Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2235
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: 26472
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Found at i:3397 original size:20 final size:20
Alignment explanation
Indices: 3326--3403 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
3316 AATGTCCAAA
3326 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACAT-TTTTCT
* *
3346 GTGTATCGATACATTTGGAAATTCA
1 ATGTATCGATACATTT-----TTCT
3371 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
3391 TTGTATCGATACA
1 ATGTATCGATACA
3404 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.04
20 28 0.60
24 2 0.04
25 15 0.32
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:3410 original size:13 final size:13
Alignment explanation
Indices: 3392--3429 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3382 CATTTTTCTT
3392 TGTATCGATACAA
1 TGTATCGATACAA
*
3405 TGTATCGATACAC
1 TGTATCGATACAA
3418 TGTATCGATACA
1 TGTATCGATACA
3430 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3588 original size:20 final size:20
Alignment explanation
Indices: 3545--3589 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3535 AAATCTTTTG
3545 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3566 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3586 CAAA
1 CAAA
3590 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:6013 original size:13 final size:13
Alignment explanation
Indices: 5995--6020 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5985 ACAACCAAGT
5995 ATGTATCGATACA
1 ATGTATCGATACA
6008 ATGTATCGATACA
1 ATGTATCGATACA
6021 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6106 original size:19 final size:20
Alignment explanation
Indices: 6074--6113 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
6064 GCTATATTTT
6074 TCAAAATATGTATCGATACA
1 TCAAAATATGTATCGATACA
6094 TCAAAAT-TGTATCGATACA
1 TCAAAATATGTATCGATACA
6113 T
1 T
6114 TCACACGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (20 bp):
TCAAAATATGTATCGATACA
Found at i:6807 original size:21 final size:21
Alignment explanation
Indices: 6783--6840 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
6773 TAAGCTTTCA
6783 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
6804 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
6825 AATGTATCGATACATT
1 AATGTATCGATACATT
6841 CCACAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:6849 original size:21 final size:21
Alignment explanation
Indices: 6781--6859 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
6771 GATAAGCTTT
**
6781 CAAATGTATCGATACATTTGTA
1 CAAATGTATCGATACA-TTCCA
* ***
6803 -GAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTCCA
**
6823 GGAATGTATCGATACATTCCA
1 CAAATGTATCGATACATTCCA
6844 CAAATGTATCGATACA
1 CAAATGTATCGATACA
6860 GGGTCCCAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.04
21 45 0.96
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCCA
Found at i:6959 original size:32 final size:32
Alignment explanation
Indices: 6897--6959 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
6887 TTCAGCGATT
* **
6897 TGTATCGATACATAAATGTTGTATTTATACAA
1 TGTATCGATACATAAATATTGTATCAATACAA
*
6929 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAATATTGTATCAATACA
6960 TAATTAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCAATACAA
Found at i:7045 original size:34 final size:33
Alignment explanation
Indices: 6982--7048 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
6972 GCCAAGGGAA
* *
6982 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCAATACATTATTCTGTGTATCGATACAT
*
7015 TGTATCAATACATCTATTCTTTGTATCGATACAT
1 TGTATCAATACAT-TATTCTGTGTATCGATACAT
7049 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
TGTATCAATACATTATTCTGTGTATCGATACAT
