Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013501.1 Kokia drynarioides strain JFW-HI SEQ_128527, 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: 27105
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:346 original size:24 final size:24
Alignment explanation
Indices: 314--452 Score: 172
Period size: 24 Copynumber: 5.8 Consensus size: 24
304 GCGTTTACGC
*
314 TTACGCTCGCCAGCTGATATGCGT
1 TTACGCTCGCCAGCTAATATGCGT
**
338 TTACGCTCGCCAGCTAATATATGT
1 TTACGCTCGCCAGCTAATATGCGT
*
362 TTACGCTCGCCAGCTAATATGTGT
1 TTACGCTCGCCAGCTAATATGCGT
* * * *
386 TTACGCTCGTCAGTTGATATACGT
1 TTACGCTCGCCAGCTAATATGCGT
* *
410 TTACGCTCGTCA-CTAATATGCAT
1 TTACGCTCGCCAGCTAATATGCGT
*
433 TTACGCTCGCTAGCTAATAT
1 TTACGCTCGCCAGCTAATAT
453 AATAAAAACA
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 17 0.17
24 82 0.83
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (24 bp):
TTACGCTCGCCAGCTAATATGCGT
Found at i:366 original size:48 final size:48
Alignment explanation
Indices: 309--453 Score: 193
Period size: 48 Copynumber: 3.0 Consensus size: 48
299 AATATGCGTT
* *
309 TACGCTTACGCTCGCCAGCTGATATGCGTTTACGCTCGCCAGCTAATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
* * * * *
357 TATGTTTACGCTCGCCAGCTAATATGTGTTTACGCTCGTCAGTTGATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
* * *
405 TACGTTTACGCTCGTCA-CTAATATGCATTTACGCTCGCTAGCTAATA
1 TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
452 TA
1 TA
454 ATAAAAACAT
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 26 0.32
48 56 0.68
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (48 bp):
TACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCAGCTAATA
Found at i:8206 original size:60 final size:58
Alignment explanation
Indices: 8120--8646 Score: 383
Period size: 59 Copynumber: 8.8 Consensus size: 58
8110 GAAAAAAAAA
*
8120 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAATCAAATT
1 TTTGGTGTTGGTCA-TGCAATGGCCGACACCCCTTTTT-ATCTGATAAAAAAATCAAATT
* * * *
8179 TTTGGATGTTGGTCATGCAATGACCGACACCTCCTTTTTGTC--A-AAAAAATTCAATTT
1 TTTGG-TGTTGGTCATGCAATGGCCGACACC-CCTTTTTATCTGATAAAAAAATCAAATT
* * *
8236 TTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGAT-AAAAAAATCAAATT
** *
8295 TTTGGGTGTTGGTCATGCCGTGGTCGACACTCCCTTTTT-T-TAGATAAAAAAATTTCAAAATTT
1 TTT-GGTGTTGGTCATGCAATGGCCGACAC-CCCTTTTTATCT-GATAAAAAAA--TC-AAA-TT
* * * * *
8358 TTTTGTGTTTG-CTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATTAAATT
1 TTTGGTGTTGGTC-ATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATT
* * *
8416 TTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTT-TCAGATAAAAAAATTTCAAAATTT
1 TTTG-GTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAA--TC-AAA-TT
* ** * * *
8478 TTTGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGT-AGATAAAAAAAAAT-AGATTTT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCC-CTTTTTATCTGAT--AAAAAAATCA-A-ATT
* * * * * * * *
8539 TTTTGTGTTAGCCATGCAATGGTCGACACCCCTTTTTGT-TAAATAAAAAAATCGATTT
1 TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCT-GATAAAAAAATCAAATT
** * ** * * *
8597 TTTTATGTCGACCATGCAATGACCGACACCTCCTTTTTATTTGGTAAAAA
1 TTTGGTGTTGGTCATGCAATGGCCGACACC-CCTTTTTATCTGATAAAAA
8647 TTAAAATTTT
