Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020099.1 Corchorus olitorius cultivar O-4 contig20132, 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: 17833
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Found at i:728 original size:44 final size:44
Alignment explanation
Indices: 666--755 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
656 AATCGGGTGT
666 TTTTCTTATATACTAGTTAGTTGCGCTCGCGCGATGCCGTGGGG
1 TTTTCTTATATACTAGTTAGTTGCGCTCGCGCGATGCCGTGGGG
710 TTTTCTTATATACTAGTTAGTTGCGCTCGCGCGATGCCGTGGGG
1 TTTTCTTATATACTAGTTAGTTGCGCTCGCGCGATGCCGTGGGG
754 TT
1 TT
756 CATCGTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (44 bp):
TTTTCTTATATACTAGTTAGTTGCGCTCGCGCGATGCCGTGGGG
Found at i:995 original size:38 final size:35
Alignment explanation
Indices: 947--1019 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 35
937 TAGAGGACAT
* *
947 AAAATGCTAATTGTGATGCAATATATTTAACAGAGGTA
1 AAAATCCTAATTGAGATGC-ATATA--TAACAGAGGTA
*
985 AAAATCCTAATTGAGGTGCATATATAACAGAGGTA
1 AAAATCCTAATTGAGATGCATATATAACAGAGGTA
1020 GAGGATAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 11 0.34
37 5 0.16
38 16 0.50
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (35 bp):
AAAATCCTAATTGAGATGCATATATAACAGAGGTA
Found at i:1101 original size:2 final size:2
Alignment explanation
Indices: 1096--1130 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1086 AAAGAGGCAA
1096 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 A
1131 CACCATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2065 original size:30 final size:30
Alignment explanation
Indices: 2029--2091 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2019 TTTACTCAAT
* *
2029 AAAGATAAATGACATTATAGAACATTATAG
1 AAAGATAAATGAAATTACAGAACATTATAG
*
2059 AAAGATAAATGAAATTACATAACATTATAG
1 AAAGATAAATGAAATTACAGAACATTATAG
2089 AAA
1 AAA
2092 TAAGTGAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.25
Consensus pattern (30 bp):
AAAGATAAATGAAATTACAGAACATTATAG
Found at i:2498 original size:27 final size:27
Alignment explanation
Indices: 2460--2512 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2450 AGTCGACCAA
2460 AAGTAGCAGGATATGAACACCATTAAG
1 AAGTAGCAGGATATGAACACCATTAAG
2487 AAGTAGCAGGATATGAACACCATTAA
1 AAGTAGCAGGATATGAACACCATTAA
2513 ACTAACACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (27 bp):
AAGTAGCAGGATATGAACACCATTAAG
Found at i:3938 original size:20 final size:20
Alignment explanation
Indices: 3913--3957 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3903 AACCTGAACT
3913 CAAATCTCTCCTGTAAACCC
1 CAAATCTCTCCTGTAAACCC
*
3933 CAAATCTCTCTTGTAAACCC
1 CAAATCTCTCCTGTAAACCC
3953 CAAAT
1 CAAAT
3958 TCAAAGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (20 bp):
CAAATCTCTCCTGTAAACCC
Found at i:4001 original size:18 final size:18
Alignment explanation
Indices: 3978--4021 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
3968 TAAAGAGGAA
3978 AAGGAAGAAAACAAACCT
1 AAGGAAGAAAACAAACCT
3996 AAGGAAGAAAACAAACCT
1 AAGGAAGAAAACAAACCT
4014 AAGGAAGA
1 AAGGAAGA
4022 GAAAGCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.61, C:0.14, G:0.20, T:0.05
Consensus pattern (18 bp):
AAGGAAGAAAACAAACCT
Found at i:4543 original size:14 final size:14
