Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012618.1 Corchorus olitorius cultivar O-4 contig12651, 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: 146327
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:75 original size:31 final size:31
Alignment explanation
Indices: 4--75 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
1 AGC
*
4 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
35 TGATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
65 GTTTTAATTTG
1 -TTTTAATTTG
76 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:544 original size:23 final size:23
Alignment explanation
Indices: 508--559 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
498 CAAACTTGAG
*
508 CCCGAACCCGACCCGAGCCCGAA
1 CCCGAACCCGACCCGAGACCGAA
* *
531 CTCGAACCCTACCCGAGACCGAA
1 CCCGAACCCGACCCGAGACCGAA
554 CCCGAA
1 CCCGAA
560 AATACCTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.48, G:0.19, T:0.04
Consensus pattern (23 bp):
CCCGAACCCGACCCGAGACCGAA
Found at i:591 original size:32 final size:32
Alignment explanation
Indices: 549--633 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
539 CTACCCGAGA
* * **
549 CCGAACCCGAAAATACCTGAACTTGACATAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
*
581 CCGAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
613 CCGAGCCCGAAAATACCCGAA
1 CCGAGCCCGAAAATACCCGAA
634 AAACCCGAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.36, G:0.15, T:0.11
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACATAAC
Found at i:600 original size:16 final size:16
Alignment explanation
Indices: 579--632 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
569 ACTTGACATA
579 ACCCGAGCCCGAAAAT
1 ACCCGAGCCCGAAAAT
* **
595 ACCCGAACCCG-ACTT
1 ACCCGAGCCCGAAAAT
610 AACCCGAGCCCGAAAAT
1 -ACCCGAGCCCGAAAAT
627 ACCCGA
1 ACCCGA
633 AAAACCCGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.35, C:0.41, G:0.17, T:0.07
Consensus pattern (16 bp):
ACCCGAGCCCGAAAAT
Found at i:4459 original size:22 final size:22
Alignment explanation
Indices: 4433--4477 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4423 AACGATTAAA
*
4433 AAAAAAAACGAACAAACACATCC
1 AAAAAAGA-GAACAAACACATCC
4456 AAAAAAGAGAACAAACACATCC
1 AAAAAAGAGAACAAACACATCC
4478 CATCAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.64, C:0.24, G:0.07, T:0.04
Consensus pattern (22 bp):
AAAAAAGAGAACAAACACATCC
Found at i:5000 original size:12 final size:12
Alignment explanation
Indices: 4983--5012 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4973 TACTAAACCA
4983 ATCCTCATCAAT
1 ATCCTCATCAAT
*
4995 ATCCTCTTCAAT
1 ATCCTCATCAAT
5007 ATCCTC
1 ATCCTC
5013 CAAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (12 bp):
ATCCTCATCAAT
Found at i:13354 original size:87 final size:87
Alignment explanation
Indices: 13172--13343 Score: 209
Period size: 87 Copynumber: 2.0 Consensus size: 87
13162 TGCAGGGTTA
* * * *
13172 AAAAAAAAATCTTTTACTCATGTCATGAATTCATATAACATTTATGTACTAAGTCAAATCTTCAA
1 AAAAAAAAATCTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCAA
*** * *
13237 TCTTCAAGAAAAAGTTATCGGT
66 TCTTCAAGAAAAACCAAGCGAT
* *
13259 AAAAAAAAATGTCTTACTCCTGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCCA
1 AAAAAAAAATCTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCT-CCA
* * *
13324 ATTTTTAAGAAAATCCAAGC
65 ATCTTCAAGAAAAACCAAGC
13344 ATGATTAAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 56 0.79
88 15 0.21
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (87 bp):
AAAAAAAAATCTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCAA
TCTTCAAGAAAAACCAAGCGAT
Found at i:13580 original size:25 final size:26
Alignment explanation
Indices: 13551--13600 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
13541 TACCTCATTA
13551 AGTATTAA-AAAAAATAAAAGTTAAG
1 AGTATTAAGAAAAAATAAAAGTTAAG
*
13576 AGTATTAAGTAAAAATAAAAGTTAA
1 AGTATTAAGAAAAAATAAAAGTTAA
13601 AATGCCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (26 bp):
AGTATTAAGAAAAAATAAAAGTTAAG
Found at i:15917 original size:22 final size:22
Alignment explanation
Indices: 15892--16060 Score: 123
Period size: 22 Copynumber: 7.8 Consensus size: 22
15882 TCAAACAAAG
15892 ATGAAATTTTGATAACCTTCCT
1 ATGAAATTTTGATAACCTTCCT
* *** *
15914 ATGAAATTTTAATAATGATACT
1 ATGAAATTTTGATAACCTTCCT
* **
15936 ATGAAATTTTGAGAACCTTTTT
1 ATGAAATTTTGATAACCTTCCT
** *
15958 AT--AATTTTTTTAACCTTCTT
1 ATGAAATTTTGATAACCTTCCT
* *
15978 ATGAAATTTTGTTAACCTCCCT
1 ATGAAATTTTGATAACCTTCCT
* * *
16000 AAGGAATTTTGA-AGATC-TCACT
1 ATGAAATTTTGATA-ACCTTC-CT
*
