Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_259
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: 111735
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2945 original size:40 final size:40
Alignment explanation
Indices: 2754--2938 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
2744 TTGAATGATG
* * * *
2754 TCCGGGCTAAGTCCCGAAGGC-TCTGTG-GTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTAAA
* * * *
2794 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
2834 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
2873 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2914 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2939 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 33 0.28
40 79 0.66
41 7 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2960 original size:79 final size:79
Alignment explanation
Indices: 2807--2971 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
2797 GGACTAAGAT
* * **
2807 CCGAAGGCATTTATGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTATGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
2872 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* * *
2886 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTATGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
2949 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
2965 CCGAAGG
1 CCGAAGG
2972 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTATGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:6353 original size:27 final size:27
Alignment explanation
Indices: 6301--6409 Score: 150
Period size: 27 Copynumber: 4.1 Consensus size: 27
6291 CATTGCTGCA
* *
6301 AGAACAGATAA-TGTGACAGAGTCACC
1 AGAACAGATAATTGTGGCAGAGCCACC
6327 AGAACAGATAATTGTGGCAGAGCCACC
1 AGAACAGATAATTGTGGCAGAGCCACC
6354 AGAACAGAT-ATATGTGGCAGAGCCACC
1 AGAACAGATAAT-TGTGGCAGAGCCACC
* * *
6381 AGATCAGATAAATGTGGCATAGCCACC
1 AGAACAGATAATTGTGGCAGAGCCACC
6408 AG
1 AG
6410 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
26 13 0.17
27 61 0.81
28 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (27 bp):
AGAACAGATAATTGTGGCAGAGCCACC
Found at i:7874 original size:24 final size:24
Alignment explanation
Indices: 7839--7884 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
7829 CCAACATCGT
7839 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCTAAATCC
*
7863 TCTCCCTTATCAGCTCCTAAAT
1 TCTCCCTAATCAGCTCCTAAAT
7885 ATTCTCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.04, T:0.33
Consensus pattern (24 bp):
TCTCCCTAATCAGCTCCTAAATCC
Found at i:7890 original size:24 final size:24
Alignment explanation
Indices: 7838--7890 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
7828 GCCAACATCG
*
7838 TTCTCCCTAATCAGCTCCTAAATC
1 TTCTCCCTAATCAGCTCCTAAATA
* *
7862 CTCTCCCTTATCAGCTCCTAAATA
1 TTCTCCCTAATCAGCTCCTAAATA
7886 TTCTC
1 TTCTC
7891 TTGACAGCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
TTCTCCCTAATCAGCTCCTAAATA
Found at i:9328 original size:18 final size:18
Alignment explanation
Indices: 9305--9341 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9295 CGGTTTGAGG
9305 ATAGAAAGCTGTACTAAA
1 ATAGAAAGCTGTACTAAA
9323 ATAGAAAGCTGTACTAAA
1 ATAGAAAGCTGTACTAAA
9341 A
1 A
9342 CTCAACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (18 bp):
ATAGAAAGCTGTACTAAA
Found at i:11961 original size:24 final size:24
Alignment explanation
Indices: 11934--11983 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
11924 CGAGCACGAA
*
11934 TAGCATAAGTTCTCGCAGATGCTC
1 TAGCATAAGTCCTCGCAGATGCTC
11958 TAGCATAAGTCCTCGCAGATGCTC
1 TAGCATAAGTCCTCGCAGATGCTC
11982 TA
1 TA
