Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012062.1 Corchorus olitorius cultivar O-4 contig12095, 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: 41713
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:21 original size:15 final size:16
Alignment explanation
Indices: 1--32 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1 ATTAAAC-AGAAAACA
1 ATTAAACTAGAAAACA
16 ATTAAACTAGAAAACA
1 ATTAAACTAGAAAACA
32 A
1 A
33 AGCAGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (16 bp):
ATTAAACTAGAAAACA
Found at i:3477 original size:15 final size:13
Alignment explanation
Indices: 3449--3492 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3439 GAGTCATGGT
3449 TTTCAAAAAA-GA
1 TTTCAAAAAATGA
3461 TTTCAATAAAATTGA
1 TTTCAA-AAAA-TGA
*
3476 TTTCCAAAAATGA
1 TTTCAAAAAATGA
3489 TTTC
1 TTTC
3493 GAAACTCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 4 0.14
15 7 0.25
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (13 bp):
TTTCAAAAAATGA
Found at i:4554 original size:28 final size:28
Alignment explanation
Indices: 4514--4611 Score: 151
Period size: 28 Copynumber: 3.4 Consensus size: 28
4504 CTTAAAGTGA
4514 CATTTTGGTCATTTTGCATGTCCAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
*
4542 CATTTTGGTCATTTTGCATGTCTAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
**
4570 CATTTTGGTCATTTTGCACATCCATGGGG
1 CATTTTGGTCATTTTGCATGTCCA-GGGG
4599 CATTTTGGGTCAT
1 CATTTT-GGTCAT
4612 CTCAAGTACT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 48 0.75
29 10 0.16
30 6 0.09
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (28 bp):
CATTTTGGTCATTTTGCATGTCCAGGGG
Found at i:5000 original size:35 final size:35
Alignment explanation
Indices: 4960--5030 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4950 GCCTCATGCA
4960 TTATTTTGATTTTCTTTGCTTGGCATTGAATGTAT
1 TTATTTTGATTTTCTTTGCTTGGCATTGAATGTAT
*
4995 TTATTTTGATTTTCTTTGCTTGGCATTGCATGTAT
1 TTATTTTGATTTTCTTTGCTTGGCATTGAATGTAT
5030 T
1 T
5031 GGAGTGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.58
Consensus pattern (35 bp):
TTATTTTGATTTTCTTTGCTTGGCATTGAATGTAT
Found at i:5207 original size:25 final size:25
Alignment explanation
Indices: 5179--5246 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
5169 GAGGTTGTAA
*
5179 TCTACATTTGCATTCTTTTTTACAT
1 TCTACATTTGCATTCTTTTTTACAC
* * *
5204 TCTACACTAGCATTC-CTTTTACAC
1 TCTACATTTGCATTCTTTTTTACAC
*
5228 TCTACATTTACATTTCTTT
1 TCTACATTTGCA-TTCTTT
5247 CGCACCAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
24 16 0.48
25 16 0.48
26 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (25 bp):
TCTACATTTGCATTCTTTTTTACAC
Found at i:6233 original size:39 final size:39
Alignment explanation
Indices: 6118--6241 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 39
6108 GGAAAAAAAG
6118 TTCACTACATCTCAAAACTTAGCCATATGCA-CTTTTCAA
1 TTCACTACATCTCAAAACTTAGCCATATGCATC-TTTCAA
* * ** * *
6157 TCCATTGTATCTTAAAACTTAGCCATATGCATTTTTCAA
1 TTCACTACATCTCAAAACTTAGCCATATGCATCTTTCAA
* *
6196 TTCACTACATCTCAAAACTTAGCCAGATGCATCTTTCAG
1 TTCACTACATCTCAAAACTTAGCCATATGCATCTTTCAA
6235 TTCACTA
1 TTCACTA
