Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014897.1 Kokia drynarioides strain JFW-HI SEQ_129940, 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: 83570
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:2787 original size:24 final size:23
Alignment explanation
Indices: 2747--2804 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
2737 TATACATTCT
*
2747 AATTAGAT-TTTATAAATAATTAA
1 AATTA-ATATTTAAAAATAATTAA
* *
2770 TATTAATTATTTAAAAATATTTAA
1 AATTAA-TATTTAAAAATAATTAA
2794 AATTAATATTT
1 AATTAATATTT
2805 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 18 0.62
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAAAAATAATTAA
Found at i:3126 original size:21 final size:20
Alignment explanation
Indices: 3086--3127 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3076 CCAGCTTTAC
3086 TTAAATTTTGAATTGGATAAA
1 TTAAATTTTGAATT-GATAAA
3107 TTAAATTAGTTGAATT-ATAAA
1 TTAAATT--TTGAATTGATAAA
3128 AAGTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (20 bp):
TTAAATTTTGAATTGATAAA
Found at i:12385 original size:16 final size:15
Alignment explanation
Indices: 12343--12390 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
12333 TAATTGTAAT
*
12343 TTATTAAATAAAA-A
1 TTATTTAATAAAATA
*
12357 TGATTTAATTAAAATA
1 TTATTTAA-TAAAATA
12373 TTATTTCAATAAAATA
1 TTATTT-AATAAAATA
12389 TT
1 TT
12391 TAAATTTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 15 0.54
17 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
TTATTTAATAAAATA
Found at i:24942 original size:20 final size:22
Alignment explanation
Indices: 24917--25033 Score: 80
Period size: 23 Copynumber: 5.2 Consensus size: 22
24907 AAAACGCATA
*
24917 AAAATAACATCC-AAACAAC-C
1 AAAATAACAACCAAAACAACAC
*
24937 AAAATAATAACCAAAACAACAGC
1 AAAATAACAACCAAAACAACA-C
*
24960 AAAATAACAACAAAAACAGTA-AC
1 AAAATAACAACCAAAACA--ACAC
* *
24983 AAAATAACAGCAAAAATAGCAACA-
1 AAAATAACAAC-CAAA-A-CAACAC
* *
25007 AAAATAACAACAAAAACAGCACC
1 AAAATAACAACCAAAACAACA-C
25030 AAAA
1 AAAA
25034 CAGTAAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
20 10 0.13
21 11 0.14
22 1 0.01
23 36 0.46
24 16 0.20
25 3 0.04
26 2 0.03
ACGTcount: A:0.67, C:0.21, G:0.04, T:0.08
Consensus pattern (22 bp):
AAAATAACAACCAAAACAACAC
Found at i:24962 original size:23 final size:21
Alignment explanation
Indices: 24929--25033 Score: 84
Period size: 23 Copynumber: 4.6 Consensus size: 21
24919 AATAACATCC
* *
24929 AAACAACCAAAATAATAACCA
1 AAACAACCAAAATAACAACAA
24950 AAACAACAGCAAAATAACAACAA
1 AAACAAC--CAAAATAACAACAA
* *
24973 AAACAGTAACAAAATAACAGCAAA
1 AAACA--ACCAAAATAACAAC-AA
*
24997 AATAGCAACAAAAATAACAACAA
1 AA-A-CAACCAAAATAACAACAA
25020 AAACAGCACCAAAA
1 AAACA--ACCAAAA
25034 CAGTAAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
21 9 0.13
22 1 0.01
23 38 0.57
24 15 0.22
25 2 0.03
26 2 0.03
ACGTcount: A:0.68, C:0.21, G:0.05, T:0.07
Consensus pattern (21 bp):
AAACAACCAAAATAACAACAA
Found at i:24998 original size:12 final size:12
Alignment explanation
Indices: 24930--25022 Score: 82
Period size: 12 Copynumber: 7.9 Consensus size: 12
24920 ATAACATCCA
*
24930 AACAACCAAAAT
1 AACAACAAAAAT
* * *
24942 AATAACCAAAAC
1 AACAACAAAAAT
*
24954 AACAGC-AAAAT
1 AACAACAAAAAT
*
24965 AACAACAAAAAC
1 AACAACAAAAAT
**
24977 AGTAAC-AAAAT
1 AACAACAAAAAT
*
24988 AACAGCAAAAAT
1 AACAACAAAAAT
