Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008644.1 Corchorus capsularis cultivar CVL-1 contig08665, 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: 78589
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:153 original size:2 final size:2
Alignment explanation
Indices: 102--138 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
92 TTAAAATTCC
102 TA TA TA 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
139 CTTGCTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14035 original size:50 final size:48
Alignment explanation
Indices: 13949--14049 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 48
13939 TTAAATATAC
*
13949 TTGCTGTTGAATATTTGCTGTTGAATGTTGATTCTATATGGTGAATAT
1 TTGCTGTTGAATATTTGCTGTTGAATGTTGATTCTATAAGGTGAATAT
*
13997 TTGCTGTTGAATATTT-CTGTTAGCAAATTTTGATTCTATAAGGTGAATAT
1 TTGCTGTTGAATATTTGCTGTT-G--AATGTTGATTCTATAAGGTGAATAT
14047 TTG
1 TTG
14050 TTTTTGTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
47 5 0.10
48 17 0.35
50 26 0.54
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (48 bp):
TTGCTGTTGAATATTTGCTGTTGAATGTTGATTCTATAAGGTGAATAT
Found at i:14944 original size:31 final size:30
Alignment explanation
Indices: 14906--15009 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
14896 TTAATTTGGC
14906 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTT-CCAAAATGCT
* * * **
14937 CAAATAAGGGCCTGATCTTT-TAATTTGGC-
1 CAAATAAGGGCCTAATGTTTCCAAAAT-GCT
* *
14966 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATGTT-TCCAAAATGCT
14997 CAAATAAGGGCCT
1 CAAATAAGGGCCT
15010 GACGTCAGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
29 19 0.33
30 5 0.09
31 34 0.59
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (30 bp):
CAAATAAGGGCCTAATGTTTCCAAAATGCT
Found at i:14978 original size:29 final size:29
Alignment explanation
Indices: 14889--14978 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
14879 AAATAAGGTT
14889 TGATCTTTTAATTTGGCCAAATAAGGGCC
1 TGATCTTTTAATTTGGCCAAATAAGGGCC
* * * **
14918 TAATGTTTGCCAAAAT-GCTCAAATAAGGGCC
1 TGATCTTT--TAATTTGGC-CAAATAAGGGCC
14949 TGATCTTTTAATTTGGCCAAATAAGGGCC
1 TGATCTTTTAATTTGGCCAAATAAGGGCC
14978 T
1 T
14979 AACGTTATCG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
29 22 0.47
30 4 0.09
31 21 0.45
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (29 bp):
TGATCTTTTAATTTGGCCAAATAAGGGCC
Found at i:14979 original size:60 final size:60
Alignment explanation
Indices: 14847--15011 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 60
14837 GCTAATTGCT
* ** * **
14847 CAAATAAGGGCCTAACATTTGTTAAAATACTCAAATAA-GGTTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
14906 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
14966 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCTGA
1 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCTGA
15012 CGTCAGTTTG
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 33 0.35
60 61 0.64
61 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:15148 original size:31 final size:29
Alignment explanation
Indices: 15113--15215 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 29
15103 AGATCGGGCC
*