Statistics
Matches: 380, Mismatches: 55, Indels: 66
0.76 0.11 0.13
Matches are distributed among these distances:
55 8 0.02
56 22 0.06
57 18 0.05
58 45 0.12
59 82 0.22
60 60 0.16
61 82 0.22
62 49 0.13
63 7 0.02
64 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (58 bp):
TTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATT
Found at i:8427 original size:181 final size:181
Alignment explanation
Indices: 8221--8571 Score: 449
Period size: 181 Copynumber: 1.9 Consensus size: 181
8211 CCTTTTTGTC
* *
8221 AAAAAAATTCAATTTTTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAA
1 AAAAAAATTCAAATTTTTGGTGTTGGTCATGCAATAGCGGACACCCCT-TTTATCAGATAAAAAA
* ** * * *
8286 A-ATC-AAATTTTTGGGTGTTGGTCATGCCGTGGTCGACACTCC-CTTTTTTTAGATAAAAAAAT
65 ATATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACAC-CCTCTTTTTGTAGATAAAAAAAA
* * *
8348 TTCAAAATTTTTTTGTGTTTGCTATGCAATGGCCAACACCCCTATTTATCTGAT
129 AT-AAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCTATTTATCTGAT
* * * *
8402 AAAAAAATT-AAATTTTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAA
1 AAAAAAATTCAAATTTTTG-GTGTTGGTCATGCAATAGCGGACACCCCTTTTATCAGATAAAAAA
* *
8466 ATTTCAAAATTTTTTGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAA
65 ATATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAA
* * * *
8531 TAGATTTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCT
130 TAAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCT
8572 TTTTGTTAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
180 23 0.16
181 73 0.50
182 49 0.34
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (181 bp):
AAAAAAATTCAAATTTTTGGTGTTGGTCATGCAATAGCGGACACCCCTTTTATCAGATAAAAAAA
TATCAAAATTTTTGGGTGTTGGCCATGCAATGATCGACACCCTCTTTTTGTAGATAAAAAAAAAT
AAAATTTTTTTGTGTTAGCCATGCAATGGCCAACACCCCTATTTATCTGAT
Found at i:8494 original size:61 final size:59
Alignment explanation
Indices: 8120--8590 Score: 353
Period size: 60 Copynumber: 7.9 Consensus size: 59
8110 GAAAAAAAAA
* * *
8120 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAA-TCAAA-TT
1 TTTGGTGTTGGTCA-TGCAATGGCTGACACCCCTTTTT--TCAGATAAAAAAATTCAAATTT
* *
8179 TTTGGATGTTGGTCATGCAATGACCGACACCTCC-TTTTT--G-TCAAAAAAATTC-AATTT
1 TTTGG-TGTTGGTCATGCAATGGCTGACACC-CCTTTTTTCAGAT-AAAAAAATTCAAATTT
* * * * *
8236 TTTGGTGTTGGTCATGCAATAGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATTT
1 TTTGGTGTTGGTCATGCAATGGCTGACACCCCT-TTTTTCAGATAAAAAAATTCAAATTT
* ** *
8296 TTGGGTGTTGGTCATGCCGTGG-TCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTT
1 TTTGGTGTTGGTCATGCAATGGCT-GACAC-CCCTTTTTTCAGATAAAAAAA-TTC-AAATTT
* * ** * *
8358 TTTTGTGTTTG-CTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATT-AAA-TT
1 TTTGGTGTTGGTC-ATGCAATGGCTGACACCCCT-TTTTTCAGATAAAAAAATTCAAATTT
*
8416 TTTGAGTGTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTT
1 TTTG-GTGTTGGTCATGCAATGGCTGACACCCCTTTTTTCAGATAAAAAAA-TTC-AAATTT
* * * *
8478 TTTGGTGTTGGCCATGCAAT-GATCGACACCCTCTTTTTGT-AGATAAAAAAAAAT-AGATTTT
1 TTTGGTGTTGGTCATGCAATGGCT-GACACCC-CTTTTT-TCAGAT-AAAAAAATTCA-AATTT
* * * * *
8539 TTTTGTGTTAGCCATGCAATGG-TCGACACCCCTTTTTGTTAAATAAAAAAAT
1 TTTGGTGTTGGTCATGCAATGGCT-GACACCCCTTTTT-TCAGATAAAAAAAT
8591 CGATTTTTTT
