Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003358.1 Hibiscus syriacus cultivar Beakdansim tig00007066_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: 55022
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1257 original size:21 final size:21
Alignment explanation
Indices: 1227--1272 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1217 AAAATATAGA
*
1227 ATATATATAGTTTTT-GAAAG
1 ATATATATAGTTTTTGGAAAC
1247 ATATAGTATAGTTTTTGGAAAC
1 ATATA-TATAGTTTTTGGAAAC
1269 ATAT
1 ATAT
1273 TTTTAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.43
Consensus pattern (21 bp):
ATATATATAGTTTTTGGAAAC
Found at i:1316 original size:35 final size:35
Alignment explanation
Indices: 1272--1338 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
1262 TGGAAACATA
*
1272 TTTTTAAAAC--ATATAATATAATTTTTTAAAATGG
1 TTTTTAAAACATATATAATAT-ATTTTTGAAAATGG
1306 TTTTTAAAAACATATATAATATATTTTTGAAAA
1 TTTTT-AAAACATATATAATATATTTTTGAAAA
1339 CATATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
35 5 0.17
36 10 0.34
37 9 0.31
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTTTAAAACATATATAATATATTTTTGAAAATGG
Found at i:1338 original size:24 final size:24
Alignment explanation
Indices: 1306--1364 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1296 TTTAAAATGG
1306 TTTTTAAAAACATAT-ATA-ATATA
1 TTTTTAAAAACATATAATATATA-A
*
1329 TTTTTGAAAACATATAATATATAA
1 TTTTTAAAAACATATAATATATAA
1353 TTTTTAAAAACA
1 TTTTTAAAAACA
1365 GTTTTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 14 0.44
24 15 0.47
25 3 0.09
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTTTAAAAACATATAATATATAA
Found at i:1369 original size:60 final size:57
Alignment explanation
Indices: 1269--1403 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 57
1259 TTTTGGAAAC
* **
1269 ATATTTTT-AAAACATATAATATAATTTTTTAAAATGGTTTTTAAAAACATATATAAT
1 ATATTTTTGAAAACATATAATATAATTTTTAAAAACAG-TTTTAAAAACATATATAAT
* *
1326 ATATTTTTGAAAACATATAATATATAATTTTTAAAAACAGTTTTGAAAATATATATAAT
1 ATATTTTTGAAAACATAT-A-ATATAATTTTTAAAAACAGTTTTAAAAACATATATAAT
1385 ATAGTTTTTGAAAACATAT
1 ATA-TTTTTGAAAACATAT
1404 TTTTGAAAAC
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
57 8 0.12
58 9 0.13
59 21 0.30
60 31 0.45
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (57 bp):
ATATTTTTGAAAACATATAATATAATTTTTAAAAACAGTTTTAAAAACATATATAAT
Found at i:1380 original size:36 final size:38
Alignment explanation
Indices: 1330--1423 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 38
1320 TATAATATAT
1330 TTTTGAAAACATATAATATATAATTTTT-AAAA-ACAG
1 TTTTGAAAACATATAATATATAATTTTTGAAAACACAG
* * * *
1366 TTTTGAAAATATAT-ATAATATAGTTTTTGAAAACATAT
1 TTTTGAAAACATATAAT-ATATAATTTTTGAAAACACAG
1404 TTTTGAAAACATATAATATA
1 TTTTGAAAACATATAATATA
1424 GTTTTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.04
36 23 0.47
37 4 0.08
38 18 0.37
39 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (38 bp):
TTTTGAAAACATATAATATATAATTTTTGAAAACACAG
Found at i:1408 original size:14 final size:14
Alignment explanation
Indices: 1389--1417 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1379 TATAATATAG
1389 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1403 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1417 T
1 T
1418 AATATAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1490 original size:37 final size:36
Alignment explanation
Indices: 1326--1545 Score: 152
Period size: 37 Copynumber: 6.1 Consensus size: 36
1316 CATATATAAT
* * *
1326 ATATTTTTGAAAACATATAATATATAATTTTTAAAA-
1 ATATTTTTGAAAATATAT-ATATATAGTTTTGAAAAC
* *
1362 ACAGTTTTGAAAATATATATAATATAGTTTTTGAAAAC
1 ATATTTTTGAAAATATATAT-ATATAG-TTTTGAAAAC
* * *
