Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008994.1 Hibiscus syriacus cultivar Beakdansim tig00112370_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: 399360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:245265 original size:12 final size:12
Alignment explanation
Indices: 245250--245284 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
245240 CGATTCTCGG
245250 CCCAATACCCGA
1 CCCAATACCCGA
*
245262 CCCAATACCCGG
1 CCCAATACCCGA
245274 CCCAATACCCG
1 CCCAATACCCG
245285 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:252092 original size:9 final size:9
Alignment explanation
Indices: 252078--252180 Score: 71
Period size: 9 Copynumber: 10.8 Consensus size: 9
252068 GGCTGCTGGA
252078 AACCGGTTT
1 AACCGGTTT
252087 AACCGGTTTT
1 AACCGG-TTT
252097 CAACCGGTTCT
1 -AACCGGTT-T
*
252108 GACCGGTTT
1 AACCGGTTT
*
252117 GACCGGTTT
1 AACCGGTTT
* *
252126 CAACCAGTTCG
1 -AACCGGTT-T
252137 AACCGGTTT
1 AACCGGTTT
* *
252146 GACCGGTCTG
1 AACCGGT-TT
*
252156 AATCGGTTT
1 AACCGGTTT
*
252165 GACCGGTTT
1 AACCGGTTT
*
252174 GACCGGT
1 AACCGGT
252181 CTGAATCGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:252103 original size:11 final size:10
Alignment explanation
Indices: 252078--252145 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
252068 GGCTGCTGGA
252078 AACCGG-TTT
1 AACCGGTTTT
252087 AACCGGTTTT
1 AACCGGTTTT
*
252097 CAACCGGTTCT
1 -AACCGGTTTT
*
252108 GACCGG-TTT
1 AACCGGTTTT
* *
252117 GACCGGTTTC
1 AACCGGTTTT
* **
252127 AACCAGTTCG
1 AACCGGTTTT
252137 AACCGGTTT
1 AACCGGTTT
252146 GACCGGTCTG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
9 14 0.30
10 23 0.50
11 9 0.20
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:252103 original size:20 final size:21
Alignment explanation
Indices: 252078--252116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
252068 GGCTGCTGGA
252078 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
252098 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
252117 GACCGGTTTC
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:252123 original size:19 final size:18
Alignment explanation
Indices: 252079--252196 Score: 92
Period size: 19 Copynumber: 6.2 Consensus size: 18
252069 GCTGCTGGAA
* *
252079 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGG-TTT-G
252099 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
* * *
252118 ACCGGTTTCAACCAGTTCG
1 ACCGGTTT-GACCGGTTTG
*
252137 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
*
252156 AATCGGTTTGACCGGTTTG
1 -ACCGGTTTGACCGGTTTG
* *
252175 ACCGGTCTGAATCGGTTTG
1 ACCGGTTTG-ACCGGTTTG
252194 ACC
1 ACC
252197 CGACCCGACC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
18 8 0.10
19 48 0.60
20 18 0.22
21 6 0.08
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:252141 original size:29 final size:28
Alignment explanation
Indices: 252079--252180 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 28
252069 GCTGCTGGAA
*
252079 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
*
252109 ACCGGTTTGACCGGTTTCAACCAGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
252137 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
252166 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
252181 CTGAATCGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
28 16 0.25
29 35 0.55
30 13 0.20
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:252178 original size:28 final size:28
Alignment explanation
Indices: 252101--252196 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
252091 GGTTTTCAAC
* * *
252101 CGGTTCTGACCGGTTTGACCGGTTTCAAC
1 CGGTT-TGACCGGTTTGACCGGTCTGAAT
* *
252130 CAGTTCGAACCGGTTTGACCGGTCTGAAT
1 CGGTTTG-ACCGGTTTGACCGGTCTGAAT
252159 CGGTTTGACCGGTTTGACCGGTCTGAAT
1 CGGTTTGACCGGTTTGACCGGTCTGAAT
252187 CGGTTTGACC
1 CGGTTTGACC
252197 CGACCCGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 32 0.54
29 27 0.46
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (28 bp):
CGGTTTGACCGGTTTGACCGGTCTGAAT
Found at i:252203 original size:5 final size:5
Alignment explanation
Indices: 252193--252267 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
252183 GAATCGGTTT
* * *
252193 GACCC GACCC GACCGTT GACCC GACCC GACCGTT GACCC GACCT GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
*
252242 GACCGTT GACCC GACCC GACCC GACC
1 GACC--C GACCC GACCC GACCC GACC
252268 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
5 44 0.79
7 12 0.21
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:252218 original size:22 final size:22
Alignment explanation
Indices: 252210--252274 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
252200 CCCGACCGTT
252210 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
