Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007562.1 Hibiscus syriacus cultivar Beakdansim tig00021412_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: 47947
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:556 original size:17 final size:17
Alignment explanation
Indices: 525--569 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 17
515 AACTCATGGG
525 AGGAGATGC-CAGTATA
1 AGGAGATGCACAGTATA
541 AGGAGATGCACAGTATA
1 AGGAGATGCACAGTATA
558 AGGAGAT-CACAG
1 AGGAGATGCACAG
570 AGAGTACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.40, C:0.13, G:0.31, T:0.16
Consensus pattern (17 bp):
AGGAGATGCACAGTATA
Found at i:1295 original size:5 final size:5
Alignment explanation
Indices: 1276--1458 Score: 71
Period size: 5 Copynumber: 36.4 Consensus size: 5
1266 GATTCATTTA
* * * * *
1276 TTATT TTATT ATTATT TTATTT TTATT TTATT TAATG TT-TT CTCTT TGA-T
1 TTATT TTATT -TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT
* *
1326 TTATT TT-TAT TTATA TTATTT TTATT TTTTT TTATCT TATATAT TT-TT
1 TTATT TTAT-T TTATT TTA-TT TTATT TTATT TTAT-T T-TAT-T TTATT
* ** *
1374 TTACAT TT-TT TCCTT TGA-T TTATT TGATATT TTATT TTATT TTATT
1 TTA-TT TTATT TTATT TTATT TTATT T--TATT TTATT TTATT TTATT
* * *
1420 TTCCTT TGA-T TTA-T TTATC TTATT TTA-T TT-TT TTATT TT
1 TT-ATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1459 TTCTCCTTTT
Statistics
Matches: 133, Mismatches: 26, Indels: 38
0.68 0.13 0.19
Matches are distributed among these distances:
4 27 0.20
5 72 0.54
6 24 0.18
7 10 0.08
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:1308 original size:11 final size:11
Alignment explanation
Indices: 1271--1421 Score: 66
Period size: 11 Copynumber: 13.5 Consensus size: 11
1261 CCTTTGATTC
1271 ATTTATTATTTT
1 ATTT-TTATTTT
*
1283 ATTATTATTTT
1 ATTTTTATTTT
1294 ATTTTTATTTT
1 ATTTTTATTTT
* *
1305 ATTTAATGTTTT
1 ATTT-TTATTTT
* *
1317 CTCTTTGA-TTT
1 AT-TTTTATTTT
1328 ATTTTTA-TTT
1 ATTTTTATTTT
*
1338 A-TATTATTTTT
1 ATTTTTA-TTTT
1349 ATTTTT-TTTT
1 ATTTTTATTTT
1359 ATCTTATATATTTT
1 AT-TT-T-TATTTT
**
1373 -TTTACATTTT
1 ATTTTTATTTT
1383 -TTCCTTTGA-TTT
1 ATT--TTT-ATTTT
*
1395 ATTTGATATTTT
1 ATTT-TTATTTT
1407 A-TTTTATTTT
1 ATTTTTATTTT
1417 ATTTT
1 ATTTT
1422 CCTTTGATTT
Statistics
Matches: 105, Mismatches: 18, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
9 4 0.04
10 28 0.27
11 38 0.36
12 24 0.23
13 7 0.07
14 4 0.04
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:1343 original size:57 final size:53
Alignment explanation
Indices: 1257--1460 Score: 156
Period size: 52 Copynumber: 3.8 Consensus size: 53
1247 ACTATTCATT
1257 TTTTCCTTTGATTCATTTATTATTTTATTATTATTTTATTTTTATTTTATTTAATG
1 TTTTCCTTTGATTCATTTATTATTTTATTA-T-TTTTATTTTT-TTTTATTTAATG
* *
1313 TTTTCTCTTTGATTTATTT-TTATTTATATTATTTTTATTTTTTTTTATCTTATATA
1 TTTTC-CTTTGATTCATTTATTATTT-TATTATTTTTATTTTTTTTTAT-TTA-ATG
* * * * * *
1369 TTTT--TTT-A--CATTTTTTCCTTTGATTTATTTGATATTTTATTTTATTT--TA
1 TTTTCCTTTGATTCATTTATT-ATTTTA-TTATTT-TTATTTTTTTTTATTTAATG
*
1418 TTTTCCTTTGATTTATTTATCTTATTTTATT-TTTTTATTTTTT
1 TTTTCCTTTGATTCATTTA--TTATTTTATTATTTTTATTTTTT
1461 CTCCTTTTGA
Statistics
Matches: 120, Mismatches: 13, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
49 6 0.05
50 4 0.03
51 6 0.05
52 20 0.17
53 18 0.15
54 12 0.10
55 17 0.14
56 20 0.17
57 17 0.14
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.73
Consensus pattern (53 bp):
TTTTCCTTTGATTCATTTATTATTTTATTATTTTTATTTTTTTTTATTTAATG
Found at i:1351 original size:21 final size:21
Alignment explanation
Indices: 1325--1365 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315 TTCTCTTTGA
1325 TTTATTTTTATTTATATTATT
1 TTTATTTTTATTTATATTATT
* *
1346 TTTATTTTTTTTTATCTTAT
1 TTTATTTTTATTTATATTAT
1366 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTATTTATATTATT
Found at i:1374 original size:21 final size:21
Alignment explanation
Indices: 1324--1375 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1314 TTTCTCTTTG
1324 ATTTATTTTTATTTATATTATT
