Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:40 original size:17 final size:18
Alignment explanation
Indices: 12--45 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2 GCATAAATAA
*
12 ATATAGGTATGTGTATAT
1 ATATAGGTATGTATATAT
30 ATATA-GTATGTATATA
1 ATATAGGTATGTATATA
46 GTATGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
ATATAGGTATGTATATAT
Found at i:43 original size:11 final size:11
Alignment explanation
Indices: 24--60 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
14 ATAGGTATGT
*
24 GTATATATATA
1 GTATGTATATA
35 GTATGTATATA
1 GTATGTATATA
46 GTATGTATATA
1 GTATGTATATA
57 GTAT
1 GTAT
61 ATAGTTGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (11 bp):
GTATGTATATA
Found at i:62 original size:18 final size:18
Alignment explanation
Indices: 12--65 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2 GCATAAATAA
*
12 ATATAGGTATGTGTATA-T
1 ATATA-GTATGTATATAGT
30 ATATAGTATGTATATAGT
1 ATATAGTATGTATATAGT
*
48 ATGTA-TATAGTATATAGT
1 ATATAGTAT-GTATATAGT
66 TGGCATGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (18 bp):
ATATAGTATGTATATAGT
Found at i:206 original size:30 final size:27
Alignment explanation
Indices: 172--240 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
162 TAATAGTTGC
172 ATTGCATATCATATAGTTTCATATCAAATA
1 ATTGCATAT--TATA-TTTCATATCAAATA
* *
202 ATTGCATATTATATTTGATATTAAATA
1 ATTGCATATTATATTTCATATCAAATA
*
229 ATTAGTATATTA
1 ATT-GCATATTA
241 CCTAGTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.43
28 11 0.31
30 9 0.26
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (27 bp):
ATTGCATATTATATTTCATATCAAATA
Found at i:209 original size:15 final size:15
Alignment explanation
Indices: 172--210 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
162 TAATAGTTGC
*
172 ATTGCATATCATATA
1 ATTGCATATCAAATA
* *
187 GTTTCATATCAAATA
1 ATTGCATATCAAATA
202 ATTGCATAT
1 ATTGCATAT
211 TATATTTGAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTGCATATCAAATA
Found at i:252 original size:30 final size:28
Alignment explanation
Indices: 183--268 Score: 75
Period size: 30 Copynumber: 3.0 Consensus size: 28
173 TTGCATATCA
* * *
183 TATAGTTTCATATCAAATAATT-GCATAT
1 TATAG-TTGATATTAAATAATTAGTATAT
*
211 TATATTTGATATTAAATAATTAGTATAT
1 TATAGTTGATATTAAATAATTAGTATAT
* **
239 TACCTAGTTGATATTATATGGTTAGTATAT
1 TA--TAGTTGATATTAAATAATTAGTATAT
269 ACTTATATAG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
27 14 0.30
28 11 0.23
30 22 0.47
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (28 bp):
TATAGTTGATATTAAATAATTAGTATAT
Found at i:978 original size:27 final size:27
Alignment explanation
Indices: 948--1014 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
938 CTATATAGTT
948 TATATATATATATATATATATATTATA
1 TATATATATATATATATATATATTATA
975 TATATATATATATATATATATATTATA
1 TATATATATATATATATATATATTATA
1002 TATATATATATAT
1 TATATATATATAT
1015 CAATGTATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATATATATATATATATATATTATA
Found at i:1023 original size:27 final size:26
Alignment explanation
Indices: 939--1030 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 26
929 ATAGCTCAAC
939 TATATAGTT-TATATATATATATAT-A
1 TATATA-TTATATATATATATATATAA
964 TATATATTATATATATATATATATATA
1 TATATATTATATATATATATATATA-A
991 TATATATTATATATATATATATATCAA
1 TATATATTATATATATATATATAT-AA
* *
1018 TGTATAGTATATA
1 TATATATTATATA
1031 GTTTACATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.03
25 21 0.34
27 37 0.61
28 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (26 bp):
TATATATTATATATATATATATATAA
Found at i:1030 original size:2 final size:2
Alignment explanation
Indices: 948--1014 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
938 CTATATAGTT
948 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
989 TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1015 CAATGTATAG
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1275 original size:29 final size:28
Alignment explanation
Indices: 1243--1306 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1233 TATAGTACAG
*
1243 ATATAAATATCA-ACTATAGTATATAGTTT
1 ATATAAATAT-ATACTATA-TAAATAGTTT
*
1272 ATATATAGTATATACTATATAAATAGTTT
1 ATATA-AATATATACTATATAAATAGTTT
1301 ATATAA
1 ATATAA
1307 TTCATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 20 0.65
30 10 0.32
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (28 bp):
ATATAAATATATACTATATAAATAGTTT
Found at i:1292 original size:18 final size:18
Alignment explanation
Indices: 1257--1303 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1247 AAATATCAAC
* *
1257 TATAGTATATAGTTTATA
1 TATAGTATATACTATATA
1275 TATAGTATATACTATATA
1 TATAGTATATACTATATA
* *
1293 AATAGTTTATA
1 TATAGTATATA
1304 TAATTCATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (18 bp):
TATAGTATATACTATATA
Found at i:1325 original size:22 final size:22
Alignment explanation
Indices: 1300--1347 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1290 ATAAATAGTT
1300 TATATAATTCAT-TAATAAACTA
1 TATATAATTCATAT-ATAAACTA
* *
1322 TATATAGTTCATATGTAAACTA
1 TATATAATTCATATATAAACTA
1344 TATA
1 TATA
1348 GTATATACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (22 bp):
TATATAATTCATATATAAACTA
Found at i:1444 original size:2 final size:2
Alignment explanation
Indices: 1425--1482 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
1415 ACTTTGAATT
*
1425 TA TA TA GTA TA AA T- TA TA TA TA T- TA TA TA T- TA -A TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1464 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
1483 ATTGTTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
1 5 0.10
2 41 0.85
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3750 original size:20 final size:18
Alignment explanation
Indices: 3727--3774 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
3717 GTGCCAGCAA
3727 TATCGATACTGACCCTTGGG
1 TATCGATACT-ACCC-TGGG
*
3747 TATCGATACCTACCCTGTG
1 TATCGATA-CTACCCTGGG
3766 TATCGATAC
1 TATCGATAC
3775 CAAAAATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 11 0.42
20 12 0.46
21 2 0.08
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (18 bp):
TATCGATACTACCCTGGG
Found at i:3770 original size:19 final size:21
Alignment explanation
Indices: 3727--3775 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
3717 GTGCCAGCAA
3727 TATCGATA-CTGACCCTTGGG
1 TATCGATACCTGACCCTTGGG
*
3747 TATCGATACCT-ACCC-TGTG
1 TATCGATACCTGACCCTTGGG
3766 TATCGATACC
1 TATCGATACC
3776 AAAAATAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
20 12 0.44
21 2 0.07
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (21 bp):
TATCGATACCTGACCCTTGGG
Found at i:5915 original size:15 final size:15
Alignment explanation
Indices: 5878--5909 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5868 ACTATTGTGA
*
5878 CAAATTTAATTTTGT
1 CAAAATTAATTTTGT
5893 CAAAATTAATTTTGT
1 CAAAATTAATTTTGT
5908 CA
1 CA
5910 CTATTAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
CAAAATTAATTTTGT
Found at i:6476 original size:180 final size:179
Alignment explanation
Indices: 6154--6594 Score: 425
Period size: 180 Copynumber: 2.4 Consensus size: 179
6144 ACAATGATAG
* * *
6154 AAAAAGTTGTCACAACAAATAATGAGATTTA-GATTTATTGTGACAAATTTTGTTTG-TGATTAT
1 AAAAAGTTGTCACAAAAAATAATGAGATTCATG-TTT-TTGTGACAAATTATGTTTGTTG-TTAT
* *
6217 ATATTTTAATTATAGTGACAAAATGTATAGTCACAAATGATTATCTCCAATTTATGGTACAAAAA
63 ATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATTTATGCTACAAAAA
* * *
6282 CAAAATCATATAGTGACATAA-TTTATAACTATAAGCT-ATAATTATTGTTATA
128 CAAAATCATATAGTGACA-AATTTTATAACTAT-AGCTGATAATAATTATTACA
* * *
6334 AAAAAGTTGTCACAATAAATAATGAGATTCATGTTTTTAGT-AAAACATTGTGTTTGTTGTTATA
1 AAAAAGTTGTCACAAAAAATAATGAGATTCATGTTTTT-GTGACAA-ATTATGTTTGTTGTTATA
** * * **
6398 TATTTTAATTATAGTGACAAAATATATTTTCACAAA-GATT-TCCCTCCATATTT-TTCTGCGCC
64 TATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTAT--CTCCA-ATTTATGCTAC-AA
