Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013770.1 Corchorus olitorius cultivar O-4 contig13803, 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: 52028
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3338 original size:22 final size:22
Alignment explanation
Indices: 3313--3365 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3303 AAATCAAACT
**
3313 AACAATTAAGACTATCT-AAGAA
1 AACAATTAAGAAAAT-TAAAGAA
*
3335 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAATTAAAGAA
3357 AACAATTAA
1 AACAATTAA
3366 TTAGAAAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAATTAAAGAA
Found at i:4675 original size:19 final size:18
Alignment explanation
Indices: 4642--4677 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4632 TTGAAATTAT
*
4642 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
4660 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
4678 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:11557 original size:14 final size:14
Alignment explanation
Indices: 11538--11565 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11528 GAGAGACAAG
11538 TTATTTTTTTTTTT
1 TTATTTTTTTTTTT
11552 TTATTTTTTTTTTT
1 TTATTTTTTTTTTT
11566 CACAAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (14 bp):
TTATTTTTTTTTTT
Found at i:19546 original size:15 final size:16
Alignment explanation
Indices: 19515--19549 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19505 TTACTTTGCT
19515 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
19531 TTGTTTTCT-TTTTAA
1 TTGTTTTCTAGTTTAA
19546 TTGT
1 TTGT
19550 GATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:20450 original size:12 final size:12
Alignment explanation
Indices: 20431--20463 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
20421 ATCTAACTTA
20431 AAGATTTTGCTT
1 AAGATTTTGCTT
*
20443 AGGATTTTGCTT
1 AAGATTTTGCTT
20455 AAGATTTTG
1 AAGATTTTG
20464 AGGATAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (12 bp):
AAGATTTTGCTT
Found at i:20642 original size:239 final size:239
Alignment explanation
Indices: 20223--20671 Score: 880
Period size: 239 Copynumber: 1.9 Consensus size: 239
20213 AGGTATCAGA
20223 TGAGGATAAGTAGTCCTCACATACTGGCTTAGGATTTTATTTCCTTTCGTACTTTTATTTTTCTC
1 TGAGGATAAGTAGTCCTCACATACTGGCTTAGGATTTTATTTCCTTTCGTACTTTTATTTTTCTC
20288 AAGTATTCTCATGACTTTAAGATTTTGCTTTATGAGTTAATTTCAAATTCAAACAAGTTGAATTT
66 AAGTATTCTCATGACTTTAAGATTTTGCTTTATGAGTTAATTTCAAATTCAAACAAGTTGAATTT
20353 TTGCTTTCAATTGGTGGCAATGAATTGTTAGCCAACTTCTATATTAGTGGCCTTTATTATTTTTA
131 TTGCTTTCAATTGGTGGCAATGAATTGTTAGCCAACTTCTATATTAGTGGCCTTTATTATTTTTA
20418 GCCATCTAACTTAAAGATTTTGCTTAGGATTTTGCTTAAGATTT
196 GCCATCTAACTTAAAGATTTTGCTTAGGATTTTGCTTAAGATTT
20462 TGAGGATAAGTAGTCCTCACATACTGGCTTAGGATTTTATTTCCTTTCGTACTTTTATTTTTCTC
1 TGAGGATAAGTAGTCCTCACATACTGGCTTAGGATTTTATTTCCTTTCGTACTTTTATTTTTCTC
*
20527 AAGTATTCTCATGACTTTAAGATTTTGCTTTATGAGTTAATTTCAATTTCAAACAAGTTGAATTT
66 AAGTATTCTCATGACTTTAAGATTTTGCTTTATGAGTTAATTTCAAATTCAAACAAGTTGAATTT
*
20592 TTGCTTTCAATTGGTGGCAATGAATTGTTAGCCAACTTTTATATTAGTGGCCTTTATTATTTTTA
131 TTGCTTTCAATTGGTGGCAATGAATTGTTAGCCAACTTCTATATTAGTGGCCTTTATTATTTTTA
20657 GCCATCTAACTTAAA
196 GCCATCTAACTTAAA
20672 CAAAATCCTT
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 208 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (239 bp):
TGAGGATAAGTAGTCCTCACATACTGGCTTAGGATTTTATTTCCTTTCGTACTTTTATTTTTCTC
AAGTATTCTCATGACTTTAAGATTTTGCTTTATGAGTTAATTTCAAATTCAAACAAGTTGAATTT
TTGCTTTCAATTGGTGGCAATGAATTGTTAGCCAACTTCTATATTAGTGGCCTTTATTATTTTTA
