Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1872
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: 47398
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:667 original size:23 final size:25
Alignment explanation
Indices: 633--690 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
623 CAAACATCCA
* *
633 AAAAATGA-TTAGTACAATA-TC-T
1 AAAAATTAGTTAGTAAAATATTCAT
655 AAAAATTAGTTAGTAAAATATTCAT
1 AAAAATTAGTTAGTAAAATATTCAT
680 AAACAATTAGT
1 AAA-AATTAGT
691 AAAATAGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 7 0.23
23 10 0.33
24 2 0.07
25 4 0.13
26 7 0.23
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.33
Consensus pattern (25 bp):
AAAAATTAGTTAGTAAAATATTCAT
Found at i:8235 original size:28 final size:28
Alignment explanation
Indices: 8195--8267 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
8185 TAAAGCCGGA
* * *
8195 GTTGGAGTATCCCC-TTGGAAGTAACGGG
1 GTTGGAGTATCCCCGAT-GAAATAACGAG
8223 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCCGATGAAATAACGAG
*
8251 GTTGGAGTATCCTCGAT
1 GTTGGAGTATCCCCGAT
8268 TATGAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GTTGGAGTATCCCCGATGAAATAACGAG
Found at i:8314 original size:52 final size:52
Alignment explanation
Indices: 8251--8420 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 52
8241 AAATAACGAG
* *
8251 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAACCGGA
* * ** *
8303 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAACC-GGA
* * * *
8356 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTATTTTTG-GAAATAAAACCGGA
8407 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
8421 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
51 3 0.03
52 77 0.79
53 17 0.18
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAACCGGA
Found at i:8466 original size:27 final size:28
Alignment explanation
Indices: 8403--8478 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
8393 GCGATAAAAC
*
8403 CGGAGTTGGAGTATCCCCTCA-GAAATAA
1 CGGAGTTGGAGTATCCCC-GATGAAATAA
* *
8431 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGAGTTGGAGTATCCCCGATGAAATAA
8458 CGGAGTTGGAGTATCCCCGAT
1 CGGAGTTGGAGTATCCCCGAT
8479 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (28 bp):
CGGAGTTGGAGTATCCCCGATGAAATAA
Found at i:8490 original size:107 final size:104
Alignment explanation
Indices: 8137--8490 Score: 276
Period size: 107 Copynumber: 3.3 Consensus size: 104
8127 CCCTCGAAAA
* * * * * *
8137 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGAGTTGGAG
1 TAACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTT-GGAATAAAACCGGAGTTGGAG
* * *
8202 TATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCC-TCGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * *
8244 TAAC-GAGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGG
1 TAACGGA-GTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGG-AATAAAACCGGAGTTGG
* * ** * ** **
8308 AGTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
63 AGTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * *
8346 AAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGT
1 -TAA-C-GGAGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTT-G-GAATAAAACCGGAGT
8409 TGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAT
60 TGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
*
8455 TAACGGAGTTGGAGTATCCCCGATTGTGAAGAAATT
1 TAACGGAGTTGGAGTATCCCCGATTATGAA-AAATT
8491 GGTGTTTTTT
Statistics
Matches: 190, Mismatches: 36, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
102 1 0.01
103 4 0.02
104 48 0.25
105 16 0.08
106 23 0.12
107 62 0.33
108 32 0.17
109 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (104 bp):
TAACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAATAAAACCGGAGTTGGAGT
ATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:8517 original size:55 final size:51
Alignment explanation
Indices: 8458--8593 Score: 148
Period size: 51 Copynumber: 2.6 Consensus size: 51
8448 CGATGATTAA
* * *
8458 CGGAGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATGAAAT
1 CGGAGTTGGAGTATCCCCGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAAT
* *
8513 CGGAGTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAAT
1 CGGAGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAAT
* *
8564 CGGAGTTGGAATATCCTCGATTGTGGAGAA
1 CGGAGTTGGAGTATCCCCGATTGT-GAGAA
8594 TTGATAAACT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
51 33 0.48
52 2 0.03
53 4 0.06
54 8 0.12
55 22 0.32
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
CGGAGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAAT
Found at i:8579 original size:51 final size:53
Alignment explanation
Indices: 8251--8585 Score: 176
Period size: 52 Copynumber: 6.3 Consensus size: 53
8241 AAATAACGAG
* * * *
8251 GTTGGAGTATCCTCGATTATGAA-AAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
* * *
8303 GTTGGAGTATCCCCGATTA--AAGGAAAATTGGCG-TTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTATGAA-G-AAATTAGTGTTTTTGAAAATAAAATC-GGA
* * ** *
8356 -TTGGAGTATCCCCGATTGTGGAA-AAATTAGTGTTTTAG-CGATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
* *** * **** ** *
8407 GTTGGAGTATCCCCTCAGA-AAT-AACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGA
1 GTTGGAGTAT-CCC-C-GATTATGAA-GAAATT--AGTGTTTTTGAAAATAAAATCGGA
* * * *
8462 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATGAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG--TTTTTGAAAATAAAATCGGA
*
8517 GTTAGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGA
* *
8568 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
8586 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 46, Indels: 49
0.69 0.15 0.16
Matches are distributed among these distances:
50 2 0.01
51 37 0.17
52 77 0.36
53 28 0.13
54 19 0.09
55 40 0.19
56 7 0.03
57 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:10972 original size:13 final size:13
Alignment explanation
Indices: 10954--10979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10944 ACAAAGATCC
10954 ATGTATCGATACA
1 ATGTATCGATACA
10967 ATGTATCGATACA
1 ATGTATCGATACA
10980 CAGAAAAATG
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:10975 original size:33 final size:33
Alignment explanation
Indices: 10933--10999 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10923 AAAATTTCCA
***
10933 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
10966 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
10999 A
1 A
11000 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:11043 original size:19 final size:18
Alignment explanation
Indices: 11019--11086 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
11009 CAGTAGCTAA
11019 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
11038 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
11053 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
11070 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
11087 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:11059 original size:13 final size:13
Alignment explanation
Indices: 11041--11065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11031 ACAATACTTA
11041 TGTATCGATACAT
1 TGTATCGATACAT
11054 TGTATCGATACA
1 TGTATCGATACA
11066 AAACTTATGT
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:11063 original size:32 final size:32
Alignment explanation
Indices: 11022--11084 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11012 TAGCTAATTA
*
11022 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
