Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003340.1 Hibiscus syriacus cultivar Beakdansim tig00007029_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: 63460
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1474 original size:19 final size:19
Alignment explanation
Indices: 1450--1486 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1440 AAATTCACAC
1450 AGGGTTTAATTATACGCGT
1 AGGGTTTAATTATACGCGT
*
1469 AGGGTTTAATTGTACGCG
1 AGGGTTTAATTATACGCG
1487 CAGTCACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (19 bp):
AGGGTTTAATTATACGCGT
Found at i:2490 original size:37 final size:37
Alignment explanation
Indices: 2417--2497 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 37
2407 AATCATACCT
2417 AAAATTTAGTTTTTGTTTCATTTTAGTACCTGTCGTTA
1 AAAATTTAGTTTTTGTTTCATTTTAGTACC-GTCGTTA
*
2455 AAAATATTAGTTTTTGTTTCATTTTAGTACC-TCGTTC
1 AAAAT-TTAGTTTTTGTTTCATTTTAGTACCGTCGTTA
2492 AAAATT
1 AAAATT
2498 AAATGTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 1 0.02
37 10 0.24
38 5 0.12
39 25 0.61
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (37 bp):
AAAATTTAGTTTTTGTTTCATTTTAGTACCGTCGTTA
Found at i:4075 original size:18 final size:18
Alignment explanation
Indices: 4052--4094 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
4042 TTGAAAAGTT
4052 GATATCAAATGTTAGAGA
1 GATATCAAATGTTAGAGA
4070 GATATCAAATGTTAGAGA
1 GATATCAAATGTTAGAGA
4088 GATATCA
1 GATATCA
4095 TTTGCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (18 bp):
GATATCAAATGTTAGAGA
Found at i:4718 original size:19 final size:20
Alignment explanation
Indices: 4683--4720 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4673 CTCTAAATCC
4683 GTTTTCAAAATTTCATTTTG
1 GTTTTCAAAATTTCATTTTG
4703 GTTTTCAAAA-TTCATTTT
1 GTTTTCAAAATTTCATTTT
4721 ACCTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (20 bp):
GTTTTCAAAATTTCATTTTG
Found at i:4727 original size:19 final size:20
Alignment explanation
Indices: 4685--4730 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4675 CTAAATCCGT
***
4685 TTTCAAAATTTCATTTTGGT
1 TTTCAAAATTTCATTTTACC
4705 TTTCAAAA-TTCATTTTACC
1 TTTCAAAATTTCATTTTACC
4724 TTTCAAA
1 TTTCAAA
4731 CGAAAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTCAAAATTTCATTTTACC
Found at i:6148 original size:19 final size:19
Alignment explanation
Indices: 6124--6196 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
6114 GAGCCTTATG
6124 GTAGTATCGATACTACCTA
1 GTAGTATCGATACTACCTA
6143 GTAGTATCGATACTACCTA
1 GTAGTATCGATACTACCTA
* *
6162 GTGGTATCGGTACTACCTA
1 GTAGTATCGATACTACCTA
* *
6181 GTGGTATCGGTACTAC
1 GTAGTATCGATACTAC
6197 TCTTACTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (19 bp):
GTAGTATCGATACTACCTA
Found at i:11335 original size:9 final size:9
Alignment explanation
Indices: 11323--11369 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
11313 CATTCGGAGC
11323 ATGAGAAGT
1 ATGAGAAGT
*
11332 ATGAGGAGT
1 ATGAGAAGT
11341 ATGAGAAGT
1 ATGAGAAGT
** *
11350 ATTCGGAGT
1 ATGAGAAGT
11359 ATGAGAAGT
1 ATGAGAAGT
11368 AT
1 AT
11370 TCGGAGCATG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.34, T:0.26
Consensus pattern (9 bp):
ATGAGAAGT
Found at i:11339 original size:18 final size:18
Alignment explanation
Indices: 11301--11381 Score: 101
Period size: 18 Copynumber: 4.5 Consensus size: 18
11291 GCTGAAGAAT
*
11301 GAGCATGA-AAGGCATTCG
1 GAGCATGAGAA-GTATTCG
**
11319 GAGCATGAGAAGTATGAG
1 GAGCATGAGAAGTATTCG
*
11337 GAGTATGAGAAGTATTCG
