Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006400.1 Hibiscus syriacus cultivar Beakdansim tig00015426_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: 1412076
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1343509 original size:129 final size:129
Alignment explanation
Indices: 1343053--1343493 Score: 686
Period size: 129 Copynumber: 3.4 Consensus size: 129
1343043 GATACATGGT
* * * * ** *
1343053 TCCTACGTGATGAAGACATCTGGTC-GAAGGATGACACTACTCATACATGATGAAGAGTTCTTGG
1 TCCTACGTGATGAGGAGATCTGATCTG-GGGATGACACGGCTCATACGTGATGAAGAGTTC-TGG
*
1343117 CCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
64 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
1343182 C
129 C
*
1343183 TCCTACGTGATGAGGAGATCTGATCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1343248 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
* * ** *
1343312 TCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGCTCATACGTGATGAAGAGTTCCGGCC
1 TCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1343377 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
* * * * *
1343441 TCCTACGTGATGAAGAGCTCTGATCTGGGGATGACACGGTTCCTACATGATGA
1 TCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGA
1343494 GGACGGCTGG
Statistics
Matches: 286, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
129 235 0.82
130 50 0.17
131 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
Found at i:1344008 original size:15 final size:15
Alignment explanation
Indices: 1343984--1344018 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1343974 AAGATGATCT
*
1343984 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
1343999 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
1344014 TGTTT
1 TGTTT
1344019 TTAATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:1344256 original size:62 final size:61
Alignment explanation
Indices: 1344185--1344306 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
1344175 AAGGTTGGTA
* * *
1344185 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCACAGATT
1 TTTTCAAAAGAA-TCGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCA-AGATT
* * *
1344247 TTTTCAAAAGAATCGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACATACTCAAGAT
1 TTTTCAAAAGAATCGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAGAT
1344307 GAATCACATC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 8 0.15
62 45 0.85
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (61 bp):
TTTTCAAAAGAATCGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAGATT
Found at i:1344573 original size:64 final size:63
Alignment explanation
Indices: 1344528--1344820 Score: 446
Period size: 64 Copynumber: 4.5 Consensus size: 63
1344518 TCATTTTAAG
* * *
1344528 AGAAACAGATTCAAAGA-TTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAC
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAA
1344591 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGAC-AAATTTTGTTTCC
1 AGAAACAAACTCAAAGA--TTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-C
1344655 AA
62 AA
1344657 AGAAACAAACTCAAAGATTTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
1 AGAAACAAACTCAAAGA---TTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-
1344722 CAA
61 CAA
1344725 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAA
1344789 AGAAACAAACTCAAAGATTTTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAA
1344821 CATCTCAAAG
Statistics
Matches: 221, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
63 15 0.07
64 76 0.34
65 3 0.01
66 33 0.15
67 62 0.28
68 32 0.14
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (63 bp):
AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAA
Found at i:1344632 original size:67 final size:67
Alignment explanation
Indices: 1344547--1344810 Score: 482
