Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010581.1 Kokia drynarioides strain JFW-HI SEQ_125506, 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: 90814
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4053 original size:20 final size:20
Alignment explanation
Indices: 4017--4068 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
4007 TTTTACAAAC
*
4017 TAAAATAT-AAT-CTTAAACA
1 TAAAATATAAATAC-TAAAAA
* *
4036 TTAAATCTAAATACTAAAAA
1 TAAAATATAAATACTAAAAA
4056 TAAAATATAAATA
1 TAAAATATAAATA
4069 TATAATGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.23
20 19 0.73
21 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATATAAATACTAAAAA
Found at i:27288 original size:72 final size:76
Alignment explanation
Indices: 27200--27357 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 76
27190 GTTTATTACA
*
27200 TTTATGCTCGCTAGCATGAATACGTTTACGCTCGTCAGCAT-AA-A-T-ACGTTTATGCTCGCCA
1 TTTATGCTCGCCAGCATGAATACGTTTACGCTCGTCAGCATGAATACTAACGTTTATGCTCGCCA
27261 GCATGAATACG
66 GCATGAATACG
* *
27272 TTTATGCTCGCCAGCATGAATACGTTTACGCTCGTCAGCATGAATACGTAAACGTTTATGGTCGT
1 TTTATGCTCGCCAGCATGAATACGTTTACGCTCGTCAGCATGAATAC-T-AACGTTTATGCTCGC
27337 CAGCATGAATACG
64 CAGCATGAATACG
27350 TTTATGCT
1 TTTATGCT
27358 TTTTAGCATG
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
72 40 0.52
73 2 0.03
74 1 0.01
76 1 0.01
78 33 0.43
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (76 bp):
TTTATGCTCGCCAGCATGAATACGTTTACGCTCGTCAGCATGAATACTAACGTTTATGCTCGCCA
GCATGAATACG
Found at i:27329 original size:30 final size:30
Alignment explanation
Indices: 27293--27350 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
27283 CAGCATGAAT
27293 ACGTTTACGCTCGTCAGCATGAATACGTAA
1 ACGTTTACGCTCGTCAGCATGAATACGTAA
* *
27323 ACGTTTATGGTCGTCAGCATGAATACGT
1 ACGTTTACGCTCGTCAGCATGAATACGT
27351 TTATGCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (30 bp):
ACGTTTACGCTCGTCAGCATGAATACGTAA
Found at i:27355 original size:24 final size:24
Alignment explanation
Indices: 27200--27372 Score: 195
Period size: 24 Copynumber: 7.0 Consensus size: 24
27190 GTTTATTACA
27200 TTTATGCTCG-CTAGCATGAATACG
1 TTTATGCTCGTC-AGCATGAATACG
* *
27224 TTTACGCTCGTCAGCATAAATACG
1 TTTATGCTCGTCAGCATGAATACG
*
27248 TTTATGCTCGCCAGCATGAATACG
1 TTTATGCTCGTCAGCATGAATACG
*
27272 TTTATGCTCGCCAGCATGAATACG
1 TTTATGCTCGTCAGCATGAATACG
*
27296 TTTACGCTCGTCAGCATGAATACGTAAACG
1 TTTATGCTCGTCAGCATG-A-A--T--ACG
*
27326 TTTATGGTCGTCAGCATGAATACG
1 TTTATGCTCGTCAGCATGAATACG
** *
27350 TTTATGCTTTTTAGCATGAATAC
1 TTTATGCTCGTCAGCATGAATAC
27373 TTGAAACATT
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
24 103 0.80
25 2 0.02
26 2 0.02
28 2 0.02
29 1 0.01
30 19 0.15
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (24 bp):
TTTATGCTCGTCAGCATGAATACG
Found at i:27367 original size:78 final size:72
Alignment explanation
Indices: 27200--27372 Score: 238
Period size: 78 Copynumber: 2.3 Consensus size: 72
27190 GTTTATTACA
27200 TTTATGCTCGCTAGCATGAATACGTTTACGCTCGTCAGCATAAATACGTTTATGCTCGCCAGCAT
1 TTTATGCTCGCTAGCATGAATACGTTTACGCTCGTCAGCATAAATACGTTTATGCTCGCCAGCAT
27265 GAATACG
66 GAATACG
* * *
27272 TTTATGCTCGCCAGCATGAATACGTTTACGCTCGTCAGCATGAATACGTAAACGTTTATGGTCGT