15113 CTTATTTGAGCATTTTCGATAATGTGAGACT
1 CTTATTTGAGCATTTT-GA-AATGTCAGACT
** * *
15144 CTTATTTG-GCCAAATT-AAAAGATCAGACC
1 CTTATTTGAG-CATTTTGAAATG-TCAGACT
*
15173 CTTATTTGAGCATTTTGACAAATGTTAGACT
1 CTTATTTGAGCATTTTG--AAATGTCAGACT
15204 CTTATTTGAGCA
1 CTTATTTGAGCA
15216 ATTAGCCTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 18 0.32
30 2 0.04
31 29 0.52
32 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (29 bp):
CTTATTTGAGCATTTTGAAATGTCAGACT
Found at i:15151 original size:60 final size:59
Alignment explanation
Indices: 15047--15211 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 59
15037 TTTTCGACGC
* * *
15047 CAGGCCCTTATTTGAGCATTTATGATAACGTTAGACCCTGATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTT-TGATAATGTTAGACTCTTATTTGGCCAAATTAAAAGAT
* *
15107 CGGGCCCTTATTTGAGCATTTTCGATAATGTGAGACTCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTT-GATAATGTTAGACTCTTATTTGGCCAAATTAAAAGAT
* *
15167 CAGACCCTTATTTGAGCATTTTGACAAATGTTAGACTCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGA-TAATGTTAGACTCTTATTTG
15212 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 3 0.03
60 91 0.97
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (59 bp):
CAGGCCCTTATTTGAGCATTTTGATAATGTTAGACTCTTATTTGGCCAAATTAAAAGAT
Found at i:15176 original size:29 final size:29
Alignment explanation
Indices: 15079--15180 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
15069 TGATAACGTT
*
15079 AGACCCTGATTTGGCCAAATTAAAAGATC
1 AGACCCTTATTTGGCCAAATTAAAAGATC
* * ** * *
15108 GGGCCCTTATTTGAG-CATTTTCGATAATG-TG
1 AGACCCTTATTTG-GCCAAATT--A-AAAGATC
*
15139 AGACTCTTATTTGGCCAAATTAAAAGATC
1 AGACCCTTATTTGGCCAAATTAAAAGATC
15168 AGACCCTTATTTG
1 AGACCCTTATTTG
15181 AGCATTTTGA
Statistics
Matches: 52, Mismatches: 15, Indels: 12
0.66 0.19 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:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (29 bp):
AGACCCTTATTTGGCCAAATTAAAAGATC
Found at i:23850 original size:28 final size:28
Alignment explanation
Indices: 23819--23878 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
23809 GATTATTTTG
** **
23819 TTGTCAAGTTTTCTTTGGATTGGTAGAT
1 TTGTCAAGTTGCCTTTGGATTCATAGAT
**
23847 TTGTTTAGTTGCCTTTGGATTCATAGAT
1 TTGTCAAGTTGCCTTTGGATTCATAGAT
23875 TTGT
1 TTGT
23879 TTAGTTGCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.17, C:0.08, G:0.23, T:0.52
Consensus pattern (28 bp):
TTGTCAAGTTGCCTTTGGATTCATAGAT
Found at i:23879 original size:28 final size:28
Alignment explanation
Indices: 23831--23886 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
23821 GTCAAGTTTT
**
23831 CTTTGGATTGGTAGATTTGTTTAGTTGC
1 CTTTGGATTCATAGATTTGTTTAGTTGC
23859 CTTTGGATTCATAGATTTGTTTAGTTGC
1 CTTTGGATTCATAGATTTGTTTAGTTGC
23887 TGATGCCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (28 bp):
CTTTGGATTCATAGATTTGTTTAGTTGC
Found at i:35130 original size:19 final size:18
Alignment explanation
Indices: 35106--35141 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35096 TGAAGATTTA
35106 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
35125 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
35142 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:35759 original size:17 final size:18