*
25000 AGCAACAAAAAT
1 AACAACAAAAAT
25012 AACAACAAAAA
1 AACAACAAAAA
25023 CAGCACCAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 16 0.25
12 47 0.75
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:24999 original size:35 final size:35
Alignment explanation
Indices: 24930--25033 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 35
24920 ATAACATCCA
* *
24930 AACAACCAAAATAATAACCAAAACAACAGCAAAAT
1 AACAACAAAAACAATAACCAAAACAACAGCAAAAT
* *
24965 AACAACAAAAACAGTAA-CAAAATAACAGCAAAAAT
1 AACAACAAAAACAATAACCAAAACAACAGC-AAAAT
* * * * * *
25000 AGCAACAAAAATAACAACAAAAACAGCACCAAAA
1 AACAACAAAAACAATAACCAAAACAACAGCAAAA
25034 CAGTAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
34 11 0.20
35 36 0.65
36 8 0.15
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (35 bp):
AACAACAAAAACAATAACCAAAACAACAGCAAAAT
Found at i:25032 original size:12 final size:12
Alignment explanation
Indices: 24960--25033 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 12
24950 AAACAACAGC
*
24960 AAAATAACAACA
1 AAAATAGCAACA
* *
24972 AAAACAGTAAC-
1 AAAATAGCAACA
* *
24983 AAAATAACAGCA
1 AAAATAGCAACA
24995 AAAATAGCAACA
1 AAAATAGCAACA
*
25007 AAAATAACAACA
1 AAAATAGCAACA
* *
25019 AAAACAGCACCA
1 AAAATAGCAACA
25031 AAA
1 AAA
25034 CAGTAAAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
11 7 0.15
12 41 0.85
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAATAGCAACA
Found at i:27388 original size:17 final size:17
Alignment explanation
Indices: 27366--27398 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27356 TTTTTACTCA
27366 TTCTATGTCTAAATGTG
1 TTCTATGTCTAAATGTG
27383 TTCTATGTCTAAATGT
1 TTCTATGTCTAAATGT
27399 TAAGCACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (17 bp):
TTCTATGTCTAAATGTG
Found at i:35326 original size:34 final size:36
Alignment explanation
Indices: 35282--35352 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
35272 TTTCACGACC
*
35282 TTTATACAACA-TCA-ATTTTAAGGATAAAATCTAT
1 TTTATACAACACTCATATCTTAAGGATAAAATCTAT
* *
35316 TTTATCCAACACTCATATCTTATGGATAAAATCTAT
1 TTTATACAACACTCATATCTTAAGGATAAAATCTAT
35352 T
1 T
35353 AGGCTTGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 10 0.31
35 3 0.09
36 19 0.59
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (36 bp):
TTTATACAACACTCATATCTTAAGGATAAAATCTAT
Found at i:41543 original size:135 final size:134
Alignment explanation
Indices: 41288--41546 Score: 358
Period size: 134 Copynumber: 1.9 Consensus size: 134
41278 AGATGGCAGA
* * * *
41288 TAAGGAGTAAGGTCCACATGGACTTATACGAATATTAAGTTGATGAACATTTTTTATGGGTCGAC
1 TAAGGAGTAAGGTCCACACGGACTCATACGAATATTAAGTTGATAAACATTTTTGATGGGTCGAC
** * *
41353 CAAGGAATAAATGGAACCCTAATGAGCTGTAAATCTAAGGGTTTTCCCGAAAATTCAATTTCAAA
66 CAAGGAATAAACAGAACCCTAATGAGCTGTAAATCTAAGGGTATCCCCGAAAATTCAATTTCAAA
41418 TAGT
131 TAGT
* * * * *
41422 TAAGGATTGAGGTTCACACGGACTCATCCGAATATTAAGTTGATAAACATTTTTGATGTGTCGAC
1 TAAGGAGTAAGGTCCACACGGACTCATACGAATATTAAGTTGATAAACATTTTTGATGGGTCGA-
* *
41487 CCAAGGAATAAACAGAACCCTTATGAGCTGTAAATCTACA-GGTATCCCCGATAATTCAAT
65 CCAAGGAATAAACAGAACCCTAATGAGCTGTAAATCTA-AGGGTATCCCCGAAAATTCAAT
41547 GTTAAGGAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
134 55 0.51
135 52 0.48
136 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (134 bp):