1 TTTATGCTCGCTAGCATGAATACGTTTACGCTCGTCAGCAT-AA-A--T--ACGTTTATGCTCGC
27337 CAGCATGAATACG
60 CAGCATGAATACG
***
27350 TTTATGCTTTTTAGCATGAATAC
1 TTTATGCTCGCTAGCATGAATAC
27373 TTGAAACATT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
72 40 0.45
73 2 0.02
74 1 0.01
76 1 0.01
78 44 0.50
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (72 bp):
TTTATGCTCGCTAGCATGAATACGTTTACGCTCGTCAGCATAAATACGTTTATGCTCGCCAGCAT
GAATACG
Found at i:30617 original size:18 final size:18
Alignment explanation
Indices: 30581--30634 Score: 83
Period size: 18 Copynumber: 3.0 Consensus size: 18
30571 CCTCAAACCT
30581 TTTAAATTG-TTTATTTA
1 TTTAAATTGTTTTATTTA
*
30598 TTTAAATTGTTTTGTTTA
1 TTTAAATTGTTTTATTTA
30616 TTTAAATTGTTTTAATTTA
1 TTTAAATTGTTTT-ATTTA
30635 GCTTGCTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.27
18 20 0.61
19 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTAAATTGTTTTATTTA
Found at i:31624 original size:25 final size:25
Alignment explanation
Indices: 31535--31781 Score: 293
Period size: 25 Copynumber: 10.3 Consensus size: 25
31525 TAAGTACATA
* *
31535 AGTGCTGGGGAAATAGAAGCACACAC
1 AGTGCT-GGGTAACAGAAGCACACAC
* **
31561 AGTGCT--G-AACAGAACCATGCAC
1 AGTGCTGGGTAACAGAAGCACACAC
31583 AGTGCTGGGGTAACAGAAGCACACAC
1 AGTGCT-GGGTAACAGAAGCACACAC
31609 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
31634 AGTGCT-GG--ACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
31656 AGTGCT-GG--ACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
31678 AGTGCTGGGTAATAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
* * *
31703 AATG-T-TG-AACAAAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
31725 AGTGCTAGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
31750 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
31775 AATGCTG
1 AGTGCTG
31782 AACAGAAGCG
Statistics
Matches: 194, Mismatches: 17, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
22 75 0.39
23 5 0.03
24 4 0.02
25 86 0.44
26 24 0.12
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:31649 original size:47 final size:47
Alignment explanation
Indices: 31535--31790 Score: 283
Period size: 47 Copynumber: 5.4 Consensus size: 47
31525 TAAGTACATA
* * **
31535 AGTGCTGGGGAAATAGAAGCACACACAGTGCT-GAACAGAACCATGCAC
1 AGTGCT-GGG-AACAGAAGCACACACAGTGCTGGAACAGAAGCACACAC
31583 AGTGCTGGGGTAACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACAC
1 AGTGCT-GGG-AACAGAAGCACACACAGTGCT-GG-AACAGAAGCACACAC
31634 AGTGCT-GG-ACAGAAGCACACACAGTGCTGG-ACAGAAGCACACAC
1 AGTGCTGGGAACAGAAGCACACACAGTGCTGGAACAGAAGCACACAC
* * * *
31678 AGTGCTGGGTAATAGAAGCACACACAATG-TTGAACAAAAGCACACAC
1 AGTGCTGGG-AACAGAAGCACACACAGTGCTGGAACAGAAGCACACAC
*
31725 AGTGCTAGGTAACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACAC
1 AGTGCT-GGGAACAGAAGCACACACAGTGCT-GG-AACAGAAGCACACAC
*
31775 AATGCT--GAACAGAAGC
1 AGTGCTGGGAACAGAAGC
31791 GTGCTAGCAT
Statistics
Matches: 181, Mismatches: 16, Indels: 23
0.82 0.07 0.10
Matches are distributed among these distances:
44 20 0.11
45 2 0.01
46 4 0.02
47 81 0.45
48 33 0.18
49 3 0.02
50 20 0.11
51 18 0.10
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.12
Consensus pattern (47 bp):
