Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 10 of 19
Found at i:1650634 original size:14 final size:15
Alignment explanation
Indices: 1650603--1650661 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 15
1650593 AATATGATAA
*
1650603 ATATAATAAA-TA-T
1 ATATATTAAATTATT
1650616 ATATATTAAATT-TT
1 ATATATTAAATTATT
1650630 ATATAATATAAATTATT
1 ATAT-AT-TAAATTATT
1650647 AATATATTATAATTA
1 -ATATATTA-AATTA
1650662 AAAAAAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 2 0.05
16 8 0.21
17 9 0.24
18 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTAAATTATT
Found at i:1650634 original size:16 final size:17
Alignment explanation
Indices: 1650613--1650661 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
1650603 ATATAATAAA
1650613 TATATATATTAAATT-T
1 TATATATATTAAATTAT
1650629 TATATA-ATATAAATTAT
1 TATATATAT-TAAATTAT
1650646 TA-ATATATTATAATTA
1 TATATATATTA-AATTA
1650662 AAAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.07
16 17 0.59
17 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATTAAATTAT
Found at i:1652181 original size:28 final size:25
Alignment explanation
Indices: 1652130--1652196 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
1652120 TTATAATTTT
*
1652130 ATATATAAATATTATAATTTTATCAA
1 ATATATAAATATTATAATTATATC-A
*
1652156 ATATATAAATATTTTATATTAATATCA
1 ATATATAAATATTATA-ATT-ATATCA
* *
1652183 TTAAATAAATATTA
1 ATATATAAATATTA
1652197 ATATAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 15 0.44
27 15 0.44
28 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATATAAATATTATAATTATATCA
Found at i:1652204 original size:11 final size:11
Alignment explanation
Indices: 1652171--1652254 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
1652161 TAAATATTTT
*
1652171 ATATTAATATC
1 ATATTAATATA
*
1652182 AT-TAAATA-A
1 ATATTAATATA
1652191 ATATTAATATA
1 ATATTAATATA
*
1652202 ATATTAATTTA
1 ATATTAATATA
1652213 ATATTTAATA-A
1 ATA-TTAATATA
*
1652224 GATCATGATATATA
1 -AT-ATTA-ATATA
**
1652238 ATAAAAATATA
1 ATATTAATATA
1652249 ATATTA
1 ATATTA
1652255 TTATTTTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
9 2 0.04
10 10 0.18
11 26 0.46
12 11 0.20
13 6 0.11
14 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATATTAATATA
Found at i:1652693 original size:30 final size:30
Alignment explanation
Indices: 1652659--1652790 Score: 103
Period size: 30 Copynumber: 4.5 Consensus size: 30
1652649 TAGTAAAAGG
1652659 TTATTTAAATATAAATAAAAAATAAAAAAT
1 TTATTTAAATATAAATAAAAAATAAAAAAT
* * * * * *
1652689 TTATTTTATTATAAATTAAAAGTTAAAAGT
1 TTATTTAAATATAAATAAAAAATAAAAAAT
* * *
1652719 TTATTTAAATATAATTTAAATATTAAAAAA-
1 TTATTTAAATATAA-ATAAAAAATAAAAAAT
*
1652749 TTATTT--ATATACAGT-AAAAATATAAAAAT
1 TTATTTAAATATA-AATAAAAAATA-AAAAAT
*
1652778 TTATATAAA-ATAA
1 TTATTTAAATATAA
1652791 TAATATTTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
27 5 0.06
28 11 0.14
29 7 0.09
30 45 0.58
31 10 0.13
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (30 bp):
TTATTTAAATATAAATAAAAAATAAAAAAT
Found at i:1654659 original size:186 final size:186
Alignment explanation
Indices: 1654340--1654777 Score: 716
Period size: 186 Copynumber: 2.3 Consensus size: 186
1654330 TGAACGGTAG
* * *
1654340 CCTGAAAATTGGTTGACACTTTTAATAATCAATGACTAAGTGCAGGTCATTTTTCAGGAGGCTTG
1 CCTGAAAATTGGTTGACACTTCTAATAATCAATGACTAAGTGCAAGTCATTTTTCACGAGGCTTG
* * * *
1654405 GATCCTAAGTCCTAACGTGTTTGCTGTTGTTGAGGAAAATGATGAAGATTGAGGGAGGCAGGCAG
66 GATCATAAGTCCTAACGAGTTTGCTGTTGTTGACGAAAATGATGAAGATTGAGGGAGGCAGACAG
*
1654470 GCTCAGCCCTGTGTGTCTAGTAGGAAGTCAAACGTCAGCAGCCCATCAGAGTGTAA
131 GCTCAGCCCTGCGTGTCTAGTAGGAAGTCAAACGTCAGCAGCCCATCAGAGTGTAA
*
1654526 CCTGAAAATTGGTTGATACTTCTAATAATCAATGACTAAGTGCAAGTCATTTTTCACGAGGCTTG
1 CCTGAAAATTGGTTGACACTTCTAATAATCAATGACTAAGTGCAAGTCATTTTTCACGAGGCTTG
1654591 GATCATAAGTCCTAACGAGTTTGCTGTTGTTGACGAAAATGATGAAGATTGAGGGAGGCAGACAG
66 GATCATAAGTCCTAACGAGTTTGCTGTTGTTGACGAAAATGATGAAGATTGAGGGAGGCAGACAG
* *
1654656 GCTCAGCCCTGCGTGTCTAGTAGGAAGTCAAACGTCAGCAGCCCGTCAGAGTGTAG
131 GCTCAGCCCTGCGTGTCTAGTAGGAAGTCAAACGTCAGCAGCCCATCAGAGTGTAA
* * **
1654712 CCTGAAAATTGGCTGACACTTACTAACAATCAATGACTAAGTG-AAGGTCATTTTTCATAAGGCT
1 CCTGAAAATTGGTTGACACTT-CTAATAATCAATGACTAAGTGCAA-GTCATTTTTCACGAGGCT
1654776 TG
64 TG
1654778 AATCCAAACA
Statistics
Matches: 234, Mismatches: 16, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
186 196 0.84
187 38 0.16
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (186 bp):
CCTGAAAATTGGTTGACACTTCTAATAATCAATGACTAAGTGCAAGTCATTTTTCACGAGGCTTG
GATCATAAGTCCTAACGAGTTTGCTGTTGTTGACGAAAATGATGAAGATTGAGGGAGGCAGACAG
GCTCAGCCCTGCGTGTCTAGTAGGAAGTCAAACGTCAGCAGCCCATCAGAGTGTAA
Found at i:1655061 original size:18 final size:19
Alignment explanation
Indices: 1655028--1655063 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1655018 ATGATCTTGC
*
1655028 GAAAACTTTCATTATATAA
1 GAAAACTTTAATTATATAA
1655047 GAAAA-TTTAATTATATA
1 GAAAACTTTAATTATATA
1655064 TTTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (19 bp):
GAAAACTTTAATTATATAA
Found at i:1655212 original size:15 final size:15
Alignment explanation
Indices: 1655169--1655227 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1655159 AATATAGATT
1655169 TGAATTTTAAAATCTTA
1 TGAA-TTTAAAAT-TTA
1655186 --AATTTAAAATTTA
1 TGAATTTAAAATTTA
*
1655199 TG-ATTTACAAATTTG
1 TGAATTTA-AAATTTA
1655214 TGAATTTAAAATTT
1 TGAATTTAAAATTT
1655228 TTTATTTGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 3 0.08
14 13 0.35
15 16 0.43
16 5 0.14
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (15 bp):
TGAATTTAAAATTTA
Found at i:1655640 original size:2 final size:2
Alignment explanation
Indices: 1655633--1655657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1655623 TAAGTATTTC
1655633 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1655658 GATAATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1655971 original size:153 final size:150
Alignment explanation
Indices: 1655791--1656094 Score: 511
Period size: 153 Copynumber: 2.0 Consensus size: 150
1655781 TAAGAGTTTG
* *
1655791 ATCAAATAAATTTGTTAATTGGACAAGTCAAGTTAA-TTCAAGTTTTTAAATTTTTAAATTATTT
1 ATCAAATAAATTTGTTAATTAGACAAGTCAAGTTAACTT-AAGTTTTTAAAATTTTAAATTATTT
*
1655855 TCATGTTCAAATTATTTTTTATTTAGCTTATTTTAAGTTATTGACTTTTTTTTTATTTAAATTTT
65 TCATGTTCAAATTATTTTTTATTTAGCTTATTTTAAGTTATT-A--ATTTTTTTATTTAAATTTT
1655920 GATATTTAAACTGTTGATTTTTTT
127 GATATTTAAACTGTTGATTTTTTT
1655944 ATCAAATAAATTTGTTAATTAGACAAGTCAAGTTAACTTAAGTTTTTAAAATTTTAAATTATTTT
1 ATCAAATAAATTTGTTAATTAGACAAGTCAAGTTAACTTAAGTTTTTAAAATTTTAAATTATTTT
*
1656009 TATGTTCAAATTATTTTTTATTTAGCTTATTTTAAGTTATTAATTTTTTTATTTAAATTTTGATA
66 CATGTTCAAATTATTTTTTATTTAGCTTATTTTAAGTTATTAATTTTTTTATTTAAATTTTGATA
**
1656074 TTTAAGTTGTTGATTTTTTT
131 TTTAAACTGTTGATTTTTTT
1656094 A
1 A
1656095 ATTATATTAA
Statistics
Matches: 144, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
150 41 0.28
152 1 0.01
153 100 0.69
154 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (150 bp):
ATCAAATAAATTTGTTAATTAGACAAGTCAAGTTAACTTAAGTTTTTAAAATTTTAAATTATTTT
CATGTTCAAATTATTTTTTATTTAGCTTATTTTAAGTTATTAATTTTTTTATTTAAATTTTGATA
TTTAAACTGTTGATTTTTTT
Found at i:1656125 original size:30 final size:29
Alignment explanation
Indices: 1656091--1656158 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1656081 TGTTGATTTT
*
1656091 TTTAATTATATTAAGTT-AATTATATTTAAA
1 TTTAATTAAATTAA-TTAAATT-TATTTAAA
* *
1656121 TTTAAATAAATTAATTAAATTTTTTTAAA
1 TTTAATTAAATTAATTAAATTTATTTAAA
1656150 TTTGAATTA
1 TTT-AATTA
1656159 GAATAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTAATTAAATTAATTAAATTTATTTAAA
Found at i:1656604 original size:17 final size:16
Alignment explanation
Indices: 1656572--1656610 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1656562 TTATTTATTT
1656572 AATATTAAATATAATA
1 AATATTAAATATAATA
*
1656588 AATATTCAATAATAATA
1 AATATTAAAT-ATAATA
*
1656605 TATATT
1 AATATT
1656611 TAGCTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATTAAATATAATA
Found at i:1657500 original size:22 final size:22
Alignment explanation
Indices: 1657465--1657519 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1657455 TTTTTATTAA
*
1657465 AAAAATTATTTTATGACAAACAT-
1 AAAAATTATATTAT-A-AAACATC
1657488 AAAAA-TATATTATAAAACATC
1 AAAAATTATATTATAAAACATC
1657509 AAAAAGTTATA
1 AAAAA-TTATA
1657520 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
22 7 0.25
23 9 0.32
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAAATTATATTATAAAACATC
Found at i:1657835 original size:22 final size:21
Alignment explanation
Indices: 1657801--1657856 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
1657791 TATTAAAAAA
1657801 TTTATA-TTTTAT-ATTAATAT
1 TTTATATTTTTATAATTAA-AT
1657821 TTATATATTTTTATAATTAAAT
1 TT-TATATTTTTATAATTAAAT
1657843 TTTAATATTTTTAT
1 TTT-ATATTTTTAT
1657857 TAAATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 20 0.62
23 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATATTTTTATAATTAAAT
Found at i:1657860 original size:19 final size:20
Alignment explanation
Indices: 1657804--1657867 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
1657794 TAAAAAATTT
1657804 ATATTTTATATT-AATATTTA
1 ATATTTTATATTAAAT-TTTA
1657824 TATATTTTTATAATTAAATTTTA
1 -ATA-TTTTAT-ATTAAATTTTA
*
1657847 ATATTTT-TATTAAATTATA
