Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold389
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: 982648
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 7 of 7
Found at i:909868 original size:116 final size:116
Alignment explanation
Indices: 909399--909911 Score: 576
Period size: 116 Copynumber: 4.4 Consensus size: 116
909389 AAAGGAGAGA
* * * * * * *
909399 GCGTCTTGCTCTTTGAGGA-TTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 GCGTCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
909463 TCCTGCTCTTTGAGGACTCA-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAG
65 TCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAG
* * * * *
909520 GCGTCCTGCTTTTTGAGGACTGGAAAATGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAAGCAT
1 GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCAT
* * *
909585 CCTACTCTTTGAGGACT-GAAAAATGCCACCAACTTGTTTGGGCTTTGAAAG
66 CCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* **
909636 GCGTCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCAT
1 GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCAT
* * * *
909695 CTTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTAAGAG
66 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* * * **
909746 GTGTCCTACTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAAGAAAAGGTGT
1 GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCAT
* * * * *
909811 CCTGCTCTTTGAAGATTAGAAAATGCCACCAACTCGTGTAGGTTTTAAAAG
66 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
* **
909862 GAGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT
1 GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT
909912 GAAAGGCGTC
Statistics
Matches: 334, Mismatches: 48, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
110 94 0.28
111 2 0.01
115 1 0.00
116 143 0.43
121 93 0.28
122 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (116 bp):
GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCAT
CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:911027 original size:11 final size:11
Alignment explanation
Indices: 911024--911071 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
911014 TTTTTCTTTG
911024 TTTTGTTTTTT
1 TTTTGTTTTTT
911035 TTTTGTTTTTT
1 TTTTGTTTTTT
* *
911046 TTTTGCCTTTTG
1 TTTTG-TTTTTT
911058 TTTTGTTTTTT
1 TTTTGTTTTTT
911069 TTT
1 TTT
911072 AGAAGAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:916904 original size:6 final size:6
Alignment explanation
Indices: 916893--916927 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
916883 TTGACGATCA
916893 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCC
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCC
916928 ATCCACCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCCT
Found at i:923720 original size:28 final size:28
Alignment explanation
Indices: 923659--923726 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
923649 ATAAATCCGG
923659 GGTTGGAGTAT-CCCTCGAAAGTAACGA
1 GGTTGGAGTATCCCCTCGAAAGTAACGA
923686 GGTTGGAGTATCCCCAAT-GAAA-TAACGA
1 GGTTGGAGTATCCCC--TCGAAAGTAACGA
923714 GGTTGGAGTATCC
1 GGTTGGAGTATCC
923727 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 11 0.29
28 22 0.58
29 4 0.11
30 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGAAAGTAACGA
Found at i:923783 original size:51 final size:51
Alignment explanation
Indices: 923715--923813 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
923705 AAATAACGAG
* * * *
923715 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCAGA
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAACAAAATCAGA
* * *
923766 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAACAAAATC
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAACAAAATC
923814 GGGGTTCGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAACAAAATCAGA
Found at i:923849 original size:79 final size:80
Alignment explanation
Indices: 923766--923941 Score: 230
Period size: 79 Copynumber: 2.2 Consensus size: 80
923756 TAAAATCAGA
* * * * * * *
923766 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAACAAAATCGGGG-TTCGAGTATGCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAACAAAACCGGGGATTCGAGTATCCC
923830 CTC-AAAAATAACGGG
66 CTCGAAAAA-AACGGG
* * *
923845 GTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGATTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAACAAAACCGGGGATTCGAGTATCCC
*
923910 CTCGAAAAAAATGGG
66 CTCGAAAAAAACGGG
923925 GTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
923942 GATTAACGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 44 0.53
80 34 0.41
81 5 0.06
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (80 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAACAAAACCGGGGATTCGAGTATCCC
CTCGAAAAAAACGGG
Found at i:924103 original size:51 final size:51
Alignment explanation
Indices: 923948--924182 Score: 274
Period size: 51 Copynumber: 4.6 Consensus size: 51
923938 CGATGATTAA
* *
923948 CGGGGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGAAAATAAAAT
*** * ** *
924000 CACAGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGAAAATAAAAT
* *
924052 CGGGGTTGGAGAATCCTCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAT
* * * *
924103 CGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-AGAAACAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAAT
* * *
924154 CGAGGTTGAAGTATCCCCGATTATGAAAA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAA
924183 GTTGAGAAAC
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.01
51 94 0.61
52 50 0.32
53 10 0.06
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAT
Found at i:926646 original size:19 final size:21
Alignment explanation
Indices: 926622--926673 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
926612 AGCGATGCAC
*
926622 TGTATCGATACATT-ACT-TA
1 TGTATCGATACATTAACTGAA
926641 TGTATCGATACATTAACTGAA
1 TGTATCGATACATTAACTGAA
926662 TGTATCGATACA
1 TGTATCGATACA
926674 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTAACTGAA
Found at i:935490 original size:14 final size:15
Alignment explanation
Indices: 935471--935503 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
935461 CTTCATACCC
*
935471 AAAAAAAA-TAAAAA
1 AAAAAAAACCAAAAA
935485 AAAAAAAACCAAAAA
1 AAAAAAAACCAAAAA
935500 AAAA
1 AAAA
935504 CCAAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAAAACCAAAAA
Found at i:935498 original size:11 final size:11
Alignment explanation
Indices: 935484--935526 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
935474 AAAAATAAAA
935484 AAAAAAAAACC
1 AAAAAAAAACC
935495 AAAAAAAAACC
1 AAAAAAAAACC
*
935506 AAGGAAAAAATAAC
1 AA--AAAAAA-ACC
935520 AAAAAAA
1 AAAAAAA
935527 CAGAAATGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 13 0.46
12 5 0.18
13 6 0.21
14 4 0.14
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:936789 original size:28 final size:28
Alignment explanation
Indices: 936749--937359 Score: 616
Period size: 28 Copynumber: 21.1 Consensus size: 28
936739 CATTCATCTC
* *
936749 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
936777 TTCAAAGCCCACAATTAAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
936806 TTCAAAGCCCACACGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CTT
*
936838 TTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
936866 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
936894 TTCAAAGCCCACAAGTTAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
936923 TTCAAAGCCCACACAAGTCGGTAGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CTT
936955 TTCAAAGCCCACAAGTCAGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
936984 TT-AAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
937011 TTCAAATCCCACAAGTCAGTTGCACGCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
937040 TTTAAAGCCCACGAGTCAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CTT
* *
937070 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
937098 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
937126 TTCAAATCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
937155 TTCAAAACCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
937183 TTCAAAGCCCATAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
937212 TTCAAAGTCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
937240 TTCAAAGCCCACAAGTCAGTGGCGCCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
937268 TTCAAAGCCCACAAGTTAGTGGCACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
** *
937296 TTCAAAGCCCACACGAGTTGGAGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CTT
* *
937328 TCCAAAGCCCACACAAGTTAGTGGCACCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCTT
937358 TT
1 TT
937360 TTAAAATAAA
Statistics
Matches: 486, Mismatches: 71, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
27 8 0.02
28 244 0.50
29 100 0.21
30 61 0.13
31 23 0.05
32 44 0.09
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:936955 original size:117 final size:115
Alignment explanation
Indices: 936749--937308 Score: 725
Period size: 117 Copynumber: 4.9 Consensus size: 115
936739 CATTCATCTC
* * *
936749 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAATTAAGTGGCATTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGC
* * *
936814 CCACACGAGTCGGTGGTAACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCT
66 CCACA--AGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
*
936866 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAG-
* *
936931 CCACACAAGTCGGTAGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
65 CC-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * ** *
936983 TTTAAAGCCCACAAGTTAGTGGCACCCTTTCAAATCCCACAAGTCAGTTGCACGCTTTTTAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGC
* * * *
937048 CCACGAGTCAGTGGTAACTCTTTTCAAAGCCCACAAGTCAATGGCACCCT
66 CCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
937098 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAATCCCACAAGTCAGTGGCATTCTTTTCAAAAC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGC
* * * *
937163 CCACAAGTTAGTGGC-AC-CCTTTCAAAGCCCATAAGTCAGTGGCATTCTT
66 CCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * * * ** *
937212 TTCAAAGTCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC-GCCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGC
*
937276 CCACAAGTTAGTGGC-ACT-TTTTCAAAGCCCACA
66 CCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACA
937309 CGAGTTGGAG
Statistics
Matches: 391, Mismatches: 48, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
113 63 0.16
114 49 0.13
115 112 0.29
116 2 0.01
117 159 0.41
118 2 0.01
