Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014698.1 Kokia drynarioides strain JFW-HI SEQ_129737, whole genome shotgun sequence
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: 100692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1857 original size:29 final size:29
Alignment explanation
Indices: 1814--1871 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1804 ATCAACATGT
* *
1814 GATAACACAATACAGATTAAAATCACACA
1 GATAACACAACACAGAATAAAATCACACA
* *
1843 GATAACATAACACAGAATAATATCACACA
1 GATAACACAACACAGAATAAAATCACACA
1872 AGGTGAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (29 bp):
GATAACACAACACAGAATAAAATCACACA
Found at i:11828 original size:30 final size:30
Alignment explanation
Indices: 11794--11855 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
11784 AAAACATATT
* *
11794 ATATATAATATATATTATTTATTTTGATTA
1 ATATAAAAAATATATTATTTATTTTGATTA
*
11824 ATATAAAAAATATATTATTTATTTTGGTTA
1 ATATAAAAAATATATTATTTATTTTGATTA
11854 AT
1 AT
11856 TTGATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
ATATAAAAAATATATTATTTATTTTGATTA
Found at i:12667 original size:17 final size:16
Alignment explanation
Indices: 12621--12672 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
12611 TAAATGGAAT
12621 ATTTCAAATAAATATA
1 ATTTCAAATAAATATA
12637 CA-TTCAAA-AAATATTA
1 -ATTTCAAATAAATA-TA
12653 ATTTCAAATAAATATA
1 ATTTCAAATAAATATA
12669 ATTT
1 ATTT
12673 AAACCTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.19
16 20 0.62
17 6 0.19
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTCAAATAAATATA
Found at i:15240 original size:128 final size:129
Alignment explanation
Indices: 15038--15306 Score: 423
Period size: 128 Copynumber: 2.1 Consensus size: 129
15028 TATATATATA
* *
15038 TATATATATTGATATGCATATTTGGTGGCTGGAAATAAATAAATAAATGTTTTTTGCCGTGTGAA
1 TATATATATTGATATGCATATTTGATGGCTGG--A-AAATAAATAAATGTTTTTTGCCATGTGAA
* * *
15103 TTATATTGAACATTTTGGATTGTTGAAATAAGCTGAGTACAAAAGATTAATGAAAGATTTGAATT
63 TTATATTGAACATTTTGGATCGTTGAAATAAGCTGAATACAAAAGAATAATGAAAGATTTGAATT
15168 GT
128 GT
*
15170 TATACATATTGATATGCATATTTGATGGCTGG-AAATAAATAAATGTTTTTTGCCATGTGAATTA
1 TATATATATTGATATGCATATTTGATGGCTGGAAAATAAATAAATGTTTTTTGCCATGTGAATTA
* * *
15234 TATTGAACATTTTGGATCGTTGAAATGAGTTGAATACAAATGAATAATGAAAGATTTGAATTGT
66 TATTGAACATTTTGGATCGTTGAAATAAGCTGAATACAAAAGAATAATGAAAGATTTGAATTGT
15298 TATATATAT
1 TATATATAT
15307 AGAGCAAGAA
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
128 97 0.76
132 30 0.24
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (129 bp):
TATATATATTGATATGCATATTTGATGGCTGGAAAATAAATAAATGTTTTTTGCCATGTGAATTA
TATTGAACATTTTGGATCGTTGAAATAAGCTGAATACAAAAGAATAATGAAAGATTTGAATTGT
Found at i:17607 original size:24 final size:24
Alignment explanation
Indices: 17562--17607 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17552 CTACAATTTA
*
17562 ATATATTTTTCATTTTAATATTGT
1 ATATATTTTTCATGTTAATATTGT
* *
17586 ATATATTTTTTATGTTATTATT
1 ATATATTTTTCATGTTAATATT
17608 AATTAGTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
ATATATTTTTCATGTTAATATTGT
Found at i:21161 original size:3 final size:3
Alignment explanation
Indices: 21155--21231 Score: 106
Period size: 3 Copynumber: 26.0 Consensus size: 3
21145 TATGATTTTC
21155 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
21203 ATT -TG A-T ATT ATAT AGTT -TT ATT ATT ATT
1 ATT ATT ATT ATT AT-T A-TT ATT ATT ATT ATT
21232 TGATTTTAAC
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
2 4 0.06
3 59 0.88
4 3 0.04
5 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:21532 original size:23 final size:23
