Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008328.1 Hibiscus syriacus cultivar Beakdansim tig00111036_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: 520947
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:353340 original size:2 final size:2
Alignment explanation
Indices: 353333--353360 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
353323 CTTCATTCAA
353333 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
353361 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:353365 original size:2 final size:2
Alignment explanation
Indices: 353360--353402 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
353350 TCTCTCTCTC
353360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
353402 T
1 T
353403 TTCACAATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:359923 original size:62 final size:63
Alignment explanation
Indices: 359802--359929 Score: 204
Period size: 62 Copynumber: 2.0 Consensus size: 63
359792 ATTAGTTGCA
* *
359802 CTCACCTGATGCCTCACTAGCTTTCTAGTAATTTTTATCGCTTTCCTTATACACCTTATCTCT
1 CTCACCAGATGCCTCACTAGCTTTCTAGCAATTTTTATCGCTTTCCTTATACACCTTATCTCT
** *
359865 CTCACCAGATGCCTCACTAGCTTTCTA-CCGTTTTTATCGCTTTCCTTATACACTTTATCTCT
1 CTCACCAGATGCCTCACTAGCTTTCTAGCAATTTTTATCGCTTTCCTTATACACCTTATCTCT
359927 CTC
1 CTC
359930 TTTTAGTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 34 0.57
63 26 0.43
ACGTcount: A:0.18, C:0.32, G:0.08, T:0.42
Consensus pattern (63 bp):
CTCACCAGATGCCTCACTAGCTTTCTAGCAATTTTTATCGCTTTCCTTATACACCTTATCTCT
Found at i:364604 original size:2 final size:2
Alignment explanation
Indices: 364534--364595 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
364524 CATTTCTTTA
364534 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
364576 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
364596 TGGTATATAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372336 original size:2 final size:2
Alignment explanation
Indices: 372329--372355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
372319 TTAAATTTTA
372329 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
372356 GAAGGGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:377271 original size:2 final size:2
Alignment explanation
Indices: 377266--377290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
377256 ACACACACAC
377266 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
377291 CAAACAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:377648 original size:2 final size:2
Alignment explanation
Indices: 377641--377694 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
377631 AACATTTGCC
377641 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
377683 AT AT AT AT AT AT
1 AT AT AT AT AT AT
377695 TCATGAAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:378480 original size:18 final size:18
Alignment explanation
Indices: 378442--378481 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
378432 AATAGAATTA
* **
378442 TAATTAAATAATAATTTT
1 TAATCAAATAATAATAAT
378460 TAATCAAATAATAATAAT
1 TAATCAAATAATAATAAT
378478 TAAT
1 TAAT
378482 TTATTTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATCAAATAATAATAAT
Found at i:385207 original size:23 final size:23
Alignment explanation
Indices: 385176--385235 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
385166 GGATATAAAT
385176 AAATATAAACGAACACAATAAACG
1 AAAT-TAAACGAACACAATAAACG
* *
385200 AAATTAAATGAACACAATAAATG
1 AAATTAAACGAACACAATAAACG
385223 AACA-TAAACGAAC
1 AA-ATTAAACGAAC
385236 GTAACCGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 27 0.84
24 5 0.16
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (23 bp):
AAATTAAACGAACACAATAAACG
Found at i:385455 original size:14 final size:14
Alignment explanation
Indices: 385421--385470 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
385411 TATTGGACTA
*
385421 AACAAACATAAATG
1 AACAAACATAAACG
385435 AAC--ACATAAACG
1 AACAAACATAAACG
*
385447 AACAAACATAAACA
1 AACAAACATAAACG
385461 AACAAACATA
1 AACAAACATA
385471 TTACTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.34
14 21 0.66
ACGTcount: A:0.66, C:0.20, G:0.04, T:0.10
Consensus pattern (14 bp):
AACAAACATAAACG
Found at i:388651 original size:21 final size:21
Alignment explanation
Indices: 388626--388670 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
388616 AAATTACACG
388626 TTTAGTATATAAACTATCAAT
1 TTTAGTATATAAACTATCAAT
* * *
388647 TTTAGTATTTAAACTTTTAAT
1 TTTAGTATATAAACTATCAAT
388668 TTT
1 TTT
388671 TTTCAAAATC
