Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 49
Found at i:3986176 original size:14 final size:14
Alignment explanation
Indices: 3986136--3986177 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
3986126 TTAGATGCTT
*
3986136 TCGGATGGCCTCAG
1 TCGGATGGCCTCGG
*
3986150 TCGGATGACCTCGG
1 TCGGATGGCCTCGG
3986164 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
3986178 ATGCCCAGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:3986253 original size:29 final size:29
Alignment explanation
Indices: 3986220--3986277 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3986210 GCAATCTCTT
*
3986220 GTAGGTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
*
3986249 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
3986278 CGGTCAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.38, T:0.14
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGACATGGCGACCTA
Found at i:3990163 original size:15 final size:18
Alignment explanation
Indices: 3990123--3990163 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3990113 TTTCGAGGGT
3990123 TGTCGTCGGAGCGGCCGG
1 TGTCGTCGGAGCGGCCGG
3990141 TGTCGTCGGAGCGGCCGG
1 TGTCGTCGGAGCGGCCGG
3990159 TGTCG
1 TGTCG
3990164 CCGGTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.27, G:0.49, T:0.20
Consensus pattern (18 bp):
TGTCGTCGGAGCGGCCGG
Found at i:3990521 original size:60 final size:60
Alignment explanation
Indices: 3990448--3990583 Score: 164
Period size: 60 Copynumber: 2.3 Consensus size: 60
3990438 ATTTCAAATT
** * *
3990448 AGTCCTTAAACTTTTAAACATTCCAATTACATCTTCAAACTATGACTCTTATTCTAAACC
1 AGTCCTTAAACTTTTAAACATTCCAATTACATCCCCAAACTATGAATCTCATTCTAAACC
* * * * **
3990508 AGTCCTTAAACTTTTGAATATTCTAATTTCATCCCCAAACTATGAATCTCATTCTAAATT
1 AGTCCTTAAACTTTTAAACATTCCAATTACATCCCCAAACTATGAATCTCATTCTAAACC
* *
3990568 GGTCCCTAAACTTTTA
1 AGTCCTTAAACTTTTA
3990584 GATCTTCCGA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (60 bp):
AGTCCTTAAACTTTTAAACATTCCAATTACATCCCCAAACTATGAATCTCATTCTAAACC
Found at i:3992386 original size:21 final size:21
Alignment explanation
Indices: 3992360--3992401 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3992350 CCAGAATGGG
*
3992360 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
3992381 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
3992402 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:3992564 original size:29 final size:31
Alignment explanation
Indices: 3992530--3992589 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3992520 AAATTTTGAA
*
3992530 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3992559 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3992590 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:3992742 original size:29 final size:28
Alignment explanation
Indices: 3992631--3992743 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 28
3992621 CATTTATATT
* *
3992631 CTTATTTTGATCAAAAAATACTCTAGATA
1 CTTATTTTGAT-AAAAAATACTTTAAATA
* *
3992660 CCTATTTTGATAAAAAAATACTTTAAGT-
1 CTTATTTTGAT-AAAAAATACTTTAAATA
* *
3992688 TTCTATTTTGATAAAAAA-A-ATTAAATA
1 CT-TATTTTGATAAAAAATACTTTAAATA
*
3992715 CTTATTTTAACTAAAAAATACTTTAAATA
1 CTTATTTTGA-TAAAAAATACTTTAAATA
3992744 TTTAAATAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
26 12 0.18
27 9 0.13
28 7 0.10
29 39 0.58
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (28 bp):
CTTATTTTGATAAAAAATACTTTAAATA
Found at i:3997146 original size:18 final size:19
Alignment explanation
Indices: 3997120--3997177 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
3997110 TCGAGGGATA
3997120 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
** *
3997139 AT-AGTGGTTATTCGGAAC
1 ATCAGTGGTCCTTCGGGAC
3997157 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
3997177 A
1 A
3997178 AATATTCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 13 0.42
19 5 0.16
20 13 0.42
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:3997166 original size:20 final size:20
Alignment explanation
Indices: 3997119--3997178 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
3997109 GTCGAGGGAT
* *
3997119 AATCAGTGGTCCTTCGGGAC
1 AATCAGTGGTCATTCGGAAC
*
3997139 -AT-AGTGGTTATTCGGAAC
1 AATCAGTGGTCATTCGGAAC
* *
3997157 AATCAGTGGTCCTTCGGGAC
1 AATCAGTGGTCATTCGGAAC
3997177 AA
1 AA
3997179 ATATTCAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 15 0.47
