Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015884.1 Corchorus olitorius cultivar O-4 contig15917, 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: 70834
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4313 original size:21 final size:21
Alignment explanation
Indices: 4289--4338 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
4279 CGGCCATCCA
*
4289 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCAGTTAAGC
*
4310 CCGTGCCACCACCAGTTATGC
1 CCGTGCCACCACCAGTTAAGC
4331 CCGTGCCA
1 CCGTGCCA
4339 TCATCATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (21 bp):
CCGTGCCACCACCAGTTAAGC
Found at i:8706 original size:15 final size:15
Alignment explanation
Indices: 8673--8714 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
8663 TTGCTTTGTT
8673 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
*
8689 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTATAA
8704 TTGTTTTCTGT
1 TTGTTTTCTGT
8715 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:8975 original size:24 final size:24
Alignment explanation
Indices: 8948--9011 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
8938 GCCATTGCAT
*
8948 CAGCCACCACCTCCTCCAGTTGAG
1 CAGCCACCACCTCCTCCAGTTCAG
** *
8972 CAGCCAATACATCCTCCAGTTCAG
1 CAGCCACCACCTCCTCCAGTTCAG
*
8996 TAGCCACCACCTCCTC
1 CAGCCACCACCTCCTC
9012 TTGTTGACCA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.45, G:0.12, T:0.19
Consensus pattern (24 bp):
CAGCCACCACCTCCTCCAGTTCAG
Found at i:10442 original size:127 final size:127
Alignment explanation
Indices: 10200--10430 Score: 288
Period size: 127 Copynumber: 1.8 Consensus size: 127
10190 TGGGAATGCA
* ** **
10200 ATGTTTCTTTCCTTTCTGACTTGTGTGTGCACTAGGTATTATAGTGGATATTCTGGTGCTTTGCT
1 ATGTTTCTTTCCTTTCTGACTTGTGTGCGCACTAACTATTATAGTCAATATTCTGGTGCTTTGCT
* ** *
10265 TGCTGATATGTTTATTTTTGGCTAAAATTGTTGTATTTGCTGCTATTTTTCCTTTGTTTTTT
66 TGCTGATATGTCTATTTTCAGCTAAAATTCTTGTATTTGCTGCTATTTTTCCTTTGTTTTTT
* * *
10327 ATGTTTCTTTCCTTTCTGACTTG-GTTGCGCAAC-AACTATTATAGTCAATATTTTGTTTCTTTG
1 ATGTTTCTTTCCTTTCTGACTTGTG-TGCGC-ACTAACTATTATAGTCAATATTCTGGTGCTTTG
* *
10390 CTTGCTGATATGTCCT-TTTTCAGCTACATTTCTTGTATTTG
64 CTTGCTGATATGT-CTATTTTCAGCTAAAATTCTTGTATTTG
10431 GTGTTGTTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
126 1 0.01
127 83 0.95
128 3 0.03
ACGTcount: A:0.16, C:0.15, G:0.17, T:0.52
Consensus pattern (127 bp):
ATGTTTCTTTCCTTTCTGACTTGTGTGCGCACTAACTATTATAGTCAATATTCTGGTGCTTTGCT
TGCTGATATGTCTATTTTCAGCTAAAATTCTTGTATTTGCTGCTATTTTTCCTTTGTTTTTT
Found at i:12683 original size:15 final size:15
Alignment explanation
Indices: 12659--12688 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12649 AAGATGAGGC
*
12659 AGAGAGTGAAGGTGA
1 AGAGAATGAAGGTGA
12674 AGAGAATGAAGGTGA
1 AGAGAATGAAGGTGA
12689 TCAGTAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (15 bp):
AGAGAATGAAGGTGA
Found at i:12858 original size:31 final size:31
Alignment explanation
Indices: 12820--12880 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
12810 TATTTTGACA
12820 TATTGTAAATTTAAATTTACAAACCTTGAAG
1 TATTGTAAATTTAAATTTACAAACCTTGAAG
*
12851 TATTGTAAATTTTAATTTACAAACCTTGAA
1 TATTGTAAATTTAAATTTACAAACCTTGAA
12881 TTTTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTGTAAATTTAAATTTACAAACCTTGAAG
Found at i:15344 original size:18 final size:18
Alignment explanation
Indices: 15321--15356 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15311 CTAGAATTTC
15321 TTATTTACCAATTTATTG
1 TTATTTACCAATTTATTG
15339 TTATTTACCAATTTATTG
1 TTATTTACCAATTTATTG
15357 AGACTTAAAC
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:0.11, G:0.06, T:0.56
