Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_31 ID=scaffold_31-JGI_221_v2.0
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: 66424
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.23
Warning! 20018 characters in sequence are not A, C, G, or T
Found at i:22037 original size:29 final size:31
Alignment explanation
Indices: 21994--22066 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
21984 TATATGTAAT
21994 ATATATATGCATGGGT-TATG-TTATATATA-
1 ATATATATGCATGGGTCT-TGATTATATATAC
*
22023 ATATATATGCGTGGGTCTTGATTATATATATC
1 ATATATATGCATGGGTCTTGATTATATATA-C
*
22055 ATATATAAGCAT
1 ATATATATGCAT
22067 ATATGGGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 17 0.46
30 10 0.27
32 10 0.27
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (31 bp):
ATATATATGCATGGGTCTTGATTATATATAC
Found at i:23116 original size:17 final size:17
Alignment explanation
Indices: 23096--23131 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23086 GAACTATTAA
23096 TTGGAATGAACTGTCAT
1 TTGGAATGAACTGTCAT
* *
23113 TTGGTATGAACTGTTAT
1 TTGGAATGAACTGTCAT
23130 TT
1 TT
23132 CATATGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.44
Consensus pattern (17 bp):
TTGGAATGAACTGTCAT
Found at i:23137 original size:17 final size:17
Alignment explanation
Indices: 23101--23140 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
23091 ATTAATTGGA
**
23101 ATGAACTGTCATTTGGT
1 ATGAACTGTCATTTCAT
*
23118 ATGAACTGTTATTTCAT
1 ATGAACTGTCATTTCAT
23135 ATGAAC
1 ATGAAC
23141 AGATGTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (17 bp):
ATGAACTGTCATTTCAT
Found at i:23230 original size:18 final size:18
Alignment explanation
Indices: 23180--23230 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
23170 TGATCTGCCA
* *
23180 ATTTTATGCGAATTACTT
1 ATTTTATGAGAACTACTT
* * *
23198 ATTATATGTGCACTACTT
1 ATTTTATGAGAACTACTT
23216 ATTTTATGAGAACTA
1 ATTTTATGAGAACTA
23231 TTGTGTCGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTTATGAGAACTACTT
Found at i:29249 original size:25 final size:25
Alignment explanation
Indices: 29215--29265 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29205 AAAAATTAAA
29215 CAACATCAGGGAACCCTAGGGTTCC
1 CAACATCAGGGAACCCTAGGGTTCC
29240 CAACATCAGGGAACCCTAGGGTTCC
1 CAACATCAGGGAACCCTAGGGTTCC
29265 C
1 C
29266 TGCCTTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (25 bp):
CAACATCAGGGAACCCTAGGGTTCC
Found at i:35274 original size:8 final size:8
Alignment explanation
Indices: 35261--35331 Score: 65
Period size: 8 Copynumber: 8.9 Consensus size: 8
35251 GTTCAGACTC
35261 AAAAAAAT
1 AAAAAAAT
35269 -AAAAAA-
1 AAAAAAAT
**
35275 AAATCAAT
1 AAAAAAAT
*
35283 CAAAAAAT
1 AAAAAAAT
*
35291 CAAAAAAT
1 AAAAAAAT
*
35299 CAAAAAAT
1 AAAAAAAT
35307 CAAAAAAAT
1 -AAAAAAAT
35316 CAAAAAAAT
1 -AAAAAAAT
35325 AAAAAAA
1 AAAAAAA
35332 ATCAAAGTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 10 0.19
8 28 0.52
9 16 0.30
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:35275 original size:9 final size:9
Alignment explanation
Indices: 35261--35333 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
35251 GTTCAGACTC
35261 AAAAAAATAA
1 AAAAAAAT-A
35271 AAAAAAATCA
1 AAAAAAAT-A
35281 ATCAAAAAAT-
1 A--AAAAAATA
*
35291 CAAAAAAT-
1 AAAAAAATA
* *
35299 CAAAAAATC
1 AAAAAAATA
*
35308 AAAAAAATC
1 AAAAAAATA
35317 AAAAAAATA
1 AAAAAAATA
35326 AAAAAAAT
1 AAAAAAAT
35334 CAAAGTCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
8 15 0.27
9 24 0.43
10 10 0.18
12 7 0.12
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:35299 original size:16 final size:16