TAAGGAGTAAGGTCCACACGGACTCATACGAATATTAAGTTGATAAACATTTTTGATGGGTCGAC
CAAGGAATAAACAGAACCCTAATGAGCTGTAAATCTAAGGGTATCCCCGAAAATTCAATTTCAAA
TAGT
Found at i:41838 original size:21 final size:21
Alignment explanation
Indices: 41814--41857 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41804 ATAAAGCGAA
*
41814 AATATTAAATTATTCATTAAC
1 AATATTAAATTATTCATGAAC
* *
41835 AATATTATATTATTGATGAAC
1 AATATTAAATTATTCATGAAC
41856 AA
1 AA
41858 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
AATATTAAATTATTCATGAAC
Found at i:42145 original size:134 final size:131
Alignment explanation
Indices: 41926--42342 Score: 360
Period size: 134 Copynumber: 3.1 Consensus size: 131
41916 GACACTCATT
* * *
41926 AGTTGATAGAAAATTTTTATGGGTCGGTTTGAGGAATAAATGAAATCTTTATGAGTTGTAAATTT
1 AGTTGAT-GAATATTTTGAGGGGTCGGTTTGAGGAATAAATGAAATCTTTA-GAGTTGTAAATTT
* * * * * *
41991 GCGGGTATCTTCGAATATTCAATGTGAAATAGTTA-AGGAGTGAAATTCATACAGACTCGTATGA
64 ACGAGTATCTCCGAAAATTCAATGTCAAATAGTTAGA-GAGTGAAATTCACACAGACTC--ATGA
42055 ATATTA
126 ATATTA
*
42061 AGTTGATGAATATTTTGAGGGGTTGGTTTGAGGAATAAATGAAATTCTTGTA-AGTTGTAAATTT
1 AGTTGATGAATATTTTGAGGGGTCGGTTTGAGGAATAAATGAAA-TCTT-TAGAGTTGTAAATTT
* ** **
42125 ATGAGTAT-TCCCGAAAATTCAATGTCAAATAGTTAGAGAGTGAGGTTCACATGGACTCATGAAT
64 ACGAGTATCT-CCGAAAATTCAATGTCAAATAGTTAGAGAGTGAAATTCACACAGACTCATGAAT
42189 ATTA
128 ATTA
* * * ** * ** *
42193 AGTTGATGAATATTTCTAATGGGTCGGCTCAAGGAATAAAT-AAAGCTCTTATGAGCCGTAAATC
1 AGTTGATGAATATTT-TGAGGGGTCGGTTTGAGGAATAAATGAAATCT-TTA-GAGTTGTAAATT
* * * * * * *
42257 TACGAGTATC-CTCAAAAATTAAATATCAAATAGTTA-ACGAGTGAGATTCACACAAATTCAAAC
63 TACGAGTATCTC-CGAAAATTCAATGTCAAATAGTTAGA-GAGTGAAATTCACACAGACTC--AT
42320 GAATATTA
124 GAATATTA
* *
42328 AATTGATGAACATTT
1 AGTTGATGAATATTT
42343 CTAATGGGTC
Statistics
Matches: 232, Mismatches: 37, Indels: 26
0.79 0.13 0.09
Matches are distributed among these distances:
131 4 0.02
132 31 0.13
133 73 0.31
134 88 0.38
135 34 0.15
136 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (131 bp):
AGTTGATGAATATTTTGAGGGGTCGGTTTGAGGAATAAATGAAATCTTTAGAGTTGTAAATTTAC
GAGTATCTCCGAAAATTCAATGTCAAATAGTTAGAGAGTGAAATTCACACAGACTCATGAATATT
A
Found at i:42286 original size:133 final size:134
Alignment explanation
Indices: 42017--42369 Score: 347
Period size: 133 Copynumber: 2.6 Consensus size: 134
42007 ATTCAATGTG
* * * * * * *
42017 AAATAGTTAAGGAGTGAAATTCATACAGACTCGTATGAATATTAAGTTGATGAATATTT-TGAGG
1 AAATAGTTAACGAGTGAGATTCACACAAACTC-AATGAATATTAAGTTGATGAATATTTCTAATG
* * ** * * ** * * * *
42081 GGTTGGTTTGAGGAATAAATGAAATTCTTGTAAGTTGTAAATTTATGAGTATTCCCGAAAATTCA
65 GGTCGGCTCAAGGAATAAATGAAACTCTTATAAGCCGTAAATCTACGAGTATTCCCAAAAATTAA
*
42146 ATGTC
130 ATATC
* ***
42151 AAATAGTTAGA-GAGTGAGGTTCACATGGACTC-ATGAATATTAAGTTGATGAATATTTCTAATG
1 AAATAGTTA-ACGAGTGAGATTCACACAAACTCAATGAATATTAAGTTGATGAATATTTCTAATG
*
42214 GGTCGGCTCAAGGAATAAAT-AAAGCTCTTATGAGCCGTAAATCTACGAGTA-TCCTCAAAAATT
65 GGTCGGCTCAAGGAATAAATGAAA-CTCTTATAAGCCGTAAATCTACGAGTATTCC-CAAAAATT
42277 AAATATC
128 AAATATC
* * * *
42284 AAATAGTTAACGAGTGAGATTCACACAAATTCAAACGAATATTAAATTGATGAACATTTCTAATG
1 AAATAGTTAACGAGTGAGATTCACACAAACTC-AATGAATATTAAGTTGATGAATATTTCTAATG
* *
42349 GGTCAGCTCAAGAAATAAATG
65 GGTCGGCTCAAGGAATAAATG
42370 GAACCCGTAT
Statistics
Matches: 180, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
132 32 0.18
133 76 0.42
