Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006183.1 Corchorus capsularis cultivar CVL-1 contig06201, 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: 45069
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:800 original size:16 final size:16
Alignment explanation
Indices: 775--805 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
765 AATTACAGTT
775 TTTTAGAAATGTAATA
1 TTTTAGAAATGTAATA
*
791 TTTTATAAATGTAAT
1 TTTTAGAAATGTAAT
806 TTAGTTATCA
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:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTTAGAAATGTAATA
Found at i:2142 original size:22 final size:22
Alignment explanation
Indices: 2117--2434 Score: 119
Period size: 22 Copynumber: 14.5 Consensus size: 22
2107 AGTTTAATTT
2117 TCAAAATTTCATAGGAGGGTTA
1 TCAAAATTTCATAGGAGGGTTA
*
2139 TCAAAATTTC--AGTG-TGG-T-
1 TCAAAATTTCATAG-GAGGGTTA
* *** *
2157 TCAACATTTCATA-GTTTGTAGA
1 TCAAAATTTCATAGGAGGGT-TA
2179 TCAAAATTTCATAGTGA-GGTTA
1 TCAAAATTTCATAG-GAGGGTTA
* *** *
2201 TAAAAAAACCATAGG-GAGCTTA
1 TCAAAATTTCATAGGAG-GGTTA
* *
2223 TCAAATTTTTACA-AGGA-GGTAA
1 TCAAA-ATTT-CATAGGAGGGTTA
2245 TCAAAATTT-ATAGTGA-GGTAATA
1 TCAAAATTTCATAG-GAGGGT--TA
* **
2268 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAGG-AGGGTTA
*
2291 TCAAAATTTCATAGTGA-GGTTT
1 TCAAAATTTCATAG-GAGGGTTA
* * *
2313 TTAAAATTTCATGGGAAGGTTA
1 TCAAAATTTCATAGGAGGGTTA
* * * *
2335 ACAAAATTCCATAGAAAGGTTA
1 TCAAAATTTCATAGGAGGGTTA
* * *
2357 TCGAAATTCCATAGTG-TGGTTA
1 TCAAAATTTCATAG-GAGGGTTA
*
2379 TCAAAATTTCATAGG-GAGATTA
1 TCAAAATTTCATAGGAG-GGTTA
* *
2401 TCACAGTTTCATAGG-GTGGTTA
1 TCAAAATTTCATAGGAG-GGTTA
*
2423 TCACAATTTCAT
1 TCAAAATTTCAT
2435 TGTGTGGTTA
Statistics
Matches: 222, Mismatches: 49, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
18 10 0.05
19 4 0.02
20 7 0.03
21 13 0.06
22 146 0.66
23 32 0.14
24 9 0.04
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAGGAGGGTTA
Found at i:2270 original size:23 final size:24
Alignment explanation
Indices: 2244--2310 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
2234 CAAGGAGGTA
2244 ATCAAAATTTATAGTGAGGTA-AT
1 ATCAAAATTTATAGTGAGGTATAT
* *
2267 ATCAAAATTTTATAG-GAAG-ATTT
1 ATCAAAA-TTTATAGTGAGGTATAT
2290 ATCAAAATTTCATAGTGAGGT
1 ATCAAAATTT-ATAGTGAGGT
2311 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.11
23 22 0.61
24 10 0.28
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (24 bp):
ATCAAAATTTATAGTGAGGTATAT
Found at i:2441 original size:22 final size:22
Alignment explanation
Indices: 2352--2444 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 22
2342 TCCATAGAAA
* *
2352 GGTTATCGA-AATTCCATAGTGT
1 GGTTATC-ACAATTTCATAGGGT
* *
2374 GGTTATCAAAATTTCATAGGGA
1 GGTTATCACAATTTCATAGGGT
* *
2396 GATTATCACAGTTTCATAGGGT
1 GGTTATCACAATTTCATAGGGT
* *
2418 GGTTATCACAATTTCATTGTGT
1 GGTTATCACAATTTCATAGGGT
2440 GGTTA
1 GGTTA
2445 AAGCTTGGGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 1 0.02
22 58 0.98
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (22 bp):
GGTTATCACAATTTCATAGGGT
Found at i:4072 original size:5 final size:5
Alignment explanation