* * * * * *
6460 AAA-ATAGTCCTATAGTGACAAATTTTGTAACTATAGGTGTTAATAATTATTACA
125 AAACAAAATCATATAGTGACAAATTTTATAACTATAGCTGATAATAATTATTACA
* * * * *
6514 AAAAACATTATCACAAAAAATAAAT-ATATTCATGTTTTTGTGACAAATTATATTTGTAGTTATA
1 AAAAA-GTTGTCACAAAAAAT-AATGAGATTCATGTTTTTGTGACAAATTATGTTTGTTGTTATA
* *
6578 AATTTTAACTATAGTGA
64 TATTTTAATTATAGTGA
6595 TAGCATATAT
Statistics
Matches: 217, Mismatches: 31, Indels: 26
0.79 0.11 0.09
Matches are distributed among these distances:
178 1 0.00
179 14 0.06
180 161 0.74
181 38 0.18
182 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (179 bp):
AAAAAGTTGTCACAAAAAATAATGAGATTCATGTTTTTGTGACAAATTATGTTTGTTGTTATATA
TTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATTTATGCTACAAAAACAA
AATCATATAGTGACAAATTTTATAACTATAGCTGATAATAATTATTACA
Found at i:7528 original size:12 final size:12
Alignment explanation
Indices: 7508--7577 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
7498 GATACATGAC
*
7508 CTGAATTCTGTT
1 CTGATTTCTGTT
*
7520 CTGATTTCTGAT
1 CTGATTTCTGTT
*
7532 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
7544 CTTATATCTGTT
1 CTGATTTCTGTT
*
7556 CTGAATTCTGTT
1 CTGATTTCTGTT
*
7568 TTGATTTCTG
1 CTGATTTCTG
7578 ATATCTCCAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:7539 original size:24 final size:24
Alignment explanation
Indices: 7509--7581 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
7499 ATACATGACC
7509 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
7533 TGGATTCTGTTCTTATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
7557 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
7581 T
1 T
7582 CTCCATTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:7542 original size:48 final size:48
Alignment explanation
Indices: 7471--7581 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
7461 AAATATTTTA
*
7471 TCTGATTTCCGACT-TGAATTCTGTTATGATA-CATGACCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTATGATATC-TGACCTGAATTCTGT
* * * **
7519 TCTGATTTCTGATATGGATTCTGTTCTTATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTATGATATCTGACCTGAATTCTGT
*
7567 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
7582 CTCCATTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTATGATATCTGACCTGAATTCTGT
Found at i:7744 original size:2 final size:2
Alignment explanation
Indices: 7737--7775 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7727 AAAGGATGGG
7737 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7776 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8142 original size:22 final size:21
Alignment explanation
Indices: 8117--8158 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
8107 GGATTCTACC
8117 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
8139 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
8159 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:9711 original size:32 final size:31
Alignment explanation
Indices: 9648--9738 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 31
9638 ATTTCTCATT
*
9648 ATAAAAAA-TGTGACAAATAATATTCTA-TCACA
1 ATAAAAAATTGTAAC-AA-AATATT-TAGTCACA
9680 ATAAAAAATTGTAACAAAATTATTTAGTCACA
1 ATAAAAAATTGTAACAAAA-TATTTAGTCACA
* * *
9712 GTCAAAAAGTTATAA-AAAATATTTAGT
1 AT-AAAAAATTGTAACAAAATATTTAGT
9739 TTCAAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
31 12 0.24
32 24 0.47
33 15 0.29
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.31
Consensus pattern (31 bp):
ATAAAAAATTGTAACAAAATATTTAGTCACA
Found at i:9845 original size:21 final size:19
Alignment explanation
Indices: 9819--9861 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9809 TTGATGTTAT
9819 AATTTAACTTAATTGTGACAA
1 AATTT-ACTT-ATTGTGACAA
* *
9840 AATTTACTTTTTGTGATAA
1 AATTTACTTATTGTGACAA
9859 AAT
1 AAT
9862 AATTGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (19 bp):
AATTTACTTATTGTGACAA
Found at i:15153 original size:8 final size:8
Alignment explanation
Indices: 15140--15198 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
15130 TGTAGCCTTT
15140 ATGCATGG
1 ATGCATGG
15148 ATGCAT-G
1 ATGCATGG
15155 --GCA-GG
1 ATGCATGG
15160 ATGCATGG
1 ATGCATGG
15168 ATGCAT-G
1 ATGCATGG
15175 --GCA-GG
1 ATGCATGG
*
15180 ATGCATCG
1 ATGCATGG
15188 ATGCATGG
1 ATGCATGG
15196 ATG
1 ATG
15199 GATGCATCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
5 8 0.20
7 8 0.20
8 25 0.61
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.22
Consensus pattern (8 bp):
ATGCATGG
Found at i:15165 original size:20 final size:20
Alignment explanation
Indices: 15140--15214 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
15130 TGTAGCCTTT
*
15140 ATGCATGGATGCATGGCAGG
1 ATGCATCGATGCATGGCAGG
*
15160 ATGCATGGATGCATGGCAGG
1 ATGCATCGATGCATGGCAGG
15180 ATGCATCGATGCATGG-ATGG
1 ATGCATCGATGCATGGCA-GG
15200 ATGCATCGATGCATG
1 ATGCATCGATGCATG
15215 CATCGATATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 52 0.98
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (20 bp):
ATGCATCGATGCATGGCAGG
Found at i:15200 original size:32 final size:32
Alignment explanation
Indices: 15180--15244 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
15170 GCATGGCAGG
*
15180 ATGCATCGATGCATGGATGGATGCATCGATGC
1 ATGCATCGATACATGGATGGATGCATCGATGC
*
15212 ATGCATCGATATATGGATGGATGCATCGATGC
1 ATGCATCGATACATGGATGGATGCATCGATGC
15244 A
1 A
15245 CTAAGTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (32 bp):
ATGCATCGATACATGGATGGATGCATCGATGC
Found at i:15202 original size:12 final size:12
Alignment explanation
Indices: 15144--15242 Score: 57
Period size: 12 Copynumber: 8.2 Consensus size: 12
15134 GCCTTTATGC
15144 ATGGATGCATGG
1 ATGGATGCATGG
15156 CA-GGATGCATGG
1 -ATGGATGCATGG
*
15168 ATGCATGGCA-GG
1 ATGGAT-GCATGG
15180 ATGCATCGATGCATGG
1 ATG----GATGCATGG
*
15196 ATGGATGCATCG
1 ATGGATGCATGG
* *
15208 ATGCATGCATCG
1 ATGGATGCATGG
15220 AT--AT--ATGG
1 ATGGATGCATGG
*
15228 ATGGATGCATCG
1 ATGGATGCATGG
15240 ATG
1 ATG
15243 CACTAAGTGC
Statistics
Matches: 69, Mismatches: 6, Indels: 23
0.70 0.06 0.23
Matches are distributed among these distances:
8 5 0.07
10 4 0.06
11 1 0.01
12 45 0.65
13 4 0.06
15 3 0.04
16 7 0.10
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.24
Consensus pattern (12 bp):
ATGGATGCATGG
Found at i:15333 original size:21 final size:21
Alignment explanation
Indices: 15307--15364 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
15297 CATTAGTGCA
15307 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
15328 GGTGCATGGATGCACTGCATG
1 GGTGCATGGATGCACTGCAGG
*
15349 GATGCATGGATGCACT
1 GGTGCATGGATGCACT
15365 TTGACACCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:15346 original size:13 final size:13
Alignment explanation
Indices: 15330--15354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15320 ACTGCAGGGG
15330 TGCATGGATGCAC
1 TGCATGGATGCAC
15343 TGCATGGATGCA
1 TGCATGGATGCA
15355 TGGATGCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:15489 original size:30 final size:29
Alignment explanation
Indices: 15444--15502 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
15434 TAACTTTGAA
*
15444 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
15473 TAAATTCAATTTAAGTCCAAAAACATTTTG
1 TAAATTCAA-TTAAGTCCAAAAACATTTTG
15503 CCTTAAAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:19455 original size:22 final size:23
Alignment explanation
Indices: 19405--19448 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19395 CATTTCATAT
*
19405 TTTCACATAAACACGTAGTTCAC
1 TTTCACATAAACACGTAGCTCAC
*
19428 TTTCACAT-AGCACGTAGCTCA
1 TTTCACATAAACACGTAGCTCA
19449 TATTCACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (23 bp):
TTTCACATAAACACGTAGCTCAC
Found at i:19600 original size:2 final size:2
Alignment explanation
Indices: 19593--19627 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19583 TTCATCTTCC
