Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001935.1 Hibiscus syriacus cultivar Beakdansim tig00003920_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: 109471
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:3818 original size:64 final size:65
Alignment explanation
Indices: 3690--3836 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 65
3680 TTCTTGTATT
* *
3690 TAATGTTAATAAAAATTAACTTTTAATGAGAATAAGTTTATAAAAAAAATTTAATTTTAGTTCAT
1 TAAT-TTAATAAAAA-TAACTTTAAATGAAAATAAGTTTATAAAAAAAATTTAATTTTAGTTCAT
3755 ATA
64 A-A
* * * * * *
3758 TATTTTAATAAAAATAGCTTTAAAT-AAAATAATTTTATCAAATATA-TTAATTTTAGTTCATAA
1 TAATTTAATAAAAATAACTTTAAATGAAAATAAGTTTATAAAAAAAATTTAATTTTAGTTCATAA
3821 TAATTTAATAATAAAT
1 TAATTTAATAA-AAAT
3837 TTTAATGGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 11 0.16
64 20 0.29
65 16 0.23
66 9 0.13
67 10 0.14
68 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (65 bp):
TAATTTAATAAAAATAACTTTAAATGAAAATAAGTTTATAAAAAAAATTTAATTTTAGTTCATAA
Found at i:14343 original size:28 final size:29
Alignment explanation
Indices: 14294--14349 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
14284 GGATAGATTT
* *
14294 AATATTTATATTAAATTCATATTTTTTAA
1 AATATTTAAATTAAATTCATATTATTTAA
14323 AATATTATAAATTAAA-T-ATATTATTTA
1 AATATT-TAAATTAAATTCATATTATTTA
14350 GTTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 7 0.29
30 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
AATATTTAAATTAAATTCATATTATTTAA
Found at i:14490 original size:68 final size:64
Alignment explanation
Indices: 14413--14548 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 64
14403 GTTTATTATC
* * * *
14413 TATTTAATTTTGAATATTAAAAGATA-ATTATATCTTTTTTTTAAATATTTTAAAATTAAAATAA
1 TATTTAATTTTAAATAGTAAAAGA-AGATTATAT-ATATTTTTAAATATTTT-AAATTAAAAT-A
14477 TAT
62 TAT
* *
14480 ATATTTAATTTTAAATAGTAAAAGAAGTTTATATATATTTTTGAATATTTTAAATTAAAATATAT
1 -TATTTAATTTTAAATAGTAAAAGAAGATTATATATATTTTTAAATATTTTAAATTAAAATATAT
14545 TATT
1 TATT
14549 ATATGTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
64 4 0.07
65 4 0.07
66 10 0.16
67 15 0.25
68 28 0.46
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (64 bp):
TATTTAATTTTAAATAGTAAAAGAAGATTATATATATTTTTAAATATTTTAAATTAAAATATAT
Found at i:26219 original size:19 final size:19
Alignment explanation
Indices: 26195--26235 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
26185 CAAATTAATG
*
26195 AAAGAAAACTGTAATCTTC
1 AAAGAAAAATGTAATCTTC
* *
26214 AAAGAAAAATGTCATTTTC
1 AAAGAAAAATGTAATCTTC
26233 AAA
1 AAA
26236 TTTCAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (19 bp):
AAAGAAAAATGTAATCTTC
Found at i:30943 original size:21 final size:21
Alignment explanation
Indices: 30904--30944 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30894 CCTAGAGAGA
* * *
30904 GTATTGATACTCTAGTTAAGG
1 GTATCGATACTCAACTTAAGG
30925 GTATCGATACTCAACTTAAG
1 GTATCGATACTCAACTTAAG
30945 TTTCTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCAACTTAAGG
Found at i:36442 original size:66 final size:66
Alignment explanation
Indices: 36248--36432 Score: 361
Period size: 66 Copynumber: 2.8 Consensus size: 66
36238 CTTCTAAATC
36248 CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTTGCGTTATTTGAC
1 CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTTGCGTTATTTGAC
36313 A
66 A
36314 CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTTGCGTTATTTGAC
1 CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTTGCGTTATTTGAC
36379 A
66 A
*
36380 CTTACCATCCTTTCACCACTCCATTATCATTATTATCATAACATTTTTGACTT
1 CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTT
36433 ATGCTATTTG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 118 1.00
ACGTcount: A:0.26, C:0.25, G:0.05, T:0.44
Consensus pattern (66 bp):
CTTACCATCCTTTCACCACTCTATTATCATTATTATCATAACATTTTTGACTTGCGTTATTTGAC
A
Found at i:37086 original size:18 final size:18
Alignment explanation
Indices: 37049--37086 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
37039 TTTTAAGATT
*
37049 TTATATTCGATTTAAATA
1 TTATATTCGATTCAAATA
*
37067 TTATATTCGATTCAATTA
1 TTATATTCGATTCAAATA
37085 TT
1 TT
37087 CGAATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTCAAATA
Found at i:39063 original size:19 final size:20
Alignment explanation