252232 GACCTGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
252254 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
252275 GTTGACCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:252274 original size:17 final size:17
Alignment explanation
Indices: 252191--252262 Score: 99
Period size: 17 Copynumber: 3.9 Consensus size: 17
252181 CTGAATCGGT
252191 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
252208 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
252225 TTGACCCGACCTGACCCGACCG
1 TTGA--C--CC-GACCCGACCG
252247 TTGACCCGACCCGACC
1 TTGACCCGACCCGACC
252263 CGACCGTTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
17 30 0.60
18 2 0.04
19 1 0.02
20 1 0.02
21 2 0.04
22 14 0.28
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:252276 original size:7 final size:7
Alignment explanation
Indices: 252264--252294 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
252254 GACCCGACCC
252264 GACCGTT
1 GACCGTT
252271 GACCGTT
1 GACCGTT
252278 GACCGTT
1 GACCGTT
*
252285 GACCATT
1 GACCGTT
252292 GAC
1 GAC
252295 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:262166 original size:56 final size:57
Alignment explanation
Indices: 262080--262189 Score: 161
Period size: 56 Copynumber: 1.9 Consensus size: 57
262070 ACAGCTCAAA
* *
262080 TGGTCTCCCGACTATAGGGCGTTGTCTTGTTGTGTCTCGA-ATTAAAAGTTACGAAG
1 TGGTCTCCCGACTATAGGGCGTTGTCTTGTTGAGTCCCGACATTAAAAGTTACGAAG
*
262136 TGGTCTCCCGATTATAGGGCGTTG-CTTTGTTGAGTCCCGACTATTAAAAGTTAC
1 TGGTCTCCCGACTATAGGGCGTTGTC-TTGTTGAGTCCCGAC-ATTAAAAGTTAC
262190 AAAATGATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
55 1 0.02
56 35 0.73
58 12 0.25
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (57 bp):
TGGTCTCCCGACTATAGGGCGTTGTCTTGTTGAGTCCCGACATTAAAAGTTACGAAG
Found at i:263026 original size:41 final size:41
Alignment explanation
Indices: 262980--263058 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
262970 AAATTGGTCC
262980 TTAAACTTTTAAATGTTTCAATTTCATCTCTTAACTATGAT
1 TTAAACTTTTAAATGTTTCAATTTCATCTCTTAACTATGAT
*
263021 TTAAACTTTTAAATGTTTCAATTTCGTCTCTTAACTAT
1 TTAAACTTTTAAATGTTTCAATTTCATCTCTTAACTAT
263059 TATTATCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.49
Consensus pattern (41 bp):
TTAAACTTTTAAATGTTTCAATTTCATCTCTTAACTATGAT
Found at i:264646 original size:36 final size:36
Alignment explanation
Indices: 264547--264647 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
264537 TTAACCCCAT
** * *
264547 CTCTTCATCTTCAGTTACTTTTTCCTTATTAAGCAG
1 CTCTTCATCTTTGGTTCCTTTTTCCTTCTTAAGCAG
* * *
264583 CTCTTCAT-TTTCGGTGCCTTCTTCCTTCTTAGGCAG
1 CTCTTCATCTTT-GGTTCCTTTTTCCTTCTTAAGCAG
264619 CTCTTCATCTTTGGTTCCTTTTTCCTTCT
1 CTCTTCATCTTTGGTTCCTTTTTCCTTCT
264648 GAGGAGATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 2 0.04
36 49 0.91
37 3 0.06
ACGTcount: A:0.11, C:0.29, G:0.11, T:0.50
Consensus pattern (36 bp):
CTCTTCATCTTTGGTTCCTTTTTCCTTCTTAAGCAG
Found at i:265927 original size:58 final size:58
Alignment explanation
Indices: 265856--265970 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
265846 ACTATTAAAA
**
265856 GTTACAAAATAGTCCTACGACTATA-GAGTCTGCTTTGTTCAGTCTCTCAACAATTAAT
1 GTTACAAAATAGTCC-ACGACTATAGGACACTGCTTTGTTCAGTCTCTCAACAATTAAT
* * * *
265914 GTTACAAAATAGTCCCCGACTATAGGACACTGCTTTGTTGAGTCTCTCGACTATTAA
1 GTTACAAAATAGTCCACGACTATAGGACACTGCTTTGTTCAGTCTCTCAACAATTAA
265971 AAGTTGCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 8 0.16
58 42 0.84
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (58 bp):
GTTACAAAATAGTCCACGACTATAGGACACTGCTTTGTTCAGTCTCTCAACAATTAAT
Found at i:266056 original size:60 final size:59
Alignment explanation
Indices: 265734--266043 Score: 269
Period size: 60 Copynumber: 5.2 Consensus size: 59
265724 CTTTTAGGGT
* * * * * *
265734 AAAGTATAC-AAATGGTCCCCAGACTATAGGGT-CTGCTTCGTTGAGTC-CGCTAACGATTA
1 AAAGT-TACAAAATAGTCCCC-GACTATAGAGTACTGCTTTGTTGAGTCTCTC-GACTATTA
* * * **
265793 AAAGTTATAAAAT-GATCCCTCAACTATAGGGTGTTGCTTTGTTGAGTAC-CTCGACTATTA
1 AAAGTTACAAAATAG-TCCC-CGACTATAGAGTACTGCTTTGTTGAGT-CTCTCGACTATTA
* * * *
265853 AAAGTTACAAAATAGTCCTACGACTATAGAGT-CTGCTTTGTTCAGTCTCTCAACAATT-
1 AAAGTTACAAAATAGTCC-CCGACTATAGAGTACTGCTTTGTTGAGTCTCTCGACTATTA
* *
265911 AATGTTACAAAATAGTCCCCGACTATAG-GACACTGCTTTGTTGAGTCTCTCGACTATTA
1 AAAGTTACAAAATAGTCCCCGACTATAGAG-TACTGCTTTGTTGAGTCTCTCGACTATTA
* * * * *
265970 AAAGTTGCAAAGTGGTCCCCTGACTATAGAGTATTGCTTTGTTGAGTAC-CCCGACTATTA
1 AAAGTTACAAAATAGTCCCC-GACTATAGAGTACTGCTTTGTTGAGT-CTCTCGACTATTA
266030 AAAGTTACAAAATA
1 AAAGTTACAAAATA
266044 ATATCTTGAC
Statistics
Matches: 206, Mismatches: 31, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
56 1 0.00
57 9 0.04
58 44 0.21
59 59 0.29
60 87 0.42
