Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006804.1 Hibiscus syriacus cultivar Beakdansim tig00017269_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: 104202
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3649 original size:246 final size:251
Alignment explanation
Indices: 3209--3749 Score: 830
Period size: 246 Copynumber: 2.2 Consensus size: 251
3199 TAATGATGCT
*
3209 TGCTACATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGG-TTGA-TATGAGTTCAATTGTTTA
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATTATGAGTTCAATTGTTTA
* * *
3272 TTGAGGTGTTCTGATGTTGTTTGATCCTCTTTTTGGCTGAGATTTTGGGTTTATAAACATGATGT
66 TTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATGT
* * *
3337 AAAATAGCATGCTTTGTTGCCTTTTGTGAACTAGGTTCTCATAAACTTCAGGAAAATTACTTGTG
131 AAAAAAGCAGGCTTTGTTGCCTTTTGTGAACCAGGTTCTCATAAACTTCAGGAAAATTACTTGTG
*
3402 CATTGTTCTTGGGTGAACCTCTGGCTTT-ATTGGTGCCTGAAGGTTCAGTAAATGA
196 CATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
*
3457 T-TTA-ATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATGTATGAGTTCAATTGTTT
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGAT-TATGAGTTCAATTGTTT
* * * *
3520 CTTGAGGCGTTTTGATGTT-TTTGATCCTCTTTTTGGATGAGA-TTTAGGTTTTTAAACCTGATG
65 ATTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATG
* * *
3583 TAAAAAAGCAGGCTTTGTTTCC-TTTGTGAACCAGGTTCTCGTAAACTTTAGGAAAATTACTTGT
130 TAAAAAAGCAGGCTTTGTTGCCTTTTGTGAACCAGGTTCTCATAAACTTCAGGAAAATTACTTGT
* *
3647 GCATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTTCCTGAAGGTTTAGTAAATGA
195 GCATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
* *
3704 TGCTAGATTTTGTATTCCTCTATAA-AAATTAAGTTTTGGGATTGAT
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGAT
3750 ATATATATAT
Statistics
Matches: 267, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
246 102 0.38
247 69 0.26
248 45 0.17
249 51 0.19
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (251 bp):
TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATTATGAGTTCAATTGTTTA
TTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATGT
AAAAAAGCAGGCTTTGTTGCCTTTTGTGAACCAGGTTCTCATAAACTTCAGGAAAATTACTTGTG
CATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
Found at i:10012 original size:29 final size:28
Alignment explanation
Indices: 9966--10039 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
9956 GTATTAGTTG
* *
9966 AATAAAAATAATT-TAAA-TAATTTTAA
1 AATAAAAAAAATTAAAAAGTAATTTTAA
*
9992 ACACTAAAAAAAATTAAAAATGTCATTTTAA
1 A-A-TAAAAAAAATTAAAAA-GTAATTTTAA
*
10023 AATAAAACAAATTAAAA
1 AATAAAAAAAATTAAAA
10040 TTTAGATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 10 0.26
29 17 0.44
30 1 0.03
31 9 0.23
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (28 bp):
AATAAAAAAAATTAAAAAGTAATTTTAA
Found at i:15515 original size:41 final size:41
Alignment explanation
Indices: 15461--15540 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
15451 AAATGCGATA
* *
15461 AATATTAATTTTAAAAATAATTATATGAAACGATAAGTGAT
1 AATAATAATTTTAAAAATAATTATATGAAACAATAAGTGAT
15502 AATAATAATTTTAAAAATAATTATATGAAACAATAAGTG
1 AATAATAATTTTAAAAATAATTATATGAAACAATAAGTG
15541 GATCCAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.35
Consensus pattern (41 bp):
AATAATAATTTTAAAAATAATTATATGAAACAATAAGTGAT
Found at i:16604 original size:17 final size:17
Alignment explanation
Indices: 16582--16644 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
16572 ATGTTTTAAA
16582 TTCAAATTCTTTCTCTT
1 TTCAAATTCTTTCTCTT
* *
16599 TTCAAAAGAATTCTTTCGTATAA
1 TTC---A-AATTCTTTC-TCT-T
16622 TTCAAATTCTTTCTCTT
1 TTCAAATTCTTTCTCTT
16639 TTCAAA
1 TTCAAA
16645 AGAATTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 9 0.25
18 2 0.06
19 9 0.25
20 2 0.06
21 9 0.25
22 2 0.06
23 3 0.08
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (17 bp):
TTCAAATTCTTTCTCTT
Found at i:16610 original size:21 final size:21
Alignment explanation
Indices: 16586--16655 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
16576 TTTAAATTCA
16586 AATTCTTTCTCTTTTCAAAAG
1 AATTCTTTCTCTTTTCAAAAG
* *
16607 AATTCTTTCGTATAATTC---A-