Statistics
Matches: 338, Mismatches: 42, Indels: 63
0.76 0.09 0.14
Matches are distributed among these distances:
55 3 0.01
56 32 0.09
57 13 0.04
58 21 0.06
59 45 0.13
60 86 0.25
61 73 0.22
62 57 0.17
63 8 0.02
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (59 bp):
TTTGGTGTTGGTCATGCAATGGCTGACACCCCTTTTTTCAGATAAAAAAATTCAAATTT
Found at i:8507 original size:120 final size:118
Alignment explanation
Indices: 8120--8508 Score: 445
Period size: 116 Copynumber: 3.3 Consensus size: 118
8110 GAAAAAAAAA
* * * *
8120 TTTGATGTTGGTCATTGC-ATGGCCGACACCCCTTTTTAATCTGATAAAAAAATCAAATTTTTGG
1 TTTGGTGTTGGCCA-TGCAATGACCGACACCCCTATTT-ATCTGATAAAAAAATCAAATTTTTGG
* * *
8184 ATGTTGGTCATGCAATGACCGACACCTCC-TTTTT-G-TCAAAAAAA-TTC--AATTT
64 -TGTTGGTCATGCCATGGCTGACACC-CCTTTTTTAGAT-AAAAAAATTTCAAAATTT
* *
8236 TTTGGTGTTGGTCATGCAAT-AGCGGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTGG
1 TTTGGTGTTGGCCATGCAATGA-CCGACACCCCTATTTATCTGAT-AAAAAAATCAAATTTTT-G
*
8300 GTGTTGGTCATGCCGTGG-TCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTT
63 GTGTTGGTCATGCCATGGCT-GACAC-CCC-TTTTTTAGATAAAAAAATTTCAAAATTT
* * * * * *
8358 TTTTGTGTTTGCTATGCAATGGCCAACACCCCTATTTATCTGATAAAAAAATTAAATTTTTGAGT
1 TTTGGTGTTGGCCATGCAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTG-GT
8423 GTTGGTCATGCCATGGCTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTT
65 GTTGGTCATGCCATGGCTGACACCCCTTTTTT-AGATAAAAAAATTTCAAAATTT
*
8478 TTTGGTGTTGGCCATGCAATGATCGACACCC
1 TTTGGTGTTGGCCATGCAATGACCGACACCC
8509 TCTTTTTGTA
Statistics
Matches: 233, Mismatches: 23, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
115 10 0.04
116 66 0.28
117 3 0.01
118 5 0.02
119 14 0.06
120 55 0.24
121 38 0.16
122 42 0.18
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (118 bp):
TTTGGTGTTGGCCATGCAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGTG
TTGGTCATGCCATGGCTGACACCCCTTTTTTAGATAAAAAAATTTCAAAATTT
Found at i:8597 original size:59 final size:58
Alignment explanation
Indices: 8138--8634 Score: 289
Period size: 61 Copynumber: 8.3 Consensus size: 58
8128 TGGTCATTGC
* * * *
8138 ATGGCCGACACCCCTTTTTAATCT-GATAAAAAAATCAAA-TTTTTGGATGTTGGTCATGCA
1 ATGGTCGACACCCCTTTTT--T-TAGATAAAAAAATCAAATTTTTTTG-TGTTAGCCATGCA
** * * * * * *
8198 ATGACCGACACCTCCTTTTTGT-CA-AAAAAATTC-AATTTTTTGGTGTTGGTCATGCA
1 ATGGTCGACACC-CCTTTTTTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * ** * * *
8254 ATAG-CGGACACCCCTATTTATCT-GATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGCC
1 ATGGTC-GACACCCCT-TTT-TTTAGAT-AAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * *
8314 GTGGTCGACACTCCCTTTTTTTAGATAAAAAAATTTCAAAATTTTTTTGTGTTTGCTATGCA
1 ATGGTCGACAC-CCCTTTTTTTAGATAAAAAAA--TC-AAATTTTTTTGTGTTAGCCATGCA
* * * * ** * * *
8376 ATGGCCAACACCCCTATTTATCT-GATAAAAAAATTAAATTTTTGAGTGTTGGTCATGCC
1 ATGGTCGACACCCCT-TTT-TTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
* * *
8435 ATGG-CTGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCA
1 ATGGTC-GACACCCCTTTTTTTAGATAAAAAAA--TC-AAATTTTTTTGTGTTAGCCATGCA
* * *
8496 ATGATCGACACCCTCTTTTTGTAGATAAAAAAAAAT-AGATTTTTTTTGTGTTAGCCATGCA
1 ATGGTCGACACCC-CTTTTTTTAGAT--AAAAAAATCA-AATTTTTTTGTGTTAGCCATGCA
* * * *