134 25 0.14
135 47 0.26
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (134 bp):
AAATAGTTAACGAGTGAGATTCACACAAACTCAATGAATATTAAGTTGATGAATATTTCTAATGG
GTCGGCTCAAGGAATAAATGAAACTCTTATAAGCCGTAAATCTACGAGTATTCCCAAAAATTAAA
TATC
Found at i:42506 original size:21 final size:20
Alignment explanation
Indices: 42481--42520 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42471 ATTGATGAAC
42481 AAAAACAAAAAAGAAAGGGAA
1 AAAAACAAAAAAG-AAGGGAA
**
42502 AAAAAGGAAAAAGAAGGGA
1 AAAAACAAAAAAGAAGGGA
42521 TTAGGGGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAGAAGGGAA
Found at i:45070 original size:22 final size:22
Alignment explanation
Indices: 45045--45097 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
45035 ATATTTGAAA
45045 TTTAATTCAGATACTTTTATTTT
1 TTTAATTCAGATA-TTTTATTTT
* *
45068 TTATAATTGAGTTATTTTATTTT
1 TT-TAATTCAGATATTTTATTTT
45091 TTTAATT
1 TTTAATT
45098 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 5 0.19
23 13 0.48
24 9 0.33
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTAATTCAGATATTTTATTTT
Found at i:45727 original size:16 final size:17
Alignment explanation
Indices: 45706--45739 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45696 CACTAACTTA
*
45706 TTAAAAATTA-ATATTT
1 TTAAAAAATATATATTT
45722 TTAAAAAATATATATTT
1 TTAAAAAATATATATTT
45739 T
1 T
45740 ATTGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAAATATATATTT
Found at i:45768 original size:17 final size:15
Alignment explanation
Indices: 45729--45785 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
45719 TTTTTAAAAA
45729 ATATATATTTTATTGT
1 ATAT-TATTTTATTGT
*
45745 ATTTTATTTTAATTCGT
1 ATATTATTTT-ATT-GT
*
45762 ATATTATTAATATATGT
1 ATATTATT-TTAT-TGT
45779 ATATTAT
1 ATATTAT
45786 AATTATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 20 0.59
18 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (15 bp):
ATATTATTTTATTGT
Found at i:45876 original size:16 final size:16
Alignment explanation
Indices: 45849--45885 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
45839 ACAATTTCAT
45849 TTTCATTTTTATTATAA
1 TTTCATTTTTATTAT-A
45866 TTTCA-TTTTATTATA
1 TTTCATTTTTATTATA
45881 TTTCA
1 TTTCA
45886 ACTTTAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCATTTTTATTATA
Found at i:45988 original size:7 final size:7
Alignment explanation
Indices: 45976--46007 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
45966 ATTCCAAATA
45976 AAATTTG
1 AAATTTG
45983 AAATTTG
1 AAATTTG
45990 AAATTTG
1 AAATTTG
45997 AAATTT-
1 AAATTTG
46003 AAATT
1 AAATT
46008 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (7 bp):
AAATTTG
Found at i:49266 original size:28 final size:27
Alignment explanation
Indices: 49202--49279 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 27
49192 TAACTTTTTT
*
49202 AATAATTTTTTAAAAAGTT-TGA-TACATA
1 AATAATTTTTT-AAAA-TTAT-ATTAAATA
49230 AATAA-TTTTTAAAATTGATATTAAATA
1 AATAATTTTTTAAAATT-ATATTAAATA
*
49257 AATTAGTTTTTTAAAATTATATT
1 AA-TAATTTTTTAAAATTATATT
49280 GAAGTTTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 13 0.30
28 12 0.28
29 11 0.26
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (27 bp):
AATAATTTTTTAAAATTATATTAAATA
Found at i:51452 original size:202 final size:201
Alignment explanation
Indices: 51063--51551 Score: 599
