Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024653.1 Corchorus olitorius cultivar O-4 contig24686, 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: 37480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:383 original size:32 final size:32
Alignment explanation
Indices: 342--402 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
332 AAATATGTTT
342 GAAAAATAAGGATATAAT-GATCGATTCAATTA
1 GAAAAATAAGGATATAATAG-TCGATTCAATTA
*
374 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
403 AAGTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:1347 original size:44 final size:42
Alignment explanation
Indices: 1296--1411 Score: 160
Period size: 44 Copynumber: 2.7 Consensus size: 42
1286 TACATCTCAA
* * *
1296 AAAATGTCTTATCCATCCCACAAATAAATTACATGTCATTATC
1 AAAATGTCTTCTCCATCCCACAAATAAATTACATGGCA-TACC
*
1339 AAAGATGTCTTCTCCATCCCACAAATAAATTACATGGCATCCC
1 AAA-ATGTCTTCTCCATCCCACAAATAAATTACATGGCATACC
1382 AAAACTGTCTTTCTCCATCCCACAAATAAA
1 AAAA-TGTC-TTCTCCATCCCACAAATAAA
1412 CAAATTCTGG
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
42 1 0.02
43 12 0.18
44 53 0.80
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (42 bp):
AAAATGTCTTCTCCATCCCACAAATAAATTACATGGCATACC
Found at i:4994 original size:74 final size:75
Alignment explanation
Indices: 4907--5057 Score: 232
Period size: 75 Copynumber: 2.0 Consensus size: 75
4897 ATGATAGATA
*
4907 TGCAAATTAAGTTTAAAATAAAAAA-AAAATTAAAATTTAGCTCAGATCAATGACAGAAAAAGCA
1 TGCAAATTAAGTTTAAAATAAAAAAGAAAATTAAAATTTAGCTCAGATCAATGACACAAAAAGCA
*
4971 TAGCAGAGGC
66 GAGCAGAGGC
** * * *
4981 TGCAAATTAAGTTTAAAATAAAAAAGAATTTTAAAATTTAGCTCGGATCAATGACACTAAGAGCA
1 TGCAAATTAAGTTTAAAATAAAAAAGAAAATTAAAATTTAGCTCAGATCAATGACACAAAAAGCA
5046 GAGCAGAGGC
66 GAGCAGAGGC
5056 TG
1 TG
5058 AAGATCTGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 25 0.36
75 44 0.64
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.23
Consensus pattern (75 bp):
TGCAAATTAAGTTTAAAATAAAAAAGAAAATTAAAATTTAGCTCAGATCAATGACACAAAAAGCA
GAGCAGAGGC
Found at i:14454 original size:22 final size:22
Alignment explanation
Indices: 14412--14455 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14402 TATTCATATG
*
14412 AAATTATGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
14434 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
14456 TTTGATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:14616 original size:23 final size:22
Alignment explanation
Indices: 14545--14905 Score: 259
Period size: 22 Copynumber: 16.6 Consensus size: 22
14535 TTTTTAACCT
* *
14545 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
14567 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
*
14589 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* * *
14612 TATGAGATGTTGATAATCAT-AC
1 TATGAAATTTTGATAA-CCTCAC
* *
14634 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
14656 TATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
*
14679 TATAAAATTTTGATAATCCTTCA-
1 TATGAAATTTTGATAA-CC-TCAC
*
14702 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
14723 TTATAAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
*
14744 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
14762 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * * *
14784 TATCAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
14806 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
14828 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
*
14850 TATAAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
14872 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
14893 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
14906 CACTCCACAA
