Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 62 of 62
Found at i:14229130 original size:23 final size:23
Alignment explanation
Indices: 14229080--14229124 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
14229070 TGCCTATTTT
*
14229080 ATTATATAATCGCTACCTATTAC
1 ATTATATAATCGCTACCTAATAC
14229103 ATTATATAAGT-GCTACCTAATA
1 ATTATATAA-TCGCTACCTAATA
14229125 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
ATTATATAATCGCTACCTAATAC
Found at i:14229217 original size:23 final size:23
Alignment explanation
Indices: 14229167--14229211 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
14229157 TGTCTATTTT
* *
14229167 ATTATATAATCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
14229190 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
14229212 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:14231941 original size:22 final size:22
Alignment explanation
Indices: 14231899--14231967 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
14231889 AGGTGTCAAT
* *
14231899 TATT-TTTTTAAATAGTGTTAA
1 TATTATTTTTAAATAATATTAA
*
14231920 TATTATTTTTAAGTAATATTAA
1 TATTATTTTTAAATAATATTAA
*
14231942 TTTTATTTTTAATATATATATATAA
1 TATTATTTTTAA-ATA-ATAT-TAA
14231967 T
1 T
14231968 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 4 0.10
22 25 0.64
23 2 0.05
24 4 0.10
25 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TATTATTTTTAAATAATATTAA
Found at i:14232505 original size:21 final size:22
Alignment explanation
Indices: 14232467--14232508 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
14232457 TATACTTTGA
14232467 ATATTTCAAATTAAAATAATAT
1 ATATTTCAAATTAAAATAATAT
**
14232489 ATATTT-AAATTTTAATAATA
1 ATATTTCAAATTAAAATAATA
14232509 AAAAGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTTCAAATTAAAATAATAT
Found at i:14234604 original size:21 final size:21
Alignment explanation
Indices: 14234578--14234617 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14234568 ATAATGTCAT
*
14234578 AGGGGTACCGATTCCCCCCAA
1 AGGGGTACCGATACCCCCCAA
*
14234599 AGGGGTACTGATACCCCCC
1 AGGGGTACCGATACCCCCC
14234618 TTGAATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
AGGGGTACCGATACCCCCCAA
Found at i:14235558 original size:23 final size:23
Alignment explanation
Indices: 14235503--14235558 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
14235493 CACTACGATT
14235503 CATTTCTACGCGGCACTTTGGTG
1 CATTTCTACGCGGCACTTTGGTG
* * *
14235526 TAATTCTACGTGGCACTTTGGTG
1 CATTTCTACGCGGCACTTTGGTG
*
14235549 CATTTATACG
1 CATTTCTACG
14235559 AGCTGTGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (23 bp):
CATTTCTACGCGGCACTTTGGTG
Found at i:14236013 original size:2 final size:2
Alignment explanation
Indices: 14236006--14236051 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
14235996 CAAATAGGGA
*
14236006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14236048 AT AT
1 AT AT
14236052 GTTGTAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14239012 original size:23 final size:23
Alignment explanation
Indices: 14238941--14239014 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
14238931 ATAATTTGCA
14238941 CCGAAGTG-CCACGTAGATTTGTC
1 CCGAAG-GACCACGTAGATTTGTC
* *
14238964 CCAAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGATTTGTC
* *
14238987 CCGAAGGACCACATAGATTTATC
1 CCGAAGGACCACGTAGATTTGTC
14239010 CCGAA
1 CCGAA
14239015 TGATCGCGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
22 1 0.02
23 43 0.98
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CCGAAGGACCACGTAGATTTGTC
Found at i:14243490 original size:18 final size:18
Alignment explanation
Indices: 14243467--14243537 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
14243457 ACTGAATATT
14243467 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
14243485 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
14243503 TGTCCCGAAGAACAACTA
1 TGTCCCGAAGGACCACTA
14243521 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
14243538 GATAATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:14244225 original size:19 final size:19
Alignment explanation
Indices: 14244182--14244228 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
14244172 GGGGGTGCAG
*
14244182 CGATGCACTCCTTATGCAT
1 CGATGCACTCCTTATACAT
**
14244201 TAATGCACTCCTTATACAT
1 CGATGCACTCCTTATACAT
14244220 CGATGCACT
1 CGATGCACT
14244229 AATGGCATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.32
