Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold905
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: 51684
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4452 original size:47 final size:47
Alignment explanation
Indices: 4286--4672 Score: 549
Period size: 47 Copynumber: 8.4 Consensus size: 47
4276 TGCCTCGGGA
* *
4286 CTTATCACATTTATACACTTTCACATCCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * * *
4332 CTCATCACATGTATACACCTTCACA-TCAATCATC-TCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTC-ATCA-CATTGGCCATTCGGC
*
4379 CTTATCTC--ATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
4424 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
4471 CTTAT-ACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
4517 CATATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
4564 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTC-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
4610 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
4657 C-T-TCACATATACACAC
1 CTTATCACATATATACAC
4673 CTTGTACATC
Statistics
Matches: 310, Mismatches: 22, Indels: 19
0.88 0.06 0.05
Matches are distributed among these distances:
44 1 0.00
45 48 0.15
46 119 0.38
47 142 0.46
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:4517 original size:93 final size:93
Alignment explanation
Indices: 4286--4672 Score: 536
Period size: 93 Copynumber: 4.2 Consensus size: 93
4276 TGCCTCGGGA
* * * *
4286 CTTATCACATTTATACACTTTCACATCCATCACA-TGGCCATTCGGCCTCATCACATGTATACAC
1 CTTAT-ACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
4350 CTTCACA-TCAATCATC-TCGGCCATTAGGT
65 TTTCACATTC-ATCA-CATCGGCCATTAGGC
4379 CTTAT-C-TCATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATACAT-ATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * *
4442 TTTCACATTCATCACATTGGCCACTCGGC
65 TTTCACATTCATCACATCGGCCATTAGGC
* *
4471 CTTATACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCATATCACATATATACACT
1 CTTATACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT
* *
4536 TTCACATTCATCACATTGGCCATTCGGC
66 TTCACATTCATCACATCGGCCATTAGGC
*
4564 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTC-GCCTTATCACATATATACAC
1 CTTAT-ACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
4628 TTTCACATTCATCACATCGGCCATTAGGC
65 TTTCACATTCATCACATCGGCCATTAGGC
* *
4657 CTT-CACATATACACAC
1 CTTATACATATATACAC
4673 CTTGTACATC
Statistics
Matches: 268, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
90 1 0.00
91 35 0.13
92 52 0.19
93 143 0.53
94 37 0.14
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (93 bp):
CTTATACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGC
Found at i:4574 original size:140 final size:140
Alignment explanation
Indices: 4286--4672 Score: 565
Period size: 140 Copynumber: 2.8 Consensus size: 140
4276 TGCCTCGGGA
* * * *
4286 CTTATCACATTTATACACTTTCACATCCATCACA-TGGCCATTCGGCCTCATCACATGTATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * *
4350 CTTCACA-TCAATCATC-TCGGCCATTAGGTCTTATCTC--ATATACACTTTCACATTCATCACA
66 TTTCACATTC-ATCA-CATCGGCCATTAGG-CCTATCACATATATACACTTTCACATTCATCACA
4411 TTGGCCATTCGGC
128 TTGGCCATTCGGC
*
4424 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCTTAT-ACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * *
4488 TTTCACATTCATCACATTGGCCACTCGGCCATATCACATATATACACTTTCACATTCATCACATT
66 TTTCACATTCATCACATCGGCCATTAGGCC-TATCACATATATACACTTTCACATTCATCACATT
4553 GGCCATTCGGC
130 GGCCATTCGGC
*
4564 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTC-GCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
4628 TTTCACATTCATCACATCGGCCATTAGGCCT-TCACATATACACAC
66 TTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACAC
4673 CTTGTACATC
Statistics
Matches: 225, Mismatches: 17, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
137 2 0.01
138 80 0.36
139 25 0.11
140 118 0.52
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (140 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACTTTCACATTCATCACATTG
GCCATTCGGC
Found at i:8127 original size:40 final size:40
Alignment explanation
Indices: 8033--8177 Score: 168
Period size: 40 Copynumber: 3.6 Consensus size: 40
8023 TACTCGAATG
*
8033 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
