Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006857.1 Hibiscus syriacus cultivar Beakdansim tig00017448_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: 95849
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:16187 original size:32 final size:30
Alignment explanation
Indices: 16118--16188 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
16108 AAGTTTATTT
* * *
16118 TTTAATTTAATTACTTAATTTTCAAATTAC
1 TTTAATTTAATCACTTAACTTTCAAATTAA
*
16148 TCATAATTTAATCACTCTAACTTTCAAATTTAA
1 T-TTAATTTAATCACT-TAACTTTCAAA-TTAA
16181 TTTAATTT
1 TTTAATTT
16189 TAATTATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 12 0.36
32 16 0.48
33 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATTTAATCACTTAACTTTCAAATTAA
Found at i:16791 original size:29 final size:29
Alignment explanation
Indices: 16757--16848 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
16747 TTTGGATGAA
*
16757 TTTGGGGATAAAATTAGAATATTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
* * *
16786 TTTGGGGATGAATTTAGAAAGATAGTC-ATAG
1 TTTGGGGATGAAATTAG--A-ATATTCAAAAG
* * *
16817 TTTAGTGATGAAATTAGAATGTTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
16846 TTT
1 TTT
16849 AAGGTGTAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
28 4 0.08
29 22 0.45
31 18 0.37
32 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
TTTGGGGATGAAATTAGAATATTCAAAAG
Found at i:17506 original size:23 final size:23
Alignment explanation
Indices: 17476--17545 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
17466 TTCCATATAG
17476 AATGTCCCGAAGGACCGCGTAGA
1 AATGTCCCGAAGGACCGCGTAGA
* *
17499 AATGTCCCGAAGGACCACGCAGA
1 AATGTCCCGAAGGACCGCGTAGA
* * *
17522 ATTGTCCTGAAGGACCGTGTAGA
1 AATGTCCCGAAGGACCGCGTAGA
17545 A
1 A
17546 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (23 bp):
AATGTCCCGAAGGACCGCGTAGA
Found at i:20578 original size:21 final size:18
Alignment explanation
Indices: 20546--20584 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
20536 AAATGCTTTG
20546 TTTTTTACAAATTATAAAT
1 TTTTTTACAAATT-TAAAT
20565 TTTTTTATCAAAATTTAAAT
1 TTTTTTA-C-AAATTTAAAT
20585 GTTTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTTACAAATTTAAAT
Found at i:23813 original size:12 final size:12
Alignment explanation
Indices: 23796--23829 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
23786 GAATACATGC
23796 CTATGTGATGAG
1 CTATGTGATGAG
23808 CTATGTGATGAG
1 CTATGTGATGAG
23820 CTATGTGATG
1 CTATGTGATG
23830 TATATATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (12 bp):
CTATGTGATGAG
Found at i:25668 original size:18 final size:18
Alignment explanation
Indices: 25645--25686 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
25635 AGAGAAGGTT
25645 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
25663 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
25681 TTATGA
1 TTATGA
25687 CGTGTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (18 bp):
TTATGATGTTAAATGATA
Found at i:29714 original size:22 final size:22
Alignment explanation
Indices: 29688--29729 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
29678 AGATTGTGCA
29688 GGGGGTA-CAGATTCCCCCCTGG
1 GGGGGTATC-GATTCCCCCCTGG
29710 GGGGGTATCGATTCCCCCCT
1 GGGGGTATCGATTCCCCCCT
29730 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCCCTGG
Found at i:30817 original size:24 final size:23
Alignment explanation
Indices: 30761--30821 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
30751 ACAATCTTAT
30761 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
**
30784 GCGGTC-CTTCGG-GACAATTTCTAC
1 ATGG-CACTTCGGTG-C-ATTTCTAC
30808 ATGGCACTTCGGTG
1 ATGGCACTTCGGTG
30822 TAATTTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 17 0.59
25 1 0.03
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGCATTTCTAC
Found at i:38368 original size:17 final size:19
