Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007763.1 Kokia drynarioides strain JFW-HI SEQ_122396, 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: 237200
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:208922 original size:97 final size:97
Alignment explanation
Indices: 208747--208922 Score: 250
Period size: 97 Copynumber: 1.8 Consensus size: 97
208737 TCGATTATCT
* *
208747 CGATTTGAAGAAGAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCAGAGATAAAGAAA
1 CGATTTGAAGAAGAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAA
*
208812 CATTGTCTCGATTTGAGGGTATTCGAATATTC
66 CATTGCCTCGATTTGAGGGTATTCGAATATTC
*
208844 CGATTTGAAGAA-AGATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTC-GAAATAAA-A
1 CGATTTGAAGAAGAG-TCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-TCAGAAATAAAGA
* *
208906 GAATATTGCCTTGATTT
64 -AACATTGCCTCGATTT
208923 TAAAGTTTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
96 3 0.04
97 65 0.93
98 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (97 bp):
CGATTTGAAGAAGAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAA
CATTGCCTCGATTTGAGGGTATTCGAATATTC
Found at i:209170 original size:27 final size:28
Alignment explanation
Indices: 209140--209200 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
209130 AAAATGTGAT
* * *
209140 TTTTGGATAATC-GGTGCAAAATGGTAA
1 TTTTGGACAATCAGGAGCAAAATGATAA
* *
209167 TTTTGAACACTCAGGAGCAAAATGATAA
1 TTTTGGACAATCAGGAGCAAAATGATAA
209195 TTTTGG
1 TTTTGG
209201 GGAAGTTCGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (28 bp):
TTTTGGACAATCAGGAGCAAAATGATAA
Found at i:209347 original size:58 final size:58
Alignment explanation
Indices: 209240--209529 Score: 243
Period size: 59 Copynumber: 4.9 Consensus size: 58
209230 AGGCATTCAA
** * *
209240 GGGTAAAATCTTAA-TTTTGGAAAAAAATCAAGGTCAAAAA-AGGAAATTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGG--AAAAATCGAGGTTAAAAATA-G-AATTTTGGAAGTTTGG
* * * * * *
209300 GGGTAAAATGGTAGTTTTTTGAGAAATCGAGGTTAAAAATAGCATTTTAGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTT-GGAAGTTTGG
* * *
209359 GGGTAAAATGGTAATTTTTGGAAAAAT-TAGGGTTAAAAAT-GAAATTTTGAAAAG-TTCG
1 GGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTTAAAAATAG-AATTTTG-GAAGTTTGG
* *
209417 GGGTAAGAAT-GTAATTTTTGGAAAAATCGAGATCAAAAAAATAGAATTTTTGGAAGTTTGG
1 GGGTAA-AATGGTAATTTTTGGAAAAATCGAGGT--TAAAAATAGAA-TTTTGGAAGTTTGG
* ** *
209478 GGGTAAAATGGTAATTTTTGGAGAAA-CAGAGGCCAAAAATGGAATTTTGGAA
1 GGGTAAAATGGTAATTTTTGGAAAAATC-GAGGTTAAAAATAGAATTTTGGAA
209530 AAATCGAGGT
Statistics
Matches: 189, Mismatches: 26, Indels: 32
0.77 0.11 0.13
Matches are distributed among these distances:
58 44 0.23
59 80 0.42
60 27 0.14
61 38 0.20
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTTGGAAGTTTGG
Found at i:209391 original size:29 final size:29
Alignment explanation
