Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005827.1 Hibiscus syriacus cultivar Beakdansim tig00013655_pilon, 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: 80989
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4665 original size:22 final size:20
Alignment explanation
Indices: 4640--4687 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
4630 AAAAGACATG
4640 AAAAAAATG-GAAAACAAAACA
1 AAAAAAATGTGAAAA-AAAA-A
4661 AAAAAAATGTGAAAAAGAAAA
1 AAAAAAATGTGAAAAA-AAAA
4682 AAAAAA
1 AAAAAA
4688 GCAAATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.06
Consensus pattern (20 bp):
AAAAAAATGTGAAAAAAAAA
Found at i:11823 original size:22 final size:22
Alignment explanation
Indices: 11797--11839 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11787 GCTTGAAAAT
*
11797 AAAAGAAAAAAGGGAAAACTTG
1 AAAAGAAAAAAGAGAAAACTTG
*
11819 AAAAGTAAAAAGAGAAAACTT
1 AAAAGAAAAAAGAGAAAACTT
11840 TAATAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAAAGAGAAAACTTG
Found at i:12922 original size:11 final size:11
Alignment explanation
Indices: 12900--12932 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12890 TTCGAACAGC
12900 TTCTTTTT-TT
1 TTCTTTTTCTT
12910 TTCTTTTTCTT
1 TTCTTTTTCTT
12921 TTCTTTTTCTT
1 TTCTTTTTCTT
12932 T
1 T
12933 CATTCAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:18533 original size:403 final size:403
Alignment explanation
Indices: 17786--18594 Score: 1429
Period size: 403 Copynumber: 2.0 Consensus size: 403
17776 CTATACCGCT
*
17786 CCGAAGAGTAATGGCACTGACATTCCCCCTCTGGTTTACTTTAGTTTTAGATGGAAGTTTACCTC
1 CCGAAGAGTAATGGCACTGACATTCCCCCTCTGGTTTACTTTAGTTTGAGATGGAAGTTTACCTC
* *
17851 GTGATTCCAAGCGACCTACGGTTTGAGCCAGTTGGCTCATCTTCTTGTCTATCTCTTGTAAGTGG
66 GTGATTCCAAGAGACCTACGGTTTGAGCCAGTTGGCTCATCTGCTTGTCTATCTCTTGTAAGTGG
*
17916 GCTTTAGTATGATTCTGGAATTTTTCCTGGGATAGTGCTAACCTCTCGACAATTGACTCTAGTGA
131 GCTTTAGTATGATTCTGGAATTTTTCCTGGGATAGTGCTAACCTCTCGACAATCGACTCTAGTGA
17981 TTTCTTTTGCGGCTGTTGTTGTGGTGGAGGTGGTCTCGCTTGACAACCTTGATTTGGTCTTGAGT
196 TTTCTTTTGCGGCTGTTGTTGTGGTGGAGGTGGTCTCGCTTGACAACCTTGATTTGGTCTTGAGT
** *
18046 TCTGAACATAGTTGAAATTTGGATGATCCATCCATCCTGGGTTGTATGTATTGTCGTAGGGATTA
261 TCTGAACATACCTGAAATTCGGATGATCCATCCATCCTGGGTTGTATGTATTGTCGTAGGGATTA
*
18111 TAAGCTCTTTGGGGAGGTCCCGAAAAATCCCCGATTGCATTGACTTGAGATGTTGCATCATCTTG
326 TAAGCTCTTTGGGGAGGTCCCGAAAAATCCCCGATTGCATTGACTTGAGATGCTGCATCATCTTG
*
18176 AATTAGTGGACAA
391 AATCAGTGGACAA
** * * *
18189 CCGAAGAGTAATGGTGCTGACGTTCCCCCTCTGGTTTACTTTAGTTTGAGATGGAAGTTTACTTG
1 CCGAAGAGTAATGGCACTGACATTCCCCCTCTGGTTTACTTTAGTTTGAGATGGAAGTTTACCTC
18254 GTGATTCCAAGAGACCTACGGTTTGAGCCAGTTGGCTCATCTGCTTGTCTATCTCTTGTAAGTGG
66 GTGATTCCAAGAGACCTACGGTTTGAGCCAGTTGGCTCATCTGCTTGTCTATCTCTTGTAAGTGG
* *
18319 GCTTTAGTATGATTCTGGAATTTTTCCTGTGATAGTGCTAACCTCTCTACAATCGACTCTAGTGA
131 GCTTTAGTATGATTCTGGAATTTTTCCTGGGATAGTGCTAACCTCTCGACAATCGACTCTAGTGA
* * * *
18384 TTTTTTTTGCGGTTGTTGTTGTGGTGGGGGTGGTCTCGCTTGACAGCCTTGATTTGGTCTTGAGT
196 TTTCTTTTGCGGCTGTTGTTGTGGTGGAGGTGGTCTCGCTTGACAACCTTGATTTGGTCTTGAGT
*
18449 TCTGAACATACCTGAAATTCGGATGATCCATCCATCCTGGGTTGTATGTATTGTCGTATGGATTA
261 TCTGAACATACCTGAAATTCGGATGATCCATCCATCCTGGGTTGTATGTATTGTCGTAGGGATTA
18514 TAAGCTCTTTGGGGAGGTCCCGAAAAATCCCCGATTGCATTGACTTGAGATGCTGCATCATCTTG
326 TAAGCTCTTTGGGGAGGTCCCGAAAAATCCCCGATTGCATTGACTTGAGATGCTGCATCATCTTG
18579 AATCAGTGGACAA
391 AATCAGTGGACAA
18592 CCG
1 CCG
18595 TGTGTCGGAT
Statistics
Matches: 385, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
403 385 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (403 bp):
CCGAAGAGTAATGGCACTGACATTCCCCCTCTGGTTTACTTTAGTTTGAGATGGAAGTTTACCTC
GTGATTCCAAGAGACCTACGGTTTGAGCCAGTTGGCTCATCTGCTTGTCTATCTCTTGTAAGTGG
GCTTTAGTATGATTCTGGAATTTTTCCTGGGATAGTGCTAACCTCTCGACAATCGACTCTAGTGA
TTTCTTTTGCGGCTGTTGTTGTGGTGGAGGTGGTCTCGCTTGACAACCTTGATTTGGTCTTGAGT
TCTGAACATACCTGAAATTCGGATGATCCATCCATCCTGGGTTGTATGTATTGTCGTAGGGATTA
TAAGCTCTTTGGGGAGGTCCCGAAAAATCCCCGATTGCATTGACTTGAGATGCTGCATCATCTTG
AATCAGTGGACAA
Found at i:20447 original size:22 final size:23
Alignment explanation
Indices: 20408--20451 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20398 ACTTGAAAAT
*
20408 AAAAGAAAAAAGGGGAAAACTTG
1 AAAAGAAAAAAGGAGAAAACTTG
*
20431 AAAAGTAAAAA-GAGAAAACTT
1 AAAAGAAAAAAGGAGAAAACTT
20452 TAATAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAAGAAAAAAGGAGAAAACTTG
Found at i:24113 original size:29 final size:29
Alignment explanation
Indices: 24071--24141 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
24061 ATAGTCATTA
24071 ATGGATTCAATTGGCCCAAAAAGATCTAT
1 ATGGATTCAATTGGCCCAAAAAGATCTAT
24100 ATGGATTCAATTGGCCCAAAAAGATCTAT