16022 ATGAAATTTTGATAA-CTTCCCA
1 ATGAAATTTTGATAACCTT-CCT
16044 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
16061 AACACTGATA
Statistics
Matches: 112, Mismatches: 27, Indels: 15
0.73 0.18 0.10
Matches are distributed among these distances:
20 16 0.14
21 3 0.03
22 90 0.80
23 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTTCCT
Found at i:15972 original size:20 final size:21
Alignment explanation
Indices: 15939--15995 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
15929 TGATACTATG
** *
15939 AAATTTTGAGAACCTTTTTAT
1 AAATTTTGTTAACCTTCTTAT
*
15960 -AATTTTTTTAACCTTCTTAT
1 AAATTTTGTTAACCTTCTTAT
15980 GAAATTTTGTTAACCT
1 -AAATTTTGTTAACCT
15996 CCCTAAGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.55
22 13 0.45
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
AAATTTTGTTAACCTTCTTAT
Found at i:16160 original size:22 final size:22
Alignment explanation
Indices: 16122--16203 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
16112 AAAACCTCCA
*
16122 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
16144 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
* * * *
16166 TATTAAATTGTGATAACCTCGC
1 TATGAAATTGTGATAATCACAC
16188 TATGAAATCT-TGATAA
1 TATGAAAT-TGTGATAA
16204 ACCTTCCTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
22 41 0.85
23 7 0.15
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:16252 original size:45 final size:45
Alignment explanation
Indices: 16148--16252 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 45
16138 TCACACTCTG
* * * *
16148 AAATTTTGATAATC-ACACTATTAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
* * * *
16192 AAATCTTGATAAACCTTC-CTATAAAATTTTGATAAACCTCCCTGTA
1 AAATTTTGAT-AACCTACACTATAAAATTGTGAT-AACCTCCCTATA
16238 AAATTTTGATAACCT
1 AAATTTTGATAACCT
16253 CCTTATGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
44 9 0.18
45 21 0.43
46 19 0.39
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (45 bp):
AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
Found at i:16254 original size:22 final size:23
Alignment explanation
Indices: 16148--16263 Score: 103
Period size: 23 Copynumber: 5.2 Consensus size: 23
16138 TCACACTCTG
* * * *
16148 AAATTTTGAT-AATCACACTATT
1 AAATTTTGATAAACCTCCCTATA
* * *
16170 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
16192 AAATCTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
16215 AAATTTTGATAAACCTCCCTGTA
1 AAATTTTGATAAACCTCCCTATA
* *
16238 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACCTCCCTATA
16260 AAAT
1 AAAT
16264 CTAAATAACT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
22 38 0.49
23 39 0.51
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:16501 original size:22 final size:21
Alignment explanation
Indices: 16146--16503 Score: 141
Period size: 22 Copynumber: 16.8 Consensus size: 21
16136 AATCACACTC
16146 TGAAATTTTGATAATCAC-ACTA
1 TGAAATTTTGATAA-C-CTACTA
* * *
16168 TTAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCT-ACTA
* *
16190 TGAAATCTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACC-TACTA
* * *
16213 TAAAATTTTGATAAACCTCCCTG
1 TGAAATTTTGAT-AACCT-ACTA
* *
16236 TAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTAC-TA
* **
16258 TGAAATCTAAATAA-CTAC--
1 TGAAATTTTGATAACCTACTA
*
16276 --AAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTAC-TA
** *
16296 TGATTTTTTGATAACC-GCGTTA
1 TGAAATTTTGATAACCTAC--TA
* * *
16318 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-ACTA
* *
16340 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACCTACTA
*
16362 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT--ACTA
* *
16384 TGAAATTTTGATAACCTTCAAA
1 TGAAATTTTGATAACCTAC-TA
* *
16406 TGAAATTTTGATATCCTAC-C
1 TGAAATTTTGATAACCTACTA
* *
16426 TGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAACCTAC-T-A
* * * *
16448 TAAAAGTTTGATAACCTTC-C
1 TGAAATTTTGATAACCTACTA
*
16468 T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAACC-TACTA
16487 TGAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
16504 CCCCAAAAAT
Statistics
Matches: 252, Mismatches: 55, Indels: 59
0.69 0.15 0.16
Matches are distributed among these distances:
16 9 0.04
17 12 0.05
18 4 0.02
19 4 0.02
20 16 0.06
21 11 0.04
22 148 0.59
23 46 0.18
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTACTA
Found at i:16547 original size:56 final size:56
Alignment explanation
Indices: 16487--16616 Score: 251
Period size: 56 Copynumber: 2.3 Consensus size: 56
16477 AACCATACTA
*
16487 TGAAATTTTGATAACCTCCCCAAAAATACCACTATGAAATTTTGGTAATCACATTC
