Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012199.1 Corchorus olitorius cultivar O-4 contig12232, 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: 66260
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2226 original size:2 final size:2
Alignment explanation
Indices: 2219--2244 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2209 CCATATGTCC
2219 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2245 TACTTGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3290 original size:2 final size:2
Alignment explanation
Indices: 3283--3321 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3273 GCATGCAACA
3283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3322 CACACAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7176 original size:26 final size:26
Alignment explanation
Indices: 7140--7189 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
7130 AATTTAATTA
7140 ACATGGTGTTATTAGTATACAAAGTC
1 ACATGGTGTTATTAGTATACAAAGTC
7166 ACATGGTGTTATTAGTATACAAAG
1 ACATGGTGTTATTAGTATACAAAG
7190 GCACCTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (26 bp):
ACATGGTGTTATTAGTATACAAAGTC
Found at i:8807 original size:17 final size:19
Alignment explanation
Indices: 8785--8819 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
8775 TACACTGCTA
8785 GTGTATTA-A-ATATGAAT
1 GTGTATTATATATATGAAT
8802 GTGTATTATATATATGAA
1 GTGTATTATATATATGAA
8820 AAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (19 bp):
GTGTATTATATATATGAAT
Found at i:12959 original size:13 final size:13
Alignment explanation
Indices: 12933--12968 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12923 AAAAGCTTGG
12933 TTTTGAAGAAGTGC
1 TTTTGAA-AAGTGC
12947 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
12960 TTTTTAAAA
1 TTTTGAAAA
12969 TTGGGGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:13726 original size:111 final size:106
Alignment explanation
Indices: 13498--13741 Score: 280
Period size: 109 Copynumber: 2.2 Consensus size: 106
13488 ATGTATTCAC
* * *
13498 AATTTCATAAAATTTAGATCCAAATTAATAAAAAAAAGTTTGACTTATAAGGTTAGTACTCAAAT
1 AATTTCATAAAGTTTAG-TCCAAATTAATAAAAAAAAGTTT-A-TTACAAGGTTAGTACTAAAAT
* * *
13563 TTAAGATTTATTATTATAGGGTTTTGGTTTGAATATTTGATCAT
63 TTAAGATTTATTATTATACGGTTTTAGTTTGAATATTTGACCAT
* * *
13607 AATTTCATAAAGTTTAGTCTCAAATTAATAAAAATAA-TATT-TTACAGGGTTGGTACTAAAATT
1 AATTTCATAAAGTTTAGTC-CAAATTAATAAAAAAAAGT-TTATTACAAGGTTAGTACTAAAATT
13670 TAAGATTTATTATTAATTATACCGGTTTTAGTTTGAATATTT-AGCCAT
64 TAAGA--T-TTATT-ATTATA-CGGTTTTAGTTTGAATATTTGA-CCAT
13718 AATTTCATAAAGTTTAG-CCAAATT
1 AATTTCATAAAGTTTAGTCCAAATT
13742 TAAAACTTAA
Statistics
Matches: 118, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
106 23 0.19
108 4 0.03
109 45 0.38
110 8 0.07
111 38 0.32
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (106 bp):
AATTTCATAAAGTTTAGTCCAAATTAATAAAAAAAAGTTTATTACAAGGTTAGTACTAAAATTTA
AGATTTATTATTATACGGTTTTAGTTTGAATATTTGACCAT
Found at i:14020 original size:68 final size:69
Alignment explanation
Indices: 13908--14043 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 69
13898 AAAACAAAAA
* ***
13908 ACTAAGGAAAAAATGATGAGAACACCATTAATTACATTTTAATGCT-AAATTACATATAAAGACA
1 ACTAAAGAAAAAATGATGAGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACA
13972 ATGC
66 ATGC
* *
13976 ACTAAAGAAAAAATGGT-AGGAACACCATTAATTACATCCAAATGCTAAAATTACTTATAAAGAC
1 ACTAAAGAAAAAATGATGA-GAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGAC
14040 AATG
65 AATG
14044 TATTTCAGGC
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 1 0.02
68 39 0.65
69 20 0.33
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (69 bp):
ACTAAAGAAAAAATGATGAGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACA
ATGC
Found at i:14995 original size:75 final size:74
Alignment explanation
