Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001881.1 Hibiscus syriacus cultivar Beakdansim tig00003821_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: 134940
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8634 original size:13 final size:13
Alignment explanation
Indices: 8616--8641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8606 GAGACGAGAT
8616 CTTTTAAAAATCA
1 CTTTTAAAAATCA
8629 CTTTTAAAAATCA
1 CTTTTAAAAATCA
8642 AATTGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CTTTTAAAAATCA
Found at i:13181 original size:33 final size:33
Alignment explanation
Indices: 13144--13209 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
13134 CTTGTTATTA
*
13144 GGGGCTTAATTTTTATTTTTGCCCAAGGCCATT
1 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
13177 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
1 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
13210 AAAATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (33 bp):
GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
Found at i:13774 original size:22 final size:22
Alignment explanation
Indices: 13743--13796 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
13733 AAATCTGAAA
*
13743 ATTTAAAAAAATTATA-AAAAAT
1 ATTTAGAAAAATTA-AGAAAAAT
*
13765 CTTTAGAAAAATTAAGAAAAAT
1 ATTTAGAAAAATTAAGAAAAAT
13787 ATTTAGAAAA
1 ATTTAGAAAA
13797 CTTTATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
ATTTAGAAAAATTAAGAAAAAT
Found at i:14353 original size:16 final size:16
Alignment explanation
Indices: 14332--14366 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
14322 TCTAGGGCAC
*
14332 AGTATTCTTTCATGTG
1 AGTATTCCTTCATGTG
14348 AGTATTCCTTCATGTG
1 AGTATTCCTTCATGTG
14364 AGT
1 AGT
14367 TTATACTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (16 bp):
AGTATTCCTTCATGTG
Found at i:17097 original size:117 final size:117
Alignment explanation
Indices: 16880--17110 Score: 356
Period size: 117 Copynumber: 2.0 Consensus size: 117
16870 TGGAAACTAG
* * * *
16880 TGCTTCAGGTCTGACTGTTGACTCTGTTAGTGCTACTGAGAAGAGTCATTCTCCATTAAGACTGG
1 TGCTTCAGGTCTAACTGTTGACACTGTTAGTGCTACTGAAAAGAGTCATACTCCATTAAGACTGG
* * *
16945 AGCAACATCTGAGTGATCAGAAATGCAACAATAGCCGAAATTCAGAAGGAAA
66 AACAACATCTGAGTGATCAGAAAGGAAACAATAGCCGAAATTCAGAAGGAAA
* *
16997 TGCTTCAGGTGTAACTGTTGACACTGTTAGTGCTGCTGAAAAGAGTCATACTCCATTAAGACTGG
1 TGCTTCAGGTCTAACTGTTGACACTGTTAGTGCTACTGAAAAGAGTCATACTCCATTAAGACTGG
*
17062 AACAA-ATTCTGAGTGATCAGAAAGGAAACATTAGCCGAAATTCAGAAGG
66 AACAACA-TCTGAGTGATCAGAAAGGAAACAATAGCCGAAATTCAGAAGG
17111 CAACGCTAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
116 1 0.01
117 102 0.99
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (117 bp):
TGCTTCAGGTCTAACTGTTGACACTGTTAGTGCTACTGAAAAGAGTCATACTCCATTAAGACTGG
AACAACATCTGAGTGATCAGAAAGGAAACAATAGCCGAAATTCAGAAGGAAA
Found at i:24551 original size:23 final size:23
Alignment explanation
Indices: 24533--24591 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
24523 CTCGTATAAA
24533 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
24556 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
24578 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
24592 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:24998 original size:2 final size:2
Alignment explanation
Indices: 24986--25059 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
24976 ATTTCATTTC
*
24986 AT AT CT 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
25028 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
25060 CCTCAAGATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25317 original size:18 final size:18
Alignment explanation
Indices: 25296--25330 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25286 TCCCATCTAG
25296 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
25314 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
25331 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:25939 original size:21 final size:21
Alignment explanation
Indices: 25915--25959 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25905 TCTTGTTCGT
* *
25915 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
25936 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
25957 TTG
1 TTG
25960 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:32787 original size:2 final size:2
Alignment explanation
Indices: 32780--32807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32770 TATGCAACTA
32780 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
32808 GAGTTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33072 original size:123 final size:125
Alignment explanation
Indices: 32849--33096 Score: 419
Period size: 123 Copynumber: 2.0 Consensus size: 125
32839 CTCTAGTTTT
* * *
32849 ACACAAATTTAAGATCGTTGGATGAGTGAAAATAGATAATTGAGATTGATTTCTCGTTTTTTTAT
1 ACACAAATTTAAGATCGTTAGATAAGTGAAAATAGATAATTGAAATTGATTTCTCGTTTTTTTAT
*
32914 TTGTAGTGAATATATTTTCAGTTCCTAATGATAATCTCAGCCATATATTTTCACACACAC
66 TTGTAGTGAATATATTTTCACTTCCTAATGATAATCTCAGCCATATATTTTCACACACAC
*
32974 ACACAAATTTAAGATCGTTAGATAAGTG-AAATAGATGATTGAAATTGATTTCTCG-TTTTTTAT
1 ACACAAATTTAAGATCGTTAGATAAGTGAAAATAGATAATTGAAATTGATTTCTCGTTTTTTTAT
* *