Indices: 39039--39086 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
39029 AACGACTTTC
*
39039 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
39058 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
39078 TTTTGAAAA
1 TTTTGAAAA
39087 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:39196 original size:14 final size:14
Alignment explanation
Indices: 39177--39203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39167 AACAAAAGAA
39177 AAATAATTCATTTT
1 AAATAATTCATTTT
39191 AAATAATTCATTT
1 AAATAATTCATTT
39204 AGTTCAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATAATTCATTTT
Found at i:40200 original size:21 final size:21
Alignment explanation
Indices: 40174--40213 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40164 AAACAATTGG
40174 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
40195 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
40214 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:40492 original size:20 final size:20
Alignment explanation
Indices: 40467--40519 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
40457 AATGCACTTA
40467 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
40487 GTGCATCGATGCATTCTGTT
1 GTGCATCGATGCATCCTGCT
*
40507 GTGCATCCATGCA
1 GTGCATCGATGCA
40520 CGAAGGCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:46961 original size:23 final size:23
Alignment explanation
Indices: 46929--47012 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
46919 TTGGTGCAGA
46929 GGGAATCGATACCCCCCTTGAAG
1 GGGAATCGATACCCCCCTTGAAG
* * *
46952 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCCCTTGAAG
* *
46975 GGGAATCGATTCCCCCC-TGTAG
1 GGGAATCGATACCCCCCTTGAAG
*
46997 AGGAATCGATACCCCC
1 GGGAATCGATACCCCC
47013 TGGAGGTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 18 0.34
23 35 0.66
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTGAAG
Found at i:47686 original size:21 final size:21
Alignment explanation
Indices: 47660--47709 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
47650 GTCTCATAAA
47660 CATTCTAGAGCTTCCTCTAGT
1 CATTCTAGAGCTTCCTCTAGT
47681 CATTCTAGAGCTTCCTCTAGT
1 CATTCTAGAGCTTCCTCTAGT
*
47702 CGTTCTAG
1 CATTCTAG
47710 CCAACCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.28, G:0.16, T:0.38
Consensus pattern (21 bp):
CATTCTAGAGCTTCCTCTAGT
Found at i:48956 original size:28 final size:28
Alignment explanation
Indices: 48925--48992 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
48915 CTTAGATTGT
48925 TGGATGTTTGAATTTGTTTGATGGATTA
1 TGGATGTTTGAATTTGTTTGATGGATTA
48953 TGGATGTTTGAATTTGTTTGATGGATTA
1 TGGATGTTTGAATTTGTTTGATGGATTA
*
48981 TGGATGCTTGAA
1 TGGATGTTTGAA
48993 CTTATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.47
Consensus pattern (28 bp):
TGGATGTTTGAATTTGTTTGATGGATTA
Found at i:50943 original size:23 final size:23
Alignment explanation
Indices: 50912--50969 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
50902 TATGTGGTCA
*
50912 TTCGGGACATTTCTACGTTGTCC
1 TTCGTGACATTTCTACGTTGTCC
50935 TTCGTGACATTTCTACGTTGTCC
1 TTCGTGACATTTCTACGTTGTCC
50958 TTCGTGACATTT
1 TTCGTGACATTT
50970 GAGATGGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (23 bp):
TTCGTGACATTTCTACGTTGTCC
Found at i:51586 original size:18 final size:18
Alignment explanation
Indices: 51551--51589 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
51541 GTAAACTTTT
* *
51551 TTATTTAATGTATGTAAA
1 TTATTCAATATATGTAAA
*
51569 TTATTCAATATATTTAAA
1 TTATTCAATATATGTAAA
51587 TTA
1 TTA
51590 AGTCTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTATTCAATATATGTAAA
Found at i:51956 original size:8 final size:8
Alignment explanation
Indices: 51940--51973 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
51930 TGTGTGACTT
*
51940 GCAAATTG
1 GCAAGTTG
51948 GCAAGTTG
1 GCAAGTTG
51956 GCAAGTTG
1 GCAAGTTG
*
51964 ACAAGTTG
1 GCAAGTTG
51972 GC
1 GC
51974 TTGCCAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (8 bp):
GCAAGTTG
Found at i:52022 original size:49 final size:50
Alignment explanation
Indices: 51960--52062 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 50
51950 AAGTTGGCAA
*
51960 GTTGACAAGTTGGC-TTGCCAACTTGTGCACATGGGATAATTCATCTTTG
1 GTTGACAAGTTGGCATGGCCAACTTGTGCACATGGGATAATTCATCTTTG
