Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002286.1 Hibiscus syriacus cultivar Beakdansim tig00004650_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: 59960
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2575 original size:12 final size:11
Alignment explanation
Indices: 2540--2624 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 11
2530 TCCGAATTGA
2540 ATTCTGTTCTG
1 ATTCTGTTCTG
*
2551 ATAC-GTTACCTG
1 ATTCTGTT--CTG
2563 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
2575 ATTCTGATCTGG
1 ATTCTGTTCT-G
*
2587 ATTATGTTCTG
1 ATTCTGTTCTG
* *
2598 ATATCTGATATG
1 AT-TCTGTTCTG
*
2610 AATTCTGTTTTG
1 -ATTCTGTTCTG
2622 ATT
1 ATT
2625 TATGATATCT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
10 3 0.05
11 18 0.32
12 28 0.49
13 5 0.09
14 3 0.05
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:2618 original size:24 final size:24
Alignment explanation
Indices: 2537--2632 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
2527 ATTTCCGAAT
*
2537 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
*
2559 CCTGAATTCTGTTCTGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
* *
2584 TGGATTATGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* * *
2608 TGAATTCTGTTTTGATTTATGATA
1 TGAATTCTGTTCTGATATCTGATA
2632 T
1 T
2633 CTCCGTTTAC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 14 0.24
24 43 0.73
25 2 0.03
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:3839 original size:2 final size:2
Alignment explanation
Indices: 3832--3876 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3822 TACATGAAAG
3832 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
3874 AT A
1 AT A
3877 AAGAACTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4715 original size:18 final size:18
Alignment explanation
Indices: 4692--4732 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4682 ACCGGTCATA
*
4692 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
* *
4710 ACCCGACCTGACCTGTTG
1 ACCCGACCCGACCCGTTG
4728 ACCCG
1 ACCCG
4733 TTGACCGGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:7234 original size:12 final size:11
Alignment explanation
Indices: 7207--7275 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 11
7197 CGTTACCTGA
*
7207 ATTCTGTTATG
1 ATTCTGATATG
7218 ATTCTGATATGG
1 ATTCTGATAT-G
* *
7230 ATTCTGTTCTG
1 ATTCTGATATG
7241 ATATCTGATATG
1 AT-TCTGATATG
* *
7253 AATTCTGTTTTG
1 -ATTCTGATATG
7265 ATTTCTGATAT
1 A-TTCTGATAT
7276 CTCCGTTTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
11 13 0.29
12 30 0.67
13 2 0.04
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (11 bp):
ATTCTGATATG
Found at i:7234 original size:47 final size:48
Alignment explanation
Indices: 7183--7275 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
7173 TCCGAATTGA
*
7183 ATTCTGTTCTGATA-C-GTTACCTGAATTCTGTTATGA-TTCTGATATGG
1 ATTCTGTTCTGATATCTGATA--TGAATTCTGTTATGATTTCTGATATGG
*
7230 ATTCTGTTCTGATATCTGATATGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTGATATCTGATATGAATTCTGTTATGATTTCTGATAT
7276 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
47 28 0.68
48 10 0.24
49 3 0.07
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATATGAATTCTGTTATGATTTCTGATATGG
Found at i:7252 original size:24 final size:23
Alignment explanation
