Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1375
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: 25040
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Found at i:6118 original size:13 final size:13
Alignment explanation
Indices: 6100--6124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6090 CATAAAGTGT
6100 TGTATCGATACAA
1 TGTATCGATACAA
6113 TGTATCGATACA
1 TGTATCGATACA
6125 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6122 original size:33 final size:33
Alignment explanation
Indices: 6080--6146 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6070 TTCAACGATT
6080 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
6113 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
6146 T
1 T
6147 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:6205 original size:13 final size:13
Alignment explanation
Indices: 6187--6211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6177 ATTACTCAAA
6187 TGTATCGATACAT
1 TGTATCGATACAT
6200 TGTATCGATACA
1 TGTATCGATACA
6212 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6276 original size:52 final size:52
Alignment explanation
Indices: 6220--6348 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
6210 CACTGATCTT
* * *
6220 TGTATCGATACATGAAGGTAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
6272 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
6324 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
6349 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:20132 original size:1 final size:1
Alignment explanation
Indices: 20126--20233 Score: 81
Period size: 1 Copynumber: 108.0 Consensus size: 1
20116 AGCGTCCTCC
** ** ** * * *
20126 AAAAAAAAAAAAACGAAAAAAAAATGAAAAACCAAAAAAAAAAAAAAAAACAAAAAACAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
20191 AAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20234 GGGGGTCCGG
Statistics
Matches: 81, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:20149 original size:18 final size:19
Alignment explanation
Indices: 20126--20226 Score: 107
Period size: 21 Copynumber: 5.2 Consensus size: 19
20116 AGCGTCCTCC
*
20126 AAAAAA-AAAAAAACGAAA
1 AAAAAATAAAAAAACAAAA
* *
20144 AAAAAATGAAAAACCAAAA
1 AAAAAATAAAAAAACAAAA
20163 AAAAAA-AAAAAAACAAAA
1 AAAAAATAAAAAAACAAAA
* *
20181 AACAAAAGAAAAAAAAAAACA
1 AA-AAAATAAAAAAACAAA-A
20202 AAAACAATAAAAAAACAAACA
1 AAAA-AATAAAAAAACAAA-A
20223 AAAA
1 AAAA
20227 CAAAAAAGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
18 18 0.26
19 19 0.27
20 12 0.17
21 21 0.30
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (19 bp):
AAAAAATAAAAAAACAAAA
Found at i:20155 original size:19 final size:18
Alignment explanation
Indices: 20126--20233 Score: 94
Period size: 18 Copynumber: 5.8 Consensus size: 18
20116 AGCGTCCTCC
20126 AAAAAAA-AAAAAACGAAA
1 AAAAAAAGAAAAAAC-AAA
* *
20144 AAAAAATGAAAAACCAAA
1 AAAAAAAGAAAAAACAAA
*
20162 AAAAAAAAAAAAAACAAA
1 AAAAAAAGAAAAAACAAA
20180 AAACAAAAGAAAAAA-AAA
1 AAA-AAAAGAAAAAACAAA
* *
20198 AACAAAAACAATAAAAAAACA
1 AA-AAAAAGAA-AAAACAA-A
*
20219 AACAAAAACAAAAAA
1 AA-AAAAAGAAAAAA
20234 GGGGGTCCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
18 38 0.49
19 21 0.27
20 6 0.08
21 12 0.16
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAAACAAA
Found at i:20167 original size:37 final size:35
Alignment explanation
