Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007916.1 Corchorus capsularis cultivar CVL-1 contig07937, 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: 66371
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:497 original size:2 final size:2
Alignment explanation
Indices: 490--519 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
480 CTAAAGCAAC
490 AT AT AT AT AT 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
520 CTACTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2290 original size:51 final size:51
Alignment explanation
Indices: 2214--2444 Score: 250
Period size: 51 Copynumber: 4.5 Consensus size: 51
2204 TAAGTTGTTA
* *
2214 ATAAAGATTCAATTTTTAATGTAAAAGGCTTTAGCTTTTGGTTAGTCAATG
1 ATAAAGATTCGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATG
* *
2265 ATAAATATTTGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATG
1 ATAAAGATTCGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATG
* * * * ** *
2316 ATAAAGATTCGATCTTTAGTGTAAAAGGCCTT-GATTTGTGGTTAAGTTGATA
1 ATAAAGATTCGATTTTTAATGTAAAAGGCTTTAG-TTTTTGGTT-AGTCAATG
* * * * * *
2368 AAAAAGATTCAATTTTTAATGTAAAAGGCTTTAGTTTTTGGCTAATTAGTG
1 ATAAAGATTCGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATG
* *
2419 ATAAAGATT-AATTTTTTAGTGTAAAA
1 ATAAAGATTCGA-TTTTTAATGTAAAA
2445 AACTTTAATT
Statistics
Matches: 150, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
50 3 0.02
51 107 0.71
52 39 0.26
53 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (51 bp):
ATAAAGATTCGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATG
Found at i:2496 original size:154 final size:154
Alignment explanation
Indices: 2204--2487 Score: 329
Period size: 154 Copynumber: 1.8 Consensus size: 154
2194 TAACTATTGA
* * * *
2204 TAAGTTGTTAATAAAGATTCAATTTTTAATGTAAAAGGCTTTAGCTTTTGGTTAGTCAATGATAA
1 TAAGTTGATAAAAAAGATTCAATTTTTAATGTAAAAGGCTTTAGCTTTTGGCTAATCAATGATAA
* * ** * * * * * * * *
2269 ATATTTGATTTTTAATGTAAAAGGCTTTAGTTTTTGGTTAGTCAATGATAAAGATTCGATCTTTA
66 AGATTTAATTTTTAATGTAAAAAACTTTAATTTTGGGTAAATCAATAATAAAAATTCAATCTTGA
2334 GTGTAAAAGGCCTTGATTTGTGGT
131 GTGTAAAAGGCCTTGATTTGTGGT
* * *
2358 TAAGTTGATAAAAAAGATTCAATTTTTAATGTAAAAGGCTTTAGTTTTTGGCTAATTAGTGATAA
1 TAAGTTGATAAAAAAGATTCAATTTTTAATGTAAAAGGCTTTAGCTTTTGGCTAATCAATGATAA
* * *
2423 AGA-TTAATTTTTTAGTGTAAAAAACTTTAATTTTGGGGTAAATTATTAATAAAAATGT-AATCT
66 AGATTTAA-TTTTTAATGTAAAAAACTTTAATTTT-GGGTAAATCAATAATAAAAAT-TCAATCT
2486 TG
128 TG
2488 GATTAAAAGA
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
153 3 0.03
154 82 0.78
155 19 0.18
156 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (154 bp):
TAAGTTGATAAAAAAGATTCAATTTTTAATGTAAAAGGCTTTAGCTTTTGGCTAATCAATGATAA
AGATTTAATTTTTAATGTAAAAAACTTTAATTTTGGGTAAATCAATAATAAAAATTCAATCTTGA
GTGTAAAAGGCCTTGATTTGTGGT
Found at i:2659 original size:20 final size:19
Alignment explanation
Indices: 2621--2658 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2611 TTAATTTGTA
*
2621 AATAAAAATGAAACCTTTT
1 AATAAAAATCAAACCTTTT
2640 AATAAAAGATCAAA-CTTTT