1 ATATTTTATATTAAATTTTA
1657866 AT
1 AT
1657868 CCGAATATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 12 0.31
20 1 0.03
21 7 0.18
22 9 0.23
23 7 0.18
24 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTTATATTAAATTTTA
Found at i:1659725 original size:2 final size:2
Alignment explanation
Indices: 1659718--1659761 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
1659708 ACATTTTGGT
1659718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1659761 T
1 T
1659762 GATACATGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1660511 original size:3 final size:3
Alignment explanation
Indices: 1660503--1660535 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1660493 AAAGGTTTGC
1660503 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1660536 TAATAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1660716 original size:2 final size:2
Alignment explanation
Indices: 1660709--1660755 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
1660699 TCTTTAAATC
* *
1660709 AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT AC AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
1660752 -T AT A
1 AT AT A
1660756 GTAGTAATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1660736 original size:23 final size:23
Alignment explanation
Indices: 1660706--1660751 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1660696 CTTTCTTTAA
* *
1660706 ATCATATATATATATATATATAT
1 ATCATATATATACAAATATATAT
1660729 ATCATATATATACAAATATATAT
1 ATCATATATATACAAATATATAT
1660752 TATAGTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATCATATATATACAAATATATAT
Found at i:1661217 original size:24 final size:24
Alignment explanation
Indices: 1661190--1661267 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
1661180 TGGGGGTGGG
1661190 GGTGGTTTTGGTGGAGGTACTGGA
1 GGTGGTTTTGGTGGAGGTACTGGA
* *
1661214 GGTGGTTTTGGTGGTGGTTCTGGA
1 GGTGGTTTTGGTGGAGGTACTGGA
* * *
1661238 GGGGGTTTTGGAGGAGG-AGCTGGT
1 GGTGGTTTTGGTGGAGGTA-CTGGA
1661262 GGTGGT
1 GGTGGT
1661268 GGTGGCTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.09, C:0.04, G:0.54, T:0.33
Consensus pattern (24 bp):
GGTGGTTTTGGTGGAGGTACTGGA
Found at i:1661231 original size:12 final size:12
Alignment explanation
Indices: 1661190--1661251 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
1661180 TGGGGGTGGG
*
1661190 GGTGGTTTTGGT
1 GGTGGTTTTGGA
* **
1661202 GGAGGTACTGGA
1 GGTGGTTTTGGA
*
1661214 GGTGGTTTTGGT
1 GGTGGTTTTGGA
*
1661226 GGTGGTTCTGGA
1 GGTGGTTTTGGA
*
1661238 GGGGGTTTTGGA
1 GGTGGTTTTGGA
1661250 GG
1 GG
1661252 AGGAGCTGGT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.08, C:0.03, G:0.53, T:0.35
Consensus pattern (12 bp):
GGTGGTTTTGGA
Found at i:1661285 original size:6 final size:6
Alignment explanation
Indices: 1661276--1661317 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1661266 GTGGTGGCTT
**
1661276 TGGAGG TGGAGG TGGAGG TGGAGG TGGATT TGGAGG TGGAGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG
1661318 CGGACATGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.00, G:0.62, T:0.21
Consensus pattern (6 bp):
TGGAGG
Found at i:1661289 original size:18 final size:17
Alignment explanation
Indices: 1661288--1661356 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
1661278 GAGGTGGAGG
1661288 TGGAGGTGGAGGTGGATT
1 TGGAGGTGGAGGTGG-TT
* **
1661306 TGGAGGTGGAGGCGGACA
1 TGGAGGTGGAGGTGG-TT
1661324 TGGTAGCGGTGGA-G-GGTT
1 TGG-A--GGTGGAGGTGGTT
1661342 TGGAGGTGGAGGTGG
1 TGGAGGTGGAGGTGG
1661357 GAAAGGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.15
16 1 0.02
17 3 0.07
18 21 0.51
19 3 0.07
20 1 0.02
21 6 0.15
ACGTcount: A:0.16, C:0.04, G:0.58, T:0.22
Consensus pattern (17 bp):
TGGAGGTGGAGGTGGTT
Found at i:1661317 original size:30 final size:30
Alignment explanation
Indices: 1661234--1661380 Score: 107
Period size: 30 Copynumber: 4.7 Consensus size: 30
1661224 GTGGTGGTTC
* * * * *
1661234 TGGAGGGGGTTTTGGAGGAGGAGCTGGTGG
1 TGGAGGTGGATTTGGAGGTGGAGGTGGAGG
* *
1661264 TGGTGGTGGCTTTGGAGGTGGAGGTGGAGG
1 TGGAGGTGGATTTGGAGGTGGAGGTGGAGG
*
1661294 TGGAGGTGGATTTGGAGGTGGAGGCGGACATGG
1 TGGAGGTGGATTTGGAGGTGGAGGTGG--A-GG
* * *
1661327 TAGCGGTGGAGGGTTTGGAGGTGGAGGTGG-GAA
1 TGGAGGTGGA---TTTGGAGGTGGAGGTGGAG-G
* *
1661360 AGGAGGTGGATTTGGTGGTGG
1 TGGAGGTGGATTTGGAGGTGG
1661381 GATTGGTAAG
Statistics
Matches: 93, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
30 58 0.62
32 2 0.02
33 17 0.18
36 16 0.17
ACGTcount: A:0.15, C:0.03, G:0.58, T:0.24
Consensus pattern (30 bp):
TGGAGGTGGATTTGGAGGTGGAGGTGGAGG
Found at i:1661455 original size:30 final size:30
Alignment explanation
Indices: 1661421--1661653 Score: 259
Period size: 30 Copynumber: 7.8 Consensus size: 30
1661411 AGTAGGAAAA
* *
1661421 GGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
* * *
1661451 GGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
*
1661481 GGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
* *** * ** ***
1661511 GGTGGAGGCATTGGTGGGGGAGTAGGAAAA
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
* *
1661541 GGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
* * *
1661571 GGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
*
1661601 GGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGGACTT
*
1661631 GGTGGAGGAATTGGTAAGGGTGG
1 GGTGGAGGAATTGGAAAGGGTGG
1661654 AGGCATTGGT
Statistics
Matches: 162, Mismatches: 41, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 162 1.00
ACGTcount: A:0.20, C:0.06, G:0.53, T:0.21
Consensus pattern (30 bp):
GGTGGAGGAATTGGAAAGGGTGGGGGACTT
Found at i:1661455 original size:60 final size:60
Alignment explanation
Indices: 1661391--1661656 Score: 325
Period size: 60 Copynumber: 4.4 Consensus size: 60
1661381 GATTGGTAAG
* ** * *
1661391 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGTAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTT
* * ****
1661451 GGTGGAGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGTAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTT
* ** * *
1661511 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGTAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTT
* * ****
1661571 GGTGGAGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGTAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTT
*
1661631 GGTGGAGGAATTGGTAAGGGTGGAGG
1 GGTGGAGGAATTGGTAAGGGAGGAGG
1661657 CATTGGTGGG
Statistics
Matches: 172, Mismatches: 34, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 172 1.00
ACGTcount: A:0.21, C:0.05, G:0.53, T:0.21
Consensus pattern (60 bp):
GGTGGAGGAATTGGTAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTT
Found at i:1661521 original size:120 final size:120
Alignment explanation
Indices: 1661391--1661645 Score: 501
Period size: 120 Copynumber: 2.1 Consensus size: 120
1661381 GATTGGTAAG
1661391 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1661456 AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
66 AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
1661511 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1661576 AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
66 AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
*
1661631 GGTGGAGGAATTGGT
1 GGTGGAGGCATTGGT
1661646 AAGGGTGGAG
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 134 1.00
ACGTcount: A:0.21, C:0.05, G:0.53, T:0.21
Consensus pattern (120 bp):
GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTT
Found at i:1661653 original size:78 final size:78
Alignment explanation
Indices: 1661571--1661734 Score: 211
Period size: 78 Copynumber: 2.1 Consensus size: 78
1661561 TGGGGGACTT
* ****
1661571 GGTGGAGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGAATTGGCAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGG
* *
1661636 AGGAATTGGTAAG
66 AGGAATTGGCAAA
* *** * *
1661649 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGAATTGGCAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGG
1661714 AGGAATTGGCAAA
66 AGGAATTGGCAAA
1661727 GGTGGAGG
1 GGTGGAGG
1661735 CCTTGGAGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.23, C:0.05, G:0.52, T:0.20
Consensus pattern (78 bp):
GGTGGAGGAATTGGCAAGGGAGGAGGAAAAGGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGG
AGGAATTGGCAAA
Found at i:1661657 original size:60 final size:60
Alignment explanation
Indices: 1661421--1661683 Score: 364
Period size: 60 Copynumber: 4.4 Consensus size: 60
1661411 AGTAGGAAAA
* *
1661421 GGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCATT
* *** * * * **
1661481 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGCATTGGTGGGGGAGTAGGAAAA
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCATT
* *
1661541 GGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCATT
*
1661601 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGTAAGGGTGGAGGCATT
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCATT
* * * *
1661661 GGTGGGGGAGTAGGAAAAGGTGG
1 GGTGGTGGAATTGGAAAGGGTGG
1661684 TGGCATTGGA
Statistics
Matches: 174, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 174 1.00
ACGTcount: A:0.21, C:0.05, G:0.53, T:0.21
Consensus pattern (60 bp):
GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAGGGTGGAGGCATT
Found at i:1661663 original size:30 final size:29