Consensus pattern (19 bp):
CGATGCACTCCTTATACAT
Found at i:14250374 original size:18 final size:18
Alignment explanation
Indices: 14250351--14250421 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
14250341 ACTGAATATT
*
14250351 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
14250369 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
14250387 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
14250405 TGTTCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
14250422 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:14256001 original size:18 final size:18
Alignment explanation
Indices: 14255968--14256036 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
14255958 ACTGAATATT
*
14255968 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
14255986 TATCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
14256004 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
14256022 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
14256037 TTGATAATCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:14258288 original size:32 final size:32
Alignment explanation
Indices: 14258247--14258372 Score: 207
Period size: 32 Copynumber: 3.9 Consensus size: 32
14258237 CATAGGTAAC
14258247 TGTCCATATGTCCCGAAAGACATAGGTAATTA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTA
*
14258279 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTA
* * *
14258311 TATCCATATGTCCCGAAATACAAAGGTAATTA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTA
*
14258343 TGTGCATATGTCCCGAAAGACATAGGTAAT
1 TGTCCATATGTCCCGAAAGACATAGGTAAT
14258373 CCTCGACTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 85 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATTA
Found at i:14258634 original size:10 final size:10
Alignment explanation
Indices: 14258619--14258649 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
14258609 TGTCATATCT
14258619 TGTTCACATA
1 TGTTCACATA
14258629 TGTTCACATA
1 TGTTCACATA
14258639 TGTTCACATA
1 TGTTCACATA
14258649 T
1 T
14258650 ACATCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (10 bp):
TGTTCACATA
Found at i:14264296 original size:219 final size:218
Alignment explanation
Indices: 14263893--14264329 Score: 865
Period size: 219 Copynumber: 2.0 Consensus size: 218
14263883 CGGTTTGTAG
14263893 ATGAGGCCACCAGGGGTGTACTCAATGTGGGATGAAGATGAATCGGGGATTAATGTACACATGAA
1 ATGAGGCCACCAGGGGTGTACTCAATGTGGGATGAAGATGAATCGGGGATTAATGTACACATGAA
14263958 GCTATCAGCTGAGGCTTTGTATGATTCAGAGTGTACATATTTCCTTCTAATACTTCCTGAAAACA
66 GCTATCAGCTGAGGCTTTGTATGATTCAGAGTGTACATATTTCCTTCTAATACTTCCTGAAAACA
14264023 GGGAAACCCAAAGTTGATGCCAGAACAATCAATTCAACGAAATCATGGACGAACACATGATCTTA
131 GGGAAACCCAAAGTTGATGCCAGAACAATCAATTCAACGAAATCATGGACGAACACATGATCTTA
14264088 TAATAGGGGTGTGAACTTTGAAA
196 TAATAGGGGTGTGAACTTTGAAA
14264111 ATGAGGCCACCAGGGGTGTACTCAATGTGGGATGAAGATGAATCGGGGATTAATGTACACATGAA
1 ATGAGGCCACCAGGGGTGTACTCAATGTGGGATGAAGATGAATCGGGGATTAATGTACACATGAA
14264176 GCTATCAGCTGAGGCTTTGTATGATTCAAGAGTGTACATATTTCCTTCTAATACTTCCTGAAAAC
66 GCTATCAGCTGAGGCTTTGTATGATTC-AGAGTGTACATATTTCCTTCTAATACTTCCTGAAAAC
14264241 AGGGAAACCCAAAGTTGATGCCAGAACAATCAATTCAACGAAATCATGGACGAACACATGATCTT
130 AGGGAAACCCAAAGTTGATGCCAGAACAATCAATTCAACGAAATCATGGACGAACACATGATCTT
14264306 ATAATAGGGGTGTGAACTTTGAAA
195 ATAATAGGGGTGTGAACTTTGAAA
14264330 GTTATATTAG
Statistics
Matches: 218, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 92 0.42
219 126 0.58
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (218 bp):
ATGAGGCCACCAGGGGTGTACTCAATGTGGGATGAAGATGAATCGGGGATTAATGTACACATGAA
GCTATCAGCTGAGGCTTTGTATGATTCAGAGTGTACATATTTCCTTCTAATACTTCCTGAAAACA
GGGAAACCCAAAGTTGATGCCAGAACAATCAATTCAACGAAATCATGGACGAACACATGATCTTA
TAATAGGGGTGTGAACTTTGAAA
Found at i:14264885 original size:2 final size:2
Alignment explanation
Indices: 14264878--14264903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14264868 TTGTCTTAAA
14264878 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
14264904 GAGTCATTTG
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:14268647 original size:3 final size:3
Alignment explanation
Indices: 14268622--14268680 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
14268612 TTGGGCTTTG
* * * *
14268622 TAA TAT TAA TAAA TAA TTAA TAA TAA TAA TAA TAA TTA TAA TTA TTA
1 TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14268669 TAA TAA TAA TAA