1 AATTCTTTC-TCT-TTTCAAAAG
16626 AATTCTTTCTCTTTTCAAAAG
1 AATTCTTTCTCTTTTCAAAAG
16647 AATTCTTTC
1 AATTCTTTC
16656 GTATTTTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 9 0.23
20 2 0.05
21 18 0.46
22 2 0.05
23 3 0.08
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.49
Consensus pattern (21 bp):
AATTCTTTCTCTTTTCAAAAG
Found at i:16635 original size:40 final size:40
Alignment explanation
Indices: 16580--16659 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
16570 TCATGTTTTA
16580 AATTCAAATTCTTTCTCTTTTCAAAAGAATTCTTTCGTAT
1 AATTCAAATTCTTTCTCTTTTCAAAAGAATTCTTTCGTAT
16620 AATTCAAATTCTTTCTCTTTTCAAAAGAATTCTTTCGTAT
1 AATTCAAATTCTTTCTCTTTTCAAAAGAATTCTTTCGTAT
16660 TTTATGGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (40 bp):
AATTCAAATTCTTTCTCTTTTCAAAAGAATTCTTTCGTAT
Found at i:18002 original size:20 final size:20
Alignment explanation
Indices: 17979--18016 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17969 AAACATCTGG
*
17979 TAGTATTGATGCTACCTAGA
1 TAGTATCGATGCTACCTAGA
17999 TAGTATCGATGCTACCTA
1 TAGTATCGATGCTACCTA
18017 AAGAGTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (20 bp):
TAGTATCGATGCTACCTAGA
Found at i:18023 original size:20 final size:20
Alignment explanation
Indices: 17980--18024 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17970 AACATCTGGT
* * *
17980 AGTATTGATGCTACCTAGAT
1 AGTATCGATGCTACCTAAAG
18000 AGTATCGATGCTACCTAAAG
1 AGTATCGATGCTACCTAAAG
18020 AGTAT
1 AGTAT
18025 GGATACTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (20 bp):
AGTATCGATGCTACCTAAAG
Found at i:19552 original size:9 final size:9
Alignment explanation
Indices: 19538--19592 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
19528 AAAGTATAGA
19538 TTTAAATAT
1 TTTAAATAT
19547 TTTAAATAT
1 TTTAAATAT
**
19556 AATAATTATTAT
1 TTTAA--A-TAT
19568 TTTAAA-A-
1 TTTAAATAT
19575 TTTAAATAT
1 TTTAAATAT
19584 TTTAAATAT
1 TTTAAATAT
19593 GATATTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
7 6 0.16
8 2 0.05
9 21 0.57
10 1 0.03
11 1 0.03
12 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAAATAT
Found at i:19948 original size:17 final size:17
Alignment explanation
Indices: 19897--19950 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
19887 AGGCCTATCG
19897 GACGGTCAAAAAGATGT
1 GACGGTCAAAAAGATGT
* *
19914 GACAGTTC--AAATATGT
1 GAC-GGTCAAAAAGATGT
19930 GACGGTCAAAAAGATGT
1 GACGGTCAAAAAGATGT
19947 GACG
1 GACG
19951 ATAAAAAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 14 0.47
18 3 0.10
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (17 bp):
GACGGTCAAAAAGATGT
Found at i:20211 original size:31 final size:31
Alignment explanation
Indices: 20139--20225 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
20129 TTTTGGGGGG
* *
20139 AAAATATGAAAGTTTAGGCATTAAAACAGACC
1 AAAAT-TGATAGTTTAGGTATTAAAACAGACC
* * * **
20171 AAAACTGATAGTTTAAGTATTAAAACGGATT
1 AAAATTGATAGTTTAGGTATTAAAACAGACC
* *
20202 AAAATTGATAATTTAGGTACTAAA
1 AAAATTGATAGTTTAGGTATTAAA
20226 CGTGTAATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
31 40 0.91
32 4 0.09
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (31 bp):
AAAATTGATAGTTTAGGTATTAAAACAGACC
Found at i:28022 original size:30 final size:30
Alignment explanation
Indices: 27988--28049 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
27978 CAATACGTGT
27988 TTATACGATCCCGTCGATTTTAGTAAGACG
1 TTATACGATCCCGTCGATTTTAGTAAGACG
** *
28018 TTATACGATCTTGTCGATTTTAGTAAGTCG
1 TTATACGATCCCGTCGATTTTAGTAAGACG
28048 TT
1 TT
28050 CTATGACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (30 bp):
TTATACGATCCCGTCGATTTTAGTAAGACG
Found at i:28061 original size:30 final size:30
Alignment explanation
Indices: 28000--28069 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
27990 ATACGATCCC
*
28000 GTCGATTTTAGTAAGACGTTATACGATCTT
1 GTCGATTTTAGTAAGACGTTATACGACCTT
* * *
28030 GTCGATTTTAGTAAGTCGTTCTATGACCTT
1 GTCGATTTTAGTAAGACGTTATACGACCTT
28060 GTCGATTTTA
1 GTCGATTTTA
28070 ATGCGGCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (30 bp):
GTCGATTTTAGTAAGACGTTATACGACCTT