1 ATTT-TTTTTATTTATATTATT
* *
1346 -TTTATTTTTTTTTATCTTATAT
1 ATTT-TTTTTATTTATATTAT-T
1368 ATTTTTTT
1 ATTTTTTT
1376 ACATTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 18 0.69
22 5 0.19
23 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
ATTTTTTTTATTTATATTATT
Found at i:1436 original size:29 final size:28
Alignment explanation
Indices: 1396--1450 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1386 CTTTGATTTA
*
1396 TTTGATATTTTATTTTATTTTATTTTCC
1 TTTGATATTTTATCTTATTTTATTTTCC
*
1424 TTTGATTTATTTATCTTATTTTATTTT
1 TTTGATAT-TTTATCTTATTTTATTTT
1451 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (28 bp):
TTTGATATTTTATCTTATTTTATTTTCC
Found at i:1450 original size:68 final size:67
Alignment explanation
Indices: 1297--1452 Score: 158
Period size: 68 Copynumber: 2.3 Consensus size: 67
1287 TTATTTTATT
* * * * *
1297 TTTATTTTATTTAATGTTTTCTCTTTGATTTATTTTTATTTATATTATTTTTATTTTTTTTTATC
1 TTTA-TTTATTTTATTTTTTCTCTTTGATTTATTTATATTTATATTATTTTTATTTTCTTTGATC
1362 TTA
65 TTA
* *
1365 TATATTT-TTTTACATTTTTTC-CTTTGATTTATTTGATATTT-TATTTTATTTTATTTTCCTTT
1 TTTATTTATTTT--ATTTTTTCTCTTTGATTTATTT-ATATTTATATTAT-TTTTATTTT-CTTT
1427 GAT-TTA
61 GATCTTA
1433 TTTATCTTATTTTATTTTTT
1 TTTAT-TTATTTTATTTTTT
1453 TATTTTTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
66 3 0.04
67 21 0.29
68 38 0.52
69 7 0.10
70 4 0.05
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (67 bp):
TTTATTTATTTTATTTTTTCTCTTTGATTTATTTATATTTATATTATTTTTATTTTCTTTGATCT
TA
Found at i:1470 original size:42 final size:44
Alignment explanation
Indices: 1408--1497 Score: 132
Period size: 42 Copynumber: 2.1 Consensus size: 44
1398 TGATATTTTA
* *
1408 TTTTATTTTATTTTCCTTTGATTTATTTA-TCTTATTTTAT-TT
1 TTTTATTTTATTCTCCTTTGATTTATTTATTATTATTTTATGTT
1450 TTTTATTTT-TTCTCCTTTTGATTTATTTATTATTATTTTATGTT
1 TTTTATTTTATTCTCC-TTTGATTTATTTATTATTATTTTATGTT
1494 TTTT
1 TTTT
1498 CCTTGATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 5 0.12
42 22 0.51
43 10 0.23
44 6 0.14
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (44 bp):
TTTTATTTTATTCTCCTTTGATTTATTTATTATTATTTTATGTT
Found at i:5830 original size:60 final size:60
Alignment explanation
Indices: 5704--5844 Score: 153
Period size: 60 Copynumber: 2.3 Consensus size: 60
5694 AAATTGGGGA
* * * *
5704 CAATATAGAATGAGGTCATAGTTTGGGGGATGACATTATAATGTTCAAAAGTTTAGGAAC
1 CAATTTAGAATGAGGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGAAC
** *
5764 TGATTTAGAATGAGAGTCATAGTTT-GAGAATGTA-ATTGGAATGTTCAAAAGTTTA-GAATC
1 CAATTTAGAATGAG-GTCATAGTTTGGAGAATG-ACATTAGAATGTTCAAAAGTTTAGGAA-C
*
5824 CAATTTAGAATAAAGGTCATA
1 CAATTTAGAAT-GAGGTCATA
5845 AATTTGGGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 3 0.04
60 51 0.76
61 13 0.19
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (60 bp):
CAATTTAGAATGAGGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGAAC
Found at i:9669 original size:37 final size:38
Alignment explanation
Indices: 9606--9681 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
9596 AGTGACGGTG
* *
9606 AGGGTGTCTCTGAAAAATCTCGAGTTCATAATCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
* **
9644 AGGGTGT-TCAGAAGAATCCCGAGTTCATTGTCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
9681 A
1 A
9682 TTGATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (38 bp):
AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
Found at i:19137 original size:15 final size:15
Alignment explanation
Indices: 19119--19184 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
19109 CTCCATAATT
*
19119 ACCACCACCATATCC
1 ACCACCACCATAGCC
*
19134 ACCACCA-TATCCA-CC
1 ACCACCACCAT--AGCC
19149 ACCACCACCATAGCC
1 ACCACCACCATAGCC
*
19164 ACCACCGCCATAGCC
1 ACCACCACCATAGCC
19179 ACCACC
1 ACCACC
19185 TCCAAAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.07
15 38 0.86
16 3 0.07
ACGTcount: A:0.32, C:0.55, G:0.05, T:0.09
Consensus pattern (15 bp):
ACCACCACCATAGCC
Found at i:19169 original size:12 final size:12
Alignment explanation
