Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008357.1 Hibiscus syriacus cultivar Beakdansim tig00111096_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: 1459476
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1428660 original size:60 final size:59
Alignment explanation
Indices: 1428602--1428880 Score: 223
Period size: 60 Copynumber: 4.6 Consensus size: 59
1428592 AATCGTAACA
*
1428602 CATAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGTAACG
1 CATAAGTCAAATTCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
* * * *
1428662 CA-ATAGTCATATTCGCAACACTGAAGTCAAATTCGCAACGCGAATCTGT-AAAAT-GCAGCG
1 CATA-AGTCAAATTCGCAACAC-GAAGTCAAATTCGCAACGCG-AT-AGTCAAATTCGCAACG
** * * *
1428722 CGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
1 C--ATAAGTCAAATTCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
* ** * *
1428782 CGAT-AGTCAAATTCGCAA-AGCGATAGTCAAATTCGTAACATTGA-ATTTCAAATTCGCAACA
1 C-ATAAGTCAAATTCGCAACA-CGA-AGTCAAATTCGCAAC-GCGATA-GTCAAATTCGCAACG
* *
1428843 CAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAA
1 CATAAGTCAAATTCGCAACACGA-AGTCAAATTCGCAA
1428881 AGCACGTTTA
Statistics
Matches: 176, Mismatches: 27, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
58 4 0.02
59 14 0.08
60 99 0.56
61 54 0.31
62 5 0.03
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (59 bp):
CATAAGTCAAATTCGCAACACGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
Found at i:1428670 original size:40 final size:40
Alignment explanation
Indices: 1428598--1428880 Score: 219
Period size: 40 Copynumber: 7.0 Consensus size: 40
1428588 TGTAAATCGT
*
1428598 AACAC-ATAAGTCAAATTCGCAACACAGA-AGTCAAATTCGC
1 AACACGAT-AGTCAAATTCGCAACGCA-ATAGTCAAATTCGC
* * *
1428638 AACGCGATAGTCAAATTCGTAACGCAATAGTCATATTCGC
1 AACACGATAGTCAAATTCGCAACGCAATAGTCAAATTCGC
* *
1428678 AACACTGA-AGTCAAATTCGCAACGCGAATCTGT-AAAAT-GC
1 AACAC-GATAGTCAAATTCGCAACGC-AAT-AGTCAAATTCGC
* * * *
1428718 AGCGCGAATTTGT-AAA-TCGCAACACAGA-AGTCAAATTCGC
1 AACACG-A-TAGTCAAATTCGCAACGCA-ATAGTCAAATTCGC
* * *
1428758 AACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 AACACGATAGTCAAATTCGCAACGCAATAGTCAAATTCGC
* *
1428798 AA-AGCGATAGTCAAATTCGTAACATTG-AAT-TTCAAATTCGC
1 AACA-CGATAGTCAAATTCGCAAC---GCAATAGTCAAATTCGC
* * *
1428839 AACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 AACACGATAGTCAAATTCGCAACGCAATAGTCAAATTCGC
1428879 AA
1 AA
1428881 AGCACGTTTA
Statistics
Matches: 190, Mismatches: 32, Indels: 42
0.72 0.12 0.16
Matches are distributed among these distances:
38 5 0.03
39 15 0.08
40 121 0.64
41 41 0.22
42 7 0.04
43 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.21
Consensus pattern (40 bp):
AACACGATAGTCAAATTCGCAACGCAATAGTCAAATTCGC
Found at i:1428760 original size:140 final size:141
Alignment explanation
Indices: 1428549--1428841 Score: 437
Period size: 140 Copynumber: 2.1 Consensus size: 141
1428539 ACCCAGTTTC
* * *
1428549 CAAATTCGCAACGCGAATATGTAAATCGAAACGTGAATTTGTAAATCGTAACACATAAGTCAAAT
1 CAAATTCGCAACGCGAATATGTAAATCGAAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
* * * *
1428614 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGTAACGCAATAGTCATATTCGCA
66 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAAGCAATAGTCAAATTCGCA
1428679 ACACTGAA-GT
131 ACACTGAATGT
* * *
1428689 CAAATTCGCAACGCGAATCTGTAAAAT-GCAGCGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 CAAATTCGCAACGCGAATATGT-AAATCGAAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
* *
1428753 TTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAAGCGATAGTCAAATTCGT
65 TTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAAGCAATAGTCAAATTCGC
* *
1428818 AACATTGAATTT
130 AACACTGAATGT
1428830 CAAATTCGCAAC
1 CAAATTCGCAAC
1428842 ACAAAAGTCA
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
140 120 0.88
141 17 0.12
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (141 bp):
CAAATTCGCAACGCGAATATGTAAATCGAAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAAGCAATAGTCAAATTCGCA
ACACTGAATGT
Found at i:1429068 original size:22 final size:22
Alignment explanation
Indices: 1429040--1429090 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1429030 CTACGGCGAC
1429040 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
1429062 ATTCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1429084 ATCCGTC
1 ATCCGTC
1429091 TATTTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1429495 original size:20 final size:19
Alignment explanation
Indices: 1429457--1429509 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1429447 AAATCGCAAC
1429457 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
1429476 GCGATTTTCATTTTCTCGTT
1 GCGATTTT-AGTTTCGCGTT
*
1429496 GCGAATTTAAGTTT
1 GCG-ATTTTAGTTT
1429510 AAGAAACTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1431171 original size:14 final size:14
Alignment explanation
Indices: 1431152--1431188 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1431142 GCTTGTTTAA
1431152 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1431166 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1431180 TTGATTTGT
1 TTGATTTGT
1431189 TGTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1431329 original size:54 final size:54
Alignment explanation
Indices: 1431243--1431377 Score: 180
Period size: 54 Copynumber: 2.5 Consensus size: 54
1431233 GTTAAAGGTA
* ** * * *
1431243 CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGATTTTATCGTTGTGATAGT
1 CAAATTCGCAACACGAAAGTCAAATTCACAACGCGAAATAAGCGTTGCGATAGT
* *
1431297 CAAATTCGCAACATGAATGTCAAATTCACAACGCGAAATAAGCGTTGCGATAGT
1 CAAATTCGCAACACGAAAGTCAAATTCACAACGCGAAATAAGCGTTGCGATAGT
* *
1431351 GAAATTCGCAACGCGAAAGTCAAATTC
1 CAAATTCGCAACACGAAAGTCAAATTC
1431378 GCGCTGCGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (54 bp):
CAAATTCGCAACACGAAAGTCAAATTCACAACGCGAAATAAGCGTTGCGATAGT
Found at i:1434953 original size:19 final size:19
Alignment explanation
Indices: 1434910--1434981 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
1434900 CAAAACATTT
* *
1434910 GTGTTGCGAAACTAAA-AC
1 GTGTTGCGAAATTAAATTC
*
1434928 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAATTAAATTC
*
1434947 GTGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAATTC
* *
1434967 -AGTTGCGAATTTAAA