11984 ACATCTGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (24 bp):
TAGCATAAGTCCTCGCAGATGCTC
Found at i:14834 original size:108 final size:110
Alignment explanation
Indices: 14690--14888 Score: 287
Period size: 108 Copynumber: 1.8 Consensus size: 110
14680 ATCCTTTTGA
* * * *
14690 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACTAA
1 AACTTACCAATGCCATGTCTTGACATGGTATTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
14753 -TGCCATGCCTTGGCATGGTCTTACATAGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTAGCATGGTCTTACATAGGACCTTTGCCTTATAGT
* * *
14798 AACTTATCAATGCCATGTCTTGACATGGTATTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
14863 TTCCATGCCTTAGCATGGTCTTACAT
66 TGCCATGCCTTAGCATGGTCTTACAT
14889 GGTATCCTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.61
109 6 0.08
110 24 0.30
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTACATAGGACCTTTGCCTTATAGT
Found at i:14845 original size:55 final size:52
Alignment explanation
Indices: 14690--14897 Score: 181
Period size: 55 Copynumber: 3.8 Consensus size: 52
14680 ATCCTTTTGA
* *
14690 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTA-CAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATG
* * * *
14743 AACTCACTAATGCCATGCCTTGGCATGGTCTTACAT-AGGA-CCTTTGCCTTATAG
1 AACTTAC-AATGCCATGTCTTGACATGGTCTTACATGA-TATCC-TTGCCTTAT-G
* *
14797 TAACTTATCAATGCCATGTCTTGACATGGTATTACATGATTTCCTTGCCTTA-G
1 -AACTTA-CAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATG
* * *
14850 AAACCTTACCAATTTCCATGCCTT-AGCATGGTCTTACATGGTATCCTT
1 -AA-CTTA-CAA-TGCCATGTCTTGA-CATGGTCTTACATGATATCCTT
14898 AAACCCTAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
52 3 0.02
53 43 0.34
54 9 0.07
55 66 0.53
56 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (52 bp):
AACTTACAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATG
Found at i:17179 original size:15 final size:14
Alignment explanation
Indices: 17147--17199 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
17137 CCAGAAAAGT
17147 AAATCATTTTCCAG
1 AAATCATTTTCCAG
17161 AAATCATTTTCCAAG
1 AAATCATTTTCC-AG
* *
17176 AAATTATTTTTCAG
1 AAATCATTTTCCAG
17190 AAATCATTTT
1 AAATCATTTT
17200 ACGAAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28333 original size:16 final size:16
Alignment explanation
Indices: 28308--28360 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
28298 GACTAGCACC
*
28308 CATATTCACATAATCA
1 CATATACACATAATCA
*
28324 CATATACACATAATCT
1 CATATACACATAATCA
* *
28340 CATGA-GCTCATAATCA
1 CAT-ATACACATAATCA
28356 CATAT
1 CATAT
28361 TTCCTAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (16 bp):
CATATACACATAATCA
Found at i:35452 original size:7 final size:7
Alignment explanation
Indices: 35440--35464 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35430 GAGTGTTTGA
35440 GGGGTGT
1 GGGGTGT
35447 GGGGTGT
1 GGGGTGT
35454 GGGGTGT
1 GGGGTGT
35461 GGGG
1 GGGG
35465 ATTGTATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (7 bp):
GGGGTGT
Found at i:41820 original size:16 final size:16
Alignment explanation
Indices: 41799--41851 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
41789 GTAGATTGAC
41799 AAAAGCCGAAATGCCA
1 AAAAGCCGAAATGCCA
* **
41815 AAAAGCTGAAATGCTG
1 AAAAGCCGAAATGCCA
*
41831 AAAAGCCAAAATGCCA
1 AAAAGCCGAAATGCCA
41847 AAAAG
1 AAAAG
41852 TCAAAAGCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:46599 original size:28 final size:28
Alignment explanation
Indices: 46560--46645 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
46550 GGTCATATGA
*
46560 ATGTGATCTGGGACTAATGGGCCACATAC
1 ATGTGAT-TGGGCCTAATGGGCCACATAC
*
46589 ATGTGATTGGGCCTAATGGGCCATATGA-