Statistics
Matches: 270, Mismatches: 45, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 12 0.04
21 13 0.05
22 169 0.63
23 59 0.22
24 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:14836 original size:44 final size:43
Alignment explanation
Indices: 14545--15316 Score: 225
Period size: 44 Copynumber: 17.4 Consensus size: 43
14535 TTTTTAACCT
* * * * * *
14545 TATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATAACCT-ACTATGAAATTTTGATA-ATCTCCC
* * * *
14589 TATGAAATTTTGATAACCAACACTATGAGATGTTGATAATCAT-AC
1 TATGAAATTTTGATAACC--TACTATGAAATTTTGATAATC-TCCC
* * * *
14634 TATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGATAACCT-ACTATGAAATTTTGAT-AATCTCCC
* * * * *
14679 TATAAAATTTTGATAATCCTTCATATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAA-CCTAC-TATGAAATTTTGATAATCTCCC
* * *
14724 TATAAAATCTTGATAA-CTAC----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTACTATGAAATTTTGATAATCTCCC
** * * *
14762 TATGATTTTTTGATAACCTCATTATCAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-ACTATGAAATTTTGATAATCTCCC
* *
14806 TATGAAATTTTGATCTACATACTATGAAATTTTGATAA-C-CCTC
1 TATGAAATTTTGAT-AACCTACTATGAAATTTTGATAATCTCC-C
* *
14849 TTATAAAATTTTGATAACCTTCATATGAAATTTTGAT-ATCCTCCC
1 -TATGAAATTTTGATAACCTAC-TATGAAATTTTGATAAT-CTCCC
* * * * * * * *
14894 --TGAAATTTTGATCACTCCACAATAAAAGTTTAATAACCTTCC
1 TATGAAATTTTGATAAC-CTACTATGAAATTTTGATAATCTCCC
* * *
14936 --T--AA-TTTGGTAAGCATACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAA-CCTACTATGAAATTTTGATAATCTCCC
* * * * * * * * *
14975 -AAGAAACACCGCTATGA-AATTCTAGTAATCACATTTTGAAAATTTGATAACCTC
1 TATG-AA-A---TTTTGATAA-CCTACT-ATGAAATTTTGATAA--T-CT--CC-C
* * * *
15029 TTCATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGA-C-CCTTC
1 -T-ATGAAATTTTGATAACCT-ACTATGAAATTTTGATAATCTCC--C
* * *
15075 TATGAAATTTTGATAATCAC-ATTAT-ATAATTTTGATAACCTCGC
1 TATGAAATTTTGATAA-C-CTACTATGA-AATTTTGATAATCTCCC
* *
15119 TTTGAAATTTTGATAACAAC-ACTATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAAC--CTACTATGAAATTTTGATAATCTCCC
* * * *
15163 TAT-AAATTTTGATAATCCAATCTCTATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAA-CC--T-ACTATGAAATTTTGATAATCTCCC
* * * * *
15209 TATGAGA-TTTGATAACCTTC-ATCAAATTTTGGT-A-CTCCT
1 TATGAAATTTTGATAACCTACTATGAAATTTTGATAATCTCCC
* * * *
15248 TATGAAATTGAGACTTTTATAACCTACATATGAAATTTTGATAACCACAC
1 TATGAAA-T-----TTTGATAACCTAC-TATGAAATTTTGATAATCTCCC
15298 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
15317 CCCCATGAAA
Statistics
Matches: 540, Mismatches: 117, Indels: 142
0.68 0.15 0.18
Matches are distributed among these distances:
38 29 0.05
39 35 0.06
40 5 0.01
41 10 0.02
42 33 0.06
43 29 0.05
44 178 0.33
45 84 0.16
46 65 0.12
47 7 0.01
48 26 0.05
49 2 0.00
50 9 0.02
51 1 0.00
52 16 0.03
53 5 0.01
54 1 0.00
55 1 0.00
56 2 0.00
57 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTACTATGAAATTTTGATAATCTCCC
Found at i:15039 original size:21 final size:23
Alignment explanation
Indices: 15011--15226 Score: 152
Period size: 22 Copynumber: 9.7 Consensus size: 23
15001 AATCACATTT
*
15011 TGAAAATTTGATAACCTCTTC-A
1 TGAAATTTTGATAACCTCTTCTA
15033 TGAAATTTTGATAACCTC-TCTA
1 TGAAATTTTGATAACCTCTTCTA
* * *
15055 TAAAATTTTGTTGACC-CTTCTA
1 TGAAATTTTGATAACCTCTTCTA
* * *
15077 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTCTTCTA
* *
15099 T-ATAATTTTGATAACCTC-GCTT
1 TGA-AATTTTGATAACCTCTTCTA
** *
15121 TGAAATTTTGATAACAAC-ACTA
1 TGAAATTTTGATAACCTCTTCTA
15143 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT-CTA
15165 T-AAATTTTGATAATCCAATC-TCTA
1 TGAAATTTTGATAA-CC--TCTTCTA
* * *
15189 TGAAATTTCGATAATCAC-TCTA
1 TGAAATTTTGATAACCTCTTCTA
*
15211 TGAGA-TTTGATAACCT