Indices: 209359--209443 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
209349 GAAAGTTTAG
209359 GGGTAAAATGGTAATTTTTGGAAAAATT-A
1 GGGTAAAAT-GTAATTTTTGGAAAAATTCA
* * *
209388 GGGTTAAAAATG-AAATTTT-GAAAAGTTCG
1 GGG-T-AAAATGTAATTTTTGGAAAAATTCA
209417 GGGTAAGAATGTAATTTTTGGAAAAAT
1 GGGTAA-AATGTAATTTTTGGAAAAAT
209444 CGAGATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
27 2 0.04
28 12 0.27
29 18 0.40
30 8 0.18
31 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTGGAAAAATTCA
Found at i:209396 original size:30 final size:29
Alignment explanation
Indices: 209355--209443 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 29
209345 TTTAGAAAGT
209355 TTAGGGGTAAAATGGTAATTTTTGGAAAAA
1 TTAGGGGTAAAAT-GTAATTTTTGGAAAAA
* * *
209385 TTAGGGTTAAAAATG-AAATTTT-GAAAAG
1 TTAGGGGT-AAAATGTAATTTTTGGAAAAA
*
209413 TTCGGGGTAAGAATGTAATTTTTGGAAAAA
1 TTAGGGGTAA-AATGTAATTTTTGGAAAAA
209443 T
1 T
209444 CGAGATCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.04
28 15 0.31
29 12 0.25
30 14 0.29
31 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (29 bp):
TTAGGGGTAAAATGTAATTTTTGGAAAAA
Found at i:209525 original size:29 final size:29
Alignment explanation
Indices: 209482--209559 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
209472 GTTTGGGGGT
*
209482 AAAATGGTAATTTTTGGAGAAA-CAGAGGCCA
1 AAAATGG-AA-TTTTGGAAAAATC-GAGGCCA
*
209513 AAAATGGAATTTTGGAAAAATCGAGGTCA
1 AAAATGGAATTTTGGAAAAATCGAGGCCA
*
209542 AAAATAGAATTTTGGAAA
1 AAAATGGAATTTTGGAAA
209560 GTTCAGGGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 33 0.77
30 3 0.07
31 7 0.16
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.24
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAAATCGAGGCCA
Found at i:209555 original size:119 final size:119
Alignment explanation
Indices: 209334--209559 Score: 280
Period size: 119 Copynumber: 1.9 Consensus size: 119
209324 AATCGAGGTT
* * **
209334 AAAAATAGCATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTTAAAAAT
1 AAAAATAGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCAGGGCCAAAAAT
* * *
209399 GAAATTTTGAAAAGTTCGGGGTAAGAATGTAATTTTTGGAAAAATCGAGATCAA
66 GAAATTTTGAAAAGATCGAGGTAAAAATGTAATTTTTGGAAAAATCGAGATCAA
* * * *
209453 AAAAATAGAATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAGAAA-CAGAGGCCAAAAA
1 AAAAATAGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCAG-GGCCAAAAA
*
209517 TGGAATTTTGGAAAA-ATCGAGGTCAAAAATAG-AA-TTTTGGAAA
65 TGAAATTTT-GAAAAGATCGAGGT-AAAAAT-GTAATTTTTGGAAA
209560 GTTCAGGGGG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
118 2 0.02
119 76 0.84
120 12 0.13
121 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (119 bp):
AAAAATAGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCAGGGCCAAAAAT
GAAATTTTGAAAAGATCGAGGTAAAAATGTAATTTTTGGAAAAATCGAGATCAA
Found at i:209600 original size:30 final size:30
Alignment explanation