Found at i:38875 original size:32 final size:33
Alignment explanation
Indices: 38816--38899 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
38806 ACCCGACCCG
* * *
38816 ACCCGACCTGACCTGAATATTACACTTAAAAAA
1 ACCCGACCTGACCCGAATATCAAACTTAAAAAA
*
38849 ACCCGACC-GACCCGAATATCAAACTTAAAATA
1 ACCCGACCTGACCCGAATATCAAACTTAAAAAA
*
38881 ACCCGATCTGAACCCGAAT
1 ACCCGACCTG-ACCCGAAT
38900 TTTTTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
32 27 0.61
33 9 0.20
34 8 0.18
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (33 bp):
ACCCGACCTGACCCGAATATCAAACTTAAAAAA
Found at i:47351 original size:3 final size:3
Alignment explanation
Indices: 47337--47400 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
47327 CATTTAAATT
* * * *
47337 TTA TTT TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
47383 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
47401 ATATATATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 1 0.02
3 46 0.92
4 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:50803 original size:27 final size:27
Alignment explanation
Indices: 50761--50855 Score: 176
Period size: 27 Copynumber: 3.6 Consensus size: 27
50751 GTGTAGGAAT
50761 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
50786 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
50813 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
50840 TATAGAGATATGATTT
1 TATAGAGATATGATTT
50856 TGTAAATAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 7 0.10
27 61 0.90
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:55923 original size:273 final size:273
Alignment explanation
Indices: 55436--55982 Score: 1046
Period size: 273 Copynumber: 2.0 Consensus size: 273
55426 TTAAAGGGTA
55436 TTGTACAGAACTCCCTTTAATAATCACACCCAAGTCGAAGGTCGTGGAAAATATGATGCCAAAGG
1 TTGTACAGAACTCCCTTTAATAATCACACCCAAGTCGAAGGTCGTGGAAAATATGATGCCAAAGG
55501 TGATAATCACGATCCCAAAGTATTTCTCTTACAGGATAATATAGATCCCAAAGTGAAGCAATAAA
66 TGATAATCACGATCCCAAAGTATTTCTCTTACAGGATAATATAGATCCCAAAGTGAAGCAATAAA
55566 GTTTTTAATGTTTCTAAGCATAGCGAGTATAACATTGTGGACCAACTGCACAAGATACCCGCTCG
131 GTTTTTAATGTTTCTAAGCATAGCGAGTATAACATTGTGGACCAACTGCACAAGATACCCGCTCG
55631 TATTTCTATGTTATAATTGTTACTAAGATTAAAAGTGCATCACGAGGCGCTGGTGAAGGTCCTGA
196 TATTTCTATGTTATAATTGTTACTAAGATTAAAAGTGCATCACGAGGCGCTGGTGAAGGTCCTGA
55696 ACTTGACATTCGT
261 ACTTGACATTCGT
55709 TTGTACAGAACTCCCTTTAATAATCACACCCAAGTCGAAGGTCGTGGAAAATATGATGCCAAAGG
1 TTGTACAGAACTCCCTTTAATAATCACACCCAAGTCGAAGGTCGTGGAAAATATGATGCCAAAGG
55774 TGATAATCACGATCCCAAAGTATTTCTCTTACAAGGATAATATATAGATCCCAAAGTGAAGCAAT
66 TGATAATCACGATCCCAAAGTATTTCTCTTAC-AGGAT-A-ATATAGATCCCAAAGTGAAGCAAT
55839 -AAGTTTTTAATGTTTCTAAGCATAGCGAGTATAACATTGTGGA-CAA-TGCACAAGATACCCGC
128 AAAGTTTTTAATGTTTCTAAGCATAGCGAGTATAACATTGTGGACCAACTGCACAAGATACCCGC
55901 TCGTATTTCTATGTTATAATTGTTACTAAGATTAAAAGTGCATCACGAGGCGCTGGTGAAGGTCC
193 TCGTATTTCTATGTTATAATTGTTACTAAGATTAAAAGTGCATCACGAGGCGCTGGTGAAGGTCC
55966 TGAACTTGACATTCGT
258 TGAACTTGACATTCGT
55982 T
1 T
55983 CCAAAAGATA
Statistics
Matches: 271, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
273 195 0.72
274 8 0.03
275 44 0.16
276 24 0.09
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (273 bp):
TTGTACAGAACTCCCTTTAATAATCACACCCAAGTCGAAGGTCGTGGAAAATATGATGCCAAAGG
TGATAATCACGATCCCAAAGTATTTCTCTTACAGGATAATATAGATCCCAAAGTGAAGCAATAAA
GTTTTTAATGTTTCTAAGCATAGCGAGTATAACATTGTGGACCAACTGCACAAGATACCCGCTCG
TATTTCTATGTTATAATTGTTACTAAGATTAAAAGTGCATCACGAGGCGCTGGTGAAGGTCCTGA
ACTTGACATTCGT
Found at i:57230 original size:10 final size:10
Alignment explanation
Indices: 57212--57242 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
57202 TTTGTGTATA
57212 TATTATATTC
1 TATTATATTC
*
57222 TATTCTATTC
1 TATTATATTC
57232 TATTATATTC
1 TATTATATTC
57242 T
1 T
57243 TTGTGTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATATTC
Found at i:59444 original size:180 final size:180
Alignment explanation
Indices: 59088--59554 Score: 641
Period size: 180 Copynumber: 2.6 Consensus size: 180
59078 GATCCAAATT
* * * * * **
