Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009102.1 Hibiscus syriacus cultivar Beakdansim tig00112562_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: 86726
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4945 original size:13 final size:12
Alignment explanation
Indices: 4912--4946 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
4902 AGTAAAACAC
4912 GATAAATTTAAT
1 GATAAATTTAAT
4924 GATAAATTTAAT
1 GATAAATTTAAT
4936 GATAAAATTTA
1 GAT-AAATTTA
4947 TAACATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (12 bp):
GATAAATTTAAT
Found at i:6927 original size:24 final size:24
Alignment explanation
Indices: 6895--6943 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6885 ATGAGTAGTG
6895 AGCATGCGAGTGGCAACAAAACAT
1 AGCATGCGAGTGGCAACAAAACAT
6919 AGCATGCGAGTGGCAACAAAACAT
1 AGCATGCGAGTGGCAACAAAACAT
6943 A
1 A
6944 ACAAGAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (24 bp):
AGCATGCGAGTGGCAACAAAACAT
Found at i:10831 original size:2 final size:2
Alignment explanation
Indices: 10795--10819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10785 CTAAAATGAA
10795 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 A
10820 ACCATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22580 original size:20 final size:21
Alignment explanation
Indices: 22555--22601 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
22545 TTATTGTGCC
22555 AGTTAC-AGAGTAATTACAAG
1 AGTTACAAGAGTAATTACAAG
* *
22575 AGTTACAAAGTGTAATTACATG
1 AGTTAC-AAGAGTAATTACAAG
22597 AGTTA
1 AGTTA
22602 TAAACGGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (21 bp):
AGTTACAAGAGTAATTACAAG
Found at i:23500 original size:28 final size:30
Alignment explanation
Indices: 23442--23500 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23432 TCCTAAAACC
*
23442 TTAAATTTCAATACCCAGATATCTAAATTT
1 TTAAATTTCAAGACCCAGATATCTAAATTT
*
23472 TTAAATTTCAAGA-CCTGA-ATCTAAATTT
1 TTAAATTTCAAGACCCAGATATCTAAATTT
23500 T
1 T
23501 AATCAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.41
29 4 0.15
30 12 0.44
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (30 bp):
TTAAATTTCAAGACCCAGATATCTAAATTT
Found at i:35777 original size:320 final size:320
Alignment explanation
Indices: 35195--35839 Score: 1290
Period size: 320 Copynumber: 2.0 Consensus size: 320
35185 CTCCTCTTCT
35195 GTTTAGCGAAATCGACTCGGTCTCGACTCAGCTACGATCCGATAATTTATCTTGCCGCTCCATTT
1 GTTTAGCGAAATCGACTCGGTCTCGACTCAGCTACGATCCGATAATTTATCTTGCCGCTCCATTT
35260 CCACGCCCTCTCGTTGGATTTGATTACGATCCCGATAGCGTCCGTCGGCCAATGCTATCCGAAAT
66 CCACGCCCTCTCGTTGGATTTGATTACGATCCCGATAGCGTCCGTCGGCCAATGCTATCCGAAAT
35325 TGCCAAATTGACATCTCAAAACCCTAAATGCTCCAACAACTATACTCTCTCTGTCACCGTGGATT
131 TGCCAAATTGACATCTCAAAACCCTAAATGCTCCAACAACTATACTCTCTCTGTCACCGTGGATT
35390 TAGGCTCACGTTGCCTCCGCAGCCCAACATCGTCCCCACATTCGAGTTCTTACCGGTACTGATCA
196 TAGGCTCACGTTGCCTCCGCAGCCCAACATCGTCCCCACATTCGAGTTCTTACCGGTACTGATCA
35455 ATCACAGCCACTGATTTTGTTCAGAACGATGATGTGGCTGTCGATAAGAGGTTGGCGTCA
261 ATCACAGCCACTGATTTTGTTCAGAACGATGATGTGGCTGTCGATAAGAGGTTGGCGTCA
35515 GTTTAGCGAAATCGACTCGGTCTCGACTCAGCTACGATCCGATAATTTATCTTGCCGCTCCATTT
1 GTTTAGCGAAATCGACTCGGTCTCGACTCAGCTACGATCCGATAATTTATCTTGCCGCTCCATTT
35580 CCACGCCCTCTCGTTGGATTTGATTACGATCCCGATAGCGTCCGTCGGCCAATGCTATCCGAAAT
66 CCACGCCCTCTCGTTGGATTTGATTACGATCCCGATAGCGTCCGTCGGCCAATGCTATCCGAAAT
35645 TGCCAAATTGACATCTCAAAACCCTAAATGCTCCAACAACTATACTCTCTCTGTCACCGTGGATT
131 TGCCAAATTGACATCTCAAAACCCTAAATGCTCCAACAACTATACTCTCTCTGTCACCGTGGATT
