Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001009.1 Kokia drynarioides strain JFW-HI SEQ_112218, 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: 44573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:568 original size:21 final size:22
Alignment explanation
Indices: 518--619 Score: 59
Period size: 21 Copynumber: 4.4 Consensus size: 22
508 TATTAATAAA
518 TATTATTAGGTTATTAATGTCAT
1 TATTATTA-GTTATTAATGTCAT
* *
541 CAATATTA-TTATTAATGT-ATT
1 TATTATTAGTTATTAATGTCA-T
562 TATTATTAGCAAAGGTTATTAATGTCAT
1 TATTATT-----A-GTTATTAATGTCAT
* *
590 CAATATTA-TTATTAATGT-ATT
1 TATTATTAGTTATTAATGTCA-T
611 TATTATTAG
1 TATTATTAG
620 CAAAAGTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 23
0.66 0.09 0.25
Matches are distributed among these distances:
20 2 0.03
21 33 0.55
23 7 0.12
26 1 0.02
28 16 0.27
29 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (22 bp):
TATTATTAGTTATTAATGTCAT
Found at i:582 original size:49 final size:49
Alignment explanation
Indices: 525--623 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
515 AAATATTATT
525 AGGTTATTAATGTCATCAATATTATTATTAATGTATTTATTATTAGCAA
1 AGGTTATTAATGTCATCAATATTATTATTAATGTATTTATTATTAGCAA
574 AGGTTATTAATGTCATCAATATTATTATTAATGTATTTATTATTAGCAA
1 AGGTTATTAATGTCATCAATATTATTATTAATGTATTTATTATTAGCAA
623 A
1 A
624 AGTATTTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (49 bp):
AGGTTATTAATGTCATCAATATTATTATTAATGTATTTATTATTAGCAA
Found at i:614 original size:18 final size:18
Alignment explanation
Indices: 593--698 Score: 72
Period size: 18 Copynumber: 5.7 Consensus size: 18
583 ATGTCATCAA
*
593 TATTATTATTAATGTATT
1 TATTATTATTAATATATT
** *
611 TATTATTAGCAAAAGTATT
1 TATTATTATTAATA-TATT
*
630 TATTAGATT-TTATAAATATT
1 TATT--ATTATTA-ATATATT
* *
650 TATTATTATTACTATTTT
1 TATTATTATTAATATATT
* *
668 TGTTATTATTAA-ATTTAT
1 TATTATTATTAATATAT-T
686 TATTATTATTAAT
1 TATTATTATTAAT
699 TCATTTAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
17 4 0.06
18 39 0.57
19 11 0.16
20 9 0.13
21 6 0.09
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
TATTATTATTAATATATT
Found at i:1358 original size:14 final size:14
Alignment explanation
Indices: 1339--1372 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1329 TTGGGCCCGA
1339 TTTGTAAATGGACT
1 TTTGTAAATGGACT
**
1353 TTTGTATTTGGACT
1 TTTGTAAATGGACT
1367 TTTGTA
1 TTTGTA
1373 TTTGAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (14 bp):
TTTGTAAATGGACT
Found at i:1373 original size:14 final size:14
Alignment explanation
Indices: 1347--1387 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1337 GATTTGTAAA
1347 TGGACTTTTGTATT
1 TGGACTTTTGTATT
1361 TGGACTTTTGTATT
1 TGGACTTTTGTATT
*
1375 TGAACTTTT-TATT
1 TGGACTTTTGTATT
1388 AAATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (14 bp):
TGGACTTTTGTATT
Found at i:1408 original size:17 final size:17
Alignment explanation
Indices: 1386--1459 Score: 78
Period size: 17 Copynumber: 4.3 Consensus size: 17
1376 GAACTTTTTA
*
1386 TTAAATTTATAA-TAATT
1 TTAAATTTA-AAGTAAAT
1403 TTAAATTTAAAAGTAAAT
1 TTAAATTT-AAAGTAAAT
* *
1421 TTAAACTTAAATTAAAT
1 TTAAATTTAAAGTAAAT
**
1438 TTAAATTTAAAACAAAT
1 TTAAATTTAAAGTAAAT
1455 TTAAA
1 TTAAA
1460 ATGGGTTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
17 37 0.76
18 12 0.24
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAGTAAAT
Found at i:1413 original size:6 final size:6
Alignment explanation
Indices: 1402--1448 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
1392 TTATAATAAT