33037 TTGTAGTGATTATATTTTCACTTCCTAATGTTAATCTCAGCCATATATTTTCACACACAC
66 TTGTAGTGAATATATTTTCACTTCCTAATGATAATCTCAGCCATATATTTTCACACACAC
33097 GCGCATGCAC
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
123 65 0.56
124 25 0.22
125 26 0.22
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (125 bp):
ACACAAATTTAAGATCGTTAGATAAGTGAAAATAGATAATTGAAATTGATTTCTCGTTTTTTTAT
TTGTAGTGAATATATTTTCACTTCCTAATGATAATCTCAGCCATATATTTTCACACACAC
Found at i:33312 original size:2 final size:2
Alignment explanation
Indices: 33305--33396 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
33295 AAATTAAACC
33305 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
33347 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
33389 AT AT AT AT
1 AT AT AT AT
33397 TTAGGGGTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33736 original size:29 final size:29
Alignment explanation
Indices: 33703--33778 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
33693 TGATGACTAG
* *
33703 AAAAGTGTAGTGCCAAAAGCAATCTATTT
1 AAAAGTTTAGTGACAAAAGCAATCTATTT
*
33732 AAAAGTTTAGTGTCAAAAGCAATCTATTT
1 AAAAGTTTAGTGACAAAAGCAATCTATTT
33761 AAAAGTTTAGTGACAAAA
1 AAAAGTTTAGTGACAAAA
33779 TCGATAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (29 bp):
AAAAGTTTAGTGACAAAAGCAATCTATTT
Found at i:33789 original size:29 final size:29
Alignment explanation
Indices: 33703--33789 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
33693 TGATGACTAG
* * **
33703 AAAAGTGTAGTGCCAAAAGCAATCTATTT
1 AAAAGTTTAGTGACAAAAGCAATAAATTT
* **
33732 AAAAGTTTAGTGTCAAAAGCAATCTATTT
1 AAAAGTTTAGTGACAAAAGCAATAAATTT
* *
33761 AAAAGTTTAGTGACAAAATCGATAAATTT
1 AAAAGTTTAGTGACAAAAGCAATAAATTT
33790 CTAAAGTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (29 bp):
AAAAGTTTAGTGACAAAAGCAATAAATTT
Found at i:36392 original size:27 final size:25
Alignment explanation
Indices: 36345--36402 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
36335 ATTTTAAGAG
* *
36345 ATAAAAATATATTATTAATAAAAAT
1 ATAAAAATATATAAATAATAAAAAT
*
36370 ATAAAAATATATAACATATATAATAAT
1 ATAAAAATATATAA-ATA-ATAAAAAT
*
36397 TTAAAA
1 ATAAAA
36403 TTTTCAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 13 0.48
26 2 0.07
27 12 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
ATAAAAATATATAAATAATAAAAAT
Found at i:40347 original size:60 final size:60
Alignment explanation
Indices: 40253--40368 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
40243 TGGTCCCTTG
* * ** *
40253 ACTATAGGATGTTGTTTTATTGAGTCCCTTAACTATTAAAAGTTATGAAATAGTCAATTT
1 ACTATAGGATGTTGATTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCAATTT
*
40313 ACTATAGTG-TGTTGATTTGTTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCA
1 ACTATAG-GATGTTGATTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCA
40369 CCCAACTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (60 bp):
ACTATAGGATGTTGATTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCAATTT
Found at i:41049 original size:21 final size:21
Alignment explanation
Indices: 41023--41064 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41013 CCAGAATGGG
*
41023 GGGAATCGGTACCACTTCATA
1 GGGAATCGATACCACTTCATA
*
41044 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCACTTCATA
41065 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCACTTCATA
Found at i:41181 original size:19 final size:19
Alignment explanation
Indices: 41157--41226 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
41147 AACCATACAA
41157 GGGGAATCTGTACCCCTGG
1 GGGGAATCTGTACCCCTGG
* *
41176 GGGGAATATGT-TCCC---
1 GGGGAATCTGTACCCCTGG
41191 GGGGAAT-TGATACCCCCTGG
1 GGGGAATCTG-TA-CCCCTGG
41211 GGGGAATCTGTACCCC
1 GGGGAATCTGTACCCC
41227 CTGGACAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.05
15 8 0.20
17 3 0.07
18 3 0.07
19 14 0.34
20 9 0.22
21 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (19 bp):
GGGGAATCTGTACCCCTGG
Found at i:41216 original size:20 final size:20
Alignment explanation
Indices: 41191--41230 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41181 ATATGTTCCC
41191 GGGGAAT-TGATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
41211 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
41231 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:43963 original size:21 final size:21
Alignment explanation
Indices: 43937--43999 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
43927 CCAGAATGGG
*
43937 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
43958 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
43979 GGAAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
44000 ATATTCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:44153 original size:21 final size:21
Alignment explanation
Indices: 44129--44169 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44119 ATCTGTTCCC
44129 GGGGAA-CCGATACCCCCTGGG
1 GGGGAATCCG-TACCCCCTGGG
*
44150 GGGGAATCTGTACCCCCTGG
1 GGGGAATCCGTACCCCCTGG
44170 ACAATCTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.17, C:0.32, G:0.37, T:0.15
Consensus pattern (21 bp):
GGGGAATCCGTACCCCCTGGG
Found at i:47182 original size:13 final size:13
Alignment explanation
Indices: 47164--47189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47154 ATCTTAATAC