1 GTGTTGCGAAATTAAA
1434982 ATTCAGTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.37
19 23 0.50
20 6 0.13
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (19 bp):
GTGTTGCGAAATTAAATTC
Found at i:1434966 original size:20 final size:20
Alignment explanation
Indices: 1434929--1435259 Score: 156
Period size: 20 Copynumber: 16.6 Consensus size: 20
1434919 AACTAAAACC
*
1434929 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
1434948 TGTTGCGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTCG
* *
1434967 AGTTGCGAATTTAAAATTC-
1 TGTTGCGAATTTGAAATTCG
* * *
1434986 AGTTGCAAATTTAAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
* *
1435007 TATTGCGAATTTG-ACTATCG
1 TGTTGCGAATTTGAAAT-TCG
* *
1435027 CGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* *
1435047 TGTTGCGAATTTG-ACTTATG
1 TGTTGCGAATTTGAAATT-CG
*
1435067 TGTTGCG-ATTTACAAATTTTC-
1 TGTTGCGAATTT-GAAA--TTCG
1435088 T-TTGCG-ATTT-ACAGATTCG
1 TGTTGCGAATTTGA-A-ATTCG
** *
1435107 CATTGCGAATTTG-ACTTCAG
1 TGTTGCGAATTTGAAATTC-G
**
1435127 TGTTGCGAATTTGACTTTCG
1 TGTTGCGAATTTGAAATTCG
* *
1435147 CGTTGCGAATTTG-ATTTCTG
1 TGTTGCGAATTTGAAATTC-G
*
1435167 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
*
1435187 TGTTGCG-ATTTACAAATTCG
1 TGTTGCGAATTT-GAAATTCG
**
1435207 CATTGCGAATTTGGAAACTT-G
1 TGTTGCGAATTT-GAAA-TTCG
* * *
1435228 -GTTGCGAAATTGGAGTTCG
1 TGTTGCGAATTTGAAATTCG
*
1435247 CGTTGCGAATTTG
1 TGTTGCGAATTTG
1435260 TTGGTCATTT
Statistics
Matches: 250, Mismatches: 37, Indels: 49
0.74 0.11 0.15
Matches are distributed among these distances:
18 6 0.02
19 67 0.27
20 141 0.56
21 32 0.13
22 2 0.01
23 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:1434981 original size:38 final size:38
Alignment explanation
Indices: 1434930--1435040 Score: 116
Period size: 38 Copynumber: 2.8 Consensus size: 38
1434920 ACTAAAACCT
* *
1434930 GTTGCGAAATTAAATTCGTGTTGCGAATTTGAAATTCA
1 GTTGCGAATTTAAATTCGAGTTGCGAATTTGAAATTCA
* *
1434968 GTTGCGAATTTAAAATTC-AGTTGCAAATTTAAAATTCA
1 GTTGCGAATTT-AAATTCGAGTTGCGAATTTGAAATTCA
* * *
1435006 GTATTGCGAATTTGACTATCGCGTTGCGAATTTGA
1 G--TTGCGAATTTAAAT-TCGAGTTGCGAATTTGA
1435041 CTTCTGTGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 28 0.47
39 8 0.14
40 12 0.20
41 11 0.19
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (38 bp):
GTTGCGAATTTAAATTCGAGTTGCGAATTTGAAATTCA
Found at i:1434983 original size:19 final size:19
Alignment explanation
Indices: 1434930--1435018 Score: 108
Period size: 19 Copynumber: 4.6 Consensus size: 19
1434920 ACTAAAACCT
* *
1434930 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTAAAATTC-A
*
1434949 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTAAAATTCA
1434968 GTTGCGAATTTAAAATTCA
1 GTTGCGAATTTAAAATTCA
*
1434987 GTTGCAAATTTAAAATTCA
1 GTTGCGAATTTAAAATTCA
1435006 GTATTGCGAATTT
1 G--TTGCGAATTT
1435019 GACTATCGCG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 47 0.76
20 6 0.10
21 9 0.15
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTAAAATTCA
Found at i:1435078 original size:80 final size:81
Alignment explanation
Indices: 1434987--1435182 Score: 215