35710 TAGGCTCACGTTGCCTCCGCAGCCCAACATCGTCCCCACATTCGAGTTCTTACCGGTACTGATCA
196 TAGGCTCACGTTGCCTCCGCAGCCCAACATCGTCCCCACATTCGAGTTCTTACCGGTACTGATCA
35775 ATCACAGCCACTGATTTTGTTCAGAACGATGATGTGGCTGTCGATAAGAGGTTGGCGTCA
261 ATCACAGCCACTGATTTTGTTCAGAACGATGATGTGGCTGTCGATAAGAGGTTGGCGTCA
35835 GTTTA
1 GTTTA
35840 TGGCGGGGAA
Statistics
Matches: 325, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 325 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (320 bp):
GTTTAGCGAAATCGACTCGGTCTCGACTCAGCTACGATCCGATAATTTATCTTGCCGCTCCATTT
CCACGCCCTCTCGTTGGATTTGATTACGATCCCGATAGCGTCCGTCGGCCAATGCTATCCGAAAT
TGCCAAATTGACATCTCAAAACCCTAAATGCTCCAACAACTATACTCTCTCTGTCACCGTGGATT
TAGGCTCACGTTGCCTCCGCAGCCCAACATCGTCCCCACATTCGAGTTCTTACCGGTACTGATCA
ATCACAGCCACTGATTTTGTTCAGAACGATGATGTGGCTGTCGATAAGAGGTTGGCGTCA
Found at i:37159 original size:17 final size:17
Alignment explanation
Indices: 37137--37179 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
37127 GCATGTCTGT
37137 TTCATTTTCTCAAACTG
1 TTCATTTTCTCAAACTG
37154 TTCATTTTCTCAAACTG
1 TTCATTTTCTCAAACTG
37171 TTCATTTTC
1 TTCATTTTC
37180 CTCTTTGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (17 bp):
TTCATTTTCTCAAACTG
Found at i:42498 original size:35 final size:35
Alignment explanation
Indices: 42447--42526 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
42437 AACACAGTCA
42447 TCAATTACATTATAAACCCCAAAGTCCAAAATACT
1 TCAATTACATTATAAACCCCAAAGTCCAAAATACT
* * * *
42482 TTAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTATAAACCCCAAAGTCCAAAATACT
42517 TCAATTACAT
1 TCAATTACAT
42527 ACCCAACCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAAGTCCAAAATACT
Found at i:42540 original size:35 final size:35
Alignment explanation
Indices: 42447--42542 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 35
42437 AACACAGTCA
* *
42447 TCAATTACATTA-TAAACCCCAAAGTCCAAAATACT
1 TCAATTACA-TACCAAACCCCAAATTCCAAAATACT
* * * *
42482 TTAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATACCAAACCCCAAATTCCAAAATACT
*
42517 TCAATTACATACCCAACCCCAAATTC
1 TCAATTACATACCAAACCCCAAATTC
42543 ATAATACATT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 1 0.02
35 50 0.98
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.28
Consensus pattern (35 bp):
TCAATTACATACCAAACCCCAAATTCCAAAATACT
Found at i:43520 original size:35 final size:35
Alignment explanation
Indices: 43481--43558 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
43471 GGGGTTGGGC
43481 ATGTAATTGAAGTATTTTGAAATTT-GAGGTTTAAA
1 ATGTAATTGAAGTATTTTGAAATTTAG-GGTTTAAA
* * *
43516 ATGTAATTTAAGTATTTTGGAATTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTAGGGTTTAAA
43551 ATGTAATT
1 ATGTAATT
43559 AATGTTTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.45
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTAGGGTTTAAA
Found at i:44959 original size:29 final size:30
Alignment explanation
Indices: 44903--44979 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
44893 ATAAATTTAA
*
44903 TTAA-AATTTAGAGATTAGAGTCTTGAAAT
1 TTAAGAATTTAGAGATTAGAGTCATGAAAT
*
44932 TTAAGAATTTAGAGATTTGAGT-ATGAAAT
1 TTAAGAATTTAGAGATTAGAGTCATGAAAT
*
44961 TTAAGATTTTAGGAGATTA
1 TTAAGAATTTA-GAGATTA
44980 ATGCCATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (30 bp):
TTAAGAATTTAGAGATTAGAGTCATGAAAT
Found at i:53702 original size:25 final size:28
Alignment explanation
Indices: 53674--53725 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
53664 TTTAAAATTA
53674 AAAAGAC-TAA-AGAAAAA-AAGAAAAG
1 AAAAGACATAATAGAAAAACAAGAAAAG
* *
