Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004350.1 Hibiscus syriacus cultivar Beakdansim tig00009532_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: 72218
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3367 original size:23 final size:23
Alignment explanation
Indices: 3338--3385 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3328 TCAAATATAC
3338 ACAGAGACATACACTCATCATTT
1 ACAGAGACATACACTCATCATTT
3361 ACAGAGACATACACTCATCATTT
1 ACAGAGACATACACTCATCATTT
3384 AC
1 AC
3386 TTAATTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (23 bp):
ACAGAGACATACACTCATCATTT
Found at i:3687 original size:25 final size:23
Alignment explanation
Indices: 3670--3724 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3660 ATGAAATTTG
3670 TCCCGAAGGACCACTATGAAATA
1 TCCCGAAGGACCACTATGAAATA
* *
3693 TCCCGAAGGATCACTAT---ATG
1 TCCCGAAGGACCACTATGAAATA
3713 TCCCGAAGGACC
1 TCCCGAAGGACC
3725 CCGTAGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.45
23 16 0.55
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (23 bp):
TCCCGAAGGACCACTATGAAATA
Found at i:8616 original size:36 final size:36
Alignment explanation
Indices: 8561--8663 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
8551 ATTTCTCCAT
*
8561 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
8597 TATCAGCTTTGGTATATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
8633 TATCATCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
8664 CCATCACCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:9940 original size:21 final size:18
Alignment explanation
Indices: 9899--9947 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
9889 GCAAATTTTG
*
9899 GTATCGATACCCAGTTGA
1 GTATCGATACCCAGGTGA
9917 GTATCGATACCCAATGGGTGA
1 GTATCGATACCC-A--GGTGA
9938 GTATCGATAC
1 GTATCGATAC
9948 TGCTGGCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 1 0.04
21 14 0.52
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (18 bp):
GTATCGATACCCAGGTGA
Found at i:13935 original size:28 final size:28
Alignment explanation
Indices: 13903--13978 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
13893 TTATATGACT
* **
13903 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
13931 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
13960 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
13979 TAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:15314 original size:3 final size:3
Alignment explanation
Indices: 15308--15376 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
15298 TAATTTTTTT
* * *
15308 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TGTA TAA TGA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA
*
15353 TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
15377 ATAAATAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.84
4 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:15331 original size:12 final size:12
Alignment explanation
Indices: 15316--15384 Score: 61
Period size: 12 Copynumber: 5.6 Consensus size: 12
15306 TTTAATAATA
15316 ATAATAATATAT
1 ATAATAATATAT
*
15328 ATAATAATATGT
1 ATAATAATATAT
*
15340 ATAATGAT-TAT
1 ATAATAATATAT
15351 AATAATAATAATAATT
1 -ATAATAAT-AT-A-T
*
15367 ATAATAATAAAT
1 ATAATAATATAT
15379 A-AATAA
1 ATAATAA
15385 ATAAAATGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 7 0.15
12 27 0.57
13 1 0.02
14 2 0.04
15 9 0.19
16 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:15387 original size:15 final size:15
Alignment explanation
Indices: 15310--15388 Score: 60
Period size: 15 Copynumber: 5.5 Consensus size: 15
15300 ATTTTTTTTA
15310 ATAATAATAAT-AAT
1 ATAATAATAATAAAT
**
15324 ATATATAATAATATGT
1 ATA-ATAATAATAAAT
* *
15340 ATAATGAT--TATA-
1 ATAATAATAATAAAT
*
15352 ATAATAATAATAATT
1 ATAATAATAATAAAT
15367 ATAATAATAAATAAAT
1 ATAATAAT-AATAAAT
15383 A-AATAA
1 ATAATAA
15389 AATGGGTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
12 7 0.14
13 3 0.06
14 5 0.10
15 25 0.49
16 11 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:15388 original size:18 final size:17
Alignment explanation