AGTGCTGGGAACAGAAGCACACACAGTGCTGGAACAGAAGCACACAC
Found at i:35709 original size:9 final size:9
Alignment explanation
Indices: 35676--35709 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
35666 AACCCAAAAC
35676 AAAAAAAGA
1 AAAAAAAGA
*
35685 ACAAAAAGA
1 AAAAAAAGA
*
35694 AAGAAAAGA
1 AAAAAAAGA
35703 AAAAAAA
1 AAAAAAA
35710 AGTCAAGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:39378 original size:27 final size:27
Alignment explanation
Indices: 39336--39398 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
39326 AGGAGTAATA
*
39336 TGATTCTGGCTCGAAAGAGCATTATTT
1 TGATTCTGGCTCGAAAGAGCATTATTC
* * *
39363 TGATTCTTGCTTGAAAGAGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
39390 TGATTCTGG
1 TGATTCTGG
39399 GCTTGTAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (27 bp):
TGATTCTGGCTCGAAAGAGCATTATTC
Found at i:39422 original size:24 final size:24
Alignment explanation
Indices: 39392--39548 Score: 233
Period size: 24 Copynumber: 6.5 Consensus size: 24
39382 CGTTATTCTG
* *
39392 ATTCTGGGCTTGTAAGAACTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
39416 ATTCTGGGCTCGTAAGAGCTAATC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
39440 ATTCTAGGCTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
39464 ATTCTAGGCTCGTAACAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
39488 ATTCTGGACTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
39512 ATTCTAGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
39536 ATTCTGGGCTCGT
1 ATTCTGGGCTCGT
39549 GTGGGCTAAG
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 119 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:44184 original size:27 final size:27
Alignment explanation
Indices: 44146--44205 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
44136 TAAGGAGTAA
*
44146 TCTGATTCTAGCTCGAAAGAGCATTAT
1 TCTGATCCTAGCTCGAAAGAGCATTAT
* *
44173 TCTGATCCTAGCTTGAAAGAGCGTTAT
1 TCTGATCCTAGCTCGAAAGAGCATTAT
*
44200 TATGAT
1 TCTGAT
44206 TTTGGGCTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (27 bp):
TCTGATCCTAGCTCGAAAGAGCATTAT
Found at i:44345 original size:24 final size:24
Alignment explanation
Indices: 44208--44336 Score: 213
Period size: 24 Copynumber: 5.4 Consensus size: 24
44198 ATTATGATTT
* *
44208 TGGGCTCGTACGAGCTAATCATTT
1 TGGGCTCGTAAGAGCTAATCATTC
44232 TGGGCTCGTAAGAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
*
44256 TGGGCTCGTAAGAGCTAACCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
44280 TGGGCTCGTAAGAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
* *
44304 TGGGCTCGTAAGAGCTAACCATTT
1 TGGGCTCGTAAGAGCTAATCATTC
44328 TGGGCTCGT
1 TGGGCTCGT
44337 GTGGGCTAAG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 99 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAATCATTC
Found at i:45391 original size:49 final size:50
Alignment explanation
Indices: 45304--45414 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 50
45294 TCACAACGAC
* * * *
45304 GAACTCGGTACCTTAGAAGATGTGATGGAAATGATTGAGGCCGCAATGGT
1 GAACCCGGTACCGTAGAAGATGTGAGGGAAATGATTGAGGCCGCAAAGGT
* * *
45354 GAATCCGGTACCGT-GAAGATGTGAAGGGAAA-GGTTGAGGCTGCAAAGGT
1 GAACCCGGTACCGTAGAAGATGTG-AGGGAAATGATTGAGGCCGCAAAGGT