59088 AAAAATATGTCGATCCAAAAAGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGA-TAAACCGATATCAAAATGATA
* * * * *
59153 AAACC-GAAAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAACCGGTAAAA-CGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
59217 CGTGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTCGATACTTTTA
129 CGTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTATCGATAC-TTTA
* * *
59270 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAACCAATATCAAAATGATAA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAACCGATATCAAAATGATAA
* * *
59335 AACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTG
66 AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
* ** *
59399 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTATCGATACTTTA
131 TGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTATCGATACTTTA
* * *
59449 AAAAAAATATCGATCCACAACGATATAACAGGTAAAAATATAATAAAACCGATATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGAT-AAACCGATATCAAAATGATA
59514 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATA
65 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATA
59555 ATTTCGTAAG
Statistics
Matches: 253, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
179 43 0.17
180 117 0.46
181 50 0.20
182 43 0.17
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (180 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAACCGATATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTATCGATACTTTA
Found at i:61750 original size:21 final size:21
Alignment explanation
Indices: 61724--61788 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
61714 AAGATAATCA
61724 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
*
61745 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAT
* *
61766 AGAGTCGAAGATACACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
61787 AG
1 AG
61789 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:61864 original size:33 final size:33
Alignment explanation
Indices: 61822--61887 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
61812 AAATAGATGG
* *
61822 AGTGGTGAAAGGAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
61855 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
61888 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.50, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:62816 original size:19 final size:19
Alignment explanation
Indices: 62792--62840 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
62782 AATGTAGGGT
62792 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
62811 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
62830 TAATTTTGTAT
1 TAATTTTGTAT
62841 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:63439 original size:200 final size:200
Alignment explanation
Indices: 63096--64251 Score: 1960
Period size: 200 Copynumber: 5.8 Consensus size: 200
63086 GTGCAACCAT
*
63096 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
*
63161 TCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
63226 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
63291 TATAA
196 TATAA
*
63296 AAAGTGTTGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* *
63361 TCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* *
63426 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGTAACAATAAAGTGTCGACCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
63491 TATAA
196 TATAA
*
63496 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAGTCTAA
1 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* *
63561 TCGGTACAAGTATACTGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* *
63626 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACATGGTGCAACAATAAAGTATCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
63691 TATAA
196 TATAA
*
63696 AAAGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* *
63761 CCGGTACAAGTATATCGGTTTTATGAGAGAATAGGTCTAAATAATATATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
*
63826 TGTGTCGATATTTTTTGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
63891 TATAA
196 TATAA
* *
63896 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