11054 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
11085 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:11167 original size:21 final size:21
Alignment explanation
Indices: 11143--11199 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
11133 CATTTGTAGG
11143 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
11164 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
11185 ATGTATCGATACATT
1 ATGTATCGATACATT
11200 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:11210 original size:1 final size:1
Alignment explanation
Indices: 11204--11259 Score: 85
Period size: 1 Copynumber: 56.0 Consensus size: 1
11194 TACATTTAAA
***
11204 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11260 CAAACACTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:11247 original size:27 final size:27
Alignment explanation
Indices: 11209--11262 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11199 TTAAATTTTT
11209 TTTTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTTTCAA
11236 TTTTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTTTCAA
11263 ACACTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.07, C:0.04, G:0.00, T:0.89
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTTTTTTTTCAA
Found at i:13421 original size:58 final size:56
Alignment explanation
Indices: 13328--13546 Score: 213
Period size: 58 Copynumber: 3.9 Consensus size: 56
13318 TAGGCCCATA
* *
13328 AATATATGCAAATTGGGCTTTAACTCTTCTTGGACATGTGAATTAGGCTCCAAGAAATG
1 AATACATGCAAATTGGGC-TTCACTCTTCTTGGACATGTGAATTAGGCTCCAAG--ATG
* *
13387 AATACATGCAAATTAGGCTTCACTCTTCTTGGACATGTGAATT-GGCTCCAAGCT-
1 AATACATGCAAATTGGGCTTCACTCTTCTTGGACATGTGAATTAGGCTCCAAGATG
* ** * *
13441 --T-C-TTC--ATT-GTTTTTATCCTCTTCTTAGACATGTGAATTAGGCTCCAAGCCATG
1 AATACATGCAAATTGGGCTTCA--CTCTTCTTGGACATGTGAATTAGGCTCCAAG--ATG
* *
13494 AATACATGCAAATTGGGCTTCACTCTTCTTGGACAAGTGAATTGGGCTCCAAG
1 AATACATGCAAATTGGGCTTCACTCTTCTTGGACATGTGAATTAGGCTCCAAG
13547 CTCTTCAATG
Statistics
Matches: 130, Mismatches: 17, Indels: 27
0.75 0.10 0.16
Matches are distributed among these distances:
47 4 0.03
48 3 0.02
49 20 0.15
50 11 0.08
51 1 0.01
52 2 0.02
55 2 0.02
56 1 0.01
57 11 0.08
58 52 0.40
59 19 0.15
60 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (56 bp):
AATACATGCAAATTGGGCTTCACTCTTCTTGGACATGTGAATTAGGCTCCAAGATG
Found at i:13537 original size:107 final size:108
Alignment explanation
Indices: 13351--13568 Score: 359
Period size: 107 Copynumber: 2.0 Consensus size: 108
13341 TGGGCTTTAA
*
13351 CTCTTCTTGGACATGTGAATTAGGCTCCAAGAAATGAATACATGCAAATTAGGCTTCACTCTTCT
1 CTCTTCTTAGACATGTGAATTAGGCTCCAAGAAATGAATACATGCAAATTAGGCTTCACTCTTCT
* *
13416 TGGACATGTGAATT-GGCTCCAAGCTTCTTCATTGTTTTT-ATC
66 TGGACAAGTGAATTGGGCTCCAAGC-TCTTCAATGTTTTTCATC
** *
13458 CTCTTCTTAGACATGTGAATTAGGCTCCAAGCCATGAATACATGCAAATTGGGCTTCACTCTTCT
1 CTCTTCTTAGACATGTGAATTAGGCTCCAAGAAATGAATACATGCAAATTAGGCTTCACTCTTCT
13523 TGGACAAGTGAATTGGGCTCCAAGCTCTTCAATGTTTTTCATC
66 TGGACAAGTGAATTGGGCTCCAAGCTCTTCAATGTTTTTCATC
13566 CTC
1 CTC
13569 ATCATATATA
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
107 87 0.84
108 16 0.16
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (108 bp):
CTCTTCTTAGACATGTGAATTAGGCTCCAAGAAATGAATACATGCAAATTAGGCTTCACTCTTCT
TGGACAAGTGAATTGGGCTCCAAGCTCTTCAATGTTTTTCATC
Found at i:18458 original size:28 final size:28
Alignment explanation
Indices: 18415--18487 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
18405 ATTGAAAAAT
* *
18415 AAGAAAGATC-AAGGAAGTGAAATCAA-C
1 AAGAAATATCAAAGGAAATGAAAT-AAGC
*
18442 AAGAAATATGAAAGGAAATGAAATAAGC
1 AAGAAATATCAAAGGAAATGAAATAAGC
*
18470 AAGAAATTTCAAAGGAAA
1 AAGAAATATCAAAGGAAA
18488 AAATCAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.26