1 TAA TAA TAA TAA
14268681 AAATGGGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:14269090 original size:106 final size:109
Alignment explanation
Indices: 14268974--14269634 Score: 1070
Period size: 106 Copynumber: 6.0 Consensus size: 109
14268964 ATGATAGATT
14268974 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC-T-TT-TTCTTCAGATGAGTTCTTCTCATT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATT
14269036 ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
66 ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269080 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGATGAGTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC---TTCTT-CTTCTTC--A-GATGAGTTCT
14269145 TCTCATTATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
59 TCTCATTATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269196 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC-T-TT-TTCTTCAGATGAGTTCTTCTCATT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATT
14269258 ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
66 ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269302 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC---TTCTT-CTTCTTCAGATGAGTTCTTCT
*
14269367 CATTATGAACTCTACCTGGCAAAGCTAATCCATTGAATGATGGATTTG
62 CATTATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269415 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC-T-TT-TTCTTCAGATGAGTTCTTCTCATT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATT
*
14269477 ATGAACTCTACCTGGCAAAGCTGATCTATTGAATGATGGATTTG
66 ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269521 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC---TTCTT-CTTCTTCAGATGAGTTCTTCT
** * *
14269586 CATTATGAACTGGAACTGGAAAAGCTGATCCATTGAATGATGGATTTG
62 CATTATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
14269634 A
1 A
14269635 ATTTTTGCTA
Statistics
Matches: 523, Mismatches: 8, Indels: 41
0.91 0.01 0.07
Matches are distributed among these distances:
106 232 0.44
107 1 0.00
108 2 0.00
109 7 0.01
110 3 0.01
111 8 0.02
112 1 0.00
113 172 0.33
115 1 0.00
116 96 0.18
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (109 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTG
Found at i:14269514 original size:219 final size:219
Alignment explanation
Indices: 14268974--14269634 Score: 1241
Period size: 219 Copynumber: 3.0 Consensus size: 219
14268964 ATGATAGATT
14268974 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
14269039 AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
66 AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
14269104 TCATTATGAACTTTTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCA
131 TCATTATGAACTTTTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCTACCTGGCA
14269169 AAGCTGATCCATTGAATGATGGATTTG
193 AAGCTGATCCATTGAATGATGGATTTG
14269196 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
14269261 AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
66 AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
14269326 TCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAAG
131 TCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAAG
*
14269391 CTAATCCATTGAATGATGGATTTG
196 CTGATCCATTGAATGATGGATTTG
14269415 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
*
14269480 AACTCTACCTGGCAAAGCTGATCTATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
66 AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
** * *
14269545 TCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTGGAACTGGAAAAG
131 TCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAAG
14269610 CTGATCCATTGAATGATGGATTTG
196 CTGATCCATTGAATGATGGATTTG
14269634 A
1 A
14269635 ATTTTTGCTA
Statistics
Matches: 432, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
219 274 0.63
220 1 0.00
222 157 0.36
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (219 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCAGATGAGTTCTTCTCATTATG
AACTCTACCTGGCAAAGCTGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
TCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAAG
CTGATCCATTGAATGATGGATTTG
Found at i:14270451 original size:92 final size:92
Alignment explanation
Indices: 14270348--14270599 Score: 504
Period size: 92 Copynumber: 2.7 Consensus size: 92
14270338 TTCCAATGAT
14270348 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