* * **
52009 GTTGGCAAGTTGGCAAGTGGTCAACTTGTGCACATGGGATTTTTCATCTTTG
1 GTTGACAAGTTGGC-A-TGGCCAACTTGTGCACATGGGATAATTCATCTTTG
52061 GT
1 GT
52063 CCCTAAACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 13 0.28
52 33 0.72
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (50 bp):
GTTGACAAGTTGGCATGGCCAACTTGTGCACATGGGATAATTCATCTTTG
Found at i:54160 original size:14 final size:14
Alignment explanation
Indices: 54143--54170 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54133 ACATTTTACT
54143 GTTATCATTTAATA
1 GTTATCATTTAATA
54157 GTTATCATTTAATA
1 GTTATCATTTAATA
54171 TACTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
GTTATCATTTAATA
Found at i:54424 original size:23 final size:23
Alignment explanation
Indices: 54381--54427 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54371 ATGTACATTT
*
54381 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTAAAAAGAAAAAAA
*
54404 TACATAAC-TAAAAATATAAAAAA
1 TACATAACTTAAAAAGA-AAAAAA
54427 T
1 T
54428 TTATATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (23 bp):
TACATAACTTAAAAAGAAAAAAA
Found at i:58242 original size:2 final size:2
Alignment explanation
Indices: 58235--58263 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58225 TTACATTAAC
58235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58264 CAAATCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58638 original size:13 final size:13
Alignment explanation
Indices: 58584--58638 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
58574 AAGATGACGT
*
58584 GCATTTATAACGT
1 GCATTTATAACGC
* *
58597 GCATTTATGATGC
1 GCATTTATAACGC
* **
58610 GCATTTATGATAC
1 GCATTTATAACGC
58623 GCATTTATAACGC
1 GCATTTATAACGC
58636 GCA
1 GCA
58639 CACATTTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (13 bp):
GCATTTATAACGC
Found at i:61157 original size:18 final size:17
Alignment explanation
Indices: 61103--61151 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
61093 TTGGACCCTT
* *
61103 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
61121 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
61139 AGTGCATTCGATG
1 AGTGCA-TCGATG
61152 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:61256 original size:65 final size:64
Alignment explanation
Indices: 61099--61282 Score: 205
Period size: 65 Copynumber: 2.8 Consensus size: 64
61089 ACCGTTGGAC
* *
61099 CCTTAGTGCATCGGTGCACT-AAGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATA
1 CCTTAGTGCATCGGTGCA-TGTA-AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATA
61162 G
64 G
** * * *
61163 CCAGAGTGCATCGATGCATAGCT-GGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAA-
1 CCTTAGTGCATCGGTGCAT-G-TAAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAAT
*
61226 AT
63 AG
*
61228 CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGCATTCGATGTT
1 CCTTAGTGCATCGGTGCAT-GTAAGTGCATCGATGCATCAAATGCATTCGATGTT
61283 CAATTTAATT
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
63 1 0.01
64 43 0.43
65 52 0.53
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
CCTTAGTGCATCGGTGCATGTAAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAG
Found at i:61301 original size:45 final size:45
Alignment explanation
Indices: 61251--61356 Score: 203
Period size: 45 Copynumber: 2.4 Consensus size: 45
61241 GTGCATGGTA
61251 AGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
1 AGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
61296 AGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
1 AGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
*
61341 GGTGCATCGATGCATG
1 AGTGCATCGATGCATG
61357 GATTGGTGCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (45 bp):
AGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
Found at i:65628 original size:18 final size:18
Alignment explanation
Indices: 65584--65628 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
65574 AGCACACAAC
*
65584 TGTGGGGATTCTTGATTA
1 TGTGGGCATTCTTGATTA
65602 TGT--GCATTC-TGATGTA
1 TGTGGGCATTCTTGAT-TA
65618 TGTGGGCATTC
1 TGTGGGCATTC
65629 CACGACATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
18 9 0.39
ACGTcount: A:0.16, C:0.11, G:0.31, T:0.42
Consensus pattern (18 bp):
TGTGGGCATTCTTGATTA