1 GAGCATGAGAAGTATTCG
*
11355 GAGTATGAGAAGTATTCG
1 GAGCATGAGAAGTATTCG
11373 GAGCATGAG
1 GAGCATGAG
11382 GAGCTTGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
18 53 0.96
19 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.36, T:0.21
Consensus pattern (18 bp):
GAGCATGAGAAGTATTCG
Found at i:19273 original size:2 final size:2
Alignment explanation
Indices: 19268--19313 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
19258 GCGAATTACC
19268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
19310 TA TA
1 TA TA
19314 AACCATCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22157 original size:6 final size:6
Alignment explanation
Indices: 22148--22172 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22138 AATCCCACTT
22148 GTACCA GTACCA GTACCA GTACCA G
1 GTACCA GTACCA GTACCA GTACCA G
22173 CGTACGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (6 bp):
GTACCA
Found at i:23221 original size:16 final size:17
Alignment explanation
Indices: 23185--23229 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
23175 TTTATGAGGA
23185 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGT-AAGG
*
23203 AATTGAAATCTGT-AGG
1 AATTGGAATCTGTAAGG
23219 AATTGGAATCT
1 AATTGGAATCT
23230 AAATCTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (17 bp):
AATTGGAATCTGTAAGG
Found at i:26667 original size:40 final size:40
Alignment explanation
Indices: 26623--26703 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
26613 ACAAGTTCGT
26623 TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
1 TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
26663 TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
1 TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
26703 T
1 T
26704 TTCGAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (40 bp):
TCTAATTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
Found at i:26717 original size:40 final size:39
Alignment explanation
Indices: 26633--26719 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
26623 TCTAATTTGG
* *
26633 TTTTTGATCCCTTGTTTTGTTTTAAATAAGTCTAATTTGG
1 TTTTTGATCCCTTGTTTTGTTTTAAATAAGTCGAA-TTGC
26673 TTTTTGATCCCTTGTTTTGTTTTAAATAAGTTTCGAA-TGC
1 TTTTTGATCCCTTGTTTTGTTTTAAATAAG--TCGAATTGC
26713 TTTTTGA
1 TTTTTGA
26720 CTCTTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 39 0.91
42 4 0.09
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (39 bp):
TTTTTGATCCCTTGTTTTGTTTTAAATAAGTCGAATTGC
Found at i:27370 original size:41 final size:46
Alignment explanation
Indices: 27274--27371 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 46
27264 GTATGCGAAC
* * *
27274 TAGAAATCATGCGGTTAGGATTATTTTCCTGAACAAACATGTGAAT
1 TAGAAATCATGCGGTTAGGATTATTTTCATGAACAAACATATGAAG
* * *
27320 TAGATATCATGCGGTTAGGA-T-TTTT-ATGAA-AAGCATATG-GG
1 TAGAAATCATGCGGTTAGGATTATTTTCATGAACAAACATATGAAG
27361 TAGAAATCATG
1 TAGAAATCATG
27372 ACTGGGTAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 10 0.22
42 7 0.16
43 4 0.09
44 4 0.09
45 1 0.02
46 19 0.42
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (46 bp):
TAGAAATCATGCGGTTAGGATTATTTTCATGAACAAACATATGAAG
Found at i:36962 original size:11 final size:12
Alignment explanation
Indices: 36935--36963 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
36925 TTTCGCCTGA
36935 AAAAATGAATGG
1 AAAAATGAATGG
36947 AAAAATGAATGG
1 AAAAATGAATGG
36959 AAAAA
1 AAAAA
36964 AAATGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAAATGAATGG
Found at i:36997 original size:22 final size:21
Alignment explanation
Indices: 36959--37015 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
36949 AAATGAATGG
36959 AAAAAAAATGAAAAAAAAAGAA
1 AAAAAAAATG-AAAAAAAAGAA
* **
36981 AGAAAAAATGAGGAAAAAGAA
1 AAAAAAAATGAAAAAAAAGAA
37002 AAATAAAAAT-AAAA
1 AAA-AAAAATGAAAA
37016 GAAGGGTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAAAAAATGAAAAAAAAGAA
Found at i:38514 original size:111 final size:111
Alignment explanation
Indices: 38170--38728 Score: 888
Period size: 111 Copynumber: 5.0 Consensus size: 111
38160 GGTTCGACCC
* * * *
38170 TGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTTAGAAGAAGTGGAACAGATCCCTCTC
1 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
38235 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
66 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
*
38281 TGATTCAATGAATCAACTTTCACAGATCTGATATTCCCTCAGAGGAAGTGGAACAGAT-CC-CTC
1 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
*
38344 TTTCAAGATTTGATATTCCCTGAGTGATAGCGGAACAAGTCTACCT
66 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
* *
38390 TGATTCAATGAATCAAATTTCCCATATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
1 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
38455 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
66 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
*
38501 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGAGGAACAGATCCCTCTC
1 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
* * *
38566 TTTCAAGATTTTATATTCCCTGAGTGACAGTGGAACAAGTCTACCC
66 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
* * * **
38612 TGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCAAATCT
1 TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATC-CCTCT
* * * ** *
38677 CTTTCAAGATTTGATATTCCATAAGTGATAATGGAACAAGTCTACCC
65 CTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
38724 TGATT
1 TGATT
38729 TAATTTTACC
Statistics
Matches: 419, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
109 103 0.25
110 4 0.01
111 262 0.63
112 50 0.12
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (111 bp):
TGATTCAATGAATCAACTTTCCCAGATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCCTCTC
TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCT
Found at i:38556 original size:220 final size:222
Alignment explanation
Indices: 38166--38728 Score: 923
Period size: 220 Copynumber: 2.5 Consensus size: 222
38156 TGCAGGTTCG
*
38166 ACCCTGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTTAGAAGAAGTGGAACAGATCCC
1 ACCCTGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTCAGAAGAAGTGGAACAGATCCC
38231 TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATGAATCA
66 TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATGAATCA
*
38296 ACTTTCACAGATCTGATATTCCCTCAGAGGAAGTGGAACAGAT-CC-CTCTTTCAAGATTTGATA
131 ACTTTCACAGATCTGATATTCCCTCAGAGGAAGAGGAACAGATCCCTCTCTTTCAAGATTTGATA
*
38359 TTCCCTGAGTGATAGCGGAACAAGTCT
196 TTCCCTGAGTGACAGCGGAACAAGTCT
* * * *
38386 ACCTTGATTCAATGAATCAAATTTCCCATATCTGATATTCCCTCAGAGGAAGTGGAACAGATCCC
1 ACCCTGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTCAGAAGAAGTGGAACAGATCCC
38451 TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATGAATCA
66 TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATGAATCA
* *
38516 ACTTTCCCAGATCTGATATTCCCTCAGAGGAAGAGGAACAGATCCCTCTCTTTCAAGATTTTATA