Indices: 4053--4103 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
4043 TTAAAACTAG
*
4053 TATATA TATAA TATAT TATAA TATAA TATAA TATAAA TATGAA T-TAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TAT-AA TAT-AA TATAA
4100 TATA
1 TATA
4104 TACCGTAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
4 3 0.08
5 25 0.62
6 12 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:4078 original size:15 final size:15
Alignment explanation
Indices: 4053--4103 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
4043 TTAAAACTAG
*
4053 TATATATATAATATAT
1 TATA-ATATAATATAA
4069 TATAATATAATATAA
1 TATAATATAATATAA
4084 TATAAATATGAAT-TAA
1 TAT-AATAT-AATATAA
4100 TATA
1 TATA
4104 TACCGTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 14 0.44
16 15 0.47
17 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TATAATATAATATAA
Found at i:14244 original size:17 final size:17
Alignment explanation
Indices: 14222--14258 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14212 ATTTTTCAGT
14222 CTTTGATTGAATGATTG
1 CTTTGATTGAATGATTG
14239 CTTTGATTGAATGATTG
1 CTTTGATTGAATGATTG
14256 CTT
1 CTT
14259 AGCAGGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (17 bp):
CTTTGATTGAATGATTG
Found at i:14801 original size:38 final size:38
Alignment explanation
Indices: 14744--14825 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
14734 TCATATTCAG
* *
14744 GTCAACACGAGGATGGTCAAATATTTACGAATACAAAT
1 GTCAACACAACGATGGTCAAATATTTACGAATACAAAT
* *
14782 GTCAACACAACGATTGTCAAATATTTATGAATACAAAT
1 GTCAACACAACGATGGTCAAATATTTACGAATACAAAT
14820 GT-AACA
1 GTCAACA
14826 TTTTATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (38 bp):
GTCAACACAACGATGGTCAAATATTTACGAATACAAAT
Found at i:15005 original size:25 final size:27
Alignment explanation
Indices: 14977--15033 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
14967 TTTTTAAAAC
14977 ATAT-TTCTAAAT-TGCCATTATCAAA
1 ATATATTCTAAATATGCCATTATCAAA
* * * *
15002 ATATATTTTAATTATGTCATTATTAAA
1 ATATATTCTAAATATGCCATTATCAAA
15029 ATATA
1 ATATA
15034 ATTTTGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.23
27 16 0.62
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (27 bp):
ATATATTCTAAATATGCCATTATCAAA
Found at i:15593 original size:26 final size:26
Alignment explanation
Indices: 15557--15607 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
15547 TTATTAAAAT
15557 ATTTTAGTTAG-AAAATTTCAATTTCA
1 ATTTTAGTTAGAAAAATTT-AATTTCA
*
15583 ATTTTATTTAGAAAAATTTAATTTC
1 ATTTTAGTTAGAAAAATTTAATTTC
15608 TATTGTACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (26 bp):
ATTTTAGTTAGAAAAATTTAATTTCA
Found at i:15734 original size:22 final size:22
Alignment explanation
Indices: 15698--15972 Score: 232
Period size: 22 Copynumber: 12.4 Consensus size: 22
15688 TACTAACATG
* * *
15698 ATTTCAAAG-GAGGTTAGCAGA
1 ATTTCATAGCGAGGTTACCAAA
*
15719 ATTTCATTGCGAGGTTACCAAA
1 ATTTCATAGCGAGGTTACCAAA
** ** *
15741 ATTTCATAGAAATATTAGCAAA
1 ATTTCATAGCGAGGTTACCAAA
* ***
15763 ATTTCATAGCGATGTTACGGGA
1 ATTTCATAGCGAGGTTACCAAA
15785 ATTTCATATG-GAGGTTACCAAA
1 ATTTCATA-GCGAGGTTACCAAA
*