GCCATCTAACTTAAAGATTTTGCTTAGGATTTTGCTTAAGATTT
Found at i:22605 original size:19 final size:18
Alignment explanation
Indices: 22572--22607 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22562 TTGAGATAAT
22572 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
22590 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
22608 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:36275 original size:22 final size:22
Alignment explanation
Indices: 36236--36298 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
36226 GAATTTCGAG
* *
36236 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATGAAATTTTGTT
36257 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* * *
36279 AACCTCCTTAAGGAATTTTG
1 AACCTTCTTATGAAATTTTG
36299 AAGACCTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:36317 original size:22 final size:22
Alignment explanation
Indices: 36292--36675 Score: 96
Period size: 22 Copynumber: 17.6 Consensus size: 22
36282 CTCCTTAAGG
*
36292 AATTTTGA-AGACCTCACTATGA
1 AATTTTGATA-ACCTCACAATGA
* *
36314 AATTTTGATAACTTCCCAATGA
1 AATTTTGATAACCTCACAATGA
* *
36336 AATTTTGATAACCAACACTATGA
1 AATTTTGATAACC-TCACAATGA
* * *
36359 GATGTTGATAAGCTC-CATATGA
1 AATTTTGATAACCTCACA-ATGA
* * * ***
36381 TATATTGATTACCAT-GTTATGA
1 AATTTTGATAACC-TCACAATGA
* * *
36403 AAATTTAAAAACCTC-CATATG-
1 AATTTTGATAACCTCACA-ATGA
* * **
36424 AATTCTT-AGTAATCACACTCTGA
1 AATT-TTGA-TAACCTCACAATGA
* * *
36447 AATTTTGATAATCACACTATGA
1 AATTTTGATAACCTCACAATGA
* * * *
36469 AATTGTGATAAGCTCGCTATGA
1 AATTTTGATAACCTCACAATGA
* *
36491 AATTTTGATAAACCTTC-CTATAA
1 AATTTTGAT-AACC-TCACAATGA
* * *
36514 AATTTTGATAAACCTCCCTATAA
1 AATTTTGAT-AACCTCACAATGA
* * *
36537 AATTTTGATAATCTC-CTTACGA
1 AATTTTGATAACCTCAC-AATGA
*
36559 AATCTTGATAA-CT-AC----A
1 AATTTTGATAACCTCACAATGA
* *
36575 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTCACAATGA
** **
36597 TTTTTTGATAACCTCATTATGA
1 AATTTTGATAACCTCACAATGA
** * * *
36619 AATTTTCTTAATCTCCCTATGA
1 AATTTTGATAACCTCACAATGA
* * *
36641 AATTTTGATCTACAT-ACTATGA
1 AATTTTGAT-AACCTCACAATGA
36663 AATTTTGATAACC
1 AATTTTGATAACC
36676 CTTTTATGAA
Statistics
Matches: 273, Mismatches: 65, Indels: 49
0.71 0.17 0.13
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
21 12 0.04
22 182 0.67
23 63 0.23
24 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
AATTTTGATAACCTCACAATGA
Found at i:36340 original size:44 final size:45
Alignment explanation
Indices: 36265--36374 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 45
36255 TTAACCTTCT
* * * *
36265 TATGAAATTTTGTTAACCTCCTTAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATAACCTCCTCAAGAAATTTTGATA-ACCAACAC
*
36309 TATGAAATTTTGATAACTTCC-CAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCTCAA-GAAATTTTGATAACCAACAC
* * *
36354 TATGAGATGTTGATAAGCTCC
1 TATGAAATTTTGATAACCTCC
36375 ATATGATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
43 2 0.04
44 31 0.57
45 21 0.39
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCTCAAGAAATTTTGATAACCAACAC
Found at i:36389 original size:45 final size:45
Alignment explanation
Indices: 36306--36394 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
36296 TTGAAGACCT
* *
36306 CACTATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAA
1 CACTATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAA
* * *
36351 CACTATGAGATGTTGATAAGC-T-CCATATGATATATTGATTACCA
1 CACTATGAAATGTTGATAA-CTTCCCA-ATGAAATATTGATAACCA
36395 TGTTATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
44 3 0.08
45 33 0.89
46 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (45 bp):
CACTATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAA
Found at i:36516 original size:23 final size:23
Alignment explanation
Indices: 36446--36547 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
36436 TCACACTCTG
* * * *
36446 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * * *
36468 AAATTGTGAT-AAGCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
*
36490 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
36513 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
36536 AAATTTTGATAA
1 AAATTTTGATAA
36548 TCTCCTTACG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
22 27 0.39
23 42 0.61
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:36568 original size:45 final size:43
Alignment explanation
Indices: 36446--36569 Score: 101
Period size: 45 Copynumber: 2.7 Consensus size: 43
36436 TCACACTCTG
* * * *
36446 AAATTTTGATAATCACAC-TATGAAATTGTGAT-AAGCTCGCTATG
1 AAATTTTGATAATCTC-CTTA-GAAATT-TGATAAACCTCCCTATA
*
36490 AAATTTTGATAAACCTTCCTATA-AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AATC-TCCT-TAGAAA-TTTGATAAACCTCCCTATA
36536 AAATTTTGATAATCTCCTTACGAAATCTTGATAA
1 AAATTTTGATAATCTCCTTA-GAAAT-TTGATAA
36570 CTACAAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
43 2 0.03
44 15 0.23
45 24 0.37
46 22 0.34
47 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (43 bp):
AAATTTTGATAATCTCCTTAGAAATTTGATAAACCTCCCTATA
Found at i:36632 original size:82 final size:84
Alignment explanation
Indices: 36490--36649 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 84
36480 GCTCGCTATG
* * * *
36490 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAATCTCCTT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTCATAATCTCCCT
36555 ACGAAATCTTGATAACTAC
66 ACGAAATCTTGATAACTAC
* ** * * *
36574 AAATTTTGAT-AACCTCCCTATGATTTTTTGAT-AACCTCATTATGAAATTTTCTTAATCTCCCT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTCATAATCTCCCT
* *
36637 ATGAAATTTTGAT
66 ACGAAATCTTGAT
36650 CTACATACTA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 36 0.56
83 18 0.28
84 10 0.16
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (84 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTCATAATCTCCCT
ACGAAATCTTGATAACTAC
Found at i:36876 original size:22 final size:22
Alignment explanation
Indices: 36849--37261 Score: 238
Period size: 22 Copynumber: 18.6 Consensus size: 22
36839 ATATTAAAAA
* *
36849 TTTGATAACCTCTTTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
*
36871 TTTGATAACCTCTCTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
36893 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * * *
36915 TTTGATAATCACAT-TAAGTAAT
1 TTTGATAACCTC-TCTATGAAAT
* *
36937 TTTGATAACCTCGCTTTGAAAT
1 TTTGATAACCTCTCTATGAAAT
** *
36959 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
36981 TTTGATAACCT-TCCTAT-AAAT
1 TTTGATAACCTCT-CTATGAAAT
37002 TTTGATAATCCGATCTCTATGAAAT
1 TTTGATAA-CC--TCTCTATGAAAT
* * * *
37027 TTCGATAATCACTCTATGATA-
1 TTTGATAACCTCTCTATGAAAT
*
37048 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
*
37069 TTTGGT-A-CTC-CTTATGAAATT
1 TTTGATAACCTCTC-TATGAAA-T
*
37090 GAGACTTTTATAACCT-TCATATGAAAT
1 -----TTTGATAACCTCTC-TATGAAAT
* * **
37117 TTTGATAACCACACTAAAAAAT
1 TTTGATAACCTCTCTATGAAAT
* **
37139 TTTGATAACCACAATATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
37161 TTTGATAACCTCCCCATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
37183 ATT-AGTAGCCTC-CGTATGAAAT
1 TTTGA-TAACCTCTC-TATGAAAT
* * *
37205 TTTGTTAACCACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