Indices: 7204--7275 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
7194 ATACGTTACC
7204 TGAATTCTGTTATGATTCTGATA
1 TGAATTCTGTTATGATTCTGATA
* *
7227 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTATGAT-TCTGATA
*
7251 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGA-TTCTGATA
7275 T
1 T
7276 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.33
24 28 0.65
25 1 0.02
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTATGATTCTGATA
Found at i:15844 original size:27 final size:27
Alignment explanation
Indices: 15802--15869 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
15792 ATGTAGGAAT
15802 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
15827 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
15854 TATAGAGATATGATTT
1 TATAGAGATATGATTT
15870 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:19603 original size:27 final size:27
Alignment explanation
Indices: 19565--19625 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
19555 GTGTAGGAAT
*
19565 TAGAGATATGATTTGTTACTATTCCTA
1 TAGAGATATGATTTGTTACCATTCCTA
19592 TAGAGATATGATTTGTTACCATTCCTA
1 TAGAGATATGATTTGTTACCATTCCTA
19619 TAGAGAT
1 TAGAGAT
19626 GATTTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (27 bp):
TAGAGATATGATTTGTTACCATTCCTA
Found at i:20439 original size:253 final size:254
Alignment explanation
Indices: 19961--20461 Score: 864
Period size: 253 Copynumber: 2.0 Consensus size: 254
19951 ATTAGTGAAT
19961 TACTTTCTGGGAAGCTAGATTTTTGTGCTATGGGATCAAATGATATCTGCATGTTTTGTTCCTTC
1 TACTTTCTGGGAAGCTAGATTTTTGTGCTATGGGATCAAATGATATCTGCATGTTTTGTTCCTTC
* *
20026 AGCATTAATGCCTAATACATTTCAGGATCTCAGAAAGACAGATTTTATTGTCTTGAGTAATTTTT
66 AGCATTAATGCCCAATACATTTCAGGATCTCAGAAAGACAGATTTTAGTGTCTTGAGTAATTTTT
20091 TTTTGGCATTGTTAATCTCCATTCACATGATAAAAGCCATTATTACTTGTGTGAGTCCATAGATT
131 TTTTGGCATTGTTAATCTCCATTCACATGATAAAAGCCATTATTACTTGTGTGAGTCCATAGATT
*
20156 TAAGAATCATATAGATAAGAATAAAACATA-T-TGAGTTTTCTCTTACCCTGACTGCAG
196 TAAGAATCATACAGATAAGAATAAAACATATTGTGAGTTTTCTCTTACCCTGACTGCAG
* *
20213 TACTTTCTGGGAAGCTAGA-TTTTGTGCTATGGGATGAAATGATATCTGCGTGTTTTGTTCCTTC
1 TACTTTCTGGGAAGCTAGATTTTTGTGCTATGGGATCAAATGATATCTGCATGTTTTGTTCCTTC
* **
20277 AGCATTAATTCCCAATACATTTCAGGATCTCAGAAAGACAGATTTTAGTGTCTTTGAGGTTTTTT
66 AGCATTAATGCCCAATACATTTCAGGATCTCAGAAAGACAGATTTTAGTGTC-TTGA-GTAATTT
*
20342 TTTTTTTGCATTGTTAATCTCCATTCACATGATAAAAGCCATTATTACTTGTGTGAGTCCATAGA
129 TTTTTTGGCATTGTTAATCTCCATTCACATGATAAAAGCCATTATTACTTGTGTGAGTCCATAGA
**
20407 TTTAAGAATTTTACAGATAAGAATAAAACATATTGTGAGTTTTCTCTTACCCTGA
194 TTTAAGAATCATACAGATAAGAATAAAACATATTGTGAGTTTTCTCTTACCCTGA
20462 TTGCGGTTTG
Statistics
Matches: 234, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
251 92 0.39
252 23 0.10
253 98 0.42
254 1 0.00
255 20 0.09
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (254 bp):
TACTTTCTGGGAAGCTAGATTTTTGTGCTATGGGATCAAATGATATCTGCATGTTTTGTTCCTTC
AGCATTAATGCCCAATACATTTCAGGATCTCAGAAAGACAGATTTTAGTGTCTTGAGTAATTTTT
TTTTGGCATTGTTAATCTCCATTCACATGATAAAAGCCATTATTACTTGTGTGAGTCCATAGATT
TAAGAATCATACAGATAAGAATAAAACATATTGTGAGTTTTCTCTTACCCTGACTGCAG
Found at i:31305 original size:6 final size:6
Alignment explanation
Indices: 31294--31334 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
31284 CCAAATCATC
*
31294 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT GCATA