15807 ATTTCATAGGGAGGTTACCAAA
1 ATTTCATAGCGAGGTTACCAAA
*
15829 GTTTCATAG-GTAGGTTACCAAA
1 ATTTCATAGCG-AGGTTACCAAA
* *
15851 ATGTCATAGCGAGATTACCAAA
1 ATTTCATAGCGAGGTTACCAAA
**
15873 ATTTCATAGCGAGGTTACTGAA
1 ATTTCATAGCGAGGTTACCAAA
* **
15895 ATTCCATAGCGAGGTAATTACCGTA
1 ATTTCATAGCGAGG---TTACCAAA
** *
15920 ATTGGATAGGGAGGTTACCAAA
1 ATTTCATAGCGAGGTTACCAAA
* *
15942 ATTTCATAGAGAGATTACCAAA
1 ATTTCATAGCGAGGTTACCAAA
*
15964 ATTTTATAG
1 ATTTCATAG
15973 GTAAGTTATC
Statistics
Matches: 204, Mismatches: 42, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
21 9 0.04
22 176 0.86
23 2 0.01
25 17 0.08
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (22 bp):
ATTTCATAGCGAGGTTACCAAA
Found at i:15995 original size:91 final size:91
Alignment explanation
Indices: 15834--16000 Score: 221
Period size: 91 Copynumber: 1.8 Consensus size: 91
15824 CCAAAGTTTC
* * * *
15834 ATAGGTAGGTTACCAAAATGTCATAGCGAGATTACCAAAATTTCATAGCGAGGTTACTGAAATTC
1 ATAGGGAGGTTACCAAAATGTCATAGAGAGATTACCAAAATTTCATAGCGAAGTTACTCAAATTC
*
15899 CATAGCGAGGTAATTACCGTAATTGG
66 CATAGCAAGGTAATTACCGTAATTGG
* *
15925 ATAGGGAGGTTACCAAAATTTCATAGAGAGATTACCAAAATTTTATAG-GTAAGTTA-TCAAACT
1 ATAGGGAGGTTACCAAAATGTCATAGAGAGATTACCAAAATTTCATAGCG-AAGTTACTCAAA-T
**
15988 TTTATAGCAAGGT
64 TCCATAGCAAGGT
16001 TAAAAAAGGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 5 0.08
91 60 0.92
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (91 bp):
ATAGGGAGGTTACCAAAATGTCATAGAGAGATTACCAAAATTTCATAGCGAAGTTACTCAAATTC
CATAGCAAGGTAATTACCGTAATTGG
Found at i:19191 original size:22 final size:21
Alignment explanation
Indices: 19154--19684 Score: 304
Period size: 22 Copynumber: 24.4 Consensus size: 21
19144 TTCTCAATAG
*
19154 AATTTCATAGATAGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
*
19176 AATTTCGTAGCGAGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
19198 AATTTCATAGTGAGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
* * **
19220 AATTTCATAGGGAGCTTCCCGG
1 AATTTCATA-GGAGGTTACCAA
*
19242 AA-TTCGATGAGGAAGTTACCAA
1 AATTTC-AT-AGGAGGTTACCAA
* * * *
19264 AATTTTATAGGCAGTTTACTAG
1 AATTTCATAGG-AGGTTACCAA
* * *
19286 AATTTCCTTGGTAGGTGACCAA
1 AATTTCATAGG-AGGTTACCAA
** *
19308 AATTTTGTAGG-GAGTTATCC-G
1 AATTTCATAGGAG-GTTA-CCAA
* *
19329 AGTTTCATAGGGAGGTTACCAG
1 AATTTCATA-GGAGGTTACCAA
* *
19351 GA-TTCATAGGTAGGTTTCCAA
1 AATTTCATAGG-AGGTTACCAA
* *
19372 AATTTCATAGCGTGGTTAGCAA
1 AATTTCATAG-GAGGTTACCAA
19394 AATTTCATAGCGAGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
* * *
19416 AATTTCATTGCAAGGTTACC-G
1 AATTTCATAG-GAGGTTACCAA
* *
19437 GATTTCGATAGTGAGTTTACCAA
1 AATTTC-ATAG-GAGGTTACCAA
*
19460 AATTTCA-AGGGAGGTTAACAA
1 AATTTCATA-GGAGGTTACCAA
* * * **
19481 AATTTCTTTGGGGGTTACCGG
1 AATTTCATAGGAGGTTACCAA
*
19502 AATTTCATAAGGAGTTTACCAA
1 AATTTCAT-AGGAGGTTACCAA
19524 AATTTCATAGTGAGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
* * * *
19546 AATTTAATAGGGGGTTTACGAG
1 AATTTCATAGGAGG-TTACCAA
****
19568 AATTTCATAGGAGGTTATTGG
1 AATTTCATAGGAGGTTACCAA
*
19589 TATTTCATAGTGA-GTATACCAA
1 AATTTCATAG-GAGGT-TACCAA
* *
19611 AATTTTATAGTGAGG-TAGTCAA
1 AATTTCATAG-GAGGTTA-CCAA
