Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2240
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: 27825
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Found at i:1835 original size:67 final size:67
Alignment explanation
Indices: 1727--1859 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
1717 ATTAGGAAGA
1727 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1792 TT
66 TT
1794 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1 GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
1859 T
66 T
1860 CTTCTGATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (67 bp):
GCAAATGTACTCAGGGTACTTTTCCTAGTATTTTCCCTCAAGGATAAATAAGATTTCATGCCAAG
TT
Found at i:2810 original size:2 final size:2
Alignment explanation
Indices: 2803--2843 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2793 ATGTGATGTG
*
2803 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2844 TCGAATACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5748 original size:28 final size:30
Alignment explanation
Indices: 5689--5748 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
5679 CTTGTAATAT
* *
5689 TTATATGTAAATGGTAATACTTTTTTGTAA
1 TTATATGTAAATGCTAATACTTTTATGTAA
*
5719 TTATATGTAAA-GCTAAT-GTTTTATGTAA
1 TTATATGTAAATGCTAATACTTTTATGTAA
5747 TT
1 TT
5749 GTAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 5 0.19
30 11 0.41
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
TTATATGTAAATGCTAATACTTTTATGTAA
Found at i:5753 original size:18 final size:18
Alignment explanation
Indices: 5732--5861 Score: 84
Period size: 18 Copynumber: 6.9 Consensus size: 18
5722 TATGTAAAGC
5732 TAATGTTTTATGTAATTG
1 TAATGTTTTATGTAATTG
* * *
5750 TAATATTTTTTATAATTG
1 TAATGTTTTATGTAATTG
5768 ATAATGTTTGTATGTAATTAG
1 -TAATGTTT-TATGTAATT-G
*
5789 T-ATATTTTATGTAACTTG
1 TAATGTTTTATGTAA-TTG
* * * **
5807 CAATATTTT-TATAACTAA
1 TAATGTTTTATGTAA-TTG
* *
5825 TAACGTTTATATATAATTAG
1 TAATGTTT-TATGTAATT-G
5845 TAATGTTTTATGTAATT
1 TAATGTTTTATGTAATT
5862 ACATGTAAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
18 34 0.40
19 31 0.36
20 20 0.23
21 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (18 bp):
TAATGTTTTATGTAATTG
Found at i:5797 original size:56 final size:56
Alignment explanation
Indices: 5732--5861 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 56
5722 TATGTAAAGC
* * * * * * *
5732 TAATGTTTTATGTAATTGTAATATTTTTTATAATTGATAATGTTTGTATGTAATTAG
1 TAATATTTTATGTAATTGCAATA-TTTTTATAACTAATAACGTTTATATATAATTAG
5789 T-ATATTTTATGTAACTTGCAATATTTTTATAACTAATAACGTTTATATATAATTAG
1 TAATATTTTATGTAA-TTGCAATATTTTTATAACTAATAACGTTTATATATAATTAG
*
5845 TAATGTTTTATGTAATT
1 TAATATTTTATGTAATT
5862 ACATGTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
56 43 0.68
57 20 0.32
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (56 bp):
TAATATTTTATGTAATTGCAATATTTTTATAACTAATAACGTTTATATATAATTAG
Found at i:7325 original size:96 final size:97
Alignment explanation
Indices: 7151--7339 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 97
7141 AGGTCTTTTG
* * * *
7151 ACATCAACATTTGGATATTTCTTAATAGTACTTAGCTTTTTTGATAAATAAATATTTAACAAAAT
1 ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAATAAAAAATTAACAAAAA
*
7216 AAGTAAATTAAAAAAAATAAATTTATGTATTC
66 AAATAAATTAAAAAAAATAAATTTATGTATTC
*
7248 ACATCAACATTTGGATATTTC-TAATAATACTTAGC-TTTTTGATAAATAAAAAAATTGACAAAA