131 ACTTTCACAGATCTGATATTCCCTCAGAGGAAGAGGAACAGATCCCTCTCTTTCAAGATTTGATA
*
38581 TTCCCTGAGTGACAGTGGAACAAGTCT
196 TTCCCTGAGTGACAGCGGAACAAGTCT
* * *
38608 ACCCTGATTCAATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCAA
1 ACCCTGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTCAGAAGAAGTGGAACAGATC-C
* * * * ** *
38673 ATCTCTTTCAAGATTTGATATTCCATAAGTGATAATGGAACAAGTCTACCCTGATT
65 CTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATT
38729 TAATTTTACC
Statistics
Matches: 316, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
220 166 0.53
221 2 0.01
222 99 0.31
223 49 0.16
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (222 bp):
ACCCTGATTCAATGGATCAACTTTCCCATATCTGATATTCCCTCAGAAGAAGTGGAACAGATCCC
TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATGAATCA
ACTTTCACAGATCTGATATTCCCTCAGAGGAAGAGGAACAGATCCCTCTCTTTCAAGATTTGATA
TTCCCTGAGTGACAGCGGAACAAGTCT
Found at i:42294 original size:33 final size:33
Alignment explanation
Indices: 42231--42382 Score: 143
Period size: 33 Copynumber: 4.6 Consensus size: 33
42221 TTTTCACCCT
42231 AAACCCGAACCCGACCCGAATAT--CAC---AAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
* *
42260 AAATCTGACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
*
42293 AACCCGACCCCAACCCGACCCGAATATCACACTTAAAA
1 AA----A-CCCGACCCGACCCGAATATCACACTTAAAA
* * *
42331 AAACCCGACCCAACCAGAATATCAAACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
**
42364 AAACCCGACCATACCCGAA
1 AAACCCGACCCGACCCGAA
42383 CCCGAATTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
28 15 0.15
29 5 0.05
30 3 0.03
33 47 0.47
34 1 0.01
37 1 0.01
38 29 0.29
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:42311 original size:38 final size:38
Alignment explanation
Indices: 42267--42389 Score: 161
Period size: 38 Copynumber: 3.3 Consensus size: 38
42257 AAAAAATCTG
42267 ACCCGACCCGAATATCACACTT-AAAAAACCCGACCCCA
1 ACCCGACCCGAATATCACACTTAAAAAAACCCGA-CCCA
42305 ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCA
1 ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCA
*
42343 A-CC-A---GAATATCAAACTTAAAAAAACCCGA-CCA
1 ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCA
42375 TACCCGAACCCGAAT
1 -ACCCG-ACCCGAAT
42390 TTTTTTAAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 15
0.83 0.01 0.16
Matches are distributed among these distances:
32 3 0.04
33 25 0.33
34 2 0.03
36 2 0.03
37 2 0.03
38 27 0.36
39 15 0.20
ACGTcount: A:0.43, C:0.37, G:0.08, T:0.11
Consensus pattern (38 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCA
Found at i:42317 original size:66 final size:69
Alignment explanation
Indices: 42233--42389 Score: 180
Period size: 71 Copynumber: 2.3 Consensus size: 69
42223 TTCACCCTAA
* * * * * *
42233 ACCCGAACCCGACCCGAATAT-CAC-AAAAAATCTGACCCGACCCGAATATCACACTT-AAAAAA
1 ACCCCAACCCGACCCGAATATACACTAAAAAACCCGACCCAACCAGAATATCAAACTTAAAAAAA
42295 CCCG
66 CCCG
42299 ACCCCAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCAACCAGAATATCAAACTTAAAA
1 ACCCCAACCCGACCCGAATAT-ACAC-T-AAAAAACCCGACCCAACCAGAATATCAAACTTAAAA
42364 AAACCCG
63 AAACCCG
42371 A--CCATACCCGAACCCGAAT
1 ACCCCA-ACCCG-ACCCGAAT
42390 TTTTTTAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
66 20 0.26
68 3 0.04
70 3 0.04
71 32 0.42
72 19 0.25
ACGTcount: A:0.43, C:0.37, G:0.09, T:0.11
Consensus pattern (69 bp):
ACCCCAACCCGACCCGAATATACACTAAAAAACCCGACCCAACCAGAATATCAAACTTAAAAAAA
CCCG
Found at i:42423 original size:29 final size:27
Alignment explanation