*
63961 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* *
64026 TGTGTCGATATTTTTGGTCCAGAATGAAAGGCAAATAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
64091 TATAA
196 TATAA
* *
64096 AAAGTGTCGATCTC-ATAAATATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTA
1 AAAGTGTCGATC-CGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTA
* * * ** * *
64160 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAA-CCTATATCGACACTTTT-TAA
65 ACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTATCGACACTTTTGTAG
* *
64223 TATTGTGTCGGTACTTTAT-GTCCAGAATG
129 T-TTGTGTCGATA-TTTTTGGTCCAGAATG
64252 GAAGAAAAAT
Statistics
Matches: 912, Mismatches: 40, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
199 3 0.00
200 902 0.99
201 7 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
TATAA
Found at i:67866 original size:87 final size:86
Alignment explanation
Indices: 67760--67926 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 86
67750 AAATAGGTCA
*
67760 ATATAAGCGCTACCTATTACATTATATAAGCGCTATC-TAATATGTTATTGTACTTGTTAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTA-CATAATATGTTATTGTACTTGATAATATT
*
67824 TCCTGTTAAATACATATTTTATT
65 TCCGGTTAAATA-ATATTTTATT
* * *
67847 ATATAAGCTCTATCTATTACATTATATAAGCGTTACATAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
67912 CCGGTTAAATAATAT
66 CCGGTTAAATAATAT
67927 AACATAATCG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 5 0.07
87 69 0.93
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATAATATTTTATT
Found at i:68383 original size:45 final size:46
Alignment explanation
Indices: 68332--68431 Score: 150
Period size: 48 Copynumber: 2.2 Consensus size: 46
68322 TCAGGTGACG
*
68332 AAAACCAAAC-A-TTATCCAAATATAAAATTGATTGGTTCGATGATC
1 AAAACCAAACAAGTTATCCAAATA-AAAATTGATTGGTCCGATGATC
68377 AAAACCAAACATAGTTTATCCAAATAAAAATTGATTGGTCCGATGATC
1 AAAACCAAACA-AG-TTATCCAAATAAAAATTGATTGGTCCGATGATC
68425 AAAACCA
1 AAAACCA
68432 GGCATTATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
45 10 0.20
47 1 0.02
48 28 0.56
49 11 0.22
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (46 bp):
AAAACCAAACAAGTTATCCAAATAAAAATTGATTGGTCCGATGATC
Found at i:79903 original size:16 final size:17
Alignment explanation
Indices: 79870--79903 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
79860 CCTTCTGTTT
*
79870 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
79887 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
79903 T
1 T
79904 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:80363 original size:12 final size:13
Alignment explanation
Indices: 80323--80351 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
80313 TATTATTTTA
80323 AAAAAAAATTA-T
1 AAAAAAAATTACT
80335 AAAAAAAATTACT
1 AAAAAAAATTACT
80348 AAAA
1 AAAA
80352 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTACT
Found at i:80372 original size:21 final size:22
Alignment explanation
Indices: 80326--80372 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
80316 TATTTTAAAA
*
80326 AAAAATTATAAAAAAAATTACT
1 AAAAATTATAAAAAAAATCACT
*
80348 -AAAATTATAAAAAAAA-CCCT
1 AAAAATTATAAAAAAAATCACT
80368 AAAAA
1 AAAAA
80373 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAATTATAAAAAAAATCACT
Found at i:84834 original size:26 final size:26
Alignment explanation
Indices: 84804--84856 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
84794 AAAAATAAAT
84804 GCAATGTTAATGAATTATCACCAATG
1 GCAATGTTAATGAATTATCACCAATG
84830 GCAATGTTAATGAATTATCACCAATG
1 GCAATGTTAATGAATTATCACCAATG
84856 G
1 G
84857 AGGCAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (26 bp):
GCAATGTTAATGAATTATCACCAATG
Found at i:95399 original size:33 final size:33
Alignment explanation
Indices: 95357--95421 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
95347 TCTGCAAACA
*
95357 AGGATGAAAAATTGAAATATTGTAGAACTACCG
1 AGGATGAAAAATTGAAATATTATAGAACTACCG
*
95390 AGGATGAAAAATTGAAATGTTATAGAACTACC
1 AGGATGAAAAATTGAAATATTATAGAACTACC
95422 AGACAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (33 bp):
AGGATGAAAAATTGAAATATTATAGAACTACCG
Done.