1 ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAAT-AAAAAATTAACAAAA
*
7311 AAAAT-AATT-AAAAAAAT-AATTTATATATT
65 AAAATAAATTAAAAAAAATAAATTTATGTATT
7340 TATTATGTTC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
93 11 0.13
94 8 0.10
95 16 0.19
96 28 0.33
97 21 0.25
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (97 bp):
ACATCAACATTTGGATATTTCTTAATAATACTTAGCTTTTTTGATAAATAAAAAATTAACAAAAA
AAATAAATTAAAAAAAATAAATTTATGTATTC
Found at i:7700 original size:20 final size:19
Alignment explanation
Indices: 7667--7722 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
7657 ATTGTAGATC
*
7667 TATTTAAA-TTAAAATTATT
1 TATTTAAATTTAAAAAT-TT
7686 TATTTAAATTTAAAAATTT
1 TATTTAAATTTAAAAATTT
7705 TATTTAATATTTTAAAAA
1 TATTTAA-A-TTTAAAAA
7723 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 17 0.52
20 8 0.24
21 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTAAATTTAAAAATTT
Found at i:7869 original size:21 final size:21
Alignment explanation
Indices: 7847--7892 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
7837 TTATTACTTA
7847 TTAATTATATATGATATAATAT
1 TTAATT-TATATGATATAATAT
*
7869 TTAATTTATATTATATAATTAT
1 TTAATTTATATGATATAA-TAT
7891 TT
1 TT
7893 CTTTTATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATTTATATGATATAATAT
Found at i:9515 original size:39 final size:39
Alignment explanation
Indices: 9437--9603 Score: 121
Period size: 39 Copynumber: 4.3 Consensus size: 39
9427 AACTAACTTT
* * *
9437 AAAGACTTAGTTTTGATG--AAAAT-GTAAAATAAATCTTA
1 AAAG-CTTAATTTTGATGTAAAAATATTAAAAT-AATTTTA
* *
9475 AAAGTTTTATTTTGATGTAAAAATATTAAAATAATTTTA
1 AAAGCTTAATTTTGATGTAAAAATATTAAAATAATTTTA
* * * * *
9514 AAAGCTTGATTTTGATGTGAAAGTGTAAAAATAATCTTTA
1 AAAGCTTAATTTTGATGTAAAAATATTAAAATAAT-TTTA
* * * *
9554 AAA-CTTAATTTTTA-ATATAAAATATTAAAATGACTTTA
1 AAAGCTTAATTTTGATGTA-AAAATATTAAAATAATTTTA
*
9592 AAAG-TTCATTTT
1 AAAGCTTAATTTT
9604 CGTCATAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
37 10 0.10
38 19 0.19
39 60 0.59
40 13 0.13
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (39 bp):
AAAGCTTAATTTTGATGTAAAAATATTAAAATAATTTTA
Found at i:9550 original size:78 final size:77
Alignment explanation
Indices: 9453--9603 Score: 173
Period size: 78 Copynumber: 1.9 Consensus size: 77
9443 TTAGTTTTGA
* * * *
9453 TGAAAATGTAAAATAAATC-TTAAAAGTTTTATTTTG-ATGTAAAAATATTAAAATAATTTTAAA
1 TGAAAATGTAAAATAAATCTTTAAAA-CTTAATTTTGAATAT-AAAATATTAAAATAACTTTAAA
*
9516 AGCTTGATTTTGATG
64 AG-TTCATTTTGATG
* * *
9531 TGAAAGTGTAAAA-ATAATCTTTAAAACTTAATTTTTAATATAAAATATTAAAATGACTTTAAAA
1 TGAAAATGTAAAATA-AATCTTTAAAACTTAATTTTGAATATAAAATATTAAAATAACTTTAAAA
9595 GTTCATTTT
65 GTTCATTTT
9604 CGTCATAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
77 8 0.13
78 45 0.73
79 9 0.15
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (77 bp):
TGAAAATGTAAAATAAATCTTTAAAACTTAATTTTGAATATAAAATATTAAAATAACTTTAAAAG
TTCATTTTGATG
Found at i:15721 original size:11 final size:12
Alignment explanation
Indices: 15688--15760 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 12
15678 GATAATATTA
15688 AATATAAAATAAT
1 AATATAAAA-AAT
*
15701 TATATAAAAAAAT
1 AATAT-AAAAAAT
*
15714 AAT-TAAAATAT
1 AATATAAAAAAT
15725 AATATAAAATAA-
1 AATATAAAA-AAT
15737 AATGATAATACAAAAT
1 AAT-AT-A-A-AAAAT
15753 AATATAAA
1 AATATAAA