1 ATGGATTCAATTGGCCCAAAAAGATCTAT
24129 ATGGATTCAATTG
1 ATGGATTCAATTG
24142 TAATACTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (29 bp):
ATGGATTCAATTGGCCCAAAAAGATCTAT
Found at i:27281 original size:21 final size:21
Alignment explanation
Indices: 27257--27309 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
27247 AAATTCAGGG
27257 GTATCGGTACATCCTATGGGT
1 GTATCGGTACATCCTATGGGT
*
27278 GTATCGGTACATCTTATGGGT
1 GTATCGGTACATCCTATGGGT
27299 GTATCGGTACA
1 GTATCGGTACA
27310 CCCTTACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
GTATCGGTACATCCTATGGGT
Found at i:30764 original size:20 final size:21
Alignment explanation
Indices: 30739--30831 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
30729 TTTTCCCAAT
*
30739 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30759 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
30780 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30800 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
30821 TCGCAATGCGA
1 TCGCAATGCGA
30832 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:30784 original size:41 final size:41
Alignment explanation
Indices: 30739--30831 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
30729 TTTTCCCAAT
30739 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
30780 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
30821 TCGCAATGCGA
1 TCGCAATGCGA
30832 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:30844 original size:41 final size:41
Alignment explanation
Indices: 30758--30892 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
30748 GAATAAGTAA
** *
30758 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
30799 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
30840 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
30881 TTCGCAACGCGA
1 ATCGCAACGCGA
30893 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:30845 original size:20 final size:20
Alignment explanation
Indices: 30820--30913 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
30810 AATTGGGAAA
*
30820 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
30840 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
30861 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
30881 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
30901 TTCGCAACGCGAT
1 ATCGCAACGCGAT
30914 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:31128 original size:22 final size:22
Alignment explanation
Indices: 31100--31143 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31090 CACTCTCTCA
31100 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
31122 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
31144 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:31416 original size:20 final size:20
Alignment explanation
Indices: 31387--31430 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31377 GCGATTTTAG
31387 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
31407 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
31427 TTTC
1 TTTC
31431 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:32760 original size:18 final size:18
Alignment explanation
Indices: 32739--32783 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
32729 TCCACTTCGG
* *
32739 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
32757 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
32775 GAGCCATCA
1 GAGCCATCA
32784 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:33329 original size:14 final size:14
Alignment explanation
Indices: 33310--33367 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
33300 ATGCGAAATG
33310 AAAATCGCAACGAA
1 AAAATCGCAACGAA
33324 AAAATCGCAACACGAA
1 AAAATCGC-A-ACGAA
*
33340 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
33356 AAAATCGCAACG
1 AAAATCGCAACG
33368 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 19 0.49
15 1 0.03
16 11 0.28
17 1 0.03
18 7 0.18
ACGTcount: A:0.52, C:0.24, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:33340 original size:33 final size:33
Alignment explanation
Indices: 33294--33381 Score: 142
Period size: 32 Copynumber: 2.7 Consensus size: 33
33284 GGAAATGGCT
*
33294 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
* *
33327 ATCGCAACACGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
33359 ATCGCAACGCGAAATGAAAATCG
1 ATCGCAACGCGAAATGAAAATCG
33382 TAATGCGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 30 0.60
33 20 0.40
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:33378 original size:19 final size:19
Alignment explanation
Indices: 33256--33381 Score: 85
