Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015274.1 Kokia drynarioides strain JFW-HI SEQ_130319, 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: 742443
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:454325 original size:71 final size:71
Alignment explanation
Indices: 454237--454378 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
454227 TCTTGGTTTT
*
454237 GTATCCTTATTCGCAAAAAGATATCTTAACACTGAGCGATCAATAAATACAGTAACTTTTGCACC
1 GTATCCTTATTCGCAAAAAGATATCTTAACACCGAGCGATCAATAAATACAGTAACTTTTGCACC
454302 GACAAG
66 GACAAG
454308 GTATCCTTATTCGCAAAAAGATATCTTAACACCGAGCGATCAATAAATACAGTAACTTTTGCACC
1 GTATCCTTATTCGCAAAAAGATATCTTAACACCGAGCGATCAATAAATACAGTAACTTTTGCACC
454373 GACAAG
66 GACAAG
454379 ATATGAACGA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (71 bp):
GTATCCTTATTCGCAAAAAGATATCTTAACACCGAGCGATCAATAAATACAGTAACTTTTGCACC
GACAAG
Found at i:460567 original size:19 final size:22
Alignment explanation
Indices: 460535--460583 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
460525 GTTTGTAAAA
460535 AAAGTCAA-TAATCAA-A-GTC
1 AAAGTCAACTAATCAACAGGTC
460554 AAAGTCAACT-ATCAACAGGTC
1 AAAGTCAACTAATCAACAGGTC
*
460575 AAAATCAAC
1 AAAGTCAAC
460584 GAGTCAGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 13 0.50
20 2 0.08
21 11 0.42
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.18
Consensus pattern (22 bp):
AAAGTCAACTAATCAACAGGTC
Found at i:465116 original size:66 final size:65
Alignment explanation
Indices: 464998--465121 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 65
464988 CATGGGATCC
* * ** *
464998 ACATAGATAGTGAGCTAAGACAATAACACACAATAGAGATAGTTTGTTGGGATAGTAAGCACAAA
1 ACATAGATAGTCAGCTAAGACAATAACACACAATAAAGATAGTCCGCTGGGATAGTAAGCACAAA
* * *
465063 ACATAGATAGTCCGCTAGGACAATAAACACATAATAAAGATAGTCCGCTGGGATAGTAA
1 ACATAGATAGTCAGCTAAGACAAT-AACACACAATAAAGATAGTCCGCTGGGATAGTAA
465122 ATACTATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
65 21 0.42
66 29 0.58
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (65 bp):
ACATAGATAGTCAGCTAAGACAATAACACACAATAAAGATAGTCCGCTGGGATAGTAAGCACAAA
Found at i:466325 original size:13 final size:13
Alignment explanation
Indices: 466307--466334 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
466297 ATCAACCTAA
466307 TAGCCCATGCATG
1 TAGCCCATGCATG
466320 TAGCCCATGCATG
1 TAGCCCATGCATG
466333 TA
1 TA
466335 TGAAACCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (13 bp):
TAGCCCATGCATG
Found at i:468161 original size:17 final size:16
Alignment explanation
Indices: 468141--468179 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
468131 TGTTGCATTC
*
468141 ATATTGTTTTTAGTATT
1 ATATTGTATTT-GTATT
468158 ATATTTGTATTTGTATT
1 ATA-TTGTATTTGTATT
468175 ATATT
1 ATATT
468180 TATGTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 11 0.55
18 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (16 bp):
ATATTGTATTTGTATT
Found at i:471574 original size:25 final size:25
Alignment explanation
Indices: 471525--471573 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
471515 TTTTAAATTA
471525 AATCCTTTTATTTTTATTATTTTTT
1 AATCCTTTTATTTTTATTATTTTTT
471550 AATCC-TTTATTTTTATTATTTTTT
1 AATCCTTTTATTTTTATTATTTTTT
471574 TTGTAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (25 bp):
AATCCTTTTATTTTTATTATTTTTT
Found at i:473298 original size:26 final size:26
Alignment explanation
Indices: 473254--473550 Score: 326
Period size: 26 Copynumber: 11.5 Consensus size: 26
473244 TCATACAAGC
* *
473254 CTAGTT-AGGATATCACTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
473279 CTAGTTCAGTATATCGCTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* * * *
473305 CCAGTTCAGTGTATAGCTCTTATGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* * *
473331 ATAGTTCAATATATCGCTCTTACTAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* * *
473357 CCAGTTTAATATATCGCTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* * * * * * *
473383 CCAGTTTAGTGTATCACTTTTACAAT
1 CTAGTTCAGTATATCGCTCTTACGAG
*
473409 CTAGTTCAGTATATCGTTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* *
473435 CAAGTTCATTATATCGCTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* *
473461 CCAGATCAGTATATCGCTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
*
473487 CTAGTTCAGTATATCTCTCTTACGAG
1 CTAGTTCAGTATATCGCTCTTACGAG
* * *
473513 CCAGTTCAGTATATTGCTCTTACAAG
1 CTAGTTCAGTATATCGCTCTTACGAG
*
473539 CTAGTTTAGTAT
1 CTAGTTCAGTAT
473551 TTTTCTTTTA
Statistics
Matches: 225, Mismatches: 46, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
25 6 0.03
26 219 0.97
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
CTAGTTCAGTATATCGCTCTTACGAG
