Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012670.1 Kokia drynarioides strain JFW-HI SEQ_127681, 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: 104971
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:410 original size:20 final size:21
Alignment explanation
Indices: 385--427 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
375 TACTTACTGC
*
385 TACTAAC-AATAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
405 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
426 TA
1 TA
428 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:814 original size:4 final size:4
Alignment explanation
Indices: 807--845 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
797 TTCCTTCTTC
*
807 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
846 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:841 original size:21 final size:21
Alignment explanation
Indices: 762--845 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
752 ACATTATCTT
*
762 TTTTTTCTTTCTCCTTCTTTCCC
1 TTTTTTCTTTCT--TTCTTTCTC
* * *
785 TTATTCTCCTTC-TTCCTTCTTC
1 TT-TTTTCTTTCTTTCTTTC-TC
*
807 TTCTTTCTTTCTTTCTTTCTC
1 TTTTTTCTTTCTTTCTTTCTC
828 TTTTTTCTTTCTTT-TTTC
1 TTTTTTCTTTCTTTCTTTC
846 CTTCAATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
20 4 0.08
21 27 0.55
22 9 0.18
23 2 0.04
24 7 0.14
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTCTTTCTTTCTTTCTC
Found at i:1201 original size:11 final size:11
Alignment explanation
Indices: 1185--1209 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1175 TTAAATATAT
1185 AAAAATAATAA
1 AAAAATAATAA
1196 AAAAATAATAA
1 AAAAATAATAA
1207 AAA
1 AAA
1210 CACGTGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:4372 original size:23 final size:24
Alignment explanation
Indices: 4328--4373 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4318 TCATTTTCAA
*
4328 TGCTATTTTACATAAAATAATTTG
1 TGCTATCTTACATAAAATAATTTG
*
4352 TGCTATCTTGCAT-AAATAATTT
1 TGCTATCTTACATAAAATAATTT
4374 TAGTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (24 bp):
TGCTATCTTACATAAAATAATTTG
Found at i:7100 original size:15 final size:15
Alignment explanation
Indices: 7080--7108 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7070 TTTCAAATTA
7080 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
7095 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
7109 ACCTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:11115 original size:10 final size:11
Alignment explanation
Indices: 11096--11134 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
11086 TCCCATTGAT
11096 TTTTTATATTA
1 TTTTTATATTA
11107 TTTTT-TATTA
1 TTTTTATATTA
11117 TTTATTATATTA
1 TTT-TTATATTA
*
11129 TATTTA
1 TTTTTA
11135 AATTCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 8 0.32
11 10 0.40
12 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:11170 original size:19 final size:19
Alignment explanation
Indices: 11122--11175 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
11112 TATTATTTAT
* * *
11122 TATATTATATTTAAATTCA
1 TATATTCTATTTTAATTAA
*
11141 TATTTTC-ATTTTAATTAA
1 TATATTCTATTTTAATTAA
11159 TATATTCTATTTTAATT
1 TATATTCTATTTTAATT
11176 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTCTATTTTAATTAA
Found at i:11351 original size:18 final size:18
Alignment explanation
Indices: 11328--11370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
11318 AATTATCAAA
11328 TATATTTTAAATGTAAAG
1 TATATTTTAAATGTAAAG
* * *
11346 TATATTATAATTGTCAAG
1 TATATTTTAAATGTAAAG
11364 TAT-TTTT
1 TATATTTT
11371 TTTTAAACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (18 bp):
TATATTTTAAATGTAAAG
Found at i:12941 original size:24 final size:23
Alignment explanation
Indices: 12914--12959 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
12904 AATAACATCA
* *
12914 TTATTATTTTGATTATTTTAATTT
1 TTATTAATTTAATTA-TTTAATTT
12938 TTATTAATTTAATTATTTAATT
1 TTATTAATTTAATTATTTAATT
12960 AAGATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATTAATTTAATTATTTAATTT
Found at i:12943 original size:15 final size:15