1 TGAAAATTTGATAACCTCCCCAAAAATACCACTATGAAATTTTGGTAATCACATTC
16543 TGAAAATTTGATAACCTCCCCAAAAATACCACTATGAAATTTTGGTAATCACATTC
1 TGAAAATTTGATAACCTCCCCAAAAATACCACTATGAAATTTTGGTAATCACATTC
16599 TGAAAATTTGATAACCTC
1 TGAAAATTTGATAACCTC
16617 TTAATGAAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (56 bp):
TGAAAATTTGATAACCTCCCCAAAAATACCACTATGAAATTTTGGTAATCACATTC
Found at i:16648 original size:22 final size:22
Alignment explanation
Indices: 16599--16992 Score: 201
Period size: 22 Copynumber: 17.9 Consensus size: 22
16589 AATCACATTC
*
16599 TGAAAATTTGATAACCTCT-TAA
1 TGAAATTTTGATAACCTCTCT-A
16621 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
16643 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
16665 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
16687 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
16709 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
16731 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
16753 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
16777 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
16799 TGAGA-TTTAATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
16819 TCAAATTTTGGT-A-CTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
16839 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
16867 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
16889 -AAAATTTTTGATAACC-C-C-A
1 TGAAA-TTTTGATAACCTCTCTA
*
16908 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * * *
16930 TAAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
16952 TGAAATTCTT-ATAATCTCACTA
1 TGAAATT-TTGATAACCTCTCTA
*
16974 TGACAA-TTTGATAATCTCT
1 TGA-AATTTTGATAACCTCT
16993 TTGATAACCT
Statistics
Matches: 283, Mismatches: 57, Indels: 64
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.00
19 11 0.04
20 21 0.07
21 30 0.11
22 178 0.63
23 8 0.03
24 6 0.02
25 12 0.04
26 4 0.01
27 3 0.01
28 9 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:16694 original size:44 final size:44
Alignment explanation
Indices: 16574--17201 Score: 203
Period size: 44 Copynumber: 14.5 Consensus size: 44
16564 AAAAATACCA
* * *
16574 CTATGAAATTTTGGTAATCACATTCTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * *
16618 -TAATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CT-ATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT
* *
16662 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * *
16706 CTTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCT
* * *
16749 CCTAT-AAATTTTGATAATC-CGATCTCTATGAAATTTCGATAATCACT
1 -CTATGAAATTTTGATAATCAC-A--T-TATGAAATTTTGATAACCTCT
* * * * *
16796 CTATGAGA-TTTAATAA-C-CTTCTATCAAATTTTGGT-A-CTCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT
* * * * * *
16836 TTATGAAATTGAGACTTTTATAACCTTCA-TATGAAATTTTGATAACCACA
1 CTATGAAA-T-----TTTGATAATC-ACATTATGAAATTTTGATAACCTCT
* ** *
16886 CTA-AAAATTTTTGATAA-C-C-CCATGAAATATT-AGTAACCTC-
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGA-TAACCTCT
* * * * * *
16926 CTTATAAAATTTTGTTAACCACACTATGAAATTCTT-ATAATCTCA
1 C-TATGAAATTTTGATAATCACATTATGAAATT-TTGATAACCTCT
* *
16971 CTATGACAA-TTTGATAAT--C----T----CTTTGATAACCTTT
1 CTATGA-AATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * ** *
17005 CTATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTAAT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCT-CT
* * * *
17050 CCTATGAAATGTTGGTAACCACACTATGAAATTTTGATAACCT-T
1 -CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * *
17094 CCCATGAAATTTTGATAACTCCCA-TATGAAATTTTGGTCACCACA
1 -CTATGAAATTTTGATAA-TCACATTATGAAATTTTGATAACCTCT
* * * * *
17139 CTATGGAATTTTGATAA-C-C-TCATGAAATTATAATAA-CTAT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
*
17179 CTTATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAATCACA
17202 CAGAGACAAG
Statistics
Matches: 437, Mismatches: 91, Indels: 112
0.68 0.14 0.17
Matches are distributed among these distances:
33 4 0.01
34 19 0.04
36 1 0.00
38 1 0.00
40 14 0.03
41 54 0.12
42 22 0.05
43 19 0.04
44 191 0.44
45 14 0.03
46 64 0.15
47 10 0.02
48 13 0.03
49 6 0.01
50 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:16737 original size:88 final size:87
Alignment explanation
Indices: 16574--16740 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 87
16564 AAAAATACCA
* * **
16574 CTATGAAATTTTGGTAATCACATTCTGAAAATTTGATAACCTCTTAATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT-ATGAAATTTTGATAACAAC
*
16639 TCTATAAAATTTTGTTGACCCCT
65 ACTATAAAATTTTGTTGACCCCT
* *
16662 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCT--CTTATGAAATTTTGATAACAA