1 TGAAATTTTGATAACCT
15227 TCATCAAATT
Statistics
Matches: 154, Mismatches: 26, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.01
21 24 0.16
22 107 0.69
23 3 0.02
24 5 0.03
25 12 0.08
26 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAACCTCTTCTA
Found at i:15291 original size:22 final size:22
Alignment explanation
Indices: 15262--15399 Score: 101
Period size: 22 Copynumber: 6.4 Consensus size: 22
15252 AAATTGAGAC
15262 TTTT-ATAACCTACATATGAAA
1 TTTTGATAACCTACATATGAAA
15283 TTTTGATAACC-ACACTATGAAA
1 TTTTGATAACCTACA-TATGAAA
* **
15305 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTACATATGAAA
*
15327 TATT-AGTAACCT-CAT-T-AAA
1 TTTTGA-TAACCTACATATGAAA
* * *
15346 TTTTGTTAAACAACACTATGAAA
1 TTTTGATAACCTACA-TATGAAA
* * *
15369 TTATGATAACCT-CGTTATGACA
1 TTTTGATAACCTAC-ATATGAAA
15391 TTTTGATAA
1 TTTTGATAA
15400 TCTCTTTGAT
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
19 10 0.11
20 3 0.03
21 10 0.11
22 55 0.61
23 12 0.13
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTACATATGAAA
Found at i:15508 original size:64 final size:66
Alignment explanation
Indices: 15433--15635 Score: 193
Period size: 66 Copynumber: 3.1 Consensus size: 66
15423 AATTGTGATG
* * *
15433 ACCACACTATGAAATTTCAATAACTTTCCTAAGAAA-TTT-A-ACCTGATCC-TATGAAATTTTG
1 ACCACACTATGAAATTTCAATAACCTTCCCAAGAAATTTTGATAACT--TCCATATGAAATTTTG
15494 GTA
64 GTA
** * *
15497 ACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTCCATTTGAAATTTTGGT
1 ACCACACTATGAAATTTCAATAACCTTCCCAAGAAATTTTGATAACTTCCATATGAAATTTTGGT
15562 A
66 A
* ** * * * *
15563 ACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACTAT-CTTATGAAATTTTG
1 ACCACACTATGAAATTTCAATAACCTTCC-CAAGAAATTTTGATAACT-TCCATATGAAATTTTG
*
15626 ATA
64 GTA
15629 ACCACAC
1 ACCACAC
15636 AGAGACAAGA
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
64 31 0.26
65 9 0.08
66 76 0.63
67 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (66 bp):
ACCACACTATGAAATTTCAATAACCTTCCCAAGAAATTTTGATAACTTCCATATGAAATTTTGGT
A
Found at i:15509 original size:22 final size:22
Alignment explanation
Indices: 15481--15635 Score: 131
Period size: 22 Copynumber: 7.0 Consensus size: 22
15471 TAACCTGATC
*
15481 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
15503 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
15525 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
15548 -TTTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
15569 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
15590 CTCATGAAATTATAATAACTATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
15613 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
15635 C
1 C
15636 AGAGACAAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 94 0.90
23 3 0.03
24 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:15579 original size:66 final size:66
Alignment explanation
Indices: 15482--15635 Score: 224
Period size: 66 Copynumber: 2.3 Consensus size: 66
15472 AACCTGATCC
* *
15482 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAACT-T
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTATAATAACTAT
15545 CCAT
65 -C-T
*
15549 T-TGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACTATC
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACTATC
15613 T
66 T
*
15614 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGGTAACCACAC
15636 AGAGACAAGA
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
65 5 0.06
66 73 0.91
67 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACTATC
T
Found at i:15777 original size:6 final size:6
Alignment explanation
Indices: 15766--15791 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15756 AGTATTGTAC
