Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 100 of 356
Found at i:31616002 original size:110 final size:111
Alignment explanation
Indices: 31615864--31616175 Score: 335
Period size: 110 Copynumber: 2.8 Consensus size: 111
31615854 ATGAAAAAGG
* *
31615864 TGGTGCTGGCCATCAGTGTCTTATAGTAAAAAAAAAGTGCATTGGGAGCCAAAAAATGTACTTGG
1 TGGTGCTGGCCATCAGTGTCTCAAAGTAAAAAAAAAGTGCATTGGGAGCC-AAAAATGTACTTGG
*
31615929 TGTCGACCATCTACTTGCCAACACCCAA-TTTTTTTT-AAATGACA-
65 TGTCGACCATCTACTGGCCAACACCCAATTTTTTTTTAAAATGACAC
* * * * * * * *
31615973 TCGGTGTTGGCCATCAGTGTCCCAAAGTAAAAAAAAAATACATTAGGAGTCGAAAATATACTTGG
1 T-GGTGCTGGCCATCAGTGTCTCAAAGTAAAAAAAAAGTGCATTGGGAGCCAAAAATGTACTTGG
* * * *
31616038 TG-CTAGCCATTTACTGGGCAGCACCCAATTTTTTTTTTTAAAAATGACAC
65 TGTCGA-CCATCTACTGGCCAACACCCAA--TTTTTTTTT-AAAATGACAC
* * *
31616088 TGGTGCAGGCCATTAGTGTCTCAAAGTAAAAAAAAAAAGTGCATTGGGACCCGAAAAATGTACTT
1 TGGTGCTGGCCATCAGTGTCTCAAAGT--AAAAAAAAAGTGCATTGGGAGCC-AAAAATGTACTT
**
31616153 GGTGTCGGTCATCTACTGGCCAA
63 GGTGTCGACCATCTACTGGCCAA
31616176 TATTAAAACT
Statistics
Matches: 159, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
108 2 0.01
109 33 0.21
110 41 0.26
112 8 0.05
114 30 0.19
115 1 0.01
116 18 0.11
117 25 0.16
118 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (111 bp):
TGGTGCTGGCCATCAGTGTCTCAAAGTAAAAAAAAAGTGCATTGGGAGCCAAAAATGTACTTGGT
GTCGACCATCTACTGGCCAACACCCAATTTTTTTTTAAAATGACAC
Found at i:31617263 original size:21 final size:20
Alignment explanation
Indices: 31617217--31617271 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
31617207 TGACAATTAC
*
31617217 TTATTTTATAAT-TTTAATT
1 TTATTTTATAATATTTAATA
*
31617236 TTAATTTATATAATATTTTATA
1 TT-ATTT-TATAATATTTAATA
31617258 TTATTTTAATAATA
1 TTATTTT-ATAATA
31617272 AATATGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 5 0.17
21 16 0.53
22 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTATAATATTTAATA
Found at i:31617664 original size:21 final size:21
Alignment explanation
Indices: 31617634--31617686 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
31617624 CATTTTTTTA
*
31617634 AAGAGGAAAAAACTGAAAATC
1 AAGAGAAAAAAACTGAAAATC
*
31617655 AAGAGAAAAAAATTGAAAATC
1 AAGAGAAAAAAACTGAAAATC
*
31617676 AGGAGAAAAAA
1 AAGAGAAAAAA
31617687 TTTGATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.66, C:0.06, G:0.19, T:0.09
Consensus pattern (21 bp):
AAGAGAAAAAAACTGAAAATC
Found at i:31623188 original size:38 final size:35
Alignment explanation
Indices: 31623140--31623210 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 35
31623130 TTAATATAAA
*
31623140 AATAATTATATTAAGAATATTATTAAATTATATTTAAT
1 AATAAATATATTAA-AATATTATTAAA--ATATTTAAT
31623178 AATAAATATATTAAAATATTATTAAAATATTTA
1 AATAAATATATTAAAATATTATTAAAATATTTA
31623211 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 7 0.22
37 12 0.38
38 13 0.41
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (35 bp):
AATAAATATATTAAAATATTATTAAAATATTTAAT
Found at i:31623202 original size:11 final size:11
Alignment explanation
Indices: 31623148--31623208 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 11
31623138 AAAATAATTA
31623148 TATTAAGAATAT
1 TATTAA-AATAT
*
31623160 TATTAAATTA-
1 TATTAAAATAT
31623170 TATTTAATAATAAAT
1 TA-TTAA-AAT--AT
31623185 ATATTAAAATAT
1 -TATTAAAATAT
31623197 TATTAAAATAT
1 TATTAAAATAT
31623208 T
1 T
31623209 TATTTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 2 0.05
11 19 0.46
12 10 0.24
14 4 0.10
15 4 0.10
16 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
TATTAAAATAT
Found at i:31623429 original size:46 final size:44
Alignment explanation
Indices: 31623339--31623430 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 44
31623329 ATATCTATTC
** **
31623339 CATTCAACCAAACACAATAATACTATTACAGTTCTATTTTATTA
1 CATTCAACCAAACACAATAATACTATTACAACTCTATTCCATTA
*
31623383 CATTCAACCAAACA-ATTGAATTACTGATTACAACTCTATTCCATTA
1 CATTCAACCAAACACAAT-AA-TACT-ATTACAACTCTATTCCATTA
31623429 CA
1 CA
31623431 GCCCTATTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.40
45 4 0.10
46 18 0.45
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (44 bp):
CATTCAACCAAACACAATAATACTATTACAACTCTATTCCATTA
Found at i:31625739 original size:42 final size:42
Alignment explanation
Indices: 31625680--31625776 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
31625670 AATCCTAATT
31625680 GAGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
1 GAGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
*
31625722 GAGAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GAGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
* *
31625764 AATAAAATA-TTCC
1 GAGAAAATAGTTCC
31625777 TAGAATATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 4 0.08
42 48 0.92
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.29
Consensus pattern (42 bp):
GAGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
Found at i:31625816 original size:19 final size:18
Alignment explanation
Indices: 31625794--31625833 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
31625784 TGAATAAAAC
31625794 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
31625813 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
31625831 TTA
1 TTA
31625834 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:31630409 original size:42 final size:42
Alignment explanation
Indices: 31630350--31630433 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
31630340 AATCCTAATT
* *
31630350 GGGAAAATAGTTTCCTTATTCTAATAAACTACTGAAACATAA
1 GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
* *
31630392 GGGAAAATAGTTCCCTTATTTTAATAAACTACTAAAAGATAA
1 GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
31630434 AATAAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (42 bp):
GGGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
Found at i:31630441 original size:42 final size:42
Alignment explanation
Indices: 31630352--31630446 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
31630342 TCCTAATTGG
* * **
31630352 GAAAATAGTTTCCTTATTCTAATAAACTACTGAAACATAAGG
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
* *
31630394 GAAAATAGTTCCCTTATTTTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
31630436 TAAAATA-TTCC
1 GAAAATAGTTCC
31630447 TAGAATATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:31630486 original size:19 final size:18
Alignment explanation
Indices: 31630464--31630503 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
31630454 TGAATAAAAC
*
31630464 TTATCTACCTATATAAGAT
1 TTATCTACCTAAATAA-AT
31630483 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
31630501 TTA
1 TTA
31630504 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:31639199 original size:7 final size:7
Alignment explanation
Indices: 31639169--31639214 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
31639159 ATAAAAATAC
31639169 ATAATTT
1 ATAATTT
*
31639176 ATTAATAT
1 A-TAATTT
*
31639184 -TAATAT
1 ATAATTT
31639190 ATAATTT
1 ATAATTT
31639197 ATAATTT
1 ATAATTT
31639204 ATAATTT
1 ATAATTT
31639211 -TAAT
1 ATAAT
31639215 AAAATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 10 0.29
7 20 0.57
8 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATAATTT
Found at i:31648795 original size:16 final size:15
Alignment explanation
Indices: 31648752--31648799 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
31648742 AAATCCTCTT
31648752 TCTC-TTTCTTTTT-
1 TCTCATTTCTTTTTC
* *
31648765 TCTCTTTTCTATTTC
1 TCTCATTTCTTTTTC
31648780 TCTCAATTTCTTTTTC
1 TCTC-ATTTCTTTTTC
31648796 TCTC
1 TCTC
31648800 TCTCTTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 4 0.14
16 13 0.45
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTCATTTCTTTTTC
Found at i:31650665 original size:26 final size:26
Alignment explanation
Indices: 31650623--31650674 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
31650613 AACACTTTTG
*
31650623 ATTTTGTTTATGTTTTGGATGTTGTT
1 ATTTTGTTTATGGTTTGGATGTTGTT
**
31650649 ATTTTGTGTT-TGGTTTGTTTGTTGTT
1 ATTTTGT-TTATGGTTTGGATGTTGTT
31650675 TGTTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.08, C:0.00, G:0.25, T:0.67
Consensus pattern (26 bp):
ATTTTGTTTATGGTTTGGATGTTGTT
Found at i:31650902 original size:12 final size:12
Alignment explanation
Indices: 31650887--31650917 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31650877 GTTTTTTTTC
31650887 TTATTTTTATGT
1 TTATTTTTATGT
*
31650899 TTATTTTTGTGT
1 TTATTTTTATGT
31650911 TTATTTT
1 TTATTTT
31650918 AGTTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (12 bp):
TTATTTTTATGT
Found at i:31650902 original size:30 final size:30
Alignment explanation
Indices: 31650868--31650930 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
31650858 GCACATTAAC
* *
31650868 TTTATGTGTGTTTTTTTTCTTA-TTTTTATG
1 TTTATGTGTGTGTTTATT-TTAGTTTTTATG
* *
31650898 TTTATTTTTGTGTTTATTTTAGTTTTTATG
1 TTTATGTGTGTGTTTATTTTAGTTTTTATG
31650928 TTT
1 TTT
31650931 TTTTATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.75
Consensus pattern (30 bp):
TTTATGTGTGTGTTTATTTTAGTTTTTATG
Found at i:31650934 original size:17 final size:17
Alignment explanation
Indices: 31650868--31650936 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
31650858 GCACATTAAC
* * *
31650868 TTTATGTGTGTTTTTTT
1 TTTATGTTTATTTTATT
*