15761 TATATAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
11 9 0.19
12 10 0.21
13 13 0.27
14 6 0.12
15 5 0.10
16 5 0.10
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:15733 original size:21 final size:18
Alignment explanation
Indices: 15688--15770 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
15678 GATAATATTA
15688 AATATAAAATAATTATAT
1 AATATAAAATAATTATAT
15706 AA-A-AAAATAATTAAAATAT
1 AATATAAAATAATT---ATAT
*
15725 AATATAAAATAA-AATGAT
1 AATATAAAATAATTAT-AT
*
15743 AATACAAAATAA-TATA-
1 AATATAAAATAATTATAT
15759 AATATATAAATA
1 AATATA-AAATA
15771 TTTTAAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
16 14 0.26
17 9 0.17
18 17 0.31
19 6 0.11
20 1 0.02
21 7 0.13
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (18 bp):
AATATAAAATAATTATAT
Found at i:15738 original size:27 final size:27
Alignment explanation
Indices: 15692--15843 Score: 90
Period size: 27 Copynumber: 5.7 Consensus size: 27
15682 ATATTAAATA
*
15692 TAAAATA-ATTATATAA-AAAAATAAT
1 TAAAATATAATATATAATAAAAATAAT
*
15717 TAAAATATAATATAAAATAAAATGATAA-
1 TAAAATATAATATATAATAAAA--ATAAT
*
15745 TACAAA-ATAATATA-AATATATAAATATTT
1 TA-AAATATAATATATAATA-A-AAATA-AT
* *
15774 TAAAAT-T--TATATAATATAAATTAT
1 TAAAATATAATATATAATAAAAATAAT
* *
15798 TTAAATATCATATATAATATAAAATATAT
1 TAAAATATAATATATAATA-AAAATA-AT
*
15827 T-AAATAAAAT-TATAATA
1 TAAAATATAATATATAATA
15844 TAATAATACA
Statistics
Matches: 100, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
24 6 0.06
25 12 0.12
26 11 0.11
27 31 0.31
28 26 0.26
29 14 0.14
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TAAAATATAATATATAATAAAAATAAT
Found at i:15746 original size:23 final size:23
Alignment explanation
Indices: 15679--15760 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
15669 ACTAGATTTG
*
15679 ATAATATTAAATATAAAATAATTAT
1 ATAATA-TAAA-ATAAAATAATAAT
*
15704 ATAA-A-AAAAT-AATTAA-AAT
1 ATAATATAAAATAAAATAATAAT
*
15723 ATAATATAAAATAAAATGATAAT
1 ATAATATAAAATAAAATAATAAT
* * *
15746 ACAAAATAATATAAA
1 ATAATATAAAATAAA
15761 TATATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 6 0.13
20 6 0.13
21 7 0.15
22 7 0.15
23 15 0.33
24 1 0.02
25 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (23 bp):
ATAATATAAAATAAAATAATAAT
Found at i:15771 original size:42 final size:39
Alignment explanation
Indices: 15681--15771 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 39
15671 TAGATTTGAT
*
15681 AATAT-TAAATATAAAATAATTATATAAAAAAATAATTA
1 AATATATAAATATAAAATAATAATATAAAAAAATAATTA
15719 AA-ATAT-AATATAAAATAA-AATGATAATACAAAATAATATA
1 AATATATAAATATAAAATAATAAT-ATAA-A-AAAATAAT-TA
15759 AATATATAAATAT
1 AATATATAAATAT
15772 TTTAAAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
36 2 0.04
37 18 0.40
38 4 0.09
39 8 0.18
40 4 0.09
41 4 0.09
42 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (39 bp):
AATATATAAATATAAAATAATAATATAAAAAAATAATTA
Found at i:15859 original size:35 final size:34
Alignment explanation
Indices: 15799--15874 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
15789 ATAAATTATT
* *
15799 TAAA-TATCATATATAATATAAAATAT-ATTAAA
1 TAAATTATAATATATAATACAAAATATGATTAAA
* *
15831 TAAAATTATAATATAATAATACACAATATGATTACA
1 T-AAATTATAATAT-ATAATACAAAATATGATTAAA
15867 TAAATTAT
1 TAAATTAT
15875 TAGATCTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.03
33 3 0.08
