Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004202.1 Hibiscus syriacus cultivar Beakdansim tig00009196_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: 71071
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Found at i:8353 original size:27 final size:27
Alignment explanation
Indices: 8313--8365 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
8303 TTTATTGTTA
* *
8313 ATAAGTCTATTCACCAAGTGACATGAT
1 ATAAGTCTACTCACCAAATGACATGAT
8340 ATAAGTCTACTCACCAAATGACATGA
1 ATAAGTCTACTCACCAAATGACATGA
8366 GTTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (27 bp):
ATAAGTCTACTCACCAAATGACATGAT
Found at i:9714 original size:3 final size:3
Alignment explanation
Indices: 9706--9870 Score: 303
Period size: 3 Copynumber: 55.0 Consensus size: 3
9696 CATTATAAAT
9706 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9754 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9802 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9850 ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
9871 TTATTATTAT
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 156 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16359 original size:17 final size:17
Alignment explanation
Indices: 16318--16353 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16308 AAGAAAAAAG
*
16318 AAAGCAGGTGATAAGGC
1 AAAGCAGTTGATAAGGC
16335 AAAGCAGTTGATAAGGC
1 AAAGCAGTTGATAAGGC
16352 AA
1 AA
16354 GTCAGTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.14
Consensus pattern (17 bp):
AAAGCAGTTGATAAGGC
Found at i:22684 original size:46 final size:46
Alignment explanation
Indices: 22552--22668 Score: 216
Period size: 46 Copynumber: 2.5 Consensus size: 46
22542 TGCATATTTG
* *
22552 ATCTCCACGGAAGAGTAGTGAAACAGATTCTTTCCAAGTCAATCCA
1 ATCTCCATGGAAGAGTATTGAAACAGATTCTTTCCAAGTCAATCCA
22598 ATCTCCATGGAAGAGTATTGAAACAGATTCTTTCCAAGTCAATCCA
1 ATCTCCATGGAAGAGTATTGAAACAGATTCTTTCCAAGTCAATCCA
22644 ATCTCCATGGAAGAGTATTGAAACA
1 ATCTCCATGGAAGAGTATTGAAACA
22669 TATTATGTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (46 bp):
ATCTCCATGGAAGAGTATTGAAACAGATTCTTTCCAAGTCAATCCA
Found at i:22731 original size:35 final size:36
Alignment explanation
Indices: 22684--22752 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
22674 TGTTTAAGTC
22684 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
1 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
22720 ATGC-AATCAAGCCTTCACAAAAGAGTAGTGAAG
1 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAG
22753 AAAGAATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (36 bp):
ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
Found at i:26609 original size:14 final size:15
Alignment explanation
Indices: 26590--26618 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
26580 ATGTGTTATT
26590 GTATTTT-TGTACTA
1 GTATTTTGTGTACTA
26604 GTATTTTGTGTACTA
1 GTATTTTGTGTACTA
26619 TGGCACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (15 bp):
GTATTTTGTGTACTA
Found at i:29465 original size:11 final size:11
Alignment explanation
Indices: 29448--29490 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
29438 TTTGCAATTC
29448 TTTTATCTT-T
1 TTTTATCTTAT
29458 TCTTTATCTTAT
1 T-TTTATCTTAT
*
29470 TTTAATCTTATT
1 TTTTATCTTA-T
29482 TTTTATCTT
1 TTTTATCTT
29491 GTTTCCAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 16 0.57
12 11 0.39
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATCTTAT
Found at i:31866 original size:19 final size:20
Alignment explanation