37227 TCTT-ATAACCTCGCTATGACAT
1 T-TTGATAACCTCTCTATGAAAT
* *
37249 TTTTATAATCTCT
1 TTTGATAACCTCT
37262 TTGATAACCT
Statistics
Matches: 300, Mismatches: 64, Indels: 54
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 30 0.10
22 214 0.71
23 5 0.02
24 6 0.02
25 12 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:36967 original size:88 final size:87
Alignment explanation
Indices: 36818--37011 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 87
36808 CGAAATACCA
* * **
36818 CTATGAAATTTTGGTAATCACATATTAAAAATTTGATAACCTCTTTATCAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACA-ATTAAAAATTTGATAACCTCCTTATCAAATTTTGATAACAAC
* * *
36883 TCTATAAAATTTTGTTGACCC-C
65 ACTATAAAATTTTGATAACCCTC
* *
36905 TCTATGAAATTTTGATAATCAC-ATTAAGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 -CTATGAAATTTTGATAATCACAATTAA--AAATTTGATAACCTC-CTTATCAAATTTTGATAAC
* *
36968 AACACTATGAAATTTTGATAACCTTC
62 AACACTATAAAATTTTGATAACCCTC
36994 CTAT-AAATTTTGATAATC
1 CTATGAAATTTTGATAATC
37012 CGATCTCTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
86 5 0.05
87 14 0.15
88 69 0.76
89 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (87 bp):
CTATGAAATTTTGATAATCACAATTAAAAATTTGATAACCTCCTTATCAAATTTTGATAACAACA
CTATAAAATTTTGATAACCCTC
Found at i:36982 original size:44 final size:42
Alignment explanation
Indices: 36818--37542 Score: 177
Period size: 44 Copynumber: 16.5 Consensus size: 42
36808 CGAAATACCA
* * *
36818 CTATGAAATTTTGGTAATCACA-TATTAAAAATTTGATAACCTC
1 CTATGAAATTTTGATAA-CACACTA-TGAAATTTTGATAACCTC
* * * * * * * *
36861 TTTATCAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCC
1 -CTATGAAATTTTGATAA-CACACTATGAAATTTTGATAACCTC
* * *
36905 TCTATGAAATTTTGATAATCACATTAAGTAATTTTGATAACCTC
1 -CTATGAAATTTTGATAA-CACACTATGAAATTTTGATAACCTC
*
36949 GCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAACCTTC
1 -CTATGAAATTTTGATAAC-ACACTATGAAATTTTGATAACC-TC
* *
36994 CTAT-AAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACT-
1 CTATGAAATTTTGATAA--C-A-CACTATGAAATTTTGATAA-C-CTC
* * * *
37040 CTATGATA-TTTGATAAC-CTTCTATCAAATTTTGGT-A-CTC
1 CTATGAAATTTTGATAACAC-ACTATGAAATTTTGATAACCTC
* * *
37079 CTTATGAAATTGAGACTTTTATAAC-CTTCATATGAAATTTTGATAACCAC
1 C-TATGAAA-T-----TTTGATAACAC-AC-TATGAAATTTTGATAACCTC
** *
37129 ACTAAAAAATTTTGATAACCACAATATGAAATTTTGATAACCTCC
1 -CTATGAAATTTTGATAA-CACACTATGAAATTTTGATAACCT-C
* * * * * *
37174 CCATGAAATATT-AGTAGC-CTCCGTATGAAATTTTGTTAACCAC
1 CTATGAAATTTTGA-TAACAC-AC-TATGAAATTTTGATAACCTC
* * * *
37217 ACTATGAAATTCTT-ATAACCTCGCTATGACATTTTTATAA--T-
1 -CTATGAAATT-TTGATAA-CACACTATGAAATTTTGATAACCTC
* * * * **
37258 C--T----CTTTGATAAC-CTTTCTATAAAATTATGATAACCAGA
1 CTATGAAATTTTGATAACAC--ACTATGAAATTTTGATAACC-TC
** * * *
37296 CTATGAAATTTCAATAAC-CTTGCTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAACAC--ACTATGAAATTTTGATAACC---TC
* ** *
37342 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTG
1 CTATGAAATTTTGATAA-CACACTATGAAATTTTGATAACC-TC
* * * *
37386 CTAAGAAATTTTAATAAC-CTGATCCTATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACAC--A--CTATGAAATTTTGATAACCTC
* * * * *
37431 ACTATGAAATTTTGATAAC-CTTCCCATGAAATTTCGGTAACCAC
1 -CTATGAAATTTTGATAACAC--ACTATGAAATTTTGATAACCTC
* * * *
37475 ACTATGGAATTTTGATAAC-CTCCTCATGAAATTATAATAACCATC
1 -CTATGAAATTTTGATAACAC-ACT-ATGAAATTTTGATAACC-TC
*
37520 ATATGAAATTTTGATAACCACAC
1 CTATGAAATTTTGATAA-CACAC
37543 AGAGACAAGA
Statistics
Matches: 510, Mismatches: 112, Indels: 117
0.69 0.15 0.16
Matches are distributed among these distances:
32 1 0.00
33 3 0.01
