Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008340.1 Hibiscus syriacus cultivar Beakdansim tig00111064_pilon, 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: 409852
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:316799 original size:84 final size:84
Alignment explanation
Indices: 316689--317061 Score: 425
Period size: 84 Copynumber: 4.5 Consensus size: 84
316679 TCGGGGGTCT
* *
316689 TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
316754 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * * * * **
316773 TTAGCAAATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGATTGT-G
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
****
316837 ATCGAACTTGGGGGTC---T-
65 -TCGAACTCAAAGGTCTTTTG
* * *
316854 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCATAG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
316918 TCGAACTCAAAGGTCTTTTG
65 TCGAACTCAAAGGTCTTTTG
* * * * ** *
316938 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
317003 CGAACTCGAAGGTCTTTGG
66 CGAACTCAAAGGTCTTTTG
* *
317022 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAAT
317062 AGTTTGTTTT
Statistics
Matches: 237, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
80 20 0.08
81 42 0.18
82 1 0.00
83 3 0.01
84 148 0.62
85 23 0.10
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTTG
Found at i:316890 original size:81 final size:80
Alignment explanation
Indices: 316644--317061 Score: 320
Period size: 84 Copynumber: 5.0 Consensus size: 80
316634 TAAATGATGT
*
316644 AAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGT-ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
316709 ACTTAAGCTACACTGC
65 ACTTAAGCTATACTGC
* * * *** * *
316725 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAAATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTA-TCGAACTCGGGGGTC-TTTG---GCAGATAGCCCTT
* *
316789 CTTGACTTAAGTTATACTGC
61 CTCGACTTAAGCTATACTGC
* *
316809 AAATGATGTGCCCTCGAAGCTGATTGTGATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGT-ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
316874 ACTTAAGCTATGCTGC
65 ACTTAAGCTATACTGC
* * ** *** * *
316890 AAATGATGTGCCGTTG-AGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTA-TCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTT
* * * **
316954 CTAGACTTAAGTTGTGTTGC
61 CTCGACTTAAGCTATACTGC
* * * * ** *
316974 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTA-TCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTT
* *
317038 CTCGACTTAAGTTATGCTGC
61 CTCGACTTAAGCTATACTGC
317058 AAAT
1 AAAT
317062 AGTTTGTTTT
Statistics
Matches: 275, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
79 2 0.01
80 42 0.15
81 56 0.20
83 8 0.03
84 143 0.52
85 23 0.08
86 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATACTGC
Found at i:316921 original size:165 final size:164
Alignment explanation
Indices: 316644--317061 Score: 561
Period size: 165 Copynumber: 2.5 Consensus size: 164
316634 TAAATGATGT
*
316644 AAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGT-ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
** *
316709 ACTTAAGCTACACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
65 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGT
* *
316774 TAGCAAATAACCCTTCTTGACTTAAGTTATACTGC
130 TAGCAAACAACCCTTCTAGACTTAAGTTATACTGC
* *
316809 AAATGATGTGCCCTCGAAGCTGATTGTGATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGT-ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
316874 ACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCATAGTCGAACTCAAAGGTCTTTTG
65 ACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTG
* * * **
316938 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGTTGC
129 TTAGCAAACAACCCTTCTAGACTTAAGTTATACTGC
* * * * ** *
316974 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTA-TCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTT
*
317038 CTCGACTTAAGTTATGCTGCAAAT
61 CTCGACTTAAGCTATGCTGCAAAT
317062 AGTTTGTTTT
Statistics
Matches: 223, Mismatches: 24, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
163 1 0.00
164 24 0.11
165 157 0.70
166 3 0.01
168 38 0.17
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTT
AGCAAACAACCCTTCTAGACTTAAGTTATACTGC
Found at i:320488 original size:18 final size:19
Alignment explanation
Indices: 320447--320491 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
320437 AGTTAATGTG
320447 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
320466 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
320484 AATGCAAA
1 AATGCAAA
320492 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:322261 original size:31 final size:32
Alignment explanation
Indices: 322226--322352 Score: 104
Period size: 36 Copynumber: 3.9 Consensus size: 32
322216 TAAATACGAA
*
322226 ATAAATAAACAACATAA-AAAATAAAAAAATG
1 ATAAATAAACAAAATAACAAAATAAAAAAATG
* *
322257 ATAAAGTAAAGAGAAATAAACAAAATAAATAGAATG
1 ATAAA-TAAACA-AAAT-AACAAAATAAA-AAAATG
* *
322293 ATAAAATAAACAAAAATAA-AACATACAAAAAA-A
1 AT-AAATAAAC-AAAATAACAAAATA-AAAAAATG
322326 AT-AATAAAC-AAA-AACAAAATAAAAAAA
1 ATAAATAAACAAAATAACAAAATAAAAAAA
322353 CAAAGGAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
28 8 0.10
29 8 0.10
31 12 0.15
32 5 0.06
33 5 0.06
34 10 0.13
35 12 0.15
36 15 0.19
37 4 0.05
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (32 bp):
ATAAATAAACAAAATAACAAAATAAAAAAATG
Found at i:322313 original size:15 final size:15
Alignment explanation
Indices: 322293--322352 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
322283 AAATAGAATG
322293 ATAAAATAAACAAAA
1 ATAAAATAAACAAAA
* *
322308 ATAAAACATACAAAA
1 ATAAAATAAACAAAA
*
322323 AAAATAATAAACAAAA
1 ATAA-AATAAACAAAA
*
322339 ACAAAATAAA-AAAA
1 ATAAAATAAACAAAA
322353 CAAAGGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 4 0.11
15 22 0.58
16 12 0.32
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (15 bp):
ATAAAATAAACAAAA
Found at i:323995 original size:32 final size:32
Alignment explanation
Indices: 323957--324311 Score: 109
Period size: 33 Copynumber: 11.0 Consensus size: 32
323947 AAAATAAAAT
323957 ACTATATAATAT-ATTTAAAAAAATGTTTTAAA
1 ACTATATAATATAATTT-AAAAAATGTTTTAAA
* * *
323989 AC--TAT-ATAT--TTCAAAATAT-TTTCAAA
1 ACTATATAATATAATTTAAAAAATGTTTTAAA
* * *
324015 ACCATATACTATAATTTTAAAAATGTTTTAAA
1 ACTATATAATATAATTTAAAAAATGTTTTAAA
* ** * *
324047 ACTCTATGTTATAATTTTCAAAAACGTTTTAAA
1 ACTATATAATATAA-TTTAAAAAATGTTTTAAA
* * ** *
324080 ACTATAT-GTTTCAA---AAAAAA-AATTT-CA
1 ACTATATAATAT-AATTTAAAAAATGTTTTAAA
*
324107 ACTATAT-ATATAAATTT--CAAATGATTTTAAA
1 ACTATATAATAT-AATTTAAAAAATG-TTTTAAA
* **
324138 ACTAT-TATTATAAGTTTTCAAAATGGTTTTAAAA
1 ACTATATAATATAA-TTTAAAAAAT-GTTTT-AAA
* * *
324172 ACTATAT-ATAT-ATGGTTCAAAAATATCTTCAAA
1 ACTATATAATATAAT--TTAAAAAATGT-TTTAAA
**
324205 ACTATATAATATGTTTTCAAAAAAATGTTTTCAAA
1 ACTATATAATATAATTT--AAAAAATGTTTT-AAA
** *
324240 ACTATAATATATATGTTTTCAAAAATGTTTTCAAAA
1 ACTAT-ATA-ATATAATTTAAAAAATGTTTT--AAA
* **
324276 ATTATATATATATAAGTTTTCAAAATGATTTTAAA
1 ACTATATA-ATATAA-TTTAAAAAATG-TTTTAAA
324311 A
1 A
324312 ATTATATATT
Statistics
Matches: 243, Mismatches: 46, Indels: 65
0.69 0.13 0.18
Matches are distributed among these distances:
26 8 0.03
27 18 0.07
28 11 0.05
29 12 0.05
30 9 0.04
31 19 0.08
32 21 0.09
33 46 0.19
34 27 0.11
35 40 0.16
36 19 0.08
37 13 0.05
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (32 bp):
ACTATATAATATAATTTAAAAAATGTTTTAAA
Found at i:324015 original size:26 final size:27
Alignment explanation
Indices: 323965--324022 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
323955 ATACTATATA
* *
323965 ATATATTTAAAAAAATGTTTTAAAACT
1 ATATATTTAAAAAAATGTTTCAAAACC
* *
323992 ATATATTTCAAAATAT-TTTCAAAACC
1 ATATATTTAAAAAAATGTTTCAAAACC
324018 ATATA
1 ATATA
324023 CTATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATATTTAAAAAAATGTTTCAAAACC
Found at i:324076 original size:91 final size:89
Alignment explanation
Indices: 323975--324180 Score: 220
Period size: 91 Copynumber: 2.3 Consensus size: 89
323965 ATATATTTAA
* * * *
323975 AAAAATGTTTTAAAACTATATATTTC-AAAATATTTTCAAAACCATATACTATAATTTTAAAAAT
1 AAAAACGTTTTAAAACTATATATTTCAAAAAAAATTTC--AACCATATA-TATAAATTT-AAAAT
* *
324039 G-TTTTAAAACTCTATGTTATAA-TTTTC
62 GATTTTAAAACTAT-TATTATAAGTTTTC
* * *
324066 AAAAACGTTTTAAAACTATATGTTTCAAAAAAAAAATTTCAACTATATATATAAATTTCAAATGA