Indices: 42382--42468 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 27
42372 CCATACCCGA
*
42382 ACCCGAATT-TTTTTAAAAAAAATCCG
1 ACCCAAATTATTTTTAAAAAAAATCCG
* * *
42408 ACCC-AATCCTGATTTTTAAAAAAGACCCA
1 ACCCAAAT--T-ATTTTTAAAAAAAATCCG
*
42437 ACCCCAAATTTTTTTTAAAAAAAATCCG
1 A-CCCAAATTATTTTTAAAAAAAATCCG
42465 ACCC
1 ACCC
42469 GAATACCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 4 0.08
28 15 0.31
29 16 0.33
30 3 0.06
31 3 0.06
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (27 bp):
ACCCAAATTATTTTTAAAAAAAATCCG
Found at i:43687 original size:14 final size:13
Alignment explanation
Indices: 43635--43710 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
43625 AACAATCTAA
43635 TTATATAT-ATAT
1 TTATATATAATAT
*
43647 ATATAT-TAAATAT
1 TTATATAT-AATAT
*
43660 TT-TA-A-AATAA
1 TTATATATAATAT
43670 TTATAATATAATAT
1 TTAT-ATATAATAT
43684 TTATTTATATAATAT
1 TTA--TATATAATAT
43699 TGTATATATAAT
1 T-TATATATAAT
43711 CTCATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
10 6 0.12
11 2 0.04
12 8 0.16
13 6 0.12
14 15 0.30
15 10 0.20
16 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (13 bp):
TTATATATAATAT
Found at i:45564 original size:138 final size:138
Alignment explanation
Indices: 45383--45651 Score: 328
Period size: 138 Copynumber: 1.9 Consensus size: 138
45373 AAGGATTATA
* * * * * *
45383 GTGAAATTGAACCCTAGATGAAGGCTCTAATATTAAACTTAATCAATTTTGCAATTTATT-GAAT
1 GTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATTATACAAATTATTAG-AT
* * *
45447 CAAATAATT-AG-TGTGGAACCTCAGTCATAAAAGCAAGAACCAAATTAAAAATTCTCCTAAATT
65 CAAAGAATTAAGAT-T-GAACCTCAGGCATAAAAGCAAGAACCAAATTAAAAATTCACCTAAATT
45510 AAAAGACTAAG
128 AAAAGACTAAG
* * * *
45521 GTGAAATTAAACCTTAGGTGAATGCTCTAAAATTAAACCTAATCAATTATACAAATTATTAGGTC
1 GTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATTATACAAATTATTAGATC
* * * * *
45586 AAAGAATTAAGATTGAACCTCGGGCATAGAAGCGAGGACCAAATTAAAATTTCACCTAAATTAAA
66 AAAGAATTAAGATTGAACCTCAGGCATAAAAGCAAGAACCAAATTAAAAATTCACCTAAATTAAA
45651 A
131 A
45652 AGTTTAGGGA
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
138 105 0.95
139 4 0.04
140 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (138 bp):
GTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATTATACAAATTATTAGATC
AAAGAATTAAGATTGAACCTCAGGCATAAAAGCAAGAACCAAATTAAAAATTCACCTAAATTAAA
AGACTAAG
Found at i:46215 original size:3 final size:3
Alignment explanation
Indices: 46209--46233 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46199 AATAATAATA
46209 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
46234 AAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:59338 original size:32 final size:32
Alignment explanation
Indices: 59297--59403 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 32
59287 ATGAAAATTT
59297 TAAATTAAAAATACTTAAAATGATATTTTTAA
1 TAAATTAAAAATACTTAAAATGATATTTTTAA
* *
59329 TAAATTAAAAATTC-T--AATGAATAGTTTTAA
1 TAAATTAAAAATACTTAAAATG-ATATTTTTAA
* *
59359 TTTTAAATTAAAAAAATACTTAAAATGACATTATTAA
1 ---TAAATT--AAAAATACTTAAAATGATATTTTTAA
*
59396 TGAATTAA
1 TAAATTAA
59404 GATTTTCAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
29 4 0.07
30 9 0.15
31 1 0.02
32 15 0.25
33 6 0.10
34 5 0.08
35 7 0.12
36 1 0.02
37 7 0.12
38 4 0.07
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (32 bp):
TAAATTAAAAATACTTAAAATGATATTTTTAA
Found at i:62501 original size:28 final size:28
Alignment explanation
Indices: 62465--62562 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