45403 GAACCCGGTACC
1 GAACCCGGTACC
45415 TTAGGAACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
49 35 0.67
50 17 0.33
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.20
Consensus pattern (50 bp):
GAACCCGGTACCGTAGAAGATGTGAGGGAAATGATTGAGGCCGCAAAGGT
Found at i:45727 original size:43 final size:41
Alignment explanation
Indices: 45537--45744 Score: 285
Period size: 41 Copynumber: 5.0 Consensus size: 41
45527 AAGAGCAAGG
*
45537 TGAAGATTCCAATCTTTTACCCC-AATCAAGAGGGGCAGAT
1 TGAAGATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
* *
45577 TGAAGATTTCAGTCTTTTACCCCTAATCAAGAGGGACAGAT
1 TGAAGATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
* * *
45618 TGAAGATTCCAAT-TTGTTACCCCTAATTAAAAGGGGCAGAT
1 TGAAGATTCCAGTCTT-TTACCCCTAATCAAGAGGGGCAGAT
* * *
45659 TGAAAATTACAGTATTTTACCCCTAATCAAGAGGGGCAGAT
1 TGAAGATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
*
45700 TGCAGTCATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
1 TGAAG--ATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
45743 TG
1 TG
45745 TAGCCATCAT
Statistics
Matches: 146, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
40 23 0.16
41 85 0.58
42 2 0.01
43 36 0.25
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
TGAAGATTCCAGTCTTTTACCCCTAATCAAGAGGGGCAGAT
Found at i:46238 original size:85 final size:85
Alignment explanation
Indices: 46095--46259 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 85
46085 CAAACCCTAT
** *
46095 CTTCTTGATAAGATACAAAGAAGTGGGTCAAAGCAATAAATCGATCATCTTCCTGATGAGATACA
1 CTTCTTGATAAGATACAAAGAAGTGAATCAAAGCAATAAATAGATCATCTTCCTGATGAGATACA
*
46160 AAGAAGTGGACCAAATTCCC
66 AAGAAGTAGACCAAATTCCC
* * * * * **
46180 CTTCTTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGTAG-TCATCTTTTTGATGAGATAC
1 CTTCTTGATAAGATACAAAGAAGTGAATCAAAGCAAT-AAATAGATCATCTTCCTGATGAGATAC
*
46244 AGAGAAGTAGACCAAA
65 AAAGAAGTAGACCAAA
46260 ATAATGAAGC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 63 0.94
86 4 0.06
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (85 bp):
CTTCTTGATAAGATACAAAGAAGTGAATCAAAGCAATAAATAGATCATCTTCCTGATGAGATACA
AAGAAGTAGACCAAATTCCC
Found at i:46258 original size:208 final size:206
Alignment explanation
Indices: 45794--46377 Score: 746
Period size: 208 Copynumber: 2.8 Consensus size: 206
45784 TGGAACGTCA
* *
45794 AAATCAATGAA-AAGGTCATCTTTCTAATGAGATATAAAGAAGTAGACCAAATCAATGAAGCGAA
1 AAATCAATGAAGAA-GTCATCTTTCTAATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAA
* * *
45858 GCTTAATACGAATGAGACTTCAAACCCTATCTTCTTGATGAGATACAAAGAAGTGGGTCAAACCA
65 GCTCAATAC-AATGAGACTTCAAACCCTATCTTCTTGATAAGATACAAAGAAGTGGGTCAAAGCA
* * * * * * * *
45923 ATAAGTGGCCATCTTCCTAACGAGATGCAGAA-AAGTGAACGAAATTCATCTTCCTAATAAGATA
129 ATAAATGGTCATCTTCCTGATGAGATACA-AAGAAGTGGACCAAATTCACCTTCCTAATAAGATA
*
45987 CAGAGAAGTGGATT
193 CAGAGAAGTGAATT
** * * *
46001 AAATCAATG-AGGCGATCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATAAAACGAA
1 AAATCAATGAAGAAG-TCATCTTTCTAATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAA
* *
46065 TCTCAACACAAGTGAGACTTCAAACCCTATCTTCTTGATAAGATACAAAGAAGTGGGTCAAAGCA
65 GCTCAATACAA-TGAGACTTCAAACCCTATCTTCTTGATAAGATACAAAGAAGTGGGTCAAAGCA
* * * * *