31650885 TCTTATTTTTATGTTTATT
1 T-TTATGTTTAT-TTTATT
*
31650904 TTTGTGTTTATTTTAGTT
1 TTTATGTTTATTTTA-TT
31650922 TTTATGTTT-TTTTAT
1 TTTATGTTTATTTTAT
31650937 GAAAAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 25 0.60
19 6 0.14
ACGTcount: A:0.12, C:0.01, G:0.12, T:0.75
Consensus pattern (17 bp):
TTTATGTTTATTTTATT
Found at i:31653644 original size:19 final size:19
Alignment explanation
Indices: 31653605--31653645 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31653595 TAGTTTTAGG
**
31653605 TTTAGTTTTTTTCTAGTTT
1 TTTAGTTTTTTTCTACATT
31653624 TTTAGTTTTTTTCTACATT
1 TTTAGTTTTTTTCTACATT
31653643 TTT
1 TTT
31653646 CTAGGGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTAGTTTTTTTCTACATT
Found at i:31659148 original size:40 final size:40
Alignment explanation
Indices: 31659085--31659434 Score: 556
Period size: 40 Copynumber: 9.0 Consensus size: 40
31659075 CACGAATGCC
* *
31659085 TCAATTCGCACAAACGCCGTCGGGTCTTAGCCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
* *
31659125 TCAGTTCGCACAAATGCCTTCGGGTCTTATCCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
* * *
31659165 TCAATTCGCACAAATTCCTTCGGGTCTTATCCCAGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
31659205 TCAATTCGCACAAATGCCTTCGGG---T------GATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
31659236 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
*
31659276 TCAATTCGCACAAATGCCTTCAGGTCTTAGCCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
*
31659316 TCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
31659356 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
31659396 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
31659435 CATTCAAATG
Statistics
Matches: 289, Mismatches: 12, Indels: 18
0.91 0.04 0.06
Matches are distributed among these distances:
31 30 0.10
34 1 0.00
37 1 0.00
40 257 0.89
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (40 bp):
TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
Found at i:31659234 original size:31 final size:31
Alignment explanation
Indices: 31659199--31659260 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
31659189 TCTTATCCCA
31659199 GATATATCAATTCGCACAAATGCCTTCGGGT
1 GATATATCAATTCGCACAAATGCCTTCGGGT
31659230 GATATATCAATTCGCACAAATGCCTTCGGGT
1 GATATATCAATTCGCACAAATGCCTTCGGGT
31659261 CTTAGCCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (31 bp):
GATATATCAATTCGCACAAATGCCTTCGGGT
Found at i:31659359 original size:151 final size:153
Alignment explanation
Indices: 31659085--31659434 Score: 551
Period size: 151 Copynumber: 2.3 Consensus size: 153
31659075 CACGAATGCC
* * * *
31659085 TCAATTCGCACAAACGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAATGCCTTCGGGT
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCAGGT
* * *
31659150 CTTATCCCGGATATATCAATTCGCACAAATTCCTTCGGGTCTTATCCCAGATATATCAATTCGCA
66 CTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCAGATATATCAATTCGCA
31659215 CAAATGCCTTCGGG-T-GATATA
131 CAAATGCCTTCGGGTTCGATATA
31659236 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCAGGT
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCAGGT
*
31659301 CTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCA
66 CTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCAGATATATCAATTCGCA
31659366 CAAATGCCTTCGGGTCTTAGCCCGGATATA
131 CAAATGCCTTCGGG--TT----C-GATATA
31659396 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
31659435 CATTCAAATG
Statistics
Matches: 182, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
151 136 0.75
154 1 0.01
160 45 0.25
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (153 bp):
TCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCAGGT
CTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAACCCAGATATATCAATTCGCA
CAAATGCCTTCGGGTTCGATATA
Found at i:31665491 original size:20 final size:21
Alignment explanation
Indices: 31665466--31665506 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31665456 CGAGACTTAA
*
31665466 TCGGAAACTTT-AAGAATTTT
1 TCGGAAACTTTCAAAAATTTT
*
31665486 TCGGAAAGTTTCAAAAATTTT
1 TCGGAAACTTTCAAAAATTTT
31665507 CCAAGTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGGAAACTTTCAAAAATTTT
Found at i:31670203 original size:124 final size:124
Alignment explanation
Indices: 31669983--31670231 Score: 489
Period size: 124 Copynumber: 2.0 Consensus size: 124
31669973 ATCATATGAC
31669983 CCGTAATATGTTAGAAATGATATGTGAAAATTTTGATATGAAAATTTTATTGATTAAGTGTTTAA
1 CCGTAATATGTTAGAAATGATATGTGAAAATTTTGATATGAAAATTTTATTGATTAAGTGTTTAA
31670048 TTACGAAAAGGACTAAATCGCATAAAATGAGAAAGTCAAATTCTAGTAGCTATAAGGAT
66 TTACGAAAAGGACTAAATCGCATAAAATGAGAAAGTCAAATTCTAGTAGCTATAAGGAT
31670107 CCGTAATATGTTAGAAATGATATGTGAAAATTTTGATATGAAAATTTTATTGATTAAGTGTTTAA
1 CCGTAATATGTTAGAAATGATATGTGAAAATTTTGATATGAAAATTTTATTGATTAAGTGTTTAA
*
31670172 TTACGAAAAGGACTAAATCGTATAAAATGAGAAAGTCAAATTCTAGTAGCTATAAGGAT
66 TTACGAAAAGGACTAAATCGCATAAAATGAGAAAGTCAAATTCTAGTAGCTATAAGGAT
31670231 C
1 C
31670232 AAATAGCTAT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (124 bp):
CCGTAATATGTTAGAAATGATATGTGAAAATTTTGATATGAAAATTTTATTGATTAAGTGTTTAA
TTACGAAAAGGACTAAATCGCATAAAATGAGAAAGTCAAATTCTAGTAGCTATAAGGAT
Found at i:31680498 original size:248 final size:245
Alignment explanation
Indices: 31680063--31680555 Score: 950
Period size: 248 Copynumber: 2.0 Consensus size: 245
31680053 GACTCCGGTG
*
31680063 AGCCTTTTTCCTCTTTATTTATTTTCCTATATACCAAAGATTAATGGATAAATCCAAGAAAAAAC
1 AGCCTTTTTCCTCTTTATTTATTTTCCTATATACCAAAGATTAATGGATAAACCCAAGAAAAAAC
31680128 AAAGGAAAACAAAGTGAAAATCACCTTTAGCAAAATCGCTTCTGTTTTTTTTATTTCTCTTTTTT
66 AAAGGAAAACAAAGTGAAAATCACCTTTAGCAAAATCGCTTCTGTTTTTTTTATTTCTCTTTTTT
31680193 GTATTGATATCGTGTGTGTTCGTTCATAGTAGAATACAATCAAAATGAAAAAACGGCTTTATATC
131 GTATTGATATCGTGTGTGTTCGTTCATAGTAGAATACAATCAAAATGAAAAAACGGCTTTATATC
31680258 CGAATAAGAAAAATAATGAAAATATTACAATATTTTATCACGTTTTCATT
196 CGAATAAGAAAAATAATGAAAATATTACAATATTTTATCACGTTTTCATT
31680308 AGCCTTTTTCCTCTTTATTTATTTTCCTATATACCAAAGATTAATGGATAAAACCCAAGAAAAAA
1 AGCCTTTTTCCTCTTTATTTATTTTCCTATATACCAAAGATTAATGGAT-AAACCCAAGAAAAAA
31680373 CAAAGGAAAACAAAGTGAAAATCACCTTTAGCAAAATCGCTTCTGTTTTTTTTTTATTTCTCTTT
65 CAAAGGAAAACAAAGTGAAAATCACCTTTAGCAAAATCGCTTCTG--TTTTTTTTATTTCTCTTT
31680438 TTTGTATTGATATCGTGTGTGTTCGTTCATAGTAGAATACAATCAAAATGAAAAAACGGCTTTAT
128 TTTGTATTGATATCGTGTGTGTTCGTTCATAGTAGAATACAATCAAAATGAAAAAACGGCTTTAT
31680503 ATCCGAATAAGAAAAATAATGAAAATATTACAATATTTTATCACGTTTTCATT
193 ATCCGAATAAGAAAAATAATGAAAATATTACAATATTTTATCACGTTTTCATT
31680556 TTACTGTTGT
Statistics
Matches: 244, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
245 49 0.20
246 59 0.24
248 136 0.56
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (245 bp):
AGCCTTTTTCCTCTTTATTTATTTTCCTATATACCAAAGATTAATGGATAAACCCAAGAAAAAAC
AAAGGAAAACAAAGTGAAAATCACCTTTAGCAAAATCGCTTCTGTTTTTTTTATTTCTCTTTTTT
GTATTGATATCGTGTGTGTTCGTTCATAGTAGAATACAATCAAAATGAAAAAACGGCTTTATATC
CGAATAAGAAAAATAATGAAAATATTACAATATTTTATCACGTTTTCATT
Found at i:31683672 original size:55 final size:55
Alignment explanation
Indices: 31683605--31683737 Score: 196
Period size: 55 Copynumber: 2.4 Consensus size: 55
31683595 TGCCCTTAGT
* * * *
31683605 CCGTGTATAACACTGACTTTAAAACATGGCCATGGCACACGCCTGTGTGGCCGGC
1 CCGTGTACAACACTGACTTTAAAACACGGCCATCGCACACGCCCGTGTGGCCGGC
* *
31683660 CCGTGTACAACACTGACTTTAAAACACGGCCATCGTACACGCCCGTGTGGCCTGC
1 CCGTGTACAACACTGACTTTAAAACACGGCCATCGCACACGCCCGTGTGGCCGGC
*
31683715 CCGTGTACAACATTGAC-TTAAAA
1 CCGTGTACAACACTGACTTTAAAA
31683738 TTTTAAGTGC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 6 0.08
55 65 0.92
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (55 bp):
CCGTGTACAACACTGACTTTAAAACACGGCCATCGCACACGCCCGTGTGGCCGGC
Found at i:31688096 original size:66 final size:66
Alignment explanation
Indices: 31688016--31688147 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
31688006 AAGCAATTTC
31688016 ATACAAATTGGTTCTAGAATCCAAGTTTTTTAATTTATTCAATTTAGTCCCTAATTTCCAATTGG
1 ATACAAATTGGTTCTAGAATCCAAGTTTTTTAATTTATTCAATTTAGTCCCTAATTTCCAATTGG
31688081 A
66 A
31688082 ATACAAATTGGTTCTAGAATCCAAGTTTTTTAATTTATTCAATTTAGTCCCTAATTTCCAATTGG
1 ATACAAATTGGTTCTAGAATCCAAGTTTTTTAATTTATTCAATTTAGTCCCTAATTTCCAATTGG
31688147 A
66 A
31688148 CACCTTACTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (66 bp):
ATACAAATTGGTTCTAGAATCCAAGTTTTTTAATTTATTCAATTTAGTCCCTAATTTCCAATTGG
A
Found at i:31689280 original size:23 final size:23
Alignment explanation
Indices: 31689254--31689298 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31689244 TATAAATTTA
31689254 AATTAGAAATTA-GAAAAATAAAT
1 AATTA-AAATTATGAAAAATAAAT
**
31689277 AATTATTATTATGAAAAATAAA
1 AATTAAAATTATGAAAAATAAA
31689299 ATTTCTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
AATTAAAATTATGAAAAATAAAT
Found at i:31689537 original size:23 final size:23
Alignment explanation
Indices: 31689507--31689555 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31689497 TATTGAAGTC
*
31689507 TTTTTATATGTATATCTTGATAA
1 TTTTTATATGTATATCTTAATAA
31689530 TTTTTATATGTATATCTTAATAA
1 TTTTTATATGTATATCTTAATAA
31689553 TTT
1 TTT
31689556 ATACATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTTTATATGTATATCTTAATAA
Found at i:31690568 original size:78 final size:78
Alignment explanation
Indices: 31690446--31690591 Score: 292