1 AAAAACGTTTTAAAACTATATATTTC--AAAAAAAATTTCAACCATATATATAAATTTAAAATGA
324131 TTTTAAAACTATTATTATAAGTTTTC
64 TTTTAAAACTATTATTATAAGTTTTC
**
324157 AAAATGGTTTTAAAAACTATATAT
1 AAAAACGTTTT-AAAACTATATAT
324181 ATATGGTTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
90 12 0.12
91 57 0.59
92 19 0.20
94 9 0.09
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (89 bp):
AAAAACGTTTTAAAACTATATATTTCAAAAAAAATTTCAACCATATATATAAATTTAAAATGATT
TTAAAACTATTATTATAAGTTTTC
Found at i:324238 original size:35 final size:34
Alignment explanation
Indices: 324125--324400 Score: 199
Period size: 35 Copynumber: 7.8 Consensus size: 34
324115 TATAAATTTC
*
324125 AAATGATTTT-AAAACTAT-TATTATAAGTTTTC-A
1 AAATG-TTTTCAAAACTATATA-TATATGTTTTCAA
* *
324158 AAATGGTTTTAAAAACTATATATATATG-GTTCAA
1 AAAT-GTTTTCAAAACTATATATATATGTTTTCAA
* *
324192 AAATATCTTCAAAACTATATA-ATATGTTTTCAAAA
1 AAATGTTTTCAAAACTATATATATATGTTTTC--AA
324227 AAATGTTTTCAAAACTATAATATATATGTTTTCAA
1 AAATGTTTTCAAAACTAT-ATATATATGTTTTCAA
*
324262 AAATGTTTTCAAAAATTATATATATATAAGTTTTC-A
1 AAATGTTTTC-AAAACTATATATATAT--GTTTTCAA
* * *
324298 AAATGATTTTAAAAATTATATATTATATATATTTTCTAA
1 AAATG-TTTTCAAAA--CTATA-TATATATGTTTTC-AA
*
324337 AAATGTTATTTTTAAAACTATATATTATATAGTTTT-AA
1 AAATG---TTTTCAAAACTATATA-TATAT-GTTTTCAA
* * *
324375 AAA-CTATTAAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATA-TATAT
324401 ACGTAGTTTC
Statistics
Matches: 203, Mismatches: 18, Indels: 43
0.77 0.07 0.16
Matches are distributed among these distances:
32 5 0.02
33 28 0.14
34 39 0.19
35 40 0.20
36 20 0.10
37 25 0.12
38 11 0.05
39 22 0.11
40 4 0.02
41 9 0.04
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (34 bp):
AAATGTTTTCAAAACTATATATATATGTTTTCAA
Found at i:324269 original size:12 final size:12
Alignment explanation
Indices: 324252--324277 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
324242 TATAATATAT
324252 ATGTTTTCAAAA
1 ATGTTTTCAAAA
324264 ATGTTTTCAAAA
1 ATGTTTTCAAAA
324276 AT
1 AT
324278 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:324312 original size:36 final size:36
Alignment explanation
Indices: 324106--324415 Score: 214
Period size: 37 Copynumber: 8.8 Consensus size: 36
324096 AAAAAATTTC
324106 AACTATATATATA-AA--TTTC-AAATGATTTT-AA
1 AACTATATATATATAAGTTTTCAAAATGATTTTAAA
*
324137 AACTAT-TAT-TATAAGTTTTCAAAATGGTTTTAAA
1 AACTATATATATATAAGTTTTCAAAATGATTTTAAA
* * *
324171 AACTATATATATAT--G-GTTCAAAAAT-ATCTTCAA
1 AACTATATATATATAAGTTTTC-AAAATGATTTTAAA
*
324204 AACTATATA-ATAT--GTTTTCAAAAAAATG-TTTTCAA
1 AACTATATATATATAAGTTTTC---AAAATGATTTTAAA
*
324239 AACTATA-ATATATATGTTTTCAAAAATG-TTTTCAAA
1 AACTATATATATATAAGTTTTC-AAAATGATTTT-AAA
*
324275 AATTATATATATATAAGTTTTCAAAATGATTTTAAA
1 AACTATATATATATAAGTTTTCAAAATGATTTTAAA
* *
324311 AATTATATATTATATATA-TTTTCTAAAAATGTTATTTTTAA
1 AACTATATA-TATATA-AGTTTTC--AAAATG--ATTTTAAA
*
324352 AACTATATAT-TATATAGTTTT-AAAA--ACTATTAAA
1 AACTATATATATATA-AGTTTTCAAAATGA-TTTTAAA
*
324386 AACTATATATTATATACGTAGTTTCAAAAT
1 AACTATATA-TATATAAGT--TTTCAAAAT
324416 ATGTATATAT
Statistics
Matches: 232, Mismatches: 15, Indels: 56
0.77 0.05 0.18
Matches are distributed among these distances:
29 2 0.01
30 5 0.02
31 6 0.03
32 9 0.04
33 30 0.13
34 29 0.12
35 40 0.17
36 33 0.14
37 41 0.18
38 5 0.02
39 12 0.05
40 5 0.02
41 15 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
AACTATATATATATAAGTTTTCAAAATGATTTTAAA
Found at i:324362 original size:16 final size:17
Alignment explanation
Indices: 324322--324362 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
324312 ATTATATATT
324322 ATATATATTTTCTAAAA
1 ATATATATTTTCTAAAA
*
324339 ATGT-TATTTT-TAAAA
1 ATATATATTTTCTAAAA
*
324354 CTATATATT
1 ATATATATT
324363 ATATAGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 10 0.50
17 3 0.15
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATATATTTTCTAAAA
Found at i:329099 original size:172 final size:172
Alignment explanation
Indices: 328835--329175 Score: 603
Period size: 172 Copynumber: 2.0 Consensus size: 172
328825 AGTTTAGTTA
*
328835 CTAAAACAAACTAAAACTGATAGTTCAAGTACTAATGCGTAGTTTACCCGAAAATAGTGAGCGTG
1 CTAAAACAAACTAAAACTGATAATTCAAGTACTAATGCGTAGTTTACCCGAAAATAGTGAGCGTG
*