Period size: 19 Copynumber: 7.2 Consensus size: 19
33246 TAGTTTACTT
* **
33256 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
33275 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
33295 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
33314 TCGCAA--CG-AA--AAAA
1 TCGCAACGCGAAATGAAAA
*
33328 TCGCAACACGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
33346 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
33360 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
33379 TCG
1 TCG
33382 TAATGCGATT
Statistics
Matches: 87, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.23
16 8 0.09
17 4 0.05
18 10 0.11
19 28 0.32
20 17 0.20
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:33407 original size:19 final size:18
Alignment explanation
Indices: 33396--33501 Score: 94
Period size: 19 Copynumber: 5.9 Consensus size: 18
33386 GCGATTTGTT
33396 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
33414 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
33430 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
33447 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
* *
33466 TTTCAGCGTTACGATAGTCA
1 TTTC-GCGTTGCGAT-TTCA
33486 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
33502 TAAGTTTCGT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
16 2 0.03
17 2 0.03
18 18 0.25
19 22 0.31
20 16 0.23
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:33482 original size:20 final size:19
Alignment explanation
Indices: 33445--33499 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
33435 TTGCGATTTT
* *
33445 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTACGATAGC
*
33464 CATTTCAGCGTTACGATAGT
1 CATTTC-GCGTTACGATAGC
*
33484 CATTTCGCGTTGCGAT
1 CATTTCGCGTTACGAT
33500 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTACGATAGC
Found at i:35514 original size:19 final size:19
Alignment explanation
Indices: 35490--35610 Score: 189
Period size: 19 Copynumber: 6.6 Consensus size: 19
35480 AAAACAGACT
* *
35490 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
35509 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35528 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35547 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35566 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
35580 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35599 ATCGCAATGCGA
1 ATCGCAATGCGA
35611 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
14 11 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 78 0.82
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35599 original size:52 final size:55
Alignment explanation
Indices: 35490--35610 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 55
35480 AAAACAGACT
* *
35490 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAAA
35547 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAAA
35599 ATCGCAATGCGA
1 ATCGCAATGCGA
35611 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
52 35 0.56
53 1 0.02
55 2 0.03
57 24 0.39
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (55 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAAA
Found at i:36748 original size:24 final size:24
Alignment explanation
Indices: 36721--36774 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36711 GTATTCGAAA
* *
36721 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
36745 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
36769 TTTGAT
1 TTTGAT
36775 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:36961 original size:12 final size:12
Alignment explanation
Indices: 36944--36968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36934 ATATAATCCT
36944 GAAGAAGAAAAA
1 GAAGAAGAAAAA
36956 GAAGAAGAAAAA
1 GAAGAAGAAAAA
36968 G
1 G
36969 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:39259 original size:19 final size:19
Alignment explanation
Indices: 39235--39398 Score: 89
Period size: 19 Copynumber: 9.7 Consensus size: 19
39225 GGAAATTACT
39235 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
39254 AACGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
39268 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
39287 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
39301 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
39320 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
39334 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
39353 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
39367 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39386 ATCGCAACGCGAA
1 ATCGCAATGCGAA
39399 TTTAATTTCT
Statistics
Matches: 104, Mismatches: 21, Indels: 40