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATA
31335 ACACACACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:31342 original size:2 final size:2
Alignment explanation
Indices: 31335--31496 Score: 317
Period size: 2 Copynumber: 81.5 Consensus size: 2
31325 CATATGCATA
31335 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31377 AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31418 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31460 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
31497 TACTCATAGA
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
1 1 0.01
2 158 0.99
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31677 original size:25 final size:25
Alignment explanation
Indices: 31647--31729 Score: 157
Period size: 25 Copynumber: 3.3 Consensus size: 25
31637 TCATATAACT
31647 TATATCATATTCTTATATAATCACA
1 TATATCATATTCTTATATAATCACA
31672 TATATCATATTCTTATATAATCACA
1 TATATCATATTCTTATATAATCACA
31697 TATATCATATTCTTATATAATCACA
1 TATATCATATTCTTATATAATCACA
*
31722 TAGATCAT
1 TATATCAT
31730 TTATACCAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.43
Consensus pattern (25 bp):
TATATCATATTCTTATATAATCACA
Found at i:35184 original size:41 final size:41
Alignment explanation
Indices: 35104--35401 Score: 357
Period size: 41 Copynumber: 7.3 Consensus size: 41
35094 TGACAAAATG
* * * * * *
35104 CAATAGTTCACCATTCGATTTAATTCAATCATGGCAACATGA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACAT-A
* * * *
35146 -AATACTTCATCATTCAACTTGATTCGGTAATGGTAACATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
* * *
35186 CAATAATTCACCATTCAACTTGATTCCATCGTGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
35227 CAATAATTCACCATTCAACTTGATTCGATCATGG-AAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAA-CATA
* *
35268 CAATAATTCACTATTCAACTTGATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
* * * *
35309 CATTAATTCATCATTCAACTTAATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
* * *
35350 CAATAATTCACCATTCAACATGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
*
35391 CATTAATTCAC
1 CAATAATTCAC
35402 AAACCAATTC
Statistics
Matches: 222, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.01
41 219 0.99
42 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
Found at i:35240 original size:123 final size:123
Alignment explanation
Indices: 35104--35401 Score: 395
Period size: 123 Copynumber: 2.4 Consensus size: 123
35094 TGACAAAATG
* * * * *
35104 CAATAGTTCACCATTCGATTTAATTCAATCATGGCAA-CATGA-AATACTTCA-TCATTCAACTT
1 CAATAATTCACCATTCAACTTGATTCAATCATGG-AAGCAT-ACAATAATTCACT-ATTCAACTT
* * *
35166 GATTCGGTAATGGTAACATACAATAATTCACCATTCAACTTGATTCCATCGTGGTAGCATA
63 GATTCGATAATGGTAACATACAATAATTCACCATTCAACTTAATTCCATCATGGTAGCATA
*
35227 CAATAATTCACCATTCAACTTGATTCGATCATGGAAGCATACAATAATTCACTATTCAACTTGAT
1 CAATAATTCACCATTCAACTTGATTCAATCATGGAAGCATACAATAATTCACTATTCAACTTGAT
* * * * *
35292 TCGATCATGGTAGCATACATTAATTCATCATTCAACTTAATTCGATCATGGTAGCATA
66 TCGATAATGGTAACATACAATAATTCACCATTCAACTTAATTCCATCATGGTAGCATA
* * *
35350 CAATAATTCACCATTCAACATGATTCAATCATGGTAGCATACATTAATTCAC
1 CAATAATTCACCATTCAACTTGATTCAATCATGGAAGCATACAATAATTCAC
35402 AAACCAATTC
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
122 3 0.02
123 150 0.97
124 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (123 bp):
