Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014668.1 Corchorus capsularis cultivar CVL-1 contig14689, 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: 49817
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:110 original size:31 final size:31
Alignment explanation
Indices: 72--207 Score: 136
Period size: 31 Copynumber: 4.5 Consensus size: 31
62 AAACTGACAA
**
72 TAGGCCCTTATTTGAGCATTTTTTATAACGT
1 TAGGCCCTTATTTGAGCATTTTCGATAACGT
*
103 TAGGCCCTTATTTGAGCATTTTCGATAATGT
1 TAGGCCCTTATTTGAGCATTTTCGATAACGT
** *
134 TAGGCCCTTATTTG-GCCAAATT--A-AAAGAT
1 TAGGCCCTTATTTGAG-CATTTTCGATAACG-T
** *
163 CGGGCCCTTATTTAAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTTCGATAACGT
*
194 TAGACCCTTATTTG
1 TAGGCCCTTATTTG
208 GCCAAATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.04
29 17 0.20
30 2 0.02
31 58 0.70
32 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTCGATAACGT
Found at i:235 original size:29 final size:29
Alignment explanation
Indices: 136--236 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
126 GATAATGTTA
136 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
* ** * **
165 GGCCCTTATTTAAG-CATTTTCGATAACG-TTA
1 GGCCCTTATTT-GGCCAAATT--A-AAAGATCG
*
196 GACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
225 GGCCCTTATTTG
1 GGCCCTTATTTG
237 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 3 0.06
29 28 0.54
30 2 0.04
31 16 0.31
32 3 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:276 original size:60 final size:61
Alignment explanation
Indices: 105--268 Score: 262
Period size: 60 Copynumber: 2.7 Consensus size: 61
95 TATAACGTTA
105 GGCCCTTATTTGAGCATTTTCGATAA-TGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACTGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
165 GGCCCTTATTTAAGCATTTTCGATAAC-GTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACTGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
225 GGCCCTTATTTGAGCATTTTGGCA-AACTTTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACTGTTAGGCCCTTATTTG
269 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
60 80 0.84
61 15 0.16
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (61 bp):
GGCCCTTATTTGAGCATTTTCGATAACTGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:558 original size:24 final size:24
Alignment explanation
Indices: 484--558 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 24
474 TGTTATAATA
484 AATTTTATCCCCCTTAATTATCTAG
1 AATTTTAT-CCCCTTAATTATCTAG
* * * * *
509 AATTGTAACCTC-T-GTTATAATA-
1 AATTTTATCCCCTTAATTAT-CTAG
531 AATTTTATCCCCTTAATTATCTAG
1 AATTTTATCCCCTTAATTATCTAG
555 AATT
1 AATT
559 GTAACCTCTC
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
22 13 0.36
23 6 0.17
24 11 0.31
25 6 0.17
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (24 bp):
AATTTTATCCCCTTAATTATCTAG
Found at i:560 original size:46 final size:47
Alignment explanation
Indices: 474--567 Score: 181
Period size: 46 Copynumber: 2.0 Consensus size: 47
464 TTCACATAAA
474 TGTTATAATAAATTTTATCCCCCTTAATTATCTAGAATTGTAACCTC
