Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 5 of 113
Found at i:1249799 original size:3 final size:3
Alignment explanation
Indices: 1249756--1249781 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1249746 ACGGACTGGC
1249756 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
1249782 CTGCTGCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:1250523 original size:17 final size:16
Alignment explanation
Indices: 1250497--1250534 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1250487 GGGTTTTTTT
1250497 TTCTTTTTCTCTTCTC
1 TTCTTTTTCTCTTCTC
*
1250513 TTCTCTTTTCTTTTCTC
1 TTCT-TTTTCTCTTCTC
1250530 TTCTT
1 TTCTT
1250535 CTTGAGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTTTTCTCTTCTC
Found at i:1254367 original size:3 final size:3
Alignment explanation
Indices: 1254359--1254395 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1254349 ACAGCTTTGT
*
1254359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1254396 AAATTCTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1258870 original size:30 final size:29
Alignment explanation
Indices: 1258806--1258905 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 29
1258796 TAAACAAAAG
* * *
1258806 ATTTATTT-AGATACAAAATAAAATTAAGG
1 ATTTATTTGA-ATATAAATTAAAATTAAGA
*
1258835 GTTTATTTGAATATAAATTAAAGATTAAGA
1 ATTTATTTGAATATAAATTAAA-ATTAAGA
** * *
1258865 ATTTATTCAAATGTAAATTAAAATTCAGAA
1 ATTTATTTGAATATAAATTAAAATTAAG-A
1258895 ATTTATTTGAA
1 ATTTATTTGAA
1258906 CCTAATTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 22 0.39
30 35 0.61
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTTATTTGAATATAAATTAAAATTAAGA
Found at i:1259729 original size:6 final size:7
Alignment explanation
Indices: 1259702--1259727 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1259692 ACTGAGATTA
1259702 AAAAAAT
1 AAAAAAT
1259709 AAAAAAT
1 AAAAAAT
1259716 AAAAAAT
1 AAAAAAT
1259723 AAAAA
1 AAAAA
1259728 TATTAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1272116 original size:2 final size:2
Alignment explanation
Indices: 1272109--1272145 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1272099 CACAACCAAA
1272109 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1272146 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1272150 original size:2 final size:2
Alignment explanation
Indices: 1272145--1272169 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1272135 TCTCTCTCTC
1272145 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
1272170 TATTATTATT
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:1281164 original size:22 final size:20
Alignment explanation
Indices: 1281118--1281159 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1281108 ATTTGTTAAA
1281118 TGATACTACTTTCACAAGTG
1 TGATACTACTTTCACAAGTG
1281138 TGATACTACTTTCACAAGTG
1 TGATACTACTTTCACAAGTG
1281158 TG
1 TG
1281160 TGATATCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (20 bp):
TGATACTACTTTCACAAGTG
Found at i:1282146 original size:15 final size:15
Alignment explanation
Indices: 1282115--1282163 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
1282105 ATTAATTTTT
1282115 AATTATTTAT-TATTA
1 AATT-TTTATATATTA
*
1282130 AATTTTTATATAATA
1 AATTTTTATATATTA
1282145 AA-TTTTA-ATATTA
1 AATTTTTATATATTA
1282158 AATTTT
1 AATTTT
1282164 ATTTCACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 7 0.23
14 13 0.43
15 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTTATATATTA
Found at i:1282161 original size:13 final size:13
Alignment explanation
Indices: 1282120--1282164 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1282110 TTTTTAATTA
*
1282120 TTTATTATTAAATT
1 TTTAATATTAAA-T
*
1282134 TTTATATAATAAAT
1 TTTA-ATATTAAAT
1282148 TTTAATATTAAAT
1 TTTAATATTAAAT
1282161 TTTA
1 TTTA
1282165 TTTCACACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.44
14 9 0.33
15 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAATATTAAAT
Found at i:1282266 original size:21 final size:21
Alignment explanation
Indices: 1282215--1282267 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1282205 ATTATTTATT
*
1282215 TTAATTTTATTATTATAATAC
1 TTAATTTTATTATTATAATAA
*
1282236 TCAATTTTATTATTATAATAA
1 TTAATTTTATTATTATAATAA
*
1282257 TTAATATTATT
1 TTAATTTTATT
1282268 GTTGTCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTTTATTATTATAATAA
Found at i:1284212 original size:18 final size:18
Alignment explanation
Indices: 1284191--1284228 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1284181 TATAAAAAAT
* *
1284191 TATTTTTTAAAATTTTCA
1 TATTTCTTAAAATTATCA
1284209 TATTTCTTAAAATTATCA
1 TATTTCTTAAAATTATCA
1284227 TA
1 TA
1284229 CGTGACATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTCTTAAAATTATCA
Found at i:1288163 original size:20 final size:22
Alignment explanation
Indices: 1288140--1288182 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
1288130 ATTAATAATT
1288140 ATATATTAAA-ATTTAT-TTAA
1 ATATATTAAACATTTATATTAA
1288160 ATATATTAAACATTTATATTAA
1 ATATATTAAACATTTATATTAA
1288182 A
1 A
1288183 ATAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATTAAACATTTATATTAA
Found at i:1292726 original size:2 final size:2
Alignment explanation
Indices: 1292719--1292767 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1292709 CCATTACTGC
1292719 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1292759 AG AG -G AG AG
1 AG AG AG AG AG
1292768 TGCAAGAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1305646 original size:10 final size:10
Alignment explanation
Indices: 1305631--1305658 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1305621 GAAAAGAAAT
1305631 GTTAAAGAGA
1 GTTAAAGAGA
1305641 GTTAAAGAGA
1 GTTAAAGAGA
1305651 GTTAAAGA
1 GTTAAAGA
1305659 AAGGACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (10 bp):
GTTAAAGAGA
Found at i:1309274 original size:5 final size:5
Alignment explanation
Indices: 1309266--1309296 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1309256 TATTTTGTCC
*
1309266 TTGCG TTGCA TTGCA TTGCA TTGCA TTGCA T
1 TTGCA TTGCA TTGCA TTGCA TTGCA TTGCA T
1309297 CGAATAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (5 bp):
TTGCA
Found at i:1320154 original size:16 final size:16
Alignment explanation
Indices: 1320135--1320166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1320125 TATCAAACAT
*
1320135 ATTATTTATATATATA
1 ATTATATATATATATA
1320151 ATTATATATATATATA
1 ATTATATATATATATA
1320167 TAATAATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATATATATATATA
Found at i:1323850 original size:24 final size:22
Alignment explanation
Indices: 1323805--1323850 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1323795 TTTATTCAAT
*
1323805 ATTTTTTTGAAAATATTAAATA
1 ATTTTTTTGAAAAAATTAAATA
*
1323827 ATTTTTTTTAATAAAATTATAATA
1 ATTTTTTTGAA-AAAATTA-AATA
1323851 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTTTTTGAAAAAATTAAATA
Found at i:1324970 original size:20 final size:21
Alignment explanation
Indices: 1324942--1324987 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1324932 CTGTCTCATT
* *
1324942 TAATTTGATAATTTA-AAATA
1 TAATATGATAATATATAAATA
1324962 TAATATGATAATATATAAATA
1 TAATATGATAATATATAAATA
1324983 TAATA
1 TAATA
1324988 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TAATATGATAATATATAAATA
Found at i:1325092 original size:28 final size:30
Alignment explanation
Indices: 1325053--1325122 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
1325043 AAATTAAAAT
* * *
1325053 AATATATTTTATAT-TAATATAA-ATTATA
1 AATAAATTTTATATAAAATATAATATAATA
1325081 AATAAATTTTATATAAAATATAATATAATA
1 AATAAATTTTATATAAAATATAATATAATA
* *
1325111 TATAAAATTTAT
1 AATAAATTTTAT
1325123 TTTTATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 13 0.37
29 7 0.20
30 15 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAAATTTTATATAAAATATAATATAATA
Found at i:1326843 original size:30 final size:30
Alignment explanation
Indices: 1326808--1326866 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1326798 TTTTAATGAA
*
1326808 ATTAAAA-AAAAAAATTTTAATATATTTAAT
1 ATTAAAATAAAAAAATTTT-ATAAATTTAAT
*
1326838 ATTAAAATTAAAAAATTTTATAAATTTAA
1 ATTAAAATAAAAAAATTTTATAAATTTAA
1326867 AATTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTAAAATAAAAAAATTTTATAAATTTAAT
Found at i:1326844 original size:24 final size:23
Alignment explanation
Indices: 1326817--1326892 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
1326807 AATTAAAAAA
1326817 AAAAATTTTAATATATTTAATATT
1 AAAAATTTTAATAT-TTTAATATT
** * *
1326841 -AAAATTAAAAAATTTTATAAATT
1 AAAAATTTTAATATTTTA-ATATT
*
1326864 TAAAATTTT-ATAATTTTTAATATT
1 AAAAATTTTAAT-A-TTTTAATATT
1326888 AAAAA
1 AAAAA
1326893 ATAAAAAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 4 0.10
23 15 0.38
24 15 0.38
25 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAAATTTTAATATTTTAATATT
Found at i:1328080 original size:11 final size:11
Alignment explanation
Indices: 1328050--1328080 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
1328040 TTATTTAAAA
1328050 AATTATTTTTT
1 AATTATTTTTT
1328061 AATTAATTTTTT
1 AATT-ATTTTTT
1328073 AATTATTT
1 AATTATTT
1328081 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTATTTTTT
Found at i:1328122 original size:30 final size:30
Alignment explanation
Indices: 1328081--1328139 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1328071 TTAATTATTT
* * *
1328081 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
1328111 ATATTTATATTTAAAAAATAATATTTTTA
1 ATATATATATTTAAAAAATAATATTTTTA
1328140 TTAATTTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:1333701 original size:15 final size:15
Alignment explanation
Indices: 1333681--1333710 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1333671 GGTTGATTAT
1333681 GGTAAAAACTATATG
1 GGTAAAAACTATATG
1333696 GGTAAAAACTATATG
1 GGTAAAAACTATATG
1333711 CAAGTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
GGTAAAAACTATATG
Found at i:1340645 original size:8 final size:8
Alignment explanation
Indices: 1340606--1340669 Score: 58
Period size: 8 Copynumber: 7.5 Consensus size: 8
1340596 CCCAAGTATA
*
1340606 TATTATTT
1 TATTTTTT
1340614 TATGTTTTT
1 TAT-TTTTT
1340623 TAATTGTTATT
1 T-ATT-TT-TT
1340634 TATTTTTT
1 TATTTTTT
1340642 TATTTTTT
1 TATTTTTT
*
1340650 TA-TTATT
1 TATTTTTT
1340657 TATTTGTTT
1 TATTT-TTT
1340666 TATT
1 TATT
1340670 GTTTATCTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.13
8 17 0.36
9 14 0.30
10 7 0.15
11 3 0.06
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (8 bp):
TATTTTTT
Found at i:1340674 original size:16 final size:15
Alignment explanation
Indices: 1340640--1340675 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1340630 TATTTATTTT
1340640 TTTATTTTTTTATTA
1 TTTATTTTTTTATTA
*
1340655 TTTATTTGTTTTATTG
1 TTTATTT-TTTTATTA
1340671 TTTAT
1 TTTAT
1340676 CTCTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTATTTTTTTATTA
Found at i:1340682 original size:27 final size:27
Alignment explanation
Indices: 1340629--1340706 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 27
1340619 TTTTTAATTG
