Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023217.1 Corchorus olitorius cultivar O-4 contig23250, 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: 111938
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:238 original size:42 final size:43
Alignment explanation
Indices: 187--281 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 43
177 AGTACATTAC
*
187 CTAA-ATTCTACT-CCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
228 CTAATATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG
273 CTAATATTC
1 CTAATATTC
282 ATTGTTGCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 4 0.08
42 8 0.16
45 37 0.76
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:1434 original size:73 final size:74
Alignment explanation
Indices: 1300--1447 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 74
1290 CAATTTTGAA
* * * * *
1300 ATATATTTGACAAATAAGGGTATAATGGACGATTCAAAAGTTTTATAAGAGGTTGTAC-TTTTTA
1 ATATATTTGAAAAATAAGGGTATAATAGACGATTCAAAAGTTTTAGAAGAGCTCGTACTTTTTTA
*
1364 ATATAGTAT
66 ATATAATAT
* *
1373 ATATGTTTGAAAAATAAGGGTATAATAGACGATTCAAAAGTTTTACGAAGA-CTCGTGCTTTTTT
1 ATATATTTGAAAAATAAGGGTATAATAGACGATTCAAAAGTTTTA-GAAGAGCTCGTACTTTTTT
1437 AATATAATAT
65 AATATAATAT
1447 A
1 A
1448 AATAGTATAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
73 46 0.71
74 19 0.29
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (74 bp):
ATATATTTGAAAAATAAGGGTATAATAGACGATTCAAAAGTTTTAGAAGAGCTCGTACTTTTTTA
ATATAATAT
Found at i:3498 original size:21 final size:21
Alignment explanation
Indices: 3453--3498 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3443 TATGCTTTGG
* *
3453 TCTATAGATTTGGGCCTATTA
1 TCTATAGAATTGGGCCTAATA
3474 TCTATAGAATTGGGCCTTAAT-
1 TCTATAGAATTGGGCC-TAATA
3495 TCTA
1 TCTA
3499 AGAGTGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (21 bp):
TCTATAGAATTGGGCCTAATA
Found at i:8439 original size:30 final size:30
Alignment explanation
Indices: 8175--8435 Score: 299
Period size: 30 Copynumber: 8.6 Consensus size: 30
8165 CATGGTGTAT
* *
8175 ATGACAACTTCTGGTGTCAATTGAATAAAATA
1 ATGACAACTTCTGGTGTCAATTG--CAAAATC
* **
8207 ATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
8237 ATGACAACTTCTGGTGTCATTTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
8267 ATGACAACTTTTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
8297 ATGACAAC-TCATGGTGTCAATTGTAAAAGC
1 ATGACAACTTC-TGGTGTCAATTGCAAAATC
* * *
8327 ATGACAACTTATGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
8357 ATGACAACTTATGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
8387 ATGACAACTTATGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
8417 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
8436 TTTGGAGAGT
Statistics
Matches: 204, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
29 1 0.00
30 182 0.89
31 1 0.00
32 20 0.10
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:10061 original size:42 final size:42
Alignment explanation
Indices: 10002--10087 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
9992 TTCTATTTTA
*
10002 ATCCCGTTTAAGATTATCTTATCATAATATGAAATTAACATC
1 ATCCCATTTAAGATTATCTTATCATAATATGAAATTAACATC
*
10044 ATCCCATTTAAGATTATCTTATCATAATATGAAATTAAGATC
1 ATCCCATTTAAGATTATCTTATCATAATATGAAATTAACATC
10086 AT
1 AT
10088 AAACATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (42 bp):
ATCCCATTTAAGATTATCTTATCATAATATGAAATTAACATC
Found at i:10492 original size:21 final size:21
Alignment explanation
Indices: 10347--10479 Score: 203
Period size: 21 Copynumber: 6.3 Consensus size: 21
10337 TTCAGTCACT
*
10347 CAAATTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
* *
10368 CATATTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
* * *
10389 CAAATTTTGATAGTCAAACCT
1 CAAAGTTTGATGGTCAAACCC
10410 CAAAGTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
*
10431 CTAAGTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
10452 CAAAGTTTGATGGTCAAACCC
1 CAAAGTTTGATGGTCAAACCC
10473 CAAAGTT
1 CAAAGTT
10480 CAATAGTCAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 103 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (21 bp):
CAAAGTTTGATGGTCAAACCC
Found at i:10584 original size:21 final size:20
Alignment explanation
Indices: 10551--10635 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 20
10541 TGTGTTTTTG
*
10551 CCCAAATTTTGATAGTCAAAC
1 CCCAAA-TTTGATGGTCAAAC
10572 CCCGAAATTTGATGGTCAAAC
1 CCC-AAATTTGATGGTCAAAC
*
10593 CCCAAATTTTGATGGTCAAAA
1 CCCAAA-TTTGATGGTCAAAC
*
10614 CCCAACTTTTGATGGTCAAAC
1 CCCAA-ATTTGATGGTCAAAC
10635 C
1 C
10636 ATGTTAAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.05