Indices: 15309--15384 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
15299 AATTTTTTTT
15309 AATAATAATAATAATATA
1 AATAATAATAATAA-ATA
* *
15327 TATAATAATATGTATAATGA
1 AATAATAATA-ATA-AAT-A
*
15347 TTATAATAATAAT-AAT-
1 -AATAATAATAATAAATA
*
15363 AATTATAATAATAAATA
1 AATAATAATAATAAATA
15380 AATAA
1 AATAA
15385 ATAAAATGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
15 10 0.22
16 3 0.07
17 4 0.09
18 12 0.26
19 4 0.09
20 3 0.07
21 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AATAATAATAATAAATA
Found at i:15646 original size:17 final size:17
Alignment explanation
Indices: 15624--15682 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
15614 TTGAACAAGC
15624 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
15641 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
15660 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
15677 TCTTCT
1 TCTTCT
15683 GGAAATGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:16018 original size:227 final size:228
Alignment explanation
Indices: 15727--16145 Score: 664
Period size: 227 Copynumber: 1.8 Consensus size: 228
15717 TAGAGTCATG
* * *
15727 CAAAAGGTCGAACAAGATCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTCGAACAAGATCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
* * * *
15792 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAA-GTTGAACAAG
66 TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAAC-AAAAGGTTGAACAAG
*
15856 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCAC
130 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCAC
15920 TGGGGATGTTGATCCATCAAATGATGAATTCAAA
195 TGGGGATGTTGATCCATCAAATGATGAATTCAAA
15954 CAAAAGGTCGAACAA-ATTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTC
1 CAAAAGGTCGAACAAGA-TCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTC
* * * * *
16018 ATTATGAACTTTTTCTGGAAAAGCTGATCTATCAAGTGATGAATTCAAACAAAAGGTTGATCAAT
65 ATTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAG
* *
16083 TTCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
130 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC
16146 TTCTTTCTTC
Statistics
Matches: 174, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
226 5 0.03
227 133 0.76
228 36 0.21
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (228 bp):
CAAAAGGTCGAACAAGATCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACT
GGGGATGTTGATCCATCAAATGATGAATTCAAA
Found at i:16141 original size:113 final size:113
Alignment explanation
Indices: 15727--16146 Score: 585
Period size: 113 Copynumber: 3.7 Consensus size: 113
15717 TAGAGTCATG
* *
15727 CAAAAGGTCGAACAAGA-TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAA-ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
15791 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAG
65 ATTATGAACTTTTTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
*
15840 CGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * *
15903 ATTATGAACTCTTTCACTGGGGATGTTGATCCATCAAATGATGAATTCAAA
65 ATTATGAACT-TTT-TCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
* * *
15954 CAAAAGGTCGAACAAATTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
16019 TTATGAACTTTTTCTGGAAAAGCTGATCTATCAAGTGATGAATTCAAA
66 TTATGAACTTTTTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
* * * *
16067 CAAAAGGTTGATCAATTTCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
16132 TTATGAACTTTTTCT
66 TTATGAACTTTTTCT
16147 TCTTTCTTCA
Statistics
Matches: 270, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
112 31 0.11
113 140 0.52
114 68 0.25
115 31 0.11
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
Found at i:16183 original size:40 final size:40
Alignment explanation
Indices: 16083--16184 Score: 170
Period size: 40 Copynumber: 2.5 Consensus size: 40
16073 GTTGATCAAT
*
16083 TTCTTCTCATTATGAA-TTTCCTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAG
*
16123 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
16163 TTCTTCTCATTATGAACTTTTT
1 TTCTTCTCATTATGAACTTTTT
16185 TCTGGAAAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 56 0.95
41 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.52
