Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018253.1 Corchorus olitorius cultivar O-4 contig18286, 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: 121490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:557 original size:2 final size:2
Alignment explanation
Indices: 550--656 Score: 196
Period size: 2 Copynumber: 53.5 Consensus size: 2
540 ATTATACCTA
* *
550 GT GT GT GT GT TT GC GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
592 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
634 GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT G
657 ATTGTTTGGT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 101 1.00
ACGTcount: A:0.00, C:0.01, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:4655 original size:319 final size:318
Alignment explanation
Indices: 4040--4907 Score: 952
Period size: 319 Copynumber: 2.7 Consensus size: 318
4030 CACGATTTTA
* * * * *
4040 ACTATAAACTGACCCGAAAA-TTTTTCCTCAATTATTTGCCATAATATTCATAAATAATATATAA
1 ACTAAAAACTGACCCAAAAAGTTTTTTCTCAATTTTTTGCCATAATATTCATAAAAAATATATAA
* * * * *
4104 TTCAACTCCCAAAAAAATTGAAGGATTTTT-CAGTCTTCTAATATCGTTTTTCCATTTTTTCCGA
66 TTCAA-TGCCAAAAAGATTGAAGGCTTTTTAC-G-CTTCTAATATCTTTTTTTCATTTTTTCCGA
* *
4168 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
128 ATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * ** *
4233 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGGTAAAAACCATACAAA
193 TGGCTGAGATTTAGTTAGACGAATATACATATTTCAAGGAGTCATTATGCAAAAAAACATACAAA
* ** * *
4298 ACTGAGTAGAGGCCTTGAAACTCGTTTTTAGTCAAAAATCATGATCGTAGATTA-T-T-TCG
258 ACTGAGTAGAAGCCCCGAAACGCGTTTTTAGCCAAAAATCATGATCGTAG-TTAGTATATCG
* * *
4357 GCTAAAAACTGA-CCAAAAAGTTTTTTTTCTTAATTTTTTGCCATAATACTT-ATAAAAAATATT
1 ACTAAAAACTGACCCAAAAAG--TTTTTTCTCAATTTTTTGCCATAATA-TTCATAAAAAATATA
*
4420 TAATTCAATGCCAAAAAGATTGAAAGCTTTTTACGCTTCTAATATCATTTTTTTCATTTTTTTCC
63 TAATTCAATGCCAAAAAGATTGAAGGCTTTTTACGCTTCTAATATC-TTTTTTTCA-TTTTTTCC
* *
4485 GAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAA-CCGTTAAATCTA
126 GAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TTAAATCCA
*
4549 ATGTGGCTG-GACTTTAGTTTGACGAATATACATATTTCAAGGAGT-ATTATGCCAAAAAAACAT
190 ATGTGGCTGAGA-TTTAGTTAGACGAATATACATATTTCAAGGAGTCATTATG-CAAAAAAACAT
* ** * *
4612 GCAAAACTGAGTCA-AAGCCCCGAAACGCGTTTTTAGCCAAAAATTGTGATGGTTGTTAGTACAC
253 ACAAAACTGAGT-AGAAGCCCCGAAACGCGTTTTTAGCCAAAAATCATGATCGTAGTTAGT----
4676 GATATCG
313 -ATATCG
* * * *
4683 ACTAAAAACTGACCCGAAAAGATTTTTCTCAATTTTTTG-CAAAATATTCAGAAAAAATATATAA
1 ACTAAAAACTGACCCAAAAAGTTTTTTCTCAATTTTTTGCCATAATATTCATAAAAAATATATAA
** * * * * *
4747 CCCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATAT-TGTTTTTCAACTTTTTTCTGA
66 TTCAATGCCAAAAAGATTGA-AGGCTTTTTACGCTTCTAATATCTTTTTTTC-A-TTTTTTCCGA
* * * * *
4811 ATTAATTTCTAATTAAATAAAAAAAAGATTCAGATGCTCGTAAAAACAAGTCCTTATACCCAATG
128 ATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * *
4876 TGGCTGAGATTTGGTTCGATGAATATATATAT
193 TGGCTGAGATTTAGTTAGACGAATATACATAT
4908 ATATATATAT
Statistics
Matches: 464, Mismatches: 62, Indels: 43
0.82 0.11 0.08
Matches are distributed among these distances:
316 6 0.01
317 21 0.05
318 40 0.09
319 198 0.43
320 3 0.01
323 9 0.02
324 126 0.27
325 40 0.09
326 14 0.03
327 7 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (318 bp):
ACTAAAAACTGACCCAAAAAGTTTTTTCTCAATTTTTTGCCATAATATTCATAAAAAATATATAA
TTCAATGCCAAAAAGATTGAAGGCTTTTTACGCTTCTAATATCTTTTTTTCATTTTTTCCGAATT
AATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
CTGAGATTTAGTTAGACGAATATACATATTTCAAGGAGTCATTATGCAAAAAAACATACAAAACT
GAGTAGAAGCCCCGAAACGCGTTTTTAGCCAAAAATCATGATCGTAGTTAGTATATCG
Found at i:4905 original size:2 final size:2
Alignment explanation
Indices: 4898--4929 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4888 GGTTCGATGA