Indices: 31823--31867 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
31813 TACTATGCTG
*
31823 GAAATTAATATTAGACTGTT
1 GAAATTAATATTAGAATGTT
*
31843 GAAATTAATGTTAGAATG-T
1 GAAATTAATATTAGAATGTT
31862 GAAATT
1 GAAATT
31868 GGATTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (20 bp):
GAAATTAATATTAGAATGTT
Found at i:33658 original size:2 final size:2
Alignment explanation
Indices: 33651--33686 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
33641 AGTTTTATGC
33651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33687 CGATTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45365 original size:40 final size:40
Alignment explanation
Indices: 45239--45364 Score: 123
Period size: 39 Copynumber: 3.1 Consensus size: 40
45229 GATATTTAGT
* *
45239 TAAAAATAATATATGTGTTTGATGCATATAATATTTTAAC
1 TAAAAATAATATATGTATTTGATACATATAATATTTTAAC
* * * **
45279 -AAAAACAAT-TATTGTAATT-ATAAATAATATATATTTTTAGT
1 TAAAAATAATATA-TGTATTTGATACAT-ATA-ATA-TTTTAAC
*
45320 TAAAATTAATATATGTATTTGATACATATAATATTTTAAC
1 TAAAAATAATATATGTATTTGATACATATAATATTTTAAC
45360 TAAAA
1 TAAAA
45365 TAAAATTATT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
38 6 0.09
39 16 0.24
40 13 0.20
41 8 0.12
42 16 0.24
43 7 0.11
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (40 bp):
TAAAAATAATATATGTATTTGATACATATAATATTTTAAC
Found at i:45587 original size:92 final size:94
Alignment explanation
Indices: 45412--45658 Score: 263
Period size: 92 Copynumber: 2.6 Consensus size: 94
45402 ATATACATTT
* * * * *
45412 AAAAGGAGATAATTATTGTCATTATCAAGCTTTATTAAATATATATTTATAAAATAGAA-CTTAA
1 AAAAGGAGATAATTATTGTAATTATCAAACTCTATTAAATATATATTTATATAATAAAACCTTAA
** *
45476 TCTCATTTGAAATGAGTTTATAGATTTTA
66 TCTCAAGTGAAATGAGTTTATAGATTTCA
*
45505 AAAAGGA-ATCATTATTGTAATTATCAAACTCTATTAAATATATATTTATATAATAAAACCTT-A
1 AAAAGGAGATAATTATTGTAATTATCAAACTCTATTAAATATATATTTATATAATAAAACCTTAA
*
45568 TCT-AAGTGAAAAT-AGGTTTATATATTTCA
66 TCTCAAGTG-AAATGA-GTTTATAGATTTCA
* * * * * *
45597 AAGA-GAGATAATTATTTTAAGTATCAAATTCTATTAAAATATACATATTTTTATGATAAAAC
1 AAAAGGAGATAATTATTGTAATTATCAAACTCTATT-AAATAT--ATATTTATATAATAAAAC
45659 ATATTCTGAG
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
91 6 0.05
92 92 0.71
93 16 0.12
95 16 0.12
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (94 bp):
AAAAGGAGATAATTATTGTAATTATCAAACTCTATTAAATATATATTTATATAATAAAACCTTAA
TCTCAAGTGAAATGAGTTTATAGATTTCA
Found at i:45681 original size:2 final size:2
Alignment explanation
Indices: 45674--45700 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45664 CTGAGTTGAA
45674 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
45701 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45685 original size:95 final size:91
Alignment explanation
Indices: 45401--45687 Score: 226
Period size: 92 Copynumber: 3.1 Consensus size: 91
45391 TAAATAATTA
* * * * * * *
45401 TATATACATTTAAAAG-GAGATAATTATTGTCATTATCAAGCTTTATTAAATATATATTTATAAA
1 TATATATATTTCAAAGAGAGATAATTATTGTAAGTATCAAACTCTATTAAATATATATTTATATA
* **
45465 ATAGAAC-TTAATCTCATTTG-AAATGAG
66 ATAAAACATT-ATCT-AAGTGAAAAT-AG
* * * * * *
45492 TTTATAGATTTTAAAAAG-GAATCATTATTGTAATTATCAAACTCTATTAAATATATATTTATAT
1 TATATATATTTCAAAGAGAG-ATAATTATTGTAAGTATCAAACTCTATTAAATATATATTTATAT
*
45556 AATAAAACCTTATCTAAGTGAAAATAGG
65 AATAAAACATTATCTAAGTGAAAATA-G
* * * *
45584 TTTATATATTTCAAAGAGAGATAATTATTTTAAGTATCAAATTCTATTAAAATATACATATTTTT
1 TATATATATTTCAAAGAGAGATAATTATTGTAAGTATCAAACTCTATT-AAATAT--ATATTTAT
* *
45649 ATGATAAAACA-TATTCTGAGTTGAAATATA-
63 ATAATAAAACATTA-TCTAAG-TGAAA-ATAG