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:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTAGTATATAAACTATCAAT
Found at i:391717 original size:20 final size:18
Alignment explanation
Indices: 391684--391724 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
391674 TAATCTGAGT
*
391684 TTTTGTTATTTTTTATTC
1 TTTTGTTATTTTTTACTC
391702 TTTTGTTGATTTTTTTACTC
1 TTTTGTT-A-TTTTTTACTC
391722 TTT
1 TTT
391725 GATTTGCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTGTTATTTTTTACTC
Found at i:391939 original size:31 final size:31
Alignment explanation
Indices: 391901--391974 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
391891 AAACTACATA
*
391901 TTTAGTATCTAAACTATCAATTTTGATTCAT
1 TTTAGTATCTAAACTATCAATTTTGATCCAT
*
391932 TTTAGTATCTAAACTATCAGTTTTGATCCAT
1 TTTAGTATCTAAACTATCAATTTTGATCCAT
*
391963 TTTAATATCTAA
1 TTTAGTATCTAA
391975 CATTTTAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (31 bp):
TTTAGTATCTAAACTATCAATTTTGATCCAT
Found at i:399719 original size:120 final size:120
Alignment explanation
Indices: 399493--399739 Score: 361
Period size: 120 Copynumber: 2.1 Consensus size: 120
399483 AAGCTTAAGT
399493 ACTAAAATGGACCAAAACTAATAGTTCAGGTACTAAACAAATTAAGTTTTTAAACGATGGGTACT
1 ACTAAAATGGACCAAAACTAATAGTTCAGGTACTAAACAAATTAAGTTTTTAAACGATGGGTACT
* * *
399558 AAAATGAAACAAAAACTAAACATTAGGTATGGTTTTGAAAAAAATGAAGTTTAGGC
66 AAAATGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAA-AAAGTTTAGAC
* * * * * * * *
399614 ACTAAAATGGATCAAAATTGATAGTTTATGTCCTAAACAAATTAAGTTTTT-AATGGTGGGTACT
1 ACTAAAATGGACCAAAACTAATAGTTCAGGTACTAAACAAATTAAGTTTTTAAACGATGGGTACT
* *
399678 AAAATGAAACAAAAACTAAACGTTAGGTATGATTTTGAAAAAAAAAAGTTTAGAT
66 AAAATGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAAAAAGTTTAGAC
399733 ACTAAAA
1 ACTAAAA
399740 CATAACAAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 15 0.13
120 53 0.47
121 45 0.40
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (120 bp):
ACTAAAATGGACCAAAACTAATAGTTCAGGTACTAAACAAATTAAGTTTTTAAACGATGGGTACT
AAAATGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAAAAAGTTTAGAC
Found at i:405830 original size:62 final size:62
Alignment explanation
Indices: 405729--405851 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
405719 GTCCACGCAT
* *
405729 TGTAAATTTTTTAGTTTCATATCATTTTAAAATTATTGAATAAATAAGTAGACGACTGAACG
1 TGTAAATTGTTTAGTTTCATATCATTTTAAAATTATTGAATAAATAAATAGACGACTGAACG
* * * * *
405791 TGTAAATTGTTTAGTTTTATATCATTTTAAAGTTGTTGAATAAATAAATAGATGATTGAAC
1 TGTAAATTGTTTAGTTTCATATCATTTTAAAATTATTGAATAAATAAATAGACGACTGAAC
405852 ATCCATTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (62 bp):
TGTAAATTGTTTAGTTTCATATCATTTTAAAATTATTGAATAAATAAATAGACGACTGAACG
Found at i:407949 original size:60 final size:59
Alignment explanation
Indices: 407865--408008 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 59
407855 ACTGGGGACC
* * *
407865 AATTTAGAATGAGGGTTATAGTTTG-GGAATGAAATTGGAAT-TCTCAAAAGTTT-AAGGATT
1 AATTTAGAATGA-GATTATAGTTTGAGGAATG-AATTGAAATAT-TCAAAA-TTTAAAGGAAT
* * *
407925 CATTTAGAATGAGATTCATGGTTTGAGGATTGAATTGAAATATTCAAAATTTAAAGGAAT
1 AATTTAGAATGAGATT-ATAGTTTGAGGAATGAATTGAAATATTCAAAATTTAAAGGAAT
*
407985 AATTCAGAATGAAGATTATAGTTT
1 AATTTAGAATG-AGATTATAGTTT
408009 AAGAATGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
59 6 0.09
60 53 0.76
61 11 0.16
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (59 bp):
AATTTAGAATGAGATTATAGTTTGAGGAATGAATTGAAATATTCAAAATTTAAAGGAAT
Found at i:409549 original size:364 final size:361
Alignment explanation
Indices: 408705--409911 Score: 1596
Period size: 352 Copynumber: 3.3 Consensus size: 361
408695 AAATAAAATT
* ** *
408705 TAATTTACCAAACCTTACTTTCCACGTGGGAT-AAATTAATAATTTATTGTACCAAAAATGCCAC
1 TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAAATGCCAC
* * * *
408769 GGAACATTCATGAAG-CAGTATGTACTTTCCTTTGACTTTATCCGCATTAAGTTTGTCGTTTTAA
66 GGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGTCGTTTTAA
* ** * *
408833 TAATTAGTATATGTTTTATTGATAAATTAATAAATAAATTTCATATTTAATATTTAAATTATTAA
131 TAATTAGTATATGATTTATTGATAAATTAATGGATAAATTTCATATTTAGTATTTAAATTATTAG
* * *
408898 TTTTA-A-TCT-AT-TTT-AATATTTACA-TTTTT-AAATTATACCTAATATTTAATTTTTATTT
196 TTTTATATTTTAATATTTAAATTTTTA-ATTTTTTAAAATTATATCTAATATTTAATTTTTATTT
* * ** * * * * *
408956 TATATTAATACTTATATATTAAAATC-TAACGATACTGTATTTTTTATAAATAAATTATAATATT
260 TATGTTAATACTTAAACGTTAAAAACTTAACGACACTATATTTTTTAT-GATAAATTATATTATT
* * *
409020 TATTACTCAACTATC--TTA-TCTGCA-TA-----AC-A
324 CATTACTTAACTATCTTTTACTCT-TATTATTCGTACTA
409049 TAATTTACCAAACCTTACTTTTCACGTGGCTTACATGATTAAATTAATAATATT-CTGTACCAAA
