Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010151.1 Corchorus capsularis cultivar CVL-1 contig10172, 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: 32042
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:3624 original size:400 final size:402
Alignment explanation
Indices: 2864--3676 Score: 1459
Period size: 400 Copynumber: 2.0 Consensus size: 402
2854 TGCAGGGCCT
* *
2864 TCCCAACAACTGGTATCAGAGCCTGGTTGAACTCGATGATTGTGGCCCATGAGCACGGTAAACCT
1 TCCCAACAAGTGGTATCAGAGCCTGGTTGAACCCGATGATTGTGGCCCATGAGCACGGTAAACCT
*
2929 GGTTGGCCGCACGCCAGAGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCCAGGGGTTA
66 GGTTGGCCGCACACCAGAGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCCAGGGGTTA
*
2994 AGTCTTGGATAACCGGTAATTGGCTTAAGACTTGACGGGTTAGGTCGCACGGGGGAGAGAGATAA
131 AGTCTTGGATAACCGGTAATTGGCTTAAGACTTGACGGGTTAGGCCGCAC-GGGGAGAGAGATAA
* *
3059 GGACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCGCATGTGAGGGAACATCCCACATCAT
195 GGACTCACAAGTGAATCGGGGGAGATTGTTAAAGGATTCACATGTGAGGGAACATCCCACATCAT
3124 GAAGAGATGGGATGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTT
260 GAAGAGATGGGATGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTT
3189 TTGGGTTCGGATTGGTGTCTGACATGTATATGGGCTGCTCGGTGGGCCTTGCTGAAGCAGACAGG
325 TTGGGTTCGGATTGGTGTCTGACATGTATATGGGCTGCTCGGTGGGCCTTGCTGAAGCAGACAGG
*
3254 GCATGGGTTCCTC
390 GCACGGGTTCCTC
* *
3267 TCCCAACAAGTGGTATCTGAGTCTGGTTGAACCCGATGATTGTGGCCCATGAGCACGGTAAACCT
1 TCCCAACAAGTGGTATCAGAGCCTGGTTGAACCCGATGATTGTGGCCCATGAGCACGGTAAACCT
* *
3332 GGTTGGCCGCACACCAGGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCTAGGGGTTA
66 GGTTGGCCGCACACCAGAGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCCAGGGGTTA
* * *
3397 AGTCTTGGATAGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCAC-GGG-GAGAGATGAG
131 AGTCTTGGATAACCGGTAATTGGCTTAAGACTTGACGGGTTAGGCCGCACGGGGAGAGAGATAAG
*
3460 GACTCACAAGTGAATCGGGGGAGATTGTTAAAGGATTCACATGTGAGGGAACATCCTACATCATG
196 GACTCACAAGTGAATCGGGGGAGATTGTTAAAGGATTCACATGTGAGGGAACATCCCACATCATG
3525 AAGAGATGGGATGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTT
261 AAGAGATGGGATGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTT
3590 TGGGTTCGGATTGGTGTCTGACATGTATATGGGCTGCTCGGTGGGCCTTGCTGAAGCAGACAGGG
326 TGGGTTCGGATTGGTGTCTGACATGTATATGGGCTGCTCGGTGGGCCTTGCTGAAGCAGACAGGG
*
3655 CCCGGGTTCCTC
391 CACGGGTTCCTC
3667 TCCCAACAAG
1 TCCCAACAAG
3677 ATGGCTGTGA
Statistics
Matches: 394, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
400 221 0.56
401 3 0.01
403 170 0.43
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (402 bp):
TCCCAACAAGTGGTATCAGAGCCTGGTTGAACCCGATGATTGTGGCCCATGAGCACGGTAAACCT
GGTTGGCCGCACACCAGAGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCCAGGGGTTA
AGTCTTGGATAACCGGTAATTGGCTTAAGACTTGACGGGTTAGGCCGCACGGGGAGAGAGATAAG
GACTCACAAGTGAATCGGGGGAGATTGTTAAAGGATTCACATGTGAGGGAACATCCCACATCATG
AAGAGATGGGATGTTGGAGTAGCTTATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTT
TGGGTTCGGATTGGTGTCTGACATGTATATGGGCTGCTCGGTGGGCCTTGCTGAAGCAGACAGGG
CACGGGTTCCTC
Found at i:5440 original size:17 final size:18
Alignment explanation
Indices: 5415--5457 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
5405 TTTGAATTTT
*
5415 TTTTCTTTTCT-TTTGTC
1 TTTTGTTTTCTATTTGTC
5432 TTTTGTTTTCTATTTGTC
1 TTTTGTTTTCTATTTGTC
5450 -TTTGTTTT
1 TTTTGTTTT
5458 TGTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTCTATTTGTC
Found at i:7096 original size:27 final size:27
Alignment explanation
Indices: 7066--7122 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
7056 TGGCATGTCA
* * *