62455 AAAAAGTTTG
*
62465 AATAATTTAGATATCTATTTTGAC-ATAA
1 AATATTTTAGATATCTATTTTGACTA-AA
*
62493 AATATTTTAGGTATCTATTTTGACTAAA
1 AATATTTTAGATATCTATTTTGACTAAA
* * *
62521 AATATAATATTAGATATTTATTTTTACCAAA
1 AATAT--T-TTAGATATCTATTTTGACTAAA
*
62552 AGATACTTTAG
1 A-ATATTTTAG
62563 GTACTTAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
28 29 0.50
29 5 0.09
30 2 0.03
31 19 0.33
32 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (28 bp):
AATATTTTAGATATCTATTTTGACTAAA
Found at i:62520 original size:27 final size:28
Alignment explanation
Indices: 62465--62544 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
62455 AAAAAGTTTG
62465 AATAATTTAGATATCTATTTTGACATAA
1 AATAATTTAGATATCTATTTTGACATAA
* * *
62493 AATATTTTAGGTATCTATTTTGACTAAAA
1 AATAATTTAGATATCTATTTTGAC-ATAA
*
62522 ATATAATATTAGATATTTATTTT
1 A-ATAAT-TTAGATATCTATTTT
62545 TACCAAAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 22 0.51
29 4 0.09
30 4 0.09
31 13 0.30
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (28 bp):
AATAATTTAGATATCTATTTTGACATAA
Found at i:63040 original size:20 final size:20
Alignment explanation
Indices: 63015--63275 Score: 151
Period size: 20 Copynumber: 12.8 Consensus size: 20
63005 AATGACCAAC
*
63015 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
63035 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
***
63055 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
63076 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* *
63097 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
63117 AAAATGGCAACG-G-TCAAA
1 AAAATCGCAACGCGATTAAG
* ***
63135 ACGAAATGGCAACGCGATATTCC
1 A--AAATCGCAACGCGAT-TAAG
*
63158 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* *
63179 -AGATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
*
63198 AAAATCGCAACG-G-TCAAACG
1 AAAATCGCAACGCGAT-TAA-G
63218 AAAATCGCAACGCGAAATTCCAAG
1 AAAATCGCAACGCG--ATT--AAG
*
63242 --AATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
63260 AGAATCGCAACGCGAT
1 AAAATCGCAACGCGAT
63276 CACAAAAACG
Statistics
Matches: 182, Mismatches: 38, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
18 7 0.04
19 20 0.11
20 103 0.57
21 10 0.05
22 37 0.20
23 1 0.01
24 2 0.01
25 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:63154 original size:82 final size:83
Alignment explanation
Indices: 63017--63275 Score: 445
Period size: 82 Copynumber: 3.2 Consensus size: 83
63007 TGACCAACAA
* *
63017 AATCGCAACGCGATTTAGAAAATCGCAACGTTGAAAA-GAAAATCGCAACGCGATATTCCAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAAACGAAAATCGCAACGCGATATTCCAAGAA
63081 TCGCAATGCGATTAAGAG
66 TCGCAATGCGATTAAGAG
* *
63099 AATCGCAACGCGATTTAGAAAATGGCAACGGTCAAAACG-AAATGGCAACGCGATATTCCAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAAACGAAAATCGCAACGCGATATTCCAAGAA
63163 TCGCAATGCGATTAAGAG
66 TCGCAATGCGATTAAGAG
*
63181 -ATCGCAACGCGATTTAGAAAATCGCAACGGTC-AAACGAAAATCGCAACGCGAAATTCCAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAAACGAAAATCGCAACGCGATATTCCAAGAA
63244 TCGCAATGCGATTAAGAG
66 TCGCAATGCGATTAAGAG
63262 AATCGCAACGCGAT
1 AATCGCAACGCGAT
63276 CACAAAAACG
Statistics
Matches: 167, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
80 5 0.03
81 72 0.43
82 89 0.53
83 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.17
Consensus pattern (83 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAAACGAAAATCGCAACGCGATATTCCAAGAA
TCGCAATGCGATTAAGAG
Done.