1 AATAAAA-ATCAAACCTTTT
2659 TGATTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAAAAATCAAACCTTTT
Found at i:2677 original size:50 final size:52
Alignment explanation
Indices: 2569--2679 Score: 124
Period size: 52 Copynumber: 2.2 Consensus size: 52
2559 GCAAAGTAAT
* **
2569 AATAAAAATGAAGCCTTTTAAATTAAAAGACTAAACTTTGAGTTAATTTGTA
1 AATAAAAATGAAACCTTTTAAATTAAAAGACTAAACTTTGAGTTAAGGTGTA
2621 AATAAAAATGAAACCTTTT-AA-TAAAAGA-TCAAACTTTTTGA-TTAAGGTG-A
1 AATAAAAATGAAACCTTTTAAATTAAAAGACT-AAAC--TTTGAGTTAAGGTGTA
*
2671 AGTAAAAAT
1 AATAAAAAT
2680 AAGATCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
49 1 0.02
50 20 0.38
51 8 0.15
52 23 0.44
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (52 bp):
AATAAAAATGAAACCTTTTAAATTAAAAGACTAAACTTTGAGTTAAGGTGTA
Found at i:2798 original size:50 final size:50
Alignment explanation
Indices: 2673--2804 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 50
2663 TAAGGTGAAG
* * * *
2673 TAAAAATAAGATCTTT-GAACTAAACAATGGAATTTGTGCTTAATTAACAA
1 TAAAAATGAGATCTTTAG-ATTAAAAAATTGAATTTGTGCTTAATTAACAA
* * * *
2723 TAAAAATGAAATCTTTAG-TAAAAAAAATTGAACTTT-TGGTTAGTTAACAA
1 TAAAAATGAGATCTTTAGAT-TAAAAAATTGAA-TTTGTGCTTAATTAACAA
2773 TAAAAATGAGATCTTTAGATT-AAAAATTGAAT
1 TAAAAATGAGATCTTTAGATTAAAAAATTGAAT
2805 ATAAATGAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
48 1 0.01
49 10 0.15
50 52 0.76
51 5 0.07
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (50 bp):
TAAAAATGAGATCTTTAGATTAAAAAATTGAATTTGTGCTTAATTAACAA
Found at i:3687 original size:40 final size:40
Alignment explanation
Indices: 3518--3798 Score: 309
Period size: 41 Copynumber: 7.0 Consensus size: 40
3508 CCCAAATTGT
* * * * *
3518 CCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAATTGGC
1 CCTTCCCTATCGGAAGGTGTTGTTTA-CATTCCTAGTTTGC
** * * *
3559 CCTTCCCTATCGGAAGGTACTGTTTACTTTTCCCAGTCTGC
1 CCTTCCCTATCGGAAGGTGTTGTTTAC-ATTCCTAGTTTGC
* * **
3600 CCTTCCCCATCGGAAGATGTTGTTTAGTTTTCCT-GTTTTGC
1 CCTTCCCTATCGGAAGGTGTTGTTTA-CATTCCTAG-TTTGC
*
3641 CCTTCCCTATCGGAAGTTGTTGTTTACATTCCTAGTTTGC
1 CCTTCCCTATCGGAAGGTGTTGTTTACATTCCTAGTTTGC
* *
3681 CATTCCCCA-CTGGAAGGTGTTGTTTACATTCCTAGTTTGC
1 CCTTCCCTATC-GGAAGGTGTTGTTTACATTCCTAGTTTGC
*
3721 CCTTCCCTATCGGAAGGTATTG-TTACATTCCT-GTTTTGC
1 CCTTCCCTATCGGAAGGTGTTGTTTACATTCCTAG-TTTGC
*
3760 CCTTCCCTATCGAAAGGTGTTGTTTACATTCCTAGTTTG
1 CCTTCCCTATCGGAAGGTGTTGTTTACATTCCTAGTTTG
3799 TCGGTGTTGT
Statistics
Matches: 206, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.00
39 36 0.17
40 78 0.38
41 91 0.44
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (40 bp):
CCTTCCCTATCGGAAGGTGTTGTTTACATTCCTAGTTTGC
Found at i:3804 original size:26 final size:26
Alignment explanation
Indices: 3775--3824 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3765 CCTATCGAAA
3775 GGTGTTGTTTACATTCCTAGTTTGTC
1 GGTGTTGTTTACATTCCTAGTTTGTC
3801 GGTGTTGTTTACATTCCTAGTTTG
1 GGTGTTGTTTACATTCCTAGTTTG
3825 CCCTTCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.50
Consensus pattern (26 bp):
