCATACTAAGTGGATGAATTTCCGTATGGGCA
1419091 GCTTAAGAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
55 1 0.01
56 88 0.98
57 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (56 bp):
AAAACTTAAGAAAGTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:1419110 original size:43 final size:43
Alignment explanation
Indices: 1419049--1419133 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
1419039 ATGTGTAAAA
*
1419049 CTTAAGAAATTAATACTAAGTGGACGAATTTCCGCATGGGCAG
1 CTTAAGAAATTAATACTAAGTGAACGAATTTCCGCATGGGCAG
* * * *
1419092 CTTAAGAAATTCATACTAAGTGAATGAATTTCTGTATGGGCA
1 CTTAAGAAATTAATACTAAGTGAACGAATTTCCGCATGGGCA
1419134 CTATATGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (43 bp):
CTTAAGAAATTAATACTAAGTGAACGAATTTCCGCATGGGCAG
Found at i:1419589 original size:44 final size:43
Alignment explanation
Indices: 1419523--1419734 Score: 236
Period size: 41 Copynumber: 5.0 Consensus size: 43
1419513 TTGGTTGAAG
* * * * *
1419523 TTTCTCAAGGCTCATCTACTGTGTACAAGGATAAGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTGCAAGG-TAAGACCTTACCA
*
1419567 TTTCTGAAGGCTCCTCTGCTGTGTGCAAGG--AGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTGCAAGGTAAGACCTTACCA
* *
1419608 TTTTTGAAGGCTCCTATGCTATGTGCAAGG--AGACCTTACCA
1 TTTCTGAAGGCTCCTCTGCTATGTGCAAGGTAAGACCTTACCA
* * ** *
1419649 TTTCTGAAGGCTCATCTGCTATGTGCCAGGGTAAGACCTTGTCG
1 TTTCTGAAGGCTCCTCTGCTATGTG-CAAGGTAAGACCTTACCA
1419693 TTTCT-ATAGGCTCCTCTGCTATGTGCAAGGATAAGACCTTAC
1 TTTCTGA-AGGCTCCTCTGCTATGTGCAAGG-TAAGACCTTAC
1419735 AGCTTTCCAC
Statistics
Matches: 145, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
41 71 0.49
42 4 0.03
43 5 0.03
44 65 0.45
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
TTTCTGAAGGCTCCTCTGCTATGTGCAAGGTAAGACCTTACCA
Found at i:1419674 original size:82 final size:84
Alignment explanation
Indices: 1419556--1419723 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 84
1419546 TACAAGGATA
* * *
1419556 AGACCTTACCATTTCTGAAGGCTCCTCTGCTGTGTG-CAAGG-AGACCTTACCATTTTTGA-AGG
1 AGACCTTACCATTTCTGAAGGCTCATCTGCTATGTGCCAAGGAAGACCTTACCATTTCT-ATAGG
1419618 CTCCTATGCTATGTGCAAGG
65 CTCCTATGCTATGTGCAAGG
* ** *
1419638 AGACCTTACCATTTCTGAAGGCTCATCTGCTATGTGCCAGGGTAAGACCTTGTCGTTTCTATAGG
1 AGACCTTACCATTTCTGAAGGCTCATCTGCTATGTGCCAAGG-AAGACCTTACCATTTCTATAGG
*
1419703 CTCCTCTGCTATGTGCAAGG
65 CTCCTATGCTATGTGCAAGG
1419723 A
1 A
1419724 TAAGACCTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
82 34 0.46
83 4 0.05
84 1 0.01
85 35 0.47
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (84 bp):
AGACCTTACCATTTCTGAAGGCTCATCTGCTATGTGCCAAGGAAGACCTTACCATTTCTATAGGC
TCCTATGCTATGTGCAAGG
Found at i:1422437 original size:17 final size:17
Alignment explanation
Indices: 1422415--1422447 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1422405 CATTATCATC
1422415 TTTATCCATTA-TCTTTA
1 TTTATCC-TTATTCTTTA
1422432 TTTATCCTTATTCTTT
1 TTTATCCTTATTCTTT
1422448 TATTACCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATCCTTATTCTTTA
Found at i:1422709 original size:32 final size:32
Alignment explanation
Indices: 1422665--1422747 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
1422655 ATATTAGTAG
* *
1422665 AGTGTTGTATTCAGATAATACAC-ATCAGTATT
1 AGTGTTGAATTCAGATAATACACAAT-AGTATC
* * *
1422697 AGTGTTGCATTCAGATAATGCACAATAGTGTC
1 AGTGTTGAATTCAGATAATACACAATAGTATC
*
1422729 AGTGTCGAATTCAGATAAT
1 AGTGTTGAATTCAGATAAT
1422748 GCATTGTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 42 0.95
33 2 0.05
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
AGTGTTGAATTCAGATAATACACAATAGTATC
Found at i:1422758 original size:32 final size:33
Alignment explanation
Indices: 1422705--1422779 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
1422695 TTAGTGTTGC
1422705 ATTCAGATAATGCACAATAGTGTCA-GTGTCG-A
1 ATTCAGATAATGCACAATAGTGTCATG-GTCGCA
***
1422737 ATTCAGATAATGCATTGTAGTGTCATGGTCGCA
1 ATTCAGATAATGCACAATAGTGTCATGGTCGCA
1422770 ATT-AGATAAT
1 ATTCAGATAAT
1422780 ACATAGAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 33 0.87
33 5 0.13
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (33 bp):
ATTCAGATAATGCACAATAGTGTCATGGTCGCA
Found at i:1428494 original size:32 final size:32
Alignment explanation
Indices: 1428420--1428495 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
1428410 TAGTGCACAG
*
1428420 TAGTGTCAATGTCGCATTCAAATAATGCATAA