14270413 GCATATTCATCTTCCAAATTCAATAAC
66 GCATATTCATCTTCCAAATTCAATAAC
14270440 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
14270505 GCATATTCATCTTCCAAATTCAATAAC
66 GCATATTCATCTTCCAAATTCAATAAC
14270532 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
14270597 GCA
66 GCA
14270600 CATGGCACTT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 160 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (92 bp):
TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCATATTCATCTTCCAAATTCAATAAC
Found at i:14271753 original size:1 final size:1
Alignment explanation
Indices: 14271749--14271821 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
14271739 CTTGACCCCC
* * * * * * * * *
14271749 TTTTTTCTTTTTTCTTTTTTTCTTTTTTTTTCTTTTCTTTTCTTTTTCTTTTTTTTTTCTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
14271814 TTCTTTTT
1 TTTTTTTT
14271822 CTCTTTAAGC
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:14271766 original size:5 final size:5
Alignment explanation
Indices: 14271751--14271820 Score: 72
Period size: 5 Copynumber: 13.8 Consensus size: 5
14271741 TGACCCCCTT
* *
14271751 TTTTC TTTT- TTCTTT TTTTC TTTTT TTTTC TTTTC TTTTC TTTTTC TTTT-
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC
*
14271801 TTTTT TCTTTC TTTTC TTTT
1 TTTTC T-TTTC TTTTC TTTT
14271821 TCTCTTTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
4 6 0.11
5 39 0.70
6 11 0.20
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:14271769 original size:15 final size:16
Alignment explanation
Indices: 14271751--14271827 Score: 108
Period size: 15 Copynumber: 4.9 Consensus size: 16
14271741 TGACCCCCTT
14271751 TTTTCTTTTTTCTTT-
1 TTTTCTTTTTTCTTTC
14271766 TTTTCTTTTTT-TTTC
1 TTTTCTTTTTTCTTTC
14271781 TTTTCTTTTCTT-TTTC
1 TTTTCTTTT-TTCTTTC
14271797 TTTT-TTTTTTCTTTC
1 TTTTCTTTTTTCTTTC
14271812 TTTTCTTTTTCTCTTT
1 TTTTCTTTTT-TCTTT
14271828 AAGCATAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.09
15 32 0.56
16 15 0.26
17 5 0.09
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTC
Found at i:14271778 original size:26 final size:26
Alignment explanation
Indices: 14271749--14271827 Score: 99
Period size: 25 Copynumber: 3.0 Consensus size: 26
14271739 CTTGACCCCC
14271749 TTTTTTCTTTTTTCTTTTTTTC-TTT
1 TTTTTTCTTTTTTCTTTTTTTCTTTT
14271774 TTTTTTCTTTTCTT-TTCTTTTTCTTTT
1 TTTTTTCTTTT-TTCTT-TTTTTCTTTT
*
14271801 TTTTTTCTTTCTTTTCTTTTTCTCTTT
1 TTTTTTC-TT-TTTTCTTTTTTTCTTT
14271828 AAGCATAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
25 13 0.28
26 8 0.17
27 10 0.21
28 12 0.26
29 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (26 bp):
TTTTTTCTTTTTTCTTTTTTTCTTTT
Found at i:14271779 original size:11 final size:11
Alignment explanation
Indices: 14271751--14271815 Score: 78
Period size: 11 Copynumber: 5.6 Consensus size: 11
14271741 TGACCCCCTT
14271751 TTTTCTTTTTTC
1 TTTT-TTTTTTC
14271763 TTTTTTTCTTT-
1 TTTTTTT-TTTC
14271774 TTTTTTCTTTTC
1 TTTTTT-TTTTC
*
14271786 TTTTCTTTTTC
1 TTTTTTTTTTC
14271797 TTTTTTTTTTC
1 TTTTTTTTTTC
14271808 TTTCTTTT
1 TTT-TTTT
14271816 CTTTTTCTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 30 0.64
12 17 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:14284460 original size:3 final size:3
Alignment explanation
Indices: 14284435--14284505 Score: 99
Period size: 3 Copynumber: 23.0 Consensus size: 3
14284425 TTGGGCTTTG
*
14284435 TAA TAT TAA TAAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14284482 TAA TAA TAA TAA T-A TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA
14284506 AAAAAATGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 51 0.82
4 9 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:14285060 original size:22 final size:21
Alignment explanation
Indices: 14285010--14285060 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
14285000 AGTTTTGAGG
*
14285010 TTATTTTAAAATTTATGCATT
1 TTATTTTAAAATTTATGAATT
*
14285031 TTCTTTTTAAAATATATAT-AATT
1 TT-ATTTTAAAAT-T-TATGAATT
14285054 TTATTTT
1 TTATTTT
14285061 TTTTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.08
22 13 0.54
23 6 0.25
24 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTTTAAAATTTATGAATT
Found at i:14287130 original size:8 final size:8
Alignment explanation
Indices: 14287117--14287161 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
14287107 AAATATAATT
14287117 TAAAAATA