Alignment explanation
Indices: 1661421--1661692 Score: 211
Period size: 30 Copynumber: 9.1 Consensus size: 29
1661411 AGTAGGAAAA
* * *
1661421 GGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGCA-TT
* *
1661451 GGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGAGGAATTGGAAAGGGTGG-GGCATT
* *
1661481 GGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGCA-TT
* *** * * * **
1661511 GGTGGAGGCATTGGTGGGGGAGTAGGAAAA
1 GGTGGAGGAATTGGAAAGGGTG-GGGCATT
* * *
1661541 GGTGGTGGCATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGCA-TT
* *
1661571 GGTGGAGGAATTGGCAAGGGTGGAGGCCTT
1 GGTGGAGGAATTGGAAAGGGTGG-GGCATT
* *
1661601 GGTGGTGGAATTGGAAAGGGTGGGGGACTT
1 GGTGGAGGAATTGGAAAGGGTGGGGCA-TT
*
1661631 GGTGGAGGAATTGGTAAGGGTGGAGGCATT
1 GGTGGAGGAATTGGAAAGGGTGG-GGCATT
* * * *
1661661 GGTGGGGGAGTAGGAAAAGGTGGTGGCATT
1 GGTGGAGGAATTGGAAAGGGTGG-GGCATT
1661691 GG
1 GG
1661693 AAAGGGTGGG
Statistics
Matches: 189, Mismatches: 46, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
29 7 0.04
30 172 0.91
31 10 0.05
ACGTcount: A:0.21, C:0.06, G:0.53, T:0.21
Consensus pattern (29 bp):
GGTGGAGGAATTGGAAAGGGTGGGGCATT
Found at i:1661713 original size:30 final size:30
Alignment explanation
Indices: 1661679--1661872 Score: 210
Period size: 30 Copynumber: 6.5 Consensus size: 30
1661669 AGTAGGAAAA
* * *
1661679 GGTGGTGGCATTGG-AAAGGGTGGGGGACTT
1 GGTGGTGGAATTGGCAAA-GGAGGAGGACTT
* * *
1661709 GGTGGAGGAATTGGCAAAGGTGGAGGCCTT
1 GGTGGTGGAATTGGCAAAGGAGGAGGACTT
*
1661739 GGAGGTGGAATTGGCAAAGGAGGAGGACTT
1 GGTGGTGGAATTGGCAAAGGAGGAGGACTT
* * *
1661769 GGTGGTGGGATTGGCAAAGGAGGAGGCCTA
1 GGTGGTGGAATTGGCAAAGGAGGAGGACTT
* * * * *
1661799 GGTGGTGGAATAGGTAAAGGTGGTGGAATT
1 GGTGGTGGAATTGGCAAAGGAGGAGGACTT
* * *
1661829 GGAGGTGGCATTGGCAAGGGAGGAGGACTT
1 GGTGGTGGAATTGGCAAAGGAGGAGGACTT
1661859 GGTGGTGGAATTGG
1 GGTGGTGGAATTGG
1661873 AGGTGGCATT
Statistics
Matches: 133, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
30 130 0.98
31 3 0.02
ACGTcount: A:0.23, C:0.07, G:0.49, T:0.21
Consensus pattern (30 bp):
GGTGGTGGAATTGGCAAAGGAGGAGGACTT
Found at i:1661746 original size:60 final size:60
Alignment explanation
Indices: 1661679--1662118 Score: 237
Period size: 60 Copynumber: 7.1 Consensus size: 60
1661669 AGTAGGAAAA
* * * *
1661679 GGTGGTGGCATTGG-AAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAAGGTGGAGGCCTT
1 GGTGGTGGAATTGGCAAA-GGTGGAGGACTTGGTGGTGGAATTGGCAAAGGAGGAGGCCTT
* * * *
1661739 GGAGGTGGAATTGGCAAAGGAGGAGGACTTGGTGGTGGGATTGGCAAAGGAGGAGGCCTA
1 GGTGGTGGAATTGGCAAAGGTGGAGGACTTGGTGGTGGAATTGGCAAAGGAGGAGGCCTT
* * * * * * * *
1661799 GGTGGTGGAATAGGTAAAGGTGGTGGAATTGGAGGTGGCATTGGCAAGGGAGGAGGACTT
1 GGTGGTGGAATTGGCAAAGGTGGAGGACTTGGTGGTGGAATTGGCAAAGGAGGAGGCCTT
** ***
1661859 GGTGGTGGAATTGG-AGGTGGCATTGGCAAAGGAGGAGGCATTGGTGGTGGAATTGG-AAAGGGA
1 GGTGGTGGAATTGGCA-AAGG---TGG---AGGACTTGG---TGG---TGGAATTGGCAAA-GGA
* *
1661922 GGTGGGCTT
52 GGAGGCCTT
* * * * * * *
1661931 GGAGGAGGTATTGGCAAAGGGGGAGG-CATTGGTGGTGGAATAGG-AAAGGGAGGTGGGCTT
1 GGTGGTGGAATTGGCAAAGGTGGAGGAC-TTGGTGGTGGAATTGGCAAA-GGAGGAGGCCTT
* * * * * * *
1661991 GGAGGAGGTATTGGCAAAGGGGGAGG-CATTGGTGGCGGAATTGG-AAAGGGTGGAGGACTT
1 GGTGGTGGAATTGGCAAAGGTGGAGGAC-TTGGTGGTGGAATTGGCAAA-GGAGGAGGCCTT
* * * * * * * * * *
1662051 GGTGGCGGAATAGGAAAAGGTGGTGGACTTGGTGGAGGAATTGGGAAGGGTGGTGGCATT
1 GGTGGTGGAATTGGCAAAGGTGGAGGACTTGGTGGTGGAATTGGCAAAGGAGGAGGCCTT
1662111 GGTGGTGG
1 GGTGGTGG
1662119 TGGTGGCTTT
Statistics
Matches: 302, Mismatches: 59, Indels: 38
0.76 0.15 0.10
Matches are distributed among these distances:
59 1 0.00
60 241 0.80
61 6 0.02
63 6 0.02
66 10 0.03
69 4 0.01
71 2 0.01
72 31 0.10
73 1 0.00
ACGTcount: A:0.23, C:0.06, G:0.50, T:0.20
Consensus pattern (60 bp):
GGTGGTGGAATTGGCAAAGGTGGAGGACTTGGTGGTGGAATTGGCAAAGGAGGAGGCCTT
Found at i:1661758 original size:78 final size:78
Alignment explanation
Indices: 1661601--1661758 Score: 235
Period size: 78 Copynumber: 2.0 Consensus size: 78
1661591 TGGAGGCCTT
* * *
1661601 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGTAAGGGTGGAGGCATTGGTGG
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAAGGTGGAGGCATTGGAGG
*
1661666 GGGAGTAGGAAAA
66 GGGAATAGGAAAA
* *
1661679 GGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAAGGTGGAGGCCTTGGAGG
1 GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAAGGTGGAGGCATTGGAGG
* * *
1661744 TGGAATTGGCAAA
66 GGGAATAGGAAAA
1661757 GG
1 GG
1661759 AGGAGGACTT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.23, C:0.05, G:0.51, T:0.20
Consensus pattern (78 bp):
GGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAATTGGCAAAGGTGGAGGCATTGGAGG
GGGAATAGGAAAA
Found at i:1661767 original size:138 final size:138
Alignment explanation
Indices: 1661511--1661831 Score: 491
Period size: 138 Copynumber: 2.3 Consensus size: 138
1661501 TGGGGGACTT
1661511 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
* * * *
1661576 AGGAATTGGCAAGGGTGGAGGCCTTGGTGGTGGAATTGGAAAGGGTGGGGGACTTGGTGGAGGAA
66 AGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGAAAGGGAGGAGGACTTGGTGGAGGAA
* *
1661641 TTGGTAAG
131 TTGGCAAA
1661649 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
1 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
* *
1661714 AGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGCAAA-GGAGGAGGACTTGGTGGTGGG
66 AGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGG-AAAGGGAGGAGGACTTGGTGGAGGA
1661778 ATTGGCAAA
130 ATTGGCAAA
* * * * * * *
1661787 GGAGGAGGCCTAGGTGGTGGAATAGGTAAAGGTGGTGGAATTGGA
1 GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGA
1661832 GGTGGCATTG
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 164 0.98
139 3 0.02
ACGTcount: A:0.23, C:0.06, G:0.51, T:0.20
Consensus pattern (138 bp):
GGTGGAGGCATTGGTGGGGGAGTAGGAAAAGGTGGTGGCATTGGAAAGGGTGGGGGACTTGGTGG
AGGAATTGGCAAAGGTGGAGGCCTTGGAGGTGGAATTGGAAAGGGAGGAGGACTTGGTGGAGGAA
TTGGCAAA
Found at i:1661864 original size:42 final size:42
Alignment explanation
Indices: 1661817--1661915 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
1661807 AATAGGTAAA
*
1661817 GGTGGTGGAATTGGAGGTGGCATTGGCAAGGGAGGAGG-ACTT
1 GGTGGTGGAATTGGAGGTGGCATTGGCAAAGGAGGAGGCA-TT
1661859 GGTGGTGGAATTGGAGGTGGCATTGGCAAAGGAGGAGGCATT
1 GGTGGTGGAATTGGAGGTGGCATTGGCAAAGGAGGAGGCATT
1661901 GGTGGTGGAATTGGA
1 GGTGGTGGAATTGGA
1661916 AAGGGAGGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
42 54 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.06, G:0.49, T:0.22
Consensus pattern (42 bp):
GGTGGTGGAATTGGAGGTGGCATTGGCAAAGGAGGAGGCATT
Found at i:1661892 original size:102 final size:102
Alignment explanation
Indices: 1661767--1661971 Score: 272
Period size: 102 Copynumber: 2.0 Consensus size: 102
1661757 GGAGGAGGAC
* * * *
1661767 TTGGTGGTGGGATTGGCAAAGGAGGAGGCCTAGGTGGTGGAATAGGTAAA-GGTGGTGGAATTGG
1 TTGGAGGTGGCATTGGCAAAGGAGGAGGCATAGGTGGTGGAATAGG-AAAGGGAGGTGGAATTGG
*
1661831 AGGTGGCATTGGC-AAGGGAGGAGG-ACTTGGTGGTGGAA
65 AGGAGGCATTGGCAAAGGG-GGAGGCA-TTGGTGGTGGAA
* * **
1661869 TTGGAGGTGGCATTGGCAAAGGAGGAGGCATTGGTGGTGGAATTGGAAAGGGAGGTGGGCTTGGA
1 TTGGAGGTGGCATTGGCAAAGGAGGAGGCATAGGTGGTGGAATAGGAAAGGGAGGTGGAATTGGA
*
1661934 GGAGGTATTGGCAAAGGGGGAGGCATTGGTGGTGGAA
66 GGAGGCATTGGCAAAGGGGGAGGCATTGGTGGTGGAA
1661971 T
1 T
1661972 AGGAAAGGGA
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
101 3 0.03
102 81 0.90
103 6 0.07
ACGTcount: A:0.23, C:0.06, G:0.49, T:0.21
Consensus pattern (102 bp):
TTGGAGGTGGCATTGGCAAAGGAGGAGGCATAGGTGGTGGAATAGGAAAGGGAGGTGGAATTGGA
GGAGGCATTGGCAAAGGGGGAGGCATTGGTGGTGGAA
Found at i:1662070 original size:120 final size:120
Alignment explanation
Indices: 1661869--1662106 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 120
1661859 GGTGGTGGAA
* * * *
1661869 TTGGAGGTGGCATTGGCAAAGGAGGAGGCATTGGTGGTGGAATTGGAAAGGGAGGTGGGCTTGGA
1 TTGGAGGAGGCATTGGCAAAGGAGGAGGCATTGGTGGCGGAATTGGAAAGGGAGGAGGACTTGGA
* * * *
1661934 GGAGGTATTGGCAAAGGGGGAGG-CATTGGTGGTGGAATAGGAAAGGGAGGTGGGC
66 GGAGGAATAGGAAAAGGGGGAGGAC-TTGGTGGAGGAATAGGAAAGGGAGGTGGGC
* * * *
1661989 TTGGAGGAGGTATTGGCAAAGGGGGAGGCATTGGTGGCGGAATTGGAAAGGGTGGAGGACTTGGT
1 TTGGAGGAGGCATTGGCAAAGGAGGAGGCATTGGTGGCGGAATTGGAAAGGGAGGAGGACTTGGA
* * * * * *
1662054 GGCGGAATAGGAAAAGGTGGTGGACTTGGTGGAGGAATTGGGAAGGGTGGTGG
66 GGAGGAATAGGAAAAGGGGGAGGACTTGGTGGAGGAATAGGAAAGGGAGGTGG
1662107 CATTGGTGGT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
120 98 0.99
121 1 0.01
ACGTcount: A:0.24, C:0.05, G:0.51, T:0.20
Consensus pattern (120 bp):
TTGGAGGAGGCATTGGCAAAGGAGGAGGCATTGGTGGCGGAATTGGAAAGGGAGGAGGACTTGGA
GGAGGAATAGGAAAAGGGGGAGGACTTGGTGGAGGAATAGGAAAGGGAGGTGGGC
Found at i:1662111 original size:18 final size:18
Alignment explanation
Indices: 1662090--1662148 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1662080 TGGTGGAGGA
1662090 ATTGGGAAGGGTGGTGGC
1 ATTGGGAAGGGTGGTGGC
1662108 ATTGGTG--GTGGTGGTGGC
1 ATTGG-GAAG-GGTGGTGGC
* * *
1662126 TTTGGTAAAGGTGGTGGC
1 ATTGGGAAGGGTGGTGGC
1662144 ATTGG
1 ATTGG
1662149 AGGTGGGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.14, C:0.05, G:0.51, T:0.31
Consensus pattern (18 bp):
ATTGGGAAGGGTGGTGGC
Found at i:1662113 original size:90 final size:89
Alignment explanation
Indices: 1661886--1662115 Score: 252
Period size: 90 Copynumber: 2.6 Consensus size: 89
1661876 TGGCATTGGC
* * * *