*
16726 CACTATGAAATTTTG
64 CACTATAAAATTTTG
16741 ATAATCTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 66 0.96
90 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (87 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTATGAAATTTTGATAACAACA
CTATAAAATTTTGTTGACCCCT
Found at i:17090 original size:22 final size:22
Alignment explanation
Indices: 17005--17202 Score: 140
Period size: 22 Copynumber: 9.0 Consensus size: 22
16995 GATAACCTTT
* *
17005 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
**
17027 CTATGAAATTTCAATAACCTA-A
1 CTATGAAATTTTGATAACC-ACA
* *
17049 TCCTATGAAATGTTGGTAACCACA
1 --CTATGAAATTTTGATAACCACA
*
17073 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
17095 CCATGAAATTTTGATAACTCCCA
1 CTATGAAATTTTGATAAC-CACA
* *
17118 -TATGAAATTTTGGTCACCACA
1 CTATGAAATTTTGATAACCACA
* *
17139 CTATGGAATTTTGATAA-C-CT
1 CTATGAAATTTTGATAACCACA
* * *
17159 C-ATGAAATTATAATAACTATC-
1 CTATGAAATTTTGATAACCA-CA
*
17180 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
17202 C
1 C
17203 AGAGACAAGA
Statistics
Matches: 133, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
19 12 0.09
20 2 0.02
21 5 0.04
22 94 0.71
23 4 0.03
24 16 0.12
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:17149 original size:66 final size:63
Alignment explanation
Indices: 17052--17202 Score: 194
Period size: 63 Copynumber: 2.3 Consensus size: 63
17042 AACCTAATCC
* * * *
17052 TATGAAATGTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTCCC
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-T--CATGAAATTATAATAACTACC
17117 A
63 A
* * * *
17118 TATGAAATTTTGGTCACCACACTATGGAATTTTGATAACCTCATGAAATTATAATAACTATCT
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCATGAAATTATAATAACTACCA
*
17181 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGGTAACCACAC
17203 AGAGACAAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
63 37 0.49
65 1 0.01
66 37 0.49
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (63 bp):
TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCATGAAATTATAATAACTACCA
Found at i:18366 original size:27 final size:26
Alignment explanation
Indices: 18312--18372 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
18302 CTAAATTTTC
18312 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
18340 ATTATTTAATAATGGTAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
18367 A-TATTT
1 ATTATTT
18373 GAAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:31196 original size:30 final size:29
Alignment explanation
Indices: 31157--31231 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
31147 TTATGCTGAG
31157 GGGGCAAAATGTCCCAAAATTGAAGTTCAA
1 GGGGCAAAATGT-CCAAAATTGAAGTTCAA
* *
31187 GGGGTAAAATGTCCAAAATTGAAGTTCAT
1 GGGGCAAAATGTCCAAAATTGAAGTTCAA
* *
31216 GAGGCAAAACGTCCAA
1 GGGGCAAAATGTCCAA
31232 TCACTATAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 29 0.73
30 11 0.28
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (29 bp):
GGGGCAAAATGTCCAAAATTGAAGTTCAA
Found at i:35903 original size:31 final size:29
Alignment explanation
Indices: 35832--35923 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
35822 TCCATTAATT
* *
35832 CCACTTCAGGGACTCAA-TTGCTCATTTTT
1 CCACTTCAGGGACT-AATTTGCACATTTTA
* *
35861 TCACTTGAGGGACTAATTTGCACATTTTCCA
1 CCACTTCAGGGACTAATTTGCACATTTT--A
* *
35892 CCACTTCAGGGACCAATTGTGTAC-TTTTA
1 CCACTTCAGGGACTAATT-TGCACATTTTA
35921 CCA
1 CCA
35924 TACTTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.04
29 26 0.51
31 19 0.37
32 4 0.08
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (29 bp):
CCACTTCAGGGACTAATTTGCACATTTTA
Found at i:36691 original size:20 final size:20
Alignment explanation
Indices: 36668--36719 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
36658 TTTTAGTGTA
*
36668 TTGGGCTAGTTTTTTTAGCT
1 TTGGGCTAGTTTATTTAGCT
* *
36688 TTGGGTTAATTTATTTAGCT
1 TTGGGCTAGTTTATTTAGCT
*
36708 TTGGGCTTGTTT
1 TTGGGCTAGTTT
36720 CTTTGTACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.25, T:0.56
Consensus pattern (20 bp):
TTGGGCTAGTTTATTTAGCT
Found at i:37306 original size:18 final size:18
Alignment explanation
Indices: 37285--37324 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
37275 GTAATCTTTG
37285 ATCACCGGGTGATCTTAC
1 ATCACCGGGTGATCTTAC
* *
37303 ATCA-CTGGTGATCTTAG
1 ATCACCGGGTGATCTTAC
37320 ATCAC
1 ATCAC
37325 TAATGATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (18 bp):
ATCACCGGGTGATCTTAC
Found at i:37314 original size:17 final size:17
Alignment explanation