Indices: 209513--209618 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 30
209503 ACAGAGGCCA
* * *
209513 AAAATGGAATTTTGGAAAA-ATC-GAGGTC
1 AAAATAGAATTTTGGAAAAGTTCAGGGGTC
209541 AAAAATAGAATTTTGG-AAAGTTCAGGGGGT-
1 -AAAATAGAATTTTGGAAAAGTTCA-GGGGTC
209571 AAGAATAGAATTTTGGAAAAGTTCAGGGGTC
1 AA-AATAGAATTTTGGAAAAGTTCAGGGGTC
*
209602 AAAATATGATTTTTGGA
1 AAAATA-GAATTTTGGA
209619 CAGTTTATGG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.05
29 18 0.27
30 22 0.33
31 23 0.35
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (30 bp):
AAAATAGAATTTTGGAAAAGTTCAGGGGTC
Found at i:210816 original size:22 final size:20
Alignment explanation
Indices: 210783--210833 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
210773 CTTTTTATTA
*
210783 TTATTATTATTAACATTCAT
1 TTATCATTATTAACATTCAT
**
210803 TCATATCATTATTATTATTCAT
1 T--TATCATTATTAACATTCAT
210825 TTATCATTA
1 TTATCATTA
210834 ATGCCATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATCATTATTAACATTCAT
Found at i:212387 original size:94 final size:94
Alignment explanation
Indices: 212223--212393 Score: 218
Period size: 94 Copynumber: 1.8 Consensus size: 94
212213 CTAGGACGTC
* * * * * *
212223 AAACATGGGGATTATAGGTGTAAAACCGTAGCTAGGCTATGACAACTAGTACTGCCCGTCAAGAT
1 AAACATGGAGATTATAGGTGTAAAACCATAGCTAGACTAAGACAACTAATACTGCCCGCCAAGAT
212288 AGTAAACACGAGAAGTCTTCCAAGACATT
66 AGTAAACACGAGAAGTCTTCCAAGACATT
* * * * **
212317 AAACATGGAGATTATAGGTGTAAGACCATAGCTCGACTAAGACGACTAATA-TAGTCCGCCGGGA
1 AAACATGGAGATTATAGGTGTAAAACCATAGCTAGACTAAGACAACTAATACT-GCCCGCCAAGA
212381 TAGTAAACACGAG
65 TAGTAAACACGAG
212394 GTTGTCCATC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
93 1 0.02
94 63 0.98
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (94 bp):
AAACATGGAGATTATAGGTGTAAAACCATAGCTAGACTAAGACAACTAATACTGCCCGCCAAGAT
AGTAAACACGAGAAGTCTTCCAAGACATT
Found at i:212412 original size:27 final size:27
Alignment explanation
Indices: 212382--212471 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
212372 CCGCCGGGAT
*
212382 AGTAAACACGAGGTTGTCCATCGGGAC
1 AGTAAACACGAGGTTGTCCATCGAGAC
*** * *
212409 AGTAAACACGAGGTTGTTTGTCTAGAT
1 AGTAAACACGAGGTTGTCCATCGAGAC
212436 AGTAAACACGAGGTTGTCCATCGAGAC
1 AGTAAACACGAGGTTGTCCATCGAGAC
212463 AGTAAACAC
1 AGTAAACAC
212472 AGGGAAGTCC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (27 bp):
AGTAAACACGAGGTTGTCCATCGAGAC
Found at i:212496 original size:54 final size:54
Alignment explanation
Indices: 212382--212497 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 54
212372 CCGCCGGGAT
* ** ** *
212382 AGTAAACACGAGGTTGTCCATCGGGACAGTAAACACGAGGTTGTTTGTCTAGAT
1 AGTAAACACGAGGTTGTCCATCGAGACAGTAAACACGAGGAAGTCCGTCTAGAC
212436 AGTAAACACGAGGTTGTCCATCGAGACAGTAAACAC-AGGGAAGTCCGT-TAGGAC
1 AGTAAACACGAGGTTGTCCATCGAGACAGTAAACACGA-GGAAGTCCGTCTA-GAC
*
212490 ATTAAACA
1 AGTAAACA
212498 TGGGGATTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 3 0.06
54 50 0.94