1400 ATATTTTTGAAAACATATA-ATATAGTTTTTAAAAGG
1 ATATTTTTGAAAATATATATATATAGTTTTGAAAA-C
* * *
1436 TTTTTTTTG---A-A-ACATATATAGTTTTGAAAAC
1 ATATTTTTGAAAATATATATATATAGTTTTGAAAAC
* *
1467 ATATTATTTGAATATATATATATATAGTTTTTAAAATC
1 ATATT-TTTGAAAATATATATATATAGTTTTGAAAA-C
** * *
1505 -GGTTTTT-AAAACGTATATAAATATAATTTTGAAAAC
1 ATATTTTTGAAAA--TATATATATATAGTTTTGAAAAC
1541 ATATT
1 ATATT
1546 ATGTTGTTTT
Statistics
Matches: 142, Mismatches: 27, Indels: 29
0.72 0.14 0.15
Matches are distributed among these distances:
31 5 0.04
32 19 0.13
33 1 0.01
35 14 0.10
36 38 0.27
37 48 0.34
38 17 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATTTTTGAAAATATATATATATAGTTTTGAAAAC
Found at i:1511 original size:68 final size:66
Alignment explanation
Indices: 1383--1523 Score: 178
Period size: 68 Copynumber: 2.1 Consensus size: 66
1373 AATATATATA
*
1383 ATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATAGTTTTTAAAAGGTTTTTTTTGAAA
1 ATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATAGTTTTTAAAAGG--TTTTTTAAAA
1448 CAT
64 CAT
* *
1451 ATATAG-TTTTGAAAACATATTATTTGAATATATATATATATAGTTTTTAAAATCGG-TTTTTAA
1 ATATAGTTTTTGAAAACATATT-TTTGAAAACATATA-ATATAGTTTTTAAAA--GGTTTTTTAA
*
1514 AACGT
62 AACAT
1519 ATATA
1 ATATA
1524 AATATAATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
67 15 0.23
68 33 0.51
69 15 0.23
71 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.45
Consensus pattern (66 bp):
ATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATAGTTTTTAAAAGGTTTTTTAAAACA
T
Found at i:1547 original size:74 final size:71
Alignment explanation
Indices: 1326--1545 Score: 225
Period size: 74 Copynumber: 3.1 Consensus size: 71
1316 CATATATAAT
* * * *
1326 ATATTTTTGAAAACATATAATATATAATTTTTAAAAACAGTTTTGAAAA-TATATATAATATAGT
1 ATATTTTTGAAAACATAT-ATATATAGTTTTT-AAAACGGTTTTTAAAAGTATATA-AATATA-A
1390 TTTTGAAAAC
62 TTTTGAAAAC
*** * * * *
1400 ATATTTTTGAAAACATATA-ATATAGTTTTTAAAA-GGTTTTT-TTTG-AAACATATATAGTTTT
1 ATATTTTTGAAAACATATATATATAGTTTTTAAAACGGTTTTTAAAAGTATATAAATATAATTTT
1461 GAAAAC
66 GAAAAC
* *
1467 ATATTATTTGAATATATATATATATAGTTTTTAAAATCGGTTTTTAAAACGTATATAAATATAAT
1 ATATT-TTTGAAAACATATATATATAGTTTTTAAAA-CGGTTTTTAAAA-GTATATAAATATAAT
1532 TTTGAAAAC
63 TTTGAAAAC
1541 ATATT
1 ATATT
1546 ATGTTGTTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
67 15 0.13
68 17 0.14
69 18 0.15
70 5 0.04
71 11 0.09
72 10 0.08
73 2 0.02
74 41 0.34
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (71 bp):
ATATTTTTGAAAACATATATATATAGTTTTTAAAACGGTTTTTAAAAGTATATAAATATAATTTT
GAAAAC
Found at i:1580 original size:26 final size:26
Alignment explanation
Indices: 1539--1602 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1529 AATTTTGAAA
1539 ACATATTATGT-T-GTTTTTGAA-ATAT
1 ACATATTAT-TATAGTTTTT-AATATAT
1564 A-ATATATATTATAGTTTTTAATATAT
1 ACATAT-TATTATAGTTTTTAATATAT
1590 ACATATTATTATA
1 ACATATTATTATA
1603 TAATATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
24 5 0.15
25 7 0.21
26 18 0.53
27 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (26 bp):
ACATATTATTATAGTTTTTAATATAT
Found at i:2162 original size:22 final size:22
Alignment explanation
Indices: 2120--2162 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2110 AAAGTATAAT
*
2120 ATATAGTTTTTGAAGATATATA
1 ATATAGTTTTTGAAGACATATA
2142 ATATAGTTTTTGGAA-ACATAT
1 ATATAGTTTTT-GAAGACATAT
2163 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (22 bp):
ATATAGTTTTTGAAGACATATA
Found at i:2230 original size:22 final size:21
Alignment explanation
Indices: 2198--2273 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 21
2188 TTTTAAAATG
2198 GTTTTTAAAAACATATAATATA
1 GTTTTT-AAAACATATAATATA
2220 GTTTTTGAAAACATAT-ATATA
1 GTTTTT-AAAACATATAATATA
*