** *
1402 TTTAAA TTTAAA AGTAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1449 ACAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:3692 original size:47 final size:42
Alignment explanation
Indices: 3581--3800 Score: 191
Period size: 41 Copynumber: 5.2 Consensus size: 42
3571 TCAAGTCATA
* *
3581 AGTCTTCCTTTAACCAT-ATTCTCGTTCTCATCTCGAGACATG
1 AGTCTTCC-TTAATCATAATTCTCATTCTCATCTCGAGACATG
3623 AGTCTTCCTTAATCATAA-TCTCATTCTCAT-TCCGAGACATG
1 AGTCTTCCTTAATCATAATTCTCATTCTCATCT-CGAGACATG
* * *
3664 AGTCTTCCTTATTCATAA-TCTCATTCTCATCTCGAGGCATT
1 AGTCTTCCTTAATCATAATTCTCATTCTCATCTCGAGACATG
* * * * * * *
3705 AGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGGCATT
1 AGTCTTCC-TTAAT-CATAATTCTCATTCTCATCTCGAGACATG
* * * * *
3748 AGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGACATG
1 AGTCTTCC-TTAAT-CATAATTCTCATTCTCATCTCGAGACATG
3791 AGTCTTCCTT
1 AGTCTTCCTT
3801 TTTATACACC
Statistics
Matches: 159, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.01
41 71 0.45
42 16 0.10
43 71 0.45
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (42 bp):
AGTCTTCCTTAATCATAATTCTCATTCTCATCTCGAGACATG
Found at i:3743 original size:43 final size:43
Alignment explanation
Indices: 3682--3808 Score: 191
Period size: 43 Copynumber: 2.9 Consensus size: 43
3672 TTATTCATAA
* * *
3682 TCTCATTCTCATCTCGAGGCATTAGTCTTCCATTTATACAATT
1 TCTCATGCTCAACCCGAGGCATTAGTCTTCCATTTATACAATT
3725 TCTCATGCTCAACCCGAGGCATTAGTCTTCCATTTATACAATT
1 TCTCATGCTCAACCCGAGGCATTAGTCTTCCATTTATACAATT
* * *
3768 TCTCATGCTCAACCCGAGACATGAGTCTTCCTTTTTATACA
1 TCTCATGCTCAACCCGAGGCATTAGTCTTCC-ATTTATACA
3809 CCACATATTC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
43 69 0.90
44 8 0.10
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (43 bp):
TCTCATGCTCAACCCGAGGCATTAGTCTTCCATTTATACAATT
Found at i:5365 original size:21 final size:20
Alignment explanation
Indices: 5336--5385 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
5326 CTGGAGTTTT
*
5336 TTGTGTCGGTAG-ATGCATGAC
1 TTGTATCGGTAGAAT-CAT-AC
5357 TTGTATCGGTAGAAATCATAC
1 TTGTATCGGTAG-AATCATAC
5378 TTGTATCG
1 TTGTATCG
5386 ATAAAACTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 21 0.81
22 3 0.12
23 2 0.08
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGTATCGGTAGAATCATAC
Found at i:5991 original size:17 final size:17
Alignment explanation
Indices: 5969--6001 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5959 TTATCGTTTG
5969 TTTATTATTC-TTATTTA
1 TTTATT-TTCGTTATTTA
5986 TTTATTTTCGTTATTT
1 TTTATTTTCGTTATTT
6002 TTTTTATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATTTTCGTTATTTA
Found at i:8384 original size:28 final size:28
Alignment explanation
Indices: 8353--8415 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
8343 AAAATGTGAT
* * * *
8353 TTTTGGATGTTTGGGGGTAAAACGGTAA
1 TTTTGGATATTCGAGGGTAAAACAGTAA
*
8381 TTTTGGGTATTCGAGGGTAAAACAGTAA
1 TTTTGGATATTCGAGGGTAAAACAGTAA
8409 TTTTGGA
1 TTTTGGA
8416 AGGTCTAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.37
Consensus pattern (28 bp):
TTTTGGATATTCGAGGGTAAAACAGTAA
Found at i:8634 original size:59 final size:58
Alignment explanation
Indices: 8571--8823 Score: 165
Period size: 59 Copynumber: 4.3 Consensus size: 58
8561 ATATTCAGGT
*
8571 GTAAAAATGTATTTTTTGGAAAATTTGGTGTCAAAAATGGAATTTTGGGACGTTTAGGG
1 GTAAAAATGTATTTTTTGGAAAATTTGG-GTCAAAAATGGAATTTTGGGAAGTTTAGGG
* ** * * ** ** * *
8630 GTAAATACATAATTTTTGGAAAATTTGGGGTTAAAAATATAATTTTAAGAAGTTCAAGG
1 GTAAAAATGTATTTTTTGGAAAATTT-GGGTCAAAAATGGAATTTTGGGAAGTTTAGGG
* * * * * *
8689 GTAAAAATGTAATTTTTT-GAAAATTCAGGGTTAAAAAAGGAATTTTGGAAAG-TTCGAGA
1 GTAAAAATGT-ATTTTTTGGAAAATT-TGGGTCAAAAATGGAATTTTGGGAAGTTTAG-GG