34 18 0.04
38 4 0.01
39 1 0.00
40 8 0.02
41 2 0.00
42 15 0.03
43 20 0.04
44 283 0.55
45 16 0.03
46 98 0.19
47 17 0.03
48 14 0.03
49 2 0.00
50 7 0.01
51 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (42 bp):
CTATGAAATTTTGATAACACACTATGAAATTTTGATAACCTC
Found at i:37312 original size:22 final size:22
Alignment explanation
Indices: 37287--37538 Score: 152
Period size: 22 Copynumber: 11.3 Consensus size: 22
37277 TAAAATTATG
* *
37287 ATAACCAGACTATGAAATTTCA
1 ATAACCTGACTATGAAATTTTA
*
37309 ATAACCTTG-CTAAGAAATTTTA
1 ATAACC-TGACTATGAAATTTTA
*
37331 ATAACCTGATCCTATGAAATTTTG
1 ATAACCTGA--CTATGAAATTTTA
* ** *
37355 GTAACCACACTATGAAATTTCA
1 ATAACCTGACTATGAAATTTTA
*
37377 ATAACCTTG-CTAAGAAATTTTA
1 ATAACC-TGACTATGAAATTTTA
*
37399 ATAACCTGATCCTATGAAATTTTG
1 ATAACCTGA--CTATGAAATTTTA
* ** *
37423 GTAACCACACTATGAAATTTTG
1 ATAACCTGACTATGAAATTTTA
** * **
37445 ATAACCTTCCCATGAAATTTCG
1 ATAACCTGACTATGAAATTTTA
* ** * *
37467 GTAACCACACTATGGAATTTTG
1 ATAACCTGACTATGAAATTTTA
* *
37489 ATAACCT-CCTCATGAAATTATA
1 ATAACCTGACT-ATGAAATTTTA
* *
37511 ATAACCATCA-TATGAAATTTTG
1 ATAACC-TGACTATGAAATTTTA
37533 ATAACC
1 ATAACC
37539 ACACAGAGAC
Statistics
Matches: 177, Mismatches: 42, Indels: 22
0.73 0.17 0.09
Matches are distributed among these distances:
21 6 0.03
22 134 0.76
23 3 0.02
24 34 0.19
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATAACCTGACTATGAAATTTTA
Found at i:37472 original size:68 final size:68
Alignment explanation
Indices: 37274--37452 Score: 304
Period size: 68 Copynumber: 2.6 Consensus size: 68
37264 GATAACCTTT
* * * *
37274 CTATAAAATTATGATAACCAGACTATGAAATTTCAATAACCTTGCTAAGAAATTTTAATAACCTG
1 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTGCTAAGAAATTTTAATAACCTG
37339 ATC
66 ATC
37342 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTGCTAAGAAATTTTAATAACCTG
1 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTGCTAAGAAATTTTAATAACCTG
37407 ATC
66 ATC
**
37410 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTT
37453 CCCATGAAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 105 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (68 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAACCTTGCTAAGAAATTTTAATAACCTG
ATC
Found at i:37515 original size:66 final size:66
Alignment explanation
Indices: 37274--37542 Score: 178
Period size: 68 Copynumber: 4.0 Consensus size: 66
37264 GATAACCTTT
* * * * **
37274 CTATAAAATTATGATAACCAGACTATGAAATT-TCAATAACCTTGCTA-A-GAAATTTTAATAAC
1 CTATGAAATTTTGATAACCACACTATGAAATTAT-AATAACCAT-C-ACATGAAATTTCGATAAC
37336 CTGATC-
63 C--A-CA
* * **
37342 CTATGAAATTTTGGTAACCACACTATGAAATT-TCAATAACCTTGCTA-A-GAAATTTTAATAAC
1 CTATGAAATTTTGATAACCACACTATGAAATTAT-AATAACCAT-C-ACATGAAATTTCGATAAC
37404 CTGATC-
63 C--A-CA
* * * * * *
37410 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTCGGTAACCAC
1 CTATGAAATTTTGATAACCACACTATGAAATTATAATAACCATCACATGAAATTTCGATAACCAC
37475 A
66 A
* * * *
37476 CTATGGAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCATATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCACACT-ATGAAATTATAATAACCATCACATGAAATTTCGATAACCA
37540 CA
65 CA
37542 C
1 C
37543 AGAGACAAGA
Statistics
Matches: 177, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
65 3 0.02
66 55 0.31
67 2 0.01
68 116 0.66
69 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACTATGAAATTATAATAACCATCACATGAAATTTCGATAACCAC
A
Found at i:37740 original size:20 final size:20
Alignment explanation
Indices: 37701--37739 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
37691 TATTGACATT