8557 ATGGTCGACACCCCTTTTTGTTAAATAAAAAAATC-GATTTTTTTATG-TCGACCATGCA
1 ATGGTCGACACCCCTTTTT-TTAGATAAAAAAATCAAATTTTTTTGTGTTAG-CCATGCA
**
8615 ATGACCGACACCTCCTTTTT
1 ATGGTCGACACC-CCTTTTT
8635 ATTTGGTAAA
Statistics
Matches: 353, Mismatches: 54, Indels: 61
0.75 0.12 0.13
Matches are distributed among these distances:
55 4 0.01
56 26 0.07
57 21 0.06
58 42 0.12
59 62 0.18
60 54 0.15
61 84 0.24
62 51 0.14
63 2 0.01
64 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (58 bp):
ATGGTCGACACCCCTTTTTTTAGATAAAAAAATCAAATTTTTTTGTGTTAGCCATGCA
Found at i:12286 original size:11 final size:12
Alignment explanation
Indices: 12246--12294 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
12236 TATTTGTGTA
12246 AAAATTAATTTG
1 AAAATTAATTTG
12258 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
12272 TTGAAATTAATTTG
1 --AAAATTAATTTG
12286 AAAATTAAT
1 AAAATTAAT
12295 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:12531 original size:83 final size:84
Alignment explanation
Indices: 12408--13117 Score: 921
Period size: 86 Copynumber: 8.5 Consensus size: 84
12398 AATTTAACAT
* * * *
12408 TATTTAAATAAAAAAATATTATTATATTACAATTTATATCAAATATTGTGTTCATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
12473 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* * *
12492 TATTTAAAT-AAAAATTATTATTATATTATAATTTTTATCAAATAATTTGTTAATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
12556 ATTATTTATCAAATTTTCA
66 ATTATTTATCAAATTTTAA
* *
12575 TATATAAATAAAAAATATTATTATTGTATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
1 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
12640 ACATTATTTATCAAATTTTCA
64 ACATTATTTATCAAATTTTAA
*
12661 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAAT
1 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
12726 ACATTATTTA-CTAAATTTAAA
64 ACATTATTTATC-AAATTTTAA
* *
12747 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
12812 ATGATTTATCAAATTTTTA
66 ATTATTTATCAAATTTTAA
*
12831 TATTTAAATAAAAAATTATTATTATATTA-AATTTTTTTTCAAATAA-----TG---T-ACAATA
1 TATTTAAATAAAAAATTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGATTTGACAATA
* *
12886 CATTATTT-GCTAAATTTAAA
65 CATTATTTATC-AAATTTTAA
* * * * *
12906 TATTTAAATAAAAAATAATTATTATATTAAAATTTTTATCTAGTAATGTATTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
12971 ATTATTTA-CTAAATTTAAA
66 ATTATTTATC-AAATTTTAA
* * *
12990 TATTTAAAT-AAAAATTATTATTATATTAAAATTTTTATCAAATAATGTGTCGATTTGATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
13054 ATTATTTA-CTAATTTTAAA
66 ATTATTTATCAAATTTT-AA
* *
13073 TATTTAAATAAAAAAATTATTATTTTATTACATTTTTTATCAAAT
1 TATTTAAAT-AAAAAATTATTATTATATTACAATTTTTATCAAAT
13118 TTTAAATTTA
Statistics
Matches: 561, Mismatches: 44, Indels: 41
0.87 0.07 0.06
Matches are distributed among these distances:
74 1 0.00
75 58 0.10
76 3 0.01
79 2 0.00
80 2 0.00
82 5 0.01
83 148 0.26
84 147 0.26
85 42 0.07
86 153 0.27
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (84 bp):
TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
ATTATTTATCAAATTTTAA
Found at i:12886 original size:75 final size:76
Alignment explanation
Indices: 12807--13117 Score: 322
Period size: 83 Copynumber: 3.9 Consensus size: 76