GGTGTTGTTTACATTCCTAGTTTGTC
Found at i:3938 original size:40 final size:40
Alignment explanation
Indices: 3801--3932 Score: 203
Period size: 40 Copynumber: 3.3 Consensus size: 40
3791 CTAGTTTGTC
*
3801 GGTGTTGTTTACATTCCTAG-TTTGCCCTTCCCAATCGGAA
1 GGTGTTGTTTACATTCCT-GTTTTGCCCTTCCCAACCGGAA
* *
3841 GGTGTTGTTTACATTCCTGTTTTGCTCTTCCCTACCGGAA
1 GGTGTTGTTTACATTCCTGTTTTGCCCTTCCCAACCGGAA
* *
3881 GGTGTTGTTTACATTTCTGTTTTGCCCTTCCCCACCGGAA
1 GGTGTTGTTTACATTCCTGTTTTGCCCTTCCCAACCGGAA
3921 GGTGTTGTTTAC
1 GGTGTTGTTTAC
3933 TTTTCTTATT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 84 0.99
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (40 bp):
GGTGTTGTTTACATTCCTGTTTTGCCCTTCCCAACCGGAA
Found at i:5818 original size:22 final size:22
Alignment explanation
Indices: 5789--5841 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5779 TGCTTGATTA
*
5789 ATGTTCGTTTAATA-TTCGGTT
1 ATGTTCGTTTAATAGCTCGGTT
*
5810 ATTGTTCGTTTAATAGCTCGTTT
1 A-TGTTCGTTTAATAGCTCGGTT
5833 ATGTTCGTT
1 ATGTTCGTT
5842 AATTAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 21 0.75
23 6 0.21
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (22 bp):
ATGTTCGTTTAATAGCTCGGTT
Found at i:8158 original size:5 final size:5
Alignment explanation
Indices: 8148--8186 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
8138 ACTAATCCTA
* *
8148 TATAT TATAT TATAT TATAT TATCT TAAAT T-TAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
8187 ATTCTTCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:11470 original size:2 final size:2
Alignment explanation
Indices: 11463--11496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11453 GGCACATAAC
11463 AT AT AT AT AT AT AT 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
11497 TGCCAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14357 original size:438 final size:437
Alignment explanation
Indices: 13526--14510 Score: 1287
Period size: 438 Copynumber: 2.2 Consensus size: 437
13516 TGGGCCCCGC
* * * * *
13526 TCTCAATAAACAAATCATA-TTTTTGCTGGATTATTTATCAAACGATCCCTATACTTTTATGCTT
1 TCTCCATAAACAAAT-ATATTTTTTTCTGGATTATTTATCAAATGATCCTTATACTTTTATGTTT
* * * * * * *
13590 TATGCTATTTAGTCCCTCACAAAATCTGGGTTGGACGATTGAACGTTTCGGCTTTAATTCTTTTA
65 TATGCTATTTAATCCTTTAC-AATTATGGGTTGGACGATTTAACGTGTCGGCTTTAATTCTTTTA
* * * *
13655 TTTTTTGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTA
129 TTTTCTATTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTA
* ** * *
13720 CAACTTTCATGAAGGACTGAAAAACCAATTTTCATGTTACGATTCTAAAAAATGCTTCTTAAATT
194 AAACTTTCATGAAAAACTCAAAAACCAATTTTAATGTTACGATTCTAAAAAATGCTTCTTAAATT
* * *
13785 TTGTGGTCTCGATTGTCGGTCTATCTAATATTGTATAATTTTCGATCAACTTGTCCGATTGAGGT
259 TTGTGGTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCAACTTGTCCGATTGAAGT
* * *
13850 TGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACATTCGTCAAAAACCTAAAAGTTGA
324 TGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACATTCATCAAAAACATAAAAGTTGA
* * *
13915 ATTTGATTAATGAGTTTCATGGAGGGTTCAAGAGAGAATTTTTATGTTTGG