Found at i:67840 original size:44 final size:44
Alignment explanation
Indices: 67777--67864 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
67767 AAGAAGCTTT
*
67777 ATGGCTTACTAGTTTAGTGAAGGAATTGGGTGTTCAGCAAGGTG
1 ATGGCTTACTAGTTTAGTGAAGGAATTGGATGTTCAGCAAGGTG
67821 ATGGCTTACTAGTTTAGTGAAGGAATTGGATGTTCAGCAAGGTG
1 ATGGCTTACTAGTTTAGTGAAGGAATTGGATGTTCAGCAAGGTG
67865 GAGTTTAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.32
Consensus pattern (44 bp):
ATGGCTTACTAGTTTAGTGAAGGAATTGGATGTTCAGCAAGGTG
Found at i:70091 original size:20 final size:20
Alignment explanation
Indices: 70066--70134 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
70056 GATAAACAAA
70066 TATCTATACTGGAGGACTAG
1 TATCTATACTGGAGGACTAG
**
70086 TATCTATACTGGATAAACTAG
1 TATCTATACTGGA-GGACTAG
* * *
70107 TAACCATGCTGGAGGACT-G
1 TATCTATACTGGAGGACTAG
70126 ATATCTATA
1 -TATCTATA
70135 TTGAATGAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 21 0.57
21 15 0.41
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (20 bp):
TATCTATACTGGAGGACTAG
Found at i:70101 original size:41 final size:41
Alignment explanation
Indices: 70056--70134 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
70046 ATCCATACAA
* *
70056 GATAAACAAATATCTATACTGGAGGACT-AGTATCTATACTG
1 GATAAACAAATAACCATACTGGAGGACTGA-TATCTATACTG
* * *
70097 GATAAACTAGTAACCATGCTGGAGGACTGATATCTATA
1 GATAAACAAATAACCATACTGGAGGACTGATATCTATA
70135 TTGAATGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (41 bp):
GATAAACAAATAACCATACTGGAGGACTGATATCTATACTG
Found at i:70107 original size:21 final size:21
Alignment explanation
Indices: 70056--70108 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
70046 ATCCATACAA
* *
70056 GATAAACAAATATCTATACTG
1 GATAAACTAGTATCTATACTG
**
70077 GA-GGACTAGTATCTATACTG
1 GATAAACTAGTATCTATACTG
70097 GATAAACTAGTA
1 GATAAACTAGTA
70109 ACCATGCTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (21 bp):
GATAAACTAGTATCTATACTG
Found at i:75705 original size:21 final size:20
Alignment explanation
Indices: 75643--75710 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
75633 AATTTGTAAA
*
75643 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* ** * *
75663 TCACAATGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
75683 TCGCAACACAAAAGTCAAAAT
1 TCGCAACACAAAAGTC-AAAT
75704 TCGCAAC
1 TCGCAAC
75711 TGAATTTCAA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:75721 original size:40 final size:39
Alignment explanation
Indices: 75614--75724 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 39
75604 GGATCTAAAC
* * *
75614 AAGTCAAATTCGCAACGCGAATTTGTAAA-TCGCAACACAG
1 AAGTCAAATTCGCAAC-TGAATTT-CAAATTCGCAACACAA
* * *
75654 AAGTCAAATTCACAA-TGCGATAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACTG-AAT-TTCAAATTCGCAACACAA
75694 AAGTCAAAATTCGCAACTGAATTTCAAATTC
1 AAGTC-AAATTCGCAACTGAATTTCAAATTC
75725 CCAGCTGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.02
39 5 0.09
40 38 0.67
41 11 0.19
42 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (39 bp):
AAGTCAAATTCGCAACTGAATTTCAAATTCGCAACACAA
Found at i:75724 original size:19 final size:19
Alignment explanation
Indices: 75700--75742 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
75690 ACAAAAGTCA
*
75700 AAATTCGCAACTGAATTTC
1 AAATTCCCAACTGAATTTC
* *
75719 AAATTCCCAGCTGAATTTT
1 AAATTCCCAACTGAATTTC
75738 AAATT
1 AAATT
75743 AGCTACACGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (19 bp):
AAATTCCCAACTGAATTTC
Found at i:76520 original size:12 final size:12
Alignment explanation
Indices: 76499--76532 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
76489 ACCACATTTC
*
76499 CAATACCAAACA
1 CAATATCAAACA
76511 CAATATCAAACA
1 CAATATCAAACA
*
76523 CAATTTCAAA
1 CAATATCAAA
76533 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:78998 original size:18 final size:18
Alignment explanation
Indices: 78975--79010 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
78965 AAGCAAAAGG
*
78975 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
78993 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
79011 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:79321 original size:20 final size:20
Alignment explanation