1 ATGTGATTGGGCCTAATGGGCCACAT-AC
* * *
46617 AAGAGATTGGGCCTAGTGGGCCACATAC
1 ATGTGATTGGGCCTAATGGGCCACATAC
46645 A
1 A
46646 AGTATGTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.82
29 8 0.16
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (28 bp):
ATGTGATTGGGCCTAATGGGCCACATAC
Found at i:46640 original size:56 final size:57
Alignment explanation
Indices: 46532--46645 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 57
46522 ATGACTGTAA
* * *
46532 ATGTGATTTGGACCTAATGGTCATATGAATGTGATCTGGGACTAATGGGCCACATAC
1 ATGTGATTTGGACCTAATGGCCATATGAAAGAGATCTGGGACTAATGGGCCACATAC
* * *
46589 ATGTGA-TTGGGCCTAATGGGCCATATGAAAGAGAT-TGGGCCTAGTGGGCCACATAC
1 ATGTGATTTGGACCTAAT-GGCCATATGAAAGAGATCTGGGACTAATGGGCCACATAC
46645 A
1 A
46646 AGTATGTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 30 0.60
57 20 0.40
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (57 bp):
ATGTGATTTGGACCTAATGGCCATATGAAAGAGATCTGGGACTAATGGGCCACATAC
Found at i:72927 original size:23 final size:22
Alignment explanation
Indices: 72896--72938 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
72886 ATAATCCATA
*
72896 CCAAATCATGCCAAAACATAAG
1 CCAAATCATACCAAAACATAAG
72918 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
72939 TGTTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:75697 original size:93 final size:93
Alignment explanation
Indices: 75538--75708 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
75528 GGATGGTTGA
* * * * *
75538 GCATCTGAACTCGTTGAGTTGAGTCTAAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
75603 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
75631 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
*
75696 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
75709 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:75711 original size:46 final size:46
Alignment explanation
Indices: 75544--75713 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 46
75534 TTGAGCATCT
** * * *
75544 GAACTCGTTGAGTTGAGTCTAAGTTCACCTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
* * *
75590 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC--CC
75637 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
* * *
75683 GAGCTCATTGAGTTGAGTCTGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
75714 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 54 0.53
47 28 0.28
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
Found at i:77653 original size:13 final size:13
Alignment explanation
Indices: 77635--77659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77625 CACAAATGTT
77635 AAAATTTTCACAC
1 AAAATTTTCACAC
77648 AAAATTTTCACA
1 AAAATTTTCACA
77660 TATATCAATT
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:81610 original size:43 final size:43
Alignment explanation
Indices: 81553--81675 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
81543 ATCACAGACA
* * * *
81553 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
** * *
81595 ATGCCTCTGTCCCAGACAGGGTCTTACACGTAATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
*
81638 ATGCCAATGTCCCAGACATGGTTTTACAC-TAAATCACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATCACA
81676 CCTCGGAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
42 6 0.09
43 61 0.91
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:87721 original size:27 final size:26
Alignment explanation
Indices: 87682--87776 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
87672 TATGTCACAA
*
87682 ATTATCTGATCTGGTGGCTCTGCCAC
1 ATTATCTGTTCTGGTGGCTCTGCCAC
87708 ATATATCTGTTCTGGTGGCTCTGCCAC
1 AT-TATCTGTTCTGGTGGCTCTGCCAC
* * **