Period size: 67 Copynumber: 4.0 Consensus size: 67
1344537 TTCAAAGATT
*
1344547 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCACAGAAACAAACTCAAAGATTTT
1 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1344612 TG
66 TG
1344614 TTTCAAAAGAAATTATCTTAAGAGAGAC-AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-TTT
1344678 TTG
65 TTG
1344681 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA--TT
1 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1344744 T-
66 TG
1344745 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1344810 T
66 T
1344811 TCAAAAGAAA
Statistics
Matches: 192, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
64 61 0.32
65 3 0.02
66 34 0.18
67 62 0.32
68 32 0.17
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (67 bp):
TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
TG
Found at i:1344827 original size:26 final size:27
Alignment explanation
Indices: 1344782--1344837 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
1344772 CAAAATTTTG
*
1344782 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
1344809 TTTCAAAAGAAAC-ATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
1344835 TTT
1 TTT
1344838 TTCACAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:1344838 original size:27 final size:28
Alignment explanation
Indices: 1344772--1344838 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
1344762 TTAAGAGAGA
*
1344772 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
1344800 CAAAGA-TTTTTTCAAAAGAAAC-ATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
1344826 CAAAGATTTTTTT
1 CAAAGATTTTTTT
1344839 TCACAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.26
27 18 0.51
28 7 0.20
29 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.34
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:1344990 original size:140 final size:141
Alignment explanation
Indices: 1344733--1345122 Score: 588
Period size: 140 Copynumber: 2.7 Consensus size: 141
1344723 AAAGAAACAA
* * * * * * * *
1344733 ACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
1 ACTCAAAGA-TTTTTC--ACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1344798 CTCAAAGATTTTTTCAAAAGAAAC-ATCTCAAAGATTTTTTTTCACAAAATTGTCTCAAGAAAGA
63 CTCAAAGA-TTTTTCAAAAGAAACAATCTCAAAGA-TTTTTTTCACAAAATTGTCTCAAGAAAGA
1344862 CAAAACTTTGTTTCAG
126 CAAAACTTTGTTTCAG
* *
1344878 ACTCAAGGATTTTTCACGAAATTGTCTCAAGAGAAAC-AAACTTTGTTTCAAAATAAATAGACTC
1 ACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTC
*
1344942 AAAGATTTTTCAAAAGAAACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAA
66 AAAGATTTTTCAAAAGAAACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAAAGACAAAA
1345007 CTTTGTTTCAG
131 CTTTGTTTCAG
*
1345018 ACTCAAAGCTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTC
1 ACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTC
*
1345083 AAAGATTTTTCAAAAGAAACAA-CTCAAAGATATTTATTCA
66 AAAGATTTTTCAAAAGAAACAATCTCAAAGAT-TTTTTTCA
1345123 AAAGGAACAA
Statistics
Matches: 227, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
140 102 0.45
141 93 0.41
142 18 0.08
144 6 0.03
145 8 0.04
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (141 bp):
ACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTC
AAAGATTTTTCAAAAGAAACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAAAGACAAAA
CTTTGTTTCAG
Found at i:1345093 original size:26 final size:25
Alignment explanation
Indices: 1345064--1345210 Score: 102
Period size: 28 Copynumber: 5.5 Consensus size: 25
1345054 CAAAACTTTG
* *
1345064 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
1345090 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
1345117 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
1345146 TATTCAAAATG-AACAAACTCAAAGATTT
1 T-TTCAAAA-GAAAC-AACTCAAAGA-TT
* *
1345174 TTTCCAAGAGAAACAAACTCAAATA-T