Alignment explanation
Indices: 21499--21543 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21489 CCATTCACCA
*
21499 AAAATTAATAAATGTA-TATTTT
1 AAAATTAATAAATATATTATTTT
21521 AAAATTATATAAATATATTATTT
1 AAAATTA-ATAAATATATTATTT
21544 AATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTAATAAATATATTATTTT
Found at i:21539 original size:21 final size:21
Alignment explanation
Indices: 21499--21539 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
21489 CCATTCACCA
21499 AAAATTAATAAATGTATATTTT
1 AAAATTAATAAA-GTATATTTT
21521 AAAATTATATAAA-TATATT
1 AAAATTA-ATAAAGTATATT
21540 ATTTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATTAATAAAGTATATTTT
Found at i:23933 original size:15 final size:15
Alignment explanation
Indices: 23913--23948 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
23903 TTTGATGTAT
23913 TTATTTATAAATAAA
1 TTATTTATAAATAAA
23928 TTATTTATAAATAAA
1 TTATTTATAAATAAA
23943 TTATTT
1 TTATTT
23949 CGTAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTTATAAATAAA
Found at i:30855 original size:2 final size:2
Alignment explanation
Indices: 30848--30872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30838 TACTCAATAC
30848 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30873 ATTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40604 original size:12 final size:13
Alignment explanation
Indices: 40582--40607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40572 CTAAATGTAG
40582 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
40595 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
40608 CAATTTTTCT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:51473 original size:36 final size:36
Alignment explanation
Indices: 51426--51509 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
51416 TTTGGGTTTT
51426 ATTATACTCGTTAAGCTTTACCGTCAAACCACGCCG
1 ATTATACTCGTTAAGCTTTACCGTCAAACCACGCCG
51462 ATTATACTCGTTAAGCTTTACCGTCAAACCACGCCG
1 ATTATACTCGTTAAGCTTTACCGTCAAACCACGCCG
51498 ATTATACTCGTT
1 ATTATACTCGTT
51510 TTCCATTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (36 bp):
ATTATACTCGTTAAGCTTTACCGTCAAACCACGCCG
Found at i:54946 original size:39 final size:39
Alignment explanation
Indices: 54866--54947 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
54856 AGGGAGAAAA
*
54866 TAATATTAAATTAAATAATAATTGAATTGAATTTTTATT
1 TAATATTAAATTAAATAATAATTGAATTGAATTATTATT
*
54905 TAATATTAAATTTAAATTATTTAATT-AATT-AATTATT-TT
1 TAATATTAAA-TTAAA-TA-ATAATTGAATTGAATTATTATT
54944 TAAT
1 TAAT
54948 TAATAAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
39 16 0.42
40 11 0.29
41 6 0.16
42 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (39 bp):
TAATATTAAATTAAATAATAATTGAATTGAATTATTATT
Found at i:64540 original size:19 final size:17
Alignment explanation
Indices: 64518--64557 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
64508 TTATATTAGG
64518 ATTTAATATTTAAGATATT
1 ATTTAATATTTAA-AT-TT
*
64537 ATTTATTATTTAAATTT
1 ATTTAATATTTAAATTT
64554 ATTT
1 ATTT
64558 TTTTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTAATATTTAAATTT
Found at i:70094 original size:6 final size:6
Alignment explanation
Indices: 70083--70108 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
70073 GGCAACCCAA
70083 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
70109 TTAATTTTTC
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:70115 original size:9 final size:8
Alignment explanation
Indices: 70083--70151 Score: 57
Period size: 8 Copynumber: 8.0 Consensus size: 8
70073 GGCAACCCAA
70083 TTATTTTT
1 TTATTTTT
*
70091 ATTTTTATTT