19593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19628 CATTTTCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20432 original size:7 final size:7
Alignment explanation
Indices: 20410--20461 Score: 90
Period size: 7 Copynumber: 7.7 Consensus size: 7
20400 ATAACAAACA
20410 CATG-TT
1 CATGCTT
20416 CATG-TT
1 CATGCTT
20422 CATGCTT
1 CATGCTT
20429 CATGCTT
1 CATGCTT
20436 CATGCTT
1 CATGCTT
20443 CATGCTT
1 CATGCTT
20450 CATGCTT
1 CATGCTT
20457 CATGC
1 CATGC
20462 ACAATACTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 10 0.22
7 35 0.78
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.42
Consensus pattern (7 bp):
CATGCTT
Found at i:25925 original size:23 final size:22
Alignment explanation
Indices: 25870--25933 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 22
25860 TTTCCCTTGA
*
25870 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
25890 AGTGTATCGATGCATCCTTAAC
1 AGTGCATCGATGCATCCTTAAC
25912 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
25934 TGCATCAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.41
21 1 0.03
22 3 0.08
23 12 0.32
24 6 0.16
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:27886 original size:3 final size:3
Alignment explanation
Indices: 27878--27925 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
27868 TTTGTTTTAT
* *
27878 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27923 TTA
1 TTA
27926 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27904 original size:22 final size:23
Alignment explanation
Indices: 27868--27912 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
27858 TTTTATTTCA
*
27868 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
27891 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
27913 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTGTTTTATATATTATTATTAT
Found at i:27933 original size:14 final size:14
Alignment explanation
Indices: 27878--27929 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
27868 TTTGTTTTAT
27878 TTATTATTATTATT-
1 TTATTA-TATTATTA
* * *
27892 TTGTTTTAATATTA
1 TTATTATATTATTA
27906 TTATTATATTATTA
1 TTATTATATTATTA
27920 TTATTA-ATTA
1 TTATTATATTA
27930 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:31438 original size:30 final size:30
Alignment explanation
Indices: 31403--31467 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
31393 AAGAGAATGT
* *
31403 CATGGAAGAAGTTGTAGTCCAGATAAGCAA
1 CATGGAAGAAGCTGTAGTCCAGACAAGCAA
* *
31433 TATGGAAGAAGCTGTAGTCCATACAAGCAA
1 CATGGAAGAAGCTGTAGTCCAGACAAGCAA
31463 CATGG
1 CATGG
31468 CCCATAAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.20
Consensus pattern (30 bp):
CATGGAAGAAGCTGTAGTCCAGACAAGCAA
Found at i:31677 original size:7 final size:7
Alignment explanation
Indices: 31665--31702 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
31655 CATACATACA
31665 TTTGCAT
1 TTTGCAT
31672 TTTGCAT
1 TTTGCAT
31679 CTTTGCAT
1 -TTTGCAT
*
31687 TTTTCAT
1 TTTGCAT
31694 TTTGCAT
1 TTTGCAT
31701 TT
1 TT
31703 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (7 bp):
TTTGCAT
Found at i:31685 original size:15 final size:14
Alignment explanation
Indices: 31665--31702 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
31655 CATACATACA
31665 TTTGCATTTTGCAT
1 TTTGCATTTTGCAT
*
31679 CTTTGCATTTTTCAT
1 -TTTGCATTTTGCAT
31694 TTTGCATTT
1 TTTGCATTT
31703 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (14 bp):
TTTGCATTTTGCAT
Found at i:31833 original size:34 final size:35
Alignment explanation
Indices: 31773--31850 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
31763 GCATTTGCAT
* *
31773 TTTTCATTTTTGCATTCTTATGTTTGTAT-TTACA
1 TTTTCATTTTTGCATTCTCATCTTTGTATATTACA
*
31807 TTTTCATTTTTTCATT-TCCATCTTTGTATAATTACA
1 TTTTCATTTTTGCATTCT-CATCTTTGTAT-ATTACA
31843 TTTT-ATTT
1 TTTTCATTT
31851 CAAACTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 1 0.03
34 24 0.63
35 4 0.11
36 9 0.24
ACGTcount: A:0.19, C:0.13, G:0.05, T:0.63
Consensus pattern (35 bp):
TTTTCATTTTTGCATTCTCATCTTTGTATATTACA
Found at i:34421 original size:17 final size:17
Alignment explanation
Indices: 34387--34421 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34377 AAGAAAAAGG
34387 AAAAAGGAAAAAAATGA
1 AAAAAGGAAAAAAATGA
* *
34404 AAAAAGGGAAAAATTGA
1 AAAAAGGAAAAAAATGA
34421 A
1 A
34422 TCAAGACGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAAGGAAAAAAATGA
Found at i:35082 original size:32 final size:32
Alignment explanation
Indices: 35046--35106 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
35036 TGGAAATAAT
* *
35046 AAGTATCTCTACGAGATGAGTATAACAACAAG
1 AAGTATCTCTACAAGATGAGCATAACAACAAG
35078 AAGTATCTCTACAAGATGAGCATAACAAC
1 AAGTATCTCTACAAGATGAGCATAACAAC
35107 CATTTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (32 bp):
AAGTATCTCTACAAGATGAGCATAACAACAAG
Found at i:39811 original size:113 final size:114
Alignment explanation
Indices: 39601--39908 Score: 408
Period size: 113 Copynumber: 2.7 Consensus size: 114
39591 TTTCAAACAT
* *
39601 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAA
1 TGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
* **
39666 GAACTTGTTCAACCTTTTGCTCGAATTAATCACTC-GGTGGATCAG-TAG
66 GAACTTGTTCAACCTTTCGCTCGAATTAATCACTCAAATGGATCAGCT-G
*
39714 TGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAA
1 TGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
* ** * * *
39779 GAATTTGTTCAACCTTTCGCTTTAATTCATCACTCAAATGGATTAGCTT
66 GAACTTGTTCAACCTTTCGCTCGAATTAATCACTCAAATGGATCAGCTG
* * * * *
39828 TTCCAGAG-AAAGTTCATAATAAGAAGAACTTATCTGAACAA-AAAGAAGAAGTTCATAATGAGA
1 TGCCAG-GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
39891 AGAGCTTGTTCAACCTTT
65 AGAACTTGTTCAACCTTT
39909 GTATGATTCT
Statistics
Matches: 172, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
113 128 0.74
114 42 0.24
115 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (114 bp):
TGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTCGCTCGAATTAATCACTCAAATGGATCAGCTG
Found at i:40405 original size:3 final size:3
Alignment explanation
Indices: 40397--40446 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
40387 TTTGTTTTAT
* *
40397 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA -TA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40441 TTA TTA
1 TTA TTA
40447 AATAATTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:40439 original size:16 final size:16
Alignment explanation
Indices: 40401--40444 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
40391 TTTTATTTAT
* * *
40401 TATTATTATTTTGTTT
1 TATTATTATTATATTA
*
40417 TAATATTATTATATTA
1 TATTATTATTATATTA
40433 TATTATTATTAT
1 TATTATTATTAT
40445 TAAATAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATTATTATATTA
Found at i:40442 original size:19 final size:18
Alignment explanation
Indices: 40393--40446 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
40383 TTCATTTGTT
*
40393 TTATTTATTATTATTATT
1 TTATTTATTATTATTATA
* *
40411 TTGTTTTAATATTATTATA
1 TT-ATTTATTATTATTATA
40430 TTATATTATTATTATTA
1 TTAT-TTATTATTATTA
40447 AATAATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTATTATTATTATA
Found at i:41891 original size:15 final size:15
Alignment explanation
Indices: 41871--41899 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41861 AATAATTTAT
41871 TTAATTATTTATGTA
1 TTAATTATTTATGTA
41886 TTAATTATTTATGT
1 TTAATTATTTATGT
41900 TTTTATTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TTAATTATTTATGTA
Found at i:49278 original size:24 final size:24
Alignment explanation
Indices: 49250--49311 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
49240 TGAGATACAC
49250 GGGTAAAAATGAGGAGATTTTAAA
1 GGGTAAAAATGAGGAGATTTTAAA
49274 GGGTAAAAATGAGGAGATTTTAAA
1 GGGTAAAAATGAGGAGATTTTAAA
*
49298 GGGTAAAACTGAGG
1 GGGTAAAAATGAGG
49312 TGGATAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.23
Consensus pattern (24 bp):