Found at i:478298 original size:22 final size:22
Alignment explanation
Indices: 478268--478321 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
478258 TGTAAAATGT
*
478268 CAATATAATTAATTGATTGCAC
1 CAATTTAATTAATTGATTGCAC
* *
478290 CAATTTAATTGATTGATTGCGC
1 CAATTTAATTAATTGATTGCAC
478312 CAATTTAATT
1 CAATTTAATT
478322 CAATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
CAATTTAATTAATTGATTGCAC
Found at i:497041 original size:93 final size:93
Alignment explanation
Indices: 496923--497796 Score: 594
Period size: 93 Copynumber: 9.4 Consensus size: 93
496913 ATTAAAAAAT
*
496923 AGATCTCAATCTCCCTGAGGTTACAGTAGAATGGAGTGAAGCACTAAATCCTATATCCCTGAAGT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACTAAATCCTATATCCCTGAAGT
* * * *
496988 TGTATTGGATTAGAGTAAAATGAGTAAC
66 TGCAATGGATTGGATTAAAATGAGTAAC
* * *
497016 GGATCTCAATCTCCCTAAGGTTACAGTGGAATGAAGTGAAGTACAACATTAAATCCTATA-CCCT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG--C-AC--TAAATCCTATATCCC-
* *
497080 TGAAGTTGCAGTGGGTTGGATTAAAA--AGT-A-
60 TGAAGTTGCAATGGATTGGATTAAAATGAGTAAC
* * * *
497110 A-ATCTCAATCTCTCTGAGGTTACAGTGGAA-GGAAGTAAAGCACCAAATCCTATATCCTTGAAG
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGG-AGTGAAGCACTAAATCCTATATCCCTGAAG
* * ** *
497173 TTACAATGTATCAGATTAAAATGAGTAAT
65 TTGCAATGGATTGGATTAAAATGAGTAAC
* * * *
497202 GGATCTCAATCTCCTTGAGGTTACAATGGAATGGAGTGAAGTACAACACCAAATCCTATA-CCCT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-----CACTAAATCCTATATCCC-
* **
497266 TGAAGTTGCAATGGGTCAGATT-AAA--A--AAC
60 TGAAGTTGCAATGGATTGGATTAAAATGAGTAAC
* ** *
497295 AGATCTCAATCTCCCTAAGGTTACAGTGGAATAAAGTAAAGCA-TCAAATCCTATATCCCTGAAG
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACT-AAATCCTATATCCCTGAAG
* *
497359 TTGTAGTGGATTGGATTAAAATGAGTAAC
65 TTGCAATGGATTGGATTAAAATGAGTAAC
* * * * * *
497388 AGATCTCAATCTTCCTAAGGTTACAGTGGAATAGAGTGAAGTACAACACAAAATCCTGTA-CTTC
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-----CACTAAATCCTATATC-CC
* * * *
497452 TGAAGTTGTAGTGGGTCGGATT-AAAT-AG---C
60 TGAAGTTGCAATGGATTGGATTAAAATGAGTAAC
** * * * * *
497481 AGATCTCAATCTCTTTGAGGTTACAGTGGAATGGAATAAAACA-TCAAATCTTATATCCCTAAAG
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACT-AAATCCTATATCCCTGAAG
*
497545 TTGCAATGGATTGGATTAAAATGAGTAAT
65 TTGCAATGGATTGGATTAAAATGAGTAAC
* * * * *
497574 GGATCTTAATCTCCCTGAGGTTACAGTGAAATGGAGTGAAGTACAACACCAAATCCTATACCCCT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-----CACTAAATCCTATATCCCT
* * ** * **
497639 AAAGTTACAGGGGGTCAGATTAAAA--AG---C
61 GAAGTTGCAATGGATTGGATTAAAATGAGTAAC
* * * * * * * * *
497667 AGATCTTAATCTCCTTGAGGTTACAATGGAATGAAGTGAAGCACCAAATCTTATCTTCTTGAAGT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACTAAATCCTATATCCCTGAAGT
* * * *** * * * *
497732 TGTAGTGAAACAGATTAAGATAAATAAT
66 TGCAATGGATTGGATTAAAATGAGTAAC
*
497760 GGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGT
1 AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGT
497797 AAAGTTACAA
Statistics
Matches: 615, Mismatches: 114, Indels: 104
0.74 0.14 0.12
Matches are distributed among these distances:
88 118 0.19
89 13 0.02
90 8 0.01
91 3 0.00
92 1 0.00
93 314 0.51
94 2 0.00
95 3 0.00
96 9 0.01
97 13 0.02
98 131 0.21
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (93 bp):
AGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACTAAATCCTATATCCCTGAAGT
TGCAATGGATTGGATTAAAATGAGTAAC
Found at i:497195 original size:186 final size:186
Alignment explanation
Indices: 496880--497872 Score: 1175
Period size: 186 Copynumber: 5.3 Consensus size: 186
496870 AGTAAATGGT
* **
496880 AAATCCTATAACCTTGAAGTTGCAGTGGGTCAGATTAAAAAATAGATCTCAATCTCCCTGAGGTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGTT
* * * * *
496945 ACAGTAGAATGG-AGTGAAGCACTAAATCCTATATCCCTGAAGTTGTATTGGATTAGAGTAAAAT
66 ACAGTGGAA-GGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAAT
* * * **
497009 GAGTAACGGATCTCAATCTCCCTAAGGTTACAGTGGAATGAAGTGAAGTACAACATT
130 GAGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACACC
** * * *
497066 AAATCCTATACCCTTGAAGTTGCAGTGGGTTGGATTAAAAAGTAAATCTCAATCTCTCTGAGGTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGTT
* ** * *
497131 ACAGTGGAAGGAAGTAAAGCACCAAATCCTATATCCTTGAAGTTACAATGTATCAGATTAAAATG
66 ACAGTGGAAGGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAATG
* *
497196 AGTAATGGATCTCAATCTCCTTGAGGTTACAATGGAATGGAGTGAAGTACAACACC
131 AGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACACC
* * *
497252 AAATCCTATACCCTTGAAGTTGCAATGGGTCAGATTAAAAAACAGATCTCAATCTCCCTAAGGTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGTT
** * * *
497317 ACAGTGGAATAAAGTAAAGCATCAAATCCTATATCCCTGAAGTTGTAGTGGATTGGATTAAAATG