46130 ATAAATCGATCATCTTCCTGATGAGATACAAAGAAGTGGACCAAATTCCCCTTCTTGATGAGATA
129 ATAAAT-GGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAATTCACCTTCCTAATAAGATA
46195 CAGAGAAGTGAATT
193 CAGAGAAGTGAATT
* * *
46209 AAATCAATGAAGTAGTCATCTTTTTGATGAGATACAGAGAAGTAGACCAAAAT-AATGAAGCGAA
1 AAATCAATGAAGAAGTCATCTTTCTAATGAGATACAGAGAAGTAGACC-AAATCAATGAAGCGAA
* * *
46273 GCTCAATATGAATGAGACTTCAAA-CCTCATCTTCTTGATAAGATATAGAGAAGTGGGTCAAAGC
65 GCTCAATA-CAATGAGACTTCAAACCCT-ATCTTCTTGATAAGATACAAAGAAGTGGGTCAAAGC
*
46337 AATAAAAAGGTCATCTTCCTGATGAGATACAAAGAAGTGGA
128 AAT-AAATGGTCATCTTCCTGATGAGATACAAAGAAGTGGA
46378 TTAAATCGAT
Statistics
Matches: 327, Mismatches: 40, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
206 4 0.01
207 120 0.37
208 191 0.58
209 12 0.04
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (206 bp):
AAATCAATGAAGAAGTCATCTTTCTAATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAG
CTCAATACAATGAGACTTCAAACCCTATCTTCTTGATAAGATACAAAGAAGTGGGTCAAAGCAAT
AAATGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAATTCACCTTCCTAATAAGATACAG
AGAAGTGAATT
Found at i:46843 original size:124 final size:122
Alignment explanation
Indices: 46472--46861 Score: 476
Period size: 123 Copynumber: 3.2 Consensus size: 122
46462 CTTCAAATTC
* * * * * *
46472 CATCTTCCTAGTGAGATACAAAGAATTGTACCAAAATAATGAGATAAAGCTCAATTGTGAGTGAA
1 CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGT-GAGCTCAAATGTGAGTGAA
* * * * *
46537 ACTTCAAA-CCTCATCTTCCTGGTGAGGTATAAAGAAGTAAGTCAAATAATGAAGTGGT
65 ACTTCAAACCCT-ATCTTCCTGGTGAGATACAAAGAAGTAGGTCAAACAATAAAGTGGT
** * * * * *
46595 CATCAACCTGATGAGATATAGAGAAGTTTACCAAAATAATAAGGTGAAGCTCAAATATGAGTGAA
1 CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGTG-AGCTCAAATGTGAGTGAA
*
46660 ACTTCATACCCTATCTTCCTGGTGAGATACAAAGAAGTAGGTCAAACAATAAAGTGGT
65 ACTTCAAACCCTATCTTCCTGGTGAGATACAAAGAAGTAGGTCAAACAATAAAGTGGT
*
46718 CATCTTCCTGGTGAGGTACAGAGAAGTGTACCAAAATAATGAGGTGAGTCTCAAAATGTGAGTGA
1 CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGTGAG-CTC-AAATGTGAGTGA
* * * * * * * *
46783 AACTTTAAACCCTATCTTCTTGGTAAGATACAAAGAAATGGGTGAAACAACAAAGCGGT
64 AACTTCAAACCCTATCTTCCTGGTGAGATACAAAGAAGTAGGTCAAACAATAAAGTGGT
46842 CATCTTCCTGGTGAGATACA
1 CATCTTCCTGGTGAGATACA
46862 AATATGTAAA
Statistics
Matches: 226, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
122 2 0.01
123 141 0.62
124 83 0.37
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (122 bp):
CATCTTCCTGGTGAGATACAGAGAAGTGTACCAAAATAATGAGGTGAGCTCAAATGTGAGTGAAA
CTTCAAACCCTATCTTCCTGGTGAGATACAAAGAAGTAGGTCAAACAATAAAGTGGT
Found at i:48880 original size:18 final size:18
Alignment explanation
Indices: 48854--48904 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
48844 CAAACCTTTT
*
48854 AATTTTTTTATTTATTTA
1 AATTGTTTTATTTATTTA
*
48872 AATTGTTTTGTTTATTTA
1 AATTGTTTTATTTATTTA
48890 AATTGTTTTAATTTA
1 AATTGTTTT-ATTTA
48905 GTTTGCTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
AATTGTTTTATTTATTTA
Found at i:50517 original size:24 final size:23
Alignment explanation
Indices: 50475--50522 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
50465 ATTTTTGTCC
50475 TCTCTCAAAAACTTGTTCTTGTTT
1 TCTCTCAAAAACTTGTTC-TGTTT
*