Alignment explanation
Indices: 35739--35774 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35729 TTTCTCTTCA
*
35739 TCTA-TTTTTCTTCTAGT
1 TCTAGTTTTTCTCCTAGT
35756 TCTAGTTTTTCTCCTAGT
1 TCTAGTTTTTCTCCTAGT
35774 T
1 T
35775 TTAGATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.19, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTAGTTTTTCTCCTAGT
Found at i:37029 original size:122 final size:122
Alignment explanation
Indices: 36792--37104 Score: 486
Period size: 122 Copynumber: 2.6 Consensus size: 122
36782 GTTATAACTA
* * * *
36792 ACCGGCAGGCGATCGACAAGGACCATCCCTGATCGAGTATAGAAAATGAAAAAG-CCCCAAGGGG
1 ACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATGAAAAAGCCCCCAAGGGG
36856 CCCAACGCCAACTGGCGAGCGCCAGGCAAACCCAAGCTCAACCTAGTATGGCCATCG
66 CCCAACGCCAACTGGCGAGCGCCAGGCAAACCCAAGCTCAACCTAGTATGGCCATCG
36913 ACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATGAAAAAGCCCCCAAGGGG
1 ACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATGAAAAAGCCCCCAAGGGG
* * *
36978 CCCAACGCCAACTGGCGAGCGCCAGGCAAGGCCGAA-CTCGACCTAGTATGGCCATCG
66 CCCAACGCCAACTGGCGAGCGCCAGGCAA-ACCCAAGCTCAACCTAGTATGGCCATCG
* * * ** *
37035 ACCGGCAGGCGATCAGCATGAACCATCCCTAACCGAGTATAAAAAATGATGAAGCCCTCAAGGGG
1 ACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATGAAAAAGCCCCCAAGGGG
37100 CCCAA
66 CCCAA
37105 TACCATGAGA
Statistics
Matches: 177, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
121 50 0.28
122 123 0.69
123 4 0.02
ACGTcount: A:0.32, C:0.31, G:0.26, T:0.11
Consensus pattern (122 bp):
ACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATGAAAAAGCCCCCAAGGGG
CCCAACGCCAACTGGCGAGCGCCAGGCAAACCCAAGCTCAACCTAGTATGGCCATCG
Found at i:37231 original size:25 final size:25
Alignment explanation
Indices: 37203--37371 Score: 153
Period size: 25 Copynumber: 6.8 Consensus size: 25
37193 CCTGTCGCGT
** *
37203 GCCAAGCCTAGAATGCCCGTCAAGC
1 GCCAAGCGGAGAATGCCCGTCGAGC
*
37228 GCCAAGGGGAGAATGCCCGTCGAGC
1 GCCAAGCGGAGAATGCCCGTCGAGC
* *
37253 GACAAGCGGAGAACGCCCGTCGAGC
1 GCCAAGCGGAGAATGCCCGTCGAGC
** * *
37278 GCCAAGCGGAGAGCGCCCGTAGAGG
1 GCCAAGCGGAGAATGCCCGTCGAGC
* * *
37303 GCCAAGTGGAGAACGCCCG-CTAG-
1 GCCAAGCGGAGAATGCCCGTCGAGC
*
37326 GCAACAAGCGGAGAACGCCCGTCGAGC
1 GC--CAAGCGGAGAATGCCCGTCGAGC
* * *
37353 ACCAACCGGAGAACGCCCG
1 GCCAAGCGGAGAATGCCCG
37372 AAGAAGGCCA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 113 0.93
26 3 0.02
27 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.34, T:0.06
Consensus pattern (25 bp):
GCCAAGCGGAGAATGCCCGTCGAGC
Found at i:37271 original size:50 final size:50
Alignment explanation
Indices: 37187--37940 Score: 448
Period size: 50 Copynumber: 14.7 Consensus size: 50
37177 CGCCAAATGT
* * * ** *
37187 AGAACGCCTGTCGCGTGCCAAGCCTAGAATGCCCGTCAAGCGCCAAGGGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * *
37237 AGAATGCCCGTCGAGCGACAAGCGGAGAACGCCCGTCGAGCGCCAAGCGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * * * *
37287 AGAGCGCCCGTAGAGGGCCAAGTGGAGAACGCCCG-CTAG-GCAACAAGCGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGC--CAAGGGG
* * ** ** *
37337 AGAACGCCCGTCGAGCACCAACCGGAGAACGCCCGAAGAAG-GCCAAATGC