61 6 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (59 bp):
AAAGTTACAAAATAGTCCCCGACTATAGAGTACTGCTTTGTTGAGTCTCTCGACTATTA
Found at i:266083 original size:29 final size:29
Alignment explanation
Indices: 266019--266088 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
266009 TGTTGAGTAC
*
266019 CCCGACTATTAAAAGTTACAAAATAATAT
1 CCCGACTATTAAAAGCTACAAAATAATAT
** **
266048 CTTGACTATTAAAAGCTACAAAATGGTCA-
1 CCCGACTATTAAAAGCTACAAAATAAT-AT
266077 CCCGACTATTAA
1 CCCGACTATTAA
266089 TATGTTTCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (29 bp):
CCCGACTATTAAAAGCTACAAAATAATAT
Found at i:270964 original size:12 final size:13
Alignment explanation
Indices: 270942--270974 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
270932 TCTTTTTCTT
270942 TTTATATTAATTAA
1 TTTA-ATTAATTAA
270956 -TTAATTAATTAA
1 TTTAATTAATTAA
270968 TTTAATT
1 TTTAATT
270975 GCAATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAATTAATTAA
Found at i:271141 original size:22 final size:23
Alignment explanation
Indices: 271116--271159 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
271106 TGGCGAATAC
271116 ATAAA-ATTACGGACTAATTTTA
1 ATAAATATTACGGACTAATTTTA
*
271138 ATAAATATTAGGGACTAATTTT
1 ATAAATATTACGGACTAATTTT
271160 GTTATCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
ATAAATATTACGGACTAATTTTA
Found at i:271528 original size:2 final size:2
Alignment explanation
Indices: 271523--271555 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
271513 AAATAAATAA
271523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
271556 ATAGAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:272066 original size:21 final size:21
Alignment explanation
Indices: 272028--272067 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
272018 ATGGGCATGA
*
272028 GACCCGAACCCGATGGGTTCC
1 GACCCGAACCCAATGGGTTCC
272049 GACCC-AACCCAATCGGGTT
1 GACCCGAACCCAAT-GGGTT
272068 GAGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
GACCCGAACCCAATGGGTTCC
Found at i:277161 original size:20 final size:20
Alignment explanation
Indices: 277136--277185 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
277126 TGGTATTTAA
277136 ATATTTAATTTTTTAAAATT
1 ATATTTAATTTTTTAAAATT
* *
277156 ATATTTAA-TATTTAATATT
1 ATATTTAATTTTTTAAAATT
*
277175 -TATTTCATTTT
1 ATATTTAATTTT
277186 AATATTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTAATTTTTTAAAATT
Found at i:277188 original size:17 final size:17
Alignment explanation
Indices: 277146--277195 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
277136 ATATTTAATT
*
277146 TTTTAAAATTATATTTAA
1 TTTTAATATT-TATTTAA
*
277164 TATTTAATATTTATTTCA
1 T-TTTAATATTTATTTAA
277182 TTTTAATATTTATT
1 TTTTAATATTTATT
277196 GTTAAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.45
18 8 0.28
19 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATATTTATTTAA
Found at i:281181 original size:31 final size:31
Alignment explanation
Indices: 281146--281213 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
281136 TCAAAAAACA
281146 TAAGATACAATCACTTTCATTTTTATTTAAT
1 TAAGATACAATCACTTTCATTTTTATTTAAT
*** *
281177 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATACAATCACTTTCATTTTTATTTAAT
*
281208 CAAGAT
1 TAAGAT
281214 TTGGCCATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (31 bp):
TAAGATACAATCACTTTCATTTTTATTTAAT
Found at i:281356 original size:25 final size:26
Alignment explanation
Indices: 281328--281376 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
281318 TAATAAATTC
*
281328 AAAT-AAATTATATATTTTTAAATGA
1 AAATAAAATAATATATTTTTAAATGA
281353 AAATAAAATAATATATTTTTAAAT
1 AAATAAAATAATATATTTTTAAAT
281377 TAAGTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATAAAATAATATATTTTTAAATGA
Found at i:281389 original size:27 final size:27
Alignment explanation
Indices: 281339--281431 Score: 95
Period size: 26 Copynumber: 3.6 Consensus size: 27
281329 AATAAATTAT
* ** *
281339 ATATTTTTAAATGAAAATAA-AATAAT
1 ATATTTTTAAATTAAGTTAATAATAAA
281365 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
*
281392 ATATATTT-AA-TAAGTTAAT-ATAAAA
1 ATATTTTTAAATTAAGTTAATAAT-AAA
*
281417 ATATTTTTAAGTTAA
1 ATATTTTTAAATTAA
281432 TATATATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.04
25 19 0.34
26 20 0.36
27 15 0.27
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTTAATAATAAA
Found at i:281410 original size:22 final size:22
Alignment explanation
Indices: 281377--281435 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 22
281367 ATTTTTAAAT
281377 TAAGTTAATAATAAAATATATTTAA
1 TAAGTTAAT-ATAAAA-ATATTT-A
*
281402 TAAGTTAATATAAAAATATTTT
1 TAAGTTAATATAAAAATATTTA
281424 TAAGTTAATATA
1 TAAGTTAATATA
281436 TATAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 12 0.36