7066 AAGAAATTTCGAGTTTAAATTAGTAGC
1 AAGAAATTGCAAGTATAAATTAGTAGC
7093 AAGAAATTGCAAGTATAAATTAGTAGC
1 AAGAAATTGCAAGTATAAATTAGTAGC
7120 AAG
1 AAG
7123 TATCTTGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (27 bp):
AAGAAATTGCAAGTATAAATTAGTAGC
Found at i:7506 original size:12 final size:12
Alignment explanation
Indices: 7489--7516 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7479 CACTGGTTTT
7489 AACAAAAAAAAA
1 AACAAAAAAAAA
7501 AACAAAAAAAAA
1 AACAAAAAAAAA
7513 AACA
1 AACA
7517 TGAACCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAAAAAAAA
Found at i:9910 original size:6 final size:6
Alignment explanation
Indices: 9899--9926 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9889 TACTAGGAGT
9899 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
9927 ATTTCAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:10710 original size:12 final size:12
Alignment explanation
Indices: 10685--10768 Score: 65
Period size: 12 Copynumber: 7.4 Consensus size: 12
10675 TTTTCCCCAA
10685 TTTCTT-TT-CT
1 TTTCTTCTTCCT
10695 TTTCTTCTTCCT
1 TTTCTTCTTCCT
*
10707 TTTCTTCTTCGT
1 TTTCTTCTTCCT
*
10719 TTTCTGCTT--T
1 TTTCTTCTTCCT
* *
10729 TATCAAT-TT-CT
1 TTTC-TTCTTCCT
10740 TTTCTTCTTCCT
1 TTTCTTCTTCCT
10752 TTTCTTC-TCCGT
1 TTTCTTCTTCC-T
10764 TTTCT
1 TTTCT
10769 GCTTTTATCA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
10 13 0.22
11 11 0.18
12 36 0.60
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.67
Consensus pattern (12 bp):
TTTCTTCTTCCT
Found at i:10741 original size:45 final size:45
Alignment explanation
Indices: 10690--10790 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 45
10680 CCCAATTTCT
*
10690 TTTCTTTTCTTCTTCCTTTTCTTCTTCGTTTTCTGCTTTTATCAA
1 TTTCTTTTCTTCTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAA
10735 TTTCTTTTCTTCTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAA
1 TTTCTTTTCTTCTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAA
10780 TTTCTTTTCTT
1 TTTCTTTTCTT
10791 AAATTTTTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.06, C:0.25, G:0.04, T:0.65
Consensus pattern (45 bp):
TTTCTTTTCTTCTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAA
Found at i:10742 original size:21 final size:21
Alignment explanation
Indices: 10718--10789 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
10708 TTCTTCTTCG
10718 TTTTCTGCTTTTATCAATTTC
1 TTTTCTGCTTTTATCAATTTC
* *
10739 TTTTCTTCTTCCTTTTC--TTCTCC
1 TTTTCTGCTT--TTATCAATT-T-C
10762 GTTTTCTGCTTTTATCAATTTC
1 -TTTTCTGCTTTTATCAATTTC
10784 TTTTCT
1 TTTTCT
10790 TAAATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 17 0.43
22 6 0.15
23 6 0.15
24 11 0.28
ACGTcount: A:0.08, C:0.24, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTCTGCTTTTATCAATTTC
Found at i:10839 original size:12 final size:12
Alignment explanation
Indices: 10818--10877 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 12
10808 TCTTACCTAA
10818 TTTCTT-AATTT
1 TTTCTTAAATTT
10829 TTTCTTAAATTT
1 TTTCTTAAATTT
*
10841 TTATACGTTGTATATTT
1 TT-T-C--T-TAAATTT
10858 TTTCTTAAATTT
1 TTTCTTAAATTT
10870 TTTCTTAA
1 TTTCTTAA
10878 TTTCACCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 6 0.15
12 21 0.51
13 2 0.05
14 1 0.02
15 1 0.02
16 2 0.05
17 8 0.20
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTCTTAAATTT
Found at i:10945 original size:31 final size:30
Alignment explanation
Indices: 10857--10946 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 30
10847 GTTGTATATT
*
10857 TTTTCTTAAATTTTTTCTTAATTTCACCTTT--
1 TTTTCTT-AATTTTTTCTTAATTT-A-TTTTCC
*