Period size: 78 Copynumber: 1.9 Consensus size: 78
31690436 TTTGTGCAAC
31690446 CCAAAGAAAATAAGGACTCAACCCTGGTACAGTCCAAAGAGTCAGACCTGGAGGAGCAACCTCAA
1 CCAAAGAAAATAAGGACTCAACCCTGGTACAGTCCAAAGAGTCAGACCTGGAGGAGCAACCTCAA
31690511 CAAGCGGTGCAGG
66 CAAGCGGTGCAGG
31690524 CCAAAGAAAATAAGGACTCAACCCTGGTACAGTCCAAAGAGTCAGACCTGGAGGAGCAACCTCAA
1 CCAAAGAAAATAAGGACTCAACCCTGGTACAGTCCAAAGAGTCAGACCTGGAGGAGCAACCTCAA
31690589 CAA
66 CAA
31690592 TCGGAAGACT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (78 bp):
CCAAAGAAAATAAGGACTCAACCCTGGTACAGTCCAAAGAGTCAGACCTGGAGGAGCAACCTCAA
CAAGCGGTGCAGG
Found at i:31696246 original size:21 final size:21
Alignment explanation
Indices: 31696213--31696261 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
31696203 ATAAATAAAA
*
31696213 TCATTCA-TGTCAATTCCCTG
1 TCATTCACTGTCAATTCACTG
*
31696233 TCATTCACTGTCAATTTACTG
1 TCATTCACTGTCAATTCACTG
31696254 TCATTCAC
1 TCATTCAC
31696262 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (21 bp):
TCATTCACTGTCAATTCACTG
Found at i:31696253 original size:11 final size:11
Alignment explanation
Indices: 31696215--31696261 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
31696205 AAATAAAATC
31696215 ATTCA-TGTCA
1 ATTCACTGTCA
*
31696225 ATTCCCTGTC-
1 ATTCACTGTCA
31696235 ATTCACTGTCA
1 ATTCACTGTCA
*
31696246 ATTTACTGTC-
1 ATTCACTGTCA
31696256 ATTCAC
1 ATTCAC
31696262 AACTTCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 18 0.58
11 13 0.42
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (11 bp):
ATTCACTGTCA
Found at i:31696472 original size:21 final size:19
Alignment explanation
Indices: 31696435--31696505 Score: 97
Period size: 19 Copynumber: 3.6 Consensus size: 19
31696425 TGATTAAGCC
31696435 AACAGAAGCTCGAAAGCTG
1 AACAGAAGCTCGAAAGCTG
31696454 AACAGAAGCTCGTGAAAGCTG
1 AACAGAAGCTC--GAAAGCTG
* * *
31696475 AATAGAAGCTCAAAAGCTA
1 AACAGAAGCTCGAAAGCTG
31696494 AACAGAAGCTCG
1 AACAGAAGCTCG
31696506 TGAGAGCTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 27 0.60
21 18 0.40
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
AACAGAAGCTCGAAAGCTG
Found at i:31696498 original size:40 final size:40
Alignment explanation
Indices: 31696438--31696516 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
31696428 TTAAGCCAAC
* *
31696438 AGAAGCTCGAAAGCTGAACAGAAGCTCGTGAAAGCTGAAT
1 AGAAGCTCAAAAGCTAAACAGAAGCTCGTGAAAGCTGAAT
*
31696478 AGAAGCTCAAAAGCTAAACAGAAGCTCGTGAGAGCTGAA
1 AGAAGCTCAAAAGCTAAACAGAAGCTCGTGAAAGCTGAA
31696517 AGTAAAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.14
Consensus pattern (40 bp):
AGAAGCTCAAAAGCTAAACAGAAGCTCGTGAAAGCTGAAT
Found at i:31696550 original size:27 final size:27
Alignment explanation
Indices: 31696519--31696576 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
31696509 GAGCTGAAAG
* *
31696519 TAAAACATGAGAGTTCGTAACAAATCC
1 TAAAACACGAGAGTTCGCAACAAATCC
31696546 TAAAACACGAGAGTTCGCAACAAATCC
1 TAAAACACGAGAGTTCGCAACAAATCC
31696573 TAAA
1 TAAA
31696577 CCCTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.19
Consensus pattern (27 bp):
TAAAACACGAGAGTTCGCAACAAATCC
Found at i:31696701 original size:17 final size:17
Alignment explanation
Indices: 31696681--31696719 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
31696671 AAATCCAATT
31696681 CAATATTAT-AATTCCAA
1 CAATATT-TCAATTCCAA
*
31696698 CAATATTTCATTTCCAA
1 CAATATTTCAATTCCAA
31696715 CAATA
1 CAATA
31696720 GAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
CAATATTTCAATTCCAA
Found at i:31701698 original size:19 final size:19
Alignment explanation
Indices: 31701652--31701698 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
31701642 TATACAAAGT
*
31701652 TAAATATATCAATAATATA
1 TAAATATATCAATAATACA
*
31701671 T-AATAATATTAATAATACA
1 TAAAT-ATATCAATAATACA
31701690 TAAATATAT
1 TAAATATAT
31701699 AAAGGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 18 0.75
20 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATATATCAATAATACA
Found at i:31703566 original size:3 final size:3
Alignment explanation
Indices: 31703558--31703592 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31703548 ATCACATGTT
31703558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31703593 TGGATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31703710 original size:72 final size:72
Alignment explanation
Indices: 31703593--31703776 Score: 350
Period size: 72 Copynumber: 2.6 Consensus size: 72
31703583 TATTATTATT
31703593 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
31703658 TTTTAAG
66 TTTTAAG
*
31703665 TGGATGTAATGATGTAACTTAGTTGCATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
31703730 TTTTAAG
66 TTTTAAG
*
31703737 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
31703777 GTCAAGTTGT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 109 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:31708002 original size:3 final size:3
Alignment explanation
Indices: 31707994--31708049 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
31707984 ATCACATGTT
31707994 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31708042 TTA TTA TT
1 TTA TTA TT
31708050 TGGATGTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31708131 original size:72 final size:72
Alignment explanation
Indices: 31708050--31708233 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
31708040 TATTATTATT
31708050 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
31708115 TTTTAAG
66 TTTTAAG
31708122 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
31708187 TTTTAAG
66 TTTTAAG
*
31708194 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
31708234 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:31720024 original size:24 final size:21
Alignment explanation
Indices: 31719970--31720013 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31719960 GTATAAGGTT
31719970 AGAGAGAGTTTTTGATGATTA
1 AGAGAGAGTTTTTGATGATTA
31719991 AGAGAGAGTTTTTGATGATTA
1 AGAGAGAGTTTTTGATGATTA
31720012 AG
1 AG
31720014 GGAGGGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (21 bp):
AGAGAGAGTTTTTGATGATTA
Found at i:31727364 original size:16 final size:16
Alignment explanation
Indices: 31727343--31727375 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31727333 CATCAATGTT
31727343 AGGAATGGTGAAATGG
1 AGGAATGGTGAAATGG
31727359 AGGAATGGTGAAATGG
1 AGGAATGGTGAAATGG
31727375 A
1 A
31727376 ATAGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.18
Consensus pattern (16 bp):
AGGAATGGTGAAATGG
Found at i:31727635 original size:27 final size:27
Alignment explanation
Indices: 31727605--31727685 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
31727595 AATATAGCCT
*
31727605 ATCAGGATAGTAAACACGAGGTAGTCC
1 ATCAGGACAGTAAACACGAGGTAGTCC
* *
31727632 ATCAGGACAGTAAATACGAGGTAGTCT
1 ATCAGGACAGTAAACACGAGGTAGTCC
* *
31727659 A-CTGGGACAATAAACACGAGGTAGTCC
1 ATC-AGGACAGTAAACACGAGGTAGTCC
31727686 GCAGGGAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (27 bp):
ATCAGGACAGTAAACACGAGGTAGTCC
Found at i:31727692 original size:27 final size:27
Alignment explanation
Indices: 31727615--31727701 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
31727605 ATCAGGATAG
*
31727615 TAAACACGAGGTAGTCCATCA-GGACAG
1 TAAACACGAGGTAGTCCA-CAGGGACAA
* * *
31727642 TAAATACGAGGTAGTCTACTGGGACAA
1 TAAACACGAGGTAGTCCACAGGGACAA
* * *
31727669 TAAACACGAGGTAGTCCGCAGGGAGAT
1 TAAACACGAGGTAGTCCACAGGGACAA
31727696 TAAACA
1 TAAACA
31727702 TAGGGTAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
26 1 0.02
27 48 0.98
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (27 bp):
TAAACACGAGGTAGTCCACAGGGACAA
Found at i:31730887 original size:47 final size:46
Alignment explanation
Indices: 31730819--31730974 Score: 183
Period size: 47 Copynumber: 3.3 Consensus size: 46
31730809 AGCTTAAGAT
*
31730819 CGAATGGCCAATGTGATGAATGTGAAAGGGTGTATATGTGATAAGGT
1 CGAATGGCCAATGTGATGAATGTGAAA-GGTGTATATGTGATAAGGC
*
31730866 CGAATGGCCAATGTGATGAATGTGAAA-GTGCATACATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGGTG--TATATGTGATAAGGC
** * *
31730913 CGAATGGTTAATGTGAT-ATATGTGTAA-GTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGGTGTATATGTGATAAGGC
*
31730958 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
31730975 AAAGTGTGCA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
45 24 0.25
46 6 0.06
47 65 0.68
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (46 bp):
CGAATGGCCAATGTGATGAATGTGAAAGGTGTATATGTGATAAGGC
Found at i:31731099 original size:39 final size:40
Alignment explanation
Indices: 31731045--31731129 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
31731035 AAATGAATTG
* * * *
31731045 TGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
31731084 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
31731124 TGCTGG
1 TGCTGG
31731130 TGAATTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:31733716 original size:40 final size:40
Alignment explanation
Indices: 31733661--31734014 Score: 559
Period size: 40 Copynumber: 8.9 Consensus size: 40
31733651 CTCGCCGATG
* **
31733661 ATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGAAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733701 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733741 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733781 ATCCGGGCTAAAT-CCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733820 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733860 ATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