15766 GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GT
15792 TTAATCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:19421 original size:42 final size:42
Alignment explanation
Indices: 19375--19465 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
19365 AACAACAATT
* * * *
19375 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATATTGATGAATTACCTACAGATGGAGTAG
*
19417 AATATTAGCTTTATATTGATGAATTACCTACAGATTGAGTAG
1 AATATTAGCTTTATATTGATGAATTACCTACAGATGGAGTAG
19459 AAT-TTAG
1 AATATTAG
19466 GTAATGCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (42 bp):
AATATTAGCTTTATATTGATGAATTACCTACAGATGGAGTAG
Found at i:21085 original size:18 final size:19
Alignment explanation
Indices: 21046--21085 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
21036 ATGGCACCAT
21046 ATCCTAGAAGAGCTGATGAAC
1 ATCCTAGAAGAGC--ATGAAC
21067 ATCCTAGAAGAGC-TGAAC
1 ATCCTAGAAGAGCATGAAC
21085 A
1 A
21086 AGTCAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (19 bp):
ATCCTAGAAGAGCATGAAC
Found at i:31414 original size:22 final size:22
Alignment explanation
Indices: 31341--31537 Score: 95
Period size: 22 Copynumber: 9.1 Consensus size: 22
31331 TCTTTTTGTT
*
31341 ATCTT-TTATAAAATTTTGATA
1 ATCTTCTTATGAAATTTTGATA
** * *
31362 ATCCCCTTA-GATATCTTGATA
1 ATCTTCTTATGAAATTTTGATA
* *** *
31383 AGCAAATTATGAAAATTTGATA
1 ATCTTCTTATGAAATTTTGATA
31405 ATCTTCTTATGAAATTTTGATA
1 ATCTTCTTATGAAATTTTGATA
* * *
31427 ATATAAC-TATGAAATTTTAATA
1 ATCT-TCTTATGAAATTTTGATA
* * *
31449 AACGTTCATATGAAAATTTGATA
1 ATC-TTCTTATGAAATTTTGATA
* * * *
31472 ATATTGTTATGACATTTTGTTA
1 ATCTTCTTATGAAATTTTGATA
*
31494 ATC-TC-TAT-AAATCTTCGAT-
1 ATCTTCTTATGAAAT-TTTGATA
**
31513 A-CTATAATATGAAATTTTGATA
1 ATCT-TCTTATGAAATTTTGATA
31535 ATC
1 ATC
31538 ACTCAATGAA
Statistics
Matches: 125, Mismatches: 39, Indels: 22
0.67 0.21 0.12
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 8 0.06
21 26 0.21
22 69 0.55
23 17 0.14
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (22 bp):
ATCTTCTTATGAAATTTTGATA
Found at i:31425 original size:44 final size:44
Alignment explanation
Indices: 31346--31537 Score: 112
Period size: 45 Copynumber: 4.4 Consensus size: 44
31336 TTGTTATCTT
** * *
31346 TTAT-AAAATTTTGATAATCCCCTTA-GATATCTTGATAAGCA-AA
1 TTATGAAAA-TTTGATAATCTTCTTATGAAATTTTGATAA-CATAA
*
31389 TTATGAAAATTTGATAATCTTCTTATGAAATTTTGATAATATAA
1 TTATGAAAATTTGATAATCTTCTTATGAAATTTTGATAACATAA
* * * * * * * **
31433 CTATGAAATTTTAATAAACGTTCATATGAAAATTTGATAATATTG
1 TTATGAAAATTTGATAATC-TTCTTATGAAATTTTGATAACATAA
* * * *
31478 TTATGACATTTTGTTAATC-TC-TAT-AAATCTTCGAT-ACTATAA
1 TTATGAAAATTTGATAATCTTCTTATGAAAT-TTTGATAAC-ATAA
*
31520 -TATGAAATTTTGATAATC
1 TTATGAAAATTTGATAATC
31538 ACTCAATGAA
Statistics
Matches: 118, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
41 20 0.17
42 10 0.08
43 21 0.18
44 32 0.27
45 35 0.30
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (44 bp):
TTATGAAAATTTGATAATCTTCTTATGAAATTTTGATAACATAA
Found at i:31471 original size:45 final size:44
Alignment explanation
Indices: 31390--31475 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
31380 ATAAGCAAAT
* * * *
31390 TATGAAAATTTGATAATCTTCTTATGAAATTTTGATAATATAAC
1 TATGAAAATTTAATAAACTTCATATGAAAATTTGATAATATAAC
*
31434 TATGAAATTTTAATAAACGTTCATATGAAAATTTGATAATAT
1 TATGAAAATTTAATAAAC-TTCATATGAAAATTTGATAATAT
31476 TGTTATGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 15 0.42
45 21 0.58
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (44 bp):
TATGAAAATTTAATAAACTTCATATGAAAATTTGATAATATAAC
Found at i:31483 original size:45 final size:44
Alignment explanation