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
Found at i:16227 original size:267 final size:267
Alignment explanation
Indices: 15854--16413 Score: 872
Period size: 267 Copynumber: 2.1 Consensus size: 267
15844 AAGTTGAACA
*
15854 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCA
1 AGTTCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCA
** * *
15919 CTGGGGATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCCCATTATG
66 CTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCCCATTATG
*
15984 AACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCTA
131 AACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCA
* * *
16049 TCAAGTGA-TGAATTCAAACAAAAGGTTGATCAATTTCTTCTCATTATGAATTTCCTCTTCCTTC
196 TCAAATGATTG-ATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTC
16113 TTCAGATG
260 TTCAGATG
*
16121 AGTTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTTT
1 AGTTCTTCTCATTATGAACTTTTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC
* * ** * * *
16185 TCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTAT
65 ACTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCCCATTAT
* *
16250 GAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCC
130 GAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCC
** * * *
16315 ATCAAATGATTGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGTATTTCTTCTTCCTTC
195 ATCAAATGATTGATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTC
16380 TTCAGATG
260 TTCAGATG
16388 AGTTCTTCTCATTATGAACTTTTTCT
1 AGTTCTTCTCATTATGAACTTTTTCT
16414 GGAAAGCTGA
Statistics
Matches: 267, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
267 234 0.88
268 33 0.12
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (267 bp):
AGTTCTTCTCATTATGAACTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCA
CTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCCCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCA
TCAAATGATTGATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTCT
TCAGATG
Found at i:16253 original size:154 final size:153
Alignment explanation
Indices: 15970--16300 Score: 536
Period size: 154 Copynumber: 2.2 Consensus size: 153
15960 GTCGAACAAA
* *
15970 TTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTG
* * * *
16035 GAAAAGCTGATCTATCAAGTGATGAATTCAAACAAAAGGTTGATCAATTTCTTCTCATTATGAAT
66 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
16100 TTCCTCTTCCTTCTTCAGATGAG
131 TTCCTCTTCCTTCTTCAGATGAG
* *
16123 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAAC-TTTTTCT
* ** *
16188 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
65 GGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
16253 TTTCTTCTTCCTTCTTCAGATGAG
130 TTTCCTCTTCCTTCTTCAGATGAG
16277 TTCTTCTCATTATGAACTTTTTCT
1 TTCTTCTCATTATGAACTTTTTCT
16301 GGAAAAGCTG
Statistics
Matches: 164, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
153 53 0.32
154 111 0.68
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (153 bp):
TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTG
GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
TTCCTCTTCCTTCTTCAGATGAG
Found at i:16478 original size:225 final size:228
Alignment explanation
Indices: 16123--16558 Score: 790
Period size: 225 Copynumber: 1.9 Consensus size: 228
16113 TTCAGATGAG
*
16123 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
16188 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
16253 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTTCTGGAAAAGCTGATCCAT
131 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTGAAAAAGCTGATCCAT
*
16317 CAAATGATTGATTTGAGCAAAAGGTTGAACAAA
196 CAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
16350 TTCTTCTCATTATGTA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTTC
1 TTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTC
16413 TGG-AAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
65 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
*
16477 ATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTGAAAAAGCTGATCCA
130 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTGAAAAAGCTGATCCA
16542 TCAAATGATGGATTTGA
195 TCAAATGATGGATTTGA
16559 ATCTTTGAAA
Statistics
Matches: 202, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
225 102 0.50
226 49 0.24
227 51 0.25
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (228 bp):
TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTGAAAAAGCTGATCCAT
CAAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:16481 original size:112 final size:114
Alignment explanation
Indices: 16123--16558 Score: 790
Period size: 113 Copynumber: 3.9 Consensus size: 114
16113 TTCAGATGAG
*
16123 TTCTTCTCATTATGAACTTT-TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTC
1 TTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTC
16187 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
65 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
16237 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
*
16301 GGAAAAGCTGATCCATCAAATGATTGATTTGAGCAAAAGGTTGAACAAA
66 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
16350 TTCTTCTCATTATGTATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
16414 GG-AAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
16462 TTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
*
16527 GAAAAAGCTGATCCATCAAATGATGGATTTGA
66 GGAAAAGCTGATCCATCAAATGATGGATTTGA
16559 ATCTTTGAAA
Statistics
Matches: 312, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
112 100 0.32
113 131 0.42
114 81 0.26
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (114 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:16971 original size:22 final size:22
Alignment explanation
Indices: 16946--17000 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
16936 GATAAAGCTT
*
16946 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
16968 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
16990 TCATCTTTGAA
1 TCATCTTTGAA
17001 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:19740 original size:115 final size:114
Alignment explanation
Indices: 19539--19765 Score: 348
Period size: 115 Copynumber: 2.0 Consensus size: 114
19529 GACGATCATG
* *
19539 TTCATCTTTCTAATCCAATGATTGGTTTTGGAATTCTTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCTAATCCAATGATTGGTTTTGGAATTCATACCAAACCAGATCAGATAACTCAAAGA
*
19604 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
** *
19653 TTCATCTTT-TAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCATATCAGATAACTCAAA
1 TTCATCTTTCT-AATCCAATGATTGG-TTTTGGAATTCATACCAAACCAGATCAGATAACTCAAA
* * *
19717 GAACACTTCAAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
64 GAACACTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCA
19766 CATGGCATTT
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
113 1 0.01
114 23 0.23
115 78 0.76
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCTAATCCAATGATTGGTTTTGGAATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
Found at i:24831 original size:20 final size:20
Alignment explanation
Indices: 24802--24842 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
24792 GGAAATATGC
*
24802 AAATGTAAATACAAACGTAA
1 AAATGCAAATACAAACGTAA
* *
24822 AAATGCAAATGCAAATGTAA
1 AAATGCAAATACAAACGTAA
24842 A
1 A
24843 TATATGAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (20 bp):
AAATGCAAATACAAACGTAA
Found at i:24936 original size:7 final size:7
Alignment explanation
Indices: 24902--24943 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
24892 ATAAGAGTAT
24902 AAATGCA
1 AAATGCA
* *
24909 CAATGAA
1 AAATGCA
24916 AAATGCA
1 AAATGCA
24923 AAGATGCA
1 AA-ATGCA
24931 AAATGC-
1 AAATGCA
24937 AAATGCA
1 AAATGCA
24944 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:27345 original size:28 final size:28
Alignment explanation
Indices: 27313--27388 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
27303 TTATATGACT
* **
27313 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
27341 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
27370 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
27389 TAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:28732 original size:3 final size:3
Alignment explanation