31733900 ATCCGGGCTAAGTCTC-AAGAGCATTCGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
31733939 ATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * *
31733979 ATTCGGGCTAGGTCCCGAAGAGCATTCATGCTGGTG
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
31734015 ATGTGTATTC
Statistics
Matches: 290, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
39 71 0.24
40 219 0.76
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
Found at i:31733890 original size:119 final size:118
Alignment explanation
Indices: 31733661--31734014 Score: 550
Period size: 119 Copynumber: 3.0 Consensus size: 118
31733651 CTCGCCGATG
* *
31733661 ATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGAAGTTATATCCGGGCTAAGTCCCGAAGAGCAT
1 ATCCGGGCTAAGT-CC-AAGAGCATTCGTGCTGGAGTTATATCCAGGCTAAGTCCCGAAGAGCAT
* * *
31733726 ACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
64 TCGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
31733781 ATCCGGGCTAAATCCGAAGAGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGAGCATT
1 ATCCGGGCTAAGTCC-AAGAGCATTCGTGCTGGAGTTATATCCAGGCTAAGTCCCGAAGAGCATT
31733846 CGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
65 CGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
31733900 ATCCGGGCTAAGTCTCAAGAGCATTCGTGCTGGAGTTATAT-CAGGGTTAAGTCCCGAAGAGCAT
1 ATCCGGGCTAAGTC-CAAGAGCATTCGTGCTGGAGTTATATCCA-GGCTAAGTCCCGAAGAGCAT
* *
31733964 TCGTGCTGGTGTTATAT-TCGGGCTAGGTCCCGAAGAGCATTCATGCTGGTG
64 TCGTGCTGGTGTTATATCT-GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
31734015 ATGTGTATTC
Statistics
Matches: 218, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
118 3 0.01
119 202 0.93
120 13 0.06
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (118 bp):
ATCCGGGCTAAGTCCAAGAGCATTCGTGCTGGAGTTATATCCAGGCTAAGTCCCGAAGAGCATTC
GTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
Found at i:31733957 original size:159 final size:159
Alignment explanation
Indices: 31733661--31734014 Score: 557
Period size: 159 Copynumber: 2.2 Consensus size: 159
31733651 CTCGCCGATG
* **
31733661 ATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGAAGTTATATCCGGGCTAAGTCCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT
* *
31733726 ACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTA
66 ACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAGGGCTA
31733791 AATCCGAAGAGCATTCGTGCTGGTGTTAT
131 AATCCGAAGAGCATTCGTGCTGGTGTTAT
* *
31733820 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT
* * * *
31733885 TCGTGCTGGTGTTATATCCGGGCTAAGTCTC-AAGAGCATTCGTGCTGGAGTTATATCAGGGTTA
66 ACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAGGGCTA
*
31733949 AGTCCCGAAGAGCATTCGTGCTGGTGTTAT
131 AAT-CCGAAGAGCATTCGTGCTGGTGTTAT
* * *
31733979 ATTCGGGCTAGGTCCCGAAGAGCATTCATGCTGGTG
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
31734015 ATGTGTATTC
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
158 31 0.17
159 147 0.83
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (159 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCAT
ACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTATATCAGGGCTA
AATCCGAAGAGCATTCGTGCTGGTGTTAT
Found at i:31734228 original size:25 final size:25
Alignment explanation
Indices: 31734178--31734228 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
31734168 TGTGTAACAA
* *
31734178 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
31734203 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
31734228 C
1 C
31734229 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:31737779 original size:47 final size:46
Alignment explanation
Indices: 31737710--31737865 Score: 192
Period size: 47 Copynumber: 3.3 Consensus size: 46
31737700 AGCTTAAGAT
31737710 CGAATGGCCAATGTGATGAATGTGAAAGGGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAA-GGTGTATATGTGATAAGGC
*
31737757 CGAATGGCCAATGTGATGAATGTGAAA-GTGCATACATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGGTG--TATATGTGATAAGGC
** * *
31737804 CGAATGGTTAATGTGAT-ATATGTGTAA-GTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGGTGTATATGTGATAAGGC
*
31737849 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
31737866 AAAGTGTGCA
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
45 24 0.25
46 6 0.06
47 66 0.69
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (46 bp):
CGAATGGCCAATGTGATGAATGTGAAAGGTGTATATGTGATAAGGC
Found at i:31737989 original size:39 final size:40
Alignment explanation
Indices: 31737935--31738020 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
31737925 TAAATGAATT
* * * *
31737935 ATGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTC
1 ATGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTA
*
31737974 ATGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTA
1 ATGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTA
31738014 ATGCTGG
1 ATGCTGG
31738021 TGAATTAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 19 0.46
40 22 0.54
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
ATGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTA
Found at i:31742785 original size:38 final size:37
Alignment explanation
Indices: 31742736--31742863 Score: 89
Period size: 38 Copynumber: 3.3 Consensus size: 37
31742726 TTTAAGATTT
31742736 AATTTATATAATTTAATTTTGACATAATTTGATACCTC
1 AATTT-TATAATTTAATTTTGACATAATTTGATACCTC
* * * * * * *
31742774 AATCTTTATAATATCATTAGTTAGTC-TAAATTTAAGA-TTT
1 AAT-TTTATAATTTAATT--TT-GACAT-AATTTGATACCTC
* *
31742814 AATTTATATAATTTAATTTTAACATAATTTGATGCCTC
1 AATTT-TATAATTTAATTTTGACATAATTTGATACCTC
31742852 AATTTTTATAAT
1 AA-TTTTATAAT
31742864 ATCATTAGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
37 7 0.11
38 25 0.38
39 7 0.11
40 17 0.26
41 9 0.14
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (37 bp):
AATTTTATAATTTAATTTTGACATAATTTGATACCTC
Found at i:31742895 original size:78 final size:78
Alignment explanation
Indices: 31742723--31742881 Score: 284
Period size: 78 Copynumber: 2.1 Consensus size: 78
31742713 ATATTTGCTC
*
31742723 AAATTTAAGATTTAATTTATATAATTTAATTTTGACATAATTTGATACCTCAATCTTTATAATAT
1 AAATTTAAGATTTAATTTATATAATTTAATTTTAACATAATTTGATACCTCAATCTTTATAATAT
31742788 CATTAGTTAGTCT
66 CATTAGTTAGTCT
* *
31742801 AAATTTAAGATTTAATTTATATAATTTAATTTTAACATAATTTGATGCCTCAATTTTTATAATAT
1 AAATTTAAGATTTAATTTATATAATTTAATTTTAACATAATTTGATACCTCAATCTTTATAATAT
31742866 CATTAGTT-GTCT
66 CATTAGTTAGTCT
31742878 AAAT
1 AAAT
31742882 ATTTTATTCT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 8 0.10
78 70 0.90
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (78 bp):
AAATTTAAGATTTAATTTATATAATTTAATTTTAACATAATTTGATACCTCAATCTTTATAATAT
CATTAGTTAGTCT
Found at i:31751783 original size:11 final size:11
Alignment explanation
Indices: 31751767--31751817 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
31751757 ACACAACAAT
*
31751767 TTATAACTTAA
1 TTATAAATTAA
*
31751778 TTATAAATTAC
1 TTATAAATTAA
*
31751789 TAATAAATTAA
1 TTATAAATTAA
* *
31751800 TTTTAAAATAA
1 TTATAAATTAA
31751811 TTATAAA
1 TTATAAA
31751818 AAACAAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (11 bp):
TTATAAATTAA
Found at i:31751998 original size:16 final size:16
Alignment explanation
Indices: 31751973--31752003 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31751963 AATACATTAC
*
31751973 CTTTTTTTTTCTTCTT
1 CTTTTCTTTTCTTCTT
31751989 CTTTTCTTTTCTTCT
1 CTTTTCTTTTCTTCT
31752004 CCTCTTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTCTTTTCTTCTT
Found at i:31752011 original size:16 final size:16
Alignment explanation
Indices: 31751979--31752012 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31751969 TTACCTTTTT
* *
31751979 TTTTCTTCTTCTTTTC
1 TTTTCTTCTCCTCTTC
31751995 TTTTCTTCTCCTCTTC
1 TTTTCTTCTCCTCTTC
31752011 TT
1 TT
31752013 CTCCTTTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCTTCTCCTCTTC
Found at i:31753036 original size:23 final size:24
Alignment explanation
Indices: 31752991--31753036 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31752981 TTATGACTTC
* *
31752991 ATTTTTTTTGAAGGGATTTAAAGA
1 ATTTTTTTTAAAGGGATTCAAAGA
31753015 ATTTTTTTTAAAGGGA-TCAAAG
1 ATTTTTTTTAAAGGGATTCAAAG
31753037 TATAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (24 bp):
ATTTTTTTTAAAGGGATTCAAAGA
Found at i:31753779 original size:48 final size:47
Alignment explanation
Indices: 31753707--31753841 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 47
31753697 AGTGATAATT
* *
31753707 TTAAATTTTCAATACTATTCGATATTTTTTTAATTTATGTAAATT-TAA
1 TTAAA-TTTCAATACTATTTGATATTTTTTTCATTTATG-AAATTATAA
* * *
31753755 TTAAATTTGCAATATTATTTGATATTTTATTCATTTATGCAATTATAA
1 TTAAATTT-CAATACTATTTGATATTTTTTTCATTTATGAAATTATAA
**
31753803 TTAAAATTTCAATACTGCTTGAT-TTTTTTTCATTTATGA
1 TT-AAATTTCAATACTATTTGATATTTTTTTCATTTATGA
31753842 TGTTTGCATT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
47 21 0.28
48 47 0.64
49 6 0.08
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.53
Consensus pattern (47 bp):
TTAAATTTCAATACTATTTGATATTTTTTTCATTTATGAAATTATAA
Found at i:31754806 original size:7 final size:7
Alignment explanation