Alignment explanation
Indices: 12919--12961 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
12909 CATCATTATT
* *
12919 ATTTTGATTATTTTA
1 ATTTTTATTAATTTA
12934 ATTTTTATTAATTTA
1 ATTTTTATTAATTTA
12949 ATTATTTAATTAA
1 ATT-TTT-ATTAA
12962 GATAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 16 0.67
16 3 0.12
17 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTTTATTAATTTA
Found at i:14929 original size:24 final size:24
Alignment explanation
Indices: 14899--14949 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
14889 GGTTAGACGA
*
14899 AAATTGCAGAATTGGGAGGTTAGG
1 AAATTGCAGAATTGGGAGGCTAGG
14923 AAATTGCAGAATTGGGAGGCTAGG
1 AAATTGCAGAATTGGGAGGCTAGG
14947 AAA
1 AAA
14950 CTTTCTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.35, T:0.22
Consensus pattern (24 bp):
AAATTGCAGAATTGGGAGGCTAGG
Found at i:16742 original size:2 final size:2
Alignment explanation
Indices: 16735--16789 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
16725 AGACTGTTTA
16735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16777 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
16790 ACAAATGCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20508 original size:14 final size:14
Alignment explanation
Indices: 20470--20511 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
20460 GATTAAAATT
*
20470 TTCATATA-TATAA
1 TTCATATATTAAAA
20483 TTACATTATATTAAAA
1 TT-CA-TATATTAAAA
20499 TTCATATATTAAA
1 TTCATATATTAAA
20512 TTACGGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 6 0.24
16 6 0.24
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TTCATATATTAAAA
Found at i:21528 original size:20 final size:20
Alignment explanation
Indices: 21503--21548 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
21493 GCCAAGGCAC
21503 CTGCCAATCCCCGCTTGGCT
1 CTGCCAATCCCCGCTTGGCT
21523 CTGCCAATCCCCGCTTGGCT
1 CTGCCAATCCCCGCTTGGCT
21543 CTGCCA
1 CTGCCA
21549 TTGAGTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.11, C:0.46, G:0.20, T:0.24
Consensus pattern (20 bp):
CTGCCAATCCCCGCTTGGCT
Found at i:29011 original size:90 final size:90
Alignment explanation
Indices: 28853--29089 Score: 411
Period size: 90 Copynumber: 2.6 Consensus size: 90
28843 CCATTTCCAA
28853 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
28918 TGTTCAAAGAGTTGCCAGCTGGAGT
66 TGTTCAAAGAGTTGCCAGCTGGAGT
* *
28943 AATTAATGAGCATTTACTTGAAGCAGAACCAAACAATGGTGTAGAGGATGAGAAAGAGATCGACT
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
*
29008 TGTTCAAAGAGTTGCCAGCTGGGGT
66 TGTTCAAAGAGTTGCCAGCTGGAGT
* * * *
29033 AATTGATGAGCATTCACTTGAAGCAAAATCAAACAACGGTGTACAGGATGAGAAAGA
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGA
29090 AGTAGAGATC
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 138 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (90 bp):
AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
TGTTCAAAGAGTTGCCAGCTGGAGT
Found at i:33131 original size:7 final size:7
Alignment explanation
Indices: 33119--33152 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
33109 ACTGGTTTCA
33119 ATTGCAG
1 ATTGCAG
33126 ATTGCAG
1 ATTGCAG
33133 ATTGCAG
1 ATTGCAG
33140 ATTGCAG
1 ATTGCAG
33147 ATTGCA
1 ATTGCA
33153 ACACCTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (7 bp):
ATTGCAG
Found at i:41412 original size:13 final size:13
Alignment explanation
Indices: 41394--41419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41384 ATCACATCAG
41394 TATATTAAAAAAA
1 TATATTAAAAAAA
41407 TATATTAAAAAAA
1 TATATTAAAAAAA
41420 AAAGAGGACG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TATATTAAAAAAA
Found at i:44354 original size:28 final size:26
Alignment explanation
Indices: 44286--44359 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
44276 ATATATAAAA
44286 TATTTTATTATATAATTACATATTTT
1 TATTTTATTATATAATTACATATTTT
**
44312 T-TTTGGTGAACATATAATTACATATTTAT
1 TATTT--T-ATTATATAATTACATATTT-T
44341 TATTTTATTTATATAATTA
1 TATTTTA-TTATATAATTA
44360 AAATAGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 2 0.05