* * * * **
8748 GTAAAAATGTA-ATTTTGGAAAGTTTGGGAGTC-AAAATGTAATTTTTGGAATGTTCGGGG
1 GTAAAAATGTATTTTTTGGAAAATTT-GG-GTCAAAAATGGAATTTTGGGAA-GTTTAGGG
8807 GTCAAAATATG-ATTTTT
1 GT-AAAA-ATGTATTTTT
8824 AGATAGTTTA
Statistics
Matches: 143, Mismatches: 39, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
57 4 0.03
58 24 0.17
59 94 0.66
60 15 0.10
61 6 0.04
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (58 bp):
GTAAAAATGTATTTTTTGGAAAATTTGGGTCAAAAATGGAATTTTGGGAAGTTTAGGG
Found at i:8718 original size:29 final size:29
Alignment explanation
Indices: 8463--8763 Score: 104
Period size: 29 Copynumber: 10.2 Consensus size: 29
8453 GGTAAAATAA
*
8463 TAATTTTTTGAGAATTC-GGGATTAAAAATAG
1 TAATTTTTTGAAAATTCAGGG--TAAAAAT-G
*
8494 -AA-TTTTT-AAACATTCAGGAT-AAAATGG
1 TAATTTTTTGAAA-ATTCAGGGTAAAAAT-G
* * *
8521 TAATTTTTT-AAAAGGTTTAGGGTTAAAACG
1 TAATTTTTTGAAAA--TTCAGGGTAAAAATG
* * *
8551 GAATTTTTAG-ATATTCAGGTGTAAAAATG
1 TAATTTTTTGAAAATTCAGG-GTAAAAATG
*
8580 T-ATTTTTTGGAAAATT-TGGTGTCAAAAATG
1 TAATTTTTT-GAAAATTCAGG-GT-AAAAATG
* * * ** * * **
8610 GAA-TTTTGGGACGTTTAGGGGTAAATACA
1 TAATTTTTTGAAAATTCA-GGGTAAAAATG
* ** *
8639 TAATTTTTGGAAAATTTGGGGTTAAAAATA
1 TAATTTTTTGAAAATTCAGGG-TAAAAATG
** *
8669 TAATTTTAAG-AAGTTCAAGGGTAAAAATG
1 TAATTTTTTGAAAATTC-AGGGTAAAAATG
*
8698 TAATTTTTTGAAAATTCAGGGTTAAAAAAG
1 TAATTTTTTGAAAATTCAGGG-TAAAAATG
* * * *
8728 GAA-TTTTGGAAAGTTCGAGAGTAAAAATG
1 TAATTTTTTGAAAATTC-AGGGTAAAAATG
8757 TAATTTT
1 TAATTTT
8764 GGAAAGTTTG
Statistics
Matches: 200, Mismatches: 48, Indels: 45
0.68 0.16 0.15
Matches are distributed among these distances:
27 6 0.03
28 17 0.09
29 86 0.43
30 84 0.42
31 7 0.04
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (29 bp):
TAATTTTTTGAAAATTCAGGGTAAAAATG
Found at i:8811 original size:30 final size:30
Alignment explanation
Indices: 8571--8823 Score: 147
Period size: 29 Copynumber: 8.6 Consensus size: 30
8561 ATATTCAGGT
* * * *
8571 GTAAAAATGTATTTTTTGGAAAATT-TGGT
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* * * **
8600 GTCAAAAATGGAA-TTTTGGGACGTTTAGGG
1 GT-AAAAATGTAATTTTTGGAAAGTTCGGGG
* ** * *
8630 GTAAATACATAATTTTTGGAAAATTTGGGG
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* * ** **
8660 TTAAAAATATAATTTTAAG-AAGTTCAAGG
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* * *
8689 GTAAAAATGTAATTTTTTGAAAATTCAGGG
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* * * * *
8719 TTAAAAAAGGAA-TTTTGGAAAGTTCGAGA
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* *
8748 GTAAAAATGTAA-TTTTGGAAAGTTTGGGA
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* *
8777 GTCAAAATGTAATTTTTGGAATGTTCGGGG
1 GTAAAAATGTAATTTTTGGAAAGTTCGGGG
* * *
8807 GTCAAAATATGATTTTT
1 GTAAAAATGTAATTTTT
8824 AGATAGTTTA
Statistics
Matches: 170, Mismatches: 49, Indels: 9
0.75 0.21 0.04
Matches are distributed among these distances:
29 85 0.50
30 85 0.50
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (30 bp):
GTAAAAATGTAATTTTTGGAAAGTTCGGGG
Found at i:9812 original size:3 final size:3
Alignment explanation
Indices: 9804--9887 Score: 125
Period size: 3 Copynumber: 28.0 Consensus size: 3
9794 TTCGATTTTC
* * *
9804 TTA TTA TTA TTA TTA TTA ATA TTA -TA TTTA CTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
9849 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9888 ATTTATGACT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.95
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11390 original size:89 final size:89
Alignment explanation
Indices: 11283--11657 Score: 360
Period size: 98 Copynumber: 4.0 Consensus size: 89
11273 TAAATTCACC