34 7 0.19
35 19 0.53
36 6 0.17
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (34 bp):
TAAATTATAATATATAATACAAAATATGATTAAA
Found at i:20887 original size:6 final size:6
Alignment explanation
Indices: 20876--20901 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20866 AATAAAACCC
20876 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
20902 TAATCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:22193 original size:41 final size:41
Alignment explanation
Indices: 22131--22209 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
22121 TAAGAAACTT
* * *
22131 AAAAGATTGATTAGGATAAAACCATAAGAGTCAATGAATGA
1 AAAAAATTGATTAGGACAAAACCATAAAAGTCAATGAATGA
22172 AAAAAATTGATCTA-GACAAAACCATAAAAGTCAATGAA
1 AAAAAATTGAT-TAGGACAAAACCATAAAAGTCAATGAA
22210 GGGTGACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.20
Consensus pattern (41 bp):
AAAAAATTGATTAGGACAAAACCATAAAAGTCAATGAATGA
Found at i:22573 original size:41 final size:41
Alignment explanation
Indices: 22522--22635 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
22512 GGAAAAACTA
* * * **
22522 TTGATTGGGATGAAACCATACGAGTCAAC-ATATGAGAAGTG
1 TTGATCGGGATGAAACCATACGAGTCAACAAAAAG-GAAAAG
* *
22563 TTGATCGGGATAAAACCATACGAGTTAACAAAAAGGAAAAG
1 TTGATCGGGATGAAACCATACGAGTCAACAAAAAGGAAAAG
* * *
22604 TTGACCGAGATGAAACCATATGAGTCAACAAA
1 TTGATCGGGATGAAACCATACGAGTCAACAAA
22636 GAATAACCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 57 0.95
42 3 0.05
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (41 bp):
TTGATCGGGATGAAACCATACGAGTCAACAAAAAGGAAAAG
Found at i:23142 original size:40 final size:40
Alignment explanation
Indices: 23036--23191 Score: 145
Period size: 40 Copynumber: 3.9 Consensus size: 40
23026 TAAGTAAAAA
* ** *
23036 AGGTTGACTAGAGCTAAACCATTTTAGTCAACAAATTA-AA
1 AGGTTGACTAGGGCTAAACCATTACA-TCAACAAATTAGAG
* ** *
23076 AGGGTTAACTAGGGCTAAACTGTTACATCAATAAATTAGAG
1 A-GGTTGACTAGGGCTAAACCATTACATCAACAAATTAGAG
* * * *
23117 AGGTTGGCTAGGGCTAAACCATTACATTTAGCCAATTAGAG
1 AGGTTGACTAGGGCTAAACCATTACA-TCAACAAATTAGAG
*
23158 TGGTTGACTAGGG-TAAACCATTACAATCAACAAA
1 AGGTTGACTAGGGCTAAACCATTAC-ATCAACAAA
23192 GGATGACTAT
Statistics
Matches: 91, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
40 48 0.53
41 43 0.47
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (40 bp):
AGGTTGACTAGGGCTAAACCATTACATCAACAAATTAGAG
Found at i:23311 original size:105 final size:106
Alignment explanation
Indices: 23150--23401 Score: 269
Period size: 105 Copynumber: 2.4 Consensus size: 106
23140 ACATTTAGCC
* * * * * * *
23150 AATTAGAGTGGTTGACTAGGG-TAAACCATTACAATCAACAAAGGATGACTATGATGAAACTTAA
1 AATTAGAGGGGTTGACCAGGGCTAAACCATTATAGTCAACAAAGGATAACTACGATGAAACCTAA
* * ** * *
23214 GTTGAAAAA-GGTTGACTAGGGCTAAACCATTATAGCCAATA
66 G-TAAAAAAGGGTTGACCAAAGCTAAACCATTACAGCCAACA
*
23255 AGTTAGAGGGGTTGACCAGGGCTAAA-CATTATAGTCAACTAAAGG-TAACTACGATGAAACCTA
1 AATTAGAGGGGTTGACCAGGGCTAAACCATTATAGTCAAC-AAAGGATAACTACGATGAAACCTA
* **
23318 AGTAAAAAAGGGTTGACCAAAGCTAAACTATTACAGTTAACA
65 AGTAAAAAAGGGTTGACCAAAGCTAAACCATTACAGCCAACA
* * * *
23360 AATTAAAAGGGTTGACCAAGGCTAAACCAGTATAGTCAACAA
1 AATTAGAGGGGTTGACCAGGGCTAAACCATTATAGTCAACAA
23402 GTTAGAAAAG
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
104 6 0.05
105 94 0.78
106 21 0.17
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (106 bp):