Alignment explanation
Indices: 4524--4553 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4514 AAAATTCAAA
4524 AAATCAAAATCATC
1 AAATCAAAATCATC
4538 AAATCAAAATCATC
1 AAATCAAAATCATC
4552 AA
1 AA
4554 GTGTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCAAAATCATC
Found at i:5202 original size:21 final size:21
Alignment explanation
Indices: 5174--5297 Score: 101
Period size: 21 Copynumber: 5.8 Consensus size: 21
5164 TGAATATTTT
5174 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAACTACC
* *
5195 TATTAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
5216 TATAAAATTGTGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* * *
5237 ATAAGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-CTACC
* *
5260 TATGAAATTTTAATAAACTTTCC
1 TATGAAATTTTGAT-AAC-TACC
5283 TATG-AATTTTG-TAAC
1 TATGAAATTTTGATAAC
5298 CTTCCAATGA
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.04
21 36 0.44
22 33 0.41
23 9 0.11
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:6647 original size:12 final size:12
Alignment explanation
Indices: 6630--6661 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
6620 TACCCTATGT
6630 AAACACGACACG
1 AAACACGACACG
6642 AAACACGACACG
1 AAACACGACACG
6654 AAACACGA
1 AAACACGA
6662 ATTGCCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:7866 original size:2 final size:2
Alignment explanation
Indices: 7859--7883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7849 GTAGTTAGAA
7859 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
7884 ATAGTTTGAG
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:8240 original size:22 final size:22
Alignment explanation
Indices: 8214--8778 Score: 148
Period size: 22 Copynumber: 26.2 Consensus size: 22
8204 ATTACACTAT
*
8214 TTTTGATGATC-TCCTTATGAAA
1 TTTTGATAATCTTCC-TATGAAA
8236 TTTTGATAATCTTCCTATGAAA
1 TTTTGATAATCTTCCTATGAAA
* * *
8258 TTTTAATAA-CGATACTATGAAA
1 TTTTGATAATC-TTCCTATGAAA
* * * ** *
8280 TTTCGAGAACCTTTTTATAAAA
1 TTTTGATAATCTTCCTATGAAA
** * *
8302 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAATCTTCCTATGAAA
* * * * *
8324 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAATCTTCCTATGAAA
8346 TTTTGA-AGATC-TCACTATGAAA
1 TTTTGATA-ATCTTC-CTATGAAA
*
8368 TTTTGATAA-CTTCCGAATGAAA
1 TTTTGATAATCTTCC-TATGAAA
* ** *
8390 TTTTGATAACCAACACTATGAGA
1 TTTTGATAATCTTC-CTATGAAA
* *
8413 TGTTGATAA-CCTCCATATG--A
1 TTTTGATAATCTTCC-TATGAAA
*
8433 TATTGATAA-C--CAC-A--AAA
1 TTTTGATAATCTTC-CTATGAAA
* * * *
8450 -TTTAAAAACCTTCATATG-AA
1 TTTTGATAATCTTCCTATGAAA
* * *
8470 TTGTT-AGTAAT-TACACTCTAAAA
1 TT-TTGA-TAATCTTC-CTATGAAA
*
8493 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAATCTTC-CTATGAAA
* * *
8515 TTGTGATAA-CCTCGCTATAAAA
1 TTTTGATAATCTTC-CTATGAAA
*
8537 TTTTGATAAGTCTTCCTATAAAA
1 TTTTGATAA-TCTTCCTATGAAA
* * *
8560 TTTTGATAAACATCGCTATAAAA
1 TTTTGATAATCTTC-CTATGAAA
*
8583 TTTTGATAA-CCTCCTTATGAAA
1 TTTTGATAATCTTCC-TATGAAA
* *
8605 TCTTGATAA-----CTA-CAAA
1 TTTTGATAATCTTCCTATGAAA
* * **
8621 TTTTGATAACCTCCCTATGACT
1 TTTTGATAATCTTCCTATGAAA
* * *
8643 TTTTAATAA-CCTCATTATGAAA
1 TTTTGATAATCTTC-CTATGAAA
*
8665 TTTTGTTAAT-TTCCCTATGAAA
1 TTTTGATAATCTT-CCTATGAAA
* * * *
8687 TTTTGAT-CTACATACTATAAAA