Found at i:7579 original size:12 final size:12
Alignment explanation
Indices: 7553--7585 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
7543 AATCCTTTAG
7553 CAAAAAAAC-CA
1 CAAAAAAACACA
7564 -AAAAAAACACA
1 CAAAAAAACACA
7575 CAAAAAAACAC
1 CAAAAAAACAC
7586 TATTCCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAACACA
Found at i:7913 original size:19 final size:19
Alignment explanation
Indices: 7889--7956 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
7879 AATTCAACGA
7889 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
7908 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
7923 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
7940 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
7957 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:7927 original size:32 final size:32
Alignment explanation
Indices: 7891--7953 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7881 TTCAACGATT
*
7891 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
7923 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
7954 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:7928 original size:13 final size:13
Alignment explanation
Indices: 7910--7934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7900 ACATAAGTTT
7910 TGTATCGATACAA
1 TGTATCGATACAA
7923 TGTATCGATACA
1 TGTATCGATACA
7935 TAAGTATTGT
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:8014 original size:13 final size:13
Alignment explanation
Indices: 7996--8021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7986 CATTTTTCTG
7996 TGTATCGATACAT
1 TGTATCGATACAT
8009 TGTATCGATACAT
1 TGTATCGATACAT
8022 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8018 original size:33 final size:33
Alignment explanation
Indices: 7976--8042 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7966 GCCAAGGAAA
***
7976 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
8009 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
8042 T
1 T
8043 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:8253 original size:992 final size:990
Alignment explanation
Indices: 6849--8836 Score: 3301
Period size: 992 Copynumber: 2.0 Consensus size: 990
6839 TTCCACAAAT
* * *
6849 GTATCGATACAGGGTCCCAACGGTCAAAATTTTTGAATTTCAGCGATTTGTATCGATACATAAAT
1 GTATCGATACAGGGTCCCAACGGTCAAAAATTTTGAAATTCAACGATTTGTATCGATACATAAAT
**
6914 GTTGTATTTATACAATGTATCGATACATAAGTATTGTATCAATACATAATTAGCTACTGCCAAGG
66 GTTGTATCGATACAATGTATCGATACATAAGTATTGTATCAATACATAATTAGCTACTGCCAAGG
* *
6979 GAATGTATCGATACATTTTTCTGTGTATCGATACATTGTATCAATACATCTATTCTTTGTATCGA
131 AAATGTATCGATACATTTTTCTGTGTATCGATACATTGTATCAATACATCGATTCTTTGTATCGA
7044 TACATCTAGGAAGTTTACCCAGATGTATCGATACATTTTACAATGTATCGATACATTCAGGCATT
196 TACATCTAGGAAGTTTACCCAGATGTATCGATACATTTTACAATGTATCGATACATTCAGGCATT
7109 TTTTGACTACTTCGAGCCACTTTTCTGCTTTGCCATTGTTCATTCAAAACATGTTTTTAACACAC
261 TTTTGACTACTTCGAGCCACTTTTCTGCTTTGCCATTGTTCATTCAAAACATGTTTTTAACACAC
* *
7174 ATATTGCATCTAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTCGGAATGCAAGTTAA
326 ATATTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTCGGAATACAAGTTAA
7239 ACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAAAGGACATGTCAGAT
391 ACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAAAGGACATGTCAGAT
*
7304 TTTTCTGAATTCTGGCAGTCTCAGGTTCAGGGCCACCACTGCATTGCAGAACCAATGGCAATGAG
456 TTTTCTGAATTCTGGCAGTCTCAGGTTCAGGACCACCACTGCATTGCAGAACCAATGGCAATGAG
*
7369 GGGCAGCCTGA-GCT-TTGCCTCCTTGGGCAAAAGGGAAAATACCATAATGCCCTTGGTTTGTCC
521 GGGCAGCCTGAGGCTGTTGCCTCCTTGGGCAAAAGGGAAAATACCATAATACCCTTGGTTTGTCC
7432 CCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTGGCTCAGTAAAAAAGGGATCATT
586 CCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTGGCTCAG-AAAAAAGGGATCATT
* *
7497 TTCTGAAAAAAAAAAACCATTTTCCAGCAGC-AAGAAACCCTTAAGAAATCCTTTAGCAAAAAAA