2241 GTTTTTAAAAAATATATATATA
1 GTTTTTAAAACATATA-ATATA
2263 GTTTTTAAAAC
1 GTTTTTAAAAC
2274 GGGTTTTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 8 0.16
21 11 0.22
22 30 0.61
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (21 bp):
GTTTTTAAAACATATAATATA
Found at i:2300 original size:74 final size:74
Alignment explanation
Indices: 2139--2342 Score: 226
Period size: 74 Copynumber: 2.7 Consensus size: 74
2129 TTGAAGATAT
* *
2139 ATAATATAGTTTTTGGAAAC--ATA---TTTTTAAAAATATATAATATATAGTTTTTTAAAATGG
1 ATAATATAGTTTTTGAAAACATATATTGTTTTTAAAAA-ATAT-ATATATAG-TTTTTAAAAGGG
2199 TTTTTAAAAACA
63 TTTTTAAAAACA
2211 TATAATATAGTTTTTGAAAACATATATATAGTTTTTAAAAAATATATATATAGTTTTTAAAACGG
1 -ATAATATAGTTTTTGAAAACATATAT-T-GTTTTTAAAAAATATATATATAGTTTTTAAAA-GG
*
2276 GTTTTT-GAAAC-
62 GTTTTTAAAAACA
* *
2287 AT-ATATAGTTTTTGAAAACATATGTTGTTTTGAAAATAATATATTATATAGTTTTT
1 ATAATATAGTTTTTGAAAACATATATTGTTTTTAAAA-AATATA-TATATAGTTTTT
2343 TAATAAATAC
Statistics
Matches: 116, Mismatches: 5, Indels: 19
0.83 0.04 0.14
Matches are distributed among these distances:
72 9 0.08
73 26 0.22
74 34 0.29
75 5 0.04
77 13 0.11
78 15 0.13
79 4 0.03
80 10 0.09
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (74 bp):
ATAATATAGTTTTTGAAAACATATATTGTTTTTAAAAAATATATATATAGTTTTTAAAAGGGTTT
TTAAAAACA
Found at i:2317 original size:18 final size:19
Alignment explanation
Indices: 2276--2322 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2266 TTTAAAACGG
2276 GTTTTTG-AAACATATATA
1 GTTTTTGAAAACATATATA
* *
2294 GTTTTTGAAAACATATGTT
1 GTTTTTGAAAACATATATA
2313 G-TTTTGAAAA
1 GTTTTTGAAAA
2323 TAATATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (19 bp):
GTTTTTGAAAACATATATA
Found at i:3448 original size:23 final size:23
Alignment explanation
Indices: 3380--3448 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3370 CACCACAGTT
* *
3380 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
* *
3403 CATAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
3426 CGTAGAAATGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
3449 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:7973 original size:20 final size:21
Alignment explanation
Indices: 7919--7981 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
7909 GATTCCCCTG
7919 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
7943 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
7963 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
7982 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:16670 original size:13 final size:13
Alignment explanation
Indices: 16652--16719 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
16642 TGCGTCATAA
16652 ATTTATGACGCAC
1 ATTTATGACGCAC
*
16665 ATTTATGACACAC
1 ATTTATGACGCAC
***
16678 ATTTATGACATGC
1 ATTTATGACGCAC
* *
16691 ATTTATGGCGCGC
1 ATTTATGACGCAC
*
16704 ATTTATGACGCTC
1 ATTTATGACGCAC
16717 ATT
1 ATT
16720 GCGCGTCATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:21343 original size:4 final size:4
Alignment explanation
Indices: 21334--21360 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21324 AACATACCAA
21334 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
21361 ATTTTACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:22369 original size:18 final size:18
Alignment explanation
Indices: 22346--22410 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
22336 GCACATATAC
22346 CATCATTATCAACATCAA
1 CATCATTATCAACATCAA
** *
22364 CATCATTATCATGATC-T
1 CATCATTATCAACATCAA
*
22381 CTATCATTATCAATATCAA
1 C-ATCATTATCAACATCAA
*
22400 TATCATTATCA
1 CATCATTATCA
22411 TGTAATACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.03
18 37 0.97
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (18 bp):