87735 GATTATCTGTATCTAGTGACTCTGTTAC
1 -ATTATCTGT-TCTGGTGGCTCTGCCAC
*
87763 ATTATCTTTTCTGG
1 ATTATCTGTTCTGG
87777 CAGCCATGCT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.10
27 38 0.64
28 15 0.25
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (26 bp):
ATTATCTGTTCTGGTGGCTCTGCCAC
Found at i:92751 original size:27 final size:27
Alignment explanation
Indices: 92721--92898 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
92711 ATATTGAGCC
* * *
92721 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
92748 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
92775 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** **
92803 CGCACACTTAGTGCCGCATGGTCATTT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
92830 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * *
92857 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
92884 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
92899 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:92860 original size:82 final size:81
Alignment explanation
Indices: 92747--92897 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
92737 TACAATCAAC
* * * *
92747 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCACACTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCACACTT
92812 AGTGCCGCATGGTCATT
65 AGTGCCGCATGGTCATT
* **
92829 TCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
92893 AGTGC
65 AGTGC
92898 TGTACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 18 0.30
82 43 0.70
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCATT
Found at i:95766 original size:436 final size:436
Alignment explanation
Indices: 94966--95822 Score: 1238
Period size: 436 Copynumber: 2.0 Consensus size: 436
94956 GCTAACAAAA
* * * * *
94966 TTAAAGATTTAGTTGCAATAGTTGCTTAACAGAGGGTTTATTCGACCGAGTGCATCTCCATGGGG
1 TTAAAGATTCAGTTGCAATAGTTGCTTAACAGAAGGTTCATTCAACAGAGTGCATCTCCATGGGG
* **
95031 TGCACCGATTTTGTTTGTGAAGAAGAAGGATGGTACGATGAAGTTGTGTATTGGTTATATTTAGT
66 TGCACCGATTTTGTTTGTGAAGAAGAAGGATGGTACGATGAAGTTGTGTATTGATTATAGATAGT
* *
95096 TGAATAAGTTGACCATCAAGAACAACTATCCTTTACCTTAAATTGACAACTTGTTTGATCAGTTT
131 TGAATAAGTTGACCATCAAGAACAACTATCCTTTACCTCAAACTGACAACTTGTTTGATCAGTTT
* * * * *
95161 CGAGGTGCAACAGTGTTTTTGAAGATTGATATAAGATTTGGGTATTATCAGTTTAAGATGAAGGA
196 CAAGGTGCAACAATGTTTTTGAAGATTGATATAAGATCTAGGTATTATCAGTTGAAGATGAAGGA
* ** ** *
95226 GTTTGACATCTTAAAAATTGCTTTTAGGACTTGGTATGGGCATTATGAGTTTTTGGTCATGATGC
261 GTCTGACATCTTAAAAATTGCTTTTAAAACTCAGTATGGGCATTATGAGTTTTTGGTCATGACGC
* *
95291 TCGGTTTAACTAATGACCCTACCGTGTTCATGGATCTAATAAA-CTGAGTATTCCATTCGTACTT
326 TCGATTTAACTAATGACCCCACCGTGTTCATGGATCTAATAAATC-GAGTATTCCATTCGTACTT
*
95355 GGATCAATTTGTGGTTGTCTTCATAGATGACAAAAGAGTTCAAAGAG
390 GGATCAATTTATGGTTGTCTTCATAGATGACAAAAGAGTTCAAAGAG
* ** * *
95402 TTAAAGATTCAGTTGC-ATGAGTTGCTTGATGGAAGGTTCATTCAACAGAGTGTATCTCCGTGGG
1 TTAAAGATTCAGTTGCAAT-AGTTGCTTAACAGAAGGTTCATTCAACAGAGTGCATCTCCATGGG
* *
95466 GTGCACC-AGTTTTGTTTGTGAAGAAGAAGGATGGTACGAT-ATGGTTGTGTATTGATTATCGAT
65 GTGCACCGA-TTTTGTTTGTGAAGAAGAAGGATGGTACGATGA-AGTTGTGTATTGATTATAGAT
* * * **
95529 AGTTGAATAAGTTGACCATCAAGAACAAGTATCTTTTGCCTCAAACTGATGACTTGTTTGATCAG
128 AGTTGAATAAGTTGACCATCAAGAACAACTATCCTTTACCTCAAACTGACAACTTGTTTGATCAG
* * *
95594 TTTCAATGTGCAACAATGTTTTTGAAGATTGATCTAAGATCTAGGTATTATCAGTTGAAGGTGAA
193 TTTCAAGGTGCAACAATGTTTTTGAAGATTGATATAAGATCTAGGTATTATCAGTTGAAGATGAA
95659 GGAGTCTGACATCTTAAAAATTGCTTTTAAAACTCAGTATGGGCATTATGAGTTTTTGGTCATGA
258 GGAGTCTGACATCTTAAAAATTGCTTTTAAAACTCAGTATGGGCATTATGAGTTTTTGGTCATGA
* * * *
95724 CGTTCGATTTAACTAATG-CTCCCGCCGTGTTCATGTATCTAATAAATCGAGTATTCCATTTGTA