1 -TTATT-TTT
70101 TTATTTTT
1 TTATTTTT
70109 TTAATTTTT
1 TT-ATTTTT
*
70118 CTATCTTATT
1 TTAT-TT-TT
*
70128 TTATTTAT
1 TTATTTTT
*
70136 TTATTTAT
1 TTATTTTT
70144 TTATTTTT
1 TTATTTTT
70152 GTCCAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 23 0.46
9 19 0.38
10 8 0.16
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (8 bp):
TTATTTTT
Found at i:70126 original size:22 final size:20
Alignment explanation
Indices: 70083--70151 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 20
70073 GGCAACCCAA
70083 TTATTTTTATT-TTTA-TT-T
1 TTATTTTT-TTATTTATTTAT
70101 TTATTTTTTTAATTT-TTCTAT
1 TTATTTTTTT-ATTTATT-TAT
70122 CTTATTTTATTTATTTATTTAT
1 -TTATTTT-TTTATTTATTTAT
70144 TTATTTTT
1 TTATTTTT
70152 GTCCAGGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.05
18 8 0.19
19 4 0.09
20 2 0.05
21 8 0.19
22 14 0.33
23 5 0.12
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTTTTTTATTTATTTAT
Found at i:71720 original size:19 final size:19
Alignment explanation
Indices: 71698--71742 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
71688 TTATATTAGG
71698 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
71717 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
71736 ATTTAAT
1 ATTTAAT
71743 TTGTGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:71765 original size:14 final size:14
Alignment explanation
Indices: 71742--71771 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71732 TTGTATTTAA
*
71742 TTTGTGTTTATCTT
1 TTTGTATTTATCTT
71756 TTTGTATTTATCTT
1 TTTGTATTTATCTT
71770 TT
1 TT
71772 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (14 bp):
TTTGTATTTATCTT
Found at i:72571 original size:22 final size:22
Alignment explanation
Indices: 72544--72589 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
72534 TTCGACTTCC
*
72544 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTAT-TTTACTTTTAATT
*
72566 CTATTTTATTTTATTTTTAATT
1 CTATTTTATTTTACTTTTAATT
72588 CT
1 CT
72590 GTTTCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTTATTTTACTTTTAATT
Found at i:72604 original size:22 final size:22
Alignment explanation
Indices: 72558--72604 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
72548 TTTCTATTTC
*
72558 TTTTAATTCTATTTTATTTTAT
1 TTTTAATTCTAGTTTATTTTAT
*
72580 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTATTTTAT
72601 TTTT
1 TTTT
72605 CCTTAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTATTTTAT
Found at i:76081 original size:60 final size:59
Alignment explanation
Indices: 75818--76083 Score: 263
Period size: 60 Copynumber: 4.5 Consensus size: 59
75808 TTGGACATCC
* * * * *
75818 GGGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAAT--AGAATTTTGGAACTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTC-AAAATCGAGATTTTTGGAAGTTT
* * * * * * * *
75876 AGGGGGTAAAATAGTAA-TTTT-GAGAGTTTCGGGATTAAAAAATTGA-ATTTTCGGAGGTTC
1 -GGGGGTAAAATGGTAATTTTTGGA-AGTTTTGGG-GT-CAAAATCGAGATTTTTGGAAGTTT
* * * * *
75936 GAGGGTGAAATGGTAATTTTTGGAAAGTTTTGAGGTCAAAATCGAGATTTTTAGAGGTTT
1 GGGGGTAAAATGGTAATTTTTGG-AAGTTTTGGGGTCAAAATCGAGATTTTTGGAAGTTT
*
75996 GGGGGTAAAACGGTAATTTTTGGAAGTTTTGGGGTCAAAATCGAGATTTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAATCGAGA-TTTTTGGAAGTTT
76056 GGGGGTAAAATGGTAATTTTTGGAAGTT
1 GGGGGTAAAATGGTAATTTTTGGAAGTT
76084 CGAGGATAAA
Statistics
Matches: 167, Mismatches: 30, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
57 1 0.01
58 11 0.07
59 62 0.37
60 83 0.50
61 9 0.05
62 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.36
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAATCGAGATTTTTGGAAGTTT
Found at i:76095 original size:59 final size:59
Alignment explanation
Indices: 75818--76144 Score: 253
Period size: 59 Copynumber: 5.5 Consensus size: 59
75808 TTGGACATCC
* * * *
75818 GGGGGTAAAAAGGTAATTTTTGAAAGTTTTTG-GGTCAAAAAT--AGAATTTTGGAACTTT
1 GGGGGTAAAATGGTAATTTTTGGAAG-TTTTGAGGTC-AAAATCGAGATTTTTGGAAGTTT
* * * * * * *
75876 AGGGGGTAAAATAGTAA-TTTT-GAGAGTTTCG-GGATTAAAAAATTGA-ATTTTCGGAGGTTC
1 -GGGGGTAAAATGGTAATTTTTGGA-AGTTTTGAGG--T-CAAAATCGAGATTTTTGGAAGTTT
* * * *
75936 GAGGGTGAAATGGTAATTTTTGGAAAGTTTTGAGGTCAAAATCGAGATTTTTAGAGGTTT
1 GGGGGTAAAATGGTAATTTTTGG-AAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTT
* *
75996 GGGGGTAAAACGGTAATTTTTGGAAGTTTTGGGGTCAAAATCGAGATTTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAATCGAGA-TTTTTGGAAGTTT
* * *
76056 GGGGGTAAAATGGTAATTTTTGGAAG-TTCGAGGAT-AAAATTG-GAATTTTGGAGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGTTTTGAGG-TCAAAATCGAG-ATTTTTG-GAAGTTT
* *
76115 GGGGGTCAAA-GTATAATTTTTGGATAGTTT
1 GGGGGTAAAATG-GTAATTTTTGGA-AGTTT
76145 AGGGACTTCC
Statistics
Matches: 218, Mismatches: 32, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
57 7 0.03
58 13 0.06
59 101 0.46
60 84 0.39
61 10 0.05
62 3 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.36
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTT
Found at i:76144 original size:30 final size:29
Alignment explanation
Indices: 75818--76144 Score: 152
Period size: 29 Copynumber: 11.0 Consensus size: 29
75808 TTGGACATCC
* *
75818 GGGGGTAAAAAGGTAATTTTTGAAAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAGTTT
** *
75847 TTGGGTCAAAAATAG-AA-TTTTGGAACTTT
1 GGGGGT-AAAAAT-GTAATTTTTGGAAGTTT
75876 AGGGGGT-AAAATAGTAA-TTTT-GAGAGTTT
1 -GGGGGTAAAAAT-GTAATTTTTGGA-AGTTT
** * * *
75905 CGGGATTAAAAAAT-TGAATTTTCGGAGGTTC
1 -GGGGGT-AAAAATGT-AATTTTTGGAAGTTT
* *
75936 GAGGGT-GAAATGGTAATTTTTGGAAAGTTT
1 GGGGGTAAAAAT-GTAATTTTTGG-AAGTTT
* * * * *
75966 TGAGGTCAAAATCG-AGATTTTTAGAGGTTT
1 GGGGGTAAAAAT-GTA-ATTTTTGGAAGTTT
**
75996 GGGGGTAAAACGGTAATTTTTGGAAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
76025 TGGGGTCAAAATCG-AGATTTTTTGGAAGTTT
1 GGGGGTAAAAAT-GTA-A-TTTTTGGAAGTTT
*
76056 GGGGGT-AAAATGGTAATTTTTGGAAGTTC
1 GGGGGTAAAAAT-GTAATTTTTGGAAGTTT
* * * * *
76085 GAGGATAAAATTGGAATTTTGGAGAAGTTT
1 GGGGGTAAAAATGTAATTTTTG-GAAGTTT
* * *
76115 GGGGGTCAAAGTATAATTTTTGGATAGTTT
1 GGGGGTAAAAATGTAATTTTTGGA-AGTTT
76145 AGGGACTTCC
Statistics
Matches: 220, Mismatches: 55, Indels: 45
0.69 0.17 0.14
Matches are distributed among these distances:
28 13 0.06
29 85 0.39
30 77 0.35
31 43 0.20
32 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGGTAAAAATGTAATTTTTGGAAGTTT
Found at i:77104 original size:13 final size:13
Alignment explanation
Indices: 77086--77134 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
77076 GTATTTGGAC
77086 ATTTGGACTTGTA
1 ATTTGGACTTGTA
77099 ATTTGGACATTGT-
1 ATTTGGAC-TTGTA
77112 A--TGGACTTGTA
1 ATTTGGACTTGTA
77123 ATCTTTGGACTT
1 A--TTTGGACTT
77135 TCAATATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.13
11 6 0.20
13 9 0.30
14 4 0.13
15 7 0.23
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.45
Consensus pattern (13 bp):
ATTTGGACTTGTA
Found at i:77104 original size:21 final size:24
Alignment explanation
Indices: 77074--77124 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
77064 ATTTGGGCTT
77074 TTGT-ATTTGGACA-T-T-TGGAC
1 TTGTAATTTGGACATTGTATGGAC
77094 TTGTAATTTGGACATTGTATGGAC
1 TTGTAATTTGGACATTGTATGGAC
77118 TTGTAAT
1 TTGTAAT
77125 CTTTGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 1 0.04
23 1 0.04
24 12 0.44