28 27 0.71
29 2 0.05
30 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TATTTTATTATATAATTACATATTTT
Found at i:45603 original size:17 final size:17
Alignment explanation
Indices: 45581--45613 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45571 ATTAATTTTT
45581 AATTATTGT-TTTTAATA
1 AATTATT-TATTTTAATA
45598 AATTATTTATTTTAAT
1 AATTATTTATTTTAAT
45614 TAGATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTATTTATTTTAATA
Found at i:63970 original size:41 final size:43
Alignment explanation
Indices: 63925--64005 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 43
63915 TGAAATAAAA
* *
63925 AAAAATACTTATAATAATATT-GTAA-TAAATTTAAATTTAAC
1 AAAAATAATTATAATAATATTAATAATTAAATTTAAATTTAAC
* * *
63966 AAAAATAATTTTAATAGTATTAATAATTATATTTAAATTT
1 AAAAATAATTATAATAATATTAATAATTAAATTTAAATTT
64006 TTTTTAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 18 0.55
42 3 0.09
43 12 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (43 bp):
AAAAATAATTATAATAATATTAATAATTAAATTTAAATTTAAC
Found at i:66248 original size:28 final size:28
Alignment explanation
Indices: 66216--66271 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
66206 ATAAGGTGGC
66216 AGCTGGTTAATATTAATTAACTATGAAT
1 AGCTGGTTAATATTAATTAACTATGAAT
66244 AGCTGGTTAATATTAATTAACTATGAAT
1 AGCTGGTTAATATTAATTAACTATGAAT
66272 GTTATATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AGCTGGTTAATATTAATTAACTATGAAT
Found at i:72913 original size:25 final size:25
Alignment explanation
Indices: 72879--72929 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
72869 GTGAATGACG
*
72879 CTACATATTATAGAAGTCGTATACC
1 CTACATATTATAGAAGTCATATACC
*
72904 CTACATATTATAGAAGTTATATACC
1 CTACATATTATAGAAGTCATATACC
72929 C
1 C
72930 AATCTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (25 bp):
CTACATATTATAGAAGTCATATACC
Found at i:74036 original size:21 final size:21
Alignment explanation
Indices: 74002--74078 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
73992 AATAGTGTAT
** *
74002 ACTTCTACTAATACATGTGAC
1 ACTTCTACCGATACAAGTGAC
*
74023 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* ***
74044 TCTTCTACCGATACAAGTCTT
1 ACTTCTACCGATACAAGTGAC
74065 ACTTCTACCGATAC
1 ACTTCTACCGATAC
74079 TAAAAACTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:77949 original size:3 final size:3
Alignment explanation
Indices: 77943--77968 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
77933 AAAAAAAAAA
77943 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
77969 AGGAGCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:79034 original size:8 final size:8
Alignment explanation
Indices: 79023--79058 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
79013 TTTAATTGAA
79023 TAATAATT
1 TAATAATT
79031 TAATAATT
1 TAATAATT
*
79039 TAATATTT
1 TAATAATT
79047 TAATAATAT
1 TAATAAT-T
79056 TAA
1 TAA
79059 AAAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 21 0.84
9 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAATAATT
Found at i:79042 original size:16 final size:17
Alignment explanation
Indices: 79023--79081 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
79013 TTTAATTGAA
79023 TAATAATTTAATAAT-T
1 TAATAATTTAATAATAT
*
79039 TAATATTTTAATAATAT
1 TAATAATTTAATAATAT
* * *
79056 TAAAAAATATAAAAATAT
1 T-AATAATTTAATAATAT
79074 T-ATAATTT
1 TAATAATTT
79082 CCCATAACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 19 0.56
17 2 0.06
18 13 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAATTTAATAATAT
Found at i:79738 original size:33 final size:33
Alignment explanation
Indices: 79696--79763 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
79686 TAATTTAACT
*
79696 TTTTTCATTTTAACATTGTACATATGTTGTTTA
1 TTTTTCATTTTAACATTGTACATATATTGTTTA
79729 TTTTTCATTTTAACATTGTACATATATTGTTTA
1 TTTTTCATTTTAACATTGTACATATATTGTTTA
79762 TT
1 TT
79764 ATTATTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (33 bp):
TTTTTCATTTTAACATTGTACATATATTGTTTA
Found at i:80871 original size:19 final size:20
Alignment explanation