1 TGTTATAATAAATTTTATCCCCCTTAATTATCTAGAATTGTAACCTC
521 TGTTATAATAAATTTTAT-CCCCTTAATTATCTAGAATTGTAACCTC
1 TGTTATAATAAATTTTATCCCCCTTAATTATCTAGAATTGTAACCTC
567 T
1 T
568 CTTCGGGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 29 0.62
47 18 0.38
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (47 bp):
TGTTATAATAAATTTTATCCCCCTTAATTATCTAGAATTGTAACCTC
Found at i:3980 original size:23 final size:23
Alignment explanation
Indices: 3950--4006 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
3940 ATAATTTGAA
3950 ACATTTTGATCCCCACACCAACC
1 ACATTTTGATCCCCACACCAACC
3973 ACATTTTGATCCCCACACCAACC
1 ACATTTTGATCCCCACACCAACC
3996 ACATTTTGATC
1 ACATTTTGATC
4007 GTCCACTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.39, G:0.05, T:0.26
Consensus pattern (23 bp):
ACATTTTGATCCCCACACCAACC
Found at i:6575 original size:32 final size:31
Alignment explanation
Indices: 6532--6625 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 31
6522 GCTCATGGGG
6532 CACACCGATCGAGTCTAAGCAGGCTCTGATAC
1 CACACCGATCGAGTCTAA-CAGGCTCTGATAC
*
6564 CACACCAATCGAGTCTAACTAGGCTC-----C
1 CACACCGATCGAGTCTAAC-AGGCTCTGATAC
6591 CACACCGATCGAGTCTAACCAGGCTCTGATAC
1 CACACCGATCGAGTCTAA-CAGGCTCTGATAC
6623 CAC
1 CAC
6626 TTGTTGGGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
27 24 0.45
28 1 0.02
31 1 0.02
32 27 0.51
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (31 bp):
CACACCGATCGAGTCTAACAGGCTCTGATAC
Found at i:6601 original size:27 final size:27
Alignment explanation
Indices: 6532--6616 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
6522 GCTCATGGGG
6532 CACACCGATCGAGTCTAAGCAGGCTCTGATAC
1 CACACCGATCGAGTCTAA-CAGGCTC----AC
*
6564 CACACCAATCGAGTCTAACTAGGCTC-C
1 CACACCGATCGAGTCTAAC-AGGCTCAC
6591 CACACCGATCGAGTCTAACCAGGCTC
1 CACACCGATCGAGTCTAA-CAGGCTC
6617 TGATACCACT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
27 24 0.49
28 1 0.02
31 1 0.02
32 23 0.47
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.18
Consensus pattern (27 bp):
CACACCGATCGAGTCTAACAGGCTCAC
Found at i:6922 original size:47 final size:47
Alignment explanation
Indices: 6848--6944 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
6838 TCCTTATCTC
*
6848 TCCCCCGTGCGGCCCAACCCGTCAAGTTTTAAGCCAATTACCGGCTA
1 TCCCCCGTGCGGCCCAACCCGTCAAGTTTTAAACCAATTACCGGCTA
*
6895 TCCCCCGTGCGGCCCAACCCGTTAAGTTTTAAACCAATTACCGGCTA
1 TCCCCCGTGCGGCCCAACCCGTCAAGTTTTAAACCAATTACCGGCTA
6942 TCC
1 TCC
6945 AAGACTTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (47 bp):
TCCCCCGTGCGGCCCAACCCGTCAAGTTTTAAACCAATTACCGGCTA
Found at i:10340 original size:23 final size:23
Alignment explanation
Indices: 10314--10368 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
10304 TTCTACAATC
*
10314 AAACCAAGACCCATTAATGTTGA
1 AAACTAAGACCCATTAATGTTGA
10337 AAACTAAGACCCATTAATGTTGA
1 AAACTAAGACCCATTAATGTTGA
10360 AAACTAAGA
1 AAACTAAGA
10369 GCCGACTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (23 bp):
AAACTAAGACCCATTAATGTTGA
Found at i:13365 original size:13 final size:13
Alignment explanation
Indices: 13347--13381 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