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (24 bp):
TTGTAATTTGGACATTGTATGGAC
Found at i:78215 original size:32 final size:32
Alignment explanation
Indices: 78179--78242 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
78169 CATATAATAA
*
78179 AATTTTAAATTACAATAAATATTAGAATTTTT
1 AATTTTAAATTAAAATAAATATTAGAATTTTT
78211 AATTTTAAATTAAAATAAATATTAGAATTTTT
1 AATTTTAAATTAAAATAAATATTAGAATTTTT
78243 TTTCACGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (32 bp):
AATTTTAAATTAAAATAAATATTAGAATTTTT
Found at i:80844 original size:20 final size:21
Alignment explanation
Indices: 80807--80848 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
80797 TTTTTTTGGG
80807 TTAAATTTTATTATTATTTTAA
1 TTAAATTTTA-TATTATTTTAA
80829 TTAAATTTTA-ATTATTTTAA
1 TTAAATTTTATATTATTTTAA
80849 AGATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAAATTTTATATTATTTTAA
Found at i:80856 original size:20 final size:20
Alignment explanation
Indices: 80809--80858 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
80799 TTTTTGGGTT
**
80809 AAATTTTATTATTATTTTAATT
1 AAATTTTA--ATTATTTTAAAG
80831 AAATTTTAATTATTTTAAAG
1 AAATTTTAATTATTTTAAAG
*
80851 ATATTTTA
1 AAATTTTA
80859 GTATAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
22 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AAATTTTAATTATTTTAAAG
Found at i:86557 original size:23 final size:23
Alignment explanation
Indices: 86522--86579 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
86512 AAAAAAACTC
* *
86522 AATTTATACTAATCATATGTTAAT
1 AATTAATA-TAATCATATGATAAT
*
86546 AATTAATATAATTATATGATAAT
1 AATTAATATAATCATATGATAAT
* *
86569 ATTTAAAATAA
1 AATTAATATAA
86580 AAATAAGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
AATTAATATAATCATATGATAAT
Found at i:87787 original size:21 final size:21
Alignment explanation
Indices: 87761--87800 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
87751 ATTTAATTAC
87761 AAATTAA-TTAATTATTCAAAG
1 AAATTAATTTAATT-TTCAAAG
87782 AAATTAATTTAATTTTCAA
1 AAATTAATTTAATTTTCAA
87801 GTCTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
AAATTAATTTAATTTTCAAAG
Found at i:88159 original size:157 final size:158
Alignment explanation
Indices: 87868--88176 Score: 478
Period size: 157 Copynumber: 2.0 Consensus size: 158
87858 TTACTTCATC
*
87868 ATTTCACAATTTTTCATTTCATCAATTAATGCAAACCATCAAGATTATATCGAGCTAGCGGAAGA
1 ATTTCACAATTTTTCATTTCATCAATTAATGCAAACCATCAAGATTATATCGAGCTAACGGAAGA
* * * ** *
87933 ATCGATTGGACATATAAAATTAGAGCTCAAATAATTTTTAATTAAGTTTCAACCTTACATCTATT
66 ACCGATTGAACATATAAAATTAGAGCTCAAATAATTTGTAATTAAGTCCCAACCCTACATCTATT
87998 AATTACAACATTATTTAGTCATGGAGTT
131 AATTACAACATTATTTAGTCATGGAGTT
* * *
88026 ATTT-ACAATTTTTCATTTCATCAATTAATGCAAACCATCAAGGTTATATCGAGCTAACGGAGGG
1 ATTTCACAATTTTTCATTTCATCAATTAATGCAAACCATCAAGATTATATCGAGCTAACGGAAGA
*
88090 ACCGATTGAACATATAAAATTAGAGCTCAAATAATTTGTAATTAAGTCCCAACCCTACGGT-TAT
66 ACCGATTGAACATATAAAATTAGAGCTCAAATAATTTGTAATTAAGTCCCAACCCTAC-ATCTAT
* *
88154 TAATTATAATATTATTTAGTCAT
130 TAATTACAACATTATTTAGTCAT
88177 AGAATCATTC
Statistics
Matches: 137, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
157 132 0.96
158 5 0.04
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (158 bp):
ATTTCACAATTTTTCATTTCATCAATTAATGCAAACCATCAAGATTATATCGAGCTAACGGAAGA
ACCGATTGAACATATAAAATTAGAGCTCAAATAATTTGTAATTAAGTCCCAACCCTACATCTATT
AATTACAACATTATTTAGTCATGGAGTT
Found at i:93088 original size:29 final size:29
Alignment explanation
Indices: 93045--93100 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
93035 TTTAACTCTT
* * *
93045 TTTAATTATATAAAAATTAAATTGATCTA