Indices: 31754794--31754826 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31754784 TAGTCGTTTC
31754794 GTATTTA
1 GTATTTA
31754801 GTATTTA
1 GTATTTA
31754808 GTATTTA
1 GTATTTA
31754815 GTATTTA
1 GTATTTA
31754822 GTATT
1 GTATT
31754827 ATGTATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31754832 original size:7 final size:7
Alignment explanation
Indices: 31754822--31754853 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
31754812 TTAGTATTTA
31754822 GTATTAT
1 GTATTAT
31754829 GTATTAT
1 GTATTAT
31754836 GTATTAT
1 GTATTAT
31754843 GTATATAT
1 GTAT-TAT
31754851 GTA
1 GTA
31754854 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (7 bp):
GTATTAT
Found at i:31754832 original size:14 final size:14
Alignment explanation
Indices: 31754801--31754846 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
31754791 TTCGTATTTA
31754801 GTATTTAGTATT-T
1 GTATTTAGTATTAT
31754814 AGTATTTAGTATTAT
1 -GTATTTAGTATTAT
31754829 GTA-TTATGTATTAT
1 GTATTTA-GTATTAT
31754843 GTAT
1 GTAT
31754847 ATATGTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.10
14 25 0.86
15 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (14 bp):
GTATTTAGTATTAT
Found at i:31754840 original size:21 final size:21
Alignment explanation
Indices: 31754794--31754833 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31754784 TAGTCGTTTC
31754794 GTATTTAGTATT-TAGTATTTA
1 GTATTTAGTATTAT-GTATTTA
31754815 GTATTTAGTATTATGTATT
1 GTATTTAGTATTATGTATT
31754834 ATGTATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
GTATTTAGTATTATGTATTTA
Found at i:31755451 original size:18 final size:18
Alignment explanation
Indices: 31755428--31755465 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31755418 TGCTAGGTGC
*
31755428 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
31755446 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
31755464 GT
1 GT
31755466 TTTCTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:31759133 original size:126 final size:126
Alignment explanation
Indices: 31758908--31759288 Score: 600
Period size: 126 Copynumber: 3.0 Consensus size: 126
31758898 TTATAGCCTC
*
31758908 ATTTTTCTACGTACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
* * * *
31758973 ACAGCGCATCCTACTTAAAGCATTTTCAACACTATTTGTTCAGAAACATCTACTCAGAATT
66 ACAGTGCATCCTACTTAAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* * * *
31759034 ATTTTTCTACGAACTACTGTAGCAAAAGAACGTCCACTTGAGAGCTTTTTTTAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
* * *
31759099 ATAGTGCTTCCTACTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
66 ACAGTGCATCCTACTTAAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* *
31759160 ATATTTCTAAGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
* * * *
31759225 ACAGTGCATCCTGCTTAAAGCGTTTTCGACTCTATTTGTTTAGAAACGTCTACTCAAAATT
66 ACAGTGCATCCTACTTAAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
31759286 ATT
1 ATT
31759289 CTTACAGAAA
Statistics
Matches: 229, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 229 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (126 bp):
ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
ACAGTGCATCCTACTTAAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:31759911 original size:35 final size:38
Alignment explanation
Indices: 31759830--31759919 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
31759820 AGGATTATGT
*
31759830 ATCAATTAACCCTAAATTAATCAATTAAACCTAAATTTA
1 ATCAATTAACCCTAATTTAATCAATT-AACCTAAATTTA
*
31759869 ATCAATTAACCCTAATTTAATCAA-T-CCCT-AATTTA
1 ATCAATTAACCCTAATTTAATCAATTAACCTAAATTTA
*
31759904 ATTAATTAACCCTAAT
1 ATCAATTAACCCTAAT
31759920 ACCTTAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 21 0.44
36 3 0.06
38 1 0.02
39 23 0.48
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (38 bp):
ATCAATTAACCCTAATTTAATCAATTAACCTAAATTTA
Found at i:31759919 original size:19 final size:19
Alignment explanation
Indices: 31759830--31759919 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
31759820 AGGATTATGT
*
31759830 ATCAATTAACCCTAAATTA
1 ATCAATTAACCCTAATTTA
*
31759849 ATCAATTAAACCTAAATTTA
1 ATCAATTAACCCT-AATTTA
31759869 ATCAATTAACCCTAATTTA
1 ATCAATTAACCCTAATTTA
31759888 ATCAA-T--CCCTAATTTA
1 ATCAATTAACCCTAATTTA
*
31759904 ATTAATTAACCCTAAT
1 ATCAATTAACCCTAAT
31759920 ACCTTAAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.22
17 1 0.02
18 1 0.02
19 30 0.48
20 17 0.27
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (19 bp):
ATCAATTAACCCTAATTTA
Found at i:31760035 original size:17 final size:17
Alignment explanation
Indices: 31760013--31760045 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31760003 CCTTAAATTC
31760013 TAAACCTTAAAAAACCA
1 TAAACCTTAAAAAACCA
31760030 TAAACCTTAAAAAACC
1 TAAACCTTAAAAAACC
31760046 CTACCCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAACCTTAAAAAACCA
Found at i:31764118 original size:23 final size:23
Alignment explanation
Indices: 31764092--31764137 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31764082 GTGTTTCATG
*
31764092 TCTGTTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
31764115 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
31764138 ACTAGCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (23 bp):
TCTGCTGCCTGATTAAGTTACAT
Found at i:31764416 original size:25 final size:26
Alignment explanation
Indices: 31764381--31764429 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
31764371 TCTCCAATTC
*
31764381 TTAAACTTGATTTTGA-AATAAAAAA
1 TTAAACATGATTTTGATAATAAAAAA
*
31764406 TTAAACATGATTTTTATAATAAAA
1 TTAAACATGATTTTGATAATAAAA
31764430 CTTATTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (26 bp):
TTAAACATGATTTTGATAATAAAAAA
Found at i:31764493 original size:45 final size:46
Alignment explanation
Indices: 31764444--31764534 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
31764434 TTCTTCACAG
*
31764444 AATTAAA-TTCCTACTATAAAATTTTTAAAAAATACAACCACTATA
1 AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
* * *
31764489 AATTAAATTTCCTACTTTGAAATTTTCAAAAAATACAATCACTATA
1 AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
31764535 GACATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 7 0.17
46 34 0.83
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.35
Consensus pattern (46 bp):
AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
Found at i:31769696 original size:120 final size:120
Alignment explanation
Indices: 31769495--31770836 Score: 2560
Period size: 120 Copynumber: 11.2 Consensus size: 120
31769485 TTTTCAAGTT
31769495 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31769560 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31769615 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
31769680 TAATATAAGAACATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31769735 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31769800 TAATATAAGAATATTAATTATTAAGAA-TTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31769854 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31769919 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31769974 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31770039 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31770094 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31770159 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31770214 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
**
31770279 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31770334 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
31770399 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
*
31770454 ATATATTTAATAATAATTATATTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
31770519 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
*
31770574 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
** *
31770639 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
*
31770694 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
31770759 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
31770814 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
31770837 TAAATATGAT
Statistics
Matches: 1208, Mismatches: 13, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
119 119 0.10
120 1089 0.90
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
Found at i:31770573 original size:18 final size:17
Alignment explanation
Indices: 31770545--31770579 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31770535 ATTATTAAGA
*
31770545 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31770562 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31770580 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31770813 original size:18 final size:17
Alignment explanation
Indices: 31770785--31770819 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31770775 ATTATTAAGA
*
31770785 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31770802 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31770820 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31771033 original size:44 final size:45
Alignment explanation
Indices: 31770984--31771074 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
31770974 ACCTCTATTC
* * *
31770984 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