4898 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
4930 TTCAAGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8366 original size:17 final size:17
Alignment explanation
Indices: 8344--8398 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
8334 ATCACCCTCC
8344 AGATCACTAGTGATCTA
1 AGATCACTAGTGATCTA
*
8361 AGATCACTAGTGATGTA
1 AGATCACTAGTGATCTA
** *
8378 AGATCACCGGTGATCGA
1 AGATCACTAGTGATCTA
8395 AGAT
1 AGAT
8399 TACATGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (17 bp):
AGATCACTAGTGATCTA
Found at i:12646 original size:20 final size:19
Alignment explanation
Indices: 12621--12661 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12611 AATTAATAAT
*
12621 AAAGTTGAATCATCTAAAAA
1 AAAGTTAAATCA-CTAAAAA
*
12641 AAAGTTAAATGACTAAAAA
1 AAAGTTAAATCACTAAAAA
12660 AA
1 AA
12662 TACTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (19 bp):
AAAGTTAAATCACTAAAAA
Found at i:12753 original size:3 final size:3
Alignment explanation
Indices: 12745--12786 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12735 GTGATTTTAT
*
12745 ATA ATA ATA ATA A-A ATA ATA ATA ATA AT- ATA AT- TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12787 TAAGATAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.15
3 29 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:12763 original size:11 final size:12
Alignment explanation
Indices: 12745--12786 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
12735 GTGATTTTAT
12745 ATAATAATAATA
1 ATAATAATAATA
12757 A-AATAATAATA
1 ATAATAATAATA
12768 ATAAT-ATAAT-
1 ATAATAATAATA
*
12778 TTAATAATA
1 ATAATAATA
12787 TAAGATAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATAATAATA
Found at i:12764 original size:14 final size:14
Alignment explanation
Indices: 12745--12777 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12735 GTGATTTTAT
12745 ATAATAATAATAAA
1 ATAATAATAATAAA
*
12759 ATAATAATAATAAT
1 ATAATAATAATAAA
12773 ATAAT
1 ATAAT
12778 TTAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:21275 original size:73 final size:73
Alignment explanation
Indices: 21189--21335 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
21179 GTTAGGATTA
*
21189 TTGTCTTTGATCTTTTGATCACCTATAAGTTGTTTTATCATGTTTTTGTAAGATTGGTTCTTTTA
1 TTGTCTTTGATCTTTTGATCACCTATAAGTTATTTTATCATGTTTTTGTAAGATTGGTTCTTTTA
21254 TGTAGTTG
66 TGTAGTTG
21262 TTGTCTTTGATCTTTTGATCACCTATAAGTTATTTTATCATGTTTTTGTAAGATTGGTTCTTTTA
1 TTGTCTTTGATCTTTTGATCACCTATAAGTTATTTTATCATGTTTTTGTAAGATTGGTTCTTTTA
21327 TGTAGTTG
66 TGTAGTTG
21335 T
1 T
21336 CTAGCTGCCA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.18, C:0.10, G:0.17, T:0.55
Consensus pattern (73 bp):
TTGTCTTTGATCTTTTGATCACCTATAAGTTATTTTATCATGTTTTTGTAAGATTGGTTCTTTTA
TGTAGTTG
Found at i:26156 original size:19 final size:19
Alignment explanation
Indices: 26134--26178 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
26124 CTTCACTACG
*
26134 ACTGTGTAGTTCAACTATA
1 ACTGTGAAGTTCAACTATA
26153 ACTGTGAAGTTCAACTATA
1 ACTGTGAAGTTCAACTATA
26172 ACTGTGA
1 ACTGTGA
26179 CGTATCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
ACTGTGAAGTTCAACTATA
Found at i:32244 original size:5 final size:6
Alignment explanation
Indices: 32212--32250 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
32202 TTGTTAGATA
32212 TTAT-T TTATGT TTATGT TTATGT TTAT-T TTAT-T TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
32251 AATATTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (6 bp):
TTATGT
Found at i:41055 original size:7 final size:6
Alignment explanation
Indices: 41024--41053 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41014 TGACTTAATA
*
41024 ATTTTC ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
41054 TAAGGAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:41229 original size:26 final size:26