23 6 0.18
24 6 0.18
25 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAGTTAATATAAAAATATTTA
Found at i:281411 original size:25 final size:25
Alignment explanation
Indices: 281359--281433 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 25
281349 ATGAAAATAA
* *
281359 AATAATATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
281386 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
*
281411 -ATAAAA-ATATTT-TTAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
281433 A
1 A
281434 TATATAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 9 0.20
23 6 0.14
24 6 0.14
25 9 0.20
26 2 0.05
27 12 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:281442 original size:25 final size:25
Alignment explanation
Indices: 281375--281443 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
281365 ATATTTTTAA
281375 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAA-ATATTT
*
281400 AATAAGTT-A-ATATAAAAATATTT
1 ATTAAGTTAATATATAAAAATATTT
281423 -TTAAGTTAATATATATAAAAT
1 ATTAAGTTAATATATA-AAAAT
281444 TATATTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.16
23 8 0.21
24 12 0.32
25 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTAAGTTAATATATAAAAATATTT
Found at i:281514 original size:15 final size:16
Alignment explanation
Indices: 281490--281521 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
281480 CATAATATTT
281490 TTATTCATTATTTAAA
1 TTATTCATTATTTAAA
281506 TTATT-ATTATTTAAA
1 TTATTCATTATTTAAA
281521 T
1 T
281522 ATATATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTCATTATTTAAA
Found at i:281649 original size:35 final size:36
Alignment explanation
Indices: 281581--281650 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
281571 CACATAAATT
* * *
281581 TTAAAAATTCAAATTACATAAATGAAATAAAATTTA
1 TTAAAAATTCAAAATAAAGAAATGAAATAAAATTTA
* *
281617 TTAAAAATT-AAAATAAAGAAATGTAATTAAATTT
1 TTAAAAATTCAAAATAAAGAAATGAAATAAAATTT
281651 CGAATGTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (36 bp):
TTAAAAATTCAAAATAAAGAAATGAAATAAAATTTA
Found at i:284601 original size:2 final size:2
Alignment explanation
Indices: 284594--284623 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
284584 ATGACTCTTT
284594 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
284624 CATGGTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:288938 original size:111 final size:111
Alignment explanation
Indices: 288715--289273 Score: 888
Period size: 111 Copynumber: 5.0 Consensus size: 111
288705 GGTAAAATTA
* ** * * * **
288715 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* * *
288780 TCCGCTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTG
65 TCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
288827 AATCAGGGTAGACTTGTTCCACTGTCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
288892 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
288938 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
289003 CCACTTCCTCTGAGGGAATATCAGATATGGGAAATTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
289049 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
289112 CCACTTCCTCTGAGGGAATATCAGATCTGTGAAAGTTGATTAATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
289158 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * * *
289223 CCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTTGATCCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
289269 AATCA
1 AATCA
289274 GGGTCGAACC
Statistics
Matches: 418, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
109 102 0.24
110 4 0.01
111 262 0.63
112 50 0.12
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (111 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:289188 original size:220 final size:222
Alignment explanation
Indices: 288710--289273 Score: 916
Period size: 220 Copynumber: 2.5 Consensus size: 222
288700 CTTCAGGTAA
* * ** * * * **
288710 AATTAAATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGAGATTTGA
1 AATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGA
* * *
288775 TCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGAC
65 TCTGTTCCACTTCTTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGAC
*
288840 TTGTTCCACTGTCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGA
130 TTGTTCCACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGA
288905 GGGAATATCAGATCTGGGAAAGTTGATT
195 GGGAATATCAGATCTGGGAAAGTTGATT
*
288933 CATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
1 AATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
* * *
288998 CTGTTCCACTTCCTCTGAGGGAATATCAGATATGGGAAATTTGATTCATTGAATCAAGGTAGACT
66 CTGTTCCACTTCTTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGACT
* *