31771028 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
31771073 CA
1 CA
31771075 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:31771076 original size:16 final size:16
Alignment explanation
Indices: 31771055--31771123 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
31771045 GATTAGCTAT
31771055 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31771071 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
31771088 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31771104 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
31771120 TACA
1 TACA
31771124 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31771097 original size:33 final size:32
Alignment explanation
Indices: 31771055--31771123 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
31771045 GATTAGCTAT
31771055 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
31771088 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
31771120 TACA
1 TACA
31771124 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:31771632 original size:16 final size:17
Alignment explanation
Indices: 31771611--31771643 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31771601 TTTTTGATGA
31771611 ATTTGGCAC-CAAATAT
1 ATTTGGCACTCAAATAT
*
31771627 ATTTGGGACTCAAATAT
1 ATTTGGCACTCAAATAT
31771644 TAAAACATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTTGGCACTCAAATAT
Found at i:31773511 original size:48 final size:49
Alignment explanation
Indices: 31773427--31773537 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 49
31773417 CTGCTGGTAG
* *
31773427 ATGTTAGTTGCTAAAAAGATTGGTGGATAAAATGGGCTACAAGTAGGGC
1 ATGTTAGTTGCTAAAAAGATTAGTGGATAAAATGGGCCACAAGTAGGGC
** * * *
31773476 ATGTTAGTTGCTAATTAGA-TAGTGGATAAATTGGGCCACTAGTAGGTC
1 ATGTTAGTTGCTAAAAAGATTAGTGGATAAAATGGGCCACAAGTAGGGC
*
31773524 ATGTTAATTGCTAA
1 ATGTTAGTTGCTAA
31773538 CCATAATGAC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
48 37 0.69
49 17 0.31
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (49 bp):
ATGTTAGTTGCTAAAAAGATTAGTGGATAAAATGGGCCACAAGTAGGGC
Found at i:31777069 original size:24 final size:24
Alignment explanation
Indices: 31777042--31777089 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31777032 TGAGTATGTG
31777042 TTAGAGAACAACATATTGAACTGA
1 TTAGAGAACAACATATTGAACTGA
31777066 TTAGAGAACAACATATTGAACTGA
1 TTAGAGAACAACATATTGAACTGA
31777090 CTTATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (24 bp):
TTAGAGAACAACATATTGAACTGA
Found at i:31780663 original size:45 final size:46
Alignment explanation
Indices: 31780596--31780719 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
31780586 CATATGACCT
*
31780596 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
31780639 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
31780685 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
31780720 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:31780702 original size:46 final size:45
Alignment explanation
Indices: 31780596--31780830 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
31780586 CATATGACCT
*
31780596 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
31780639 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
31780685 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
31780722 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
31780759 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
31780796 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
31780831 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:31780723 original size:37 final size:37
Alignment explanation
Indices: 31780681--31780857 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
31780671 AGCTGAAGCT
* **
31780681 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
31780718 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
31780755 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
31780792 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
31780829 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
31780858 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:31788331 original size:45 final size:46
Alignment explanation
Indices: 31788264--31788387 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
31788254 CATATGACCT
*
31788264 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
31788307 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
31788353 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
31788388 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:31788370 original size:46 final size:45
Alignment explanation
Indices: 31788264--31788461 Score: 207
Period size: 37 Copynumber: 4.8 Consensus size: 45
31788254 CATATGACCT
*
31788264 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
31788307 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
31788353 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
31788390 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
31788427 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
31788462 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:31788391 original size:37 final size:37
Alignment explanation
Indices: 31788350--31788488 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
31788340 GCTGAAGCTA
* *
31788350 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
31788387 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
31788424 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
31788461 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
31788489 AGTACTCAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:31792961 original size:22 final size:22
Alignment explanation
Indices: 31792930--31792985 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
31792920 CTTCCAAGGA
*
31792930 TAAGTGTTGAATCAGCTCATGG
1 TAAGTCTTGAATCAGCTCATGG
31792952 TAAGTCTTGAATCAGCTCATGG
1 TAAGTCTTGAATCAGCTCATGG
31792974 TAAGTCTTGAAT
1 TAAGTCTTGAAT
31792986 ATATACTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (22 bp):
TAAGTCTTGAATCAGCTCATGG
Found at i:31800700 original size:17 final size:18
Alignment explanation
Indices: 31800664--31800704 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31800654 TCATTATGAG
* *
31800664 ATAAGAAAATTTTAGTAA
1 ATAAAAAAATTTTAGAAA
31800682 ATAAAAAAATTTTA-AAA
1 ATAAAAAAATTTTAGAAA
31800699 ATAAAA
1 ATAAAA
31800705 TGAATACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
ATAAAAAAATTTTAGAAA
Found at i:31805709 original size:18 final size:18
Alignment explanation
Indices: 31805686--31805728 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
31805676 TGCCAAGTAC
*
31805686 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
31805704 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
31805722 GTTTCCT
1 GTATCCT
31805729 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:31805994 original size:21 final size:21
Alignment explanation
Indices: 31805970--31806009 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31805960 CAATAGCCAC
*
31805970 AACCA-AATCCCTTGCCGGAGG
1 AACCACAA-CCCTCGCCGGAGG
31805991 AACCACAACCCTCGCCGGA
1 AACCACAACCCTCGCCGGA
31806010 AGCTGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.40, G:0.20, T:0.10
Consensus pattern (21 bp):
AACCACAACCCTCGCCGGAGG
Found at i:31809409 original size:126 final size:127
Alignment explanation
Indices: 31809184--31809691 Score: 702
Period size: 126 Copynumber: 4.0 Consensus size: 127
31809174 TTATAGCCTC
* * * *
31809184 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGC-TTTTTCCAGAAATTTTGCT
1 ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAACTTTTTTCAAGAAATTTTACT
*
31809248 GACAGTGCATCCTGCTTGAAACGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
66 GACAGTGCATCATGCTTGAAACGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
* * *
31809310 ATTTTTCCACGAACTACTATAGCAAAAGAGTGCCCACGTGGGAACTTTTTTC-AGAAATTTTACT
1 ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAACTTTTTTCAAGAAATTTTACT
* * * * *
31809374 GACAGTGCATCCTGCTTGAAGCGTTTTCGGTACTATTTGTTTAGAAACGTCTATTCAGAATT
66 GACAGTGCATCATGCTTGAAACGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
* *
31809436 ATTTTTCCACGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGC-TTTTTCAAGAAATTTTACT
1 ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAACTTTTTTCAAGAAATTTTACT
** * * *
31809500 GACAGTGCATCATGCTTGAAGTGTTTTCGGCACTATTTATTCAGAAATGTCTACTCAAAATT
66 GACAGTGCATCATGCTTGAAACGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
* * * *
31809562 ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTAGG-AGTTTTTTCTAGAAATTTTGCT
1 ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAACTTTTTTCAAGAAATTTTACT
* * * * *
31809626 GACAGTGTATCATGCTTGAAACATTTTCCGACACTATTT-TTCCAGAAATGTCTGCTCAGAATT
66 GACAGTGCATCATGCTTGAAACGTTTT-CGGCACTATTTGTT-CAGAAACGTCTACTCAGAATT
31809689 ATT
1 ATT
31809692 CTTGCAGAAA
Statistics
Matches: 341, Mismatches: 36, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
125 6 0.02
126 297 0.87
127 38 0.11
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (127 bp):
ATTTTTCCACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAACTTTTTTCAAGAAATTTTACT
GACAGTGCATCATGCTTGAAACGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:31810167 original size:16 final size:17
Alignment explanation