*
11283 GTTGCGGCTTAAATCTTTCCTTTCAAG-CTTCTAAGGTATAAGGTTTGCCATTGCGACTTAAACC
1 GTTGCGGCTTAAATCTTTCCCTTCAAGTC-TCTAAGGTATAAGGTTTGCCATTGCGACTTAAACC
*
11347 TTTCTCTTTGTATCTTCATGGTACT
65 TTTCCCTTTGTATCTTCATGGTACT
* *
11372 GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTTAGGTATAAGGTTTGCCATTGCGACTTAAACCT
1 GTTGCGGCTTAAATCTTTCCCTTCAAGTCTCTAAGGTATAAGGTTTGCCATTGCGACTTAAACCT
*
11437 TTCCCTTTGTATCTTCGTGGTACTAGATT
66 TTCCCTTTGTATCTTCATGGTAC-----T
* * * *
11466 CGCCGTTGCGGCTTAAATCTTTCCCCTT-ATGTCTCTGAGGTATAAGGTTTGCCATTGTGGCTTA
1 ----GTTGCGGCTTAAATCTTT-CCCTTCAAGTCTCTAAGGTATAAGGTTTGCCATTGCGACTTA
* *
11530 AACCTTTCCCTTCGTGTGTTCGTGGT-ACTGGATTCGT
61 AACCTTTCCCTT--TGT-ATC-T--TCA-TGG-TAC-T
* * * * *
11567 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTTAACC
1 -GTTGCGGCTTAAATCTTTCCCTTCAAGTCTCTAAGGTATAAGGTTTGCCATTGCGACTTAAACC
** **
11632 TTTCCCTCCGTATCTTCGCGGTACT
65 TTTCCCTTTGTATCTTCATGGTACT
11657 G
1 G
11658 AGACTTGTAG
Statistics
Matches: 242, Mismatches: 23, Indels: 42
0.79 0.07 0.14
Matches are distributed among these distances:
89 82 0.34
90 2 0.01
91 2 0.01
92 3 0.01
94 2 0.01
95 2 0.01
96 2 0.01
97 5 0.02
98 124 0.51
99 5 0.02
100 3 0.01
101 3 0.01
102 1 0.00
104 4 0.02
105 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (89 bp):
GTTGCGGCTTAAATCTTTCCCTTCAAGTCTCTAAGGTATAAGGTTTGCCATTGCGACTTAAACCT
TTCCCTTTGTATCTTCATGGTACT
Found at i:11432 original size:49 final size:49
Alignment explanation
Indices: 11373--11638 Score: 231
Period size: 49 Copynumber: 5.4 Consensus size: 49
11363 CATGGTACTG
* *
11373 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTTAGGTATAAGGTTTGCCA
1 TTGCGGCTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* * * * *
11422 TTGCGACTTAAACCTTTCCCTT--TGTATCTTCGTGGTACT-AGATTCGCCG
1 TTGCGGCTTAAACCTTTCCCTTCATGTCTCTT--AGGTA-TAAGGTTCGCCA
* * *
11471 TTGCGGCTTAAATCTTTCCCCTT-ATGTCTCTGAGGTATAAGGTTTGCCA
1 TTGCGGCTTAAACCTTT-CCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* * * * * *
11520 TTGTGGCTTAAACCTTTCCCTTCGTGTGTTCGT-GGTACT--GGATTCGTCG
1 TTGCGGCTTAAACCTTTCCCTTCATGT-CTCTTAGGTA-TAAGG-TTCGCCA
* * *
11569 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCA
1 TTGCGGCTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* *
11618 TTGCGACTTTAACCTTTCCCT
1 TTGCGGCTTAAACCTTTCCCT
11639 CCGTATCTTC
Statistics
Matches: 168, Mismatches: 36, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
47 7 0.04
48 10 0.06
49 134 0.80
50 11 0.07
51 6 0.04
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (49 bp):
TTGCGGCTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
Found at i:11657 original size:98 final size:98
Alignment explanation
Indices: 11372--11657 Score: 439
Period size: 98 Copynumber: 2.9 Consensus size: 98
11362 TCATGGTACT
*
11372 GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTTAGGTATAAGGTTTGCCATTGCGACTTAAACCT
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCT
* *
11437 TTCCCTTTGTATCTTCGTGGTACTAGATTCGCC
66 TTCCCTTCGTATCTTCGTGGTACTGGATTCGCC
* *
11470 GTTGCGGCTTAAATCTTTCCCCTT-ATGTCTCTGAGGTATAAGGTTTGCCATTGTGGCTTAAACC
1 GTTGCGGCTTAAATCTTT-CCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACC
* * *
11534 TTTCCCTTCGTGTGTTCGTGGTACTGGATTCGTC
65 TTTCCCTTCGTATCTTCGTGGTACTGGATTCGCC
* * *
11568 GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTTAACCT
1 GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCT
* *
11633 TTCCCTCCGTATCTTCGCGGTACTG
66 TTCCCTTCGTATCTTCGTGGTACTG
11658 AGACTTGTAG
Statistics
Matches: 169, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
97 5 0.03
98 159 0.94
99 5 0.03