1 TTTTGATAAT-CTTCCTATGAAA
* * *
8709 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAATCTTCCTATGAAA
* **
8731 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAATCT-TCCTATGAAA
* *
8753 TTTTGATAACCTTCATATGAAA
1 TTTTGATAATCTTCCTATGAAA
8775 TTTT
1 TTTT
8779 TATATCCTGA
Statistics
Matches: 403, Mismatches: 94, Indels: 92
0.68 0.16 0.16
Matches are distributed among these distances:
16 16 0.04
17 5 0.01
18 2 0.00
19 3 0.01
20 12 0.03
21 21 0.05
22 275 0.68
23 65 0.16
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTGATAATCTTCCTATGAAA
Found at i:8279 original size:44 final size:43
Alignment explanation
Indices: 8229--8778 Score: 269
Period size: 44 Copynumber: 12.8 Consensus size: 43
8219 ATGATCTCCT
* *
8229 TATGAAATTTTGATAATCTTCCTATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAAC-ATAC
* * ** * ** * *
8273 TATGAAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACATAC
* * * *
8316 TTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGATC-TCAC
1 -TATGAAATTTTGATAACCTTCCTATGAAATTTTGATA-A-CAT-AC
* *
8361 TATGAAATTTTGATAA-CTTCCGAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTCC-TATGAAATTTTGATAA-C-ATAC
* * * *
8406 TATGAGATGTTGATAACC-TCCATATG--ATATTGATAAC-CAC
1 TATGAAATTTTGATAACCTTCC-TATGAAATTTTGATAACATAC
* * * * *
8446 -A--AAA-TTTAAAAACCTTCATATG-AATTGTT-AGTAATTACAC
1 TATGAAATTTTGATAACCTTCCTATGAAATT-TTGA-TAA-CATAC
* * * * * * *
8486 TCTAAAATTTTGATAATC-ACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAACAT-AC
* * * *
8530 TATAAAATTTTGATAAGTCTTCCTATAAAATTTTGATAAACATCGC
1 TATGAAATTTTGATAA-CCTTCCTATGAAATTTTGAT-AACAT-AC
* *
8576 TATAAAATTTTGATAACC-TCCTTATGAAATCTTGATAAC-TAC
1 TATGAAATTTTGATAACCTTCC-TATGAAATTTTGATAACATAC
* ** * * *
8618 ----AAATTTTGATAACCTCCCTATGACTTTTTAATAACCTCAT
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACAT-AC
* * *
8658 TATGAAATTTTGTTAA-TTTCCCTATGAAATTTTGATCTACATAC
1 TATGAAATTTTGATAACCTT-CCTATGAAATTTTGAT-AACATAC
* * * * *
8702 TATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAAC-ATAC
*
8746 TATGAAATTTTGATAACCTTCATATGAAATTTT
1 TATGAAATTTTGATAACCTTCCTATGAAATTTT
8779 TATATCCTGA
Statistics
Matches: 381, Mismatches: 87, Indels: 76
0.70 0.16 0.14
Matches are distributed among these distances:
36 11 0.03
37 7 0.02
38 32 0.08
39 4 0.01
40 7 0.02
42 2 0.01
43 24 0.06
44 207 0.54
45 62 0.16
46 25 0.07
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACATAC
Found at i:8582 original size:46 final size:44
Alignment explanation
Indices: 8488--8591 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 44
8478 AATTACACTC
* *
8488 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAATCACACTATAAAATTGTGATAACATCGCTA
* *
8532 TAAAATTTTGATAAGTCTTC-CTATAAAATTTTGATAAACATCGCTA
1 TAAAATTTTGATAA-TC-ACACTATAAAATTGTGAT-AACATCGCTA
8578 TAAAATTTTGATAA
1 TAAAATTTTGATAA
8592 CCTCCTTATG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
44 14 0.26
45 15 0.28
46 24 0.45
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (44 bp):
TAAAATTTTGATAATCACACTATAAAATTGTGATAACATCGCTA
Found at i:8776 original size:66 final size:61
Alignment explanation
Indices: 8552--8778 Score: 163
Period size: 66 Copynumber: 3.6 Consensus size: 61
8542 ATAAGTCTTC
* * * *