Indices: 20126--20233 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 35
20116 AGCGTCCTCC
*
20126 AAAAAAAAAAAAACGAAAAAA-AAATGAAAAACCAAAA
1 AAAAAAAAAAAAAC-AAAAAACAAAAGAAAAA--AAAA
20163 AAAAAAAAAAAAACAAAAAACAAAAGAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAACAAAAGAAAAAAAAA
* * * * *
20198 AACAAAAACAATA-AAAAAAC-AAACAAAAACAAA
1 AAAAAAAAAAAAACAAAAAACAAAAGAAAAAAAAA
20231 AAA
1 AAA
20234 GGGGGTCCGG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
33 13 0.21
34 7 0.11
35 14 0.22
36 6 0.10
37 23 0.37
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (35 bp):
AAAAAAAAAAAAACAAAAAACAAAAGAAAAAAAAA
Found at i:20181 original size:33 final size:31
Alignment explanation
Indices: 20124--20233 Score: 107
Period size: 33 Copynumber: 3.5 Consensus size: 31
20114 ACAGCGTCCT
*
20124 CCAAAAAAAAAAAAACGAAAA-AAAAATGAAAAA
1 CCAAAAAAAAAAAAA--AAAACAAAAA-AAAAAA
*
20157 CCAAAAAAAAAAAAAAAAACAAAAAACAAAA
1 CCAAAAAAAAAAAAAAAAACAAAAAAAAAAA
* *
20188 -GAAAAAAAAAAACAAAAACAATAAAAAAACAA
1 CCAAAAAAAAAAAAAAAAACAA-AAAAAAA-AA
* *
20220 ACAAAAACAAAAAA
1 CCAAAAAAAAAAAA
20234 GGGGGTCCGG
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
30 19 0.29
31 14 0.22
32 7 0.11
33 25 0.38
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (31 bp):
CCAAAAAAAAAAAAAAAAACAAAAAAAAAAA
Found at i:20231 original size:18 final size:17
Alignment explanation
Indices: 20126--20233 Score: 98
Period size: 17 Copynumber: 6.2 Consensus size: 17
20116 AGCGTCCTCC
20126 AAAAA-AAAAAAAACGAA
1 AAAAACAAAAAAAAC-AA
*
20143 AAAAA-AATGAAAAACCAA
1 AAAAACAA--AAAAAACAA
*
20161 AAAAA-AAAAAAAAAACA
1 AAAAACAAAAAAAACA-A
20178 AAAAACAAAAGAAAA-AA
1 AAAAACAAAA-AAAACAA
* *
20195 AAAAACAAAAACAATAA
1 AAAAACAAAAAAAACAA
20212 AAAAACAAACAAAAACAA
1 AAAAACAAA-AAAAACAA
20230 AAAA
1 AAAA
20234 GGGGGTCCGG
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
16 9 0.12
17 35 0.45
18 24 0.31
19 10 0.13
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (17 bp):
AAAAACAAAAAAAACAA
Found at i:21644 original size:29 final size:27
Alignment explanation
Indices: 21587--21970 Score: 286
Period size: 29 Copynumber: 13.6 Consensus size: 27
21577 CATCATCACC
*
21587 TTCAAAAGTCCACAAGTCAGTGGCATT
1 TTCAAAAGCCCACAAGTCAGTGGCATT
***
21614 TTTTCAAGCCC-CAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA---TT
**
21643 TTCAAAAGCCCACAAGTC-GTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGC-ATT
*
21670 TTC-AAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA---TT
21699 TTC-AAAGCCCCACAAGTCAGTGGCATATT
1 TTCAAAAG-CCCACAAGTCAGTGGC--ATT
21728 TTCAAAAGCCCACAAGTCAGTGGCACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--TT
21757 TT--AAAG-CCACAAGTCAGTGGCATATTTT
1 TTCAAAAGCCCACAAGTCAGTGGC--A--TT
*
21785 TTAAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGC--A-TT
*
21815 TTCAAAAGCCCACAAGTCAGTGGCGTCCT
1 TTCAAAAGCCCACAAGTCAGTGGCAT--T
* **
21844 TT-ACAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGC-ATT
21871 TTCAAAAAGCCCACAAGTCAGTGGCATATTT
1 TTC-AAAAGCCCACAAGTCAGTGGC--A-TT
*
21902 TTC-AAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGC-A-TT
* **
21930 TT-ACAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGC-ATT
21957 TTCAAAA-CCCACAA
1 TTCAAAAGCCCACAA
21971 CGGCGTGGCA
Statistics
Matches: 297, Mismatches: 31, Indels: 58
0.77 0.08 0.15
Matches are distributed among these distances:
26 42 0.14