0.63 0.13 0.24
Matches are distributed among these distances:
14 34 0.33
15 4 0.04
16 8 0.08
17 8 0.08
18 4 0.04
19 46 0.44
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:39272 original size:33 final size:33
Alignment explanation
Indices: 39234--39399 Score: 219
Period size: 33 Copynumber: 5.0 Consensus size: 33
39224 CGGAAATTAC
*
39234 TATCGCAATGCGAAATGAAAAACGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
**
39268 -ATCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* **
39300 TTTCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
39333 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 TATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
39367 -ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
39399 T
1 T
39400 TTAATTTCTC
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.03
33 115 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:39563 original size:14 final size:14
Alignment explanation
Indices: 39544--39580 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39534 CATCAATTAA
39544 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
39558 ACAAATCACCTTTT
1 ACAAATCAACTTTT
39572 ACAAATCAA
1 ACAAATCAA
39581 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41002 original size:21 final size:21
Alignment explanation
Indices: 40936--41002 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
40926 GTGAATCGGG
*
40936 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
40956 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
40978 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
40999 CTCT
1 CTCT
41003 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:41021 original size:42 final size:41
Alignment explanation
Indices: 40936--41058 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
40926 GTGAATCGGG
* * * * *
40936 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
40978 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
41020 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
41059 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:43089 original size:20 final size:19
Alignment explanation
Indices: 43058--43237 Score: 128
Period size: 19 Copynumber: 9.8 Consensus size: 19
43048 TCTTTTGGTT
43058 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
43077 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
43098 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
43117 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
**
43131 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
43147 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
43164 GAAATGAAAATCGCAACCA
1 GAAATGAAAATCGCAACGA
* *
43183 CGAAATAAAAATCGCAACGC
1 -GAAATGAAAATCGCAACGA
*
43203 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
43222 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
43238 TGCGATTTTG
Statistics
Matches: 126, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
14 17 0.13
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 52 0.41
20 45 0.36
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:43140 original size:33 final size:33
Alignment explanation
Indices: 43083--43182 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
43073 ACGAGATAAT
*
43083 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
43117 GAGAATCGCAACGTGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
43150 GACAATCGCAACGCGAAATGAAAATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
43183 CGAAATAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:43175 original size:19 final size:19
Alignment explanation
Indices: 43153--43242 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
43143 GCGACCAGAC
43153 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
43172 AATCGCAACCACGAAATAAA
1 AATCGCAA-CGCGAAATGAA
43192 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
43211 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
43230 AATCGCAATGCGA
1 AATCGCAACGCGA
43243 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 48 0.74
20 17 0.26
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:43196 original size:39 final size:38
Alignment explanation
Indices: 43153--43242 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
43143 GCGACCAGAC
43153 AATCGCAACGCGAAATGAAAATCGCAACCACGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CACGAAATAAA
* *
43192 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
*
43230 AATCGCAATGCGA
1 AATCGCAACGCGA
43243 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
Found at i:43271 original size:19 final size:19
Alignment explanation