47164 TCAAATCCTTAAA
1 TCAAATCCTTAAA
47177 TCAAATCCTTAAA
1 TCAAATCCTTAAA
47190 ACCCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TCAAATCCTTAAA
Found at i:55758 original size:2 final size:2
Alignment explanation
Indices: 55745--55774 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55735 CATTTCCTCC
*
55745 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
55775 TGGCTCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:55926 original size:19 final size:19
Alignment explanation
Indices: 55902--55939 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55892 CTACAGGTGC
55902 CACTTATTCCTTTCTTCCA
1 CACTTATTCCTTTCTTCCA
55921 CACTTATTCCTTTCTTCCA
1 CACTTATTCCTTTCTTCCA
55940 TATGTTCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (19 bp):
CACTTATTCCTTTCTTCCA
Found at i:65479 original size:24 final size:23
Alignment explanation
Indices: 65435--65479 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
65425 AATAAAATAC
* * *
65435 AAAAATTCTATTTTTTTATTTAT
1 AAAAATTCAATTTTATAATTTAT
65458 AAAAACTTCAATTTTATAATTT
1 AAAAA-TTCAATTTTATAATTT
65480 TTCGCAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
AAAAATTCAATTTTATAATTTAT
Found at i:67801 original size:2 final size:2
Alignment explanation
Indices: 67794--67838 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
67784 AGATACATGC
67794 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
67836 TA T
1 TA T
67839 GCACGAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70092 original size:7 final size:7
Alignment explanation
Indices: 70080--70105 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
70070 TTTGTTGTTA
70080 AAAATTT
1 AAAATTT
70087 AAAATTT
1 AAAATTT
70094 AAAATTT
1 AAAATTT
70101 AAAAT
1 AAAAT
70106 AATATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:74670 original size:4 final size:4
Alignment explanation
Indices: 74658--74692 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
74648 TATATATATT
* *
74658 TATG CATG TATG TATA TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
74693 ACTTATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:74675 original size:20 final size:20
Alignment explanation
Indices: 74650--74693 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
74640 AACTACAATA
*
74650 TATATATTTATGCATGTATG
1 TATATATGTATGCATGTATG
*
74670 TATATATGTATGTATGTATG
1 TATATATGTATGCATGTATG
74690 TATA
1 TATA
74694 CTTATAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (20 bp):
TATATATGTATGCATGTATG
Found at i:75137 original size:18 final size:17
Alignment explanation
Indices: 75116--75154 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
75106 TTAAAACTAA
* *
75116 TAAAATATTAACTATTAT
1 TAAAATATAAAATATT-T
75134 TAAAATATAAAATATTT
1 TAAAATATAAAATATTT
75151 TAAA
1 TAAA
75155 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATATAAAATATTT
Found at i:77053 original size:3 final size:3
Alignment explanation
Indices: 77045--77076 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
77035 AACCAATCCA
77045 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
77077 GAAATGAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:87026 original size:12 final size:12
Alignment explanation
Indices: 87009--87040 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
86999 CTCTGTAATT
87009 TCTCTCTCTTTC
1 TCTCTCTCTTTC
87021 TCTCTCTCTTTC
1 TCTCTCTCTTTC
*
87033 TCACTCTC
1 TCTCTCTC
87041 AATTCGCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:90709 original size:29 final size:29
Alignment explanation
Indices: 90655--90860 Score: 136
Period size: 29 Copynumber: 7.0 Consensus size: 29
90645 TTCAATTTGG
* *
90655 TATTATTATCTT-CACTTAAAACTATATTT
1 TATTATTATCTTAAATTTAAAA-TATATTT
* *
90684 TATTCTTATTTTAAATTTAAAATATATATTT
1 TATTATTATCTTAAATTT-AAA-ATATATTT
* * * *
90715 TATTTTTGTCTT-AACTTATAAATCTATTT
1 TATTATTATCTTAAATTTA-AAATATATTT
* * *
90744 TATTCTTAT-TTTAATATAAAA-ATATTT
1 TATTATTATCTTAAATTTAAAATATATTT
* * * * *
90771 TATTATTGTCTTCACTTAAAAATATCTTT
1 TATTATTATCTTAAATTTAAAATATATTT
90800 TATTATTAT-TATAAA-TTAAATATATATTT
1 TATTATTATCT-TAAATTTAAA-ATATATTT
* *
90829 TATTAGTATCTTAACTTTTTAAAATATATTT
1 TATTATTATCTTAA--ATTTAAAATATATTT
90860 T
1 T
90861 TAAAATATAT
Statistics
Matches: 136, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
27 12 0.09
28 18 0.13
29 62 0.46
30 10 0.07
31 28 0.21
32 6 0.04
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTATTATCTTAAATTTAAAATATATTT
Found at i:90769 original size:27 final size:27
Alignment explanation
Indices: 90678--90774 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 27
90668 ACTTAAAACT
*
90678 ATATTTTATTCTTATTTTAAATTTAAAATA
1 ATATTTTATTCTTATTTT-AATAT-AAA-A
* * * *
90708 TATATTTTATTTTTGTCTTAACTTATAAAT
1 -ATATTTTATTCTTATTTTAA--TATAAAA
*
90738 CTATTTTATTCTTATTTTAATATAAAA
1 ATATTTTATTCTTATTTTAATATAAAA
90765 ATATTTTATT
1 ATATTTTATT
90775 ATTGTCTTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
27 15 0.28
29 16 0.30
30 2 0.04
31 18 0.34
32 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTTTATTCTTATTTTAATATAAAA
Found at i:90801 original size:56 final size:58
Alignment explanation
Indices: 90655--90860 Score: 220