1 TAATTTACCAAACCTTACTTTTCACGTGGC---C-T-A--AAATTAATAAT-TTACTGTACCAAA
*
409113 AATGCCACGTTACATTCAT-AAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGT
58 AATGCCACGGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGT
* * *
409177 CGTTTTAATAATTAGTATATGATTTATTGATAAATTAATGGGTAAATTTTATATTTAGTATTTAT
123 CGTTTTAATAATTAGTATATGATTTATTGATAAATTAATGGATAAATTTCATATTTAGTATTTAA
**
409242 ATTATTAGTTTTATCAGTTTTAATATTTAAATTTTTAATTTTTTAAAATTATATCTAACGTTTAA
188 ATTATTAGTTTTAT-A-TTTTAATATTTAAATTTTTAATTTTTTAAAATTATATCTAATATTTAA
* * *
409307 TTTTTATTTTATGTTAGTGCTTAGACGTTAAAAACTTAACGACACTATA-TTTTTATGAGTAAAT
251 TTTTTATTTTATGTTAATACTTAAACGTTAAAAACTTAACGACACTATATTTTTTATGA-TAAAT
409371 TATATTATTCATTACTTAACTATCTTGTTACTCTTATTATTCGTACTA
315 TATATTATTCATTACTTAACTATCTT-TTACTCTTATTATTCGTACTA
*
409419 TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAGATGCCAC
1 TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAAATGCCAC
409484 GGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGTCGTTTTAA
66 GGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGTCGTTTTAA
* * *
409549 TAATTAGTATATTATTTATTGATAAATTAATGGATAAATGTCATATTTAGTATCTAAATTATTAG
131 TAATTAGTATATGATTTATTGATAAATTAATGGATAAATTTCATATTTAGTATTTAAATTATTAG
* * *
409614 TTTTGATATATTTTAATATTTAAATTTTTTATTTTTTAAAATTATATTTAATATTTAGTTTTTAT
196 -TTT--TATATTTTAATATTTAAATTTTTAATTTTTTAAAATTATATCTAATATTTAATTTTTAT
* *
409679 TTCATGTTAATACTTAAACGTTAAAAACTTAACGACACTATATTTTTTATGCATAAATTATATCA
258 TTTATGTTAATACTTAAACGTTAAAAACTTAACGACACTATATTTTTTATG-ATAAATTATATTA
* *
409744 TTCATTACTTAACTATCTTTTTCACTCCTATTATTCGTAGTA
322 TTCATTACTTAACTATC-TTTT-ACTCTTATTATTCGTACTA
*
409786 TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAAATGACAC
1 TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAAATGCCAC
* * *
409851 GGTACATTCATGAAGCCACTATGTGCTTTCCTTTGGCTTTATCCACATTAAGTTTGTCGTT
66 GGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGTCGTT
409912 CTATGTATAA
Statistics
Matches: 761, Mismatches: 61, Indels: 59
0.86 0.07 0.07
Matches are distributed among these distances:
344 28 0.04
348 1 0.00
351 3 0.00
352 145 0.19
353 2 0.00
354 1 0.00
356 2 0.00
357 2 0.00
358 4 0.01
359 13 0.02
360 78 0.10
361 11 0.01
362 2 0.00
363 42 0.06
364 117 0.15
365 92 0.12
366 40 0.05
367 145 0.19
369 2 0.00
370 31 0.04
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (361 bp):
TAATTTACCAAACCTTACTTTTCACGTGGCCTAAAATTAATAATTTACTGTACCAAAAATGCCAC
GGTACATTCATGAAGCCACTATGTACTTTCCTTTGACTTTATCCACATTAAGGTTGTCGTTTTAA
TAATTAGTATATGATTTATTGATAAATTAATGGATAAATTTCATATTTAGTATTTAAATTATTAG
TTTTATATTTTAATATTTAAATTTTTAATTTTTTAAAATTATATCTAATATTTAATTTTTATTTT
ATGTTAATACTTAAACGTTAAAAACTTAACGACACTATATTTTTTATGATAAATTATATTATTCA
TTACTTAACTATCTTTTACTCTTATTATTCGTACTA
Found at i:410927 original size:31 final size:31
Alignment explanation
Indices: 410871--410942 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
410861 AAAAATTAAT
*
410871 TTAATTTGAT-TTCTAAATTTAAAATAAAATA
1 TTAATTTAATATT-TAAATTTAAAATAAAATA
* *
410902 TTTATTTAATATTTAAATTTTAAATAAAATA
1 TTAATTTAATATTTAAATTTAAAATAAAATA
410933 TTAATTTAAT
1 TTAATTTAAT
410943 CTATACATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TTAATTTAATATTTAAATTTAAAATAAAATA
Found at i:411425 original size:53 final size:53
Alignment explanation
Indices: 411326--411426 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
411316 TAAACATATA
* * *
411326 TTATTAACTTCTAATGTATTAAGGTATATAGTTCTATAGATTATTAGTCATTC
1 TTATTAACTTCTAATGTATTAAGGTATATAATTCTATACATCATTAGTCATTC
* * *
411379 TTATTAACTTGTAATTTATTAAGGTATATAATTCTGTACATCATTAGT
1 TTATTAACTTCTAATGTATTAAGGTATATAATTCTATACATCATTAGT
411427 TAATAAGATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (53 bp):
TTATTAACTTCTAATGTATTAAGGTATATAATTCTATACATCATTAGTCATTC
Found at i:415904 original size:22 final size:23
Alignment explanation
Indices: 415863--415921 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
415853 CAAACCATTC
415863 AGGGGGGAATCGGTACCCCCTTG
1 AGGGGGGAATCGGTACCCCCTTG
415886 AGGGGGGAATCGGTACCCCCTTG
1 AGGGGGGAATCGGTACCCCCTTG
415909 -GGGGGGAATCGGT
1 AGGGGGGAATCGGT
415922 TCCCTCTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (23 bp):
AGGGGGGAATCGGTACCCCCTTG
Found at i:416292 original size:19 final size:19
Alignment explanation
Indices: 416268--416307 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
416258 ACACTTCTCC
416268 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
416287 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