GGGTAAAAATGAGGAGATTTTAAA
Found at i:50945 original size:20 final size:19
Alignment explanation
Indices: 50916--50960 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
50906 TCCTTTAAAA
*
50916 AATATAAAATATAAAATTTT
1 AATATTAAATA-AAAATTTT
50936 AATATTAAATAAAAATTTT
1 AATATTAAATAAAAATTTT
50955 AA-ATTA
1 AATATTA
50961 TCAGATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTAAATAAAAATTTT
Found at i:51373 original size:12 final size:13
Alignment explanation
Indices: 51353--51412 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 13
51343 ACTATTATAG
51353 AATATAAATAAAT
1 AATATAAATAAAT
51366 AA-ATAAATAATAT
1 AATATAAATAA-AT
*
51379 AATAGT--ATTAAT
1 AATA-TAAATAAAT
51391 AATATATAATAAAT
1 AATATA-AATAAAT
51405 AATTATAA
1 AA-TATAA
51413 TACTAAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
11 1 0.03
12 14 0.37
13 9 0.24
14 9 0.24
15 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
AATATAAATAAAT
Found at i:51407 original size:17 final size:18
Alignment explanation
Indices: 51353--51407 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
51343 ACTATTATAG
51353 AATATA-AATAAATAAATA
1 AATATATAATAAAT-AATA
*
51371 AATAATATAATAGTATTAAT-
1 AAT-ATATAATA--AATAATA
51391 AATATATAATAAATAAT
1 AATATATAATAAATAAT
51408 TATAATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 11 0.35
20 7 0.23
21 3 0.10
22 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AATATATAATAAATAATA
Found at i:54975 original size:96 final size:96
Alignment explanation
Indices: 54802--55001 Score: 292
Period size: 96 Copynumber: 2.1 Consensus size: 96
54792 TTCAAGTAGT
* *
54802 AACCAGTAGATTCCATGATCAATAATTCAGGAACGATCATATTTTCCAGTAAAAACAGGTAACCA
1 AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
* *
54867 GATAACACATTTCAGGTAACCATAGTTCATA
66 GAGAACACATTTCAAGTAACCATAGTTCATA
* * * * *
54898 AACCGGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTACAGTGAAAACAGGTAACTA
1 AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
* *
54963 GAGAACATATTTCAAGTAACCATAGTTCGTA
66 GAGAACACATTTCAAGTAACCATAGTTCATA
*
54994 GACCAGTA
1 AACCAGTA
55002 AATCAGTGAT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCAATAAATCAGGAACGATCATATTTTACAGTAAAAACAGGTAACCA
GAGAACACATTTCAAGTAACCATAGTTCATA
Found at i:62351 original size:21 final size:23
Alignment explanation
Indices: 62299--62351 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
62289 AAAAAATAAT
* *
62299 ATATAATATTAATTATATTGATA
1 ATATAATATTAATTAAATTGAAA
62322 AT-TATATATT-A-TAAATTGAAA
1 ATATA-ATATTAATTAAATTGAAA
62343 ATATAATAT
1 ATATAATAT
62352 CATATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
23 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATAATATTAATTAAATTGAAA
Found at i:62430 original size:50 final size:51
Alignment explanation
Indices: 62371--62483 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 51
62361 TAATATATTG
* *
62371 ATTACATATTAATATAATATTAA-AAATAA-AATATTATTAAAATTATATTAT
1 ATTA-ATATTAATAT-ATATTAATAAATAATAATATTATTAAAATGATATTAA
* * * *
62422 ATGT-ATATTAA-ATATTTTAATAATTAATATTTTTATTAAAATGATATTAA
1 AT-TAATATTAATATATATTAATAAATAATAATATTATTAAAATGATATTAA
62472 ATTAATATTAAT
1 ATTAATATTAAT
62484 TAAATAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
48 6 0.12
49 8 0.16
50 34 0.67
51 2 0.04
52 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (51 bp):
ATTAATATTAATATATATTAATAAATAATAATATTATTAAAATGATATTAA
Found at i:66937 original size:20 final size:21
Alignment explanation
Indices: 66912--66950 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66902 GGCTGCTGGA
66912 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
66932 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
66951 GATCGATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:66948 original size:10 final size:9
Alignment explanation
Indices: 66913--67011 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
66903 GCTGCTGGAA
*
66913 ACCGGTTTA
1 ACCGGTTTG
*
66922 ACCGGTTTTCA
1 ACCGG-TTT-G
66933 ACCGGTTCTG
1 ACCGGTT-TG
66943 ACCGGTTTG
1 ACCGGTTTG
* * *
66952 ATCGATTTCA
1 ACCGGTTT-G
*
66962 ACCGGTTCG
1 ACCGGTTTG
66971 AACCGGTTTG
1 -ACCGGTTTG
*
66981 ACCGGTCTG
1 ACCGGTTTG
66990 AGCCGGTTTG
1 A-CCGGTTTG
*
67000 ACCGGTCTG
1 ACCGGTTTG
67009 ACC
1 ACC
67012 TGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:66984 original size:19 final size:19
Alignment explanation
Indices: 66912--67005 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 19
66902 GGCTGCTGGA
*
66912 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
66932 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
* * *
66952 -ATCGATTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
66971 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
66990 AGCCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
67006 CTGACCTGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.05
19 35 0.60
20 14 0.24
21 6 0.10
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:67006 original size:19 final size:19
Alignment explanation
Indices: 66973--67009 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
66963 CCGGTTCGAA
66973 CCGGTTTGACCGGTCTGAG
1 CCGGTTTGACCGGTCTGAG
66992 CCGGTTTGACCGGTCTGA
1 CCGGTTTGACCGGTCTGA
67010 CCTGACCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.35, T:0.27
Consensus pattern (19 bp):
CCGGTTTGACCGGTCTGAG
Found at i:67010 original size:9 final size:9
Alignment explanation
Indices: 66972--67011 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
66962 ACCGGTTCGA
*
66972 ACCGGTTTG
1 ACCGGTCTG
66981 ACCGGTCTG
1 ACCGGTCTG
*
66990 AGCCGGTTTG
1 A-CCGGTCTG
67000 ACCGGTCTG
1 ACCGGTCTG
67009 ACC
1 ACC
67012 TGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:67033 original size:17 final size:17
Alignment explanation
Indices: 67007--67045 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
66997 TTGACCGGTC
*
67007 TGACCTGACCCGACCGT
1 TGACCCGACCCGACCGT
67024 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
67041 TGACC
1 TGACC
67046 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:74164 original size:20 final size:20
Alignment explanation
Indices: 74139--74223 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
74129 GGCTGCTGGA
74139 AACCGGTT-TAACCGGTTTT
1 AACCGGTTCTAACCGGTTTT
*
74158 CAACCGGTTCTGACCGGTTTT
1 -AACCGGTTCTAACCGGTTTT
*
74179 AACCGGTTCGAACCGG-TTT
1 AACCGGTTCTAACCGGTTTT
* *
74198 GACCGG-TCTGAGCCGG-TTT
1 AACCGGTTCT-AACCGGTTTT
74217 AACCGGT
1 AACCGGT
74224 CTGACCCGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
18 2 0.04
19 21 0.38
20 22 0.40
21 10 0.18
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTT
Found at i:74175 original size:10 final size:10
Alignment explanation
Indices: 74160--74229 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
74150 CCGGTTTTCA
74160 ACCGGTTCTG
1 ACCGGTTCTG
* *
74170 ACCGGTTTTA
1 ACCGGTTCTG
74180 ACCGGTTC-G
1 ACCGGTTCTG
74189 AACCGGTT-TG
1 -ACCGGTTCTG
74199 ACCGG-TCTG
1 ACCGGTTCTG
*
74208 AGCCGGTT-TA
1 A-CCGGTTCTG
74218 ACCGG-TCTG
1 ACCGGTTCTG
74227 ACC
1 ACC
74230 CGACCCGACC
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.04
9 16 0.33
10 29 0.60
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:74204 original size:19 final size:20
Alignment explanation
Indices: 74139--74227 Score: 91
Period size: 19 Copynumber: 4.6 Consensus size: 20
74129 GGCTGCTGGA
74139 AACCGGTT-T-AACCGGTTTT
1 AACCGGTTCTGAACCGG-TTT
74158 CAACCGGTTCTG-ACCGGTTTT
1 -AACCGGTTCTGAACCGG-TTT
74179 AACCGGTTC-GAACCGGTTT
1 AACCGGTTCTGAACCGGTTT
* *
74198 GACCGG-TCTGAGCCGGTTT
1 AACCGGTTCTGAACCGGTTT
74217 AACCGG-TCTGA
1 AACCGGTTCTGA
74228 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.03
19 28 0.45
20 22 0.35
21 10 0.16
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTCTGAACCGGTTT
Found at i:74251 original size:18 final size:18
Alignment explanation