6242 TCCTTTTGAC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.35
Consensus pattern (39 bp):
TTCACTACATCTCAAAACTTAGCCATATGCATCTTTCAA
Found at i:8799 original size:16 final size:16
Alignment explanation
Indices: 8778--8810 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8768 AAGAGGTAAT
*
8778 AAAAGGTTTTTTTCAA
1 AAAAGGTTTTTCTCAA
8794 AAAAGGTTTTTCTCAA
1 AAAAGGTTTTTCTCAA
8810 A
1 A
8811 TCATGTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
AAAAGGTTTTTCTCAA
Found at i:10506 original size:69 final size:69
Alignment explanation
Indices: 10355--10508 Score: 168
Period size: 69 Copynumber: 2.2 Consensus size: 69
10345 AAATGCTTGA
* * * ** *
10355 CTTTTTCATAAGACAAACTCGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAGCCACA
1 CTTTTACATAAGCCAAACTCGTTTCCATACGAGACAATTTAAGCATTGGTTCCATCCAAGCCACA
10420 TAGG
66 TAGG
* * * * *
10424 CTTTTCCACAAGCCAAATTCGTTTCCATATGAGACAATTTAAGCATTGGTTCCATCCATACGGCA
1 CTTTTACATAAGCCAAACTCGTTTCCATACGAGACAATTTAAGCATTGGTTCCATCCA-A-GCCA
*
10489 -A-GGG
64 CATAGG
10493 CTTTTACATAAGCCAA
1 CTTTTACATAAGCCAA
10509 GTTTAATGAG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
69 65 0.93
70 2 0.03
71 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (69 bp):
CTTTTACATAAGCCAAACTCGTTTCCATACGAGACAATTTAAGCATTGGTTCCATCCAAGCCACA
TAGG
Found at i:10894 original size:169 final size:168
Alignment explanation
Indices: 10608--11052 Score: 653
Period size: 169 Copynumber: 2.6 Consensus size: 168
10598 AGTTTCAATA
* * *
10608 CGGGTATCATTTCATTTCATCAAGTATTTCATCAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
1 CGGGTACCATTTCATTTCATCAAGT-TTTCATCAAAGATTCATGTTTAAGTTTAAAATCCTTGTT
*
10673 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCT-TTGGGCACAAATTCAGAAACCTCCGGGT
65 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCT-GGCACAAATTCAGAAACCTCCGGGT
*
10737 ATTAATTCTGATAAGTCCTCCGGGCAATCAGTAAAACCAC-
129 ACTAATTCTGATAAGTCCTCCGGGCAATCAGTAAAACC-CG
* * *
10777 CGGGTACCATTTCATTTCATTAAGCTTTTCATTAAAGATTCTTGTTTAAGTTTAAAATCCTTGTT
1 CGGGTACCATTTCATTTCATCAAG-TTTTCATCAAAGATTCATGTTTAAGTTTAAAATCCTTGTT
* * * * *
10842 CAAGGTTTCAATTCAAAGTTTGCATTGGTAAGTCCTCCTGGCACAAATTCAGAAACCTGCGGGTA
65 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCTGGCACAAATTCAGAAACCTCCGGGTA
* *
10907 CTAATTCTGATAAGTCCTCCGGGCAATCTGTAAAGCCCG
130 CTAATTCTGATAAGTCCTCCGGGCAATCAGTAAAACCCG
* * *
10946 CGGGAACCATTTCATTTTATCAAGTTTTCATCATAGATTCATGTTTAAGTTTAAAATCCTT-TGT
1 CGGGTACCATTTCATTTCATCAAGTTTTCATCAAAGATTCATGTTTAAGTTTAAAATCCTTGT-T
*
11010 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCA
65 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCTGGCA
11053 ACTGATAAGT
Statistics
Matches: 246, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
167 1 0.00
168 74 0.30
169 169 0.69
170 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (168 bp):
CGGGTACCATTTCATTTCATCAAGTTTTCATCAAAGATTCATGTTTAAGTTTAAAATCCTTGTTC
AAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCTGGCACAAATTCAGAAACCTCCGGGTAC
TAATTCTGATAAGTCCTCCGGGCAATCAGTAAAACCCG
Found at i:11338 original size:38 final size:38
Alignment explanation