328900 GCCTATTGTCTAATGAGCTTAAAATAACCAAACGACATCGTATAGAAATCAAAATTATACACAAA
66 GCCTATTGTCTAATGAGCTTAAAATAACCAAACGACATCGAATAGAAATCAAAATTATACACAAA
* *
328965 GGTGCAAATGACACCGCTTGGAAAATAAATAATTAAAATGGC
131 GGTGCAAACGACACCGCTTGGAAAAGAAATAATTAAAATGGC
* *
329007 CTAAAACAAAC-AAAATTGATAATTTAAGTACTAAATGCGTAGTTTACCCGAAAATAGTGAGCGT
1 CTAAAACAAACTAAAACTGATAATTCAAGTACT-AATGCGTAGTTTACCCGAAAATAGTGAGCGT
329071 GGCCTATTGTCTAATGAGCTTAAAATAACCAAACGACATCGAATAGAAATCAAAATTATACACAA
65 GGCCTATTGTCTAATGAGCTTAAAATAACCAAACGACATCGAATAGAAATCAAAATTATACACAA
*
329136 AGGTGCAAACGACATCGCTTGGAAAAGAAATAATTAAAAT
130 AGGTGCAAACGACACCGCTTGGAAAAGAAATAATTAAAAT
329176 AGCCCATGCA
Statistics
Matches: 161, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
171 18 0.11
172 143 0.89
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (172 bp):
CTAAAACAAACTAAAACTGATAATTCAAGTACTAATGCGTAGTTTACCCGAAAATAGTGAGCGTG
GCCTATTGTCTAATGAGCTTAAAATAACCAAACGACATCGAATAGAAATCAAAATTATACACAAA
GGTGCAAACGACACCGCTTGGAAAAGAAATAATTAAAATGGC
Found at i:335326 original size:21 final size:21
Alignment explanation
Indices: 335297--335351 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
335287 CGTGGGGGGT
*
335297 ATCGATTCCCTC-AAGGAGGGA
1 ATCGGTTCCCTCAAAGGA-GGA
335318 ATCGGTTCCCATTCAAAGGAGGA
1 ATCGGTTCCC--TCAAAGGAGGA
335341 ATCGGTTCCCT
1 ATCGGTTCCCT
335352 TATGGGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.33
23 15 0.50
24 5 0.17
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (21 bp):
ATCGGTTCCCTCAAAGGAGGA
Found at i:335369 original size:20 final size:20
Alignment explanation
Indices: 335291--335371 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
335281 AGAACCCGTG
* *
335291 GGGGGTATCGATTCCCTCAA
1 GGGGGAATCGATTCCCTTAA
*
335311 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCC-TT--AA
* * *
335335 GGAGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAA
*
335355 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
335372 CTGCCAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 17 0.35
21 12 0.24
22 3 0.06
23 13 0.27
24 4 0.08
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAA
Found at i:344432 original size:36 final size:36
Alignment explanation
Indices: 344385--344463 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
344375 AGATTTTGGA
*
344385 CACTTAGGAGAGAATTAGGTTTAGCTGACCTATCTT
1 CACTTAGGAGAGAATTAGGTTTAACTGACCTATCTT
344421 CACTTAGGAGAGAATTAGGTTTAACTGACCTATCTT
1 CACTTAGGAGAGAATTAGGTTTAACTGACCTATCTT
344457 CACTTAG
1 CACTTAG
344464 TGTTTAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (36 bp):
CACTTAGGAGAGAATTAGGTTTAACTGACCTATCTT
Found at i:346794 original size:25 final size:25
Alignment explanation
Indices: 346764--346826 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
346754 TATTTTTATT
346764 TTGGATGTTTGAATTTGTTGGATGA
1 TTGGATGTTTGAATTTGTTGGATGA
346789 TTGGATGTTTGAATTTGTTGGATGA
1 TTGGATGTTTGAATTTGTTGGATGA
*
346814 TTGAATGTTTGAA
1 TTGGATGTTTGAA
346827 CTTAATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (25 bp):
TTGGATGTTTGAATTTGTTGGATGA
Found at i:351987 original size:60 final size:59
Alignment explanation
Indices: 351923--352048 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
351913 ATATGTCCCT
* * * * *
351923 AAACTATAACCCTGATTTTAAATTGATT-TTTAAACTTTGGAATATTTTAATTTTATCCTC
1 AAACTAT-ACCCTCATTCTAAATT-ATTACTTAAACTTTGGAACATTTTAATTTCATCCTC
** * * *
351983 AAACTATACTTTCATTCTAAATTATTACTTAAACTTTTGAACATTTTAGTTTCATCCTT
1 AAACTATACCCTCATTCTAAATTATTACTTAAACTTTGGAACATTTTAATTTCATCCTC
352042 AAACTAT
1 AAACTAT
352049 GACTCACTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 3 0.05
59 45 0.82
60 7 0.13
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (59 bp):
AAACTATACCCTCATTCTAAATTATTACTTAAACTTTGGAACATTTTAATTTCATCCTC
Found at i:353495 original size:21 final size:21
Alignment explanation
Indices: 353462--353511 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
353452 CCGAATTGCT
353462 ACATAGAATGTCCCGAAGGACC
1 ACATAG-ATGTCCCGAAGGACC
353484 ACATAGATGTCCCGAAGGACC
1 ACATAGATGTCCCGAAGGACC
*
353505 ACGTAGA
1 ACATAGA
353512 AATGTCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (21 bp):
ACATAGATGTCCCGAAGGACC