Alignment explanation
Indices: 35280--35337 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 16
35270 AAAAAAAATC
35280 AATCAAAAAATCAAAA
1 AATCAAAAAATCAAAA
35296 AATCAAAAAATCAAAAA
1 AATCAAAAAATC-AAAA
*
35313 AATCAAAAAAATAAAAAA
1 AATC-AAAAAAT-CAAAA
35331 AATCAAA
1 AATCAAA
35338 GTCAAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
16 12 0.32
17 11 0.29
18 15 0.39
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (16 bp):
AATCAAAAAATCAAAA
Found at i:36211 original size:9 final size:9
Alignment explanation
Indices: 36197--36237 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
36187 AAAAAAAGAG
36197 ATGAAAAAA
1 ATGAAAAAA
36206 ATG-AAAAA
1 ATGAAAAAA
36214 ATG--AAAA
1 ATGAAAAAA
36221 ATGAAAAAA
1 ATGAAAAAA
36230 ATGAAAAA
1 ATGAAAAA
36238 GTAAAAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.23
8 8 0.27
9 15 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:36220 original size:7 final size:8
Alignment explanation
Indices: 36201--36237 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
36191 AAAGAGATGA
36201 AAAAAATG
1 AAAAAATG
36209 AAAAAATG
1 AAAAAATG
36217 -AAAAATG
1 AAAAAATG
36224 AAAAAAATG
1 -AAAAAATG
36233 AAAAA
1 AAAAA
36238 GTAAAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:36224 original size:24 final size:23
Alignment explanation
Indices: 36197--36246 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
36187 AAAAAAAGAG
36197 ATGAAAAAAATGAAAAAATGAAAA
1 ATGAAAAAAATGAAAAAAT-AAAA
*
36221 ATGAAAAAAATGAAAAAGTAAAA
1 ATGAAAAAAATGAAAAAATAAAA
36244 ATG
1 ATG
36247 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (23 bp):
ATGAAAAAAATGAAAAAATAAAA
Found at i:36244 original size:16 final size:16
Alignment explanation
Indices: 36202--36237 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
36192 AAGAGATGAA
36202 AAAAATG-AAAAAATG
1 AAAAATGAAAAAAATG
36217 AAAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
36233 AAAAA
1 AAAAA
36238 GTAAAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:37973 original size:44 final size:44
Alignment explanation
Indices: 37925--38151 Score: 165
Period size: 44 Copynumber: 5.2 Consensus size: 44
37915 GACAACCGAT
*
37925 CTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTTCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* * * * * * * *
37969 CTTGCCTCTCT-CGATTG-TAGTGGAGCTGGTTGAAGACAACAGAT
1 CTTGCCTTTCTGC-ATTGACAGCGAAGCAGGTCGAAGAC-ACAAAC
* *
38013 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTTCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* * * * * * * * * *
38057 ATTACCTCTCT-CGGTTG-TAGCGGAGCTGGTTGAAGACAACAGAT
1 CTTGCCTTTCTGC-ATTGACAGCGAAGCAGGTCGAAGAC-ACAAAC
* * * *
38101 CTGGCCTTCCTGCATTAACATCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTTCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
38145 CTTGCCT
1 CTTGCCT
38152 CTCTCGGTTG
Statistics
Matches: 129, Mismatches: 46, Indels: 16
0.68 0.24 0.08
Matches are distributed among these distances:
43 31 0.24
44 67 0.52
45 31 0.24
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (44 bp):
CTTGCCTTTCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:37998 original size:88 final size:87
Alignment explanation
Indices: 37432--38201 Score: 924
Period size: 87 Copynumber: 8.8 Consensus size: 87
37422 ATCTGTGAAC
* * * * *
37432 ATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGATAACAGATATTGCAT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
37497 TCCTGCGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