Indices: 31810146--31810184 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
31810136 TAAATTTTTT
*
31810146 CCTAAAACCTT-AAAAC
1 CCTAAAACATTAAAAAC
31810162 CCTAAAACATTACAAAAC
1 CCTAAAACATTA-AAAAC
31810180 CCTAA
1 CCTAA
31810185 CTTAACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (17 bp):
CCTAAAACATTAAAAAC
Found at i:31814298 original size:23 final size:23
Alignment explanation
Indices: 31814270--31814319 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
31814260 AAAATAATCC
*
31814270 TAATTA-AATTTTTGTGTCTTTTT
1 TAATTACAATTTTTGGGT-TTTTT
31814293 TAATTATCAATTTTTGGGTTTTTT
1 TAATTA-CAATTTTTGGGTTTTTT
31814317 TAA
1 TAA
31814320 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 8 0.33
25 10 0.42
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.62
Consensus pattern (23 bp):
TAATTACAATTTTTGGGTTTTTT
Found at i:31823612 original size:33 final size:33
Alignment explanation
Indices: 31823548--31823619 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
31823538 TCATTTCAAG
*
31823548 TTTCACATCTCATTTCATCATTTCAT-TTTTTCA
1 TTTCACATCTCATTTCAT-ATTTCATATTTTCCA
*
31823581 TTTCCCATCTCATATTCAT-TTGTCATATTTTCCA
1 TTTCACATCTCAT-TTCATATT-TCATATTTTCCA
31823615 TTTCA
1 TTTCA
31823620 ATATTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 2 0.06
33 16 0.48
34 15 0.45
ACGTcount: A:0.21, C:0.25, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTCACATCTCATTTCATATTTCATATTTTCCA
Found at i:31826463 original size:80 final size:80
Alignment explanation
Indices: 31826347--31826532 Score: 222
Period size: 80 Copynumber: 2.3 Consensus size: 80
31826337 AGTAACTCAT
* *
31826347 ACAATGCCTTCGGGACTTAACCC-GAATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 ACAAAGCCTTCGGGACTTAACCCGGAA-TTTAAAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
31826410 GGA-ATTAGT-A-TCTCGC
64 GGATA-TAGTCACT-TAGC
**
31826426 ACAAAGGCCTTCGGGACTTAACCCGGAA-TTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGAATTTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
31826490 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
31826507 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
31826533 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
79 11 0.12
80 69 0.73
81 13 0.14
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGAATTTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:31826492 original size:40 final size:40
Alignment explanation
Indices: 31826349--31826532 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
31826339 TAACTCATAC
*
31826349 AATGCCTTCGGGACTTAACCC-GAATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAA--TTAATAACTCGCACA
* *
31826389 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31826429 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
31826469 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
31826510 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31826533 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
39 8 0.06
40 102 0.82
41 14 0.11
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:31834287 original size:39 final size:40
Alignment explanation
Indices: 31834244--31834411 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
31834234 CTCGTTCAAG
* * * *
31834244 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
31834283 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
31834323 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
31834363 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
31834403 TGCCTTCGG
1 TGCCTTCGG
31834412 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:31834395 original size:80 final size:80
Alignment explanation
Indices: 31834279--31834464 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
31834269 AGTAACTCAT
* * *
31834279 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
31834343 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
31834358 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
31834422 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
31834439 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
31834465 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:31834424 original size:40 final size:40
Alignment explanation
Indices: 31834281--31834464 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
31834271 TAACTCATAC
* *
31834281 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
31834321 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31834361 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
31834401 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
31834442 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31834465 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:31855413 original size:20 final size:18
Alignment explanation
Indices: 31855359--31855414 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
31855349 AATCTAATAG
*
31855359 ATTTAATATTAGATTAA-
1 ATTTAATATTAAATTAAT
31855376 ATTTAATATTAAGA-TAAT
1 ATTTAATATTAA-ATTAAT
31855394 CACTTTAATATTAAATTAAT
1 -A-TTTAATATTAAATTAAT
31855414 A
1 A
31855415 AAATACTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 14 0.42
18 1 0.03
19 3 0.09
20 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (18 bp):
ATTTAATATTAAATTAAT
Found at i:31855455 original size:17 final size:17
Alignment explanation
Indices: 31855360--31855458 Score: 53
Period size: 17 Copynumber: 5.8 Consensus size: 17
31855350 ATCTAATAGA
* *
31855360 TTTAATATTAGATTAAA
1 TTTAATATTAAATTAAG
* *
31855377 TTTAATATTAAGATAATCAC
1 TTTAATATTAA-AT--TAAG
31855397 TTTAATATTAAATTAA-
1 TTTAATATTAAATTAAG
** * *
31855413 TAAAATACT--ATGAAG
1 TTTAATATTAAATTAAG
*
31855428 -ATAAGTATTAAATTAAG
1 TTTAA-TATTAAATTAAG
31855445 TTTAATATTAAATT
1 TTTAATATTAAATT
31855459 TATTAAAGTA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
14 7 0.11
15 3 0.05
16 6 0.10
17 26 0.42
18 5 0.08
19 2 0.03
20 13 0.21
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TTTAATATTAAATTAAG
Found at i:31858135 original size:43 final size:43
Alignment explanation
Indices: 31858082--31858196 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
31858072 TGAGATTACA
* *
31858082 TGTAAGACCATGTCTGGGACATTGGCATTG-TATTGTGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTA-TATGATTATG
* *
31858125 TGTAAAACCATGTCTGGGACATTGGCATCGTTATATGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTATG
*
31858168 TGTAAGACCATGTCTGGAACATTGGCATC
1 TGTAAGACCATGTCTGGGACATTGGCATC
31858197 AATATGAGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 63 0.97
44 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTATG
Found at i:31858215 original size:43 final size:42
Alignment explanation
Indices: 31858071--31858245 Score: 153
Period size: 43 Copynumber: 4.1 Consensus size: 42
31858061 GATTGTTGAG
* *
31858071 ATGAGATTACATGTAAGACCATGTCTGGGACATTGGCAT-TGT
1 ATGAGATTA-GTGTAAGACCATGTCTGGGACATTGGCATCTAT
* *
31858113 ATTGTGATTATGTGTAAAACCATGTCTGGGACATTGGCATCGTTAT
1 A-TGAGATTA-GTGTAAGACCATGTCTGGGACATTGGCATC--TAT
* * * *
31858159 ATGA-TTTTGTGTAAGACCATGTCTGGAACATTGGCATCAAT
1 ATGAGATTAGTGTAAGACCATGTCTGGGACATTGGCATCTAT
* * *
31858200 ATGAGA-TAGCATGTAAGACCATATCTGGGATA-TGGCAT-TTT
1 ATGAGATTAG--TGTAAGACCATGTCTGGGACATTGGCATCTAT
31858241 ATGAG
1 ATGAG
31858246 CTTTATGTGA
Statistics
Matches: 108, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
41 14 0.13
42 7 0.06
43 80 0.74
44 2 0.02
45 2 0.02
46 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (42 bp):
ATGAGATTAGTGTAAGACCATGTCTGGGACATTGGCATCTAT
Found at i:31860850 original size:43 final size:42
Alignment explanation
Indices: 31860739--31860899 Score: 130
Period size: 44 Copynumber: 3.8 Consensus size: 42
31860729 AAGGCGAACA
* * *
31860739 TCCCAGACGTGGTCTTACATGTAATCAAATATTGATGCCTCTAT-
1 TCCCAGACATGGTCTTACATGAAATCAAATA-TGAT-CC-CAATG
* * * *
31860783 CCCCA-ACAGGGTCTTATATGAAATCAAATATGATCCCGATG
1 TCCCAGACATGGTCTTACATGAAATCAAATATGATCCCAATG
* * *
31860824 TCCCAGACATGGTCTTACATGTAAATCTCAAAT-CGATGCCAACG
1 TCCCAGACATGGTCTTACATG-AAA--TCAAATATGATCCCAATG
* * *
31860868 TCCCAGACGTGGTCTTACACGAAATCACATAT
1 TCCCAGACATGGTCTTACATGAAATCAAATAT
31860900 CGGAATCCTA
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
40 3 0.03
41 11 0.12
42 17 0.18
43 27 0.29
44 30 0.32
45 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACATGAAATCAAATATGATCCCAATG
Found at i:31863778 original size:42 final size:42
Alignment explanation
Indices: 31863715--31863867 Score: 198
Period size: 42 Copynumber: 3.6 Consensus size: 42
31863705 TGAGATGCCA
* * * * *
31863715 ATGCCATGTCCCAGATGTGGTCTTACATGAGATCTCACATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
31863757 ATGCCATATCCCAGATATGGTCTTATACGACATCTCATTTCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
31863799 ATGCCATGTCCCAGATGTGGTCTTACACGAAATCTCATATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
31863841 AGGCCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
31863868 TGATAACACA
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 95 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:31863886 original size:84 final size:84
Alignment explanation
Indices: 31863715--31863893 Score: 234
Period size: 84 Copynumber: 2.1 Consensus size: 84
31863705 TGAGATGCCA
* * * *
