Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3844254 original size:66 final size:66
Alignment explanation
Indices: 3844168--3844493 Score: 508
Period size: 66 Copynumber: 4.9 Consensus size: 66
3844158 GAATACCATG
* * *
3844168 AGTGGCACATTTTATGCCGATAATGCACCATTATGCATTATTCAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
3844233 T
66 T
*
3844234 AGTGGCACCTTTTATACCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
3844299 T
66 T
* * * *
3844300 AGTGGCACCTTTTAGGTCGATAATGCACCGTTATTCATTAATCAAAATCGATCAATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
3844365 T
66 T
* *
3844366 AGTGGCACCTTTTATGCTGATAATGCATCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
3844431 T
66 T
* * * * * *
3844432 AGTGGCACCTTTTATGCTGATAATGTACCATTATGCAATAATCAAAATTGATCAATAATTTT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTT
3844494 TATTCATTCA
Statistics
Matches: 239, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 239 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (66 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
T
Found at i:3847033 original size:15 final size:15
Alignment explanation
Indices: 3846983--3847034 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
3846973 TGAAGCTTAT
* *
3846983 CTTACTAATTCCTAG
1 CTTACCAATTCCTAA
*
3846998 CTTACAAATTCCTAA
1 CTTACCAATTCCTAA
3847013 CTTACCAATTCCTAA
1 CTTACCAATTCCTAA
3847028 CTTACCA
1 CTTACCA
3847035 TTTGGACCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.35
Consensus pattern (15 bp):
CTTACCAATTCCTAA
Found at i:3848191 original size:226 final size:226
Alignment explanation
Indices: 3847811--3848264 Score: 732
Period size: 226 Copynumber: 2.0 Consensus size: 226
3847801 TTGATAATAC
* *
3847811 TGATAACAAATCAAAGTAATTAATCGGTTATGTTATCGTCGAATTTCTAAGGCTCCATCAGCTTA
1 TGATAACAAATCAAAGTAATTAACCGGTTATGTTATCGTCGAATTTATAAGGCTCCATCAGCTTA
*
3847876 AACTTTGGTAACATTTTAAGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTA
66 AACTTTGGTAACATTTTAAGCGTTACCTAATATATTGATAATACTGATAACAAATTAAGTAATTA
*
3847941 ACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCACCAACTTTAAAAAGACATTA-CTTATTATA
131 ACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCACCAAC-TTAAAAAGACACTAGC-TATTATA
3848005 TTACATAAGCGCTACCTAATATGTTATTATGGT
194 TTACATAAGCGCTACCTAATATGTTATTATGGT
3848038 TGATAACAAATC-AAGTAATTAACCGGTTATGTTATCGTCGAATTTATAAGGCTCCATCAGCTTA
1 TGATAACAAATCAAAGTAATTAACCGGTTATGTTATCGTCGAATTTATAAGGCTCCATCAGCTTA
* *
3848102 AACTTTGGTAACATTTTAGGCGTTACCTAATATATTGATAATATTGATAACAAATTAAGTAATTA
66 AACTTTGGTAACATTTTAAGCGTTACCTAATATATTGATAATACTGATAACAAATTAAGTAATTA
* * * * ** * * * *
3848167 ACCTATTTTGTTATCGTTGGATTTCTATGGCTCTATTAGCTTAAAAAGGCGCTAGCTATTATGTT
131 ACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCACCAACTTAAAAAGACACTAGCTATTATATT
3848232 ACATAAGCGCTACCTAATATGTTATTATGGT
196 ACATAAGCGCTACCTAATATGTTATTATGGT
3848263 TG
1 TG
3848265 GTAATGTTTC
Statistics
Matches: 210, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
225 52 0.25
226 146 0.70
227 12 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (226 bp):
TGATAACAAATCAAAGTAATTAACCGGTTATGTTATCGTCGAATTTATAAGGCTCCATCAGCTTA
AACTTTGGTAACATTTTAAGCGTTACCTAATATATTGATAATACTGATAACAAATTAAGTAATTA
ACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCACCAACTTAAAAAGACACTAGCTATTATATT
ACATAAGCGCTACCTAATATGTTATTATGGT
Found at i:3849033 original size:17 final size:17
Alignment explanation
Indices: 3849011--3849051 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3849001 TGTGGTGTCC
3849011 ATCGCAGATGCGGTTGT
1 ATCGCAGATGCGGTTGT
3849028 ATCGCAGATGCGGTTGT
1 ATCGCAGATGCGGTTGT
*
3849045 GTCGCAG
1 ATCGCAG
3849052 TTGCAGACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.27
Consensus pattern (17 bp):
ATCGCAGATGCGGTTGT
Found at i:3853454 original size:3 final size:3
Alignment explanation
Indices: 3853446--3853486 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3853436 TATTTATTTT
*
3853446 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3853487 TAAATGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3856390 original size:21 final size:20
Alignment explanation
Indices: 3856304--3856461 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3856294 AAATGACCAA
**
3856304 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3856323 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3856343 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3856363 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3856384 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3856405 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3856425 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
3856446 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3856462 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3856454 original size:20 final size:20
Alignment explanation
Indices: 3856429--3856622 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
3856419 GATTTTCAAT
* *
3856429 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
3856449 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
3856469 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3856489 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
3856509 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
3856529 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3856549 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
3856569 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
3856590 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
3856610 AATCGCAACGCGA
1 AATCGCAACGCGA
3856623 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:3856474 original size:40 final size:39
Alignment explanation
Indices: 3856429--3856622 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
3856419 GATTTTCAAT
* ** *
3856429 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