27 33 0.11
28 53 0.18
29 90 0.30
30 57 0.19
31 21 0.07
32 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (27 bp):
TTCAAAAGCCCACAAGTCAGTGGCATT
Found at i:21752 original size:86 final size:86
Alignment explanation
Indices: 21591--21970 Score: 492
Period size: 86 Copynumber: 4.5 Consensus size: 86
21581 ATCACCTTCA
* * ** *
21591 AAAGTCCACAAGTCAGTGGC-A-TTTTTTCAAGCCC-CAAGTCAGTGGCATTTTTTTCAAAAGCC
1 AAAGCCCACAAGTCAGTGGCAACCTTTTAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCC
*
21653 CACAAGTC-GTGGCAACCTTC
66 CACAAGTCAGTGGCAACCTTT
* * *
21673 AAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCCACAAGTCAGTGGCATA-TTTTCAAAAGC
1 AAAGCCCACAAGTCAGTGGCAACCTTTTAAAAG-CCCACAAGTCAGTGGCATATTTTTCAAAAGC
21737 CCACAAGTCAGTGGC-ACCTTTT
65 CCACAAGTCAGTGGCAACC-TTT
**
21759 AAAG-CCACAAGTCAGTGGCATATTTTTTAAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAG
1 AAAGCCCACAAGTCAGTGGCA-ACCTTTT-AAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAG
**
21823 CCCACAAGTCAGTGGCGTCCTTT
64 CCCACAAGTCAGTGGCAACCTTT
**
21846 ACAAGCCCACAAGTCAGTGGCAACCTTCAAAAAGCCCACAAGTCAGTGGCATATTTTTC-AAAGC
1 A-AAGCCCACAAGTCAGTGGCAACCTTTTAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGC
21910 CCACAAGTCAGTGGCAACCTTT
65 CCACAAGTCAGTGGCAACCTTT
*
21932 ACAAGCCCACAAGTCAGTGGCAACC-TTCAAAA-CCCACAA
1 A-AAGCCCACAAGTCAGTGGCAACCTTTTAAAAGCCCACAA
21971 CGGCGTGGCA
Statistics
Matches: 264, Mismatches: 22, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
82 18 0.07
84 14 0.05
85 46 0.17
86 98 0.37
87 64 0.24
88 8 0.03
89 16 0.06
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (86 bp):
AAAGCCCACAAGTCAGTGGCAACCTTTTAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCC
CACAAGTCAGTGGCAACCTTT
Found at i:21799 original size:57 final size:56
Alignment explanation
Indices: 21591--21953 Score: 366
Period size: 57 Copynumber: 6.4 Consensus size: 56
21581 ATCACCTTCA
* * **
21591 AAAGTCCACAAGTCAGTGGCAT-TTTTT-CAAGCCC-CAAGTCAGTGGCATTTTTTT
1 AAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGCA-CCTTTT
** * *
21645 CAAAAGCCCACAAGTC-GTGGCA-A-CCTTCAAAGCCCACAAGTTAGTGGCACCCTTTT
1 --AAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGCA-CCTTTT
*
21701 CAAAGCCCCACAAGTCAGTGGCATATTTTCAAAAGCCCACAAGTCAGTGGCACCTTTT
1 -AAAG-CCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGCACCTTTT
**
21759 AAAG-CCACAAGTCAGTGGCATATTTTTTAAAAAGCCCACAAGTCAGTGGCATATTTTT
1 AAAGCCCACAAGTCAGTGGCATA-TTTTT-AAAAGCCCACAAGTCAGTGGCA-CCTTTT
* ** * **
21817 CAAAAGCCCACAAGTCAGTGGCGT-CCTTTACAAGCCCACAAGTCAGTGGCAACCTTCAA
1 --AAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGC-ACCTT-TT
*
21876 AAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCAACC-TTT
1 AAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGC-ACCTTTT
21932 ACAAGCCCACAAGTCAGTGGCA
1 A-AAGCCCACAAGTCAGTGGCA
21954 ACCTTCAAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
54 2 0.01
55 34 0.13
56 44 0.17
57 74 0.29
58 59 0.23
59 25 0.10
60 4 0.02
61 16 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGCATATTTTTAAAAGCCCACAAGTCAGTGGCACCTTTT
Found at i:21988 original size:57 final size:57
Alignment explanation
Indices: 21596--22005 Score: 306
Period size: 57 Copynumber: 7.2 Consensus size: 57
21586 CTTCAAAAGT
*** * **** *
21596 CCACAAGTCAGTGGCATTTTTTC-AAGCCC-CAAGTCAGTGGCATTTTTTTCAAAAGC