1661886 AAAGGAGGAGG-CATTGGTGGTGGAATTGGAAAGGGAGGTGGGC-TTGGAGGAGGTATTGGCAAA
1 AAAGGAGGTGGAC-TTGGTGGAGGAATTGGAAAGGG-GGT-GGCATTGGTGGAGGAATTGGCAAA
*
1661949 GGGGGAGGCATTGGTGGTGGAATAGGA
63 GGGGGAGGCATTGGTGGCGGAATAGGA
* * * * * *
1661976 AAGGGAGGTGGGCTTGGAGGAGGTATTGGCAAAGGGGGAGGCATTGGTGGCGGAATTGG-AAAGG
1 AAAGGAGGTGGACTTGGTGGAGGAATTGG-AAAGGGGGTGGCATTGGTGGAGGAATTGGCAAAGG
1662040 GTGGAGG-ACTTGGTGGCGGAATAGGA
65 G-GGAGGCA-TTGGTGGCGGAATAGGA
* *
1662066 AAAGGTGGTGGACTTGGTGGAGGAATTGGGAAGGGTGGTGGCATTGGTGG
1 AAAGGAGGTGGACTTGGTGGAGGAATTGGAAAGGG-GGTGGCATTGGTGG
1662116 TGGTGGTGGC
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
89 15 0.13
90 95 0.81
91 7 0.06
ACGTcount: A:0.24, C:0.05, G:0.51, T:0.20
Consensus pattern (89 bp):
AAAGGAGGTGGACTTGGTGGAGGAATTGGAAAGGGGGTGGCATTGGTGGAGGAATTGGCAAAGGG
GGAGGCATTGGTGGCGGAATAGGA
Found at i:1662166 original size:30 final size:30
Alignment explanation
Indices: 1661859--1662181 Score: 188
Period size: 30 Copynumber: 10.6 Consensus size: 30
1661849 AGGAGGACTT
* * * *
1661859 GGTGGTGGAATTGGAGGTGGCATTGGCAAA
1 GGTGGTGGCATTGGTGGTGGAATTGGAAAA
* * *
1661889 GGAGGAGGCATTGGTGGTGGAATTGGAAAG
1 GGTGGTGGCATTGGTGGTGGAATTGGAAAA
* * * * *
1661919 GGAGGTGGGC-TTGGAGGAGGTATTGGCAAA
1 GGTGGT-GGCATTGGTGGTGGAATTGGAAAA
* * * *
1661949 GGGGGAGGCATTGGTGGTGGAATAGGAAAG
1 GGTGGTGGCATTGGTGGTGGAATTGGAAAA
* * * * *
1661979 GGAGGTGGGC-TTGGAGGAGGTATTGGCAAA
1 GGTGGT-GGCATTGGTGGTGGAATTGGAAAA
* * * *
1662009 GGGGGAGGCATTGGTGGCGGAATTGGAAAG
1 GGTGGTGGCATTGGTGGTGGAATTGGAAAA
* * *
1662039 GGTGGAGG-ACTTGGTGGCGGAATAGGAAAA
1 GGTGGTGGCA-TTGGTGGTGGAATTGGAAAA
* * *
1662069 GGTGGTGG-ACTTGGTGGAGGAATTGGGAAG
1 GGTGGTGGCA-TTGGTGGTGGAATTGGAAAA
** *
1662099 GGTGGTGGCATTGGTGGTGGTGGTGGCTTTGGTAAA
1 GGTGGTGGCA----T--TGGTGGTGGAATTGGAAAA
* *
1662135 GGTGGTGGCATTGGAGGTGGGATTGGAAAA
1 GGTGGTGGCATTGGTGGTGGAATTGGAAAA
1662165 GGTGGTGG-ATTTGGTGG
1 GGTGGTGGCA-TTGGTGG
1662182 CGGTGCTGGT
Statistics
Matches: 226, Mismatches: 55, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
29 8 0.04
30 185 0.82
31 7 0.03
32 1 0.00
34 1 0.00
36 24 0.11
ACGTcount: A:0.22, C:0.05, G:0.51, T:0.22
Consensus pattern (30 bp):
GGTGGTGGCATTGGTGGTGGAATTGGAAAA
Found at i:1662198 original size:66 final size:66
Alignment explanation
Indices: 1662066--1662220 Score: 163
Period size: 66 Copynumber: 2.3 Consensus size: 66
1662056 CGGAATAGGA
* * * * * * *
1662066 AAAGGTGGTGGACTTGGTGGAGGAATTGGGAAGGGTGGTGGCATTGGTGGTGGTGGTGGCTTTGG
1 AAAGGTGGTGGACTTGGAGGTGGAATTGGAAAAGGTGGTGGCATTGGTGGCGGTGCTGGCTGTGG
1662131 T
66 T
*
1662132 AAAGGTGGTGG-CATTGGAGGTGGGATTGGAAAAGGTGGTGG-ATTTGGTGGCGGTGCTGG-TGG
1 AAAGGTGGTGGAC-TTGGAGGTGGAATTGGAAAAGGTGGTGGCA-TTGGTGGCGGTGCTGGCT-G
1662194 TGGT
63 TGGT
** *
1662198 ACTGGTGGTGGATTTGGAGGTGG
1 AAAGGTGGTGGACTTGGAGGTGG
1662221 TGCCGGCGGT
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
65 3 0.04
66 71 0.96
ACGTcount: A:0.15, C:0.05, G:0.52, T:0.28
Consensus pattern (66 bp):
AAAGGTGGTGGACTTGGAGGTGGAATTGGAAAAGGTGGTGGCATTGGTGGCGGTGCTGGCTGTGG
T
Found at i:1662219 original size:24 final size:24
Alignment explanation
Indices: 1662192--1662238 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1662182 CGGTGCTGGT
* *
1662192 GGTGGTACTGGTGGTGGATTTGGA
1 GGTGGTACCGGCGGTGGATTTGGA
*
1662216 GGTGGTGCCGGCGGTGGATTTGG
1 GGTGGTACCGGCGGTGGATTTGG
1662239 CGGAGGTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.53, T:0.30
Consensus pattern (24 bp):
GGTGGTACCGGCGGTGGATTTGGA
Found at i:1662266 original size:18 final size:18
Alignment explanation
Indices: 1662243--1662296 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1662233 ATTTGGCGGA
1662243 GGTGGAGCTGGTTCCGGT
1 GGTGGAGCTGGTTCCGGT
*
1662261 GGTGGA-----TT-CGGA
1 GGTGGAGCTGGTTCCGGT
1662273 GGTGGAGCTGGTTCCGGT
1 GGTGGAGCTGGTTCCGGT
1662291 GGTGGA
1 GGTGGA
1662297 TTCGGAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 9 0.32
13 2 0.07
17 2 0.07
18 15 0.54
ACGTcount: A:0.09, C:0.13, G:0.52, T:0.26
Consensus pattern (18 bp):
GGTGGAGCTGGTTCCGGT
Found at i:1662273 original size:30 final size:30
Alignment explanation
Indices: 1662212--1662424 Score: 204
Period size: 30 Copynumber: 7.1 Consensus size: 30
1662202 GTGGTGGATT
* * *
1662212 TGGAGGTGGTGCCGGCGGTGGATTTGGCGGAGG
1 TGGAGCTGGTTCCGGTGGTGGA-TT--CGGAGG
1662245 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
1 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
1662275 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
1 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
* * *
1662305 TGGAGGTGGTTCTGGAGGTGGATT------
1 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
* * *
1662329 TGGAGCTGGTGCCGGCGGTGGATTTGGTGGAGG
1 TGGAGCTGGTTCCGGTGGTGGA-TT--CGGAGG
1662362 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
1 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
* * * * *
1662392 TGAAGGTGGTTCTGGAGGTGGATTTGGAGG
1 TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
1662422 TGG
1 TGG
1662425 TTTTGGCGAA
Statistics
Matches: 152, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
24 18 0.12
25 2 0.01
30 89 0.59
32 4 0.03
33 39 0.26
ACGTcount: A:0.11, C:0.10, G:0.52, T:0.27
Consensus pattern (30 bp):
TGGAGCTGGTTCCGGTGGTGGATTCGGAGG
Found at i:1662312 original size:18 final size:18
Alignment explanation
Indices: 1662291--1662326 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1662281 TGGTTCCGGT
1662291 GGTGGATTC-GGAGGTGGA
1 GGTGG-TTCTGGAGGTGGA
1662309 GGTGGTTCTGGAGGTGGA
1 GGTGGTTCTGGAGGTGGA
1662327 TTTGGAGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.14, C:0.06, G:0.56, T:0.25
Consensus pattern (18 bp):
GGTGGTTCTGGAGGTGGA
Found at i:1662332 original size:24 final size:24
Alignment explanation
Indices: 1662305--1662426 Score: 68
Period size: 24 Copynumber: 5.5 Consensus size: 24
1662295 GATTCGGAGG
1662305 TGGAGGTGGTTCTGGAGGTGGATT
1 TGGAGGTGGTTCTGGAGGTGGATT
* * * *
1662329 TGGAGCTGGTGCCGGCGGTGGATT
1 TGGAGGTGGTTCTGGAGGTGGATT
* * *
1662353 TGGTGGAGG---TGGAGCTGG-TT
1 TGGAGGTGGTTCTGGAGGTGGATT
* *
1662373 CCGGTGGTGGATTC-GGAGGT-GA--
1 -TGGAGGTGG-TTCTGGAGGTGGATT
1662395 ---AGGTGGTTCTGGAGGTGGATT
1 TGGAGGTGGTTCTGGAGGTGGATT
1662416 TGGAGGTGGTT
1 TGGAGGTGGTT
1662427 TTGGCGAAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 26
0.64 0.13 0.23
Matches are distributed among these distances:
17 3 0.04
18 11 0.15
19 2 0.03
20 2 0.03
21 13 0.18
23 1 0.01
24 39 0.55
ACGTcount: A:0.11, C:0.08, G:0.51, T:0.30
Consensus pattern (24 bp):
TGGAGGTGGTTCTGGAGGTGGATT
Found at i:1662342 original size:117 final size:117
Alignment explanation
Indices: 1662192--1662424 Score: 385
Period size: 117 Copynumber: 2.0 Consensus size: 117
1662182 CGGTGCTGGT
* *
1662192 GGTGGTACTGGTGGTGGATTTGGAGGTGGTGCCGGCGGTGGATTTGGCGGAGGTGGAGCTGGTTC
1 GGTGGTACTGGAGGTGGATTTGGAGCTGGTGCCGGCGGTGGATTTGGCGGAGGTGGAGCTGGTTC
* *
1662257 CGGTGGTGGATTCGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGGA
66 CGGTGGTGGATTCGGAGGTGAAGCTGGTTCCGGAGGTGGATTCGGAGGTGGA
* *
1662309 GGTGGTTCTGGAGGTGGATTTGGAGCTGGTGCCGGCGGTGGATTTGGTGGAGGTGGAGCTGGTTC
1 GGTGGTACTGGAGGTGGATTTGGAGCTGGTGCCGGCGGTGGATTTGGCGGAGGTGGAGCTGGTTC
* * *
1662374 CGGTGGTGGATTCGGAGGTGAAGGTGGTTCTGGAGGTGGATTTGGAGGTGG
66 CGGTGGTGGATTCGGAGGTGAAGCTGGTTCCGGAGGTGGATTCGGAGGTGG
1662425 TTTTGGCGAA
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.11, C:0.10, G:0.52, T:0.27
Consensus pattern (117 bp):
GGTGGTACTGGAGGTGGATTTGGAGCTGGTGCCGGCGGTGGATTTGGCGGAGGTGGAGCTGGTTC
CGGTGGTGGATTCGGAGGTGAAGCTGGTTCCGGAGGTGGATTCGGAGGTGGA
Found at i:1662363 original size:87 final size:84
Alignment explanation
Indices: 1662245--1662425 Score: 290
Period size: 87 Copynumber: 2.1 Consensus size: 84
1662235 TTGGCGGAGG
* * *
1662245 TGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGGAG
1 TGGAGCTGGTGCCGGCGGTGGATTCGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAG
1662310 GTGGTTCTGGAGGTGGATT
66 GTGGTTCTGGAGGTGGATT
*
1662329 TGGAGCTGGTGCCGGCGGTGGATTTGGTGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTG
1 TGGAGCTGGTGCCGGCGGTGGA-TT--CGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTG
1662394 AAGGTGGTTCTGGAGGTGGATT
63 AAGGTGGTTCTGGAGGTGGATT
*
1662416 TGGAGGTGGT
1 TGGAGCTGGT
1662426 TTTGGCGAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 20 0.22
85 2 0.02
87 67 0.75
ACGTcount: A:0.11, C:0.10, G:0.51, T:0.28
Consensus pattern (84 bp):
TGGAGCTGGTGCCGGCGGTGGATTCGGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAG
GTGGTTCTGGAGGTGGATT
Found at i:1662429 original size:12 final size:12
Alignment explanation
Indices: 1662395--1662430 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1662385 TCGGAGGTGA
*
1662395 AGGTGGTTCTGG
1 AGGTGGTTTTGG
*
1662407 AGGTGGATTTGG
1 AGGTGGTTTTGG
1662419 AGGTGGTTTTGG
1 AGGTGGTTTTGG
1662431 CGAAGGGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.03, G:0.50, T:0.36
Consensus pattern (12 bp):
AGGTGGTTTTGG
Found at i:1662446 original size:87 final size:87
Alignment explanation
Indices: 1662270--1662451 Score: 256
Period size: 87 Copynumber: 2.1 Consensus size: 87
1662260 TGGTGGATTC
*
1662270 GGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGGAGGTGGTTCTGGAGGTGGATTTGGAGC
1 GGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAGGTGGTTCTGGAGGTGGATTTGGAGC
** ****
1662335 TGGTGCCGGCGGTGGATTTGGT