Period size: 60 Copynumber: 3.5 Consensus size: 58
90645 TTCAATTTGG
* * *
90655 TATTATTATCTTCACTTAAAACTATATTTTATTCTTATTTTAAATTTAAAATATATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTT-AATAT-AAATATATATTT
* * * *
90715 TATTTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAA-A-ATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATATAAATATATATTT
* * *
90771 TATTATTGTCTTCACTTAAAAATATCTTTTATTATTATTATAA-ATTAAATATATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATA-TAAATATATATTT
* * * *
90829 TATTAGTATCTTAACTTTTTAAAATATATTTT
1 TATTATTGTCTTCAC--TTAAAAATATATTTT
90861 TAAAATATAT
Statistics
Matches: 122, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
55 1 0.01
56 46 0.38
57 2 0.02
58 21 0.17
59 4 0.03
60 48 0.39
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (58 bp):
TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATATAAATATATATTT
Found at i:90862 original size:13 final size:13
Alignment explanation
Indices: 90844--90871 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
90834 GTATCTTAAC
90844 TTTTTAAAATATA
1 TTTTTAAAATATA
90857 TTTTTAAAATATA
1 TTTTTAAAATATA
90870 TT
1 TT
90872 AATTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:90874 original size:116 final size:118
Alignment explanation
Indices: 90655--90890 Score: 275
Period size: 116 Copynumber: 2.0 Consensus size: 118
90645 TTCAATTTGG
* * * *
90655 TATTATTATCTTCACTTAAAACTATATTTTATTCTTATTTTAAATTTAAAATATATATTTTATTT
1 TATTATTATCTTCACTTAAAAATATATTTTATTATTATTATAAATTTAAAATATATATTTTATTA
* * * *** *
90720 TTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATAT-AAAA-ATATTT
66 GTATCTTAACTTATAAATATATTTTATAAATATATTAATATCAAAAGATATTT
* *
90771 TATTATTGTCTTCACTTAAAAATATCTTTTATTATTATTATAAA-TT-AAATATATATTTTATTA
1 TATTATTATCTTCACTTAAAAATATATTTTATTATTATTATAAATTTAAAATATATATTTTATTA
* *
90834 GTATCTTAACTTTTTAAAATATATTTT-TAAAATATATTAATTTCAAAAGATATTT
66 GTATCTTAAC-TTAT-AAATATATTTTAT-AAATATATTAATATCAAAAGATATTT
90889 TA
1 TA
90891 ACTTAAGAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
114 24 0.24
115 6 0.06
116 58 0.58
117 4 0.04
118 8 0.08
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (118 bp):
TATTATTATCTTCACTTAAAAATATATTTTATTATTATTATAAATTTAAAATATATATTTTATTA
GTATCTTAACTTATAAATATATTTTATAAATATATTAATATCAAAAGATATTT
Found at i:90984 original size:30 final size:30
Alignment explanation
Indices: 90934--91093 Score: 97
Period size: 30 Copynumber: 5.4 Consensus size: 30
90924 TTAAAATCAT
*
90934 TTTTTAAAGGTTAATATAAGAATAAAATATAA
1 TTTTT-AA-GTTAATGTAAGAATAAAATATAA
90966 TTTTTAAGTTAATGTAAGAAT-AAATAT-A
1 TTTTTAAGTTAATGTAAGAATAAAATATAA
* * *
90994 CTTTTAAGTGAA-GATAAG-ATAAAACATATA
1 TTTTTAAGTTAATG-TAAGAATAAAATATA-A
*
91024 TTTTTATA-TTAAAT-TAA-AA-AAAATA-GA
1 TTTTTA-AGTT-AATGTAAGAATAAAATATAA
* * *
91051 TTTATAAGTTAA-GACAAAAATAAAATATAA
1 TTTTTAAGTTAATG-TAAGAATAAAATATAA
*
91081 TTTTAAAAGTTAA
1 TTTT-TAAGTTAA
91094 GAATATAAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
26 3 0.03
27 13 0.13
28 22 0.22
29 17 0.17
30 28 0.28
31 12 0.12
32 5 0.05
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.37
Consensus pattern (30 bp):
TTTTTAAGTTAATGTAAGAATAAAATATAA
Found at i:91011 original size:28 final size:30
Alignment explanation
Indices: 90949--91016 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
90939 AAAGGTTAAT
* *
90949 ATAAGAATAAAATATAATTTTTAAGTTAATG
1 ATAAGAAT-AAATATAACTTTTAAGTGAATG
90980 -TAAGAATAAATAT-ACTTTTAAGTGAA-G
1 ATAAGAATAAATATAACTTTTAAGTGAATG
91007 ATAAG-ATAAA
1 ATAAGAATAAA
91017 ACATATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.18
28 15 0.44
29 6 0.18
30 7 0.21
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.34
Consensus pattern (30 bp):
ATAAGAATAAATATAACTTTTAAGTGAATG
Found at i:91084 original size:57 final size:57
Alignment explanation
Indices: 90954--91093 Score: 135
Period size: 57 Copynumber: 2.4 Consensus size: 57
90944 TTAATATAAG
* * *
90954 AATAAAATATAATTTTTAAGTTAATGTAAGAATAAATATACTTTTAAGTGAAGATAA
1 AATAAAATATAATTTTTAAGTTAATGTAAGAAAAAATAGACTTTTAAGTGAAGAAAA
* * *
91011 GATAAAACATATATTTTTATA-TTAAAT-TAA-AAAAAATAGA-TTTATAAGTTAAGACAAA
1 AATAAAATATA-ATTTTTA-AGTT-AATGTAAGAAAAAATAGACTTT-TAAGTGAAGA-AAA
*
91069 AATAAAATATAATTTTAAAAGTTAA
1 AATAAAATATAATTTT-TAAGTTAA
91094 GAATATAAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
56 3 0.04
57 34 0.51
58 26 0.39
59 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (57 bp):
AATAAAATATAATTTTTAAGTTAATGTAAGAAAAAATAGACTTTTAAGTGAAGAAAA
Found at i:93457 original size:25 final size:23
Alignment explanation
Indices: 93429--93491 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
93419 TGTTCGGGTG
93429 AATTTATAAAATTTTAAGAGTGATA
1 AATTTATAAAATTTTAA-AG-GATA
* *
93454 AATTTAT-AAATTTTCAAGGATG
1 AATTTATAAAATTTTAAAGGATA
*
93476 AATTTGTAAAATTTTA
1 AATTTATAAAATTTTA
93492 GGGACAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.27
23 9 0.27
24 8 0.24
25 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (23 bp):
AATTTATAAAATTTTAAAGGATA
Found at i:94477 original size:17 final size:18
Alignment explanation
Indices: 94450--94483 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
94440 TCTTTTAAAA
*
94450 TTTTCAAATTTCTATATC