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (54 bp):
AGTAAACACGAGGTTGTCCATCGAGACAGTAAACACGAGGAAGTCCGTCTAGAC
Found at i:216682 original size:21 final size:21
Alignment explanation
Indices: 216656--216704 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
216646 CCTATGACAG
* *
216656 TTCTACCGACACAAGTAAAGC
1 TTCTACCGAAACAAATAAAGC
* *
216677 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATAAAGC
216698 TTCTACC
1 TTCTACC
216705 AGTACTTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (21 bp):
TTCTACCGAAACAAATAAAGC
Found at i:217536 original size:36 final size:35
Alignment explanation
Indices: 217487--217586 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 35
217477 CGATATTGGA
*
217487 TTTACTCCATGTTGAGCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGA-CCAAAGGTCATGATGCTCAT
217523 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGA-CCAAAGGTCATGATGCTCAT
* *
217559 TTTACTCCCTATTGACTCAAAAGTCATG
1 TTTACTCCCTGTTGAC-CAAAGGTCATG
217587 CCTCTTACCA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 1 0.02
36 58 0.98
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (35 bp):
TTTACTCCCTGTTGACCAAAGGTCATGATGCTCAT
Found at i:225325 original size:2 final size:2
Alignment explanation
Indices: 225318--225345 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
225308 CTATACCTTT
225318 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
225346 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:225721 original size:23 final size:23
Alignment explanation
Indices: 225691--225835 Score: 108
Period size: 23 Copynumber: 6.5 Consensus size: 23
225681 AGTGCTGGGC
225691 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
**
225714 AACAGAGAGTGCACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
225733 -AC--TGAGCACACAAAATGCTA
1 AACAGAGAGCACACAAAGTGCTA
** *
225753 ATTAGAGAGCACACAAAGTGTTAA
1 AACAGAGAGCACACAAAGTGCT-A
*
225777 TAACAGAGAGCACGA-AACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
* * *
225801 AACAGAGAACATACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
225824 AACAGAGAGCAC
1 AACAGAGAGCAC
225836 GCTAGTGTTC
Statistics
Matches: 91, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
16 9 0.10
18 3 0.03
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 56 0.62
24 2 0.02
25 16 0.18
26 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:225740 original size:39 final size:39
Alignment explanation
Indices: 225697--225771 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
225687 GGGCAACAGA
* **
225697 GAGCACACAAAGTGCTAAACAGAGAGTGCACAAAGTACT
1 GAGCACACAAAATGCTAAACAGAGAGCACACAAAGTACT
**
225736 GAGCACACAAAATGCTAATTAGAGAGCACACAAAGT
1 GAGCACACAAAATGCTAAACAGAGAGCACACAAAGT
225772 GTTAATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAATGCTAAACAGAGAGCACACAAAGTACT
Found at i:227387 original size:18 final size:18