12797 TTGATTTGAT
* ** * *
12807 AATACATGATTTA-TCAAATTTTTATATTTAAATAAAAAATTATTATTATATTAAATTTTTTTTC
1 AATACATTATTTACT-AAATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATC
12871 AAATAATGT-AC
65 AAATAATGTGAC
* *
12882 AATACATTATTTGCTAAATTTAAATATTTAAATAAAAAATAATTATTATATTAAAATTTTTATCT
1 AATACATTATTTACTAAATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATC-
*
12947 AGTAATGTATTGATTTGAC
65 A--AA--TA---ATGTGAC
12966 AATACATTATTTACTAAATTTAAATATTTAAAT-AAAAATTATTATTATATTAAAATTTTTATCA
1 AATACATTATTTACTAAATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATCA
*
13030 AATAATGTGTCGATTTGAT
66 AATAA----T-G---TGAC
* * * *
13049 AATACATTATTTACTAATTTTAAATATTTAAATAAAAAAATTATTATTTTATTACATTTTTTATC
1 AATACATTATTTACTAAATTTAAATATTTAAAT-AAAAAATTATTATTATATTAAAATTTTTATC
13114 AAAT
65 AAAT
13118 TTTAAATTTA
Statistics
Matches: 200, Mismatches: 16, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
75 56 0.28
76 2 0.01
78 4 0.02
79 1 0.00
80 4 0.02
82 1 0.00
83 67 0.34
84 34 0.17
85 31 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (76 bp):
AATACATTATTTACTAAATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATCA
AATAATGTGAC
Found at i:13243 original size:22 final size:22
Alignment explanation
Indices: 13209--13269 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
13199 TGGACCACCC
* *
13209 AAATTTCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCG
* * *
13231 AAATTCCAACTCAGCAAAATCG
1 AAATTCCAGCTCACCAAAACCG
13253 AAATTCCAGCTCACCAA
1 AAATTCCAGCTCACCAA
13270 CATCTCAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Found at i:14351 original size:29 final size:29
Alignment explanation
Indices: 14296--14352 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
14286 ATGTAAGATA
14296 TATTTTCGAATTTTTTATAATATTTTTTC
1 TATTTTCGAATTTTTTATAATATTTTTTC
*
14325 TATTTTCGAAATGTTTTT-TTATATTTTT
1 TATTTTCG-AAT-TTTTTATAATATTTTT
14353 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (29 bp):
TATTTTCGAATTTTTTATAATATTTTTTC
Found at i:15490 original size:17 final size:18
Alignment explanation
Indices: 15463--15496 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15453 TTTAAATTTA
15463 ATTTGTAATTTCGTTTTT
1 ATTTGTAATTTCGTTTTT
*
15481 ATTT-TAATTTTGTTTT
1 ATTTGTAATTTCGTTTT
15497 CTAATTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (18 bp):
ATTTGTAATTTCGTTTTT
Found at i:15924 original size:60 final size:61
Alignment explanation
Indices: 15816--15950 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 61
15806 TAGTTGATGG
* ** *
15816 CCAACACCAAAAAATTTTGAAATTTTTTATCTGAAAAAAAGGGGTGTCGATCATGGCATGA
1 CCAACACCAAAAAATTTTGAAATTTTTTATCAGAAAAAAAGAAGTGTCGACCATGGCATGA
* ** * * *
15877 CCAACACCTAAAAA-TTTGATTTTTTTTATCAGATAAATAGAAGTGTCGACCATTGCATGA
1 CCAACACCAAAAAATTTTGAAATTTTTTATCAGAAAAAAAGAAGTGTCGACCATGGCATGA
*
15937 CCAACACAAAAAAA
1 CCAACACCAAAAAA
15951 AATGAATTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 49 0.79
61 13 0.21
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (61 bp):
CCAACACCAAAAAATTTTGAAATTTTTTATCAGAAAAAAAGAAGTGTCGACCATGGCATGA
Found at i:16289 original size:19 final size:19
Alignment explanation
Indices: 16265--16303 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16255 AGCTTGGATC