1 TTTTCAAATTTCAATATC
94468 TTTT-AAATTTCAATAT
1 TTTTCAAATTTCAATAT
94484 ATATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTCAAATTTCAATATC
Found at i:94490 original size:25 final size:26
Alignment explanation
Indices: 94439--94491 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
94429 TTAATTTTAC
* *
94439 ATCTTTTAAAATTTTCAAATTTCTAT
1 ATCTTTTAAAATTTTCAAATATATAT
94465 ATCTTTT-AAA-TTTCAATATATATAT
1 ATCTTTTAAAATTTTCAA-ATATATAT
94490 AT
1 AT
94492 ATATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 11 0.46
26 7 0.29
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (26 bp):
ATCTTTTAAAATTTTCAAATATATAT
Found at i:99349 original size:20 final size:20
Alignment explanation
Indices: 99324--99368 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
99314 GTCATCCAAT
*
99324 TTTTTAAACCCCAGACTGGA
1 TTTTTAAACCCCAGACCGGA
*
99344 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
99364 TTTTT
1 TTTTT
99369 TTCCAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:99737 original size:15 final size:15
Alignment explanation
Indices: 99717--99774 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
99707 TAACCGATTT
99717 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
99732 CGGTTTTTTTAAAAAAAAC
1 CGG---TTTT-AAAAAAAC
*
99751 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
99766 CGATTTTAA
1 CGGTTTTAA
99775 TATTATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 18 0.50
16 3 0.08
18 4 0.11
19 11 0.31
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:99743 original size:18 final size:19
Alignment explanation
Indices: 99720--99755 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
99710 CCGATTTCGG
99720 TTTT-AAAAAAACCGGTTT
1 TTTTAAAAAAAACCGGTTT
99738 TTTTAAAAAAAACCGGTT
1 TTTTAAAAAAAACCGGTT
99756 ATAAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (19 bp):
TTTTAAAAAAAACCGGTTT
Found at i:99863 original size:33 final size:33
Alignment explanation
Indices: 99816--99918 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
99806 ACAAAGTTTA
* *
99816 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
99848 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
99881 CGATAAATTCAAATACTTAAAAACTT-CATGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
99913 CGATAA
1 CGATAA
99919 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.22
33 51 0.78
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:99937 original size:21 final size:21
Alignment explanation
Indices: 99913--99954 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
99903 ACTTCATGTT
99913 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
99934 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
99955 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:102327 original size:28 final size:28
Alignment explanation
Indices: 102294--102352 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
102284 AAAAAATCGA
102294 TTTTTCCCAAAATCCGG-T-TTCGGATATT
1 TTTTTCCCAAAAT-CGGATATTCGGAT-TT
**
102322 TTTTTCGTAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAATCGGATATTCGGATTT
102350 TTT
1 TTT
102353 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 17 0.63
29 7 0.26
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (28 bp):
TTTTTCCCAAAATCGGATATTCGGATTT
Found at i:115550 original size:21 final size:21
Alignment explanation
Indices: 115524--115568 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
115514 GATTTCTGGG
* *
115524 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
115545 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
115566 CAA
1 CAA
115569 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:116247 original size:23 final size:24
Alignment explanation
Indices: 116204--116250 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
116194 ATATGGCATG
*
116204 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
116228 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
116251 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:116504 original size:31 final size:31
Alignment explanation
Indices: 116466--116590 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
116456 AGGGTCGAGG
*
116466 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
116497 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
116528 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
116559 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
116590 G
1 G
116591 GTCATTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:119784 original size:21 final size:21
Alignment explanation
Indices: 119747--119791 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
119737 GATTTCTGGG
*
119747 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
119768 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
119789 CAA
1 CAA
119792 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:120678 original size:31 final size:31
Alignment explanation
Indices: 120640--120764 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
120630 AGGGTCGAGG
*
120640 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
120671 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
120702 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
