Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003678.1 Hibiscus syriacus cultivar Beakdansim tig00007858_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: 77782
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3532 original size:10 final size:9
Alignment explanation
Indices: 3515--3562 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
3505 ATTTAATAAA
3515 ATAAAATAG
1 ATAAAATAG
3524 ATAATAATAG
1 ATAA-AATAG
3534 ATAGAAA-AG
1 ATA-AAATAG
3543 A-AAAATA-
1 ATAAAATAG
3550 ATAAAATA-
1 ATAAAATAG
3558 ATAAA
1 ATAAA
3563 TTATAATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.11
8 13 0.37
9 7 0.20
10 10 0.29
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (9 bp):
ATAAAATAG
Found at i:3644 original size:16 final size:18
Alignment explanation
Indices: 3610--3647 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
3600 TTGTTTTTAC
3610 AATAAAAGATAATAATTA
1 AATAAAAGATAATAATTA
3628 AATAAAAGA-AA-AATTA
1 AATAAAAGATAATAATTA
3644 AATA
1 AATA
3648 CATAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAAAAGATAATAATTA
Found at i:4121 original size:12 final size:12
Alignment explanation
Indices: 4106--4137 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4096 AAAAGTATGC
4106 GAAAAATAGAGA
1 GAAAAATAGAGA
*
4118 GAAAACTAGAGA
1 GAAAAATAGAGA
4130 GAAAAATA
1 GAAAAATA
4138 AGATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.22, T:0.09
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:4944 original size:12 final size:12
Alignment explanation
Indices: 4927--4952 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4917 TTTTGAATTC
4927 AGGTTACAATCA
1 AGGTTACAATCA
4939 AGGTTACAATCA
1 AGGTTACAATCA
4951 AG
1 AG
4953 AAAAGACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (12 bp):
AGGTTACAATCA
Found at i:6435 original size:21 final size:21
Alignment explanation
Indices: 6411--6466 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
6401 GCTAAAAATT
6411 AAATAAAACGAAATA-AAAAGA
1 AAATAAAACGAAATAGAAAA-A
* * *
6432 AAATGAAATGAAATAGAATAA
1 AAATAAAACGAAATAGAAAAA
*
6453 AAATAGAACGAAAT
1 AAATAAAACGAAAT
6467 GGGTTGCCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (21 bp):
AAATAAAACGAAATAGAAAAA
Found at i:17058 original size:22 final size:22
Alignment explanation
Indices: 17010--17058 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
17000 GGATGTTTTG
*
17010 TTTATCTTGAATATTTTGGTTA
1 TTTATCTTGAATATTTTGGTGA
* *
17032 TTTATGTTGGATATTTTGG-GA
1 TTTATCTTGAATATTTTGGTGA
17053 TGTTAT
1 T-TTAT
17059 TTATGCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.57
Consensus pattern (22 bp):
TTTATCTTGAATATTTTGGTGA
Found at i:24233 original size:9 final size:9
Alignment explanation
Indices: 24215--24313 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
24205 GGTCGGGTCG
*
24215 GGTCAGACC
1 GGTCAAACC
24224 GGTCAAACC
1 GGTCAAACC
*
24233 GGTTCAGACC
1 GG-TCAAACC
24243 GGTCAAACC
1 GGTCAAACC
*
24252 GGTTCGAACC
1 GG-TCAAACC
* *
24262 AGTTGAAACC
1 -GGTCAAACC
24272 GGTCAAACC
1 GGTCAAACC
24281 GGTCAGAACC
1 GGTCA-AACC
*
24291 GGTTGAAAACC
1 GG-T-CAAACC
*
24302 GGTTAAACC
1 GGTCAAACC
24311 GGT
1 GGT
24314 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
9 38 0.52
10 26 0.36
11 8 0.11
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:24239 original size:19 final size:19
Alignment explanation
Indices: 24217--24314 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
24207 TCGGGTCGGG
24217 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
24236 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
24255 TC-GAACCAGTTGAAACCGG-
1 TCAG-ACC-GGTCAAACCGGT
*
24274 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
24294 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
24314 T
1 T
24315 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.06
19 35 0.53
20 18 0.27
21 9 0.14
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:24273 original size:29 final size:31
Alignment explanation
Indices: 24240--24314 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
24230 ACCGGTTCAG
24240 ACCGGTCAAACCGGTTC-GAACCAGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
*
24269 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
*
24299 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
24315 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 15 0.37