Period size: 202 Copynumber: 2.4 Consensus size: 201
51053 AATCTCTGTT
* * * * *
51063 CATGTTCGATTCAGTTTAATGAGTGAGCCTCAAAATATTGTTCATGTTCATTTATTTAGCTTGAT
1 CATGTTTGGTTCAGTTTAATAAATGAGCCTCAAAATCTTGTTCATGTTCATTTATTTAGCTTGAT
* * * ** *
51128 AAACGAAGC-TAAACAAACTGAAACTGAACGATTTATGAACTATTCATGGATATATTCATGGCTG
66 AAATGAA-CATAAACAAACAGAAACAGAACGATTTATGAACTATTCATCAATATATTCACGGCTG
* * * *
51192 TAAATTAACTGAGCTTGAACTAAGGAATCTCTGGTCATGTTCGTTTATGTTTAAACTTGTT-TAT
130 TAAATGAACTGAGCTTGAACAAAGGAATCTCTGGTCATATTAGTTTATGTTTAAACTTGTTCT-T
51256 GCTAGGTC
194 GCTAGGTC
* * * *
51264 CGTGTTTGGTTCAGTTTAATAAATTGAGCTTCAAAATCTTGTTCATATTCATTTATTTAGTTTGA
1 CATGTTTGGTTCAGTTTAATAAA-TGAGCCTCAAAATCTTGTTCATGTTCATTTATTTAGCTTGA
** * * * * *
51329 TAAATGAACATAAATGAACAGGATCAGAATGATTTATGAACTGTTTATCAATATATTCACGGCTG
65 TAAATGAACATAAACAAACAGAAACAGAACGATTTATGAACTATTCATCAATATATTCACGGCTG
* * *
51394 TAAATGAACTGAGCTTGGACAAAGGAATCTTTGTTCATATTAGTTTAT-TTTCAAACTTGTTCTT
130 TAAATGAACTGAGCTTGAACAAAGGAATCTCTGGTCATATTAGTTTATGTTT-AAACTTGTTCTT
* *
51458 GTTAGGTT
194 GCTAGGTC
* * *
51466 CATGTTTGGTTCA-ATTAAGAAATGAACCTCAAAATCTTGTTCATGTTCATTTATTTAGCTTGAT
1 CATGTTTGGTTCAGTTTAATAAATGAGCCTCAAAATCTTGTTCATGTTCATTTATTTAGCTTGAT
*
51530 AAATGAACATAAACAAATAGAA
66 AAATGAACATAAACAAACAGAA
51552 CCGAGCTTGA
Statistics
Matches: 242, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
200 56 0.23
201 29 0.12
202 156 0.64
203 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (201 bp):
CATGTTTGGTTCAGTTTAATAAATGAGCCTCAAAATCTTGTTCATGTTCATTTATTTAGCTTGAT
AAATGAACATAAACAAACAGAAACAGAACGATTTATGAACTATTCATCAATATATTCACGGCTGT
AAATGAACTGAGCTTGAACAAAGGAATCTCTGGTCATATTAGTTTATGTTTAAACTTGTTCTTGC
TAGGTC
Found at i:60263 original size:21 final size:21
Alignment explanation
Indices: 60238--60280 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
60228 TTGAATTAGT
*
60238 ACTCTAATACTCTCTTAATTA
1 ACTCTAACACTCTCTTAATTA
60259 ACTCTAACACTCTCTTAATTA
1 ACTCTAACACTCTCTTAATTA
60280 A
1 A
60281 GGAGGTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.40
Consensus pattern (21 bp):
ACTCTAACACTCTCTTAATTA
Found at i:60300 original size:3 final size:3
Alignment explanation
Indices: 60292--60316 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
60282 GAGGTTGAGG
60292 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
60317 CCATTAACTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:61227 original size:29 final size:30
Alignment explanation
Indices: 61195--61252 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
61185 ATATAAAATA
*
61195 ATCATTGAA-TTATTCGAAAATTCTCATTT
1 ATCATTAAACTTATTCGAAAATTCTCATTT
* * *
61224 ATCATTAAACTTATTTGAAAGTTTTCATT
1 ATCATTAAACTTATTCGAAAATTCTCATT
61253 CAAAACACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (30 bp):
ATCATTAAACTTATTCGAAAATTCTCATTT
Found at i:65689 original size:17 final size:17
Alignment explanation
Indices: 65667--65701 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
65657 ATCAAACATG
65667 ATAAAACTTAAAATAAA
1 ATAAAACTTAAAATAAA
* *
65684 ATAAAATTTAAACTAAA
1 ATAAAACTTAAAATAAA
65701 A
1 A
65702 ACACACCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAACTTAAAATAAA
Found at i:65806 original size:21 final size:20
Alignment explanation
Indices: 65772--65825 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
65762 TGTAATCACT
*