Indices: 74228--74264 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
74218 ACCGGTCTGA
74228 CCCGACCCGACCGTTGAC
1 CCCGACCCGACCGTTGAC
74246 CCCGACCCGACCGTTGAC
1 CCCGACCCGACCGTTGAC
74264 C
1 C
74265 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCCGACCCGACCGTTGAC
Found at i:76185 original size:22 final size:23
Alignment explanation
Indices: 76133--76184 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
76123 CATAAACACA
*
76133 AAAAAAATTAATTTTGTCATGAC
1 AAAAAAATTAATTTTGCCATGAC
76156 AAAAAAATTAATTTTGCCATGAC
1 AAAAAAATTAATTTTGCCATGAC
76179 AAAAAA
1 AAAAAA
76185 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAAAAATTAATTTTGCCATGAC
Found at i:77983 original size:16 final size:16
Alignment explanation
Indices: 77938--78016 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 16
77928 TTCACGGAAT
77938 ATAAGATTACCAGTGAGA
1 ATAAGATTACCAG-G-GA
77956 ATGTAAGATTACCAGGGA
1 A--TAAGATTACCAGGGA
* *
77974 ATAGGATTA-CTGGGA
1 ATAAGATTACCAGGGA
77989 ATGTAAGATTACCAGGGA
1 A--TAAGATTACCAGGGA
*
78007 ATATGATTAC
1 ATAAGATTAC
78017 TGAGAATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 6 0.12
16 15 0.29
17 7 0.14
18 10 0.20
19 1 0.02
20 12 0.24
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (16 bp):
ATAAGATTACCAGGGA
Found at i:77992 original size:33 final size:33
Alignment explanation
Indices: 77951--78025 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
77941 AGATTACCAG
77951 TGAGAATGTAAGATTACCAGGGAATAGGATTAC
1 TGAGAATGTAAGATTACCAGGGAATAGGATTAC
* *
77984 TGGGAATGTAAGATTACCAGGGAATATGATTAC
1 TGAGAATGTAAGATTACCAGGGAATAGGATTAC
78017 TGAGAATGT
1 TGAGAATGT
78026 TGTATATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.27
Consensus pattern (33 bp):
TGAGAATGTAAGATTACCAGGGAATAGGATTAC
Found at i:78000 original size:17 final size:17
Alignment explanation
Indices: 77933--78008 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 17
77923 TTTGGTTCAC
*
77933 GGAATATAAGATTACCAG
1 GGAATGTAAGATTA-CAG
77951 TGAGAATGTAAGATTACCAG
1 -G-GAATGTAAGATTA-CAG
* *
77971 GGAA--TAGGATTACTG
1 GGAATGTAAGATTACAG
77986 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTA-CAG
78004 GGAAT
1 GGAAT
78009 ATGATTACTG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.12
16 7 0.15
17 7 0.15
18 10 0.21
19 2 0.04
20 16 0.33
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (17 bp):
GGAATGTAAGATTACAG
Found at i:81759 original size:13 final size:13
Alignment explanation
Indices: 81741--81768 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
81731 GGAATCTTCA
81741 TCAATTTTCAGAT
1 TCAATTTTCAGAT
81754 TCAATTTTCAGAT
1 TCAATTTTCAGAT
81767 TC
1 TC
81769 TGAAGATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (13 bp):
TCAATTTTCAGAT
Found at i:81922 original size:11 final size:11
Alignment explanation
Indices: 81906--81954 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
81896 CTGTTAAGAG
81906 TGTTATTAGTT
1 TGTTATTAGTT
*
81917 TGTTA-TGGTT
1 TGTTATTAGTT
* **
81927 TATTATTAACT
1 TGTTATTAGTT
81938 TGTTATTAGTT
1 TGTTATTAGTT
81949 TGTTAT
1 TGTTAT
81955 GTTGGTTACT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:83856 original size:11 final size:11
Alignment explanation
Indices: 83840--83888 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
83830 ATATTAAGAG
83840 TGTTATTAGTT
1 TGTTATTAGTT
*
83851 TGTTA-TGGTT
1 TGTTATTAGTT
*
83861 TGTTATTAGCT
1 TGTTATTAGTT
*
83872 TGTTATTAATT
1 TGTTATTAGTT
83883 TGTTAT
1 TGTTAT
83889 GTTGGTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:90571 original size:15 final size:15
Alignment explanation
Indices: 90547--90580 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
90537 CTAGATAAGT
*
90547 TTCTCTTTGCTTAGA
1 TTCTCATTGCTTAGA
90562 TTCTCATTGCTTAGA
1 TTCTCATTGCTTAGA
90577 TTCT
1 TTCT
90581 TCAACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.53
Consensus pattern (15 bp):
TTCTCATTGCTTAGA
Found at i:92086 original size:18 final size:18
Alignment explanation
Indices: 92063--92097 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
92053 TGACCGGTCA
92063 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
92081 CGACCCGACCCGTTGAC
1 CGACCCGACCCGTTGAC
92098 TGGTGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:99248 original size:18 final size:18
Alignment explanation
Indices: 99225--99277 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
99215 TGACCGGTCA
99225 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
99243 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
99261 CGACCCGACCCGTTGAC
1 CGACCCGACCCGTTGAC
99278 TGGTTCTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:106091 original size:36 final size:37
Alignment explanation
Indices: 106046--106115 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
106036 TTTCATTCAA
* *
106046 TAAATCTAGTTCACTAATTAAACTAGCTCATTTATTT
1 TAAATCTAGTTCACTAAGTAAACTAGATCATTTATTT
*
106083 TAAA-CTAGTTCATTAAGTAAACTAGATCATTTA
1 TAAATCTAGTTCACTAAGTAAACTAGATCATTTA
106116 AAGCTTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (37 bp):
TAAATCTAGTTCACTAAGTAAACTAGATCATTTATTT
Found at i:106105 original size:17 final size:17
Alignment explanation
Indices: 106037--106113 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
106027 AAGTATGTTT
106037 TTCATTCAA-TAAATCTAG
1 TTCATT-AATTAAA-CTAG
*
106055 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* *
106072 CTCATTTATTTTAAACTAG
1 TTCA-TTA-ATTAAACTAG
*
106091 TTCATTAAGTAAACTAG
1 TTCATTAATTAAACTAG
*
106108 ATCATT
1 TTCATT
106114 TAAAGCTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
17 22 0.46
18 14 0.29
19 12 0.25
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:114594 original size:3 final size:3
Alignment explanation
Indices: 114582--114635 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
114572 AATATTCTAG
114582 ATA A-A 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
114629 ATA ATA A
1 ATA ATA A
114636 ACATGGACTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:115261 original size:40 final size:40
Alignment explanation
Indices: 115176--115271 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
115166 TCTCAAGATT
* * *
115176 CAAACCACAATATTAACTCTAGAACAATAAAATCCATAAG
1 CAAACCATAATATTAACTCTAAAACAATAAAATCCATAAA
* *
115216 GAAACCATAATATTAAGTCTAAAACAATAAAATCCATAAA
1 CAAACCATAATATTAACTCTAAAACAATAAAATCCATAAA
*
115256 CAAACCATAATTTTAA
1 CAAACCATAATATTAA
115272 AGTTTCAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.23
Consensus pattern (40 bp):
CAAACCATAATATTAACTCTAAAACAATAAAATCCATAAA
Found at i:119063 original size:6 final size:6
Alignment explanation
Indices: 119052--119655 Score: 1104
Period size: 6 Copynumber: 102.2 Consensus size: 6
119042 AACCCACGAG
*
119052 TACATA TACATA TGCATA TAC--A TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119098 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119146 TACATA TACATA TACATA TACATA TACATA TAC--A TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119192 TACATA -ACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119239 TACATA TACATA TACATACA TACATA TACATA TACATA TACATA TAC--A
1 TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA TACATA
119287 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119335 TACATA TACATA TACATA TACATA TAC--A TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119381 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119429 TACATA TAC--A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119475 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119523 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119571 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
119619 TACATA TACATA TACATA TACATA TACATA TACATA T
1 TACATA TACATA TACATA TACATA TACATA TACATA T
119656 TCATGGAAAA
Statistics
Matches: 583, Mismatches: 2, Indels: 26
0.95 0.00 0.04
Matches are distributed among these distances:
4 20 0.03
5 5 0.01
6 552 0.95
8 6 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:119961 original size:2 final size:2
Alignment explanation
Indices: 119954--120019 Score: 100
Period size: 2 Copynumber: 33.0 Consensus size: 2
119944 ATGACCCATA
119954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119995 CAT AT AT AT AT AT -T CAT AT AT AT AT
1 -AT AT AT AT AT AT AT -AT AT AT AT AT
120020 TAGTGTAAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.03
2 56 0.93
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123544 original size:30 final size:30
Alignment explanation
Indices: 123508--123588 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
123498 CGAAATACAC
*
123508 AATAACATAAAATACACTACCA-ACAATTAA
1 AATAACATAAAATACAATACCATA-AATTAA
123538 AATAACATAAAATACAATACCATAAATTAA
1 AATAACATAAAATACAATACCATAAATTAA
123568 AATAACATAAAATACAATACC
1 AATAACATAAAATACAATACC
123589 GAAAAATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (30 bp):
AATAACATAAAATACAATACCATAAATTAA
Found at i:123561 original size:15 final size:15
Alignment explanation
Indices: 123506--123618 Score: 86
Period size: 15 Copynumber: 7.5 Consensus size: 15
123496 CCCGAAATAC
*
123506 ACAATAACATAAAAT
1 ACAATACCATAAAAT
* *
123521 ACACTACCA-ACAATT
1 ACAATACCATA-AAAT
* *
123536 AAAATAACATAAAAT
1 ACAATACCATAAAAT
*
123551 ACAATACCATAAATT
1 ACAATACCATAAAAT
* *
123566 AAAATAACATAAAAT
1 ACAATACCATAAAAT
123581 ACAATACCGA-AAAAT
1 ACAATACC-ATAAAAT
* * *
123596 ATAATACGAGAAAAAT
1 ACAATACCA-TAAAAT
123612 ACAATAC
1 ACAATAC
123619 AAGAAAATAA
Statistics
Matches: 75, Mismatches: 18, Indels: 9
0.74 0.18 0.09
Matches are distributed among these distances:
14 2 0.03
15 60 0.80
16 13 0.17
ACGTcount: A:0.62, C:0.16, G:0.03, T:0.19
Consensus pattern (15 bp):
ACAATACCATAAAAT
Found at i:123627 original size:15 final size:15
Alignment explanation
Indices: 123576--123625 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
123566 AAAATAACAT
*
123576 AAAATACAATACCGA
1 AAAATACAATACAGA
*
123591 AAAATATAATACGAGA
1 AAAATACAATAC-AGA
123607 AAAATACAATACAAGA
1 AAAATACAATAC-AGA
123623 AAA
1 AAA
123626 TAAATTACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.66, C:0.12, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAATACAATACAGA
Found at i:126548 original size:102 final size:102
Alignment explanation
Indices: 126399--126633 Score: 242
Period size: 102 Copynumber: 2.3 Consensus size: 102
126389 TTCTAATCCA
* * * ** * * *
126399 TTGAACTTGAAGGCATATTGCCATATATG-TTCTGAACAGATTGTTGTGTTGATGGAATTTCGAT
1 TTGAACTTGACGGCATATTGCCATAT-GGATTCTAAATGGACTATTGTGTCGATGGAATTTCGAT
* *
126463 GTTCAAATCAAACAAGTT-GATAGATGAATGCC-TTCCTC
65 GTTCAAATCAAACAAGTTGGA-AAATGAACGCCTTTCC-C
* * *
126501 TTGAACTTGACGTCATATTTCCATATGGATTCTAAATGGACTATTGTGTCGATGGCATTTCGATG
1 TTGAACTTGACGGCATATTGCCATATGGATTCTAAATGGACTATTGTGTCGATGGAATTTCGATG
* ** **
126566 TTGAGGTTGAACAAGTTGGAAAATGAACGCCTTTCCC
66 TTCAAATCAAACAAGTTGGAAAATGAACGCCTTTCCC
* *
126603 TTGAACTTGACGGGATGTTGCCATATGGATT
1 TTGAACTTGACGGCATATTGCCATATGGATT
126634 ATTCGTTGAT
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
101 1 0.01
102 101 0.94
103 6 0.06
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (102 bp):
TTGAACTTGACGGCATATTGCCATATGGATTCTAAATGGACTATTGTGTCGATGGAATTTCGATG
TTCAAATCAAACAAGTTGGAAAATGAACGCCTTTCCC
Found at i:131333 original size:32 final size:32
Alignment explanation
Indices: 131275--131339 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
131265 TAAGGTGACC
* * * *
131275 CTTGGGTAGGCTTTTAGGCCCCAAGGTATTCT
1 CTTGGGTAGGCTATAAGGACCCAAGGTACTCT
*
131307 CTTGGGTAGGCTATAAGGACCTAAGGTACTCT
1 CTTGGGTAGGCTATAAGGACCCAAGGTACTCT
131339 C
1 C
131340 CTAGGTTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (32 bp):
CTTGGGTAGGCTATAAGGACCCAAGGTACTCT
Found at i:132837 original size:2 final size:2
Alignment explanation
Indices: 132830--132863 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
132820 AATTACGAGT
132830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132864 AATTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132966 original size:2 final size:2
Alignment explanation
Indices: 132959--133009 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
132949 GATCCTAATC
132959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133001 AT AT AT AT A
1 AT AT AT AT A
133010 ATGTGGAAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:133568 original size:58 final size:58
Alignment explanation
Indices: 133445--133566 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
133435 GTCGGATGAT
* * *
133445 CATTTTATAACTTTTAATAGTTAGGGGACTCAACAAAGTAGTACCTTGTAATAATGGA
1 CATTTTATAACTTTTAATAGTTAGGGGACTCAACAAAGTAATACCTTATAATAAGGGA
*
133503 CATTTTATAACTTTTAATAGTT-GTGGACTCAACAGAA-TAATATCC-TATAATTAAGGGA
1 CATTTTATAACTTTTAATAGTTAGGGGACTCAACA-AAGTAATA-CCTTATAA-TAAGGGA
133561 CCATTT
1 -CATTT
133567 ATGCACTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
57 19 0.34
58 32 0.57
59 5 0.09
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (58 bp):
CATTTTATAACTTTTAATAGTTAGGGGACTCAACAAAGTAATACCTTATAATAAGGGA
Found at i:134094 original size:31 final size:31
Alignment explanation
Indices: 134059--134118 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
134049 ACAAAGATAG
134059 GTTAGTTAGATTATAATGAGAAAGAAAAGAT
1 GTTAGTTAGATTATAATGAGAAAGAAAAGAT
134090 GTTAGTTAGATTATAATGAGAAAGAAAAG
1 GTTAGTTAGATTATAATGAGAAAGAAAAG
134119 CATAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.28
Consensus pattern (31 bp):
GTTAGTTAGATTATAATGAGAAAGAAAAGAT
Found at i:134200 original size:18 final size:18
Alignment explanation
Indices: 134177--134213 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
134167 TTATATGCAT
134177 CACATTTCTAGATTTCTC
1 CACATTTCTAGATTTCTC
134195 CACATTTCTAGATTTCTC
1 CACATTTCTAGATTTCTC
134213 C
1 C
134214 TACACAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.30, G:0.05, T:0.43
Consensus pattern (18 bp):
CACATTTCTAGATTTCTC
Found at i:134849 original size:17 final size:17
Alignment explanation
Indices: 134827--134860 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
134817 TTAATTATTA
134827 TTATTTCTATTATTTTT
1 TTATTTCTATTATTTTT
*
134844 TTATTTTTATTATTTTT
1 TTATTTCTATTATTTTT
134861 GTTTCCGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTCTATTATTTTT
Found at i:134860 original size:9 final size:9
Alignment explanation
Indices: 134824--134860 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
134814 TATTTAATTA
134824 TTATTATTT
1 TTATTATTT
*
134833 CTATTATTT
1 TTATTATTT
134842 TT-TTATTT
1 TTATTATTT
134850 TTATTATTT
1 TTATTATTT
134859 TT
1 TT
134861 GTTTCCGCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTATTT
Found at i:137620 original size:12 final size:12
Alignment explanation
Indices: 137603--137627 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
137593 TTCGATAGCT
137603 TGGGGACTTTGC
1 TGGGGACTTTGC
137615 TGGGGACTTTGC
1 TGGGGACTTTGC
137627 T
1 T
137628 TTTAGAGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.40, T:0.36
Consensus pattern (12 bp):
TGGGGACTTTGC
Found at i:145386 original size:231 final size:231
Alignment explanation
Indices: 144983--145727 Score: 925
Period size: 231 Copynumber: 3.2 Consensus size: 231
144973 TTTATATGTT
*
144983 AAAAATGAGATAGGTTTCTCATTT-AATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTG-AAAGTAAGAAAAGTTTC
* * *
145047 TTACATAATAAACTATTTCCAAAGTTGGTAAGTCCT-TCAGGCCATCAATAAGTCTATCAAGCAT
65 TTAC-TAATAAACTATTTCCAAAATTGGTAAGT-CTATCGGGCCATCAATAAGTCTTTCAAGCAT
* *
145111 GATGCTAAAATTCC-TCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCAT
128 GATGCTTAAA-TCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTTGGGCCAT
145175 CCATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTC-
192 CCATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCA
* * * *