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (20 bp):
AATCAGTGGTCATTCGGAAC
Found at i:4005134 original size:20 final size:19
Alignment explanation
Indices: 4005094--4005144 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
4005084 AGTGAACTTG
4005094 GTATCGATA-CCACCACGA
1 GTATCGATACCCACCACGA
4005112 GTATCGATACCTCACCTAC-A
1 GTATCGATACC-CACC-ACGA
4005132 GTATCGATACCCA
1 GTATCGATACCCA
4005145 TTGTATGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.30
19 3 0.10
20 16 0.53
21 2 0.07
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (19 bp):
GTATCGATACCCACCACGA
Found at i:4007407 original size:2 final size:2
Alignment explanation
Indices: 4007400--4007436 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4007390 ATCAAGAGTA
4007400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4007437 CAAACATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4010492 original size:22 final size:23
Alignment explanation
Indices: 4010472--4010519 Score: 60
Period size: 27 Copynumber: 1.9 Consensus size: 23
4010462 AATCATTCAG
4010472 CGCTGAATGTTAAATCGTTCAACATTC
1 CGCTGAATGTTAAATCGTT---CA-TC
4010499 CGCTGAATGTTAAATCGTTCA
1 CGCTGAATGTTAAATCGTTCA
4010520 ACATTCAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.10
27 19 0.90
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (23 bp):
CGCTGAATGTTAAATCGTTCATC
Found at i:4010498 original size:29 final size:29
Alignment explanation
Indices: 4010465--4010559 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
4010455 GTTTTGGAAT
4010465 CATTCAGCGCTGAATGTTAAATCGTTCAA
1 CATTCAGCGCTGAATGTTAAATCGTTCAA
4010494 CATTC--CGCTGAATGTTAAATCGTTCAA
1 CATTCAGCGCTGAATGTTAAATCGTTCAA
*
4010521 CATTCAGCGCTGAATGTTAAATCATTCAA
1 CATTCAGCGCTGAATGTTAAATCGTTCAA
4010550 CATTCAGCGC
1 CATTCAGCGC
4010560 GTTTGTTTCG
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
27 27 0.43
29 36 0.57
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (29 bp):
CATTCAGCGCTGAATGTTAAATCGTTCAA
Found at i:4010644 original size:26 final size:27
Alignment explanation
Indices: 4010614--4010678 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
4010604 AAAATAGTGT
*
4010614 TGAATAATTCAGCATAGAAGT-CATTC
1 TGAATAATTCAGCACAGAAGTACATTC
* *
4010640 TGAATGATTCAGCACAGAAGTACATTT
1 TGAATAATTCAGCACAGAAGTACATTC
4010667 TGAATAATTCAG
1 TGAATAATTCAG
4010679 AATCATTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (27 bp):
TGAATAATTCAGCACAGAAGTACATTC
Found at i:4011804 original size:61 final size:62
Alignment explanation
Indices: 4011729--4011853 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
4011719 AGGCTCGAAT
4011729 AAGATGGCATGGAATTCATTTAGTGACCA-ATCACAACCCTTACAAAAGCTTGAGGGACCTA
1 AAGATGGCATGGAATTCATTTAGTGACCAGATCACAACCCTTACAAAAGCTTGAGGGACCTA
4011790 AAGATGGCATGGAATTCATTTAGTGACCAGATCACAACCCTTACAAAAGCTTGAGGGACCTA
1 AAGATGGCATGGAATTCATTTAGTGACCAGATCACAACCCTTACAAAAGCTTGAGGGACCTA
4011852 AA
1 AA
4011854 CTGTTGTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 29 0.46
62 34 0.54
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (62 bp):
AAGATGGCATGGAATTCATTTAGTGACCAGATCACAACCCTTACAAAAGCTTGAGGGACCTA
Found at i:4012943 original size:25 final size:25
Alignment explanation
Indices: 4012720--4012939 Score: 413
Period size: 25 Copynumber: 8.8 Consensus size: 25
4012710 TAATTTGTTC
*
4012720 TAGGGTTTGAAACCCTAATCTGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012745 TAGGGTTTGAAACCCTAATCCGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012770 TAGGGTTTGAAACCCTAATCCGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012795 TAGGGTTTGAAACCCTAATCCGATT
1 TAGGGTTTGAAACCCTAATCCGATT
*
4012820 TAGGGTTTGAAACCCTAATCTGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012845 TAGGGTTTGAAACCCTAATCCGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012870 TAGGGTTTGAAACCCTAATCCGATT
1 TAGGGTTTGAAACCCTAATCCGATT
*
4012895 TAGGGTTTGAAACCCTAATCTGATT
1 TAGGGTTTGAAACCCTAATCCGATT
4012920 TAGGGTTTGAAACCCTAATC
1 TAGGGTTTGAAACCCTAATC
4012940 TGATAGGTTG
Statistics
Matches: 191, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 191 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (25 bp):
TAGGGTTTGAAACCCTAATCCGATT
Found at i:4013045 original size:3 final size:3
Alignment explanation
Indices: 4013037--4013079 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