13337 AATCTAAATC
*
13347 TAAAGCAGATTAA
1 TAAAGCAAATTAA
13360 TAAAGCAAATTAA
1 TAAAGCAAATTAA
13373 TAAAGCAAA
1 TAAAGCAAA
13382 CAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:36236 original size:29 final size:29
Alignment explanation
Indices: 36183--36245 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
36173 ATGATTTAGG
* *
36183 TTTTTTTAACAATATACCCTAAATTGAGC
1 TTTTTTGAACAATATACCCTAAATTAAGC
* *
36212 TTTTTTGAACAATATACCTTGAATTAAGC
1 TTTTTTGAACAATATACCCTAAATTAAGC
*
36241 ATTTT
1 TTTTT
36246 CGCAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTTTTGAACAATATACCCTAAATTAAGC
Found at i:38021 original size:19 final size:19
Alignment explanation
Indices: 37997--38033 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37987 TCATAATTTC
37997 TGACAATGAATATAGCACA
1 TGACAATGAATATAGCACA
*
38016 TGACAATGGATATAGCAC
1 TGACAATGAATATAGCAC
38034 CTAACCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (19 bp):
TGACAATGAATATAGCACA
Found at i:38719 original size:18 final size:19
Alignment explanation
Indices: 38681--38726 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
38671 TCTCAATCTA
38681 AAATAAA-T-TAAATAAAT
1 AAATAAATTATAAATAAAT
*
38698 AAATATATTATAAATAAA-
1 AAATAAATTATAAATAAAT
38716 AAATAAATTAT
1 AAATAAATTAT
38727 TAATTACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 11 0.44
19 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAATTATAAATAAAT
Found at i:39573 original size:28 final size:28
Alignment explanation
Indices: 39533--39616 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
39523 ATACTATAGC
*
39533 ATTAAGGAG-ATTTTAGCAATTGACTAAT
1 ATTAAGG-GTATTTTAACAATTGACTAAT
*
39561 ATTAAGGGTATTTTAATAATTGACTAAT
1 ATTAAGGGTATTTTAACAATTGACTAAT
* *
39589 ATTAAGGGTATTTTAATAATTGATTAAT
1 ATTAAGGGTATTTTAACAATTGACTAAT
39617 TAAGATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 1 0.02
28 51 0.98
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (28 bp):
ATTAAGGGTATTTTAACAATTGACTAAT
Found at i:39668 original size:5 final size:5
Alignment explanation
Indices: 39658--39698 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
39648 ATATATATAG
*
39658 TAAGA TAAGA TAAGA TAAGA TAAGA T-ATA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
39699 GTAACTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:40700 original size:64 final size:67
Alignment explanation
Indices: 40612--40759 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 67
40602 TTCAGAGTGT
* * * * *
40612 GGTTATCAAAATTTCA-GAGGAAGGTTAT-CAAATTTTCATAGTGTAAAAACCAAAAT-TTTTAG
1 GGTTATCAAAATTTCATCAGAAAGGTTATCCAAAATATCATAGTGTAAAAACCAAAATATTATAG
*
40674 -G
66 TA
* * *
40675 GGATTATCAAAATTTCATCA-AAAGGTTATCCAAAATATCATATTGTAATAATCAAAATATTATA
1 GG-TTATCAAAATTTCATCAGAAAGGTTATCCAAAATATCATAGTGTAAAAACCAAAATATTATA
40739 GTTA
65 G-TA
40743 GGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
40760 TCGGAGGTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 22 0.31
65 24 0.34
66 5 0.07
67 15 0.21
68 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (67 bp):