66 ACAGTGGAAGGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAATG
** * * * *
497382 AGTAACAGATCTCAATCTTCCTAAGGTTACAGTGGAATAGAGTGAAGTACAACACA
131 AGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACACC
* * * * * **
497438 AAATCCTGTA-CTTCTGAAGTTGTAGTGGGTCGGATTAAATAGCAGATCTCAATCTCTTTGAGGT
1 AAATCCTATACCCT-TGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGT
* * * * * *
497502 TACAGTGGAATGGAA-TAAAACATCAAATCTTATATCCCTAAAGTTGCAATGGATTGGATTAAAA
65 TACAGTGGAA-GGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAA
* *
497566 TGAGTAATGGATCTTAATCTCCCTGAGGTTACAGTGAAATGGAGTGAAGTACAACACC
129 TGAGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACACC
* * * * * *
497624 AAATCCTATACCCCTAAAGTTACAGGGGGTCAGATTAAAAAGCAGATCTTAATCTCCTTGAGGTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGTT
* * * * * * * * * ** * *
497689 ACAATGGAATGAAGTGAAGCACCAAATCTTATCTTCTTGAAGTTGTAGTGAAACAGATTAAGATA
66 ACAGTGGAAGGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAATG
* *
497754 AATAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACC
131 AGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-TACAACACC
* * * * * * *
497811 AAATCTTATACCCCTAAAGTTACAATAGGTC-GAACTAAAAAGCAGATCTCAATCTCCCTGAG
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCAG-ATTAAAAAGCAGATCTCAATCTCCCTGAG
497873 TTTTCAATGG
Statistics
Matches: 687, Mismatches: 113, Indels: 13
0.85 0.14 0.02
Matches are distributed among these distances:
185 7 0.01
186 615 0.90
187 65 0.09
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (186 bp):
AAATCCTATACCCTTGAAGTTGCAGTGGGTCAGATTAAAAAGCAGATCTCAATCTCCCTGAGGTT
ACAGTGGAAGGAAGTAAAGCACCAAATCCTATATCCCTGAAGTTGTAATGGATTAGATTAAAATG
AGTAATGGATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACACC
Found at i:498197 original size:21 final size:22
Alignment explanation
Indices: 498171--498221 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
498161 CGGGCCCAAC
498171 TAAAAACCAAACAAAAAAATATAA
1 TAAAAACCAAAC-AAAAAATA-AA
*
498195 -AAAAA-TAAACAAAAAATAAA
1 TAAAAACCAAACAAAAAATAAA
498215 TAAAAAC
1 TAAAAAC
498222 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 4 0.17
23 5 0.21
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (22 bp):
TAAAAACCAAACAAAAAATAAA
Found at i:499895 original size:21 final size:22
Alignment explanation
Indices: 499871--499912 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
499861 AGTTTTCCCC
499871 TTTTATT-TTTTTAAAATTTTA
1 TTTTATTCTTTTTAAAATTTTA
499892 TTTTATTCTTTTTAAAATTTT
1 TTTTATTCTTTTTAAAATTTT
499913 CCTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTCTTTTTAAAATTTTA
Found at i:499921 original size:30 final size:29
Alignment explanation
Indices: 499887--499973 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 29
499877 TTTTTTAAAA
499887 TTTTATTTTATTCTTTTTAAAATTT-TCCTT
1 TTTTATTTTATTCTTTTT-AAATTTATCC-T
* *
499917 TTTTATTCTGTT-TTTATTAAATTTAATCCT
1 TTTTATTTTATTCTTT-TTAAATTT-ATCCT
499947 TTTTATTATTTATTCTTTTGT-AATTTA
1 TTTTA-T-TTTATTCTTTT-TAAATTTA
499974 AATTTAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
29 9 0.20
30 18 0.39
31 5 0.11
32 10 0.22
33 4 0.09
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTATTTTATTCTTTTTAAATTTATCCT
Found at i:503687 original size:30 final size:27
Alignment explanation
Indices: 503636--503691 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
503626 TAAAATCGAT
503636 TTAATTGATCGAATCGAATTAATTTGG
1 TTAATTGATCGAATCGAATTAATTTGG
*
503663 TTAATTGATCGGTTAATTGAATTAATTTG
1 TTAATTGATC-G--AATCGAATTAATTTG
503692 ATCGGGTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 10 0.40
28 1 0.04
30 14 0.56
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (27 bp):
TTAATTGATCGAATCGAATTAATTTGG
Found at i:503992 original size:9 final size:9
Alignment explanation
Indices: 503966--504007 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
503956 CAATTAACGA
503966 TTAA-TAAT
1 TTAATTAAT
**
503974 TTAAAAAAT
1 TTAATTAAT
503983 TTAATTAAT
1 TTAATTAAT
503992 TTAATTAAT
1 TTAATTAAT
504001 ATTAATT
1 -TTAATT
504008 TGAATCGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 4 0.14
9 19 0.66
10 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAATTAAT
Found at i:504853 original size:9 final size:9
Alignment explanation
Indices: 504820--504862 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
504810 AAAATCTGAT
*
504820 ATTTTCATA
1 ATTTTTATA
*
504829 ATTTTTAGA
1 ATTTTTATA
* *
504838 ATATTTATT
1 ATTTTTATA
504847 ATTTTTATA
1 ATTTTTATA
504856 ATTTTTA
1 ATTTTTA
504863 GGAAAATTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:526094 original size:26 final size:26
Alignment explanation