4013027 ATTTGTAAAT
* **
4013037 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA CGA -AA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4013080 TAAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4013475 original size:88 final size:90
Alignment explanation
Indices: 4013276--4013519 Score: 316
Period size: 90 Copynumber: 2.7 Consensus size: 90
4013266 TCTAAGGGTG
* * ** * * * *
4013276 ACACGGCTCCTACGTGATGAGGA-GATCTGGTCA-GGGGATGACACTGCTCCTACATGATGAAGA
1 ACACGGTTCCTACGTGATGAGGACGA-CTGGTTATTAGGTTGACACGGCTCATACGTGATGAAGA
* * *
4013339 ATTCTTGGCCATCTTTAGGGATGATA
65 GTTCTTGGCCATCTTAAAGGATGATA
*
4013365 ACACGGTTCCTACGTGATGAGGACGACTGGTTATTAGGTTGACACGGCTCTTACGTGATGAAGAG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATTAGGTTGACACGGCTCATACGTGATGAAGAG
4013430 TTCTTGGCCATC-TAAAGG-TGATA
66 TTCTTGGCCATCTTAAAGGATGATA
*
4013453 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTAT-TA-GGTTGACACGGCTCATACGTGATGAAG
4013518 AG
64 AG
4013520 ATTTGGTCTG
Statistics
Matches: 138, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
88 38 0.28
89 34 0.25
90 66 0.48
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (90 bp):
ACACGGTTCCTACGTGATGAGGACGACTGGTTATTAGGTTGACACGGCTCATACGTGATGAAGAG
TTCTTGGCCATCTTAAAGGATGATA
Found at i:4027576 original size:25 final size:25
Alignment explanation
Indices: 4027544--4027707 Score: 301
Period size: 25 Copynumber: 6.6 Consensus size: 25
4027534 TTAGGGTTAT
* *
4027544 AACCCTAATTTGTTTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
4027569 AACCCTAATCTGATTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
4027594 AACCCTAATCTGATTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
4027619 AACCCTAATCTGATTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
*
4027644 AATCCTAATCTGATTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
4027669 AACCCTAATCTGATTTAGGGTTTGA
1 AACCCTAATCTGATTTAGGGTTTGA
4027694 AACCCTAATCTGAT
1 AACCCTAATCTGAT
4027708 GGGTTGGTTC
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 135 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (25 bp):
AACCCTAATCTGATTTAGGGTTTGA
Found at i:4027809 original size:3 final size:3
Alignment explanation
Indices: 4027801--4027847 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
4027791 ATTTGTAAAT
* **
4027801 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
4027846 TA
1 TA
4027848 TAAAAAAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4028289 original size:29 final size:29
Alignment explanation
Indices: 4028247--4028343 Score: 185
Period size: 29 Copynumber: 3.3 Consensus size: 29
4028237 GTTTTGGAAT
4028247 CATTCAGCGCTGAATGATAAATCGTTCAA
1 CATTCAGCGCTGAATGATAAATCGTTCAA
*
4028276 CATTCAGCGCTGAATGTTAAATCGTTCAA
1 CATTCAGCGCTGAATGATAAATCGTTCAA
4028305 CATTCAGCGCTGAATGATAAATCGTTCAA
1 CATTCAGCGCTGAATGATAAATCGTTCAA
4028334 CATTCAGCGC
1 CATTCAGCGC
4028344 GTTTGTTTCG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (29 bp):
CATTCAGCGCTGAATGATAAATCGTTCAA
Found at i:4033559 original size:12 final size:12
Alignment explanation
Indices: 4033542--4033566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4033532 TTGTGCAGGA
4033542 GGTGCGGCTGAG
1 GGTGCGGCTGAG
4033554 GGTGCGGCTGAG
1 GGTGCGGCTGAG
4033566 G
1 G
4033567 CAGTGGCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.60, T:0.16
Consensus pattern (12 bp):
GGTGCGGCTGAG
Found at i:4046540 original size:21 final size:22
Alignment explanation
Indices: 4046499--4046541 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4046489 TACTTATATA
*
4046499 TTTTATTAATTTAATCTTAAAC
1 TTTTATTAATTAAATCTTAAAC
*
4046521 TTTTTTTAATTAAATC-TAAAC
1 TTTTATTAATTAAATCTTAAAC
4046542 ATTGTAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATTAATTAAATCTTAAAC
Found at i:4053823 original size:18 final size:18
Alignment explanation
Indices: 4053799--4053867 Score: 104
Period size: 18 Copynumber: 3.8 Consensus size: 18
4053789 TGACCAGTTT
*
4053799 TGAACCGTTTGACCGGT-
1 TGAACCGGTTGACCGGTC
4053816 TCGAACCGGTTGACCGGTC
1 T-GAACCGGTTGACCGGTC
4053835 TGAACCGGTTTGACCGGTC
1 TGAACCGG-TTGACCGGTC
4053854 TGAACCGGTTGACC
1 TGAACCGGTTGACC
4053868 CGACCCGACT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 1 0.02
18 28 0.58
19 19 0.40
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (18 bp):