1 TAAAAATA
14287125 TAAAAATA
1 TAAAAATA
* *
14287133 TTAAATTA
1 TAAAAATA
14287141 TAAAAATA
1 TAAAAATA
* *
14287149 TTAAATTA
1 TAAAAATA
14287157 TAAAA
1 TAAAA
14287162 GTTTAATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAAATA
Found at i:14287144 original size:16 final size:16
Alignment explanation
Indices: 14287094--14287161 Score: 84
Period size: 16 Copynumber: 4.1 Consensus size: 16
14287084 CTTTATATTT
14287094 AATATTAAATT-TAAA
1 AATATTAAATTATAAA
*
14287109 ATATAATTTAAAAATATAAA
1 A-AT-A-TT-AAATTATAAA
14287129 AATATTAAATTATAAA
1 AATATTAAATTATAAA
14287145 AATATTAAATTATAAA
1 AATATTAAATTATAAA
14287161 A
1 A
14287162 GTTTAATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
15 1 0.02
16 28 0.61
17 3 0.07
18 3 0.07
19 6 0.13
20 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATTAAATTATAAA
Found at i:14287262 original size:19 final size:19
Alignment explanation
Indices: 14287237--14287278 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
14287227 TTATAATTTA
*
14287237 ATATATTTATAATTCATTTTT
1 ATAT-TTTAAAATT-ATTTTT
14287258 ATATTTTAAAATTATTTTT
1 ATATTTTAAAATTATTTTT
14287277 AT
1 AT
14287279 TGTAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTAAAATTATTTTT
Found at i:14289552 original size:29 final size:29
Alignment explanation
Indices: 14289518--14289575 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
14289508 CACTCAAAAG
14289518 AATATGGTGTGATGAAAGTAACAAAGGAT
1 AATATGGTGTGATGAAAGTAACAAAGGAT
*
14289547 AATATGGTGTGATGAAAGTAACAGAGGAT
1 AATATGGTGTGATGAAAGTAACAAAGGAT
14289576 GGGAGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.29, T:0.24
Consensus pattern (29 bp):
AATATGGTGTGATGAAAGTAACAAAGGAT
Found at i:14290180 original size:20 final size:21
Alignment explanation
Indices: 14290155--14290206 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
14290145 TTTTCCCAAT
*
14290155 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
14290175 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
14290196 TCGCAATGCGA
1 TCGCAATGCGA
14290207 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:14290219 original size:41 final size:41
Alignment explanation
Indices: 14290192--14290323 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
14290182 GCGAATTGGG
* * *
14290192 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
14290233 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAAT-AC
** * * *
14290275 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
14290314 ATAATCGCAA
1 AAAATCGCAA
14290324 TGCGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:14290220 original size:20 final size:20
Alignment explanation
Indices: 14290195--14290309 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
14290185 AATTGGGAAA
*
14290195 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
14290215 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
14290236 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
14290256 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
14290276 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
14290296 TTCGCAACGCGATA
1 ATCGCAACGCGATA
14290310 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:14290525 original size:22 final size:22
Alignment explanation
Indices: 14290497--14290540 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14290487 CACTCTCTCA
14290497 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
14290519 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
14290541 TATCTCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:14292161 original size:18 final size:18
Alignment explanation
Indices: 14292137--14292177 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
14292127 CTTCGGGAGT
*
14292137 CATCACCTCGCCCAGAGC
1 CATCACCTCACCCAGAGC
*
14292155 TATCACCTCACCCAGAGC
1 CATCACCTCACCCAGAGC
14292173 CATCA
1 CATCA
14292178 TCTGATCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
CATCACCTCACCCAGAGC
Found at i:14292713 original size:19 final size:20
Alignment explanation
Indices: 14292659--14292724 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
14292649 TAGTTTACTT
* *
14292659 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
14292679 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
14292699 TCGCAATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
14292717 TCGCAACG
1 TCGCAACG