28 29 0.74
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (28 bp):
AAGAAATATCAAAGGAAATGAAATAAGC
Found at i:26475 original size:151 final size:151
Alignment explanation
Indices: 26201--26504 Score: 536
Period size: 151 Copynumber: 2.0 Consensus size: 151
26191 GCTACAATGG
* *
26201 TTGAGTGATGAAGAGGAGTTGGTTGTTAATAGGTAGGTTTTGATTACTTTTTCTATTGGCAAGTA
1 TTGAGTGATGAAGAGGAGTTGGTTGATAATAGGCAGGTTTTGATTACTTTTTCTATTGGCAAGTA
26266 CGAGGATGAAGTCTTGTGTGATGTAGTGCCAATGGAAGCAAGCCACATCCTCTTGGGAAGACCTT
66 CGAGGATGAAGTCTTGTGTGATGTAGTGCCAATGGAAGCAAGCCACATCCTCTTGGGAAGACCTT
*
26331 GGCAGTTCAACAAGAAAGCTA
131 GGAAGTTCAACAAGAAAGCTA
*
26352 TTGAGTGATGAAGGGGAGTTGGTTGATAATAGGCAGGTTTTGATTACTTTTTCTATTGGCAAGTA
1 TTGAGTGATGAAGAGGAGTTGGTTGATAATAGGCAGGTTTTGATTACTTTTTCTATTGGCAAGTA
* * * *
26417 TGAGGATGAAGTCTTGTGTGATGTAGTGCCTATGGAAGCAAGCCACGTCTTCTTGGGAAGACCTT
66 CGAGGATGAAGTCTTGTGTGATGTAGTGCCAATGGAAGCAAGCCACATCCTCTTGGGAAGACCTT
26482 GGAAGTTCAACAAGAAAGCTA
131 GGAAGTTCAACAAGAAAGCTA
26503 TT
1 TT
26505 CATGATGGTC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 145 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (151 bp):
TTGAGTGATGAAGAGGAGTTGGTTGATAATAGGCAGGTTTTGATTACTTTTTCTATTGGCAAGTA
CGAGGATGAAGTCTTGTGTGATGTAGTGCCAATGGAAGCAAGCCACATCCTCTTGGGAAGACCTT
GGAAGTTCAACAAGAAAGCTA
Found at i:34890 original size:50 final size:49
Alignment explanation
Indices: 34818--34950 Score: 189
Period size: 49 Copynumber: 2.7 Consensus size: 49
34808 TTTTATAATT
*
34818 TGTATCGATA-ATTGTTCCTTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGG-TTTACCCAGA
*
34867 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCTGA
1 TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
* * *
34916 TGTATCAATACATT-TTGCAATGTGTCGATACATTC
1 TGTATCGATACATTGTT-CATTGTATCGATACATTC
34951 AGACATTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
48 2 0.03
49 48 0.62
50 27 0.35
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTACCCAGA
Found at i:37319 original size:79 final size:81
Alignment explanation
Indices: 37185--37341 Score: 237
Period size: 79 Copynumber: 2.0 Consensus size: 81
37175 TTTTCATCTC
* * * * *
37185 GGGGATACTCCAACCCCGGTTTTATTTCCAAAATATCAATTTTTCATAATCGGGGATACTCCAA-
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATAGGGGATACTCCAAC
*
37249 TCCCG-TTATTTCCGA
66 TCCAGCTTATTTCCGA
*
37264 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACAATAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATAGGGGATACTCCAAC
37329 TCCAGCTTATTTC
66 TCCAGCTTATTTC
37342 TAAATTATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
79 58 0.84
80 4 0.06
81 7 0.10
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (81 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATAGGGGATACTCCAAC
TCCAGCTTATTTCCGA
Found at i:37372 original size:129 final size:130
Alignment explanation
Indices: 37185--37461 Score: 306
Period size: 129 Copynumber: 2.1 Consensus size: 130
37175 TTTTCATCTC
* * * *
37185 GGGGATACTCCAACCCCGGTTTTATTTCCAAAATATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCAGTCTTATTTCCAAAATATCAATTTCTCACAATCGGGGATACTCCAA-
* * * **
37250 CCC-GTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACAAT
65 CCCTATTATTTCCGAGAGGATACTCCAACCCCAGCCTTATTTCTAAAACACCAATTTTCCACAAT
37314 A
130 A
* * * ** *
37315 GGGGATACTCCAACTCCAG-CTTATTTCTAAATTATTGATTTCTCACAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCAGTCTTATTTCCAAAATATCAATTTCTCACAATCGGGGATACTCCAAC
** * * **** *
37379 CCTATTATTTTGGCGAGGATACTCCAACCCCAGCCTTATTTCTAAAGCTTTGATTTTCCACAATC
66 CCTATTATTTCCGAGAGGATACTCCAACCCCAGCCTTATTTCTAAAACACCAATTTTCCACAATA
*
37444 GGTGATACTCCAACCCCA
1 GGGGATACTCCAACCCCA
37462 TTATCTTCGA
Statistics
Matches: 120, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