650 TTCTGAAAAAAAAAAA-CA-TTTCCAGCAACAAAAAAACCCTTAAGAAATCCTTTAGCAAAAAAA
7561 CCAAAA-AAAACACACAA-AAAAACACTATTCCATTAGTTTCCAAACTCCATTCCCGTAGCTCCA
713 --AAAACAAAA-ACA-AAGAAAAACACTATTCCATTAGTTTCCAAACTCCATTCCCGTAGCTCCA
* *
7624 AAAGCCACCACCAAAAACCCTCCAAAAACTCCATATTCCTCACACTTTCACCCAAAAACAG-CTC
774 AAAACCACCACCAAAAAACCTCCAAAAACTCCATATTCCTCACACTTTCACCCAAAAACAGCCTC
* * * *
7688 TTCTCTCAACCATACTACCCAAAAGCTACATCCTTTCATCCTTTTCTTGCTAAATAATAGCAAAG
839 -TCCCTCAACCAGACTACCAAAAAGCTACATCATTTCATCCTTTTCTTGCTAAATAATAGCAAAG
* * *
7753 AGAGGGAGAAAACTAGGCCAACAACCCTTATTTCGGGAAACAAGGAAAGTTCAAGCCTTTTGGTA
903 AGAGGGAGAAAACTAGGCCAACAACCCTTATTCCGAGAAACAAGGAAAGCTCAAG-C-TTTGGTA
7818 TATTCTCTCTACCTTGATCTTTTGG
966 TATTCTCTCTACCTTGATCTTTTGG
* *
7843 GTATCGATATAGGGTCCCAACGGTCAAAAATTTTGAAATTCAACGATTTGTATCGATACATAAGT
1 GTATCGATACAGGGTCCCAACGGTCAAAAATTTTGAAATTCAACGATTTGTATCGATACATAAAT
* *
7908 TTTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACATAATTAGCTACTGCCAAGG
66 GTTGTATCGATACAATGTATCGATACATAAGTATTGTATCAATACATAATTAGCTACTGCCAAGG
* *
7973 AAATGTATCGATACATTTTTCTGTGTATCGATACATTGTATCGATACATGGA-TCTTTGTATCGA
131 AAATGTATCGATACATTTTTCTGTGTATCGATACATTGTATCAATACATCGATTCTTTGTATCGA
* *
8037 TACAT-TTGGAAATTTTACCCAGATGTATCGATACATTTTACAATGTATCGATACATTCAGGCA-
196 TACATCTAGG-AAGTTTACCCAGATGTATCGATACATTTTACAATGTATCGATACATTCAGGCAT
8100 TTTTTGACTACTTCGAGCCACTTTTCTGCTTTGCCATTGTTCATTCAAAACATGTTTTTAACACA
260 TTTTTGACTACTTCGAGCCACTTTTCTGCTTTGCCATTGTTCATTCAAAACATGTTTTTAACACA
*
8165 CATTTTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTCGGAATACAAGTTA
325 CATATTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTCGGAATACAAGTTA
8230 AACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAAAGGACATGTCAGA
390 AACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAAAGGACATGTCAGA
8295 TTTTTCTGAATTCTGGCAGTCTCAGGTTCAGGACCACCACTGCATTGCAGAACCAATGGCAATGA
455 TTTTTCTGAATTCTGGCAGTCTCAGGTTCAGGACCACCACTGCATTGCAGAACCAATGGCAATGA
8360 GGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATACCATAATACCCTTG
520 GGGGCAGCCTGA------GGCT-GTTGCCTCCTTGGGCAAAAGGGAAAATACCATAATACCCTTG
* **
8425 GTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTGGCTCAGCAAAGGGG
578 GTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTGGCTCAGAAAAAAGG
* * * *
8490 GATCCTTTTCTGAAAAAAAAACAGATTTCCAGCAACAAAAAAACCCTTAGGAAATCCTTTAGCAA
643 GATCATTTTCTGAAAAAAAAAAACATTTCCAGCAACAAAAAAACCCTTAAGAAATCCTTTAGCAA
* *
8555 AAAAAAAAACCAAAAACAAAGAAAAACACTATTCCATTGGTTTTCAAACTCCATTCCCGTAGCTC
708 AAAAAAAAA-CAAAAACAAAGAAAAACACTATTCCATTAGTTTCCAAACTCCATTCCCGTAGCTC
* **
8620 CAAAAACCACCACCAAAAAACCTCCAAAAACTCCATATTCCTTACACTTTCACCCCCAAACAGCC
772 CAAAAACCACCACCAAAAAACCTCCAAAAACTCCATATTCCTCACACTTTCACCCAAAAACAGCC
* * * *
8685 TCTCCCTTAGCTAGACTACCAAAAAGCTACCTCATTTCATCCTTTTCTTGCTAAATAATAGCAAA
837 TCTCCCTCAACCAGACTACCAAAAAGCTACATCATTTCATCCTTTTCTTGCTAAATAATAGCAAA
* *
8750 GAGAGGGAGAAAACTAGGCCACCAACCTTTATTCCGAGAAACAAGGAAAGCTCAAGCTTTGGTAT
902 GAGAGGGAGAAAACTAGGCCAACAACCCTTATTCCGAGAAACAAGGAAAGCTCAAGCTTTGGTAT
8815 ATTCTCTCTACCTTGATCTTTT
967 ATTCTCTCTACCTTGATCTTTT
8837 TGGTTTCTGT
Statistics
Matches: 930, Mismatches: 49, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
992 271 0.29
993 69 0.07
994 169 0.18
996 30 0.03
997 7 0.01
998 219 0.24
999 42 0.05
1000 26 0.03
1001 97 0.10
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (990 bp):
GTATCGATACAGGGTCCCAACGGTCAAAAATTTTGAAATTCAACGATTTGTATCGATACATAAAT
GTTGTATCGATACAATGTATCGATACATAAGTATTGTATCAATACATAATTAGCTACTGCCAAGG
AAATGTATCGATACATTTTTCTGTGTATCGATACATTGTATCAATACATCGATTCTTTGTATCGA
TACATCTAGGAAGTTTACCCAGATGTATCGATACATTTTACAATGTATCGATACATTCAGGCATT
TTTTGACTACTTCGAGCCACTTTTCTGCTTTGCCATTGTTCATTCAAAACATGTTTTTAACACAC
ATATTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTCGGAATACAAGTTAA
ACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAAAGGACATGTCAGAT
TTTTCTGAATTCTGGCAGTCTCAGGTTCAGGACCACCACTGCATTGCAGAACCAATGGCAATGAG
GGGCAGCCTGAGGCTGTTGCCTCCTTGGGCAAAAGGGAAAATACCATAATACCCTTGGTTTGTCC
CCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTGGCTCAGAAAAAAGGGATCATTT
TCTGAAAAAAAAAAACATTTCCAGCAACAAAAAAACCCTTAAGAAATCCTTTAGCAAAAAAAAAA
ACAAAAACAAAGAAAAACACTATTCCATTAGTTTCCAAACTCCATTCCCGTAGCTCCAAAAACCA
CCACCAAAAAACCTCCAAAAACTCCATATTCCTCACACTTTCACCCAAAAACAGCCTCTCCCTCA
ACCAGACTACCAAAAAGCTACATCATTTCATCCTTTTCTTGCTAAATAATAGCAAAGAGAGGGAG
AAAACTAGGCCAACAACCCTTATTCCGAGAAACAAGGAAAGCTCAAGCTTTGGTATATTCTCTCT
ACCTTGATCTTTTGG
Found at i:10441 original size:51 final size:53
Alignment explanation
Indices: 10377--10507 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
10367 AGTTTCTCAA
* * * *
10377 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
10428 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
10482 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
10508 CCCGTTAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
53 9 0.13
54 20 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:10521 original size:27 final size:25
Alignment explanation
Indices: 10491--10563 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 25
10481 TTTCTTCACA
10491 ATCGGGGATACTCCAACCCCGTTAAT
1 ATCGGGGATACTCCAACCCCGTT-AT
10517 CATCGGGGATACTCCAACCCCGTTAT
1 -ATCGGGGATACTCCAACCCCGTTAT
*
10543 TTCGAGGGGATACTCCAACCC
1 ATC--GGGGATACTCCAACCC
10564 TGACTTTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 2 0.05
26 2 0.05
27 39 0.91
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (25 bp):
ATCGGGGATACTCCAACCCCGTTAT
Found at i:10714 original size:52 final size:50
Alignment explanation
Indices: 10550--10716 Score: 158
Period size: 51 Copynumber: 3.3 Consensus size: 50
10540 TATTTCGAGG
* *** * *
10550 GGATACTCCAACCCTGACTTTATTTCCAAAATATTGACTTTTCATAATCGA
1 GGATACTCCAACCC-GATTTTATTTCCAAAATACCAATTTTTCACAATCGA
* * * * *
10601 GGATACTCCACCCCCGGTTTTATTTTC-AAACACCAATTTTTC-CTTAATCGG
1 GGATACTCCA-ACCCGATTTTATTTCCAAAATACCAATTTTTCAC--AATCGA
*
10652 GGATACTCCAACTCCGATTTTATTTCCAAGAATACCAATTTTTCACAGTCGA
1 GGATACTCCAAC-CCGATTTTATTTCCAA-AATACCAATTTTTCACAATCGA
10704 GGATACTCCAACC
1 GGATACTCCAACC
10717 TCGTTATGTC
Statistics
Matches: 92, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
50 11 0.12
51 47 0.51
52 20 0.22
53 13 0.14
54 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (50 bp):
GGATACTCCAACCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGA
Found at i:10736 original size:28 final size:28
Alignment explanation
Indices: 10704--10775 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
10694 TCACAGTCGA
* **
10704 GGATACTCCAACCTCGTTA-TGTCATCGG
1 GGATACTCCAACCCCGTTACT-TCAGAGG
*
10732 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
10760 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
10776 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:10770 original size:210 final size:210
Alignment explanation
Indices: 10385--10826 Score: 642
Period size: 210 Copynumber: 2.1 Consensus size: 210
10375 AATTCTCCAC
* * *
10385 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* *
10450 TAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCGTTA
66 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTA
* * *
10515 ATCATCGGGGATACTCCAACCCCGTTATTTCGAGGGGATACTCCAACCCTGACTTTATTTCCAAA
131 ATCATCGGGGATACTCCAACCCCGTTATTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAA
10580 ATATTGACTTT-TCAT
196 ATATTGA-TTTCTCAT
* * *
10595 AATCGAGGATACTCCACCCCCGGTTTTATTTTC-AAACACCAATTTTTCCT-TAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGGGGATAC
* * * *
10658 TCCAACTCCGATTTTATTTCC-AAGAATACCAATTT-TTCACAGTCGAGGATACTCCAACCTCGT