Indices: 37292--37325 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37282 TTGATCACCG
37292 GGTGATCTTACATCACT
1 GGTGATCTTACATCACT
*
37309 GGTGATCTTAGATCACT
1 GGTGATCTTACATCACT
37326 AATGATCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (17 bp):
GGTGATCTTACATCACT
Found at i:37331 original size:17 final size:17
Alignment explanation
Indices: 37294--37333 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
37284 GATCACCGGG
**
37294 TGATCTTACATCACTGG
1 TGATCTTACATCACTAA
*
37311 TGATCTTAGATCACTAA
1 TGATCTTACATCACTAA
37328 TGATCT
1 TGATCT
37334 GGGAGGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (17 bp):
TGATCTTACATCACTAA
Found at i:38267 original size:69 final size:69
Alignment explanation
Indices: 38137--38274 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 69
38127 AAAAACTAAC
** * * *
38137 AACTAAGGAAAAAATGGTGGGAACACCATTAATTACATTTCAATGCTAAAATTACATATAAAGAC
1 AACTAAGGAAAAAATGGTAAGAACACCATTAATTACATTCCAATACTAAAATTACACATAAAGAC
38202 AATG
66 AATG
*
38206 AACTGAGGAAAAAATGGTAAGAACACCATTAATTACA-TCCAAATACTAAAATTACACATAAAGA
1 AACTAAGGAAAAAATGGTAAGAACACCATTAATTACATTCC-AATACTAAAATTACACATAAAGA
38270 CAATG
65 CAATG
38275 CATTTCAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
68 2 0.03
69 60 0.97
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.22
Consensus pattern (69 bp):
AACTAAGGAAAAAATGGTAAGAACACCATTAATTACATTCCAATACTAAAATTACACATAAAGAC
AATG
Found at i:39094 original size:4 final size:4
Alignment explanation
Indices: 39085--39111 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39075 TGAATTGGTA
39085 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
39112 TTTTGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:40388 original size:3 final size:3
Alignment explanation
Indices: 40380--40418 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
40370 CGGCTGCCAA
40380 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40419 GGGAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:50313 original size:18 final size:18
Alignment explanation
Indices: 50290--50329 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50280 GATATCCCTA
*
50290 AAGACAATGAAGATAGTG
1 AAGACAATGAAGAAAGTG
* *
50308 AAGACAGTGAGGAAAGTG
1 AAGACAATGAAGAAAGTG
50326 AAGA
1 AAGA
50330 AAATACAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.33, T:0.12
Consensus pattern (18 bp):
AAGACAATGAAGAAAGTG
Found at i:52681 original size:5 final size:5
Alignment explanation
Indices: 52671--52696 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52661 ACAGAATCCA
52671 TCTTC TCTTC TCTTC TCTTC TCTTC T
1 TCTTC TCTTC TCTTC TCTTC TCTTC T
52697 GCCCTACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:58618 original size:15 final size:16
Alignment explanation
Indices: 58581--58619 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
58571 TGAATTGATC
*
58581 TTCTATTTCTTTTTTGT
1 TTCT-TTTCTATTTTGT
58598 TTCTTTTCTATTTTG-
1 TTCTTTTCTATTTTGT
58613 TTCTTTT
1 TTCTTTT
58620 TTCCTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.77
Consensus pattern (16 bp):
TTCTTTTCTATTTTGT
Found at i:58622 original size:22 final size:23
Alignment explanation
Indices: 58581--58627 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
58571 TGAATTGATC
58581 TTCTATTTCTTTTTTGTTT-CTT
1 TTCTATTTCTTTTTTGTTTCCTT
58603 TTCTATTT-TGTTCTTT-TTTCCTT
1 TTCTATTTCT-TT-TTTGTTTCCTT
58626 TT
1 TT
58628 TGGGGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 8 0.36
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (23 bp):
TTCTATTTCTTTTTTGTTTCCTT
Found at i:61234 original size:30 final size:30
Alignment explanation
Indices: 61200--61426 Score: 190
Period size: 30 Copynumber: 7.9 Consensus size: 30
61190 ACCACCAATT
* *
61200 AAGCCACCCACAACTCCAGCGCCTCCTTAC
1 AAGCCACCAACAACTCCAGCACCTCCTTAC
**
61230 AAGCCA-C--CAACT-C--CACC-AGTT--
1 AAGCCACCAACAACTCCAGCACCTCCTTAC
*
61251 AAGCCACCAACAACTCCAGCACCGCCTTAC
1 AAGCCACCAACAACTCCAGCACCTCCTTAC
* * * * *
61281 AAGCCACCAACCACCCCAGCTCCTCCAGT-G
1 AAGCCACCAACAACTCCAGCACCTCC-TTAC
*
61311 AAGCCACCAACAACTCCAGCACCGCCTTAC
1 AAGCCACCAACAACTCCAGCACCTCCTTAC
* *
61341 AAGCCACCAACAACCCCAGCTCCTCCAGTT--
1 AAGCCACCAACAACTCCAGCACCTCC--TTAC
* *
61371 AAGCCACCCACAACTCCAGCACCGCCTTAC
1 AAGCCACCAACAACTCCAGCACCTCCTTAC
* *
61401 AAACCACCAACAACTCCAGCTCCTCC
1 AAGCCACCAACAACTCCAGCACCTCC
61427 AGTCAAGCCA
Statistics
Matches: 154, Mismatches: 28, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
21 6 0.04
22 1 0.01
23 2 0.01
24 8 0.05
25 1 0.01
26 1 0.01
27 9 0.06
28 4 0.03
29 2 0.01
30 117 0.76
31 1 0.01
32 2 0.01