*
37519 ATCGAAAACAAAGCCTTCCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
37584 TCCTGCGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * * *
37606 ATCAAAAACAAAGCCTGGCCTCCATCAGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
37671 TCCTGCGTTACCAGCAAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
37693 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
37758 TCCTGCGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
*
37780 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAGAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
37845 TCCGGCGTTAACAACGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * * ** * * * *
37867 ATCGAAAATAAAGTCTTGCCTCTC-TCGATTGTGGTGGAGCTGGTTGAAGACAACCGATCTTGCC
1 ATCGAAAACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC
* * *
37931 TTTCTGCATTGACAGCGAAGCAG
65 TTCCTGCGTTAACAGCGAAGCAG
* * * * *
37954 ATCGAAGACACAAA-CCTTGCCTCTC-TCGATTGTAGTGGAGCTGGTTGAAGACAACAGATCTTG
1 ATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* *
38017 CCTTCCTGCATTGACAGCGAAGCAG
63 CCTTCCTGCGTTAACAGCGAAGCAG
* * * * * * * *
38042 ATCGAAGACACAAA-CATTACCTCTC-TCGGTTGTAGCGGAGCTGGTTGAAGACAACAGATCTGG
1 ATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* *
38105 CCTTCCTGCATTAACATCGAAGCAG
63 CCTTCCTGCGTTAACAGCGAAGCAG
* ** * * * * *
38130 GTCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTGGTGGAGCTGGATGAGGACAGCAGATATTG
1 ATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
*
38193 CCCTCCTGC
63 CCTTCCTGC
38202 ATCGACAGCG
Statistics
Matches: 620, Mismatches: 60, Indels: 5
0.91 0.09 0.01
Matches are distributed among these distances:
87 402 0.65
88 214 0.35
89 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (87 bp):
ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
TCCTGCGTTAACAGCGAAGCAG
Found at i:38411 original size:95 final size:95
Alignment explanation
Indices: 38216--38398 Score: 307
Period size: 95 Copynumber: 1.9 Consensus size: 95
38206 ACAGCGGGGC
* *
38216 AGATCAAATATAGAAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
1 AGATTAAATATAGAAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
*
38281 ATCTCCCTGGTTGGCAGTGGAATAGACTAA
66 ATCTCCCTGGTTAGCAGTGGAATAGACTAA
38311 AGATTAAATAT-GATAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTC
1 AGATTAAATATAGA-AGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTC
38375 TATCTCCCTAGG-TAGCAGTGGAAT
65 TATCTCCCT-GGTTAGCAGTGGAAT
38399 GAATTGAAGA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
94 2 0.02
95 79 0.95
96 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (95 bp):
AGATTAAATATAGAAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
ATCTCCCTGGTTAGCAGTGGAATAGACTAA
Found at i:38560 original size:129 final size:128
Alignment explanation
Indices: 38415--38652 Score: 404
Period size: 128 Copynumber: 1.9 Consensus size: 128
38405 AAGATTACAG
* *
38415 ATCCTATTTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAGATTCTGTCTCCCTAAGCAGT
1 ATCCTATCTCCCTAAGCAGTAGGGGAGTAGGTTGAAGATTGC-AGATTCTGTCTCCCTAAGCAGT
* *
38480 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGTACATTGAGCCGTTA
65 AGTGGAGCAGATCGAAGATGCTAAATCTTATCTTCCCAAGATAGTGGAGTACATTGAGCCGTTA
38544 ATCCTATCTCCCTAAGCAGTAGGGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTA
1 ATCCTATCTCCCTAAGCAGTAGGGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTA
* * *
38609 GTGGAGCAGATCGAAGATGCTAAATTTTATCTTCTCAAGGTAGT
66 GTGGAGCAGATCGAAGATGCTAAATCTTATCTTCCCAAGATAGT
38653 AGGGAAGCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 62 0.61