CAATAATTCACCATTCAACTTGATTCAATCATGGAAGCATACAATAATTCACTATTCAACTTGAT
TCGATAATGGTAACATACAATAATTCACCATTCAACTTAATTCCATCATGGTAGCATA
Found at i:35422 original size:41 final size:41
Alignment explanation
Indices: 35066--35403 Score: 315
Period size: 41 Copynumber: 8.2 Consensus size: 41
35056 CAGCATGTAT
* ** ** *
35066 TAATTCACAATTCAA-TTCAATTCAATCATGACAAAATGCAA
1 TAATTCACAATTCAACTT-AATTCGATCATGGTAGCATACAA
* * * * * * *
35107 TAGTTCACCATTCGATTTAATTCAATCATGGCAACATGA-AA
1 TAATTCACAATTCAACTTAATTCGATCATGGTAGCAT-ACAA
* * * * *
35148 TACTTCATC-ATTCAACTTGATTCGGTAATGGTAACATACAA
1 TAATTCA-CAATTCAACTTAATTCGATCATGGTAGCATACAA
* * * *
35189 TAATTCACCATTCAACTTGATTCCATCGTGGTAGCATACAA
1 TAATTCACAATTCAACTTAATTCGATCATGGTAGCATACAA
* * *
35230 TAATTCACCATTCAACTTGATTCGATCATGGAAGCATACAA
1 TAATTCACAATTCAACTTAATTCGATCATGGTAGCATACAA
* * *
35271 TAATTCACTATTCAACTTGATTCGATCATGGTAGCATACAT
1 TAATTCACAATTCAACTTAATTCGATCATGGTAGCATACAA
35312 TAATTCATC-ATTCAACTTAATTCGATCATGGTAGCATACAA
1 TAATTCA-CAATTCAACTTAATTCGATCATGGTAGCATACAA
* * * * *
35353 TAATTCACCATTCAACATGATTCAATCATGGTAGCATACAT
1 TAATTCACAATTCAACTTAATTCGATCATGGTAGCATACAA
35394 TAATTCACAA
1 TAATTCACAA
35404 ACCAATTCAA
Statistics
Matches: 257, Mismatches: 33, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
40 3 0.01
41 250 0.97
42 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (41 bp):
TAATTCACAATTCAACTTAATTCGATCATGGTAGCATACAA
Found at i:35422 original size:82 final size:81
Alignment explanation
Indices: 35064--35402 Score: 376
Period size: 82 Copynumber: 4.1 Consensus size: 81
35054 ATCAGCATGT
* ** ** * * * * *
35064 ATTAATTCACAATTCAA-TTCAATTCAATCATGACAAAATGCAATAGTTCACCATTCGATTTAAT
1 ATTAATTCAC-ATTCAACTT-AATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGAT
* *
35128 TCAATCATGGCAACATGA-
64 TCAATCATGGTAGCAT-AC
* * * * * *
35146 AATACTTCATCATTCAACTTGATTCGGTAATGGTAACATACAATAATTCACCATTCAACTTGATT
1 ATTAATTCA-CATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGATT
* *
35211 CCATCGTGGTAGCATAC
65 CAATCATGGTAGCATAC
* * * *
35228 AATAATTCACCATTCAACTTGATTCGATCATGGAAGCATACAATAATTCACTATTCAACTTGATT
1 ATTAATTCA-CATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGATT
*
35293 CGATCATGGTAGCATAC
65 CAATCATGGTAGCATAC
*
35310 ATTAATTCATCATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAACATGATT
1 ATTAATTCA-CATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGATT
35375 CAATCATGGTAGCATAC
65 CAATCATGGTAGCATAC
35392 ATTAATTCACA
1 ATTAATTCACA
35403 AACCAATTCA
Statistics
Matches: 220, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
81 3 0.01
82 214 0.97
83 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (81 bp):
ATTAATTCACATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGATTC
AATCATGGTAGCATAC
Found at i:35437 original size:123 final size:123
Alignment explanation
Indices: 35180--35456 Score: 340
Period size: 123 Copynumber: 2.3 Consensus size: 123
35170 CGGTAATGGT
* * *
35180 AACATACAATAATTCACCATTCAACTTGATTCCATCGTGGTAGCATACAATAATTCACCATTCAA
1 AACATACATTAATTCACCATTCAACTTAATTCCATCATGGTAGCATACAATAATTCACCATTCAA
* * * ** * * * *
35245 CTTGATTCGATCATGGAAGCATACAATAATTCACTATTCAACTTGATTCGATCATGGT
66 CATGATTCAATCATGGAAGCATACAATAATTCACAAACCAACTTAATTAGATCATAGC
* * *
35303 AGCATACATTAATTCATCATTCAACTTAATTCGATCATGGTAGCATACAATAATTCACCATTCAA