389 ATTTGATGAATGAGTTTCATGAAGGATTCAAGAGAGAATTTTTATG-TT-G
*
13966 T-TCCATAAACAAATATATTTTTTTCTGGATTATTTATCAAATGATTCTTATACTTTTATGTTTT
1 TCTCCATAAACAAATATATTTTTTTCTGGATTATTTATCAAATGATCCTTATACTTTTATGTTTT
* * *
14030 ATGCTATTTAATCATTTACAATTATGGGTTGGATGATTTAACGTGTCGGCTTTTATT-TTTGTAT
66 ATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTTAACGTGTCGGCTTTAATTCTTT-TAT
* *
14094 TTTCTATTCTATTTGTCCGATCAATGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTAA
130 TTTCTATTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTAA
* * ** * * *
14159 AACTTTCATGAAAAACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAGTGTTTCTTAATTTT
195 AACTTTCATGAAAAACTCAAAAACCAATTTTAATGTTACGATTCTAAAAAATGCTTCTTAAATTT
* * * * * * *
14224 TTTTGTTTCGATTGCCGGTCTATTTAATATCGTATAATTTTTGGTCCACTTGTCCGATTGAAGTT
260 TGTGGTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCAACTTGTCCGATTGAAGTT
* *** *
14289 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGAC-TTGCATTAAGGGCATGAAAGTTGA
325 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACATT-CATCAAAAACATAAAAGTTGA
* *
14353 ATTTGATGAATGAGTTTCGTGAAGGATTCAAGAGGGAATTTTTATGTTG
389 ATTTGATGAATGAGTTTCATGAAGGATTCAAGAGAGAATTTTTATGTTG
* * * *
14402 TCTCCATAAACTAATATTTTTTTTTGCTGGATTATTTATCTAATGA-CCATCATACTTTTATGTT
1 TCTCCATAAACAAATATATTTTTTT-CTGGATTATTTATCAAATGATCC-TTATACTTTTATGTT
* * *
14466 TCATGCTATTGAATCCTTTACAATTATAGGTTGGACGATTTAACG
64 TTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTTAACG
14511 CTTTGACTTT
Statistics
Matches: 472, Mismatches: 67, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
436 2 0.00
437 29 0.06
438 372 0.79
439 68 0.14
440 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (437 bp):
TCTCCATAAACAAATATATTTTTTTCTGGATTATTTATCAAATGATCCTTATACTTTTATGTTTT
ATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTTAACGTGTCGGCTTTAATTCTTTTATT
TTCTATTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTAAA
ACTTTCATGAAAAACTCAAAAACCAATTTTAATGTTACGATTCTAAAAAATGCTTCTTAAATTTT
GTGGTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCAACTTGTCCGATTGAAGTTG
TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACATTCATCAAAAACATAAAAGTTGAAT
TTGATGAATGAGTTTCATGAAGGATTCAAGAGAGAATTTTTATGTTG
Found at i:19246 original size:2 final size:2
Alignment explanation
Indices: 19233--19275 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
19223 TAGCTGTAAT
19233 TA TA TA TCA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19274 TA
1 TA
19276 CCCATAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29002 original size:14 final size:15
Alignment explanation
Indices: 28983--29012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28973 GTTAACCGTG
28983 GAATTT-TATTTTAA
1 GAATTTGTATTTTAA
28997 GAATTTGTATTTTAA
1 GAATTTGTATTTTAA
29012 G
1 G
29013 GGGTTTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
GAATTTGTATTTTAA
Found at i:30652 original size:34 final size:34
Alignment explanation
Indices: 30609--30680 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