1340629 TTATTTATTT-TTTTATT-TTT-T-TA
1 TTATTTATTTGTTTTATTGTTTATCTA
*
1340652 TTATTTATTTGTTTTATTGTTTATCTC
1 TTATTTATTTGTTTTATTGTTTATCTA
* *
1340679 TTATTTTTTCTGTTTAATTGATTTATCT
1 TTATTTATT-TGTTTTATTG-TTTATCT
1340707 TCAGCTTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.22
24 7 0.15
25 3 0.07
26 1 0.02
27 9 0.20
28 9 0.20
29 7 0.15
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (27 bp):
TTATTTATTTGTTTTATTGTTTATCTA
Found at i:1340707 original size:27 final size:26
Alignment explanation
Indices: 1340652--1340707 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
1340642 TATTTTTTTA
*
1340652 TTATTTATTTGTTTTATTGTTTATCTC
1 TTATTTATTTGTTTAATTGTTTA-CTC
*
1340679 TTATTTTTTCTGTTTAATTGATTTA-TC
1 TTATTTATT-TGTTTAATTG-TTTACTC
1340706 TT
1 TT
1340708 CAGCTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 12 0.48
28 9 0.36
29 4 0.16
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (26 bp):
TTATTTATTTGTTTAATTGTTTACTC
Found at i:1342162 original size:58 final size:58
Alignment explanation
Indices: 1342030--1342442 Score: 443
Period size: 58 Copynumber: 7.1 Consensus size: 58
1342020 GCTTTTGTAC
* * * **
1342030 AAAGAAAATTAATACTTTCAACTTTTT-TCAAAAAT-TTTTTTTTAAATTTTAATTTCG
1 AAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTT-ATTTTT
* *
1342087 AAA-AAAATTAATACTTTCAACTTTTTCTCAAAAAT-TTATTTTTGAAAACTTATTTTT
1 AAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATT-TTTTTGAAAATTTATTTTT
*
1342144 AAAGAAAATGGATACTTTCAAC-TTTTCTCCAAAAATATTTTTTTGAAAATTTATTTTT
1 AAAGAAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTTGAAAATTTATTTTT
* *
1342202 AAAGAAAATTGATACTTTCAACTTTTTCCTAAAAATATATATTTTTTAGAAAGTTTA-TTTT
1 AAAGAAAATTGATACTTTCAACTTTTT-CTCAAAA-ATAT-TTTTTT-GAAAATTTATTTTT
* * * * ** *
1342263 CAAGAAAAATTGATAATTTTAACTTTTCCTCAAAAATATTTTTTAAAAAATTTATTTTC
1 AAAG-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTT
* * *
1342322 AAGGAAAATTGATACTTTTAAC-TTTTCTTCAAAAATATTTTTTTGAAAACTTATTTTT
1 AAAGAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTTGAAAATTTATTTTT
* * * *
1342380 AAGGAGAATTGATACTTTCAAC-TTTTCTTCAAAAATATTTTCTTG--AATTT-TATTT
1 AAAGAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTTGAAAATTTATTTTT
1342435 AAAGAAAA
1 AAAGAAAA
1342443 GAAAATAATA
Statistics
Matches: 308, Mismatches: 35, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
55 10 0.03
56 27 0.09
57 30 0.10
58 164 0.53
59 20 0.06
60 10 0.03
61 19 0.06
62 28 0.09
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (58 bp):
AAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTT
Found at i:1342338 original size:178 final size:172
Alignment explanation
Indices: 1342030--1342420 Score: 498
Period size: 178 Copynumber: 2.2 Consensus size: 172
1342020 GCTTTTGTAC
* * *
1342030 AAAGAAAATTAATACTTTCAACTTTTTTCAAAAATTTTTTTTTAAATTTTAATTTCGAAAAAAAT
1 AAAGAAAATTGATACTTTCAACTTTTTCCAAAAATTTTTTTTTAAAGTTTAATTTCGAAAAAAAT
* * ** *
1342095 TAATACTTTCAACTTTTTCTCAAAAATTTATTTTTGAAAACTTATTTTTAAAGAAAATGGATACT
66 TAATAATTTCAACTTTTCCTCAAAAATTTATTTTAAAAAACTTATTTTCAAAGAAAATGGATACT
*
1342160 TTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTTATTTTT
131 TTCAACTTTTCTCCAAAAATATTTTTTTGAAAACTTATTTTT
*
1342202 AAAGAAAATTGATACTTTCAACTTTTTCCTAAAAATATATATTTTTTAGAAAGTTTATTTTC-AA
1 AAAGAAAATTGATACTTTCAACTTTTTCC-AAAAAT-T-T-TTTTTT--AAAGTTTAATTTCGAA
* * * *
1342266 GAAAAATTGATAATTTTAACTTTTCCTCAAAAATATT-TTTTAAAAAATTTATTTTCAAGGAAAA
60 -AAAAATTAATAATTTCAACTTTTCCTCAAAAAT-TTATTTTAAAAAACTTATTTTCAAAGAAAA
* * *
1342330 TTGATACTTTTAACTTTTCTTCAAAAATATTTTTTTGAAAACTTATTTTT
123 TGGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAACTTATTTTT
* * * *
1342380 AAGGAGAATTGATACTTTCAACTTTTCTTCAAAAATATTTT
1 AAAGAAAATTGATACTTTCAACTTTT-TCCAAAAATTTTTT
1342421 CTTGAATTTT
Statistics
Matches: 189, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
172 27 0.14
173 6 0.03
174 1 0.01
175 4 0.02
176 7 0.04
177 2 0.01
178 138 0.73
179 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (172 bp):
AAAGAAAATTGATACTTTCAACTTTTTCCAAAAATTTTTTTTTAAAGTTTAATTTCGAAAAAAAT
TAATAATTTCAACTTTTCCTCAAAAATTTATTTTAAAAAACTTATTTTCAAAGAAAATGGATACT
TTCAACTTTTCTCCAAAAATATTTTTTTGAAAACTTATTTTT
Found at i:1342457 original size:5 final size:5
Alignment explanation
Indices: 1342449--1342527 Score: 79
Period size: 5 Copynumber: 15.0 Consensus size: 5
1342439 AAAAGAAAAT
*
1342449 AATAA AATAA AATAAA AATAA AGA-AA AGTAA AATAAA AATAAA AATAA
1 AATAA AATAA AAT-AA AATAA A-ATAA AATAA AAT-AA AAT-AA AATAA
* *
1342497 AATAA AGATAA AATAA AATAA TATTA AATAA
1 AATAA A-ATAA AATAA AATAA AATAA AATAA
1342528 TTCTAATCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
5 41 0.65
6 22 0.35
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1342468 original size:6 final size:6
Alignment explanation
Indices: 1342452--1342514 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
1342442 AGAAAATAAT
*
1342452 AAAAT- AAAATA AAAATA AAGAAAA GTAAAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AA-AATA --AAAATA AAAATA AAAATA AAAATA
*
1342501 AAGAT- AAAATA AAA
1 AAAATA AAAATA AAA
1342515 TAATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
5 14 0.29
6 26 0.54
7 3 0.06
8 3 0.06
9 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1342468 original size:11 final size:11
Alignment explanation
Indices: 1342452--1342517 Score: 75
Period size: 11 Copynumber: 6.1 Consensus size: 11
1342442 AGAAAATAAT
1342452 AAAATAAAATA
1 AAAATAAAATA
*
1342463 AAAAT-AAAGA
1 AAAATAAAATA
*
1342473 AAAGTAAAATA
1 AAAATAAAATA
1342484 AAAATAAAA-A
1 AAAATAAAATA
1342494 TAAAATAAAGAT-
1 -AAAATAAA-ATA
1342506 AAAATAAAATA
1 AAAATAAAATA
1342517 A
1 A
1342518 TATTAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
10 11 0.24
11 34 0.74
12 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1342471 original size:33 final size:33
Alignment explanation
Indices: 1342434--1342519 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
1342424 GAATTTTATT
1342434 TAAAGAAAAGAAAATAATAAAAT-AAAATAAAAA
1 TAAAGAAAAGAAAATAATAAAATAAAAAT-AAAA
1342467 TAAAGAAAAGTAAAAT-A-AAAATAAAAATAAAA
1 TAAAGAAAAG-AAAATAATAAAATAAAAATAAAA
*
1342499 TAAAGATAAAATAAAATAATA
1 TAAAG--AAAAGAAAATAATA
1342520 TTAAATAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
32 14 0.30
33 21 0.46
34 10 0.22
35 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (33 bp):
TAAAGAAAAGAAAATAATAAAATAAAAATAAAA
Found at i:1342496 original size:38 final size:33
Alignment explanation
Indices: 1342434--1342519 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 33
1342424 GAATTTTATT
1342434 TAAAGAAAAGAAAATAATAAAATAAAATAAAAA
1 TAAAGAAAAGAAAATAATAAAATAAAATAAAAA
1342467 TAAAGAAAAGTAAAAT-A-AAAATAAAA-ATAAAA
1 TAAAGAAAAG-AAAATAATAAAATAAAATA-AAAA
*
1342499 TAAAGATAAAATAAAATAATA
1 TAAAG--AAAAGAAAATAATA
1342520 TTAAATAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
31 1 0.02
32 18 0.39
33 16 0.35
34 10 0.22
35 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (33 bp):
TAAAGAAAAGAAAATAATAAAATAAAATAAAAA
Found at i:1342524 original size:16 final size:15
Alignment explanation
Indices: 1342449--1342524 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 15
1342439 AAAAGAAAAT
*
1342449 AATAAAATAAAATAAA
1 AATAAATTAAAAT-AA
*
1342465 AATAAA-GAAAAGTAA
1 AATAAATTAAAA-TAA
*
1342480 AATAAAAATAAAAATAA
1 AAT--AAATTAAAATAA
*
1342497 AATAAAGATAAAATAA
1 AATAAA-TTAAAATAA
1342513 AATAATATTAAA
1 AATAA-ATTAAA
1342525 TAATTCTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
15 12 0.24
16 23 0.47
17 10 0.20
18 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (15 bp):
AATAAATTAAAATAA
Found at i:1343104 original size:13 final size:13
Alignment explanation
Indices: 1343086--1343127 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1343076 AAAATTTTCC
1343086 AAAAATTTCCAAA
1 AAAAATTTCCAAA
1343099 AAAAA-TTCACAAA
1 AAAAATTTC-CAAA
1343112 AAAAATTCTCCAAA
1 AAAAATT-TCCAAA
1343126 AA
1 AA
1343128 TTTCTACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 14 0.54
14 7 0.27
15 2 0.08
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATTTCCAAA
Found at i:1343496 original size:14 final size:14
Alignment explanation
Indices: 1343479--1343546 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 14
1343469 GATAAATTAA
1343479 AAATAATAATAGAT
1 AAATAATAATAGAT
* *
1343493 AAATTATAATATAT
1 AAATAATAATAGAT
*
1343507 AAATAGATAAATAATAAT
1 AAATA-AT-AAT-A-GAT
1343525 AAATATATAACTAGAT
1 AAATA-ATAA-TAGAT
1343541 AAATAA
1 AAATAA
1343547 AAAATATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 16 0.37
15 3 0.07
16 10 0.23
17 4 0.09
18 10 0.23
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAATAATAGAT
Found at i:1343514 original size:22 final size:22
Alignment explanation
Indices: 1343442--1343544 Score: 88
Period size: 26 Copynumber: 4.6 Consensus size: 22
1343432 TTAAAAGAAA
* *
1343442 ATAATTAGATAAATCATAATAT
1 ATAAATAGATAAATTATAATAT
* *
1343464 -T-AACAGATAAATTA-AAAAT
1 ATAAATAGATAAATTATAATAT
1343483 A-ATAATAGATAAATTATAATAT
1 ATA-AATAGATAAATTATAATAT
1343505 ATAAATAGATAAATAATAATAAATAT
1 ATAAATAGATAAAT--T-AT-AATAT
*
1343531 ATAACTAGATAAAT
1 ATAAATAGATAAAT
1343545 AAAAAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.06
20 10 0.15
21 13 0.20
22 16 0.25
23 1 0.02
24 1 0.02
25 2 0.03
26 18 0.28
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (22 bp):
ATAAATAGATAAATTATAATAT
Found at i:1343526 original size:42 final size:42
Alignment explanation
Indices: 1343417--1343526 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
1343407 TCAAATAAAA
* *
1343417 AATAT-TAATAGATAATTAAAAGAAAATAATTAGATAAATCAT
1 AATATATAATAGATAAATAAAA-ATAATAATTAGATAAATCAT
* *
1343459 AATAT-TAACAGATAAATTAAAAATAATAA-TAGATAAATTAT
1 AATATATAATAGATAAA-TAAAAATAATAATTAGATAAATCAT
*
1343500 AATATATAAATAGATAAATAATAATAA
1 AATATAT-AATAGATAAATAAAAATAA
1343527 ATATATAACT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
41 16 0.27
42 29 0.49
43 14 0.24
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (42 bp):
AATATATAATAGATAAATAAAAATAATAATTAGATAAATCAT
Found at i:1343651 original size:7 final size:7
Alignment explanation
Indices: 1343621--1343709 Score: 55
Period size: 7 Copynumber: 12.7 Consensus size: 7
1343611 ATATATATAT
1343621 ATAAATA
1 ATAAATA
*
1343628 GT-AATA
1 ATAAATA
1343634 ATAAATAA
1 ATAAAT-A
1343642 ATAAATA
1 ATAAATA
1343649 ATAAATA
1 ATAAATA
1343656 CATAAGATA
1 -ATAA-ATA
*
1343665 A-AAAGGA
1 ATAAA-TA
*
1343672 ATATAT-
1 ATAAATA
1343678 ATATAAT-
1 ATA-AATA
1343685 ATAAAATA
1 AT-AAATA
1343693 A-AAATA
1 ATAAATA
1343699 A-AAATA
1 ATAAATA
1343705 ATAAA
1 ATAAA
1343710 ATATAAAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
6 21 0.32
7 26 0.39
8 16 0.24
9 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (7 bp):
ATAAATA
Found at i:1343700 original size:34 final size:34
Alignment explanation
Indices: 1343662--1343730 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
1343652 AATACATAAG
* * *
1343662 ATAAAAAGGAAT-ATATATATAATATAAAATAAAA
1 ATAAAAA-GAATAAAATATAAAATACAAAATAAAA
*
1343696 ATAAAAATAATAAAATATAAAATACAAAATAAAA
1 ATAAAAAGAATAAAATATAAAATACAAAATAAAA
