Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007962.1 Hibiscus syriacus cultivar Beakdansim tig00110391_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: 1774241
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:366357 original size:156 final size:156
Alignment explanation
Indices: 366071--366380 Score: 496
Period size: 156 Copynumber: 2.0 Consensus size: 156
366061 ATTCAGAAAC
* * * * *
366071 CATAGTAATCCCTCCAGCCCAACATATCATAATGTGTAGGTTCCCCAGAACCATACACCCACCGT
1 CATAGTAATCCCTCCAACCCAACACAGCATAATATGTAGGTTCCCCAGAACCATACACCAACCGT
*
366136 CACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTACTAGTACACTTACTCCAACAATA-C
66 CACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTACAAGTACACTTACTCCAACAATACC
366200 CCCCAAATAAAAACATTTATCAAAATT
131 CCCCAAAT-AAAACATTTATCAAAATT
*
366227 CATAGTAATCCCTCCAACCGAACACAGCATAATATGTAGGTTCCCCAGAACCATACACCAACCGT
1 CATAGTAATCCCTCCAACCCAACACAGCATAATATGTAGGTTCCCCAGAACCATACACCAACCGT
* * * * *
366292 CACATCGAGTAAGGCCCTGAGTACAAAGCCGAGGAGCCTGCAAGTACACTTCCTCCAACATTACC
66 CACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTACAAGTACACTTACTCCAACAATACC
366357 CCCCAAATAAAACATTTATCAAAA
131 CCCCAAATAAAACATTTATCAAAA
366381 ATCAAAACAT
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
156 132 0.94
157 9 0.06
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.19
Consensus pattern (156 bp):
CATAGTAATCCCTCCAACCCAACACAGCATAATATGTAGGTTCCCCAGAACCATACACCAACCGT
CACATCGAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTACAAGTACACTTACTCCAACAATACC
CCCCAAATAAAACATTTATCAAAATT
Found at i:366413 original size:24 final size:24
Alignment explanation
Indices: 366381--366465 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
366371 TTTATCAAAA
*
366381 ATCAAAACATAAGT-CAGGTCAGAT
1 ATCAGAACATAA-TCCAGGTCAGAT
*
366405 ATTAGAACATAATCCAGGTCAGAT
1 ATCAGAACATAATCCAGGTCAGAT
** *
366429 ATCAGAACATAATCCATTTCAGGT
1 ATCAGAACATAATCCAGGTCAGAT
*
366453 ATCATAACATAAT
1 ATCAGAACATAAT
366466 TCAAATTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 1 0.02
24 52 0.98
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAGAACATAATCCAGGTCAGAT
Found at i:371385 original size:16 final size:18
Alignment explanation
Indices: 371356--371392 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
371346 ATCTCTTTTC
371356 TTTTTCTTTCTTGTTGTT
1 TTTTTCTTTCTTGTTGTT
371374 TTTTTC-TT-TTGTTGTT
1 TTTTTCTTTCTTGTTGTT
371390 TTT
1 TTT
371393 GAAAACTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 2 0.11
18 6 0.32
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTCTTGTTGTT
Found at i:371702 original size:20 final size:21
Alignment explanation
Indices: 371665--371704 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
371655 ACTTTGATTT
*
371665 GTTTTTGTGACTGATTGATGC
1 GTTTTTGTCACTGATTGATGC
371686 GTTTTTGTCACTG-TTGATG
1 GTTTTTGTCACTGATTGATG
371705 ATAACATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.10, G:0.28, T:0.50
Consensus pattern (21 bp):
GTTTTTGTCACTGATTGATGC
Found at i:374726 original size:2 final size:2
Alignment explanation
Indices: 374719--374745 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
374709 CCCCTCCGAC
374719 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
374746 AAATGCAGAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:375789 original size:2 final size:2
Alignment explanation
Indices: 375782--375825 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
375772 AATAATTCAT
*
375782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375824 TA
1 TA
375826 AACTAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:378931 original size:50 final size:49
Alignment explanation
Indices: 378857--379111 Score: 275
Period size: 50 Copynumber: 5.1 Consensus size: 49
378847 ACAGATATAG
*
378857 AAACTCTTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGGT
1 AAACTCTTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
* *
378906 AAACTCTTTATTTTTTTAGGTAAATTAATCATTTGAATATTAAAAGTGAT
1 AAACTC-TTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
* ** * * * **
378956 AAACTCTTAATAATTTGTAAGACAAACATACGATACATTT--TTATTGACCGAT-AT
1 AAACTCTTAAT--TTT-TTAGGTAAA-TTA--ATA-ATTTGAATATTAAAAG-TGAT
*
379010 AGAAACTCTTAATTATTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
1 --AAACTCTTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
379061 AAACTCTTAA-TTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
1 AAACTCTTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
379109 AAA
1 AAA
379112 AAAAATTATT
Statistics
Matches: 169, Mismatches: 23, Indels: 29
0.76 0.10 0.13
Matches are distributed among these distances:
48 40 0.24
49 24 0.14
50 50 0.30
51 11 0.07
52 8 0.05
53 8 0.05
54 10 0.06
55 3 0.02
56 15 0.09
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (49 bp):
AAACTCTTAATTTTTTAGGTAAATTAATAATTTGAATATTAAAAGTGAT
Found at i:378982 original size:155 final size:154
Alignment explanation
Indices: 378809--379111 Score: 518
Period size: 155 Copynumber: 2.0 Consensus size: 154
378799 AGTGTCATTC
* * *
378809 ATAATATTGTAAGACAAACATATGATATATTTTTATTGACAGATATAGAAACTCTTAATTTTTTA
1 ATAATATTGTAAGACAAACATACGATACATTTTTATTGACAGATATAGAAACTCTTAATTATTTA
* * *
378874 GGTAAATTAATAATTTGAATATTAAAAGTGGTAAACTCTTTATTTTTTTAGGTAAATTAATCATT
66 GGTAAATTAATAATTTGAATATTAAAAGTGATAAACTC-TTA-ATTTTTAGGTAAATTAATAATT
378939 TGAATATTAAAAGTGATAAACTCTTA
129 TGAATATTAAAAGTGATAAACTCTTA
*
378965 ATAAT-TTGTAAGACAAACATACGATACATTTTTATTGACCGATATAGAAACTCTTAATTATTTA
1 ATAATATTGTAAGACAAACATACGATACATTTTTATTGACAGATATAGAAACTCTTAATTATTTA
379029 GGTAAATTAATAATTTGAATATTAAAAGTGATAAACTCTTAATTTTTAGGTAAATTAATAATTTG
66 GGTAAATTAATAATTTGAATATTAAAAGTGATAAACTCTTAATTTTTAGGTAAATTAATAATTTG
379094 AATATTAAAAGTGATAAA
131 AATATTAAAAGTGATAAA
379112 AAAAATTATT
Statistics
Matches: 140, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
153 40 0.29
154 3 0.02
155 92 0.66
156 5 0.04
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (154 bp):
ATAATATTGTAAGACAAACATACGATACATTTTTATTGACAGATATAGAAACTCTTAATTATTTA
GGTAAATTAATAATTTGAATATTAAAAGTGATAAACTCTTAATTTTTAGGTAAATTAATAATTTG
AATATTAAAAGTGATAAACTCTTA
Found at i:384995 original size:2 final size:2
Alignment explanation
Indices: 384988--385014 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
384978 ATCAAGAATC
384988 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
385015 GAAAAACGTA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:386207 original size:13 final size:14
Alignment explanation
Indices: 386189--386217 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
386179 ATTATCAACA
386189 TTCA-TTTTATAAT
1 TTCATTTTTATAAT
386202 TTCATTTTTATAAT
1 TTCATTTTTATAAT
386216 TT
1 TT
386218 TAGGGACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCATTTTTATAAT
Found at i:388835 original size:3 final size:3
Alignment explanation
Indices: 388827--388900 Score: 87
Period size: 3 Copynumber: 23.7 Consensus size: 3
388817 ATATTTGTTT
* *
388827 ATA ATA ATA ATA ATA ATA TTA ATTA ATA ATA ATAA ATA ATA TTA A-A
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA
388873 ATTA ATAA ATA ATA ATA ATA ATA ATA AT
1 A-TA AT-A ATA ATA ATA ATA ATA ATA AT
388901 TTATAATCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 2 0.03
3 49 0.79
4 11 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:388897 original size:19 final size:19
Alignment explanation
Indices: 388827--388899 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
388817 ATATTTGTTT
388827 ATAATAATAATAAT-AATA
1 ATAATAATAATAATAAATA
*
388845 TTAATTAATAATAATAAATA
1 ATAA-TAATAATAATAAATA
*
388865 ATATTAA-AATTAATAAATA
1 ATAATAATAA-TAATAAATA
388884 ATAATAATAATAATAA
1 ATAATAATAATAATAA
388900 TTTATAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.11
19 34 0.72
20 8 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAATAATAATAATAAATA
Found at i:388906 original size:19 final size:19
Alignment explanation
Indices: 388824--388907 Score: 82
Period size: 19 Copynumber: 4.4 Consensus size: 19
388814 GGCATATTTG
388824 TTTATAATAATAATAATAA
1 TTTATAATAATAATAATAA
*
388843 TATTA-ATTAATAATAATAA
1 T-TTATAATAATAATAATAA
* * *
388862 ATAATATTAA-AATTAATAA
1 TTTATAATAATAA-TAATAA
* *
388881 ATAATAATAATAATAATAA
1 TTTATAATAATAATAATAA
388900 TTTATAAT
1 TTTATAAT
388908 CAAATAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
18 4 0.07
19 46 0.84
20 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAATAATAATAATAA
Found at i:389280 original size:28 final size:28
Alignment explanation
Indices: 389249--389319 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
389239 CACATGCTTT
389249 TCATTATGAACTTCTGAACAAGTTCTTC
1 TCATTATGAACTTCTGAACAAGTTCTTC
389277 TCATTATGAACTTCTGAACAAGTTCTTC
1 TCATTATGAACTTCTGAACAAGTTCTTC
389305 TCATTATGAACTTCT
1 TCATTATGAACTTCT
389320 TGTCTTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (28 bp):
TCATTATGAACTTCTGAACAAGTTCTTC
Found at i:389390 original size:79 final size:80
Alignment explanation
Indices: 389294--389446 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
389284 GAACTTCTGA
* * ** * *
389294 ACAAGTTCTTCTCATTATGAACTTCTTGTCTT-AAAATTTTGATCCAACTTCTTCTGTGAAGGAA
1 ACAAGTTCTTCTCATTATGAACTTATTCTCTTGAAAATACTGATCCAACTCCTTCTGTGAAGCAA
389358 TCGAGCAAAAGTTGT
66 TCGAGCAAAAGTTGT
* * * *
389373 ACAAGTTCTTCTTATTATGAACTTATTCTCTTGGAAATACTGATCCAACTCCTTCTGTGATGCAG
1 ACAAGTTCTTCTCATTATGAACTTATTCTCTTGAAAATACTGATCCAACTCCTTCTGTGAAGCAA
389438 TCGAGCAAA
66 TCGAGCAAA
389447 TGTGATGTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 29 0.46
80 34 0.54
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (80 bp):
ACAAGTTCTTCTCATTATGAACTTATTCTCTTGAAAATACTGATCCAACTCCTTCTGTGAAGCAA
TCGAGCAAAAGTTGT
Found at i:392107 original size:31 final size:31
Alignment explanation
Indices: 392069--392161 Score: 141
Period size: 32 Copynumber: 3.0 Consensus size: 31
392059 GTCGAGGGTC
* * *
392069 ACCTATGTCTTTCGAGACATATGGATAGTTT
1 ACCTATGTCCTTCGGGACATATGGACAGTTT
*
392100 ACCTATGTCCTTCGGGACATATGGACAGGATT
1 ACCTATGTCCTTCGGGACATATGGACA-GTTT
392132 ACCTATGTCCTTCGGGACATATGGACAGTT
1 ACCTATGTCCTTCGGGACATATGGACAGTT