1 CCACAAGTCAGTGGCATACCTTCAAAACCCACAAGTCAGTGGCACACCTTT-ACAAGC
* * *
21652 CCACAAGTC-GTGGCA-ACCTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTTCAAAGCC
1 CCACAAGTCAGTGGCATACCTTCAAAACCCACAAGTCAGTGGCACACCTTTAC-AAG-C
** *
21708 CCACAAGTCAGTGGCATATTTTCAAAAGCCCACAAGTCAGTGGCAC-CTTTTA-AAG-
1 CCACAAGTCAGTGGCATACCTTCAAAA-CCCACAAGTCAGTGGCACACCTTTACAAGC
** * * ** *
21763 CCACAAGTCAGTGGCATATTTTTTAAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGC
1 CCACAAGTCAGTGGCATA--CCTTCAAAA-CCCACAAGTCAGTGGCACACCTTT-ACAAGC
* * * * *
21824 CCACAAGTCAGTGGCGT-CCTTTACAAGCCCACAAGTCAGTGGCA-ACCTTCAAAAAGC
1 CCACAAGTCAGTGGCATACCTTCA-AAACCCACAAGTCAGTGGCACACCTT-TACAAGC
** *
21881 CCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTTACAAGC
1 CCACAAGTCAGTGGCATA-CCTTCAAAACCCACAAGTCAGTGGCACACCTTTACAAGC
* *
21938 CCACAAGTCAGTGGCA-ACCTTCAAAACCCACAACGGC-GTGGCACACCCTTTTCCGAAGC
1 CCACAAGTCAGTGGCATACCTTCAAAACCCACAA-GTCAGTGGCACA-CC-TTTAC-AAGC
21997 CCACAAGTC
1 CCACAAGTC
22006 CGGTGGTACC
Statistics
Matches: 295, Mismatches: 37, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
54 3 0.01
55 55 0.19
56 35 0.12
57 83 0.28
58 60 0.20
59 40 0.14
60 3 0.01
61 16 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (57 bp):
CCACAAGTCAGTGGCATACCTTCAAAACCCACAAGTCAGTGGCACACCTTTACAAGC
Found at i:22020 original size:116 final size:113
Alignment explanation
Indices: 21641--22005 Score: 343
Period size: 116 Copynumber: 3.2 Consensus size: 113
21631 AGTGGCATTT
** * * *
21641 TTTTCAAAAGCCCACAAGTC-GTGGCA-A-CCTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 TTTTC-AAAGCCCACAAGTCAGTGG-ATATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAC-
**
21703 AAGCCCCACAAGTCAGTGGCATATTTTCAAAAGCCCACAAGTCAGTGG--CACC
63 AAG-CCCACAAGTCAGTGGCA-ACCTTCAAAA-CCCACAAGTCAGTGGCACACC
* **
21755 TTTT-AAAG-CCACAAGTCAGTGGCATATTTTTTAAAAAGCCCACAAGTCAGTGGCATATTTTTC
1 TTTTCAAAGCCCACAAGTCAGTGG-ATA-TTTTT-CAAAGCCCACAAGTCAGTGGCA-ACCTTT-
* ** * *
21818 AAAAGCCCACAAGTCAGTGGCGTCCTTTACAAGCCCACAAGTCAGTGGCA-ACC
61 ACAAGCCCACAAGTCAGTGGCAACCTTCA-AAACCCACAAGTCAGTGGCACACC
***
21871 TTCAAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTACAA
1 TTTTCAAAGCCCACAAGTCAGTGG-ATATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTACAA
*
21936 GCCCACAAGTCAGTGGCAACCTTCAAAACCCACAACGGC-GTGGCACACCC
65 GCCCACAAGTCAGTGGCAACCTTCAAAACCCACAA-GTCAGTGGCACA-CC
*
21986 TTTTCCGAAGCCCACAAGTC
1 TTTT-CAAAGCCCACAAGTC
22006 CGGTGGTACC
Statistics
Matches: 205, Mismatches: 30, Indels: 30
0.77 0.11 0.11
Matches are distributed among these distances:
111 9 0.04
112 10 0.05
113 16 0.08
114 32 0.16
115 28 0.14
116 77 0.38
117 15 0.07
118 18 0.09
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (113 bp):
TTTTCAAAGCCCACAAGTCAGTGGATATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTACAAG
CCCACAAGTCAGTGGCAACCTTCAAAACCCACAAGTCAGTGGCACACC
Found at i:22092 original size:43 final size:43
Alignment explanation
Indices: 22023--22112 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
22013 ACCTTTTCCT
22023 CTTTAAGTCCAATGTAGCGGAACTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCGGAACTTGAATCAGCACATTGGCAC
* *
22066 CTTTAAGTCCAATAG-AGCTGG-CCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAAT-GTAGC-GGAACTTGAATCAGCACATTGGCAC
22109 CTTT
1 CTTT
22113 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 40 0.93
44 3 0.07