Indices: 79296--79335 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
79286 ATATTGCGAT
* *
79296 CAACGCGAAAGTTAAATTCG
1 CAACGCAAAAGTCAAATTCG
79316 CAACGCAAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
79336 TAAACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
CAACGCAAAAGTCAAATTCG
Found at i:79344 original size:20 final size:20
Alignment explanation
Indices: 79297--79345 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
79287 TATTGCGATC
* * *
79297 AACGCGAAAGTTAAATTCGC
1 AACGCAAAAGTCAAATTCGA
79317 AACGCAAAAGTCAAATTCGTA
1 AACGCAAAAGTCAAATTCG-A
79338 AAC-CAAAA
1 AACGCAAAA
79346 TCGCGTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
AACGCAAAAGTCAAATTCGA
Found at i:79393 original size:53 final size:53
Alignment explanation
Indices: 79313--79425 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
79303 AAAGTTAAAT
*
79313 TCGCAACGCAAAAGTCAAATTCGTAAACCAAAATCGCGTTGTGAATTTGACTA
1 TCGCAACGCAAAAGTCAAATTCGTAAACCAAAATCGCGTTGCGAATTTGACTA
79366 TCGCAACGCAAAAGTCAAATTCGTAAACCAAAATCGCGTTGCGAATTTGACTA
1 TCGCAACGCAAAAGTCAAATTCGTAAACCAAAATCGCGTTGCGAATTTGACTA
79419 TCGCAAC
1 TCGCAAC
79426 ACTTATTTCG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (53 bp):
TCGCAACGCAAAAGTCAAATTCGTAAACCAAAATCGCGTTGCGAATTTGACTA
Found at i:81042 original size:21 final size:21
Alignment explanation
Indices: 80982--81049 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
80972 GTGAATCGGG
* * * *
80982 CTCTTAAACGGTTGGCGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
81003 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
81024 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
81045 TTCTT
1 CTCTT
81050 CAATGATGAG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:83215 original size:20 final size:20
Alignment explanation
Indices: 83203--83265 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
83193 AAACTTAAAT
83203 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
83223 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
83243 TCGCAACACGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
83262 TCGC
1 TCGC
83266 GTCGCGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 8 0.20
20 33 0.80
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:83781 original size:20 final size:20
Alignment explanation
Indices: 83756--84003 Score: 256
Period size: 20 Copynumber: 12.4 Consensus size: 20
83746 GCATAAAAAC
*
83756 ATTTGACTTTCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
83776 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
83796 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* *
83815 ATTT-ACAAATTT-GTGTTGTGA
1 ATTTGAC---TTTCGCGTTGCGA
* *
83836 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * *
83856 AATTGACTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
83876 ATTTGACTATCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCGA
*
83896 ATTTGACTTT-GTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
83915 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
83935 ATTTGACTATCACGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
83955 ATTTGA-TTATCGCATTGCGA
1 ATTTGACTT-TCGCGTTGCGA
83975 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
83995 ATTTGACTT
1 ATTTGACTT
84004 CTGTGTTGCG
Statistics
Matches: 195, Mismatches: 22, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.01
19 26 0.13
20 157 0.81
21 6 0.03
22 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:83899 original size:60 final size:60
Alignment explanation
Indices: 83756--84060 Score: 270
Period size: 60 Copynumber: 5.1 Consensus size: 60
83746 GCATAAAAAC
* * * *
83756 ATTTGACTTTCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCG-
1 ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATC-GCGTTGCGA
* * * * * * * *
83815 ATTT-ACAAATTTGTGTTGTGAATTTGACTTTTGTGTTGCGAAATTGACTATCGTGTTGCGA
1 ATTTGAC-TA-TCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGA
* *
83876 ATTTGACTATCGCGTTGCAAATTTGACTTT-GTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGA
* * *
83935 ATTTGACTATCACGTTGCGAATTTGA-TTATCGCATTGCGAATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGAATTTGACTT-TCGCGTTGCGAATTTGACTATCGCGTTGCGA
* * *
83995 ATTTGACT-TCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGATTTATAGA-T-TCGCGTTGCGA