1 TTT-CAAAAGAAAC-AACTCAAAGATT
1345200 TTT-AAAAGAAA
1 TTTCAAAAGAAA
1345211 TTGTCTTTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
24 7 0.07
25 8 0.08
26 16 0.15
27 8 0.08
28 32 0.31
29 32 0.31
30 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:1345147 original size:29 final size:29
Alignment explanation
Indices: 1345065--1345202 Score: 144
Period size: 29 Copynumber: 4.9 Consensus size: 29
1345055 AAAACTTTGT
* * *
1345065 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
1345091 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
1345119 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
1345148 TTCAAAATG-AACAAACTCAAAGATTTTT-
1 TTCAAAA-GAAACAAACTCAAAGATTTTTA
* * *
1345176 TCCAAGAGAAACAAACTCAAATATTTT
1 TTCAAAAGAAACAAACTCAAAGATTTT
1345203 AAAAGAAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
25 9 0.09
26 10 0.10
27 4 0.04
28 33 0.34
29 39 0.41
30 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:1345189 original size:57 final size:57
Alignment explanation
Indices: 1345065--1345202 Score: 144
Period size: 57 Copynumber: 2.5 Consensus size: 57
1345055 AAAACTTTGT
* * *
1345065 TTCAAAATAAATAGACTCAAAGA--TTT-TTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAAGAAACAACTCAAAGATATTTA
* *
1345119 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAATG-AACAAACTCAAAGAT-TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAA-GAAAC-AACTCAAAGATATTTA
* *
1345175 TTCCAAGAGAAACAAACTCAAATATTTT
1 TT-CAAAAGAAACAAACTCAAAGATTTT
1345203 AAAAGAAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
54 18 0.26
56 5 0.07
57 34 0.49
58 12 0.17
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (57 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAAGAAACAACTCAAAGATATTTA
Found at i:1345533 original size:35 final size:35
Alignment explanation
Indices: 1345440--1345553 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 35
1345430 TTATATTATG
* *
1345440 AGAGAAATGATGTCTCAAGCGAGACGAAATT-TGCTTT
1 AGAGAAAT--TGTCTCAAGCGAGACAAAATTGT-TTTT
* * **
1345477 A-AGATATAGTCTCAAATGAGACAAAATTGTTTTT
1 AGAGAAATTGTCTCAAGCGAGACAAAATTGTTTTT
*
1345511 AGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTT
1 AGAGAAATTGTCTCAAGCGAGACAAA-ATTGTTTTT
*
1345547 TGAGAAA
1 AGAGAAA
1345554 ACGATCTCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
34 21 0.34
35 21 0.34
36 19 0.31
37 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (35 bp):
AGAGAAATTGTCTCAAGCGAGACAAAATTGTTTTT
Found at i:1345562 original size:37 final size:35
Alignment explanation
Indices: 1345451--1345569 Score: 91
Period size: 34 Copynumber: 3.4 Consensus size: 35
1345441 GAGAAATGAT
* * *
1345451 GTCTCAAGCGAGACGAAATT-TGCTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTGT-TTTTAGAGA-AAAC
** **
1345485 GTCTCAAATGAGACAAAATTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTGTTTTTAGAGAAAAC
* *
1345520 GTCTCAAGCGAGACAAAGTTTGTTTTTTGAGAAAAC
1 GTCTCAAGCGAGACAAA-ATTGTTTTTAGAGAAAAC
*
1345556 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
1345570 TCAACTTTGT
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
34 22 0.33
35 19 0.28
36 15 0.22
37 11 0.16
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (35 bp):
GTCTCAAGCGAGACAAAATTGTTTTTAGAGAAAAC
Found at i:1345579 original size:37 final size:35
Alignment explanation
Indices: 1345451--1345581 Score: 106
Period size: 35 Copynumber: 3.7 Consensus size: 35
1345441 GAGAAATGAT
* * *
1345451 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGAC-AAATTTGTTTTTAGAGA-AAAC
* * **
1345485 GTCTCAAATGAGACAAAATTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAATTTGTTTTTAGAGAAAAC
* *
1345520 GTCTCAAGCGAGACAAAGTTTGTTTTTTGAGAAAAC
1 GTCTCAAGTGAGACAAA-TTTGTTTTTAGAGAAAAC
*
1345556 GATCTCAAGTGAGATCAACTTTGTTT
1 G-TCTCAAGTGAGA-CAAATTTGTTT