GGTTATCAAAATTTCATCAGAAAGGTTATCCAAAATATCATAGTGTAAAAACCAAAATATTATAG
TA
Found at i:40842 original size:23 final size:24
Alignment explanation
Indices: 40789--40848 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
40779 ATAGTGTTGC
* * *
40789 TATCGAATTTTCATAGGGAGAGGT
1 TATCGAAATTTCACAAGGAGAGGT
*
40813 TATCGAAATTTCACAAGGAG-GTT
1 TATCGAAATTTCACAAGGAGAGGT
40836 TATCGAAATTTCA
1 TATCGAAATTTCA
40849 TTGTGTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (24 bp):
TATCGAAATTTCACAAGGAGAGGT
Found at i:41073 original size:44 final size:44
Alignment explanation
Indices: 40810--41084 Score: 153
Period size: 44 Copynumber: 6.3 Consensus size: 44
40800 CATAGGGAGA
* * * *
40810 GGTTATCGAAATTTCACAAGGAGGTTTATCGAAATTTCATTGTGT
1 GGTTATCAAAATTTTATAAGGAGG-TTATCGAAATTTCATAGTGT
* * * * * *
40855 AGTTATCAAAGTTTCATAAAGAGG-T-TCAAAATTTCATAGTGA
1 GGTTATCAAAATTTTATAAGGAGGTTATCGAAATTTCATAGTGT
* * * *
40897 CGTTATCAAAATTTTATTAGGATG-TA-CCAATATTTCATAGTGCGT
1 GGTTATCAAAATTTTATAAGGAGGTTATCGAA-ATTTCATAGT--GT
* * * * * *
40942 GGTTATC-AAATTTTCAT-TGTATAAGTTGTCGAAATTTCTTAAG-GA
1 GGTTATCAAAATTTT-ATAAG--GAGGTTATCGAAATTTCAT-AGTGT
* * * *
40987 GG-T-TCAAAATTTCAT---GAGGCTATCTAAAGTTT-ATAGTAT
1 GGTTATCAAAATTTTATAAGGAGGTTATCGAAA-TTTCATAGTGT
41026 GGTTATCAAAATTTTATAAGGAGGTTATCGAAATTTCATAGTGT
1 GGTTATCAAAATTTTATAAGGAGGTTATCGAAATTTCATAGTGT
*
41070 GGTTATCAAATTTTT
1 GGTTATCAAAATTTT
41085 TTCATAAGAG
Statistics
Matches: 173, Mismatches: 38, Indels: 39
0.69 0.15 0.16
Matches are distributed among these distances:
38 2 0.01
39 11 0.06
40 4 0.02
41 11 0.06
42 36 0.21
43 18 0.10
44 46 0.27
45 31 0.18
46 2 0.01
47 7 0.04
48 5 0.03
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (44 bp):
GGTTATCAAAATTTTATAAGGAGGTTATCGAAATTTCATAGTGT
Found at i:41082 original size:21 final size:22
Alignment explanation
Indices: 40591--41079 Score: 124
Period size: 22 Copynumber: 22.4 Consensus size: 22
40581 GCCGTTGTCA
* *
40591 GTTATTAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
40613 GTTATCAAAATTTCAGAG-GAAG
1 GTTATCAAAATTTCATAGTG-TG
* *
40635 GTTATCAAATTTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTG
*** * *
40657 AAAACCAAAATTT-TTAG-G-G
1 GTTATCAAAATTTCATAGTGTG
***
40676 GATTATCAAAATTTCATCA-AAAG
1 G-TTATCAAAATTTCAT-AGTGTG
* * *
40699 GTTATCCAAAATATCATATTGTA
1 GTTAT-CAAAATTTCATAGTGTG
* *
40722 ATAATCAAAATATT-ATAGT-TAG
1 GTTATCAAAAT-TTCATAGTGT-G
* *
40744 GTTATCAAAATTTCATTCG-GAG
1 GTTATCAAAATTTCA-TAGTGTG
* *
40766 G-TACCAAAATTTCATAGTGTT
1 GTTATCAAAATTTCATAGTGTG
* * * * *
40787 GCTATCGAATTTTCATAGGGAGAG
1 GTTATCAAAATTTCATA--GTGTG
* * *
40811 GTTATCGAAATTTCACAAG-GAG
1 GTTATCAAAATTTCA-TAGTGTG
* * *
40833 GTTTATCGAAATTTCATTGTGTA
1 G-TTATCAAAATTTCATAGTGTG
* ** *
40856 GTTATCAAAGTTTCATAAAGAG
1 GTTATCAAAATTTCATAGTGTG
**
40878 G-T-TCAAAATTTCATAGTGAC
1 GTTATCAAAATTTCATAGTGTG
*
40898 GTTATCAAAATTTTATTAG-GAT-
1 GTTATCAAAATTTCA-TAGTG-TG
* *
40920 G-TACCAATATTTCATAGTGCGTG
1 GTTATCAAAATTTCATAGT--GTG
* * * *
40943 GTTATCAAATTTTCATTGTATAA
1 GTTATCAAAATTTCATAGTGT-G
* * * *
40966 GTTGTCGAAATTTCTTAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