1 AACATACATTAATTCACCATTCAACTTAATTCCATCATGGTAGCATACAATAATTCACCATTCAA
* *
35368 CATGATTCAATCATGGTAGCATACATTAATTCACAAACCAA-TTCAATTAGATCATAGC
66 CATGATTCAATCATGGAAGCATACAATAATTCACAAACCAACTT-AATTAGATCATAGC
** * * *
35426 AACATGTATTAATTCACAATCCAATTTAATT
1 AACATACATTAATTCACCATTCAACTTAATT
35457 TAAATCAAGG
Statistics
Matches: 129, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
122 2 0.02
123 127 0.98
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (123 bp):
AACATACATTAATTCACCATTCAACTTAATTCCATCATGGTAGCATACAATAATTCACCATTCAA
CATGATTCAATCATGGAAGCATACAATAATTCACAAACCAACTTAATTAGATCATAGC
Found at i:36539 original size:23 final size:23
Alignment explanation
Indices: 36493--36581 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
36483 GTGGCATATA
***
36493 AAATATCCCGAAGGACCGTGTAG
1 AAATATCCCGAAGGACCACATAG
*
36516 AAATGTCCCGAAGGACCACATAG
1 AAATATCCCGAAGGACCACATAG
*
36539 --ATATCCTGAAGGACCACATAG
1 AAATATCCCGAAGGACCACATAG
* * *
36560 AATTGTCCCTAAGGACCACATA
1 AAATATCCCGAAGGACCACATA
36582 TATGTTCCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 19 0.35
23 35 0.65
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
AAATATCCCGAAGGACCACATAG
Found at i:36561 original size:44 final size:44
Alignment explanation
Indices: 36495--36581 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
36485 GGCATATAAA
***
36495 ATATCCCGAAGGACCGTGTAGAAATGTCCCGAAGGACCACATAG
1 ATATCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAG
* * *
36539 ATATCCTGAAGGACCACATAGAATTGTCCCTAAGGACCACATA
1 ATATCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATA
36582 TATGTTCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (44 bp):
ATATCCCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAG
Found at i:36595 original size:44 final size:44
Alignment explanation
Indices: 36513--36666 Score: 138
Period size: 44 Copynumber: 3.6 Consensus size: 44
36503 AAGGACCGTG
* * * *
36513 TAGAAATGTCCCGAAGGACCACATAGAT-ATCCTGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCACATATATGTTCC-AAAGGACCACA
*
36557 TAGAATTGTCCCTAAGGACCACATATATGTTCCAAAGGACCA-A
1 TAGAATTGTCCCGAAGGACCACATATATGTTCCAAAGGACCACA
* * ** *
36600 -ACATTTGTCCCGAAGGGACTGCATATATGTTCCAAAGGATCACA
1 TAGAATTGTCCCGAA-GGACCACATATATGTTCCAAAGGACCACA
* * *
36644 TA-TA-TGTCCCAAATGACCACATA
1 TAGAATTGTCCCGAAGGACCACATA
36667 GAACCCTCGA
Statistics
Matches: 89, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
42 18 0.20
43 33 0.37
44 34 0.38
45 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (44 bp):
TAGAATTGTCCCGAAGGACCACATATATGTTCCAAAGGACCACA
Found at i:36596 original size:21 final size:21
Alignment explanation
Indices: 36518--36666 Score: 118
Period size: 21 Copynumber: 7.0 Consensus size: 21
36508 CCGTGTAGAA
* *
36518 ATGTCCCGAAGGACCACATAG
1 ATGTCCCAAAGGACCACATAT
* ** *
36539 ATATCCTGAAGGACCACATAGA
1 ATGTCCCAAAGGACCACATA-T
*
36561 ATTGTCCCTAAGGACCACATAT
1 A-TGTCCCAAAGGACCACATAT
* * *
36583 ATGTTCCAAAGGACCAAACAT
1 ATGTCCCAAAGGACCACATAT
* * **
36604 TTGTCCCGAAGGGACTGCATAT
1 ATGTCCC-AAAGGACCACATAT
* *
36626 ATGTTCCAAAGGATCACATAT
1 ATGTCCCAAAGGACCACATAT
*
36647 ATGTCCCAAATGACCACATA
1 ATGTCCCAAAGGACCACATA
36667 GAACCCTCGA
Statistics
Matches: 98, Mismatches: 27, Indels: 6
0.75 0.21 0.05
Matches are distributed among these distances:
21 66 0.67