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
Found at i:24303 original size:30 final size:29
Alignment explanation
Indices: 24257--24313 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
24247 AAACCGGTTC
24257 GAACCAGTTGAAACCGGTCAAACCGGTCA
1 GAACCAGTTGAAACCGGTCAAACCGGTCA
* *
24286 GAACCGGTTGAAAACCGGTTAAACCGGT
1 GAACCAGTTG-AAACCGGTCAAACCGGT
24314 TTCCAGCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (29 bp):
GAACCAGTTGAAACCGGTCAAACCGGTCA
Found at i:31482 original size:7 final size:7
Alignment explanation
Indices: 31470--31500 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31460 GTCAAAGAAA
31470 GTCAACG
1 GTCAACG
31477 GTCAACG
1 GTCAACG
31484 GTCAACG
1 GTCAACG
31491 GTCAACG
1 GTCAACG
31498 GTC
1 GTC
31501 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:31507 original size:5 final size:5
Alignment explanation
Indices: 31497--31537 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
31487 AACGGTCAAC
*
31497 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
31538 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:31552 original size:9 final size:9
Alignment explanation
Indices: 31534--31601 Score: 82
Period size: 9 Copynumber: 7.3 Consensus size: 9
31524 GGTCGGGTCG
*
31534 GGTCAGACC
1 GGTCAAACC
31543 GGTCAAACC
1 GGTCAAACC
*
31552 GGTTCAGACC
1 GG-TCAAACC
31562 GGTCAAACC
1 GGTCAAACC
*
31571 GGTTCAGACC
1 GG-TCAAACC
31581 GGTCAAACC
1 GGTCAAACC
*
31590 GGTTAAACC
1 GGTCAAACC
31599 GGT
1 GGT
31602 TTCCAGCAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
9 35 0.69
10 16 0.31
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:31558 original size:19 final size:19
Alignment explanation
Indices: 31536--31593 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
31526 TCGGGTCGGG
31536 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
31555 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
31574 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
31593 T
1 T
31594 AAACCGGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:31565 original size:28 final size:27
Alignment explanation
Indices: 31534--31601 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
31524 GGTCGGGTCG
* *
31534 GGTCAGACCGGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTCAAACCGG-TCAAACC
*
31562 GGTCAAACCGGTTCAGACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
*
31590 GGTTAAACCGGT
1 GGTCAAACCGGT
31602 TTCCAGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.03
28 26 0.74
29 8 0.23
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.16
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:33065 original size:90 final size:90
Alignment explanation
Indices: 32912--33122 Score: 386
Period size: 90 Copynumber: 2.3 Consensus size: 90
32902 AAAATTATTT
** * *
32912 TCCATATAGCTTACTTTATGCACATAGCAAAAAGAAAGCCGACTTAAGGATAGGCTCTGAAGCTT
1 TCCATATAGCTTACCCTAAGCACACAGCAAAAAGAAAGCCGACTTAAGGATAGGCTCTGAAGCTT
32977 GTATCCTTAAGCCCAAGTCAATAAG
66 GTATCCTTAAGCCCAAGTCAATAAG
33002 TCCATATAGCTTACCCTAAGCACACAGCAAAAAGAAAGCCGACTTAAGGATAGGCTCTGAAGCTT
1 TCCATATAGCTTACCCTAAGCACACAGCAAAAAGAAAGCCGACTTAAGGATAGGCTCTGAAGCTT
33067 GTATCCTTAAGCCCAAGTCAATAAG
66 GTATCCTTAAGCCCAAGTCAATAAG
33092 TCCATATAGCTTACCCTAAGCACACAGCAAA
1 TCCATATAGCTTACCCTAAGCACACAGCAAA
33123 GGGAAGCCGA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 117 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (90 bp):
TCCATATAGCTTACCCTAAGCACACAGCAAAAAGAAAGCCGACTTAAGGATAGGCTCTGAAGCTT
GTATCCTTAAGCCCAAGTCAATAAG
Found at i:33974 original size:5 final size:5
Alignment explanation
Indices: 33964--34023 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
33954 AACGGTCAAC
* *
33964 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
34013 GGTCG GGTCG G
1 GGTCG GGTCG G
34024 ACCGGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
5 39 0.83
7 8 0.17
ACGTcount: A:0.07, C:0.22, G:0.53, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:33985 original size:22 final size:22
Alignment explanation
Indices: 33957--34023 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
33947 AACGGTCAAC
33957 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33979 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
34001 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
34023 G
1 G