Indices: 11286--11407 Score: 165
Period size: 39 Copynumber: 3.2 Consensus size: 38
11276 TGTATTCTTT
11286 TTTATTTGGTTAA-TTCTGATCCTGGTTTAGGATCATTGC
1 TTTA-TTGGTTAATTTC-GATCCTGGTTTAGGATCATTGC
*
11325 TTTATTGGTTAATTTCGATCATGGTTTAGGATCATTGC
1 TTTATTGGTTAATTTCGATCCTGGTTTAGGATCATTGC
* * * *
11363 TTTATCAGCTTATTTTCAATCCTGGTTTAGGATCATTGC
1 TTTAT-TGGTTAATTTCGATCCTGGTTTAGGATCATTGC
11402 TTTATT
1 TTTATT
11408 TATTTATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
38 34 0.46
39 40 0.54
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (38 bp):
TTTATTGGTTAATTTCGATCCTGGTTTAGGATCATTGC
Found at i:11415 original size:39 final size:38
Alignment explanation
Indices: 11304--11421 Score: 155
Period size: 39 Copynumber: 3.1 Consensus size: 38
11294 GTTAATTCTG
** * *
11304 ATCCTGGTTTAGGATCATTGCTTTATTGGTTAATTTCG
1 ATCCTGGTTTAGGATCATTGCTTTATTACTTATTTTCA
* *
11342 ATCATGGTTTAGGATCATTGCTTTATCAGCTTATTTTCA
1 ATCCTGGTTTAGGATCATTGCTTTATTA-CTTATTTTCA
*
11381 ATCCTGGTTTAGGATCATTGCTTTATTTATTTATTTTCA
1 ATCCTGGTTTAGGATCATTGCTTTA-TTACTTATTTTCA
11420 AT
1 AT
11422 TTTATTCTGG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 25 0.36
39 42 0.61
40 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (38 bp):
ATCCTGGTTTAGGATCATTGCTTTATTACTTATTTTCA
Found at i:16838 original size:21 final size:21
Alignment explanation
Indices: 16784--16838 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
16774 GTCAATCTCT
* *
16784 AATGAATTTGGGGATGGTGCTA
1 AATG-ATTTGGGGATGATGATA
*
16806 ATGATTATTTGGGGATGATGATA
1 A--ATGATTTGGGGATGATGATA
16829 AATGATTTGG
1 AATGATTTGG
16839 ATATAGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 8 0.30
22 1 0.04
23 16 0.59
24 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (21 bp):
AATGATTTGGGGATGATGATA
Found at i:17821 original size:224 final size:221
Alignment explanation
Indices: 17424--17855 Score: 679
Period size: 224 Copynumber: 1.9 Consensus size: 221
17414 AAACAATCAC
* * * * *
17424 TATTAGATGACACTAAATTTATATAGACGTGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAAATGACACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
*
17489 TAGAACACGTTTAAAGCCAATTTTGGGTATATAAGAAAAAATGCCAATCTCTAAAGAATTTGGGG
66 TAGAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAAAATGCCAATCTCTAAAGAATTTGGGG
* *
17554 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
131 ATGGTGCATATGATTATTTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATAAGTTTGGGG
17619 ATACTGAATTTTGTATTTCGTTTAAT
196 ATACTGAATTTTGTATTTCGTTTAAT
*
17645 TATTAAATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAAATGACACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* * *
17710 TA-AAGCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTT
66 TAGAA-CAC-GTTTAAAGCCAATTTTGGGTATAT-A-AAAAAAAATGCCAATCTCTAAAGAATTT
* *
17774 GGGTATGGTGCTTATGATTATTTAGGGATGATGAGAAA-GTATTTGGGTATAAAGTATATAAGTT
127 GGGGATGGTGCATATGATTATTTAGGGATGATGAGAAATG-ATTTGGGTATAAAGTATATAAGTT
17838 TGGGGATACTGAATTTTG
191 TGGGGATACTGAATTTTG
17856 CACAAGTAAA
Statistics
Matches: 192, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
220 2 0.01