21 51 0.89
22 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (20 bp):
CCCAAATTTGATGGTCAAAC
Found at i:10611 original size:42 final size:42
Alignment explanation
Indices: 10551--10635 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
10541 TGTGTTTTTG
*
10551 CCCAAATTTTGATAGTCAAACCCCGAA-ATTTGATGGTCAAAC
1 CCCAAATTTTGATAGTCAAAACCC-AACATTTGATGGTCAAAC
* *
10593 CCCAAATTTTGATGGTCAAAACCCAACTTTTGATGGTCAAAC
1 CCCAAATTTTGATAGTCAAAACCCAACATTTGATGGTCAAAC
10635 C
1 C
10636 ATGTTAAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
CCCAAATTTTGATAGTCAAAACCCAACATTTGATGGTCAAAC
Found at i:10673 original size:143 final size:142
Alignment explanation
Indices: 10410--10801 Score: 559
Period size: 143 Copynumber: 2.7 Consensus size: 142
10400 AGTCAAACCT
* * *
10410 CAAAGTTTGATGGTCAAACCCCTAAGTTTGATGGTCAAACCCCAAAGTTTGATGGTCAAACCCCA
1 CAAATTTTGATGGTCAAACCCC-AAATTTGATGGTCAAACCCCAAATTTTGATGGTCAAACCCCA
* ** * ** *
10475 AAGTTCAATAGTCAAACCATGTTAAACCTTATAAATTGAAATACCCGCCAAATTTTTGCCCAAAA
65 AATTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCACCAAATTTTTGCCCAAAA
*
10540 CTGTGTTTTTGCC
130 CTGTGTTTTCGCC
* *
10553 CAAATTTTGATAGTCAAACCCCGAAATTTGATGGTCAAACCCCAAATTTTGATGGTCAAAACCCA
1 CAAATTTTGATGGTCAAACCCC-AAATTTGATGGTCAAACCCCAAATTTTGATGGTCAAACCCCA
* * *
10618 ACTTTTGATGGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCACCATATTTTTGCCCAAAA
65 AATTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCACCAAATTTTTGCCCAAAA
*
10683 TTGTGTTTTCGCC
130 CTGTGTTTTCGCC
* * *
10696 CAAATTTTGATGGTGAAACCCCAAATTTTGATGGTCAAACCCCAAATTTTGATGGTTATACCCCA
1 CAAATTTTGATGGTCAAACCCCAAA-TTTGATGGTCAAACCCCAAATTTTGATGGTCAAACCCCA
* *
10761 AATTTTGATAGTCAAACCATGTTTAATCTTATCAATTGAAG
65 AATTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAG
10802 GTACCCAAAA
Statistics
Matches: 221, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
142 3 0.01
143 218 0.99
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (142 bp):
CAAATTTTGATGGTCAAACCCCAAATTTGATGGTCAAACCCCAAATTTTGATGGTCAAACCCCAA
ATTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCACCAAATTTTTGCCCAAAAC
TGTGTTTTCGCC
Found at i:10720 original size:21 final size:21
Alignment explanation
Indices: 10694--10778 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
10684 TGTGTTTTCG
*
10694 CCCAAATTTTGATGGTGAAAC
1 CCCAAATTTTGATGGTCAAAC
10715 CCCAAATTTTGATGGTCAAAC
1 CCCAAATTTTGATGGTCAAAC
* *
10736 CCCAAATTTTGATGGTTATAC
1 CCCAAATTTTGATGGTCAAAC
*
10757 CCCAAATTTTGATAGTCAAAC
1 CCCAAATTTTGATGGTCAAAC
10778 C
1 C
10779 ATGTTTAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (21 bp):
CCCAAATTTTGATGGTCAAAC
Found at i:11322 original size:43 final size:43
Alignment explanation
Indices: 11261--11421 Score: 231
Period size: 43 Copynumber: 3.8 Consensus size: 43
11251 CCAATGACCA
*
11261 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATATC
* *
11304 AAAGTCCTCAAACACATATATAACACAGAGGCA--ACTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATATC
11345 AAAGTCCCCAAACACATATATAACACA-AGGGCATCTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGA-GGCATCTCTATAT-C
* *
11388 AAAGTCCTCAAATACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
11422 TTCCCCTTAT
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
40 1 0.01
41 37 0.35
42 1 0.01
43 66 0.62
44 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.20
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATATC
Found at i:11358 original size:84 final size:84
Alignment explanation
Indices: 11261--11420 Score: 286
Period size: 84 Copynumber: 1.9 Consensus size: 84
11251 CCAATGACCA
*
11261 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTA-TATCAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTA-CAAAGTCCTCAAACACATATAT
11325 AACACAGAGGCAACTATATC
65 AACACAGAGGCAACTATATC
*
11345 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTACAAAGTCCTCAAATACATATATA
1 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
11410 ACACAGAGGCA
66 ACACAGAGGCA
11421 TTTCCCCTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
84 71 0.97
85 2 0.03
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCAACTATATC
Found at i:24061 original size:43 final size:42
Alignment explanation
Indices: 24000--24201 Score: 311
Period size: 43 Copynumber: 4.8 Consensus size: 42
23990 CCAATGACCA
*
24000 AAAGTCCCCAAACACATATATAACACAGAGACATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TC
* *
24043 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATTC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTC
24085 -AAGT-CCCAAACACATATATAACACAG-GGCATCTCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TC