30599 ATACTTGAAA
* *
30609 CCAACAAGATATATACCTCTTCTTTTTGATGAGT
1 CCAACAAGATACATACATCTTCTTTTTGATGAGT
*
30643 CCAAGAAGATACATACATCTTCTTTTTGATGAGT
1 CCAACAAGATACATACATCTTCTTTTTGATGAGT
30677 CCAA
1 CCAA
30681 ATACATATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (34 bp):
CCAACAAGATACATACATCTTCTTTTTGATGAGT
Found at i:42355 original size:3 final size:3
Alignment explanation
Indices: 42347--42405 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
42337 TTGATGTCTC
* *
42347 AAT AAT AAT GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42395 AAT AAT AAT AA
1 AAT AAT AAT AA
42406 ATGACAATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:48306 original size:21 final size:21
Alignment explanation
Indices: 48240--48306 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
48230 AAGTGCATAA
48240 CTTGGAATCGATTGGAATATT
1 CTTGGAATCGATTGGAATATT
* * *
48261 CCTAGAATCGATTGTGAGA-A-G
1 CTTGGAATCGATTG-GA-ATATT
48282 CTTGGAATCGATTGGAATATT
1 CTTGGAATCGATTGGAATATT
48303 CTTG
1 CTTG
48307 CTCAAAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 28 0.78
22 3 0.08
23 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (21 bp):
CTTGGAATCGATTGGAATATT
Found at i:53982 original size:75 final size:75
Alignment explanation
Indices: 53854--54263 Score: 579
Period size: 75 Copynumber: 5.5 Consensus size: 75
53844 GGAATCCTGT
* * * * * *
53854 GGGTGACGTCTGTTTGGACGTTCGACCCCGCTTGGAGCTATACGGGGGTGCCAGTCTATGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
*
53919 GGCCGTCTGC
66 AGCCGTCTGC
* * **
53929 GGATGACGTCTACTTGGACGTTCGACCTCGCTTAGAGTTACGCGGGGGCGCCAGTCTAGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
* *
53994 AGCCGTCCGT
66 AGCCGTCTGC
* * * * *
54004 GGGTGACGTTTGCTTGGACATTCGACCTCGCTTAAAGTTATACGAGGGCACCAGTCTAGGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
54069 AGCCGTCTGC
66 AGCCGTCTGC
* * * *
54079 GGTTGACGTCTGCTTGGACGTTCGGCCTCGCTTAGAGTTATACGGGGGCACCAGTCTAAGCGCTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
54144 AGCCGTCTGC
66 AGCCGTCTGC
* * *
54154 GGGTGACGTCTGCTTGGACATTCGACCTCGCTTAGAGTTATGC-GGGGCGCCAGTCTAGGCACTC
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
*
54218 AGTCGTCTGC
66 AGCCGTCTGC
54228 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGA
1 GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGA
54264 TTTTTCATGA
Statistics
Matches: 295, Mismatches: 40, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
74 62 0.21
75 233 0.79
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (75 bp):
GGGTGACGTCTGCTTGGACGTTCGACCTCGCTTAGAGTTATACGGGGGCGCCAGTCTAGGCGCTC
AGCCGTCTGC
Found at i:60996 original size:21 final size:21
Alignment explanation
Indices: 60970--61022 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
60960 GCACTGGAGT
* * *
60970 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
60991 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
61012 ACAT-GGGCGCC
1 ACATGGGGCGCC
61023 CAGCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Done.