129 40 0.39
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (128 bp):
ATCCTATCTCCCTAAGCAGTAGGGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGATGCTAAATCTTATCTTCCCAAGATAGTGGAGTACATTGAGCCGTTA
Found at i:38625 original size:44 final size:44
Alignment explanation
Indices: 38371--38626 Score: 197
Period size: 44 Copynumber: 5.9 Consensus size: 44
38361 GAAGCCGATA
* * * * *
38371 ATTCTATCTCCCTAGGTAGCAGTGGAAT-GAATTGAAGATTACAG
1 ATTCTATCTCCCTAAGCAGTAGTGGAGTAG-ATTGAAGATTGCAG
* * *
38415 ATCCTATTTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAG
1 ATTCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGC-AG
* * * **
38460 ATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTG
1 ATTCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG
* * *
38503 AATCTTATCTTCCC-AAG-A-TAGTGGAGTACATTG-AGCCGTT--A-
1 ATTC-TATC-TCCCTAAGCAGTAGTGGAGTAGATTGAAG--ATTGCAG
* * *
38544 ATCCTATCTCCCTAAGCAGTAGGGGAGTAGGTTGAAGATTGCAG
1 ATTCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG
* * *
38588 ATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 ATTCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGAT
38627 GCTAAATTTT
Statistics
Matches: 163, Mismatches: 35, Indels: 28
0.72 0.15 0.12
Matches are distributed among these distances:
39 4 0.02
40 7 0.04
41 7 0.04
42 24 0.15
43 8 0.05
44 74 0.45
45 39 0.24
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
ATTCTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG
Found at i:48568 original size:19 final size:19
Alignment explanation
Indices: 48544--48582 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
48534 TGAAACAAGG
*
48544 TTAGTACATTGTCAGTCCC
1 TTAGTACATTGCCAGTCCC
48563 TTAGTACATTGCCAGTCCC
1 TTAGTACATTGCCAGTCCC
48582 T
1 T
48583 AACAAGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (19 bp):
TTAGTACATTGCCAGTCCC
Found at i:53106 original size:24 final size:25
Alignment explanation
Indices: 53059--53110 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
53049 TCCCAATTCC
53059 CTCCTTACATCTCACCGCCTTATTT
1 CTCCTTACATCTCACCGCCTTATTT
*
53084 CTCCTT-C-TCTCACCTTCCTTATTT
1 CTCCTTACATCTCACC-GCCTTATTT
53108 CTC
1 CTC
53111 TAAAAATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.12, C:0.42, G:0.02, T:0.44
Consensus pattern (25 bp):
CTCCTTACATCTCACCGCCTTATTT
Found at i:57506 original size:2 final size:2
Alignment explanation
Indices: 57499--57537 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57489 TGATTGGATT
57499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57538 TGTTATTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59735 original size:32 final size:31
Alignment explanation
Indices: 59674--59748 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
59664 TATATGCAAT
59674 ATATATATGCATGGGTTATGTTATATATATA
1 ATATATATGCATGGGTTATGTTATATATATA
* *
59705 ATATATATGCGTGGGTCT-TGATTATATATATC
1 ATATATATGCATGGGT-TATG-TTATATATATA
*
59737 ATATATAAGCAT
1 ATATATATGCAT
59749 ATATGGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 17 0.45
32 21 0.55
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
ATATATATGCATGGGTTATGTTATATATATA
Found at i:60924 original size:18 final size:18
Alignment explanation
Indices: 60874--60924 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
60864 TGATCTGCCA
* *
60874 ATTTTATGCGAATTACTT
1 ATTTTATGAGAACTACTT
* * *
60892 ATTATATGTGCACTACTT
1 ATTTTATGAGAACTACTT
60910 ATTTTATGAGAACTA
1 ATTTTATGAGAACTA
60925 TTGTGTCGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTTATGAGAACTACTT
Done.