1345582 AATGTGAAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
33 6 0.08
34 17 0.22
35 18 0.23
36 15 0.19
37 18 0.23
38 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (35 bp):
GTCTCAAGTGAGACAAATTTGTTTTTAGAGAAAAC
Found at i:1345634 original size:103 final size:105
Alignment explanation
Indices: 1345520--1345753 Score: 273
Period size: 104 Copynumber: 2.2 Consensus size: 105
1345510 TAGAGAAATT
*** *
1345520 GTCTCAAGCGAGACAAAGTTTGTTTTTTGAG-AA-AACGATCTCAA-GTGAGATCAACTTTG-TT
1 GTCTCAAGCGAGACAAA-TTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATCAACTTTGTTT
*
1345581 TAATGTGAAACAAATTCGA-AATTTGGATCTCAAAGG-GAAAAG
64 TAA-GTGAAACAAATTC-ACAATTTGGATCTCAAAGGAAAAAAG
* * *
1345623 GTCTCAAGCGAGCCAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTTA
1 GTCTCAAGCGAGACAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTTA
* * *
1345688 AGTGAATCAAATTCACAATTTGTATCTCAAAGGAAAAAAT
66 AGTGAAACAAATTCACAATTTGGATCTCAAAGGAAAAAAG
*
1345728 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGAC-AAATTTGTTTT
1345754 AAAATTCTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
102 10 0.09
103 21 0.19
104 48 0.43
105 22 0.20
106 10 0.09
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (105 bp):
GTCTCAAGCGAGACAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTTA
AGTGAAACAAATTCACAATTTGGATCTCAAAGGAAAAAAG
Found at i:1346236 original size:14 final size:14
Alignment explanation
Indices: 1346217--1346243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1346207 GTATCAGGTA
1346217 TGTATGTATGTATG
1 TGTATGTATGTATG
1346231 TGTATGTATGTAT
1 TGTATGTATGTAT
1346244 ATACTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TGTATGTATGTATG
Found at i:1353559 original size:3 final size:3
Alignment explanation
Indices: 1353553--1353613 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1353543 AAAAAATATG
* **
1353553 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1353597 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
1353614 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:1355984 original size:30 final size:30
Alignment explanation
Indices: 1355948--1356055 Score: 137
Period size: 30 Copynumber: 3.6 Consensus size: 30
1355938 TAGAGAATAA
*
1355948 TTTACGTAAAATGGATTACTTGAAAACTGT
1 TTTACGTAAAATGAATTACTTGAAAACTGT
* *
1355978 TTTACGTAAAATAAATTATTTGAAAACTGT
1 TTTACGTAAAATGAATTACTTGAAAACTGT
* ** *
1356008 TTTACGTAACATGAATTA-TCAAAAATTGT
1 TTTACGTAAAATGAATTACTTGAAAACTGT
*
1356037 TTTACTTAAAATGAATTAC
1 TTTACGTAAAATGAATTAC
1356056 ATTTTTTGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 24 0.36
30 43 0.64
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACTTGAAAACTGT
Found at i:1356481 original size:16 final size:17
Alignment explanation
Indices: 1356451--1356482 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1356441 ATTTAAAAAA
1356451 ATAATATCATTATTACT
1 ATAATATCATTATTACT
1356468 ATAATATC-TTATTAC
1 ATAATATCATTATTAC
1356483 GTAAGTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATCATTATTACT
Found at i:1361837 original size:15 final size:15
Alignment explanation
Indices: 1361817--1361855 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1361807 AAAAAATAAC
* *
1361817 ATAACTAGATTGTAG
1 ATAACTAAATTATAG
1361832 ATAACTAAATTATAG
1 ATAACTAAATTATAG
1361847 ATAACTAAA
1 ATAACTAAA
1361856 CCATCCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (15 bp):
ATAACTAAATTATAG
Found at i:1372253 original size:40 final size:40
Alignment explanation
Indices: 1372204--1372292 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
1372194 ATATATATAT
*
1372204 ATATATTAAAACAAATTAATTCATATTATGACTATGTCTG
1 ATATTTTAAAACAAATTAATTCATATTATGACTATGTCTG
1372244 ATATTTTAAAACAAATTAATTCATATTATGACTATGTCTG
1 ATATTTTAAAACAAATTAATTCATATTATGACTATGTCTG
1372284 ATATTTTAA