*
24125 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATT-C
*
24168 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
24202 TTCTCCTTAT
Statistics
Matches: 147, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
39 10 0.07
40 23 0.16
41 8 0.05
42 25 0.17
43 81 0.55
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTC
Found at i:25780 original size:96 final size:96
Alignment explanation
Indices: 25616--25812 Score: 340
Period size: 96 Copynumber: 2.1 Consensus size: 96
25606 TCCTCTTCTG
* * *
25616 GGGAGATTTGGGCTAGGCTTGAGCCCATAGTGAGCCAAACCAGGCCTTTCTCACATTCCCTCAAA
1 GGGAGATTTGGGCTAGGCTTGAGCCCATAGTGAACCAAACCAGGCCTTTCTCACACTCCCACAAA
*
25681 AAGGCTCCCACATTTTCTGGCGACTCGACTA
66 AAGGCTCCCACATTTTCTGGCGACTCCACTA
*
25712 GGGAGATTTGGGCTAGGCTTGAGCCCATAGTGAACCGAACCAGGCCTTTCTCACACTCCCACAAA
1 GGGAGATTTGGGCTAGGCTTGAGCCCATAGTGAACCAAACCAGGCCTTTCTCACACTCCCACAAA
*
25777 AAGGCTCCCACATTTTCTGGCGACTCCACTG
66 AAGGCTCCCACATTTTCTGGCGACTCCACTA
25808 GGGAG
1 GGGAG
25813 CCTTTAGGAA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (96 bp):
GGGAGATTTGGGCTAGGCTTGAGCCCATAGTGAACCAAACCAGGCCTTTCTCACACTCCCACAAA
AAGGCTCCCACATTTTCTGGCGACTCCACTA
Found at i:28223 original size:17 final size:17
Alignment explanation
Indices: 28181--28223 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28171 GGAGAGCGGG
*
28181 GAAGAAGAAGAACAGTA
1 GAAGAAGAAGAACAGAA
*
28198 G-AGAGAGAAGAACTGAA
1 GAAGA-AGAAGAACAGAA
28215 GAAGAAGAA
1 GAAGAAGAA
28224 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.58, C:0.05, G:0.33, T:0.05
Consensus pattern (17 bp):
GAAGAAGAAGAACAGAA
Found at i:29892 original size:2 final size:2
Alignment explanation
Indices: 29885--29913 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29875 CAAATGTCTT
29885 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 T
29914 CAATGCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42432 original size:3 final size:3
Alignment explanation
Indices: 42424--42448 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42414 TCCTCTCTGT
42424 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
42449 CTCATCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:47005 original size:19 final size:20
Alignment explanation
Indices: 46955--47011 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
46945 GCTACTCTAA
46955 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGTA-C
* * * *
46976 TAATTTGATATATACAGT-G
1 TAATCTCATATGTACAGTAC
46995 TAATCTCATATGTACAG
1 TAATCTCATATGTACAG
47012 GATCTAAACG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TAATCTCATATGTACAGTAC
Found at i:103062 original size:23 final size:23
Alignment explanation
Indices: 103023--103066 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
103013 ATTCAATAAC
*
103023 AATAAATTAATTAAAATCAAACT
1 AATAAATTAAGTAAAATCAAACT
103046 AATAAATTAAAGT-AAATCAAA
1 AATAAATT-AAGTAAAATCAAA
103067 GTTAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAATTAAGTAAAATCAAACT
Found at i:106773 original size:42 final size:42
Alignment explanation
Indices: 106713--106795 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
106703 CCTAAGTCTT
106713 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
* * *
106755 GAAAATTCTTTGTTAATTAAGAAATACTCAACTCAAATCAT
1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCAT
106796 GATCCTTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
Found at i:106929 original size:55 final size:56
Alignment explanation
Indices: 106859--106970 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
106849 TTTATTTTGT
106859 AGAATAATTAAGTAGAGATA-GGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
106914 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
106970 A
1 A
106971 AGGAAACACA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 20 0.36
56 36 0.64
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:107189 original size:7 final size:7
Alignment explanation
Indices: 107177--107214 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
107167 TATATATATA
107177 ATAGTTT
1 ATAGTTT
107184 ATAGTTT
1 ATAGTTT
107191 ATAGTTT
1 ATAGTTT
107198 ATAGTTT
1 ATAGTTT
107205 ATAGTTT
1 ATAGTTT
107212 ATA
1 ATA
107215 TATGATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (7 bp):
ATAGTTT
Found at i:111881 original size:2 final size:2
Alignment explanation
Indices: 111874--111938 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
111864 GAAGATGAAC
111874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
111916 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.