120733 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
120764 G
1 G
120765 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:125516 original size:2 final size:2
Alignment explanation
Indices: 125509--125566 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
125499 TCTATAAACA
125509 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
125551 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
125567 TAATAAATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:125590 original size:18 final size:20
Alignment explanation
Indices: 125559--125607 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
125549 ATATATATAT
*
125559 ATATATATTAATAAATAAATAA
1 ATATATAATAAT-AA-AAATAA
125581 AT-TATAATAATAAAAATAA
1 ATATATAATAATAAAAATAA
125600 ATATATAA
1 ATATATAA
125608 AACCCGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 7 0.28
21 8 0.32
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATATAATAATAAAAATAA
Found at i:126261 original size:105 final size:104
Alignment explanation
Indices: 126057--127415 Score: 1791
Period size: 105 Copynumber: 13.3 Consensus size: 104
126047 ATTGCTCCGT
* ** * * * **
126057 GTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGGAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAAT-TGGAAGTTG-TTGTTGACAAC
* * * * *
126122 CAGTC-GCCCCTTCGTTGTGAAGTTGAGCTTGCGTTATCTTGA
63 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
126164 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTGTTGACAACCA
*
126229 GCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTGGA
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
126269 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTGTTGACAACCA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAGTTGTTGTTGACAACCA
* *
126334 GCGGTCCATTCGTTGTGAAGTTGAACTTGCGTTGTCTGGA
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
126374 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTG-TTGTTGACAACC
*
126439 AGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
** *
126480 GTCCAATATGTTTCGTTGTGAACTT-AAAGTTGG----GAAATT----G-T-TTGTTGACAACCA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAA-TTGGCTCTGAAATTGGAAGTTGTTGTTGACAACCA
126534 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
126574 GCCCAATGTCCTTCGTTGTGAAGTTGAAATTGG----GAAATT----G-T-TTGTTGACAACCAG
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTGTTGACAACCAG
126629 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
126668 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTG-TTGTTGACAACC
**
126732 AGCGGTCCCTTCGTCGTGAAGTTGAACTTATGTTGTCTGGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
126773 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTG-TTGTTGACAACC
126838 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
126879 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTG-TTGTTGACAACC
126943 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
126984 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTG-TTGTTGACAACC
*
127048 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
127089 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTATTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTT-GTTGTTGACAACC
127154 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
127195 GTCCAATATCCTTCGTTGCGAAGTTGAAATTGG----GAAATT----G-T-TTATTGACAACCAG
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTGTTGACAACCAG
127250 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
127289 GTCCAACATCCTTCGTTGCGAAGTTGAAATTGG----GAAATT----G-T-TTATTGACAACCAG
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTGTTGACAACCAG
* * *
127344 TGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGTCTGGA
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
127383 GTCCAATATCCTTCTTTATGAAGTTGAAATTGG
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
127416 AATCTAAAAG
Statistics
Matches: 1165, Mismatches: 64, Indels: 59
0.90 0.05 0.05
Matches are distributed among these distances:
94 339 0.29
95 3 0.00
96 2 0.00
97 2 0.00
98 6 0.01
102 12 0.01
103 1 0.00
104 2 0.00
105 495 0.42
106 268 0.23
107 35 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (104 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
Found at i:126482 original size:211 final size:212
Alignment explanation
Indices: 126057--127415 Score: 1849
Period size: 211 Copynumber: 6.7 Consensus size: 212
126047 ATTGCTCCGT
* ** * * * **
126057 GTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGGAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAAATTGTTTGTTGACAAC
* * * * *
126122 CAGTC-GCCCCTTCGTTGTGAAGTTGAGCTTGCGTTATCTTGAGTCCAATATCCTTCGCTGTGAA
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
126186 GTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
129 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
126250 TTAACTTGCGTTGTCTGGA
194 TGAACTTGCGTTGTCTGGA
126269 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTG-TTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAACC
* *
126333 AGCGGTCCATTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
*
126398 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCCTCGTCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