1343730 A
1 A
1343731 GCAAAAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (34 bp):
ATAAAAAGAATAAAATATAAAATACAAAATAAAA
Found at i:1343705 original size:22 final size:23
Alignment explanation
Indices: 1343680--1343728 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 23
1343670 GAATATATAT
1343680 ATAATATAAAATA-AAAATA-AAA
1 ATAA-ATAAAATATAAAATACAAA
1343702 AT-AATAAAATATAAAATACAAA
1 ATAAATAAAATATAAAATACAAA
1343724 ATAAA
1 ATAAA
1343729 AAGCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 7 0.29
23 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAATAAAATATAAAATACAAA
Found at i:1343715 original size:7 final size:7
Alignment explanation
Indices: 1343676--1343730 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
1343666 AAAGGAATAT
*
1343676 ATATATA
1 ATATAAA
1343683 ATATAAA
1 ATATAAA
1343690 ATA-AAA
1 ATATAAA
1343696 ATA-AAA
1 ATATAAA
1343702 ATAATAAA
1 AT-ATAAA
1343710 ATATAAA
1 ATATAAA
*
1343717 ATACAAA
1 ATATAAA
1343724 ATA-AAA
1 ATATAAA
1343730 A
1 A
1343731 GCAAAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 15 0.34
7 24 0.55
8 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
ATATAAA
Found at i:1343737 original size:27 final size:27
Alignment explanation
Indices: 1343682--1343739 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1343672 ATATATATAT
*
1343682 AATATAAAATAAAAATAAAAATAATAA
1 AATATAAAATAAAAATAAAAAGAATAA
*
1343709 AATATAAAATACAAAATAAAAAGCA-AA
1 AATATAAAATA-AAAATAAAAAGAATAA
1343736 AATA
1 AATA
1343740 GGTCTACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (27 bp):
AATATAAAATAAAAATAAAAAGAATAA
Found at i:1343943 original size:26 final size:24
Alignment explanation
Indices: 1343889--1343946 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
1343879 ATCTAATGAT
*
1343889 AAAATTTTTAAAAATTTTAAATGG
1 AAAATTTTTAAAAATTTTAAATGC
* **
1343913 TAAATTTTTATAAAATTCTTAGGTGC
1 AAAATTTTTA-AAAATT-TTAAATGC
1343939 AAAATTTT
1 AAAATTTT
1343947 GTCTAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 9 0.33
25 6 0.22
26 12 0.44
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (24 bp):
AAAATTTTTAAAAATTTTAAATGC
Found at i:1344126 original size:26 final size:28
Alignment explanation
Indices: 1344097--1344152 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1344087 TGAGATTTTT
*
1344097 AAAAATTTC-AAATGATAAATTTCT-TA
1 AAAAATTTCTAAATGAGAAATTTCTCTA
*
1344123 AAAAATTTCTAGATGAGAAATTTCTCTA
1 AAAAATTTCTAAATGAGAAATTTCTCTA
1344151 AA
1 AA
1344153 TTTGTCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 13 0.50
28 4 0.15
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (28 bp):
AAAAATTTCTAAATGAGAAATTTCTCTA
Found at i:1344281 original size:25 final size:26
Alignment explanation
Indices: 1344253--1344302 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1344243 ACAATTATCT
1344253 AATGATAGAA-TTTTT-AAAAATTTCA
1 AATGATA-AATTTTTTAAAAAATTTCA
*
1344278 AATGGTAAATTTTTTAAAAAATTTC
1 AATGATAAATTTTTTAAAAAATTTC
1344303 TAGGTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 11 0.50
26 9 0.41
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (26 bp):
AATGATAAATTTTTTAAAAAATTTCA
Found at i:1344763 original size:47 final size:46
Alignment explanation
Indices: 1344699--1344794 Score: 133
Period size: 47 Copynumber: 2.1 Consensus size: 46
1344689 GTGTGTGTTT
1344699 TTATAACTTTTTCTATATGTAATTAAACTTTCGAACTT-TATTGTGTA
1 TTATAACTTTTTCTATATGTAATTAAACTTTCGAA-TTCTATTGTG-A
* *
1344746 TTATAA-TTTTCTTTATATGTAATTGAACTTTCGAATTCTATTGTGA
1 TTATAACTTTT-TCTATATGTAATTAAACTTTCGAATTCTATTGTGA
1344792 TTA
1 TTA
1344795 GTAGATTCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
46 10 0.22
47 35 0.78
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (46 bp):
TTATAACTTTTTCTATATGTAATTAAACTTTCGAATTCTATTGTGA
Found at i:1351317 original size:39 final size:39
Alignment explanation
Indices: 1351247--1351327 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
1351237 GAACTGATGA
* * *
1351247 GAAATCCTTTGCACTGGCAAATACATGCAATTCTCTTTG
1 GAAATCCTTTGCAATGGCAAATACATCCAATTCTCTTCG
* * * *
1351286 GAAATCCTTTTCAATTGCAATTGCATCCAATTCTCTTCG
1 GAAATCCTTTGCAATGGCAAATACATCCAATTCTCTTCG
1351325 GAA
1 GAA
1351328 TTAATTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (39 bp):
GAAATCCTTTGCAATGGCAAATACATCCAATTCTCTTCG
Found at i:1361160 original size:39 final size:39
Alignment explanation
Indices: 1361101--1361181 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
1361091 GAACTGATGA
* * *
1361101 GAAATCCTTTGCACTGGCAATTACATGCAATTCTCTTTG
1 GAAATCCTTTGCAATGGCAATTACATCCAATTCTCTTCG
* * *
1361140 GAAATCCTTTTCAATTGCAATTGCATCCAATTCTCTTCG
1 GAAATCCTTTGCAATGGCAATTACATCCAATTCTCTTCG
1361179 GAA
1 GAA
1361182 TTAATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (39 bp):
GAAATCCTTTGCAATGGCAATTACATCCAATTCTCTTCG
Found at i:1367670 original size:24 final size:24
Alignment explanation
Indices: 1367618--1367671 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1367608 AATTATCATA
*
1367618 ATAATTTATTATTAAAGTAATTTT
1 ATAATTTATGATTAAAGTAATTTT
* *
1367642 ATAATTTATGATTTAAATTTATTTT
1 ATAATTTATGA-TTAAAGTAATTTT
1367667 -TAATT
1 ATAATT
1367672 AAAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATAATTTATGATTAAAGTAATTTT
Found at i:1380330 original size:2 final size:2
Alignment explanation
Indices: 1380325--1380352 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1380315 AAATAAATAA
1380325 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
1380353 CTCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1383754 original size:25 final size:25
Alignment explanation
Indices: 1383726--1383780 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
1383716 CTATCTTTGC
1383726 TATTTG-AAAT-AACATATAAAATAAA
1 TATTTGTAAATAAACAT-TAAAA-AAA
1383751 TATTTGTAAATAAACATTAAAAAAA
1 TATTTGTAAATAAACATTAAAAAAA
1383776 TATTT
1 TATTT
1383781 CTAATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.50
26 9 0.32
27 5 0.18
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
TATTTGTAAATAAACATTAAAAAAA
Found at i:1385617 original size:3 final size:3
Alignment explanation
Indices: 1385572--1385598 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1385562 CTACATTTTT
1385572 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1385599 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1399203 original size:35 final size:35
Alignment explanation
Indices: 1399164--1399332 Score: 117
Period size: 36 Copynumber: 4.8 Consensus size: 35
1399154 TATATATACC
* *
1399164 TGGCTTGAGGTTCAATCCCAGTCATTTTTAATATT
1 TGGCTTGCGGTTTAATCCCAGTCATTTTTAATATT
* * * * *
1399199 TGGCTCGTGGTTTAATCTCAGTCATTTTTTTATTTT
1 TGGCTTGCGGTTTAATCCCAGTCA-TTTTTAATATT
* * * *
1399235 TGACTTGCGATTTAATCCCAATC-TCTTTT-ATCTCT
1 TGGCTTGCGGTTTAATCCCAGTCAT-TTTTAATAT-T
* * * * *
1399270 CTAGCTTGCGATTCAGTCCGAGTCATTTTTAATATT
1 -TGGCTTGCGGTTTAATCCCAGTCATTTTTAATATT
* * *
1399306 TGGCTCGTGGTTTAATCCTAGTCATTT
1 TGGCTTGCGGTTTAATCCCAGTCATTT
1399333 CTTTATTTTT
Statistics
Matches: 101, Mismatches: 27, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
34 4 0.04
35 45 0.45
36 48 0.48
37 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (35 bp):
TGGCTTGCGGTTTAATCCCAGTCATTTTTAATATT
Found at i:1399356 original size:107 final size:106
Alignment explanation
Indices: 1399174--1399474 Score: 387
Period size: 107 Copynumber: 2.8 Consensus size: 106
1399164 TGGCTTGAGG
1399174 TTCAATCCCAGTCATTTTTAATATTTGGCTCGTGGTTTAAT-CTCAGTCATTTTTT-TATTTTTG
1 TTCAATCCCAGTCATTTTTAATATTTGGCTCGTGGTTTAATCCT-AGTCATTTTTTAT-TTTTTG
* * *
1399237 ACTTGCGATTTAATCCCAATCTCTTTTATCTCTCTAGCTTGCGA
64 ACTCGCG-TTTAATCCCAGTCTCTTTTATCTCTCTAACTTGCGA
* *
1399281 TTCAGTCCGAGTCATTTTTAATATTTGGCTCGTGGTTTAATCCTAGTCATTTCTTTATTTTTTGA
1 TTCAATCCCAGTCATTTTTAATATTTGGCTCGTGGTTTAATCCTAGTCATTT-TTTATTTTTTGA
* * *
1399346 CTCGCGTTTAATCTCAGTCTCTTTTATCTCTCTAACTTGTGG
65 CTCGCGTTTAATCCCAGTCTCTTTTATCTCTCTAACTTGCGA
* ** *
1399388 TTCAATCCCAGTCGTCATCAATATTTGGCTCGTGGTTTAATCCT-GATCA--TTTTATTTTTTGA
1 TTCAATCCCAGTCATTTTTAATATTTGGCTCGTGGTTTAATCCTAG-TCATTTTTTATTTTTTGA
* *
1399450 CTCACGGTTTAATCCCGGTCTCTTT
65 CTCGC-GTTTAATCCCAGTCTCTTT
1399475 ATTCTTCGAT
Statistics
Matches: 172, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
104 16 0.09
105 18 0.10
106 1 0.01
107 119 0.69
108 17 0.10
109 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (106 bp):
TTCAATCCCAGTCATTTTTAATATTTGGCTCGTGGTTTAATCCTAGTCATTTTTTATTTTTTGAC
TCGCGTTTAATCCCAGTCTCTTTTATCTCTCTAACTTGCGA
Found at i:1399863 original size:170 final size:168
Alignment explanation
Indices: 1399441--1399989 Score: 732
Period size: 170 Copynumber: 3.2 Consensus size: 168
1399431 TGATCATTTT
* *
1399441 ATTTTTTGACTCACGGTTTAATCCCGGTCTCTTTATTCTTCGATTCGCGATTCAATCCCGATC-T
1 ATTTTTTGACTCACGGTTTAATCCCGATCTCTTTATTCTTCGATTCGCGGTTCAATCCCGATCTT
1399505 TTTAATTTAAAATCGTAATTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCCC
66 TTTAATTTAAAATCGTAATTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCCC
1399570 AGTCTTTTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
131 -GTCTTTTTATTTTTTGACTTATGATTCAATCCAAG-T----TC
* **
1399614 ATTTTTTGACTCGCGGTTTAATCCC-AGTCTCTTTATTCTTCGATTCGCGGTTCAATCTTGATCT
1 ATTTTTTGACTCACGGTTTAATCCCGA-TCTCTTTATTCTTCGATTCGCGGTTCAATCCCGATCT
*
1399678 TTTTAATTTAAAATCGTAGTTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCC
65 TTTTAATTTAAAATCGTAATTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCC
**
1399743 CGTTCTTTTTTATTTTTTGACTCGTGATTCAATCCAAGTTC
130 CG-TC-TTTTTATTTTTTGACTTATGATTCAATCCAAGTTC
*
1399784 ATTTTTTGACTCACGATTTAATCCCGATCTCTTTA-TCTTTCGATTCGCGGTTCAATCCCGATCT
1 ATTTTTTGACTCACGGTTTAATCCCGATCTCTTTATTC-TTCGATTCGCGGTTCAATCCCGATCT
* * * * *
1399848 TTTTAATTTAAAATCGTAATTTAATCTCGA---TTGTTGTTAACCTCTGATTCGTAGCTTATTCT
65 TTTTAATTTAAAATCGTAATTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCC
* *
1399910 CGATCATTTTATTTTCTGACTTATGATTCAATCCAAGTTAATGTC
130 CG-TCTTTTTATTTTTTGACTTATGATTCAATCCAAG----T-TC
* ** *
1399955 ATTTTCTGACTCGTGGTTTAATCTCGATCTCTTTA
1 ATTTTTTGACTCACGGTTTAATCCCGATCTCTTTA
1399990 GTCTATAATT
Statistics
Matches: 337, Mismatches: 28, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
166 28 0.08
167 32 0.09
169 2 0.01
170 86 0.26
171 33 0.10
173 58 0.17
174 68 0.20
175 30 0.09
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (168 bp):
ATTTTTTGACTCACGGTTTAATCCCGATCTCTTTATTCTTCGATTCGCGGTTCAATCCCGATCTT
TTTAATTTAAAATCGTAATTTAATCTCAATTTTTGTTGTTAACCTCTGACTCGTGGTTTATTCCC
GTCTTTTTATTTTTTGACTTATGATTCAATCCAAGTTC
Found at i:1400166 original size:37 final size:37
Alignment explanation
Indices: 1400123--1400241 Score: 130
Period size: 37 Copynumber: 3.2 Consensus size: 37
1400113 TCGTGATTTT
* * * *
1400123 GACTTACAGTGTTGTCTCGATTGATTCTTTATTTATC
1 GACTTACGGTGTTGTCCCGATCGATTCTTTACTTATC
* * * *
1400160 GACTTACGGTATTATCCCGGTCGATTCTTTACTTCTC
1 GACTTACGGTGTTGTCCCGATCGATTCTTTACTTATC
** * *
1400197 GACTCGCGGTGTTGTCCCGATCGATTCTTTACTTCTT
1 GACTTACGGTGTTGTCCCGATCGATTCTTTACTTATC
1400234 GACTTACG
1 GACTTACG
1400242 ATTTAATTCC
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (37 bp):