Alignment explanation
Indices: 38329--38375 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
38319 AAAATGAAAA
* *
38329 TATTTTTTTACTATTTTTC
1 TATTTTTTAAATATTTTTC
38348 TATTTTTTAAATA-TTTT-
1 TATTTTTTAAATATTTTTC
38365 TATTTTTTAAA
1 TATTTTTTAAA
38376 AATTCAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 11 0.42
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTTAAATATTTTTC
Found at i:40594 original size:95 final size:95
Alignment explanation
Indices: 40431--40621 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
40421 TAAAATTGTG
40431 TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
1 TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
40496 GCTAGAATAAACTTAAGTCTTAAACCAGAC
66 GCTAGAATAAACTTAAGTCTTAAACCAGAC
40526 TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
1 TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
*
40591 GCTAGAATAAACTTAAGTCTTAAACCGGAC
66 GCTAGAATAAACTTAAGTCTTAAACCAGAC
40621 T
1 T
40622 TGACTCTTTT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (95 bp):
TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
GCTAGAATAAACTTAAGTCTTAAACCAGAC
Found at i:50169 original size:31 final size:31
Alignment explanation
Indices: 50133--50192 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
50123 AACTTAAAAG
*
50133 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
50164 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
50193 CATACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:50214 original size:31 final size:31
Alignment explanation
Indices: 50140--50215 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
50130 AAGAGTTTTG
* ***
50140 CAATACTGAAATTTAAATAATTTTAGTTTTA
1 CAATACTGAAATTTAAATAATTATACAATTA
*
50171 TAATACTGAAATTTAAATAATTCATACAATTA
1 CAATACTGAAATTTAAATAATT-ATACAATTA
50203 CAATACT-AAATTT
1 CAATACTGAAATTT
50216 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
CAATACTGAAATTTAAATAATTATACAATTA
Found at i:50240 original size:22 final size:22
Alignment explanation
Indices: 50215--50711 Score: 746
Period size: 22 Copynumber: 22.6 Consensus size: 22
50205 ATACTAAATT
*
50215 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
50237 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
50259 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
50281 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
50303 TTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATCCATA
50325 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
50347 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
50369 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
50391 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
50413 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
50435 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATCCATA
*
50457 TTTTAAAATAAATCTATCCATA
1 TTTTAAAATAAATCAATCCATA
50479 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
50501 TTTTAAAATAAGTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
50523 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
50545 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
50567 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
50589 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
50611 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
50633 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
50655 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
50677 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
50699 TTTTAAAATAAAT
1 TTTTAAAATAAAT
50712 TTTAAAATAA
Statistics
Matches: 429, Mismatches: 42, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
21 8 0.02
22 413 0.96
23 8 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:50715 original size:12 final size:12
Alignment explanation