392162 ATGTTCTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 26 0.46
32 30 0.54
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (31 bp):
ACCTATGTCCTTCGGGACATATGGACAGTTT
Found at i:400228 original size:54 final size:55
Alignment explanation
Indices: 400146--400256 Score: 215
Period size: 54 Copynumber: 2.0 Consensus size: 55
400136 TGCCTATAGC
400146 CAGCTCTCTTATGCAGCGAACTACGTAT-CCCATATAAGCTATCACCTTACCCAT
1 CAGCTCTCTTATGCAGCGAACTACGTATCCCCATATAAGCTATCACCTTACCCAT
400200 CAGCTCTCTTATGCAGCGAACTACGTATCCCCATATAAGCTATCACCTTACCCAT
1 CAGCTCTCTTATGCAGCGAACTACGTATCCCCATATAAGCTATCACCTTACCCAT
400255 CA
1 CA
400257 TCTGCTCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 28 0.50
55 28 0.50
ACGTcount: A:0.28, C:0.34, G:0.11, T:0.27
Consensus pattern (55 bp):
CAGCTCTCTTATGCAGCGAACTACGTATCCCCATATAAGCTATCACCTTACCCAT
Found at i:405705 original size:3 final size:3
Alignment explanation
Indices: 405697--405751 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
405687 GTTTGTTTAC
405697 AAT AAT AAT AACT -AT AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
405743 AAT ATT AAT
1 AAT AAT AAT
405752 TATTATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:405756 original size:3 final size:3
Alignment explanation
Indices: 405745--405793 Score: 71
Period size: 3 Copynumber: 15.3 Consensus size: 3
405735 ATAATAATAA
405745 TAT TAAT TAT TAT TAT TAT TAT TAT TAAT TAAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT T-AT T-AT TAT TAT TAT TAT TAT
405793 T
1 T
405794 TGTAATCGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 34 0.77
4 10 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:406122 original size:37 final size:37
Alignment explanation
Indices: 406063--406154 Score: 89
Period size: 39 Copynumber: 2.4 Consensus size: 37
406053 ATATTTTCGA
*
406063 AAAACGTATAACATATAGTTTT-AGAAAACGG-TTATTG
1 AAAACATATAA-ATATAGTTTTAAGAAAACGGATT-TTG
* *
406100 AAAACATATAAATATATTTTTTAAAGAAATCGGATTTTG
1 AAAACATATAAATATA-GTTTT-AAGAAAACGGATTTTG
*
406139 AAAATATATATAATAT
1 AAAACATATA-AATAT
406155 GGCTTTGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.11
37 14 0.30
39 20 0.43
40 7 0.15
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (37 bp):
AAAACATATAAATATAGTTTTAAGAAAACGGATTTTG
Found at i:406243 original size:34 final size:34
Alignment explanation
Indices: 406175--406353 Score: 188
Period size: 34 Copynumber: 5.2 Consensus size: 34
406165 ATACGATTTA
406175 AAAACATA-TATATA-TTTTGAAATTAC-ATTTTTG
1 AAAACATATTATATAGTTTTGAAA--ACAATTTTTG
* *
406208 AAAACATATTATCTTGTTTTGAAAACAATTTTTG
1 AAAACATATTATATAGTTTTGAAAACAATTTTTG
* *
406242 AAAATATTATTATATAG-TTTGAAAATAATTTTTG
1 AAAACA-TATTATATAGTTTTGAAAACAATTTTTG
* *
406276 AAAATATA-TATATAGTTTTGAAAACAGTTTTTG
1 AAAACATATTATATAGTTTTGAAAACAATTTTTG
* *
406309 AAACATATATAATATATAGTTTTGAAAAAAATATTTTG
1 AAA-ACATAT--TATATAGTTTTGAAAACAAT-TTTTG
406347 AAAACAT
1 AAAACAT
406354 TTTGAAAACG
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
32 7 0.06
33 30 0.24
34 43 0.34
35 16 0.13
37 21 0.17
38 8 0.06
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (34 bp):
AAAACATATTATATAGTTTTGAAAACAATTTTTG
Found at i:406355 original size:11 final size:11
Alignment explanation
Indices: 406336--406372 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
406326 AGTTTTGAAA
*
406336 AAAATATTTTG
1 AAAACATTTTG
406347 AAAACATTTTG
1 AAAACATTTTG
*
406358 AAAACGTTTTG
1 AAAACATTTTG
406369 AAAA
1 AAAA
406373 AAATAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (11 bp):
AAAACATTTTG
Found at i:406387 original size:37 final size:37
Alignment explanation
Indices: 406327--406399 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
406317 ATAATATATA
*
406327 GTTTTGAAAAAAATATTTTGAAAACATTTT-GAAAAC
1 GTTTTGAAAAAAATATTTAGAAAACATTTTCGAAAAC
406363 GTTTTGAAAAAAATAATTTAGAAAACATTTTCGAAAA
1 GTTTTGAAAAAAAT-ATTTAGAAAACATTTTCGAAAA
406400 TATATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 14 0.41
37 15 0.44
38 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.34
Consensus pattern (37 bp):
GTTTTGAAAAAAATATTTAGAAAACATTTTCGAAAAC
Found at i:418277 original size:44 final size:45
Alignment explanation
Indices: 418229--418334 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
418219 TTTATTCTGC
*
418229 TTTTTTACTTATTTTAAAAAATTTACATTTCTT-TC-TTTTATTTA
1 TTTTTTACTTATTTTAAAAAATTAACATTTCTTATCTTTTTA-TTA
* * *
418273 TTTTTTATCTTCTTTTTAAAAATTAACATTTTTTAATCTTTTTATTA
1 TTTTTTA-CTTATTTTAAAAAATTAACATTTCTT-ATCTTTTTATTA
*
418320 TTTATTTATTTATTT
1 TTT-TTTACTTATTT
418335 ATTTCCTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 7 0.14
45 22 0.43
47 13 0.25
48 9 0.18
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (45 bp):
TTTTTTACTTATTTTAAAAAATTAACATTTCTTATCTTTTTATTA
Found at i:418379 original size:54 final size:55
Alignment explanation
Indices: 418265--418380 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 55
418255 ATTTCTTTCT
*
418265 TTTATTTATTTTTTATCTTCTTTTTAAAAATTAACATTTTTTAATCTTTTTATTA
1 TTTATTTATTTTTTATCTTCTCTTTAAAAATTAACATTTTTTAATCTTTTTATTA
*
418320 TTTATTTATTTATTTAT-TTC-CTTT-AAAATTGAA-ATTTTCTTCAT-TTTTTATTTA
1 TTTATTTATTT-TTTATCTTCTCTTTAAAAATT-AACATTTT-TTAATCTTTTTA-TTA
418374 TTTATTT
1 TTTATTT
418381 TTGTTATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
53 17 0.31
54 19 0.35
55 14 0.25
56 5 0.09
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (55 bp):
TTTATTTATTTTTTATCTTCTCTTTAAAAATTAACATTTTTTAATCTTTTTATTA
Found at i:429138 original size:22 final size:22
Alignment explanation
Indices: 429113--429172 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
429103 GAATCGATAC
429113 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
429135 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
* *
429157 CCCCCCTGTAGGGGAA
1 CCCCCTTGAAGGGGAA
429173 TTGATACCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:429182 original size:22 final size:22
Alignment explanation
Indices: 429107--429183 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
429097 CAGAGAGAAT
429107 CGATACCCCCCTTGAAGGGGAAC
1 CGATACCCCCC-TGAAGGGGAAC
* *
429130 CGATTCCCCCTTGAAGGGGAAC
1 CGATACCCCCCTGAAGGGGAAC
* * *
429152 CGATTCCCCCCTGTAGGGGAAT
1 CGATACCCCCCTGAAGGGGAAC
*
429174 TGATACCCCC
1 CGATACCCCC
429184 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 38 0.81
23 9 0.19
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
CGATACCCCCCTGAAGGGGAAC
Found at i:432958 original size:21 final size:21
Alignment explanation
Indices: 432932--432971 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
432922 CAGAACCCCA
*
432932 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
432953 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
432972 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:433006 original size:20 final size:21
Alignment explanation
Indices: 432954--433014 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
432944 TTCCCCTGTG
432954 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
432977 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
432997 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
433015 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:437037 original size:36 final size:37
Alignment explanation
Indices: 436973--437217 Score: 215
Period size: 36 Copynumber: 6.8 Consensus size: 37
436963 AAAACGGTTA
* * * *
436973 TTGAAAATATATAATATATAG--TTAAAAATCAGTTT
1 TTGAAAACATATATTATATAGTTTTGAAAATCAATTT
* * *
437008 TTGAAAA-ATATATAATATGGTTTTGAAAATACGA--T
1 TTGAAAACATATATTATATAGTTTTGAAAAT-CAATTT
* * *
437043 TTAAAAACATATATTACATAATTTTGAAAA-CACATTT
1 TTGAAAACATATATTATATAGTTTTGAAAATCA-ATTT
* *
437080 TTGAAAAC--ATATTATATAGTTTCGAAAA-CAATAT
1 TTGAAAACATATATTATATAGTTTTGAAAATCAATTT
* *
437114 TTGAATATATATATTATATAGTTTTGAAAAT-AATTT
1 TTGAAAACATATATTATATAGTTTTGAAAATCAATTT
* *
437150 TTGAAAATATATATTATATAGTTTT-AAAAACAATTT
1 TTGAAAACATATATTATATAGTTTTGAAAATCAATTT
* *
437186 TTAAAAACATATATAATCTATAGTTTTGAAAA
1 TTGAAAACATATAT--TATATAGTTTTGAAAA
437218 AACATTTTGA
Statistics
Matches: 170, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
34 20 0.12
35 38 0.22
36 89 0.52
37 9 0.05
38 10 0.06
39 4 0.02
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (37 bp):
TTGAAAACATATATTATATAGTTTTGAAAATCAATTT
Found at i:437138 original size:107 final size:105
Alignment explanation
Indices: 437007--437197 Score: 256
Period size: 107 Copynumber: 1.8 Consensus size: 105
436997 AAAATCAGTT
* * *
437007 TTTGAAAAATATATAATATGGTTTTGAAAATACGATTTAAAAACATATATTACATAATTTTGAAA
1 TTTGAAAAATATATAATATAGTTTTGAAAATAAGATTTAAAAACATATATTACATAATTTTAAAA
*
437072 ACACATTTTTGAAAACATATTATATAGTTTCGAAAACAATA
66 ACA-ATTTTTAAAAACATATTATATAGTTTCGAAAACAATA
* * ** * * * *
437113 TTTGAATATATATATTATATAGTTTTGAAAATAATTTTTGAAAATATATATTATATAGTTTTAAA
1 TTTGAA-AAATATATAATATAGTTTTGAAAATAAGATTTAAAAACATATATTACATAATTTTAAA
437178 AACAATTTTTAAAAACATAT
65 AACAATTTTTAAAAACATAT
437198 ATAATCTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
106 21 0.29
107 51 0.71
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (105 bp):
TTTGAAAAATATATAATATAGTTTTGAAAATAAGATTTAAAAACATATATTACATAATTTTAAAA
ACAATTTTTAAAAACATATTATATAGTTTCGAAAACAATA
Found at i:437335 original size:36 final size:36
Alignment explanation
Indices: 437221--437326 Score: 131
Period size: 38 Copynumber: 2.9 Consensus size: 36
437211 TTGAAAAAAC
* * *
437221 ATTTTGAAAACGTTTTGAAAAAATATATAATATATA
1 ATTTTGAAAACATTTTTAAAATATATATAATATATA
* *
437257 ATTTAGAAAACATTTTTGAATATATATATATATATATA
1 ATTTTGAAAACATTTTT-AAAATATATATA-ATATATA
*
437295 ATTTTGAAAACATTTTCTAAAATATATGTAAT
1 ATTTTGAAAACATTTT-TAAAATATATATAAT
437327 TTTCATTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 14 0.24
37 12 0.20
38 32 0.54
39 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (36 bp):
ATTTTGAAAACATTTTTAAAATATATATAATATATA
Found at i:440295 original size:7 final size:7
Alignment explanation
Indices: 440283--440314 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
440273 AAAAGGAAAT
440283 TATTAAG
1 TATTAAG
440290 TATTAAG
1 TATTAAG
440297 TATTAAG
1 TATTAAG
440304 TATTAAG
1 TATTAAG
440311 TATT
1 TATT