TGAACCGGTTGACCGGTC
Found at i:4053883 original size:17 final size:17
Alignment explanation
Indices: 4053861--4053918 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
4053851 GTCTGAACCG
4053861 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
4053878 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
4053895 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
4053912 GTTGACC
1 GTTGACC
4053919 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:4053920 original size:7 final size:7
Alignment explanation
Indices: 4053908--4053944 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
4053898 GACCCGACCC
4053908 GACCGTT
1 GACCGTT
4053915 GACCGTT
1 GACCGTT
4053922 GACCG-T
1 GACCGTT
4053928 GACCGTT
1 GACCGTT
4053935 GACCGTT
1 GACCGTT
4053942 GAC
1 GAC
4053945 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:4053932 original size:13 final size:13
Alignment explanation
Indices: 4053908--4053940 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4053898 GACCCGACCC
4053908 GACCGTTGACCGTT
1 GACCG-TGACCGTT
4053922 GACCGTGACCGTT
1 GACCGTGACCGTT
4053935 GACCGT
1 GACCGT
4053941 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:4054705 original size:279 final size:281
Alignment explanation
Indices: 4054205--4054764 Score: 1081
Period size: 279 Copynumber: 2.0 Consensus size: 281
4054195 CCAAATTCAG
4054205 ACTCGAAATACCCCAAATTGATAGTCAAACTCGAAAAAATGCTTATATACTTAAGAAGACTAGCT
1 ACTCGAAATACCCCAAATTGATAGTCAAACTCGAAAAAATGCTTATATACTTAAGAAGACTAGCT
4054270 TTGAACAATTAAATAGGATTTGGACTGATAGATTATTGTTTGATGGTACAAGAGACTCTCTGGAT
66 TTGAACAATTAAATAGGATTTGGACTGATAGATTATTGTTTGATGGTACAAGAGACTCTCTGGAT
4054335 CGTCGACAGCTCGACCCAGCTCTTCTAGATCAGTTAAACCACGTGTGCCAGTATTCACCCGTTCG
131 CGTCGACAGCTCGACCCAGCTCTTCTAGATCAGTTAAACCACGTGTGCCAGTATTCACCCGTTCG
4054400 AAAATTGTAGCAGAGCGTGGTGAAACCAGCAATCAGTAAA-TT-CTATTTGAACCTATTGTCGAG
196 AAAATTGTAGCAGAGCGTGGTGAAACCAGCAATCAGTAAATTTGCTATTTGAACCTATTGTCGAG
4054463 GTGTGTTCCCTGCTTATTATT
261 GTGTGTTCCCTGCTTATTATT
4054484 ACTCGAAATACCCCAAATTGATAGTCAAACTCGAAAAAATGCTTATATACTTAAGAAGACTAGCT
1 ACTCGAAATACCCCAAATTGATAGTCAAACTCGAAAAAATGCTTATATACTTAAGAAGACTAGCT
*
4054549 TTGAACAATTAAATAGGATTTGGACTGATATTATTATTGTTTGATGGTACAAGAGACTCTCTGGA
66 TTGAACAATTAAATAGGATTTGGACTGATA-GATTATTGTTTGATGGTACAAGAGACTCTCTGGA
4054614 T-GTCGACAGCTCGACCCAGCTCTTCTAGATCAGTTAAACCACGTGTGCCAGTATTCACCCGTTC
130 TCGTCGACAGCTCGACCCAGCTCTTCTAGATCAGTTAAACCACGTGTGCCAGTATTCACCCGTTC
4054678 GAAAATTGTAGCAGAGCGTGGTGAAACCAGCAATCAGTAAATTTGCTATTTGAACCTATTGTCGA
195 GAAAATTGTAGCAGAGCGTGGTGAAACCAGCAATCAGTAAATTTGCTATTTGAACCTATTGTCGA
4054743 GGTGTGTTCCCTGCTTATTATT
260 GGTGTGTTCCCTGCTTATTATT
4054765 GAACTGTTTA
Statistics
Matches: 277, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
279 199 0.72
280 36 0.13
281 42 0.15
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (281 bp):
ACTCGAAATACCCCAAATTGATAGTCAAACTCGAAAAAATGCTTATATACTTAAGAAGACTAGCT
TTGAACAATTAAATAGGATTTGGACTGATAGATTATTGTTTGATGGTACAAGAGACTCTCTGGAT
CGTCGACAGCTCGACCCAGCTCTTCTAGATCAGTTAAACCACGTGTGCCAGTATTCACCCGTTCG
AAAATTGTAGCAGAGCGTGGTGAAACCAGCAATCAGTAAATTTGCTATTTGAACCTATTGTCGAG
GTGTGTTCCCTGCTTATTATT
Found at i:4061326 original size:10 final size:10
Alignment explanation
Indices: 4061313--4061384 Score: 87
Period size: 10 Copynumber: 7.5 Consensus size: 10
4061303 TTTGACCAGT
4061313 TTTGAACCGG
1 TTTGAACCGG
4061323 TTTG-ACCGG
1 TTTGAACCGG
*
4061332 TTCGAACCGG
1 TTTGAACCGG
4061342 TTTG-ACCGG
1 TTTGAACCGG
*
4061351 TCTGAACCGG
1 TTTGAACCGG
4061361 TTTG-ACCGG
1 TTTGAACCGG
*
4061370 TCTGAACCGG
1 TTTGAACCGG
*
4061380 GTTGA
1 TTTGA
4061385 CCCGACCCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 24 0.46
10 28 0.54
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.28
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:4061340 original size:19 final size:19
Alignment explanation
Indices: 4061296--4061386 Score: 121
Period size: 19 Copynumber: 4.7 Consensus size: 19
4061286 GCTGCTGGAA
* *
4061296 AACCGGTTTTGACCAGTTTTG
1 AACCGG-TTTGACC-GGTCTG
4061317 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
4061336 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
4061355 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
4061374 AACCGGGTTGACC
1 AACCGGTTTGACC
4061387 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 8 0.12