Indices: 50698--50724 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
50688 ATCAATCTAT
50698 ATTTTAAAATAA
1 ATTTTAAAATAA
50710 ATTTTAAAATAA
1 ATTTTAAAATAA
50722 ATT
1 ATT
50725 ATTTTTCGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:57535 original size:19 final size:19
Alignment explanation
Indices: 57511--57551 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
57501 TTGGGTTAAG
57511 TAACTAACACATAAACTAT
1 TAACTAACACATAAACTAT
57530 TAACTAACACATAAACTAT
1 TAACTAACACATAAACTAT
57549 TAA
1 TAA
57552 TTTATCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (19 bp):
TAACTAACACATAAACTAT
Found at i:61316 original size:137 final size:137
Alignment explanation
Indices: 61070--61342 Score: 417
Period size: 137 Copynumber: 2.0 Consensus size: 137
61060 CTGCCTTTTG
*
61070 GAATTTGATATCAAATCTCATTCTCTTTCACAATTTAGGTGGTGTTTGGTTCCCTGAAATCTCTT
1 GAATTTGATATCAAATCTCATTCTCTTTCACAATTTAGGTGGTGTTTGGTTCCCTGAAATCCCTT
* * *
61135 AGAATTAGGGAGAATTGAAATTCAATTCTATCACTTTCTCATGTTTAGTTCAAGTTTTCAAAGAA
66 AGAATTAGGGAGAATTAAAATTCAATTCTACCACTTTCCCATGTTTAGTTCAAGTTTTCAAAGAA
*
61200 TGAATTA
131 GGAATTA
* * *
61207 GAATTTGATATCAAATCTCATTCTCTTTCATAATTTAGGTGGTGTTTGGTTCGCTGGAATCCCTT
1 GAATTTGATATCAAATCTCATTCTCTTTCACAATTTAGGTGGTGTTTGGTTCCCTGAAATCCCTT
*
61272 -GTAATTAGGG-GAAATTAAAATTCAATT-TCACCACTTTCCCATGTTTGGTTCAAGTTTTCAAA
66 AG-AATTAGGGAG-AATTAAAATTCAATTCT-ACCACTTTCCCATGTTTAGTTCAAGTTTTCAAA
61334 GAAGGAATT
128 GAAGGAATT
61343 GAAATCCAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
136 3 0.02
137 121 0.98
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (137 bp):
GAATTTGATATCAAATCTCATTCTCTTTCACAATTTAGGTGGTGTTTGGTTCCCTGAAATCCCTT
AGAATTAGGGAGAATTAAAATTCAATTCTACCACTTTCCCATGTTTAGTTCAAGTTTTCAAAGAA
GGAATTA
Found at i:61557 original size:15 final size:16
Alignment explanation
Indices: 61528--61558 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61518 TGTGATATTC
61528 GGGTCGGGTTCAGGTT
1 GGGTCGGGTTCAGGTT
61544 GGGTCGGG-TCAGGTT
1 GGGTCGGGTTCAGGTT
61559 TTTTTAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.13, G:0.52, T:0.29
Consensus pattern (16 bp):
GGGTCGGGTTCAGGTT
Found at i:61572 original size:49 final size:49
Alignment explanation
Indices: 61491--61584 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
61481 AAAAAATTTG
*
61491 GGTTCGGGTTGGGTCAGGTTTTTTAAATGTGATATTCGGGTCGGGTTCA
1 GGTTCGGGTCGGGTCAGGTTTTTTAAATGTGATATTCGGGTCGGGTTCA
* *
61540 GGTT-GGGTCGGGTCAGGTTTTTTTAAGTGTGATATTTGGGTCGGG
1 GGTTCGGGTCGGGTCAGG-TTTTTTAAATGTGATATTCGGGTCGGG
61585 GTCGGGGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 12 0.29
49 29 0.71
ACGTcount: A:0.13, C:0.09, G:0.39, T:0.39
Consensus pattern (49 bp):
GGTTCGGGTCGGGTCAGGTTTTTTAAATGTGATATTCGGGTCGGGTTCA
Found at i:62509 original size:21 final size:21
Alignment explanation
Indices: 62483--62535 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
62473 GTTTCCAGAT
*
62483 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTAGACTA
62504 TCGCAACGCGAACTTAGACTA
1 TCGCAACGCGAACTTAGACTA
*
62525 TCGCAATGCGA
1 TCGCAACGCGA
62536 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTAGACTA
Found at i:62681 original size:82 final size:82
Alignment explanation
Indices: 62569--62829 Score: 450
Period size: 82 Copynumber: 3.2 Consensus size: 82
62559 TCCAAGTTCG
62569 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
62634 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* *
62651 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTTGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
62716 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* * *
62733 CGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTTAAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTTCAAATTCGTTGCGATAGTCGAAGTTCGCG
*
62798 TTGCGATTTATTCTAAATT
64 TTGCGATTTATTCCAAATT
62817 CGTTGCGATAGTC
1 CGTTGCGATAGTC