Indices: 526057--526118 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
526047 GTATTTTGTT
*
526057 AAATGTGATGATT-TTGTTGAGATGAG
1 AAATGT-ATGATTACTGTTGAGATGAG
* *
526083 AGAATGTATGATTACTGTTGAGTTGTG
1 A-AATGTATGATTACTGTTGAGATGAG
526110 AAATGTATG
1 AAATGTATG
526119 TTGATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39
Consensus pattern (26 bp):
AAATGTATGATTACTGTTGAGATGAG
Found at i:531057 original size:28 final size:28
Alignment explanation
Indices: 530986--531051 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
530976 GTAAAACTGC
* * *
530986 CACATAATTGTCATAAATGGCCACATAT
1 CACATAATTGCCAAAAACGGCCACATAT
*
531014 CACATCATTGCCAAAAACGGCCACATAT
1 CACATAATTGCCAAAAACGGCCACATAT
531042 CACATAATTG
1 CACATAATTG
531052 GGAAAATTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (28 bp):
CACATAATTGCCAAAAACGGCCACATAT
Found at i:533993 original size:11 final size:11
Alignment explanation
Indices: 533977--534010 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
533967 TCGAAGCTTC
533977 ACTTTTAGCTA
1 ACTTTTAGCTA
533988 ACTTTTAGCTA
1 ACTTTTAGCTA
*
533999 ATTTTTAGCTA
1 ACTTTTAGCTA
534010 A
1 A
534011 AAGTTGCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (11 bp):
ACTTTTAGCTA
Found at i:534218 original size:18 final size:18
Alignment explanation
Indices: 534195--534229 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
534185 TCTCCAAAAC
* *
534195 CTTTTCGTCGGAGCAACT
1 CTTTTCATCGCAGCAACT
534213 CTTTTCATCGCAGCAAC
1 CTTTTCATCGCAGCAAC
534230 CATCGCTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (18 bp):
CTTTTCATCGCAGCAACT
Found at i:535051 original size:27 final size:27
Alignment explanation
Indices: 535007--535069 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
534997 ATCTGAAGGA
*
535007 GAACCAAACAACCCTGAACCAAGAGTG
1 GAACCAAATAACCCTGAACCAAGAGTG
* * * *
535034 GAACCAAATAGCCTTGAATCAGGAGTG
1 GAACCAAATAACCCTGAACCAAGAGTG
*
535061 GAGCCAAAT
1 GAACCAAAT
535070 GTTGTTGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (27 bp):
GAACCAAATAACCCTGAACCAAGAGTG
Found at i:539201 original size:138 final size:130
Alignment explanation
Indices: 538920--539266 Score: 471
Period size: 138 Copynumber: 2.6 Consensus size: 130
538910 ACATAGATAA
* * * *
538920 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAAATATGTTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* * *
538985 TAAATAGTTATATTTCGCTCAAAATATAAAAAGACATGGAAATTAATATTCTTTGGAAAGAATAT
66 TAAACAGTTATATTTCGCTCAAAATATAAAAAGAAATGGAAATTAATATTCTTTGAAAAGAATAT
* *
539050 AATTAATATATGAATTTTATTCATACACAATATTAATTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
539115 TAAACAGTTACATGAATGAATTTCGGTCAAAATAT-AAAAGAAATGGAAATTAATATTATTTTGA
66 TAAACAG-T---T--AT--ATTTCGCTCAAAATATAAAAAGAAATGGAAATTAATATT-CTTTGA
539179 AAAGAATAT
122 AAAGAATAT
* * *
539188 AATTAATATATGAATTTAATTCATAAAAAATATTAATTGTATATATTTTATCGAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
*
539253 TAAACAATTATATT
66 TAAACAGTTATATT
539267 AATTAATTTT
Statistics
Matches: 192, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
130 69 0.36
131 1 0.01
132 2 0.01
134 2 0.01
136 2 0.01
137 22 0.11
138 94 0.49
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (130 bp):
AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
TAAACAGTTATATTTCGCTCAAAATATAAAAAGAAATGGAAATTAATATTCTTTGAAAAGAATAT
Found at i:542547 original size:58 final size:58
Alignment explanation
Indices: 542477--542593 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
542467 ACTTCATTGC
542477 TTTCTTTGATGACTTCAGTAAATATAGGTATATTTATCTTATGTGCCATAAGTCTGGA
1 TTTCTTTGATGACTTCAGTAAATATAGGTATATTTATCTTATGTGCCATAAGTCTGGA
*
542535 TTTCTTTGATGACTTCTGTAAATATAGGTATATTTATCTTATGTGCCATAAGTCTGGA
1 TTTCTTTGATGACTTCAGTAAATATAGGTATATTTATCTTATGTGCCATAAGTCTGGA
542593 T
1 T
542594 CCCTTGAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (58 bp):
TTTCTTTGATGACTTCAGTAAATATAGGTATATTTATCTTATGTGCCATAAGTCTGGA
Found at i:548881 original size:20 final size:20
Alignment explanation
Indices: 548856--548897 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
548846 TTAATCGATC
548856 CAAAGAAATGGTGCCTATAT
1 CAAAGAAATGGTGCCTATAT
548876 CAAAGAAATGGTGCCTATAT
1 CAAAGAAATGGTGCCTATAT
548896 CA
1 CA
548898 TACTTATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (20 bp):
CAAAGAAATGGTGCCTATAT
Found at i:551737 original size:41 final size:41
Alignment explanation
Indices: 551680--551761 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
551670 TAAACGTACC
551680 TCCATAATTGTTGTACAATTCAACGGCTCCATATGGATAAA
1 TCCATAATTGTTGTACAATTCAACGGCTCCATATGGATAAA
551721 TCCATAATTGTTGTACAATTCAACGGCTCCATATGGATAAA