Found at i:353555 original size:23 final size:23
Alignment explanation
Indices: 353529--353585 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
353519 TGCATAGATG
*
353529 TCCTGAAGGACCATGTAGAAA-TA
1 TCCTGAAGGACCACGTA-AAATTA
353552 TCCTGAAGGACCACGTAAAATTA
1 TCCTGAAGGACCACGTAAAATTA
*
353575 TCCCGAAGGAC
1 TCCTGAAGGAC
353586 TGCGTAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TCCTGAAGGACCACGTAAAATTA
Found at i:354953 original size:4 final size:4
Alignment explanation
Indices: 354944--354972 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
354934 ATCTCTGATT
354944 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
354973 CCCCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:358671 original size:88 final size:89
Alignment explanation
Indices: 358518--358686 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 89
358508 TGTCGATGTA
* * * * * *
358518 ATGAGTTTCAAGTTACTGTAATAAATGTCGTAAATCTCAAATTAATTTTTAAGATGATCTTATAG
1 ATGAGTTTCAAGTTAATGCAACAAATGTCGCAAATCTCAAATTAATTATGAAGATGATCTTATAG
358583 GCCAATTTTTTTACCCACGATATG
66 GCCAATTTTTTTACCCACGATATG
* * *
358607 ATGAGTTTTAAGTTAATGCAACAAATGT-GCAGATCTCAAATTAATTATGGAGATGA-CTTAATA
1 ATGAGTTTCAAGTTAATGCAACAAATGTCGCAAATCTCAAATTAATTATGAAGATGATCTT-ATA
358670 GGCCAATTTTTTTACCC
65 GGCCAATTTTTTTACCC
358687 GCATGGTCTA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 3 0.04
88 43 0.61
89 24 0.34
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (89 bp):
ATGAGTTTCAAGTTAATGCAACAAATGTCGCAAATCTCAAATTAATTATGAAGATGATCTTATAG
GCCAATTTTTTTACCCACGATATG
Found at i:363806 original size:24 final size:24
Alignment explanation
Indices: 363777--363825 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
363767 TAATATATAT
363777 TAAAATAATATATGAAGTTGATAA
1 TAAAATAATATATGAAGTTGATAA
363801 TAAAATAATATATGAAGTTGATAA
1 TAAAATAATATATGAAGTTGATAA
363825 T
1 T
363826 TATTCTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
TAAAATAATATATGAAGTTGATAA
Found at i:364469 original size:14 final size:14
Alignment explanation
Indices: 364458--364517 Score: 120
Period size: 14 Copynumber: 4.3 Consensus size: 14
364448 ACATCAATTG
364458 TCGTAAATCAATAA
1 TCGTAAATCAATAA
364472 TCGTAAATCAATAA
1 TCGTAAATCAATAA
364486 TCGTAAATCAATAA
1 TCGTAAATCAATAA
364500 TCGTAAATCAATAA
1 TCGTAAATCAATAA
364514 TCGT
1 TCGT
364518 TTAAGTTCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (14 bp):
TCGTAAATCAATAA
Found at i:364891 original size:23 final size:23
Alignment explanation
Indices: 364866--364919 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
364856 AACATGTTTA
* *
364866 AAAATAAAACTT-AAAATAAATG
1 AAAATAAAACTTGAAAAGAAAAG
364888 AAAATGAAAACTTGAAAAGAAAAG
1 AAAAT-AAAACTTGAAAAGAAAAG
364912 AAAATAAA
1 AAAATAAA
364920 GAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 5 0.18
23 10 0.36
24 13 0.46
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (23 bp):
AAAATAAAACTTGAAAAGAAAAG
Found at i:365700 original size:2 final size:2
Alignment explanation
Indices: 365693--365721 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
365683 TATAAGACAT
365693 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 T
365722 TTAAACACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:366332 original size:54 final size:54
Alignment explanation
Indices: 366269--366748 Score: 617
Period size: 54 Copynumber: 8.9 Consensus size: 54
366259 AATATGGAAA
* * * * * * *
366269 TTCACAAACTCATTTTGAAATCCTTGGGGTGCACA-TATAGGGCCGATACGGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACT-TAGTGCCGATACGGTCG
* * * *
366323 TTCACAAACTCATTGTGAATTTCGTAGGTTGCACACTTAGTGCCGATACGGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
366377 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
*
366431 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACAGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* *
366485 TTCATAAACAT-ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGATCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* *
366539 TTCATAAACTCATTATGAATTCCGTGGGTTTCACACTTAGTGCCGATACGGTGG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
** * * * *
366593 TTCATAAACAT-ATTATGAATTATGTTGGTTGCACACTTAGTACCTATACGGTCA
