Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014174.1 Corchorus capsularis cultivar CVL-1 contig14195, 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: 19514
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2704 original size:51 final size:51
Alignment explanation
Indices: 2637--2902 Score: 168
Period size: 51 Copynumber: 5.3 Consensus size: 51
2627 TAGTTTCGAT
* *
2637 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
** * * * *
2688 GTTCTCACAAAGAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG---C--C
* *
2736 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
** * * * *
2787 GTTCTCACAAAGAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG---C--C
* *
2835 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
2886 GTTCTCACAAAGAGTCC
1 GTTCTCACAAAGAGTCC
2903 AGGGCTTACG
Statistics
Matches: 155, Mismatches: 34, Indels: 52
0.64 0.14 0.22
Matches are distributed among these distances:
43 18 0.12
44 2 0.01
46 12 0.08
47 2 0.01
48 32 0.21
49 4 0.03
50 4 0.03
51 47 0.30
52 2 0.01
53 12 0.08
55 2 0.01
56 18 0.12
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (51 bp):
GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
Found at i:3071 original size:99 final size:99
Alignment explanation
Indices: 2080--3069 Score: 1513
Period size: 99 Copynumber: 10.0 Consensus size: 99
2070 ACTTAGGTTG
* * *
2080 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGACTTACGTTCGGCCAACTTAGTTTAGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
*
2145 TCTCACGATGAGTCCAGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
** * * *
2179 AATACGAACTTAGCCAATCTTACAAAGAGTCCATGGCTTACGTTCAG-CAACTTAGTTTTGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
* *
2243 TCTCACGATGAGTCTGGATCGAAATCTAAGGCCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
2277 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCTAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
2342 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * *
2376 ATTACGAACGTT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGGCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
* ** *
2440 TTCTCATGGGGAGTTCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
** *
2475 GTTACGAACGTT-GCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
2539 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * * * *
2574 ATTACAAACGTT-GCTGTTTTCACAAAGAGTCCATGGCTTACATTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
2638 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
2673 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
2738 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
2772 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
2837 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
2871 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCTAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
** *
2936 TCTCACGGGGAGTCTGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * *
2970 ATTACGAACGTT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAATTTTGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
**
3034 TTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
3069 A
1 A
3070 TTCGGAAATT
Statistics
Matches: 830, Mismatches: 57, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
98 91 0.11
99 735 0.89
100 4 0.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (99 bp):
AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
Found at i:4027 original size:231 final size:231
Alignment explanation
Indices: 3487--4270 Score: 1446
Period size: 231 Copynumber: 3.4 Consensus size: 231
3477 GGTCTACAAA
* *
3487 CTTGCCGCTCTTCATGGTCTAGCTGCCATGACTTTTGGATCAGATGGGGGATTGATCCCTTTCAA
1 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
3552 ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
66 ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
* * *
3617 GTGGATCTCCCTTAACACATAGACAGCTTCATCTGGGTCTACAAACTTCAAAAAAGAAAAGGTGA
131 GTGGATCTCCCTTAACACATAGACAGTTTCATCT-GGTCTACATACTTCAAAAAAG-GAAGGTGA
3682 AGGAT-TTCTTATATAGTTCATCATCAATCAACACATAC
194 AGGATATT-TTATATAGTTCATCATCAATCAACACATAC
*
3720 CTTGCCGCTCTTCATGGTCTGGCTGCCATGATTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
1 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
*
3785 ATACTCCACTATCTCGATCATCTACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
66 ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
3850 GTGGATCTCCCTTAACACATAGACAGTTTCATCTGGTCTACATACTTC-AAAAAGGAAGGGTGAA
131 GTGGATCTCCCTTAACACATAGACAGTTTCATCTGGTCTACATACTTCAAAAAAGGAA-GGTGAA
3914 GGATATTTTATATAGTTCATCATCAATCAACACATAC
195 GGATATTTTATATAGTTCATCATCAATCAACACATAC
3951 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