1 TTTAATAATAAAAAAACTAAATTGATCTA
*
93074 TTTAATAATAAAAAAACTAATTTGATC
1 TTTAATAATAAAAAAACTAAATTGATC
93101 AAGTCCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTAATAATAAAAAAACTAAATTGATCTA
Found at i:94117 original size:31 final size:31
Alignment explanation
Indices: 94081--94139 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
94071 CCCAATTTGG
*
94081 TACCTGAATTTAGCATTTTTTCCTAATTCGA
1 TACCTGAACTTAGCATTTTTTCCTAATTCGA
*
94112 TACCTGAACTTGGCATTTTTTCCTAATT
1 TACCTGAACTTAGCATTTTTTCCTAATT
94140 TGGTACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (31 bp):
TACCTGAACTTAGCATTTTTTCCTAATTCGA
Found at i:94486 original size:61 final size:59
Alignment explanation
Indices: 94332--94489 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 59
94322 AAAGATTAGG
** * * **
94332 TACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACCCCAAAAAGTTTAAA
1 TACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAACTGAACCAAAAAAAGTTTAAA
* * * **
94391 TACCAACTTAAAAAAAAGTGTCAAGTTTAAGTACCAAGCTGAACCAAAAAAGAGTTTAGG
1 TACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAACTGAACCAAAAAA-AGTTTAAA
* * * *
94451 TACCAAAATTAAAGAAACGTGTTAAGTTCAGGTACCAAA
1 TACC-AAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAA
94490 TATTATATTA
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 42 0.53
60 10 0.13
61 27 0.34
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (59 bp):
TACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAACTGAACCAAAAAAAGTTTAAA
Found at i:97005 original size:39 final size:40
Alignment explanation
Indices: 96953--97029 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
96943 TGGTCTGGTT
*
96953 TAAACCCGAT-AAAAATTCGAGTATAATATAAAGGAGTAG
1 TAAACCCGATAAAAAATACGAGTATAATATAAAGGAGTAG
* * * *
96992 TAAACTCGGTAAAAAATACGAGTGTAGTATAAAGGAGT
1 TAAACCCGATAAAAAATACGAGTATAATATAAAGGAGT
97030 GGTGCCAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 8 0.25
40 24 0.75
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (40 bp):
TAAACCCGATAAAAAATACGAGTATAATATAAAGGAGTAG
Found at i:97099 original size:26 final size:26
Alignment explanation
Indices: 97063--97156 Score: 107
Period size: 26 Copynumber: 3.4 Consensus size: 26
97053 CACAAAAAAA
*
97063 TATGTTAATGTTTGTATTTAATTAAT
1 TATGTTTATGTTTGTATTTAATTAAT
*
97089 TATGTTTATGTTTAAATTTGTATTTAATCAAT
1 TATGTTTATG------TTTGTATTTAATTAAT
97121 TATGTTTATGTTTGTATTTAATTAAT
1 TATGTTTATGTTTGTATTTAATTAAT
*
97147 TATATTTATG
1 TATGTTTATG
97157 CTTATGTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
26 33 0.57
32 25 0.43
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.59
Consensus pattern (26 bp):
TATGTTTATGTTTGTATTTAATTAAT
Found at i:97109 original size:32 final size:32
Alignment explanation
Indices: 97073--97133 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
97063 TATGTTAATG
*
97073 TTTGTATTTAATTAATTATGTTTATGTTTAAA
1 TTTGTATTTAATCAATTATGTTTATGTTTAAA
97105 TTTGTATTTAATCAATTATGTTTATGTTT
1 TTTGTATTTAATCAATTATGTTTATGTTT
97134 GTATTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.61
Consensus pattern (32 bp):
TTTGTATTTAATCAATTATGTTTATGTTTAAA
Found at i:97156 original size:32 final size:32
Alignment explanation
Indices: 97063--97165 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 32
97053 CACAAAAAAA
* *
97063 TATGTTAATGTTTGTATTTAATTAATTATGTT
1 TATGTTTATGTTTGTATTTAATTAATTATATT
** *
97095 TATGTTTAAATTTGTA--T--TTAATCA-A-T
1 TATGTTTATGTTTGTATTTAATTAATTATATT
97121 TATGTTTATGTTTGTATTTAATTAATTATATT
1 TATGTTTATGTTTGTATTTAATTAATTATATT
*
97153 TATGCTTATGTTT
1 TATGTTTATGTTT
