Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003154.1 Hibiscus syriacus cultivar Beakdansim tig00006634_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: 65657
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5451 original size:70 final size:71
Alignment explanation
Indices: 5182--5459 Score: 407
Period size: 71 Copynumber: 3.9 Consensus size: 71
5172 AAACCGAATA
* * *
5182 ACTTCTTAAAAGATCATAAAAGCACATAAGCTTTACGACAACTTAGAAA-ATCATCGTATGATCC
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAAGATCATCATATGATCC
***
5246 TAACAG
66 TAATTC
* * * *
5252 ACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAACAGATCATCATATGATC
1 ACTTCTTAAAAGATC-ATAAAAGCACATAAGCGTTACGACAACTTAAAAAGATCATCATATGATC
5317 CTAATTC
65 CTAATTC
* *
5324 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAAGGTCATCATATGATCC
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAAGATCATCATATGATCC
5389 TAATTC
66 TAATTC
* *
5395 ACTTCTTAAAAGGTCAT-AAAGCACATATGCGTTACGACAACTTAAAAAGATCATCATATGATCC
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAAGATCATCATATGATCC
5459 T
66 T
5460 CATTGAATGC
Statistics
Matches: 186, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
70 61 0.33
71 94 0.51
72 31 0.17
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (71 bp):
ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAAGATCATCATATGATCC
TAATTC
Found at i:5454 original size:141 final size:142
Alignment explanation
Indices: 5182--5459 Score: 418
Period size: 141 Copynumber: 2.0 Consensus size: 142
5172 AAACCGAATA
* * *
5182 ACTTCTTAAAAGATCATAAAAGCACATAAGCTTTACGACAACTTAGAAAATCATCGTATGATCCT
1 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAATCATCATATGATCCT
* *
5247 AACAGACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAACAGATCATCATA
66 AACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCATA
5312 TGATCCTAATTC
131 TGATCCTAATTC
5324 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTA-AAAAGGTCATCATATGATC
1 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAA--TCATCATATGATC
** * * **
5388 CTAATTCACTTCTTAAAAGGTC-A-TAAAGCACATATGCGTTACGACAACTTAAAAAGATCATCA
64 CTAACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCA
5451 TATGATCCT
129 TATGATCCT
5460 CATTGAATGC
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
141 49 0.40
142 44 0.36
143 30 0.24
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (142 bp):
ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAATCATCATATGATCCT
AACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCATA
TGATCCTAATTC
Found at i:9659 original size:264 final size:265
Alignment explanation
Indices: 9219--10405 Score: 1555
Period size: 265 Copynumber: 4.5 Consensus size: 265
9209 TCTGGGACTA
** * * * * * * * *
9219 ACGCGCTTGAAAAAACTCTCTTTGTTACTGTGTGAAAACGTTAGATCATATCACTATCTAGTCAA
1 ACGCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAA
* * *
9284 ATTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATGTAACA
66 ACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAACA
* * *
9349 CGTGTTATGAAAATTGAAATGTACATGAGAAACTATACTAATAAATATTGTTGCCGTTTACTATG
131 CGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTACTATG
* * *
9414 ACATCAATAATTTAATTTATCAATC-AAAAAATTCTAAAATGATTGGATCTGTTGTAATAAATGG
196 ACATCAATAATTTAATCTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAAATGG
9478 AGTTC
261 AGTTC
* *
9483 ACGCGCTTGAAAAAGTTATTTTTGTTATTGAGTGAAAATGTTAGATCATGTTATTATCAAATCAA
1 ACGCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAA
* *
9548 ACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACATACATCTATCA
66 ACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAACA
*
9613 CGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTA-AAGT
131 CGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTACTA-T
9677 GACATCAATAATTTAATCTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAAATG
195 GACATCAATAATTTAATCTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAAATG
9742 GAGTTC
260 GAGTTC
** * *
9748 ACGTACTTGACAAAGTTATTTTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAA
1 ACGCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAA
** * * **
9813 ACTATAACGATAATATTTATTGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACA
66 ACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAACA
* * * * *
9878 CTTGTTATGAAAATTGAAATGTATATGTAAAACTATACTGATAAATATTGTTGTCGTTTATTGTG
131 CGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTACTATG
* * * * *
9943 ACGTCAATGATTTGATTTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAACTGG
196 ACATCAATAATTTAATCTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAAATGG
10008 AGTTC
261 AGTTC
* * ** *
10013 -CTACGCTTGAGAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCACATTATCATCAAGTCA
1 AC-GCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCA
** *
10077 AACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACCTATATCTAAC
65 AACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAAC
* * * * *
10142 ACGTGTTATGAAAATTAAAATGTACATGTGAAATTGTACTGATAAATATTGTTGTTGTTTACTGT
130 ACGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTACTAT
* * * * **
10207 AACATCAATAATTTAATCTATCAATCGAAAGAGTTCTAAAAATAAATGGATCTATTGTAATAACC
195 GACATCAATAATTTAATCTATCAATCGAAAGAATTCT-AAAATGATTGGATCTATTGTAATAAAT
10272 GGAGTT-
259 GGAGTTC
* * * * * * *
10278 ---CGCTTTAGAAAGTTCTCTTTGTTACTGAGTGAAAATGTTAGATCATGTTATCACCAA-ACAA
1 ACGCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTC-A
* * * * * * * ** *
10339 AATTATAATGATCTTATTTGTTTTATTTATTCAACTTAAATGATTGTT-TTTGTAGACATATAAC
65 AACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAAC
10403 ACG
130 ACG
10406 GGATAGAGAA
Statistics
Matches: 815, Mismatches: 102, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
261 14 0.02
262 93 0.11
263 1 0.00
264 197 0.24
265 480 0.59
266 30 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (265 bp):
ACGCGCTTGAAAAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAA
ACTATAACGATCTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACAGACATCTAACA
CGTGTTATGAAAATTGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTACTATG
ACATCAATAATTTAATCTATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAAATGG
AGTTC
Found at i:12862 original size:21 final size:21
Alignment explanation
Indices: 12838--12897 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
12828 AACTTTGAAA
12838 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
12859 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
12873 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
12894 AAAT
1 AAAT
12898 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:12944 original size:36 final size:36
Alignment explanation
Indices: 12830--12949 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
12820 TGGTAACCAA
12830 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
12867 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
12902 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
12939 -GTTGAAAAATG
1 CTTTGAAAAATG
12950 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:12949 original size:72 final size:69
Alignment explanation
Indices: 12803--12946 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 69
12793 TGAAAGTATT
*
12803 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
*
12868 TTTG
66 GTTG
* * * *
12872 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGTAAACA--ACTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATG
12936 TTT-GTTG
62 TTTCGTTG
12943 AAAA
1 AAAA
12947 ATGATAATGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 12 0.18
70 12 0.18
71 13 0.20
72 28 0.43
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
GTTG
Found at i:13380 original size:16 final size:16
Alignment explanation
Indices: 13359--13391 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13349 TACTATTCAT
*
13359 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
13375 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
13391 G
1 G
13392 ATCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:17479 original size:21 final size:21