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (98 bp):
GTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCT
TTCCCTTCGTATCTTCGTGGTACTGGATTCGCC
Found at i:12089 original size:18 final size:18
Alignment explanation
Indices: 12063--12097 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12053 AAAAATAACG
*
12063 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
12081 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
12098 GTATTAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:16380 original size:18 final size:19
Alignment explanation
Indices: 16338--16380 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
16328 GTCAGTCGTG
16338 CTTTTCTCATCTCTCGCTT
1 CTTTTCTCATCTCTCGCTT
* **
16357 CCTTTCT-ATCTCTTTCTT
1 CTTTTCTCATCTCTCGCTT
16375 CTTTTC
1 CTTTTC
16381 CTTCACATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.05, C:0.35, G:0.02, T:0.58
Consensus pattern (19 bp):
CTTTTCTCATCTCTCGCTT
Found at i:23511 original size:30 final size:29
Alignment explanation
Indices: 23426--23671 Score: 113
Period size: 29 Copynumber: 8.4 Consensus size: 29
23416 AAATGGTAAT
**
23426 TTTTTGGAAGGTTCGGGGTTAAAAATGAAA
1 TTTTTGGAAAATTCGGGG-TAAAAATGAAA
** * * *
23456 TTTTTATATATTTGGGGGTAAAAATGAAA
1 TTTTTGGAAAATTCGGGGTAAAAATGAAA
* *
23485 TTTTTGGAAAATTCGTGGTAAAAAATGGAA
1 TTTTTGGAAAATTCGGGGT-AAAAATGAAA
* * **
23515 TTTTAGG-AAGTTCAATGGTAAAAAT-ATAA
1 TTTTTGGAAAATTC-GGGGTAAAAATGA-AA
* * *
23544 TTTTTGGAAAATTCGAGGTCAAACT-AGAA
1 TTTTTGGAAAATTCGGGGTAAAAATGA-AA
* ** ** *
23573 TTTTGGGAAGTTTATGGGT-AAAATGTAA
1 TTTTTGGAAAATTCGGGGTAAAAATGAAA
*** * * *
23601 TTTTCAAAAAATTCGAGGTCAAAATGGAA
1 TTTTTGGAAAATTCGGGGTAAAAATGAAA
* ** * *
23630 TTTTAGGAAGTTTAGGGGTAAAAATGTAA
1 TTTTTGGAAAATTCGGGGTAAAAATGAAA
*
23659 TTTTTAGAAAATT
1 TTTTTGGAAAATT
23672 TTATGTTAAA
Statistics
Matches: 156, Mismatches: 54, Indels: 13
0.70 0.24 0.06
Matches are distributed among these distances:
28 17 0.11
29 103 0.66
30 36 0.23
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
TTTTTGGAAAATTCGGGGTAAAAATGAAA
Found at i:23710 original size:29 final size:29
Alignment explanation
Indices: 23471--23729 Score: 118
Period size: 29 Copynumber: 8.9 Consensus size: 29
23461 ATATATTTGG
* *
23471 GGGTAAAAATGAAATTTTTGGAAAATTC--
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCAA
23499 GTGGTAAAAAATGGAATTTTAGG-AAGTTCAA
1 G-GGT-AAAAATGGAATTTT-GGAAAGTTCAA
* ** * *
23530 TGGTAAAAATATAATTTTTGGAAAATTCGA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCAA
* * * * * *
23560 -GGTCAAACTAGAATTTTGGGAAGTTTAT
1 GGGTAAAAATGGAATTTTGGAAAGTTCAA
* ** * *
23588 GGGT-AAAATGTAATTTTCAAAAAATTCGA
1 GGGTAAAAATGGAATTTT-GGAAAGTTCAA
* * *
23617 -GGTCAAAATGGAATTTTAGG-AAGTTTAG
1 GGGTAAAAATGGAATTTT-GGAAAGTTCAA
* * * **
23645 GGGTAAAAATGTAATTTTTAGAAAATTTTA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCAA
* *
23675 TGTTAAAAATGGAATTTTGGAAAGTTCAA
1 GGGTAAAAATGGAATTTTGGAAAGTTCAA
* * *
23704 GGGTAAAAATGTAATATTGTAAAGTT
1 GGGTAAAAATGGAATTTTGGAAAGTT
23730 TAGGGGGTCA
Statistics
Matches: 167, Mismatches: 51, Indels: 25
0.69 0.21 0.10
Matches are distributed among these distances:
28 28 0.17
29 95 0.57
30 44 0.26
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGGAAAGTTCAA
Found at i:23715 original size:59 final size:58
Alignment explanation
Indices: 23471--23718 Score: 275
Period size: 59 Copynumber: 4.3 Consensus size: 58
23461 ATATATTTGG
* * *
23471 GGGTAAAAATGAAATTTTTGGAAAATTCGTGGTAAAAAATGGAATTTTAGGAAGTTCAA
1 GGGTAAAAATGTAATTTTTAGAAAATTCGAGGT-AAAAATGGAATTTTAGGAAGTTCAA
* * * * * * * * *