Alignment explanation
Indices: 227361--227396 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
227351 TTTTCTATCA
*
227361 ATTTCTCTTTATAAAAAT
1 ATTTCTCTTAATAAAAAT
*
227379 ATTTTTCTTAATAAAAAT
1 ATTTCTCTTAATAAAAAT
227397 GGTAAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTCTCTTAATAAAAAT
Found at i:231871 original size:26 final size:27
Alignment explanation
Indices: 231808--231874 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
231798 TATCAACATT
231808 ACTG-CTGCTAACCAA-CTTAACCAACA
1 ACTGACTGCTAA-CAACCTTAACCAACA
*
231834 ACTGA-TGATAACAACCTTAACCAACA
1 ACTGACTGCTAACAACCTTAACCAACA
231860 ACT-ACTGCTAACAAC
1 ACTGACTGCTAACAAC
231875 TTCCATTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 4 0.11
26 32 0.89
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.19
Consensus pattern (27 bp):
ACTGACTGCTAACAACCTTAACCAACA
Found at i:232959 original size:18 final size:19
Alignment explanation
Indices: 232926--232964 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
232916 CTCATAAATA
*
232926 TATATAAAATGATTTTTATT
1 TATATAAAAT-ATTTTAATT
232946 TATATAAAAT-TTTTAATT
1 TATATAAAATATTTTAATT
232964 T
1 T
232965 TACTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATATAAAATATTTTAATT
Found at i:233652 original size:604 final size:608
Alignment explanation
Indices: 232490--233706 Score: 2030
Period size: 604 Copynumber: 2.0 Consensus size: 608
232480 TGATTTGCAG
* *
232490 ATAGCTCGTGGATTCGAATTTTAAGGGAGATTTGCGAATTCAGATTCAAATAATCTAAAATCGTA
1 ATAGCTCGTGGATTCGAATTTTAAGAGAGATTTGCGAATTCAGATTCAAATAACCTAAAATCGTA
*
232555 GATTTTTAACTCGTTGCCATCCCTAGTTGATAAATTAAGTTGCTTTCAAGTTTATTGGTAGAATG
66 GATTTTTAACTCGTAGCCATCCCTAGTTGATAAATTAAGTTGCTTTCAA---TA---GT--AA--
232620 CAATGTGTTTAGATCTCTTTTTTCTTAATTGTAGTCTAAAATGTTGCTTGAATAACCCATGATGT
121 CAATGTGTTTAGATCTCTTTTTTCTTAATTGTAGTCTAAAATGTTGCTTGAATAACCCATGATGT
*
232685 GGTTCAGTTGCATGTTTGCACCATACCAGAGTACTATTTTCTCACTAATGAATTATACTCTATTT
186 GGTTCAGTTGCATGTTTGCACCATACCAGAGTACTATTTTCTCACTAATGAATTATACTCTAATT
* * *
232750 GATTTTCGGTTTAACTGGTTCAATGAGTCAATCTAATCCAATTCAAACAACAAGAGCATTTTATT
251 GATTTTCGGTTCAACCGGTTCAATCAGTCAATCTAATCCAATTCAAACAACAAGAGCATTTTATT
232815 TTCCCATGCTAACTCTTCACTTTTTTTATTAAGAAAACGCATGCCGATTTGATTCATTTTTCTCT
316 TTCCCATGCTAACTCTTCACTTTTTTTATTAAGAAAACGCATGCCGATTTGATTCATTTTTCTCT
* *
232880 CGGTACCTATAGGCATGTAAAATTTGATTAATTTTTCTCATAAATATATATAAAATGATTTTTAT
381 CAGTACCTATAGACATGTAAAATTTGATTAATTTTTCTCATAAATATATATAAAATGATTTTTAT
* *
232945 TTATATAAAATTTTTAATTTTACTTTTATAATAGTTTAATAAATATATAATAAAATCTATATAGT
446 TTATATAAAATATTTAATTTTACTTTTATAATAGTTTAATAAATATATAAGAAAATCTATATAGT
* *
233010 TAATCATATATAAGTGATTATATGACTAGTAAAATGATACAAATATAATTAATATATTTATAGAA
511 TAATCATATATAAGTAATTATAAGACTAGTAAAATGATACAAATATAATTAATATATTTATAGAA
233075 TTTAAATTATTTATTACTACAATTATTAACTAT
576 TTTAAATTATTTATTACTACAATTATTAACTAT
* * * * *