221 64 0.33
222 22 0.11
223 2 0.01
224 102 0.53
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (221 bp):
TATTAAATGACACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
TAGAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAAAATGCCAATCTCTAAAGAATTTGGGG
ATGGTGCATATGATTATTTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATAAGTTTGGGG
ATACTGAATTTTGTATTTCGTTTAAT
Found at i:18442 original size:224 final size:221
Alignment explanation
Indices: 18055--18469 Score: 677
Period size: 224 Copynumber: 1.9 Consensus size: 221
18045 AATAATCTAC
* *
18055 TATTAGATGACACTAAATTTATATAGACGGGGTTTATTCAATTAATTACAATGAAAAATATGGAT
1 TATTAGATGACACTAAAATCATATAGACGGGGTTTATTCAATTAATTACAATGAAAAATATGGAT
*
18120 TAAAACACAATTGAAGCCAATTTTGGGTATATAAGAAAAAATGTCAATCTCTAAAGAATTTGGCC
66 TAAAACACAATTAAAGCCAATTTTGGGTATATAAGAAAAAATGTCAATCTCTAAAGAATTTGGCC
*
18185 ATGGTGGATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
131 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
18250 ATACTGAATTTTTCATTTTGTTTAAT
196 ATACTGAATTTTTCATTTTGTTTAAT
* **
18276 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATGGAAAAATATGGA
1 TATTAGATGACACTAAAATCATATAGACGGGGTTTATTCAATTAATTACAAT-GAAAAATATGGA
* ** * *
18341 TTAAATCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAATGTCAATCTCTAAAGAATTTG
65 TTAAAACAC-AATTAAAGCCAATTTTGGGTATATAAG-AAAAAATGTCAATCTCTAAAGAATTTG
**
18406 GGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTT
128 GCCATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTT
18470 TGTCGTAACA
Statistics
Matches: 177, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
221 47 0.27
222 20 0.11
223 22 0.12
224 88 0.50
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (221 bp):
TATTAGATGACACTAAAATCATATAGACGGGGTTTATTCAATTAATTACAATGAAAAATATGGAT
TAAAACACAATTAAAGCCAATTTTGGGTATATAAGAAAAAATGTCAATCTCTAAAGAATTTGGCC
ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
ATACTGAATTTTTCATTTTGTTTAAT
Found at i:18461 original size:631 final size:630
Alignment explanation
Indices: 17259--18469 Score: 2140
Period size: 631 Copynumber: 1.9 Consensus size: 630
17249 AAAAGATCAT
17259 TTCAAATGAAAACAAGATGTATTGTTGCACAAGTAAATTGAATCTCTAGACATTCTTGAAGATAG
1 TTCAAATGAAAACAAGATGTATTGTTGCACAAGTAAATTGAATCTCTAGACATTCTTGAAGATAG
* *
17324 ATTAAAAGGTATTCCACACTAGTCAAAATTGCATACTTGACAATATTCCTACATAACTTGAATGG
66 ATTAAAAGGTATTCCACACTAGCCAAAATTGCATACTTGACAATATTCCTACATAACTTGAACGG
*
17389 GTAAGAAATGCTTGATACAACAAAAAAACAATCACTATTAGATGACACTAAATTTATATAGACGT
131 GTAAGAAATGCTTGATACAACAAAAAAACAATCACTATTAGATGACACTAAATTTATATAGACGG
** * **
17454 GGTTTATTCAATTAATTAGGATGAAAAATATGGATTAGAACACGTTTAAAGCCAATTTTGGGTAT
196 GGTTTATTCAATTAATTACAATGAAAAATATGGATTAAAACACAATTAAAGCCAATTTTGGGTAT
**
17519 ATAAGAAAAAATGCCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGA
261 ATAAGAAAAAATGCCAATCTCTAAAGAATTTGGCCATGGTGCATATGATTATTTGGGGATGATGA
17584 GAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTCGTTTAATTATT
326 GAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTCGTTTAATTATT
17649 AAATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGATTAAA
391 AAATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGATTAAA
*
17714 GCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTTGGGTA
456 GCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTTGGGGA
*
17779 TGGTGCTTATGATTATTTAGGGATGATGAGAAAGTATTTGGGTATAAAGTATATAAGTTTGGGGA
521 TGGTGCATATGATTATTTAGGGATGATGAGAAAGTATTTGGGTATAAAGTATATAAGTTTGGGGA
17844 TACTGAATTTTGCACAAGTAAATTGAATCTTTAGACATTCTTGAA
586 TACTGAATTTTGCACAAGTAAATTGAATCTTTAGACATTCTTGAA
17889 TTCAAATGAAAACAAGATGTATTGTTGCACAAGTAAATTGAATCTCTAGACATTCTTGAAGATAG
1 TTCAAATGAAAACAAGATGTATTGTTGCACAAGTAAATTGAATCTCTAGACATTCTTGAAGATAG
* *
17954 ATTAAAAGGTATTCCACACTAGCCAAAATTGCATACTTGACCATATTCCTACATAACTTGAGCGG
66 ATTAAAAGGTATTCCACACTAGCCAAAATTGCATACTTGACAATATTCCTACATAACTTGAACGG
* *
18019 GTAAGAAATGCTTGGTACAACAAAAAAATAATCTACTATTAGATGACACTAAATTTATATAGACG
131 GTAAGAAATGCTTGATACAACAAAAAAACAATC-ACTATTAGATGACACTAAATTTATATAGACG
*
18084 GGGTTTATTCAATTAATTACAATGAAAAATATGGATTAAAACACAATTGAAGCCAATTTTGGGTA
195 GGGTTTATTCAATTAATTACAATGAAAAATATGGATTAAAACACAATTAAAGCCAATTTTGGGTA
* *
18149 TATAAGAAAAAATGTCAATCTCTAAAGAATTTGGCCATGGTGGATATGATTATTTGGGGATGATG
260 TATAAGAAAAAATGCCAATCTCTAAAGAATTTGGCCATGGTGCATATGATTATTTGGGGATGATG
*
18214 AGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTT-TCATTTTGTTTAATTA
325 AGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGT-ATTTCGTTTAATTA
* *
18278 TTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATGGAAAAATATGGATT
389 TTAAATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGAT-GAAAAATATGGATT
*
18343 AAATCACTTTTTAAAGTCAATTTTGGGTATATGAG-AAAAAAATGTCAATCTCTAAAGAATTTGG
453 AAAGCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTTGG
* *
18407 GGATGGTGCATATGATTATTTGGGGATGATGAGAAA-TGATTTGGGTATAAAGTATATCAGTTT
518 GGATGGTGCATATGATTATTTAGGGATGATGAGAAAGT-ATTTGGGTATAAAGTATATAAGTTT
18470 TGTCGTAACA
Statistics
Matches: 552, Mismatches: 25, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
630 159 0.29
631 345 0.62
632 48 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (630 bp):
TTCAAATGAAAACAAGATGTATTGTTGCACAAGTAAATTGAATCTCTAGACATTCTTGAAGATAG
ATTAAAAGGTATTCCACACTAGCCAAAATTGCATACTTGACAATATTCCTACATAACTTGAACGG
GTAAGAAATGCTTGATACAACAAAAAAACAATCACTATTAGATGACACTAAATTTATATAGACGG
GGTTTATTCAATTAATTACAATGAAAAATATGGATTAAAACACAATTAAAGCCAATTTTGGGTAT
ATAAGAAAAAATGCCAATCTCTAAAGAATTTGGCCATGGTGCATATGATTATTTGGGGATGATGA
GAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTCGTTTAATTATT
AAATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGATTAAA
GCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAAAATGTCAATCTCTAAAGAATTTGGGGA
TGGTGCATATGATTATTTAGGGATGATGAGAAAGTATTTGGGTATAAAGTATATAAGTTTGGGGA
TACTGAATTTTGCACAAGTAAATTGAATCTTTAGACATTCTTGAA
Found at i:19964 original size:26 final size:27
Alignment explanation
Indices: 19910--19971 Score: 99
Period size: 26 Copynumber: 2.3 Consensus size: 27
19900 CTAACAAAAC
19910 AAGCCCAAATGCATGAAAAATAAGCTAA
1 AAGCCCAAATGCATG-AAAATAAGCTAA
*
19938 AAGCCCAAATGCATG-AAATAAGTTAA
1 AAGCCCAAATGCATGAAAATAAGCTAA
19964 AAGCCCAA
1 AAGCCCAA
19972 GTATAGGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 18 0.55