66 TGGTGCCGGCGAAGGAGCAAGT
*
1662357 GGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAGGTGGTTCTGGAGGTGGATTTGGAGG
1 GGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAGGTGGTTCTGGAGGTGGATTTGGAGC
*** *
1662422 TGGTTTTGGCGAAGGGGCAAGT
66 TGGTGCCGGCGAAGGAGCAAGT
1662444 GGAGGTGG
1 GGAGGTGG
1662452 TGGAATTGGA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.13, C:0.09, G:0.52, T:0.26
Consensus pattern (87 bp):
GGAGGTGGAGCTGGTTCCGGTGGTGGATTCGGAGGTGAAGGTGGTTCTGGAGGTGGATTTGGAGC
TGGTGCCGGCGAAGGAGCAAGT
Found at i:1662970 original size:28 final size:28
Alignment explanation
Indices: 1662938--1662994 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1662928 ATAATATTAG
1662938 ATAAATATCTGAATTGAAGCCACGTTTT
1 ATAAATATCTGAATTGAAGCCACGTTTT
1662966 ATAAATATCTGAATTGAAGCCACGTTTT
1 ATAAATATCTGAATTGAAGCCACGTTTT
1662994 A
1 A
1662995 ACGTGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (28 bp):
ATAAATATCTGAATTGAAGCCACGTTTT
Found at i:1664919 original size:266 final size:264
Alignment explanation
Indices: 1664415--1665717 Score: 1282
Period size: 266 Copynumber: 5.0 Consensus size: 264
1664405 AAAAGCAAAC
* *
1664415 TTTATGTATCTTCTCCAAAAAAACCTCTGCAACTCCATAAATAAAGGCACAGAAAGAGCATCGAG
1 TTTATGTATCTTCTCC--AATAA-CTCTGCAACTCCATAAATAAAAGCACAGAAAGAG-ATCGAG
* * * *
1664480 AGGACTTCGATGTGAGTCCATTAGCATTCAAAGCTACACAGTGCCAACTCAGGGCTAGTAGCTTC
62 AGGACTTCAATGTGAGTCCATTAGCATTCAAAGCTACACATTGCCAACTCAAGGCTAGTAGCTTT
* * * * * * *
1664545 ACCAAGATGGACTGAGGTACAGAGTTTACGAGCACTTGAATATATCATTTCAGTTTCAACCTTCC
127 GCCAAGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTTCAGTTCCAAACTTCC
* * * *
1664610 AATGAACAATATTCACTTCATCTTGCTGATAAATAA-CAATATGCACAGAACATGGAGATATTGA
192 AATGAACAATATTCACTTCATC-T-ATGATAAATAATAAATATGCACAGAACATGCAGATATCGA
* * **
1664674 GAGATGTAAA
255 CACACATAAA
* * * * * *
1664684 TTTATGTATCTTCTCGAATAACTCTGCAATTCCATAAATGAAAGCAAAGAAAGAGGGTCGAGATG
1 TTTATGTATCTTCTCCAATAACTCTGCAACTCCATAAATAAAAGCACAGAAAGA-GATCGAGAGG
* * *
1664749 ACTTCGATGTGAGTCCATTAGCATTCAAAGCCACACATTGCCAGCTCAAGGCTAGTAGCTTTGCC
65 ACTTCAATGTGAGTCCATTAGCATTCAAAGCTACACATTGCCAACTCAAGGCTAGTAGCTTTGCC
* * * * *
1664814 AAGATGGACTGAGGTAAAGGGTTTGCGAGCTCTTAAATAGATTACTTAAGTTCCAAACTTCCAAT
130 AAGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTTCAGTTCCAAACTTCCAAT
* *
1664879 -AAGCAATATTCACTTCATCGTAATGATAAAT-ATAAATATGCACGGAACATGTAGATATCGACA
195 GAA-CAATATTCACTTCATC-T-ATGATAAATAATAAATATGCACAGAACATGCAGATATCGACA
1664942 CACATAAAA
257 CACAT-AAA
* *
1664951 TTTATGCATCTTCTCCAATAACT-TGCAACTCCATAAATAAAATCACA-AAAGAG-TAC-A-AGG
1 TTTATGTATCTTCTCCAATAACTCTGCAACTCCATAAATAAAAGCACAGAAAGAGAT-CGAGAGG
* * *
1665011 ACTTCAATGTGAGTCCATGAGCATTCAAAGCTACAAATTGCCAACTCAAGGCTAGTAGCTTTGTC
65 ACTTCAATGTGAGTCCATTAGCATTCAAAGCTACACATTGCCAACTCAAGGCTAGTAGCTTTGCC
* * * * *
1665076 AAGATGGACTGAGATAAAGGGTTTATGAGCTCTTGAATGGATTATTTCTGTTCCAAACTTCCAAT
130 AAGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTTCAGTTCCAAACTTCCAAT
* * * *
1665141 GAACAATGTTTACTTCATCT-TG-T---TGATAAA-AT----A-AACATGCAGATA-CCA-ACAC
195 GAACAATATTCACTTCATCTATGATAAATAATAAATATGCACAGAACATGCAGATATCGACACAC
1665193 ATAAA
260 ATAAA
* * * *
1665198 TTTATGTATCTTATCTAATAACTCTGCAACTCCATAGATGAAAGCACAG-AAGA-ATACTGAGAG
1 TTTATGTATCTTCTCCAATAACTCTGCAACTCCATAAATAAAAGCACAGAAAGAGAT-C-GAGAG
* * * * * *
1665261 GACTTCAATGTGAGCCCATTAGAATTC-AAGCTACA-AGTTGCCAATTTAAGGCTAGCATCTTTG
64 GACTTCAATGTGAGTCCATTAGCATTCAAAGCTACACA-TTGCCAACTCAAGGCTAGTAGCTTTG
* *
1665324 CCAAGAGGGACTGAGGTAAAGGGTTTACGAGCACTTGAATCGATTATTTCCA-TTCCAAACTT-C
128 CCAAGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTT-CAGTTCCAAACTTCC
* ** * * *
1665387 AATGAACAATATTCACTTCATCTAGTTGATAGATAATAAGCATGCCCATAACATGCAGATATATG
192 AATGAACAATATTCACTTCATCTA--TGATAAATAATAAATATGCACAGAACATGCAGATAT-CG
1665452 ACACA-ATAAAA
254 ACACACAT-AAA
* * * * *
1665463 TATT-TGTTTCTCCTCCAATAACTCTGCAACTTCATAGATACAAAAGCACAG-AAGCGTATCGAG
1 T-TTATGTATCTTCTCCAATAACTCTGCAACTCCATA-A-ATAAAAGCACAGAAAGAG-ATCGAG
* * * * * * *
1665526 AGGGCTTCAATGTGAGTCTATTAGCATTCAAAGTTATACATTGCCAACTTAAGGTTAATAGCTTT
62 AGGACTTCAATGTGAGTCCATTAGCATTCAAAGCTACACATTGCCAACTCAAGGCTAGTAGCTTT
* * * * * *
1665591 GCCAAGATGGACTGAGGTAAAGGATTTACAAGCTCTGGAATAGATCATTTCTGCTT-CAAACTTC
127 GCCAAGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTTCAG-TTCCAAACTTC
* * * * * * * * *
1665655 CCATGACCAATATTTACTTCATCTTGTGGATAAATAACAAGTATTCACATACCATGCAGATAT
191 CAATGAACAATATTCACTTCATC-TAT-GATAAATAATAAATATGCACAGAACATGCAGATAT
1665718 TGACTCATTG
Statistics
Matches: 864, Mismatches: 126, Indels: 88
0.80 0.12 0.08
Matches are distributed among these distances:
247 23 0.03
248 34 0.04
249 25 0.03
250 95 0.11
251 27 0.03
252 2 0.00
253 1 0.00
255 3 0.00
256 10 0.01
257 2 0.00
258 1 0.00
259 2 0.00
261 2 0.00
262 144 0.17
263 4 0.00
264 5 0.01
265 42 0.05
266 223 0.26
267 71 0.08
268 78 0.09
269 69 0.08
270 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (264 bp):
TTTATGTATCTTCTCCAATAACTCTGCAACTCCATAAATAAAAGCACAGAAAGAGATCGAGAGGA
CTTCAATGTGAGTCCATTAGCATTCAAAGCTACACATTGCCAACTCAAGGCTAGTAGCTTTGCCA
AGATGGACTGAGGTAAAGGGTTTACGAGCACTTGAATAGATTATTTCAGTTCCAAACTTCCAATG
AACAATATTCACTTCATCTATGATAAATAATAAATATGCACAGAACATGCAGATATCGACACACA
TAAA
Found at i:1666750 original size:16 final size:17
Alignment explanation
Indices: 1666729--1666762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1666719 TTAGTTTTGT
*
1666729 TTTAATTTTTA-TTAAA
1 TTTAATTTATACTTAAA
1666745 TTTAATTTATACTTAAA
1 TTTAATTTATACTTAAA
1666762 T
1 T
1666763 AAATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAATTTATACTTAAA
Found at i:1670664 original size:33 final size:30
Alignment explanation
Indices: 1670597--1670664 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 30
1670587 ATTTAATTAT
* *
1670597 ATAAATTATAATATAAAAAAATTATATAAT
1 ATAAATTATAAAATAAAAAAATTATATAAA
* *
1670627 ATAAATTATTAAAATATTAAAATTTATATAAAA
1 ATAAATTA-TAAAATA-AAAAAATTATAT-AAA
1670660 ATAAA
1 ATAAA
1670665 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 10 0.32
33 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
ATAAATTATAAAATAAAAAAATTATATAAA
Found at i:1670742 original size:45 final size:45
Alignment explanation
Indices: 1670613--1670720 Score: 121
Period size: 45 Copynumber: 2.3 Consensus size: 45
1670603 TATAATATAA
1670613 AAAAATTA-TATAATATAAATTATTAA-AATATTAAAATTTATATAAAAAT
1 AAAAATTATTA-AATAT-AATTA-TAATAATA-TAAAA--TATATAAAAAT
* * *
1670662 AAAATTTTTTAAATATAATTATAATAATATAAAATATATAAATAT
1 AAAAATTATTAAATATAATTATAATAATATAAAATATATAAAAAT
1670707 AAAAATTATTAAAT
1 AAAAATTATTAAAT
1670721 TTATTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 22 0.42
47 8 0.15
48 9 0.17
49 11 0.21
50 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (45 bp):
AAAAATTATTAAATATAATTATAATAATATAAAATATATAAAAAT
Found at i:1670796 original size:2 final size:2
Alignment explanation
Indices: 1670789--1670819 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1670779 TAAAAATTTA
*
1670789 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1670820 AAAGATCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1675395 original size:15 final size:15
Alignment explanation
Indices: 1675364--1675393 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1675354 TTAGGGGAAT
1675364 GAGGAGGGGGAGGGG
1 GAGGAGGGGGAGGGG
1675379 GAGG-GGGGGAGGGG
1 GAGGAGGGGGAGGGG
1675393 G
1 G
1675394 GAACTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (15 bp):
GAGGAGGGGGAGGGG
Found at i:1676202 original size:2 final size:2
Alignment explanation
Indices: 1676195--1676223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1676185 GAATTTCTTT
1676195 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 T
1676224 CCAGGTATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1676814 original size:18 final size:17
Alignment explanation
Indices: 1676780--1676830 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1676770 AATTTAAAAT
1676780 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1676797 ATTTT-TATTTAT-TAA
1 ATTTTATATTTATATAA
* *
1676812 TAATTTATA-TCATATAA
1 -ATTTTATATTTATATAA
1676829 AT
1 AT
1676831 ATTTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.11
16 15 0.54
17 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1676827 original size:32 final size:33
Alignment explanation
Indices: 1676777--1676840 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
1676767 TTAAATTTAA
* *
1676777 AATATTTTATATTTATATAAAT-TTTTATTTATT
1 AATAATTTATATTCATATAAATATTTT-TTTATT
1676810 AATAATTTATA-TCATATAAATATTTTTTTAT
1 AATAATTTATATTCATATAAATATTTTTTTAT
1676841 GCTTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (33 bp):
AATAATTTATATTCATATAAATATTTTTTTATT
Found at i:1680870 original size:20 final size:21
Alignment explanation
Indices: 1680831--1680871 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1680821 AATAGTATTT
1680831 TTTATATTAAATTAATATATA
1 TTTATATTAAATTAATATATA
1680852 TTTAT-TTAAATTTAA-ATATA
1 TTTATATTAAA-TTAATATATA
1680872 AAATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATATTAAATTAATATATA
Found at i:1680983 original size:7 final size:7
Alignment explanation
Indices: 1680959--1680996 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1680949 AATTCAGTTA
1680959 AATTTA-
1 AATTTAT
1680965 AATTTA-
1 AATTTAT