440315 TTGATAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (7 bp):
TATTAAG
Found at i:441154 original size:48 final size:45
Alignment explanation
Indices: 441048--441172 Score: 164
Period size: 48 Copynumber: 2.8 Consensus size: 45
441038 GTAAGTATGC
* *
441048 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* *
441091 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAATATTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAATA-TATTGATA
*
441139 AAATAAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
441173 GAGATTTTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
46 11 0.15
47 9 0.12
48 29 0.40
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
Found at i:447039 original size:7 final size:7
Alignment explanation
Indices: 447027--447051 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
447017 AAAAGGAAAT
447027 TATTAAG
1 TATTAAG
447034 TATTAAG
1 TATTAAG
447041 TATTAAG
1 TATTAAG
447048 TATT
1 TATT
447052 TTGATAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (7 bp):
TATTAAG
Found at i:447894 original size:47 final size:45
Alignment explanation
Indices: 447788--447911 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 45
447778 GTAAGTATGC
** *
447788 AAATAAGCTTACGAGCTTAT-GAAT-AATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* * *
447831 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAATTTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAATATATTGATA
*
447878 AAATAAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
447912 GAGATTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
43 20 0.29
44 3 0.04
45 10 0.14
46 1 0.01
47 36 0.51
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
Found at i:454936 original size:48 final size:50
Alignment explanation
Indices: 454856--454952 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 50
454846 AGGGTGAAAA
454856 ATCTGGCTCAACCCAAGAATAATAGTAATTGACCTTTATATGTTTAGAGT
1 ATCTGGCTCAACCCAAGAATAATAGTAATTGACCTTTATATGTTTAGAGT
454906 ATCTGGCTCAACCC-A-AATAATAGTAATTGACCTTTATATGTTTAGAG
1 ATCTGGCTCAACCCAAGAATAATAGTAATTGACCTTTATATGTTTAGAG
454953 AAAATTGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 32 0.68
49 1 0.02
50 14 0.30
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (50 bp):
ATCTGGCTCAACCCAAGAATAATAGTAATTGACCTTTATATGTTTAGAGT
Found at i:457102 original size:31 final size:32
Alignment explanation
Indices: 457064--457126 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
457054 GTTGAAAAGA
457064 TAGCCTTCGATCACAAAC-TAAAAACTTCCGC
1 TAGCCTTCGATCACAAACTTAAAAACTTCCGC
457095 TAGCCTTCGATCACAAACTTAAAAACTTCCGC
1 TAGCCTTCGATCACAAACTTAAAAACTTCCGC
457127 ACAAAGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.24
Consensus pattern (32 bp):
TAGCCTTCGATCACAAACTTAAAAACTTCCGC
Found at i:458364 original size:58 final size:58
Alignment explanation
Indices: 458254--458364 Score: 127
Period size: 58 Copynumber: 1.9 Consensus size: 58
458244 CTGATTTTCA
* * * * *
458254 TTTTAAATTGATCCTAAAAATCTGAATATTCCAATTTCATCTCTCAACTATGACTTTT
1 TTTTAAATTAATCCTAAAAATCTGAATACTCCAAATTCATCTCCCAAATATGACTTTT
* *
458312 TTTTAAATTAATCTCT-AAAATTTTAATACTCCAAATTCATC-CCCAAAATATGA
1 TTTTAAATTAATC-CTAAAAATCTGAATACTCCAAATTCATCTCCC-AAATATGA
458365 TCATCATTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
57 2 0.05
58 40 0.91
59 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (58 bp):
TTTTAAATTAATCCTAAAAATCTGAATACTCCAAATTCATCTCCCAAATATGACTTTT
Found at i:461051 original size:41 final size:40
Alignment explanation
Indices: 460989--461469 Score: 295
Period size: 41 Copynumber: 11.7 Consensus size: 40
460979 TAACATTAAC
* *
460989 GGCGTTTTTCAACAAATGCCGCTAAAACTCATACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAACTCATACTTTAGT
** *
461029 GGCGTTTATTCGACAAACGCCGCTAAAGA-TAAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAA-ACTCA-TACTTTAGT
* * *
461071 GGCGTTTTTAAACAAACGCCGCCATAGAA-TCGTTCTTTAGT
1 GGCGTTTTTAAACAAACGCCG-C-TAAAACTCATACTTTAGT
* * ** *
461112 GGCGTTTTTAAATAAATGCCG-TAATAGGGT-ATA-TATATTGT
1 GGCGTTTTTAAACAAACGCCGCTAA-A-ACTCATACT-T-TAGT
* * * * *
461153 GGTGTTTTTAGATAAACGCCGCTAAAAC-CTAGTACTTCAGA
1 GGCGTTTTTAAACAAACGCCGCTAAAACTC-A-TACTTTAGT
* *
461194 GGCGTTTTATGCAA-AAACGCCGCTAAAACTCGTACTTTAGT
1 GGCGTTTT-T-AAACAAACGCCGCTAAAACTCATACTTTAGT
** *
461235 GGCGTTTATTCGACAAACGCCGCTAAAGA-TAAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAA-ACTCA-TACTTTAGT
* * *
461277 GGCGTTTGTAAACAAACGCCGCCATAGAA-T-ATTTCTTTAGT
1 GGCGTTTTTAAACAAACGCCG-C-TAAAACTCA-TACTTTAGT
** * *
461318 GGCGTTTTTAAACAAACGCCGC-AATAGGGTACATA-TATCGT
1 GGCGTTTTTAAACAAACGCCGCTAA-A-ACT-CATACTTTAGT
* * *
461359 TGCGTTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAA-CTCATACTTTAGT
*
461400 GGCGTTTTATTCAA-AAACGCCGCTAAATACTCATACTTTAGT
1 GGCG-TTT-TTAAACAAACGCCGCTAAA-ACTCATACTTTAGT
* * * *
461442 GACGATTTTAGACAAACACCGCTAAAAC
1 GGCGTTTTTAAACAAACGCCGCTAAAAC
461470 CTAGTACTCT
Statistics
Matches: 345, Mismatches: 60, Indels: 72
0.72 0.13 0.15
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 20 0.06
41 207 0.60
42 97 0.28
43 15 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (40 bp):
GGCGTTTTTAAACAAACGCCGCTAAAACTCATACTTTAGT
Found at i:461327 original size:165 final size:165
Alignment explanation
Indices: 460989--461339 Score: 374
Period size: 165 Copynumber: 2.1 Consensus size: 165
460979 TAACATTAAC
* * * * * *
460989 GGCGTTTTTCAACAAATGCCGCTAAAA-CTCA-TACTTTAGTGGCG-TTTATTCGACAAACGCCG
1 GGCGTTTTTAAACAAACGCCGCTAAAACCT-AGTACTTCAGAGGCGTTTTATGC-AAAAACGCCG
* * *
461051 CTAAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCG
64 CTAAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCCAAAGAATAGTACTTTAGTGGCG
* * * * **
461116 TTTTTAAATAAATGCCGTAATAGGGTATATATATTGT
129 TTTGTAAACAAACGCCGCAATAGAATATATATATTGT
* * *
461153 GGTGTTTTTAGATAAACGCCGCTAAAACCTAGTACTTCAGAGGCGTTTTATGCAAAAACGCCGCT
1 GGCGTTTTTAAACAAACGCCGCTAAAACCTAGTACTTCAGAGGCGTTTTATGCAAAAACGCCGCT
* ** *
461218 AAA-ACT-CGTACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAG-ATAAGTACTTTAGTGGC
66 AAAGA-TAAGTACTTTAGTGGCGTTT-TTAAACAAACGCCGCCAAAGAAT-AGTACTTTAGTGGC
* * *
461280 GTTTGTAAACAAACGCCGCCATAGAATATTTCT-TTAGT
128 GTTTGTAAACAAACGCCGCAATAGAATATATATATT-GT
461318 GGCGTTTTTAAACAAACGCCGC
1 GGCGTTTTTAAACAAACGCCGC
461340 AATAGGGTAC
Statistics
Matches: 152, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
164 45 0.30
165 101 0.66
166 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (165 bp):
GGCGTTTTTAAACAAACGCCGCTAAAACCTAGTACTTCAGAGGCGTTTTATGCAAAAACGCCGCT
AAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCCAAAGAATAGTACTTTAGTGGCGTT
TGTAAACAAACGCCGCAATAGAATATATATATTGT
Found at i:461489 original size:206 final size:206
Alignment explanation
Indices: 460989--461467 Score: 730
Period size: 206 Copynumber: 2.3 Consensus size: 206
460979 TAACATTAAC
*
460989 GGCG-TTT-TTCAACAAATGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGC
1 GGCGTTTTATTCAA-AAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGC
* *
461052 TAAAGATAAGTACTTTAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCGT
65 TAAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAATAGTTCTTTAGTGGCGT
* * * * * * *
461117 TTTTAAATAAATGCCGTAATAGGGTATATATATTGTGGTGTTTTTAGATAAACGCCGCTAAAACC
130 TTTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCGTTTTTAAATAAACGCCGCTAAAACC
*
461182 TAGTACTTCAGA
195 TAATACTTCAGA
* *
461194 GGCGTTTTATGCAAAAACGCCGCTAAAACTCGTACTTTAGTGGCGTTTATTCGACAAACGCCGCT
1 GGCGTTTTATTCAAAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCT
*
461259 AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAATATTTCTTTAGTGGCGTT
66 AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAATAGTTCTTTAGTGGCGTT
*
461324 TTTAAACAAACGCCGCAATAGGGTACATATATCGTTGCGTTTTTAAATAAACGCCGCTAAAACCT
131 TTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCGTTTTTAAATAAACGCCGCTAAAACCT
* *
461389 AATACTTTAGT
196 AATACTTCAGA
* * * *
461400 GGCGTTTTATTCAAAAACGCCGCTAAATACTCATACTTTAGTGACGATT-TTAGACAAACACCGC
1 GGCGTTTTATTCAAAAACGCCGCTAAA-ACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGC
461464 TAAA
65 TAAA
461468 ACCTAGTACT
Statistics
Matches: 248, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
205 4 0.02
206 222 0.90
207 22 0.09
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (206 bp):
GGCGTTTTATTCAAAAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCT
AAAGATAAGTACTTTAGTGGCGTTTGTAAACAAACGCCGCCATAGAATAGTTCTTTAGTGGCGTT
TTTAAACAAACGCCGCAATAGGGTACATATATCGTGGCGTTTTTAAATAAACGCCGCTAAAACCT
AATACTTCAGA
Found at i:463428 original size:21 final size:21
Alignment explanation
Indices: 463369--463429 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
463359 TGATTTATTA
*
463369 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTGTTG
463390 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
463411 TTATGGATTTCAAGTTTGT
1 TTATGGATTTCAAGTTTGT
463430 GTTTTAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.07, G:0.21, T:0.52
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:463688 original size:43 final size:43
Alignment explanation
Indices: 463564--463943 Score: 584
Period size: 43 Copynumber: 8.9 Consensus size: 43
463554 GTTTTTATAG
* * * *
463564 AAAAGCGCCGCTATAAATCTCGACCTTTTACGACATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
463607 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTTCT
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
463649 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
* *
463692 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
463734 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
463777 AAAAACGCCGCTATAGATCTCGACCTTTTGTGACGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
*
463820 AAAAACGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
* *
463863 AAAAACGCCGCTATAGATCTCGACCTTTTACGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
* * *
463906 AAAAATGCCGCTATATATCTCGACCTTTTGTGGCGTTT
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTT
463944 TTTGTTCTCA
Statistics
Matches: 309, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
42 78 0.25
43 231 0.75