Indices: 31387--31489 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 44
31377 TTGATAAGCA
* * * * *
31387 AATTATGAAAATTTGATAATCTTCTTATGAAATTTTGATAATAT
1 AATTATGAAATTTTAATAAACTTCATATGAAAATTTGATAATAT
*
31431 AACTATGAAATTTTAATAAACGTTCATATGAAAATTTGATAATAT
1 AATTATGAAATTTTAATAAAC-TTCATATGAAAATTTGATAATAT
** *
31476 TGTTATGACATTTT
1 AATTATGAAATTTT
31490 GTTAATCTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 17 0.35
45 31 0.65
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.44
Consensus pattern (44 bp):
AATTATGAAATTTTAATAAACTTCATATGAAAATTTGATAATAT
Found at i:32330 original size:1 final size:1
Alignment explanation
Indices: 32324--32351 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
32314 GGACTTCAGG
32324 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
32352 ACTATTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34555 original size:158 final size:158
Alignment explanation
Indices: 34267--34581 Score: 594
Period size: 158 Copynumber: 2.0 Consensus size: 158
34257 GAAAATGAAG
34267 GAAGCCACTTTGAACTTCATTGTCTCAAACATGAAGGATGTTGTTTCCACATTGAAGTATGAAGA
1 GAAGCCACTTTGAACTTCATTGTCTCAAACATGAAGGATGTTGTTTCCACATTGAAGTATGAAGA
*
34332 TTTTGCATCTAGCAACCCGAATCTTTGTCTGCAGATTACAAGGGCATTTGTTAATGCAAATGCCA
66 TTTTGCATCCAGCAACCCGAATCTTTGTCTGCAGATTACAAGGGCATTTGTTAATGCAAATGCCA
*
34397 AGTTTTGTCAGGGGCGGCACTGGCAGGC
131 AGTTTTGTCAGGGGCGGCACTCGCAGGC
34425 GAAGCCACTTTGAACTTCATTGTCTCAAACATGAAGGATGTTGTTTCCACATTGAAGTATGAAGA
1 GAAGCCACTTTGAACTTCATTGTCTCAAACATGAAGGATGTTGTTTCCACATTGAAGTATGAAGA
34490 TTTTGCATCCAGCAACCCGAATCTTTGTCTGCAGATTACAAGGGCATTTGTTAATGCAAATGCCA
66 TTTTGCATCCAGCAACCCGAATCTTTGTCTGCAGATTACAAGGGCATTTGTTAATGCAAATGCCA
* *
34555 ATTTTTGTCAGGGGTGGCACTCGCAGG
131 AGTTTTGTCAGGGGCGGCACTCGCAGG
34582 GGTGGGGTAT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 153 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (158 bp):
GAAGCCACTTTGAACTTCATTGTCTCAAACATGAAGGATGTTGTTTCCACATTGAAGTATGAAGA
TTTTGCATCCAGCAACCCGAATCTTTGTCTGCAGATTACAAGGGCATTTGTTAATGCAAATGCCA
AGTTTTGTCAGGGGCGGCACTCGCAGGC
Found at i:35018 original size:53 final size:53
Alignment explanation
Indices: 34955--35062 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
34945 GCCAAAGCTT
34955 CAAGTTCATAATTGTATCTCTTTTTTATGATTGAAAACTTTTGAGACCTTTGC
1 CAAGTTCATAATTGTATCTCTTTTTTATGATTGAAAACTTTTGAGACCTTTGC
35008 CAAGTTCATAATTGTATCTCTTTTTTATGATTGAAAACTTTTGAGACCTTTGC
1 CAAGTTCATAATTGTATCTCTTTTTTATGATTGAAAACTTTTGAGACCTTTGC
35061 CA
1 CA
35063 TTAGCCAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (53 bp):
CAAGTTCATAATTGTATCTCTTTTTTATGATTGAAAACTTTTGAGACCTTTGC
Found at i:35200 original size:73 final size:73
Alignment explanation
Indices: 35081--35227 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
35071 AGCTTCAAGT
35081 TCATAATTGTATCTCTTTTTTATGATTGAAAAAGAGTGATTTTCTTGTTATCTAAAATCTAAAAC
1 TCATAATTGTATCTCTTTTTTATGATTGAAAAAGAGTGATTTTCTTGTTATCTAAAATCTAAAAC
35146 ACATATAA
66 ACATATAA
35154 TCATAATTGTATCTCTTTTTTATGATTGAAAAAGAGTGATTTTCTTGTTATCTAAAATCTAAAAC
1 TCATAATTGTATCTCTTTTTTATGATTGAAAAAGAGTGATTTTCTTGTTATCTAAAATCTAAAAC
35219 ACATATAA
66 ACATATAA
35227 T
1 T
35228 AGTAATACCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (73 bp):
TCATAATTGTATCTCTTTTTTATGATTGAAAAAGAGTGATTTTCTTGTTATCTAAAATCTAAAAC
ACATATAA
Found at i:36530 original size:22 final size:22
Alignment explanation
Indices: 36504--36546 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
36494 AAAATAATTG
* *
36504 AATTAACAAATAAGCTAAAGGA
1 AATTAAAAAAAAAGCTAAAGGA
36526 AATTAAAAAAAAAGCTAAAGG
1 AATTAAAAAAAAAGCTAAAGG
36547 GCGAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (22 bp):
AATTAAAAAAAAAGCTAAAGGA
Done.