97166 ATGTTTGGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
26 15 0.27
28 7 0.12
30 7 0.12
31 1 0.02
32 26 0.46
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (32 bp):
TATGTTTATGTTTGTATTTAATTAATTATATT
Found at i:97166 original size:26 final size:26
Alignment explanation
Indices: 97109--97166 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
97099 TTTAAATTTG
* * *
97109 TATTTAATCAATTATGTTTATGTTTG
1 TATTTAATCAATTATATTTATGCTTA
*
97135 TATTTAATTAATTATATTTATGCTTA
1 TATTTAATCAATTATATTTATGCTTA
*
97161 TGTTTA
1 TATTTA
97167 TGTTTGGGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (26 bp):
TATTTAATCAATTATATTTATGCTTA
Found at i:97372 original size:38 final size:38
Alignment explanation
Indices: 97321--97410 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
97311 CCATATACCC
* *
97321 CAAACATAAACATAAGCATGAAGATAATT-AAT-TAAATA
1 CAAACATAAACATAAACAT-AA-ATAATTAAATACAAATA
*
97359 CAAACATAAACATAAACATAATTAATTAAATACAAATA
1 CAAACATAAACATAAACATAAATAATTAAATACAAATA
*
97397 TAAACATAAACATA
1 CAAACATAAACATA
97411 TTTTTTTGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 5 0.11
37 5 0.11
38 36 0.78
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.23
Consensus pattern (38 bp):
CAAACATAAACATAAACATAAATAATTAAATACAAATA
Found at i:97380 original size:32 final size:32
Alignment explanation
Indices: 97328--97410 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
97318 CCCCAAACAT
* * *
97328 AAACATAAGCATGAAGATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
97360 AAACATAAACATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
*
97392 AAATATAAACATAAACATA
1 AAACATAAACATAAACATA
97411 TTTTTTTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (32 bp):
AAACATAAACATAAACATAATTAATTAAATAC
Found at i:97462 original size:27 final size:27
Alignment explanation
Indices: 97420--97474 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
97410 ATTTTTTTGG
*
97420 TGGTGATGCCTGTCAGGTAGGCACCAC
1 TGGTGATGCCTATCAGGTAGGCACCAC
*
97447 TGGTGATGCTTATCAGGTAGGCACCAC
1 TGGTGATGCCTATCAGGTAGGCACCAC
97474 T
1 T
97475 CCTTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (27 bp):
TGGTGATGCCTATCAGGTAGGCACCAC
Found at i:100398 original size:4 final size:4
Alignment explanation
Indices: 100389--100474 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
100379 AAATAAACGG
* * *
100389 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
100439 G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
100475 GTAATGTGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
3 6 0.09
4 51 0.74
5 12 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:100411 original size:17 final size:19
Alignment explanation
Indices: 100388--100474 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 19
100378 CAAATAAACG
100388 GGAAAGAAAGAAAGAA-AA
1 GGAAAGAAAGAAAGAAGAA
100406 -GAAAGAAAGAAAGGAAGAA
1 GGAAAGAAAGAAA-GAAGAA
*
100425 GGAGAGGAAAGAAAGAAGAA
1 GGA-AAGAAAGAAAGAAGAA
*
100445 GGAGAGGAAAGAAAGAAGAA
1 GGA-AAGAAAGAAAGAAGAA
100465 GGAAAGAAAG
1 GGAAAGAAAG
100475 GTAATGTGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
17 12 0.19
18 3 0.05
19 8 0.13
20 31 0.49
21 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAAGAAGAA
Found at i:100548 original size:19 final size:18
Alignment explanation
Indices: 100514--100558 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
100504 GTATGATATC
*
100514 TTTTTAAAATTGTATTTTA
1 TTTTT-AAATTGTATTTAA
*
100533 TTTATTAAATTTTATTTAA
1 TTT-TTAAATTGTATTTAA
100552 TTTTTAA
1 TTTTTAA
100559 CAGATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTAAATTGTATTTAA
Done.