1 TCCATAATTGTTGTACAATTCAACGGCTCCATATGGATAAA
551762 CTATGTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (41 bp):
TCCATAATTGTTGTACAATTCAACGGCTCCATATGGATAAA
Found at i:558994 original size:16 final size:15
Alignment explanation
Indices: 558969--558998 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
558959 ATCATAATTT
558969 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
558984 TTTTTCTTTCTTTTT
1 TTTTTC-TTCTTTTT
558999 ATGTGACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:564592 original size:15 final size:15
Alignment explanation
Indices: 564572--564634 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 15
564562 TTAAAATTAA
564572 ATGCAATTTATCTAG
1 ATGCAATTTATCTAG
564587 ATGCAATTTATCCCTA-
1 ATGCAATTTAT--CTAG
*
564603 ATGCAAATTAATCTAAG
1 ATGC-AATTTATCT-AG
*
564620 TATGAAATTTATCTA
1 -ATGCAATTTATCTA
564635 TATGAATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 13 0.33
16 6 0.15
17 17 0.44
18 3 0.08
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (15 bp):
ATGCAATTTATCTAG
Found at i:564608 original size:16 final size:14
Alignment explanation
Indices: 564571--564618 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
564561 ATTAAAATTA
564571 AATGCAATTTATCT
1 AATGCAATTTATCT
564585 AGATGCAATTTATCCCT
1 A-ATGCAATTTAT--CT
*
564602 AATGCAAATTAATCT
1 AATGC-AATTTATCT
564617 AA
1 AA
564619 GTATGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.03
15 15 0.52
16 4 0.14
17 9 0.31
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (14 bp):
AATGCAATTTATCT
Found at i:565476 original size:8 final size:8
Alignment explanation
Indices: 565463--565511 Score: 50
Period size: 7 Copynumber: 6.4 Consensus size: 8
565453 AAAATGGAAT
*
565463 TGAGAGGA
1 TGAGAGAA
565471 TGAGAGAA
1 TGAGAGAA
565479 TGAGAGAAA
1 TGAGAG-AA
*
565488 TGA-TGAA
1 TGAGAGAA
565495 TGA-AGAA
1 TGAGAGAA
565502 TGA-AGAA
1 TGAGAGAA
565509 TGA
1 TGA
565512 TTCAGGGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.49
8 14 0.38
9 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.35, T:0.16
Consensus pattern (8 bp):
TGAGAGAA
Found at i:569926 original size:54 final size:54
Alignment explanation
Indices: 569868--569976 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
569858 TAAAGTCTAA
* * *
569868 TCATATTAC-AAGGCATCATATAGGGAAATGAA-ATCCATATAGTGTAAGGCCTAG
1 TCATATTACTAAGGCATCATAT-GGCAAATGAAGA-CCACATAGTGTAAGACCTAG
* * *
569922 TCATATTGCTAGGGCATCATATGGCAAATGAAGACCACATTGTGTAAGACCTAG
1 TCATATTACTAAGGCATCATATGGCAAATGAAGACCACATAGTGTAAGACCTAG
569976 T
1 T
569977 ACGGGACTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 35 0.74
55 12 0.26
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (54 bp):
TCATATTACTAAGGCATCATATGGCAAATGAAGACCACATAGTGTAAGACCTAG
Found at i:570290 original size:61 final size:59
Alignment explanation
Indices: 570141--570290 Score: 162
Period size: 59 Copynumber: 2.5 Consensus size: 59
570131 ATATATGTGG
* * * * *
570141 AAGCCTTTGTGGCCATTTT-TGTTATATGTGAGCCATAGTGGCAGAATCTGGTATATGT
1 AAGCCTTTGTGGCTATTTTCTATTATATGTGAGCCATAGTGGCAGAACCTGATATATGA
* * *
570199 GAGCTTTTGTGGCT-TTTCTCTATTATATGTGAGCCTTAGTGGC-GAAACCTGATATAAATGA
1 AAGCCTTTGTGGCTATTT-TCTATTATATGTGAGCCATAGTGGCAG-AACCTGATAT--ATGA
*
570260 AAGCCTTTGTGGCTATTTTCTATTACATGTG
1 AAGCCTTTGTGGCTATTTTCTATTATATGTG
570291 GGTCTTGTGG
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
57 3 0.04
58 13 0.17
59 29 0.39
61 27 0.36
62 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (59 bp):
AAGCCTTTGTGGCTATTTTCTATTATATGTGAGCCATAGTGGCAGAACCTGATATATGA
Found at i:584450 original size:16 final size:18
Alignment explanation
Indices: 584421--584453 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
584411 GTAATTTTTA
584421 TTTTATATTGTTTAATTT
1 TTTTATATTGTTTAATTT
584439 TTTTA-ATT-TTTAATT
1 TTTTATATTGTTTAATT
584454 AATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTATATTGTTTAATTT
Found at i:587308 original size:25 final size:23
Alignment explanation
Indices: 587263--587322 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
587253 TGCCTAAGCC
587263 CAAACCTCAAACCAATACCCAACTT
1 CAAACC-CAAACCAATACCCAAC-T
**
587288 CAAACCCAAACCCTTATCCCAACT
1 CAAACCCAAACCAATA-CCCAACT
587312 -AAACCCAAACC
1 CAAACCCAAACC
587323 TAAACCTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 11 0.34
24 9 0.28
25 12 0.38
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.13
Consensus pattern (23 bp):
CAAACCCAAACCAATACCCAACT
Found at i:588869 original size:3 final size:3
Alignment explanation
Indices: 588861--588899 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
588851 TAAATAAATA
*
588861 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