62830 CAAAATCGCA
Statistics
Matches: 169, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
82 108 0.64
83 2 0.01
84 59 0.35
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:62832 original size:42 final size:42
Alignment explanation
Indices: 62569--62829 Score: 440
Period size: 42 Copynumber: 6.3 Consensus size: 42
62559 TCCAAGTTCG
62569 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TT-CAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
62609 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
62651 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
62691 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* **
62733 CGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTTAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
62775 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
62817 CGTTGCGATAGTC
1 CGTTGCGATAGTC
62830 CAAAATCGCA
Statistics
Matches: 208, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
40 69 0.33
41 6 0.03
42 133 0.64
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:63592 original size:42 final size:42
Alignment explanation
Indices: 63530--63802 Score: 397
Period size: 42 Copynumber: 6.5 Consensus size: 42
63520 TGCTATTTTG
*
63530 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
63572 GACTATTGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
63614 GACTATCGCAACGAATTTGGAATAAATCGTAACGCAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
63656 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
63698 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
63740 GACTATCGCAACGAA-TTTGAA-AAATCGCAACGCGAATTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
63780 GACTATCGCAACGCAAACTTGGA
1 GACTATCGCAACG--AACTTGGA
63803 CTATCACAAT
Statistics
Matches: 209, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
40 30 0.14
41 5 0.02
42 170 0.81
43 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:63777 original size:21 final size:21
Alignment explanation
Indices: 63679--63778 Score: 66
Period size: 21 Copynumber: 4.9 Consensus size: 21
63669 AACTTGGAAT
* * *
63679 AAATCACAACGCGAACTTGGA
1 AAATCGCAACGCGAATTTGAA
**
63700 CTATCGCAA--CGAATTTGGAA
1 AAATCGCAACGCGAATTT-GAA
*
63720 TAAATCGCAACGCAAACTTTG-A
1 -AAATCGCAACGCGAA-TTTGAA
**
63742 CTATCGCAA--CGAATTTGAA
1 AAATCGCAACGCGAATTTGAA
63761 AAATCGCAACGCGAATTT
1 AAATCGCAACGCGAATTT
63779 TGACTATCGC
Statistics
Matches: 58, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
18 4 0.07
19 17 0.29
20 2 0.03
21 27 0.47
22 1 0.02
23 4 0.07
24 3 0.05
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGAA
Found at i:68870 original size:20 final size:20
Alignment explanation
Indices: 68841--68910 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
68831 TTGAATTTTA
68841 TTTTTATTTTATTTAGAAGAG
1 TTTTT-TTTTATTTAGAAGAG
68862 TTTTTTTTTATTTAGAAGAG
1 TTTTTTTTTATTTAGAAGAG
68882 --TTTTTTTATTTAGAAGAG
1 TTTTTTTTTATTTAGAAGAG
68900 TTTTTTATTTA
1 TTTTTT-TTTA
68911 GAAGAAAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 18 0.39
20 19 0.41
21 9 0.20
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (20 bp):
TTTTTTTTTATTTAGAAGAG
Found at i:68885 original size:18 final size:18
Alignment explanation
Indices: 68847--68915 Score: 113
Period size: 18 Copynumber: 3.8 Consensus size: 18
68837 TTTATTTTTA
68847 TTTTATTTAGAAGAGTTTTT
1 TTTTATTTAGAAGAG--TTT
68867 TTTTATTTAGAAGAGTTT
1 TTTTATTTAGAAGAGTTT
68885 TTTTATTTAGAAGAG-TT
1 TTTTATTTAGAAGAGTTT
68902 TTTTATTTAGAAGA
1 TTTTATTTAGAAGA
68916 AAGTTTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
17 16 0.33
18 18 0.37
20 15 0.31
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (18 bp):
TTTTATTTAGAAGAGTTT
Found at i:68916 original size:20 final size:19
Alignment explanation
Indices: 68847--68921 Score: 84
Period size: 20 Copynumber: 4.1 Consensus size: 19