Consensus pattern (18 bp):
TTATTTACCAATTTATTG
Found at i:18420 original size:27 final size:27
Alignment explanation
Indices: 18390--18475 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
18380 ATGACGCATG
18390 TGCCCCTGAATATGCAAATGACCAAAA
1 TGCCCCTGAATATGCAAATGACCAAAA
* * * **
18417 TG-CCCTTATTGTAAAAATGACCAAAA
1 TGCCCCTGAATATGCAAATGACCAAAA
* * * *
18443 TGACCCTGAACATGCGAATGATCAAAA
1 TGCCCCTGAATATGCAAATGACCAAAA
*
18470 CGCCCC
1 TGCCCC
18476 CTGGGTGACC
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
26 21 0.49
27 22 0.51
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (27 bp):
TGCCCCTGAATATGCAAATGACCAAAA
Found at i:20019 original size:14 final size:14
Alignment explanation
Indices: 19995--20028 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19985 GGTTGATTTT
19995 AATTT-TAATATAA
1 AATTTATAATATAA
20008 AATTTATAATATAA
1 AATTTATAATATAA
20022 AGATTTA
1 A-ATTTA
20029 ACGAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 9 0.47
15 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AATTTATAATATAA
Found at i:21216 original size:22 final size:22
Alignment explanation
Indices: 21184--21247 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
21174 GAATCTCGAG
* *
21184 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
21206 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* * *
21228 AACCTCCCTAAGAAATTTTG
1 AACCTTCTTATGAAATTTTG
21248 AAGACCTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:21458 original size:23 final size:22
Alignment explanation
Indices: 21391--21596 Score: 132
Period size: 22 Copynumber: 9.5 Consensus size: 22
21381 AAACACACTC
* *
21391 TGAAATTTTGATAATCAC-ACTA
1 TGAAATTTTGATAAAC-CTCCTA
*
21413 TGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAACCTC-CTA
21435 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGATAAACC-TCCTA
*
21458 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAACCT-CCTA
*
21481 TAAAATTTTGAT-AACCTCCTTA
1 TGAAATTTTGATAAACCTCC-TA
*
21503 TGAAATCTTGAT-AA----CTA
1 TGAAATTTTGATAAACCTCCTA
*
21520 -CAAATTTTGAT-AACCTCCCTA
1 TGAAATTTTGATAAACCT-CCTA
* *
21541 TG-ATTTTTCGAT-AACCTCATTA
1 TGAAATTTT-GATAAACCTC-CTA
* * *
21563 CGAAATTTTG-TTAATCTCCATA
1 TGAAATTTTGATAAACCTCC-TA
21585 TGAAATTTTGAT
1 TGAAATTTTGAT
21597 CTACATACTT
Statistics
Matches: 149, Mismatches: 17, Indels: 35
0.74 0.08 0.17
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
20 1 0.01
21 14 0.09
22 73 0.49
23 45 0.30
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAAACCTCCTA
Found at i:21603 original size:19 final size:20
Alignment explanation
Indices: 21576--21617 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
21566 AATTTTGTTA
*
21576 ATCTCCATA-TGAAATTTTG
1 ATCTACATATTGAAATTTTG
21595 ATCTACATACTTTGAAATTTTG
1 ATCTACATA--TTGAAATTTTG
21617 A
1 A
21618 AAACTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
22 11 0.58
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
ATCTACATATTGAAATTTTG
Found at i:21800 original size:22 final size:22
Alignment explanation
Indices: 21775--21941 Score: 108
Period size: 22 Copynumber: 7.6 Consensus size: 22
21765 AATCACATTT
* *
21775 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTCTA
*
21797 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
21819 T-AAAATTTCGTTGACCCCTCTA
1 TGAAAATTT-GATAACCTCTCTA
* * *
21841 TGAAATTTTGATAATCACAT-TA
1 TGAAAATTTGATAACCTC-TCTA
* * *
21863 TGTAATTTTGATAACCTCGCTA
1 TGAAAATTTGATAACCTCTCTA
* ** *
21885 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* *
21907 TGAAATTTTGATAATCT-TCCTA
1 TGAAAATTTGATAACCTCT-CTA
*