53699 AAAATACATAATATAAAAACAAGAAAA
1 AAAAGACATAATAGAAAAACAAGAAAA
53726 TTAATAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 6 0.27
28 7 0.32
ACGTcount: A:0.75, C:0.06, G:0.10, T:0.10
Consensus pattern (28 bp):
AAAAGACATAATAGAAAAACAAGAAAAG
Found at i:57315 original size:53 final size:53
Alignment explanation
Indices: 57202--57320 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
57192 TGGGCATGTT
*
57202 CCCACCCTGAAATCCAAATTTTCTTCGATTAGGTACTTATTTTACTAATAGTG
1 CCCACCCTGAAATCCAAATTTTCTTCGATTAGGTACTTATTTTACGAATAGTG
** * * *
57255 CCCACCCTGAAATCTGAGTTTTCTTCGATTAGTTACTTATTTTACGGAT-GATG
1 CCCACCCTGAAATCCAAATTTTCTTCGATTAGGTACTTATTTTACGAATAG-TG
*
57308 CCTACCCTGAAAT
1 CCCACCCTGAAAT
57321 TTTATTTGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 1 0.02
53 57 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (53 bp):
CCCACCCTGAAATCCAAATTTTCTTCGATTAGGTACTTATTTTACGAATAGTG
Found at i:59029 original size:2 final size:2
Alignment explanation
Indices: 59022--59055 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
59012 AGGTTGCACT
59022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
59056 AAGTCCGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:60266 original size:10 final size:9
Alignment explanation
Indices: 60247--60271 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60237 ACCCGGTTAG
60247 TTTTTATTT
1 TTTTTATTT
60256 TTTTTATTT
1 TTTTTATTT
60265 TTTTTAT
1 TTTTTAT
60272 ATATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:60490 original size:17 final size:16
Alignment explanation
Indices: 60468--60518 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
60458 TGATTACCGA
60468 GTACCCGCAAAATCCGG
1 GTACCCG-AAAATCCGG
**
60485 GTACCCGATTA-CCGG
1 GTACCCGAAAATCCGG
*
60500 GTACCCGTAACATCCGG
1 GTACCCG-AAAATCCGG
60517 GT
1 GT
60519 CGGGACACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (16 bp):
GTACCCGAAAATCCGG
Found at i:66018 original size:30 final size:28
Alignment explanation
Indices: 65984--66042 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
65974 CTGTTAATAC
* *
65984 TATTTTTATTCTTTAAATTTTTGTTTGTAT
1 TATTTTGATACTTTAAATTTTT-TTT-TAT
*
66014 TATTTTGGTACTTTAAATTTTTTTTTAT
1 TATTTTGATACTTTAAATTTTTTTTTAT
66042 T
1 T
66043 TAATCCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 3 0.12
30 19 0.73
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.69
Consensus pattern (28 bp):
TATTTTGATACTTTAAATTTTTTTTTAT
Found at i:67119 original size:17 final size:17
Alignment explanation
Indices: 67097--67137 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
67087 TTTTTGTATT
*
67097 TTTTTTTTCTTTCG-TTA
1 TTTTTTTTATTT-GTTTA
67114 TTTTTTTTATTTGTTTA
1 TTTTTTTTATTTGTTTA
67131 TTTTTTT
1 TTTTTTT
67138 ACTAACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTTTATTTGTTTA
Found at i:69810 original size:39 final size:39
Alignment explanation
Indices: 69756--69835 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
69746 CACCCGGAGT
* *
69756 ATTACCCGAGGACTCATCCGCTACTAAAGGGAAAGTTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
*
69795 ATTACCCG-GTGACTCATCCTCTACCAAAGGGAAAGCTGC
1 ATTACCCGAG-GACTCATCCGCTACCAAAGGGAAAGCTGC
69834 AT
1 AT
69836 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
Found at i:76567 original size:71 final size:72
Alignment explanation
Indices: 76492--76625 Score: 173
Period size: 71 Copynumber: 1.9 Consensus size: 72
76482 AATACTTCGC
* * * * *
76492 TTAGGATGAAAACTCGAGATGGCATC-CTAAGTCG-AAAAAGAAAAAAAAAAAAAAACAAAAAAG