50499 TCTCTCAAATA-TTGCTTCTGTTT
1 TCTCTCAAAAACTTG-TTCTGTTT
50522 T
1 T
50523 TTGGTGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.19, C:0.21, G:0.08, T:0.52
Consensus pattern (23 bp):
TCTCTCAAAAACTTGTTCTGTTT
Found at i:52766 original size:29 final size:30
Alignment explanation
Indices: 52724--52780 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
52714 AAGAGATAAG
52724 AGAACCACTTGAAAATGTGAGG-GTGTCCT
1 AGAACCACTTGAAAATGTGAGGTGTGTCCT
52753 AGAACCACTTGAAAATGTGAGGTGTGTC
1 AGAACCACTTGAAAATGTGAGGTGTGTC
52781 TTGTTAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (30 bp):
AGAACCACTTGAAAATGTGAGGTGTGTCCT
Found at i:56855 original size:14 final size:14
Alignment explanation
Indices: 56836--56864 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56826 TTTGTCCTCT
56836 ATTTTGCTTTCTTA
1 ATTTTGCTTTCTTA
56850 ATTTTGCTTTCTTA
1 ATTTTGCTTTCTTA
56864 A
1 A
56865 AATTCATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (14 bp):
ATTTTGCTTTCTTA
Found at i:57663 original size:16 final size:16
Alignment explanation
Indices: 57642--57674 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
57632 CTAACCACCC
57642 AAACTCAATCCAATAT
1 AAACTCAATCCAATAT
57658 AAACTCAATCCAATAT
1 AAACTCAATCCAATAT
57674 A
1 A
57675 TATAAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACTCAATCCAATAT
Found at i:63640 original size:50 final size:50
Alignment explanation
Indices: 63579--63714 Score: 227
Period size: 50 Copynumber: 2.7 Consensus size: 50
63569 TTTTCGATTT
*
63579 TTGTTTTGTTCAGATCTTGTGTTTTACGTAAATATAAATAGTTATTTATA
1 TTGTTTTGTTCAGATCTTGTGTTTTACATAAATATAAATAGTTATTTATA
* *
63629 TTGTTTTGTTCAGATATTGTGTTTTACATAAATATAAATATTTATTTATA
1 TTGTTTTGTTCAGATCTTGTGTTTTACATAAATATAAATAGTTATTTATA
*
63679 TTATTTTGTTCAGATCTTGTGTTTTTACATAAATAT
1 TTGTTTTGTTCAGATCTTGTG-TTTTACATAAATAT
63715 TTTAAATTTA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 66 0.82
51 14 0.17
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.54
Consensus pattern (50 bp):
TTGTTTTGTTCAGATCTTGTGTTTTACATAAATATAAATAGTTATTTATA
Found at i:65860 original size:11 final size:11
Alignment explanation
Indices: 65844--65869 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65834 CTGATACGTG
65844 TTTTTTTTTAT
1 TTTTTTTTTAT
65855 TTTTTTTTTAT
1 TTTTTTTTTAT
65866 TTTT
1 TTTT
65870 ATATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:66193 original size:4 final size:4
Alignment explanation
Indices: 66184--66258 Score: 80
Period size: 4 Copynumber: 18.5 Consensus size: 4
66174 CAAATAAACG
* * * *
66184 AGAA AGAA AGAA AGAAA AGAA AGAA AGAA AGGA AGGA AGGA AGAA GGAGA
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A
*
66234 GGAA AGAA AG-A AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
66259 GTAATGTGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
3 3 0.05
4 53 0.83
5 8 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:66206 original size:17 final size:16
Alignment explanation
Indices: 66184--66258 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 16
66174 CAAATAAACG
66184 AGAAAGAAAGAAAGAAA
1 AGAAAGAAAGAAAG-AA
*
66201 AGAAAGAAAGAAAGGA
1 AGAAAGAAAGAAAGAA
* * *
66217 AGGAAGGAAGAAGGAGA
1 AGAAAGAAAGAAAGA-A