3856469 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
3856509 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
3856549 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
3856590 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
3856623 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:3856512 original size:60 final size:60
Alignment explanation
Indices: 3856429--3856621 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3856419 GATTTTCAAT
* ** * *
3856429 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
3856489 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
3856549 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
3856610 AATCGCAACGCG
1 AATCGCAACGCG
3856622 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:3857041 original size:33 final size:33
Alignment explanation
Indices: 3857002--3857072 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3856992 TTCACTTAGA
*
3857002 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3857035 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3857068 TTTCA
1 TTTCA
3857073 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3857212 original size:14 final size:14
Alignment explanation
Indices: 3857193--3857247 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3857183 AGAATGACTG
3857193 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3857207 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
3857226 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3857240 TCGCAACG
1 TCGCAACG
3857248 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3857230 original size:33 final size:33
Alignment explanation
Indices: 3857193--3857263 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3857183 AGAATGACTG
**
3857193 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3857226 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3857259 TCGCA
1 TCGCA
3857264 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3857281 original size:19 final size:19
Alignment explanation
Indices: 3857259--3857356 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3857249 GAAACCAAAA
*
3857259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3857278 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3857292 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3857311 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3857325 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3857344 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3857357 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3857300 original size:14 final size:14
Alignment explanation
Indices: 3857281--3857370 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3857271 TTTCATTTCG
3857281 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3857295 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3857314 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3857328 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3857345 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3857361 CGTTGCGATT
1 CGTTGCGATT
3857371 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3857306 original size:33 final size:33
Alignment explanation
Indices: 3857264--3857378 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3857254 CAAAATCGCA
3857264 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3857297 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3857330 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3857363 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3857379 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3859283 original size:92 final size:93
Alignment explanation
Indices: 3859077--3859454 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
3859067 TAGATTGCTT
*
3859077 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3859142 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3859170 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3859234 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3859262 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3859326 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3859353 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3859418 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3859446 AGTAAATTT
1 AGTAAATTT
3859455 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 72 0.26
92 130 0.46
93 80 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3859557 original size:19 final size:18
Alignment explanation
Indices: 3859498--3859625 Score: 110
Period size: 19 Copynumber: 7.3 Consensus size: 18
3859488 TAGTTTACTT
*
3859498 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
*
3859518 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACAAAA
*
3859536 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
3859555 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
3859569 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
3859588 TCGCAA--CG--ACAAGA
1 TCGCAACGCGAAACAAAA
3859602 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
3859621 TCGCA
1 TCGCA
3859626 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 18 0.20
19 28 0.32
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:3859576 original size:33 final size:32
Alignment explanation
Indices: 3859532--3859625 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
3859522 AACGCGAAAC
**
3859532 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAACCAAAATCGCAACGA
3859564 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAAATCGCAACGA
3859597 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACCAAAATCGCA
3859626 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.05
33 55 0.95
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (32 bp):
CAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:3859643 original size:19 final size:19