23530 TGGTAAAAATATAATTTTTGGAAAATTCGAGGTCAAACTAGAATTTTGGGAAGTTTAT
1 GGGTAAAAATGTAATTTTTAGAAAATTCGAGGTAAAAATGGAATTTTAGGAAGTTCAA
* * * * *
23588 GGGT-AAAATGTAATTTTCAAAAAATTCGAGGTCAAAATGGAATTTTAGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTAGAAAATTCGAGGTAAAAATGGAATTTTAGGAAGTTCAA
** *
23645 GGGTAAAAATGTAATTTTTAGAAAATTTTATGTTAAAAATGGAATTTT-GGAAAGTTCAA
1 GGGTAAAAATGTAATTTTTAGAAAATTCGA-GGTAAAAATGGAATTTTAGG-AAGTTCAA
23704 GGGTAAAAATGTAAT
1 GGGTAAAAATGTAAT
23719 ATTGTAAAGT
Statistics
Matches: 159, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
57 49 0.31
58 45 0.28
59 65 0.41
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTAGAAAATTCGAGGTAAAAATGGAATTTTAGGAAGTTCAA
Found at i:23743 original size:59 final size:59
Alignment explanation
Indices: 23506--23751 Score: 186
Period size: 59 Copynumber: 4.2 Consensus size: 59
23496 TTCGTGGTAA
* * * * *
23506 AAAATGGAATTTTAGGAAGTTCAATGGTAAAAATATAATTTTTGGAAAA--TTCGAGGTC
1 AAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTATTAGAAAAGTTTAG-GGTC
* * * * * * *
23564 AAACTAGAATTTTGGGAAGTTTATGGGT-AAAATGTAATT-TTCA-AAAA-ATTCGAGGTC
1 AAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTATT-AGAAAAGTTTAG-GGTC
* * * * * * *
23621 AAAATGGAATTTTAGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAAATTTTATGTTA
1 AAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTATTAGAAAAGTTTAGGGTC
*
23680 AAAATGGAATTTT-GGAAAGTTCAAGGGTAAAAATGTAA-TATT-GTAAAGTTTAGGGGGTC
1 AAAATGGAATTTTAGG-AAGTTCAAGGGTAAAAATGTAATTATTAGAAAAGTTTA--GGGTC
*
23739 AAAATGTAATTTT
1 AAAATGGAATTTT
23752 TTAAAAGTTT
Statistics
Matches: 153, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
56 6 0.04
57 51 0.33
58 39 0.25
59 55 0.36
60 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTATTAGAAAAGTTTAGGGTC
Found at i:23744 original size:30 final size:30
Alignment explanation
Indices: 23703--23773 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
23693 GGAAAGTTCA
*
23703 AGGGTAAAAATGTAATATTGT-AAAGTTTAG
1 AGGGTCAAAATGTAATATTGTAAAAGTTT-G
* * *
23733 GGGGTCAAAATGTAATTTTTTAAAAGTTTG
1 AGGGTCAAAATGTAATATTGTAAAAGTTTG
23763 AGGGTCAAAAT
1 AGGGTCAAAAT
23774 ATGATTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
AGGGTCAAAATGTAATATTGTAAAAGTTTG
Found at i:23781 original size:30 final size:31
Alignment explanation
Indices: 23724--23782 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
23714 GTAATATTGT
* *
23724 AAAGTTTAGGGGGTCAAAATGTAATTTTTTA
1 AAAGTTTAGAGGGTCAAAATATAATTTTTTA
*
23755 AAAGTTT-GAGGGTCAAAATATGATTTTT
1 AAAGTTTAGAGGGTCAAAATATAATTTTT
23783 GGATAGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (31 bp):
AAAGTTTAGAGGGTCAAAATATAATTTTTTA
Found at i:23795 original size:29 final size:30
Alignment explanation
Indices: 23535--23783 Score: 79
Period size: 29 Copynumber: 8.5 Consensus size: 30
23525 TTCAATGGTA
*
23535 AAAATATAATTTTTGGAAAA-TTCGA-GGTC
1 AAAATATAATTTTT-GAAAAGTTTGAGGGTC
* * **
23564 AAACTAGAA-TTTTGGGAAGTTT-ATGGGT-
1 AAAATATAATTTTTGAAAAGTTTGA-GGGTC
* ** * *
23592 AAAATGTAATTTTCAAAAAATTCGA-GGTC
1 AAAATATAATTTTTGAAAAGTTTGAGGGTC
** * * *
23621 AAAATGGAATTTTAG-GAAGTTT-AGGGGTA
1 AAAATATAATTTTTGAAAAGTTTGA-GGGTC
* * * * *
23650 AAAATGTAATTTTTAGAAAA-TTTTATGTTA
1 AAAATATAATTTTT-GAAAAGTTTGAGGGTC
** * ** *
23680 AAAATGGAA-TTTTGGAAAGTTCAAGGGTA
1 AAAATATAATTTTTGAAAAGTTTGAGGGTC
* * * *
23709 AAAATGTAA-TATTGTAAAGTTTAGGGGGTC
1 AAAATATAATTTTTGAAAAGTTT-GAGGGTC
* *
23739 AAAATGTAATTTTTTAAAAGTTTGAGGGTC
1 AAAATATAATTTTTGAAAAGTTTGAGGGTC
*
23769 AAAATATGATTTTTG
1 AAAATATAATTTTTG
23784 GATAGTTTAG
Statistics
Matches: 160, Mismatches: 46, Indels: 27
0.69 0.20 0.12