* *
19633 AATTTAATAGTGAGGTTACTAA
1 AATTTCATAG-GAGGTTACCAA
* *
19655 AATTTCATAATGAGGTTATCAA
1 AATTTCAT-AGGAGGTTACCAA
*
19677 TATTTCAT
1 AATTTCAT
19685 TTTACTTGAA
Statistics
Matches: 388, Mismatches: 95, Indels: 52
0.73 0.18 0.10
Matches are distributed among these distances:
20 3 0.01
21 90 0.23
22 280 0.72
23 15 0.04
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (21 bp):
AATTTCATAGGAGGTTACCAA
Found at i:19559 original size:65 final size:63
Alignment explanation
Indices: 19154--19684 Score: 288
Period size: 65 Copynumber: 8.1 Consensus size: 63
19144 TTCTCAATAG
* ** *
19154 AATTTCATAGATAGGTTACCAAAATTTCGTAGCGAGGTTACCAAAATTTCATAGTGAGGTTACCA
1 AATTTCATAG-GAGGTTACCGGAATTTCATAG-GA-GTTACCAAAATTTCATAGTGAGGTTACCA
19219 A
63 A
* * * *
19220 AATTTCATAGGGAGCTTCCCGGAA-TTCGATGAGGAAGTTACCAAAATTTTATAG-GCAGTTTAC
1 AATTTCATA-GGAGGTTACCGGAATTTC-AT-AGG-AGTTACCAAAATTTCATAGTG-AGGTTAC
* *
19283 TAG
61 CAA
* * * ** ** * * *
19286 AATTTCCTTGGTAGGTGACCAAAATTTTGTAGGGAGTTATCC-GAGTTTCATAGGGAGGTTACCA
1 AATTTCATAGG-AGGTTACCGGAATTTCATA-GGAGTTA-CCAAAATTTCATAGTGAGGTTACCA
*
19350 G
63 A
* * ** * * *
19351 GA-TTCATAGGTAGGTTTCCAAAATTTCATAGCGTGGTTAGCAAAATTTCATAGCGAGGTTACCA
1 AATTTCATAGG-AGGTTACCGGAATTTCATAG-G-AGTTACCAAAATTTCATAGTGAGGTTACCA
19415 A
63 A
* * * *
19416 AATTTCATTGCAAGGTTACCGG-ATTTCGATAGTGAGTTTACCAAAATTTCA-AGGGAGGTTAAC
1 AATTTCATAG-GAGGTTACCGGAATTTC-ATAG-GAG-TTACCAAAATTTCATAGTGAGGTTACC
19479 AA
62 AA
* * *
19481 AATTTCTTTGGGGGTTACCGGAATTTCATAAGGAGTTTACCAAAATTTCATAGTGAGGTTACCAA
1 AATTTCATAGGAGGTTACCGGAATTTCAT-AGGAG-TTACCAAAATTTCATAGTGAGGTTACCAA
* * *****
19546 AATTTAATAGGGGGTTTA-CGAGAATTTCATAGGAGGTTATTGGTATTTCATAGTGA-GTATACC
1 AATTTCATAGGAGG-TTACCG-GAATTTCATAGGA-GTTACCAAAATTTCATAGTGAGGT-TACC
19609 AA
62 AA
* * ** * * * *
19611 AATTTTATAGTGAGG-TAGTCAAAATTTAATAGTGAGGTTACTAAAATTTCATAATGAGGTTATC
1 AATTTCATAG-GAGGTTA-CCGGAATTTCATAG-GA-GTTACCAAAATTTCATAGTGAGGTTACC
19675 AA
62 AA
*
19677 TATTTCAT
1 AATTTCAT
19685 TTTACTTGAA
Statistics
Matches: 362, Mismatches: 74, Indels: 58
0.73 0.15 0.12
Matches are distributed among these distances:
63 1 0.00
64 57 0.16
65 155 0.43
66 141 0.39
67 8 0.02
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (63 bp):
AATTTCATAGGAGGTTACCGGAATTTCATAGGAGTTACCAAAATTTCATAGTGAGGTTACCAA
Found at i:19609 original size:87 final size:86
Alignment explanation
Indices: 19438--19674 Score: 239
Period size: 87 Copynumber: 2.7 Consensus size: 86
19428 AGGTTACCGG
* * * * * * *
19438 ATTTCGATAGTGAGTTTACCAAAATTTCA-AGGGAGGTTAACAAAATTTCTTTGGGGGTTACCGG
1 ATTTC-ATAGTGAGGTTACCAAAATTTAATAGGG-GGTTTACAAAATTTCATAGGAGGTTATCGG
*
19502 AATTTCATAAGGAGTTTACCAAA
64 AATTTCATAAGGAGTATACCAAA
* * *
19525 ATTTCATAGTGAGGTTACCAAAATTTAATAGGGGGTTTACGAGAATTTCATAGGAGGTTATTGGT
1 ATTTCATAGTGAGGTTACCAAAATTTAATAGGGGGTTTAC-AAAATTTCATAGGAGGTTATCGGA
19590 ATTTCAT-AGTGAGTATACCAAA
65 ATTTCATAAG-GAGTATACCAAA
* * * *
19612 ATTTTATAGTGAGG-TAGTCAAAATTTAATAGTGAGG-TTACTAAAATTTCATAATGAGGTTATC
1 ATTTCATAGTGAGGTTA-CCAAAATTTAATAG-GGGGTTTAC-AAAATTTCAT-AGGAGGTTATC
19675 AATATTTCAT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