45679 TATATATAT
1 TATATATAT
45688 ATATATATAT
Statistics
Matches: 160, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
91 17 0.11
92 95 0.59
93 9 0.06
94 2 0.01
95 29 0.18
96 5 0.03
97 3 0.02
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.41
Consensus pattern (91 bp):
TATATATATTTCAAAGAGAGATAATTATTGTAAGTATCAAACTCTATTAAATATATATTTATATA
ATAAAACATTATCTAAGTGAAAATAG
Found at i:45845 original size:17 final size:18
Alignment explanation
Indices: 45823--45856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45813 CATTGAAAAT
45823 ATAATAT-TCAAATTAAG
1 ATAATATATCAAATTAAG
*
45840 ATAATATATCTAATTAA
1 ATAATATATCAAATTAA
45857 ATCTATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATATATCAAATTAAG
Found at i:46903 original size:16 final size:17
Alignment explanation
Indices: 46882--46915 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46872 AGGTGTCACA
46882 TTGACT-TTTCAAAACT
1 TTGACTCTTTCAAAACT
*
46898 TTGACTCTTTGAAAACT
1 TTGACTCTTTCAAAACT
46915 T
1 T
46916 ATTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (17 bp):
TTGACTCTTTCAAAACT
Found at i:47501 original size:23 final size:24
Alignment explanation
Indices: 47474--47518 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
47464 AAACTGTCAC
*
47474 ATAGAAT-TGCACTGAAGTGCCGT
1 ATAGAATATGCACCGAAGTGCCGT
47497 ATAGAATATGCACCGAAGTGCC
1 ATAGAATATGCACCGAAGTGCC
47519 ACATAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (24 bp):
ATAGAATATGCACCGAAGTGCCGT
Found at i:47524 original size:24 final size:24
Alignment explanation
Indices: 47471--47546 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 24
47461 TCAAAACTGT
*
47471 CACATAGAAT-TGCACTGAAGTGC
1 CACATAGAATATGCACCGAAGTGC
**
47494 CGTATAGAATATGCACCGAAGTGC
1 CACATAGAATATGCACCGAAGTGC
47518 CACATAGAA-ATGTCA-CGAAG-GAC
1 CACATAGAATATG-CACCGAAGTG-C
47541 CACATA
1 CACATA
47547 AAATTATCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.02
23 23 0.51
24 21 0.47
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.18
Consensus pattern (24 bp):
CACATAGAATATGCACCGAAGTGC
Found at i:47543 original size:23 final size:23
Alignment explanation
Indices: 47517--47564 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
47507 CACCGAAGTG
*
47517 CCACATAGAAA-TGTCACGAAGGA
1 CCACATA-AAATTATCACGAAGGA
*
47540 CCACATAAAATTATCCCGAAGGA
1 CCACATAAAATTATCACGAAGGA
47563 CC
1 CC
47565 GCTTAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.15
Consensus pattern (23 bp):
CCACATAAAATTATCACGAAGGA
Found at i:55229 original size:19 final size:18
Alignment explanation
Indices: 55205--55245 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
55195 ACTTTAGTTT
55205 TATTTACATTATTTTTGAA
1 TATTTA-ATTATTTTTGAA
* *
55224 TATTTATTTATTTTTTAA
1 TATTTAATTATTTTTGAA
55242 TATT
1 TATT
55246 AAAGAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TATTTAATTATTTTTGAA
Found at i:56778 original size:36 final size:36
Alignment explanation
Indices: 56727--56798 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
56717 GAGCTATGCA
56727 CACAAAGATCATGTTAGATTGATACCAAAAGTATTC
1 CACAAAGATCATGTTAGATTGATACCAAAAGTATTC
*
56763 CACAAAGATCCTGTTAGATTGATACCAAAAGTATTC
1 CACAAAGATCATGTTAGATTGATACCAAAAGTATTC
56799 AACGGTAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (36 bp):
CACAAAGATCATGTTAGATTGATACCAAAAGTATTC
Found at i:57346 original size:42 final size:43
Alignment explanation
Indices: 57265--57346 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
57255 TGGCTTTAGA
* *
57265 GAAGTTAGGAGTAAAAGTTATCCCCTATATTTAAAGTTTTGTT