21 6 0.09
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:4061402 original size:17 final size:17
Alignment explanation
Indices: 4061380--4061437 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
4061370 TCTGAACCGG
4061380 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
4061397 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
4061414 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
4061431 GTTGACC
1 GTTGACC
4061438 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:4061439 original size:7 final size:7
Alignment explanation
Indices: 4061427--4061463 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
4061417 GACCCGACCC
4061427 GACCGTT
1 GACCGTT
4061434 GACCGTT
1 GACCGTT
4061441 GACCG-T
1 GACCGTT
4061447 GACCGTT
1 GACCGTT
4061454 GACCGTT
1 GACCGTT
4061461 GAC
1 GAC
4061464 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:4061451 original size:13 final size:13
Alignment explanation
Indices: 4061427--4061459 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4061417 GACCCGACCC
4061427 GACCGTTGACCGTT
1 GACCG-TGACCGTT
4061441 GACCGTGACCGTT
1 GACCGTGACCGTT
4061454 GACCGT
1 GACCGT
4061460 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:4068650 original size:10 final size:10
Alignment explanation
Indices: 4068637--4068707 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 10
4068627 TTTGACCAGT
4068637 TTTGAACCGG
1 TTTGAACCGG
4068647 TTTG-ACCGG
1 TTTGAACCGG
*
4068656 TTCGAACCGG
1 TTTGAACCGG
4068666 TTTG-ACCGG
1 TTTGAACCGG
*
4068675 TCTGAACCGG
1 TTTGAACCGG
4068685 TTTG-ACC-G
1 TTTGAACCGG
*
4068693 TCTGAACCGG
1 TTTGAACCGG
*
4068703 GTTGA
1 TTTGA
4068708 CCCGACCCGA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
8 4 0.08
9 22 0.44
10 24 0.48
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.28
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:4068656 original size:9 final size:9
Alignment explanation
Indices: 4068621--4068692 Score: 72
Period size: 10 Copynumber: 7.4 Consensus size: 9
4068611 CTGCTGGAAA
4068621 ACCGGTTTTG
1 ACCGG-TTTG
*
4068631 ACCAGTTTTG
1 ACC-GGTTTG
4068641 AACCGGTTTG
1 -ACCGGTTTG
*
4068651 ACCGGTTCG
1 ACCGGTTTG
4068660 AACCGGTTTG
1 -ACCGGTTTG
*
4068670 ACCGGTCTG
1 ACCGGTTTG
4068679 AACCGGTTTG
1 -ACCGGTTTG
4068689 ACCG
1 ACCG
4068693 TCTGAACCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
9 20 0.38
10 28 0.54
11 4 0.08
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4068664 original size:19 final size:19
Alignment explanation
Indices: 4068620--4068709 Score: 112
Period size: 19 Copynumber: 4.7 Consensus size: 19
4068610 GCTGCTGGAA
* *
4068620 AACCGGTTTTGACCAGTTTTG
1 AACCGG-TTTGACC-GGTCTG
4068641 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
4068660 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
4068679 AACCGGTTTGACC-GTCTG
1 AACCGGTTTGACCGGTCTG
*
4068697 AACCGGGTTGACC
1 AACCGGTTTGACC
4068710 CGACCCGACT
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
18 18 0.28
19 33 0.51
20 8 0.12
21 6 0.09
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:4068725 original size:17 final size:17
Alignment explanation
Indices: 4068703--4068759 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
4068693 TCTGAACCGG
4068703 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
4068720 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
4068737 GTTGACCCGA-CCGACC
1 GTTGACCCGACCCGACT
4068753 GTTGACC
1 GTTGACC
4068760 GTTGACCGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
16 12 0.31
17 27 0.69
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.18
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:4068761 original size:7 final size:7
Alignment explanation
Indices: 4068749--4068784 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
4068739 TGACCCGACC
4068749 GACCGTT
1 GACCGTT
4068756 GACCGTT
1 GACCGTT
4068763 GACCG-T
1 GACCGTT
4068769 GACCG-T
1 GACCGTT
4068775 GACCGTT
1 GACCGTT
4068782 GAC
1 GAC
4068785 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:4085435 original size:12 final size:11
Alignment explanation
Indices: 4085409--4085434 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4085399 GGGTGATTCG
4085409 AAAACAAAAAA
1 AAAACAAAAAA
4085420 AAAACAAAAAA
1 AAAACAAAAAA
4085431 AAAA
1 AAAA