64 TCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGT
* *
10721 TATGTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCC
129 TA-ATCATCGGGGATACTCCAACCCCGTTA-TTCCGAGGGGATACTCCAACCCCGACTTTATTCC
10786 CAAAATATTGATTTCTCAT
192 CAAAATATTGATTTCTCAT
*
10805 AATTGGGGATACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
10827 TTATTTTCGA
Statistics
Matches: 207, Mismatches: 20, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
208 27 0.13
209 49 0.24
210 129 0.62
211 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (210 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTATTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAA
ATATTGATTTCTCAT
Found at i:10960 original size:79 final size:77
Alignment explanation
Indices: 10729--10961 Score: 241
Period size: 79 Copynumber: 2.9 Consensus size: 77
10719 GTTATGTCAT
* * * *
10729 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GTTTTATT-CCAAAACAT
* *
10794 TGATTTCTCATAAT
64 TGATTTCTCACAAC
* * * * * *
10808 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG--TTTTATTCCAAAACAT
*
10873 CGATTTCTCACAAC
64 TGATTTCTCACAAC
* * * *
10887 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCGTTATTATCTCCAAAACAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTT-TTAT-TCCAAAACAT
* *
10952 TAAATTCTCA
64 TGATTTCTCA
10962 TCGAGAAATA
Statistics
Matches: 124, Mismatches: 26, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 113 0.91
80 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (77 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTTTTATTCCAAAACATTG
ATTTCTCACAAC
Found at i:23339 original size:11 final size:10
Alignment explanation
Indices: 23323--23374 Score: 68
Period size: 11 Copynumber: 4.9 Consensus size: 10
23313 ACCTTCTCTT
23323 CAAAAAAAAA
1 CAAAAAAAAA
23333 GCAAAAAAAAA
1 -CAAAAAAAAA
*
23344 AAAAAAAAAA
1 CAAAAAAAAA
23354 CAAAAAACAAA
1 CAAAAAA-AAA
23365 CAAAGAAAAA
1 CAAA-AAAAA
23375 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 15 0.41
11 19 0.51
12 3 0.08
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:23349 original size:20 final size:22
Alignment explanation
Indices: 23323--23375 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
23313 ACCTTCTCTT
23323 CAAAAAAAAAGCAAAAAA-AAA
1 CAAAAAAAAAGCAAAAAACAAA
*
23344 -AAAAAAAAAACAAAAAACAAA
1 CAAAAAAAAAGCAAAAAACAAA
*
23365 CAAAGAAAAAG
1 CAAAAAAAAAG
23376 AGAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
21 3 0.11
22 8 0.30
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAGCAAAAAACAAA
Found at i:24530 original size:55 final size:56
Alignment explanation
Indices: 24390--25005 Score: 631
Period size: 55 Copynumber: 10.8 Consensus size: 56
24380 TTTCCTTTTC
* ***
24390 AAAGCCCACACAAGTTGGT-GCATTTTCCAGTCCTCAAAGAGCAGGATGTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGA--CACTCTCTT
*
24447 AAAGCCCACCACAAGTTTGGTGGCACCTTCCAGTCCTC-AAGAGCAGGGACACTCTCTT
1 AAAGCCCA-CACAAG-TTGGTGGCACTTTCCAGTCCTCAAAGAGCA-GGACACTCTCTT
*
24505 -AAGCCCACACAAGTTGGTGGCACCTT-CAGTCCCTCAAAGAGCA-GACAC-CTCTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGT-CCTCAAAGAGCAGGACACTCTCTT
* *
24558 AAAGCCCACACAAGTTGGTGGCCCCTTCCAGTCCCTCAAAGAGCCAGGACAGC-CTCTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGT-CCTCAAAGAG-CAGGACA-CTCTCTT
* * *
24616 TAAGCCCCCACAAGTTGGTGG-ACATTTCCAGTCCTC-AAGAGCAGGA-GCT-TGCCTTT
1 AAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCTCAAAGAGCAGGACACTCT--C-TT
* *
24672 CAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTCAAAGAGCGGGAC-CTTTTCTTT
1 -AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACAC-TCTC-TT
*
24729 CAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCCCCAAAGAGCAGGACAC-CT-TT
1 -AAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACTCTCTT
*