1 TAGTGTCATTGTCGCATTCAAATAATGCATAA
* * * * *
1428452 CAGTGGCATTGTTGCATTCAAATAATGTATAT
1 TAGTGTCATTGTCGCATTCAAATAATGCATAA
1428484 TAGTGTCATTGT
1 TAGTGTCATTGT
1428496 AACATTAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TAGTGTCATTGTCGCATTCAAATAATGCATAA
Found at i:1431255 original size:47 final size:47
Alignment explanation
Indices: 1431168--1431584 Score: 613
Period size: 47 Copynumber: 8.9 Consensus size: 47
1431158 TAGCATCCTT
*
1431168 TTCATGCCTTAATGCATCATTTACATGCATTTTCAATTATGGCA-CACG
1 TTCATGCCTTAATGCATCCTTT-CATGCATTTTCAATTATGGCATC-CG
* * *
1431216 TTCATGTCTTAATGCATCCTTTCATGCATTTTTAATTATGGCTTCCG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
*
1431263 TTCATGCCTTAATGCATCCTTTTATGCATTTTCAATTATGGCATCCG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
* *
1431310 TTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATGG-ATTTCG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCA-TCCG
* * * *
1431357 TTCATGCCTTAGTGCATCATTTCATGCATTTTCAATTATAGTATCCG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
* * **
1431404 TTCATACCTTAATGCATCCTTTCATACATTTTCAATTATGGCATTTG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
* *
1431451 TTTATGCCTTAATGCATCCTTTCATGCTTTTTCAATTATGGCATCCG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
* *
1431498 TTCATGCCTTAATGCATCCTTTTATGCATTTTCAATTATGGCATCCA
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
*
1431545 TTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
1431585 AATTTGATTT
Statistics
Matches: 332, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.00
47 309 0.93
48 22 0.07
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (47 bp):
TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCATCCG
Found at i:1431477 original size:20 final size:20
Alignment explanation
Indices: 1431454--1431571 Score: 56
Period size: 20 Copynumber: 5.2 Consensus size: 20
1431444 GCATTTGTTT
1431454 ATGCCTTAATGCATCCTTTC
1 ATGCCTTAATGCATCCTTTC
* *
1431474 ATGCTTTTTCAATTATGGCATCCGTTC
1 ATGC--CTT--A--AT-GCATCCTTTC
*
1431501 ATGCCTTAATGCATCCTTTT
1 ATGCCTTAATGCATCCTTTC
* *
1431521 ATGCATTTTCAATTATGGCATCCATTC
1 ATGC--CTT--A--AT-GCATCCTTTC
*
1431548 ATGCCTTAATGCATCATTTC
1 ATGCCTTAATGCATCCTTTC
1431568 ATGC
1 ATGC
1431572 ATTTTCAATT
Statistics
Matches: 73, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
20 28 0.38
21 4 0.05
22 4 0.05
23 2 0.03
24 2 0.03
25 4 0.05
26 4 0.05
27 25 0.34
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGCCTTAATGCATCCTTTC
Found at i:1431502 original size:27 final size:26
Alignment explanation
Indices: 1431464--1431551 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
1431454 ATGCCTTAAT
1431464 GCATCCTTTCATGCTTTTTCAATTATG
1 GCATCCTTTCATGC-TTTTCAATTATG
* *
1431491 GCATCCGTTCATGC-CTT--A--AT-
1 GCATCCTTTCATGCTTTTCAATTATG
*
1431511 GCATCCTTTTATGCATTTTCAATTATG
1 GCATCCTTTCATGC-TTTTCAATTATG
*
1431538 GCATCCATTCATGC
1 GCATCCTTTCATGC
1431552 CTTAATGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 12 0.26
21 2 0.04
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 2 0.04
27 25 0.53
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (26 bp):
GCATCCTTTCATGCTTTTCAATTATG
Found at i:1431679 original size:2 final size:2
Alignment explanation
Indices: 1431672--1431709 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1431662 ATTATAAAAC
1431672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1431710 TCAAATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1432495 original size:26 final size:26
Alignment explanation
Indices: 1432466--1432520 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1432456 ATCCTTCCTT
1432466 ATACTTCTATCCAACTCAAATCTTTA
1 ATACTTCTATCCAACTCAAATCTTTA
1432492 ATACTTCTATCCAACTCAAATCTTTA
1 ATACTTCTATCCAACTCAAATCTTTA
1432518 ATA
1 ATA
1432521 ACCAACTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.38
Consensus pattern (26 bp):
ATACTTCTATCCAACTCAAATCTTTA
Found at i:1439574 original size:16 final size:17
Alignment explanation
Indices: 1439553--1439586 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1439543 CTGCACAACC
1439553 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
1439569 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
1439586 T
1 T
1439587 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Done.