1 ATTTGACTATC-GCGTTGCGAATTTGAC--TTTCGCGTTGCGAATT-T-GACTATCGCGTTGCGA
*
84055 AATTGA
1 ATTTGA
84061 AAACTGGGTT
Statistics
Matches: 207, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
58 5 0.02
59 62 0.30
60 126 0.61
61 10 0.05
62 4 0.02
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (60 bp):
ATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:84013 original size:40 final size:40
Alignment explanation
Indices: 83756--84060 Score: 254
Period size: 40 Copynumber: 7.7 Consensus size: 40
83746 GCATAAAAAC
*
83756 ATTTGACTT-TCGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTCT-GCGTTGCGAATTTGACTATCGCGTTGCGA
* * * * *
83796 ATTTGACTTCTGTGTTGCG-ATTT-ACAAATTTGTGTTGTGA
1 ATTTGACTTCTGCGTTGCGAATTTGAC-TA-TCGCGTTGCGA
* * * *
83836 ATTTGACTTTTGTGTTGCGAAATTGACTATCGTGTTGCGA
1 ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTGCGA
* * *
83876 ATTTGACTATC-GCGTTGCAAATTTGACT-TTGTGTTGCGA
1 ATTTGACT-TCTGCGTTGCGAATTTGACTATCGCGTTGCGA
*
83915 ATTTGACTATC-GCGTTGCGAATTTGACTATCACGTTGCGA
1 ATTTGACT-TCTGCGTTGCGAATTTGACTATCGCGTTGCGA
* * *
83955 ATTTGA-TTATCGCATTGCGAATTTGACTTTCGCGTTGCGA
1 ATTTGACTTCT-GCGTTGCGAATTTGACTATCGCGTTGCGA
* *
83995 ATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTTCTGCGTTGCGAATTTGAC-TA-TCGCGTTGCGA
* *
84035 TTTATAGA-TTC-GCGTTGCGAAATTGA
1 ATT-T-GACTTCTGCGTTGCGAATTTGA
84061 AAACTGGGTT
Statistics
Matches: 217, Mismatches: 32, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
38 5 0.02
39 47 0.22
40 144 0.66
41 16 0.07
42 5 0.02
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:84031 original size:20 final size:20
Alignment explanation
Indices: 84008--84054 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
83998 TGACTTCTGT
84008 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
84028 GTTGCGATTTATAGATTCGC
1 GTTGCGATTTACAAATTCGC
84048 GTTGCGA
1 GTTGCGA
84055 AATTGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:89695 original size:12 final size:12
Alignment explanation
Indices: 89678--89702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89668 ACAATCGAGC
89678 TGATAAACAAGT
1 TGATAAACAAGT
89690 TGATAAACAAGT
1 TGATAAACAAGT
89702 T
1 T
89703 ACTCCTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TGATAAACAAGT
Found at i:97459 original size:2 final size:2
Alignment explanation
Indices: 97445--97485 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
97435 TTGAGTACAC
* *
97445 AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97486 TGTCAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:98070 original size:18 final size:18
Alignment explanation
Indices: 98047--98081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
98037 ATATTTATTA
98047 ATATTTCTAATAATATAT
1 ATATTTCTAATAATATAT
* *
98065 ATATTTTTAATATTATA
1 ATATTTCTAATAATATA
98082 ATAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTCTAATAATATAT
Found at i:98083 original size:26 final size:26
Alignment explanation
Indices: 98037--98143 Score: 71
Period size: 31 Copynumber: 4.0 Consensus size: 26
98027 AATATTTAAC
*
98037 ATATTTATTAATATTTCTAATAATATAT
1 ATATTT-TTAATA-TTATAATAATATAT
*
98065 ATATTTTTAATATTATAATAAAATAAT
1 ATATTTTTAATATTATAATAATAT-AT
* * *
98092 CAATTATATTATAATAATATAA-GATAT-T
1 --A-TAT-TTTTAATATTATAATAATATAT
98120 ATATTTTT-AT-TT-TAATAATATAT
1 ATATTTTTAATATTATAATAATATAT
98143 A
1 A
98144 ATAAATTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
21 3 0.05
22 5 0.08
23 4 0.06
24 3 0.05
25 3 0.05
26 11 0.17
27 8 0.13
28 7 0.11
29 1 0.02
30 6 0.10
31 12 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (26 bp):
ATATTTTTAATATTATAATAATATAT
Found at i:98226 original size:21 final size:21
Alignment explanation
Indices: 98186--98265 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 21
98176 ATTTCATAGA
* *
98186 AATAATATTATTAA-ATTATT
1 AATAATAATAATAATATTATT
98206 AATAATGAATAAT-ATATTATTT
1 AATAAT-AATAATAATATTA-TT
*
98228 AATAAATATTAATAATATT-TT
1 AAT-AATAATAATAATATTATT
98249 AATAATACATAA-AATAT
1 AATAATA-ATAATAATAT
98266 ACTAATTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 16 0.32
21 16 0.32
22 10 0.20
23 8 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
AATAATAATAATAATATTATT
Found at i:98240 original size:29 final size:28