Alignment explanation
Indices: 3859621--3859755 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3859611 GAAACCAAAA
*
3859621 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3859640 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3859656 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3859673 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3859689 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3859706 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3859725 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3859745 TCGTGTTGCGA
1 TCGCGTTGCGA
3859756 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3859662 original size:14 final size:14
Alignment explanation
Indices: 3859643--3859699 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3859633 TTTCATTTCG
3859643 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3859657 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3859674 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3859690 CGTTGCGATT
1 CGTTGCGATT
3859700 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3859668 original size:33 final size:33
Alignment explanation
Indices: 3859626--3859718 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3859616 CAAAATCGCA
*
3859626 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3859659 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3859692 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3859719 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3861669 original size:14 final size:14
Alignment explanation
Indices: 3861650--3861685 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3861640 ATTGTTTAAT
3861650 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3861664 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3861678 TGATTTGT
1 TGATTTGT
3861686 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3861866 original size:20 final size:19
Alignment explanation
Indices: 3861824--3861873 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
3861814 GCAACGAGAG
3861824 AATCGCAATGC-GAAATGA
1 AATCGCAATGCGGAAATGA
3861842 AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGGAAATG-A
3861862 AATCGCAATGCG
1 AATCGCAATGCG
3861874 TTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.37
19 6 0.20
20 13 0.43
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGGAAATGA
Found at i:3861920 original size:52 final size:52
Alignment explanation
Indices: 3861880--3862147 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
3861870 TGCGTTTATA
*
3861880 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3861932 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3861984 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3862041 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3862093 ATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
3862146 AT
1 AT
3862148 GTTGGGATTT
Statistics
Matches: 206, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 130 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3861922 original size:33 final size:35
Alignment explanation
Indices: 3861880--3862175 Score: 230
Period size: 33 Copynumber: 8.5 Consensus size: 35
3861870 TGCGTTTATA
3861880 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
3861913 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
3861949 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
3861984 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-CATCTCG-ATTGCGATTTTC
*
3862022 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
3862058 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
3862093 ATTTCGCATTGTGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
* *
3862126 ATTTCCGCATTGCGATT-TTCAT-G-TTGGGATTTTC
1 ATTT-CGCATTGCGATTCATC-TCGATTGCGATTTTC
*
3862160 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
3862176 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 8, Indels: 40
0.83 0.03 0.14
Matches are distributed among these distances:
33 90 0.38
34 28 0.12
35 22 0.09
36 23 0.10
37 3 0.01
38 66 0.28
39 3 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
Found at i:3861926 original size:19 final size:19
Alignment explanation
Indices: 3861902--3862175 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
3861892 GATTATCTCG
3861902 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3861921 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3861940 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3861954 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3861973 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3861992 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3862011 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3862030 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3862049 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3862063 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3862082 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
3862101 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3862115 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3862135 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3862149 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3862168 TTGCGATT
1 TTGCGATT
3862176 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 28 0.12
16 24 0.11
17 21 0.09
18 3 0.01
19 136 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3862024 original size:109 final size:105
Alignment explanation
Indices: 3861880--3862147 Score: 450
Period size: 109 Copynumber: 2.5 Consensus size: 105
3861870 TGCGTTTATA
3861880 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
3861944 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3861984 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