GACTTACGGTGTTGTCCCGATCGATTCTTTACTTATC
Found at i:1400409 original size:110 final size:109
Alignment explanation
Indices: 1400234--1400506 Score: 386
Period size: 109 Copynumber: 2.5 Consensus size: 109
1400224 TTTACTTCTT
* * * * * * *
1400234 GACTTACGATTTAATTCCGGTCACTTTTA-CTTTCTGACTTGCGATTTAATCTCAGTTATTCCTA
1 GACTTACGATTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGATTTAATCCCAATCATTCCTA
*
1400298 TAGTTTCTCAACTCATGGTTTAATCCCAATCGTTTTTATTTCTCC
66 TAGTTTCTCAACTCATGGTTTAAT-CCAATCGCTTTTATTTCTCC
* * *
1400343 GACTTGCGGTTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGATTTAATCCCAATCATTTCTA
1 GACTTACGATTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGATTTAATCCCAATCATTCCTA
1400408 TAGTTTCTCAACTCATGGTTTAATCCAATCGCTTTTATTTCTCC
66 TAGTTTCTCAACTCATGGTTTAATCCAATCGCTTTTATTTCTCC
* * * * *
1400452 GACTTACGATTTAATCCTAGTCATTTTTATTTCTCCGACTTGTGATTCAATCCCA
1 GACTTACGATTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGATTTAATCCCA
1400507 GTTGTCGTTA
Statistics
Matches: 145, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
109 91 0.63
110 54 0.37
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (109 bp):
GACTTACGATTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGATTTAATCCCAATCATTCCTA
TAGTTTCTCAACTCATGGTTTAATCCAATCGCTTTTATTTCTCC
Found at i:1400504 original size:36 final size:36
Alignment explanation
Indices: 1400316--1400506 Score: 192
Period size: 36 Copynumber: 5.3 Consensus size: 36
1400306 CAACTCATGG
* *
1400316 TTTAATCCCAATCGTTTTTATTTCTCCGACTTGCGG
1 TTTAATCCCAATCATTTTTATTTCTCCGACTTGCGA
* * *
1400352 TTTAATCCCAGTCATTTTTATTTTTCTGACTTGCGA
1 TTTAATCCCAATCATTTTTATTTCTCCGACTTGCGA
*
1400388 TTTAATCCCAATCATTTCTATAGTTTCT-CAACTCATG-G-
1 TTTAATCCCAATCATTT-T-TA-TTTCTCCGACT--TGCGA
** *
1400426 TTTAAT-CCAATCGCTTTTATTTCTCCGACTTACGA
1 TTTAATCCCAATCATTTTTATTTCTCCGACTTGCGA
* * *
1400461 TTTAATCCTAGTCATTTTTATTTCTCCGACTTGTGA
1 TTTAATCCCAATCATTTTTATTTCTCCGACTTGCGA
*
1400497 TTCAATCCCA
1 TTTAATCCCA
1400507 GTTGTCGTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
33 1 0.01
34 6 0.05
35 12 0.10
36 79 0.63
37 9 0.07
38 11 0.09
39 5 0.04
40 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (36 bp):
TTTAATCCCAATCATTTTTATTTCTCCGACTTGCGA
Found at i:1400748 original size:25 final size:25
Alignment explanation
Indices: 1400702--1400749 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1400692 CTACATTTTT
*
1400702 TAATAATAATATATATTTTTTAAAA
1 TAATAATAATATATATTGTTTAAAA
1400727 TAATAATAATA-ATATTGGTTTAA
1 TAATAATAATATATATT-GTTTAA
1400750 TCATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TAATAATAATATATATTGTTTAAAA
Found at i:1400855 original size:11 final size:12
Alignment explanation
Indices: 1400832--1400857 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1400822 AAAAAAGTCC
1400832 AAACAGAAAAAA
1 AAACAGAAAAAA
1400844 AAACAGAAAAAA
1 AAACAGAAAAAA
1400856 AA
1 AA
1400858 GGGTTGGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAACAGAAAAAA
Found at i:1401862 original size:29 final size:30
Alignment explanation
Indices: 1401818--1401877 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
1401808 AAAAAAAATT
1401818 TTTTTTTTAATTTTTAAATTTATATATATTA
1 TTTTTTTTAATTTTTAAATTTATATAT-TTA
* *
1401849 TTTTTTTT-A-TTTTAAGTTTTTATATTTA
1 TTTTTTTTAATTTTTAAATTTATATATTTA
1401877 T
1 T
1401878 GCATGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 14 0.52
30 1 0.04
31 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (30 bp):
TTTTTTTTAATTTTTAAATTTATATATTTA
Found at i:1402298 original size:13 final size:13
Alignment explanation
Indices: 1402280--1402305 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1402270 CGCGTTTTAA
1402280 TTAAACCCTAAAC
1 TTAAACCCTAAAC
1402293 TTAAACCCTAAAC
1 TTAAACCCTAAAC
1402306 CTTTACCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
TTAAACCCTAAAC
Found at i:1404384 original size:24 final size:24
Alignment explanation
Indices: 1404352--1404403 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1404342 TGGTTCCAGT
1404352 ACCCCAGCTTTCAGTGCCACAAGC
1 ACCCCAGCTTTCAGTGCCACAAGC
* *
1404376 ACCCCAGCTTTCGGTGTCACAAGC
1 ACCCCAGCTTTCAGTGCCACAAGC
1404400 ACCC
1 ACCC
1404404 TTGGTGCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.17
Consensus pattern (24 bp):
ACCCCAGCTTTCAGTGCCACAAGC
Found at i:1404458 original size:24 final size:25
Alignment explanation
Indices: 1404404--1404473 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
1404394 ACAAGCACCC
1404404 TTGGTGCCACGAGCACCCTCTGCAT
1 TTGGTGCCACGAGCACCCTCTGCAT
*
1404429 TTGGTGCCACGAGCACCC-CTTCAT
1 TTGGTGCCACGAGCACCCTCTGCAT
* *
1404453 TTGGTGCTACGATCACTCCTC
1 TTGGTGCCACGAGCAC-CCTC
1404474 CCTTTGGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.47
25 20 0.50
26 1 0.03
ACGTcount: A:0.16, C:0.36, G:0.21, T:0.27
Consensus pattern (25 bp):
TTGGTGCCACGAGCACCCTCTGCAT
Found at i:1404479 original size:24 final size:24
Alignment explanation
Indices: 1404404--1404481 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
1404394 ACAAGCACCC
*
1404404 TTGGTGCCACGAGCACCCTCTGCAT
1 TTGGTGCCACGAGCACCC-CTCCAT
*
1404429 TTGGTGCCACGAGCACCCCTTCAT
1 TTGGTGCCACGAGCACCCCTCCAT
* * * *
1404453 TTGGTGCTACGATCACTCCTCCCT
1 TTGGTGCCACGAGCACCCCTCCAT
1404477 TTGGT
1 TTGGT
1404482 TCAACTGGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 29 0.62
25 18 0.38
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (24 bp):
TTGGTGCCACGAGCACCCCTCCAT
Found at i:1406277 original size:24 final size:24
Alignment explanation
Indices: 1406245--1406291 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1406235 TCAACAATCC
*
1406245 AGCATTTGCTACTGGTTTAAATTT
1 AGCATTTGCTACTGGTTCAAATTT
1406269 AGCATTTGCTACTGGTTCAAATT
1 AGCATTTGCTACTGGTTCAAATT
1406292 CTACCCTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (24 bp):
AGCATTTGCTACTGGTTCAAATTT
Found at i:1414339 original size:20 final size:20
Alignment explanation
Indices: 1414314--1414352 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1414304 TTCTTAATTA
*
1414314 TTATAATTAATATAATAATG
1 TTATAAATAATATAATAATG
*
1414334 TTATAAATAATATATTAAT
1 TTATAAATAATATAATAAT
1414353 TTTTTTAGTA
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:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATAAATAATATAATAATG
Found at i:1416785 original size:11 final size:11
Alignment explanation
Indices: 1416765--1416795 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1416755 CCCCCCCCCC
1416765 AAAA-AAAAAA
1 AAAAGAAAAAA
1416775 AAAAGAAAAAA
1 AAAAGAAAAAA
1416786 AAAAGAAAAA
1 AAAAGAAAAA
1416796 GATGCTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:1416787 original size:17 final size:17
Alignment explanation
Indices: 1416765--1416797 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1416755 CCCCCCCCCC
1416765 AAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAGAA
*
1416782 AAAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAGA
1416798 TGCTTGGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGAA
Found at i:1418106 original size:251 final size:251
Alignment explanation
Indices: 1417251--1418769 Score: 2336
Period size: 251 Copynumber: 6.0 Consensus size: 251
1417241 CAGTTTAACA
1417251 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* *
1417315 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTGCTTTAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
* *
1417380 TGACATTGTCATTCATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGA
131 TGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGGA
* *
1417445 CTGAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGG
196 CTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* *
1417501 ATTAGTGGAATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* * * *
1417566 AAAAGATCATTGTCAATACAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTCAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
*
1417631 TGACATTGTCATTTATATACTTATATACTTATATTTTGTCATTGAAAGTGGTGTCTTTATAAGTC
131 TGACATTGTCATTTATATACTTATAT--TT-CA-----TCATTGAAAGTGGTGTCTTTATAAGTC
** * *
1417696 TTCAGGGACTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCC----T--GGTGG
188 TTCAGGGACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* * * * * *
1417754 ATTGGTGGAATATTAGGCAATCTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
*
1417819 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
*
1417884 TGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGGG
131 TGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTG-GTGTCTTTATAAGTCTTCAGGG
1417949 ACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
195 ACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
*
1418006 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
*
1418070 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
* * *
1418135 TGACATTGTCATCTATATACTTATATTTCATCATTGAAAATGTTGTCTTTATAAGTCTTCAGGGA
131 TGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGGA
* * *
1418200 CTAAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGG
196 CTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* *
1418256 ATTAGTGGAATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* * *
1418321 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTCAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
*
1418386 TGACATTGTCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTC
131 TGACATTGTC------AT--TTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTC
*
1418451 TTCAGGGACTGAGAACCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
188 TTCAGGGACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* * * *
1418515 ATTGGTGGAATGCTAGGCAATCTAAGACGAATTTTATTCCTTAAGGAACTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* *
1418580 AAAAGATCGTTGTCAATAGAAGCATCTGCTTT-AATGTCATCTTTTGATGTAATTTACTTTGGCT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAT-TCATCTTTTGATGTAATTTACTTTAGCT
* * * * *
1418644 TTGACATTGTCATTTATGTATTTATATTTCGTCATTGAAAGTGGTGTCTTTGTAAGTCTTCAAGG
130 TTGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGG
*
1418709 ATTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAAACGTGG
195 ACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAAT-AACGTGG
1418767 ATT
1 ATT
1418770 GTTTATTAAA
Statistics
Matches: 1162, Mismatches: 80, Indels: 52
0.90 0.06 0.04
Matches are distributed among these distances:
245 12 0.01
246 63 0.05
250 156 0.13
251 424 0.36
252 50 0.04
253 151 0.13
254 1 0.00
255 1 0.00
257 2 0.00
258 2 0.00
259 300 0.26
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (251 bp):
ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTCATCTTTTGATGTAATTTACTTTAGCTT
TGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGGA
CTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
Found at i:1419591 original size:16 final size:17
Alignment explanation
Indices: 1419552--1419596 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1419542 TGCACATATA
* *
1419552 TATATATATATTATTTT
1 TATATTTATATTAATTT
1419569 TATTATTTAT-TTAATTT
1 TA-TATTTATATTAATTT
1419586 TATATTTATAT
1 TATATTTATAT