126463 AACTTGCGTTGTCTGGA
196 AACTTGCGTTGTCTGGA
** *
126480 GTCCAATATGTTTCGTTGTGAACTT-AAA---G-T-TG-----GG-AAATTGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAACC
* *
126533 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGCCCAATGTCCTTCG-T-T---G-
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
*
126592 TG-AA---G-T-TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
126651 AACTTGCGTTGTCTGGA
196 AACTTGCGTTGTCTGGA
*
126668 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAACC
**
126732 AGCGGTCCCTTCGTCGTGAAGTTGAACTTATGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
126797 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
126862 AACTTGCGTTGTCTGGA
196 AACTTGCGTTGTCTGGA
* *
126879 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAA-TCGAGAAA-TGTTTGTTGACAAC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGA-AAATTGTTTGTTGACAAC
*
126942 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* * * *
127007 TTGAAATTGACTCTGAAATCGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
127071 GAACTTGCGTTGTCTTGA
195 GAACTTGCGTTGTCTGGA
* *
127089 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAAGTTATTTGTTGACAAC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAA-TTGTTTGTTGACAAC
127153 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-T-T---G
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* * *
127213 -CG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
127271 GAACTTGCGTTGTCTGGA
195 GAACTTGCGTTGTCTGGA
* * *
127289 GTCCAACATCCTTCGTTGCGAAGTTGAAA-----T-TG-----GG-AAATTGTTTATTGACAACC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAACC
* * * ** *
127342 AGTGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCTTTATGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
127407 TGAAATTGG
131 TGAAATTGG
127416 AATCTAAAAG
Statistics
Matches: 1040, Mismatches: 64, Indels: 100
0.86 0.05 0.08
Matches are distributed among these distances:
188 156 0.15
189 8 0.01
190 3 0.00
192 1 0.00
193 4 0.00
194 7 0.01
195 4 0.00
198 2 0.00
199 86 0.08
200 151 0.15
201 1 0.00
204 3 0.00
205 5 0.00
206 4 0.00
207 1 0.00
209 6 0.01
210 198 0.19
211 366 0.35
212 34 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (212 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
AACTTGCGTTGTCTGGA
Found at i:126552 original size:51 final size:50
Alignment explanation
Indices: 126491--126649 Score: 147
Period size: 51 Copynumber: 3.3 Consensus size: 50
126481 TCCAATATGT
* *
126491 TTCGTTGTGAACTTAAAGTTGGGAAATTGTTTGTTGACAACCAGCGGTCCC
1 TTCGTCGTGAAGTTAAA-TTGGGAAATTGTTTGTTGACAACCAGCGGTCCC
* * * **
126542 TTCGTCGTGAAGTTGAACTTGCG---TTGTCTG--GAGC--CCA-ATGT-CC
1 TTCGTCGTGAAGTT-AAATTGGGAAATTGTTTGTTGA-CAACCAGCGGTCCC
*
126585 TTCGTTGTGAAGTTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCC
1 TTCGTCGTGAAGTT-AAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCC
126636 TTCGTCGTGAAGTT
1 TTCGTCGTGAAGTT
126650 GAACTTGCGT
Statistics
Matches: 83, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
43 22 0.27
44 2 0.02
45 3 0.04
46 8 0.10
47 2 0.02
48 8 0.10
49 3 0.04
50 2 0.02
51 31 0.37
52 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (50 bp):
TTCGTCGTGAAGTTAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCC
Found at i:126580 original size:94 final size:94
Alignment explanation
Indices: 126410--127415 Score: 1267
Period size: 94 Copynumber: 10.1 Consensus size: 94
126400 AAATTGGCTC
* *
126410 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
** *
126475 CTGGAGTCCAATATGTTTCGTTGTGAACT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
126504 T-AAAGTTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 TGAAA-TTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
126568 TCTGGAGCCCAATGTCCTTCGTTGTGAAGT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGT
126598 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
126663 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
126692 TGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 TGAAATTGG----GAAA-T------TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
**
126757 ACTTATGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
55 ACTTGCGTTGTCTGGAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T
*
126808 CTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 -TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
126873 TCTGGAGTCCAATATCCTTCGTTGTGAAGT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
126903 TGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 TGAAATTG-----G-----GA-AATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
126968 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
55 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
127008 TGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 TGAAATTG-----G-----GA-AATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
127073 ACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGT
55 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
127113 TGAAATTGGCTCTGAAATTGAAAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATTGG----GAAATT-----G---TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