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
Found at i:463712 original size:85 final size:86
Alignment explanation
Indices: 463564--463943 Score: 620
Period size: 85 Copynumber: 4.4 Consensus size: 86
463554 GTTTTTATAG
* * * *
463564 AAAAGCGCCGCTATAAATCTCGACCTTTTACGACATTTGTTCCAAAAACGCCGCTATAGATCT-G
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
*
463628 ACCTTTTGCGGCATTTGTTCT
66 ACCTTTTGCGGCATTTGTTCC
463649 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-G
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
463713 ACCTTTTGCGGCATTTGTTCC
66 ACCTTTTGCGGCATTTGTTCC
463734 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
* * *
463799 ACCTTTTGTGACGTTTGTTCC
66 ACCTTTTGCGGCATTTGTTCC
*
463820 AAAAACGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
* *
463885 ACCTTTTACGGCGTTTGTTCC
66 ACCTTTTGCGGCATTTGTTCC
* * *
463906 AAAAATGCCGCTATATATCTCGACCTTTTGTGGCGTTT
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTT
463944 TTTGTTCTCA
Statistics
Matches: 278, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
85 143 0.51
86 135 0.49
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (86 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCG
ACCTTTTGCGGCATTTGTTCC
Found at i:470149 original size:21 final size:21
Alignment explanation
Indices: 470124--470174 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
470114 CTCAGGAAAT
470124 TATCGATACCCTAAATAAGAA
1 TATCGATACCCTAAATAAGAA
*
470145 TATCGATACCCTAAATAAGAG
1 TATCGATACCCTAAATAAGAA
*
470166 TATCAATAC
1 TATCGATAC
470175 TGAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (21 bp):
TATCGATACCCTAAATAAGAA
Found at i:475282 original size:22 final size:21
Alignment explanation
Indices: 475254--475309 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
475244 ATATGCTTGA
* *
475254 GGGTATCGGTACCATTGCATGG
1 GGGTATCGGTACCATTAC-GGG
*
475276 GGGTATCGATACC--TACGGG
1 GGGTATCGGTACCATTACGGG
475295 GGGTATCGGTACCAT
1 GGGTATCGGTACCAT
475310 CTGAGCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 14 0.50
20 2 0.07
22 12 0.43
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGTATCGGTACCATTACGGG
Found at i:478025 original size:21 final size:21
Alignment explanation
Indices: 477999--478081 Score: 96
Period size: 21 Copynumber: 3.8 Consensus size: 21
477989 ACATTCAAAG
477999 GGGGTATCGATACCTATTATA
1 GGGGTATCGATACCTATTATA
* *
478020 GGGGTATCTATACCTATTCAAA
1 GGGGTATCGATACCTATT-ATA
*
478042 TGGGGTATCGATACC-AGTATTA
1 -GGGGTATCGATACCTATTA-TA
478064 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
478082 GCACAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 31 0.61
22 6 0.12
23 14 0.27
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
GGGGTATCGATACCTATTATA
Found at i:478047 original size:44 final size:44
Alignment explanation
Indices: 477954--478081 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 44
477944 TAAACCCGAC
* * * *
477954 ATGGGGTATCGATACCATAAGAAGAGTATCAATACAC-ATTCAA
1 ATGGGGTATCGATACCATTATAGGGGTATCAATACACTATTCAA
* *
477997 AGGGGGTATCGATACCTATTATAGGGGTATCTATAC-CTATTCAA
1 ATGGGGTATCGATACC-ATTATAGGGGTATCAATACACTATTCAA
* * *
478041 ATGGGGTATCGATACCAGTATTAGGGGTATCGATACTCTAT
1 ATGGGGTATCGATACCATTA-TAGGGGTATCAATACACTAT
478082 GCACAAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 19 0.26
44 49 0.68
45 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (44 bp):
ATGGGGTATCGATACCATTATAGGGGTATCAATACACTATTCAA
Found at i:478296 original size:28 final size:28
Alignment explanation
Indices: 478264--478322 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
478254 AACTATTAGC
478264 ATAGAATGCTCTTAAAAATGTTACTTTT
1 ATAGAATGCTCTTAAAAATGTTACTTTT
478292 ATAGAATGCTCTTAAAAATGTTACTTTT
1 ATAGAATGCTCTTAAAAATGTTACTTTT
478320 ATA
1 ATA
478323 AGCATTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (28 bp):
ATAGAATGCTCTTAAAAATGTTACTTTT
Found at i:484631 original size:24 final size:26
Alignment explanation
Indices: 484583--484633 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
484573 GTCGATATAT
*
484583 AAAATATCACATAAATCATAGTATGA
1 AAAATATCACATAAATAATAGTATGA
*
484609 AAAATATCATAT-AATAATA-TATGA
1 AAAATATCACATAAATAATAGTATGA
484633 A
1 A
484634 TATGTAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 6 0.26
26 11 0.48
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (26 bp):
AAAATATCACATAAATAATAGTATGA
Found at i:487678 original size:13 final size:13
Alignment explanation
Indices: 487621--487684 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
487611 CAACTATAAA
487621 ATAAAACATATCGAT
1 ATAAAA-ATATC-AT
*
487636 ATATAAAATATCAC
1 ATA-AAAATATCAT
*
487650 AT--AAATCATAAT
1 ATAAAAAT-ATCAT
487662 ATAAAAATATCAT
1 ATAAAAATATCAT
*
487675 ATAATAATAT
1 ATAAAAATAT
487685 ATGAACATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 4 0.10
12 5 0.12
13 13 0.32
14 7 0.17
15 8 0.20
16 3 0.08
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (13 bp):
ATAAAAATATCAT
Found at i:493911 original size:2 final size:2
Alignment explanation
Indices: 493904--493935 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
493894 TACACATATT
493904 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
493936 TTTTCAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:505607 original size:60 final size:59
Alignment explanation
Indices: 505534--505689 Score: 188
Period size: 60 Copynumber: 2.6 Consensus size: 59
505524 TTTGAATGAA
* * * * *
505534 TTTAGGGATGAAATTGGAATATTC-AAATATTTAGGGGCTCATTTAGAAAGAGGGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAT-TTTAAGGACTAATTTAGAAAGAGAGTCA-AG
* * * *
505594 TTTAGGGATGAAATTAAAATGTTCAAAATTTTAAGGATTAATTTAGAATGAGAGTCAAG
1 TTTAGGGATGAAATTAGAATATTCAAAATTTTAAGGACTAATTTAGAAAGAGAGTCAAG
* *
505653 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGA
1 TTTAGGGATGAAATTAGAATATTCAAAATTTTAAGGA
505690 TCGATTTGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 35 0.43
60 43 0.52
61 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (59 bp):
TTTAGGGATGAAATTAGAATATTCAAAATTTTAAGGACTAATTTAGAAAGAGAGTCAAG
Found at i:505668 original size:59 final size:60
Alignment explanation
Indices: 505534--505712 Score: 184
Period size: 59 Copynumber: 3.0 Consensus size: 60
505524 TTTGAATGAA
** * ** * *
505534 TTTAGGGATGAAATTGGAATATTCAAATA-TTTAGGGGCTCATTTAGAAAGAGGGTCATAG
1 TTTAGGGATGAAATTAAAATATTCAAA-AGTTTAAGGATTAATTTAGAAAGAGAGTCATAG
* * *
505594 TTTAGGGATGAAATTAAAATGTTCAAAATTTTAAGGATTAATTTAGAATGAGAGTCA-AG
1 TTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGATTAATTTAGAAAGAGAGTCATAG
* * ** *
505653 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGATCGATTT-GAAAAGAGAGTTATAG
1 TTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGATTAATTTAG-AAAGAGAGTCATAG
505713 CTTGGGGAGA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
58 1 0.01
59 50 0.51
60 48 0.48
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (60 bp):
TTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGATTAATTTAGAAAGAGAGTCATAG
Found at i:505690 original size:29 final size:29
Alignment explanation
Indices: 505592--505690 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 29
505582 AGAGGGTCAT
* * *
505592 AGTTTAGGGATGAAATTAAAATGTTCAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
* * * *
505621 ATTTTAAGGATTAATTTAGAATGAGAGTC--A
1 AGTTTAAGGATGAAATTAGAAT---ATTCAAA
**
505651 AGTTTGGGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATATTCAAA
505680 AGTTTAAGGAT
1 AGTTTAAGGAT
505691 CGATTTGAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
27 3 0.06
29 27 0.54
30 18 0.36
32 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.33
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATATTCAAA
Found at i:508003 original size:4 final size:4
Alignment explanation
Indices: 507978--508017 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
507968 ATTCCTCATC
* * *
507978 TACA TACA TGCA TGCA TGCA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
508018 CGATAAAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:513330 original size:32 final size:32
Alignment explanation
Indices: 513294--513368 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
513284 GATGTTTTTA
*
513294 TAAAATGAAGTGATATATCATTGGAAAGTTTC
1 TAAAATGAAGTGATATATCATTGAAAAGTTTC
*
513326 TAAAATGAAGTTATATATCATTGAAAAGTTTC
1 TAAAATGAAGTGATATATCATTGAAAAGTTTC
*
513358 TAAAGTGAAGT
1 TAAAATGAAGT
513369 AATTGGGCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (32 bp):
TAAAATGAAGTGATATATCATTGAAAAGTTTC
Found at i:513355 original size:139 final size:138
Alignment explanation
Indices: 513189--513602 Score: 533
Period size: 139 Copynumber: 3.0 Consensus size: 138
513179 TATAACACTG
* * * * * *
513189 AAATGAAGTGACATATCACTGAAAAGTTTCTAAATTAAAGTGATTGAGCACTAAAAAGTTTTTGT
1 AAATGAAGTTATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGAGCACTGAAAAGTTTTTGT
* * * * * * *
513254 TATTATGTATTAAATGGTGTGTGAGAAAATGATGTTTTTATAAAATGAAGTGATATATCATTGGA
66 CATTGTGCATTAAATGGTGTATGAGAAAA-GATATTTTTATGAAATGAAGTGATATATCATTGAA
513319 AAGTTTCTA
130 AAGTTTCTA
* * *
513328 AAATGAAGTTATATATCATTGAAAAGTTTCTAAAGTGAAGTAATTGGGCGCTGAAAAGTTTTTGT
1 AAATGAAGTTATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGAGCACTGAAAAGTTTTTGT
* * * *
513393 CATTGTGCATTAAATGATGTATGAGAAGAAGACATTTTTGTGAAATTAAGTGATATATCATTGAA
66 CATTGTGCATTAAATGGTGTATGAGAA-AAGATATTTTTATGAAATGAAGTGATATATCATTGAA
*
513458 AATTTTCTA
130 AAGTTTCTA
* * *
513467 AAATTAAGTTATATATCACTGAAAAAGTTTCTGAAGTGAAGTAATTGAGCATTGAAAAGTTTTTG
1 AAATGAAGTTATATATCACTG-AAAAGTTTCTAAAGTGAAGTAATTGAGCACTGAAAAGTTTTTG
* * * *
513532 TCATTGTGCATTAAATAGTTTATGAGAAAA-ACTTTTTTTTTGAAATGAAGTGATATATCATTGA
65 TCATTGTGCATTAAATGGTGTATGAGAAAAGA-TATTTTTATGAAATGAAGTGATATATCATTGA
513596 AAAGTTT
129 AAAGTTT
513603 TTGTCACCTA
Statistics
Matches: 237, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
138 1 0.00
139 170 0.72
140 66 0.28
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (138 bp):
AAATGAAGTTATATATCACTGAAAAGTTTCTAAAGTGAAGTAATTGAGCACTGAAAAGTTTTTGT
CATTGTGCATTAAATGGTGTATGAGAAAAGATATTTTTATGAAATGAAGTGATATATCATTGAAA
AGTTTCTA
Found at i:518897 original size:21 final size:19