22 16 0.16
23 16 0.16
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (21 bp):
ATGTCCCAAAGGACCACATAT
Found at i:38120 original size:21 final size:22
Alignment explanation
Indices: 38096--38138 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
38086 TTGTTTTCTC
38096 TCTCTC-TTTTTCTTTCTTAAT
1 TCTCTCATTTTTCTTTCTTAAT
38117 TCTCTCAAATTTTTCTTTCTTA
1 TCTCTC--ATTTTTCTTTCTTA
38139 GGTCGGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
24 13 0.68
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (22 bp):
TCTCTCATTTTTCTTTCTTAAT
Found at i:38540 original size:43 final size:43
Alignment explanation
Indices: 38481--38819 Score: 543
Period size: 43 Copynumber: 7.9 Consensus size: 43
38471 TGTGAACAAA
* *
38481 AAACGCCGCAATAGGTCGAGATCTATAGCGACATTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
38524 AAACGCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
38567 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTAGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * * *
38610 AAACGTCGTAATAGGTCGAGATCTATAGCGGTGTTTTAGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
38653 AAACGCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
38696 AAACGCTGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* *
38739 AAACACCGCAATAGGTCGAGATCTATAACGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * *
38782 AAACGCCTCAATAGGTCGAGATTTATAGCGGTGTTTTT
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTT
38820 TTATACAAAC
Statistics
Matches: 275, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 275 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
Found at i:39982 original size:21 final size:20
Alignment explanation
Indices: 39958--40000 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
39948 AACAAGTAAT
39958 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
39979 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
39999 AT
1 AT
40001 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:42913 original size:41 final size:41
Alignment explanation
Indices: 42868--42996 Score: 97
Period size: 41 Copynumber: 3.1 Consensus size: 41
42858 TCCAAAAATA
*
42868 CCACTAAAGTACGTGATTTTAGCGGCGTTTTTGT-GA-AAACG
1 CCACTAAAGTACG-GATTTTAGCGGCGTTTTT-TACATAAACG
* * *
42909 CCACTATATA-TTCGGATATT-GCGGCGTTTTTTACATAAATG
1 CCACTA-A-AGTACGGATTTTAGCGGCGTTTTTTACATAAACG
* * ** *
42950 CCACTAAAGTACACGTTTTTAGCGGCG-TTTGCACAAAAACG
1 CCACTAAAGTAC-GGATTTTAGCGGCGTTTTTTACATAAACG
42991 CCACTA
1 CCACTA
42997 TATATTTGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
39 2 0.03
40 15 0.22
41 41 0.59
42 10 0.14
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
CCACTAAAGTACGGATTTTAGCGGCGTTTTTTACATAAACG
Found at i:42977 original size:82 final size:82
Alignment explanation
Indices: 42634--43019 Score: 414
Period size: 82 Copynumber: 4.7 Consensus size: 82
42624 TATTGCACAA
* * * * *
42634 GTTTATAGCGGCGTTTTTACAAAAACGCCACTATATATCTGGGCTATTGCGGCGTTTTATACATA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATAT-TCGGATATTGCGGCGTTTTTTACATA
* *
42699 AACGCCACTAAAGTACAT
65 AATGCCACTAAAGTACAC
* * *
42717 GTTTTTAGCGGCGTTTTCGCAAAAAACGCCGCTATATATTCTGATATTGCGGCGTTTTTTTACAT
1 GTTTTTAGCGGCGTTTTCAC-AAAAACGCCACTATATATTCGGATATTGCGGCG-TTTTTTACAT
**
42782 AAATGCCACTAAAGTATGC
64 AAATGCCACTAAAGTACAC