16265 ATTTTTGTAAATAATAAAA
1 ATTTTTGTAAATAATAAAA
16284 ATTTTTGTAAATAATAAAA
1 ATTTTTGTAAATAATAAAA
16303 A
1 A
16304 CTTTGGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTTTGTAAATAATAAAA
Found at i:16308 original size:18 final size:19
Alignment explanation
Indices: 16268--16308 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
16258 TTGGATCATT
*
16268 TTTGTAAATAATAAAAATT
1 TTTGTAAATAATAAAAATC
16287 TTTGTAAATAATAAAAA-C
1 TTTGTAAATAATAAAAATC
16305 TTTG
1 TTTG
16309 GTGTCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (19 bp):
TTTGTAAATAATAAAAATC
Found at i:19008 original size:26 final size:29
Alignment explanation
Indices: 18954--19009 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 29
18944 ATTATTGAGA
*
18954 GTATCATCAAAATGAGAGTGTTTCGTAGT
1 GTATCATCAAAATGAGAGTGTTTCATAGT
*
18983 GTATCATC-AAATGA-A-TGTTTTATAGT
1 GTATCATCAAAATGAGAGTGTTTCATAGT
19009 G
1 G
19010 GATTGTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 1 0.04
28 6 0.24
29 8 0.32
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (29 bp):
GTATCATCAAAATGAGAGTGTTTCATAGT
Found at i:19456 original size:89 final size:90
Alignment explanation
Indices: 19314--19527 Score: 315
Period size: 89 Copynumber: 2.4 Consensus size: 90
19304 TCGTATTATA
* * *
19314 TTCTTGTATCTGTAAATTTAATTTAGTCCGTATT-TTTTGTTGTTCGAAATTTATATTTTCGTGA
1 TTCTTATATCTGTAAATTTAATTTAGTCTGTATTATTTGGTTGTTCGAAATTTATATTTTCGTGA
19378 ATTAATTTTCTAAAATGTTTGTATT
66 ATTAATTTTCTAAAATGTTTGTATT
* * * * *
19403 TTCTTATATCTGTAAATTTAATTTAGTGTGTATTATTTGGTT-TTTGAATTTTATATTTTTGTGT
1 TTCTTATATCTGTAAATTTAATTTAGTCTGTATTATTTGGTTGTTCGAAATTTATATTTTCGTGA
*
19467 ATTAATTTTCTAGAATGTTTGTATT
66 ATTAATTTTCTAAAATGTTTGTATT
* *
19492 TTCTTATATCTATAAATTTAATTTAGTTTGTATTAT
1 TTCTTATATCTGTAAATTTAATTTAGTCTGTATTAT
19528 AATAATAATA
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
89 107 0.95
90 6 0.05
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.57
Consensus pattern (90 bp):
TTCTTATATCTGTAAATTTAATTTAGTCTGTATTATTTGGTTGTTCGAAATTTATATTTTCGTGA
ATTAATTTTCTAAAATGTTTGTATT
Found at i:19556 original size:3 final size:3
Alignment explanation
Indices: 19550--19595 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
19540 AATAATAATA
19550 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19596 TCGAATTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23487 original size:60 final size:61
Alignment explanation
Indices: 23418--23584 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 61
23408 TATATATATA
* * * * **
23418 TGATAAAGTTGGTGTTTG-CCATTAATGTCCCAAAACGAAAAAAAAT-AATTTTTTAAAATC
1 TGATAAAGTTAGTGTTCGACCATCAATGTCCCAAAACCAAAAAAAATCAAAATTTT-AAATC
* * * *
23478 TGATAAAGTTAGTG-TCGACCATCAGTGTCCCAACACCAAAAAAATTCAAAATTTTAAATT
1 TGATAAAGTTAGTGTTCGACCATCAATGTCCCAAAACCAAAAAAAATCAAAATTTTAAATC
* * * *
23538 TGATAAAGTTAGTGTT-GATCATCAATGTTCCAATACCCTAAAAAAAT
1 TGATAAAGTTAGTGTTCGACCATCAATGTCCCAA-AACCAAAAAAAAT
23585 TTTCGTGTCT
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 68 0.79
61 16 0.19
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (61 bp):
TGATAAAGTTAGTGTTCGACCATCAATGTCCCAAAACCAAAAAAAATCAAAATTTTAAATC
Done.