289063 TGTTCCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTTCCACTTCCTCTGAG
131 TGTTCCACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAG
*
289126 GGAATATCAGATCTGTGAAAGTTGATT
196 GGAATATCAGATCTGGGAAAGTTGATT
289153 AATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
1 AATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
*
289218 CTGTTCCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCA
66 CTGTTCCACTTCTTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCA
289274 GGGTCGAACC
Statistics
Matches: 316, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
220 169 0.53
221 2 0.01
222 93 0.29
223 52 0.16
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (222 bp):
AATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
CTGTTCCACTTCTTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGACT
TGTTCCACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAG
GGAATATCAGATCTGGGAAAGTTGATT
Found at i:290481 original size:12 final size:12
Alignment explanation
Indices: 290463--290518 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
290453 TTCTTTTTCC
290463 TCATTTTTTCTT
1 TCATTTTTTCTT
290475 TC-TTTTTT-TT
1 TCATTTTTTCTT
*
290485 TCATTTTTTTTT
1 TCATTTTTTCTT
* *
290497 TCATTTTTCCAT
1 TCATTTTTTCTT
290509 TCATTTTTTC
1 TCATTTTTTC
290519 AGGCGAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 4 0.11
11 12 0.32
12 22 0.58
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (12 bp):
TCATTTTTTCTT
Found at i:290481 original size:22 final size:21
Alignment explanation
Indices: 290443--290518 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
290433 CCATTCTTTT
*
290443 ATTTTTATTTTTCTTTTTCCTC
1 ATTTTT-TCTTTCTTTTTCCTC
**
290465 ATTTTTTCTTTCTTTTTTTTTC
1 ATTTTTTCTTTC-TTTTTCCTC
*
290487 ATTTTTTTTTTCATTTTTCCATTC
1 ATTTTTTCTTTC-TTTTTCC--TC
290511 ATTTTTTC
1 ATTTTTTC
290519 AGGCGAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.12
22 29 0.67
24 9 0.21
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTTTTCTTTCTTTTTCCTC
Found at i:303822 original size:59 final size:59
Alignment explanation
Indices: 303703--303825 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 59
303693 TAAAAAAAGA
* *
303703 ATAGTTGGTGACTATTTTGTAACATTAAATAGTTAGGGGACTCAACAAAATATCATTTT
1 ATAGTTGGAGACCATTTTGTAACATTAAATAGTTAGGGGACTCAACAAAATATCATTTT
* *
303762 ATAGTTAGGAGACCATTTTGTAAC-TTCTAATAGTTAGGGGACTTAA-AAAATAAT-ATTTT
1 ATAGTT-GGAGACCATTTTGTAACATT-AAATAGTTAGGGGACTCAACAAAAT-ATCATTTT
303821 ATAGT
1 ATAGT
303826 CGAGGACCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
59 23 0.40
60 34 0.60
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (59 bp):
ATAGTTGGAGACCATTTTGTAACATTAAATAGTTAGGGGACTCAACAAAATATCATTTT
Found at i:304041 original size:2 final size:2
Alignment explanation
Indices: 304034--304059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
304024 ATTATACCTC
304034 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
304060 TTCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:310610 original size:20 final size:20
Alignment explanation
Indices: 310585--310657 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
310575 CAAGAAAAAT
310585 CAGATTCCCCCCAGGGGGAA
1 CAGATTCCCCCCAGGGGGAA
* *
310605 CAGATTCCCCCCTAGAGGGTA
1 CAGATTCCCCCC-AGGGGGAA
* *
310626 CCGATTCCCCCTAGGGGGAA
1 CAGATTCCCCCCAGGGGGAA
310646 CAGATTCCCCCC
1 CAGATTCCCCCC
310658 CCCAGGGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.22, C:0.38, G:0.25, T:0.15
Consensus pattern (20 bp):
CAGATTCCCCCCAGGGGGAA
Found at i:310644 original size:41 final size:42
Alignment explanation
Indices: 310587--310681 Score: 147
Period size: 43 Copynumber: 2.3 Consensus size: 42
310577 AGAAAAATCA
* *
310587 GATTCCCCCCAGGGGGAACAGATT-CCCCCCTAGAGGGTACC
1 GATTCCCCCTAGGGGGAACAGATTCCCCCCCCAGAGGGTACC
*
310628 GATTCCCCCTAGGGGGAACAGATTCCCCCCCCCAGGGGGTACC
1 GATTCCCCCTAGGGGGAACAGATT-CCCCCCCCAGAGGGTACC
310671 GATTCCCCCTA
1 GATTCCCCCTA
310682 TCTAACGGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 23 0.47
43 26 0.53
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.16
Consensus pattern (42 bp):
GATTCCCCCTAGGGGGAACAGATTCCCCCCCCAGAGGGTACC
Found at i:311978 original size:19 final size:20
Alignment explanation
Indices: 311954--312001 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
311944 AATGATTTTC
*
311954 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
311973 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
311993 TTTTGAAAA
1 TTTTGAAAA
312002 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:313442 original size:21 final size:21
Alignment explanation
Indices: 313416--313456 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
313406 AATCAGATTG