1 TTAGGATGAAAACCCGAAAGGGCA-CACTAAATAGAAAAAAGAAAAAAAAAAAAAAACAAAAAAG
76555 AAAAATGT
65 AAAAATGT
* * *
76563 TTAGGGTGAAAACCCGAAAGGGCACACTAAATAGAAAAAAGAGAAGAAAAAAAAAACAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACACTAAATAGAAAAAAGAAAAAAAAAAAAAAACAAAAAA
76626 AAATAAGGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 26 0.49
72 26 0.49
ACGTcount: A:0.60, C:0.10, G:0.18, T:0.11
Consensus pattern (72 bp):
TTAGGATGAAAACCCGAAAGGGCACACTAAATAGAAAAAAGAAAAAAAAAAAAAAACAAAAAAGA
AAAATGT
Found at i:77562 original size:80 final size:80
Alignment explanation
Indices: 77463--77737 Score: 194
Period size: 80 Copynumber: 3.3 Consensus size: 80
77453 ACAACATTGG
*
77463 ATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
1 ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
77528 TTTCATTCAGAGCCA
66 TTTCATTCAGAGCCA
* * ** *
77543 ATTTCAACTTCAC-GACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCAC-GACGAA
1 ATTTCAACTTCACAG-CGAAGGATA-T---C-C---A-ATTCA-AAGCTCAACTCCACAG-CGAA
* * *
77606 --GGATAT--C-GTGCTCA--CA-AACAACA
54 GGGGCT-TCCCAGT-TTCATTCAGAGC--CA
*
77629 TTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
1 ----ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
77694 CCAGTTTCATTCAGAGCCA
62 CCAGTTTCATTCAGAGCCA
77713 ATTTCAACTTCAC-GACGAAGGATAT
1 ATTTCAACTTCACAG-CGAAGGATAT
77738 TGGACTCGAA
Statistics
Matches: 145, Mismatches: 19, Indels: 62
0.64 0.08 0.27
Matches are distributed among these distances:
79 2 0.01
80 57 0.39
81 7 0.05
82 4 0.03
83 4 0.03
84 7 0.05
85 6 0.04
86 7 0.05
87 4 0.03
88 4 0.03
89 7 0.05
90 35 0.24
91 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (80 bp):
ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
TTTCATTCAGAGCCA
Found at i:77637 original size:170 final size:170
Alignment explanation
Indices: 77355--78133 Score: 1342
Period size: 170 Copynumber: 4.7 Consensus size: 170
77345 CATAACTTTG
77355 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
1 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
*
77420 TCAACTTCACGACGAAGGATATCGTGGTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
66 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
77485 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
131 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
77525 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
1 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
77590 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
66 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
77655 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
131 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
77695 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
1 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
77760 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
66 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
77825 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
131 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
* *
77865 CAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGATT
1 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
* * *
77930 TCAA--T------------T-TC---ATCACAAACAACATTGGATTTCAACTTTATAGCGAATGA
66 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
77977 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
131 TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
* * *
78017 CAATTTCATTCAGAGCCAATTACAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGATT
1 CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
*
78082 TCAACTTCACGACGAAGGATATTGTGCTCACAAACAACATTGGATTTCAACT
66 TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACT
78134 CTACGATAAA
Statistics
Matches: 582, Mismatches: 9, Indels: 36
0.93 0.01 0.06
Matches are distributed among these distances:
152 144 0.25
154 1 0.00
155 2 0.00
156 1 0.00
166 1 0.00
167 1 0.00
168 1 0.00
170 431 0.74
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (170 bp):
CAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATT
TCAACTTCACGACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGA
TATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCC
Found at i:78063 original size:152 final size:152
Alignment explanation
Indices: 77787--78090 Score: 572
Period size: 152 Copynumber: 2.0 Consensus size: 152
77777 GATATCGTGC
77787 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
1 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
*
77852 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGA
66 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTACAACTTCATGACGAAGGATATTGGACTCGA
*
77917 AACATCCACGATTTCAATTTCA
131 AACATCCACGATTTCAACTTCA
* *
77939 TCACAAACAACATTGGATTTCAACTTTATAGCGAATGATATCCAATTCAAAGCTCAACTCCACAG
1 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
78004 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTACAACTTCATGACGAAGGATATTGGACTCGA
66 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTACAACTTCATGACGAAGGATATTGGACTCGA
78069 AACATCCACGATTTCAACTTCA
131 AACATCCACGATTTCAACTTCA
78091 CGACGAAGGA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 148 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (152 bp):
TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTACAACTTCATGACGAAGGATATTGGACTCGA
AACATCCACGATTTCAACTTCA
Found at i:85090 original size:11 final size:11
Alignment explanation
Indices: 85076--85149 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
85066 GTGAAAAAAG
85076 ATAATAACAA-A
1 ATAATAA-AATA
85087 ATAATAAAATA
1 ATAATAAAATA
*
85098 AT--GAAAATA
1 ATAATAAAATA
85107 A-AATAAAAATA
1 ATAAT-AAAATA
85118 A-AATAAAATAA
1 ATAATAAAAT-A
85129 ATGAATAAAATA
1 AT-AATAAAATA
85141 A-AATAAAAT
1 ATAATAAAAT
85150 GTATGGGTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
9 7 0.13
10 15 0.28
11 22 0.41
12 2 0.04
13 8 0.15
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:85106 original size:9 final size:8
Alignment explanation
Indices: 85078--85141 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
85068 GAAAAAAGAT
*
85078 AATAACAA
1 AATAATAA
85086 AATAATAA
1 AATAATAA
85094 AATAATGAA
1 AATAAT-AA
85103 AATAA-AA
1 AATAATAA
*
85110 TAAAAATAA
1 -AATAATAA
*
85119 AATAAAATA
1 AATAATA-A
85128 AATGAATAA
1 AAT-AATAA
85137 AATAA
1 AATAA
85142 AATAAAATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
7 2 0.04
8 24 0.52
9 17 0.37
10 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (8 bp):
AATAATAA
Found at i:85109 original size:5 final size:5
Alignment explanation
Indices: 85089--85149 Score: 67
Period size: 5 Copynumber: 12.6 Consensus size: 5
85079 ATAACAAAAT
*
85089 AATAA AAT-- AATGAA AATAA AATAAA AATAA AATAA AAT-A AAT-G AATAA
1 AATAA AATAA AAT-AA AATAA AAT-AA AATAA AATAA AATAA AATAA AATAA
85137 AATAA AATAA AAT
1 AATAA AATAA AAT
85150 GTATGGGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
3 3 0.06
4 7 0.14
5 31 0.63
6 8 0.16
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:85125 original size:10 final size:10