588900 TGGGGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:593592 original size:23 final size:23
Alignment explanation
Indices: 593566--593620 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
593556 ATAACTTGAC
* *
593566 CCGTTGATTGAACCTAACCCGAT
1 CCGTTGACTGAACCTAACCCGAA
* *
593589 CCGTTGACTGAACTTGACCCGAA
1 CCGTTGACTGAACCTAACCCGAA
593612 CCGTTGACT
1 CCGTTGACT
593621 TTGATCGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (23 bp):
CCGTTGACTGAACCTAACCCGAA
Found at i:593659 original size:21 final size:21
Alignment explanation
Indices: 593635--593674 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
593625 TCGTTAACCG
593635 TTGACTGTTGACAGTTGACCA
1 TTGACTGTTGACAGTTGACCA
*
593656 TTGACTGTTGACCGTTGAC
1 TTGACTGTTGACAGTTGAC
593675 TTTTGGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
TTGACTGTTGACAGTTGACCA
Found at i:593675 original size:14 final size:14
Alignment explanation
Indices: 593611--593675 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
593601 CTTGACCCGA
593611 ACCGTTGACT-TTG
1 ACCGTTGACTGTTG
* * *
593624 ATCGTTAACCGTTG
1 ACCGTTGACTGTTG
* *
593638 ACTGTTGACAGTTG
1 ACCGTTGACTGTTG
*
593652 ACCATTGACTGTTG
1 ACCGTTGACTGTTG
593666 ACCGTTGACT
1 ACCGTTGACT
593676 TTTGGGTTGA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
13 7 0.17
14 33 0.82
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (14 bp):
ACCGTTGACTGTTG
Found at i:599050 original size:28 final size:28
Alignment explanation
Indices: 599009--599063 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
598999 GATATTCGAT
* *
599009 TTACTCCATGTTGACCCAATGGTCATGC
1 TTACTCCATATTGACCCAAAGGTCATGC
* *
599037 TTACTCCCTATTGACGCAAAGGTCATG
1 TTACTCCATATTGACCCAAAGGTCATG
599064 ATATTCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (28 bp):
TTACTCCATATTGACCCAAAGGTCATGC
Found at i:607946 original size:24 final size:24
Alignment explanation
Indices: 607914--607973 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
607904 AGTCACTTGT
*
607914 AAAAGGAAAATGAGAAAA-AGAAAG
1 AAAAAGAAAATGAGAAAAGA-AAAG
*
607938 AAAAAGAAAAAGAGAAAAGAAAAG
1 AAAAAGAAAATGAGAAAAGAAAAG
607962 AAGAAA-AAAATG
1 AA-AAAGAAAATG
607974 CTGGATGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (24 bp):
AAAAAGAAAATGAGAAAAGAAAAG
Found at i:615238 original size:21 final size:21
Alignment explanation
Indices: 615186--615260 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
615176 CAGCAGAATA
* *
615186 CTACCAATACAATTAAGAGTT
1 CTACCGATACAATTAAGACTT
* *
615207 CTACTGGTACAATTCAA-ACTT
1 CTACCGATACAATT-AAGACTT
**
615228 CTACCGATACAACCAAGACTT
1 CTACCGATACAATTAAGACTT
* *
615249 CTATCGACACAA
1 CTACCGATACAA
615261 CATACTCAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (21 bp):
CTACCGATACAATTAAGACTT
Found at i:624148 original size:27 final size:27
Alignment explanation
Indices: 624096--624150 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
624086 GTAAAGTCAC
*
624096 TATGGGGGTTATTACTATAAGTCCATT
1 TATGGGGGTTATTACTATAAGACCATT
* *
624123 TATGGGGGTTATTACTCTCAGACCATT
1 TATGGGGGTTATTACTATAAGACCATT
624150 T
1 T
624151 CTATGATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (27 bp):
TATGGGGGTTATTACTATAAGACCATT
Found at i:630393 original size:18 final size:19
Alignment explanation
Indices: 630370--630406 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
630360 ATATTTTTTT
630370 TATTTTT-TATTTTTCTCG
1 TATTTTTCTATTTTTCTCG
*
630388 TATTTTTCTTTTTTTCTCG
1 TATTTTTCTATTTTTCTCG
630407 ACTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (19 bp):
TATTTTTCTATTTTTCTCG
Found at i:633605 original size:29 final size:30
Alignment explanation
Indices: 633550--633612 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
633540 TAGACATTTA
*
633550 ATTTAAAAAAATTAAAAATCATTAAAAT-T
1 ATTTAAAAAAATTAAAAATCATAAAAATAT
633579 ATTTAAAAAGAA-TAAAAAT-ATAAAAAATAT
1 ATTTAAAAA-AATTAAAAATCAT-AAAAATAT
633609 ATTT
1 ATTT
633613 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
ATTTAAAAAAATTAAAAATCATAAAAATAT
Found at i:636366 original size:42 final size:43
Alignment explanation
Indices: 636297--636438 Score: 160
Period size: 43 Copynumber: 3.3 Consensus size: 43
636287 GTACACACAG
* *
636297 TGCATCATCGGATATACCGAAGTAATTGTACTGGCACATACAA
1 TGCATCATCGGATATACTGAAGCAATTGTACTGGCACATACAA
* * * ** *
636340 T-TATCATTGGATATACTGAAGCAATTGTATTGGCACATTTAG
1 TGCATCATCGGATATACTGAAGCAATTGTACTGGCACATACAA
** * *
636382 TGCATCATCAAATAAACTGAAGCTATTGTACTGGCACATACAA
1 TGCATCATCGGATATACTGAAGCAATTGTACTGGCACATACAA
*
636425 TGCATCATCAGATA
1 TGCATCATCGGATA
636439 AATCGAAGTG
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 34 0.43
43 45 0.57
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (43 bp):