65772 ATATAGTAATTAATTAATAAA
1 ATATAGTATTTAATT-ATAAA
*
65793 ACTAT-GTATTTAATTATATA
1 A-TATAGTATTTAATTATAAA
65813 ATATAGTATTTAA
1 ATATAGTATTTAA
65826 AGAATAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 10 0.34
22 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (20 bp):
ATATAGTATTTAATTATAAA
Found at i:65823 original size:20 final size:19
Alignment explanation
Indices: 65772--65825 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
65762 TGTAATCACT
*
65772 ATATAGTAATTAATTAATA
1 ATATAGTATTTAATTAATA
*
65791 AAACTATGTATTTAATTATATA
1 ATA-TA-GTATTTAATTA-ATA
65813 ATATAGTATTTAA
1 ATATAGTATTTAA
65826 AGAATAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 12 0.41
22 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATAGTATTTAATTAATA
Found at i:73222 original size:267 final size:267
Alignment explanation
Indices: 72720--73253 Score: 811
Period size: 267 Copynumber: 2.0 Consensus size: 267
72710 ATTTGTGGTC
* *
72720 CTTCCTTATATCATTCAGATCAACCGGCTGCAACCCGAGTTCCTCCAAATGAGCAGGCTTATCCC
1 CTTCCTTACATCATTCAGATCAACCGGCTGCAACCCGAGTTCCTCCAAATGAGCAAGCTTATCCC
*
72785 CTGGAAACTACAACAAAGGGGAAGAACTTTGGCAGGCTAAAACCAATTGGCTGCAGAAAAAACCT
66 CTGGAAACTACAACAAAGGGGAAGAACTTTGGCAAGCTAAAACCAATTGGCTGCAGAAAAAACCT
*
72850 CCATAGGCAGATAATATAATAGCCTATGTGTGATAAACTCGAACATGCAATAACAATAATAACAA
131 CCATAGGCAGATAATATAATAGCCTATGTGTGATAAACTCGAACATGCAATAACAACAATAACAA
* * *
72915 TACAAAAGAAACCAACCCAAAACTGACTTGAATATAAAGAGCATACACAATCAAGGATTTAACTG
196 TACAAAAGAAACCAACCCAAAACCGACTCGAATATAAAGAGCATACACAATCAAGGATTTAACCG
72980 ATGTGGG
261 ATGTGGG
** *
72987 CTTCCTTACATCATTTGGATCAACCGGTTG-ACACCCGAGTTCCTCCAAATGAGCAAGCTTATCC
1 CTTCCTTACATCATTCAGATCAACCGGCTGCA-ACCCGAGTTCCTCCAAATGAGCAAGCTTATCC
* * *
73051 CCTGGAAACTACAACAAAGGGGAAGAACTTTGGCAAGCT-AAACCAATTGGCTGCGGTAAATACC
65 CCTGGAAACTACAACAAAGGGGAAGAACTTTGGCAAGCTAAAACCAATTGGCTGCAGAAAAAACC
*
73115 TCCATAGGCAGATAATATAATAGCCTATCGTGTGATAAACTTGAACATGCAATAACAACAATAAC
130 TCCATAGGCAGATAATATAATAGCCTAT-GTGTGATAAACTCGAACATGCAATAACAACAATAAC
* * ** ** * * * **
73180 AATATAACAGAATTCAACTTAAAGCCGACTCGAATGTAAAGAGCATACGCAATCCCGGATTTAAC
194 AATACAAAAGAAACCAACCCAAAACCGACTCGAATATAAAGAGCATACACAATCAAGGATTTAAC
73245 CGATGTGGG
259 CGATGTGGG
73254 ATGACAAACA
Statistics
Matches: 240, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
266 51 0.21
267 189 0.79
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (267 bp):
CTTCCTTACATCATTCAGATCAACCGGCTGCAACCCGAGTTCCTCCAAATGAGCAAGCTTATCCC
CTGGAAACTACAACAAAGGGGAAGAACTTTGGCAAGCTAAAACCAATTGGCTGCAGAAAAAACCT
CCATAGGCAGATAATATAATAGCCTATGTGTGATAAACTCGAACATGCAATAACAACAATAACAA
TACAAAAGAAACCAACCCAAAACCGACTCGAATATAAAGAGCATACACAATCAAGGATTTAACCG
ATGTGGG
Found at i:76021 original size:22 final size:21
Alignment explanation
Indices: 75996--76036 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
75986 TGGAAAGATA
* *
75996 TATGTAGTTATCTTTAAAAAAT
1 TATGAAGTTAT-TTGAAAAAAT
76018 TATGAAGTTATTTGAAAAA
1 TATGAAGTTATTTGAAAAA
76037 CAGGCAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (21 bp):
TATGAAGTTATTTGAAAAAAT
Found at i:78434 original size:29 final size:29
Alignment explanation
Indices: 78362--78440 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
78352 TTTGGATGCC
* * *
78362 CGAGGGTAAAATTGCGATTTTGGACACTT
1 CGAGGGCAAAATAGTGATTTTGGACACTT