127178 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
127219 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
127284 CTGGAGTCCAACATCCTTCGTTGCGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
127313 TGAAATTGGGAAATTGTTTATTGACAACCAGTGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
127378 CTGGAGTCCAATATCCTTCTTTATGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
127407 TGAAATTGG
1 TGAAATTGG
127416 AATCTAAAAG
Statistics
Matches: 833, Mismatches: 35, Indels: 88
0.87 0.04 0.09
Matches are distributed among these distances:
93 3 0.00
94 360 0.43
95 4 0.00
96 1 0.00
97 1 0.00
98 7 0.01
99 6 0.01
100 3 0.00
101 1 0.00
102 6 0.01
103 1 0.00
104 3 0.00
105 262 0.31
106 154 0.18
107 1 0.00
110 1 0.00
111 2 0.00
112 3 0.00
113 3 0.00
115 1 0.00
116 1 0.00
117 9 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:126588 original size:43 final size:43
Alignment explanation
Indices: 126540--126695 Score: 143
Period size: 43 Copynumber: 3.4 Consensus size: 43
126530 ACCAGCGGTC
126540 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGCCCAATGT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGCCCAATGT
* * * * **
126583 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTGTTGA-CAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTGTCTG--GAGC--CCA-ATGT
* *
126633 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGCCCAATGT
*
126677 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
126696 ATTGGCTCTG
Statistics
Matches: 88, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
43 40 0.45
44 1 0.01
45 3 0.03
46 8 0.09
47 1 0.01
48 8 0.09
49 3 0.03
50 2 0.02
51 22 0.25
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGCCCAATGT
Found at i:127209 original size:43 final size:43
Alignment explanation
Indices: 127161--127316 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
127151 ACCAGCGGTC
* *
127161 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAACAT
* * * * * ** * *
127204 CCTTCGTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGCGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCAAC-AT
*
127254 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAACAT
1 -CCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAACAT
*
127298 CCTTCGTTGCGAAGTTGAA
1 CCTTCGTCGCGAAGTTGAA
127317 ATTGGGAAAT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 38 0.46
44 1 0.01
45 4 0.05
46 7 0.09
48 7 0.09
49 3 0.04
50 1 0.01
51 21 0.26
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (43 bp):
CCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAACAT
Found at i:130960 original size:24 final size:24
Alignment explanation
Indices: 130915--130969 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
130905 TATAATAATG
*
130915 ATAAATAAAATAAATAACAAAATA
1 ATAAATAAAATAAATAACAAAAGA
* *
130939 ATAAATAAAAGTTAGTAA-AAAAGA
1 ATAAATAAAA-TAAATAACAAAAGA
130963 A-AAATAA
1 ATAAATAA
130970 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (24 bp):
ATAAATAAAATAAATAACAAAAGA
Found at i:130974 original size:17 final size:17
Alignment explanation
Indices: 130954--130986 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
130944 TAAAAGTTAG
130954 TAAAAAAGA-AAAATAAT
1 TAAAAAA-ATAAAATAAT
130971 TAAAAAAATAAAATAA
1 TAAAAAAATAAAATAA
130987 ATGATGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAAAATAAAATAAT
Found at i:133617 original size:32 final size:33
Alignment explanation
Indices: 133560--133635 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 33
133550 TTAACGAAGC
133560 TCAAATCCCAATTCTTTTATATGCCCAATCCAAT
1 TCAAATCCCAATTC-TTTATATGCCCAATCCAAT
133594 TCAAATCCCAATTC-TTATATGCCCAATCCAAT
1 TCAAATCCCAATTCTTTATATGCCCAATCCAAT
*
133626 TAACAATCCC
1 TCA-AATCCC
133636 CCTGTTGCAC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 20 0.50
33 6 0.15
34 14 0.35
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (33 bp):
TCAAATCCCAATTCTTTATATGCCCAATCCAAT
Found at i:134422 original size:2 final size:2
Alignment explanation
Indices: 134415--134444 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
134405 CCGCCTCAAT
134415 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
134445 TTTATACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:134482 original size:17 final size:18
Alignment explanation
Indices: 134460--134493 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
134450 ACTTTTTATA
134460 TTAATTATATA-TAATTT
1 TTAATTATATATTAATTT
*
134477 TTAATTTTATATTAATT
1 TTAATTATATATTAATT
134494 ATATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTATATATTAATTT
Found at i:134485 original size:28 final size:31
Alignment explanation
Indices: 134433--134507 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 31
134423 TATATATATA
134433 TATATATAATATTTTATACTTTTTATATTAAT
1 TATATATAATATTTTATAC-TTTTATATTAAT
134465 TATATATAAT-TTTTA-A-TTTTATATTAAT
1 TATATATAATATTTTATACTTTTATATTAAT
*
134493 TATATAAAATATTTT
1 TATATATAATATTTT
134508 CTGGTTTGGA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 21 0.51
29 4 0.10
30 1 0.02
31 5 0.12
32 10 0.24
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TATATATAATATTTTATACTTTTATATTAAT
Done.