37701 TAAAAAATTGAAATTAAAAA
1 TAAAAAATTGAAATTAAAAA
*
37721 TAAAATATT-AAATTAAAAA
1 TAAAAAATTGAAATTAAAAA
37740 AATAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAA
Found at i:37746 original size:19 final size:19
Alignment explanation
Indices: 37711--37751 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
37701 TAAAAAATTG
*
37711 AAATTAAAAATAAAATATT
1 AAATTAAAAATAAAATAGT
37730 AAATTAAAAA-AATAATAGT
1 AAATTAAAAATAA-AATAGT
37749 AAA
1 AAA
37752 GGAAATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATTAAAAATAAAATAGT
Found at i:41690 original size:35 final size:35
Alignment explanation
Indices: 41651--41725 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
41641 TTATATAAAC
*
41651 GAACACTTAAATGAACACTAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
*
41686 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
41721 GAACA
1 GAACA
41726 TAAACGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:49570 original size:297 final size:292
Alignment explanation
Indices: 49017--49598 Score: 837
Period size: 297 Copynumber: 2.0 Consensus size: 292
49007 AGTGTTTATA
* *
49017 GAAATTACTTAAAGGTCAAATTGAGGATTAATGTGGTGTCTCCTTTTGATTTTTTTTGTCTTTTC
1 GAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGGCTCCTTTTGATTTTTTTTGTCTTTTC
* * * *
49082 TCACTTTTCGAGTGCCTAAAAAGTCCCTTGATGAATTTCCTCCATTACTTTTCCTCCTGCCTTTT
66 TCACTTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTCCATTACTTTTCCTCCTGCCCTTT
* **
49147 TTTGTAATTTACTATTTTTGTAATTTATGATTAAGTGTGTTTTAATTATGTATTAATTGTGTGTG
131 TTTGTAATTTACTATTTTTATAATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTG
* * * * *
49212 GATATTAGGATTTACTGGTTCAACTCCTTTGTCAGATTCCGAAGGATTGGTGCTATAAATGTATT
196 GATATTAGGATTTACCGGTTCAACTCCTCTGTCAGATTCCAAAGGATTAGTGCTATAAATGTATC
*
49277 TAGCCGAGTTCATTAATTTAACAATTGCTATG
261 TACCCGAGTTCATTAATTTAACAATTGCTATG
* *
49309 GAAATTACTTAAAAGGCCAAATTGAGGATTCATGTGGTGGCTCCTTTTGGCCTTTTTTTTTTGTC
1 GAAATTACTT-AAAGGCCAAATTGAGGATTAATGTGGTGGCTCCTTTT-G---ATTTTTTTTGTC
* * * *
49374 TTTTCTCACTTTTCGGGTGACTAAAAAGGCTCTCGATTAATTTCCTCTC-TTACTTTTCCTGCTG
61 TTTTCTCACTTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTC-CATTACTTTTCCTCCTG
*
49438 CCCTTTTTTGTAATTTA-TAATTTTTAT-ATTTATGATTAAGTGTGTTTTAATTACATATTGATT
125 CCCTTTTTTGTAATTTACT-ATTTTTATAATTTATGATTAAGTGTGTTTTAATTACATATTAATT
** *
49501 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGTTGGAATTCCAAAGGATTAGTGCTGTA
189 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGTCAG-ATTCCAAAGGATTAGTGCTATA
*
49566 AATGTGTCTACCCGAGTTCATTAATTTAACAAT
253 AATGTATCTACCCGAGTTCATTAATTTAACAAT
49599 AGCAATCAAG
Statistics
Matches: 256, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
292 10 0.04
293 34 0.13
294 1 0.00
296 72 0.28
297 138 0.54
298 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (292 bp):
GAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGGCTCCTTTTGATTTTTTTTGTCTTTTC
TCACTTTTCGAGTGACTAAAAAGGCCCTCGATGAATTTCCTCCATTACTTTTCCTCCTGCCCTTT
TTTGTAATTTACTATTTTTATAATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTG
GATATTAGGATTTACCGGTTCAACTCCTCTGTCAGATTCCAAAGGATTAGTGCTATAAATGTATC
TACCCGAGTTCATTAATTTAACAATTGCTATG
Found at i:51247 original size:16 final size:16
Alignment explanation
Indices: 51228--51258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51218 CCGAAAAACC
51228 CAAAACCCGAATGACT
1 CAAAACCCGAATGACT
*
51244 CAAAACCCGAGTGAC
1 CAAAACCCGAATGAC
51259 CTAAGGCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.32, G:0.16, T:0.10
Consensus pattern (16 bp):
CAAAACCCGAATGACT
Done.