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCG-TCAAGCGCCAAGGGG
* ** * * * *
37387 AGAACGCCCG-CCAGACATCAAGGGGACAACGCCGAGTGGAGAACGCCCCGCCAGGCGCCAAGGG
1 AGAACGCCCGTCGAG-CGCCAAGCGGAGAACGCC----------CG-----TCAAGCGCCAAGGG
37451 G
50 G
* * * * * * *
37452 AGAACGCCCGGCAAGCGCCAAGTGGAGAACGCCCGCCAGGTGCCAAGCGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * *
37502 AGAACACCCGACGAGCGCCAAGCGGAGAACGCCCGCCAGGCGCCAAGGGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * *
37552 AGAACGCCCGTCGAGCGCCAAGCGGAGAGCGCCCGT-AGAGGGCCAAGTGT
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCA-AGCGCCAAGGGG
* * * *
37602 AGAACGCCCG-CCAGGCGCCAAGGGGAAAACGCCCGTCGAA-CGCCAAGCGG
1 AGAACGCCCGTCGA-GCGCCAAGCGGAGAACGCCCGTC-AAGCGCCAAGGGG
* * * * *
37652 AGAACGCCCGAT-GGGCGCTAAGTGGAGAACGCCCGTAGAGGGAGCGCCAAGAGG
1 AGAACGCCCG-TCGAGCGCCAAGCGGAGAACGCCCGT-CA---AGCGCCAAGGGG
* * ** *
37706 AGAACGCCCGTCGAGCGCCAAGAGGAGAACGCCCGACGGGCGCCAAGTGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * * * * * * *
37756 AGAACGGCCGTAGAGGGCCACGTGTAGATCGCCCG-CAAGGCACCAAAGGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAA-GCGCCAAGGGG
* * * * ** *
37806 AGAACG-CCGGCGAGCACCAAGCGAAAAACGCCCACCAGGCGCCAAGGGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * * *
37855 AGAACGCCCGTCGAGCGCCAAGCAGAGAACGCCCGCCAGGCGCCAATGGG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* * *
37905 AGAATGCCAGTCGAGCGCAAAGCGGAGAACGCCCGT
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGT
37941 AGAGCGCGAG
Statistics
Matches: 548, Mismatches: 120, Indels: 72
0.74 0.16 0.10
Matches are distributed among these distances:
48 2 0.00
49 43 0.08
50 417 0.76
51 1 0.00
52 5 0.01
53 2 0.00
54 39 0.07
55 2 0.00
60 2 0.00
64 2 0.00
65 30 0.05
66 3 0.01
ACGTcount: A:0.28, C:0.32, G:0.35, T:0.05
Consensus pattern (50 bp):
AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
Found at i:37296 original size:75 final size:75
Alignment explanation
Indices: 37187--37947 Score: 477
Period size: 75 Copynumber: 9.9 Consensus size: 75
37177 CGCCAAATGT
* * * ** * *
37187 AGAACGCCTGTCGCGTGCCAAGCCTAGAATGCCCGTCAAGCGCCAAGGGGAGAATGCCCGTCGAG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCGAG
*
37252 CGACAAGCGG
66 CGCCAAGCGG
* * * *
37262 AGAACGCCCGTCGAGCGCCAAGCGGAGAGCGCCCGT-AGAGGGCCAAGTGGAGAACGCCCG-CTA
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCA-AGCGCCAAGGGGAGAACGCCCGTCGA
37325 G-GCAACAAGCGG
65 GCGC--CAAGCGG
* * ** ** * *
37337 AGAACGCCCGTCGAGCACCAACCGGAGAACGCCCGAAGAAG-GCCAAATGCAGAACGCCCG-CCA
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCG-TCAAGCGCCAAGGGGAGAACGCCCGTCGA
** *
37400 GACATCAAGGGG
65 G-CGCCAAGCGG
* * * * *
37412 ACAACGCCGAGTGGAGAACGCCCCGCCAGGCGCCAAGGGGAGAACGCCCGGCAAGCGCCAAGTGG
1 AGAACGCC----------CG--TCG--A-GCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGG
* *
37477 AGAACGCCCG-CCAGGTGCCAAGCGG
51 AGAACGCCCGTCGA-GCGCCAAGCGG
* * * *
37502 AGAACACCCGACGAGCGCCAAGCGGAGAACGCCCGCCAGGCGCCAAGGGGAGAACGCCCGTCGAG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCGAG
37567 CGCCAAGCGG
66 CGCCAAGCGG
* * * * * * * * *
37577 AGAGCGCCCGTAGAGGGCCAAGTGTAGAACGCCCGCCAGGCGCCAAGGGGAAAACGCCCGTCGAA