Alignment explanation
Indices: 41200--41252 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41190 AAAATTCTTA
41200 TACTAATTAAATTTAGTAATATATCT
1 TACTAATTAAATTTAGTAATATATCT
41226 TACTAATTAAATTTAGTAATATATCT
1 TACTAATTAAATTTAGTAATATATCT
41252 T
1 T
41253 GCATTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
TACTAATTAAATTTAGTAATATATCT
Found at i:41286 original size:2 final size:2
Alignment explanation
Indices: 41281--41319 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
41271 TGTATGTGTC
* *
41281 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41320 TTAGGGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41896 original size:23 final size:24
Alignment explanation
Indices: 41866--41911 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
41856 ATACTTTATC
41866 GATAAATAGTAAGAGAA-TGTATT
1 GATAAATAGTAAGAGAATTGTATT
*
41889 GATAAATAGTAGGAGAATTGTAT
1 GATAAATAGTAAGAGAATTGTAT
41912 AAAGGCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (24 bp):
GATAAATAGTAAGAGAATTGTATT
Found at i:42061 original size:17 final size:17
Alignment explanation
Indices: 42039--42074 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42029 TTCTAGGAAA
42039 CAATAAATTGAACGATC
1 CAATAAATTGAACGATC
*
42056 CAATAAATTGAATGATC
1 CAATAAATTGAACGATC
42073 CA
1 CA
42075 TAACCTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (17 bp):
CAATAAATTGAACGATC
Found at i:43483 original size:18 final size:18
Alignment explanation
Indices: 43460--43499 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
43450 GAACATATCT
43460 ACAACACTATATAAAAAC
1 ACAACACTATATAAAAAC
43478 ACAACACTATATAAAAAC
1 ACAACACTATATAAAAAC
43496 ACAA
1 ACAA
43500 TGTTGGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (18 bp):
ACAACACTATATAAAAAC
Found at i:43892 original size:30 final size:30
Alignment explanation
Indices: 43856--43920 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
43846 AAAATTATAA
*
43856 GTGTTTTGTGTTT-AGCCATAGAAAGCACAG
1 GTGTTTTGTGTTTGAG-AATAGAAAGCACAG
* *
43886 GTGTTTTGTTTTTGAGAATAGAAAGGACAG
1 GTGTTTTGTGTTTGAGAATAGAAAGCACAG
43916 GTGTT
1 GTGTT
43921 AATTTTGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (30 bp):
GTGTTTTGTGTTTGAGAATAGAAAGCACAG
Found at i:44707 original size:2 final size:2
Alignment explanation
Indices: 44700--44736 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44690 ACAATATGTA
44700 AT AT AT AT AT 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 AT AT AT AT AT A
44737 ACTTAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45559 original size:18 final size:19
Alignment explanation
Indices: 45527--45564 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
45517 GACTAAGAAC
45527 TTCATGACTAAGAACAAAT
1 TTCATGACTAAGAACAAAT
45546 TTCATGAC-AAGAACAAAT
1 TTCATGACTAAGAACAAAT
45564 T
1 T
45565 AGGTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
TTCATGACTAAGAACAAAT
Found at i:48019 original size:3 final size:3
Alignment explanation
Indices: 48011--48035 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48001 TGAAGAAACT
48011 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
48036 TAGATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53913 original size:30 final size:30
Alignment explanation
Indices: 53872--53930 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
53862 AAAGTTTCTG
*
53872 CTATATGGTTGATGATACGACTGTTGGTAT
1 CTATATGGTTGATGATACGACTCTTGGTAT
* *
53902 CTATTTGGTTGATGATATGACTCTTGGTA
1 CTATATGGTTGATGATACGACTCTTGGTA
53931 ATCCGCCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.42
Consensus pattern (30 bp):
CTATATGGTTGATGATACGACTCTTGGTAT
Found at i:60992 original size:72 final size:72
Alignment explanation
Indices: 60777--60972 Score: 365