145214 AAAAATGAGAAAGGTTTCTCATTTAAATTTGAAATTTGAAATGTTTGATAAGTAAGAAAAGTTTA
1 AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGA-AAGTAAGAAAAGTTTC
* * * * *
145279 TTACCAGTAAACTATTTCCAAATTTGGTAAGTCTATCGGGCCATCAGTAAGTCTTTCAACCATGA
65 TTACTAATAAACTATTTCCAAAATTGGTAAGTCTATCGGGCCATCAATAAGTCTTTCAAGCATGA
*
145344 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTTGGGCCATCCA
* * *
145409 TAAGACCTTCGAGCAGGATGTTTTCACATGTTTTTCG
195 TAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCA
* * *
145446 AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTG-ATTTTTTTAAAGTAATAAAAGTTTCT
1 AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAGTAAGAAAAGTTTCT
** * * * * *
145510 TAACTAATAAACTATTTCCAAAATTAATAAATC-ATTCGGGCCATTATTAAATCTTTCGAGCATG
66 T-ACTAATAAACTATTTCCAAAATTGGTAAGTCTA-TCGGGCCATCAATAAGTCTTTCAAGCATG
*** * * *
145574 ATAAATAAATCCCTT-GGGTCATCTATAAGCCTTCTGAGCAAGATGATAAGTCCTTCT--GCCAT
129 ATGCTTAAAT-CCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTT-TGGGCCAT
* * ** *
145636 CCATAAGACCTT-TGGCTATGACATTTTCACATATTTTTACA
192 CCATAAGACCTTCGGGC-AAGATGTTTTCACATGTTTTT-CA
* * *
145677 AAAAATGAGAAAAGTTTCTCATTTAAATATGAAATTTCAAAATTTTTGAAA
1 AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATT-GAAATTTTTGAAA
145728 AAAAAATGAG
Statistics
Matches: 447, Mismatches: 54, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
229 2 0.00
230 56 0.13
231 302 0.68
232 78 0.17
233 9 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (231 bp):
AAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAGTAAGAAAAGTTTCT
TACTAATAAACTATTTCCAAAATTGGTAAGTCTATCGGGCCATCAATAAGTCTTTCAAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTTGGGCCATCCAT
AAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCA
Found at i:146155 original size:134 final size:134
Alignment explanation
Indices: 145905--146362 Score: 485
Period size: 134 Copynumber: 3.4 Consensus size: 134
145895 GCAAATCAAA
*
145905 CTCGATTCAATCTTCCCTAAGAAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGAAACAGTAGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * * ** * *
145970 AGAATAAGCGAAATGGATCTCCCTTTTTCAAGATTTGATATGCCCTGAGTAATAGTGGAACAAGT
66 AGAAGAAGCGAAATAGATCACTCTCTTTCAAAATTTGATATTTCCTTAGTAACAGTGGAACAAGT
146035 CTGC
131 CTGC
* * *
146039 CTCGATTCAATATTCCCTGATG-AACAATAGAATGAATCAACATTTCCAGATCTGATTTTCCCTC
1 CTCGATTCAATCTTCCCT-AAGAAACAGTAGAATGAATCAACATTTCCAGATCTGATTTTCCCTC
* * * * *
146103 AAGAAGAAGTGTAATAGATCACTCTCTTTCAAAATTTGTTATTTCCTTAGTAACAATGGAACAAA
65 AAGAAGAAGCGAAATAGATCACTCTCTTTCAAAATTTGATATTTCCTTAGTAACAGTGGAACAAG
*
146168 TCGGC
130 TCTGC
* * * * * * * * *
146173 CTCTATTTAATCTTTCCTAAGTAGCAGTGGAATGAGTCAAC-GTCCCTAGATCTGATTTTCCCTC
1 CTCGATTCAATCTTCCCTAAGAAACAGTAGAATGAATCAACATTTCC-AGATCTGATTTTCCCTC
* * * * * *
146237 GAGAAGAAGCGAAACATATCCCTTTCTTTCAATATTTGATA-TTCCTTGAGTAACAGTGGAACAA
65 AAGAAGAAGCGAAATAGATCACTCTCTTTCAAAATTTGATATTTCCTT-AGTAACAGTGGAACAA
*
146301 GTCTAC
129 GTCTGC
* * *
146307 CCCGATTCAATCTTCCCTAA-AGAACAGCAGAATAAATCAACATTTCTC-GATCTGAT
1 CTCGATTCAATCTTCCCTAAGA-AACAGTAGAATGAATCAACATTTC-CAGATCTGAT
146363 CTACCCTGAA
Statistics
Matches: 261, Mismatches: 56, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
133 11 0.04
134 245 0.94
135 4 0.02
136 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAGAAACAGTAGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
AGAAGAAGCGAAATAGATCACTCTCTTTCAAAATTTGATATTTCCTTAGTAACAGTGGAACAAGT
CTGC
Found at i:146530 original size:3 final size:3
Alignment explanation
Indices: 146522--146583 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
146512 CCATAGATCT
* * *
146522 TTA TTA TTA TTA ATA TTAA TTA TTA TTA TTA TTA TT- TAA TAA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
146567 TT- TTT TCTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TT
146584 TTTCTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.84
4 5 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:146545 original size:16 final size:16
Alignment explanation
Indices: 146524--146555 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
146514 ATAGATCTTT
146524 ATTATTATTAATATTA
1 ATTATTATTAATATTA
*
146540 ATTATTATTATTATTA
1 ATTATTATTAATATTA
146556 TTTAATAATT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATTAATATTA
Found at i:146577 original size:26 final size:26
Alignment explanation
Indices: 146522--146584 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
146512 CCATAGATCT
146522 TTATTATTA-TTAATATTAATTATTA
1 TTATTATTATTTAATATTAATTATTA
*
146547 TTATTATTATTTAATAATT-ATT-TTT
1 TTATTATTATTTAAT-ATTAATTATTA
146572 TCTATTATTATTT
1 T-TATTATTATTT
146585 TTCTATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.35
26 19 0.56
27 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTATTATTTAATATTAATTATTA
Found at i:146585 original size:14 final size:14
Alignment explanation
Indices: 146545--146601 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
146535 TATTAATTAT
146545 TATTATTATTATTT-
1 TATTATTATT-TTTC
* *
146559 AATAATTATTTTTTC
1 TATTATTA-TTTTTC
146574 TATTATTATTTTTC
1 TATTATTATTTTTC
*
146588 TATTTTCTATTTTT
1 TATTAT-TATTTTT
146602 ATTATTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 20 0.57
15 15 0.43
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTATTTTTC
Found at i:155680 original size:14 final size:14
Alignment explanation
Indices: 155661--155693 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
155651 TTGTATGTTT
155661 AAGATTAGTAAATG
1 AAGATTAGTAAATG
155675 AAGATTAGTAAATG
1 AAGATTAGTAAATG
155689 AAGAT
1 AAGAT
155694 AAGTTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (14 bp):
AAGATTAGTAAATG
Found at i:156603 original size:23 final size:22
Alignment explanation
Indices: 156573--156638 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
156563 GTCGAGGGTT
156573 CTATGTGGCACTTCGGTGCAAA
1 CTATGTGGCACTTCGGTGCAAA
*
156595 CCTATGTGGCACTTTGG-G-ACAA
1 -CTATGTGGCACTTCGGTGCA-AA
* *
156617 TTATGTGGTACTTCGGTGCAAA
1 CTATGTGGCACTTCGGTGCAAA
156639 TTACGAGCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 14 0.39
22 6 0.17
23 16 0.44
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (22 bp):
CTATGTGGCACTTCGGTGCAAA
Found at i:164429 original size:16 final size:16
Alignment explanation
Indices: 164408--164443 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
164398 GAAGTAATAC
164408 TGAAATTGAGGGAAAA
1 TGAAATTGAGGGAAAA
164424 TGAAATTGAGGGAAAA
1 TGAAATTGAGGGAAAA
164440 TGAA
1 TGAA
164444 TGTTAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (16 bp):
TGAAATTGAGGGAAAA
Found at i:180504 original size:21 final size:20
Alignment explanation
Indices: 180479--180517 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
180469 GGAATAAAAA
180479 TATAA-TAATATTGTAAATATT
1 TATAATTAA-ATT-TAAATATT
180500 TATAATTAAATTTAAATA
1 TATAATTAAATTTAAATA
180518 GGAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 8 0.47
22 3 0.18
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAATTAAATTTAAATATT
Found at i:182732 original size:16 final size:18
Alignment explanation
Indices: 182711--182746 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
182701 ATTTATAAAA
182711 TTATTTAAAT-TAA-TAT
1 TTATTTAAATATAATTAT
182727 TTATTTAAATATAATTAT
1 TTATTTAAATATAATTAT
182745 TT
1 TT
182747 GATTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTTAAATATAATTAT
Found at i:182767 original size:38 final size:38
Alignment explanation
Indices: 182710--182785 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
182700 CATTTATAAA
* * *
182710 ATTATTTAAATTAATATTTATTTAAA-TATAATTATTTG
1 ATTATTTAAATTAAAATTTAATAAAATTATAA-TATTTG
**
182748 ATTATTTATTTTAAAATTTAATAAAATTATAATATTTG
1 ATTATTTAAATTAAAATTTAATAAAATTATAATATTTG
182786 TAATTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 27 0.84
39 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (38 bp):
