Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009021.1 Hibiscus syriacus cultivar Beakdansim tig00112411_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: 1242735
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1097459 original size:83 final size:83
Alignment explanation
Indices: 1097200--1097459 Score: 324
Period size: 85 Copynumber: 3.1 Consensus size: 83
1097190 TACCATGCGG
* * * * * ***
1097200 TTGATATGTCATCGAGCTGAATGGAATCAAACTCGATAGTTTTTGTTGACAGATAGATTTTCTCG
1 TTGATATATCATTGAGCTGAATGTAATCGAACTCGA-AG-GTTTGTTGACAGATAGCCCTTCTCG
* *
1097265 ACTTAAGCTATGCTGTAAAT
64 CCTTGAGCTATGCTGTAAAT
* * * *
1097285 TTGATATGA-CCTTAAGATGAATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAGCCCTTCTC
1 TTGATAT-ATCATTGAGCTGAATGTAATCGAACTCGAAGG-TTT-GTTGACAGATAGCCCTTCTC
1097349 GCCTTGAGCTATGCTGTAAAT
63 GCCTTGAGCTATGCTGTAAAT
*
1097370 TTGATATATCATTGAGCTGAATGTAATTGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
1 TTGATATATCATTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
*
1097435 TTGAGCTATGATGTAAAT
66 TTGAGCTATGCTGTAAAT
1097453 TTGATAT
1 TTGATAT
1097460 GTCCTTGAAC
Statistics
Matches: 151, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
83 46 0.30
84 9 0.06
85 96 0.64
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (83 bp):
TTGATATATCATTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
TTGAGCTATGCTGTAAAT
Found at i:1098463 original size:32 final size:32
Alignment explanation
Indices: 1098427--1098513 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
1098417 TTCACATTAG
* * *
1098427 GATGTAAAATCCCCAAATATTCCCCAATATTT
1 GATGTAAAATCCCCAAAGATGCCCCAACATTT
** *
1098459 GATGTTGAATCTCCAAAGATGCCCCAACATTT
1 GATGTAAAATCCCCAAAGATGCCCCAACATTT
** **
1098491 GATGTTGAATCTTCAAAGATGCC
1 GATGTAAAATCCCCAAAGATGCC
1098514 ACTATTGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (32 bp):
GATGTAAAATCCCCAAAGATGCCCCAACATTT
Found at i:1099314 original size:20 final size:20
Alignment explanation
Indices: 1099289--1099336 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1099279 GTTACATTTT
1099289 CAAATCACTTCTCATATGAA
1 CAAATCACTTCTCATATGAA
1099309 CAAATCACTTCTCATATGAA
1 CAAATCACTTCTCATATGAA
1099329 CAAATCAC
1 CAAATCAC
1099337 ATGTGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (20 bp):
CAAATCACTTCTCATATGAA
Found at i:1100443 original size:16 final size:17
Alignment explanation
Indices: 1100422--1100456 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1100412 CGGTTTCGAC
*
1100422 CCGACCCGTTGA-CCGA
1 CCGACCAGTTGACCCGA
1100438 CCGACCAGTTGACCCGA
1 CCGACCAGTTGACCCGA
1100455 CC
1 CC
1100457 TGTTGACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.20, C:0.46, G:0.23, T:0.11
Consensus pattern (17 bp):
CCGACCAGTTGACCCGA
Found at i:1100586 original size:30 final size:30
Alignment explanation
Indices: 1100478--1100586 Score: 134
Period size: 30 Copynumber: 3.7 Consensus size: 30
1100468 GATAGGGTGA
1100478 TATTTTGGGAA-TTAATTC--AAAATGGGTGC
1 TATTTTGGGAATTTAATTCGAAAAAT--GTGC
* *
1100507 TATTTTGGGAATTTAATTCAAAAAATATGC
1 TATTTTGGGAATTTAATTCGAAAAATGTGC
* *
1100537 TATATTGGGAATTTAATTCGAAAAATGTGT
1 TATTTTGGGAATTTAATTCGAAAAATGTGC
*
1100567 TATTCTGGGAATTTAATTCG
1 TATTTTGGGAATTTAATTCG
1100587 GAAAGGTACT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.16
30 54 0.77
32 5 0.07
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (30 bp):
TATTTTGGGAATTTAATTCGAAAAATGTGC
Found at i:1107703 original size:29 final size:29
Alignment explanation
Indices: 1107548--1107696 Score: 162
Period size: 29 Copynumber: 5.2 Consensus size: 29
1107538 ACCGGGTGAC
* * *
1107548 ATTTTGGGGA-TTAATTCGAAATGATTGCT
1 ATTTTGGGAATTTAATTCGAAAAG-GTGCT