4085435 AATATAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:4088331 original size:20 final size:21
Alignment explanation
Indices: 4088306--4088345 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4088296 TTTAGGGTAA
*
4088306 ATTATATAA-ATAGTTTTATG
1 ATTATAGAATATAGTTTTATG
*
4088326 ATTATAGAATATTGTTTTAT
1 ATTATAGAATATAGTTTTAT
4088346 TAAGTCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTATAGAATATAGTTTTATG
Found at i:4094962 original size:30 final size:30
Alignment explanation
Indices: 4094928--4094988 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4094918 ACAGGCGACC
4094928 TGATGAACAAGCATGGTTGAGGCAAAAACG
1 TGATGAACAAGCATGGTTGAGGCAAAAACG
4094958 TGATGAACAAGCATGGTTGAGGCAAAAACG
1 TGATGAACAAGCATGGTTGAGGCAAAAACG
4094988 T
1 T
4094989 AATGGCGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.18
Consensus pattern (30 bp):
TGATGAACAAGCATGGTTGAGGCAAAAACG
Found at i:4097392 original size:17 final size:17
Alignment explanation
Indices: 4097370--4097407 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4097360 CCGCAACTTA
4097370 ACGGGTAACGGCCGATC
1 ACGGGTAACGGCCGATC
*
4097387 ACGGGTAACGGTCGATC
1 ACGGGTAACGGCCGATC
4097404 ACGG
1 ACGG
4097408 TGATAGCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.37, T:0.13
Consensus pattern (17 bp):
ACGGGTAACGGCCGATC
Found at i:4098201 original size:13 final size:13
Alignment explanation
Indices: 4098183--4098217 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
4098173 GTAATTCGCA
4098183 TGCGAAAATTTGT
1 TGCGAAAATTTGT
4098196 TGCGAAAATTTGT
1 TGCGAAAATTTGT
4098209 TGCGAAAAT
1 TGCGAAAAT
4098218 AAATGCGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (13 bp):
TGCGAAAATTTGT
Found at i:4098331 original size:20 final size:20
Alignment explanation
Indices: 4098267--4098333 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
4098257 TGACTTTTGT
*
4098267 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGC
*
4098287 GTTACGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
4098307 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
4098327 ATTGCGA
1 GTTGCGA
4098334 ATTTGACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:4098346 original size:20 final size:20
Alignment explanation
Indices: 4098323--4098537 Score: 169
Period size: 20 Copynumber: 10.8 Consensus size: 20
4098313 ATTTACAGAT
*
4098323 TCGCATTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
4098343 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
4098363 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
4098383 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
*
4098402 TCTGTGTTGCGAATTTGACT-
1 TC-GCGTTGCGAATTTGACTA
* * *
4098422 TCTGTGTTGTG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
4098442 TTCACGTTGCGAATTTAGA--A
1 -TCGCGTTGCGAATTT-GACTA
* * * *
4098462 ACTGGGTTGCGAAATTG-CAA
1 TC-GCGTTGCGAATTTGACTA
* *
4098482 TTCGCGTTGCGAAATTG-CAA
1 -TCGCGTTGCGAATTTGACTA
*
4098502 TTCGCGTTGCGAATTTGGAAT-
1 -TCGCGTTGCGAATTT-GACTA
4098523 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
4098538 ATTGGTTATT
Statistics
Matches: 166, Mismatches: 16, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.01
19 8 0.05
20 147 0.89
21 8 0.05
23 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:4098347 original size:40 final size:40
Alignment explanation
Indices: 4098238--4098537 Score: 194
Period size: 40 Copynumber: 7.5 Consensus size: 40
4098228 TGCGAATTTG
* * * *
4098238 AAATTCAGGGTTGCGAATTTGACTTTTGTGTTGCGATTTAC
1 AAATTC-GCGTTGCGAATTTGACTATCGCGTTGCGATTTAC
* *
4098279 AAATTCGCGTTACG-ATTT-ACAGATTCGCGTTGCGATTTAC
1 AAATTCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGATTTAC
* *
4098319 AGATTCGCATTGCGAATTTGACTATCGCGTTGCGAATTTGAC
1 AAATTCGCGTTGCGAATTTGACTATCGCGTTGCG-ATTT-AC
*
4098361 -TA-TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC
1 AAATTCGCGTTGCGAATTTGACTATCGCGTTGCG-ATTT-AC
* * *
4098401 ---TTCTGTGTTGCGAATTTGACT-TCTGTGTTGTGATTTAC
1 AAATTC-GCGTTGCGAATTTGACTATC-GCGTTGCGATTTAC
* * * * *
4098439 AAATTCACGTTGCGAATTTAGA--AACTGGGTTGCGAAATTGC
1 AAATTCGCGTTGCGAATTT-GACTATC-GCGTTGCG-ATTTAC
* * *
4098480 -AATTCGCGTTGCGAAATTG-CAATTCGCGTTGCGAATTT-G
1 AAATTCGCGTTGCGAATTTGACTA-TCGCGTTGCG-ATTTAC
*
4098519 GAATTCGCGTTGCGAATTT
1 AAATTCGCGTTGCGAATTT
4098538 ATTGGTTATT
Statistics
Matches: 211, Mismatches: 29, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.02