78391 CGAGGGCAAAATAGTGATTTTGGACACTT
1 CGAGGGCAAAATAGTGATTTTGGACACTT
*
78420 CGAGGGCAAAATAGTAATTTT
1 CGAGGGCAAAATAGTGATTTT
78441 CAAAAGGTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (29 bp):
CGAGGGCAAAATAGTGATTTTGGACACTT
Found at i:78572 original size:29 final size:29
Alignment explanation
Indices: 78536--78852 Score: 258
Period size: 29 Copynumber: 10.8 Consensus size: 29
78526 ATTATTTATA
78536 TTCGAGGGT-AAAATGGTAATTTTTGAAAG
1 TTCGAGGGTAAAAAT-GTAATTTTTGAAAG
* *
78565 TTCGAGGGTATAAATGTAATTTTTGGAAG
1 TTCGAGGGTAAAAATGTAATTTTTGAAAG
*
78594 TTCGAGGGTAAAAATGTAATTTTTGGAAG
1 TTCGAGGGTAAAAATGTAATTTTTGAAAG
*
78623 TTCGAGGGTAAAAATGTAATTTTTTGGAAAA
1 TTCGAGGGTAAAAATGTAA-TTTTT-GAAAG
*
78654 TTCGA-GGTAAAAAATAG-AATTTTAGAAAG
1 TTCGAGGGT-AAAAAT-GTAATTTTTGAAAG
*
78683 TTCGAGGGT-AAAATGGTAATTTTAGGAGAA-
1 TTCGAGGGTAAAAAT-GTAATTTT-TGA-AAG
* *
78713 TTTG-GGGTCAAAAATGGAATTTTTGGAAA-
1 TTCGAGGGT-AAAAATGTAATTTTT-GAAAG
* * *
78742 TTCGAGGGT-AAAATATAATTATTGGAAG
1 TTCGAGGGTAAAAATGTAATTTTTGAAAG
* * * *
78770 TTTG-GTGTCAAAAATATAATTTTTAGAAAA
1 TTCGAGGGT-AAAAATGTAATTTTT-GAAAG
* * * * *
78800 TT-TAAGGTCAAAAATGAAATTTTAGAAAA
1 TTCGAGGGT-AAAAATGTAATTTTTGAAAG
*
78829 TTCGAGGGTAAAAATGTATTTTTT
1 TTCGAGGGTAAAAATGTAATTTTT
78853 TTGGAAAATT
Statistics
Matches: 236, Mismatches: 33, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
27 6 0.03
28 20 0.08
29 125 0.53
30 61 0.26
31 23 0.10
32 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGTAATTTTTGAAAG
Found at i:78584 original size:147 final size:147
Alignment explanation
Indices: 78389--78841 Score: 351
Period size: 146 Copynumber: 3.1 Consensus size: 147
78379 TTTTGGACAC
* * * *
78389 TTCGAGGGCAAAATAGTGATTTTGGACACTTCGAGGGCAAAATAGTAATTTTCAAAAGGTTCG-G
1 TTCGAGGGTAAAATGGTAATTTTGGAAACTTCGAGGGCAAAATAGTAATTTTCAAAA-GTTCGAG
* * ** **
78453 GGTTGAAAATAG-AATTTTTAGACA--TCTGAGGGTAAAATTGTAATTTTTTGGAATTTTTTAGG
65 GG-TAAAAAT-GTAATTTTTAGA-AGTTC-GAGGGTAAAAATGTAATTTTTTGGAAAATTCGAGG
* * * *
78515 TCAAAAATGGAATTATT-TATA-
126 TAAAAAATAGAATT-TTAGAAAG
* * * ***
78536 TTCGAGGGTAAAATGGTAATTTTTGAAAGTTCGAGGGTATAAAT-GTAATTTTTGGAAGTTCGAG
1 TTCGAGGGTAAAATGGTAATTTTGGAAACTTCGAGGGCA-AAATAGTAATTTTCAAAAGTTCGAG
*
78600 GGTAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTTGGAAAATTCGAGGTAAA
65 GGTAAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTTGGAAAATTCGAGGTAAA
78665 AAATAGAATTTTAGAAAG
130 AAATAGAATTTTAGAAAG
* * **
78683 TTCGAGGGTAAAATGGTAATTTTAGGAGAA-TTTG-GGGTCAAAA-ATGGAATTTTTGGAAA-TT
1 TTCGAGGGTAAAATGGTAATTTT-GGA-AACTTCGAGGG-CAAAATA-GTAA-TTTTCAAAAGTT
* * * * * * * **
78744 CGAGGGT-AAAATATAATTATTGGAAGTTTG-GTGTCAAAAATATAA-TTTTTAGAAAATTTAAG
61 CGAGGGTAAAAATGTAATTTTTAGAAGTTCGAGGGT-AAAAATGTAATTTTTTGGAAAATTCGAG
* *
78806 GTCAAAAAT-GAAATTTTAGAAAA
125 GTAAAAAATAG-AATTTTAGAAAG
78829 TTCGAGGGTAAAA
1 TTCGAGGGTAAAA
78842 ATGTATTTTT
Statistics
Matches: 254, Mismatches: 37, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
145 5 0.02
146 113 0.44
147 105 0.41
148 22 0.09
149 9 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (147 bp):
TTCGAGGGTAAAATGGTAATTTTGGAAACTTCGAGGGCAAAATAGTAATTTTCAAAAGTTCGAGG
GTAAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTTGGAAAATTCGAGGTAAAA
AATAGAATTTTAGAAAG
Found at i:78663 original size:59 final size:61
Alignment explanation