ATTATTTAAATTAAAATTTAATAAAATTATAATATTTG
Found at i:186117 original size:28 final size:27
Alignment explanation
Indices: 186082--186135 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
186072 TTCAATTTTA
*
186082 TGAAAAATA-CAAATTTAAGAATTAAAT
1 TGAAAAATATCAAA-TTAAAAATTAAAT
*
186109 TGAACAAATATGAAATTAAAAATTAAA
1 TGAA-AAATATCAAATTAAAAATTAAA
186136 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 16 0.70
29 3 0.13
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (27 bp):
TGAAAAATATCAAATTAAAAATTAAAT
Found at i:186470 original size:209 final size:209
Alignment explanation
Indices: 186104--186567 Score: 732
Period size: 209 Copynumber: 2.2 Consensus size: 209
186094 ATTTAAGAAT
* *
186104 TAAATTGAACAAATATGAAATTAAAAATTAAAATTTAAATAAATTAAACAACACACAATGGTGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAC------GAG
* *
186169 GGATCAAATTGAAATAATTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
60 GGATCAAATCGAAATAATTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
* * * *
186234 CATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGAT
125 CATTTAAAAAGTTATAGGCCAATTAAAAAATAGAAATAAGTAATAACTATAGGTCAATTTCAGAT
*
186299 GCAAATATAATTTGGAGGAC
190 GCAAATAAAATTTGGAGGAC
* * *
186319 TAAATTGAACAAATATGAAACTACAAATAAAAATTTAAATAAATTAAATAACACAC-AGGGTTCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACGAGGGATCA
186383 AATCGAAATAATTTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
66 AATCGAAATAA-TTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
* *
186448 AAAAAGTTATAGGCCAATTAAAAAATAGAAATAAGTAATAACTATAGGTTAATTTTAGATGCAAA
130 AAAAAGTTATAGGCCAATTAAAAAATAGAAATAAGTAATAACTATAGGTCAATTTCAGATGCAAA
186513 TAAAATTTGGAGGAC
195 TAAAATTTGGAGGAC
186528 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAAT
186568 TTAAATAAAT
Statistics
Matches: 233, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
208 17 0.07
209 164 0.70
215 52 0.22
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (209 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACGAGGGATCA
AATCGAAATAATTTAAATTGTAAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTTA
AAAAGTTATAGGCCAATTAAAAAATAGAAATAAGTAATAACTATAGGTCAATTTCAGATGCAAAT
AAAATTTGGAGGAC
Found at i:186679 original size:2 final size:2
Alignment explanation
Indices: 186672--186835 Score: 85
Period size: 2 Copynumber: 82.5 Consensus size: 2
186662 AACAACAATA
* *
186672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AA AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
186712 ACT AC AT AGT TT AT AT AT AA AGT AT AT GT AT -T AT AT AT AT A-
1 A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
186753 AGT -T AT AT AGT TT AA AT TT AT AT -T AT -T AT AT ACT AT AT AT
1 A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
186793 AA ACT AT AT AT AT -T AT AT AT AT AT -T AT GT AT AA ACT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
186835 A
1 A
186836 CCATGTATAA
Statistics
Matches: 122, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
1 9 0.07
2 105 0.86
3 8 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:186793 original size:9 final size:9
Alignment explanation
Indices: 186779--186861 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
186769 TTTATATTAT
186779 TATATACTA
1 TATATACTA
186788 TATATAAACTA
1 TATAT--ACTA
186799 TATATA-T-
1 TATATACTA
186806 TATATA-TA
1 TATATACTA
*
186814 TAT-TA-TG
1 TATATACTA
*
186821 TATAAACTA
1 TATATACTA
*
186830 TATATACCATG
1 TATATA-C-TA
*
186841 TATAAACTA
1 TATATACTA
186850 TA-ATACTA
1 TATATACTA
186858 TATA
1 TATA
186862 GTTTATATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
7 13 0.22
8 12 0.21
9 16 0.28
10 2 0.03
11 15 0.26
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:186798 original size:11 final size:11
Alignment explanation
Indices: 186779--186835 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
186769 TTTATATTAT
*
186779 TATATACTATA
1 TATAAACTATA
186790 TATAAACTATA
1 TATAAACTATA
*
186801 TAT--ATTATA
1 TATAAACTATA
* * *
186810 TATATATTATG
1 TATAAACTATA
186821 TATAAACTATA
1 TATAAACTATA
186832 TATA
1 TATA
186836 CCATGTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 8 0.21
11 30 0.79
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (11 bp):
TATAAACTATA
Found at i:186841 original size:20 final size:20
Alignment explanation
Indices: 186808--186855 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
186798 ATATATATTA
**
186808 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
186828 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
186848 TATA-ATAC
1 TATATATAC
186856 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:186937 original size:31 final size:31
Alignment explanation
Indices: 186879--186937 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
186869 TATGAACTAT
* *
186879 TGAACTATATAGAAACTACATAGTTTATATA
1 TGAACTATATAGAAACTACACAATTTATATA
* * *
186910 TGAATTATATATAAACTATACAATTTAT
1 TGAACTATATAGAAACTACACAATTTAT
186938 GTTTATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (31 bp):
TGAACTATATAGAAACTACACAATTTATATA
Found at i:187008 original size:22 final size:22
Alignment explanation
Indices: 186976--187023 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
186966 ATATATATTG
* *
186976 TATAAATTATATAGTTTATTA-A
1 TATAAACTATATACTTT-TTATA
186998 TATAAACTATATACTTTTTATA
1 TATAAACTATATACTTTTTATA
187020 TATA
1 TATA
187024 GTATATATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAAACTATATACTTTTTATA
Found at i:187394 original size:2 final size:2
Alignment explanation
Indices: 187389--187489 Score: 170
Period size: 2 Copynumber: 51.0 Consensus size: 2
187379 TTATATAGTT
187389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
187431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
187473 -A TA GTT TA TA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA
187490 CATGGTTTAC
Statistics
Matches: 94, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
1 2 0.02
2 91 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:187913 original size:2 final size:2
Alignment explanation
Indices: 187906--187937 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
187896 TAAAAATAAT
187906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
187938 ATAAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:187964 original size:33 final size:32
Alignment explanation
Indices: 187927--187998 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
187917 ATATATATAT
187927 ATATATATATAATAAATTTA-AT-TTAAATTAAAA
1 ATATATATATAAT--ATTTATATATTAAATT-AAA
*
187960 ATATATATATAATATTTATATATTTAATTAAA
1 ATATATATATAATATTTATATATTAAATTAAA
187992 ATATATA
1 ATATATA
187999 GATACCCGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 5 0.14
32 12 0.33
33 19 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATATATATAATATTTATATATTAAATTAAA
Found at i:188324 original size:7 final size:7
Alignment explanation
Indices: 188303--188367 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
188293 TCTATTTACA
*
188303 TTAGGAT
1 TTAGGGT
*
188310 TTATGGT
1 TTAGGGT
188317 TTAGGGT
1 TTAGGGT
**
188324 TTAATGT
1 TTAGGGT
*
188331 TTAGTGT
1 TTAGGGT
* *
188338 TTATGTT
1 TTAGGGT
188345 TTAGGGT
1 TTAGGGT
188352 TTAGGGT
1 TTAGGGT
188359 TTAGGGT
1 TTAGGGT
188366 TT
1 TT
188368 CTATAACTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (7 bp):
TTAGGGT
Found at i:188326 original size:14 final size:14
Alignment explanation
Indices: 188303--188367 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
188293 TCTATTTACA
*
188303 TTAGGATTTATGGT
1 TTAGGGTTTATGGT
188317 TTAGGGTTTAAT-GT
1 TTAGGGTTT-ATGGT
* *
188331 TTAGTGTTTATGTT
1 TTAGGGTTTATGGT
*
188345 TTAGGGTTTAGGGT
1 TTAGGGTTTATGGT
188359 TTAGGGTTT
1 TTAGGGTTT
188368 CTATAACTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.05
14 39 0.91
15 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Done.