ACGTcount: A:0.31, C:0.48, G:0.10, T:0.11
Consensus pattern (30 bp):
AAGCCACCAACAACTCCAGCACCTCCTTAC
Found at i:61240 original size:60 final size:60
Alignment explanation
Indices: 61167--61438 Score: 337
Period size: 60 Copynumber: 4.7 Consensus size: 60
61157 TACTCCCCCA
* * * * * * * * *
61167 TACAAACCCCCAACAACGCCAGCACCACCAATTAAGCCACCCACAACTCCAGCGCCTCCT
1 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCAACAACTCCAGCACCGCCT
*
61227 TACAAGCCA-C--C-A----A-CTCCACCAGTTAAGCCACCAACAACTCCAGCACCGCCT
1 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCAACAACTCCAGCACCGCCT
* *
61278 TACAAGCCACCAACCACCCCAGCTCCTCCAGTGAAGCCACCAACAACTCCAGCACCGCCT
1 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCAACAACTCCAGCACCGCCT
*
61338 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCCACAACTCCAGCACCGCCT
1 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCAACAACTCCAGCACCGCCT
* * *
61398 TACAAACCACCAACAACTCCAGCTCCTCCAGTCAAGCCACC
1 TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACC
61439 TTACAAGGCA
Statistics
Matches: 188, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
51 42 0.22
52 2 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 1 0.01
59 2 0.01
60 138 0.73
ACGTcount: A:0.32, C:0.47, G:0.10, T:0.11
Consensus pattern (60 bp):
TACAAGCCACCAACAACCCCAGCTCCTCCAGTTAAGCCACCAACAACTCCAGCACCGCCT
Found at i:61269 original size:21 final size:21
Alignment explanation
Indices: 61230--61269 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
61220 GCCTCCTTAC
**
61230 AAGCCACCAACTCCACCAGTT
1 AAGCCACCAACAACACCAGTT
*
61251 AAGCCACCAACAACTCCAG
1 AAGCCACCAACAACACCAG
61270 CACCGCCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.42, G:0.10, T:0.10
Consensus pattern (21 bp):
AAGCCACCAACAACACCAGTT
Found at i:63600 original size:16 final size:17
Alignment explanation
Indices: 63575--63612 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
63565 CTAATTTGGA
63575 TTGCTTAGAGT-TT-AT
1 TTGCTTAGAGTCTTAAT
63590 TTGCATTAGAGTCTTAAT
1 TTGC-TTAGAGTCTTAAT
63608 TTGCT
1 TTGCT
63613 AATAGAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 3 0.15
18 6 0.30
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGCTTAGAGTCTTAAT
Found at i:66752 original size:35 final size:35
Alignment explanation
Indices: 66706--66775 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
66696 TGCACTTACC
66706 CTAGCTTCCTTGTATTGACCGACCATTTGTCATTT
1 CTAGCTTCCTTGTATTGACCGACCATTTGTCATTT
*
66741 CTAGCTTCCTTGTATTGACCGACCTTTTGTCATTT
1 CTAGCTTCCTTGTATTGACCGACCATTTGTCATTT
66776 TTATGCCTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.16, C:0.26, G:0.14, T:0.44
Consensus pattern (35 bp):
CTAGCTTCCTTGTATTGACCGACCATTTGTCATTT
Found at i:73540 original size:39 final size:39
Alignment explanation
Indices: 73487--73604 Score: 227
Period size: 39 Copynumber: 3.0 Consensus size: 39
73477 TTGCATTTTG
73487 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
1 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
73526 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
1 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
*
73565 TTATTATGTTGATTAAATTTTCTGCAATCTAATTTCTGA
1 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
73604 T
1 T
73605 CAACGTCTTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (39 bp):
TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
Found at i:75839 original size:78 final size:74
Alignment explanation
Indices: 75589--75846 Score: 351
Period size: 74 Copynumber: 3.4 Consensus size: 74
75579 GACAAAAGCC
*
75589 AAATCCAAAGGCGCCGGCGGTAAAAGCTT-AGAAATTTCTTCATTATCTTTTCATTCAGATCTAG
1 AAATCCAAAGGCGCCGGCGG-AAAAGCTTAAGAATTTTCTTCATTATCTTTTCATTCAGATCTAG
75653 GGTTCCATCA
65 GGTTCCATCA
* *
75663 AAATCCAAAGGTGCCGACGGAAAAGCTTAAGAATTTTCTTCATTATCTTTTCATTCAGAAT-TAG
1 AAATCCAAAGGCGCCGGCGGAAAAGCTTAAGAATTTTCTTCATTATCTTTTCATTCAG-ATCTAG
*
75727 AGTTCCATCA
65 GGTTCCATCA
*
75737 AAATCCAAAGGCGCCGGCGGAAAAGCTTAAGAATTTTCATCATTATCTAGCTTTTCATTCAGATC
1 AAATCCAAAGGCGCCGGCGGAAAAGCTTAAGAATTTTCTTCATTA--T--CTTTTCATTCAGATC
75802 TAGGGTTCCATCA
62 TAGGGTTCCATCA
*** *
75815 AAAT-CTTTGGCGGCGGCGGCAAAAGCTTAAGA
1 AAATCCAAAGGCGCCGGCGG-AAAAGCTTAAGA
75847 TTTAGGGCAC
Statistics
Matches: 164, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
73 8 0.05
74 100 0.61
75 2 0.01
76 1 0.01
77 13 0.08
78 40 0.24
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (74 bp):
AAATCCAAAGGCGCCGGCGGAAAAGCTTAAGAATTTTCTTCATTATCTTTTCATTCAGATCTAGG
GTTCCATCA
Found at i:81917 original size:39 final size:39
Alignment explanation