Period size: 72 Copynumber: 2.7 Consensus size: 72
60767 ATAAGTACTG
60777 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAACACAAGACTAAAC
1 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAACACAAGACTAAAC
60842 CCTAGTA
66 CCTAGTA
60849 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAACACAAGACTAAAC
1 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAACACAAGACTAAAC
60914 CCTAGTA
66 CCTAGTA
* * *
60921 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTCAATTGGCTGATAAAA
1 ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAA
60973 ACATAAGCAA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 121 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (72 bp):
ATTTTGGGAATTCCTTAATTTAAAACCCTAAAAATTTAATCGGTTGATAAAACACAAGACTAAAC
CCTAGTA
Found at i:71686 original size:24 final size:24
Alignment explanation
Indices: 71659--71737 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
71649 TATGCCATAG
*
71659 AACAGAATCAACATCATTACAAGC
1 AACAGAATCAACATCATTACAAGA
*
71683 AACAGAATCAACATCATTACAAGG
1 AACAGAATCAACATCATTACAAGA
* *
71707 AATAGAATCAACAT-TTGTACAAGA
1 AACAGAATCAACATCAT-TACAAGA
71731 AACAGAA
1 AACAGAA
71738 GCATCCAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 48 0.98
ACGTcount: A:0.52, C:0.19, G:0.11, T:0.18
Consensus pattern (24 bp):
AACAGAATCAACATCATTACAAGA
Found at i:89844 original size:42 final size:42
Alignment explanation
Indices: 89785--89872 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
89775 GACATTCCAA
*
89785 TTCTGTTTTCCTTTCGTCTTTATTTCTATTTGGGTGGGTTTC
1 TTCTGTTTTCCTTTCGTCTTCATTTCTATTTGGGTGGGTTTC
89827 TTCTGTTTTCCTTTCGTCTTCATTTCTATTTGGGTGGGTTTC
1 TTCTGTTTTCCTTTCGTCTTCATTTCTATTTGGGTGGGTTTC
89869 TTCT
1 TTCT
89873 TCCCTAACAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.05, C:0.18, G:0.18, T:0.59
Consensus pattern (42 bp):
TTCTGTTTTCCTTTCGTCTTCATTTCTATTTGGGTGGGTTTC
Found at i:92687 original size:13 final size:13
Alignment explanation
Indices: 92669--92695 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
92659 AAACAACTGA
92669 AAAACACTTTTGG
1 AAAACACTTTTGG
92682 AAAACACTTTTGG
1 AAAACACTTTTGG
92695 A
1 A
92696 TTTCCCGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:101176 original size:19 final size:19
Alignment explanation
Indices: 101156--101192 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
101146 AATTAATTAT
101156 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
101174 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
101193 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:111725 original size:18 final size:18
Alignment explanation
Indices: 111702--111737 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
111692 ATTACACACT
111702 ACGATTCGCTGTAACAGC
1 ACGATTCGCTGTAACAGC
111720 ACGATTCGCTGTAACAGC
1 ACGATTCGCTGTAACAGC
111738 GCATAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
ACGATTCGCTGTAACAGC
Found at i:120312 original size:25 final size:25
Alignment explanation
Indices: 120284--120344 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
120274 AGCCTGGCTT
*
120284 GGCCCGCGCGCCTGGGCCATGCACA
1 GGCCCGCGCGCCTGGGCCACGCACA
*
120309 GGCCCGCGTGCCTGGGCCACGCACA
1 GGCCCGCGCGCCTGGGCCACGCACA
120334 GGCCCGCGCGC
1 GGCCCGCGCGC
120345 AGGCCGGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.10, C:0.46, G:0.38, T:0.07
Consensus pattern (25 bp):
GGCCCGCGCGCCTGGGCCACGCACA
Found at i:120586 original size:14 final size:14
Alignment explanation
Indices: 120567--120601 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
120557 TTCAAAACAT
120567 CAAATTTCTATCAC
1 CAAATTTCTATCAC
*
120581 CAAATTTCTATCAT
1 CAAATTTCTATCAC
120595 CAAATTT
1 CAAATTT
120602 ATAACCCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (14 bp):
CAAATTTCTATCAC
Done.