233108 ATAGCTCGTGGATTCGGATTTTTAGAGAGATTTGCGAATTCAGATTCGAATAACCTAGAATTGTA
1 ATAGCTCGTGGATTCGAATTTTAAGAGAGATTTGCGAATTCAGATTCAAATAACCTAAAATCGTA
233173 GATTTTTAACTCGTAGCCATCCCTAGTTGATAAATTAAGTTGCTTTC-A-A-T-A-AATGTGTTT
66 GATTTTTAACTCGTAGCCATCCCTAGTTGATAAATTAAGTTGCTTTCAATAGTAACAATGTGTTT
233233 AGATCTCTTTTTTTCTTAATTGTAGTCTAAAATGTTGCTTGAATAACCCATGATGTGGTTCAGTT
131 AGATCTC-TTTTTTCTTAATTGTAGTCTAAAATGTTGCTTGAATAACCCATGATGTGGTTCAGTT
*
233298 GCATGTTTGCACCATACCAGAGTACTATTTTCTCACTAATGAATTATACTTTAATTGATTTTCGG
195 GCATGTTTGCACCATACCAGAGTACTATTTTCTCACTAATGAATTATACTCTAATTGATTTTCGG
* * * ***
233363 TTCAACCGGTTCGATCAGTCAATCTGATCCAATTCAAACAACAAGATCATTTTATTTTTTTATGC
260 TTCAACCGGTTCAATCAGTCAATCTAATCCAATTCAAACAACAAGAGCATTTTATTTTCCCATGC
**
233428 TAACTCTTCACTTTTTTTATTAAGAAAACGCATGTTGATTTGATTCATTTTTCTCTCAGTACCTA
325 TAACTCTTCACTTTTTTTATTAAGAAAACGCATGCCGATTTGATTCATTTTTCTCTCAGTACCTA
* *
233493 TAGACATGTAAAATTTGATTAATTTTTCTCGTAAATATATGTAAAATGATTTTTATTTATATAAA
390 TAGACATGTAAAATTTGATTAATTTTTCTCATAAATATATATAAAATGATTTTTATTTATATAAA
*
233558 ATATTTAATTTTACTTTTGTAATAGTTTAATAAATATATAAGAAAATCTATATAGTTAATCATAT
455 ATATTTAATTTTACTTTTATAATAGTTTAATAAATATATAAGAAAATCTATATAGTTAATCATAT
233623 ATAAGTAATTATAAGACTAGTAAAATGATACAAATATAATTAATATATTTATAGAATTTAAATTA
520 ATAAGTAATTATAAGACTAGTAAAATGATACAAATATAATTAATATATTTATAGAATTTAAATTA
233688 TTTATTACTACAATTATTA
585 TTTATTACTACAATTATTA
233707 TTTAACATAA
Statistics
Matches: 568, Mismatches: 30, Indels: 16
0.93 0.05 0.03
Matches are distributed among these distances:
603 16 0.03
604 444 0.78
606 1 0.00
609 1 0.00
613 1 0.00
617 1 0.00
618 104 0.18
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (608 bp):
ATAGCTCGTGGATTCGAATTTTAAGAGAGATTTGCGAATTCAGATTCAAATAACCTAAAATCGTA
GATTTTTAACTCGTAGCCATCCCTAGTTGATAAATTAAGTTGCTTTCAATAGTAACAATGTGTTT
AGATCTCTTTTTTCTTAATTGTAGTCTAAAATGTTGCTTGAATAACCCATGATGTGGTTCAGTTG
CATGTTTGCACCATACCAGAGTACTATTTTCTCACTAATGAATTATACTCTAATTGATTTTCGGT
TCAACCGGTTCAATCAGTCAATCTAATCCAATTCAAACAACAAGAGCATTTTATTTTCCCATGCT
AACTCTTCACTTTTTTTATTAAGAAAACGCATGCCGATTTGATTCATTTTTCTCTCAGTACCTAT
AGACATGTAAAATTTGATTAATTTTTCTCATAAATATATATAAAATGATTTTTATTTATATAAAA
TATTTAATTTTACTTTTATAATAGTTTAATAAATATATAAGAAAATCTATATAGTTAATCATATA
TAAGTAATTATAAGACTAGTAAAATGATACAAATATAATTAATATATTTATAGAATTTAAATTAT
TTATTACTACAATTATTAACTAT
Found at i:234677 original size:12 final size:12
Alignment explanation
Indices: 234660--234702 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
234650 TGAAAAGAAT
234660 GAAAAAGAAAAA
1 GAAAAAGAAAAA
*
234672 GAAAAAGAAAAT
1 GAAAAAGAAAAA
* *
234684 TAAAAATATAAAA
1 GAAAAAGA-AAAA
234697 GAAAAA
1 GAAAAA
234703 AATTAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:237178 original size:2 final size:2
Alignment explanation
Indices: 237171--237200 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
237161 ATGTATTGAT
237171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.