39 13 0.06
40 164 0.78
41 26 0.12
42 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
AAATTCGCGTTGCGAATTTGACTATCGCGTTGCGATTTAC
Found at i:4098348 original size:60 final size:60
Alignment explanation
Indices: 4098283--4098420 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 60
4098273 ATTTACAAAT
4098283 TCGCGTTACG-ATTT-ACAGATTCGCGTTGCG-ATTT-ACAGATTCGCATTGCGAATTTGACTA
1 TCGCGTTACGAATTTGAC-GA-TCGCGTTGCGAATTTGAC-GA-TCGCATTGCGAATTTGACTA
* * * *
4098343 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-
1 TCGCGTTACGAATTTGACGATCGCGTTGCGAATTTGACGATCGCATTGCGAATTTGACTA
* *
4098402 TCTGTGTTGCGAATTTGAC
1 TC-GCGTTACGAATTTGAC
4098421 TTCTGTGTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
59 2 0.03
60 52 0.76
61 10 0.15
62 4 0.06
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
TCGCGTTACGAATTTGACGATCGCGTTGCGAATTTGACGATCGCATTGCGAATTTGACTA
Found at i:4098421 original size:60 final size:61
Alignment explanation
Indices: 4098303--4098537 Score: 206
Period size: 60 Copynumber: 3.9 Consensus size: 61
4098293 ATTTACAGAT
*
4098303 TCGCGTTGCG-ATTT-ACAGATTCGCATTGCGAATTT-GACTATCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACA-ATTCGCGTTGCGAATTTAGACT-TCGCGTTGCGAATTTGACTA
* *
4098363 TCGCGTTGCGAATTTGACTA-TCGCGTTGCGAATTT-GACTTCTGTGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACAATTCGCGTTGCGAATTTAGACTTC-GCGTTGCGAATTTGACTA
* * * * * *
4098422 TCTGTGTTGTG-ATTT-ACAAATTCACGTTGCGAATTTAGAAAC-T-GGGTTGCGAAATTG-CAA
1 TC-GCGTTGCGAATTTGAC-AATTCGCGTTGCGAATTTAG--ACTTCGCGTTGCGAATTTGACTA
* * *
4098482 TTCGCGTTGCGAAATTG-CAATTCGCGTTGCGAATTTGGAATTCGCGTTGCGAATTT
1 -TCGCGTTGCGAATTTGACAATTCGCGTTGCGAATTTAGACTTCGCGTTGCGAATTT
4098538 ATTGGTTATT
Statistics
Matches: 142, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
58 3 0.02
59 11 0.08
60 111 0.78
61 12 0.08
62 3 0.02
63 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (61 bp):
TCGCGTTGCGAATTTGACAATTCGCGTTGCGAATTTAGACTTCGCGTTGCGAATTTGACTA
Found at i:4099933 original size:20 final size:21
Alignment explanation
Indices: 4099880--4099933 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
4099870 GAGGCATTTC
*
4099880 ACGTGTTGGTTCACAATGATG
1 ACGTGATGGTTCACAATGATG
* ** *
4099901 ACGTGGTATTTCAC-ATGTTG
1 ACGTGATGGTTCACAATGATG
4099921 ACGTGATGGTTCA
1 ACGTGATGGTTCA
4099934 TTATGCTGAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (21 bp):
ACGTGATGGTTCACAATGATG
Found at i:4103466 original size:23 final size:22
Alignment explanation
Indices: 4103440--4103486 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
4103430 ATAAAGTACA
*
4103440 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGC-TAT
**
4103463 ATAATGTAATAGGTAGCGCTAT
1 ATAACATAATAGGTAGCGCTAT
4103485 AT
1 AT
4103487 TTACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (22 bp):
ATAACATAATAGGTAGCGCTAT
Found at i:4103884 original size:23 final size:23
Alignment explanation
Indices: 4103856--4103923 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
4103846 GACACTTTAC
*
4103856 ATATAACCACTACCTATTACATT
1 ATATAACGACTACCTATTACATT
4103879 ATATAAACGA-TACCTATTACATT
1 ATAT-AACGACTACCTATTACATT
* *
4103902 ATATAAGGGCTACCTATTACAT
1 ATATAACGACTACCTATTACAT
4103924 CATAGTTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.08
23 33 0.82
24 4 0.10
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAACGACTACCTATTACATT
Found at i:4104436 original size:38 final size:39
Alignment explanation
Indices: 4104326--4104450 Score: 216
Period size: 39 Copynumber: 3.2 Consensus size: 39
4104316 TCAAGTTGTA
*
4104326 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTT
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
4104365 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
4104404 GATTTTGATTTCCTTTTGC-TGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
4104442 GATTTTGAT
1 GATTTTGAT
4104451 GAGCATCGGA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
38 26 0.31
39 57 0.69
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:4104754 original size:23 final size:22
Alignment explanation
Indices: 4104700--4104754 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
4104690 GAGCCGAAAT
4104700 ATATGAAATTCAAACTCAATTG
1 ATATGAAATTCAAACTCAATTG
* *
4104722 AAATTTAAATTCAAACTCCAATT-
1 ATA-TGAAATTCAAACT-CAATTG
4104745 ACTATGAAAT
1 A-TATGAAAT