21929 T-AAATTTTGATAA
1 TGAAAATTTGATAA
21942 TCCGGTCTCT
Statistics
Matches: 116, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
21 18 0.16
22 91 0.78
23 7 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:21805 original size:44 final size:44
Alignment explanation
Indices: 21750--21943 Score: 173
Period size: 44 Copynumber: 4.4 Consensus size: 44
21740 AGAAATACCA
* * * *
21750 CTATAAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTTT
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * * * * *
21794 TTATGAAATTTTGATAACCTC-TCTAT-AAAATTTCGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAAATTT-GATAACCTCT
* * *
21838 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * *
21882 CTATGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAATC-ACATTATGAAAATTTGATAACCTCT
21925 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
21944 CGGTCTCTAC
Statistics
Matches: 120, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
43 21 0.17
44 93 0.77
45 6 0.05
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
Found at i:21864 original size:66 final size:66
Alignment explanation
Indices: 21794--21922 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 66
21784 GATAACCTTT
* * * ** *
21794 TTATGAAATTTTGATAACCTCTCTATAAAATTTCGTTGACCCCTCTATGAAATTTTGATAATCAC
1 TTATGAAATTTTGATAACCTCGCTATAAAATTTCGATAACAACACTATGAAATTTTGATAATCAC
21859 A
66 A
* * *
21860 TTATGTAATTTTGATAACCTCGCTATGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTCGCTATAAAATTTCGATAACAACACTATGAAATTTTGATAATC
21923 TTCCTATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCGCTATAAAATTTCGATAACAACACTATGAAATTTTGATAATCAC
A
Found at i:21943 original size:21 final size:22
Alignment explanation
Indices: 21795--21941 Score: 120
Period size: 22 Copynumber: 6.7 Consensus size: 22
21785 ATAACCTTTT
* *
21795 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACATCAC
* * * * ** *
21817 TATAAAATTTCGTTGACCCCTC
1 TATGAAATTTTGATAACATCAC
*
21839 TATGAAATTTTGATAATCA-CAT
1 TATGAAATTTTGATAA-CATCAC
* * *
21861 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACATCAC
*
21883 TATGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACATCAC
*
21905 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAA-CATCAC
21927 TAT-AAATTTTGATAA
1 TATGAAATTTTGATAA
21942 TCCGGTCTCT
Statistics
Matches: 100, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
21 13 0.13
22 84 0.84
23 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACATCAC
Found at i:22056 original size:22 final size:22
Alignment explanation
Indices: 22041--22102 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
22031 ATAACCTTCA
*
22041 TATAAAATTTTGATAATCACAC
1 TATAAAATTTTGATAACCACAC
*
22063 TAAAAAATTTTGATAACCACAC
1 TATAAAATTTTGATAACCACAC
*
22085 TATGAAATTTTGATAACC
1 TATAAAATTTTGATAACC
22103 TCCCCATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (22 bp):
TATAAAATTTTGATAACCACAC
Found at i:22111 original size:22 final size:22
Alignment explanation
Indices: 22027--22188 Score: 91
Period size: 22 Copynumber: 7.4 Consensus size: 22
22017 AAATTGAGAC
* * *
22027 TTTT-ATAACCTTCATATAAAA
1 TTTTGATAACCTCCCTATGAAA
* * * **
22048 TTTTGATAATCACACTAAAAAA
1 TTTTGATAACCTCCCTATGAAA
* *
22070 TTTTGATAACCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
22092 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
22114 -TATCAGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTCCCTATGAAA
* * * *
22136 TTTTGTTGACCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
22158 TTCTT-ATAACC-CCGCTATGACAA
1 TT-TTGATAACCTCC-CTATGA-AA
22181 -TTTGATAA
1 TTTTGATAA
22189 TCTATTTGAT