8074 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * * *
8114 ATATCCGAGCTAAGTCCCGAAGGCATTTATTG-TAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTT-GTGCTAGCGACT
* *
8154 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
8178 CTTGTGCGAG
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 57 0.64
41 30 0.34
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:15541 original size:47 final size:47
Alignment explanation
Indices: 15478--15772 Score: 459
Period size: 47 Copynumber: 6.3 Consensus size: 47
15468 CCCTTCGGGA
* *
15478 CTTATCACATTTATACACTTTCACA-TCAATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTC-ATCACATTGGCCATTAGGC
* * *
15525 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
15572 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
15619 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATT-AGGC
* *
15666 CTTATCACATATATACACTTTCACATTCATCACACTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
15713 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
15760 CTTATCACATATA
1 CTTATCACATATA
15773 CATATCTTGT
Statistics
Matches: 228, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
46 1 0.00
47 225 0.99
48 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:15697 original size:25 final size:25
Alignment explanation
Indices: 15623--15699 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
15613 TTAGGCCTTG
15623 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
** * *
15648 TCACAT-T-GGC-CATTCAGCCTT-A
1 TCACATATATACACTTTCA-CATTCA
15670 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
15695 TCACA
1 TCACA
15700 CTGGCCATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 12 0.31
23 5 0.13
24 5 0.13
25 17 0.44
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:29811 original size:37 final size:37
Alignment explanation
Indices: 29752--29897 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
29742 AGCGCAGATG
* *
29752 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
29789 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
29826 TAATCTCCACACGTAATCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
29863 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
29898 ATATATTTCC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:30099 original size:48 final size:48
Alignment explanation
Indices: 30044--30444 Score: 570
Period size: 48 Copynumber: 8.1 Consensus size: 48
30034 ACACATCGCC
*
30044 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * *
30092 TACATATTTCACACTAGTCACTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* *
30144 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
30192 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC------A
* * *
30246 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
*
30296 TATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
30344 TACATATTTCACATTAGACATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
30392 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
30440 TACAT
1 TACAT
30445 CAATTTCAGC
Statistics
Matches: 323, Mismatches: 18, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
48 187 0.58
49 1 0.00
50 48 0.15
51 1 0.00
52 41 0.13
54 45 0.14
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:30165 original size:100 final size:100
Alignment explanation
Indices: 30047--30437 Score: 605
Period size: 100 Copynumber: 3.9 Consensus size: 100
30037 CATCGCCTAC
* * *
30047 ATATTTCACACT-AGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGTC
1 ATATTTCACATTGA-CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCC
*
30111 ACTCGGCTTTACCACATATACATATCTCATATATAT
65 ATTCGGCTTTACCACATATACATATCTCATATATAT
*
30147 ATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
30212 TTCGGCTTTACCACATATACATATCTCATATATATAT
66 TTCGGCTTTACCACATATACATATCTC--ATATATAT
* * *
30249 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATATATATTTCACATTAGC
1 ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATTAGC
*
30314 CATTCGGCTTTACCACATATACATATCTC----ATAC
64 CATTCGGCTTTACCACATATACATATCTCATATATAT
30347 ATATTTCACATTAGA-CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCC
1 ATATTTCACATT-GACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCC
30411 ATTCGGCTTTACCACATATACATATCT
65 ATTCGGCTTTACCACATATACATATCT
30438 TATACATCAA
Statistics
Matches: 272, Mismatches: 13, Indels: 16
0.90 0.04 0.05
Matches are distributed among these distances:
96 46 0.17
98 43 0.16
99 1 0.00
100 85 0.31
101 1 0.00
102 49 0.18
104 47 0.17
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (100 bp):
ATATTTCACATTGACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
TTCGGCTTTACCACATATACATATCTCATATATAT
Found at i:30352 original size:152 final size:147
Alignment explanation
Indices: 30044--30437 Score: 621
Period size: 152 Copynumber: 2.6 Consensus size: 147
30034 ACACATCGCC
* *
30044 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
* *
30109 TCACTCGGCTTTACCACATATACATATCTCATATATATATATTTCACATTGACCATTCGGCTTTA
66 CCATTCGGCTTTACCACATATACATATCTCA-ATATATATATTTCACATTGACCATTCGGCTTTA
*
30174 CCACATATGCATATCTCA
130 CCACATATACATATCTCA
*
30192 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATATATTTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC------ATACATATTTCA
* *
30257 CATTAACCATTCAGCTTTACCACATATACATATCTC-ATATATATATTTCACATT-AGCCATTCG
60 CATTAGCCATTCGGCTTTACCACATATACATATCTCAATATATATATTTCACATTGA-CCATTCG
30320 GCTTTACCACATATACATATCTCA
124 GCTTTACCACATATACATATCTCA
*
30344 TACATATTTCACATTAGACATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
30409 CCATTCGGCTTTACCACATATACATATCT
66 CCATTCGGCTTTACCACATATACATATCT
30438 TATACATCAA
Statistics
Matches: 227, Mismatches: 12, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
146 44 0.19
148 46 0.20
151 1 0.00
152 94 0.41
154 42 0.19
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (147 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCTTTACCACATATACATATCTCAATATATATATTTCACATTGACCATTCGGCTTTAC
CACATATACATATCTCA
Found at i:35791 original size:29 final size:28
Alignment explanation
Indices: 35717--35863 Score: 145
Period size: 29 Copynumber: 5.2 Consensus size: 28
35707 TACATACCTG
* *
35717 CATATGGCCCA-CTAGGCCCAATCTCTTT
1 CATATGGCCCATC-AGGCCCAATCACATT
* ** *
35745 TATAAAGCCCATCTGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCACATT
35774 CATATGGCCCATCAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCACATT
* * *
35803 CATAGGGCCCATTAGGCCCAATCTCATT
1 CATATGGCCCATCAGGCCCAATCACATT
* *
35831 TATATGGCCCATCCGGCCCAAATCACATT
1 CATATGGCCCATCAGGCCC-AATCACATT
35860 -ATAT
1 CATAT
35864 TCATGCTCAC
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
28 40 0.41
29 58 0.59
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (28 bp):
CATATGGCCCATCAGGCCCAATCACATT
Found at i:35836 original size:57 final size:58
Alignment explanation
Indices: 35717--35859 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 58
35707 TACATACCTG
* * * **
35717 CATATGGCCCA-CTAGGCCC-AATCTCTTTTATAAAGCCCATCTGGCCCAATTCACATT
1 CATATGGCCCATC-AGGCCCAAATCACATTCATAGGGCCCATCTGGCCCAATTCACATT
* *
35774 CATATGGCCCATCAGGCCCAATTCACATTCATAGGGCCCAT-TAGGCCCAA-TCTCATT
1 CATATGGCCCATCAGGCCCAAATCACATTCATAGGGCCCATCT-GGCCCAATTCACATT
* *
35831 TATATGGCCCATCCGGCCCAAATCACATT
1 CATATGGCCCATCAGGCCCAAATCACATT
35860 ATATTCATGC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 50 0.68
58 23 0.32
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.26
Consensus pattern (58 bp):
CATATGGCCCATCAGGCCCAAATCACATTCATAGGGCCCATCTGGCCCAATTCACATT
Found at i:37459 original size:13 final size:13
Alignment explanation
Indices: 37441--37465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37431 CCGAAACTAG
37441 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
37454 AAAGAAAAAAAA
1 AAAGAAAAAAAA
37466 TGCTCATCCT
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:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:38654 original size:38 final size:39
Alignment explanation
Indices: 38596--38669 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
38586 GGACTAAGAT
38596 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGC
*
38635 CCGAAGGCA-TTGTGCGAGATACTAATTCCGGGCTA
1 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTA
38670 TGCGAGTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGC
Found at i:38707 original size:62 final size:61
Alignment explanation