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCGGAACTTGAATCAGCACATTGGCAC
Found at i:22314 original size:51 final size:53
Alignment explanation
Indices: 22237--22347 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 53
22227 CATCATCATT
* * *
22237 TTTAAGTCCATAT-CGCTGGCCTTGAATCAGCATATTGGCCA-CC-TTTTCCATC
1 TTTAAGTCCATATAAGCTGGCCTTGAATCAGCACATT-G-CATCCTTTTTCCAGC
*
22289 TTTAAGTTCA-AT-AGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGC
1 TTTAAGTCCATATAAGCTGGCCTTGAATCAGCACATTG-CATCCTTTTTC-CAGC
22342 TTTAAG
1 TTTAAG
22348 CCCAATATCG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 3 0.06
51 25 0.49
52 14 0.27
53 9 0.18
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.36
Consensus pattern (53 bp):
TTTAAGTCCATATAAGCTGGCCTTGAATCAGCACATTGCATCCTTTTTCCAGC
Found at i:22364 original size:169 final size:170
Alignment explanation
Indices: 22067--22617 Score: 829
Period size: 169 Copynumber: 3.3 Consensus size: 170
22057 CATTGGCACC
** *
22067 TTTAAGTCCAATAGAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCATGT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA-AT
22132 AGCTGGCCTTGAATCAGCACATTGACATCCTTTTTC-CAGCTTTAAGCCCAATATCGTTGGCCGT
65 AGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGT
22196 GAATTACATATTGCATCTTTATCACTTTTCTCATCATCATT
130 GAATTACATATTGCATCTTTATCACTTTTCTCATCATCATT
22237 TTTAAGTCC-ATATCGCTGGCCTTGAATCAGCATATTGGCCACCTTTTCCATCTTTAAGTTCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG-CACCTTTTCCATCTTTAAGTTCAAT
22301 AGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCG-TGGCCGT
65 AGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGT
*
22365 GAATTAACA-ATGGCCATCTTTATCACTTTTCTCATCATCATT
130 GAATT-ACATATTG-CATCTTTATCACTTTTCTCATCATCATT
22407 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCCATCTTTAAGTTCAAT-
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATA
* * * *
22470 GTACTGGCCTTGGACTCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCC--CAGCGTTGGCC
66 G--CTGGCCTT-GAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCC
* * * *
22533 GT-AATCACATATTGGATCTTT-TCACTTTTCTCATTCTTCATC
128 GTGAATTACATATTGCATCTTTATCACTTTTCTCA-TCATCATT
*
22575 TTTAAGTCCAATATTGCTGGCCTTGAATCAG-ATA-TGGCACCTT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
22618 CATTATCTTT
Statistics
Matches: 355, Mismatches: 14, Indels: 27
0.90 0.04 0.07
Matches are distributed among these distances:
166 5 0.01
167 18 0.05
168 46 0.13
169 110 0.31
170 109 0.31
171 67 0.19
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (170 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATA
GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTG
AATTACATATTGCATCTTTATCACTTTTCTCATCATCATT
Found at i:23619 original size:49 final size:50
Alignment explanation
Indices: 23519--23633 Score: 155
Period size: 49 Copynumber: 2.3 Consensus size: 50
23509 CACTGATCTT
* * *
23519 TGTATCGATACATGCAGGCAATTTGCCCAATGTATCGATATATTATAAAA
1 TGTATCGATACATGCAGGAAATTTGCCCAATGTATCGATACACTATAAAA
*
23569 TGTATCGATACA-GCAGGTAAATTTGCCCAGAT-T-TCGATACACTATTAAA
1 TGTATCGATACATGCAGG-AAATTTGCCCA-ATGTATCGATACACTATAAAA
23618 TGTATCGATACATGCA
1 TGTATCGATACATGCA
23634 AGCAACTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
49 30 0.52
50 26 0.45
51 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTATCGATACATGCAGGAAATTTGCCCAATGTATCGATACACTATAAAA
Done.