1680971 AATTTAT
1 AATTTAT
1680978 AATTTAT
1 AATTTAT
1680985 AATTTAT
1 AATTTAT
1680992 AATTT
1 AATTT
1680997 TTTTGAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTAT
Found at i:1681233 original size:19 final size:19
Alignment explanation
Indices: 1681211--1681251 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1681201 CTACATAATA
1681211 TTAAAT-TTTATGTTATATT
1 TTAAATATTTAT-TTATATT
*
1681230 TTAATTATTTATTTATATT
1 TTAAATATTTATTTATATT
1681249 TTA
1 TTA
1681252 TTCGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTAAATATTTATTTATATT
Found at i:1681805 original size:15 final size:16
Alignment explanation
Indices: 1681779--1681808 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1681769 ATAAATTTTT
1681779 TAATTAAATAAAATTA
1 TAATTAAATAAAATTA
1681795 TAATT-AATAAAATT
1 TAATTAAATAAAATT
1681809 TATTTACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAATAAAATTA
Found at i:1681811 original size:16 final size:17
Alignment explanation
Indices: 1681769--1681811 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1681759 TTTAATATTT
* *
1681769 ATAAATTTTTTAATTAA
1 ATAAAATTTATAATTAA
1681786 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1681801 ATAAAATTTAT
1 ATAAAATTTAT
1681812 TTACAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1682641 original size:153 final size:151
Alignment explanation
Indices: 1682365--1682641 Score: 329
Period size: 153 Copynumber: 1.8 Consensus size: 151
1682355 TATTGACATA
* *
1682365 TAAAAATTTATATAAATTTATAATAATTTTGACACATAAAAAATAATATGAATACGTTATGAACA
1 TAAAAATTTATATAAATTTATAATAATTTTAACACATAAAAAATAACATGAATACGTTATGAACA
* * ** **
1682430 CACAAAATTTTCACTGAATTAAAACATGATGAAAAATTATGCAAAATATGTGGTGAATTGAAATA
66 CACAAAATTTTCACTAAATTAAAACATGATGAAAAATTATACAAAATAAATAATGAATTGAAATA
1682495 GGACCACCGGATATTAATATT
131 GGACCACCGGATATTAATATT
* * * * * *
1682516 TAAAATTTTATATAAAAATTTATAATACTTTTAACACTTCAAAAATAACATGAATATGTTATTAA
1 TAAAAATTTATAT--AAATTTATAATAATTTTAACACATAAAAAATAACATGAATACGTTATGAA
* ** * * * * * *
1682581 CACATAATTTTTTCATTAAATTGAAATATTATGATAAATTATATAAAATAAATAATGAATT
64 CACACAAAATTTTCACTAAATTAAAACATGATGAAAAATTATACAAAATAAATAATGAATT
1682642 ATGACAGGAT
Statistics
Matches: 101, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
151 12 0.12
153 89 0.88
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (151 bp):
TAAAAATTTATATAAATTTATAATAATTTTAACACATAAAAAATAACATGAATACGTTATGAACA
CACAAAATTTTCACTAAATTAAAACATGATGAAAAATTATACAAAATAAATAATGAATTGAAATA
GGACCACCGGATATTAATATT
Found at i:1683014 original size:14 final size:14
Alignment explanation
Indices: 1682995--1683039 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1682985 ATTAATAATT
1682995 TATTTTATTTTATA
1 TATTTTATTTTATA
*
1683009 TATTTT-TTTATGTA
1 TATTTTATTT-TATA
1683023 TATTTTATTTTATA
1 TATTTTATTTTATA
1683037 TAT
1 TAT
1683040 GGGAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (14 bp):
TATTTTATTTTATA
Found at i:1683109 original size:19 final size:19
Alignment explanation
Indices: 1683081--1683145 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1683071 TATTATTGAG
1683081 AATA-TTATAAATTTATGT
1 AATATTTATAAATTTATGT
*
1683099 AATATTTATAAATATT-TTT
1 AATATTTATAAAT-TTATGT
* * *
1683118 TATATTTATATATTCATGT
1 AATATTTATAAATTTATGT
*
1683137 CATATTTAT
1 AATATTTAT
1683146 TTTTTGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 5 0.13
19 31 0.82
20 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
AATATTTATAAATTTATGT
Found at i:1683554 original size:14 final size:12
Alignment explanation
Indices: 1683525--1683553 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1683515 TATACTTAAA
1683525 ATATAATTTTTT
1 ATATAATTTTTT
1683537 ATATAATTTTTT
1 ATATAATTTTTT
1683549 ATATA
1 ATATA
1683554 TTAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATAATTTTTT
Found at i:1683562 original size:18 final size:18
Alignment explanation
Indices: 1683539--1683590 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
1683529 AATTTTTTAT
1683539 ATAATTTTTTATATATTA-
1 ATAATTTTTT-TATATTAC
*
1683557 ATAATTTATTTTATTTTAC
1 ATAATTT-TTTTATATTAC
1683576 ATATATTTTTATTAT
1 ATA-ATTTTT-TTAT
1683591 GTGCGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 13 0.45
19 8 0.28
20 8 0.28
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATAATTTTTTTATATTAC
Found at i:1683735 original size:31 final size:32
Alignment explanation
Indices: 1683690--1683752 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1683680 AATAAAACAA
*
1683690 ATTTATATAAATTTTTACACATTAAT-TATTC
1 ATTTATATAAATTTTGACACATTAATGTATTC
* * *
1683721 ATTTATCTACATTTTGACATATTAATGTATTC
1 ATTTATATAAATTTTGACACATTAATGTATTC
1683753 TTATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTTATATAAATTTTGACACATTAATGTATTC
Found at i:1683993 original size:13 final size:13
Alignment explanation
Indices: 1683975--1683999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1683965 TTATCTTATA
1683975 TTTTATATAAATT
1 TTTTATATAAATT
1683988 TTTTATATAAAT
1 TTTTATATAAAT
1684000 AAATTTAACT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTATATAAATT
Found at i:1684090 original size:17 final size:18
Alignment explanation
Indices: 1684050--1684090 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1684040 AATTTTAATG
*
1684050 ATTAAAATTTTATTTAAT
1 ATTAAAATTTTATTAAAT
*
1684068 -TAAAAATTTTA-TAAAT
1 ATTAAAATTTTATTAAAT
1684084 ATTAAAA
1 ATTAAAA
1684091 CCCGAGCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAAATTTTATTAAAT
Found at i:1684248 original size:3 final size:3
Alignment explanation
Indices: 1684240--1684264 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1684230 TCTTCATCAC
1684240 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1684265 TTAAATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1684807 original size:14 final size:15
Alignment explanation
Indices: 1684787--1684855 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 15
1684777 AAATATATTT
1684787 ATTT-TATTTTTA-A
1 ATTTATATTTTTATA
*
1684800 ATTTTTATTTATTTAAATA
1 ATTTATA-TT-TTT-A-TA
1684819 AT-TATATTTTTATA
1 ATTTATATTTTTATA
1684833 A-TTATATTTTTATA
1 ATTTATATTTTTATA
1684847 A-TTATATTT
1 ATTTATATTT
1684856 AAATATATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
13 4 0.08
14 26 0.54
15 3 0.06
16 6 0.12
17 3 0.06
18 3 0.06
19 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATATTTTTATA
Found at i:1684841 original size:28 final size:27
Alignment explanation
Indices: 1684809--1684884 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
1684799 AATTTTTATT
1684809 TATTTAAATAATTATATTTTTATAATTA
1 TATTTAAATAATTATATTTTTATAA-TA
**
1684837 TATTTTTATAATTATA--TTTA-AATA
1 TATTTAAATAATTATATTTTTATAATA
*
1684861 TATATTAAAT-ATTATTTTTTTATA
1 TAT-TTAAATAATTATATTTTTATA
1684885 TAAAATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 10 0.26
25 6 0.15
26 8 0.21
27 1 0.03
28 14 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTAAATAATTATATTTTTATAATA
Found at i:1684864 original size:12 final size:13
Alignment explanation
Indices: 1684816--1684877 Score: 53
Period size: 14 Copynumber: 5.0 Consensus size: 13
1684806 ATTTATTTAA
*
1684816 ATAATTATATTTTT
1 ATAA-TATATATTT
*
1684830 ATAATTATATTTTT
1 ATAA-TATATATTT
1684844 ATAAT-TATATTT
1 ATAATATATATTT
1684856 A-AATATATA-TT
1 ATAATATATATTT
1684867 A-AATAT-TATTT
1 ATAATATATATTT
1684878 TTTTATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
10 2 0.04
11 13 0.29
12 11 0.24
13 1 0.02
14 18 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATAATATATATTT
Found at i:1689359 original size:15 final size:14
Alignment explanation
Indices: 1689339--1689381 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1689329 ATAATTAAAT
1689339 TATTAATTTTAATA
1 TATTAATTTTAATA
1689353 TATTTAATTATTAA-A
1 TA-TTAATT-TTAATA
*
1689368 TATTAATTTAAATA
1 TATTAATTTTAATA
1689382 GATCAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 9 0.36
16 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTAATTTTAATA
Found at i:1689364 original size:22 final size:20
Alignment explanation
Indices: 1689321--1689366 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
1689311 AAATATAAAT
1689321 TTAATTTAATAATTAAATTA
1 TTAATTTAATAATTAAATTA
*
1689341 TTAATTTTAATATATTTAATTA
1 TTAA-TTTAATA-ATTAAATTA
1689363 TTAA
1 TTAA
1689367 ATATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTTAATAATTAAATTA
Found at i:1689381 original size:29 final size:30
Alignment explanation
Indices: 1689324--1689381 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1689314 TATAAATTTA
*
1689324 ATTTAATAATTAAATTATTAATTTTAATAT
1 ATTTAATAATTAAATTATTAATTTAAATAT
*
1689354 ATTTAATTATTAAA-TATTAATTTAAATA
1 ATTTAATAATTAAATTATTAATTTAAATA
1689382 GATCAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTAATAATTAAATTATTAATTTAAATAT
Found at i:1698648 original size:21 final size:22
Alignment explanation
Indices: 1698604--1698663 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
1698594 ATCTATCTAT
* *
1698604 ATATAAATATAATTTATATTTAAA
1 ATATTAATAT-ATTTATATAT-AA
1698628 ATATT-ATATATTT-TATATAA
1 ATATTAATATATTTATATATAA
*
1698648 ATTTTAATATATTTAT
1 ATATTAATATATTTAT
1698664 TTTTTGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.19
21 12 0.39
22 5 0.16
23 4 0.13
24 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTAATATATTTATATATAA
Found at i:1698712 original size:11 final size:10
Alignment explanation
Indices: 1698696--1698786 Score: 68
Period size: 11 Copynumber: 9.1 Consensus size: 10
1698686 TAAATTTATA
1698696 TATTTATGTTT
1 TATTTAT-TTT
1698707 TATTTATATTT
1 TATTTAT-TTT
1698718 TATATTATTTT
1 TAT-TTATTTT
*
1698729 TAATTA--TT
1 TATTTATTTT
1698737 T-TTTATTTT
1 TATTTATTTT
1698746 ATATTCATATTTT
1 -TATT--TATTTT
1698759 TA-TTA-TTT
1 TATTTATTTT
*
1698767 TAATTATTTT
1 TATTTATTTT
1698777 T-TTTATTTT
1 TATTTATTTT
1698786 T
1 T
1698787 GTGTTCTATA
Statistics
Matches: 67, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
7 3 0.04
8 8 0.12
9 15 0.22
10 8 0.12
11 21 0.31
12 6 0.09
13 6 0.09
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (10 bp):
TATTTATTTT
Found at i:1698743 original size:27 final size:28
Alignment explanation
Indices: 1698709--1698786 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 28
1698699 TTATGTTTTA
1698709 TTTA-TATTTTATATTATTTTTAATTAT
1 TTTATTATTTTATATTATTTTTAATTAT
*
1698736 TTT-TTATTTTATATTCATATTTTTATTAT
1 TTTATTATTTTATATT-AT-TTTTAATTAT
*
1698765 TTTAATTATTTT-TTTTATTTTT
1 TTT-ATTATTTTATATTATTTTT
1698787 GTGTTCTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 14 0.32
28 6 0.14
29 14 0.32
30 3 0.07
31 7 0.16
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTATTATTTTATATTATTTTTAATTAT
Found at i:1698776 original size:17 final size:17
Alignment explanation
Indices: 1698720--1698776 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
1698710 TTATATTTTA
1698720 TATTATTTTTAATTATTT
1 TATTA-TTTTAATTATTT
1698738 T-TTATTTTATATTCATATTTT
1 TATTATTTTA-A-T--TA-TTT
1698759 TATTATTTTAATTATTT
1 TATTATTTTAATTATTT
1698776 T
1 T
1698777 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
16 5 0.15
17 8 0.24
18 4 0.12
20 3 0.09
21 5 0.15
22 8 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTTAATTATTT
Found at i:1698785 original size:40 final size:39
Alignment explanation
Indices: 1698698--1698778 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 39
1698688 AATTTATATA
*
1698698 TTTATGTTTTATTTATATTTTATATTATTTTTAATTATTT
1 TTTAT-TTTTATTCATATTTTATATTATTTTTAATTATTT
1698738 TTTATTTTATATTCATATTTT-TATTA-TTTTAATTATTT
1 TTTATTTT-TATTCATATTTTATATTATTTTTAATTATTT
1698776 TTT
1 TTT
1698779 TTATTTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 15 0.38
39 8 0.21
40 16 0.41
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (39 bp):
TTTATTTTTATTCATATTTTATATTATTTTTAATTATTT
Found at i:1706240 original size:22 final size:23
Alignment explanation
Indices: 1706215--1706264 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1706205 TTTAAATAAG
1706215 AATTACGTAGATTTAA-CA-TTTA
1 AATTA-GTAGATTTAATCATTTTA
*
1706237 AATTTATTAGATTTAATCATTTTA
1 AA-TTAGTAGATTTAATCATTTTA
1706261 AATT
1 AATT
1706265 CAAGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 11 0.46
23 7 0.29
24 6 0.25
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (23 bp):
AATTAGTAGATTTAATCATTTTA
Found at i:1711301 original size:20 final size:20
Alignment explanation
Indices: 1711263--1711301 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1711253 CAAATATTTT
* *
1711263 TATATTAAATAAGTAATAAA
1 TATAATAAATAAATAATAAA
*
1711283 TATAATAAATAAATTATAA
1 TATAATAAATAAATAATAA
1711302 GAATATATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TATAATAAATAAATAATAAA
Found at i:1712348 original size:14 final size:13
Alignment explanation
Indices: 1712319--1712355 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1712309 GTTCAAAGCC
*
1712319 TGAAACAAGAACA
1 TGAAACATGAACA
1712332 TGAAACATGACACA
1 TGAAACATGA-ACA
1712346 TGAAACATGA
1 TGAAACATGA
1712356 GATCTGGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.54, C:0.16, G:0.16, T:0.14
Consensus pattern (13 bp):
TGAAACATGAACA
Found at i:1712648 original size:19 final size:17
Alignment explanation
Indices: 1712616--1712666 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
1712606 ATTATTTTAT
* *
1712616 TATTTTAAAAATTAAAA
1 TATTTTATATATTAAAA
*
1712633 TAATATTTATATATTAATA
1 T-AT-TTTATATATTAAAA
1712652 TATTTTATAT-TTAAA
1 TATTTTATATATTAAA
1712667 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 4 0.14
17 8 0.29
18 4 0.14
19 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTTATATATTAAAA
Found at i:1712876 original size:2 final size:2
Alignment explanation
Indices: 1712869--1712893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1712859 TATTTTTATT
1712869 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 T
1712894 GTAGAACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1712968 original size:14 final size:15
Alignment explanation
Indices: 1712949--1712978 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1712939 TTAAAATTAT
1712949 ATTAAAAA-TAATAA
1 ATTAAAAAGTAATAA
1712963 ATTAAAAAGTAATAA
1 ATTAAAAAGTAATAA
1712978 A
1 A
1712979 ACTGAGTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
ATTAAAAAGTAATAA
Found at i:1714673 original size:39 final size:38
Alignment explanation
Indices: 1714609--1714684 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1714599 AATCAGAAGA
1714609 AAAAATATATAATGATAATATTAATATATAAATATTTT
1 AAAAATATATAATGATAATATTAATATATAAATATTTT
* *
1714647 AAAATTATATAAT-ATAAATTATTAATATATTAATATTT
1 AAAAATATATAATGAT-AA-TATTAATATATAAATATTT
1714685 ATTTATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 2 0.06
38 14 0.41
39 18 0.53
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
AAAAATATATAATGATAATATTAATATATAAATATTTT
Found at i:1715306 original size:15 final size:15
Alignment explanation
Indices: 1715288--1715348 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
1715278 AAAAACTAAT
1715288 TTATTAATTAAATTA
1 TTATTAATTAAATTA
1715303 TTATTAATT-AATTAA
1 TTATTAATTAAATT-A
* *
1715318 TTAATTATATAAAAATA
1 TT-ATTA-ATTAAATTA
1715335 TTAGTTAA-TAAATT
1 TTA-TTAATTAAATT
1715349 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 4 0.11
15 16 0.43
16 6 0.16
17 8 0.22
18 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTATTAATTAAATTA
Found at i:1715312 original size:4 final size:4
Alignment explanation
Indices: 1715284--1715324 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1715274 TTTTAAAAAC
*
1715284 TAAT TTAT TAAT TAAAT T-AT T-AT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT T-AAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1715325 TATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 23 0.70
5 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TAAT
Found at i:1715343 original size:25 final size:23
Alignment explanation
Indices: 1715309--1715356 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
1715299 ATTATTATTA
*
1715309 ATTAATTAATTAATTATATAAAAAT
1 ATTAATTAATAAATT-TA-AAAAAT
*
1715334 ATTAGTTAATAAATTTAAAAAAT
1 ATTAATTAATAAATTTAAAAAAT
1715357 TATATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTAATTAATAAATTTAAAAAAT
Found at i:1721679 original size:20 final size:17
Alignment explanation
Indices: 1721638--1721672 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1721628 TAATCATAAA
*
1721638 AATATATAAATATTTTT
1 AATATAAAAATATTTTT
1721655 AATATAAAATATATTTTT
1 AATATAAAA-ATATTTTT
1721673 TCAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATAAAAATATTTTT
Found at i:1721700 original size:28 final size:29
Alignment explanation
Indices: 1721646--1721700 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1721636 AAAATATATA
* *
1721646 AATATTTTTAATATAAAATATATTTTTTC
1 AATATTTTTAAAATAAAATATAGTTTTTC
1721675 AATA-TTTTAAAATAATAA-ATAGTTTT
1 AATATTTTTAAAATAA-AATATAGTTTT
1721701 AAGCTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
AATATTTTTAAAATAAAATATAGTTTTTC
Found at i:1722040 original size:20 final size:21
Alignment explanation
Indices: 1722017--1722069 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
1722007 ATTAATATTT
1722017 ATAATTAAATTTAAATAAA-A
1 ATAATTAAATTTAAATAAATA
**
1722037 ATAATT-TTTATTAAATAAATA
1 ATAATTAAAT-TTAAATAAATA
1722058 ATAATTTAAATT
1 ATAA-TTAAATT
1722070 GAATTATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 1 0.04
20 15 0.60
21 5 0.20
22 3 0.12
23 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAAATTTAAATAAATA
Found at i:1727112 original size:27 final size:27
Alignment explanation
Indices: 1727064--1727115 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1727054 AAAAAAAGAA
*
1727064 TTATTTAAATTATTATATAAATATATT
1 TTATTTAAATTATCATATAAATATATT
*
1727091 TTATTTATATTATACATA-AAATATA
1 TTATTTAAATTAT-CATATAAATATA
1727116 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATTTAAATTATCATATAAATATATT
Found at i:1727238 original size:5 final size:5
Alignment explanation
Indices: 1727224--1727260 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
1727214 AATTTATTTT
1727224 ATTAA A-TAA ATTAA ATTAA ATT-A ATTAA A-TAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1727261 TATTTATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 12 0.41
5 17 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:1727241 original size:14 final size:14
Alignment explanation
Indices: 1727224--1727257 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1727214 AATTTATTTT
1727224 ATTAAATAAATTAA
1 ATTAAATAAATTAA
*
1727238 ATTAAATTAATTAA
1 ATTAAATAAATTAA