68837 TTTATTTTTA
**
68847 TTTTATTTAGAAGAGTTTTT
1 TTTTATTTAGAAGAG-AGTT
*
68867 TTTTATTTAGAAGAG-TTT
1 TTTTATTTAGAAGAGAGTT
68885 TTTTATTTAG-A-AGAGTT
1 TTTTATTTAGAAGAGAGTT
*
68902 TTTTATTTAGAAGAAAGTT
1 TTTTATTTAGAAGAGAGTT
68921 T
1 T
68922 AATTTTATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
16 2 0.04
17 13 0.26
18 14 0.28
19 6 0.12
20 15 0.30
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (19 bp):
TTTTATTTAGAAGAGAGTT
Found at i:73275 original size:20 final size:20
Alignment explanation
Indices: 73250--73298 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
73240 TGTTTATATA
73250 TGTTTGTGTATTTTTGAAGG
1 TGTTTGTGTATTTTTGAAGG
73270 TGTTTGTGTATTTTTGAAGG
1 TGTTTGTGTATTTTTGAAGG
*
73290 TGTTCGTGT
1 TGTTTGTGT
73299 TTGGTCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.02, G:0.31, T:0.55
Consensus pattern (20 bp):
TGTTTGTGTATTTTTGAAGG
Found at i:74258 original size:28 final size:28
Alignment explanation
Indices: 74226--74299 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
74216 GGCACGTAGA
74226 ATATGTCCCGAAGGACCACATATAACAC
1 ATATGTCCCGAAGGACCACATATAACAC
* * *
74254 ATATGACTCAAAGGACCACATATAACAC
1 ATATGTCCCGAAGGACCACATATAACAC
*
74282 ATATATCCCGAAGGACCA
1 ATATGTCCCGAAGGACCA
74300 TGTAGAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (28 bp):
ATATGTCCCGAAGGACCACATATAACAC
Found at i:78594 original size:28 final size:28
Alignment explanation
Indices: 78554--78626 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
78544 GAAAGACCAC
*
78554 TATGTCCCGAAGGAGCACATATAACACA
1 TATGTCCCGAAGGACCACATATAACACA
*
78582 TATGTCTCGAAGGACCACATATAACACA
1 TATGTCCCGAAGGACCACATATAACACA
78610 TATGTCCCGAAGGACCA
1 TATGTCCCGAAGGACCA
78627 TGTAGAACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACATATAACACA
Found at i:80934 original size:3 final size:3
Alignment explanation
Indices: 80926--81012 Score: 111
Period size: 3 Copynumber: 29.0 Consensus size: 3
80916 TTTTTTCATT
* * * *
80926 TTA TTA TTA TTA TTA TAA TTA TTT TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
80974 TTA TTA TTA TTA TTA TTA TTA TAA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81013 CAAGCCAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:83159 original size:26 final size:24
Alignment explanation
Indices: 83120--83172 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
83110 AATTCTTTCC
*
83120 TTTCAAAATTTTTATATACTTATTAT
1 TTTCAAAATATTTATATA--TATTAT
* *
83146 TTTCATAATATTTATGTATATTAT
1 TTTCAAAATATTTATATATATTAT
83170 TTT
1 TTT
83173 TTATTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
26 15 0.62
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTCAAAATATTTATATATATTAT
Found at i:84557 original size:8 final size:7
Alignment explanation
Indices: 84526--84566 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
84516 TTTTCATACA
84526 TGCATTT
1 TGCATTT
84533 T-CATTT
1 TGCATTT
84539 TGCATTT
1 TGCATTT
84546 TGCATCTT
1 TGCAT-TT
84554 TGCATTT
1 TGCATTT
84561 T-CATTT
1 TGCATTT
84567 ATACTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.34
7 14 0.44
8 7 0.22
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:84557 original size:15 final size:13
Alignment explanation
Indices: 84526--84566 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
84516 TTTTCATACA
84526 TGCATTTTCATTT
1 TGCATTTTCATTT
84539 TGCATTTTGCATCTT
1 TGCATTTT-CAT-TT
84554 TGCATTTTCATTT
1 TGCATTTTCATTT
84567 ATACTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 6 0.23
15 10 0.38
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (13 bp):
TGCATTTTCATTT
Found at i:87929 original size:32 final size:32
Alignment explanation
Indices: 87889--87955 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
87879 AGAGTCTGGA
** *
87889 AACAAGAAGTATCTCTAGGAGATGAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