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * * * **
366647 CTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGACGATACGGTTA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * *
366701 TTCATTAACAT-ATTATGAATTCAGTGGGTTACACACTTAGTGCCGATA
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATA
366749 ATACACATAG
Statistics
Matches: 380, Mismatches: 40, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.01
54 374 0.98
55 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
Found at i:368453 original size:2 final size:2
Alignment explanation
Indices: 368446--368487 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
368436 TGAAAATGAG
368446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
368488 GCATGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:369378 original size:65 final size:65
Alignment explanation
Indices: 369305--369542 Score: 343
Period size: 65 Copynumber: 3.7 Consensus size: 65
369295 CATCATAGAT
* * *
369305 TCCACCTCATGCACTACAAAGGTACACGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
1 TCCACCTCATGCACCACAAAGATACATGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
* *
369370 TCCACCTCATGCACCACAAAGATACATAAGTAATATGAGTGGTCTA-TACAATATTCAATTATCA
1 TCCACCTCATGCACCACAAAGATACATGAGTAATATGAGTGATC-AGTACAATATTCAATTATCA
369434 C
65 C
* * * ** *
369435 TCCACCTCATGCACCACAAAGGTACATGAGTTATATTAGTGATTTGTACATTATTCAATTATCAC
1 TCCACCTCATGCACCACAAAGATACATGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
* *
369500 TCCACCTCATACACCACAAAGATACATGAGTCATATGAGTGAT
1 TCCACCTCATGCACCACAAAGATACATGAGTAATATGAGTGAT
369543 ATGTGACGTA
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
65 153 0.99
66 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (65 bp):
TCCACCTCATGCACCACAAAGATACATGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
Found at i:369538 original size:130 final size:130
Alignment explanation
Indices: 369305--369540 Score: 382
Period size: 130 Copynumber: 1.8 Consensus size: 130
369295 CATCATAGAT
*
369305 TCCACCTCATGCACTACAAAGGTACACGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
1 TCCACCTCATGCACCACAAAGGTACACGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
*
369370 TCCACCTCATGCACCACAAAGATACATAAGTAATATGAGTGGTCTATACAATATTCAATTATCAC
66 TCCACCTCATACACCACAAAGATACATAAGTAATATGAGTGGTCTATACAATATTCAATTATCAC
* * * ** *
369435 TCCACCTCATGCACCACAAAGGTACATGAGTTATATTAGTGATTTGTACATTATTCAATTATCAC
1 TCCACCTCATGCACCACAAAGGTACACGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
* *
369500 TCCACCTCATACACCACAAAGATACATGAGTCATATGAGTG
66 TCCACCTCATACACCACAAAGATACATAAGTAATATGAGTG
369541 ATATGTGACG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 96 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (130 bp):
TCCACCTCATGCACCACAAAGGTACACGAGTAATATGAGTGATCAGTACAATATTCAATTATCAC
TCCACCTCATACACCACAAAGATACATAAGTAATATGAGTGGTCTATACAATATTCAATTATCAC
Found at i:372573 original size:29 final size:29
Alignment explanation
Indices: 372538--372619 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
372528 AAACTAAATT
*
372538 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
372567 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
372596 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
372620 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:377334 original size:29 final size:29
Alignment explanation
Indices: 377299--377380 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
377289 AAACTAAATT
*
377299 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
377328 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
377357 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
377381 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:379044 original size:53 final size:53
Alignment explanation
Indices: 378986--379092 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
378976 AGGTAATGAC
*
378986 ACATCAATATTAAACATAATTAAAAATATCATGTCATCATCACAATAATTTTT
1 ACATCAATATTAAAAATAATTAAAAATATCATGTCATCATCACAATAATTTTT
*
379039 ACATCAATATTAAAAATAATTAAAAATATCATGTCATCATCACAGTAATTTTT
1 ACATCAATATTAAAAATAATTAAAAATATCATGTCATCATCACAATAATTTTT
379092 A
1 A