Alignment explanation
Indices: 85089--85149 Score: 67
Period size: 9 Copynumber: 6.3 Consensus size: 10
85079 ATAACAAAAT
85089 AATAAAAT--
1 AATAAAATAA
85097 AATGAAAATAA
1 AAT-AAAATAA
85108 AATAAAAATAA
1 AAT-AAAATAA
85119 AATAAAAT-A
1 AATAAAATAA
*
85128 AAT-GAATAA
1 AATAAAATAA
85137 AATAAAATAA
1 AATAAAATAA
85147 AAT
1 AAT
85150 GTATGGGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
8 6 0.13
9 13 0.29
10 13 0.29
11 13 0.29
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AATAAAATAA
Found at i:85137 original size:18 final size:17
Alignment explanation
Indices: 85078--85147 Score: 90
Period size: 18 Copynumber: 4.1 Consensus size: 17
85068 GAAAAAAGAT
* *
85078 AATAACAAAATAATA-A
1 AATAATAAAATAAAATA
85094 AATAATGAAAATAAAATA
1 AATAAT-AAAATAAAATA
85112 AA-AATAAAATAAAATA
1 AATAATAAAATAAAATA
85128 AATGAATAAAATAAAATA
1 AAT-AATAAAATAAAATA
85146 AA
1 AA
85148 ATGTATGGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 18 0.38
17 11 0.23
18 19 0.40
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (17 bp):
AATAATAAAATAAAATA
Found at i:85144 original size:34 final size:33
Alignment explanation
Indices: 85067--85148 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
85057 TAAAAGTTAG
* * * *
85067 TGAAAA-AAGATAATAACAAAATAATAAAATAA
1 TGAAAATAAAATAAAAATAAAATAAAAAAATAA
85099 TGAAAATAAAATAAAAATAAAATAAAATAAATGAA
1 TGAAAATAAAATAAAAATAAAATAAAA-AAAT-AA
85134 T-AAAATAAAATAAAA
1 TGAAAATAAAATAAAA
85149 TGTATGGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 6 0.14
33 16 0.37
34 18 0.42
35 3 0.07
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (33 bp):
TGAAAATAAAATAAAAATAAAATAAAAAAATAA
Found at i:86251 original size:84 final size:84
Alignment explanation
Indices: 86113--86655 Score: 505
Period size: 81 Copynumber: 6.6 Consensus size: 84
86103 GTTTGCCTCT
* * *
86113 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCT-GTTGGCAGATAGCCCTTTTCGACTTAAGCTAT
1 GAGCTGAGTGTAGTCGAACTCGAAGGTCTT-TGGTTGGCAGATAACCCTTCTCGACTTAAGCTAT
86177 GCTGCAAATGATGTGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * *
86197 GAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATG
* * *
86262 TTGCAAATGACGTGCCCTCG
66 CTGCAAATGATGTG-CCTTG
* * * *
86282 AAGCTGAGTGTAATCGAACTCG-GGAGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 GAGCTGAGTGTAGTCGAACTCGAAG-GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTAT
*
86342 GATGCAAATGATGTGCCTT-
65 GCTGCAAATGATGTGCCTTG
* ** * *
86361 GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGG-TGATAGATAACCCTTCTAGACTTAAG-TTTG
1 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATG
* * *
86424 CTG-ATAATGATATGCCCTC
66 CTGCA-AATGATGTGCCTTG
* * * * *
86443 GATGCT-AATGTAATCGAACTC-AGGGGTC--T--TTGGCAGATAGCCCTTCTCAAACTTAAGCT
1 GA-GCTGAGTGTAGTCGAACTCGA-AGGTCTTTGGTTGGCAGATAACCCTTCTC-GACTTAAGCT
* *
86502 ATGCTGCAAATGATGAGCCTTA
63 ATGCTGCAAATGATGTGCCTTG
** ** * * * * *
86524 GAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGG-TGATAGATAACCTTTCTAGCCTTGAGTTAT
1 GAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTAT
*
86588 GCTG-TAATGATGTG-CTTG
65 GCTGCAAATGATGTGCCTTG
*
86606 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCACGAT-ACCCTTC
1 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCA-GATAACCCTTC
86656 GTCGTGAAGT
Statistics
Matches: 371, Mismatches: 63, Indels: 52
0.76 0.13 0.11
Matches are distributed among these distances:
79 36 0.10
80 16 0.04
81 100 0.27
82 82 0.22
83 16 0.04
84 83 0.22
85 38 0.10