1419597 ATTATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
18 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTATATTAATTT
Found at i:1419603 original size:13 final size:13
Alignment explanation
Indices: 1419550--1419671 Score: 67
Period size: 13 Copynumber: 9.2 Consensus size: 13
1419540 TATGCACATA
*
1419550 TATATATATATAT
1 TATATTTATATAT
*
1419563 TATTTTTAT-TAT
1 TATATTTATATAT
*
1419575 T-TATTTA-ATTT
1 TATATTTATATAT
1419586 TATATTTATATAT
1 TATATTTATATAT
* *
1419599 TATATTAATAAAAT
1 TATATTTAT-ATAT
1419613 TAGTATTTA-ATAGT
1 TA-TATTTATATA-T
*
1419627 T-TAATTTAAGATAT
1 TAT-ATTT-ATATAT
1419641 TA-ATTTAATAAAATAT
1 TATATTT-AT---ATAT
1419657 TATATTTATATAT
1 TATATTTATATAT
1419670 TA
1 TA
1419672 AAAATAATAT
Statistics
Matches: 85, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
11 8 0.09
12 11 0.13
13 36 0.42
14 10 0.12
15 8 0.09
16 8 0.09
17 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:1419673 original size:21 final size:21
Alignment explanation
Indices: 1419650--1419694 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1419640 TTAATTTAAT
*
1419650 AAAATATTATATTTATATATTA
1 AAAATAATAT-TTTATATATTA
1419672 AAAATAATATTTTATATATTA
1 AAAATAATATTTTATATATTA
1419693 AA
1 AA
1419695 TTAATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATAATATTTTATATATTA
Found at i:1423348 original size:2 final size:2
Alignment explanation
Indices: 1423343--1423382 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1423333 CCAAAAAAAA
1423343 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
1423383 GAAATACGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1435216 original size:24 final size:24
Alignment explanation
Indices: 1435184--1435260 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
1435174 TGGTTCCAGT
1435184 ACCCCAGCTTTCAGTGCCACAAGC
1 ACCCCAGCTTTCAGTGCCACAAGC
*
1435208 ACCCCAGCTTTCTGTGCCACAAGC
1 ACCCCAGCTTTCAGTGCCACAAGC
* * *
1435232 ACCCCTGTCTTT-GGTGCTACAAGC
1 ACCCCAG-CTTTCAGTGCCACAAGC
1435256 ACCCC
1 ACCCC
1435261 CTGCATTTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 44 0.92
25 4 0.08
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.21
Consensus pattern (24 bp):
ACCCCAGCTTTCAGTGCCACAAGC
Found at i:1435261 original size:25 final size:25
Alignment explanation
Indices: 1435197--1435297 Score: 113
Period size: 24 Copynumber: 4.2 Consensus size: 25
1435187 CCAGCTTTCA
* *
1435197 GTGCCACAAGCACCCCAG-C-TTTCT
1 GTGCCACAAGCACCCCTGTCATTT-G
1435221 GTGCCACAAGCACCCCTGTC-TTTG
1 GTGCCACAAGCACCCCTGTCATTTG
*
1435245 GTGCTACAAGCACCCCCTG-CATTTG
1 GTGCCACAAGCA-CCCCTGTCATTTG
*
1435270 GTGCCACGAGCACCCCT-TCATTTG
1 GTGCCACAAGCACCCCTGTCATTTG
1435294 GTGC
1 GTGC
1435298 TACGATCACT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
24 44 0.65
25 24 0.35
ACGTcount: A:0.18, C:0.38, G:0.21, T:0.24
Consensus pattern (25 bp):
GTGCCACAAGCACCCCTGTCATTTG
Found at i:1435317 original size:24 final size:24
Alignment explanation
Indices: 1435221--1435319 Score: 83
Period size: 24 Copynumber: 4.1 Consensus size: 24
1435211 CCAGCTTTCT
* *
1435221 GTGCCACAAGCACCCCTGTC-TTTG
1 GTGCCACGAGCACCCCT-CCATTTG
* * *
1435245 GTGCTACAAGCACCCCCTGCATTTG
1 GTGCCACGAGCA-CCCCTCCATTTG
*
1435270 GTGCCACGAGCACCCCTTCATTTG
1 GTGCCACGAGCACCCCTCCATTTG
* * * *
1435294 GTGCTACGATCACTCCTCCCTTTG
1 GTGCCACGAGCACCCCTCCATTTG
1435318 GT
1 GT
1435320 TCAACTGGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
24 44 0.70
25 19 0.30
ACGTcount: A:0.16, C:0.36, G:0.20, T:0.27
Consensus pattern (24 bp):
GTGCCACGAGCACCCCTCCATTTG
Found at i:1437185 original size:643 final size:648
Alignment explanation
Indices: 1436395--1437631 Score: 2103
Period size: 643 Copynumber: 1.9 Consensus size: 648
1436385 ATATACATGC
*
1436395 AGGAACCCAATATTCTGTACTGGCATTTGGGAGCACTAGCTTTGGCCAGTCAACTTTTAGGGGTC
1 AGGAACCCAATATTCTGTACTGGCATTTGGAAGCACTAGCTTTGGCCAGTCAACTTTTAGGGGTC
* * *
1436460 AACGTGGGGGAAGTAGAGTAGCTCCATATACACCTAAAACTGAAGCAGATAGTTCGAGTGGTACA
66 AACATGGGGGAAGTAGAGTAGCTCCATAGACACCTAAAACTAAAGCAGATAGTTCGAGTGGTACA
*
1436525 GAGTCAGCTGAAAAGTTGGAGTCAATATTAGCGATGCCTGTTTACAAAGATAAAAGTCATGAGGA
131 GAGTCAGCTGAAAAGTTGGAGTCAATATCAGCGATGCCTGTTTACAAAGATAAAAGTCATGAGGA
*
1436590 GCTGAGATGGGAGGATTATCAGTTAGGAGATAAAGGTACCTTTGTAAAATATTGTACAACCCTGA
196 GCTGAGATGGAAGGATTATCAGTTAGGAGATAAAGGTACCTTTGTAAAATATTGTACAACCCTGA
*
1436655 AAGTTAATCATTCTTC-TTCTGTGTTTGACATTCCCTACCTTGCTATATTAATTTGAAA-TTCAG
261 AAGTTAATCATTCTTCTTTCTGTGTTTGACATTCCCTACCTTGCTATATCAATTTGAAATTTCAG
* *
1436718 GTGGACCACAGCCAGCTG-CTCATCCTTCTGGAGGGATTGGCTTTGGTGTGTCAACTGCACCTAA
326 GTGGACCACAGCCACCTGCCT-AGCCTTCTGGAGGGATTGGCTTTGGTGTGTCAACTGCACCTAA
*
1436782 AAGTCCTTTTGGTTCTTCTTCAACATTTGGTCAAACATCTTCAAATCCTTTTTCCGGCACAAGTA
390 AAGTCCTTTTGGTTCTTCTTCAACATTTGGTCAAACATCTTCAAATCCTTTTTCCCGCACAAGTA
1436847 CCAAC-CCATTTAGTCTAAAACCTCCATCC-T-T-TACAGGTTTTACAACCTCGACTGCTATATC
455 CC-ACTCCATTTAGTCTAAAACCTCCATCCTTATATACAGGTTTTACAACCTCGACTGCTATATC
* *
1436908 AAATCCTTTTCAATGGACATCATCAAGCCTTTTTATCCTAACTTCGGCATCAACATCTTCAATAT
519 AAATCCTTTTCAATGGACATCATCAAGCCTTTTTAGCCCAACTTCGGCATCAACATCTTCAATAT
1436973 GTGGTTCCTTTTGAGTGCAAGTTCATATCATATATAAATAATTAAATTCTTTTGAGTTCTCTTGT
584 GTGGTTCCTTTTGAGTGCAAGTTCATATCATATATAAATAATTAAATTCTTTTGAGTTCTCTTGT
* *
1437038 AGGAACCCAATCTTCTGTACTGGCATTTGGAAGCACTAGCTTTGGCCAGTCACCTTTT-GGGGAT
1 AGGAACCCAATATTCTGTACTGGCATTTGGAAGCACTAGCTTTGGCCAGTCAACTTTTAGGGG-T
* *
1437102 CAACATGGGGGAAGTAGAGTAGCTCCTTAGACACCTACAACTAAAGCAGATAGTTCGAGTGGTAC
65 CAACATGGGGGAAGTAGAGTAGCTCCATAGACACCTAAAACTAAAGCAGATAGTTCGAGTGGTAC
*
1437167 AGAGTCAGCTGCAAAGTTGGAGTCAATATCAGCGATGCCTGTTTACAAAGATAAAAGTCATGAGG
130 AGAGTCAGCTGAAAAGTTGGAGTCAATATCAGCGATGCCTGTTTACAAAGATAAAAGTCATGAGG
1437232 AGCTGAGATGGAAGGATTATCAGTTAGGAGATAAAGGTACCTTTGTAAAATATTGTACAACCCTG
195 AGCTGAGATGGAAGGATTATCAGTTAGGAGATAAAGGTACCTTTGTAAAATATTGTACAACCCTG
1437297 AAAGTTAATCATTCTTCTTTTCTGTGTTTGACATTCCCTACCTTGCTATATCAATTTGAAATTTC
260 AAAGTTAATCATTCTTC-TTTCTGTGTTTGACATTCCCTACCTTGCTATATCAATTTGAAATTTC
** *
1437362 AGGTGGACGGCAGCCACCTGCCTAGCCTTCTGGAGTGATTGGCTTTGGTGTGTCAACTGCACCTA
324 AGGTGGACCACAGCCACCTGCCTAGCCTTCTGGAGGGATTGGCTTTGGTGTGTCAACTGCACCTA
* * *
1437427 CAAGTCCTTTTGGTTGTTCTTCAACATTTGGTCAAACATCTTCAAATCCTTTTTCCCGCACAATT
389 AAAGTCCTTTTGGTTCTTCTTCAACATTTGGTCAAACATCTTCAAATCCTTTTTCCCGCACAAGT
*
1437492 ACCACTCCATTTAGTCTAAAACCTCCATCCTTTAATAGTACAGGTTTTACAACCTTGACTGCTAT
454 ACCACTCCATTTAGTCTAAAACCTCCATCC-TT-ATA-TACAGGTTTTACAACCTCGACTGCTAT
* * *
1437557 ATCAAATCCTTTTCAATGGACATCATCAAGCCTTTTTGGCCCAACTTTGTCATCAACATCTTCAA
516 ATCAAATCCTTTTCAATGGACATCATCAAGCCTTTTTAGCCCAACTTCGGCATCAACATCTTCAA
*
1437622 TATTTGGTTC
581 TATGTGGTTC
1437632 TTCTTCCACT
Statistics
Matches: 554, Mismatches: 28, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
642 4 0.01
643 260 0.47
645 43 0.08
646 148 0.27
647 2 0.00
648 1 0.00
650 1 0.00
652 95 0.17
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (648 bp):
AGGAACCCAATATTCTGTACTGGCATTTGGAAGCACTAGCTTTGGCCAGTCAACTTTTAGGGGTC
AACATGGGGGAAGTAGAGTAGCTCCATAGACACCTAAAACTAAAGCAGATAGTTCGAGTGGTACA
GAGTCAGCTGAAAAGTTGGAGTCAATATCAGCGATGCCTGTTTACAAAGATAAAAGTCATGAGGA
GCTGAGATGGAAGGATTATCAGTTAGGAGATAAAGGTACCTTTGTAAAATATTGTACAACCCTGA
AAGTTAATCATTCTTCTTTCTGTGTTTGACATTCCCTACCTTGCTATATCAATTTGAAATTTCAG
GTGGACCACAGCCACCTGCCTAGCCTTCTGGAGGGATTGGCTTTGGTGTGTCAACTGCACCTAAA
AGTCCTTTTGGTTCTTCTTCAACATTTGGTCAAACATCTTCAAATCCTTTTTCCCGCACAAGTAC
CACTCCATTTAGTCTAAAACCTCCATCCTTATATACAGGTTTTACAACCTCGACTGCTATATCAA
ATCCTTTTCAATGGACATCATCAAGCCTTTTTAGCCCAACTTCGGCATCAACATCTTCAATATGT
GGTTCCTTTTGAGTGCAAGTTCATATCATATATAAATAATTAAATTCTTTTGAGTTCTCTTGT
Found at i:1445839 original size:20 final size:20
Alignment explanation
Indices: 1445814--1445852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1445804 TTATTAATTA
*
1445814 TTATAATTAATATAATAATG
1 TTATAAATAATATAATAATG
*
1445834 TTATAAATAATATATTAAT
1 TTATAAATAATATAATAAT
1445853 TTTTTTAGTA
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:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATAAATAATATAATAATG
Found at i:1448282 original size:13 final size:12
Alignment explanation
Indices: 1448264--1448292 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1448254 CCCCCCCCCC
1448264 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1448276 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1448288 AAAAA
1 AAAAA
1448293 GATGCTTGGT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1449595 original size:251 final size:250
Alignment explanation
Indices: 1448748--1450513 Score: 2574
Period size: 251 Copynumber: 7.0 Consensus size: 250
1448738 CAGTTTAACA
*
1448748 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGCTCCTTGTACAACTA
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
*
1448813 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATC-TTTGATGTAATTTGCTTTAGCTTT
66 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
*
1448877 GACATTGTCATTCATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
131 GACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
* *
1448942 TGAGAACCTCATGTCATATTGATGTGAACAAAATTTATGAAGCCAAAATAACGTGG
196 TGAGAACCTCATGTCATA-TGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* *
1448998 ATTAGTGGAATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAACT
* * * * *
1449063 AAAAGATCATTGTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCT
65 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTA-TCTTTTGATGTAATTTACTTTAGCT
* *
1449128 TTGGACATTGTCATTTATATACTTATATACTTATATTTTGTCATTGAAAGTGGTGTCTTTATAAG
129 TT-GACATTGTCATTTATATACTTATAT--TT-CA-----TCATTGAAAGTGTTGTCTTTATAAG
** * *
1449193 TCTTCA-GGACTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCC----T--GGTG
185 TCTTCAGGGACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTG
1449251 G
250 G
* * * * * *
1449252 ATTGGTGGAATATTAGGCAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAG
1 ATTAGTGGAATACTAGGCAATC-TAAGACGAATTTTATTC-CTAATGAACTGGTCCTTGTACAAC
1449317 TAAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCT
64 TAAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCT
1449382 TTGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGG
129 TTGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTG-TTGTCTTTATAAGTCTTCAGG
1449447 GACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
193 GACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
1449505 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
1449570 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
66 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
*
1449635 GACATTGTCATCTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
131 GACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
* * *
1449700 TAAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGG
196 TGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* *
1449755 ATTAGTGGAATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAACT
* * * *
1449820 AAAAGATCATTGTCAATACAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCTT
65 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTT
* *