Indices: 14851--14997 Score: 172
Period size: 75 Copynumber: 2.0 Consensus size: 74
14841 GTAATTAACT
* * ** * *
14851 AAGCGAGAAAAGACGAAAAGGGAGCGAAAAGGTTGTCCCTTATCGAAAGTTGAAAGGAGCCTTTG
1 AAGCGAGAAAAGACCAAAAGGGAGCGAAAAGGTTATCCCACATCAAAAGTTGAAAGGAGCCTTTA
14916 GTAAATTCC
66 GTAAATTCC
* **
14925 AAGCGAGAAAAGACCAAAACGGG-GCGAAAAAGGTTATCCCACATTAAAAGTTGATGGGAG-CTA
1 AAGCGAGAAAAGACCAAAA-GGGAGCG-AAAAGGTTATCCCACATCAAAAGTTGAAAGGAGCCT-
14988 TTAGTAAATT
63 TTAGTAAATT
14998 TTAGAGGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
74 23 0.38
75 38 0.62
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (74 bp):
AAGCGAGAAAAGACCAAAAGGGAGCGAAAAGGTTATCCCACATCAAAAGTTGAAAGGAGCCTTTA
GTAAATTCC
Found at i:16038 original size:14 final size:14
Alignment explanation
Indices: 16015--16059 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
16005 ATATGCGAAT
*
16015 TATTTGTTTCGATG
1 TATTTATTTCGATG
16029 TATTTATTTCGATG
1 TATTTATTTCGATG
*
16043 TA-TGAGTTTCGATG
1 TATTTA-TTTCGATG
16057 TAT
1 TAT
16060 GAGTTTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 25 0.93
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (14 bp):
TATTTATTTCGATG
Found at i:16060 original size:14 final size:14
Alignment explanation
Indices: 16020--16066 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
16010 CGAATTATTT
*
16020 GTTTCGATGTATTTA
1 GTTTCGATGTA-TGA
16035 -TTTCGATGTATGA
1 GTTTCGATGTATGA
16048 GTTTCGATGTATGA
1 GTTTCGATGTATGA
16062 GTTTC
1 GTTTC
16067 TCCTAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 28 0.93
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (14 bp):
GTTTCGATGTATGA
Found at i:16357 original size:2 final size:2
Alignment explanation
Indices: 16350--16383 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16340 TTAAATTAGT
16350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16384 AAAAGAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17940 original size:2 final size:2
Alignment explanation
Indices: 17929--17964 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
17919 TCTTTTACAC
17929 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17965 TAACCGGCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18270 original size:22 final size:18
Alignment explanation
Indices: 18227--18261 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18217 TCAACCATCA
18227 TTGAGTAAGTGATTATCT
1 TTGAGTAAGTGATTATCT
18245 TTGAGTAAGTGATTATC
1 TTGAGTAAGTGATTATC
18262 CTTTCTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (18 bp):
TTGAGTAAGTGATTATCT
Found at i:22521 original size:25 final size:27
Alignment explanation
Indices: 22493--22543 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
22483 TGAAAAATGT
22493 GCAAACTCCAAA-CAAC-AAAAGATAA
1 GCAAACTCCAAATCAACTAAAAGATAA
*
22518 GCAACCTCCAAATCAACTAAAAGATA
1 GCAAACTCCAAATCAACTAAAAGATA
22544 CTCCTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 4 0.17
27 8 0.35
ACGTcount: A:0.55, C:0.25, G:0.08, T:0.12
Consensus pattern (27 bp):
GCAAACTCCAAATCAACTAAAAGATAA
Found at i:24335 original size:15 final size:15
Alignment explanation
Indices: 24315--24344 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24305 CAATAGCTCC
24315 TTTTTTTTCTTTTTG
1 TTTTTTTTCTTTTTG
*
24330 TTTTTTTTTTTTTTG
1 TTTTTTTTCTTTTTG
24345 AAAAGTAGAT
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:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCTTTTTG
Found at i:24890 original size:24 final size:24
Alignment explanation
Indices: 24862--24910 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
24852 TTGGCACGAG
* *
24862 TGAGGAGACATCGGCGTTGGTTGT
1 TGAGGAGACATCGACGTTGGCTGT
24886 TGAGGAGACATCGACGTTGGCTGT
1 TGAGGAGACATCGACGTTGGCTGT
24910 T
1 T
24911 TCTTCACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.29
Consensus pattern (24 bp):