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCGAG
37642 CGCCAAGCGG
66 CGCCAAGCGG
* * * * *
37652 AGAACGCCCGAT-GGGCGCTAAGTGGAGAACGCCCGTAGAGGGAGCGCCAAGAGGAGAACGCCCG
1 AGAACGCCCG-TCGAGCGCCAAGCGGAGAACGCCCGT-CA---AGCGCCAAGGGGAGAACGCCCG
*
37716 TCGAGCGCCAAGAGG
61 TCGAGCGCCAAGCGG
* * * * * * * * * *
37731 AGAACGCCCGACGGGCGCCAAGTGGAGAACGGCCGT-AGAGGGCCACGTGTAGATCGCCCG-CAA
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCA-AGCGCCAAGGGGAGAACGCCCGTCGA
*
37794 GGCACCAAAG-GG
65 -GCGCC-AAGCGG
* * * * ** *
37806 AGAACG-CCGGCGAGCACCAAGCGAAAAACGCCCACCAGGCGCCAAGGGGAGAACGCCCGTCGAG
1 AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCGAG
*
37870 CGCCAAGCAG
66 CGCCAAGCGG
* * * * * * *
37880 AGAACGCCCG-CCAGGCGCCAATG-GGAGAATGCCAGTCGAGCGCAAAGCGGAGAACGCCCGTAG
1 AGAACGCCCGTCGA-GCGCCAA-GCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCG
37943 AGCGC
64 AGCGC
37948 GAGCATGAAT
Statistics
Matches: 541, Mismatches: 106, Indels: 78
0.75 0.15 0.11
Matches are distributed among these distances:
73 4 0.01
74 55 0.10
75 342 0.63
76 11 0.02
77 2 0.00
78 2 0.00
79 64 0.12
80 2 0.00
85 2 0.00
87 2 0.00
89 4 0.01
90 50 0.09
91 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.35, T:0.05
Consensus pattern (75 bp):
AGAACGCCCGTCGAGCGCCAAGCGGAGAACGCCCGTCAAGCGCCAAGGGGAGAACGCCCGTCGAG
CGCCAAGCGG
Found at i:37382 original size:25 final size:24
Alignment explanation
Indices: 37228--37944 Score: 222
Period size: 25 Copynumber: 29.0 Consensus size: 24
37218 CCCGTCAAGC
* * *
37228 GCCAAGGGGAGAATGCCCGTCGAG
1 GCCAAGCGGAGAACGCCCGTAGAG
* *
37252 CGACAAGCGGAGAACGCCCGTCGAG
1 -GCCAAGCGGAGAACGCCCGTAGAG
*
37277 CGCCAAGCGGAGAGCGCCCGTAGAGG
1 -GCCAAGCGGAGAACGCCCGTAGA-G
*
37303 GCCAAGTGGAGAACGCCCGCT--AG
1 GCCAAGCGGAGAACGCCCG-TAGAG
*
37326 GCAACAAGCGGAGAACGCCCGTCGAG
1 GC--CAAGCGGAGAACGCCCGTAGAG
* * *
37352 CACCAACCGGAGAACGCCCGAAGAAG
1 -GCCAAGCGGAGAACGCCCGTAG-AG
** * * *
37378 GCCAAATGCAGAACGCCCGCCAGAC
1 GCCAAGCGGAGAACGCCCG-TAGAG
** * * *
37403 ATCAAGGGGACAACG-CCG-AGTG
1 GCCAAGCGGAGAACGCCCGTAGAG
** *** **
37425 GAGAA-C-G-CCCCG-CC--AGGC
1 GCCAAGCGGAGAACGCCCGTAGAG
* *
37443 GCCAAGGGGAGAACGCCCGGCA-AG
1 GCCAAGCGGAGAACGCCC-GTAGAG
* *
37467 CGCCAAGTGGAGAACGCCCGCCAG-G
1 -GCCAAGCGGAGAACGCCCG-TAGAG
*
37492 TGCCAAGCGGAGAACACCCG-ACGAG
1 -GCCAAGCGGAGAACGCCCGTA-GAG
*
37517 CGCCAAGCGGAGAACGCCCGCCAG-G
1 -GCCAAGCGGAGAACGCCCG-TAGAG
* *
37542 CGCCAAGGGGAGAACGCCCGTCGAG
1 -GCCAAGCGGAGAACGCCCGTAGAG
*
37567 CGCCAAGCGGAGAGCGCCCGTAGAGG
1 -GCCAAGCGGAGAACGCCCGTAGA-G
* * *
37593 GCCAAGTGTAGAACGCCCGCCAG-G
1 GCCAAGCGGAGAACGCCCG-TAGAG
* * * *
37617 CGCCAAGGGGAAAACGCCCGTCGAAC
1 -GCCAAGCGGAGAACGCCCGTAG-AG
37643 GCCAAGCGGAGAACGCCCG-ATG-G
1 GCCAAGCGGAGAACGCCCGTA-GAG
*
37666 GCGCTAAGTGGAGAACGCCCGTAGAGGGAG
1 GC-C-AAGCGGAGAACGCCCGT--A--GAG
* *
37696 CGCCAAGAGGAGAACGCCCGTCGAG
1 -GCCAAGCGGAGAACGCCCGTAGAG
* *
37721 CGCCAAGAGGAGAACGCCCG-ACGGG
1 -GCCAAGCGGAGAACGCCCGTA-GAG
* *
37746 CGCCAAGTGGAGAACGGCCGTAGAGG
1 -GCCAAGCGGAGAACGCCCGTAGA-G
* * * * *
37772 GCCACGTGTAGATCGCCCGCA-AG
1 GCCAAGCGGAGAACGCCCGTAGAG
**
37795 GCACCAAAG-GGAGAACG-CCGGCGAG
1 G--CC-AAGCGGAGAACGCCCGTAGAG
* * * **
37820 CACCAAGCGAAAAACGCCCACCAG-G
1 -GCCAAGCGGAGAACGCCC-GTAGAG