313416 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
313437 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
313457 TCCTGTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:316397 original size:20 final size:20
Alignment explanation
Indices: 316372--316423 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
316362 ACGCGATATC
* *
316372 AAAATCGCAACGTTGAAAAG
1 AAAATCGCAACGGTCAAAAG
316392 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
316412 AAAATCGCAACG
1 AAAATCGCAACG
316424 CGATATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAG
Found at i:316459 original size:20 final size:20
Alignment explanation
Indices: 316434--316490 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
316424 CGATATTCCA
316434 AGAATCGCAACGCGATTAAG
1 AGAATCGCAACGCGATTAAG
316454 AGAATCGCAACGCGATTAAG
1 AGAATCGCAACGCGATTAAG
316474 AGAATCGCAACGCGATT
1 AGAATCGCAACGCGATT
316491 CAGAAAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (20 bp):
AGAATCGCAACGCGATTAAG
Found at i:316480 original size:62 final size:58
Alignment explanation
Indices: 316353--316489 Score: 152
Period size: 62 Copynumber: 2.3 Consensus size: 58
316343 AATGACCAAC
*
316353 AAAATCGCAACGCGATATCAAAATCGCAACGTTGAAAAGAAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGCGATATCAAAATCGCAACGTCGAAAAGAAAATCGCAACGGT-AAAAG
* * *
316412 AAAATCGCAACGCGATATTCCAAGAATCGCAACG-CGATTAAGAGAATCGCAACGCG-ATTAAG
1 AAAATCGCAACGCGATA-T-CAA-AATCGCAACGTCGA-AAAGAAAATCGCAACG-GTA-AAAG
*
316474 AGAATCGCAACGCGAT
1 AAAATCGCAACGCGAT
316490 TCAGAAAATG
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
59 17 0.25
60 1 0.01
61 6 0.09
62 42 0.63
63 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (58 bp):
AAAATCGCAACGCGATATCAAAATCGCAACGTCGAAAAGAAAATCGCAACGGTAAAAG
Found at i:322873 original size:175 final size:169
Alignment explanation
Indices: 322591--322906 Score: 578
Period size: 175 Copynumber: 1.8 Consensus size: 169
322581 TGTGATATGA
322591 TATTATTATATTTATTATATACAATAAAAATAAAAATAAATTGAAATTGGACCTATTGTGGCGTT
1 TATTATTATATTTATTATATACAATAAAAATAAAAATAAATTGAAATTGGACCTATTGTGGCGTT
322656 TATTAAAAACCCACTATAGATAAACGCTATTGCGGTGTTTTCATAAAACCGCCGCTAAAGTTCTA
66 TATTAAAAACCCACTATAGATAAACGCTATTGCGGTGTTTTCATAAAACCGCCGCTAAAGTTCTA
322721 ATTTGTTGCGATTAATAATTTTTGTGATATGATATTTAT
131 ATTTGTTGCGATTAATAATTTTTGTGATATGATATTTAT
322760 TATTATTATTATTTATTAATATACAATTAAAAATAAAAAATAAAATTGAAATTGGACCTATTGTG
1 TATTATTA-TATTTATT-ATATACAA-TAAAAAT-AAAAAT-AAATTGAAATTGGACCTATTGTG
322825 GCGTTTATTAAAAACCCCACTATAGATAAACGCTATTGCGGTGTTTTCATAAAACCGCCGCTAAA
61 GCGTTTATTAAAAA-CCCACTATAGATAAACGCTATTGCGGTGTTTTCATAAAACCGCCGCTAAA
322890 GTTCTAATTTGTTGCGA
125 GTTCTAATTTGTTGCGA
322907 AATTTAGAGG
Statistics
Matches: 141, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
169 8 0.06
170 8 0.06
171 8 0.06
172 7 0.05
173 6 0.04
174 37 0.26
175 67 0.48
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (169 bp):
TATTATTATATTTATTATATACAATAAAAATAAAAATAAATTGAAATTGGACCTATTGTGGCGTT
TATTAAAAACCCACTATAGATAAACGCTATTGCGGTGTTTTCATAAAACCGCCGCTAAAGTTCTA
ATTTGTTGCGATTAATAATTTTTGTGATATGATATTTAT
Found at i:323014 original size:40 final size:40
Alignment explanation
Indices: 322964--323039 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
322954 AAGTACTAGT
*
322964 CTATTGCGGCGTATATTAAAAAA-CGACACTATAGATACCC
1 CTATTACGGCGTATA-TAAAAAAGCGACACTATAGATACCC
* *
323004 CTATTACGGCGTTTATAAAAAAGCGCCACTATAGAT
1 CTATTACGGCGTATATAAAAAAGCGACACTATAGAT
323040 TAACTCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (40 bp):
CTATTACGGCGTATATAAAAAAGCGACACTATAGATACCC
Found at i:323240 original size:27 final size:27
Alignment explanation
Indices: 323210--323262 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
323200 ATTCATACAT
323210 ATTTAATATTTAATTACTTTAAAAAAA
1 ATTTAATATTTAATTACTTTAAAAAAA
* * *
323237 ATTTAATGTTTAATTATTTTATAAAA
1 ATTTAATATTTAATTACTTTAAAAAA
323263 TATAAAAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTTAATATTTAATTACTTTAAAAAAA
Found at i:324387 original size:16 final size:16
Alignment explanation
Indices: 324366--324451 Score: 61
Period size: 16 Copynumber: 5.4 Consensus size: 16
324356 TTAATCATTC
324366 TAATTTATTTTATTAA
1 TAATTTATTTTATTAA
* * *
324382 TAATTT-TTGTGACATGA
1 TAATTTATT-TTA-TTAA
*
324399 T-ATTTATTATTATTAT
1 TAATTTATT-TTATTAA
* * *
324415 TATTTTA-TTAATAAA
1 TAATTTATTTTATTAA
324430 TAATTTATTTTATTAA
1 TAATTTATTTTATTAA
324446 TAATTT
1 TAATTT
324452 TTGTGACATG
Statistics
Matches: 50, Mismatches: 15, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
15 12 0.24
16 27 0.54
17 11 0.22
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTTATTTTATTAA
Found at i:324404 original size:32 final size:33
Alignment explanation