1449885 TGACATTGTCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTC
130 TGACATTGTC------AT--TTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTC
** * *
1449950 TTCAGGGACTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCC----T--GGTGG
187 TTCAGGGACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* * * * * * *
1450008 ATTGGTGGAATATTAGGCAATGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTC-CTAATGAACTGGTCCTTGTACAACT
1450073 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTT
65 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTT
* *
1450138 TGACATTG-CAATTTATATACTTTTATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCGGGG
130 TGACATTGTC-ATTTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGG
*
1450202 ACTGAGAACCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
194 ACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
* * * *
1450259 ATTGGTGGAATGCTAGGCAATCTAAGACGAATTTTATTCCTTAACGAACTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAACT
* * *
1450324 AAAAGATCGTTGTCAATAGAAGCATCTGCTTT-AATGTCATCTTTTGATGTAATTTACTTTGGCT
65 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAT-TTATCTTTTGATGTAATTTACTTTAGCT
* * * * * *
1450388 TTGACATTGTCATTTATGTATTTATATTTCGTCATTGAAAGTGGTGTCTTTGTAAGTCTTCAAGG
129 TTGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGG
* *
1450453 ATTGAGAATCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAAACGTGG
194 ACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAAT-AACGTGG
1450511 ATT
1 ATT
1450514 GTTTATTAAA
Statistics
Matches: 1369, Mismatches: 105, Indels: 82
0.88 0.07 0.05
Matches are distributed among these distances:
245 103 0.08
246 18 0.01
247 46 0.03
249 1 0.00
250 158 0.12
251 503 0.37
252 29 0.02
253 199 0.15
254 73 0.05
255 73 0.05
256 3 0.00
257 3 0.00
259 88 0.06
260 20 0.01
261 22 0.02
262 30 0.02
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (250 bp):
ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
GACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
TGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
Found at i:1450138 original size:504 final size:497
Alignment explanation
Indices: 1448748--1450498 Score: 2470
Period size: 504 Copynumber: 3.5 Consensus size: 497
1448738 CAGTTTAACA
*
1448748 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGCTCCTTGTACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* *
1448812 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAA-T-TTATCTTTGATGTAATTTGCTTTAGCT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATAT-TTTGATGTAATTTACTTTAGCT
* *
1448875 TTGACATTGTCATTCATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGG
130 TTGACATTGTC-TTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGG
* *
1448940 ACTGAGAACCTCATGTCATATTGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTG
194 ACTGAGAACCTCATGTCATA-TGATGTGAACATAATTTATGTAGCC---AT-ACGTGGATTAGTG
*
1449005 GAATACTAGGCAATCTAAGA-TGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGA
254 GAATACTAGGCAATCTAAGACT-AATTTTATT-CTTAATGAACTGGTCCTTGTACAACTAAAAGA
* * * * *
1449069 TCATTGTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCTTTGGAC
317 TCATTGTCAATAGAAGCATCTGCTTTAAATTTA-TCTTTTGATGTAATTTACTTTAGCTTT-GAC
** *
1449134 ATTGTCATTTATATACTTATATACTTATATTTTGTCATTGAAAGTGGTGTCTTTATAAGTCTTCA
380 ATTGTC-----TAT-C-TATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCA
* * *
1449199 -GGACTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCC----T--GGTGG
438 GGGACTGAGAACCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
* * * * * *
1449252 ATTGGTGGAATATTAGGCAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAG
1 ATTAGTGGAATACTAGGCAATC-TAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAAC
* * *
1449317 TAAAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCT
65 TAAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCT
*
1449382 TTGACATTGTCATTTATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGG
130 TTGACATTGTC-TTTATATACTTATATTTCATCATTGAAAGTG-GTGTCTTTATAAGTCTTCAGG
1449447 GACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGGATTAGTG
193 GACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCC---AT-ACGTGGATTAGTG
* *
1449512 GAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTAAAAGATC
254 GAATACTAGGCAATCTAAGACTAATTTTATTCTTAATGAACTGGTCCTTGTACAACTAAAAGATC
1449577 ATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTG
319 ATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTG
*
1449642 TC-ATCTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGACTAAGAA
384 TCTATCTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGACTGAGAA
* * *
1449706 CCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGG
449 CCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
* *
1449755 ATTAGTGGAATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
*
1449820 AAAAGATCATTGTCAATACAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCTT
*
1449885 TGACATTGTCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTC
131 TGACATTGTC-------T--TTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTC
** * * *
1449950 TTCAGGGACTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCC-T-GGTGGATTGG
187 TTCAGGGACTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCATACGTGGATTAG
* * * *
1450013 TGGAATATTAGGCAATGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAG
252 TGGAATACTAGGCAATCTAAGACTAATTTTATTC-TTAATGAACTGGTCCTTGTACAACTAAAAG
1450078 ATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACA
316 ATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACA
* * * *
1450143 TTG-CAATTTATATACTTTTATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCGGGGACTGA
381 TTGTCTATCTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGACTGA
1450207 GAACCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
446 GAACCTCATGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
* * * *
1450259 ATTGGTGGAATGCTAGGCAATCTAAGACGAATTTTATTCCTTAACGAACTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
* * * *
1450324 AAAAGATCGTTGTCAATAGAAGCATCTGCTTTAATGTCATCTTTTGATGTAATTTACTTTGGCTT
66 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCTT
* * * * *
1450389 TGACATTGTCATTTATGTATTTATATTTCGTCATTGAAAGTGGTGTCTTTGTAAGTCTTCAAGGA
131 TGACATTGTC-TTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGGA
* *
1450454 TTGAGAATCTCATGTCATATGATGTGAACATAATTTATGTAGCCA
195 CTGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCA
1450499 AAATAAACGT
Statistics
Matches: 1138, Mismatches: 85, Indels: 55
0.89 0.07 0.04
Matches are distributed among these distances:
496 131 0.12
497 42 0.04
498 4 0.00
501 1 0.00
502 108 0.09
503 64 0.06
504 357 0.31
505 42 0.04
506 116 0.10
507 135 0.12
508 46 0.04
509 62 0.05
510 30 0.03
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (497 bp):
ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTTAATGAACTGGTCCTTGTACAACT
AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAGTCATATTTTGATGTAATTTACTTTAGCTT
TGACATTGTCTTTATATACTTATATTTCATCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGGAC
TGAGAACCTCATGTCATATGATGTGAACATAATTTATGTAGCCATACGTGGATTAGTGGAATACT
AGGCAATCTAAGACTAATTTTATTCTTAATGAACTGGTCCTTGTACAACTAAAAGATCATTGTCA
ATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTGTCTATCT
ATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGACTGAGAACCTCATG
TCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
Found at i:1450311 original size:755 final size:756
Alignment explanation
Indices: 1448748--1450513 Score: 3159
Period size: 755 Copynumber: 2.3 Consensus size: 756
1448738 CAGTTTAACA
*
1448748 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGCTCCTTGTACAACTA
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
*
1448813 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATC-TTTGATGTAATTTGCTTTAGCTTT
66 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
1448877 GACATTGTCATTCATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
131 GACATTGTCATT-ATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
1448942 TGAGAACCTCATGTCATATTGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTGGA
195 TGAGAACCTCATGTCATA-TGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTGGA
1449007 ATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGATCA
259 ATACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGATCA
1449072 TTGTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCTTTGGACATT
324 TTGTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCTTTGGACATT
** *
1449137 GTCATTTATATACTTATATACTTATATTTTGTCATTGAAAGTGGTGTCTTTATAAGTCTTCAGGA
389 GTCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTCTTCAGGA
1449202 CTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCCTGGTGGATTGGTGGAATATTA
454 CTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCCTGGTGGATTGGTGGAATATTA
1449267 GGCAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAGATCATTGTC
519 GGCAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAGATCATTGTC
1449332 AATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTGTCATTT
584 AATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTGTCATTT
1449397 ATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGGGACTGAGAACCTCAT
649 ATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGGGACTGAGAACCTCAT
*
1449462 GTCATATGATGTGAACATAATTTATGTAGCCAAAATAACGTGG
714 GTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
1449505 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
1449570 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
66 AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
1449635 GACATTGTCATCTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
131 GACATTGTCAT-TATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGAC
*
1449700 TAAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTGGAA
195 TGAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTGGAA
1449765 TACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGATCAT
260 TACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGATCAT
*
1449830 TGTCAATACAAGCATCTGCTTTAAAGTCA-TATTTTGATGTAATTTACTTTAGCTTT-GACATTG
325 TGTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCTTTGGACATTG
1449893 TCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTCTTCAGGGA
390 TCATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTCTTCA-GGA
1449958 CTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCCTGGTGGATTGGTGGAATATTA
454 CTGAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCCTGGTGGATTGGTGGAATATTA
1450023 GGCAAT-GTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAGATCATTGTC
519 GGCAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAGATCATTGTC
1450087 AATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTG-CAATT
584 AATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTGTC-ATT
* *
1450151 TATATACTTTTATTTCATCATTGAAAGTG-TTGTCTTTATAAGTCTTCGGGGACTGAGAACCTCA
648 TATATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGGGACTGAGAACCTCA
1450215 TGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