Alignment explanation
Indices: 17455--17515 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
17445 AACTTTGAAA
17455 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
17476 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
17490 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
17511 AAATG
1 AAATG
17516 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:17561 original size:36 final size:36
Alignment explanation
Indices: 17447--17565 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
17437 TGGTAACCAA
*
17447 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
17484 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
17519 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
17556 -GTTGAAAAAT
1 CTTTGAAAAAT
17566 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:32837 original size:27 final size:27
Alignment explanation
Indices: 32804--32865 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
32794 TTTCGACCTT
32804 GCAACTGCATGGAATCCTGTCTTTGCA
1 GCAACTGCATGGAATCCTGTCTTTGCA
32831 GCAACTGCATGGAATCCTGTCTTTGCA
1 GCAACTGCATGGAATCCTGTCTTTGCA
32858 GCAACTGC
1 GCAACTGC
32866 TGCAGGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (27 bp):
GCAACTGCATGGAATCCTGTCTTTGCA
Found at i:36807 original size:2 final size:2
Alignment explanation
Indices: 36789--36832 Score: 63
Period size: 2 Copynumber: 21.5 Consensus size: 2
36779 ATTTGTTAGG
36789 AT AT AT CAT AT -T CAT 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 AT AT AT AT
36832 A
1 A
36833 AGATATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 1 0.03
2 35 0.90
3 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38457 original size:54 final size:55
Alignment explanation
Indices: 38399--38541 Score: 175
Period size: 54 Copynumber: 2.6 Consensus size: 55
38389 TATTCTCAGG
* * * *
38399 GCTAGCCCTCTCT-TTCCTGTACGGACTTCGACTGGAGCCACGAGCATGG-TCCAA
1 GCTAGCCCTCTCTCTTCCGGGA-GGACTACGACTGGACCCACGAGCATGGTTCCAA
* *
38453 GCTAGCCCTCTCTCTTCGGGGAGGACTACGACTGGACCCACGAGCATGGTTCGAA
1 GCTAGCCCTCTCTCTTCCGGGAGGACTACGACTGGACCCACGAGCATGGTTCCAA
* * *
38508 -CCAGCCCTCTCTCTTCGGGGAGGACTACGGCTGG
1 GCTAGCCCTCTCTCTTCCGGGAGGACTACGACTGG
38542 TGATATGGCC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 70 0.89
55 9 0.11
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (55 bp):
GCTAGCCCTCTCTCTTCCGGGAGGACTACGACTGGACCCACGAGCATGGTTCCAA
Found at i:43427 original size:3 final size:3
Alignment explanation
Indices: 43419--43450 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43409 TAATTATGAA
43419 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
43451 ATTAGCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44500 original size:3 final size:3
Alignment explanation
Indices: 44492--44521 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
44482 ACAGAACTCA
44492 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
44522 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:56112 original size:27 final size:28
Alignment explanation
Indices: 56062--56150 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
56052 TTAGTCATTA
*
56062 TTTTAAATAAATTTTAACATAAAATATATAT
1 TTTTAAATAAA-GTT-A-ATAAAATATATAT
*
56093 TTTTAAATGAAAG-TAA-AAAATAAAATAT
1 TTTTAAAT-AAAGTTAATAAAAT-ATATAT
*
56121 TTTTAAATTAAGTTAATAAAATATATAT
1 TTTTAAATAAAGTTAATAAAATATATAT
56149 TT
1 TT
56151 AATAAGTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 8 0.16
28 24 0.48
29 6 0.12
30 1 0.02
31 8 0.16
32 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTTAAATAAAGTTAATAAAATATATAT
Found at i:56142 original size:24 final size:24
Alignment explanation
Indices: 56111--56186 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
56101 GAAAGTAAAA
56111 AATAAAATAT-T-TTTAAATTAAGTT
1 AATAAAATATATATTT-AA-TAAGTT
56135 AATAAAATATATATTTAATAAGTT
1 AATAAAATATATATTTAATAAGTT
* **
56159 AATATAAA-AAATATTTTTTAAGTT
1 AATA-AAATATATATTTAATAAGTT
56183 AATA
1 AATA
56187 TATATAACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 37 0.80
25 6 0.13