323 CGCTCGATTTAACTAATGAC-CCCACCGTGTTCATGGATCTAATAAATCGAGTATTCCATTCGTA
*
95788 CTTGGATCAATTTATGGTTGTTTTCATAGATGACA
387 CTTGGATCAATTTATGGTTGTCTTCATAGATGACA
95823 TTTTGGTGTC
Statistics
Matches: 372, Mismatches: 44, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
435 5 0.01
436 366 0.98
437 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (436 bp):
TTAAAGATTCAGTTGCAATAGTTGCTTAACAGAAGGTTCATTCAACAGAGTGCATCTCCATGGGG
TGCACCGATTTTGTTTGTGAAGAAGAAGGATGGTACGATGAAGTTGTGTATTGATTATAGATAGT
TGAATAAGTTGACCATCAAGAACAACTATCCTTTACCTCAAACTGACAACTTGTTTGATCAGTTT
CAAGGTGCAACAATGTTTTTGAAGATTGATATAAGATCTAGGTATTATCAGTTGAAGATGAAGGA
GTCTGACATCTTAAAAATTGCTTTTAAAACTCAGTATGGGCATTATGAGTTTTTGGTCATGACGC
TCGATTTAACTAATGACCCCACCGTGTTCATGGATCTAATAAATCGAGTATTCCATTCGTACTTG
GATCAATTTATGGTTGTCTTCATAGATGACAAAAGAGTTCAAAGAG
Found at i:103168 original size:30 final size:30
Alignment explanation
Indices: 103079--103306 Score: 143
Period size: 30 Copynumber: 7.5 Consensus size: 30
103069 ATATGTTTTA
*
103079 TATATTGCCGAATTTG-ATTCATATATGGTTA-T
1 TATATTGCCGAA-TTGAATT-ATATAT--ATACT
103111 T-TATTGCCGAATTGAATTGTATATATATATACT
1 TATATTGCCGAATTGAA---T-TATATATATACT
*
103144 TATATTGTCGAATTG-A--AT-TATATA--
1 TATATTGCCGAATTGAATTATATATATACT
* * *
103168 TATATTGCCAAATTGAATTGTATAGGTATACA
1 TATATTGCCGAATTGAATTATATA--TATACT
**
103200 CCTATTGCCGAATTGAATTATATATATACT
1 TATATTGCCGAATTGAATTATATATATACT
* * *
103230 TATATTGCCGAACTGAATTGTATATATATT
1 TATATTGCCGAATTGAATTATATATATACT
* *
103260 TATATT-CTCGAATTGAATTGTATAGGTATACA
1 TATATTGC-CGAATTGAATTATATA--TATACT
* *
103292 TCTATTGCTGAATTG
1 TATATTGCCGAATTG
103307 GCTTGTATAT
Statistics
Matches: 157, Mismatches: 20, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
24 13 0.08
25 1 0.01
26 6 0.04
27 3 0.02
28 2 0.01
29 1 0.01
30 58 0.37
31 11 0.07
32 38 0.24
33 4 0.03
34 19 0.12
35 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (30 bp):
TATATTGCCGAATTGAATTATATATATACT
Found at i:103171 original size:24 final size:24
Alignment explanation
Indices: 103144--103227 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 24
103134 TATATATACT
*
103144 TATATTGTCGAATTGAATTATATA
1 TATATTGCCGAATTGAATTATATA
*
103168 TATATTGCCAAATTGAATTGTATAGGTA
1 TATATTGCCGAATTGAA-T-TATA--TA
103196 TACACCTATTGCCGAATTGAATTATATA
1 T--A--TATTGCCGAATTGAATTATATA
103224 TATA
1 TATA
103228 CTTATATTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
24 17 0.35
25 1 0.02
26 5 0.10
28 6 0.12
30 5 0.10
31 1 0.02
32 14 0.29
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (24 bp):
TATATTGCCGAATTGAATTATATA
Found at i:103218 original size:56 final size:57
Alignment explanation
Indices: 103112--103227 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 57
103102 TATGGTTATT
* * * *
103112 TATTGCCGAATTGAATTGTATATATATATACTTATATTGTCGAATTGAATTATATATA
1 TATTGCCAAATTGAATTGTATAGATATACAC-TATATTGCCGAATTGAATTATATATA
* *
103170 TATTGCCAAATTGAATTGTATAGGTATACAC-CTATTGCCGAATTGAATTATATATA
1 TATTGCCAAATTGAATTGTATAGATATACACTATATTGCCGAATTGAATTATATATA
103226 TA
1 TA
103228 CTTATATTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 25 0.48
58 27 0.52
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (57 bp):
TATTGCCAAATTGAATTGTATAGATATACACTATATTGCCGAATTGAATTATATATA
Found at i:103287 original size:92 final size:88
Alignment explanation
Indices: 103112--103306 Score: 250
Period size: 92 Copynumber: 2.1 Consensus size: 88
103102 TATGGTTATT
* *
103112 TATTGCCGAATTGAATTGTATATATATATACTTATATTGTCGAATTGAATTATATATATATTGCC
1 TATTGCCGAATTGAA-T-TATATATATATACTTATATTGCCGAACTGAATTATATATATATTGCC
103177 AAATTGAATTGTATAGGTATACACC
64 AAATTGAATTGTATAGGTATACACC