Indices: 81873--81951 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
81863 TTGCATTTTG
81873 TTATTATGTTGATTAAACTTTCTGAAAACTAATTTCTGA
1 TTATTATGTTGATTAAACTTTCTGAAAACTAATTTCTGA
* *
81912 TTATTATGTTGATTAAATTTTCTGAAATCTAATTTCTGA
1 TTATTATGTTGATTAAACTTTCTGAAAACTAATTTCTGA
81951 T
1 T
81952 CAACATCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (39 bp):
TTATTATGTTGATTAAACTTTCTGAAAACTAATTTCTGA
Found at i:83859 original size:32 final size:32
Alignment explanation
Indices: 83812--83872 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
83802 TGTAGAACTT
* * *
83812 TTGAATCGACTATTATATCCTTATTTTTCTAA
1 TTGAATCAACCATTATACCCTTATTTTTCTAA
83844 TTGAATCAACCATTATACCCTTATTTTTC
1 TTGAATCAACCATTATACCCTTATTTTTC
83873 AAACATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (32 bp):
TTGAATCAACCATTATACCCTTATTTTTCTAA
Found at i:88498 original size:31 final size:31
Alignment explanation
Indices: 88463--88521 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
88453 AAAATTACTA
*
88463 ATTGACCCTATTAAAATGAAAGATTTATTGT
1 ATTGACCCCATTAAAATGAAAGATTTATTGT
*
88494 ATTGACCCCATTAAAATGAAAGTTTTAT
1 ATTGACCCCATTAAAATGAAAGATTTAT
88522 AATATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTGACCCCATTAAAATGAAAGATTTATTGT
Found at i:88528 original size:31 final size:31
Alignment explanation
Indices: 88463--88529 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
88453 AAAATTACTA
* **
88463 ATTGACCCTATTAAAATGAAAGATTTATTGT
1 ATTGACCCCATTAAAATGAAAGATTTATAAT
*
88494 ATTGACCCCATTAAAATGAAAGTTTTATAAT
1 ATTGACCCCATTAAAATGAAAGATTTATAAT
88525 ATTGA
1 ATTGA
88530 TCTTAGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTGACCCCATTAAAATGAAAGATTTATAAT
Found at i:89277 original size:2 final size:2
Alignment explanation
Indices: 89270--89320 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
89260 AGAGGGGGTA
* *
89270 AT AT AT AT AT AT AT AT AT AT AT AT -T CAT A- AC AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
89311 AT AT AT AT AT
1 AT AT AT AT AT
89321 TCATAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:89314 original size:27 final size:27
Alignment explanation
Indices: 89276--89331 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
89266 GGTAATATAT
89276 ATATATATATATATATATTCATAACAA
1 ATATATATATATATATATTCATAACAA
89303 ATATATATATATATATATTCATAACAA
1 ATATATATATATATATATTCATAACAA
89330 AT
1 AT
89332 TTCTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATATATATATATATATTCATAACAA
Found at i:89488 original size:31 final size:29
Alignment explanation
Indices: 89420--89494 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 29
89410 CCAACTTGCT
* *
89420 CAATTTGAGGCTAAACCTTTAAACTGAAC
1 CAATTTGAGCCTAAACCTTTAAAATGAAC
* *
89449 CAAATTGAGCCTAAACCTTATCAAAATGCAC
1 CAATTTGAGCCTAAACCTT-T-AAAATGAAC
89480 CAATTTGAGCCTAAA
1 CAATTTGAGCCTAAA
89495 TTTCACGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 17 0.44
30 1 0.03
31 21 0.54
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (29 bp):
CAATTTGAGCCTAAACCTTTAAAATGAAC
Found at i:89663 original size:31 final size:31
Alignment explanation
Indices: 89592--89668 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
89582 ATCAAATTAC
* ** *
89592 CAATTTGAGCCTAAACCTTTCAAAAGTTGTT
1 CAATTTGAGTCTAAACAATTCAAAAATTGTT
89623 CAATTTGAGTCTAAACAATTCAAAAATTGTT
1 CAATTTGAGTCTAAACAATTCAAAAATTGTT
* *
89654 GAATTTGAGTGTAAA
1 CAATTTGAGTCTAAA
89669 AACAGAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (31 bp):
CAATTTGAGTCTAAACAATTCAAAAATTGTT
Found at i:93443 original size:21 final size:21
Alignment explanation
Indices: 93407--93448 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
93397 CGGATAAAAC
*
93407 TTTTAAAATATCAAATCAAATT
1 TTTTAAAAAATCAAAT-AAATT
93429 TTTTAAAAAAT-AAATAAATT
1 TTTTAAAAAATCAAATAAATT
93449 ATGGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAATCAAATAAATT
Found at i:100576 original size:33 final size:33
Alignment explanation
Indices: 100537--100601 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
100527 GCTGCCGGAG
100537 GCAAGTATAAAACACAGAGGATTCCTTGGAGGA
1 GCAAGTATAAAACACAGAGGATTCCTTGGAGGA
100570 GCAAGTATAAAACACAGAGGATTCCTTGGAGG
1 GCAAGTATAAAACACAGAGGATTCCTTGGAGG
100602 TTTCAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (33 bp):
GCAAGTATAAAACACAGAGGATTCCTTGGAGGA
Found at i:107610 original size:24 final size:24
Alignment explanation
Indices: 107583--107629 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
107573 ATGTACGATT
107583 AAGTTGAT-TTAAGTGTCTATTATC
1 AAGTTG-TCTTAAGTGTCTATTATC
*
107607 AAGTTGTCCTTAATTGTCTATTA