* *
37845 CGCCAAGGGGAGAACGCCCGTCGAG
1 -GCCAAGCGGAGAACGCCCGTAGAG
* *
37870 CGCCAAGCAGAGAACGCCCGCCAG-G
1 -GCCAAGCGGAGAACGCCCG-TAGAG
* * *
37895 CGCCAATG-GGAGAATGCCAGTCGAG
1 -GCCAA-GCGGAGAACGCCCGTAGAG
*
37920 CGCAAAGCGGAGAACGCCCGTAGAG
1 -GCCAAGCGGAGAACGCCCGTAGAG
37945 CGCGAGCATG
Statistics
Matches: 524, Mismatches: 114, Indels: 108
0.70 0.15 0.14
Matches are distributed among these distances:
18 5 0.01
19 5 0.01
20 2 0.00
21 2 0.00
22 6 0.01
23 11 0.02
24 26 0.05
25 424 0.81
26 19 0.04
27 2 0.00
28 1 0.00
29 17 0.03
30 2 0.00
31 2 0.00
ACGTcount: A:0.28, C:0.32, G:0.36, T:0.04
Consensus pattern (24 bp):
GCCAAGCGGAGAACGCCCGTAGAG
Found at i:37945 original size:25 final size:25
Alignment explanation
Indices: 37424--37947 Score: 338
Period size: 25 Copynumber: 20.8 Consensus size: 25
37414 AACGCCGAGT
* *
37424 GGAGAACGCCCCGCCAG-GCGCCAAGG
1 GGAGAACG-CCCG-TAGAGCGCCAAGC
* *
37450 GGAGAACGCCCGGCA-AGCGCCAAGT
1 GGAGAACGCCC-GTAGAGCGCCAAGC
* *
37475 GGAGAACGCCCGCCAG-GTGCCAAGC
1 GGAGAACGCCCG-TAGAGCGCCAAGC
*
37500 GGAGAACACCCG-ACGAGCGCCAAGC
1 GGAGAACGCCCGTA-GAGCGCCAAGC
* *
37525 GGAGAACGCCCGCCAG-GCGCCAAGG
1 GGAGAACGCCCG-TAGAGCGCCAAGC
*
37550 GGAGAACGCCCGTCGAGCGCCAAGC
1 GGAGAACGCCCGTAGAGCGCCAAGC
* * *
37575 GGAGAGCGCCCGTAGAGGGCCAAGT
1 GGAGAACGCCCGTAGAGCGCCAAGC
* * *
37600 GTAGAACGCCCGCCAG-GCGCCAAGG
1 GGAGAACGCCCG-TAGAGCGCCAAGC
* * *
37625 GGAAAACGCCCGTCGAACGCCAAGC
1 GGAGAACGCCCGTAGAGCGCCAAGC
* * *
37650 GGAGAACGCCCG-ATGGGCGCTAAGT
1 GGAGAACGCCCGTA-GAGCGCCAAGC
*
37675 GGAGAACGCCCGTAGAGGGAGCGCCAAGA
1 GGAGAACGCCCGT--A--GAGCGCCAAGC
* *
37704 GGAGAACGCCCGTCGAGCGCCAAGA
1 GGAGAACGCCCGTAGAGCGCCAAGC
* *
37729 GGAGAACGCCCG-ACGGGCGCCAAGT
1 GGAGAACGCCCGTA-GAGCGCCAAGC
* * * *
37754 GGAGAACGGCCGTAGAGGGCCACGT
1 GGAGAACGCCCGTAGAGCGCCAAGC
* * * *
37779 GTAGATCGCCCGCA-AGGCACCAAAG-
1 GGAGAACGCCCGTAGA-GCGCC-AAGC
** *
37804 GGAGAACG-CCGGCGAGCACCAAGC
1 GGAGAACGCCCGTAGAGCGCCAAGC
* * ** *
37828 GAAAAACGCCCACCAG-GCGCCAAGG
1 GGAGAACGCCC-GTAGAGCGCCAAGC
*
37853 GGAGAACGCCCGTCGAGCGCCAAGC
1 GGAGAACGCCCGTAGAGCGCCAAGC
* *
37878 AGAGAACGCCCGCCAG-GCGCCAATG-
1 GGAGAACGCCCG-TAGAGCGCCAA-GC
* * * *
37903 GGAGAATGCCAGTCGAGCGCAAAGC
1 GGAGAACGCCCGTAGAGCGCCAAGC
37928 GGAGAACGCCCGTAGAGCGC
1 GGAGAACGCCCGTAGAGCGC
37948 GAGCATGAAT
Statistics
Matches: 390, Mismatches: 79, Indels: 59
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.01
24 22 0.06
25 323 0.83
26 18 0.05
27 1 0.00
28 1 0.00
29 21 0.05
ACGTcount: A:0.27, C:0.32, G:0.36, T:0.04
Consensus pattern (25 bp):
GGAGAACGCCCGTAGAGCGCCAAGC
Found at i:38044 original size:26 final size:26
Alignment explanation
Indices: 37992--38044 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
37982 AGAATGCTCG
* * *
37992 AGGTTGGAATGGAGAATGATCGTCGA
1 AGGTCGGAACGGAGAATGATCGCCGA
* *
38018 AGGTCGGAACGGAGAATGCTTGCCGA
1 AGGTCGGAACGGAGAATGATCGCCGA
38044 A
1 A
38045 TGTGAAACAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.38, T:0.19
Consensus pattern (26 bp):
AGGTCGGAACGGAGAATGATCGCCGA
Found at i:39009 original size:17 final size:17
Alignment explanation
Indices: 38983--39023 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
38973 GCCTTTCCGC
*