1 GAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGTTTTGTT
57308 GAAGTTAGGAATAAAAGTTAT-CCCTATATGTAAAGTTTT
1 GAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGTTTT
57347 ATTTGATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 17 0.46
43 20 0.54
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (43 bp):
GAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGTTTTGTT
Found at i:57435 original size:6 final size:7
Alignment explanation
Indices: 57422--57461 Score: 57
Period size: 6 Copynumber: 5.9 Consensus size: 7
57412 TTTTCATACA
57422 TGCATTT
1 TGCATTT
57429 T-CATTT
1 TGCATTT
57435 TGCATCTT
1 TGCAT-TT
57443 TGCATTT
1 TGCATTT
57450 T-CATTT
1 TGCATTT
57456 TGCATT
1 TGCATT
57462 CCGTACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (7 bp):
TGCATTT
Found at i:57457 original size:13 final size:14
Alignment explanation
Indices: 57422--57461 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
57412 TTTTCATACA
57422 TGCATTTT-CATTT
1 TGCATTTTGCATTT
57435 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
57450 T-CATTTTGCATT
1 TGCATTTTGCATT
57462 CCGTACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 6 0.24
15 6 0.24
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:60423 original size:10 final size:10
Alignment explanation
Indices: 60408--60482 Score: 71
Period size: 10 Copynumber: 7.1 Consensus size: 10
60398 TCAGAAAAGG
*
60408 AAAAAAAG-G
1 AAAAAAAGAA
60417 AAAAAAAGAA
1 AAAAAAAGAA
60427 AAAAAAAGAA
1 AAAAAAAGAA
60437 AAAAAAAGAAAA
1 AAAAAAAG--AA
60449 AGAAAAAAGAGA
1 A-AAAAAAGA-A
*
60461 AAATGAAAGAA
1 AAA-AAAAGAA
*
60472 CAAAAAAGAA
1 AAAAAAAGAA
60482 A
1 A
60483 TTGAATCAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
9 8 0.15
10 24 0.44
11 6 0.11
12 10 0.18
13 7 0.13
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.01
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:60442 original size:9 final size:9
Alignment explanation
Indices: 60402--60482 Score: 76
Period size: 9 Copynumber: 8.9 Consensus size: 9
60392 CATTCATCAG
*
60402 AAAAGGAAA
1 AAAAGAAAA
*
60411 AAAAGGAAA
1 AAAAGAAAA
60420 AAAAGAAAA
1 AAAAGAAAA
60429 AAAA-AGAAA
1 AAAAGA-AAA
*
60438 AAAA-AAGA
1 AAAAGAAAA
60446 AAAAGAAAA
1 AAAAGAAAA
*
60455 AAGAGAAAA
1 AAAAGAAAA
*
60464 TGAAAGAACAA
1 -AAAAGAA-AA
60475 AAAAGAAA
1 AAAAGAAA
60483 TTGAATCAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.11
9 41 0.67
10 11 0.18
11 2 0.03
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:60450 original size:35 final size:35
Alignment explanation
Indices: 60410--60482 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
60400 AGAAAAGGAA
60410 AAAAAGGAAAAAA-AGAAAAAAAAAGAAAAAAAAAG
1 AAAAA-GAAAAAAGAGAAAAAAAAAGAAAAAAAAAG
** *
60445 AAAAAGAAAAAAGAGAAAATGAAAGAACAAAAAAG
1 AAAAAGAAAAAAGAGAAAAAAAAAGAAAAAAAAAG
60480 AAA
1 AAA
60483 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (35 bp):
AAAAAGAAAAAAGAGAAAAAAAAAGAAAAAAAAAG
Found at i:60468 original size:15 final size:15
Alignment explanation
Indices: 60402--60482 Score: 69
Period size: 15 Copynumber: 5.5 Consensus size: 15
60392 CATTCATCAG
* *
60402 AAAAGGAAAAAAAGG
1 AAAAGAAAAAAAAGA
*
60417 AAAA-AAAGAAAA-A
1 AAAAGAAAAAAAAGA
60430 AAAAGAAAAAAAAAGA
1 AAAAG-AAAAAAAAGA
*
60446 AAAAGAAAAAAGAGA
1 AAAAGAAAAAAAAGA
* * *
60461 AAATGAAAGAACA-A
1 AAAAGAAAAAAAAGA
60475 AAAAGAAA
1 AAAAGAAA
60483 TTGAATCAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.07
14 14 0.26
15 30 0.56
16 6 0.11