TGAGGAGACATCGACGTTGGCTGT
Found at i:37825 original size:21 final size:21
Alignment explanation
Indices: 37799--37858 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
37789 CCAAACTCAC
37799 CTTCTTCATCTTCATTTTCTTCTT
1 CTTCTTCATCTTCA---TCTTCTT
*
37823 CTTGTTCATCTTCATCTTCTT
1 CTTCTTCATCTTCATCTTCTT
* **
37844 CATGATCATCTTCAT
1 CTTCTTCATCTTCAT
37859 AATAAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.61
24 13 0.39
ACGTcount: A:0.13, C:0.28, G:0.03, T:0.55
Consensus pattern (21 bp):
CTTCTTCATCTTCATCTTCTT
Found at i:39060 original size:11 final size:12
Alignment explanation
Indices: 39043--39071 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
39033 CAGGGAAAGA
39043 AAGAAACAGGGG
1 AAGAAACAGGGG
39055 -AGAAACAGGGG
1 AAGAAACAGGGG
39066 AAGAAA
1 AAGAAA
39072 GAAACAGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.55, C:0.07, G:0.38, T:0.00
Consensus pattern (12 bp):
AAGAAACAGGGG
Found at i:39060 original size:27 final size:27
Alignment explanation
Indices: 39030--39082 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39020 CAAAACTCAA
39030 AAACAGGGAAAGAAAGAAACAGGGGAG
1 AAACAGGGAAAGAAAGAAACAGGGGAG
*
39057 AAACAGGGGAAGAAAGAAACAGGGGA
1 AAACAGGGAAAGAAAGAAACAGGGGA
39083 AAAGGAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.38, T:0.00
Consensus pattern (27 bp):
AAACAGGGAAAGAAAGAAACAGGGGAG
Found at i:39081 original size:16 final size:16
Alignment explanation
Indices: 39030--39083 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
39020 CAAAACTCAA
*
39030 AAACAGGGAAAGAAAG
1 AAACAGGGGAAGAAAG
39046 AAACA-GGG--G--AG
1 AAACAGGGGAAGAAAG
39057 AAACAGGGGAAGAAAG
1 AAACAGGGGAAGAAAG
39073 AAACAGGGGAA
1 AAACAGGGGAA
39084 AAGGAAAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 1 0.03
14 1 0.03
15 2 0.06
16 18 0.56
ACGTcount: A:0.56, C:0.07, G:0.37, T:0.00
Consensus pattern (16 bp):
AAACAGGGGAAGAAAG
Found at i:39562 original size:10 final size:10
Alignment explanation
Indices: 39547--39585 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
39537 CAAGGTAGAA
39547 GAAGAAAAGT
1 GAAGAAAAGT
*
39557 GAAGAAAGAGAA
1 GAAGAAA-AG-T
39569 GAAGAAAAGT
1 GAAGAAAAGT
39579 GAAGAAA
1 GAAGAAA
39586 GAGAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.56
11 4 0.16
12 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (10 bp):
GAAGAAAAGT
Found at i:39593 original size:25 final size:22
Alignment explanation
Indices: 39543--39598 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
39533 ACAACAAGGT
39543 AGAAGAAGAAAAGTGAAGAAAG
1 AGAAGAAGAAAAGTGAAGAAAG
39565 AGAAGAAGAAAAGTGAAGAAAG
1 AGAAGAAGAAAAGTGAAGAAAG
39587 AGAAGAAGAAAA
1 AGAAGAAGAAAA
39599 AATGGGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (22 bp):
AGAAGAAGAAAAGTGAAGAAAG
Found at i:42172 original size:39 final size:39
Alignment explanation
Indices: 42128--42204 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
42118 ACGTTGATGT
42128 TAAGTACTAATAATTCTTCATGTTAAAATATATTTCATG
1 TAAGTACTAATAATTCTTCATGTTAAAATATATTTCATG
* *
42167 TAAGTACTAATAATTGTTCATGTTAAAGTATATTTCAT
1 TAAGTACTAATAATTCTTCATGTTAAAATATATTTCAT
42205 TCATATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (39 bp):
TAAGTACTAATAATTCTTCATGTTAAAATATATTTCATG
Found at i:43702 original size:99 final size:99
Alignment explanation
Indices: 43508--43705 Score: 362
Period size: 99 Copynumber: 2.0 Consensus size: 99
43498 TGAATCTCCA
*
43508 AACCAATCTCCCAATTCTATTTCAATTAATTTGGAAAATGGCTTTTTAGTGATTAGAATTCAAAT
1 AACCAATCTCCCAATTCTATTTCAATTAATTTGGAAAATGGCTTCTTAGTGATTAGAATTCAAAT
*
43573 TGAAGAATTGTTTTAAACCTCAAAATTTTGAAAG
66 TGAAGAATTGTTTTAAACCTCAAAAATTTGAAAG
43607 AACCAATCTCCCAATTCTATTTCAATTAATTTGGAAAATGGCTTCTTAGTGATTAGAATTCAAAT
1 AACCAATCTCCCAATTCTATTTCAATTAATTTGGAAAATGGCTTCTTAGTGATTAGAATTCAAAT
43672 TGAAG-ATTGTTTTAAACCTCACAAAATTTGAAAG