Period size: 80 Copynumber: 2.4 Consensus size: 81
1434977 TTAAAATTCA
* * * *
1434987 GTTGCAAATTTAAAATTCAGTATTGCGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGTGTT
1 GTTGCGAATTTAAAATTCTGT-TTGCGAATTTGACTATTCGCATTGCGAATTTGACTTCAGTGTT
*
1435051 GCGAATTTGACTTAT-GT
65 GCGAATTTGACTT-TCGC
* * *
1435068 GTTGCG-ATTTACAAATTTTCTTTGCG-ATTT-ACAGATTCGCATTGCGAATTTGACTTCAGTGT
1 GTTGCGAATTTA-AAATTCTGTTTGCGAATTTGAC-TATTCGCATTGCGAATTTGACTTCAGTGT
1435130 TGCGAATTTGACTTTCGC
64 TGCGAATTTGACTTTCGC
* *
1435148 GTTGCGAATTT-GATTTCTGTGTTGCGAATTTGACT
1 GTTGCGAATTTAAAATTCTGT-TTGCGAATTTGACT
1435183 TCTGTGTTGC
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
78 2 0.02
79 11 0.12
80 60 0.64
81 19 0.20
82 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (81 bp):
GTTGCGAATTTAAAATTCTGTTTGCGAATTTGACTATTCGCATTGCGAATTTGACTTCAGTGTTG
CGAATTTGACTTTCGC
Found at i:1435112 original size:100 final size:100
Alignment explanation
Indices: 1434994--1435219 Score: 284
Period size: 100 Copynumber: 2.3 Consensus size: 100
1434984 TCAGTTGCAA
* *
1434994 ATTTA-AAATTCAGTATTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-TTCTGTGTTGCGAA
1 ATTTACAAATTC-GCATTGCGAATTTGACT-TCAGCGTTGCGAATTTGACTTTC-GCGTTGCGAA
*
1435056 TTTGACTTATGTGTTGCG-ATTT-ACAAATTTTCT-TTGCG
63 TTTGACTTATGTGTTGCGAATTTGAC---TTCTCTGTTGCG
* *
1435094 ATTTACAGATTCGCATTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTTCGCGTTGCGAATTT
1 ATTTACAAATTCGCATTGCGAATTTGACTTCAGCGTTGCGAATTTGACTTTCGCGTTGCGAATTT
* * *
1435159 GATTTCTGTGTTGCGAATTTGACTTCTGTGTTGCG
66 GACTTATGTGTTGCGAATTTGACTTCTCTGTTGCG
1435194 ATTTACAAATTCGCATTGCGAATTTG
1 ATTTACAAATTCGCATTGCGAATTTG
1435220 GAAACTTGGT
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
99 6 0.05
100 91 0.82
101 12 0.11
102 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (100 bp):
ATTTACAAATTCGCATTGCGAATTTGACTTCAGCGTTGCGAATTTGACTTTCGCGTTGCGAATTT
GACTTATGTGTTGCGAATTTGACTTCTCTGTTGCG
Found at i:1435183 original size:40 final size:40
Alignment explanation
Indices: 1435009--1435183 Score: 182
Period size: 40 Copynumber: 4.4 Consensus size: 40
1434999 AAATTCAGTA
*
1435009 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
* * *
1435049 TTGCGAATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTTTCT-
1 TTGCGAATTTGACTT-TCGCGTTGCGAATTTGAC---TTCTGTG
* * *
1435089 TTGCG-ATTT-ACAGATTCGCATTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGAC--TTTCGCGTTGCGAATTTGACTTCTGTG
*
1435129 TTGCGAATTTGACTTTCGCGTTGCGAATTTGATTTCTGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
1435169 TTGCGAATTTGACTT
1 TTGCGAATTTGACTT
1435184 CTGTGTTGCG
Statistics
Matches: 109, Mismatches: 14, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
38 4 0.04
39 12 0.11
40 76 0.70
41 13 0.12
42 4 0.04
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
Found at i:1435232 original size:60 final size:59
Alignment explanation
Indices: 1435024--1435235 Score: 173
Period size: 60 Copynumber: 3.5 Consensus size: 59
1435014 AATTTGACTA
* ** * *
1435024 TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTATGTGTTGCGATTTACAAAT
1 TCGCATTGCGAATTTGAAAT-TGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAAT
** * * * *
1435084 TTTCTTTGCG-ATTT-ACAGATTCGCATTGCGAATTTGACTTCAGTGTTGCGAATTTGAC--TT
1 TCGCATTGCGAATTTGA-A-ATT-GCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAAT
* ** *
1435144 TCGCGTTGCGAATTTGATTTCTGTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAAT
1 TCGCATTGCGAATTTGAAAT-TGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAAT
1435204 TCGCATTGCGAATTTGGAAACTTG-GTTGCGAA
1 TCGCATTGCGAATTT-GAAA-TTGCGTTGCGAA
1435236 ATTGGAGTTC
Statistics
Matches: 118, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
58 3 0.03
59 9 0.08
60 89 0.75
61 13 0.11
62 4 0.03
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (59 bp):
TCGCATTGCGAATTTGAAATTGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAAT
Found at i:1435232 original size:100 final size:96
Alignment explanation
Indices: 1434994--1435259 Score: 279
Period size: 100 Copynumber: 2.7 Consensus size: 96
1434984 TCAGTTGCAA
* * * *
1434994 ATTTA-AAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATT
1 ATTTACAAATTC-GCATTGCGAATTTGACT-TAGTGTTGCGAATTTGACTTC-GCGTTGCGAATT
*
1435058 TGACTTATGTGTTGCGATTTACAAATTTTCTTTGCG
63 TGACTTATGTGTTGCGATTTAC--ATTCTCTTTGCG
*
1435094 ATTTACAGATTCGCATTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTTCGCGTTGCGAATTT
1 ATTTACAAATTCGCATTGCGAATTTGACTT-AGTGTTGCGAATTTGAC-TTCGCGTTGCGAATTT
* * *
1435159 GATTTCTGTGTTGCGAATTTGAC-TTCTGTGTTGCG
64 GACTTATGTGTTGCG-ATTT-ACATTCTCT-TTGCG
* *
1435194 ATTTACAAATTCGCATTGCGAATTTGGAAACTT-G-GTTGCGAAATTGGAGTTCGCGTTGCGAAT
1 ATTTACAAATTCGCATTGCGAATTT-G--ACTTAGTGTTGCG-AATTTGACTTCGCGTTGCGAAT
1435257 TTG
62 TTG
1435260 TTGGTCATTT
Statistics
Matches: 144, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
99 5 0.03
100 113 0.78
101 20 0.14
102 2 0.01
103 4 0.03
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (96 bp):
ATTTACAAATTCGCATTGCGAATTTGACTTAGTGTTGCGAATTTGACTTCGCGTTGCGAATTTGA
CTTATGTGTTGCGATTTACATTCTCTTTGCG
Found at i:1438363 original size:21 final size:21
Alignment explanation
Indices: 1438332--1438391 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
1438322 GGCATTTGTA
1438332 AAGGTAGTATCGATACTCTCTC
1 AAGG-AGTATCGATACTCTCTC
*
1438354 AATGAGTATCGATACTCTCTC
1 AAGGAGTATCGATACTCTCTC
1438375 AAGGAGTATCGATACTC
1 AAGGAGTATCGATACTC
1438392 GTGGTCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
AAGGAGTATCGATACTCTCTC
Found at i:1438787 original size:59 final size:59
Alignment explanation
Indices: 1438695--1438815 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
1438685 AATAGATGGA
* *
1438695 TAAGTGTCCTATCAAACCCTCCTATTCACAATGAAAAGGAAAACTCGATAATATTGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
* * * *
1438754 TAAGTGTCTTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
1438813 TAA
1 TAA
1438816 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
Found at i:1442165 original size:26 final size:26
Alignment explanation
Indices: 1442129--1442180 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1442119 GGCAAGTAAG
1442129 TTGATCTTGTACTCTTTAAAACTCAC
1 TTGATCTTGTACTCTTTAAAACTCAC
1442155 TTGATCTTGTACTCTTTAAAACTCAC