TGCATCATCGGATATACTGAAGCAATTGTACTGGCACATACAA
Found at i:636869 original size:15 final size:15
Alignment explanation
Indices: 636849--636895 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
636839 TATTTTTTTT
636849 ATTAAAACTTAATTA
1 ATTAAAACTTAATTA
*
636864 ATTAAAA-TTAACCTA
1 ATTAAAACTTAA-TTA
*
636879 ATTAAACCTTAATTA
1 ATTAAAACTTAATTA
636894 AT
1 AT
636896 CAAACATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAACTTAATTA
Found at i:639970 original size:27 final size:28
Alignment explanation
Indices: 639940--639995 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
639930 TGATTGCACA
639940 AAAAAAAAAT-ATTA-ACTTATGAAAAAT
1 AAAAAAAAATGATTATACTT-TGAAAAAT
*
639967 -AAAAAAAATGATTATACTTTGTAAAAT
1 AAAAAAAAATGATTATACTTTGAAAAAT
639994 AA
1 AA
639996 GATATTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 9 0.36
27 11 0.44
28 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAAAAAAATGATTATACTTTGAAAAAT
Found at i:641612 original size:38 final size:40
Alignment explanation
Indices: 641526--641668 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 40
641516 AAGTTACGTT
* * * *
641526 TGATAAAGTTCAAGCTACGGCTTAGTAGGTTATGAGCTAG
1 TGATAAAGTTCAAGCTATGACTTAGCAGGTTATGAGCCAG
* *
641566 TGACAAAGTTCAAGCTATGACTAAGCAGG-T-TGAGCCAG
1 TGATAAAGTTCAAGCTATGACTTAGCAGGTTATGAGCCAG
* * * * *
641604 TGATAAAGTTTAAGTTATGGCTTAGCAGGTTATGAGTCGG
1 TGATAAAGTTCAAGCTATGACTTAGCAGGTTATGAGCCAG
* * *
641644 TGATAAAATACAAGCTATGATTTAG
1 TGATAAAGTTCAAGCTATGACTTAG
641669 AAGGCTATAA
Statistics
Matches: 82, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 31 0.38
39 2 0.02
40 49 0.60
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (40 bp):
TGATAAAGTTCAAGCTATGACTTAGCAGGTTATGAGCCAG
Found at i:651153 original size:26 final size:26
Alignment explanation
Indices: 651124--651182 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
651114 TGAACTTGTT
** * *
651124 CAGAACTATTGCTGCGTGACTATGTC
1 CAGAACTATCACTGCATGACTAGGTC
* *
651150 CAGAATTATCACTGCATGAGTAGGTC
1 CAGAACTATCACTGCATGACTAGGTC
651176 CAGAACT
1 CAGAACT
651183 GTGCCCAGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
CAGAACTATCACTGCATGACTAGGTC
Found at i:651335 original size:5 final size:5
Alignment explanation
Indices: 651325--651355 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
651315 ATAAAAAAAG
651325 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
651356 AGATATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:659436 original size:29 final size:30
Alignment explanation
Indices: 659403--659463 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
659393 ATCACATGGT
*
659403 AACAACATATCATCG-TAAACAAATGAACA
1 AACAACATATCATCGCAAAACAAATGAACA
*
659432 AACAACATATCATCGCAAAACAAATGGACA
1 AACAACATATCATCGCAAAACAAATGAACA
659462 AA
1 AA
659464 TGGAAGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (30 bp):
AACAACATATCATCGCAAAACAAATGAACA
Found at i:675506 original size:16 final size:15
Alignment explanation
Indices: 675461--675506 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
675451 TCAGTCACTT
**
675461 GAAAAAGAAAAATGA
1 GAAAAAGAAAAAAAA
*
675476 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAAAAAAA
675492 GAAAAAGAAAAAAAA
1 GAAAAAGAAAAAAAA
675507 TTATGATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:686675 original size:17 final size:17
Alignment explanation
Indices: 686620--686681 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
686610 TATTATTATC
* * *
686620 ACATTCCCATTATCATT
1 ACATTTCCATTGTCACT
**
686637 ACATTTTAATTGTCACT
1 ACATTTCCATTGTCACT
* *
686654 ACATTTGCATTGTCATT
1 ACATTTCCATTGTCACT
*
686671 GCATTTCCATT
1 ACATTTCCATT
686682 TGTTAGTGCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (17 bp):
ACATTTCCATTGTCACT
Found at i:688933 original size:214 final size:214
Alignment explanation
Indices: 688555--688988 Score: 724
Period size: 214 Copynumber: 2.0 Consensus size: 214
688545 TATTCTGCTG
688555 ACTGTTCACCTAGGGGACCCATTTCATTATTATTGAATTTTATCTTTAATTTTACATTATTGCTT
1 ACTGTTCACCTAGGGGACCCATTTCATTATTATTGAATTTTATCTTTAATTTTACATTATTGCTT
* * *
688620 CGACAATCACTCTCATAATTTTCTTGCTTTTACTTATTATTAACACCGACAATTATAGATAACAA
66 CGACAATCACTCTCATAATTTTATTGCTTTTACTTATTATTAACACCGAAAATTATAGATAAAAA
* * *
688685 ACATCCATCCTCGTGGGATTGATATCTAATGGATTCACATCAATCTACTATACTTGCATTGACAG
131 ACATCCACCCTCGTGGGATCGATATCCAATGGATTCACATCAATCTACTATACTTGCATTGACAG
* * *
688750 TGTACATTTGCACATATTT
196 TGTAAACTTACACATATTT
*
688769 ACTGTTCACCTTGGGGACCCATTTCATTATTATTGAATTTTATCTTTAATTTTACATTATTGCTT
1 ACTGTTCACCTAGGGGACCCATTTCATTATTATTGAATTTTATCTTTAATTTTACATTATTGCTT
* *
688834 CGACAATCAGTCTCATAATTTTATTGCTTTTACTTATTATTTACACCGAAAATTATAGATAAAAA