* * *
1107577 ATTTTAGGAA-TTAATTCAAAATAGGTGTT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
1107606 ATTTTGGGAATTTAATTC-AAAA-GTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
1107633 ATATTGGGAATTTAATTCGAAAAATGTGCT
1 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
*
1107663 ATTTTGGGAATTTAATTCGAAAAGGTGTT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
1107692 ATTTT
1 ATTTT
1107697 AGTAATTATT
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
27 21 0.20
28 1 0.01
29 50 0.49
30 31 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:1107713 original size:57 final size:57
Alignment explanation
Indices: 1107548--1107724 Score: 171
Period size: 57 Copynumber: 3.1 Consensus size: 57
1107538 ACCGGGTGAC
* * * * *
1107548 ATTTTGGGGA-TTAATTCGAAATGATTGCTATTTTAGGAATTAATTCAAAATAGGTGTT
1 ATTTTGGGAATTTAATTCGAAAAG-GTGCTATTTTAGGAATTATTTCAAAA-AGGTGCT
* * * *
1107606 ATTTTGGGAATTTAATTC-AAAA-GTGCTATATTGGGAATTTAATTCGAAAAATGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAA-TTATTTC-AAAAAGGTGCT
* * * *
1107663 ATTTTGGGAATTTAATTCGAAAAGGTGTTATTTTAGTAATTATTTTAAAAAGGATGCC
1 ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAATTATTTCAAAAAGG-TGCT
1107721 ATTT
1 ATTT
1107725 CTGTAAAATA
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
56 12 0.12
57 36 0.37
58 32 0.33
59 18 0.18
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (57 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAATTATTTCAAAAAGGTGCT
Found at i:1109212 original size:16 final size:19
Alignment explanation
Indices: 1109169--1109206 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1109159 CGTTTCAAAG
1109169 ATGGTATCGATACCGTCCTT
1 ATGGTATCGATACCG-CCTT
1109189 ATGGTATCGATACC-CCTT
1 ATGGTATCGATACCGCCTT
1109207 GGTATCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (19 bp):
ATGGTATCGATACCGCCTT
Found at i:1111085 original size:17 final size:19
Alignment explanation
Indices: 1111060--1111097 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1111050 TTATTTTCTC
1111060 TTTGATTCTTT-TTTTATT
1 TTTGATTCTTTCTTTTATT
1111078 TTTG-TTCTTTGCTTTTATT
1 TTTGATTCTTT-CTTTTATT
1111097 T
1 T
1111098 ATGCTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTGATTCTTTCTTTTATT
Found at i:1111956 original size:16 final size:18
Alignment explanation
Indices: 1111924--1111957 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1111914 CAGTCGTTTA
1111924 AAAGATTAAACAAACATG
1 AAAGATTAAACAAACATG
1111942 AAAGA-TAAA-AAACATG
1 AAAGATTAAACAAACATG
1111958 TTCAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.12, T:0.15
Consensus pattern (18 bp):
AAAGATTAAACAAACATG
Found at i:1113109 original size:15 final size:15
Alignment explanation
Indices: 1113085--1113114 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1113075 TGTAAATGAT
*
1113085 GAAAATAAAATGAAA
1 GAAAACAAAATGAAA
1113100 GAAAACAAAATGAAA
1 GAAAACAAAATGAAA
1113115 AGAGTTAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (15 bp):
GAAAACAAAATGAAA
Found at i:1115138 original size:17 final size:17
Alignment explanation
Indices: 1115116--1115161 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1115106 ATTAGGTTAT
1115116 GATAGTGGGTAGTAGTG
1 GATAGTGGGTAGTAGTG
*
1115133 GATAGTGGGTAGTGGTG
1 GATAGTGGGTAGTAGTG
1115150 GATAGTGGGTAG
1 GATAGTGGGTAG
1115162 GTTAGGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.50, T:0.28
Consensus pattern (17 bp):
GATAGTGGGTAGTAGTG
Found at i:1121418 original size:30 final size:30
Alignment explanation
Indices: 1121378--1121441 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1121368 TACACTAAAA
* *
1121378 TCATTCAATTAATTGATTGTAATAATCGTG
1 TCATTCAATTAATTGATTGTAACAATCATG
*