10888 TTTCCTTAATTTTTTCTT--TTCT-TTTTCC
1 TTTTCTTAATTTTTTCTTAATT-TATTTTCC
10916 TTTTCTTAATTTTTTCTTAAATTTATTTTCC
1 TTTTCTTAATTTTTTCTT-AATTTATTTTCC
10947 ACCATCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
26 3 0.06
28 19 0.39
29 1 0.02
30 12 0.24
31 14 0.29
ACGTcount: A:0.16, C:0.17, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTCTTAATTTTTTCTTAATTTATTTTCC
Found at i:11099 original size:24 final size:23
Alignment explanation
Indices: 11055--11101 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11045 TTTCTAAAGA
*
11055 ATTTGGGAATGGTGCATATGATT
1 ATTTGGGAATGGTGCAAATGATT
* *
11078 ATTTGGGGATGGTGAGAAATGATT
1 ATTTGGGAATGGTG-CAAATGATT
11102 TGGGTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (23 bp):
ATTTGGGAATGGTGCAAATGATT
Found at i:11340 original size:221 final size:220
Alignment explanation
Indices: 10950--11687 Score: 1133
Period size: 220 Copynumber: 3.3 Consensus size: 220
10940 ATTTTCCACC
*
10950 ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAGAT-CCAAAAATATGGATTAAAGCACTTTTTAAA
* * * * *
11015 GTCAAATTTGTGTATATGAGAAAATATCAATTTCTAAAGAATTTGGGAATGGTGCATATGATTAT
65 GTCAAATTTGTGTATATGAGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTAA
* * **
11080 TTGGGGATGGTGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACATT
130 TTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCATTTTGGGGATACTGAATTTTGCATT
*
11145 TTGTTTAATTATGAGATGGCGCTAAA
195 TTGTTTAATTATGAGACGGCGCTAAA
* *
11171 ATCATATAGACGTGGTTTATTCAATTAATTAGAAT-GAAAAATATGGATTAAAGCACGTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAG-ATCCAAAAATATGGATTAAAGCACTTTTTAAA
* * *
11235 GTCAAATTTGTGTATACGAAAAAAATGTCAATCCCTAAAGAATTTGGGGATGGTGCATAAGATTA
65 GTCAAATTTGTGTATATG-AGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTA
*
11300 ATTGGGGATGATGA-AAACTGATTTGGGTATAAACTATATCATTTTGGGGATACTGAATTTTGCA
129 ATTGGGGATGATGAGAAA-TGATTTGGGTATAAAGTATATCATTTTGGGGATACTGAATTTTGCA
*
11364 TTTTGTTTAATTATGAGACGGTGCTAAA
193 TTTTGTTTAATTATGAGACGGCGCTAAA
* *
11392 ATCATATATACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCAC-TTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAGAT-CCAAAAATATGGATTAAAGCACTTTTTAAA
*
11456 GTCAAATTTGTGTATATGAGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTCA
65 GTCAAATTTGTGTATATGAGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTAA
* * *
11521 TTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATCATTTTGGTGATACTAAATTTTGCATT
130 TTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCATTTTGGGGATACTGAATTTTGCATT
* *
11586 TTGTTTAATTACGAGAGGGCGCTAAA
195 TTGTTTAATTATGAGACGGCGCTAAA
* *
11612 ATCATATAGACGTGGTTTATTCAATTAATTAGAAT-AAAAAATATGGTTTAAAGCACTTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAG-ATCCAAAAATATGGATTAAAGCACTTTTTAAA
*
11676 GTCAAAATTGTG
65 GTCAAATTTGTG
11688 AAATTCAGTA
Statistics
Matches: 472, Mismatches: 37, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
219 18 0.04
220 221 0.47
221 212 0.45
222 21 0.04
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (220 bp):
ATCATATAGACGTGGTTTATTCAATTAATTAGATCCAAAAATATGGATTAAAGCACTTTTTAAAG
TCAAATTTGTGTATATGAGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTAAT
TGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCATTTTGGGGATACTGAATTTTGCATTT
TGTTTAATTATGAGACGGCGCTAAA
Found at i:12170 original size:220 final size:219
Alignment explanation
Indices: 11678--12314 Score: 978
Period size: 220 Copynumber: 2.9 Consensus size: 219
11668 TTTTTAAAGT
*
11678 CAAAATTGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCT
1 CAAAA-TGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCC
* *
11743 CCAAATAATCATATGCACCATTCCCAAATTCCTTAGAAATTGACATTTTCTCATATACACAACTT
65 CCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATT
*
11808 TGACTTTAAAAAGTGCTTTAATCCATATTTTAGGGATCTAATTAATTGAATAAACCACGT-TA-T
130 TGACTTTAAAAAGTGATTTAATCCATATTTTA-GGATCTAATTAATTGAATAAACCACGTCTATT
**
11871 GATTTTAGCGCCGTCTCATAATTAAA
194 GATTTTAGCGCAATCTCATAATTAAA
** * *
11897 CAAAATGCAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATTTTTCATCATCCC
1 CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
* * * *
11962 CAATTAATCTTAAGCACCA-TCTCCAAATTCTTTAGAGATTGACATTTTCTCATATACACAAATT
66 CAAATAATCATATGCACCATTC-CCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATT
* * **
12026 GGACTTTAAAAAGTGTTTTAATCCATATTTT-TCATTCTAATTAATTGAATAAACCACGTCTATT
130 TGACTTTAAAAAGTGATTTAATCCATATTTTAGGA-TCTAATTAATTGAATAAACCACGTCTA-T
12090 TGATTTTAGCGCAATCTCATAATTAAA
193 TGATTTTAGCGCAATCTCATAATTAAA
*
12117 CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCACCATCCC
1 CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
*
12182 CAAATAATCATATGCACTATTCCCAAATTCTTTAGAAATTG-CTATTTTCTCATATACACAAATT
66 CAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGAC-ATTTTCTCATATACACAAATT
*
12246 TGACTTTAAAAAGTGATTTAATCCATATTTTAGGGATCTAATTAATTGAATGAACCACGTCTATA
130 TGACTTTAAAAAGTGATTTAATCCATATTTTA-GGATCTAATTAATTGAATAAACCACGTCTAT-
12311 TGAT
193 TGAT
12315 GGTGGAAAAT
Statistics
Matches: 376, Mismatches: 32, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
216 1 0.00
217 26 0.07
218 141 0.38
219 6 0.02
220 169 0.45
221 32 0.09
222 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.35
Consensus pattern (219 bp):
CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
CAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATTT
GACTTTAAAAAGTGATTTAATCCATATTTTAGGATCTAATTAATTGAATAAACCACGTCTATTGA
TTTTAGCGCAATCTCATAATTAAA
Found at i:12373 original size:11 final size:11
Alignment explanation
Indices: 12359--12448 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
12349 GGAAAAAGAA
12359 AAGAAAAAATT
1 AAGAAAAAATT
12370 AAGAAAAAA--
1 AAGAAAAAATT
* *
12379 AAGGGTAGAAATT
1 AA--GAAAAAATT
*
12392 AAGAAAAATTT
1 AAGAAAAAATT
12403 AAGAAAAAATAT
1 AAGAAAAAAT-T
12415 ACAACGTATAAAAACTT
1 --AA-G-A-AAAAA-TT
12432 AAGAAAAAATT
1 AAGAAAAAATT
12443 AAGAAA
1 AAGAAA
12449 TTGGGGAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
9 2 0.03
11 37 0.60
12 6 0.10
13 3 0.05
14 3 0.05
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:12375 original size:22 final size:22
Alignment explanation
Indices: 12350--12399 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12340 TTAAGAAAAG
12350 GAAAAAGAAA-AGAAAAAATTAA
1 GAAAAA-AAAGAGAAAAAATTAA
* * *
12372 GAAAAAAAAGGGTAGAAATTAA
1 GAAAAAAAAGAGAAAAAATTAA
12394 GAAAAA
1 GAAAAA
12400 TTTAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (22 bp):
GAAAAAAAAGAGAAAAAATTAA
Found at i:25160 original size:1 final size:1
Alignment explanation
Indices: 25154--25205 Score: 77
Period size: 1 Copynumber: 52.0 Consensus size: 1
25144 ATCACAAGCA
* * *
25154 TTTTTTTTTCTTTGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25206 CTGAAAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.04, G:0.02, T:0.94
Consensus pattern (1 bp):
T
Found at i:26255 original size:3 final size:3
Alignment explanation
Indices: 26247--26278 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
26237 AAAGCAAAGT
26247 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
26279 TTATTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Done.