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATG
CTGCAAATGATGTGCCTTG
Found at i:86335 original size:81 final size:80
Alignment explanation
Indices: 86106--86521 Score: 371
Period size: 84 Copynumber: 5.1 Consensus size: 80
86096 AAATTTGGTT
** *
86106 TGCCTCTG-AGCTGAGTGTAATCGAACTCGAAGGTCTTCTGTTGGCAGATAGCCCTTTTCGACTT
1 TGCCTC-GAAGCTGAGTGTAATCGAACTCG--GG-AGTCT-TTGGCAGATAGCCCTTCTCGACTT
86170 AAGCTATGCTGCAAATGATG
61 AAGCTATGCTGCAAATGATG
* * * * * *
86190 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA-TTTGGTTGGCAGATAACCCTTCTCGACTT
1 TGCCTCGAAGCTGAGTGTAATCGAACTCG--GG-AGTCT--TTGGCAGATAGCCCTTCTCGACTT
* * *
86254 AAGTTATGTTGCAAATGACG
61 AAGCTATGCTGCAAATGATG
86274 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
1 TG-CCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGC
*
86339 TATGATGCAAATGATG
65 TATGCTGCAAATGATG
* * ** * * *
86355 TGCCTTG-AGCTGAGTGTAGTCGAACTC-AAAGGTCTTTGGTGATAGATAACCCTTCTAGACTTA
1 TGCCTCGAAGCTGAGTGTAATCGAACTCGGGA-GTCTTT-G-G-CAGATAGCCCTTCTCGACTTA
* *
86418 AG-TTTGCTG-ATAATGATA
62 AGCTATGCTGCA-AATGATG
* * *
86436 TGCCCTCGATGCT-AATGTAATCGAACTCAGGG-GTCTTTGGCAGATAGCCCTTCTCAAACTTAA
1 TG-CCTCGAAGCTGAGTGTAATCGAACTC-GGGAGTCTTTGGCAGATAGCCCTTCTC-GACTTAA
86499 GCTATGCTGCAAATGATG
63 GCTATGCTGCAAATGATG
*
86517 AGCCT
1 TGCCT
86522 TAGAGCTGAA
Statistics
Matches: 274, Mismatches: 42, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
78 1 0.00
79 37 0.14
80 17 0.06
81 70 0.26
82 45 0.16
83 10 0.04
84 71 0.26
85 23 0.08
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
TGCCTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATGCTGCAAATGATG
Found at i:86625 original size:163 final size:162
Alignment explanation
Indices: 86113--86627 Score: 637
Period size: 164 Copynumber: 3.1 Consensus size: 162
86103 GTTTGCCTCT
** *
86113 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCTGTTGGCAGATAGCCCTTTTCGACTTAAGCTATG
1 GAGCTGAGTGTAATCGAACTCG--GG-AGTCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* **
86178 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACC
62 CTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGATAGATAACC
* * * *
86243 CTTCTCGACTTAAGTTATGTTGCA-AATGACGTGCCCTCG
125 CTTCTAGACTTAAGTTATGCTG-ATAATGATGTG-CCTTG
* *
86282 AAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGC
1 GAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* *
86347 AAATGATGTGCCTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTGATAGATAACCCTTCTA
66 AAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTA
* * *
86412 GACTTAAGTT-TGCTGATAATGATATGCCCTC
131 GACTTAAGTTATGCTGATAATGATGTGCCTTG
* *
86443 GATGCT-AATGTAATCGAACTCAGGG-GTCTTTGGCAGATAGCCCTTCTCAAACTTAAGCTATGC
1 GA-GCTGAGTGTAATCGAACTC-GGGAGTCTTTGGCAGATAGCCCTTCTC-GACTTAAGCTATGC
* * *
86506 TGCAAATGATGAGCCTTAGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACCT
63 TGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGATAGATAACCC
* *
86571 TTCTAGCCTTGAGTTATGCTG-TAATGATGTG-CTTG
126 TTCTAGACTTAAGTTATGCTGATAATGATGTGCCTTG
* *
86606 GAGCTGAGCGTAGTCGAACTCG
1 GAGCTGAGTGTAATCGAACTCG
86628 AAGGTCTTTG
Statistics
Matches: 304, Mismatches: 34, Indels: 23
0.84 0.09 0.06
Matches are distributed among these distances:
161 41 0.13
162 49 0.16
163 66 0.22
164 69 0.23
165 53 0.17
166 3 0.01
167 2 0.01
169 21 0.07
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (162 bp):
GAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
AAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTA
GACTTAAGTTATGCTGATAATGATGTGCCTTG
Done.