713 TGTCATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
* * * *
1450259 ATTGGTGGAATGCTAGGCAATCTAAGACGAATTTTATTCCTTAACGAACTGGTCCTTGTACAAGT
1 ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCC-TAATGAACTGGTCCTTGTACAACT
* * *
1450324 AAAAGATCGTTGTCAATAGAAGCATCTGCTTT-AATGTCATCTTTTGATGTAATTTACTTTGGCT
65 AAAAGATCATTGTCAATAGAAGCATCTGCTTTAAAT-TTATCTTTTGATGTAATTTACTTTAGCT
* * * * * *
1450388 TTGACATTGTCATTTATGTATTTATATTTCGTCATTGAAAGTGGTGTCTTTGTAAGTCTTCAAGG
129 TTGACATTGTCA-TTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGG
* * * *
1450453 ATTGAGAATCTCATGTCATATGATGTGAACATAATTTATGTAGCCAAAATAAACGTGGATT
193 ACTGAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAAT-AACGTGGATT
1450514 GTTTATTAAA
Statistics
Matches: 973, Mismatches: 28, Indels: 17
0.96 0.03 0.02
Matches are distributed among these distances:
754 119 0.12
755 394 0.40
756 111 0.11
757 245 0.25
758 103 0.11
759 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (756 bp):
ATTAGTGGAATACTAGGCAATCTAAGACGAATTTTATTCCTAATGAACTGGTCCTTGTACAACTA
AAAGATCATTGTCAATAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTT
GACATTGTCATTATATACTTATATTTCATCATTGAAAGTGTTGTCTTTATAAGTCTTCAGGGACT
GAGAACCTCATGTCATATGATGTGAACAAAATTTATGAAGCCAAAATAACGTGGATTAGTGGAAT
ACTAGGCAATCTAAGATGAATTTTATTCCTTAATGAACTGGTCCTTGCACAACTAAAAGATCATT
GTCAATACAAGCATCTGCTTTAAAGTCAGTATTTTGATGTAATTTACTTCAGCTTTGGACATTGT
CATTTATATACTTATATACTTATATTTCATCATTGAAAGTGGTGACTTTATAAGTCTTCAGGACT
GAGAACCTCATGTCATATGATGCAAACATAATTTATGTGGCCTGGTGGATTGGTGGAATATTAGG
CAATCGTAAGACTAATTTTATTCTTTAATGAAGTGGTCCTTGTACAAGTAAAAGATCATTGTCAA
TAGAAGCATCTGCTTTAAATTTATCTTTTGATGTAATTTACTTTAGCTTTGACATTGTCATTTAT
ATACTTATATTTCATCATTGAAAGTGTTTGTCTTTATAAGTCTTCAGGGACTGAGAACCTCATGT
CATATGATGCGAACATAATTTATGTAGCCAAAATAACGTGG
Found at i:1451334 original size:13 final size:13
Alignment explanation
Indices: 1451280--1451403 Score: 62
Period size: 13 Copynumber: 9.2 Consensus size: 13
1451270 ATATGCACAC
*
1451280 ATATATATATATAT
1 ATATTTATATAT-T
1451294 ATATTT-TATTATT
1 ATATTTATA-TATT
*
1451307 -TATTTA-ATTTT
1 ATATTTATATATT
1451318 ATATTTATATATT
1 ATATTTATATATT
* *
1451331 ATATTAATAAAATT
1 ATATTTAT-ATATT
1451345 ATTATTTA-ATAGTT
1 A-TATTTATATA-TT
*
1451359 -TAATTTAAGATATT
1 AT-ATTT-ATATATT
1451373 A-ATTTAATAAAATATT
1 ATATTT-AT---ATATT
1451389 ATATTTATATATT
1 ATATTTATATATT
1451402 AT
1 AT
1451404 TAATAATAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 31
0.69 0.06 0.25
Matches are distributed among these distances:
11 3 0.03
12 13 0.15
13 33 0.38
14 18 0.21
15 8 0.09
16 8 0.09
17 4 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTATATATT
Found at i:1451346 original size:41 final size:42
Alignment explanation
Indices: 1451301--1451401 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 42
1451291 TATATATTTT
*
1451301 ATTATTTATTTAAT-TTTATATTT-ATATATT-ATATTAATAAA
1 ATTATTTATTTAATATTTA-ATTTAAGATATTAAT-TTAATAAA
1451342 ATTA-TTATTTAATAGTTTAATTTAAGATATTAATTTAATAAA
1 ATTATTTATTTAATA-TTTAATTTAAGATATTAATTTAATAAA
1451384 A-TATTATATTTATATATT
1 ATTATT-TATTTA-ATATT
1451402 ATTAATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
40 9 0.17
41 10 0.19
42 20 0.38
43 10 0.19
44 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (42 bp):
ATTATTTATTTAATATTTAATTTAAGATATTAATTTAATAAA
Found at i:1451445 original size:19 final size:18
Alignment explanation
Indices: 1451389--1451445 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
1451379 ATAAAATATT
*
1451389 ATATTTATATATTATTAATA
1 ATATTT-TATATT-TAAATA
* *
1451409 ATAATTTATATTAAAAATA
1 ATATTTTATATT-TAAATA
1451428 ATATTTTATATGTTAAAT
1 ATATTTTATAT-TTAAAT
1451446 TAATTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATTTTATATTTAAATA
Found at i:1455007 original size:2 final size:2
Alignment explanation
Indices: 1455000--1455025 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1454990 AGCAACCAAA
1455000 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
1455026 GAAATACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1469245 original size:2 final size:2
Alignment explanation
Indices: 1469238--1469264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1469228 TTTCGTCCAT
1469238 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1469265 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1473519 original size:21 final size:21
Alignment explanation
Indices: 1473493--1473534 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1473483 GAAAAGCTAA
*
1473493 AACAAATATCTTATATAAATG
1 AACAAAGATCTTATATAAATG
1473514 AACAAAGATCTTATATAAATG
1 AACAAAGATCTTATATAAATG
1473535 CTACTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (21 bp):
AACAAAGATCTTATATAAATG
Found at i:1485115 original size:3 final size:3
Alignment explanation
Indices: 1485107--1485146 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1485097 AGTTTTTGTT
1485107 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1485147 GGTTTAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1486547 original size:3 final size:3
Alignment explanation
Indices: 1486539--1486596 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
1486529 TATAAAAAGG
1486539 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1486587 ATA ACA ATA A
1 ATA ATA ATA A
1486597 CTTTTTATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1486786 original size:15 final size:15
Alignment explanation
Indices: 1486750--1486849 Score: 73
Period size: 15 Copynumber: 6.7 Consensus size: 15
1486740 CCCAAAATTG
1486750 AAACCCTAAATCCT-T
1 AAACCCTAAA-CCTCT
1486765 CAAACCCTAAACCTCT
1 -AAACCCTAAACCTCT
*
1486781 AAACCCTAAA-AT-T
1 AAACCCTAAACCTCT
*
1486794 AAACTCTAAACC-CTT
1 AAACCCTAAACCTC-T
** *
1486809 CAAACCCTAAAAATCC
1 -AAACCCTAAACCTCT
* *
1486825 AAACCCCAAACCTCC
1 AAACCCTAAACCTCT
1486840 AAACCCTAAA
1 AAACCCTAAA
1486850 ATTAAGTCGT
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
13 10 0.15
14 1 0.01
15 35 0.52
16 20 0.30
17 1 0.01
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCCTAAACCTCT
Found at i:1486789 original size:7 final size:7
Alignment explanation
Indices: 1486750--1486819 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
1486740 CCCAAAATTG
1486750 AAACCCT
1 AAACCCT
*
1486757 AAATCCTT
1 AAA-CCCT
1486765 CAAACCCT
1 -AAACCCT
1486773 AAACCTCT
1 AAACC-CT
1486781 AAACCCT
1 AAACCCT
**
1486788 AAA-ATT
1 AAACCCT
*
1486794 AAACTCT
1 AAACCCT
1486801 AAACCCTT
1 AAACCC-T
1486809 CAAACCCT
1 -AAACCCT
1486817 AAA
1 AAA
1486820 AATCCAAACC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
6 4 0.08
7 22 0.44
8 15 0.30
9 9 0.18
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:1486812 original size:44 final size:45
Alignment explanation
Indices: 1486735--1486834 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 45
1486725 AATAATAGAA
*
1486735 TAAACCCCAAAATTGAAACCCTAAATCCTTCAAACCCTAAACCTC
1 TAAACCCCAAAATTGAAACCCTAAACCCTTCAAACCCTAAACCTC
* * **
1486780 TAAACCCTAAAATT-AAACTCTAAACCCTTCAAACCCTAAAAATC
1 TAAACCCCAAAATTGAAACCCTAAACCCTTCAAACCCTAAACCTC
*
1486824 CAAACCCCAAA
1 TAAACCCCAAA
1486835 CCTCCAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 35 0.73
45 13 0.27
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (45 bp):
TAAACCCCAAAATTGAAACCCTAAACCCTTCAAACCCTAAACCTC
Found at i:1486983 original size:28 final size:29
Alignment explanation
Indices: 1486935--1487003 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
1486925 TAAAAAATTC
**
1486935 TAAAACCTCTAAACCCCAAAATCTGAAA-CT
1 TAAAACC-CT-AACCCCAAAATCCAAAATCT
*
1486965 TAAAACCCTAATCCCAAAATCCAAAATCT
1 TAAAACCCTAACCCCAAAATCCAAAATCT
1486994 T-AAACCCTAA
1 TAAAACCCTAA
1487004 AAGTCCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 23 0.66
29 5 0.14
30 7 0.20
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.20
Consensus pattern (29 bp):
TAAAACCCTAACCCCAAAATCCAAAATCT
Found at i:1487020 original size:16 final size:15
Alignment explanation
Indices: 1486966--1487028 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
1486956 TCTGAAACTT
1486966 AAAACCCT--AATCCC
1 AAAACCCTAAAAT-CC
* *
1486980 AAAATCC-AAAATCT
1 AAAACCCTAAAATCC
*
1486994 TAAACCCTAAAAGTCC
1 AAAACCCTAAAA-TCC
*
1487010 AAAACCTTAAAATCC
1 AAAACCCTAAAATCC
1487025 AAAA
1 AAAA
1487029 TTCTAAAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
14 12 0.32
15 14 0.37
16 12 0.32
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAACCCTAAAATCC
Found at i:1487027 original size:15 final size:16
Alignment explanation
Indices: 1486995--1487028 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1486985 CCAAAATCTT
1486995 AAACCCTAAAAGTCCA
1 AAACCCTAAAAGTCCA
*
1487011 AAACCTTAAAA-TCCA
1 AAACCCTAAAAGTCCA
1487026 AAA
1 AAA
1487029 TTCTAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.26, G:0.03, T:0.15
Consensus pattern (16 bp):
AAACCCTAAAAGTCCA
Found at i:1494961 original size:15 final size:15
Alignment explanation
Indices: 1494938--1494967 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1494928 ATAAGAAAGA
1494938 CATTCGCATTTGCAT
1 CATTCGCATTTGCAT
*
1494953 CATTTGCATTTGCAT
1 CATTCGCATTTGCAT
1494968 TCACACCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.43
Consensus pattern (15 bp):
CATTCGCATTTGCAT
Found at i:1495339 original size:41 final size:41
Alignment explanation
Indices: 1495260--1495345 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
1495250 GCAAGTTTTT
*
1495260 AAGATTTCAAAGCCTCTGTTTAAGAGGAACCAATTTCAATC
1 AAGATTTCAAAGCCTCTGTTTAAGAGGAACCAATTTCAAAC
*
1495301 AAGATTTCAAAGCCTCTGTTTAAGAGGAACC-TTCTTCAAAC
1 AAGATTTCAAAGCCTCTGTTTAAGAGGAACCAAT-TTCAAAC
1495342 AAGA
1 AAGA
1495346 CCTTTAGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (41 bp):
AAGATTTCAAAGCCTCTGTTTAAGAGGAACCAATTTCAAAC
Found at i:1495770 original size:22 final size:22
Alignment explanation
Indices: 1495725--1495775 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1495715 TTTGTAAGAC
*
1495725 CTCCGGGCATAATCTTTAAAAT
1 CTCCGGGCACAATCTTTAAAAT
* *
1495747 CTTCGGGCACAA-CTTTCAAGAT
1 CTCCGGGCACAATCTTT-AAAAT
1495769 CTCCGGG
1 CTCCGGG
1495776 TAAAAGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (22 bp):
CTCCGGGCACAATCTTTAAAAT
Found at i:1495902 original size:22 final size:22
Alignment explanation
Indices: 1495847--1495904 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1495837 TAAGATTTGT
** *
1495847 AAGACCTCCGGACATAATCTCT
1 AAGACCTCCGGGTATAATCTCC
*
1495869 AAGACCTTCGGGTATAA-CTTCC
1 AAGACCTCCGGGTATAATC-TCC
1495891 AAGACCTCCGGGTA
1 AAGACCTCCGGGTA
1495905 AAAGATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (22 bp):
AAGACCTCCGGGTATAATCTCC
Found at i:1495902 original size:127 final size:128
Alignment explanation
Indices: 1495413--1496021 Score: 636
Period size: 127 Copynumber: 4.7 Consensus size: 128
1495403 AATTTTTAAA
* * * *
1495413 ATTGCCTCTGATTAGGAGGAGTATTCAAAGATTTTGAGATTTTTCAA-ACCTCC-AAGCATAATT
1 ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGT-AAGACCTCCGGA-CATAATC
* * * * * *
1495476 TCTAATACTTTTGGGCATAAATTTCAAGACCTCCGGGTAATAAAATTTTTTTAAAAAAATTTTTA