Alignment explanation
Indices: 98190--98244 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
98180 CATAGAAATA
* *
98190 ATATTATTAAATTATTAATAATGAATAAT
1 ATATTATTAAATAAATAATAAT-AATAAT
* *
98219 ATATTATTTAATAAATATTAATAATA
1 ATATTATTAAATAAATAATAATAATA
98245 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.18
29 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATAAATAATAATAATAAT
Found at i:98381 original size:29 final size:30
Alignment explanation
Indices: 98317--98383 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
98307 TTAATAAATT
98317 TATAATA-TTTTATTTCAATAAAATAAAAA
1 TATAATATTTTTATTTCAATAAAATAAAAA
98346 TATTAATATTTTTA-TT-AATAAAATTATAAAA
1 TA-TAATATTTTTATTTCAATAAAA-TA-AAAA
98377 -ATAATAT
1 TATAATAT
98384 AATACTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
29 15 0.44
30 10 0.29
31 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
TATAATATTTTTATTTCAATAAAATAAAAA
Found at i:98630 original size:14 final size:14
Alignment explanation
Indices: 98611--98667 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
98601 TCTAGAAATG
*
98611 TAATTCATTTTCCA
1 TAATTCAATTTCCA
*
98625 TAATTCAAATTTCAA
1 TAATTC-AATTTCCA
* *
98640 TAATTTATTTTCCA
1 TAATTCAATTTCCA
*
98654 GAATTCAATTTCCA
1 TAATTCAATTTCCA
98668 GAAAACCAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (14 bp):
TAATTCAATTTCCA
Found at i:98653 original size:29 final size:28
Alignment explanation
Indices: 98611--98665 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
98601 TCTAGAAATG
*
98611 TAATTCATTTTCCATAATTCAAATTTCAA
1 TAATTCATTTTCCAGAATTC-AATTTCAA
*
98640 TAATTTATTTTCCAGAATTCAATTTC
1 TAATTCATTTTCCAGAATTCAATTTC
98666 CAGAAAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (28 bp):
TAATTCATTTTCCAGAATTCAATTTCAA
Found at i:98994 original size:2 final size:2
Alignment explanation
Indices: 98987--99028 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
98977 ATCCAATTCG
98987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99029 TTATTAGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104590 original size:101 final size:102
Alignment explanation
Indices: 104425--104957 Score: 461
Period size: 97 Copynumber: 5.4 Consensus size: 102
104415 TCGTTGATAG
* * *
104425 CCAGCCGTCCCTTCGCTATGAAGTTGAA--TGTGCTATCTCGAGTCCAATATCCTTCGCTGTGAA
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
104488 GTTGAAATTGGCTCTGAAA-TGGGAAGTTGTTGACAA
66 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGACAA
*
104524 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* * * *
104589 GTTGAGATTGACTCTGAAACT-----GTTGTTGACAG
66 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGACAA
* * * * * * *
104621 TCAGTCGCCCCTTCGCTGTGAAGTTGAGC-T-TG-TG-CTTGAGT--TATATCCTTAGCTGTGAA
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
104680 GTTGAAATTGGCTCTGAAATTGGGAAATGTTGTTGACAA
66 GTTGAAATTGGCTCTGAAATTGGG-AA-GTTGTTGACAA
* * * *
104719 CCAGCCGT-CCTTCGTTGTGAAGTTGAACTTG-GTGTATCTCGAGTCCAAAATCCTT-GTTGTGA
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGT-TGTCTCGAGTCCAATATCCTTCGCTGTGA
* ** *
104781 AGTTGAGATTGGCTCCAAAATT------TTGTTGACAG
65 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGACAA
* * * * * * *
104813 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGGGTAGCGCGATATCCTCCGTTGT
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGCTGT
* * ** *
104878 GGAGTT--TATCAGCTCTGAAATTGGGAAATTGTTCATTGACAA
63 GAAGTTGAAATTGGCTCTGAAATTGGG-AA--GTT-GTTGACAA
* *
104920 -CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTC
104958 GAATAGCACG
Statistics
Matches: 347, Mismatches: 54, Indels: 59
0.75 0.12 0.13
Matches are distributed among these distances:
91 34 0.10
93 6 0.02
94 17 0.05
95 31 0.09
96 3 0.01
97 64 0.18
98 24 0.07
99 36 0.10
100 1 0.00
101 56 0.16
102 26 0.07
103 7 0.02
106 36 0.10
107 6 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (102 bp):
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGACAA
Found at i:104731 original size:97 final size:99
Alignment explanation
Indices: 104379--104795 Score: 374
Period size: 97 Copynumber: 4.2 Consensus size: 99
104369 TCCTCCACCA
* ** * * * *
104379 TGAAGTTGAAATTGGCTCCGGAGCTGGGAAATTTGTTCGTTGATAGCCAGCCGTCCCTTCGCTAT