119 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (115 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGC
CCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:937048 original size:57 final size:56
Alignment explanation
Indices: 936749--937308 Score: 611
Period size: 57 Copynumber: 9.7 Consensus size: 56
936739 CATTCATCTC
* * * *
936749 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAATTAAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * * *
936806 TTCAAAGCCCACACGAGTCGGTGGTAACTCTTTTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
936866 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
936923 TTCAAAGCCCACACAAGTCGGTAGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
936984 TT-AAAGCCCACAAGTTAGTGGCACCCTTTCAAATCCCACAAGTCAGTTGCACGCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * * * * *
937040 TTTAAAGCCCACGAGTCAGTGGTAACTCTTTTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
937098 TTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAATCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * * *
937155 TTCAAAACCCACAAGTTAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * * * * *
937212 TTCAAAGTCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCGCCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* **
937268 TTCAAAGCCCACAAGTTAGTGGCACTTTTTCAAAGCCCACA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
937309 CGAGTTGGAG
Statistics
Matches: 434, Mismatches: 55, Indels: 29
0.84 0.11 0.06
Matches are distributed among these distances:
55 1 0.00
56 120 0.28
57 144 0.33
58 45 0.10
59 45 0.10
60 22 0.05
61 57 0.13
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:938478 original size:13 final size:13
Alignment explanation
Indices: 938460--938485 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
938450 TACACAAAGT
938460 ATGTATCGATACA
1 ATGTATCGATACA
938473 ATGTATCGATACA
1 ATGTATCGATACA
938486 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:938483 original size:32 final size:33
Alignment explanation
Indices: 938442--938505 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
938432 TAGCCAAACT
**
938442 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
938474 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
938506 TTGGCTTGTA
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:945968 original size:86 final size:86
Alignment explanation
Indices: 945871--946044 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
945861 ATGTATGTGC
945871 AAATAAATTTTTGATATGTGTGTAAATTACCTTATAAAGGGGGAGATTTTTTTTTAATAAAAGGG
1 AAATAAATTTTTGATATGTGTGTAAATTACCTTATAAAGGGGGAGATTTTTTTTTAATAAAAGGG
945936 GAGAATGCGTAAATTTGCTAA
66 GAGAATGCGTAAATTTGCTAA
945957 AAATAAATTTTTGATATGTGTGTAAATTACCTTATAAAGGGGGAGATTTTTTTTTAATAAAAGGG
1 AAATAAATTTTTGATATGTGTGTAAATTACCTTATAAAGGGGGAGATTTTTTTTTAATAAAAGGG
946022 GAGAATGCGTAAATTTGCTAA
66 GAGAATGCGTAAATTTGCTAA
946043 AA
1 AA
946045 TTATCTTATT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (86 bp):
AAATAAATTTTTGATATGTGTGTAAATTACCTTATAAAGGGGGAGATTTTTTTTTAATAAAAGGG
GAGAATGCGTAAATTTGCTAA
Found at i:946762 original size:13 final size:13
Alignment explanation
Indices: 946744--946769 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
946734 TACACAAAGT
946744 ATGTATCGATACA
1 ATGTATCGATACA
946757 ATGTATCGATACA
1 ATGTATCGATACA
946770 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:946767 original size:32 final size:33
Alignment explanation
Indices: 946726--946789 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
946716 TAGCCAAACT
**
946726 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
946758 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
946790 TTGGCTTGTA
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:950552 original size:20 final size:20
Alignment explanation
Indices: 950527--950581 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
950517 CTGCCAGTTT
**
950527 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
950547 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
950566 CATATATCGATACAAT
1 CATGTATCGATACAAT
950582 GTATTGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:951542 original size:33 final size:33
Alignment explanation
Indices: 951505--951570 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
951495 AAGTGCATTA
*
951505 AAGTGCTCATCCATATGCTACGATAGTAAAGTG
1 AAGTGCTCATCCATATGCTACGAAAGTAAAGTG
* * * *
951538 AAGTGCTCATTCATGTGCTGCGAAAGTGAAGTG
1 AAGTGCTCATCCATATGCTACGAAAGTAAAGTG
951571 TTCAACTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (33 bp):
AAGTGCTCATCCATATGCTACGAAAGTAAAGTG
Found at i:953123 original size:20 final size:20
Alignment explanation
Indices: 953098--953151 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
953088 GTTTTTCCAG
953098 ATGTATCGATACATCTTTCA
1 ATGTATCGATACATCTTTCA
953118 ATGTATCGATACATCTTTCA
1 ATGTATCGATACATCTTTCA
953138 ATGTATCGATACAT
1 ATGTATCGATACAT
953152 TCTGGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATCTTTCA
Found at i:959268 original size:20 final size:19
Alignment explanation
Indices: 959243--959312 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
959233 CCAGTTTCAT
**
959243 GTATCGATACAATTGTGCAA
1 GTATCGATACAA-TGAACAA
*
959263 GTATCGATACAATGAACAT
1 GTATCGATACAATGAACAA
* * *
959282 GTATCGATACAAAGCATAA