Indices: 324368--324477 Score: 133
Period size: 32 Copynumber: 3.4 Consensus size: 33
324358 AATCATTCTA
324368 ATTTATT-TTATTAATAATTTTTGTGACATGAT
1 ATTTATTATTATTAATAATTTTTGTGACATGAT
* *
324400 ATTTATTATTATT-ATTATTTTAT-T-A-ATAAAT
1 ATTTATTATTATTAATAATTTT-TGTGACAT-GAT
324431 AATTTATT-TTATTAATAATTTTTGTGACATGAT
1 -ATTTATTATTATTAATAATTTTTGTGACATGAT
324464 ATTTATTATTATTA
1 ATTTATTATTATTA
324478 TTATTTTATT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
30 2 0.03
31 9 0.14
32 37 0.57
33 15 0.23
34 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTATTATTATTAATAATTTTTGTGACATGAT
Found at i:324436 original size:64 final size:64
Alignment explanation
Indices: 324366--324498 Score: 266
Period size: 64 Copynumber: 2.1 Consensus size: 64
324356 TTAATCATTC
324366 TAATTTATTTTATTAATAATTTTTGTGACATGATATTTATTATTATTATTATTTTATTAATAAA
1 TAATTTATTTTATTAATAATTTTTGTGACATGATATTTATTATTATTATTATTTTATTAATAAA
324430 TAATTTATTTTATTAATAATTTTTGTGACATGATATTTATTATTATTATTATTTTATTAATAAA
1 TAATTTATTTTATTAATAATTTTTGTGACATGATATTTATTATTATTATTATTTTATTAATAAA
324494 TAATT
1 TAATT
324499 ACAAATAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (64 bp):
TAATTTATTTTATTAATAATTTTTGTGACATGATATTTATTATTATTATTATTTTATTAATAAA
Found at i:328756 original size:43 final size:43
Alignment explanation
Indices: 328672--328916 Score: 282
Period size: 43 Copynumber: 5.7 Consensus size: 43
328662 CACAATGTCA
*
328672 AGATCTATAGCGGCGTTTTT-GAAACAAACG-TCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCT-GCAAAAGGTC
* *
328714 AGATCTATAGCGGTGTTTTTGGATACAAATGCTGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCTGCAAAAGGTC
* * ** *
328757 AAATCTATATCGGTTTTTTTGGATACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCTGCAAAAGGTC
* * * * **
328800 A-AGCCTATAGCGGCATTTTTTGATACAAATGCCACAAAAGGTC
1 AGA-TCTATAGCGGCGTTTTTGGATACAAACGCTGCAAAAGGTC
* * * *
328843 AGA-ATATAGCGGCATTTTTGGATACGAACACTGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCTGCAAAAGGTC
328885 AGATCTATAGCGGCGTTTTTGGATACAAACGC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGC
328917 CGCTAATTAC
Statistics
Matches: 172, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
42 55 0.32
43 115 0.67
44 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (43 bp):
AGATCTATAGCGGCGTTTTTGGATACAAACGCTGCAAAAGGTC
Found at i:328904 original size:128 final size:128
Alignment explanation
Indices: 328676--328919 Score: 337
Period size: 128 Copynumber: 1.9 Consensus size: 128
328666 ATGTCAAGAT
* * * **
328676 CTATAGCGGCGTTTTTGAAACAAACGTCGCAAAAGGTCAGATCTATAGCGGTGTTTTTGGATACA
1 CTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCAGATATATAGCGGCATTTTTGGATACA
** * **
328741 AATGCTGCAAAAGGTCAAATCTATATCGGTTTTTTTGGATACAAACGCCGCAAAAGGTCAAGC
66 AACACTGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGC
* * *
328804 CTATAGCGGCATTTTTTGATACAAATGCCACAAAAGGTCAGA-ATATAGCGGCATTTTTGGATAC
1 CTATAGCGGC-GTTTTTGAAACAAACGCCACAAAAGGTCAGATATATAGCGGCATTTTTGGATAC
* *
328868 GAACACTGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
65 AAACACTGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGATACAAACGCCGC
328920 TAATTACCAT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
128 74 0.74
129 26 0.26
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (128 bp):
CTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCAGATATATAGCGGCATTTTTGGATACA
AACACTGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGC
Found at i:328969 original size:15 final size:15
Alignment explanation
Indices: 328951--328995 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
328941 GATTAATTTA
*
328951 ATATCTTGTAACTTT
1 ATATCATGTAACTTT
328966 ATATCATGTAA----
1 ATATCATGTAACTTT
328977 ATATCATGTAACTTT
1 ATATCATGTAACTTT
328992 ATAT
1 ATAT
328996 AAATAACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
11 11 0.44
15 14 0.56
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (15 bp):
ATATCATGTAACTTT
Found at i:331416 original size:37 final size:37
Alignment explanation
Indices: 331344--331417 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
331334 TTGGAAAATG
* *
331344 TTTATATATTTTCTTTAAAAAATTTAAATTCATAAAA
1 TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
* *
331381 TTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
331418 GGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
Found at i:336324 original size:21 final size:21
Alignment explanation
Indices: 336298--336343 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
336288 TATGTCACTT
336298 TAGACTACTT-TATCAATATCG
1 TAGACTA-TTATATCAATATCG
* *
336319 TAGACTATTATGTCAGTATCG
1 TAGACTATTATATCAATATCG
336340 TAGA
1 TAGA
336344 TTGTCACATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