8552 CTATAAAATTTTGATAAACATCGCTATAAAATTTTGATAACCTCCTTATGAAATCTTG-ATAA
1 CTATGAAATTTTGATAACCTTC-CTATAAAATTTTGATAACCT-CTTATGAAATTTTGAATAA
* * * ** * *
8614 CTA-CAAATTTTGATAACCTCCCTATGACTTTTTAATAACCTCATTATGAAATTTTGTTAATTTC
1 CTATGAAATTTTGATAACCTTCCTATAAAATTTTGATAACCTC-TTATGAAATTTTG--AA--TA
*
8678 C
61 A
* * *
8679 CTATGAAATTTTGATCTA-CATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
1 CTATGAAATTTTGAT-AACCTTCCTATAAAATTTTGATAA-CCTCTTATGAAATTTTG--AA-T-
8743 AA
60 AA
* *
8745 CTATGAAATTTTGATAACCTTCATATGAAATTTT
1 CTATGAAATTTTGATAACCTTCCTATAAAATTTT
8779 TATATCCTGA
Statistics
Matches: 124, Mismatches: 30, Indels: 18
0.72 0.17 0.10
Matches are distributed among these distances:
59 1 0.01
60 28 0.23
61 14 0.11
62 3 0.02
63 1 0.01
65 6 0.05
66 66 0.53
67 5 0.04
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (61 bp):
CTATGAAATTTTGATAACCTTCCTATAAAATTTTGATAACCTCTTATGAAATTTTGAATAA
Found at i:8865 original size:22 final size:22
Alignment explanation
Indices: 8835--9129 Score: 72
Period size: 22 Copynumber: 13.2 Consensus size: 22
8825 ACCTTCCTAA
*
8835 TTTGGTAACCATACTATGAAAT
1 TTTGATAACCATACTATGAAAT
*
8857 TTTGATAACCTCCCCAGACTATGAAAT
1 TTTGATAA-----CCATACTATGAAAT
** * * * *
8884 TTTCG-TAATAAAATTTTGAAAA
1 TTT-GATAACCATACTATGAAAT
8906 TTTGATAACC-T-CTTTATGAAAT
1 TTTGATAACCATAC--TATGAAAT
* *
8928 TTTGATAACC-TCTCTATAAAAT
1 TTTGATAACCAT-ACTATGAAAT
* * *
8950 TTTGTTGACCCCT-CTATGAAAT
1 TTTGAT-AACCATACTATGAAAT
* * * *
8972 TTTGATAATCACATTATGTAAT
1 TTTGATAACCATACTATGAAAT
* *
8994 TTTGATAA-CATTGCTTTGAAAT
1 TTTGATAACCA-TACTATGAAAT
* ** * *
9016 TTTGATGATAACACTATAAAAT
1 TTTGATAACCATACTATGAAAT
* * *
9038 TTTGAAAATC-TTCTTAT-AAAT
1 TTTGATAACCATAC-TATGAAAT
* *
9059 TTTGATAATCTAATCTCTATGAAAT
1 TTTGATAA-C-CAT-ACTATGAAAT
* *
9084 TTTGATGACCACT-CTATGAGA-
1 TTTGATAACCA-TACTATGAAAT
* *
9105 TTTGATAACC-TTCTATCAAAT
1 TTTGATAACCATACTATGAAAT
9126 TTTG
1 TTTG
9130 GTACTCCTTA
Statistics
Matches: 198, Mismatches: 50, Indels: 51
0.66 0.17 0.17
Matches are distributed among these distances:
19 1 0.01
20 6 0.03
21 30 0.15
22 115 0.58
23 5 0.03
24 8 0.04
25 13 0.07
27 19 0.10
28 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTGATAACCATACTATGAAAT
Found at i:8989 original size:66 final size:65
Alignment explanation
Indices: 8900--9129 Score: 207
Period size: 66 Copynumber: 3.5 Consensus size: 65
8890 AATAAAATTT
* * * * * *
8900 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATCTC-TTATGAAATTTTGATAACATCTCTATGAAATTTTGATGACCACTCT
8965 A
65 A
* * * ** *
8966 TGAAATTTTGATAATCACATTATGTAATTTTGATAACAT-TGCTTTGAAATTTTGATGATAACAC
1 TGAAATTTTGATAATCTC-TTATGAAATTTTGATAACATCT-CTATGAAATTTTGATGACCACTC
9030 TA
64 TA
* *
9032 TAAAATTTTGAAAATCTTCTTAT-AAATTTTGATAATCTAATCTCTATGAAATTTTGATGACCAC
1 TGAAATTTTGATAATC-TCTTATGAAATTTTGATAA-C--ATCTCTATGAAATTTTGATGACCAC
9096 TCTA
62 TCTA
* * *
9100 TGAGA-TTTGATAACCT-TCTATCAAATTTTG
1 TGAAATTTTGATAATCTCT-TATGAAATTTTG
9130 GTACTCCTTA
Statistics
Matches: 131, Mismatches: 25, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
65 13 0.10
66 74 0.56
67 17 0.13
68 26 0.20
69 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (65 bp):
TGAAATTTTGATAATCTCTTATGAAATTTTGATAACATCTCTATGAAATTTTGATGACCACTCTA