28 15 0.45
ACGTcount: A:0.52, C:0.19, G:0.15, T:0.15
Consensus pattern (27 bp):
AAGCCCAAATGCATGAAAATAAGCTAA
Found at i:25633 original size:218 final size:217
Alignment explanation
Indices: 24968--25646 Score: 907
Period size: 222 Copynumber: 3.1 Consensus size: 217
24958 TGTCTACAAG
* * * *
24968 TTTGGGGATACTGAATTTTGCATTTCGTTTAATTATTAGATGGCACTAAAATCATATAGACGGGG
1 TTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGGCACTAAATTCATATAGACGAGA
* *
25033 TTTATTCAATTAATTAGGATGGAAAAATATGGATTAAAACACTTTTAAAAGTCAATTTTGGGTAT
66 TTTATTCAATTAATTAGGAT-GAAAAATATGGATTAAAACACGTTTAAAA-CCAATTTTGGGTAT
*
25098 ATGAGAAAAAAATGTCAATCTCTAAAGAATTTGGG-TTGTGCTTATGATTATTT-GGGATGATGA
129 AT----AAAAAATGTCAATCTCTAAAGAATTTGGGATGGTGCTTATGATTATTTGGGGATGATGA
*
25161 GAAAGTATTTGGGTATAAAGTATATCAG
190 GAAAGTATTTGGGTATAAAGTATATCAC
* * *
25189 TTTGGCGATACTGAATTTTGCATTTTGTTTAATTATTTGATGGCAGTAAATTCATATAGACGAGG
1 TTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGGCACTAAATTCATATAGACGA-G
* * * *
25254 ATGATTATTCAATTAATTTAGGAAGAAAAATATGGATTAAATCACGTTTAAAGCCAATTTTGGGC
65 AT--TTATTCAATTAA-TTAGGATGAAAAATATGGATTAAAACACGTTTAAAACCAATTTTGGGT
* * **
25319 ATATAAAAAATGCCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAAAAG
127 ATATAAAAAATGTCAATCTCTAAAGAATTT-GGGATGGTGCTTATGATTATTTGGGGATGATGAG
* * *
25384 AACGGATTTGGGTATAAAGCATATCAC
191 AAAGTATTTGGGTATAAAGTATATCAC
* * *
25411 TTTGGGGATACTGAATTTCGCATTTTGTTTCATTATTAGATGACACTAAATTCATATAGACGAGA
1 TTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGGCACTAAATTCATATAGACGAGA
**
25476 TTTATTCAATTAATTAGGATG-ATGATATGGATTAAAACACGTTTAAAACCAATTTTGGGTATAT
66 TTTATTCAATTAATTAGGATGAAAAATATGGATTAAAACACGTTTAAAACCAATTTTGGGTATAT
* *
25540 AAAAAATTGTTAATCTTTAAA-AACTTTGTGGATGGTGCTTATGATTATTTGGGGATGATGAGAA
131 AAAAAA-TGTCAATCTCTAAAGAA-TTTG-GGATGGTGCTTATGATTATTTGGGGATGATGAGAA
* * *
25604 ATTATTTGGGTATAAAGTAAATAAC
193 AGTATTTGGGTATAAAGTATATCAC
*
25629 TTTGGGGATACTGGATTT
1 TTTGGGGATACTGAATTT
25647 ATAGCATAAA
Statistics
Matches: 401, Mismatches: 47, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
217 47 0.12
218 89 0.22
219 37 0.09
220 3 0.01
221 76 0.19
222 91 0.23
223 14 0.03
224 38 0.09
225 6 0.01
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (217 bp):
TTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGGCACTAAATTCATATAGACGAGA
TTTATTCAATTAATTAGGATGAAAAATATGGATTAAAACACGTTTAAAACCAATTTTGGGTATAT
AAAAAATGTCAATCTCTAAAGAATTTGGGATGGTGCTTATGATTATTTGGGGATGATGAGAAAGT
ATTTGGGTATAAAGTATATCAC
Found at i:31316 original size:42 final size:43
Alignment explanation
Indices: 31265--31358 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
31255 AGTGCATTAC
*
31265 CTAA-ATTCTACT-CTATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTATCTCTAGATAATTCATCAAAATAAAA
*
31306 CTAATATTCTACTCCACTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-C-CTATCTCTAGATAATTCATCAAAATAAAA
*
31351 TTAATATT
1 CTAATATT
31359 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
45 34 0.74
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACTCCTATCTCTAGATAATTCATCAAAATAAAA
Done.