Matches are distributed among these distances:
27 5 0.03
28 23 0.14
29 72 0.45
30 47 0.29
31 13 0.08
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTTGAGGGTC
Found at i:24823 original size:3 final size:3
Alignment explanation
Indices: 24815--24865 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
24805 AGTTTTCTTT
* *
24815 TTA TTA TTA TTA TTA TTA TTA -TA TTTG TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
24860 TTA TTA
1 TTA TTA
24866 ATTTATGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.93
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25556 original size:17 final size:17
Alignment explanation
Indices: 25530--25598 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
25520 TTGAACTTTA
25530 TTTAAATAAATTTAAAT
1 TTTAAATAAATTTAAAT
*
25547 TTTCAATAAATTTAAAT
1 TTTAAATAAATTTAAAT
* *
25564 TTAAAATAAACTT-AAT
1 TTTAAATAAATTTAAAT
25580 TTTAAAATAAATTTAAAT
1 TTT-AAATAAATTTAAAT
25598 T
1 T
25599 CTGTTGGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.11
17 35 0.80
18 4 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATAAATTTAAAT
Found at i:29211 original size:14 final size:13
Alignment explanation
Indices: 29193--29217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29183 TAACCCCAAT
29193 TTTTTTTAAAAAC
1 TTTTTTTAAAAAC
29206 TTTTTTTAAAAA
1 TTTTTTTAAAAA
29218 AATATTTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTTTAAAAAC
Found at i:31140 original size:9 final size:9
Alignment explanation
Indices: 31126--31154 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
31116 AACCCTTTAA
31126 TTTCACAAT
1 TTTCACAAT
31135 TTTCACAAT
1 TTTCACAAT
31144 TTTCACAAT
1 TTTCACAAT
31153 TT
1 TT
31155 AATCCCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTCACAAT
Found at i:34729 original size:24 final size:24
Alignment explanation
Indices: 34697--34746 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
34687 ACGCGGCGGC
34697 GGTGGTGGTGGCGGTTATGGAGGT
1 GGTGGTGGTGGCGGTTATGGAGGT
* *
34721 GGTGGTGGTGGTGGTTATGGCGGT
1 GGTGGTGGTGGCGGTTATGGAGGT
34745 GG
1 GG
34747 ATCTGGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.04, G:0.60, T:0.30
Consensus pattern (24 bp):
GGTGGTGGTGGCGGTTATGGAGGT
Found at i:34745 original size:21 final size:21
Alignment explanation
Indices: 34694--34761 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
34684 CGGACGCGGC
*
34694 GGCGGTGGTGGTGGCGGTTAT
1 GGCGGTGGTGGTGGTGGTTAT
*
34715 GGAGGTGGTGGTGGTGGTGGTTAT
1 ---GGCGGTGGTGGTGGTGGTTAT
*
34739 GGCGGTGGAT-CTGGTGGTTAT
1 GGCGGTGG-TGGTGGTGGTTAT
34760 GG
1 GG
34762 TGGAGGGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 19 0.49
22 1 0.03
24 19 0.49
ACGTcount: A:0.07, C:0.06, G:0.56, T:0.31
Consensus pattern (21 bp):
GGCGGTGGTGGTGGTGGTTAT
Found at i:34753 original size:24 final size:24
Alignment explanation
Indices: 34697--34756 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
34687 ACGCGGCGGC
* *
34697 GGTGGTGGTGGCGGTTATGGAGGT
1 GGTGCTGGTGGTGGTTATGGAGGT
* *
34721 GGTGGTGGTGGTGGTTATGGCGGT
1 GGTGCTGGTGGTGGTTATGGAGGT
34745 GGAT-CTGGTGGT
1 GG-TGCTGGTGGT
34757 TATGGTGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.07, C:0.05, G:0.57, T:0.32
Consensus pattern (24 bp):
GGTGCTGGTGGTGGTTATGGAGGT
Found at i:34804 original size:15 final size:15
Alignment explanation
Indices: 34786--34815 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34776 GAGGCGGTTA
34786 TGGTGGAGGAGGCGG
1 TGGTGGAGGAGGCGG
*
34801 TGGTGGAGGTGGCGG
1 TGGTGGAGGAGGCGG
34816 ATGTTACAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.67, T:0.17
Consensus pattern (15 bp):