1 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
4016 ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
66 ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
4081 GTGGATCTCCCTTAACACATAGACAGTTTCATCTGGTCTACATACTTCAAAAAAGGAAGGTGAAG
131 GTGGATCTCCCTTAACACATAGACAGTTTCATCTGGTCTACATACTTCAAAAAAGGAAGGTGAAG
4146 GATATTTTATATAGTTCATCATCAATCAACACATAC
196 GATATTTTATATAGTTCATCATCAATCAACACATAC
4182 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
1 CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
*
4247 ATACTTCACTATCTCGATCATCCA
66 ATACTCCACTATCTCGATCATCCA
4271 GTTAGATCAT
Statistics
Matches: 538, Mismatches: 10, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
230 2 0.00
231 353 0.66
232 24 0.04
233 159 0.30
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (231 bp):
CTTGCCGCTCTTCATGGTCTGGCTGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAA
ATACTCCACTATCTCGATCATCCACCTTCGTGGATCAGACTTACATTCGGGGGTTTTCCACCTTC
GTGGATCTCCCTTAACACATAGACAGTTTCATCTGGTCTACATACTTCAAAAAAGGAAGGTGAAG
GATATTTTATATAGTTCATCATCAATCAACACATAC
Found at i:5888 original size:99 final size:99
Alignment explanation
Indices: 5628--5880 Score: 425
Period size: 99 Copynumber: 2.5 Consensus size: 99
5618 TTGTGGGGAA
*
5628 GATCTTCATATCTGACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
1 GATCTCCATATCTGACAC-TCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
5693 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAG
65 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAG
* * *
5728 GATCTCCATATCTGACGCTCTGCCGATCTTCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCA
1 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATCA
* * *
5793 CCATCAGATCTTTCAAGCTTGTAACCAACGTAAG
66 CCATCAAACCTTTCAAGCTTGTAACCAACATAAG
*
5827 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTC
1 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTC
5881 ATGTTCTACG
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 126 0.89
100 16 0.11
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.36
Consensus pattern (99 bp):
GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATCA
CCATCAAACCTTTCAAGCTTGTAACCAACATAAG
Found at i:5953 original size:66 final size:65
Alignment explanation
Indices: 5826--5954 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 65
5816 ACCAACGTAA
* *
5826 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTACG
1 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTATCGTTCTACCATGTTCAGGTTCTACG
* * * *
5891 GGATCTCCATATC-GAACACTTTTGTCGATCTTCGATGTTATCGTTCTTCCATGTTCGGGTTCTA
1 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTATCGTTCTACCATGTTCAGGTTCTA
5955 TCACCATCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
64 1 0.02
65 17 0.30
66 38 0.68
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.39
Consensus pattern (65 bp):
GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTATCGTTCTACCATGTTCAGGTTCTACG
Found at i:6122 original size:264 final size:264
Alignment explanation
Indices: 5628--6210 Score: 1089
Period size: 264 Copynumber: 2.2 Consensus size: 264
5618 TTGTGGGGAA
* *
5628 GATCTTCATATCTG-ACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTAT
1 GATCTCCATATC-GAACACTTCTGTCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTAT
*
5692 CACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACGCTCTGCCGATCT
65 CACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCT
5757 TCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCACCATCAGATCTTTCAAGCTTGTAACCAAC
130 TCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCACCATCAGATCTTTCAAGCTTGTAACCAAC
5822 GTAAGGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTC
195 GTAAGGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTC
5887 TACGG
260 TACGG
* *
5892 GATCTCCATATCGAACACTTTTGTCGATCTTCGATGTTATCGTTCTTCCATGTTCGGGTTCTATC
1 GATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
5957 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
66 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
6022 CGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCACCATCAGATCTTTCAAGCTTGTAACCAACG
131 CGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCACCATCAGATCTTTCAAGCTTGTAACCAACG
6087 TAAGGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCT
196 TAAGGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCT
6152 ACGG
261 ACGG
6156 GATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTT-TTACCATGTTC
1 GATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTCTT-CCATGTTC
6211 ATGTTCTACG
Statistics
Matches: 310, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
263 3 0.01
264 307 0.99
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (264 bp):
GATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
CGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCACCATCAGATCTTTCAAGCTTGTAACCAACG
TAAGGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCT
ACGG
Found at i:6152 original size:99 final size:99
Alignment explanation
Indices: 5891--6144 Score: 402
Period size: 99 Copynumber: 2.6 Consensus size: 99
5881 ATGTTCTACG
* * *
5891 GGATCTCCATATC-GAACACTTTTGTCGATCTTCGATGTTATCGTTCTTCCATGTTCGGGTTCTA
1 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTA
5955 TCACCATCAAACCTTTCAAGCTTGTAACCAACATAA
64 TCACCATCAAACCTTTCAAGCTTGTAACCAACATAA
* *
5991 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATC
1 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
* * *
6056 ACCATCAGATCTTTCAAGCTTGTAACCAACGTAA
66 ACCATCAAACCTTTCAAGCTTGTAACCAACATAA
*
6090 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTC
1 GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTC
6145 ATGTTCTACG
Statistics
Matches: 142, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
99 124 0.87
100 17 0.12
101 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (99 bp):
GGATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
ACCATCAAACCTTTCAAGCTTGTAACCAACATAA
Found at i:6197 original size:66 final size:66
Alignment explanation
Indices: 6090--6350 Score: 445
Period size: 66 Copynumber: 4.0 Consensus size: 66
6080 ACCAACGTAA
6090 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
1 GGATCTCCATATC-GAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
6153 CG
65 CG
* *
6155 GGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
6220 G
66 G
*
6221 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
6286 G
66 G
** *
6287 GGATCTCCATATCTCACACTTCTGCTGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
6351 TCACCATCAA
Statistics
Matches: 187, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
64 1 0.01
65 17 0.09
66 169 0.90
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (66 bp):
GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
G
Found at i:6670 original size:43 final size:43
Alignment explanation
Indices: 6549--6672 Score: 178
Period size: 43 Copynumber: 2.9 Consensus size: 43
6539 AATCTACATA
*
6549 TCTGAAACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGT
1 TCTGACACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGT
* *
6592 TCTTACACTTCTGCCGATCTTCGAGGTTTCTGTTCTCCTATGT
1 TCTGACACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGT
* * *
6635 TCTGACACTTCTGCCAATCTACAATGTTGTC-GTTCTCC
1 TCTGACACTTCTGCCGATCTTCGATGTT-TCTGTTCTCC
6673 CTTATTCAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 70 0.97
44 2 0.03
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (43 bp):
TCTGACACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGT
Found at i:10836 original size:13 final size:13
Alignment explanation
Indices: 10814--10843 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10804 GGATCTTTTT
10814 ATTTGCTGCTTTG
1 ATTTGCTGCTTTG
*
10827 ATTTGTTGCTTTG
1 ATTTGCTGCTTTG
10840 ATTT
1 ATTT
10844 TTTGGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (13 bp):
ATTTGCTGCTTTG
Found at i:14859 original size:2 final size:2
Alignment explanation
Indices: 14852--14909 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
14842 CTCGTACTTT
* * * * *
14852 TA TA TA TA GTA TA GA TA GA TA TA GA TA TA TA GA TA TA GA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14895 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
14910 TTGTTTATGT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (2 bp):
TA
Found at i:14885 original size:14 final size:14
Alignment explanation
Indices: 14855--14909 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
14845 GTACTTTTAT
*
14855 ATATAGTATAGATAG
1 ATATAG-ATATATAG
14870 ATATAGATATATAG
1 ATATAGATATATAG
*
14884 ATATAGATATATAT
1 ATATAGATATATAG
*
14898 ATATATATATAT
1 ATATAGATATAT
14910 TTGTTTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 31 0.84
15 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (14 bp):
ATATAGATATATAG
Found at i:15317 original size:13 final size:13
Alignment explanation
Indices: 15284--15309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15274 TATACAAATT
15284 AATAAAAGGAGGA
1 AATAAAAGGAGGA
15297 AATAAAAGGAGGA
1 AATAAAAGGAGGA
15310 TATGAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (13 bp):
AATAAAAGGAGGA
Found at i:17076 original size:1 final size:1
Alignment explanation
Indices: 17070--17094 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17060 TTAGATCTTG
17070 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17095 CTACTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.