Indices: 43238--43304 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
43228 AAAATCGCAA
**
43238 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
43257 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
43276 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
43296 TGCGATTTT
1 TGCGATTTT
43305 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:43914 original size:20 final size:20
Alignment explanation
Indices: 43821--43914 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
43811 CGCTATGTAA
* *
43821 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
43841 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
43861 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
43882 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
43902 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
43915 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:43932 original size:21 final size:21
Alignment explanation
Indices: 43903--43995 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
43893 ATAGTAAGTA
43903 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
43924 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
43944 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
43965 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
43985 TCGCATTGCGA
1 TCGCATTGCGA
43996 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:43933 original size:41 final size:41
Alignment explanation
Indices: 43842--43976 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
43832 AAAGTCAGTA
* * * ** *
43842 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
43882 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
43924 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
43965 TCGCGTTGCGAT
1 TCGCGTTGCGAT
43977 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:43977 original size:41 final size:41
Alignment explanation
Indices: 43903--43995 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
43893 ATAGTAAGTA
43903 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
43944 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
43985 TCGCATTGCGA
1 TCGCATTGCGA
43996 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:45541 original size:18 final size:19
Alignment explanation
Indices: 45499--45541 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
45489 CCCCTACTAG
*
45499 GAGTATTGATACTCTACCAT
1 GAGTATCGATACTC-ACCAT
*
45519 CAGTATCGATACTC-CCAT
1 GAGTATCGATACTCACCAT
45537 GAGTA
1 GAGTA
45542 CTGATACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (19 bp):
GAGTATCGATACTCACCAT
Found at i:48909 original size:19 final size:19
Alignment explanation
Indices: 48887--48926 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
48877 GTGAAGCGGC
48887 AGGAAAGTGACAAAGCATT
1 AGGAAAGTGACAAAGCATT
48906 AGGAAAGTGACAAAGCATT
1 AGGAAAGTGACAAAGCATT
48925 AG
1 AG
48927 TATTTGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.28, T:0.15
Consensus pattern (19 bp):
AGGAAAGTGACAAAGCATT
Found at i:51982 original size:23 final size:23
Alignment explanation
Indices: 51937--51982 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
51927 ATCAGTTTCT
*
51937 CTTCAAAGGGGGAATCGGCTCCC
1 CTTCAAAGGGGGAATCGACTCCC
* * *
51960 CTTCAAGGGGGGTATCGATTCCC
1 CTTCAAAGGGGGAATCGACTCCC
51983 TCTGCACTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (23 bp):
CTTCAAAGGGGGAATCGACTCCC
Found at i:65211 original size:22 final size:22
Alignment explanation
Indices: 65173--65215 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
65163 GCTTGAAAAT
*
65173 AAAATAAAGAAGGGAAAACTTG
1 AAAATAAAGAAGAGAAAACTTG
65195 AAAAGTAAA-AAGAGAAAACTT
1 AAAA-TAAAGAAGAGAAAACTT
65216 TAATAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.63, C:0.05, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAATAAAGAAGAGAAAACTTG
Found at i:73007 original size:19 final size:19
Alignment explanation
Indices: 72980--73035 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
72970 ACCCCTACAA
*
72980 AAGTTTCGATACTTTCTAC
1 AAGTATCGATACTTTCTAC
72999 AAGTATCGATACTTTCTAC
1 AAGTATCGATACTTTCTAC
*
73018 AAGTATCTATACTTTCTA
1 AAGTATCGATACTTTCTA
73036 TAAGCATCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (19 bp):
AAGTATCGATACTTTCTAC
Found at i:74509 original size:14 final size:14
Alignment explanation
Indices: 74490--74525 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
74480 ACGCTGAGAG
74490 GTATTGCTTTAGCA
1 GTATTGCTTTAGCA
74504 GTATTGCTTTAGCA
1 GTATTGCTTTAGCA
74518 GTATTGCT
1 GTATTGCT
74526 ATCAAGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (14 bp):
GTATTGCTTTAGCA
Done.