AATTAGAGGGGTTGACCAGGGCTAAACCATTATAGTCAACAAAGGATAACTACGATGAAACCTAA
GTAAAAAAGGGTTGACCAAAGCTAAACCATTACAGCCAACA
Found at i:23401 original size:41 final size:41
Alignment explanation
Indices: 23323--23401 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
23313 ACCTAAGTAA
* * *
23323 AAAAGGGTTGACCAAAGCTAAACTATTACAGTTAACAAATT
1 AAAAGGGTTGACCAAAGCTAAACCAGTACAGTCAACAAATT
* *
23364 AAAAGGGTTGACCAAGGCTAAACCAGTATAGTCAACAA
1 AAAAGGGTTGACCAAAGCTAAACCAGTACAGTCAACAA
23402 GTTAGAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAAGGGTTGACCAAAGCTAAACCAGTACAGTCAACAAATT
Found at i:23415 original size:41 final size:41
Alignment explanation
Indices: 23323--23416 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
23313 ACCTAAGTAA
* * * *
23323 AAAAGGGTTGACCAAAGCTAAACTATTACAGTTAACAAATT
1 AAAAGAGTTGACCAAAGCTAAACCAGTACAGTCAACAAATT
* * * *
23364 AAAAGGGTTGACCAAGGCTAAACCAGTATAGTCAACAAGTT
1 AAAAGAGTTGACCAAAGCTAAACCAGTACAGTCAACAAATT
23405 AGAAA-AGTTGAC
1 A-AAAGAGTTGAC
23417 TAGGGTGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 42 0.93
42 3 0.07
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAAGAGTTGACCAAAGCTAAACCAGTACAGTCAACAAATT
Found at i:23520 original size:65 final size:65
Alignment explanation
Indices: 23407--23569 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 65
23397 AACAAGTTAG
* * * *
23407 AAAAGTTGACTAGGGTGAAACAT-TAGTCGAAAAGGATTGAACATGGCTAAACTAGTACAGTCAA
1 AAAAGTTGACTAGGATGAAACCTATA-TCGAAAAAGATTGAACAGGGCTAAACTAGTACAGTCAA
23471 CT
65 -T
* *
23473 AAAAG-TGACTAGGATGAAACCTATATCGAGAAAAG-TTGACCAGGGCTAAACTAGTATAGTCAA
1 AAAAGTTGACTAGGATGAAACCTATATCGA-AAAAGATTGAACAGGGCTAAACTAGTACAGTCAA
23536 T
65 T
* *
23537 TAAAGTTGACTAGGATGAAACCTAAATCGAAAA
1 AAAAGTTGACTAGGATGAAACCTATATCGAAAA
23570 GGGTCGATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
64 8 0.09
65 67 0.78
66 11 0.13
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (65 bp):
AAAAGTTGACTAGGATGAAACCTATATCGAAAAAGATTGAACAGGGCTAAACTAGTACAGTCAAT
Found at i:24938 original size:33 final size:33
Alignment explanation
Indices: 24895--24982 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
24885 CCCAGATGTT
*
24895 TCGATACATATTACTTTGTATCGATATATTATA
1 TCGATACATATTGCTTTGTATCGATATATTATA
* *
24928 TCGATGCATATTGCTTTGTATCGATATATTGTA
1 TCGATACATATTGCTTTGTATCGATATATTATA
*
24961 TTGATACATATTGCTTTGTATC
1 TCGATACATATTGCTTTGTATC
24983 AATACATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (33 bp):
TCGATACATATTGCTTTGTATCGATATATTATA
Found at i:26640 original size:3 final size:3
Alignment explanation
Indices: 26632--26679 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
26622 AACCATCAAA
* * *
26632 GAT GAT GAT GAA GAT GAT GAT GAA GAT GAT GAT AAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
26680 AAAGAAGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:26645 original size:12 final size:12
Alignment explanation
Indices: 26630--26678 Score: 82
Period size: 12 Copynumber: 4.1 Consensus size: 12
26620 TCAACCATCA
26630 AAGATGATGATG
1 AAGATGATGATG
26642 AAGATGATGATG
1 AAGATGATGATG
26654 AAGATGATGAT-
1 AAGATGATGATG
26665 AATGATGATGATG
1 AA-GATGATGATG
26678 A
1 A
26679 TAAAGAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.91
13 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (12 bp):
AAGATGATGATG
Done.