Indices: 38609--38733 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 61
38599 AAGGCATTTG
* *
38609 TGCGAGATACTAATTCCAGGCTAAGCCCGAAGGCATTGTGCGAGATACTA-ATTCCGGGCTA
1 TGCGAGATACTAAATCCAGGCTAAGCCCGAAGGCATTGTGCGAGATACTATA-ACCGGGCTA
* * * *
38670 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTATAACCGGGCTA
1 TGCGAGATACTAAATCCAGGCTAAG-CCCGAAGGCATTGTGCGAGATACTATAACCGGGCTA
38732 TG
1 TG
38734 TCCCGAAGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 21 0.38
62 34 0.61
63 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (61 bp):
TGCGAGATACTAAATCCAGGCTAAGCCCGAAGGCATTGTGCGAGATACTATAACCGGGCTA
Found at i:38728 original size:39 final size:39
Alignment explanation
Indices: 38670--38746 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
38660 TTCCGGGCTA
*
38670 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTG
1 TGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTG
*
38709 TGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
38747 TGAACGAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTG
Found at i:45293 original size:29 final size:28
Alignment explanation
Indices: 45221--45364 Score: 136
Period size: 29 Copynumber: 5.2 Consensus size: 28
45211 CTACATACCG
*
45221 CATATGGCCCA-CTAGGCCCAATCTC-TT
1 CATATGGCCCATC-AGGCCCAATCACATT
* * *
45248 TATA-AGCCCATCTGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCACATT
45276 CATATGGCCCATCAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCACATT
* * *
45305 CATAGGGCCCATTA-GCCCAATCTCATT
1 CATATGGCCCATCAGGCCCAATCACATT
* *
45332 TATATGGCCCATCCGGCCCAAATCACATT
1 CATATGGCCCATCAGGCCC-AATCACATT
45361 -ATAT
1 CATAT
45365 TCATGCTCAC
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
26 12 0.12
27 23 0.24
28 19 0.20
29 42 0.44
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATCAGGCCCAATCACATT
Found at i:45341 original size:56 final size:58
Alignment explanation
Indices: 45221--45360 Score: 157
Period size: 56 Copynumber: 2.5 Consensus size: 58
45211 CTACATACCG
* * * *
45221 CATATGGCCCA-CTAGGCCC-AATCTC-TTTATA-AGCCCATCTGGCCCAATTCACATT
1 CATATGGCCCATC-AGGCCCAAATCACATTCATAGGGCCCATCTAGCCCAATTCACATT
* *
45276 CATATGGCCCATCAGGCCCAATTCACATTCATAGGGCCCAT-TAGCCCAA-TCTCATT
1 CATATGGCCCATCAGGCCCAAATCACATTCATAGGGCCCATCTAGCCCAATTCACATT
* *
45332 TATATGGCCCATCCGGCCCAAATCACATT
1 CATATGGCCCATCAGGCCCAAATCACATT
45361 ATATTCATGC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
55 17 0.24
56 37 0.51
57 12 0.17
58 6 0.08
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (58 bp):
CATATGGCCCATCAGGCCCAAATCACATTCATAGGGCCCATCTAGCCCAATTCACATT
Found at i:48161 original size:37 final size:39
Alignment explanation
Indices: 48063--48225 Score: 173
Period size: 38 Copynumber: 4.3 Consensus size: 39
48053 GGACTAAGAT
*
48063 CCGAA-GCATTTGTGCGAGATACTAATTCCAGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
48101 CCGAAGGCA-TTGTGCGAGATACTAATTCCGGGCT-AG-
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* * *
48137 CCGAAGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
* * *
48176 CCGAA-GCATTTGTGC--GATACT-ATAACCGCGGCTATGT
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCG-GGCTAAGC
48213 CCGAAGGCATTTG
1 CCGAAGGCATTTG
48226 AACGAGGAGC
Statistics
Matches: 106, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
35 1 0.01
36 19 0.18
37 27 0.25
38 51 0.48
39 8 0.08
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
Found at i:48161 original size:75 final size:76
Alignment explanation
Indices: 48062--48225 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 76
48052 CGGACTAAGA
*
48062 TCCGAA-GCATTTGTGCGAGATACTAATTCCAGGCTAAG-CCCGAAGGCA-TTGTGCGAGATACT
1 TCCGAAGGCATTTGTGCGAGATACTAAATCC-GGCTAAGTCCCGAA-GCATTTGTGC--GATACT
*
48124 A-ATTCCG-GGCTA-G
62 ATA-ACCGCGGCTATG
* *
48137 -CCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGCATTTGTGCGATACTATAA
1 TCCGAAGGCATTTGTGCGAGATACTAAATCCGGCTAAGTCCCGAAGCATTTGTGCGATACTATAA
48201 CCGCGGCTATG
66 CCGCGGCTATG
48212 TCCGAAGGCATTTG
1 TCCGAAGGCATTTG
48226 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
73 10 0.13
74 20 0.26
75 35 0.45
76 13 0.17
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (76 bp):
TCCGAAGGCATTTGTGCGAGATACTAAATCCGGCTAAGTCCCGAAGCATTTGTGCGATACTATAA
CCGCGGCTATG
Done.