14292725 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.21
19 6 0.15
20 25 0.64
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:14292749 original size:19 final size:19
Alignment explanation
Indices: 14292659--14292760 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 19
14292649 TAGTTTACTT
* **
14292659 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
14292679 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
14292699 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
14292717 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
14292731 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
14292750 TCGCAATGCGA
1 TCGCAACGCGA
14292761 TTTGTGTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.15
16 4 0.06
18 8 0.12
19 20 0.30
20 24 0.36
21 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:14292791 original size:14 final size:14
Alignment explanation
Indices: 14292772--14292829 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
14292762 TTGTGTTTCG
14292772 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
14292786 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
14292802 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
14292818 CGTTGCGATTTT
1 CGTTGCGATTTT
14292830 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:14292806 original size:32 final size:33
Alignment explanation
Indices: 14292767--14292845 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
14292757 GCGATTTGTG
14292767 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
14292799 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* *
14292832 TTTTGCATTGCGAT
1 TTTCGCGTTGCGAT
14292846 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 27 0.61
33 17 0.39
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:14292864 original size:20 final size:20
Alignment explanation
Indices: 14292839--14292885 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
14292829 TCATTTTGCA
14292839 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
14292859 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
14292879 TTGCGAT
1 TTGCGAT
14292886 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:14294726 original size:14 final size:14
Alignment explanation
Indices: 14294707--14294742 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
14294697 ATTGTTTAAT
14294707 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
14294721 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
14294735 TGATTTGT
1 TGATTTGT
14294743 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:14294881 original size:19 final size:19
Alignment explanation
Indices: 14294859--14294945 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
14294849 ATCGCAACGA
14294859 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
14294878 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
14294897 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
14294916 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
14294930 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
14294946 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:14294910 original size:38 final size:33
Alignment explanation
Indices: 14294830--14294945 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
14294820 AAAACAGACT
* ***
14294830 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
14294863 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
14294901 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
14294934 ATCGCAATGCGA
1 ATCGCAATGCGA
14294946 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:14294989 original size:20 final size:20
Alignment explanation
Indices: 14294964--14295021 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
14294954 TCGCATTGCG
*
14294964 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
14294984 ATTTTCGCATTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
14295004 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
14295022 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:14296104 original size:24 final size:24
Alignment explanation
Indices: 14296077--14296130 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
14296067 GTATTCAAAA
* *
14296077 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
14296101 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
14296125 TTTGAT
1 TTTGAT