Indices: 28726--28808 Score: 118
Period size: 3 Copynumber: 28.0 Consensus size: 3
28716 ATTATTTTTT
*
28726 TAA TAA TAA TAA TAA T-A TAA TAA T-A TATA TAA TGA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA
28771 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28809 ATAAATAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
2 6 0.08
3 61 0.84
4 6 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28813 original size:4 final size:4
Alignment explanation
Indices: 28804--28829 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28794 TAATAATAAT
28804 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
28830 ATTGGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:28820 original size:36 final size:36
Alignment explanation
Indices: 28727--28828 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 36
28717 TTATTTTTTT
* *
28727 AATAATAATAATAATATAATAATATAT-ATAATGAT
1 AATAATAATAATAATATAATAATAAATAATAATAAT
28762 AATATATAATAATAATATAATAAT-AATAATAATAAT
1 AATA-ATAATAATAATATAATAATAAATAATAATAAT
28798 AATAATAATAAATAA-ATAAATAAATAAATAA
1 AATAATAAT-AATAATAT-AAT-AATAAATAA
28829 AATTGGTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
35 13 0.22
36 38 0.64
37 3 0.05
38 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (36 bp):
AATAATAATAATAATATAATAATAAATAATAATAAT
Found at i:40501 original size:42 final size:42
Alignment explanation
Indices: 40454--40544 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
40444 TACAAACGCA
* **
40454 ACAATAGAGTA-GTAATTATGCGGCGTTTTTAGCCCAAATGCC
1 ACAATAGAGTAGGTAATTA-GCGGCGTTTGTAGCAAAAATGCC
* *
40496 GCAATAGAGTAGGTATTTAGCGGCGTTTGTAGCAAAAATGCC
1 ACAATAGAGTAGGTAATTAGCGGCGTTTGTAGCAAAAATGCC
40538 ACAATAG
1 ACAATAG
40545 GGTTTTTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 36 0.86
43 6 0.14
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (42 bp):
ACAATAGAGTAGGTAATTAGCGGCGTTTGTAGCAAAAATGCC
Found at i:43334 original size:13 final size:13
Alignment explanation
Indices: 43316--43340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43306 CAAAATACGT
43316 TTTTCATTAACCC
1 TTTTCATTAACCC
43329 TTTTCATTAACC
1 TTTTCATTAACC
43341 TCATTATCGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTCATTAACCC
Found at i:45320 original size:19 final size:20
Alignment explanation
Indices: 45288--45351 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
45278 GGAGTACATA
*
45288 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGAGCCG
*
45308 ATGCGGT-TGATGCGGGCCG
1 ATGCGGTCTGATGCGAGCCG
* * * *
45327 ATGCGGGCCGATGCGTGGCG
1 ATGCGGTCTGATGCGAGCCG
45347 ATGCG
1 ATGCG
45352 TTTAGTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.12, C:0.23, G:0.44, T:0.20
Consensus pattern (20 bp):
ATGCGGTCTGATGCGAGCCG
Found at i:45352 original size:10 final size:10
Alignment explanation
Indices: 45316--45351 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
45306 CGATGCGGTT
45316 GATGCGGGCC
1 GATGCGGGCC
45326 GATGCGGGCC
1 GATGCGGGCC
45336 GATGCGTGG-C
1 GATGCG-GGCC
45346 GATGCG
1 GATGCG
45352 TTTAGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 23 0.92
11 2 0.08
ACGTcount: A:0.11, C:0.25, G:0.50, T:0.14
Consensus pattern (10 bp):
GATGCGGGCC
Found at i:47396 original size:63 final size:63
Alignment explanation
Indices: 47315--47440 Score: 182
Period size: 63 Copynumber: 2.0 Consensus size: 63
47305 AAAGTTAAAA
* *
47315 AAATTAAAGCTTATGTTTAGGTTCTAATTTTCTCTATAATATTAGCAATTAA-ATGTGAAATT
1 AAATTAAAGCTTATGTTTAGGTTCTAATTTTATCTATAATATAAGCAATTAACATGTGAAATT
* * * *
47377 AAATGTAATGCTTCTGTTTAGGTTCTAATTTTATTTATAATATAAGCAATTAACATTTGAAATT
1 AAAT-TAAAGCTTATGTTTAGGTTCTAATTTTATCTATAATATAAGCAATTAACATGTGAAATT
47441 GAAACTCCAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 4 0.07
63 43 0.77
64 9 0.16
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (63 bp):
AAATTAAAGCTTATGTTTAGGTTCTAATTTTATCTATAATATAAGCAATTAACATGTGAAATT
Found at i:54906 original size:14 final size:14
Alignment explanation
Indices: 54887--54917 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54877 ATCTACTTTA
54887 CTTTTTCACCTCAC
1 CTTTTTCACCTCAC
*
54901 CTTTTTCACTTCAC