1121408 TCATTTAATTAATTGATTGTAACAATCATG
1 TCATTCAATTAATTGATTGTAACAATCATG
1121438 TCAT
1 TCAT
1121442 GTGTTACTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (30 bp):
TCATTCAATTAATTGATTGTAACAATCATG
Found at i:1123583 original size:2 final size:2
Alignment explanation
Indices: 1123578--1123635 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1123568 ATCTCTCTCA
1123578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1123620 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1123636 GTACATCACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1140041 original size:18 final size:17
Alignment explanation
Indices: 1140018--1140051 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1140008 CAGTCTGTTT
1140018 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1140036 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1140052 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1147987 original size:18 final size:17
Alignment explanation
Indices: 1147964--1147997 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1147954 CAGTCTGTTT
1147964 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1147982 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1147998 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1169278 original size:9 final size:10
Alignment explanation
Indices: 1169260--1169304 Score: 67
Period size: 9 Copynumber: 4.7 Consensus size: 10
1169250 ACCTTCCAGG
1169260 CATCCGAGGC
1 CATCCGAGGC
1169270 CATCC-AGGC
1 CATCCGAGGC
*
1169279 CATCCGAAG-
1 CATCCGAGGC
1169288 CATCCGAGGC
1 CATCCGAGGC
1169298 CATCCGA
1 CATCCGA
1169305 ACGAGCTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1169284 original size:19 final size:18
Alignment explanation
Indices: 1169254--1169305 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
1169244 CGGGCGACCT
*
1169254 TCCAGG-CATCCGAGGCCA
1 TCCAGGCCATCCGAAG-CA
1169272 TCCAGGCCATCCGAAGCA
1 TCCAGGCCATCCGAAGCA
1169290 TCCGAGGCCATCCGAA
1 TCC-AGGCCATCCGAA
1169306 CGAGCTATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (18 bp):
TCCAGGCCATCCGAAGCA
Found at i:1169343 original size:33 final size:33
Alignment explanation
Indices: 1169287--1169375 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
1169277 GCCATCCGAA
* * *
1169287 GCATCCGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGGCAACCGAGCGAGCTATGCGAGG
*
1169320 GCATTCGAGGGCAACCGAGCGAGCTATGCGAGG
1 GCATCCGAGGGCAACCGAGCGAGCTATGCGAGG
*
1169353 GAATCCGAGGGCAACCGAGCGAG
1 GCATCCGAGGGCAACCGAGCGAG
1169376 GGTAGGTCGG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.26, C:0.27, G:0.37, T:0.10
Consensus pattern (33 bp):
GCATCCGAGGGCAACCGAGCGAGCTATGCGAGG
Found at i:1169443 original size:13 final size:13
Alignment explanation
Indices: 1169421--1169452 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1169411 GCCCCGCATA
*
1169421 GCTCGTTCGGATG
1 GCTCGGTCGGATG
1169434 GCTCGGTCGGATG
1 GCTCGGTCGGATG
1169447 GCTCGG
1 GCTCGG
1169453 ATGCTCTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.25, G:0.44, T:0.25
Consensus pattern (13 bp):
GCTCGGTCGGATG
Found at i:1179630 original size:178 final size:179
Alignment explanation
Indices: 1179331--1179688 Score: 709
Period size: 178 Copynumber: 2.0 Consensus size: 179
1179321 AGGAATATCA
1179331 TATTGCTGGCTAGAACCTGCAGGAACAAATCATCAAATAATGAAAGAATAATGTTAATTGGGGGA
1 TATTGCTGGCTAGAACCTGCAGGAACAAATCATCAAATAATGAAAGAATAATGTTAATTGGGGGA
1179396 AGGCTAAAATTTGTGTTTAGTTTCTTTTCTTAGTACATACTCTATCGCAGATTGTCACAATTTAA
66 AGGCTAAAATTTGTGTTTAGTTTCTTTTCTTAGTACATACTCTATCGCAGATTGTCACAATTTAA
1179461 AGCTCTAAGATTTAAAGAAGAGAAAAGGCA-TAGCATGTCTTTGACAAT
131 AGCTCTAAGATTTAAAGAAGAGAAAAGGCATTAGCATGTCTTTGACAAT