103202 TATTGCCGAATTGAA-T-TATATATATACTTATATTGCCGAACTGAATTGTATATATATTTATAT
1 TATTGCCGAATTGAATTATATATATATACTTATATTGCCGAACTGAA-T-TATATATA--TAT-T
* * *
103265 TCTCGAATTGAATTGTATAGGTATACATC
61 GC-CAAATTGAATTGTATAGGTATACACC
*
103294 TATTGCTGAATTG
1 TATTGCCGAATTG
103307 GCTTGTATAT
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
86 27 0.29
87 2 0.02
88 8 0.09
90 18 0.19
91 2 0.02
92 36 0.39
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (88 bp):
TATTGCCGAATTGAATTATATATATATACTTATATTGCCGAACTGAATTATATATATATTGCCAA
ATTGAATTGTATAGGTATACACC
Found at i:103290 original size:62 final size:60
Alignment explanation
Indices: 103112--103326 Score: 156
Period size: 62 Copynumber: 3.5 Consensus size: 60
103102 TATGGTTATT
* *
103112 TATTGCCGAATTGAATTGTATATATATATACTTATATTGTCGAATTG-A--AT-TATAT--ATA
1 TATTGCCGAACTGAATTG--TATATATAT--TTATATTCTCGAATTGAATTATATATATACATA
* * **** *
103170 TATTGCCAAATTGAATTGTATAGGTATACACCTATTGC-CGAATTGAATTATATATATACTTA
1 TATTGCCGAACTGAATTGTATA--TATATTTATATT-CTCGAATTGAATTATATATATACATA
* *
103232 TATTGCCGAACTGAATTGTATATATATTTATATTCTCGAATTGAATTGTATAGGTATACATC
1 TATTGCCGAACTGAATTGTATATATATTTATATTCTCGAATTGAATTATATA--TATACATA
* * ** *
103294 TATTGCTGAATTGGCTTGTATATGTATTTATAT
1 TATTGCCGAACTGAATTGTATATATATTTATAT
103327 ATTGTTGATT
Statistics
Matches: 124, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
56 15 0.12
57 1 0.01
58 21 0.17
59 3 0.02
60 28 0.23
62 56 0.45
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (60 bp):
TATTGCCGAACTGAATTGTATATATATTTATATTCTCGAATTGAATTATATATATACATA
Found at i:103330 original size:32 final size:33
Alignment explanation
Indices: 103068--103330 Score: 124
Period size: 30 Copynumber: 8.6 Consensus size: 33
103058 TATAAATATA
*
103068 TATATGT-TTTATATATTGC-CGAATTTG-ATTCA
1 TATATGTATTTATATATTGCTCGAA-TTGAATT-G
* *
103100 TATATG--GTTATTTATTGC-CGAATTGAATTG
1 TATATGTATTTATATATTGCTCGAATTGAATTG
* *
103130 TATATATATATACTTATATTG-TCGAATTGAA---
1 TATATGTATTTA--TATATTGCTCGAATTGAATTG
*
103161 T-TA--TA--TATATATTGC-CAAATTGAATTG
1 TATATGTATTTATATATTGCTCGAATTGAATTG
* ** ** *
103188 TATAGGTATACACCTATTGC-CGAATTGAATTA
1 TATATGTATTTATATATTGCTCGAATTGAATTG
* * *
103220 TATATATA-CT-TATATTGC-CGAACTGAATTG
1 TATATGTATTTATATATTGCTCGAATTGAATTG
*
103250 TATATATA-TT-TATATT-CTCGAATTGAATTG
1 TATATGTATTTATATATTGCTCGAATTGAATTG
* ** * **
103280 TATAGGTATACATCTATTGCT-GAATTGGCTTG
1 TATATGTATTTATATATTGCTCGAATTGAATTG
103312 TATATGTATTTATATATTG
1 TATATGTATTTATATATTG
103331 TTGATTTGAT
Statistics
Matches: 178, Mismatches: 34, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
24 15 0.08
26 2 0.01
27 1 0.01
28 4 0.02
29 1 0.01
30 60 0.34
31 18 0.10
32 60 0.34
33 2 0.01
34 15 0.08
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (33 bp):
TATATGTATTTATATATTGCTCGAATTGAATTG
Found at i:110343 original size:32 final size:32
Alignment explanation
Indices: 110302--110486 Score: 192
Period size: 32 Copynumber: 5.7 Consensus size: 32
110292 ATGTTTTATT
** ***
110302 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATATATACTTA
110334 TATTGCCGAATTGAATTGTATATATATACTTA
1 TATTGCCGAATTGAATTGTATATATATACTTA
* * *
110366 TATTGCCG-ACTAAATTGTAAATATATACTTACA
1 TATTGCCGAATTGAATTGTATATATATACTT--A
*
110399 TCTATTGCTGAATTGAATTGTATATATATACTTA
1 --TATTGCCGAATTGAATTGTATATATATACTTA
***
110433 TATTATTGAATTGAATTGTATATATATACTTA
1 TATTGCCGAATTGAATTGTATATATATACTTA
* * *
110465 TATTGTCGAATTAAACTGTATA
1 TATTGCCGAATTGAATTGTATA
110487 GGTATACCCC
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
31 19 0.15
32 83 0.64
33 1 0.01
34 1 0.01
35 7 0.05
36 19 0.15
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATATATACTTA
Done.