24784 AAAGCCCACACAAGTTGGTGGCACTTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 AAAGCCCACACAAGTTGGTGGCACTTT-CCAGTCCTCAAAGAGCAGGAC-AC-TCT-C-TT
* * * *
24845 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACAC---TCTCTT
*
24904 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGC-CT-TT
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACTCTCTT
* * **
24958 CAAAGCCCACACGAGTTGGTGGCAGTTTTTAGTCCTCAAAGAGCAGGA
1 -AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGA
25006 TACACTTTAT
Statistics
Matches: 493, Mismatches: 28, Indels: 78
0.82 0.05 0.13
Matches are distributed among these distances:
53 11 0.02
54 64 0.13
55 99 0.20
56 35 0.07
57 82 0.17
58 64 0.13
59 66 0.13
60 40 0.08
61 32 0.06
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (56 bp):
AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACTCTCTT
Found at i:24792 original size:226 final size:229
Alignment explanation
Indices: 24357--25014 Score: 800
Period size: 226 Copynumber: 2.9 Consensus size: 229
24347 TTCGCTTTTT
* *
24357 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGT-GCATTTTCCAGT
1 AGTCCTCAAAGAGCAGGACGCC-TCTCC-TTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* *
24421 CCTCAAAGAGCAGGATG-TTTTCTCTTAAAGCCCACCACAAGTTTGGTGGCACCTTCCAGTCCTC
63 CCTCAAAGAGCAGGACGCTTTTCT-TTAAAGCCCA-CACAAG-TTGGTGGCACTTTCCAGTCCTC
24485 -AAGAGCAGGGACAC-TCTCTT--AAGCCCACACAAGTTGGTGGCACC-TTCAGTCCCTCAAAGA
125 AAAGAGC-GGGACACTTCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCC-CAAAGA
*
24545 GCA-GACACCTCTTAAAGCCCACACAAGTTGGTGGCCCCTT-CC
187 GCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCACCTTCCC
*
24587 AGTCCCTCAAAGAGCCAGGACAG-C-CT-CTTT-AAGCCCCCACAAGTTGGTGGACA-TTTCCAG
1 AGT-CCTCAAAGAG-CAGGAC-GCCTCTCCTTTAAAGCCCACACAAGTTGGTGG-CATTTTCCAG
**
24647 TCCTC-AAGAGCAGGA-GCTTGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTCA
62 TCCTCAAAGAGCAGGACGCTTTTCTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
*
24709 AAGAGCGGGAC-CTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGC
126 AAGAGCGGGACAC--TTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGC
*
24773 AGGACACCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCC
189 AGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCTTCCC
24814 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACGCC-TCTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* *
24879 TCAAAGAGCGGGACCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
65 TCAAAGAGCAGGACGCTTTTC-TTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAA
* * * ** * *
24943 GAGCAGGACGC--CTTTCAAAGCCCACACGAGTTGGTGGCAGTTTTTAGTCCTCAAAGAGCAGGA
128 GAGCGGGACACTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA
*
25006 TACACTTTA
193 CAC-CTTTA
25015 TTTTCCTCTT
Statistics
Matches: 377, Mismatches: 22, Indels: 58
0.82 0.05 0.13
Matches are distributed among these distances:
222 1 0.00
223 16 0.04
224 18 0.05
225 19 0.05
226 109 0.29
227 35 0.09
228 11 0.03
229 80 0.21
230 18 0.05
231 37 0.10
232 28 0.07
233 5 0.01
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (229 bp):
AGTCCTCAAAGAGCAGGACGCCTCTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
CAAAGAGCAGGACGCTTTTCTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAG
CGGGACACTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACAC
CTTTAAAGCCCACACAAGTTGGTGGCACCTTCCC
Found at i:25611 original size:34 final size:33
Alignment explanation
Indices: 25548--25614 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
25538 GCCAAGGGAA
* *
25548 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCAATACATTATTCTGTGTATCGATACAT
*
25581 TGTATCAATACATCTATTCTTTGTATCGATACAT
1 TGTATCAATACAT-TATTCTGTGTATCGATACAT
25615 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
TGTATCAATACATTATTCTGTGTATCGATACAT
Done.