66 TGAAGAATTGTTTTAAACCTCA-AAAATTTGAAAG
43706 CAAGAATGAC
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 16 0.17
99 80 0.83
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (99 bp):
AACCAATCTCCCAATTCTATTTCAATTAATTTGGAAAATGGCTTCTTAGTGATTAGAATTCAAAT
TGAAGAATTGTTTTAAACCTCAAAAATTTGAAAG
Found at i:45425 original size:22 final size:22
Alignment explanation
Indices: 45395--45479 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
45385 TCCAACTTAG
*
45395 AAATATTGATAACCACACCGTGA
1 AAAT-TTGATAACCACACCATGA
* **
45418 AAATTTGATAACCTCATTATG-
1 AAATTTGATAACCACACCATGA
*
45439 AAATTTCGATAACCTC-CCTATGA
1 AAATTT-GATAACCACACC-ATGA
45462 AAATTTGATAACCACACC
1 AAATTTGATAACCACACC
45480 GTGAGGTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 33 0.65
23 12 0.24
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (22 bp):
AAATTTGATAACCACACCATGA
Found at i:45482 original size:66 final size:67
Alignment explanation
Indices: 45395--45545 Score: 187
Period size: 67 Copynumber: 2.3 Consensus size: 67
45385 TCCAACTTAG
45395 AAATATTGATAACCACACCGTGAAAATTTGATAACCTCA-TTATGAAATTTCGATAACCTCCCTA
1 AAAT-TTGATAACCACACCGTGAAAATTTGATAACCTCAGTTATGAAATTTCGATAACCTCCCTA
45459 TGA
65 TGA
*** * * * * * *
45462 AAATTTGATAACCACACCGTGAGGTTTTGATAACCTTAGTTGTGAAATTTTGATACCCTTCTTAT
1 AAATTTGATAACCACACCGTGAAAATTTGATAACCTCAGTTATGAAATTTCGATAACCTCCCTAT
45527 GA
66 GA
* *
45529 AATTTTGATAATCACAC
1 AAATTTGATAACCACAC
45546 TATAATGCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 30 0.42
67 42 0.58
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (67 bp):
AAATTTGATAACCACACCGTGAAAATTTGATAACCTCAGTTATGAAATTTCGATAACCTCCCTAT
GA
Found at i:45532 original size:22 final size:23
Alignment explanation
Indices: 45415--45539 Score: 87
Period size: 22 Copynumber: 5.6 Consensus size: 23
45405 AACCACACCG
* *
45415 TGAAAATTTGATAACCTCA-TTA
1 TGAAATTTTGATAACCTTACTTA
* * *
45437 TGAAATTTCGATAACC-TCCCTA
1 TGAAATTTTGATAACCTTACTTA
* ** **
45459 TGAAAATTTGATAACCACAC-CG
1 TGAAATTTTGATAACCTTACTTA
** * *
45481 TGAGGTTTTGATAACCTTAGTTG
1 TGAAATTTTGATAACCTTACTTA
*
45504 TGAAATTTTGATACCCTT-CTTA
1 TGAAATTTTGATAACCTTACTTA
45526 TGAAATTTTGATAA
1 TGAAATTTTGATAA
45540 TCACACTATA
Statistics
Matches: 76, Mismatches: 24, Indels: 6
0.72 0.23 0.06
Matches are distributed among these distances:
22 59 0.78
23 17 0.22
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (23 bp):
TGAAATTTTGATAACCTTACTTA
Found at i:47472 original size:45 final size:45
Alignment explanation
Indices: 47408--47496 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
47398 AACAAAAATT
**
47408 AATATTAGCTTTATTTTGATGAATTTTCTAGAGATGGAAG-AGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT-GAAGTAGTAG
47453 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTA
47497 TTTAGGTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAGTAG
Found at i:47905 original size:70 final size:74
Alignment explanation
Indices: 47785--47922 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 74
47775 TTGCATACTC
*
47785 AGTCAAATTTTAAGAAAATACAAGCATAATCGATTGTAAAGGAAAAAGTTATAGGT-GAAAAGAA
1 AGTCAAATTTTAAGAAAATACAAG-ATAATCGATTGTAAAGGAAAAAGTTATAGGTAGAAAACAA
47849 AAACGTGCTA
65 AAACGTGCTA
* * *
47859 AGTCAAATTTTAAGAAAATTCAAG-T-AT-GATTGTAAAGGGAAAAGTTATTGGTAGAAAACAAA
1 AGTCAAATTTTAAGAAAATACAAGATAATCGATTGTAAAGGAAAAAGTTATAGGTAGAAAACAAA
47921 AA
66 AA
47923 GGGAAAAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
70 23 0.39
71 12 0.20
72 1 0.02
74 23 0.39
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (74 bp):
AGTCAAATTTTAAGAAAATACAAGATAATCGATTGTAAAGGAAAAAGTTATAGGTAGAAAACAAA
AACGTGCTA
Found at i:49236 original size:26 final size:26
Alignment explanation
Indices: 49207--49257 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
49197 ATTATTAAAA