38983 TTTTTC-TTTCTTCCTT
1 TTTTTCTTTTCATCCTT
38999 TTTTTCTTTTCATCCTT
1 TTTTTCTTTTCATCCTT
*
39016 TTTCTCTT
1 TTTTTCTT
39024 ATTTCTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTCTTTTCATCCTT
Found at i:41179 original size:41 final size:41
Alignment explanation
Indices: 41122--41204 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
41112 GGCACAGGCG
41122 TTCTCCGTGCCTGTATTTCAGGAATGGAACAACCCCGTGCC
1 TTCTCCGTGCCTGTATTTCAGGAATGGAACAACCCCGTGCC
* * *
41163 TTCTCCGTGCCTGTATTTCTGGAATGGCACAACCTCGTGCC
1 TTCTCCGTGCCTGTATTTCAGGAATGGAACAACCCCGTGCC
41204 T
1 T
41205 AGCACTTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.30
Consensus pattern (41 bp):
TTCTCCGTGCCTGTATTTCAGGAATGGAACAACCCCGTGCC
Found at i:41564 original size:50 final size:49
Alignment explanation
Indices: 41439--41630 Score: 366
Period size: 49 Copynumber: 3.9 Consensus size: 49
41429 TTTTATTGAT
41439 CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
1 CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
41488 CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
1 CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
41537 CAATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
1 C-ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
*
41587 CATTATCGACAGTAACACCCCCTTGACGGGTAGTAAGACCGGAT
1 CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGAT
41631 GAAGAACCCT
Statistics
Matches: 141, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
49 92 0.65
50 49 0.35
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.19
Consensus pattern (49 bp):
CATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGA
Found at i:41611 original size:99 final size:99
Alignment explanation
Indices: 41440--41630 Score: 373
Period size: 99 Copynumber: 1.9 Consensus size: 99
41430 TTTATTGATC
*
41440 ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGACATTATCGGCAGTAACA
1 ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGACATTATCGACAGTAACA
41505 CCCCCTTGACGGGTAGTAAGACCGGATCGAGACA
66 CCCCCTTGACGGGTAGTAAGACCGGATCGAGACA
41539 ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGACATTATCGACAGTAACA
1 ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGACATTATCGACAGTAACA
41604 CCCCCTTGACGGGTAGTAAGACCGGAT
66 CCCCCTTGACGGGTAGTAAGACCGGAT
41631 GAAGAACCCT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (99 bp):
ATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGACCGGATCGAGACATTATCGACAGTAACA
CCCCCTTGACGGGTAGTAAGACCGGATCGAGACA
Found at i:52961 original size:7 final size:7
Alignment explanation
Indices: 52949--52973 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52939 AAAAATCCGA
52949 AAAATTC
1 AAAATTC
52956 AAAATTC
1 AAAATTC
52963 AAAATTC
1 AAAATTC
52970 AAAA
1 AAAA
52974 CAAAATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:54921 original size:23 final size:24
Alignment explanation
Indices: 54891--54941 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
54881 GTTTAAACCA
54891 CCAAAAGAG-TATTAACTTGTTGT
1 CCAAAAGAGATATTAACTTGTTGT
*
54914 CCAAAAGAGTATATTAACTTGTTTT
1 CCAAAAGAG-ATATTAACTTGTTGT
54939 CCA
1 CCA
54942 TATTTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