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:60471 original size:25 final size:26
Alignment explanation
Indices: 60402--60456 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
60392 CATTCATCAG
*
60402 AAAAGGAAAAAAAGGAA-AAAAAGAAAA
1 AAAAAGAAAAAAA--AAGAAAAAGAAAA
60429 AAAAAGAAAAAAAAAGAAAAAGAAAA
1 AAAAAGAAAAAAAAAGAAAAAGAAAA
60455 AA
1 AA
60457 GAGAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAAAAGAAAAAGAAAA
Found at i:60481 original size:20 final size:19
Alignment explanation
Indices: 60412--60487 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
60402 AAAAGGAAAA
* **
60412 AAAGGAAAAAAAGAAAAAA
1 AAAGAAAAAAAAGAAAATG
*
60431 AAAGAAAAAAAA-AGAA--
1 AAAGAAAAAAAAGAAAATG
*
60447 AAAGAAAAAAGAGAAAATG
1 AAAGAAAAAAAAGAAAATG
*
60466 AAAGAACAAAAAAGAAATTG
1 AAAGAA-AAAAAAGAAAATG
60486 AA
1 AA
60488 TCAAGATGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 11 0.23
17 3 0.06
18 3 0.06
19 17 0.36
20 13 0.28
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAGAAAAAAAAGAAAATG
Found at i:61726 original size:78 final size:76
Alignment explanation
Indices: 61581--61753 Score: 215
Period size: 78 Copynumber: 2.2 Consensus size: 76
61571 TTGTTCTAAA
* ** *
61581 GGGGCATTCTGAAAGCTCATTTCAACTAGAAATGATATGTGAGGTGTTTTGAAAGATCACATTAG
1 GGGGCATTTTGAAAGCTCATTTCAACTAGAAATGATATGTGAGGCATTTTGAAAGATCACATCAG
**
61646 TATGAAAGTTT
66 TATGAAAAATT
* * *
61657 GGGGCATTTTGAACGC-CTATTTCAAAC-AGAAATGATTCATGTGGGGCATTTTGAAAGCTCACA
1 GGGGCATTTTGAAAGCTC-ATTTC-AACTAGAAATGA-T-ATGTGAGGCATTTTGAAAGATCACA
61720 TCAGTATGAAAAATT
62 TCAGTATGAAAAATT
61735 GGGGCATTTTGAAAGCTCA
1 GGGGCATTTTGAAAGCTCA
61754 CATGAACAAG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
75 1 0.01
76 27 0.33
77 4 0.05
78 49 0.60
79 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (76 bp):
GGGGCATTTTGAAAGCTCATTTCAACTAGAAATGATATGTGAGGCATTTTGAAAGATCACATCAG
TATGAAAAATT
Found at i:62213 original size:54 final size:54
Alignment explanation
Indices: 62128--62239 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
62118 CAATTATTGA
* * * * *
62128 GAACATCTGTACAGAAACCACAGGAAGTGATGAATGTGTTGTCAAATGTTTTAT
1 GAACATCTGTACAAAAACCACAAGAAATGATGAATGTGTTATCAAATGTTTTAC
* * *
62182 GAACATCTGTGCAAAAACCACAAGAAATGATGATTGTGTTATCAATTGTTTTAC
1 GAACATCTGTACAAAAACCACAAGAAATGATGAATGTGTTATCAAATGTTTTAC
62236 GAAC
1 GAAC
62240 CAGTTATTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (54 bp):
GAACATCTGTACAAAAACCACAAGAAATGATGAATGTGTTATCAAATGTTTTAC
Found at i:63430 original size:73 final size:73
Alignment explanation
Indices: 63306--63785 Score: 791
Period size: 73 Copynumber: 6.6 Consensus size: 73
63296 AGATGTTTTC
*
63306 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTATTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
63371 TTCACTCG
66 TTCACTCG
* *
63379 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
*
63444 TCCACTCG
66 TTCACTCG
*
63452 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCCTAAAACAATA-TGTTTCTCGCTAGAGAAAG
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-ACTGTTTCTCGCTAGAGAAAG
*
63516 TTTCACTTG
65 TTTCACTCG
* * * *
63525 AAATAACAATTTATCTCACTTGAGATTGTTTTACTTAAAACAAATTGTTTCTCGCTAAAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
*
63590 TTCACTTG
66 TTCACTCG
*
63598 AAATAGCAATTTATCTCACTTGATATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
*
63663 TTCACTTG
66 TTCACTCG
** * *
63671 AAATAATAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGATAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
63736 TTCACTCG
66 TTCACTCG