Indices: 80835--80872 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
80825 TGAAAAATGT
**
80835 TTTTTTTTGTTTGGATTTAA
1 TTTTTTTTGTTTAAATTTAA
80855 TTTTTTTT-TTTAAATTTA
1 TTTTTTTTGTTTAAATTTA
80873 CCTTCTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTTTTTGTTTAAATTTAA
Found at i:84938 original size:23 final size:23
Alignment explanation
Indices: 84889--84940 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
84879 TACAATATCC
* * *
84889 AAATAATATTAATAATGGATGCC
1 AAATAATAATAAAAATGGATGCA
84912 AAATAATAATAAAAATGGCA-GCA
1 AAATAATAATAAAAATGG-ATGCA
84935 AAATAA
1 AAATAA
84941 CATAAACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (23 bp):
AAATAATAATAAAAATGGATGCA
Found at i:85892 original size:41 final size:41
Alignment explanation
Indices: 85818--86046 Score: 235
Period size: 41 Copynumber: 5.5 Consensus size: 41
85808 TTATGCTCTT
* * * * *
85818 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCATC
* * *
85860 GCGAGACATGAGTCTTCTTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
** *
85901 TCGAGACATGAGTCTTCCTTCTTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* * *
85942 TCGAGACATGAGTCTTCCTTATATCAAAGTCACATTCTCATT
1 TCGAGACATGAGTCTTCCTTA-ATCAAAATCTCATTCTCATC
*** * *
85984 TCGAGACATGAGTCTTCCATTTATAT-ACTTTCTCATGCTCAAC
1 TCGAGACATGAGTCTTCC--TTA-ATCAAAATCTCATTCTCATC
86027 TCGAGACATGAGTCTTCCTT
1 TCGAGACATGAGTCTTCCTT
86047 TTTATACACC
Statistics
Matches: 157, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
41 76 0.48
42 47 0.30
43 28 0.18
44 6 0.04
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
Found at i:85979 original size:83 final size:82
Alignment explanation
Indices: 85816--86046 Score: 304
Period size: 83 Copynumber: 2.8 Consensus size: 82
85806 CCTTATGCTC
* * * * *
85816 TTTCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATCGCGAGACATGAGTCTTCTTTA
1 TTTCGAGACATGAGTCTTCCTTT-ATCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
*
85881 ATCAAAATCTCATTCTCA
65 ATCAAAATCACATTCTCA
*
85899 TTTCGAGACATGAGTCTTCCTTCT-TCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
1 TTTCGAGACATGAGTCTTCCTT-TATCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
*
85963 TATCAAAGTCACATTCTCA
65 -ATCAAAATCACATTCTCA
* *
85982 TTTCGAGACATGAGTCTTCCATTTAT-ATACTTTCTCATGCTCAACTCGAGACATGAGTCTTCCT
1 TTTCGAGACATGAGTCTTCC-TTTATCATA--TTCTCATTCTCATCTCGAGACATGAGTCTTCCT
86046 T
63 T
86047 TTTATACACC
Statistics
Matches: 131, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
82 36 0.27
83 60 0.46
84 4 0.03
85 31 0.24
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (82 bp):
TTTCGAGACATGAGTCTTCCTTTATCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAA
TCAAAATCACATTCTCA
Found at i:91326 original size:21 final size:22
Alignment explanation
Indices: 91302--91349 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
91292 AACAGATTGA
*
91302 AAAATAAA-AAATAGC-GTAATT
1 AAAATAAAGAAAAAGCAG-AATT
91323 AAAA-AAAGAAAAAGCAGAATT
1 AAAATAAAGAAAAAGCAGAATT
91344 AAAATA
1 AAAATA
91350 TCTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATAAAGAAAAAGCAGAATT
Found at i:92359 original size:3 final size:3
Alignment explanation
Indices: 92351--92375 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
92341 ATACACAACG
92351 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
92376 AGTTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:95967 original size:6 final size:6
Alignment explanation
Indices: 95956--95987 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
95946 GAAATCTTGA
95956 ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT AT
1 ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT AT
95988 CCTGTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTCT
Found at i:102827 original size:15 final size:16
Alignment explanation
Indices: 102809--102838 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
102799 AATTCTATTT
102809 CAAAATAT-GCTATGC
1 CAAAATATGGCTATGC
102824 CAAAATATGGCTATG
1 CAAAATATGGCTATG
102839 AAAAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (16 bp):
CAAAATATGGCTATGC
Done.