CATCATTATCAACATCAA
Found at i:22374 original size:6 final size:6
Alignment explanation
Indices: 22365--22411 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
22355 CAACATCAAC
* * *
22365 ATCATT ATCATG ATC-TCT ATCATT ATCAAT ATCAAT ATCATT ATCAT
1 ATCATT ATCATT ATCAT-T ATCATT ATCATT ATCATT ATCATT ATCAT
22412 GTAATACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.94
7 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (6 bp):
ATCATT
Found at i:22719 original size:23 final size:23
Alignment explanation
Indices: 22686--22749 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
22676 CAACTCGTAT
22686 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * *
22709 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
*
22732 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
22750 TAAAAGATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:45084 original size:23 final size:22
Alignment explanation
Indices: 45058--45112 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
45048 TAGAATCAAC
*
45058 TTCAAATCGGGTTCGAGAGCCAA
1 TTCAAAT-GGGTTCGAGAGACAA
*
45081 TTCAGATGGGTTCGAGAGACAA
1 TTCAAATGGGTTCGAGAGACAA
45103 TTCAGAATGG
1 TTCA-AATGG
45113 ATTCAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (22 bp):
TTCAAATGGGTTCGAGAGACAA
Found at i:45091 original size:22 final size:22
Alignment explanation
Indices: 45066--45108 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
45056 ACTTCAAATC
*
45066 GGGTTCGAGAGCCAATTCAGAT
1 GGGTTCGAGAGACAATTCAGAT
45088 GGGTTCGAGAGACAATTCAGA
1 GGGTTCGAGAGACAATTCAGA
45109 ATGGATTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (22 bp):
GGGTTCGAGAGACAATTCAGAT
Found at i:45858 original size:201 final size:201
Alignment explanation
Indices: 45506--45918 Score: 546
Period size: 201 Copynumber: 2.1 Consensus size: 201
45496 AGAGGAACCG
* ** * *
45506 TTCACAACATAGCTCAAGGCAAGAAGGGTTATTTGTCAATGAAAACTTTCGAGTTTGATTCCATT
1 TTCACAACATAGCTCAAGGCAAGAAGGGCTATCAGTCAACGAAAACTTTCGAGTTCGATTCCATT
* *
45571 CAGCTCGAGGGCGTATCAACTGCATAGTAGCAACGAGGAACTACTTTCTAACTAAATTTTAGACC
66 CAACTCGAGGGCGTATCAACTGCATAGTAGCAACGAGGAACTACTTTCTAACTAAATTTTAAACC
* * * * *
45636 GATGTCTTTAAGCCAAGAAGAAGGCCTAGGTTGGTTACGATTTAGCTACAAGGAATTATC-TCCT
131 GAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATCTTCC-
45700 AGCCTAA
195 AGCCTAA
*
45707 TTCACAGCATAGCTCAAGGCAAGAAGGGCTATCAGTCAACGAAAACTTTCGAGTTCGATTCCATT
1 TTCACAACATAGCTCAAGGCAAGAAGGGCTATCAGTCAACGAAAACTTTCGAGTTCGATTCCATT
* * * * * * *
45772 CAACTCGATGGCTTATCAA-TCGCATGGTAG-AAGCGAGGAACTA-TTTTTCGATTGAATTTTAA
66 CAACTCGAGGGCGTATCAACT-GCATAGTAGCAA-CGAGGAACTACTTTCT-AACTAAATTTTAA
** *
45834 ACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTGTGATTTAGCAACAATGAACTATCTT
128 ACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATCTT
45899 CCAGCCTAA
193 CCAGCCTAA
*
45908 TTTACAACATA
1 TTCACAACATA
45919 ACTTAAAGTC
Statistics
Matches: 183, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
200 7 0.04
201 173 0.95
202 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (201 bp):
TTCACAACATAGCTCAAGGCAAGAAGGGCTATCAGTCAACGAAAACTTTCGAGTTCGATTCCATT
CAACTCGAGGGCGTATCAACTGCATAGTAGCAACGAGGAACTACTTTCTAACTAAATTTTAAACC
GAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATCTTCCA
GCCTAA
Found at i:46789 original size:21 final size:22
Alignment explanation
Indices: 46763--46804 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
46753 ATATGTATAT
*
46763 ATATATA-TATATTTTTTGAAG
1 ATATATAGTATAGTTTTTGAAG
46784 ATATATAGTATAGTTTTTGAA
1 ATATATAGTATAGTTTTTGAA
46805 AACATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATATATAGTATAGTTTTTGAAG
Found at i:46790 original size:2 final size:2