1 TGAAGTTGAAATTGGCT-CTGAAATGGGAAA--TGTT-GTTGACAACCAGCCGT-CCTTCGTTGT
* *
104444 GAAGTTGAA-TGTGCTATCTCGAGTCCAATATCCTTCGCTG
61 GAAGTTGAACT-TGTTGTCTCGAGT-CAATATCCTTCGCTG
104484 TGAAGTTGAAATTGGCTCTGAAATGGG-AA-GTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAG
1 TGAAGTTGAAATTGGCTCTGAAATGGGAAATGTTGTTGACAACCAGCCGT-CCTTCGTTGTGAAG
104547 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTG
65 TTGAAC-T-TGTTGTCTCGAGT-CAATATCCTTCGCTG
* * * ** * * *
104585 TGAAGTTGAGATTGACTCTG--A----AACTGTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAG
1 TGAAGTTGAAATTGGCTCTGAAATGGGAAATGTTGTTGACAACCAGCCG-TCCTTCGTTGTGAAG
* * * *
104644 TTGAGCTTG-TG-CTTGAGT-TATATCCTTAGCTG
65 TTGAACTTGTTGTCTCGAGTCAATATCCTTCGCTG
104676 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTGTTGACAACCAGCCGTCCTTCGTTGTGAAG
1 TGAAGTTGAAATTGGCTCTGAAA-TGGGAAATGTTGTTGACAACCAGCCGTCCTTCGTTGTGAAG
* * *
104741 TTGAACTTGGTGTATCTCGAGTCCAAAATCCTT-GTTG
65 TTGAACTT-GT-TGTCTCGAGT-CAATATCCTTCGCTG
*
104778 TGAAGTTGAGATTGGCTC
1 TGAAGTTGAAATTGGCTC
104796 CAAAATTTTG
Statistics
Matches: 258, Mismatches: 36, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
91 30 0.12
93 7 0.03
94 2 0.01
95 2 0.01
96 2 0.01
97 53 0.21
98 19 0.07
99 33 0.13
100 4 0.02
101 53 0.21
102 20 0.08
103 9 0.03
104 7 0.03
105 17 0.07
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (99 bp):
TGAAGTTGAAATTGGCTCTGAAATGGGAAATGTTGTTGACAACCAGCCGTCCTTCGTTGTGAAGT
TGAACTTGTTGTCTCGAGTCAATATCCTTCGCTG
Found at i:104809 original size:192 final size:192
Alignment explanation
Indices: 104471--104846 Score: 607
Period size: 192 Copynumber: 2.0 Consensus size: 192
104461 CTCGAGTCCA
*
104471 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAGTTGTTGACAACCAGCCGTCCCT
1 ATATCCTTAGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAGTTGTTGACAACCAGCCGTCCCT
* *
104536 TCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGAC
66 TCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAAATCCTTCGCTGTGAAGTTGAGATTGAC
* * *
104601 TCTGAAACTGTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTTGAGTT
131 TCTCAAAATGTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTTGAGTT
104663 ATATCCTTAGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTGTTGACAACCAGCCGT-
1 ATATCCTTAGCTGTGAAGTTGAAATTGGCTCTGAAA-TGGG-AA-GTTGTTGACAACCAGCCGTC
*
104727 CCTTCGTTGTGAAGTTGAACTTG-GTGTATCTCGAGTCCAAAATCCTT-GTTGTGAAGTTGAGAT
63 CCTTCGTTGTGAAGTTGAACTTGTGT-TATCTCGAGTCCAAAATCCTTCGCTGTGAAGTTGAGAT
* *
104790 TGGCTC-CAAAATTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
127 TGACTCTCAAAATGTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
104847 TTGTCTCGGG
Statistics
Matches: 171, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
192 82 0.48
193 26 0.15
194 44 0.26
195 19 0.11
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (192 bp):
ATATCCTTAGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAGTTGTTGACAACCAGCCGTCCCT
TCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAAATCCTTCGCTGTGAAGTTGAGATTGAC
TCTCAAAATGTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTTGAGTT
Found at i:105046 original size:39 final size:40
Alignment explanation
Indices: 104965--105074 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 40
104955 GTCGAATAGC
* * *
104965 ACGATATCCTCATCGTGGGGTTGTAATCGTGGATGTAGGGGT
1 ACGATATCC-CATCGTGGAGTTGAAATC-TAGATGTAGGGGT
*
105007 ACGATATCCCATCGTGGAGTTGAAAT-TAGATGTATGGGT
1 ACGATATCCCATCGTGGAGTTGAAATCTAGATGTAGGGGT
* *
105046 ACGACATCCTCCGTCGTGGAGTTGAAATC
1 ACGATAT-C-CCATCGTGGAGTTGAAATC
105075 GTTGATGACC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 17 0.29
40 1 0.02
41 32 0.54
42 9 0.15
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (40 bp):
ACGATATCCCATCGTGGAGTTGAAATCTAGATGTAGGGGT
Found at i:105815 original size:15 final size:15
Alignment explanation
Indices: 105780--105829 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
105770 TGAATCCACC
105780 TTTTTGTTC--TTCT
1 TTTTTGTTCTTTTCT
105793 TTCCTTTGTTCTTTTCT
1 TT--TTTGTTCTTTTCT
105810 TTTTTGTTCTTTCTCT
1 TTTTTGTTCTTT-TCT
105826 TTTT
1 TTTT
105830 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.06
15 17 0.53
16 7 0.22
17 6 0.19
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Done.