379093 ATAGTAGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.36
Consensus pattern (53 bp):
ACATCAATATTAAAAATAATTAAAAATATCATGTCATCATCACAATAATTTTT
Found at i:381588 original size:17 final size:17
Alignment explanation
Indices: 381566--381600 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
381556 TAATTTGCAC
381566 ATTGCTACTAATCGTAT
1 ATTGCTACTAATCGTAT
381583 ATTGCTACTAATCGTAT
1 ATTGCTACTAATCGTAT
381600 A
1 A
381601 ATTTTTCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (17 bp):
ATTGCTACTAATCGTAT
Found at i:387790 original size:23 final size:23
Alignment explanation
Indices: 387764--387808 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
387754 CACCACAGCT
*
387764 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
387787 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
387809 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:387951 original size:25 final size:25
Alignment explanation
Indices: 387923--387991 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
387913 TATATATATA
387923 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
387948 TCCCGAAGGACCGCATAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
* *
387973 TCCCGAATGATCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
387992 CCCTCTACTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:389667 original size:21 final size:21
Alignment explanation
Indices: 389643--389687 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
389633 TGTTGTTCGT
* *
389643 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
389664 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
389685 TTG
1 TTG
389688 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:393124 original size:25 final size:25
Alignment explanation
Indices: 393096--393164 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
393086 TATATATATA
*
393096 TCCCGAAAGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
393121 TCCCGAAGGACCGCATAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
393146 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
393165 CCCTCTACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:394854 original size:21 final size:21
Alignment explanation
Indices: 394830--394874 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
394820 TGTTGTTCGT
* *
394830 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
394851 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
394872 TTG
1 TTG
394875 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:397142 original size:14 final size:15
Alignment explanation
Indices: 397109--397170 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 15
397099 AAGGACCGAA
397109 AATTAATAATAATAT
1 AATTAATAATAATAT
397124 AATTAA-AATAAT-T
1 AATTAATAATAATAT
397137 ACATTAATTAA-AA-A-
1 A-ATTAA-TAATAATAT
397151 AATTAGATAATAATAAT
1 AATTA-ATAATAAT-AT
397168 AAT
1 AAT
397171 ACTAACAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
13 9 0.24
14 15 0.39
15 8 0.21
16 3 0.08
17 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
AATTAATAATAATAT
Found at i:397832 original size:31 final size:31
Alignment explanation
Indices: 397792--397864 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
397782 AGGTGAATTT
* * *
397792 GTCAGAAATTTGTGACGGTTCTACATATTCC
1 GTCACAAATTTATGACGGGTCTACATATTCC
* *
397823 GTCACAAATTTATGATGGGTCTACATATTTC
1 GTCACAAATTTATGACGGGTCTACATATTCC
*
397854 ATCACAAATTT
1 GTCACAAATTT
397865 TAAAAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (31 bp):
GTCACAAATTTATGACGGGTCTACATATTCC
Found at i:398492 original size:20 final size:20
Alignment explanation
Indices: 398469--398514 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
398459 ACTTCACCAA
*
398469 TGATCCCCAACTTTCAGAAG
1 TGATCCCCAACTTTCAAAAG
*
398489 TGATCCTCAACTTTCAAAAG
1 TGATCCCCAACTTTCAAAAG
398509 TGATCC
1 TGATCC
398515 AAGGTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (20 bp):
TGATCCCCAACTTTCAAAAG
Found at i:399006 original size:48 final size:48
Alignment explanation
Indices: 398928--399022 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
398918 TAAAAAAAAA
* * * *
398928 TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTTTTTAT
1 TTCCGACGGAATCATTATCCCATCACAAATTAAATTGATATATTTTAT
* *
398976 TTCCGACGGAATGATTATTCCATCACAAATTAAATTGATATATTTTA
1 TTCCGACGGAATCATTATCCCATCACAAATTAAATTGATATATTTTA
399023 ATTAAAGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (48 bp):
TTCCGACGGAATCATTATCCCATCACAAATTAAATTGATATATTTTAT
Found at i:399096 original size:107 final size:105
Alignment explanation
Indices: 398858--399086 Score: 287
Period size: 107 Copynumber: 2.1 Consensus size: 105
398848 AAAATAATGT
* * *
398858 ATATTTTTTATTTCCGACGGAATTATTATTCCATCACAAATTAAATTGCTATATTTTAATTAAAA
1 ATATATTTTATTT-C-ACGGAATGATTATTCCATCACAAATTAAATTGATATATTTTAATTAAAA
398923 AAAAATTCCGACGGAATCATTGTCCCGTCATAAATTAAATTG
64 AAAAATTCCGACGGAATCATTGTCCCGTCATAAATTAAATTG
*
398965 ATATTTTTTATTTCCGACGGAATGATTATTCCATCACAAATTAAATTGATATATTTTAATTAAAG
1 ATATATTTTATTT-C-ACGGAATGATTATTCCATCACAAATTAAATTGATATATTTTAATTAAA-
** * *
399030 TTAAACACAATTTTTGACGGAATCATTGTCTCGTCATAAATTAAATTA
63 --AAA-A-AA-TTCCGACGGAATCATTGTCCCGTCATAAATTAAATTG
*
399078 ATATTTTTT
1 ATATATTTT
399087 TACTTAATGA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
107 62 0.56
110 3 0.03
111 1 0.01
112 2 0.02
113 42 0.38
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (105 bp):
ATATATTTTATTTCACGGAATGATTATTCCATCACAAATTAAATTGATATATTTTAATTAAAAAA
AAATTCCGACGGAATCATTGTCCCGTCATAAATTAAATTG
Found at i:399723 original size:73 final size:72
Alignment explanation
Indices: 399604--399751 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 72
399594 CTAGTCAGCG
* *
399604 TGGAAGTCATTCCAATGCACGTAGAGTTAATAGTGAAGGAGGACAAGAAGCTGAAACAAAATACA
1 TGGAAGTCATTCCAATGCACGTAGAGCTAATAGTGAAGGAAGACAAGAAGCTGAAAC-AAATACA
399669 ACATGTTC
65 ACATGTTC
*
399677 TGGAAGTCATTCCAATGCACGTAGAGCTAATATTGAAGGAAGACAAGAAGCTGAAACAAATACAA
1 TGGAAGTCATTCCAATGCACGTAGAGCTAATAGTGAAGGAAGACAAGAAGCTGAAACAAATACAA
*
399742 CCTGTTC
66 CATGTTC
399749 TGG
1 TGG
399752 CAGTAGTCCT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 17 0.24
73 54 0.76
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (72 bp):
TGGAAGTCATTCCAATGCACGTAGAGCTAATAGTGAAGGAAGACAAGAAGCTGAAACAAATACAA
CATGTTC
Found at i:405102 original size:31 final size:31
Alignment explanation
Indices: 405067--405130 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
405057 ATTATCATAA
* * * *
405067 TTGTAATAGTTTGATAATTTTAATAATCATT
1 TTGTAACAGTTTAATAAATATAATAATCATT
405098 TTGTAACAGTTTAATAAATATAATAATCATT
1 TTGTAACAGTTTAATAAATATAATAATCATT
405129 TT
1 TT
405131 ACATTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (31 bp):
TTGTAACAGTTTAATAAATATAATAATCATT
Found at i:408156 original size:13 final size:14
Alignment explanation
Indices: 408131--408160 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
408121 AAACATCAAC
408131 TTAGAGTTTATAAG
1 TTAGAGTTTATAAG
408145 TTAGAG-TTATAAG
1 TTAGAGTTTATAAG
408158 TTA
1 TTA
408161 AAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (14 bp):
TTAGAGTTTATAAG
Found at i:409358 original size:19 final size:18
Alignment explanation
Indices: 409323--409365 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
409313 CGATATACCA
409323 GGTAAAAATGATAAAAACC
1 GGTAAAAATGATAAAAA-C
409342 GGTAACAAATGAT-AAAAC
1 GGTAA-AAATGATAAAAAC
409360 GGTAAA
1 GGTAAA
409366 TTTAAAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 6 0.26
19 9 0.39
20 7 0.30
ACGTcount: A:0.56, C:0.09, G:0.19, T:0.16
Consensus pattern (18 bp):
GGTAAAAATGATAAAAAC
Found at i:409502 original size:20 final size:19
Alignment explanation
Indices: 409479--409524 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
409469 CGATATAACA
*
409479 GGTAAAAAATAGATAAAACC
1 GGTAAAAAAT-GATAAAAAC
*
409499 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
409519 GGTAAA
1 GGTAAA
409525 TGATACCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:409517 original size:21 final size:20
Alignment explanation
Indices: 409484--409522 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
409474 TAACAGGTAA
409484 AAAATAGATAAAACCGGTATC
1 AAAATAGATAAAA-CGGTATC
409505 AAAAT-GATAAAAACGGTA
1 AAAATAGAT-AAAACGGTA
409523 AATGATACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (20 bp):
AAAATAGATAAAACGGTATC
Done.