Statistics
Matches: 108, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
21 10 0.09
22 92 0.85
23 6 0.06
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAAA
Found at i:22304 original size:22 final size:21
Alignment explanation
Indices: 22276--22426 Score: 90
Period size: 22 Copynumber: 6.9 Consensus size: 21
22266 ACCTGATCCT
22276 ATGAAATTTT-AGTAACCACACA
1 ATGAAATTTTGA-TAACCAC-CA
* * *
22298 ATGAAATCTTGATAACCTTCCC
1 ATGAAATTTTGATAACC-ACCA
**
22320 ATGAAATTTTGATAACTTCCA
1 ATGAAATTTTGATAACCACCA
* *
22341 TATGAAATTTTGGTAACCACACT
1 -ATGAAATTTTGATAACCAC-CA
* * *
22364 ATGGAATTTTGATAACCTCCTC
1 ATGAAATTTTGATAACCACC-A
* **
22386 ATGAAA-TTAGAATAACCATCTT
1 ATGAAATTTTG-ATAACCA-CCA
*
22408 ATGAAATTTTTATAACCAC
1 ATGAAATTTTGATAACCAC
22427 ACAGAGACAA
Statistics
Matches: 100, Mismatches: 21, Indels: 17
0.72 0.15 0.12
Matches are distributed among these distances:
21 8 0.08
22 86 0.86
23 6 0.06
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (21 bp):
ATGAAATTTTGATAACCACCA
Found at i:22346 original size:44 final size:42
Alignment explanation
Indices: 22272--22424 Score: 114
Period size: 44 Copynumber: 3.5 Consensus size: 42
22262 AATAACCTGA
* *
22272 TCCTATGAAATTTT-AGTAACCACAC-AATGAAATCTTGATAACC
1 TCCTATGAAATTTTGA-TAACCTC-CTCATGAAAT-TTGATAACC
* * *
22315 TTCCCATGAAATTTTGATAACTTCCAT-ATGAAATTTTGGTAACC
1 -TCCTATGAAATTTTGATAACCTCC-TCATGAAA-TTTGATAACC
* * *
22359 ACACTATGGAATTTTGATAACCTCCTCATGAAATTAGAATAACC
1 TC-CTATGAAATTTTGATAACCTCCTCATGAAATTTG-ATAACC
* *
22403 ATCTTATGAAATTTTTATAACC
1 -TCCTATGAAATTTTGATAACC
22425 ACACAGAGAC
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
43 6 0.07
44 78 0.90
45 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (42 bp):
TCCTATGAAATTTTGATAACCTCCTCATGAAATTTGATAACC
Found at i:22376 original size:66 final size:66
Alignment explanation
Indices: 22193--22428 Score: 226
Period size: 66 Copynumber: 3.5 Consensus size: 66
22183 TGATAATCTA
* * * * * ** * * *
22193 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAACTTCAATAATCTTCCTAAGAAA
1 TTTGATAACCTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
22258 T
66 T
* * * *
22259 TTTAATAACCTGATCCTATGAAATTTTAGTAACCACACAATGAAATCTTGATAACCTTCCCATGA
1 TTTGATAACCT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGA
22324 AAT
64 AAT
*
22327 TTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGA
1 TTTGATAACCTTCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGA
22390 AA-
64 AAT
* * * **
22392 TTAGAATAACCATCTTATGAAATTTTTATAACCACAC
1 TTTG-ATAACCTTCCTATGAAATTTTGGTAACCACAC
22429 AGAGACAAGA
Statistics
Matches: 140, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
65 9 0.06
66 77 0.55
67 5 0.04
68 49 0.35
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (66 bp):
TTTGATAACCTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
T
Found at i:22629 original size:20 final size:20
Alignment explanation
Indices: 22591--22629 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22581 TATTGACATT
22591 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
22611 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
22630 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:25393 original size:65 final size:65
Alignment explanation
Indices: 25321--25446 Score: 243
Period size: 65 Copynumber: 1.9 Consensus size: 65
25311 GATTTCATTG
*
25321 TATTTTCCATCGTTAAATATATGTTGGAAATATTGAAAAATCTTAGAATCTTAATCAATATATTA
1 TATTTTCCATCATTAAATATATGTTGGAAATATTGAAAAATCTTAGAATCTTAATCAATATATTA
25386 TATTTTCCATCATTAAATATATGTTGGAAATATTGAAAAATCTTAGAATCTTAATCAATAT
1 TATTTTCCATCATTAAATATATGTTGGAAATATTGAAAAATCTTAGAATCTTAATCAATAT