Found at i:9014 original size:44 final size:44
Alignment explanation
Indices: 8919--9068 Score: 119
Period size: 44 Copynumber: 3.4 Consensus size: 44
8909 GATAACCTCT
* * * *** **
8919 TTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGA-CCCC
1 TTATGAAATTTTGATAATCACACTATAAAATTTTGAAAATCTGC
* **
8962 TCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACAT-TGC
1 T-TATGAAATTTTGATAATCACACTATAAAATTTTGA-AA-ATCTGC
* * *
9008 TT-TGAAATTTTGATGATAACACTATAAAATTTTGAAAATCTTC
1 TTATGAAATTTTGATAATCACACTATAAAATTTTGAAAATCTGC
9051 TTAT-AAATTTTGATAATC
1 TTATGAAATTTTGATAATC
9069 TAATCTCTAT
Statistics
Matches: 82, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
42 2 0.02
43 19 0.23
44 57 0.70
45 1 0.01
46 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (44 bp):
TTATGAAATTTTGATAATCACACTATAAAATTTTGAAAATCTGC
Found at i:9060 original size:21 final size:24
Alignment explanation
Indices: 9029--9088 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
9019 GATGATAACA
*
9029 CTATAAAATTTTGAAAATCT-TCT
1 CTATGAAATTTTGAAAATCTATCT
*
9052 -TAT-AAATTTTGATAATCTAATCT
1 CTATGAAATTTTGAAAATCT-ATCT
9075 CTATGAAATTTTGA
1 CTATGAAATTTTGA
9089 TGACCACTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 14 0.44
22 3 0.09
23 3 0.09
24 3 0.09
25 9 0.28
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (24 bp):
CTATGAAATTTTGAAAATCTATCT
Found at i:12731 original size:18 final size:18
Alignment explanation
Indices: 12708--12742 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12698 AAATAATAAA
12708 AAATAAAAATAAATATTT
1 AAATAAAAATAAATATTT
*
12726 AAATAATAATAAATATT
1 AAATAAAAATAAATATT
12743 AATTAGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAAAATAAATATTT
Found at i:13395 original size:80 final size:78
Alignment explanation
Indices: 13264--13425 Score: 297
Period size: 80 Copynumber: 2.1 Consensus size: 78
13254 CATGGAATTC
*
13264 AGATTAAAGTGAAACCGCCGCCTCTATGTTCTTTTCTAATCATCCATGGATTAATAAAGTTACGA
1 AGATTAAAGTGAAACCGCCGCCTCTATGTTCTTTTCTAATCATCCATGGATTAATAAAGTTACCA
13329 ACTATCACCCATA
66 ACTATCACCCATA
13342 AGATTAAAGTGAAACCGCCGCGCCTCTATGTTCTTTTCTAATCATCCATGGATTAATAAAGTTAC
1 AGATTAAAGTGAAACCG-C-CGCCTCTATGTTCTTTTCTAATCATCCATGGATTAATAAAGTTAC
13407 CAACTATCACCCATA
64 CAACTATCACCCATA
13422 AGAT
1 AGAT
13426 AATTGTGCTT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
78 17 0.21
79 1 0.01
80 63 0.78
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (78 bp):
AGATTAAAGTGAAACCGCCGCCTCTATGTTCTTTTCTAATCATCCATGGATTAATAAAGTTACCA
ACTATCACCCATA
Found at i:17138 original size:78 final size:78
Alignment explanation
Indices: 17048--17207 Score: 275
Period size: 78 Copynumber: 2.1 Consensus size: 78
17038 TTTCTAGTTG
* * * *
17048 AAATAGTTAAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGT
1 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAAGT
17113 TTTTAGTTGAGTA
66 TTTTAGTTGAGTA
*
17126 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAAAGT
1 AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAAGT
17191 TTTTAGTTGAGTA
66 TTTTAGTTGAGTA
17204 AAAT
1 AAAT
17208 TATAAATCTA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (78 bp):
AAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAAAGT
TTTTAGTTGAGTA
Done.