Indices: 78535--78842 Score: 263
Period size: 59 Copynumber: 5.2 Consensus size: 61
78525 AATTATTTAT
* *
78535 ATTCGAGGGT--AAAATGGTAATTTTTGAAAGTTCGAGGGTATAAATGTAATTTTTGG-AA
1 ATTCGAGGGTAAAAAATAGTAATTTTTGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAA
* *
78593 GTTCGAGGGT-AAAAAT-GTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTTGGAAA
1 ATTCGAGGGTAAAAAATAGTAATTTTTGAAAGTTCGAGGGTAAAAATGTAA-TTTTTGGAAA
* * *
78653 ATTCGA-GGTAAAAAATAG-AATTTTAGAAAGTTCGAGGGT-AAAATGGTAATTTTAGGAGA
1 ATTCGAGGGTAAAAAATAGTAATTTTTGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAA
* * * * *
78712 ATTTG-GGGTCAAAAAT-GGAATTTTTGGAAA-TTCGAGGGT-AAAATATAATTATTGG-AA
1 ATTCGAGGGTAAAAAATAGTAATTTTT-GAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAA
* * * * * * * * *
78769 GTTTG-GTGTCAAAAATA-TAATTTTTAGAAAATT-TAAGGTCAAAAATG-AAATTTTAGAAA
1 ATTCGAGGGTAAAAAATAGTAATTTTT-GAAAGTTCGAGGGT-AAAAATGTAATTTTTGGAAA
78828 ATTCGAGGGTAAAAA
1 ATTCGAGGGTAAAAA
78843 TGTATTTTTT
Statistics
Matches: 206, Mismatches: 29, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
57 30 0.15
58 57 0.28
59 71 0.34
60 47 0.23
61 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (61 bp):
ATTCGAGGGTAAAAAATAGTAATTTTTGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAA
Found at i:78688 original size:89 final size:90
Alignment explanation
Indices: 78535--78754 Score: 260
Period size: 89 Copynumber: 2.5 Consensus size: 90
78525 AATTATTTAT
* * * *
78535 ATTCGAGGGT-AAAATGGTAATTTTT-GAAAGTTCGAGGGT-ATAAATGTAATTTTTGGAAGTTC
1 ATTCGAGGGTAAAAAT-GTAATTTTTGGAAAATTCGAGGGTAAAAAATGTAATTTTAGAAAGTTC
*
78597 GAGGGTAAAAAT-GTAATTTTTGGA-A
65 GAGGGT-AAAATGGTAATTTTAGGAGA
*
78622 GTTCGAGGGTAAAAATGTAATTTTTTGGAAAATTCGA-GGTAAAAAATAG-AATTTTAGAAAGTT
1 ATTCGAGGGTAAAAATGTAA-TTTTTGGAAAATTCGAGGGTAAAAAAT-GTAATTTTAGAAAGTT
78685 CGAGGGTAAAATGGTAATTTTAGGAGA
64 CGAGGGTAAAATGGTAATTTTAGGAGA
* *
78712 ATTTG-GGGTCAAAAATGGAATTTTTGG-AAATTCGAGGGTAAAA
1 ATTCGAGGGT-AAAAATGTAATTTTTGGAAAATTCGAGGGTAAAA
78755 TATAATTATT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
87 13 0.11
88 26 0.23
89 62 0.54
90 14 0.12
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (90 bp):
ATTCGAGGGTAAAAATGTAATTTTTGGAAAATTCGAGGGTAAAAAATGTAATTTTAGAAAGTTCG
AGGGTAAAATGGTAATTTTAGGAGA
Found at i:78865 original size:32 final size:32
Alignment explanation
Indices: 78789--78884 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
78779 AAAAATATAA
** *
78789 TTTTTAGAAAATTTAAGGTCAAAA-ATGA--A
1 TTTTTAGAAAATTCGAGGTCAAAATATGATTT
*
78818 ATTTTAGAAAATTCGAGGGT-AAAA-ATGTATTT
1 TTTTTAGAAAATTCGA-GGTCAAAATATG-ATTT
*
78850 TTTTTGGAAAATTCGAGGTCAAAATATGATTT
1 TTTTTAGAAAATTCGAGGTCAAAATATGATTT
78882 TTT
1 TTT
78885 GAGAGTCTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
29 20 0.36
30 4 0.07
31 3 0.05
32 25 0.45
33 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (32 bp):
TTTTTAGAAAATTCGAGGTCAAAATATGATTT
Found at i:80481 original size:11 final size:11
Alignment explanation
Indices: 80455--80507 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
80445 TTTTGAACTC
80455 AATTTAAAATTA
1 AATTTAAAA-TA
80467 AATTTAAAATA
1 AATTTAAAATA
***
80478 AATTTTAGTTTA
1 AA-TTTAAAATA
80490 AATTTAAAATA
1 AATTTAAAATA
80501 AATTTAA
1 AATTTAA
80508 TTAAAGATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
AATTTAAAATA
Done.