31863715 ATGCCATGTCCCAGATGTGGTCTTACATGAGATCTCACATCGATGCCATATCCCAGATATGGTCT
1 ATGCCATGTCCCAGATGTGGTCTTACACGAAATCTCACATCAAGGCCATATCCCAGATATGGTCT
* * * *
31863780 TATACGACATCTCATTTCG
66 TACACGACAACACATCTCG
*
31863799 ATGCCATGTCCCAGATGTGGTCTTACACGAAATCTCATATCAAGGCCATATCCCAGATATGGTCT
1 ATGCCATGTCCCAGATGTGGTCTTACACGAAATCTCACATCAAGGCCATATCCCAGATATGGTCT
* *
31863864 TACATGATAACACATACT-G
66 TACACGACAACACAT-CTCG
31863883 ATGCCGATGTC
1 ATGCC-ATGTC
31863894 ATATCCCAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
84 76 0.93
85 6 0.07
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (84 bp):
ATGCCATGTCCCAGATGTGGTCTTACACGAAATCTCACATCAAGGCCATATCCCAGATATGGTCT
TACACGACAACACATCTCG
Found at i:31878620 original size:46 final size:46
Alignment explanation
Indices: 31878570--31878746 Score: 166
Period size: 46 Copynumber: 3.8 Consensus size: 46
31878560 TGGTTGAGCA
*
31878570 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
31878616 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * * *
31878661 CATCCGAACTCGTTAAGTTGACTCCAAAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCC-GAGTTCACTTATGGATGCGAATG
* *
31878710 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31878747 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 16, Indels: 22
0.73 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 44 0.42
47 36 0.35
48 5 0.05
49 3 0.03
51 4 0.04
52 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31878727 original size:94 final size:93
Alignment explanation
Indices: 31878567--31878739 Score: 267
Period size: 94 Copynumber: 1.8 Consensus size: 93
31878557 GGATGGTTGA
* * * * * *
31878567 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGACTCCAAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
31878632 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
31878660 GCATCCGAACTCGTTAAGTTGACTCCAAAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGA
1 GCATCCGAACTCGTTAAGTTGACTCC-AAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGA
31878724 GTTGAGTCCGAGTTCG
64 GTTGAGTCCGAGTTCG
31878740 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
93 27 0.38
94 45 0.62
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGACTCCAAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31881701 original size:15 final size:15
Alignment explanation
Indices: 31881681--31881748 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 15
31881671 GTATCTTGGG
31881681 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
31881696 TCTC-TTATTCTAGA
1 TTTCTTTATCCTGGA
* *
31881710 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
31881725 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
31881740 TTTCTTTAT
1 TTTCTTTAT
31881749 TCGATTTTCT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 11 0.27
15 30 0.73
ACGTcount: A:0.13, C:0.18, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:31881744 original size:30 final size:29
Alignment explanation
Indices: 31881672--31881750 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
31881662 CATAGTATCG
* *
31881672 TATCTTGGGTTTCTTTATCCTGGATCTCT
1 TATCTTGGATTTCTTTATTCTGGATCTCT
* * *
31881701 TAT-TCTAGATTTCTTTATTCTGGGTTTCT
1 TATCT-TGGATTTCTTTATTCTGGATCTCT
31881730 CTATCTTGGATTTCTTTATTC
1 -TATCTTGGATTTCTTTATTC
31881751 GATTTTCTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 22 0.54
30 17 0.41
31 1 0.02
ACGTcount: A:0.13, C:0.18, G:0.14, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCTGGATCTCT
Found at i:31884194 original size:46 final size:45
Alignment explanation
Indices: 31884144--31884319 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
31884134 TGGTTGAGCA
31884144 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
31884190 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
31884235 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
31884283 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31884320 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:31884300 original size:93 final size:93
Alignment explanation
Indices: 31884141--31884312 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31884131 GGATGGTTGA
* *
31884141 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31884206 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
31884234 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31884299 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
31884313 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31887363 original size:42 final size:43
Alignment explanation
Indices: 31887256--31887365 Score: 109
Period size: 44 Copynumber: 2.6 Consensus size: 43
31887246 ATATGCGTTA
* * * *
31887256 TCGTATAAGACCATATTTAGAACATTGGCATCGACTTATGATT
1 TCGTGTAAGACCCTATTTGGGACATTGGCATCGACTTATGATT
* * *
31887299 TACGTGTAAGACCAC-GTCTGGGACGTTGGCATCGTA-TT-TGATT
1 T-CGTGTAAGACC-CTATTTGGGACATTGGCATCG-ACTTATGATT
31887342 TCGTGTAAGACCCTATTTGGGACA
1 TCGTGTAAGACCCTATTTGGGACA
31887366 GAGGCTTCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.02
42 18 0.34
43 7 0.13
44 26 0.49
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (43 bp):
TCGTGTAAGACCCTATTTGGGACATTGGCATCGACTTATGATT
Found at i:31896632 original size:42 final size:42
Alignment explanation
Indices: 31896571--31896694 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
31896561 GTAATCACAT
* * *
31896571 ATCGATGCCACTGTCCCAGACAGGGTCTTACACGAACTCATAA
1 ATCGATGCCA-TGTCCCAGACAGGGTCTTACACGAAATAAAAA
* *
31896614 A-CGATGCCGATGTCCCAGACATGGCCTTACACGCAAATAAAAA
1 ATCGATGCC-ATGTCCCAGACAGGGTCTTACACG-AAATAAAAA
* *
31896657 ATCGATGCCAATGTCCTAGAC-GTCGTCTTACACGAAAT
1 ATCGATGCC-ATGTCCCAGACAG-GGTCTTACACGAAAT
31896695 CACATATCGA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 28 0.42
43 13 0.19
44 26 0.39
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCGATGCCATGTCCCAGACAGGGTCTTACACGAAATAAAAA
Found at i:31896687 original size:44 final size:43
Alignment explanation
Indices: 31896535--31896694 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
31896525 TTGTACAACA
* * * * * * *
31896535 CCAACGTCCCAGACGTGTTCTTACATGTAATCACATATCGATG
1 CCAATGTCCCAGACGTGGTCTTACACGAAATAAAAAATCGATG
* * * *
31896578 CCACTGTCCCAGACAG-GGTCTTACACGAACTCATAAA-CGATG
1 CCAATGTCCCAGAC-GTGGTCTTACACGAAATAAAAAATCGATG
* * *
31896620 CCGATGTCCCAGACATGGCCTTACACGCAAATAAAAAATCGATG
1 CCAATGTCCCAGACGTGGTCTTACACG-AAATAAAAAATCGATG
* *
31896664 CCAATGTCCTAGACGTCGTCTTACACGAAAT
1 CCAATGTCCCAGACGTGGTCTTACACGAAAT
31896695 CACATATCGA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
42 27 0.29
43 38 0.41
44 28 0.30
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
CCAATGTCCCAGACGTGGTCTTACACGAAATAAAAAATCGATG
Found at i:31897845 original size:15 final size:13
Alignment explanation
Indices: 31897813--31897837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31897803 ACAAACGATA
31897813 AAATTTTCACACG
1 AAATTTTCACACG
31897826 AAATTTTCACAC
1 AAATTTTCACAC
31897838 ATATAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:31903608 original size:43 final size:43
Alignment explanation
Indices: 31903467--31903609 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 43
31903457 ATACCACGTT
* *
31903467 TGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCATGTC
1 TGGGACGTTGGCATCG--ATATGTGATTACGTGTAAGACCATATC
* * * * * *
31903512 TGGGACATCGGTATCG-TATTTGATT-TGTGTAAGACCCTATC
1 TGGGACGTTGGCATCGATATGTGATTACGTGTAAGACCATATC
* * *
31903553 TGGGATAG-TGGCATCGATATGTGATTACATGTAAGACCAAATC
1 TGGGA-CGTTGGCATCGATATGTGATTACGTGTAAGACCATATC
31903596 TGGGACGTTGGCAT
1 TGGGACGTTGGCAT
31903610 TGTACGATAT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
41 24 0.32
42 16 0.21
43 23 0.30
45 13 0.17
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (43 bp):
TGGGACGTTGGCATCGATATGTGATTACGTGTAAGACCATATC
Found at i:31909590 original size:23 final size:25
Alignment explanation
Indices: 31909544--31909597 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
31909534 ACTTTTCATT
* *
31909544 ATTTTTAAAGACTTGGATATTTTTA
1 ATTTTTAAAGACTTAGATACTTTTA
31909569 ATTTTT-AAG-CTTAGATACTTTTA
1 ATTTTTAAAGACTTAGATACTTTTA
31909592 ATTTTT
1 ATTTTT
31909598 TAGGTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 18 0.67
24 3 0.11
25 6 0.22
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.56
Consensus pattern (25 bp):
ATTTTTAAAGACTTAGATACTTTTA
Found at i:31911196 original size:22 final size:22
Alignment explanation
Indices: 31911146--31911199 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
31911136 CAGCCTCCAG
*
31911146 CACGGGCGTG-CCCCAGGATCA
1 CACGGGCGTGTCCCCAGGACCA
* **
31911167 CACCGGCGTGTCCCTTGGACCA
1 CACGGGCGTGTCCCCAGGACCA
31911189 CACGGGCGTGT
1 CACGGGCGTGT
31911200 GAGCCTTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (22 bp):
CACGGGCGTGTCCCCAGGACCA
Found at i:31913134 original size:10 final size:10
Alignment explanation
Indices: 31913110--31913156 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
31913100 TCTATCAACT
31913110 AACATT-AAA
1 AACATTCAAA
31913119 ATACATTCAAA
1 A-ACATTCAAA
31913130 AACA-T-AAA
1 AACATTCAAA
31913138 ATACATTCAAA
1 A-ACATTCAAA
31913149 AACATTCA
1 AACATTCA
31913157 TGGAAAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.12
9 5 0.15
10 16 0.48
11 8 0.24
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (10 bp):
AACATTCAAA
Done.