*
40988 G-T-TCAAAATTTC--A-TGAG
1 GTTATCAAAATTTCATAGTGTG
* * *
41005 GCTATCTAAAGTTT-ATAGTATG
1 GTTATC-AAAATTTCATAGTGTG
* *
41027 GTTATCAAAATTTTATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
*
41049 GTTATCGAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
41071 GTTATCAAA
1 GTTATCAAA
41080 TTTTTTTCAT
Statistics
Matches: 333, Mismatches: 92, Indels: 84
0.65 0.18 0.17
Matches are distributed among these distances:
17 5 0.02
18 1 0.00
19 2 0.01
20 45 0.14
21 44 0.13
22 151 0.45
23 55 0.17
24 29 0.09
25 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:47431 original size:130 final size:130
Alignment explanation
Indices: 47224--47836 Score: 757
Period size: 130 Copynumber: 4.7 Consensus size: 130
47214 CGCAATGATC
* * * * *
47224 TTTTTAATTGTTGCCAATACTTATAGTTTTCGTAACAAAAAAAAACAAAGTCGTTGCGAAATCAT
1 TTTTTAGTTGTTGCCAATGCTTACAATTTTCGTAAC-AACAAAAACAAAGTCGTTGCGAAATCAT
* ***
47289 -AACTTATTCGTAACAATTTTATAAAGTGGTTGTCTAAGTGATTTTGATGGTATTTTACACAACA
65 AAAC-TATTCGTAACAACTTTATAAAAACGTTGTCTAAGTGATTTTGATGGTATTTTACACAACA
*
47353 CA
129 CT
* *
47355 TTTTTAGTTGTTGCCAATGCTTACAATTTTCGTAACAACACAAACAAAGTCGTTGCGAAATCCTA
1 TTTTTAGTTGTTGCCAATGCTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATA
* * *
47420 AACCATTCGTAACAATTTTATAAAAACGTTGTCTAAGTGATTTTGATGGTATTTTACATAACACT
66 AACTATTCGTAACAACTTTATAAAAACGTTGTCTAAGTGATTTTGATGGTATTTTACACAACACT
*
47485 TTTTTAGTTGTTGCCAATGCTTACAATTTTCATAACAACAAAAACAAAGTCGTTGCGAAATCATA
1 TTTTTAGTTGTTGCCAATGCTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATA
* * * *
47550 AATTATTCGTAACAACTTTATAAAACCGTTG-CTTAAGTGATTTTGATGATATTTTACAGAACAC
66 AACTATTCGTAACAACTTTATAAAAACGTTGTC-TAAGTGATTTTGATGGTATTTTACACAACAC
47614 T
130 T
* * *** * * *
47615 TTTTTAGTTGTTGCCAATGTTTACAGTATTT-GTAACAACAACTTCTTAAGTTGTTGCGGAATCA
1 TTTTTAGTTGTTGCCAATGCTTACAAT-TTTCGTAACAACAAAAAC-AAAGTCGTTGCGAAATCA
* * *
47679 TAAACTATTCGTAATAACTTTAAAAAAACGTTGCCTAAGTGATTTTGATGGTATTTTACACAACA
64 TAAACTATTCGTAACAACTTTATAAAAACGTTGTCTAAGTGATTTTGATGGTATTTTACACAACA
47744 CT
129 CT
* * ** ** * *
47746 ATTTTAGTTGTTACCAATATTTAC-ATTATTCGTAACAACAAATTCTTAAGTTTGTTGCGAAATC
1 TTTTTAGTTGTTGCCAATGCTTACAATT-TTCGTAACAACAAAAAC-AAAG-TCGTTGCGAAATC
* *
47810 ATAATCTATTCATAACAACTTTATAAA
63 ATAAACTATTCGTAACAACTTTATAAA
47837 TCATTGTGCA
Statistics
Matches: 427, Mismatches: 47, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
129 2 0.00
130 238 0.56
131 151 0.35
132 36 0.08
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (130 bp):
TTTTTAGTTGTTGCCAATGCTTACAATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATA
AACTATTCGTAACAACTTTATAAAAACGTTGTCTAAGTGATTTTGATGGTATTTTACACAACACT
Found at i:49648 original size:2 final size:2
Alignment explanation
Indices: 49641--49691 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
49631 ACATAGTATC
*
49641 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT 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
49683 AT AT AT AT A
1 AT AT AT AT A
49692 CAATAACATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Done.