1 AAGTTGT-CTTAAGTGTCTATTA
107630 ATTTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 6 0.30
25 13 0.65
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (24 bp):
AAGTTGTCTTAAGTGTCTATTATC
Found at i:107860 original size:22 final size:23
Alignment explanation
Indices: 107816--107876 Score: 97
Period size: 22 Copynumber: 2.6 Consensus size: 23
107806 GGACCAAATT
107816 TGGTTGGATCCTTTCATAAAAAAAA
1 TGGTTGGATCC-TT-ATAAAAAAAA
107841 TGGTTGGATCCTT-TAAAAAAAA
1 TGGTTGGATCCTTATAAAAAAAA
107863 TGGTTGGATCCTTA
1 TGGTTGGATCCTTA
107877 CTTAAATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 22 0.63
24 2 0.06
25 11 0.31
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (23 bp):
TGGTTGGATCCTTATAAAAAAAA
Found at i:110315 original size:30 final size:31
Alignment explanation
Indices: 110279--110349 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
110269 ATTGAATTGT
110279 TCAAATCCT-TTGGTTTGAACCTAAGCCTAA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTAA
*
110309 TCAAAT-CTGTTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTAA
110339 TCAAAT-CTGTT
1 TCAAATCCTGTT
110350 ACTAGTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (31 bp):
TCAAATCCTGTTGGTTTGAACCTAAGCCTAA
Found at i:116850 original size:17 final size:17
Alignment explanation
Indices: 116823--116877 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
116813 AATCCATGTA
* *
116823 ATCTTTGATCACCAGTG
1 ATCTTAGATCACTAGTG
*
116840 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
116857 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTAGTG
116874 ATCT
1 ATCT
116878 GGGGGTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:120158 original size:16 final size:16
Alignment explanation
Indices: 120134--120164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
120124 AATCCGAATC
*
120134 GAAATGACCTGAACCT
1 GAAACGACCTGAACCT
120150 GAAACGACCTGAACC
1 GAAACGACCTGAACC
120165 AAAATTACCC
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:0.39, C:0.29, G:0.19, T:0.13
Consensus pattern (16 bp):
GAAACGACCTGAACCT
Found at i:132634 original size:18 final size:18
Alignment explanation
Indices: 132611--132648 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
132601 TTTATAACCC
*
132611 TACATATTTAACTAGGAA
1 TACATATTTAACCAGGAA
132629 TACATATTTAACCAGGAA
1 TACATATTTAACCAGGAA
132647 TA
1 TA
132649 TATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (18 bp):
TACATATTTAACCAGGAA
Found at i:145304 original size:22 final size:22
Alignment explanation
Indices: 145276--145464 Score: 114
Period size: 22 Copynumber: 8.5 Consensus size: 22
145266 TAGATTATTG
*
145276 AAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGTGTGGTTATCA
*
145298 AAATTTCATAATGTGGTTA-CAA
1 AAATTTCATAGTGTGGTTATC-A
** *
145320 AAATTTCATAG-AAGGTAATCA
1 AAATTTCATAGTGTGGTTATCA
* * * *
145341 AAGTTTCAAATTGTGTTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
145363 AAATTTCATAGTGAGATTAACA
1 AAATTTCATAGTGTGGTTATCA
* ** *
145385 CTAAA-TTCTATAGGGAAGTTATTA
1 --AAATTTC-ATAGTGTGGTTATCA
* * * *
145409 ACATTCCATAGCGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
145431 AAATTTCATAGTTTGATTATCC
1 AAATTTCATAGTGTGGTTATCA
145453 AAATTTCATAGT
1 AAATTTCATAGT
145465 CTACCAAATC
Statistics
Matches: 124, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
21 14 0.11
22 92 0.74
23 5 0.04
24 13 0.10
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:145718 original size:22 final size:21
Alignment explanation
Indices: 145571--145718 Score: 93
Period size: 22 Copynumber: 6.8 Consensus size: 21
145561 ATACCGTCCC
* *
145571 TATCAAAATTTCAGAGTGTGGT
1 TATCAAAATTTCATAG-GAGGT
* *
145593 GACCAAAATTTCATAGGATGGT
1 TATCAAAATTTCATAGGA-GGT
**
145615 TATCGGAATTTCATAGTGTA-GT
1 TATCAAAATTTCATAG-G-AGGT
* * *
145637 TATTAAAGTTTCACATGGAGGT
1 TATCAAAATTTCATA-GGAGGT
* *
145659 TATCACAATTTCTTAAGGAGGT
1 TATCAAAATTTCAT-AGGAGGT
* *
145681 TATCAAAATAAT-ATAGCGAGAT
1 TATCAAAAT-TTCATAG-GAGGT
145703 TATCAAAATTTCATAG
1 TATCAAAATTTCATAG
145719 TAAAACTATG
Statistics
Matches: 94, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
21 5 0.05
22 84 0.89
23 4 0.04
24 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAGGT
Found at i:145966 original size:22 final size:22
Alignment explanation
Indices: 145941--145982 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
145931 TCAGAATTTT
145941 ATAGGGTAATTATCAAAATTCC
1 ATAGGGTAATTATCAAAATTCC
* **
145963 ATAGTGTGGTTATCAAAATT
1 ATAGGGTAATTATCAAAATT
145983 TAATTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATAGGGTAATTATCAAAATTCC
Done.