3862049 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3862093 ATTTCGCATTGTGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
3862148 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 94 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3864691 original size:24 final size:23
Alignment explanation
Indices: 3864652--3864697 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3864642 CTGAAACATC
3864652 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
3864675 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
3864698 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:3865396 original size:20 final size:20
Alignment explanation
Indices: 3865371--3865755 Score: 456
Period size: 20 Copynumber: 19.2 Consensus size: 20
3865361 TTCAGTGTGT
* * *
3865371 GATTTACAGATTCTCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865391 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACGCGTTGC
* * *
3865411 GATTTACAGATTCTCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865431 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACGCGTTGC
3865451 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865471 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACGCGTTGC
3865491 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865511 GATTTACGGATACGCATTGC
1 GATTTACGGATACGCGTTGC
3865531 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865551 GATTTACGGATACACGTTGC
1 GATTTACGGATACGCGTTGC
3865571 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
* * *
3865591 GATTTTATGTATTA-TCGTTGC
1 GA-TTTACGGA-TACGCGTTGC
3865612 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
* *
3865632 GATATACGGATACGCATTGC
1 GATTTACGGATACGCGTTGC
**
3865652 GATTTACCCATACGCGTTGC
1 GATTTACGGATACGCGTTGC
*
3865672 GATTTACGGATACACGTTGC
1 GATTTACGGATACGCGTTGC
3865692 GATTTACGGATACGCGTTGC
1 GATTTACGGATACGCGTTGC
* *
3865712 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATACGCGTTGC
* ** *
3865732 GATTTTCATATTCGCGTTGC
1 GATTTACGGATACGCGTTGC
3865752 GATT
1 GATT
3865756 ATTGAAAATC
Statistics
Matches: 319, Mismatches: 35, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 291 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
GATTTACGGATACGCGTTGC
Found at i:3868648 original size:21 final size:21
Alignment explanation
Indices: 3868614--3868653 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3868604 GATGTTGTAT
3868614 AGCCTTTGGAGATG-TTTTGG
1 AGCCTTTGGAGATGATTTTGG
*
3868634 AGCCGTTTGGGGATGATTTT
1 AGCC-TTTGGAGATGATTTT
3868654 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (21 bp):
AGCCTTTGGAGATGATTTTGG
Found at i:3869028 original size:29 final size:29
Alignment explanation
Indices: 3869007--3869064 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
3868997 AAACTTTGAA
3869007 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTAAAGTCCAAAAACA-TTTG
3869036 TAAATTCAATTAAAGTCCAAAAACCATTT
1 TAAATTCAATTAAAGTCCAAAAA-CATTT
3869065 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTAAAGTCCAAAAACATTTG
Found at i:3869054 original size:30 final size:30
Alignment explanation
Indices: 3869007--3869066 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
3868997 AAACTTTGAA
3869007 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
3869036 TAAATTCAATTAAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
3869067 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3870381 original size:19 final size:20
Alignment explanation
Indices: 3870338--3870385 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3870328 TCTAAATCCT
*
3870338 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3870358 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3870377 TTTTCAAAA
1 TTTTCAAAA
3870386 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3871777 original size:21 final size:21
Alignment explanation
Indices: 3871751--3871793 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3871741 TTTCTGGGTT
* *
3871751 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3871772 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3871793 A
1 A
3871794 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3871868 original size:67 final size:67
Alignment explanation
Indices: 3871773--3871922 Score: 205
Period size: 67 Copynumber: 2.2 Consensus size: 67
3871763 ACCCATTCAA
* * *
3871773 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC-TAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTA-AGGGGAATCGATA-CCCCA
3871837 -GGG
64 GGGG
* * *
3871840 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
3871905 GG
66 GG
*
3871907 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
3871923 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 5 0.07
67 67 0.91
68 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTAAGGGGAATCGATACCCCAGG
GG
Found at i:3872256 original size:28 final size:29
Alignment explanation
Indices: 3872223--3872293 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
3872213 CATATTATGA
**
3872223 TACATGACATGAATTTGTATTA-ATGTAT
1 TACATGACATGAATTCATATTATATGTAT
*
3872251 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
3872280 TACATGACATGAAT
1 TACATGACATGAAT
3872294 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 19 0.49
29 20 0.51
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:3872348 original size:30 final size:31
Alignment explanation
Indices: 3872308--3872366 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
3872298 AGAAAAGTTC
*
3872308 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
3872339 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
3872367 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:3872659 original size:22 final size:22
Alignment explanation
Indices: 3872585--3872651 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3872575 TTATGGACAA