* * * * * * * * * * * *
42801 ATTTTTAGCAGTGTTTGCACAAAAACACCATTATATATTTGGATATCGCGTCG-TTTGTCCAAAA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
* **
42865 ATACCACTAAAGTACGT
66 ATGCCACTAAAGTACAC
* ****
42882 GATTTTAGCGGCGTTTTTGTGAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
42947 ATGCCACTAAAGTACAC
66 ATGCCACTAAAGTACAC
* * * *
42964 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGACGTTT
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTT
43020 GTCAAAAAAC
Statistics
Matches: 241, Mismatches: 59, Indels: 7
0.79 0.19 0.02
Matches are distributed among these distances:
81 61 0.25
82 69 0.29
83 55 0.23
84 56 0.23
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (82 bp):
GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
ATGCCACTAAAGTACAC
Found at i:42982 original size:163 final size:165
Alignment explanation
Indices: 42703--43028 Score: 494
Period size: 163 Copynumber: 2.0 Consensus size: 165
42693 TACATAAACG
* * *
42703 CCACTAAAGTACATGTTTTTAGCGGCGTTTTCGCAAAAAACGCCGCTATATATTCTGATATTGCG
1 CCACTAAAGTACATGATTTTAGCGGCGTTTTCGCAAAAAACGCCACTATATATTCGGATATTGCG
** * *
42768 GCGTTTTTTTACATAAATGCCACTAAAGTATGCATTTTTAGCAGTGTTTGCACAAAAACACCATT
66 GCGTTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCAGCGTTTGCACAAAAACACCACT
* *
42833 ATATATTTGGATATCGCGTCGTTTGTCCAAAAATA
131 ATATATTTGGATATCGCGACGTTTGTCAAAAAATA
* * **
42868 CCACTAAAGTACGTGATTTTAGCGGCGTTTTTG-TGAAAACGCCACTATATATTCGGATATTGCG
1 CCACTAAAGTACATGATTTTAGCGGCGTTTTCGCAAAAAACGCCACTATATATTCGGATATTGCG
* * *
42932 GCG-TTTTTTACATAAATGCCACTAAAGTACACGTTTTTAGCGGCGTTTGCACAAAAACGCCACT
66 GCGTTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCAGCGTTTGCACAAAAACACCACT
42996 ATATATTTGGATATCGCGACGTTTGTCAAAAAA
131 ATATATTTGGATATCGCGACGTTTGTCAAAAAA
43029 CGCCGCTACA
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
163 85 0.59
164 30 0.21
165 30 0.21
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (165 bp):
CCACTAAAGTACATGATTTTAGCGGCGTTTTCGCAAAAAACGCCACTATATATTCGGATATTGCG
GCGTTTTTTTACATAAATGCCACTAAAGTACACATTTTTAGCAGCGTTTGCACAAAAACACCACT
ATATATTTGGATATCGCGACGTTTGTCAAAAAATA
Found at i:43072 original size:163 final size:164
Alignment explanation
Indices: 42738--43073 Score: 417
Period size: 163 Copynumber: 2.1 Consensus size: 164
42728 CGTTTTCGCA
* * **
42738 AAAAACGCCGCTATATATTCTGATATTGCGGCGTTTTTTTACATAAATGCCACTAAAGTATGCAT
1 AAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTTACATAAATGCCACTAAAGTACACAT
* * * * *
42803 TTTTAGCAGTGTTTGCACAAAAACACCATTATATATTTGGATATCGCGTCGTTTGTCCAAAAATA
66 TTTTAGCAGCGTTTGCACAAAAACACCACTATATATTTGGATATCGCGACGTTTGTCAAAAAACA
*** ** * *
42868 CCACTAAAGTACGTGATTTTAGCGGCGTTTTTGT
131 CCACTAAAGTACAAAAAATCAGCGGCGTTTCTGT
* *
42902 GAAAACGCCACTATATATTCGGATATTGCGGCG-TTTTTTACATAAATGCCACTAAAGTACACGT
1 AAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTTACATAAATGCCACTAAAGTACACAT
* * *
42966 TTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGACGTTTGTCAAAAAACG
66 TTTTAGCAGCGTTTGCACAAAAACACCACTATATATTTGGATATCGCGACGTTTGTCAAAAAACA
* * *
43031 CCGCTACA-TATAAAAAATCA-CTGGCGTTTGCTGT
131 CCACTAAAGTACAAAAAATCAGC-GGCGTTT-CTGT
43065 AAAAACGCC
1 AAAAACGCC
43074 GCTAAATCTG
Statistics
Matches: 145, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
161 1 0.01
162 12 0.08
163 102 0.70
164 30 0.21