86 31 0.25
87 83 0.66
88 12 0.10
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.35
Consensus pattern (86 bp):
ATTTCATAGTGAGGTTACCAAAATTTAATAGGGGGTTTACAAAATTTCATAGGAGGTTATCGGAA
TTTCATAAGGAGTATACCAAA
Found at i:19754 original size:22 final size:22
Alignment explanation
Indices: 19693--19789 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
19683 ATTTTACTTG
19693 AATTTCAT-TGTTAAGTTATCAA
1 AATTTCATATG-TAAGTTATCAA
* * * *
19715 AATTTTATAAGAAAGTTATTAA
1 AATTTCATATGTAAGTTATCAA
*
19737 AATTTCATATGTAGGTTAGT-AA
1 AATTTCATATGTAAGTTA-TCAA
* * * *
19759 GATTTTATA-GTGAGATTACCAA
1 AATTTCATATGTAAG-TTATCAA
19781 AATTTCATA
1 AATTTCATA
19790 AGGTAGTTGC
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
21 3 0.05
22 51 0.91
23 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.41
Consensus pattern (22 bp):
AATTTCATATGTAAGTTATCAA
Found at i:29195 original size:22 final size:22
Alignment explanation
Indices: 29167--29212 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29157 ATGAAAAAAC
29167 TATGTGACTGTAAGCAAATCAA
1 TATGTGACTGTAAGCAAATCAA
29189 TATGTGACTGTAAGCAAATCAA
1 TATGTGACTGTAAGCAAATCAA
29211 TA
1 TA
29213 ACTGGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (22 bp):
TATGTGACTGTAAGCAAATCAA
Found at i:29822 original size:2 final size:2
Alignment explanation
Indices: 29815--29845 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29805 GGAATCGTTA
29815 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 A
29846 CTAGTTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37896 original size:3 final size:3
Alignment explanation
Indices: 37888--37926 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
37878 GTACTTGTAC
*
37888 ATT ATT ATT ATT AGT ATT ATAT ATT ATT ATT AATT ATT A
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT -ATT ATT A
37927 ATTAATCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:37925 original size:13 final size:12
Alignment explanation
Indices: 37888--37926 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
37878 GTACTTGTAC
37888 ATTATTATTATT
1 ATTATTATTATT
*
37900 AGTATTATATATT
1 ATTATTAT-TATT
37913 ATTATTAATTATT
1 ATTATT-ATTATT
37926 A
1 A
37927 ATTAATCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 14 0.61
14 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:38111 original size:27 final size:28
Alignment explanation
Indices: 38060--38112 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
38050 TCCTTTAATT
* *
38060 AAAATCTCTAAACGTTTATTTCAAAAAA
1 AAAATCTCTAAACGTTTAGTACAAAAAA
38088 AAAATCTCTAAACG-TTAGTACAAAA
1 AAAATCTCTAAACGTTTAGTACAAAA
38113 TTTACTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (28 bp):
AAAATCTCTAAACGTTTAGTACAAAAAA
Found at i:42735 original size:24 final size:24
Alignment explanation
Indices: 42689--42735 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
42679 GTTGTGTAGG
* * **
42689 TTTTTTTTTTGTTTGTTCTTTTTC
1 TTTTTCTTTTATTTGTTAATTTTC
42713 TTTTTCTTTTATTTGTTAATTTT
1 TTTTTCTTTTATTTGTTAATTTT
42736 ATTAATTTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (24 bp):
TTTTTCTTTTATTTGTTAATTTTC
Done.