1727252 A-TAAAT
1 ATTAAAT
1727258 TAATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAATAAATTAA
Found at i:1727341 original size:21 final size:22
Alignment explanation
Indices: 1727311--1727355 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1727301 TTATAAATAC
* *
1727311 TAAAAATAAT-AATTTATTTTT
1 TAAAAATAATGAATATATTATT
*
1727332 TAAAATTAATGAATATATTATT
1 TAAAAATAATGAATATATTATT
1727354 TA
1 TA
1727356 TAATATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAAATAATGAATATATTATT
Found at i:1727561 original size:17 final size:17
Alignment explanation
Indices: 1727539--1727582 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1727529 ATATGATATG
1727539 ATATAATATAAAAAATA
1 ATATAATATAAAAAATA
*
1727556 ATATAA-ATAAAATATA
1 ATATAATATAAAAAATA
1727572 A-AT-ATATAAAA
1 ATATAATATAAAA
1727583 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 8 0.32
16 10 0.40
17 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAATATAAAAAATA
Found at i:1727571 original size:11 final size:12
Alignment explanation
Indices: 1727541--1727580 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1727531 ATGATATGAT
*
1727541 ATAATATAAAAA
1 ATAATATAAATA
1727553 ATAATATAAATA
1 ATAATATAAATA
1727565 A-AATATAAATA
1 ATAATATAAATA
1727576 TATAA
1 -ATAA
1727581 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 13 0.52
13 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:1727571 original size:28 final size:28
Alignment explanation
Indices: 1727514--1727614 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
1727504 TTTATAATTT
1727514 TAAAAAATAATTAAAATATGATATGATATAATA
1 TAAAAAATAA-TAAAATAT-A-A--ATATAATA
1727547 TAAAAAATAATATAAATA-AAATATAAATA
1 TAAAAAATAATA-AAATATAAATAT-AATA
* ** *
1727576 TATAAAATTTTAAAATATAATTATAATA
1 TAAAAAATAATAAAATATAAATATAATA
1727604 TATAAAAATAA
1 TA-AAAAATAA
1727615 ACGAATTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
28 15 0.26
29 23 0.40
30 1 0.02
31 1 0.02
32 2 0.04
33 15 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAAAAATAATAAAATATAAATATAATA
Found at i:1727820 original size:16 final size:16
Alignment explanation
Indices: 1727799--1727833 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1727789 AATTTCACGT
1727799 AAAAAAAT-AAAAATA
1 AAAAAAATGAAAAATA
1727814 AAAAAAATGAAAAATA
1 AAAAAAATGAAAAATA
1727830 AAAA
1 AAAA
1727834 TATTAGGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAAAATA
Found at i:1729265 original size:14 final size:14
Alignment explanation
Indices: 1729213--1729269 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1729203 TCTCATATCT
*
1729213 TATATATATTT-AA
1 TATAAATATTTAAA
1729226 TAT--ATATTTAAA
1 TATAAATATTTAAA
*
1729238 TATAAATATATAAA
1 TATAAATATTTAAA
* *
1729252 TATAATTTTTTAAA
1 TATAAATATTTAAA
1729266 TATA
1 TATA
1729270 TAAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 6 0.16
12 5 0.14
13 3 0.08
14 23 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATATTTAAA
Found at i:1729484 original size:14 final size:15
Alignment explanation
Indices: 1729467--1729496 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1729457 CTATTAGTCA
1729467 ATTATTATT-AATTT
1 ATTATTATTCAATTT
1729481 ATTATTATTCAATTT
1 ATTATTATTCAATTT
1729496 A
1 A
1729497 AGCACTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTATTCAATTT
Found at i:1731162 original size:16 final size:16
Alignment explanation
Indices: 1731122--1731166 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1731112 TATACTCGAT
**
1731122 AATTATATATTTTTAA
1 AATTATATATTTAAAA
* *
1731138 ATTTTTATATTTAAAA
1 AATTATATATTTAAAA
1731154 AATTATATATTTA
1 AATTATATATTTA
1731167 TTTAAATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTATATATTTAAAA
Found at i:1731179 original size:32 final size:30
Alignment explanation
Indices: 1731122--1731185 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 30
1731112 TATACTCGAT
*
1731122 AATTATATATTTTTAAATTTTTATATTTAAAA
1 AATTATATATTTTTAAA-TTATATA-TTAAAA
1731154 AATTATATATTTATTTAAA-TATATATTAAAA
1 AATTATATA-TT-TTTAAATTATATATTAAAA
1731185 A
1 A
1731186 TTCGGATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 7 0.24
32 14 0.48
33 2 0.07
34 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTATATATTTTTAAATTATATATTAAAA
Found at i:1731416 original size:2 final size:2
Alignment explanation
Indices: 1731411--1731441 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1731401 TCACAAAGGT
1731411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1731442 TGTAATGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1731736 original size:25 final size:24
Alignment explanation
Indices: 1731692--1731739 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1731682 AAAAATAAAA
1731692 AAATTATTATTTAAATAATAATTT
1 AAATTATTATTTAAATAATAATTT
*
1731716 AAATTAATTAATTTATA-AATAATT
1 AAATT-ATT-ATTTAAATAATAATT
1731740 ATTTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATTATTATTTAAATAATAATTT
Found at i:1731740 original size:15 final size:15
Alignment explanation
Indices: 1731703--1731747 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1731693 AATTATTATT
1731703 TAAATAA-TAATTTA
1 TAAATAATTAATTTA
*
1731717 -AATTAATTAATTTA
1 TAAATAATTAATTTA
*
1731731 TAAATAATTATTTTA
1 TAAATAATTAATTTA
1731746 TA
1 TA
1731748 TATTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATAATTAATTTA
Found at i:1732179 original size:20 final size:18
Alignment explanation
Indices: 1732128--1732252 Score: 63
Period size: 20 Copynumber: 7.2 Consensus size: 18
1732118 TTATATTAAA
*
1732128 ATTATTTTATATTTTTAT
1 ATTATTTTATATATTTAT
*
1732146 ATAAGTTTTGATATATTTAT
1 ATTA-TTTT-ATATATTTAT
1732166 AATTTATTTTATATA---A-
1 -A-TTATTTTATATATTTAT
* *
1732182 A-T-TTTGATATAGTTAT
1 ATTATTTTATATATTTAT
*
1732198 ATTATATTTATATTATTTTT
1 ATTAT-TTTATA-TATTTAT
* *
1732218 ATTATATAATAT-TTTA-
1 ATTATTTTATATATTTAT
1732234 ATTATTTT-TAT-TTTAT
1 ATTATTTTATATATTTAT
1732250 ATT
1 ATT
1732253 TATAATTATA
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
12 8 0.10
13 1 0.01
15 9 0.11
16 10 0.12
17 5 0.06
18 5 0.06
19 13 0.16
20 24 0.29
21 5 0.06
22 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTATTTTATATATTTAT
Found at i:1732181 original size:32 final size:30
Alignment explanation
Indices: 1732140--1732210 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 30
1732130 TATTTTATAT
* *
1732140 TTTTATATAAGTTTTGATATATTTATAATTTA
1 TTTTATATAAATTTTGATATAGTTAT-A-TTA
1732172 TTTTATATAAATTTTGATATAGTTATATTA
1 TTTTATATAAATTTTGATATAGTTATATTA
1732202 TATTTATAT
1 T-TTTATAT
1732211 TATTTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 4 0.11
31 8 0.22
32 24 0.67
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (30 bp):
TTTTATATAAATTTTGATATAGTTATATTA
Found at i:1732208 original size:6 final size:6
Alignment explanation
Indices: 1732189--1732268 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
1732179 TAAATTTTGA
* * * *
1732189 TATAGT TATA-T TATATT TATA-T TATTTT TATTATAT AATATT T-TAAT
1 TATATT TATATT TATATT TATATT TATATT TA-TAT-T TATATT TATATT
* *
1732236 TATTTT TAT-TT TATATT TATAAT TATAATT TAT
1 TATATT TATATT TATATT TATATT TAT-ATT TAT
1732269 CACATAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
5 18 0.31
6 28 0.48
7 10 0.17
8 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:1732222 original size:25 final size:26
Alignment explanation
Indices: 1732194--1732261 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
1732184 TTTGATATAG
1732194 TTATATTATATTTAT-ATTATTTTTA
1 TTATATTATATTTATAATTATTTTTA
*
1732219 TTATATAATATTT-TAATTATTTTTA
1 TTATATTATATTTATAATTATTTTTA
1732244 -T-T-TTATATTTATAATTAT
1 TTATATTATATTTATAATTAT
1732262 AATTTATCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.18
23 8 0.21
24 2 0.05
25 22 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTATATTTATAATTATTTTTA
Found at i:1732676 original size:24 final size:24
Alignment explanation
Indices: 1732649--1732696 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1732639 TTTAAAAAAT
* * *
1732649 TATATTTTTATATTTATATTTAAA
1 TATATATTAATATATATATTTAAA
*
1732673 TATATATTAATATATATTTTTAAA
1 TATATATTAATATATATATTTAAA
1732697 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATATTAATATATATATTTAAA
Found at i:1732812 original size:26 final size:26
Alignment explanation
Indices: 1732798--1732860 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
1732788 TTAATTTTTT
*
1732798 TAATTAT-TTTTTATATATATTTAAA
1 TAATTATATTTTTATATTTATTTAAA
*
1732823 TAATTATATTTTTATATTCATATTAAAA
1 TAATTATATTTTTATATT--TATTTAAA
1732851 TATATTATAT
1 TA-ATTATAT
1732861 AGATCTGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.22
26 9 0.28
28 9 0.28
29 7 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TAATTATATTTTTATATTTATTTAAA
Found at i:1732835 original size:28 final size:29
Alignment explanation
Indices: 1732800--1732860 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1732790 AATTTTTTTA
*
1732800 ATTAT-TTTTTATA-T-ATATTTAAATA-
1 ATTATATTTTTATATTCATATTAAAATAT
1732825 ATTATATTTTTATATTCATATTAAAATAT
1 ATTATATTTTTATATTCATATTAAAATAT
1732854 ATTATAT
1 ATTATAT
1732861 AGATCTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 5 0.16
26 8 0.26
27 1 0.03
28 10 0.32
29 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTATATTTTTATATTCATATTAAAATAT
Done.