1 CTTTTTCACCTCAC
54915 CTT
1 CTT
54918 CATTCATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.39, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTTTTCACCTCAC
Found at i:60562 original size:45 final size:45
Alignment explanation
Indices: 60506--60765 Score: 416
Period size: 45 Copynumber: 5.8 Consensus size: 45
60496 TATAAAATTT
*
60506 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTACTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
60551 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
60596 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACTAATATA
1 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
60641 CTTACCATTTACTACATAAGCTCGTAAGTTTATTTTACCAATATA
1 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
60686 CTTACCATTTACTCCATAAGCTCGTAAACTTATTTTACCAATATA
1 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
** *
60731 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTT
60766 CATGTTTACC
Statistics
Matches: 201, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
44 26 0.13
45 172 0.86
46 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:60918 original size:40 final size:40
Alignment explanation
Indices: 60839--60918 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
60829 ATAGGAGTCA
* * *
60839 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
* * *
60879 AATAATGCACCGTAGTGCTGAGGTCGGGTTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
60919 TGTACACTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
Found at i:67158 original size:21 final size:21
Alignment explanation
Indices: 67140--67199 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
67130 ATGAAGCAAG
*
67140 GGAAACAGAGAGAGCAGCAGC
1 GGAAACACAGAGAGCAGCAGC
* *
67161 GGAAGCACAGAGAGCAGC-TC
1 GGAAACACAGAGAGCAGCAGC
* *
67181 GGAAGCACAGAGAGAAGCA
1 GGAAACACAGAGAGCAGCA
67200 ACATATCAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.42, C:0.20, G:0.37, T:0.02
Consensus pattern (21 bp):
GGAAACACAGAGAGCAGCAGC
Found at i:67185 original size:20 final size:21
Alignment explanation
Indices: 67148--67199 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
67138 AGGGAAACAG
67148 AGAGAGCAGCAGCGGAAGCAC
1 AGAGAGCAGCAGCGGAAGCAC
*
67169 AGAGAGCAGC-TCGGAAGCAC
1 AGAGAGCAGCAGCGGAAGCAC
*
67189 AGAGAGAAGCA
1 AGAGAGCAGCA
67200 ACATATCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.40, C:0.21, G:0.37, T:0.02
Consensus pattern (21 bp):
AGAGAGCAGCAGCGGAAGCAC
Found at i:67600 original size:44 final size:44
Alignment explanation
Indices: 67544--67692 Score: 226
Period size: 44 Copynumber: 3.4 Consensus size: 44
67534 AAAAATGCCA
* *
67544 CTATATACAAGTCCTTTAGCGACGTTTATATCCGATAAACGCCG
1 CTATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCG
* * * *
67588 CTATATACAAGTCCTTTAGAGGCGTTTATATACGACAAATGCTG
1 CTATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCG
*
67632 ATATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCG
1 CTATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCG
*
67676 CTATATACAAGACCTTT
1 CTATATACAAGTCCTTT
67693 TACAGTATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 92 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (44 bp):
CTATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCG
Found at i:67708 original size:44 final size:43
Alignment explanation
Indices: 67534--67766 Score: 198
Period size: 44 Copynumber: 5.3 Consensus size: 43
67524 GGCGTTTGTA
* * *
67534 AAAAATGCCACTATATACAAGTCCTTTAGC-GACGTTTATATCCG
1 AAAAACGCCGCTATATACAAGACCTTTA-CAG-CGTTTATATCCG
* * * *
67578 ATAAACGCCGCTATATACAAGTCCTTTAGAGGCGTTTATATACG
1 AAAAACGCCGCTATATACAAGACCTTTACA-GCGTTTATATCCG
* * * * * *
67622 ACAAATGCTGATATATACAAGTCCTTTAGCGGCGTTTATATCCG
1 AAAAACGCCGCTATATACAAGACCTTTA-CAGCGTTTATATCCG
* ** * *
67666 ACAAACGCCGCTATATACAAGACCTTTTACAGTATTTGTATCCA
1 AAAAACGCCGCTATATACAAGACC-TTTACAGCGTTTATATCCG
* * * * *
67710 AAAAACACCGCTATATACCACACCTATTGCAGCGTTTGTATCCG
1 AAAAACGCCGCTATATACAAGACCT-TTACAGCGTTTATATCCG
67754 AAAAACGCCGCTA
1 AAAAACGCCGCTA
67767 AATATCTTAA
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
43 1 0.01