14296131 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:14296321 original size:12 final size:12
Alignment explanation
Indices: 14296304--14296328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14296294 ATATAATCCT
14296304 GAAGAAGAAAAA
1 GAAGAAGAAAAA
14296316 GAAGAAGAAAAA
1 GAAGAAGAAAAA
14296328 G
1 G
14296329 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:14298659 original size:33 final size:33
Alignment explanation
Indices: 14298612--14298738 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
14298602 GAAAATTACT
* *
14298612 ATCGTAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
14298645 ATCGCAATGCGAAATGAAAATCGCAAC-ACTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
* *
14298677 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
14298711 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
14298739 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
32 2 0.02
33 79 0.95
34 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:14298668 original size:19 final size:19
Alignment explanation
Indices: 14298612--14298742 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
14298602 GAAAATTACT
* *
14298612 ATCGTAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
14298631 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
14298645 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
14298664 ATCGCAA--C--ACT-AAT
1 ATCGCAATGCGAAATGAAA
*
14298678 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
14298697 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
14298711 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
14298730 ATCGCAACGCGAA
1 ATCGCAATGCGAA
14298743 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 4 0.05
16 5 0.06
17 5 0.06
18 4 0.05
19 38 0.46
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:14298745 original size:66 final size:66
Alignment explanation
Indices: 14298617--14298745 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 66
14298607 TTACTATCGT
*
14298617 AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACTAATTTCG
1 AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACGAATTTCG
14298682 C
66 C
* * *
14298683 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACGAATTT
14298746 AATTTCGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (66 bp):
AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACGAATTTCG
C
Found at i:14298824 original size:33 final size:33
Alignment explanation
Indices: 14298747--14298826 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 33
14298737 CGCGAATTTA
* *
14298747 ATTTCGCGTTGTGATTCTCTCGTTGCCATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTACCATTTTC
*
14298780 A-TTCGCGTTGCGATTCTCTCGTTACGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTACCATTTTC
*
14298812 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
14298827 AGTACTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 29 0.69
33 13 0.31
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTACCATTTTC
Found at i:14298952 original size:14 final size:14
Alignment explanation
Indices: 14298933--14298969 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
14298923 CATCAATTAA
14298933 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
14298947 ACAAATCACCTTTT
1 ACAAATCAACTTTT
14298961 ACAAATCAA
1 ACAAATCAA
14298970 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:14300366 original size:21 final size:21
Alignment explanation
Indices: 14300342--14300417 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
14300332 GTGGGAGAGA
14300342 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
14300363 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGATGACAGTGG
* * * *
14300384 ACTC-TCGAGGAATGATAGTGG
1 CCTCTTCAACG-ATGACAGTGG
14300405 CCTCTTCAACGAT
1 CCTCTTCAACGAT
14300418 AGGAGTGGAC
Statistics
Matches: 37, Mismatches: 16, Indels: 4
0.65 0.28 0.07
Matches are distributed among these distances:
20 3 0.08
21 30 0.81
22 4 0.11
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:14300404 original size:42 final size:42
Alignment explanation
Indices: 14300353--14300443 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
14300343 CTCTTCAACG
* * *
14300353 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
1 ATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
* * * *
14300395 ATGATAGTGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