64 TCTAAAACCTTCGGGCACAACTTTCAAGACCTCCGGGTAA-AAGA--TTTTT----AAATTTTTA
*
1495541 AAGTTTT
122 AAGTTTC
* * * * **
1495548 TTTACCCCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTTCAGG-TGTAATCT
1 ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACC-TCCGGACATAATCT
* * ** *** *
1495612 TTAAAACCTCCGGGCACAAC-TTCTAAGATTTTTAGGTAAAAGATTTTAAAATTTTTAAAGTTTC
65 CTAAAACCTTCGGGCACAACTTTC-AAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
* ** * * *
1495676 ATTGCCTTTGATTATAAGTAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGGCATAATCTT
1 ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGACATAATCTC
* *
1495741 TAAAATCTTCGGGCACAACTTTCAAGATCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
66 TAAAACCTTCGGGCACAACTTTCAAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
* * *
1495804 ATTGCCTCTTATTAGGATGAGCATTCAAAGA-TTTAAGATTTGTAAGACCTCCGGACATAATCTC
1 ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGACATAATCTC
* * * *
1495868 TAAGACCTTCGGGTATAACTTCCAAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
66 TAAAACCTTCGGGCACAACTTTCAAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
* * * * * * **
1495931 ATTACCTCTGATTA-GAGGATCATTCAAAGATTTTAAGATTTATAAGACTTTCGGGTATAATCTC
1 ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGACATAATCTC
*
1495995 TAAAATCTTCGGGCACAACTTTCAAGA
66 TAAAACCTTCGGGCACAACTTTCAAGA
1496022 TTTTTACGTA
Statistics
Matches: 396, Mismatches: 71, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
126 14 0.04
127 153 0.39
128 142 0.36
129 3 0.01
132 4 0.01
134 8 0.02
135 70 0.18
136 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (128 bp):
ATTGCCTCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGACATAATCTC
TAAAACCTTCGGGCACAACTTTCAAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTC
Found at i:1496033 original size:127 final size:128
Alignment explanation
Indices: 1495417--1496116 Score: 635
Period size: 127 Copynumber: 5.5 Consensus size: 128
1495407 TTTAAAATTG
* * * ** *
1495417 CCTCTGATTAGGAGGAGTATTCAAAGATTTTGAGATTTTTCAA-ACCTCCAAGCATAATTTCTAA
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGT-AAGACCTCCGGGCATAATCTCTAA
* * * * * * * *
1495481 TACTTTTGGGCATAAATTTCAAGACCTCCGGGTAATAAAATTTTTTTAAAAAAATTTTTAAAGTT
65 AACCTTCGGGCACAACTTTCAAGATCTCCAGGTAA-AAGA--TTTTT----AAATTTTTAAAGTT
**
1495546 TTTTTA
123 TCATTA
* * * * ** *
1495552 CCCCTGATTAGGAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTTCAGGTGTAATCTTTAAA
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAATCTCTAAA
* * ** * *
1495617 ACCTCCGGGCACAAC-TTCTAAGATTTTTAGGTAAAAGATTTTAAAATTTTTAAAGTTTCATTG
66 ACCTTCGGGCACAACTTTC-AAGATCTCCAGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTA
* ** * * *
1495680 CCTTTGATTATAAGTAGCATTCAAAGATTTTGAGATTTGTAAGACCTCCGGGCATAATCTTTAAA
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAATCTCTAAA
* * *
1495745 ATCTTCGGGCACAACTTTCAAGATCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTG
66 ACCTTCGGGCACAACTTTCAAGATCTCCAGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTA
* * * *
1495808 CCTCTTATTAGGATGAGCATTCAAAGA-TTTAAGATTTGTAAGACCTCCGGACATAATCTCTAAG
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAATCTCTAAA
* * * * *
1495872 ACCTTCGGGTATAACTTCCAAGACCTCCGGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTA
66 ACCTTCGGGCACAACTTTCAAGATCTCCAGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTA
* * * * *
1495935 CCTCTGATTA-GAGGATCATTCAAAGATTTTAAGATTTATAAGACTTTCGGGTATAATCTCTAAA
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAATCTCTAAA
* * ** * * * **
1495999 ATCTTCGGGCACAACTTTCAAGATTTTTACGTAAAAAATTTTTAAA-TTTTCAA-TATTCACAGA
66 ACCTTCGGGCACAACTTTCAAGATCTCCAGGTAAAAGATTTTTAAATTTTTAAAGT-TTCA-TTA
* * * * * *
1496062 CCTCTGATTA-GAAGAACATTCAAAGATGTT--GATATCTAAGACCTCCAGGCATAAT
1 CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAAT
1496117 TTTGATTCTC
Statistics
Matches: 470, Mismatches: 89, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
125 20 0.04
126 24 0.05
127 193 0.41
128 146 0.31
129 3 0.01
132 4 0.01
134 8 0.02
135 72 0.15
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (128 bp):
CCTCTGATTAGGAGGAGCATTCAAAGATTTTAAGATTTGTAAGACCTCCGGGCATAATCTCTAAA
ACCTTCGGGCACAACTTTCAAGATCTCCAGGTAAAAGATTTTTAAATTTTTAAAGTTTCATTA
Found at i:1496262 original size:44 final size:44
Alignment explanation
Indices: 1496186--1496294 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
1496176 GTCGATTCTG
* * * * * * *
1496186 TAAGACCTCCGAACATGATTTTTAATATCTCTGAGCATGATTTT
1 TAAGACCTCCGAACATAATCTCTAAAACCTCTGAGCATAATCTT
* *
1496230 TAAGACCTCCGGACATAATCTCTAAAACCTCTGCGCATAATCTT
1 TAAGACCTCCGAACATAATCTCTAAAACCTCTGAGCATAATCTT
* *
1496274 TAAGACCTCTGAGCATAATCT
1 TAAGACCTCCGAACATAATCT
1496295 TTAAGACATC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (44 bp):
TAAGACCTCCGAACATAATCTCTAAAACCTCTGAGCATAATCTT
Found at i:1496295 original size:22 final size:22
Alignment explanation
Indices: 1496186--1496301 Score: 108
Period size: 22 Copynumber: 5.3 Consensus size: 22
1496176 GTCGATTCTG
* * * *
1496186 TAAGACCTCCGAACATGATTTT
1 TAAGACCTCTGAGCATAATCTT
* * * *
1496208 TAATATCTCTGAGCATGATTTT
1 TAAGACCTCTGAGCATAATCTT
* *
1496230 TAAGACCTCCG-GACATAATCTC
1 TAAGACCTCTGAG-CATAATCTT
* *
1496252 TAAAACCTCTGCGCATAATCTT
1 TAAGACCTCTGAGCATAATCTT
1496274 TAAGACCTCTGAGCATAATCTT
1 TAAGACCTCTGAGCATAATCTT
1496296 TAAGAC
1 TAAGAC
1496302 ATCCGGACAT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
21 1 0.01
22 75 0.97
23 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (22 bp):
TAAGACCTCTGAGCATAATCTT
Found at i:1496312 original size:22 final size:22
Alignment explanation
Indices: 1496228--1496313 Score: 95
Period size: 22 Copynumber: 3.9 Consensus size: 22
1496218 GAGCATGATT
1496228 TTTAAGACCTCCGGACATAATC
1 TTTAAGACCTCCGGACATAATC
* * *
1496250 TCTAAAACCTCTGCG-CATAATC
1 TTTAAGACCTCCG-GACATAATC
*
1496272 TTTAAGACCT-CTGAGCATAATC
1 TTTAAGACCTCCGGA-CATAATC
*
1496294 TTTAAGACATCCGGACATAA
1 TTTAAGACCTCCGGACATAA
1496314 ATTCGATTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.02
22 46 0.90
23 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (22 bp):
TTTAAGACCTCCGGACATAATC
Found at i:1496894 original size:15 final size:15
Alignment explanation
Indices: 1496871--1496905 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1496861 AGTTTTTGTT
1496871 TAATATTAATAATAA
1 TAATATTAATAATAA
*
1496886 TAATTTTAATAATAA
1 TAATATTAATAATAA
1496901 TAATA
1 TAATA
1496906 ATATTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATTAATAATAA
Found at i:1498316 original size:3 final size:3
Alignment explanation
Indices: 1498308--1498335 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1498298 TATAAAAAGG
1498308 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1498336 CTTTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1498559 original size:29 final size:29
Alignment explanation
Indices: 1498481--1498603 Score: 113
Period size: 29 Copynumber: 4.2 Consensus size: 29
1498471 ATAAACCTCG
* * *
1498481 AAATTGAAACCCTAAATTCTCCAAACCCTA
1 AAATTTAAACCCTAAA-CCTTCAAACCCTA
* * *
1498511 AAATTTGAACCCTAAACCTTTAAACCATA
1 AAATTTAAACCCTAAACCTTCAAACCCTA
*
1498540 AAA-TTAAACTCTAAACCCTTCAAACCCTAA
1 AAATTTAAACCCTAAA-CCTTCAAACCCT-A
* * * *
1498570 AAATTCAAACCCCAAACCTCCAAACCTTA
1 AAATTTAAACCCTAAACCTTCAAACCCTA
1498599 AAATT
1 AAATT
1498604 AAGTTCCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
28 10 0.13
29 28 0.37
30 28 0.37
31 9 0.12
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.24
Consensus pattern (29 bp):
AAATTTAAACCCTAAACCTTCAAACCCTA
Found at i:1498628 original size:58 final size:59
Alignment explanation
Indices: 1498481--1498630 Score: 144
Period size: 59 Copynumber: 2.6 Consensus size: 59
1498471 ATAAACCTCG
* ** * **
1498481 AAATTGAAAC-CCTAAATTCTCCAAACCCT-AAAATTTGAACCCTAAACCTTTAAACCATA
1 AAATT-AAACTCC-AAACTCTCCAAACCCTAAAAATTCAAACCCCAAACCTCCAAACCATA
* * * *
1498540 AAATTAAACTCTAAACCCTTCAAACCCTAAAAATTCAAACCCCAAACCTCCAAACCTTA
1 AAATTAAACTCCAAACTCTCCAAACCCTAAAAATTCAAACCCCAAACCTCCAAACCATA
** *
1498599 AAATTAAGTTCCAAA-TCTCCAAACTCTAAAAA
1 AAATTAAACTCCAAACTCTCCAAACCCTAAAAA
1498631 CGAAACCCTA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
58 31 0.42
59 42 0.58
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (59 bp):
AAATTAAACTCCAAACTCTCCAAACCCTAAAAATTCAAACCCCAAACCTCCAAACCATA
Found at i:1498687 original size:30 final size:30
Alignment explanation
Indices: 1498624--1498690 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1498614 TCTCCAAACT
* * **
1498624 CTAAAAACGAAACCCTAAGCCCTTTGAGTC
1 CTAAAAACGAAACCCTAAACCCTTTCAACC
* *
1498654 CTAAAAATGAAACCTTAAACCCTTTCAACC
1 CTAAAAACGAAACCCTAAACCCTTTCAACC
1498684 CTAAAAA
1 CTAAAAA
1498691 ATTATAAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.21
Consensus pattern (30 bp):
CTAAAAACGAAACCCTAAACCCTTTCAACC
Found at i:1498748 original size:7 final size:7
Alignment explanation
Indices: 1498738--1498794 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
1498728 AACCTTAATC
1498738 CCAAAAT
1 CCAAAAT
1498745 CCAAAAT
1 CCAAAAT
1498752 CCAAAAT
1 CCAAAAT
* *
1498759 CCTAAAC
1 CCAAAAT
* *
1498766 CCTAAGT
1 CCAAAAT
*
1498773 CCAAAAA
1 CCAAAAT
*
1498780 CTTAAAAT
1 C-CAAAAT
1498788 CCAAAAT
1 CCAAAAT
1498795 TCTAAAAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.18
Consensus pattern (7 bp):
CCAAAAT
Found at i:1500446 original size:18 final size:19
Alignment explanation
Indices: 1500400--1500443 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1500390 TTTACTTAAC
1500400 TATTTATTAATAATAAATA
1 TATTTATTAATAATAAATA
1500419 -ATTTATTAATAA-AAATA
1 TATTTATTAATAATAAATA
1500436 TTATTTAT
1 -TATTTAT
1500444 AATCAACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 12 0.52
19 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTATTAATAATAAATA
Found at i:1515028 original size:15 final size:14
Alignment explanation
Indices: 1515002--1515044 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1514992 TGAAGGGAGG
*
1515002 GGAAGAAAAATAAA
1 GGAAAAAAAATAAA
1515016 GGAAAATAAAATAAA
1 GGAAAA-AAAATAAA
* *
1515031 GTAATAAAAATAAA
1 GGAAAAAAAATAAA
1515045 AAAAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
GGAAAAAAAATAAA
Found at i:1515228 original size:19 final size:19
Alignment explanation
Indices: 1515174--1515230 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
1515164 AAAGAAAATT
*
1515174 AAAAATTTTTATTTTTATAA
1 AAAAATTATTATTTTTAT-A
1515194 AAAAATTA-TATTTTTATA
1 AAAAATTATTATTTTTATA
*
1515212 AAAAATTATTATATTTATA
1 AAAAATTATTATTTTTATA
1515231 TTTTTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 9 0.26
19 18 0.53
20 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAAATTATTATTTTTATA
Found at i:1516226 original size:15 final size:16
Alignment explanation
Indices: 1516206--1516240 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1516196 ACGGTTAAAA
1516206 TTTTTAATT-ATTTTT
1 TTTTTAATTAATTTTT
1516221 TTTTTAATTCAATTTTT
1 TTTTTAATT-AATTTTT
1516238 TTT
1 TTT
1516241 CAATCACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTAATTAATTTTT
Done.