416306 CA
1 CA
416308 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:418515 original size:8 final size:8
Alignment explanation
Indices: 418504--418529 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
418494 AACGGCAGAA
418504 GGGTTTTG
1 GGGTTTTG
418512 GGGTTTTG
1 GGGTTTTG
418520 GGGTTTTG
1 GGGTTTTG
418528 GG
1 GG
418530 TGTTCTGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (8 bp):
GGGTTTTG
Found at i:424845 original size:15 final size:15
Alignment explanation
Indices: 424799--424845 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
424789 TTGTCGGCTT
*
424799 ATATATCAAAATATA
1 ATATATTAAAATATA
*
424814 ATA-ATTTATAATATA
1 ATATA-TTAAAATATA
*
424829 ATATATTAAAATTTA
1 ATATATTAAAATATA
424844 AT
1 AT
424846 TAATTGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATTAAAATATA
Found at i:425062 original size:20 final size:18
Alignment explanation
Indices: 425037--425077 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
425027 AACATTTCAA
425037 TTTCATCCCTAAATTATATC
1 TTTCAT-CCTAAATTA-ATC
*
425057 TTTCATTCTAAATTAATC
1 TTTCATCCTAAATTAATC
425075 TTT
1 TTT
425078 AAACTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCATCCTAAATTAATC
Found at i:425092 original size:60 final size:60
Alignment explanation
Indices: 425008--425146 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
424998 CTCATTTCAG
* * * * * *
425008 ATTAATCCTTAAACTTCTAAACATT-TCAATTTCATCCCTAAATTAT-ATCTTTCATTCTAA
1 ATTAATCCTTAAACTTTTGAACATTCT-AATTTCATCCCCAAACTATGA-ATATCATTCTAA
*
425068 ATTAATCTTTAAACTTTTGAACATTCTAATTTCATCCCCAAACTATGAATATCATTCTAA
1 ATTAATCCTTAAACTTTTGAACATTCTAATTTCATCCCCAAACTATGAATATCATTCTAA
* *
425128 ATTAGTCCTTAAATTTTTG
1 ATTAATCCTTAAACTTTTG
425147 CATATTTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 65 0.97
61 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (60 bp):
ATTAATCCTTAAACTTTTGAACATTCTAATTTCATCCCCAAACTATGAATATCATTCTAA
Found at i:425368 original size:58 final size:61
Alignment explanation
Indices: 425252--425389 Score: 185
Period size: 58 Copynumber: 2.3 Consensus size: 61
425242 AAACATATAA
*
425252 TTTA-GGATTAAATTGAAATGTTAAAAATGTGTAGGGACCAATTTAGAATGAAAATCATAG
1 TTTAGGGATGAAATTGAAATGTTAAAAATGTGTAGGGACCAATTTAGAATGAAAATCATAG
* * * * * *
425312 TTT-GGGATGAAAATGAAATGTTAAAAGTTTG-A-GGACTAATTTAGAATGATAGTCATAG
1 TTTAGGGATGAAATTGAAATGTTAAAAATGTGTAGGGACCAATTTAGAATGAAAATCATAG
425370 TTTAGGGATGAAATTGAAAT
1 TTTAGGGATGAAATTGAAAT
425390 TTTTAAAGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 26 0.38
59 16 0.24
60 26 0.38
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (61 bp):
TTTAGGGATGAAATTGAAATGTTAAAAATGTGTAGGGACCAATTTAGAATGAAAATCATAG
Found at i:425411 original size:59 final size:58
Alignment explanation
Indices: 425256--425412 Score: 165
Period size: 59 Copynumber: 2.7 Consensus size: 58
425246 ATATAATTTA
* * *
425256 GGATTAAATTGAAATGTTAAAAATGTGTAG-GGACCAATTTAGAATGAAAATCATAGTTTG
1 GGATGAAAATGAAATGTT-AAAA-GT-TAGAGGACTAATTTAGAATGAAAATCATAGTTTG
* * *
425316 GGATGAAAATGAAATGTTAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAG
1 GGATGAAAATGAAATGTTAAAAGTTAGAGGACTAATTTAGAATGAAAATCATAGTTT-G
* * * *
425375 GGATGAAATTGAAATTTTTAAAGATTAGA-GATTAATTT
1 GGATGAAAATGAAATGTTAAAAG-TTAGAGGACTAATTT
425413 GAAATAATGC
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.02
58 28 0.34
59 33 0.40
60 20 0.24
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (58 bp):
GGATGAAAATGAAATGTTAAAAGTTAGAGGACTAATTTAGAATGAAAATCATAGTTTG
Found at i:431326 original size:2 final size:2
Alignment explanation
Indices: 431319--431343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
431309 ATCTTAAATT
431319 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 T
431344 TGTTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:437002 original size:2 final size:2
Alignment explanation
Indices: 436995--437050 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
436985 AATAAAACTT
436995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
437037 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
437051 GACAGCAACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:439248 original size:21 final size:21
Alignment explanation
Indices: 439221--439279 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
439211 GTCCGAGTTA
439221 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
* *
439242 TCCGCGACGACCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
* *
439263 CCCGCAACGGTCGCAAT
1 CCCGCGACGGCCGCAAT
439280 CACGGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.41, G:0.29, T:0.08