34024 ACCGGTCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:34037 original size:19 final size:19
Alignment explanation
Indices: 34015--34056 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
34005 AACGGTCGGG
*
34015 TCGGGTCGGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
34034 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
34053 TCGG
1 TCGG
34057 TTCGAACCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.19
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:34065 original size:19 final size:19
Alignment explanation
Indices: 34023--34059 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
34013 GGTCGGGTCG
34023 GACCGGTCAAATCGGTTCA
1 GACCGGTCAAATCGGTTCA
34042 GACCGGTCAAATCGGTTC
1 GACCGGTCAAATCGGTTC
34060 GAACCGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (19 bp):
GACCGGTCAAATCGGTTCA
Found at i:40358 original size:29 final size:28
Alignment explanation
Indices: 40326--40382 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40316 ATTTTATTTT
* *
40326 AAAAAACCTAAAACTTTTGAAAATCTTTA
1 AAAAAAACTAAAAC-TTTGAAAACCTTTA
*
40355 AAAAAAACTCAAACTTTGAAAACCTTTA
1 AAAAAAACTAAAACTTTGAAAACCTTTA
40383 TTACAATCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAAACTAAAACTTTGAAAACCTTTA
Found at i:40498 original size:16 final size:16
Alignment explanation
Indices: 40477--40507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40467 GCCATCGATG
40477 ACACAACCACATGAAT
1 ACACAACCACATGAAT
*
40493 ACACAACCACCTGAA
1 ACACAACCACATGAA
40508 GAACCCCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.35, G:0.06, T:0.10
Consensus pattern (16 bp):
ACACAACCACATGAAT
Found at i:41573 original size:27 final size:28
Alignment explanation
Indices: 41521--41572 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
41511 TAATTTTATT
41521 TTAAAAAAACATAAAACTTTTGAAAATC
1 TTAAAAAAACATAAAACTTTTGAAAATC
*
41549 TTAAAAAAAC-TCAAAC-TTTGAAAA
1 TTAAAAAAACATAAAACTTTTGAAAA
41573 ACTTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 5 0.22
28 10 0.43
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.27
Consensus pattern (28 bp):
TTAAAAAAACATAAAACTTTTGAAAATC
Found at i:42680 original size:26 final size:27
Alignment explanation
Indices: 42651--42712 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
42641 AAAGTTAACT
42651 TTTTTATAAACAT-AATAATATTTTTA
1 TTTTTATAAACATAAATAATATTTTTA
* ** *
42677 TTTTT-TTAATTTAAATAATTTTTTTA
1 TTTTTATAAACATAAATAATATTTTTA
*
42703 ATTTTATAAA
1 TTTTTATAAA
42713 GGTGACACGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.14
26 21 0.75
27 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTTATAAACATAAATAATATTTTTA
Found at i:43953 original size:26 final size:27
Alignment explanation
Indices: 43902--43953 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
43892 CTAACTGCTT
* *
43902 AATACATGTGCATATTTCTTTAACAGC
1 AATACACGTGCATAGTTCTTTAACAGC
43929 AATACACGTGCAT-GTTCTTTAACAG
1 AATACACGTGCATAGTTCTTTAACAG
43954 TCTAACATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
AATACACGTGCATAGTTCTTTAACAGC
Found at i:44050 original size:36 final size:35
Alignment explanation
Indices: 44003--44215 Score: 277
Period size: 36 Copynumber: 5.9 Consensus size: 35
43993 AGATGAACAA
* *
44003 TTGAATCGAAAGTGCGGATGCTTTCTTCCGTTCACT
1 TTGAATCGAAAGTGC-GATGCTTCCTTTCGTTCACT
*
44039 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTG-CGATGCTTCCTTTCGTTCACT
*
44074 ATTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGC-GATGCTTCCTTTCGTTCACT
*
44111 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTG-CGATGCTTCCTTTCGTTCACT
44146 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCACT
1 -TTGAATCGAAAGTG-CGATGCTTCCTTTCGTTCACT
* *
44183 TTGAATCGAAATTGCTGATGTTTCCTTTCGTTC
1 TTGAATCGAAAGTGC-GATGCTTCCTTTCGTTC
44216 TTCTTATTCA
Statistics
Matches: 158, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
35 4 0.03
36 150 0.95
37 4 0.03
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGCGATGCTTCCTTTCGTTCACT
Found at i:44152 original size:108 final size:108
Alignment explanation
Indices: 44003--44215 Score: 313
Period size: 108 Copynumber: 2.0 Consensus size: 108
43993 AGATGAACAA
* *
44003 TTGAATCGAAAGTGCGGATGCTTTCTTCCGTTCACTTTGAATCGAAAGTGTCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTCGATGCTTCCTTTC
*
44068 GTTC-TTATTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACT
66 GTTCACT-TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACT
* *
44111 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-TTCTTGAATCGAAAGTGTCGATGCTTCCTTT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT-TTGAATCGAAAGTGTCGATGCTTCCTTT
* * * *
44175 CGTTCACTTTGAATCGAAATTGCTGATGTTTCCTTTCGTTC
65 CGTTCACTTTGAATCGAAAGTGCGGATGCTTCCTTCCGTTC
44216 TTCTTATTCA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 92 0.98
109 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (108 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGTCGATGCTTCCTTTC
GTTCACTTTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACT
Found at i:44218 original size:72 final size:72
Alignment explanation
Indices: 44003--44220 Score: 350
Period size: 72 Copynumber: 3.0 Consensus size: 72
43993 AGATGAACAA
*
44003 TTGAATCGAAAGTGCGGATGCTTTCTTCCGTTCACTTTGAATCGAAAGTG-TCGATGCTTCCTTT
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCT-GATGCTTCCTTT
*
44067 CGTTCTTA
65 CGTTCTTC
*
44075 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
44140 GTTCTTC
66 GTTCTTC
* * *
44147 TTGAATCGAAAGTGTC-GATGCTTCCTTTCGTTCACTTTGAATCGAAATTGCTGATGTTTCCTTT
1 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTT
44211 CGTTCTTC
65 CGTTCTTC
44219 TT
1 TT
44221 ATTCACCTTC
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
72 136 0.99
73 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (72 bp):
TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
GTTCTTC
Found at i:51070 original size:26 final size:26
Alignment explanation
Indices: 51041--51111 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
51031 CCATTGCATT
*
51041 GGAGAGTAAAATGTTTCTCAGATAGA
1 GGAGGGTAAAATGTTTCTCAGATAGA
51067 GGAGGGTAAAATGTTTCTCAGATAGA
1 GGAGGGTAAAATGTTTCTCAGATAGA
51093 GGAGGGTAAAATGTTTCTC
1 GGAGGGTAAAATGTTTCTC
51112 CATGGCGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (26 bp):
GGAGGGTAAAATGTTTCTCAGATAGA
Found at i:58043 original size:21 final size:21
Alignment explanation
Indices: 58003--58051 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
57993 TTTTTATTTC
*
58003 TTTTTTCACACTTTTGTTGTT
1 TTTTTTCACACTTTTGTTGTA
* *
58024 TTGTTTTC-CATTTTTTTTGTA
1 TT-TTTTCACACTTTTGTTGTA
58045 TTTTTTC
1 TTTTTTC
58052 TCTCCCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.71
Consensus pattern (21 bp):
TTTTTTCACACTTTTGTTGTA
Found at i:69064 original size:45 final size:46
Alignment explanation
Indices: 69004--69105 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 46
68994 TGCACTAAGT
* * * *
69004 GTGCATCGATGCATAAAATACATTCGATGTTTTGAAT-AAGCCTAA
1 GTGCATCGATGCATAAAATACAATCAATGTTTTCAATAAAACCTAA
* * *
69049 GTGCATCGATGCATAAAATGCAATCAATGTTTTCATTAAAACCTGA
1 GTGCATCGATGCATAAAATACAATCAATGTTTTCAATAAAACCTAA
69095 GTGCATCGATG
1 GTGCATCGATG
69106 TATGGAGAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 32 0.65
46 17 0.35
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATACAATCAATGTTTTCAATAAAACCTAA
Found at i:71796 original size:44 final size:44
Alignment explanation
Indices: 71741--71837 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
71731 GGCTTTTTTC
* *
71741 ATCGATGCACATTC-AA-GGAGTGCATCGGTGCA-TCTTCATGATGT
1 ATCGATGCACATACAAAGGGA-TGCATCGATGCACTCTTCA-G-TGT
*
71785 ATCGATGCACATACAAAGGGATGCATCGATGCACTGTTCAGTGT
1 ATCGATGCACATACAAAGGGATGCATCGATGCACTCTTCAGTGT
71829 ATCGATGCA
1 ATCGATGCA
71838 TTAAGCATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 25 0.53
45 14 0.30
46 8 0.17
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATACAAAGGGATGCATCGATGCACTCTTCAGTGT
Found at i:77645 original size:63 final size:65
Alignment explanation
Indices: 77560--77736 Score: 202
Period size: 63 Copynumber: 2.8 Consensus size: 65
77550 TGGAACACTT
* * * * *
77560 AGTGCATCGGTGCACT-AAGTGTGCATTGATGCATAAAATGC-TTCGATGTTTTGAAT-AAGCCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCT
77622 A
65 A
* * * *
77623 AGTGCATCGATGCATGGTGTGTGCATCGATGCATAAAA--CAATCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
* * *
77686 AGTGCATCGATGTATGGAGAGTGCATCGATGCATAAACTGCATTCGATGTT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTT
77737 CAATTTATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 1 0.01
62 13 0.14
63 71 0.75
65 10 0.11
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
Done.