Indices: 19120--19152 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
19110 TCCATAATTA
19120 CCACCACCATAT
1 CCACCACCATAT
19132 CCACCACCATAT
1 CCACCACCATAT
19144 CCACCACCA
1 CCACCACCA
19153 CCACCATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.55, G:0.00, T:0.12
Consensus pattern (12 bp):
CCACCACCATAT
Found at i:19184 original size:18 final size:18
Alignment explanation
Indices: 19132--19169 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19122 ACCACCATAT
*
19132 CCACCACCATATCCACCA
1 CCACCACCATAGCCACCA
19150 CCACCACCATAGCCACCA
1 CCACCACCATAGCCACCA
19168 CC
1 CC
19170 GCCATAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.58, G:0.03, T:0.08
Consensus pattern (18 bp):
CCACCACCATAGCCACCA
Found at i:23511 original size:18 final size:19
Alignment explanation
Indices: 23474--23512 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
23464 GTTTGTCATA
*
23474 ATTATATGTGATTATATGT
1 ATTATATGTAATTATATGT
*
23493 ATTATAT-TAATTGTATGT
1 ATTATATGTAATTATATGT
23511 AT
1 AT
23513 GCATGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
ATTATATGTAATTATATGT
Found at i:24131 original size:30 final size:29
Alignment explanation
Indices: 24092--24150 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
24082 GAGAATTAAC
* *
24092 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
24121 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
24151 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:24414 original size:23 final size:23
Alignment explanation
Indices: 24381--24447 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
24371 ATCTTATATG
24381 GCACTTTGGTGCATTTCTACGCA
1 GCACTTTGGTGCATTTCTACGCA
* * **
24404 GCACTTAGGTGCAATTCTACGTG
1 GCACTTTGGTGCATTTCTACGCA
*
24427 GCACTTTGGTGCATTTATACG
1 GCACTTTGGTGCATTTCTACG
24448 AGTTGTGGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (23 bp):
GCACTTTGGTGCATTTCTACGCA
Found at i:39005 original size:432 final size:432
Alignment explanation
Indices: 38200--39059 Score: 1326
Period size: 432 Copynumber: 2.0 Consensus size: 432
38190 GCTTCTTGAA
* * * * * *
38200 AATTCTCATAACTGACAGGTTTAGGTGATTCCAGCTTGTTTTCTAACAAGTGTGTTTCAAATAAA
1 AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
* *
38265 GAGGCCGGGATGCCTCTTGATCTATCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
66 GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
* *
38330 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGTCTGATCTCTTCACGAG
131 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
* *
38395 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATGCTGCTGTTTGCTCCTTTGCCACCTCGAT
196 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
* * *
38460 TCATAGCTCTTTCCGGAATAATGGTGCAGATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
261 TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
* **
38525 ACTGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCTGTCCCTTATTTTCACCACTGAATTCAT
326 ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
38590 CTGTACACTTAAAACT-AGGACATCTGCCCCTGCTTCTCAGAC
391 CTGTACACTTAAAA-TGAGGACATCTGCCCCTGCTTCTCAGAC
* *
38632 AATTCTCATAACCGAAAGGATTAGGCGTTTCCTGCTTATTTTCTAACAAATGTGTTTCAAATAAA
1 AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
* * * * *
38697 GAGGTCGGGGTGTCTCTAGATCTAGCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTG
66 GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
** *
38762 AAAATGGGCACCTACATCACCAGAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
131 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
* * *
38827 CATTGTTAGTCCTAGAAGTATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTTGAT
196 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
* * * *
38892 TCGTAACTCTTGCCTGAATCATGGTGCAAATAACGACAAGACATTCCACGGTAGCACTTGCCTCG
261 TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
* *
38957 ACGGAAGTGAAAACAGAATGGCATCTGTCCCTTCACCAATCTCTTATTTTCACCACTGAATTCAT
326 ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
** * * *
39022 CTGTATGCTTAAAATGGGGAGATCTGCTCCTGCTTCTC