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:439738 original size:75 final size:80
Alignment explanation
Indices: 439639--439828 Score: 231
Period size: 75 Copynumber: 2.5 Consensus size: 80
439629 TTGTAAACGG
*
439639 TTTTTGAA-AATATATATATAATATATAGTTTTAAAAAAAACA-TTTTG-A-AAA-TATGGGTAA
1 TTTTTGAATAA-AT-TATATAATATATAGTTTTAAAAAAAACATTTTTGAATAAATTAT--ATAA
*
439699 CATATAGTTTT-AAAATCA
62 CATATAGTTTTAAAAAACA
*
439717 -TTTT-AA-AAACTTATATAATATATAGTTTT--AAAAAACATTTTTGAATAAATTATATAATAT
1 TTTTTGAATAAA-TTATATAATATATAGTTTTAAAAAAAACATTTTTGAATAAATTATATAACAT
439777 ATAGTTTTAAAAAACA
65 ATAGTTTTAAAAAACA
439793 TTTTTGAATAAATTATATAATATATAGTTTTAAAAA
1 TTTTTGAATAAATTATATAATATATAGTTTTAAAAA
439829 CGTTTTTTTA
Statistics
Matches: 98, Mismatches: 3, Indels: 20
0.81 0.02 0.17
Matches are distributed among these distances:
73 8 0.08
74 5 0.05
75 33 0.34
76 14 0.14
77 11 0.11
78 21 0.21
79 3 0.03
80 3 0.03
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (80 bp):
TTTTTGAATAAATTATATAATATATAGTTTTAAAAAAAACATTTTTGAATAAATTATATAACATA
TAGTTTTAAAAAACA
Found at i:439779 original size:39 final size:38
Alignment explanation
Indices: 439639--439936 Score: 241
Period size: 39 Copynumber: 8.2 Consensus size: 38
439629 TTGTAAACGG
439639 TTTTTGAAAATATATATATAATATATAGTTTTAAAAAAAACA
1 TTTTTGAAAA-AT-TATATAATATATAGTTTT--AAAAAACA
* * *
439681 -TTTTG-AAAA-TATGGGTAACATATAGTTTT-AAAATCA
1 TTTTTGAAAAATTAT--ATAATATATAGTTTTAAAAAACA
439717 -TTTT-AAAAACTTATATAATATATAGTTTTAAAAAACA
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAAACA
439754 TTTTTGAATAAATTATATAATATATAGTTTTAAAAAACA
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAAACA
*
439793 TTTTTGAATAAATTATATAATATATAGTTTT-AAAAACGT
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAAAC-A
* *
439832 TTTTTTAAAACTTATAT-A-ATAT--TTTT--AAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAAACA
* *
439864 -TTTTG-AAAACTATAT-A-ATATAGTTTT-GAAAAC-
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAAACA
* *
439896 TTTTT---TAA--ATATAATATATAG-TTTAAAAAATA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAAACA
439928 TTTTTGAAA
1 TTTTTGAAA
439937 TATATGTATT
Statistics
Matches: 218, Mismatches: 17, Indels: 49
0.77 0.06 0.17
Matches are distributed among these distances:
29 4 0.02
30 17 0.08
31 16 0.07
32 9 0.04
33 14 0.06
34 4 0.02
36 31 0.14
37 10 0.05
38 21 0.10
39 81 0.37
40 6 0.03
41 5 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (38 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAAACA
Found at i:439918 original size:31 final size:31
Alignment explanation
Indices: 439810--439925 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 31
439800 ATAAATTATA
439810 TAATATATAGTTTTAAAAACGTTTTTTTAAAAC
1 TAATATATAGTTTTAAAAAC--TTTTTTAAAAC
* * * *
439843 TTATATAATA-TTTTTAAAACATTTTGAAAAC
1 TAATAT-ATAGTTTTAAAAACTTTTTTAAAAC
*
439874 TATATAATATAGTTTTGAAAACTTTTTTAAATA-
1 TA-AT-ATATAGTTTTAAAAACTTTTTTAAA-AC
*
439907 TAATATATAGTTTAAAAAA
1 TAATATATAGTTTTAAAAA
439926 TATTTTTGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
31 23 0.34
32 7 0.10
33 34 0.50
34 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (31 bp):
TAATATATAGTTTTAAAAACTTTTTTAAAAC
Found at i:442908 original size:19 final size:19
Alignment explanation
Indices: 442874--442918 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
442864 ATTTAGACAT
442874 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
442892 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
442911 TTTGCATT
1 TTTGCATT
442919 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:446600 original size:165 final size:164
Alignment explanation
Indices: 446309--447049 Score: 855
Period size: 165 Copynumber: 4.5 Consensus size: 164
446299 TATCTGCCAA
* * * * * * *
446309 CCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGAATAACTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
* ** * * * *
446373 CGAGAAGGGCTATCT---ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
66 CGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
446435 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
130 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
*
446470 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
* *
446535 CGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCA
66 CGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
446600 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
130 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
*