1 TTGATCTTGTACTCTTTAAAACTCAC
1442181 CTTACCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (26 bp):
TTGATCTTGTACTCTTTAAAACTCAC
Found at i:1442196 original size:26 final size:26
Alignment explanation
Indices: 1442137--1442196 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1442127 AGTTGATCTT
* **
1442137 GTACTCTTTAAAACTCACTTGATCTT
1 GTACTCTTTAAAACTCACTTGACCAA
1442163 GTACTCTTTAAAACTCACCTT-ACCAA
1 GTACTCTTTAAAACTCA-CTTGACCAA
*
1442189 GTAGTCTT
1 GTACTCTT
1442197 CCACAGTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (26 bp):
GTACTCTTTAAAACTCACTTGACCAA
Found at i:1443389 original size:59 final size:59
Alignment explanation
Indices: 1443297--1443417 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 59
1443287 AATAGATGGA
* * *
1443297 TAAGTGTTTTATCGAACCCTCTTAGTCGCAATAAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTTCTATCGAACCCTCTTAGTCGCAATAAAAAGGAAAAATCGATAATATGGCTC
1443356 TAAGTGTTCTATCGAACCCTAC-TAGTCGCAATAAAAAGGAAAAATCGATAATATGGCTC
1 TAAGTGTTCTATCGAACCCT-CTTAGTCGCAATAAAAAGGAAAAATCGATAATATGGCTC
1443415 TAA
1 TAA
1443418 CCAACCCTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 57 0.98
60 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (59 bp):
TAAGTGTTCTATCGAACCCTCTTAGTCGCAATAAAAAGGAAAAATCGATAATATGGCTC
Found at i:1444311 original size:259 final size:261
Alignment explanation
Indices: 1443809--1444317 Score: 828
Period size: 260 Copynumber: 2.0 Consensus size: 261
1443799 TAATCAATAG
*
1443809 AAATATTGAAAATTCGTAATATTTACAAAATCACGTATTAATCTCGTATAGGAATTTCTGATTGC
1 AAATATTGAAAATTCGTAATATTTACAAAATCACATATTAATCTCGTATAGGAATTTCTGATTGC
** * *
1443874 GTTATCTTCACTAAAATGGGTATATCTTGAGTTCCCAATATCGGATTGATGCGATTCAAGAACCG
66 GTTATCTTCACTAAAACAGGCATATCTTGAGTTCCCAACATCGGATTGATGCGATTCAAGAACCG
* *
1443939 TTGGAAAGATAAGAGACAGACAGTTGTATTTTCAGAAGACATATTGACCAAATAAGATCAGAATC
131 TTGGAAAGATAAGAGACAGACAGTTGTATTTCCAGAAGACATATTGACAAAATAAGATCAGAATC
** *
1444004 CCATTCAAAAAGTTGTCGCAAGTCTGCTGCTGTTATGGTCTTCTTTTCCAAGGCTGTCTTCACTA
196 CCATTCAAAAAGTCATCGCAAGTCTACTGCTGTTATGGTCTTCTTTTCCAAGGCTGTCTTCACTA
1444069 T
261 T
*
1444070 AAATATTGAAATTTCGTAATATTTACAAAATCACATATTAATCTC-TATAGGAATTTCTGCA-TG
1 AAATATTGAAAATTCGTAATATTTACAAAATCACATATTAATCTCGTATAGGAATTTCTG-ATTG
* * *
1444133 CGTTGTCTTCACTAAAACAGGCGTATCTTGAGTTCCCAACATTGGATTGATGCGATTCAAGAACC
65 CGTTATCTTCACTAAAACAGGCATATCTTGAGTTCCCAACATCGGATTGATGCGATTCAAGAACC
*
1444198 GTTGGAAAGATAAGTGACAGA-AGGTTG-ATTTCCAGAAGACATATTGACAAAATAAGATCAGAA
130 GTTGGAAAGATAAGAGACAGACA-GTTGTATTTCCAGAAGACATATTGACAAAATAAGATCAGAA
*
1444261 TCCCATTCAAAAAGTCATCGCAAGTCTACTGCTGTTATGGTCTTCTTTTCCCAGGCT
194 TCCCATTCAAAAAGTCATCGCAAGTCTACTGCTGTTATGGTCTTCTTTTCCAAGGCT
1444318 TGGACGAGTG
Statistics
Matches: 230, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
259 88 0.38
260 98 0.43
261 44 0.19
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (261 bp):
AAATATTGAAAATTCGTAATATTTACAAAATCACATATTAATCTCGTATAGGAATTTCTGATTGC
GTTATCTTCACTAAAACAGGCATATCTTGAGTTCCCAACATCGGATTGATGCGATTCAAGAACCG
TTGGAAAGATAAGAGACAGACAGTTGTATTTCCAGAAGACATATTGACAAAATAAGATCAGAATC
CCATTCAAAAAGTCATCGCAAGTCTACTGCTGTTATGGTCTTCTTTTCCAAGGCTGTCTTCACTA