391 CTGTACACTTAAAATGAGGACATCTGCCCCTGCTTCTC
39060 CGATTTCTGG
Statistics
Matches: 385, Mismatches: 42, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
431 1 0.00
432 384 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (432 bp):
AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
CTGTACACTTAAAATGAGGACATCTGCCCCTGCTTCTCAGAC
Found at i:39079 original size:30 final size:30
Alignment explanation
Indices: 39038--39405 Score: 414
Period size: 30 Copynumber: 12.3 Consensus size: 30
39028 GCTTAAAATG
* *
39038 GGGAGATCTGCTCCTGCTTCTCCGATTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * **
39068 GGGAGACCTGCTCCTGCTCCTCAGACTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * * **
39098 GGGAGACCTGCTCTTGCTCCTCAGACTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
39128 GGGAGACCTGCTCCTGCTTCTCTGATTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
39158 GGGAGACCTGCTCCTGCTACTCCGGTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
39188 GGGAAACCTGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * * *
39218 GGGAGACCTGCTCCTGCTACTCTGTTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
39248 GGGAGACCTGCTCCTGCTACTCTGGTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
39278 AGGAGACCTGCTCCTG-TTACTCTGGTTTCC
1 GGGAGACCTGCTCCTGCTT-CTCCGGTTTCT
* *
39308 GGGAGATCTGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
39338 GGGAGACCAGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
39368 GGGAGACCTGCTCCTGCTTCTCTGATTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
39398 GGGAGACC
1 GGGAGACC
39406 AACTAAAACA
Statistics
Matches: 299, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
29 1 0.00
30 296 0.99
31 2 0.01
ACGTcount: A:0.11, C:0.32, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
Found at i:43561 original size:6 final size:6
Alignment explanation
Indices: 43550--43576 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43540 TTTCTTTTCT
43550 CCCTAA CCCTAA CCCTAA CCCTAA CCC
1 CCCTAA CCCTAA CCCTAA CCCTAA CCC
43577 CTAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.56, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTAA
Found at i:45436 original size:6 final size:6
Alignment explanation
Indices: 45425--45451 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45415 GGGATGATAA
45425 ACGGGG ACGGGG ACGGGG ACGGGG ACG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACG
45452 AGGAAAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.63, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:45529 original size:13 final size:13
Alignment explanation
Indices: 45513--45548 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
45503 GCCCCGATTA
*
45513 CCCGATTACCCTC
1 CCCGATTACCCGC
45526 CCCGATTACCCGC
1 CCCGATTACCCGC
45539 CCCGA-TACCC
1 CCCGATTACCC
45549 AACCCGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.17, C:0.56, G:0.11, T:0.17
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:45610 original size:32 final size:32
Alignment explanation
Indices: 45558--45654 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
45548 CAACCCGATA
*
45558 AATATTAA-AAATAATT-ATTTATATATATATAT
1 AATATTAATAAAT--TTAATTTAAATATATATAT
* *
45590 AATATTAATAAATTTAATTTAAATA-AAAAAT
1 AATATTAATAAATTTAATTTAAATATATATAT
* * *
45621 CTATATTTATATATTTAATTTAAATATATATAT
1 -AATATTAATAAATTTAATTTAAATATATATAT
45654 A
1 A
45655 TACCCGGCCC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
31 6 0.12
32 38 0.73
33 8 0.15
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATTAATAAATTTAATTTAAATATATATAT
Found at i:46907 original size:16 final size:15
Alignment explanation
Indices: 46882--46916 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
46872 ATGTCACGTT
46882 TATA-TTTTAAAAAA
1 TATATTTTTAAAAAA
46896 TGATATTTTTAAAAAA
1 T-ATATTTTTAAAAAA
46912 TATAT
1 TATAT
46917 AATAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 7 0.37
16 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATATTTTTAAAAAA
Done.