26 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AATAAAATATATATTTAATAAGTT
Found at i:56187 original size:24 final size:25
Alignment explanation
Indices: 56127--56199 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
56117 ATATTTTTAA
*
56127 ATTAAGTTAATA-AAATATATATTT
1 ATTAAGTTAATATAAATAAATATTT
*
56151 AATAAGTTAATATAAA-AAATATTT
1 ATTAAGTTAATATAAATAAATATTT
* *
56175 TTTAAGTTAATATATATAACATATT
1 ATTAAGTTAATATAAATAA-ATATT
56200 ACGTATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 31 0.76
25 5 0.12
26 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (25 bp):
ATTAAGTTAATATAAATAAATATTT
Found at i:56189 original size:26 final size:26
Alignment explanation
Indices: 56114--56199 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 26
56104 AGTAAAAAAT
*
56114 AAAATA-TTTTTAAATTAAGT-TAATAA
1 AAAATATTTTTTAAGTTAA-TAT-ATAA
**
56140 AATATATATTTAATAAGTT-A-ATATAA
1 AA-A-ATATTTTTTAAGTTAATATATAA
*
56166 AAAATATTTTTTAAGTTAATATATAT
1 AAAATATTTTTTAAGTTAATATATAA
*
56192 AACATATT
1 AAAATATT
56200 ACGTATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
24 12 0.26
25 2 0.04
26 20 0.43
27 2 0.04
28 4 0.09
29 7 0.15
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (26 bp):
AAAATATTTTTTAAGTTAATATATAA
Found at i:57750 original size:13 final size:13
Alignment explanation
Indices: 57732--57757 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57722 TATATTTATA
57732 AATTATTAGAATT
1 AATTATTAGAATT
57745 AATTATTAGAATT
1 AATTATTAGAATT
57758 TTATCTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATTATTAGAATT
Found at i:62911 original size:10 final size:10
Alignment explanation
Indices: 62898--62951 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
62888 CATTCGGTAA
62898 TATGTTCGTT
1 TATGTTCGTT
*
62908 TATGTTCATT
1 TATGTTCGTT
62918 TATGTTCGTTCGTT
1 TA---T-GTTCGTT
*
62932 TATGTTTGTT
1 TATGTTCGTT
62942 TATGTTCGTT
1 TATGTTCGTT
62952 CGTTTATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 26 0.72
11 1 0.03
13 1 0.03
14 8 0.22
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:62933 original size:14 final size:14
Alignment explanation
Indices: 62911--62975 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
62901 GTTCGTTTAT
*
62911 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
62925 GTTCGTTTATG-T-
1 GTTCGTTTATGTTC
62937 -TT-GTTTATGTTC
1 GTTCGTTTATGTTC
*
62949 GTTCGTTTATGTGC
1 GTTCGTTTATGTTC
**
62963 GTTTATTTATGTT
1 GTTCGTTTATGTT
62976 TAGCCTAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.17
11 3 0.07
13 3 0.07
14 29 0.69
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.60
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:62966 original size:24 final size:24
Alignment explanation
Indices: 62901--62968 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
62891 TCGGTAATAT
*
62901 GTTCGTTTATGTTCATTTATGTTC
1 GTTCGTTTATGTTCGTTTATGTTC
*
62925 GTTCGTTTATGTTTGTTTATGTTC
1 GTTCGTTTATGTTCGTTTATGTTC
*
62949 GTTCGTTTATGTGCGTTTAT
1 GTTCGTTTATGTTCGTTTAT
62969 TTATGTTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTTATGTTC
Found at i:63206 original size:24 final size:24
Alignment explanation
Indices: 63177--63262 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
63167 TCATTTATTG
*
63177 TGTTCGTTTACATTCGTTCATTTG
1 TGTTCGTTTACATTCGTTCATTTA
*
63201 TGTTCGTTT--ATT-GTGTCTGTTTA
1 TGTTCGTTTACATTCGT-TC-ATTTA
*
63224 TGTTCGTTTACATTC-TTTAGTTTA
1 TGTTCGTTTACATTCGTTCA-TTTA
63248 TGTTCGTTTATCATT
1 TGTTCGTTTA-CATT
63263 TAAATGAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.04
22 5 0.10
23 12 0.24
24 24 0.47
25 8 0.16
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (24 bp):
TGTTCGTTTACATTCGTTCATTTA
Found at i:65479 original size:25 final size:25
Alignment explanation
Indices: 65451--65499 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
65441 ATTATCTTGC
65451 ATTCATTTCAGATTTATAAAAAAAT
1 ATTCATTTCAGATTTATAAAAAAAT
65476 ATTCATTTCAGATTTATAAAAAAA
1 ATTCATTTCAGATTTATAAAAAAA
65500 AGAACGCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTCATTTCAGATTTATAAAAAAAT
Done.