TAGACTATTATATCAATATCG
Found at i:337819 original size:33 final size:32
Alignment explanation
Indices: 337765--337826 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
337755 GACGTTTTTT
*
337765 AAAATTAATTTTAAATGTATATTTATATTACA
1 AAAATTAATTTTAAATGTATATATATATTACA
337797 AAAATTAATTTTTAAAAT-TATATATATATT
1 AAAATTAA-TTTT-AAATGTATATATATATT
337827 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 8 0.30
33 15 0.56
34 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
AAAATTAATTTTAAATGTATATATATATTACA
Found at i:338109 original size:43 final size:43
Alignment explanation
Indices: 338061--338146 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
338051 GACGGCTTGT
* *
338061 AAACTCTCAGAACTGCACTAAAAATACAATGAGGCAGGTGATC
1 AAACTCTCAGAACTGCACTAAAAATACAACGAGCCAGGTGATC
*
338104 AAACTCTCAGAACTGCACTAAAAATACGACGAGCCAGGTGATC
1 AAACTCTCAGAACTGCACTAAAAATACAACGAGCCAGGTGATC
338147 GGGGATCCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (43 bp):
AAACTCTCAGAACTGCACTAAAAATACAACGAGCCAGGTGATC
Found at i:338974 original size:13 final size:13
Alignment explanation
Indices: 338956--338980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338946 GGAAAGCACT
338956 CAGAGAGAACTCA
1 CAGAGAGAACTCA
338969 CAGAGAGAACTC
1 CAGAGAGAACTC
338981 TAGAAAACAC
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:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (13 bp):
CAGAGAGAACTCA
Found at i:343186 original size:18 final size:18
Alignment explanation
Indices: 343149--343182 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
343139 TAAATATTGA
*
343149 AATTAAAAAATGATAAAT
1 AATTAAAAAATCATAAAT
343167 AATT-AAAAATCATAAA
1 AATTAAAAAATCATAAA
343183 ATAAAATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AATTAAAAAATCATAAAT
Found at i:343928 original size:62 final size:64
Alignment explanation
Indices: 343819--343944 Score: 193
Period size: 62 Copynumber: 2.0 Consensus size: 64
343809 AAAAATTTTG
*
343819 TTCATTATCATTTATTTAGCTTAATAAATTAAATATAAACGAACATTATACAAACAGTTCACGA
1 TTCATTATCATTTATTTAGCTTAATAAATTAAACATAAACGAACATTATACAAACAGTTCACGA
* * * *
343883 TTCATTCTCATTT-TTTAGCTTGATAAA-TGAACATAAACGAACATTATATAAACAGTTCACGA
1 TTCATTATCATTTATTTAGCTTAATAAATTAAACATAAACGAACATTATACAAACAGTTCACGA
343945 ACAATTTTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 32 0.56
63 13 0.23
64 12 0.21
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (64 bp):
TTCATTATCATTTATTTAGCTTAATAAATTAAACATAAACGAACATTATACAAACAGTTCACGA
Found at i:345367 original size:24 final size:24
Alignment explanation
Indices: 345347--345392 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
345337 GTATTTAGAT
*
345347 TATAAATTTTAGTTTATTTTAATA
1 TATAAATTTTAATTTATTTTAATA
* *
345371 TATAATTTTTAATTTTTTTTAA
1 TATAAATTTTAATTTATTTTAA
345393 AAATTATACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TATAAATTTTAATTTATTTTAATA
Found at i:345862 original size:26 final size:26
Alignment explanation
Indices: 345832--345907 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
345822 TATTTTGTTG
345832 AGTTCTCCGACTATTAAAAGTTACAC
1 AGTTCTCCGACTATTAAAAGTTACAC
* * *
345858 AGTTCCCCGACTATTAAAATTTACAG
1 AGTTCTCCGACTATTAAAAGTTACAC
*
345884 AGTTCTCTGACTATTAAAAGTTAC
1 AGTTCTCCGACTATTAAAAGTTAC
345908 GAAATGGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (26 bp):
AGTTCTCCGACTATTAAAAGTTACAC
Found at i:361904 original size:34 final size:34
Alignment explanation
Indices: 361864--361933 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
361854 AGAACAAATT
*
361864 ATGATTGCACAAACATAACCAAATATTATACCAA
1 ATGATTGCACAAACACAACCAAATATTATACCAA
* *
361898 ATGATTGCATAAACACAACCAATTATTATACCAA
1 ATGATTGCACAAACACAACCAAATATTATACCAA
361932 AT
1 AT
361934 TTCCATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (34 bp):
ATGATTGCACAAACACAACCAAATATTATACCAA
Found at i:366392 original size:30 final size:31
Alignment explanation
Indices: 366356--366423 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
366346 TGACCTTTGA
* * *
366356 AATAATAATAAA-ATTATTTTTATA-TTAAAT
1 AATAATAATAAATATCA-TTTTAAACTAAAAT
366386 AATAATAATAAATATCATTTTAAACTAAAAT
1 AATAATAATAAATATCATTTTAAACTAAAAT
366417 AATAATA
1 AATAATA
366424 GATTAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
AATAATAATAAATATCATTTTAAACTAAAAT
Found at i:388807 original size:22 final size:22
Alignment explanation
Indices: 388773--388825 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
388763 AAATCATATA
* *
388773 TTTAGAATCTAAACTATCAGTT
1 TTTAAAATTTAAACTATCAGTT
388795 TTTAAAATTTAAACTATCAGTT
1 TTTAAAATTTAAACTATCAGTT
388817 TTTAAAATT
1 TTTAAAATT
388826 ATATCTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (22 bp):
TTTAAAATTTAAACTATCAGTT
Done.