87921 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
87953 AAC
1 AAC
87956 CATTTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.18
Consensus pattern (32 bp):
AACAAGAAGTATCTCTACCAGATAAGCATAAC
Found at i:90356 original size:75 final size:73
Alignment explanation
Indices: 90233--90481 Score: 242
Period size: 75 Copynumber: 3.4 Consensus size: 73
90223 ATCAACAAGA
* * * * *
90233 AACAAATGTTGGGGTATGTTGAAAGCCCATTTCAATCA-TAATCAGGAATATCGATGCGTTTTGA
1 AACAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGGAATAT-GA-GCATTTTGA
*
90297 ATGTTCACGTC
63 ATGTTCATGTC
* *
90308 AACAAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAAATTGGAATATTGGCGCATTTTGAA
1 AACAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATA-T-GAGCATTTTGAA
*
90373 CG-T-ATGT-
64 TGTTCATGTC
* *
90380 ATTAGCAAATGCTGGGGCATGCTGAAAGACCATTTCAATCAGAAATTGGAATA--A-CATTTTGA
1 A--A-CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATGAGCATTTTGA
*
90442 ATGTTCATATC
63 ATGTTCATGTC
* * *
90453 AGCAAATATTGGGGCATGCTGAAGGCCCA
1 AACAAATGTTGGGGCATGCTGAAAGCCCA
90482 CATCATCATG
Statistics
Matches: 145, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
70 33 0.23
71 1 0.01
72 4 0.03
73 4 0.03
74 2 0.01
75 96 0.66
76 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (73 bp):
AACAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATGAGCATTTTGAATG
TTCATGTC
Found at i:91832 original size:22 final size:22
Alignment explanation
Indices: 91804--91882 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
91794 ACATCTACAT
91804 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
91826 TCTTCAAATATGGTAGATTATC
1 TCTTCAAAGATGATAGATTCTC
91848 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
91870 TTTTCAAAGATGA
1 TCTTCAAAGATGA
91883 AAGCCTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:92611 original size:45 final size:45
Alignment explanation
Indices: 92546--92940 Score: 578
Period size: 45 Copynumber: 8.8 Consensus size: 45
92536 CTATTTCCCA
* *
92546 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
92591 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
92636 CATATGTAAGCCCTTTAGTGCATGATTTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
92681 CATCTGTAATCCCTTAAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
92726 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
92771 TATCTGTAAGCCCTTCAGTGCATAATGTTTTCAAAAACCTTC-GGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
92816 CATCTGTAAGCCCTT-AGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
92860 CATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
* * *
92906 CATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
92941 TGAGATTTTA
Statistics
Matches: 321, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
43 9 0.03
44 31 0.10
45 230 0.72
46 51 0.16
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:93261 original size:3 final size:3
Alignment explanation
Indices: 93183--93248 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
93173 ACTAATTTTT
* * * * *
93183 TTA TT- TTA TTA TTA -TA TTTA TTT TTA TAA ATA TTT TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
93227 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
93249 AAATAATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93382 original size:23 final size:23
Alignment explanation
Indices: 93352--93428 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
93342 TTAGCATCTT
*
93352 CTCCGCCGCCTCTACTCTAACTG
1 CTCCGCCGCCTCTACTCCAACTG
93375 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
** ***
93398 CTATGTTACCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
*
93421 CTCTGCCG
1 CTCCGCCG
93429 TCATGTTCCC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.14, C:0.45, G:0.13, T:0.27
Consensus pattern (23 bp):
CTCCGCCGCCTCTACTCCAACTG
Done.