Alignment explanation
Indices: 518869--518914 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
518859 TCATTGAATC
518869 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
518889 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
518908 ACTTAGT
1 A-TTAGT
518915 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:521614 original size:25 final size:24
Alignment explanation
Indices: 521586--521639 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
521576 TAGTTTTATA
521586 AAGTTATC-TCCTTTATTTTATTTT
1 AAGTTATCAT-CTTTATTTTATTTT
* *
521610 CAAGTTTTCATTTTTATTTTATTTT
1 -AAGTTATCATCTTTATTTTATTTT
521635 AAGTT
1 AAGTT
521640 TTATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.06, T:0.63
Consensus pattern (24 bp):
AAGTTATCATCTTTATTTTATTTT
Found at i:521641 original size:12 final size:12
Alignment explanation
Indices: 521601--521646 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
521591 ATCTCCTTTA
521601 TTTTATTTTCAAG
1 TTTTATTTT-AAG
*
521614 TTTTCATTTTTA-
1 TTTT-ATTTTAAG
521626 TTTTATTTTAAG
1 TTTTATTTTAAG
521638 TTTTATTTT
1 TTTTATTTT
521647 TAAACATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 13 0.45
13 5 0.17
14 5 0.17
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:521647 original size:24 final size:25
Alignment explanation
Indices: 521597--521648 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
521587 AGTTATCTCC
521597 TTTATTTTATTTTCAAGTTTTCATT
1 TTTATTTTATTTTCAAGTTTTCATT
521622 TTTATTTTATTTT-AAGTTTT-ATT
1 TTTATTTTATTTTCAAGTTTTCATT
521645 TTTA
1 TTTA
521649 AACATGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTATTTTATTTTCAAGTTTTCATT
Found at i:524382 original size:19 final size:21
Alignment explanation
Indices: 524358--524469 Score: 135
Period size: 19 Copynumber: 5.5 Consensus size: 21
524348 TGCAAAAATG
524358 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
524377 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
524399 GTATCGATACCATAG-TAG-A
1 GTATCGATACCATAGATAGTA
524418 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* **
524440 GTATCGATACCAT-GGTAGGG
1 GTATCGATACCATAGATAGTA
524460 GTATCGATAC
1 GTATCGATAC
524470 TAAAAAGCCA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
19 29 0.35
20 16 0.20
21 8 0.10
22 29 0.35
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:524418 original size:41 final size:41
Alignment explanation
Indices: 524358--524469 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
524348 TGCAAAAATG
* *
524358 GTATCGATACCATAATAGAGTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAGTAGAGTATCGATACCATAGTATAGTA
524399 GTATCGATACCATAGTAGAGTATCGATACCATAGTATAGTA
1 GTATCGATACCATAGTAGAGTATCGATACCATAGTATAGTA
* *
524440 GTATCGATACCATGGTAGGGGTATCGATAC
1 GTATCGATACCATAGTA-GAGTATCGATAC
524470 TAAAAAGCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 55 0.83
42 11 0.17
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (41 bp):
GTATCGATACCATAGTAGAGTATCGATACCATAGTATAGTA
Found at i:524876 original size:55 final size:55
Alignment explanation
Indices: 524792--524958 Score: 266
Period size: 55 Copynumber: 3.0 Consensus size: 55
524782 ATTTCCTAAT
*
524792 GGCACTGA-GTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACT-ATGTGTGCAAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
524848 GGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
524903 GGCACTATATGTGC-GAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
524957 GG
1 GG
524959 AAATATATGT
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
54 41 0.39
55 48 0.46
56 16 0.15
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:524946 original size:54 final size:55
Alignment explanation
Indices: 524801--524968 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 55
524791 TGGCACTGAG
* * *
524801 TGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTG
1 TGTGCAAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATA
524857 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATA
1 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATA
* * *
524912 TGTGC-GAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGAAATATA
1 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATA
524966 TGT
1 TGT
524969 ACAATTATCA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 49 0.46
55 48 0.45
56 9 0.08
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATA
Found at i:525262 original size:68 final size:68
Alignment explanation
Indices: 525172--525713 Score: 771
Period size: 68 Copynumber: 8.0 Consensus size: 68
525162 AGATTAATGC
* *
525172 CCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525237 AGG
66 AGG
* * * * ** * * *
525240 TCTAATTGTGCATTTGAAAGAAAGGTGTCAAATATATCAATTAGATGAAAGGCTAATTACCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
*
525305 AGA
66 AGG
* * *
525308 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAGGTACCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525373 AGG
66 AGG
*
525376 CCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525441 AGG
66 AGG
* * **
525444 CCTAACTATGTATTTGACAGAAATATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525509 AGG
66 AGG
* * * *
525512 CCTAAATGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGAT-AAAGGCTAACTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525576 AGG
66 AGG
* *
525579 TCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525644 AGG
66 AGG
* * * * * * * *
525647 CCTAATTATGCATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATAAAAGGTTAAATACCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
525712 AG
66 AG
525714 TAAAAGACTG
Statistics
Matches: 419, Mismatches: 54, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
67 61 0.15
68 358 0.85
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AGG
Found at i:525800 original size:45 final size:46
Alignment explanation
Indices: 525734--525878 Score: 188
Period size: 45 Copynumber: 3.2 Consensus size: 46
525724 GATGTACAAC
* *
525734 AATGCATAAT-GTCGTATAAAAGGGCATGAAATGATGTTATAAATGA
1 AATGCATAATAG-CGTATAAAAGGGCATGAAAGGATGTCATAAATGA
* * *
525780 AATGTATCATAGCGTA-AAAAGGGCATGAAAGGATGTCATAAATTA
1 AATGCATAATAGCGTATAAAAGGGCATGAAAGGATGTCATAAATGA
* *
525825 AATGCATAATAGCGTATAAAA-GACATGAAAGGATGCCATAAATGA
1 AATGCATAATAGCGTATAAAAGGGCATGAAAGGATGTCATAAATGA
*
525870 AAGGCATAA
1 AATGCATAA
525879 GGGTGCATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
45 69 0.80
46 16 0.19
47 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.23
Consensus pattern (46 bp):
AATGCATAATAGCGTATAAAAGGGCATGAAAGGATGTCATAAATGA
Found at i:527671 original size:18 final size:19
Alignment explanation
Indices: 527640--527686 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
527630 GTAATGAGAT
527640 ATTTAAAT-AATAAAAACA
1 ATTTAAATAAATAAAAACA
**
527658 A-TTAAATAAATAAAAGTA
1 ATTTAAATAAATAAAAACA
527676 ATTTAAATAAA
1 ATTTAAATAAA
527687 AATAAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
ATTTAAATAAATAAAAACA
Found at i:534738 original size:118 final size:119
Alignment explanation
Indices: 534529--534760 Score: 457
Period size: 118 Copynumber: 2.0 Consensus size: 119
534519 AAAATTAATT
534529 TCTTCTAAGCCTAAGGTTCTGCCTTCTGTTTTGCAGGCGCCTGAAGTTGAACTAAAACCGTTACC
1 TCTTCTAAGCCTAAGGTTCTGCCTTCTGTTTTGCAGGCGCCTGAAGTTGAACTAAAACCGTTACC
534594 GGATCACATGAAGTTCGTTTTTCTTGGGGCAAATAACACTTTTCCAGTTTGATC
66 GGATCACATGAAGTTCGTTTTTCTTGGGGCAAATAACACTTTTCCAGTTTGATC
534648 TCTTCTAAGCCTAAGGTTCTGCCTT-TGTTTTGCAGGCGCCTGAAGTTGAACTAAAACCGTTACC
1 TCTTCTAAGCCTAAGGTTCTGCCTTCTGTTTTGCAGGCGCCTGAAGTTGAACTAAAACCGTTACC
534712 GGATCACATGAAGTTCGTTTTTCTTGGGGCAAATAACACTTTTCCAGTT
66 GGATCACATGAAGTTCGTTTTTCTTGGGGCAAATAACACTTTTCCAGTT
534761 ATCATATAGA
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 88 0.78
119 25 0.22
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (119 bp):
TCTTCTAAGCCTAAGGTTCTGCCTTCTGTTTTGCAGGCGCCTGAAGTTGAACTAAAACCGTTACC
GGATCACATGAAGTTCGTTTTTCTTGGGGCAAATAACACTTTTCCAGTTTGATC
Found at i:537637 original size:5 final size:5
Alignment explanation
Indices: 537629--537657 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
537619 TTCATTGCAT
537629 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
537658 GGTTAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:541704 original size:24 final size:25
Alignment explanation
Indices: 541658--541704 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
541648 ATCTCCTTTA
*
541658 TTTTCTTTTCGAGTTTTCATTTTTC
1 TTTTATTTTCGAGTTTTCATTTTTC
541683 TTTTATTTT-GAGTTTT-ATTTTT
1 TTTTATTTTCGAGTTTTCATTTTT
541705 AAACATGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.72
Consensus pattern (25 bp):
TTTTATTTTCGAGTTTTCATTTTTC
Found at i:543371 original size:12 final size:12
Alignment explanation
Indices: 543354--543381 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
543344 CTTCAATATT
543354 GTAGCAAATGTC
1 GTAGCAAATGTC
543366 GTAGCAAATGTC
1 GTAGCAAATGTC
543378 GTAG
1 GTAG
543382 ATTCCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (12 bp):
GTAGCAAATGTC
Found at i:553132 original size:23 final size:26
Alignment explanation
Indices: 553089--553138 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
553079 TTATAATTAA
*
553089 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
553115 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
553138 A
1 A
553139 TCAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:554785 original size:3 final size:3
Alignment explanation
Indices: 554779--554847 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
554769 ATTATTTTTT
* *
554779 TAA TAA TAA TAA TAA T-A TATA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
554824 TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
554848 ATAAAAATGG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:554844 original size:24 final size:24
Alignment explanation
Indices: 554779--554847 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
554769 ATTATTTTTT
554779 TAATAATAATAATAAT-ATATATTA
1 TAATAATAATAATAATAATA-ATTA
*
554803 TTATAATAATAATAATAATAATTA
1 TAATAATAATAATAATAATAATTA
554827 TAATAATAATAATAATAATAA