*
66234 GGAAAGAAAG-AAGAA
1 AGAAAGAAAGAAAGAA
66249 AGAAAGAAAG
1 AGAAAGAAAG
66259 GTAATGTGTT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 10 0.21
16 15 0.32
17 22 0.47
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAGAA
Found at i:70222 original size:14 final size:14
Alignment explanation
Indices: 70203--70255 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
70193 TCCTTAATCA
70203 ATTTAGTGTTTACG
1 ATTTAGTGTTTACG
* *
70217 ATTTAGAGTTTTAAG
1 ATTTAGTG-TTTACG
70232 -TTTAGTGTTTACG
1 ATTTAGTGTTTACG
* *
70245 GTTTAGGGTTT
1 ATTTAGTGTTT
70256 TAAGTCTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.51
Consensus pattern (14 bp):
ATTTAGTGTTTACG
Found at i:70244 original size:28 final size:28
Alignment explanation
Indices: 70204--70260 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
70194 CCTTAATCAA
70204 TTTAGTGTTTACGATTTAGAGTTTTAAG
1 TTTAGTGTTTACGATTTAGAGTTTTAAG
* *
70232 TTTAGTGTTTACGGTTTAGGGTTTTAAG
1 TTTAGTGTTTACGATTTAGAGTTTTAAG
70260 T
1 T
70261 CTAGGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.51
Consensus pattern (28 bp):
TTTAGTGTTTACGATTTAGAGTTTTAAG
Found at i:70270 original size:28 final size:28
Alignment explanation
Indices: 70206--70277 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
70196 TTAATCAATT
* *
70206 TAGTGTTTACGATTTAGAGTTTTAAGTT
1 TAGTGTTTACGGTTTAGAGTTTTAAGTC
*
70234 TAGTGTTTACGGTTTAGGGTTTTAAGTC
1 TAGTGTTTACGGTTTAGAGTTTTAAGTC
*
70262 TAG-GATTTAGGGTTTA
1 TAGTG-TTTACGGTTTA
70278 ATGTTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.47
Consensus pattern (28 bp):
TAGTGTTTACGGTTTAGAGTTTTAAGTC
Found at i:70664 original size:45 final size:45
Alignment explanation
Indices: 70535--70671 Score: 177
Period size: 45 Copynumber: 3.0 Consensus size: 45
70525 GGGAGGAGTA
* * **
70535 GAGTATTGCGGTGGCTCGTCAAACTCAGCCTGATATCCTTCTCTT
1 GAGTATTGCGGTGGCTCGTCAAACTTAGGCTGATATCCTTAGCTT
* * *
70580 GAGTATTGCGGTGACTCGTTAAA-TTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTT-AGGCTGATATCCTTAGCTT
* *
70625 GAGTATTGCGGTGGCTCGTCAAACTTAGGTTGATCTCCTTAGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTTAGGCTGATATCCTTAGCTT
70670 GA
1 GA
70672 TGAGCTATGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.01
45 76 0.96
46 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTTAGGCTGATATCCTTAGCTT
Found at i:72534 original size:30 final size:29
Alignment explanation
Indices: 72495--72589 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
72485 CCAAAAAGAG
72495 TTATTTACTAAAATGGTACAAAATATATAT
1 TTATTTACTAAAATGGTACAAAATA-ATAT
* * * * * **
72525 TTATATACTAAAATAGTATCCACACACCA-
1 TTATTTACTAAAATGGTA-CAAAATAATAT
72554 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAAT-AATAT
72584 TTATTT
1 TTATTT
72590 TGTACCATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
28 3 0.06
29 18 0.38
30 23 0.48
31 4 0.08
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (29 bp):
TTATTTACTAAAATGGTACAAAATAATAT
Found at i:72643 original size:16 final size:16
Alignment explanation
Indices: 72622--72671 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
72612 TGATAGGGAT
72622 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