66 CGACAATCACTCTCATAATTTTATTGCTTTTACTTATTATTAACACCGAAAATTATAGATAAAAA
* ***
688899 ACATCCACCCTCGTGGGATCGATATCCGATGGATTCACATTTGTCTACTATACTTGCATTGACAG
131 ACATCCACCCTCGTGGGATCGATATCCAATGGATTCACATCAATCTACTATACTTGCATTGACAG
688964 TGTAAACTTACACATATTT
196 TGTAAACTTACACATATTT
688983 ACTGTT
1 ACTGTT
688989 ACATTCATAG
Statistics
Matches: 204, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
214 204 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (214 bp):
ACTGTTCACCTAGGGGACCCATTTCATTATTATTGAATTTTATCTTTAATTTTACATTATTGCTT
CGACAATCACTCTCATAATTTTATTGCTTTTACTTATTATTAACACCGAAAATTATAGATAAAAA
ACATCCACCCTCGTGGGATCGATATCCAATGGATTCACATCAATCTACTATACTTGCATTGACAG
TGTAAACTTACACATATTT
Found at i:693827 original size:18 final size:18
Alignment explanation
Indices: 693802--693855 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
693792 CTGTTATTGA
693802 AAGATCTTCTTCTTCTTC
1 AAGATCTTCTTCTTCTTC
* *
693820 AGGATCTTCCTCTTCTTC
1 AAGATCTTCTTCTTCTTC
*
693838 AAGACCTTCTTCTTCTTC
1 AAGATCTTCTTCTTCTTC
693856 TTCAGCTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.15, C:0.31, G:0.07, T:0.46
Consensus pattern (18 bp):
AAGATCTTCTTCTTCTTC
Found at i:713633 original size:10 final size:10
Alignment explanation
Indices: 713609--713642 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
713599 ATCAATTTAT
713609 TAAAAAT-AA
1 TAAAAATAAA
713618 -AAAAATAAA
1 TAAAAATAAA
713627 TAAAAATAAA
1 TAAAAATAAA
713637 TAAAAA
1 TAAAAA
713643 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:723145 original size:139 final size:139
Alignment explanation
Indices: 722930--723210 Score: 490
Period size: 139 Copynumber: 2.0 Consensus size: 139
722920 TTGGTGAAAG
* * * *
722930 GAAAAGTCTTACCCTTATAAGACGGAGAGGGCGTACTTCTTGTTCATACGAGTTAAAACATCCCT
1 GAAAAGTCTTACCCTTATAAGACGAAGAGGGCATAATTCTTGTTCATACAAGTTAAAACATCCCT
*
722995 ATCGATCTTCATAATTGATTCCCTTCCCCCTGTAAGGCATTCCCAGTTCCCTTCCAGTAATTTCC
66 ATCGATCTTCATAATTGATTACCTTCCCCCTGTAAGGCATTCCCAGTTCCCTTCCAGTAATTTCC
723060 AGCTTAATA
131 AGCTTAATA
* *
723069 GAAAAGTCTTACTCTTATAAGATGAAGAGGGCATAATTCTTGTTCATACAAGTTAAAACATCCCT
1 GAAAAGTCTTACCCTTATAAGACGAAGAGGGCATAATTCTTGTTCATACAAGTTAAAACATCCCT
*
723134 ATCGATCTTCATAATTGATTACCTTCCCCCTGTAAGGCATTCCCAGTTCCCTTCCAGTAATTTCT
66 ATCGATCTTCATAATTGATTACCTTCCCCCTGTAAGGCATTCCCAGTTCCCTTCCAGTAATTTCC
723199 AGCTTAATA
131 AGCTTAATA
723208 GAA
1 GAA
723211 TCCTAAGAGG
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 134 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (139 bp):
GAAAAGTCTTACCCTTATAAGACGAAGAGGGCATAATTCTTGTTCATACAAGTTAAAACATCCCT
ATCGATCTTCATAATTGATTACCTTCCCCCTGTAAGGCATTCCCAGTTCCCTTCCAGTAATTTCC
AGCTTAATA
Found at i:726050 original size:21 final size:21
Alignment explanation
Indices: 726008--726051 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
725998 TGGTTCGAAA
* * **
726008 GACAAGAAGAGGAAGCGTAAG
1 GACAAAAAGAAGAAGCACAAG
726029 GACAAAAAGAAGAAGCACAAG
1 GACAAAAAGAAGAAGCACAAG
726050 GA
1 GA
726052 GGAAGGAGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.32, T:0.02
Consensus pattern (21 bp):
GACAAAAAGAAGAAGCACAAG
Found at i:729091 original size:24 final size:24
Alignment explanation
Indices: 729059--729124 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
729049 GCGATCAAGG
729059 AATTTGCCTCTGATTTTTAATTTA
1 AATTTGCCTCTGATTTTTAATTTA
*
729083 AATTTGCCTCT-TTTTTATAATTTA
1 AATTTGCCTCTGATTTT-TAATTTA
* *
729107 AATTTGTCTATGATTTTT
1 AATTTGCCTCTGATTTTT
729125 TCAACTGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.11
24 28 0.78
25 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (24 bp):
AATTTGCCTCTGATTTTTAATTTA
Found at i:734836 original size:58 final size:58
Alignment explanation
Indices: 734746--734875 Score: 242
Period size: 58 Copynumber: 2.2 Consensus size: 58
734736 CTTTAAACTA
734746 TCGTTCTAGTTTGATCTAGTTTACTTCTTGCTGTTTAGGGTTACTGATTTAGTTGTTT
1 TCGTTCTAGTTTGATCTAGTTTACTTCTTGCTGTTTAGGGTTACTGATTTAGTTGTTT
734804 TCGTTCTAGTTTGATCTAGTTTACTTCTTGCTGTTTAGGGTTACTGATTTAGTTGTTT
1 TCGTTCTAGTTTGATCTAGTTTACTTCTTGCTGTTTAGGGTTACTGATTTAGTTGTTT
* *
734862 TCATTCTAGGTTGA
1 TCGTTCTAGTTTGA
734876 AATTGATTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.52
Consensus pattern (58 bp):
TCGTTCTAGTTTGATCTAGTTTACTTCTTGCTGTTTAGGGTTACTGATTTAGTTGTTT
Found at i:735531 original size:19 final size:19
Alignment explanation
Indices: 735509--735545 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
735499 TCAAAAAGTC
735509 GAGAAAAA-AAGAAAAATAT
1 GAGAAAAATAA-AAAAATAT
735528 GAGAAAAATAAAAAAATA
1 GAGAAAAATAAAAAAATA
735546 AAAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
GAGAAAAATAAAAAAATAT
Done.