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (164 bp):
AAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTTACATAAATGCCACTAAAGTACACAT
TTTTAGCAGCGTTTGCACAAAAACACCACTATATATTTGGATATCGCGACGTTTGTCAAAAAACA
CCACTAAAGTACAAAAAATCAGCGGCGTTTCTGT
Found at i:53304 original size:23 final size:23
Alignment explanation
Indices: 53263--53365 Score: 124
Period size: 23 Copynumber: 4.7 Consensus size: 23
53253 TAGTGCAGGA
* *
53263 GGAATCGATACCCCC-TTGAAGG
1 GGAATCGATTCCCCCTTTGAATG
*
53285 GGAACCGATTCCCCCTTTGAATG
1 GGAATCGATTCCCCCTTTGAATG
*
53308 GGAATCAATTCCCCCTTTGAATG
1 GGAATCGATTCCCCCTTTGAATG
*
53331 GGAATCGATTCCCTCTTT--A-G
1 GGAATCGATTCCCCCTTTGAATG
*
53351 GGAATCGATACCCCC
1 GGAATCGATTCCCCC
53366 ATCGGGTTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
20 14 0.20
21 1 0.01
22 13 0.18
23 43 0.61
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (23 bp):
GGAATCGATTCCCCCTTTGAATG
Found at i:55724 original size:64 final size:63
Alignment explanation
Indices: 55651--55827 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 63
55641 TCAAATATTG
* * * * *
55651 AACAACGAATGCCAATAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCGTTTAA-AATACA
1 AACATCGAATGTCATTAGTGTATCGATGCATAAGGAGTGCATCGATGCACCC-CTTAATAATA-A
* * * *
55715 AACATCGAATGTCATTAGTGTATCGATGCACAAGTAGTTCATCGATGCACCCCTTAATATTAA
1 AACATCGAATGTCATTAGTGTATCGATGCATAAGGAGTGCATCGATGCACCCCTTAATAATAA
* * * *
55778 AACATCGAAGGTGATTTGTGTATCGATGCAT-GGGTAGTGCATCGATGCAC
1 AACATCGAATGTCATTAGTGTATCGATGCATAAGG-AGTGCATCGATGCAC
55828 ATGTTAAAGG
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
62 1 0.01
63 46 0.48
64 48 0.51
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (63 bp):
AACATCGAATGTCATTAGTGTATCGATGCATAAGGAGTGCATCGATGCACCCCTTAATAATAA
Found at i:55806 original size:63 final size:64
Alignment explanation
Indices: 55666--55827 Score: 202
Period size: 63 Copynumber: 2.5 Consensus size: 64
55656 CGAATGCCAA
* * * *
55666 TAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCGTTTAAAATACAAACATCGAATGTCAT
1 TAGTGTATCGATGCATAAGTAGTGCATCGATGCACCCGCTTAAAATACAAACATCGAAGGTCAT
* * * *
55730 TAGTGTATCGATGCACAAGTAGTTCATCGATGCACCC-CTTAATATTA-AAACATCGAAGGTGAT
1 TAGTGTATCGATGCATAAGTAGTGCATCGATGCACCCGCTTAA-AATACAAACATCGAAGGTCAT
* **
55793 TTGTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TAGTGTATCGATGCATAAGTAGTGCATCGATGCAC
55828 ATGTTAAAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 48 0.57
64 36 0.43
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
TAGTGTATCGATGCATAAGTAGTGCATCGATGCACCCGCTTAAAATACAAACATCGAAGGTCAT
Found at i:55863 original size:20 final size:22
Alignment explanation
Indices: 55815--55872 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
55805 GCATGGGTAG
*
55815 TGCATCGATGCACATGTTAAAGGA
1 TGCATCGATGCAC-TGTT-AAGAA
55839 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
55859 TGCATCGATGCACT
1 TGCATCGATGCACT
55873 TCAAGGGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:56769 original size:20 final size:21
Alignment explanation
Indices: 56744--56782 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
56734 ATATGTGTTA
56744 TATGTGGTCCTTCG-GATATC
1 TATGTGGTCCTTCGAGATATC
56764 TATGTGGTCCTTCGAGATA
1 TATGTGGTCCTTCGAGATA
56783 AATTCTACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTCGAGATATC
Done.