T
Found at i:1444579 original size:20 final size:20
Alignment explanation
Indices: 1444554--1444610 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1444544 TATCATACTC
*
1444554 AGGGTCAGTATGGATACCCA
1 AGGGTCAGTATCGATACCCA
1444574 AGGGTCAGTATCGATACCCA
1 AGGGTCAGTATCGATACCCA
1444594 AGGGTCAGTATCGATAC
1 AGGGTCAGTATCGATAC
1444611 TGCTGGCACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (20 bp):
AGGGTCAGTATCGATACCCA
Found at i:1447735 original size:9 final size:9
Alignment explanation
Indices: 1447723--1447756 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1447713 AAATATTTTG
1447723 TATTTAATT
1 TATTTAATT
*
1447732 TATTTAA-G
1 TATTTAATT
1447740 TATTTAATT
1 TATTTAATT
1447749 TATTTAAT
1 TATTTAAT
1447757 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1447762 original size:17 final size:17
Alignment explanation
Indices: 1447722--1447760 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1447712 AAAATATTTT
1447722 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1447739 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1447756 -TATTT
1 GTATTT
1447761 TACTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1449780 original size:12 final size:12
Alignment explanation
Indices: 1449763--1449788 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1449753 AGCTGCTCAG
1449763 GACGACAACGAC
1 GACGACAACGAC
1449775 GACGACAACGAC
1 GACGACAACGAC
1449787 GA
1 GA
1449789 TGACGACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.31, G:0.27, T:0.00
Consensus pattern (12 bp):
GACGACAACGAC
Found at i:1456999 original size:15 final size:16
Alignment explanation
Indices: 1456952--1456998 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1456942 AAAGTATTAA
*
1456952 ATATAAAAATGAAGAAA
1 ATATAAAAATGAA-AAG
*
1456969 ATAATAAAAA-GTAAAG
1 AT-ATAAAAATGAAAAG
1456985 ATATAAAAATGAAA
1 ATATAAAAATGAAA
1456999 GTAATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 4 0.16
18 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (16 bp):
ATATAAAAATGAAAAG
Found at i:1457413 original size:22 final size:21
Alignment explanation
Indices: 1457378--1457419 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1457368 CATAATTATT
1457378 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
1457399 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
1457420 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:1457563 original size:14 final size:15
Alignment explanation
Indices: 1457535--1457567 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1457525 GGTAAACCAT
1457535 ATTATAATAAATATA
1 ATTATAATAAATATA
*
1457550 ATTAT-ATAACTATA
1 ATTATAATAAATATA
1457564 ATTA
1 ATTA
1457568 AAAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATAATAAATATA
Found at i:1457892 original size:18 final size:16
Alignment explanation
Indices: 1457871--1457901 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1457861 CTTCTAATTT
1457871 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
1457887 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
1457902 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Done.