63744 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
63786 TCTCTAGATA
Statistics
Matches: 380, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
72 1 0.00
73 378 0.99
74 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
TTCACTCG
Found at i:63863 original size:39 final size:39
Alignment explanation
Indices: 63817--64004 Score: 268
Period size: 39 Copynumber: 4.8 Consensus size: 39
63807 ATCTCATATT
*
63817 AAGAGGAAGAAGGAGTTCATAATCTTAAGAACTCATCTG
1 AAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTG
* *
63856 AAGAGGAAGAAGGAGTTCATAGTCTGAAGAACTCGTCTG
1 AAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTG
* * * * *
63895 AAAAGGAAGAAGAAGTTCATAGTCTGAAGAACTAATATG
1 AAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTG
* * *
63934 AAGAGGAAGAAGGGGTTCATAATCTAAAGAACTCATCTA
1 AAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTG
*
63973 AAGAGGAAGAAGAAGTTCATAATCTGAAGAAC
1 AAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
64005 GTATTCAACC
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 130 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (39 bp):
AAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCATCTG
Found at i:64110 original size:123 final size:123
Alignment explanation
Indices: 63941--64272 Score: 522
Period size: 123 Copynumber: 2.7 Consensus size: 123
63931 ATGAAGAGGA
* * ** *
63941 AGAAGGGGTTCATAATCTAAAGAACTCATCT-AAAGAGGAAGAAGAAGTTCATAATCTGAAGAAC
1 AGAAGGAGTTCGTAATAAAAAGAACTCATCTGAAA-AGGAAGAAGAAGTTCATAATCTAAAGAAC
*
64005 GTATTCAACCTTTTGCTCGACTCTATAGCAGAAGAAGATAAAGCAGCATCAATATTTCC
65 TTATTCAACCTTTTGCTCGACTCTATAGCAGAAGAAGATAAAGCAGCATCAATATTTCC
* *
64064 AGATGGAGTTCGTAATAAAAAGAACTCATCTGAAAAAGAAGAAGAAGTTCATAATCTAAAGAACT
1 AGAAGGAGTTCGTAATAAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATCTAAAGAACT
* *
64129 TATTCAACCTTTTGCTCGACTCTATCGCAGAAGAAGATAAAGCAGCATCAATATTTCT
66 TATTCAACCTTTTGCTCGACTCTATAGCAGAAGAAGATAAAGCAGCATCAATATTTCC
* *
64187 AGAAGGAGTTTGTAATAAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATCTAAAGAACT
1 AGAAGGAGTTCGTAATAAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATCTAAAGAACT
* *
64252 TATTCAATCTTTTTCTCGACT
66 TATTCAACCTTTTGCTCGACT
64273 TATCACAGAG
Statistics
Matches: 192, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
123 189 0.98
124 3 0.02
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (123 bp):
AGAAGGAGTTCGTAATAAAAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATCTAAAGAACT
TATTCAACCTTTTGCTCGACTCTATAGCAGAAGAAGATAAAGCAGCATCAATATTTCC
Found at i:65740 original size:2 final size:2
Alignment explanation
Indices: 65733--65761 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65723 GCTTATAAAA
65733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65762 CTTTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65795 original size:19 final size:18
Alignment explanation
Indices: 65771--65811 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
65761 ACTTTATTTT
65771 TATTTACATTATTTTTTAA
1 TATTTA-ATTATTTTTTAA
*
65790 TATTTATTTATTTTTTAA
1 TATTTAATTATTTTTTAA
65808 TATT
1 TATT
65812 AAAGAAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTAATTATTTTTTAA
Found at i:69061 original size:19 final size:19
Alignment explanation
Indices: 69039--69075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
69029 AACTAAAATC
69039 ATATATAATTTTAAAATAA
1 ATATATAATTTTAAAATAA
* *
69058 ATATATATTTTTAGAATA
1 ATATATAATTTTAAAATA
69076 TTGAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATATAATTTTAAAATAA
Done.