1179509 TATTGCTGGCTAGAACCTGCAGGAACAAATCATCAAATAATGAAAGAATAATGTTAATTGGGGGA
1 TATTGCTGGCTAGAACCTGCAGGAACAAATCATCAAATAATGAAAGAATAATGTTAATTGGGGGA
1179574 AGGCTAAAATTTGTGTTTAGTTTCTTTTCTTAGTACATACTCTATCGCAGATTGTCACAATTTAA
66 AGGCTAAAATTTGTGTTTAGTTTCTTTTCTTAGTACATACTCTATCGCAGATTGTCACAATTTAA
1179639 AGCTCTAAGATTTAAAGAAGAGAAAAGGCATTAGCATGTCTTTGACAAT
131 AGCTCTAAGATTTAAAGAAGAGAAAAGGCATTAGCATGTCTTTGACAAT
1179688 T
1 T
1179689 GAAGTAATTC
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 160 0.89
179 19 0.11
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (179 bp):
TATTGCTGGCTAGAACCTGCAGGAACAAATCATCAAATAATGAAAGAATAATGTTAATTGGGGGA
AGGCTAAAATTTGTGTTTAGTTTCTTTTCTTAGTACATACTCTATCGCAGATTGTCACAATTTAA
AGCTCTAAGATTTAAAGAAGAGAAAAGGCATTAGCATGTCTTTGACAAT
Found at i:1184928 original size:2 final size:2
Alignment explanation
Indices: 1184921--1184947 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1184911 AAAATGACAA
1184921 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 A
1184948 AAATTTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1186012 original size:53 final size:54
Alignment explanation
Indices: 1185906--1186013 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
1185896 ATCTTGTGAC
* * *
1185906 AATTAAATAATGTCATTCATTATTGTTTTTTTGTTAATTTAGGTAGAGATAGTA
1 AATTAAATAATGTCATTCATTATAGTTTTTTGGTTAATTTAGGTAAAGATAGTA
*
1185960 AATTAAATAATGTCATTCATTATAG-TTTTTGGTTAGTTTAGGTAAAGATAGTA
1 AATTAAATAATGTCATTCATTATAGTTTTTTGGTTAATTTAGGTAAAGATAGTA
1186013 A
1 A
1186014 TGAGGTGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 26 0.52
54 24 0.48
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (54 bp):
AATTAAATAATGTCATTCATTATAGTTTTTTGGTTAATTTAGGTAAAGATAGTA
Found at i:1193030 original size:14 final size:15
Alignment explanation
Indices: 1192989--1193034 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1192979 AATTACTGAA
*
1192989 ACTGGAAAATGAATT
1 ACTGAAAAATGAATT
**
1193004 ACTGAAATTTGAATT
1 ACTGAAAAATGAATT
1193019 -CTGAAAAATGAATT
1 ACTGAAAAATGAATT
1193033 AC
1 AC
1193035 ATTTCTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (15 bp):
ACTGAAAAATGAATT
Found at i:1193328 original size:32 final size:32
Alignment explanation
Indices: 1193264--1193326 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1193254 TTTATTATTA
*
1193264 AATATTATTTTTATAATTTTATTAATAAAAAT
1 AATATTATTTTTATAATTTTATAAATAAAAAT
*
1193296 AATATTTTTTTTAT-ATTTTAGTGAAATAAAA
1 AATATTATTTTTATAATTTTA-T-AAATAAAA
1193327 TATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 14 0.52
33 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
AATATTATTTTTATAATTTTATAAATAAAAAT
Found at i:1193372 original size:20 final size:21
Alignment explanation
Indices: 1193326--1193373 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1193316 GTGAAATAAA
* *
1193326 ATATTATAAATTATATTAATT
1 ATATTATAAATAATAGTAATT
*
1193347 AT-TTATAAATAATAGT-GTT
1 ATATTATAAATAATAGTAATT
1193366 ATATTATA
1 ATATTATA
1193374 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 17 0.74
21 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
ATATTATAAATAATAGTAATT
Found at i:1193481 original size:28 final size:28
Alignment explanation
Indices: 1193405--1193583 Score: 89
Period size: 28 Copynumber: 6.1 Consensus size: 28
1193395 TATTTTAAAT
*
1193405 ATTTTATTAAAATATTATTTAAATATATAA
1 ATTTTATT-ATATATTA-TTAAATATATAA
** *
1193435 ATAATATTAT-TCATCATTAAATATATAA
1 ATTTTATTATAT-ATTATTAAATATATAA
1193463 ATTTTATTATATATTATTAAA-ATA-AA
1 ATTTTATTATATATTATTAAATATATAA
* * * *
1193489 TATATAATATCTATATTATTATAATATA-ACTG
1 -ATTTTAT-TATATATTATTA-AATATATA--A
* *
1193521 ATTATT-TTATATAATATTAAAAATATAA
1 ATT-TTATTATATATTATTAAATATATAA