TGGTGGAGGAGGCGG
Found at i:38950 original size:31 final size:29
Alignment explanation
Indices: 38915--38992 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
38905 TTAATAGCTC
* *
38915 AGTGACTAAAATGTTACAATACAGTAACGTA
1 AGTGACTAAAATGTAACAATACA--AACATA
* * *
38946 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAATACAAACATA
38975 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
38993 TGAGGCAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 22 0.54
31 19 0.46
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAATACAAACATA
Found at i:39264 original size:2 final size:2
Alignment explanation
Indices: 39257--39282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39247 TCATATTAGG
39257 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
39283 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40971 original size:39 final size:35
Alignment explanation
Indices: 40893--40971 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 35
40883 CATTTTGGAG
***
40893 ATTAAAAAGAGAAATATACTTTTATTAAGTGGGGG
1 ATTAAAAAGAGAAATATACTTTTATTAAGTGGACA
*
40928 ATTAAAAAGGGAAATATACTTTATTTTATTAAGTGGACA
1 ATTAAAAAGAGAAATATAC----TTTTATTAAGTGGACA
40967 ATTAA
1 ATTAA
40972 GCCTATGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 18 0.50
39 18 0.50
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (35 bp):
ATTAAAAAGAGAAATATACTTTTATTAAGTGGACA
Found at i:43980 original size:11 final size:11
Alignment explanation
Indices: 43964--44010 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
43954 AGGGACCAAC
* *
43964 GAAAAATGAAG
1 GAAAAAAGAAA
43975 GAAAAAAGAAA
1 GAAAAAAGAAA
*
43986 GAAAAAA-AGA
1 GAAAAAAGAAA
43996 GAAAGAAAGAAA
1 GAAA-AAAGAAA
44008 GAA
1 GAA
44011 GAAGGAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 6 0.20
11 19 0.63
12 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:43998 original size:14 final size:14
Alignment explanation
Indices: 43976--44009 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43966 AAAATGAAGG
43976 AAAAA-AGAAAGAA
1 AAAAAGAGAAAGAA
43989 AAAAAGAGAAAGAA
1 AAAAAGAGAAAGAA
*
44003 AGAAAGA
1 AAAAAGA
44010 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAAGAA
Found at i:44020 original size:22 final size:21
Alignment explanation
Indices: 43964--44029 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 21
43954 AGGGACCAAC
*
43964 GAAAAATGAAGGAAAAAAGAAA
1 GAAAAA-GAAGGAAGAAAGAAA
43986 GAAAAA-AA-G-AGAAAGAAA
1 GAAAAAGAAGGAAGAAAGAAA
*
44004 GAAAGAAGAAGGAAGAAGGAGAA
1 GAAA-AAGAAGGAAGAAAGA-AA
44027 GAA
1 GAA
44030 GGGGAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 4 0.11
21 1 0.03
22 12 0.32
23 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.02
Consensus pattern (21 bp):
GAAAAAGAAGGAAGAAAGAAA
Found at i:44029 original size:9 final size:9
Alignment explanation
Indices: 44007--44052 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
43997 AAAGAAAGAA
44007 AGAAGAA-G
1 AGAAGAAGG
44015 -GAAGAAGG
1 AGAAGAAGG
44023 AGAAGAAGG
1 AGAAGAAGG
*
44032 GGAAGAAGG
1 AGAAGAAGG
*
44041 GGAAGAAGG
1 AGAAGAAGG
44050 AGA
1 AGA
44053 GGAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 6 0.18
8 1 0.03
9 27 0.79
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:44441 original size:20 final size:21
Alignment explanation
Indices: 44400--44442 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
44390 TAATTTATTT
44400 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
44421 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
44441 TA
1 TA
44443 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.