49207 TATTTTATTTAGAAAAATTCAAATTT
1 TATTTTATTTAGAAAAATTCAAATTT
*
49233 TATTTTATTTATAAAAATTCAAATT
1 TATTTTATTTAGAAAAATTCAAATT
49258 CTAAAATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAAATTT
Found at i:52379 original size:57 final size:58
Alignment explanation
Indices: 52315--52426 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
52305 TAATAAAAAA
52315 GTTTAATGACTAAAAAAAATATTAA-TTAAAAA-TATT-TTATAATATAATACTAAGAAG
1 GTTTAATGACT--AAAAAATATTAAGTTAAAAATTATTATTATAATATAATACTAAGAAG
* *
52372 GTTTAATGACTAAAAAATATTAAGTTAAAAATTATTATTATACTATAATATTAAG
1 GTTTAATGACTAAAAAATATTAAGTTAAAAATTATTATTATAATATAATACTAAG
52427 GGTATTTTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
55 12 0.24
56 7 0.14
57 15 0.30
58 16 0.32
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (58 bp):
GTTTAATGACTAAAAAATATTAAGTTAAAAATTATTATTATAATATAATACTAAGAAG
Found at i:52558 original size:21 final size:19
Alignment explanation
Indices: 52532--52576 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
52522 ATGATCCTAA
*
52532 TTCATTTCTTGGCTTTTTTAT
1 TTCATTT-TTGG-TATTTTAT
*
52553 TTCATTTTTTGTATTTTAT
1 TTCATTTTTGGTATTTTAT
52572 TTCAT
1 TTCAT
52577 AGAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 3 0.14
21 7 0.32
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (19 bp):
TTCATTTTTGGTATTTTAT
Found at i:52983 original size:108 final size:109
Alignment explanation
Indices: 52849--53063 Score: 369
Period size: 108 Copynumber: 2.0 Consensus size: 109
52839 GTCATTTTGG
* *
52849 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTCTGGTATGTGTGTTTAT
1 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTCTGATATGTGTGCTTAT
52914 TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGA
66 TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGA
* * *
52958 TGCTTGTATTTTT-TTTAAATCCAATAGTTTATTGCATTTTGTATTGTTTGATATGTGTGCTTAT
1 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTCTGATATGTGTGCTTAT
*
53022 TTAATAGGTTCAATTGAATAAACTACACAATTAATAATAATA
66 TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
53064 TATATAATAG
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 87 0.87
109 13 0.13
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (109 bp):
TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTCTGATATGTGTGCTTAT
TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGA
Found at i:55649 original size:4 final size:4
Alignment explanation
Indices: 55640--55668 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55630 CGTCAAATAC
55640 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
55669 AAAATCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:57341 original size:13 final size:13
Alignment explanation
Indices: 57323--57352 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
57313 CGTGAGGCCA
57323 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
57336 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
57349 AAAA
1 AAAA
57353 TCAAAACTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:58789 original size:19 final size:19
Alignment explanation
Indices: 58765--58802 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58755 GCCGACAGGC
* *
58765 GTCGGTTGCTTCGGTGGCG
1 GTCGGTAGCGTCGGTGGCG
58784 GTCGGTAGCGTCGGTGGCG
1 GTCGGTAGCGTCGGTGGCG
58803 ATTTACAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.21, G:0.50, T:0.26
Consensus pattern (19 bp):
GTCGGTAGCGTCGGTGGCG
Found at i:59665 original size:20 final size:21
Alignment explanation
Indices: 59640--59678 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59630 CTACCGCACA
59640 CTCCA-TTCCCCACTTTTGCT
1 CTCCATTTCCCCACTTTTGCT
*
59660 CTCCATTTCTCCACTTTTG
1 CTCCATTTCCCCACTTTTG
59679 TTTTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.41, G:0.05, T:0.44
Consensus pattern (21 bp):
CTCCATTTCCCCACTTTTGCT
Done.