25 16 0.64
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (24 bp):
CCAAAAGAGATATTAACTTGTTGT
Found at i:57920 original size:12 final size:12
Alignment explanation
Indices: 57903--57928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57893 GAGTAAACTG
57903 TTAAGATGTTAT
1 TTAAGATGTTAT
57915 TTAAGATGTTAT
1 TTAAGATGTTAT
57927 TT
1 TT
57929 TTGAAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
TTAAGATGTTAT
Found at i:70249 original size:17 final size:17
Alignment explanation
Indices: 70227--70276 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
70217 TGAGAATCTC
70227 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
70244 ACCAGGTGAGTA-TT-T
1 ACCAGGTGAGTATTTGT
*
70259 ACCAAGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
70276 A
1 A
70277 TATGGGTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 12 0.40
16 4 0.13
17 14 0.47
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:70267 original size:15 final size:15
Alignment explanation
Indices: 70199--70273 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 15
70189 GGTGAGTGTG
*
70199 GGTGAGTATCTCACCA
1 GGTGAGTAT-TTACCA
* * *
70215 GATGAGAATCTCACCA
1 GGTGAGTAT-TTACCA
70231 GGTGAGTATTTGTACCA
1 GGTGAGTA-TT-TACCA
70248 GGTGAGTATTTACCA
1 GGTGAGTATTTACCA
*
70263 AGTGAGTATTT
1 GGTGAGTATTT
70274 GTATATGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
15 15 0.29
16 23 0.45
17 13 0.25
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (15 bp):
GGTGAGTATTTACCA
Found at i:75510 original size:71 final size:68
Alignment explanation
Indices: 75417--75556 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 68
75407 TTTTAATAAC
* * *
75417 TTTGCTTTTTTTTTATTGTATTAACCTCATTCCTCCTTTAATTAAAGAAAAAGGGAAATGTATTT
1 TTTGCTTTTCTTTTATTATATTAACCTCATTCCTCCTTTAATT-AA-AAAAAGAGAAATGTATTT
75482 ATTTT
64 ATTTT
*
75487 TTTGCCTTTTCTTTTATTATATTAACCTTATTCCTCCTTTAATTAAAAAAAGAGAAATGTATTTA
1 TTTG-CTTTTCTTTTATTATATTAACCTCATTCCTCCTTTAATTAAAAAAAGAGAAATGTATTTA
75552 TTTT
65 TTTT
75556 T
1 T
75557 GCCTTAAGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 23 0.35
70 6 0.09
71 36 0.55
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (68 bp):
TTTGCTTTTCTTTTATTATATTAACCTCATTCCTCCTTTAATTAAAAAAAGAGAAATGTATTTAT
TTT
Found at i:77115 original size:29 final size:29
Alignment explanation
Indices: 77052--77131 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
77042 GCTTAATACC
*
77052 CAAATTAGCCCCTTAACTATCTATTTTTGGA
1 CAAATTAGCCCCTTAACT-T-TATTTTGGGA
77083 CAAATTAGCCCCTTAACTTTATTTTGGGA
1 CAAATTAGCCCCTTAACTTTATTTTGGGA
*
77112 CAAATTGGCCCCTTAACTTT
1 CAAATTAGCCCCTTAACTTT
77132 TAAAAACGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 28 0.60
30 1 0.02
31 18 0.38
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (29 bp):
CAAATTAGCCCCTTAACTTTATTTTGGGA
Found at i:77852 original size:29 final size:29
Alignment explanation
Indices: 77816--77873 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
77806 TCTCGTTTTT
77816 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
77845 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
77874 TTGATAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Done.