44 148 0.96
45 5 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
AAAAACGCCGCTATATACAAGACCTTTACAGCGTTTATATCCG
Found at i:67725 original size:88 final size:88
Alignment explanation
Indices: 67544--67766 Score: 234
Period size: 88 Copynumber: 2.5 Consensus size: 88
67534 AAAAATGCCA
* * * *
67544 CTATATACAAGTCCTTTAGCGACGTTTATATCCGATAAACGCCGCTATATACAAGTCCTTTAGAG
1 CTATATACAAGTCCTTTAGCGGCGTTTATATCCGAAAAACGCCGCTATATACAAGACCTTTACAG
* * * ** *
67609 GCGTTTATATACGACAAATGCTG
66 GCATTTATATACAAAAAACACCG
* *
67632 ATATATACAAGTCCTTTAGCGGCGTTTATATCCGACAAACGCCGCTATATACAAGACCTTTTACA
1 CTATATACAAGTCCTTTAGCGGCGTTTATATCCGAAAAACGCCGCTATATACAAGACC-TTTACA
* * *
67697 -GTATTTGTATCCAAAAAACACCG
65 GGCATTTATATACAAAAAACACCG
* ** * *
67720 CTATATACCACACCTATT-GCAGCGTTTGTATCCGAAAAACGCCGCTA
1 CTATATACAAGTCCT-TTAGCGGCGTTTATATCCGAAAAACGCCGCTA
67767 AATATCTTAA
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
88 105 0.94
89 7 0.06
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (88 bp):
CTATATACAAGTCCTTTAGCGGCGTTTATATCCGAAAAACGCCGCTATATACAAGACCTTTACAG
GCATTTATATACAAAAAACACCG
Found at i:68391 original size:78 final size:78
Alignment explanation
Indices: 68262--68408 Score: 195
Period size: 78 Copynumber: 1.9 Consensus size: 78
68252 GTTAACACAG
* * * * * * *
68262 ACACCTTACTGTTCCAATGTATGATGCTATATGGATTGGACATTGTATTGATCATTGGTTTGATG
1 ACACCTTACTGTTCCAATGCATGATACTATATGAATTAGACATTATATTGATAATTGGTATGATG
68327 CTTAGAGTTCCAT
66 CTTAGAGTTCCAT
* * * *
68340 ACACCTTATTGTTCCAATGCATGATACTATGTGAATTAGATATTATGTTGATAATTGGTATGATG
1 ACACCTTACTGTTCCAATGCATGATACTATATGAATTAGACATTATATTGATAATTGGTATGATG
68405 CTTA
66 CTTA
68409 ATGGATCGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 58 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (78 bp):
ACACCTTACTGTTCCAATGCATGATACTATATGAATTAGACATTATATTGATAATTGGTATGATG
CTTAGAGTTCCAT
Found at i:70805 original size:40 final size:40
Alignment explanation
Indices: 70741--70850 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
70731 TTGATACTAT
* *
70741 AATTACAATACTAGTATTAGAATTATAGTACAAATATTGG
1 AATTACAATACTAGTACTAGAATTACAGTACAAATATTGG
* * * *
70781 AATTACAATATTGGTACTATAATTACAGTACCAATATTGG
1 AATTACAATACTAGTACTAGAATTACAGTACAAATATTGG
* * *
70821 AATTACAATACCAGTACTGGAATTAAAGTA
1 AATTACAATACTAGTACTAGAATTACAGTA
70851 TCGATATTGG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (40 bp):
AATTACAATACTAGTACTAGAATTACAGTACAAATATTGG
Found at i:70841 original size:20 final size:20
Alignment explanation
Indices: 70741--70845 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
70731 TTGATACTAT
* *
70741 AATTACAATACTAGTATTAG
1 AATTACAATACCAGTATTGG
* * * *
70761 AATTATAGTACAAATATTGG
1 AATTACAATACCAGTATTGG
*** * **
70781 AATTACAATATTGGTACTAT
1 AATTACAATACCAGTATTGG
* *
70801 AATTACAGTACCAATATTGG
1 AATTACAATACCAGTATTGG
*
70821 AATTACAATACCAGTACTGG
1 AATTACAATACCAGTATTGG
70841 AATTA
1 AATTA
70846 AAGTATCGAT
Statistics
Matches: 60, Mismatches: 25, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (20 bp):
AATTACAATACCAGTATTGG
Found at i:70842 original size:60 final size:60
Alignment explanation
Indices: 70725--70845 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
70715 TACTTGATGA
* * * * *
70725 ACAATATTGATACTATAATTACAATACTAGTATTAGAATTATAGTACAAATATTGGAATT
1 ACAATATTGATACTATAATTACAATACCAATATTAGAATTACAATACAAATACTGGAATT
* * * * *
70785 ACAATATTGGTACTATAATTACAGTACCAATATTGGAATTACAATACCAGTACTGGAATT
1 ACAATATTGATACTATAATTACAATACCAATATTAGAATTACAATACAAATACTGGAATT
70845 A
1 A
70846 AAGTATCGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (60 bp):
ACAATATTGATACTATAATTACAATACCAATATTAGAATTACAATACAAATACTGGAATT
Found at i:71789 original size:17 final size:19
Alignment explanation
Indices: 71767--71805 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
71757 GAGTGTTATC
71767 ATTGTGT-TTG-TATGATG
1 ATTGTGTGTTGATATGATG
71784 ATTGTGTGTTGCATATGATG
1 ATTGTGTGTTG-ATATGATG
71804 AT
1 AT
71806 GCATTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
20 9 0.47
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.49
Consensus pattern (19 bp):
ATTGTGTGTTGATATGATG
Done.