* *
1193549 TATATATTATTATAAATATTAATAAATAAATAA
1 -AT-T-TTATTAT--ATATTATTAAATATATAA
1193582 AT
1 AT
1193584 AATATTTTGA
Statistics
Matches: 113, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
26 2 0.02
27 8 0.07
28 40 0.35
29 14 0.12
30 25 0.22
31 7 0.06
32 3 0.03
33 14 0.12
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (28 bp):
ATTTTATTATATATTATTAAATATATAA
Found at i:1193554 original size:21 final size:22
Alignment explanation
Indices: 1193528--1193589 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
1193518 CTGATTATTT
1193528 TATATAATATTAAAAATA-TAA
1 TATATAATATTAAAAATATTAA
* *
1193549 TATATATTATTATAAATATTAA
1 TATATAATATTAAAAATATTAA
*
1193571 TAAATAA-A-TAAATAATATT
1 TATATAATATTAAA-AATATT
1193590 TTGATGAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.09
21 23 0.68
22 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATAATATTAAAAATATTAA
Found at i:1193558 original size:33 final size:32
Alignment explanation
Indices: 1193521--1193591 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 32
1193511 AATATAACTG
*
1193521 ATTATTTTATATAATATTAA-AAATATAATATAT
1 ATTATTTTATA-AATATTAATAAATA-AATAAAT
1193554 ATTA--TTATAAATATTAATAAATAAATAAAT
1 ATTATTTTATAAATATTAATAAATAAATAAAT
*
1193584 AATATTTT
1 ATTATTTT
1193592 GATGAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
30 17 0.52
31 10 0.30
32 2 0.06
33 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTATTTTATAAATATTAATAAATAAATAAAT
Found at i:1200114 original size:33 final size:32
Alignment explanation
Indices: 1200041--1200116 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
1200031 AAACCTGAAC
* **
1200041 CCGACCCAAATATCACACTTAAAAAAAATTGA
1 CCGACCCGAATATCACACTTAAAAAAAACCGA
*
1200073 CCTAACCCGAATATCACACTTAAAAAAAACCGA
1 CC-GACCCGAATATCACACTTAAAAAAAACCGA
1200106 TCCGACCCGAA
1 -CCGACCCGAA
1200117 CCCGAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.46, C:0.30, G:0.08, T:0.16
Consensus pattern (32 bp):
CCGACCCGAATATCACACTTAAAAAAAACCGA
Found at i:1200690 original size:22 final size:21
Alignment explanation
Indices: 1200656--1200696 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1200646 ATAATTATTT
*
1200656 AAAAAATTAAATACAAATACA
1 AAAAAATTAAATAAAAATACA
*
1200677 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1200697 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:1203507 original size:12 final size:12
Alignment explanation
Indices: 1203490--1203518 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1203480 CCAGAACCAT
1203490 ACACCCACCTAC
1 ACACCCACCTAC
1203502 ACACCCACCTAC
1 ACACCCACCTAC
1203514 ACACC
1 ACACC
1203519 AAGTAAGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.07
Consensus pattern (12 bp):
ACACCCACCTAC
Found at i:1224066 original size:27 final size:27
Alignment explanation
Indices: 1224028--1224094 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
1224018 CAAAACAATG
1224028 CTGAATGATTCAGCACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
* *
1224055 CTGAATAATTCAACACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
1224082 CTGAATGATTCAG
1 CTGAATGATTCAG
1224095 AGTCATTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAGTACATT
Found at i:1227849 original size:40 final size:42
Alignment explanation
Indices: 1227805--1227912 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
1227795 CTCGAATTCT
*
1227805 CGTGTTTGTTTCACGTAATTTGTTTT-CGGAAAAAAATTT-C
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCC
* * * ***
1227845 CGTGTTTGTTTCAAGTAATTCCTTTTCCGGAATATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCC
*
1227887 CGTGTTTGTTTCACGTAATTGGTTTT
1 CGTGTTTGTTTCACGTAATTCGTTTT