72638 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
72653 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
72668 ATTA
1 ATTA
72672 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:72882 original size:11 final size:11
Alignment explanation
Indices: 72851--72883 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
72841 AAATATTTAA
*
72851 AATTTTATTTT
1 AATTTTATTAT
72862 AATTTT-TTAT
1 AATTTTATTAT
72872 AATTTTATTAT
1 AATTTTATTAT
72883 A
1 A
72884 TAACTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTATTAT
Found at i:73361 original size:12 final size:12
Alignment explanation
Indices: 73346--73370 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73336 AGATTAAAAT
73346 ATTTTAAAATTA
1 ATTTTAAAATTA
73358 ATTTTAAAATTA
1 ATTTTAAAATTA
73370 A
1 A
73371 CCAAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:73572 original size:9 final size:9
Alignment explanation
Indices: 73543--73591 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
73533 ACTTTTTTTT
*
73543 TTCTTCTCT
1 TTCTTCTCC
73552 TTCTTC-CC
1 TTCTTCTCC
*
73560 --CTTCTTC
1 TTCTTCTCC
73567 TTCTTCTCC
1 TTCTTCTCC
*
73576 TTCTTCACC
1 TTCTTCTCC
73585 TTCTTCT
1 TTCTTCT
73592 TTCTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
6 4 0.12
7 1 0.03
8 1 0.03
9 26 0.81
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:73573 original size:24 final size:24
Alignment explanation
Indices: 73543--73592 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
73533 ACTTTTTTTT
* *
73543 TTCTTCTCTTTCTTCCCCTTCTTC
1 TTCTTCTCCTTCTTCACCTTCTTC
73567 TTCTTCTCCTTCTTCACCTTCTTC
1 TTCTTCTCCTTCTTCACCTTCTTC
73591 TT
1 TT
73593 TCTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (24 bp):
TTCTTCTCCTTCTTCACCTTCTTC
Found at i:73607 original size:16 final size:17
Alignment explanation
Indices: 73588--73626 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
73578 CTTCACCTTC
73588 TTCTTTCT-TATTTTAT
1 TTCTTTCTCTATTTTAT
* *
73604 TTCTTTCTCTTTTTTCT
1 TTCTTTCTCTATTTTAT
73621 TTCTTT
1 TTCTTT
73627 TTTCCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTCTCTATTTTAT
Found at i:75121 original size:20 final size:20
Alignment explanation
Indices: 75077--75119 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
75067 TTTAACTATA
*
75077 TTTTACATATTTTATTTAAT
1 TTTTACATATTATATTTAAT
*
75097 TTTTACATA-TATATTTTAT
1 TTTTACATATTATATTTAAT
75116 TTTT
1 TTTT
75120 TATTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACATATTATATTTAAT
Found at i:81077 original size:17 final size:18
Alignment explanation
Indices: 81040--81079 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
81030 AACAAAAGGG
*
81040 ATGCAGTGACAAAATAAA
1 ATGCAATGACAAAATAAA
*
81058 ATGCAATGACAATA-AAA
1 ATGCAATGACAAAATAAA
81075 ATGCA
1 ATGCA
81080 TGAAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (18 bp):
ATGCAATGACAAAATAAA
Found at i:83434 original size:14 final size:15
Alignment explanation
Indices: 83407--83435 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
83397 ACAACAAAAG
83407 TAAAAGTGAAATAAA
1 TAAAAGTGAAATAAA
83422 TAAAAGT-AAATAAA
1 TAAAAGTGAAATAAA
83436 CAAATGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
TAAAAGTGAAATAAA
Done.