446635 CCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
* *
446700 CTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA
66 CGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
* * * * *
446765 TTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGG
130 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-G
* * * * * * * * *
446801 CAACAAAAGACCTTTGAGTTTGACTACGCTCAGC-TCAACGGCACATCATTTACAGCATAACTCA
1 C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTA
* * ** * * *
446865 AGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCAACTCCGCTCAGATCCAAGGCACA
63 AGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
*
446930 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG
127 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * * * * * * * * *
446968 CTAAAGACCTTTGAGTTCGATTATATTCAACTTAGA-GGCAAATCAAGTTTGCAGAATAGCTCAA
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC-A-TTTGCAGCATAACTTAA
* *
447032 GGCAAGAAGGGTTATCTG
64 GTCGAGAAGGGTTATCTG
447050 TCAATAAAAT
Statistics
Matches: 505, Mismatches: 62, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
161 26 0.05
162 44 0.09
164 30 0.06
165 203 0.40
166 60 0.12
167 5 0.01
168 114 0.23
169 23 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
Found at i:446617 original size:84 final size:81
Alignment explanation
Indices: 446291--446987 Score: 783
Period size: 84 Copynumber: 8.4 Consensus size: 81
446281 GCTCAAGGCC
*
446291 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
446356 TGCAGAATAACTTAAGTCG
63 TGCAGCATAACTTAAGTCG
* ** * * * *
446375 AGAAGGGCTATCT-ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTG
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTG
*
446439 CAGCATAGCTTAAGTCG
65 CAGCATAACTTAAGTCG
* ** * * * *
446456 AGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTG
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTG
446520 CAGCATAACTTAAGTCG
65 CAGCATAACTTAAGTCG
* *
446537 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
446602 TGCAGCATAGCTTAAGTCG
63 TGCAGCATAACTTAAGTCG
* * * * * * *
446621 AGAAGGGCTATCTG-CCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTG
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTG
*
446685 CAGCATAACTTAAGTCT
65 CAGCATAACTTAAGTCG
*
446702 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
446767 TGCAGCACAACTTAAGTCT
63 TGCAGCATAACTTAAGTCG
* * * *
446786 AGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCT-G--ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * * *
446850 TTACAGCATAACTCAAGGCT
62 TTGCAGCATAACTTAAGTCG
* * *
446870 AGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCAACTCCGCTCAGATCCAAGGCACATCATT
1 AGAAGGGTTATC--TGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
446935 TGCAGCATAGCTTAAGTCG
63 TGCAGCATAACTTAAGTCG
* *
446954 AGAAGGGTTATCTG-CTAAAGACCTTTGAGTTCGA
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGA
446988 TTATATTCAA
Statistics
Matches: 533, Mismatches: 63, Indels: 38
0.84 0.10 0.06
Matches are distributed among these distances:
80 69 0.13
81 168 0.32
82 2 0.00
83 5 0.01
84 230 0.43
85 58 0.11
86 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGCATAACTTAAGTCG
Found at i:447810 original size:39 final size:37
Alignment explanation
Indices: 447712--447945 Score: 191
Period size: 39 Copynumber: 6.7 Consensus size: 37
447702 TATGGGTAAC
*
447712 ATATAGTTTTAAAATCA-TTTT-AAAAACTTATAT-A-
1 ATATAGTTTTAAAAACATTTTTGAAAAA-TTATATAAT
* *
447746 ATATAGTTTTAAAAAAAATTTTGAATAAATTATATAAT
1 ATATAGTTTTAAAAACATTTTTGAA-AAATTATATAAT
447784 ATATAGTTTTAAAAAACATTTTTGAATAAATTATATAAT
1 ATATAGTTTT-AAAAACATTTTTGAA-AAATTATATAAT
* * *
447823 ATATAGTTTTAAAAACGTTTTTTTAAAACTTATAT-A-
1 ATATAGTTTTAAAAAC-ATTTTTGAAAAATTATATAAT
*
447859 ATAT--TTTT-AAAACA-TTTTG-AAAACTATAT-A-
1 ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
* *
447889 ATATAGTTTTGAAAAC-TTTTT---TAA--ATATAAT
1 ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
* *
447920 ATATAGTTTAAAAAATATTTTTGAAA
1 ATATAGTTTTAAAAACATTTTTGAAA
447946 TATATGTATT
Statistics
Matches: 167, Mismatches: 16, Indels: 33
0.77 0.07 0.15
Matches are distributed among these distances:
29 4 0.02
30 14 0.08
31 19 0.11
32 9 0.05
33 14 0.08
34 19 0.11
35 4 0.02
36 12 0.07
37 5 0.03
38 24 0.14
39 43 0.26
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
Found at i:447927 original size:31 final size:31
Alignment explanation
Indices: 447819--447934 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 31
447809 ATAAATTATA
447819 TAATATATAGTTTTAAAAACGTTTTTTTAAAAC