1 TAATAATAATAATAATAATAA
554848 ATAAAAATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 39 0.93
25 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAATAATAATAATAATAATAATTA
Found at i:555329 original size:119 final size:119
Alignment explanation
Indices: 554999--555396 Score: 620
Period size: 119 Copynumber: 3.3 Consensus size: 119
554989 ATTCTTCTCT
* * ** * * * * * * *
554999 TTCTTCAGATGAGTTTTTCTCATTATGAACTT-TC-CGATGGGGATGAAGTTGACCTATTTCCTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGA-AAGGTTGATGCTAATCTATCTCTTT
* * * * *
555062 CTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTCTTC
65 CTGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
555117 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAGGTTGATGCTAATCTATCTCTTT
555182 CTGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
65 CTGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
555237 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTC
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTC
555302 TGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
66 TGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
555356 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAA
555397 AGCTGATCAT
Statistics
Matches: 261, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
118 29 0.11
119 132 0.51
120 98 0.38
121 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (119 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTC
TGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
Found at i:555653 original size:113 final size:113
Alignment explanation
Indices: 555316--556093 Score: 1075
Period size: 113 Copynumber: 7.0 Consensus size: 113
555306 ATAGAATTAT
* * *
555316 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
555377 ATTATGAACTTC--TCTGGAAAAGCTGAT-CATCAAGTGATGGATTTGA
66 ATTATGAAC-TCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
*
555423 GCAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * * * *
555484 CTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAA
63 CTCATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
* *
555535 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
555600 ATTATGAACTCGAACTGGTAATGCTGATCCATCAAGTGATGGATTTTA
66 ATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
*
555648 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-T-T-
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
555710 ATTATGAACTCGAACTAGTAATGCTGATCCATCAAGTGATGGATTTTA
66 ATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
* *
555758 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
555823 ATTATGAACTCGAACTGGTAATGCTGATCCATCAAGTGATGGATTTTA
66 ATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
*
555871 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
555936 ATTATGAACTCGAACTGGAAAAGCTGATCCATTAAGTGATGGATTTGA
66 ATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
* *
555984 GC-AAAAGATTGAACAAGTTCTTCTCATTATGAAC-TCTACCTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
**** * *
556047 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTT
65 CATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTT
556094 GAATCTTTGC
Statistics
Matches: 615, Mismatches: 41, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
107 45 0.07
109 2 0.00
110 127 0.21
111 12 0.02
112 122 0.20
113 290 0.47
114 1 0.00
115 5 0.01
116 11 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGAACTGGAAATGCTGATCCATCAAGTGATGGATTTTA
Found at i:555765 original size:223 final size:225
Alignment explanation
Indices: 555316--556093 Score: 1080
Period size: 223 Copynumber: 3.5 Consensus size: 225
555306 ATAGAATTAT
* * *
555316 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
555378 TTATGAACTTC--TCTGGAAAAGCTGAT-CATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAA
66 TTATGAAC-TCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAG
* * *
555440 TTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
130 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCGAA
* * * * *
555501 CTGGCAATGTTAATCCATCAAATGATGAATTTAA
192 CTGGAAATGCTGATCCATCAAGTGATGGATTTAA
* *
555535 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
555600 ATTATGAACTCGAACTGGTAATGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAG
65 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAG
*
555665 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-T-T-ATTATGAACTCGAACTA
130 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
555727 GTAATGCTGATCCATCAAGTGATGGATTTTA
195 GAAATGCTGATCCATCAAGTGATGGATTTAA
* *
555758 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
555823 ATTATGAACTCGAACTGGTAATGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAG
65 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAG
555888 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
130 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * *
555953 GAAAAGCTGATCCATTAAGTGATGGATTTGA
195 GAAATGCTGATCCATCAAGTGATGGATTTAA
* *
555984 GC-AAAAGATTGAACAAGTTCTTCTCATTATGAACTCTACCTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**** *
556048 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTT
65 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTT
556094 GAATCTTTGC
Statistics
Matches: 506, Mismatches: 38, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
219 29 0.06
222 8 0.02
223 240 0.47
224 14 0.03
225 122 0.24
226 76 0.15
227 1 0.00
228 5 0.01
229 11 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (225 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAGT
TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAATGCTGATCCATCAAGTGATGGATTTAA
Found at i:555902 original size:336 final size:331
Alignment explanation
Indices: 555316--556095 Score: 1070
Period size: 336 Copynumber: 2.3 Consensus size: 331
555306 ATAGAATTAT
* * *
555316 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTC-T-TCA
* *
555378 TTATGAACTTCTCTGGAAAAGCTGATCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTC
64 TTATGAACTTCACTAGAAAAGCTGATCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTC
* *
555443 TTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
129 TTCTCATTATGAATTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCGAACTGGCAA
*
555508 TGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
192 TGCTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * *
555573 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGCTGATCCATCAAGTG
257 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTG
*
555638 ATGGATTTTA
322 ATGGATTTGA
*
555648 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-AT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCAT
* * * *
555712 TATGAAC-TCGAACTAGTAATGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAGT
65 TATGAACTTC--ACTAGAAAAGCTGAT-CATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* *
555776 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTTATTATGAACTCGAACTG
127 TCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATAGAGTTCTTCTCATTATGAACTCGAACTG
* * * * * * *
555840 GTAATGCTGATCCATCAAGTGATGGATTTTAGCAAAAAGTTGAACAAGTTCTTCTTATTATGAAC
188 GCAATGCTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
555905 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATTA
253 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCA
555970 AGTGATGGATTTGA
318 AGTGATGGATTTGA
* *
555984 GC-AAAAGATTGAACAAGTTCTTCTCATTATGAACTCTACCTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAG-TTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTC-T-TC
* * *
556048 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
63 ATTATGAAC-TTCACTAGAAAAGCTGAT-CATCAAGTGATGGATTTGA
556096 ATCTTTGCTA
Statistics
Matches: 395, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
332 31 0.08
333 9 0.02
334 12 0.03
335 84 0.21
336 201 0.51
337 2 0.01
338 43 0.11
339 11 0.03
340 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (331 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCATT
ATGAACTTCACTAGAAAAGCTGATCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTT
CTCATTATGAATTTCTTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCGAACTGGCAATGCT
AATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGG
ATTTGA
Found at i:556943 original size:115 final size:115
Alignment explanation
Indices: 556782--557245 Score: 785
Period size: 115 Copynumber: 4.1 Consensus size: 115
556772 GATCATGCAG
* * * * *
556782 TTCATCTTTTAATTCCAATGATTGG-TTTTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
556846 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
*
556896 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCACAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
556961 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
*
557011 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
557076 AACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAGCATA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
* *
557126 TTCATCTTGT----TCTAATGATTGGTTTTTGGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTT-TCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
557187 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
65 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
557238 TTCATCTT
1 TTCATCTT
557246 GTTCCAATTA
Statistics
Matches: 335, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
112 107 0.32
114 23 0.07
115 204 0.61
116 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
Found at i:557223 original size:227 final size:226
Alignment explanation
Indices: 556782--557245 Score: 779
Period size: 227 Copynumber: 2.0 Consensus size: 226
556772 GATCATGCAG
* * * *
556782 TTCATCTTTTAATTCCAATGATTGGTTTTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
556847 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTCAAATCC
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTT---ATCC
*
556912 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCACAGAACACTTCCAGAAGAT
128 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
556977 GCTATTGGGTCTTCTTATTTCTACTATGAGCACA
193 GCTATTGGGTCTTCTTATTTCTACTATGAGCACA