25447 GAAGATATTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (65 bp):
TATTTTCCATCATTAAATATATGTTGGAAATATTGAAAAATCTTAGAATCTTAATCAATATATTA
Found at i:30607 original size:19 final size:18
Alignment explanation
Indices: 30583--30621 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30573 TGAAGATTTC
*
30583 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
30602 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
30620 TT
1 TT
30622 ATTTCAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:40095 original size:24 final size:24
Alignment explanation
Indices: 40068--40114 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40058 AGTTATCTAG
40068 TTTATGTTT-TATCCTTATTTTTCC
1 TTTAT-TTTATATCCTTATTTTTCC
* *
40092 TTTATTTTATGTCTTTATTTTTC
1 TTTATTTTATATCCTTATTTTTC
40115 AAGTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTTTATATCCTTATTTTTCC
Found at i:40855 original size:17 final size:18
Alignment explanation
Indices: 40835--40869 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40825 AAAAGGGTAG
40835 TTAAAAAAAAGT-TTTTC
1 TTAAAAAAAAGTGTTTTC
*
40852 TTAAAAAGAAGTGTTTTC
1 TTAAAAAAAAGTGTTTTC
40870 ATGAAAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TTAAAAAAAAGTGTTTTC
Found at i:56363 original size:142 final size:142
Alignment explanation
Indices: 56098--56391 Score: 516
Period size: 142 Copynumber: 2.1 Consensus size: 142
56088 TGAAAGCTAA
56098 CATAATGCCATCCTCTAATGGTCCAAATGACATGATAAAGGGCAGAGAGATTTTTCAATCTAGAA
1 CATAATG--ATCCTCTAATGGTCCAAATGACATGATAAAGGGCAGAGAGATTTTTCAATCTAGAA
* * * *
56163 AATGGTATTCTTCTATTAATTGGATTCATGCTTTGATATCAGCCTCCCTTTGCACATCAGCTTGT
64 AATGGTATTCTTCTATGAAATGGAATCAAGCTTTGATATCAGCCTCCCTTTGCACATCAGCTTGT
56228 AAATGTCATGATGG
129 AAATGTCATGATGG
56242 CATAATGATCCTCTAATGGTCCAAATGACATGATAAAGGGCAGAGAGATTTTTCAATCTAGAAAA
1 CATAATGATCCTCTAATGGTCCAAATGACATGATAAAGGGCAGAGAGATTTTTCAATCTAGAAAA
* *
56307 TGGTATTCTTCTATGAAATGGAATCAAGCTTTGATCTCAGCCTCCCTTTGCTCATCAGCTTGTAA
66 TGGTATTCTTCTATGAAATGGAATCAAGCTTTGATATCAGCCTCCCTTTGCACATCAGCTTGTAA
56372 ATGTCATGATGG
131 ATGTCATGATGG
56384 CATAATGA
1 CATAATGA
56392 AATTTTTGTG
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
142 137 0.95
144 7 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (142 bp):
CATAATGATCCTCTAATGGTCCAAATGACATGATAAAGGGCAGAGAGATTTTTCAATCTAGAAAA
TGGTATTCTTCTATGAAATGGAATCAAGCTTTGATATCAGCCTCCCTTTGCACATCAGCTTGTAA
ATGTCATGATGG
Found at i:60602 original size:13 final size:13
Alignment explanation
Indices: 60584--60609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60574 AAGGTAACAA
60584 CAAAAATCATCAC
1 CAAAAATCATCAC
60597 CAAAAATCATCAC
1 CAAAAATCATCAC
60610 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:61237 original size:11 final size:11
Alignment explanation
Indices: 61221--61251 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61211 TCCTTATGAA
*
61221 ATTAGGTTAGG
1 ATTAGGTCAGG
61232 ATTAGGTCAGG
1 ATTAGGTCAGG
61243 ATTAGGTCA
1 ATTAGGTCA
61252 AACCTAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (11 bp):
ATTAGGTCAGG
Found at i:68880 original size:23 final size:24
Alignment explanation
Indices: 68846--68908 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
68836 TCGAAAAAAA
*
68846 AAAAAAACAATTTTTT-TGCGTCAT
1 AAAAAAA-AATTTTTTCTGCATCAT
68870 AAAAAAAAATTTGTTTCTGCATCAT
1 AAAAAAAAATTT-TTTCTGCATCAT
*
68895 AAAAAAAAGTTTTT
1 AAAAAAAAATTTTT
68909 GCGTTTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 5 0.14
24 12 0.34
25 18 0.51
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (24 bp):
AAAAAAAAATTTTTTCTGCATCAT
Done.