128 3 0.03
129 100 0.83
130 17 0.14
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (130 bp):
GGGGATACTCCAACCCCAGTCTTATTTCCAAAATATCAATTTCTCACAATCGGGGATACTCCAAC
CCTATTATTTCCGAGAGGATACTCCAACCCCAGCCTTATTTCTAAAACACCAATTTTCCACAATA
Found at i:37432 original size:79 final size:78
Alignment explanation
Indices: 37317--37619 Score: 245
Period size: 79 Copynumber: 3.8 Consensus size: 78
37307 CCACAATAGG
* * *
37317 GGATACTCCAACTCCAGCTTATTTCTAAATTATTGA-TTTCTCACAATCGGGGATACTCTAACCC
1 GGATACTCCAACCCCAGCTTATTTCTAAACTATTGATTTTC-CACAATCGGGGATACTCCAACCC
* * * *
37381 TATTATTTTGGCGA
65 CATTATCTTCGAGA
*
37395 GGATACTCCAACCCCAGCCTTATTTCTAAAGCT-TTGATTTTCCACAATCGGTGATACTCCAACC
1 GGATACTCCAACCCCAG-CTTATTTCTAAA-CTATTGATTTTCCACAATCGGGGATACTCCAACC
*
37459 CCATTATCTTCGAGG
64 CCATTATCTTCGAGA
** * *** * * * *
37474 GGATACTCCAACCCCGATTTTATTTTCAAAAC-GCCGATTTTCTATAATCAGGGATGCTCCAACC
1 GGATACTCCAACCCC-AGCTTA-TTTCTAAACTATTGATTTTCCACAATCGGGGATACTCCAACC
** * *
37538 CTGTTATTTTCGAGG
64 CCATTATCTTCGAGA
** ** * *
37553 GGATACTCCAACCCCAATTTTATTTCTAGAAC-ACCGATTTTCCATAATCAGGGGATACTCCAGC
1 GGATACTCCAACCCC-AGCTTATTTCTA-AACTATTGATTTTCCACAATC-GGGGATACTCCAAC
37617 CCC
63 CCC
37620 GTTGTCATCT
Statistics
Matches: 187, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
78 21 0.11
79 140 0.75
80 26 0.14
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (78 bp):
GGATACTCCAACCCCAGCTTATTTCTAAACTATTGATTTTCCACAATCGGGGATACTCCAACCCC
ATTATCTTCGAGA
Found at i:42688 original size:20 final size:20
Alignment explanation
Indices: 42665--42738 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
42655 ACAATTCAAA
42665 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
42685 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
42706 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
42726 GTATCGATACATG
1 GTATCGATACATG
42739 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:42709 original size:21 final size:21
Alignment explanation
Indices: 42683--42758 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
42673 ACATGTTGCA
42683 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
42704 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
42724 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
42745 ATGTATCGATACAT
1 ATGTATCGATACAT
42759 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:42716 original size:41 final size:41
Alignment explanation
Indices: 42665--42758 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
42655 ACAATTCAAA
42665 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
42706 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
42747 GTATCGATACAT
1 GTATCGATACAT
42759 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:42815 original size:13 final size:13
Alignment explanation
Indices: 42797--42822 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42787 TACACAAAGT
42797 ATGTATCGATACA
1 ATGTATCGATACA
42810 ATGTATCGATACA
1 ATGTATCGATACA
42823 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:42820 original size:32 final size:33
Alignment explanation
Indices: 42779--42842 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
42769 TAGCCAAACT
**
42779 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
42811 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
42843 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:43343 original size:34 final size:35
Alignment explanation
Indices: 43280--43346 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
43270 CTAAGTGATT
43280 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
43316 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
43347 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Done.