557011 TTCATCTTTCAAATCCAATGATTGGTTTT-TGGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGT-GG-TTCATACCAAACCAGATCAGATAACTCAAA
* * *
557075 GAACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAGCATATTCATCTTGT-TCT
64 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTT-TATCC
*
557139 AATGATTGGTTTTTGGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
128 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
557204 GCTATTGGGTCTTCTTATTTCTACTATGAGCACA
193 GCTATTGGGTCTTCTTATTTCTACTATGAGCACA
557238 TTCATCTT
1 TTCATCTT
557246 GTTCCAATTA
Statistics
Matches: 223, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
227 107 0.48
228 1 0.00
229 29 0.13
230 85 0.38
231 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (226 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTATCCAAT
GATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
ATTGGGTCTTCTTATTTCTACTATGAGCACA
Found at i:559149 original size:22 final size:22
Alignment explanation
Indices: 559132--559198 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
559122 CTCGTATAAA
559132 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
559154 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
559176 TGCACCGAAGTGCTCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
559198 T
1 T
559199 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:559459 original size:30 final size:31
Alignment explanation
Indices: 559418--559477 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
559408 TAGACATAGT
*
559418 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
559448 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
559478 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:559534 original size:29 final size:29
Alignment explanation
Indices: 559492--559563 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
559482 TTTTCTGCAT
**
559492 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
559521 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
559550 ATTCATGTCATGTA
1 ATTCATGTCATGTA
559564 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:559984 original size:68 final size:67
Alignment explanation
Indices: 559866--560017 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
559856 TTTTTCTCAT
* * * *
559866 GGGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
559931 TGA
65 TGA
* * * *
559934 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
559999 GA
66 GA
*
560001 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
560018 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 27 0.36
68 48 0.64
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
GA
Found at i:560027 original size:21 final size:21
Alignment explanation
Indices: 559997--560039 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
559987 ATCATATTCG
* *
559997 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
560018 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
560039 T
1 T
560040 AGCCCGAAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:560029 original size:67 final size:67
Alignment explanation
Indices: 559867--560039 Score: 206
Period size: 68 Copynumber: 2.6 Consensus size: 67
559857 TTTTCTCATG
* * *
559867 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
559932 GAG
65 GAA
* * * *
559935 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
559999 GAA
65 GAA
* *
560002 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
560040 AGCCCGAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.42
68 45 0.49
69 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:568175 original size:15 final size:15
Alignment explanation
Indices: 568152--568183 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
568142 TGAAATGAAT
568152 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
568167 AATGTATGTATGCAA
1 AATGAATGTATGCAA
568182 AA
1 AA
568184 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:572047 original size:23 final size:26
Alignment explanation
Indices: 572004--572053 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
571994 TTATAATTAA
*
572004 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
572030 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
572053 A
1 A
572054 TCAGAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:573703 original size:3 final size:3
Alignment explanation
Indices: 573697--573768 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
573687 ATTATTTTTT
*
573697 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
573742 TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
573769 ATAAAAATGG
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:576143 original size:2 final size:2
Alignment explanation
Indices: 576131--576186 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
576121 TATCAAAATA
* * *
576131 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576173 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
576187 TTGCTCCTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:585362 original size:14 final size:14
Alignment explanation
Indices: 585343--585389 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
585333 AAAACTAATG
585343 AAAATAAATGAATA
1 AAAATAAATGAATA
*
585357 AAAATAAATAAAT-
1 AAAATAAATGAATA
*
585370 AAAAT-ATTGAATA
1 AAAATAAATGAATA
585383 AAAATAA
1 AAAATAA
585390 TAATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 13 0.46
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (14 bp):
AAAATAAATGAATA
Found at i:585373 original size:27 final size:28
Alignment explanation
Indices: 585338--585405 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
585328 ATTCTAAAAC
585338 TAATGAAAATAAATGAATAAAAAT-A-AA
1 TAAT-AAAATAAATGAATAAAAATAATAA
*
585365 TAAATAAAAT-ATTGAATAAAAATAATAA
1 T-AATAAAATAAATGAATAAAAATAATAA
585393 TAATAAAATAAAT
1 TAATAAAATAAAT
585406 AAAGTAGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 12 0.34
27 15 0.43
28 8 0.23
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.26
Consensus pattern (28 bp):
TAATAAAATAAATGAATAAAAATAATAA
Found at i:585382 original size:26 final size:27
Alignment explanation
Indices: 585351--585402 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
585341 TGAAAATAAA
585351 TGAATAAAAAT-A-AATAAATAAAATAT
1 TGAATAAAAATAATAAT-AATAAAATAT
585377 TGAATAAAAATAATAATAATAAAATA
1 TGAATAAAAATAATAATAATAAAATA
585403 AATAAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
27 10 0.42
28 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (27 bp):
TGAATAAAAATAATAATAATAAAATAT
Found at i:586001 original size:13 final size:13
Alignment explanation
Indices: 585983--586015 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
585973 AGCATTGTGA
*
585983 AAAGAAAATAATG
1 AAAGAAAATAAAG
585996 AAAGAAAATAAAG
1 AAAGAAAATAAAG
586009 AAA-AAAA
1 AAAGAAAA
586016 GATAGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:589802 original size:3 final size:3
Alignment explanation
Indices: 589796--589824 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
589786 CTACTACTTC
589796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
589825 TTTTTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:591715 original size:22 final size:22
Alignment explanation
Indices: 591687--591738 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
591677 GTATGAACAT
591687 TATCGATACCCTATGGAAGA-GG
1 TATCGATACCCTAT-GAAGAGGG
*
591709 TATCGATA-CCTATGTAGAGGG
1 TATCGATACCCTATGAAGAGGG
591730 TATCGATAC
1 TATCGATAC
591739 AAAGGGAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (22 bp):
TATCGATACCCTATGAAGAGGG
Found at i:592620 original size:28 final size:28
Alignment explanation
Indices: 592579--592684 Score: 133
Period size: 28 Copynumber: 3.8 Consensus size: 28
592569 AGAGTCGAGG
* *
592579 GTTCTACGTAGTCCTTCGGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
* * *
592607 GTTCTGTGTGGTCCTTCGGAACATATAT
1 GTTCTATGTGGTCCTTCGGGACATATGT
* * *
592635 GTTCTATGTGGTCCTTCTGGATATATGA
1 GTTCTATGTGGTCCTTCGGGACATATGT
592663 GTT-TATGTGGTCCTTCGGGACA
1 GTTCTATGTGGTCCTTCGGGACA
592685 ATTTCTATGC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
27 17 0.26
28 48 0.74
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (28 bp):
GTTCTATGTGGTCCTTCGGGACATATGT
Found at i:617723 original size:55 final size:54
Alignment explanation
Indices: 617664--617911 Score: 282
Period size: 55 Copynumber: 4.5 Consensus size: 54
617654 TAGAATTAAC
617664 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAA-T
* ***
617719 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-T-AGCCAAAAT
* ** * * *
617778 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
* * *
617832 GATTGAGCACCTCTGTGCTTCAATCGAG-GATTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAT
* *
617887 GACTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
617912 TAAAATCAAG
Statistics
Matches: 163, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 47 0.29
55 68 0.42
56 1 0.01
58 1 0.01
59 40 0.25
60 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
Found at i:617762 original size:27 final size:27
Alignment explanation
Indices: 617671--617876 Score: 91
Period size: 27 Copynumber: 7.4 Consensus size: 27
617661 AACGATTGAG
*
617671 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
* ** * *
617698 CACCTCTGTG-TAGCCAAAAGTG-ATTGA
1 CACCTCTGTGCT--TCAATCGAGAACTGA
617725 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
* *** *
617753 CACCTCTGTGCAGTTAAAAAAAAATGACTGA
1 CACCTCTGTGC--TTCAATCGAGA--ACTGA
** * *
617784 GCACCTCTGTGCTTCAGCCGGGAGCTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
* *
617812 CACCTCTGTG-TAGCTAA--GATG-ATTGA
1 CACCTCTGTGCT-TC-AATCGA-GAACTGA
* *
617838 GCACCTCTGTGCTTCAATCGAGGATTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
617866 CACCTCTGTGC
1 CACCTCTGTGC
617877 AGCCAACTAT
Statistics
Matches: 131, Mismatches: 30, Indels: 36
0.66 0.15 0.18
Matches are distributed among these distances:
26 8 0.06
27 64 0.49
28 32 0.24
29 7 0.05
30 4 0.03
31 5 0.04
32 11 0.08
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:617873 original size:113 final size:114