14300437 ATGACAG
1 ATGACAG
14300444 GCGAGTCAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
ATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
Found at i:14300841 original size:90 final size:89
Alignment explanation
Indices: 14300662--14300844 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 89
14300652 ATTTCAAACT
* *
14300662 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTAGCA
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTAGCA
14300727 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
14300754 TTCAACCAAAAGACAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCAG
1 TTCAACCAAAAGACAAA-AAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAG-TTAGCAG
**
14300818 TTTTGGCAGCAACCGAATAAATTTAC
64 AATTGGCAGCAACCGAATAAATTTAC
14300844 T
1 T
14300845 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
89 8 0.09
90 32 0.38
92 17 0.20
93 28 0.33
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:14302590 original size:34 final size:33
Alignment explanation
Indices: 14302547--14302646 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 33
14302537 CGAGATAATA
**
14302547 AGAATCGCAACGCGGAAATGACTATCGCAACGAG
1 AGAATCGCAACGC-GAAATGAAAATCGCAACGAG
*
14302581 AGAATCGCAACGCGAAATGAAAATCGCAACTCGAAAT
1 AGAATCGCAACGCGAAATGAAAATCGCAA--CG--AG
*
14302618 AAAATCGCAACGCGAAATGAAAATCGCAA
1 AGAATCGCAACGCGAAATGAAAATCGCAA
14302647 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
33 14 0.24
34 13 0.22
35 2 0.03
37 29 0.50
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (33 bp):
AGAATCGCAACGCGAAATGAAAATCGCAACGAG
Found at i:14302623 original size:18 final size:19
Alignment explanation
Indices: 14302521--14302651 Score: 114
Period size: 19 Copynumber: 7.1 Consensus size: 19
14302511 TCTTTTGGTT
** *
14302521 GAAATGAAAATTACAACGA
1 GAAATGAAAATCGCAACGC
14302540 GATAAT-AAGAATCGCAACGC
1 GA-AATGAA-AATCGCAACGC
**
14302560 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
14302578 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
14302594 GAAATGAAAATCGCAACTC
1 GAAATGAAAATCGCAACGC
14302613 GAAAT-AAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
14302631 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
14302650 GA
1 GA
14302652 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 19 0.21
19 35 0.38
20 21 0.23
21 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:14302683 original size:19 final size:19
Alignment explanation
Indices: 14302647--14302718 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
14302637 AAAATCGCAA
** *
14302647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTCCGCGT
14302666 TGCGATTTTTATTCCGCGT
1 TGCGATTTTTATTCCGCGT
**
14302685 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTA-TTCCGCGT
*
14302705 TGCGATTTTCATTC
1 TGCGATTTTTATTC
14302719 TCGAAACTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TGCGATTTTTATTCCGCGT
Found at i:14303298 original size:20 final size:20
Alignment explanation
Indices: 14303273--14303326 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
14303263 GATTTTGTAT
14303273 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
14303293 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
14303313 TATCGCATTGCGAT
1 TATCGCATTGCGAT
14303327 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:14303345 original size:61 final size:61
Alignment explanation
Indices: 14303233--14303347 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
14303223 CGCTATGTAA
* * * ** *
14303233 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
14303294 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
14303348 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:14307991 original size:57 final size:57
Alignment explanation
Indices: 14307903--14308021 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 57
14307893 GCATATTAAA
* *
14307903 GGGACTGTTAGCAACTAAATTTGAGACTAAGGACTTCT-GTTGTCTTAGATACTTCTT
1 GGGACTGTTAGAAACTAAATTTGAGACTAAGGACTT-TGGTTGTCTTAAATACTTCTT
14307960 GGGACTGTTAGAAACTAAATTTGAGACTAAGGACTTTGGTTGTCTTAAATACTTCTT
1 GGGACTGTTAGAAACTAAATTTGAGACTAAGGACTTTGGTTGTCTTAAATACTTCTT
14308017 GGGAC
1 GGGAC
14308022 AGGTAGTTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
56 1 0.02
57 58 0.98
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (57 bp):
GGGACTGTTAGAAACTAAATTTGAGACTAAGGACTTTGGTTGTCTTAAATACTTCTT
Done.