1 TAATATATAGTTTTAAAAAC--TTTTTTAAAAC
* * * *
447852 TTATATAATA-TTTTTAAAACATTTTGAAAAC
1 TAATAT-ATAGTTTTAAAAACTTTTTTAAAAC
*
447883 TATATAATATAGTTTTGAAAACTTTTTTAAATA-
1 TA-AT-ATATAGTTTTAAAAACTTTTTTAAA-AC
*
447916 TAATATATAGTTTAAAAAA
1 TAATATATAGTTTTAAAAA
447935 TATTTTTGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
31 23 0.34
32 7 0.10
33 34 0.50
34 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (31 bp):
TAATATATAGTTTTAAAAACTTTTTTAAAAC
Found at i:447941 original size:31 final size:32
Alignment explanation
Indices: 447777--447949 Score: 106
Period size: 32 Copynumber: 5.2 Consensus size: 32
447767 TGAATAAATT
*
447777 ATATAATATATAGTTTTAAAAAACATTTTTGAATAAA
1 ATATAATATATAGTTTT-AAAAA-ATTTTT---TGAA
* *
447814 TTATATAATATATAGTTTTAAAAACGTTTTTTTAA
1 --ATATAATATATAGTTTTAAAAA-ATTTTTTGAA
* * *
447849 A-ACTTATATAATATTTTTAAAACA--TTTTGAA
1 ATA-TAATAT-ATAGTTTTAAAAAATTTTTTGAA
* *
447880 A-ACTATATAATATAGTTTTGAAAACTTTTTT-AA
1 ATA-TA-AT-ATATAGTTTTAAAAAATTTTTTGAA
447913 ATATAATATATAG-TTTAAAAAATATTTTTGAA
1 ATATAATATATAGTTTTAAAAAAT-TTTTTGAA
447945 ATATA
1 ATATA
447950 TGTATTAATT
Statistics
Matches: 111, Mismatches: 14, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
30 8 0.07
31 21 0.19
32 22 0.20
33 13 0.12
34 16 0.14
35 3 0.03
38 11 0.10
39 17 0.15
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (32 bp):
ATATAATATATAGTTTTAAAAAATTTTTTGAA
Found at i:455099 original size:37 final size:36
Alignment explanation
Indices: 455024--455099 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
455014 TTTTTATATT
*
455024 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
455060 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
455097 TTT
1 TTT
455100 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:455281 original size:20 final size:20
Alignment explanation
Indices: 455245--455282 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
455235 ATCCTATTCC
**
455245 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
455265 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
455283 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:458950 original size:21 final size:20
Alignment explanation
Indices: 458924--459021 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
458914 GCGTTGCATT
* *
458924 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGAT-TTTCAAAA
* **
458945 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCAAAA
* * **
458965 TCGCGTTGTGATTTTCCAGT
1 TCGCGTTGCGATTTTCAAAA
* *
458985 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCAAAA
459006 TCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTC
459022 CGGTTCGCGT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:458970 original size:20 final size:20
Alignment explanation
Indices: 458945--459037 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
458935 TAATTGAAAA
*
458945 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
458965 TCGCGTTGTGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
458985 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
459006 TCGCGTTGCGATTTTCCGGT
1 TCGCGTTGCGATTTTCCAGT
459026 TCGCGTTGCGAT
1 TCGCGTTGCGAT
459038 AGTCTACAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:459087 original size:22 final size:22
Alignment explanation
Indices: 459029--459081 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
459019 TTCCGGTTCG
459029 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
459051 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
459073 CGTTGCGAT
1 CGTTGCGAT
459082 TTTCTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:460099 original size:16 final size:15
Alignment explanation
Indices: 460080--460109 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
460070 TTGTTTATGT
460080 TATATTTTAATATATA
1 TATATTTTAA-ATATA
460096 TATATTTTAAATAT
1 TATATTTTAAATAT
460110 TTAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTTTAAATATA
Found at i:460857 original size:18 final size:19
Alignment explanation
Indices: 460816--460857 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
460806 ATTGATTATT
*
460816 TAAATATTTTTAAAATAATA
1 TAAACATTTTTAAAAT-ATA
460836 TAAACATTTTTAAAAT-TA
1 TAAACATTTTTAAAATATA
460854 TAAA
1 TAAA
460858 GTCTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAACATTTTTAAAATATA
Found at i:487128 original size:23 final size:26
Alignment explanation
Indices: 487084--487138 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
487074 TTATAACTTT
*
487084 TAATAGTCGAGGGATCTTTTAA-AAAA