3872585 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3872607 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3872629 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3872651 A
1 A
3872652 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:3878658 original size:21 final size:21
Alignment explanation
Indices: 3878632--3878673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3878622 TTTCTGGGTT
* *
3878632 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3878653 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3878674 CGAATATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3878783 original size:66 final size:66
Alignment explanation
Indices: 3878654--3878802 Score: 212
Period size: 66 Copynumber: 2.3 Consensus size: 66
3878644 ACCCATTCAA
* * *
3878654 GGGGAACCGATACCCCTTCACGAATATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAGG
1 GGGGAACCGATACCCCCTCACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
3878719 G
66 G
* *
3878720 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTA-AGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCA-CGAATATGAATTCCAGAATGC-TAGAGGGGAATCGATACCCCCA
3878783 GGG
64 GGG
*
3878786 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
3878803 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
66 43 0.57
67 30 0.40
68 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
G
Found at i:3879161 original size:28 final size:28
Alignment explanation
Indices: 3879098--3879173 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 28
3879088 CATATTATGA
*
3879098 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAA-TTGCATTAAATGTAT
*
3879127 TACATGACATGAATT-CATCTATATGTAT
1 TACATGACATGAATTGCAT-TAAATGTAT
3879155 TACATGACATGAATATGCA
1 TACATGACATGAAT-TGCA
3879174 GAAAAGTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 2 0.05
28 24 0.57
29 14 0.33
30 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (28 bp):
TACATGACATGAATTGCATTAAATGTAT
Found at i:3879531 original size:22 final size:22
Alignment explanation
Indices: 3879457--3879523 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3879447 TTATGGACAA
3879457 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3879479 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3879501 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
3879523 A
1 A
3879524 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:3880771 original size:21 final size:21
Alignment explanation
Indices: 3880721--3880780 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
3880711 ACCGTTGCAG
* *
3880721 CCTTCATGCATGGATGCACAA
1 CCTTGATGCATCGATGCACAA
**
3880742 -CAGGATGCATCGATGCACAA
1 CCTTGATGCATCGATGCACAA
3880762 CCTTGATGCATCGATGCAC
1 CCTTGATGCATCGATGCAC
3880781 TAATTGCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
CCTTGATGCATCGATGCACAA
Found at i:3880992 original size:29 final size:31
Alignment explanation
Indices: 3880960--3881019 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
3880950 AAACTTTGAA
*
3880960 TAAATTCAATT-AAGTCC-AAAAA-CATTTTG
1 TAAAATCAATTCAAG-CCTAAAAACCATTTTG
3880989 TAAAATCAATTCAAGCCTAAAAACCATTTTG
1 TAAAATCAATTCAAGCCTAAAAACCATTTTG
3881020 CATTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 12 0.44
30 8 0.30
31 7 0.26
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (31 bp):
TAAAATCAATTCAAGCCTAAAAACCATTTTG
Found at i:3881324 original size:20 final size:21
Alignment explanation
Indices: 3881301--3881341 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3881291 GTACGTTCGA
3881301 GTTTACGGGTT-AATTTGGAG
1 GTTTACGGGTTCAATTTGGAG
*
3881321 GTTTTCGGGTTCGAATTTGGA
1 GTTTACGGGTTC-AATTTGGA
3881342 AAAACAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.17, C:0.07, G:0.34, T:0.41
Consensus pattern (21 bp):
GTTTACGGGTTCAATTTGGAG
Found at i:3881439 original size:19 final size:19
Alignment explanation
Indices: 3881415--3881452 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3881405 TTGACTTTTT
*
3881415 GGTCAAAGTCAACGTCAAC
1 GGTCAAAGTCAAAGTCAAC
*
3881434 GGTCAAATTCAAAGTCAAC
1 GGTCAAAGTCAAAGTCAAC
3881453 TGGCAGAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (19 bp):
GGTCAAAGTCAAAGTCAAC
Found at i:3881918 original size:13 final size:12
Alignment explanation
Indices: 3881897--3881967 Score: 69
Period size: 13 Copynumber: 5.9 Consensus size: 12
3881887 AAAGATTAGA
3881897 ATAAAATAAAAG
1 ATAAAATAAAAG
3881909 ATAAAGAT-AAA-
1 ATAAA-ATAAAAG
3881920 AT-AAATAAACA-
1 ATAAAATAAA-AG
*
3881931 ATTAAATAAAAG
1 ATAAAATAAAAG
3881943 ATAAGAATAAAAG
1 ATAA-AATAAAAG
3881956 ATAAGAATAAAA
1 ATAA-AATAAAA
3881968 TAAATAATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
9 2 0.04
10 4 0.08
11 6 0.12
12 18 0.35
13 22 0.42
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.18
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:3881971 original size:18 final size:18
Alignment explanation
Indices: 3881880--3881954 Score: 84
Period size: 18 Copynumber: 4.3 Consensus size: 18
3881870 AATTTGTTTT
*
3881880 TAAAATAAAAGATTAGAA
1 TAAAATAAAAGATAAGAA
3881898 TAAAATAAAAGATAA-AGA
1 TAAAATAAAAGATAAGA-A
* *
3881916 TAAAAT-AAATA-AACAA
1 TAAAATAAAAGATAAGAA
*
3881932 TTAAATAAAAGATAAGAA
1 TAAAATAAAAGATAAGAA
3881950 TAAAA
1 TAAAA
3881955 GATAAGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.17
17 10 0.21
18 29 0.62
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAGATAAGAA
Found at i:3882364 original size:36 final size:36
Alignment explanation
Indices: 3882313--3882381 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
3882303 GGACCACCGG
*
3882313 TAAGTTTGTTTACATGAAGTCGAACTTGCTACCCGC
1 TAAGTTTGTTCACATGAAGTCGAACTTGCTACCCGC
3882349 TAAGTTTGTTCACATGAAGTCGAACTTGCTACC
1 TAAGTTTGTTCACATGAAGTCGAACTTGCTACC
3882382 AGCTGATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (36 bp):
TAAGTTTGTTCACATGAAGTCGAACTTGCTACCCGC
Done.