1227913 TCAGAATGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 23 0.41
41 9 0.16
42 24 0.43
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCC
Found at i:1228239 original size:26 final size:28
Alignment explanation
Indices: 1228202--1228345 Score: 70
Period size: 28 Copynumber: 5.0 Consensus size: 28
1228192 TTTTTTTTAA
1228202 TAATATATAATAA-A-AAATTATATATT
1 TAATATATAATAATATAAATTATATATT
* *
1228228 TAATA-ATGAATAATATTATTTATATATT
1 TAATATAT-AATAATATAAATTATATATT
* *
1228256 TAAAGATATTTAA-AATATACTAATTAATATTTT
1 T--A-ATATATAATAATATA--AATT-ATATATT
*
1228289 TAA-A-ATAA-AATATAATACTAT-TACTT
1 TAATATATAATAATATAA-ATTATATA-TT
* *
1228315 TAATAAATAATTAATATAATTTATAATATT
1 TAATATATAA-TAATATAAATTAT-ATATT
1228345 T
1 T
1228346 TATTTCACTA
Statistics
Matches: 89, Mismatches: 11, Indels: 32
0.67 0.08 0.24
Matches are distributed among these distances:
25 3 0.03
26 18 0.20
27 4 0.04
28 24 0.27
29 4 0.04
30 17 0.19
31 8 0.09
32 4 0.04
33 7 0.08
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATATATAATAATATAAATTATATATT
Found at i:1228243 original size:19 final size:19
Alignment explanation
Indices: 1228200--1228249 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1228190 TATTTTTTTT
1228200 AATAATATA--TAATAAAA
1 AATAATATATTTAATAAAA
* **
1228217 AATTATATATTTAATAATG
1 AATAATATATTTAATAAAA
1228236 AATAATATTATTTA
1 AATAATA-TATTTA
1228250 TATATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.31
19 12 0.46
20 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATAATATATTTAATAAAA
Found at i:1228258 original size:57 final size:56
Alignment explanation
Indices: 1228119--1228286 Score: 139
Period size: 57 Copynumber: 2.9 Consensus size: 56
1228109 ATTAATATTT
* * *
1228119 ATAATAATATAATATAGTATTTTTAATATTATATAAAATAATCAATTATATTATAATA
1 ATAATAATATTATTTA-TATTTTTAATAATATATAAAATAA-CAATTATATTATAATA
* *
1228177 ATATAAAATATTATATT-T-TTTTTAATAATATATAATAA-AA-AATTATATATTTAATA
1 ATA-ATAATATTAT-TTATATTTTTAATAATATATAA-AATAACAATTATAT-TATAATA
* *
1228233 ATGAATAATATTATTTATATATTTAA-AGATATTTAAAATATACTAATTAATATT
1 AT-AATAATATTATTTATATTTTTAATA-ATATATAAAATA-AC-AATT-ATATT
1228287 TTTAAAATAA
Statistics
Matches: 89, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
55 10 0.11
56 21 0.24
57 33 0.37
58 7 0.08
59 8 0.09
60 6 0.07
61 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (56 bp):
ATAATAATATTATTTATATTTTTAATAATATATAAAATAACAATTATATTATAATA
Found at i:1228670 original size:21 final size:21
Alignment explanation
Indices: 1228640--1228683 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1228630 TCAAAATTCA
* *
1228640 AATTCTAGTAATTTATTTTTC
1 AATTCCAGTAATTCATTTTTC
1228661 AATTCCAGTAATTCATTTTTC
1 AATTCCAGTAATTCATTTTTC
1228682 AA
1 AA
1228684 AAAATCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (21 bp):
AATTCCAGTAATTCATTTTTC
Found at i:1230324 original size:16 final size:16
Alignment explanation
Indices: 1230303--1230346 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1230293 TAATAAATAA
1230303 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1230319 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1230335 ACGAACATAAAC
1 ACGAACATAAAC
1230347 ATTGGAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1242151 original size:24 final size:22
Alignment explanation
Indices: 1242104--1242154 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1242094 TATGATTTTT
*
1242104 ATAA-TATTTCTAATTTTTATA
1 ATAATTATTTCTAATTTTTAAA
*
1242125 ATAATTATTTTTAATTTTTTCAAA
1 ATAATTATTTCTAA-TTTTT-AAA
1242149 ATAATT
1 ATAATT
1242155 TAATCTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 5 0.20
24 8 0.32
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATTATTTCTAATTTTTAAA
Done.