1 TAATAGTCAAGGGATC-TTTAATAAAA
*
487110 TAATAGTCAAGGGA-C-TTAATAAAG
1 TAATAGTCAAGGGATCTTTAATAAAA
487134 TAATA
1 TAATA
487139 CCTTATAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 8 0.31
25 1 0.04
26 13 0.50
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (26 bp):
TAATAGTCAAGGGATCTTTAATAAAA
Found at i:487810 original size:39 final size:39
Alignment explanation
Indices: 487693--487811 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 39
487683 TTAAATTTTT
* *
487693 ATTCATAA-TTCTCAAATTATTTCAC-TCTAACATGCTAA
1 ATTCATAATTTCTAAAATTATTTCACAT-TAACATTCTAA
* * ** *
487731 ATTCCTAATTTCTTAAATCT-TGACACCA-TAATATTCTAA
1 ATTCATAATTTCTAAAAT-TATTTCA-CATTAACATTCTAA
* *
487770 ATTCTTAATTTCTAAAATTATTTCACATTAACATTTTAA
1 ATTCATAATTTCTAAAATTATTTCACATTAACATTCTAA
487809 ATT
1 ATT
487812 ATTTTTTAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
38 10 0.16
39 51 0.81
40 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.44
Consensus pattern (39 bp):
ATTCATAATTTCTAAAATTATTTCACATTAACATTCTAA
Found at i:487889 original size:25 final size:26
Alignment explanation
Indices: 487844--487894 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
487834 ACTTCAAAAC
*
487844 ATTTGAAATTTAATTATA-TTTCTTT
1 ATTTGAAATTTAATTAAATTTTCTTT
*
487869 ATTTTAAATTTTAA-TAAATTTTCTTT
1 ATTTGAAA-TTTAATTAAATTTTCTTT
487895 CAATTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTGAAATTTAATTAAATTTTCTTT
Found at i:489419 original size:42 final size:41
Alignment explanation
Indices: 489347--489431 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 41
489337 AGATTGGGGT
*
489347 AATGCTTAGGGTTTTCTTTAGGTGAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
489388 AATGCTTAGGGTTTTGCTTTAGGTAAAGGCAACTTCCATACG
1 AATGCTTAGGGTTTT-CTTTAGGTAAAGGCAACTTCCATACG
489430 AA
1 AA
489432 GCGATGGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (41 bp):
AATGCTTAGGGTTTTCTTTAGGTAAAGGCAACTTCCATACG
Found at i:490261 original size:24 final size:24
Alignment explanation
Indices: 490215--490263 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
490205 TTTAAATAGT
*
490215 ATATTATATATTTAAAAACATATA
1 ATATTATATATATAAAAACATATA
*
490239 ATATTATAATATATATAAAATATAT
1 ATATTAT-ATATATA-AAAACATAT
490264 CAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 6 0.29
26 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTATATATATAAAAACATATA
Found at i:492072 original size:2 final size:2
Alignment explanation
Indices: 492067--492093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
492057 ATATAAAACA
492067 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
492094 AAGAGGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:498421 original size:30 final size:31
Alignment explanation
Indices: 498387--498459 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
498377 ATTTGTATAC
* *
498387 TTTTAGTCACTTA-GTTATTGTTTTATTAAA
1 TTTTAGTCACTTACGTAATCGTTTTATTAAA
498417 TTTTAGTCACTTACGTAATCGTTTTATTAAA
1 TTTTAGTCACTTACGTAATCGTTTTATTAAA
*
498448 TTTTAGTTACTT
1 TTTTAGTCACTT
498460 GAAAATGAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTTAGTCACTTACGTAATCGTTTTATTAAA
Found at i:499745 original size:6 final size:6
Alignment explanation
Indices: 499734--499758 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
499724 ATCTTGTATT
499734 GGTTTC GGTTTC GGTTTC GGTTTC G
1 GGTTTC GGTTTC GGTTTC GGTTTC G
499759 CAGGACCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (6 bp):
GGTTTC
Found at i:500595 original size:16 final size:16
Alignment explanation
Indices: 500574--500604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
500564 ATAGTTTGAT
500574 ATTTATCTACTTATTA
1 ATTTATCTACTTATTA
*
500590 ATTTATCTATTTATT
1 ATTTATCTACTTATT
500605 TATACTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATCTACTTATTA
Found at i:510273 original size:2 final size:2
Alignment explanation
Indices: 510266--510296 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
510256 AAACTAATAA
510266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
510297 ATCTAGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:516295 original size:31 final size:30
Alignment explanation
Indices: 516260--516321 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
516250 TAAGTATGCA
516260 AAATTAAGTATAATATAAAAGATA-AATAAAT
1 AAATT-AGTAT-ATATAAAAGATATAATAAAT
* * *
516291 AAATTATTGTATATAGAAGATATAATAAAT
1 AAATTAGTATATATAAAAGATATAATAAAT
516321 A
1 A
516322 TTATATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (30 bp):
AAATTAGTATATATAAAAGATATAATAAAT
Done.