1 ATATTTTAA
1372293 TAGATTAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (40 bp):
ATATTTTAAAACAAATTAATTCATATTATGACTATGTCTG
Found at i:1374728 original size:18 final size:18
Alignment explanation
Indices: 1374685--1374728 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1374675 ACTTGGGGAT
* *
1374685 GATGATTAGACGTGCTAG
1 GATGATTGGACATGCTAG
1374703 GATGATTGGACATGCTAG
1 GATGATTGGACATGCTAG
1374721 GATGATTG
1 GATGATTG
1374729 AAGGTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (18 bp):
GATGATTGGACATGCTAG
Found at i:1399676 original size:25 final size:25
Alignment explanation
Indices: 1399644--1399715 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
1399634 AGCCCGAAGG
1399644 CCGGTTACAAAGCAGGCTCACAGGC
1 CCGGTTACAAAGCAGGCTCACAGGC
* *
1399669 CCTGTTACAAAGCAGGCTCACAGTC
1 CCGGTTACAAAGCAGGCTCACAGGC
* *
1399694 TCGGTTACAAAGCAAGCTCACA
1 CCGGTTACAAAGCAGGCTCACA
1399716 ACCCATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.17
Consensus pattern (25 bp):
CCGGTTACAAAGCAGGCTCACAGGC
Found at i:1405065 original size:22 final size:23
Alignment explanation
Indices: 1405026--1405071 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1405016 TTTGAATATC
1405026 ATTAGATTAAAAACTCTTT-ACA
1 ATTAGATTAAAAACTCTTTGACA
*
1405048 ATTAGAGTTATAAA-TCTTTGACA
1 ATTAGA-TTAAAAACTCTTTGACA
1405071 A
1 A
1405072 AGTATCAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (23 bp):
ATTAGATTAAAAACTCTTTGACA
Found at i:1407139 original size:64 final size:65
Alignment explanation
Indices: 1407038--1407169 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 65
1407028 AACCTCGTTC
* *
1407038 GAGATCTTATTAGATGTGGGGACATGAAAGGAATTAGGATAAATCCAT-TTATGA-GTTATTTCA
1 GAGATCTTATTAGATGTGGAGACACGAAAGGAATTAGGATAAATCCATCTTATGACG-TATTTCA
1407101 A
65 A
* *
1407102 GAGAT-TTGATTAGATGTGGAGACACGAAAGGAATTAGGATAAATCCTTCTTATGACGTGTTTCA
1 GAGATCTT-ATTAGATGTGGAGACACGAAAGGAATTAGGATAAATCCATCTTATGACGTATTTCA
1407166 A
65 A
1407167 GAG
1 GAG
1407170 TCAAATCAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
63 2 0.03
64 42 0.69
65 16 0.26
66 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (65 bp):
GAGATCTTATTAGATGTGGAGACACGAAAGGAATTAGGATAAATCCATCTTATGACGTATTTCAA
Found at i:1407280 original size:20 final size:22
Alignment explanation
Indices: 1407239--1407289 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1407229 CTACATTCTG
1407239 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTT
*
1407261 CAAAGATGATAGATTCTTTTTT
1 CAAAGATGATAGATTCTCTTTT
1407283 CAAAGAT
1 CAAAGAT
1407290 AAGAGCTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTT
Found at i:1408486 original size:17 final size:15
Alignment explanation
Indices: 1408433--1408488 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
1408423 CTGAGTGACG
1408433 ATTATTATATAT-AT
1 ATTATTATATATAAT
1408447 ACGTTATTATATATAAT
1 A--TTATTATATATAAT
*
1408464 AATATTATATTATAAAT
1 ATTATTATA-TAT-AAT
1408481 ATTATTAT
1 ATTATTAT
1408489 TCATAAAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 7 0.20
16 14 0.40
17 13 0.37
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTATTATATATAAT
Found at i:1409609 original size:2 final size:2
Alignment explanation
Indices: 1409602--1409628 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1409592 TAGTCACTAT
1409602 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1409629 TTATGATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1410669 original size:16 final size:17
Alignment explanation
Indices: 1410642--1410675 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1410632 TCATTCATTC
1410642 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1410659 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
1410675 T
1 T
1410676 GACAGCTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Done.