Alignment explanation
Indices: 617667--617878 Score: 354
Period size: 113 Copynumber: 1.9 Consensus size: 114
617657 AATTAACGAT
*
617667 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
617732 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * * *
617781 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
* *
617845 TGTGCTTCAATCGAGGATTGACACCTCTGTGCAG
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG
617879 CCAACTATGA
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 46 0.51
114 45 0.49
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (114 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:623185 original size:17 final size:16
Alignment explanation
Indices: 623160--623191 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
623150 TTCTTCCTCA
623160 TTCCCTCTTCACTCTT
1 TTCCCTCTTCACTCTT
623176 TTCCCTTCTTCACTCT
1 TTCCC-TCTTCACTCT
623192 GTAACTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (16 bp):
TTCCCTCTTCACTCTT
Found at i:637056 original size:19 final size:19
Alignment explanation
Indices: 637027--637071 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
637017 ATCATAAATT
637027 ATTTT-AACATAAAATAAA
1 ATTTTAAACATAAAATAAA
637045 ATTTTAAACATAAAATAAA
1 ATTTTAAACATAAAATAAA
637064 ATTTTAAA
1 ATTTTAAA
637072 GACTAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTTAAACATAAAATAAA
Found at i:645847 original size:21 final size:21
Alignment explanation
Indices: 645821--645878 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
645811 AAAACAGAGA
***
645821 AGGGATCGATCTTTTCTTTCG
1 AGGGATCGATCTTTTCCCACG
645842 AGGGATCGATCTTTTCCCACG
1 AGGGATCGATCTTTTCCCACG
645863 AGGGATCGATCCTTTT
1 AGGGATCGAT-CTTTT
645879 TAAAGGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (21 bp):
AGGGATCGATCTTTTCCCACG
Found at i:646197 original size:27 final size:27
Alignment explanation
Indices: 646156--646224 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
646146 CATCTGTGAC
* * * *
646156 GGCGGCGGTGGCATCGGGTAAGGGAAT
1 GGCGGCGGCGACATCGGATAAGGGAAA
* *
646183 GGCGGCGGCGACATCTGATAATGGAAA
1 GGCGGCGGCGACATCGGATAAGGGAAA
* *
646210 GGCAGTGGCGACATC
1 GGCGGCGGCGACATC
646225 ATATATGGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.19, G:0.43, T:0.14
Consensus pattern (27 bp):
GGCGGCGGCGACATCGGATAAGGGAAA
Found at i:647926 original size:9 final size:9
Alignment explanation
Indices: 647914--647947 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
647904 TAAGTAAAAT
647914 ATTAAATAA
1 ATTAAATAA
647923 ATTAAAT-A
1 ATTAAATAA
*
647931 CTTAAATAA
1 ATTAAATAA
647940 ATTAAATA
1 ATTAAATA
647948 TAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:647928 original size:17 final size:16
Alignment explanation
Indices: 647899--647954 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
647889 TGCAAAAAAG
* *
647899 TTAAATAAGTAAAATA
1 TTAAATAAATTAAATA
647915 TTAAATAAATTAAATA
1 TTAAATAAATTAAATA
647931 CTTAAATAAATTAAATA
1 -TTAAATAAATTAAATA
*
647948 TAAAATA
1 TTAAATA
647955 TTAAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
TTAAATAAATTAAATA
Found at i:656925 original size:24 final size:23
Alignment explanation
Indices: 656891--656935 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
656881 TTGGTGAATC
*
656891 ATTGTTGCCAACTATACAACCATT
1 ATTGTTACCAACT-TACAACCATT
*
656915 ATTGTTACCAACTTTCAACCA
1 ATTGTTACCAACTTACAACCA
656936 CCAAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTGTTACCAACTTACAACCATT
Found at i:660526 original size:15 final size:15
Alignment explanation
Indices: 660508--660542 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
660498 TAAAATTTTA
660508 AAATTTAAATTACAG
1 AAATTTAAATTACAG
* *
660523 AAATTTAGATTACTG
1 AAATTTAAATTACAG
660538 AAATT
1 AAATT
660543 AAAACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTACAG
Found at i:662247 original size:2 final size:2
Alignment explanation
Indices: 662240--662285 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
662230 TACGTAGAAT
662240 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
662282 TA TA
1 TA TA
662286 AACAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:663171 original size:20 final size:20
Alignment explanation
Indices: 663121--663175 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
663111 ATTAACATCT
*
663121 CAATTTAATAAAAATGAATA
1 CAATTAAATAAAAATGAATA
*
663141 CAATTATATAAAAAT-ATATA
1 CAATTAAATAAAAATGA-ATA
663161 -AACTTAAATAAAAAT
1 CAA-TTAAATAAAAAT
663176 TAACTATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
CAATTAAATAAAAATGAATA
Found at i:663329 original size:16 final size:16
Alignment explanation
Indices: 663308--663340 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
663298 CTACAAATGG
663308 ATGAGATCAAAATTCA
1 ATGAGATCAAAATTCA
663324 ATGAGATCAAAATTCA
1 ATGAGATCAAAATTCA
663340 A
1 A
663341 GCTTTAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (16 bp):
ATGAGATCAAAATTCA
Found at i:663652 original size:22 final size:22
Alignment explanation
Indices: 663627--663853 Score: 127
Period size: 22 Copynumber: 10.0 Consensus size: 22
663617 TAATATATGG
*
663627 TTTTTGAAAATATATAGTATAA
1 TTTTTGAAAATATATAATATAA
** *
663649 TTTTT-AAAAGTATATGGTATAG
1 TTTTTGAAAA-TATATAATATAA
663671 TTTTTGAAAATATATAATAT-A
1 TTTTTGAAAATATATAATATAA
* * * * *
663692 GTTTTAAAAACATATAGTATAG
1 TTTTTGAAAATATATAATATAA
** * *
663714 TTTTTGAAAGCATATTATATAG
1 TTTTTGAAAATATATAATATAA
*** *
663736 TTTAAAAAAACATATAATATATA
1 TTTTTGAAAATATATAATATA-A
*
663759 GTTTTTGAAAATATATAATATAG
1 -TTTTTGAAAATATATAATATAA
* * *
663782 TTTTTAAAAACATATTGTTATATAA
1 TTTTT-GAAA-ATA-TATAATATAA
*
663807 -TTTTGAAAACATATAATATATA
1 TTTTTGAAAATATATAATATA-A
*
663829 TAGATTTTGAATATATATATATATA
1 T---TTTTGAAAATATATA-ATATA
663854 TATATATATA
Statistics
Matches: 155, Mismatches: 36, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
21 27 0.17
22 69 0.45
23 10 0.06
24 24 0.15
25 7 0.05
26 13 0.08
27 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTTTGAAAATATATAATATAA
Found at i:663768 original size:46 final size:43
Alignment explanation
Indices: 663616--663796 Score: 200
Period size: 43 Copynumber: 4.0 Consensus size: 43
663606 TGTCAAAAAA
* * **
663616 ATAATATATGGTTTTTGAAAATATATAGTATAATTTTTAAAAGTAT
1 ATAATATA--GTTTTTGAAAATATATAATAT-AGTTTTAAAAACAT
**
663662 ATGGTATAGTTTTTGAAAATATATAATATAGTTTTAAAAACAT
1 ATAATATAGTTTTTGAAAATATATAATATAGTTTTAAAAACAT
* ** * *
663705 ATAGTATAGTTTTTGAAAGCATATTATATAGTTTAAAAAAACAT
1 ATAATATAGTTTTTGAAAATATATAATATAGTTT-TAAAAACAT
663749 ATAATATATAGTTTTTGAAAATATATAATATAGTTTTTAAAAACAT
1 AT-A-ATATAGTTTTTGAAAATATATAATATAG-TTTTAAAAACAT
663795 AT
1 AT
663797 TGTTATATAA
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
43 41 0.36
44 30 0.26
45 1 0.01
46 40 0.35
47 3 0.03
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (43 bp):
ATAATATAGTTTTTGAAAATATATAATATAGTTTTAAAAACAT
Found at i:663811 original size:46 final size:43
Alignment explanation
Indices: 663587--663826 Score: 214
Period size: 46 Copynumber: 5.3 Consensus size: 43
663577 AATATATGAT
* * *
663587 AATATATAATGTATAGTTTTGTCAAAAAAATAATATATGGTTTTTGAA
1 AATATATAA--TATAGTTTT-T-AAAAACAT-ATGTATAGTTTTTGAA
* * **
663635 AATATATAGTATAATTTTTAAAAGTATATGGTATAGTTTTTGAA
1 AATATATAATATAGTTTTTAAAAACATAT-GTATAGTTTTTGAA
663679 AATATATAATATAG-TTTTAAAAACATATAGTATAGTTTTTGAA
1 AATATATAATATAGTTTTTAAAAACATAT-GTATAGTTTTTGAA
** * ** *
663722 AGCATATTATATAGTTTAAAAAAACATATAATATATAGTTTTTGAA
1 AATATATAATATAGTTTTTAAAAAC--AT-ATGTATAGTTTTTGAA
663768 AATATATAATATAGTTTTTAAAAACATATTGTTATA-TAATTTTGAA
1 AATATATAATATAGTTTTTAAAAACATA-TG-TATAGT--TTTTGAA
*
663814 AACATATAATATA
1 AATATATAATATA
663827 TATAGATTTT
Statistics
Matches: 159, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
43 40 0.25
44 42 0.26
45 5 0.03
46 62 0.39
47 2 0.01
48 8 0.05
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.42
Consensus pattern (43 bp):
AATATATAATATAGTTTTTAAAAACATATGTATAGTTTTTGAA
Found at i:663844 original size:2 final size:2
Alignment explanation
Indices: 663839--663872 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
663829 TAGATTTTGA
663839 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
663873 TTGAAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663880 original size:64 final size:55
Alignment explanation
Indices: 663800--663917 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 55
663790 AACATATTGT
*
663800 TATATAATTTTGAAAACATATAATATATATAGATTTTGAATATATATATATATATATATATA
1 TATATAATTTTGAAAAC--AT-AT-TATAT-GATTTTGAAAATATA-ATATAT-TATATATA
663862 TATATATATATTTGAAAACATATTATATGATTTTGAAAATATAATATATTATATAT
1 TATATA-AT-TTTGAAAACATATTATATGATTTTGAAAATATAATATATTATATAT
663918 TTTTTTAAGC
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
57 7 0.13
58 6 0.11
59 14 0.26
60 5 0.09
61 2 0.04
62 8 0.15
63 2 0.04
64 9 0.17
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (55 bp):
TATATAATTTTGAAAACATATTATATGATTTTGAAAATATAATATATTATATATA
Found at i:663884 original size:22 final size:22
Alignment explanation
Indices: 663673--663919 Score: 94
Period size: 22 Copynumber: 11.1 Consensus size: 22
663663 TGGTATAGTT
*
663673 TTTGAAAATATATA-ATATAGT-
1 TTTGAAAACATATATATATA-TA
*
663694 TTTAAAAACATATAGTATAGT-T-
1 TTTGAAAACATATA-TATA-TATA
*
663716 TTTGAAAGCATAT-TATATAGT-
1 TTTGAAAACATATATATATA-TA
** *
663737 TTAAAAAAACATATAATATATAGTT
1 TT-TGAAAACATAT-ATATATA-TA
* *
663762 TTTGAAAATATATA-ATATAGTT
1 TTTGAAAACATATATATATA-TA
* *
663784 TTTAAAAACATAT-TGTTATATAA
1 TTTGAAAACATATAT-ATATAT-A
663807 TTTTGAAAACATATAATATATATAGA
1 -TTTGAAAACATAT-ATATATAT--A
663833 TTTTG---A-ATATATATATATA
1 -TTTGAAAACATATATATATATA
* * *
663852 TAT--ATATATATATATATATA
1 TTTGAAAACATATATATATATA
663872 TTTGAAAACATAT-TATATGAT-
1 TTTGAAAACATATATATAT-ATA
*
663893 TTTGAAAATATAATATATTATATA
1 TTTGAAAACAT-ATATA-TATATA
663917 TTT
1 TTT
663920 TTTTAAGCTT
Statistics
Matches: 178, Mismatches: 22, Indels: 49
0.71 0.09 0.20
Matches are distributed among these distances:
18 2 0.01
19 3 0.02
20 19 0.11
21 38 0.21
22 54 0.30
23 13 0.07
24 35 0.20
25 7 0.04
26 7 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
TTTGAAAACATATATATATATA
Done.