1 GTATCGATACAATGAACAA
959301 TGTATCGATACA
1 -GTATCGATACA
959313 TTTGGATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 19 0.45
20 23 0.55
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (19 bp):
GTATCGATACAATGAACAA
Found at i:964000 original size:20 final size:20
Alignment explanation
Indices: 963975--964069 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
963965 TCCTGAGTGA
963975 AATGTATCGATACATGGGAC
1 AATGTATCGATACATGGGAC
963995 AATGTATCGATACATGGGAC
1 AATGTATCGATACATGGGAC
964015 AATGTATCGATACATGGGAC
1 AATGTATCGATACATGGGAC
*
964035 AATGTATCGATACATGAAGA-
1 AATGTATCGATACATG-GGAC
*
964055 ATTGTATCGATACAT
1 AATGTATCGATACAT
964070 TATGCCCAAC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
20 70 0.97
21 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACATGGGAC
Found at i:967008 original size:19 final size:19
Alignment explanation
Indices: 966984--967051 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
966974 AATTCAACAA
966984 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
967003 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
967018 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
967035 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
967052 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:967023 original size:13 final size:13
Alignment explanation
Indices: 967005--967029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
966995 ACATAAGTTT
967005 TGTATCGATACAA
1 TGTATCGATACAA
967018 TGTATCGATACA
1 TGTATCGATACA
967030 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:967027 original size:32 final size:32
Alignment explanation
Indices: 966986--967048 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
966976 TTCAACAATT
*
966986 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
967018 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
967049 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:967109 original size:13 final size:13
Alignment explanation
Indices: 967091--967116 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
967081 CATTTTTCTG
967091 TGTATCGATACAT
1 TGTATCGATACAT
967104 TGTATCGATACAT
1 TGTATCGATACAT
967117 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:967113 original size:33 final size:33
Alignment explanation
Indices: 967071--967175 Score: 102
Period size: 33 Copynumber: 3.0 Consensus size: 33
967061 GCCAAGGAAA
*
967071 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTTTTCTATGTATCGATACAT
*** *
967104 TGTATCGATACATGGATCTTTGTATCGATACATCT
1 TGTATCGATACATTTTTCTATGTATCGATACA--T
* *
967139 GGGTGTATCGATACATTTTACAATGTATCGATACAT
1 ---TGTATCGATACATTTTTCTATGTATCGATACAT
967175 T
1 T
967176 CAGGCATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
33 29 0.51
35 1 0.02
36 1 0.02
38 26 0.46
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTTTTCTATGTATCGATACAT
Found at i:969513 original size:51 final size:53
Alignment explanation
Indices: 969449--969579 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
969439 AGTTTCTCAA
* * * *
969449 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
969500 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
969554 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
969580 CCTGTTAATC
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:969706 original size:52 final size:50
Alignment explanation
Indices: 969650--969791 Score: 121
Period size: 52 Copynumber: 2.7 Consensus size: 50
969640 TTTTATCACT
* * *
969650 AAAACACTAATTTTTTTACAATCAGGGATACTCCAACCCTAGTTTTATTTTC
1 AAAACACCAATTTTTTTACAATC-GGGATACTCCAACCC-AATTTTATTTCC
* *
969702 AAAACGCCAATATTCCTTT--AATCGGGGATACTCCAACTCCAATTTTATTTCC
1 AAAACACCAAT-TT-TTTTACAATC-GGGATACTCCAAC-CCAATTTTATTTCC
*
969754 AAAA-ATGCCAA-TTTTTCACAATCGAGGATACTCCAACC
1 AAAACA--CCAATTTTTTTACAATCG-GGATACTCCAACC
969792 TTGTTATTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
50 2 0.03
51 4 0.05
52 56 0.77
53 8 0.11
54 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (50 bp):
AAAACACCAATTTTTTTACAATCGGGATACTCCAACCCAATTTTATTTCC
Found at i:969810 original size:28 final size:28
Alignment explanation
Indices: 969774--969848 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
969764 ATTTTTCACA
* ** *
969774 ATCGAGGATACTCCAACCTTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
969802 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
969830 CGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
969849 AGGCTTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:980731 original size:11 final size:11
Alignment explanation
Indices: 980715--980743 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
980705 CTGATGGAAA
980715 TCACTACCCTT
1 TCACTACCCTT
980726 TCACTACCCTT
1 TCACTACCCTT
980737 TCACTAC
1 TCACTAC
980744 TTTGAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (11 bp):
TCACTACCCTT
Found at i:982433 original size:1 final size:1
Alignment explanation
Indices: 982427--982471 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
982417 CCTTCTCTTC
* * *
982427 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAACAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
982472 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.04, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Done.