Alignment explanation
Indices: 46570--46774 Score: 229
Period size: 2 Copynumber: 103.5 Consensus size: 2
46560 CTTTATTTAG
* *
46570 TA TA TA TGA TA -A TA TA TA TA -A TA -A TT TCA AA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
46611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
46653 TG TA TA TA TA TA CA TA TA TA TA TA TA TG TA TA CA -A TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
46694 TA TA TA TA TA TG TA TA TA TA TG TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
46736 TG TA TA TG TA TA CA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46775 TTTTTGAAGA
Statistics
Matches: 168, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
1 4 0.02
2 162 0.96
3 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46811 original size:22 final size:21
Alignment explanation
Indices: 46765--46811 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
46755 ATGTATATAT
* * *
46765 ATATATATATTTTTTGAAGAT
1 ATATATATAGTTTTTGAAAAC
46786 ATATAGTATAGTTTTTGAAAAC
1 ATATA-TATAGTTTTTGAAAAC
46808 ATAT
1 ATAT
46812 TTTTGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATATATAGTTTTTGAAAAC
Found at i:46835 original size:38 final size:37
Alignment explanation
Indices: 46775--46911 Score: 136
Period size: 38 Copynumber: 3.6 Consensus size: 37
46765 ATATATATAT
* *
46775 TTTTTGAAGATATAT-A-GTATAGTTTTTGAAAACATA
1 TTTTTGAAAATATATAATATATAGTTTTT-AAAACATA
*
46811 TTTTTGAAAATATATAATATATAGTTTTTAAAA-ATGGT
1 TTTTTGAAAATATATAATATATAGTTTTTAAAACAT--A
* * *
46849 TTTTTGAAAACATATAATATATAGTTTTTAAAAAACGA
1 TTTTTGAAAATATATAATATATAGTTTTTAAAACA-TA
*
46887 TTCTTGAAAACGTATATAATATATA
1 TTTTTGAAAA--TATATAATATATA
46912 TAATCTTTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
36 16 0.19
37 5 0.06
38 51 0.60
39 1 0.01
40 12 0.14
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAATATATAATATATAGTTTTTAAAACATA
Found at i:46960 original size:28 final size:30
Alignment explanation
Indices: 46926--46989 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
46916 CTTTGAAAAC
*
46926 ATATTATATTGTTTTTGAA-ATATA-ATAT
1 ATATTATATAGTTTTTGAATATATACATAT
*
46954 ATATTATATAGTTTTTTAATATATACATAT
1 ATATTATATAGTTTTTGAATATATACATAT
46984 -TATTAT
1 ATATTAT
46990 TATTAGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 17 0.53
29 11 0.34
30 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (30 bp):
ATATTATATAGTTTTTGAATATATACATAT
Found at i:51422 original size:99 final size:99
Alignment explanation
Indices: 51241--51428 Score: 243
Period size: 99 Copynumber: 1.9 Consensus size: 99
51231 GAAGGTGCGC
* * * * * * *
51241 CTAATATAAACAATGGAAGTGGTTGTGTTGGTAACTCACGTGGGGTCCAAGGTAATTGTCATGGT
1 CTAATATAAACAATGAAAGTGGTTGTGTTGGCAACTCACATGGGGTCCAAGGAAACTATCAAGGT
* *
51306 GCGTCAATTATATATAATAGGAGTAGTGGTGATG
66 GCGACAATTATAAATAATAGGAGTAGTGGTGATG
* * *
51340 CTAATATAAATAATGAAAGTGGTTGTGTTGGCAACTCACATGGGGTTCAAGGAAACTATGAAGGT
1 CTAATATAAACAATGAAAGTGGTTGTGTTGGCAACTCACATGGGGTCCAAGGAAACTATCAAGGT
*
51405 GCGACAAATT-TAAATAATGGGAGT
66 GCGAC-AATTATAAATAATAGGAGT
51429 GGTTGTGTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
99 71 0.95
100 4 0.05
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (99 bp):
CTAATATAAACAATGAAAGTGGTTGTGTTGGCAACTCACATGGGGTCCAAGGAAACTATCAAGGT
GCGACAATTATAAATAATAGGAGTAGTGGTGATG
Found at i:54213 original size:22 final size:22
Alignment explanation
Indices: 54185--54226 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54175 AACTGTGATA
*
54185 CCTACAATGATCGTAATAACTT
1 CCTACAATGACCGTAATAACTT
54207 CCTACAATGACCGTAATAAC
1 CCTACAATGACCGTAATAAC
54227 ATCCGTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (22 bp):
CCTACAATGACCGTAATAACTT
Done.