4104755 GAATTTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.08
23 18 0.69
24 6 0.23
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (22 bp):
ATATGAAATTCAAACTCAATTG
Found at i:4105007 original size:24 final size:25
Alignment explanation
Indices: 4104980--4105029 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4104970 TTAATCCAAA
*
4104980 TAATGTA-CCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
4105004 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
4105029 T
1 T
4105030 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:4105353 original size:22 final size:23
Alignment explanation
Indices: 4105292--4105358 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
4105282 ACACTTTACA
* *
4105292 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
4105315 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
**
4105338 ATA-AAGGGCTACCTATTACAT
1 ATATAAACGCTACCTATTACAT
4105359 CATGTTTACC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:4105691 original size:20 final size:20
Alignment explanation
Indices: 4105666--4105704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4105656 TCCACAGTGA
* *
4105666 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
4105686 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
4105705 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:4105732 original size:20 final size:21
Alignment explanation
Indices: 4105707--4105754 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
4105697 ACACTTTACA
4105707 ATATAAC-CACCTATTACATT
1 ATATAACACACCTATTACATT
*
4105727 ATATAACGATACCTATTACATT
1 ATATAAC-ACACCTATTACATT
4105749 ATATAA
1 ATATAA
4105755 GGGCTAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAACACACCTATTACATT
Found at i:4105971 original size:29 final size:28
Alignment explanation
Indices: 4105922--4105976 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
4105912 TCATTTGCAC
*
4105922 AAAAAATTATTTGATTGTTTTATATTTTT
1 AAAAAATTATTTGAATGTTTTA-ATTTTT
*
4105951 AAAATATTATTTAGAAT-TTTTAATTT
1 AAAAAATTATTT-GAATGTTTTAATTT
4105977 AATAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 16 0.70
30 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
AAAAAATTATTTGAATGTTTTAATTTTT
Found at i:4106154 original size:20 final size:20
Alignment explanation
Indices: 4106125--4106192 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
4106115 GATAGACACT
* **
4106125 TTACAATATAACCCTACCTA
1 TTACATTATAACGATACCTA
4106145 TTACATTATATAACGATACCTA
1 TTACA-T-TATAACGATACCTA
* *
4106167 TTACATTATAAGGGTACCTA
1 TTACATTATAACGATACCTA
4106187 TTACAT
1 TTACAT
4106193 CATGTTTACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 23 0.56
21 1 0.02
22 17 0.41
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (20 bp):
TTACATTATAACGATACCTA
Found at i:4106158 original size:22 final size:22
Alignment explanation
Indices: 4106130--4106176 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4106120 ACACTTTACA
*
4106130 ATATAACCCTACCTATTACATT
1 ATATAACCATACCTATTACATT
*
4106152 ATATAACGATACCTATTACATT
1 ATATAACCATACCTATTACATT
4106174 ATA
1 ATA
4106177 AGGGTACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATAACCATACCTATTACATT
Found at i:4106574 original size:23 final size:23
Alignment explanation
Indices: 4106548--4106609 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
4106538 ATATAACCAC
4106548 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
4106571 TACCTATT-CATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
4106593 TACCTATTACATCATAT
1 TACCTATTACATTATAT
4106610 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:4106596 original size:22 final size:23
Alignment explanation
Indices: 4106538--4106609 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
4106528 ACACTTTACA
* *
4106538 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
4106561 ATATAAACGATACCTATT-CATT
1 ATATAAACGCTACCTATTACATT
** *
4106583 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
4106606 ATAT
1 ATAT
4106610 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:4109633 original size:22 final size:22
Alignment explanation
Indices: 4109603--4109647 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
4109593 TTCCACAGTG
4109603 AAAAAGTATCGACAC-TTTTAT
1 AAAAAGTATCGACACATTTTAT
4109624 AAAAAGGTATCGACACATTTTAT
1 AAAAA-GTATCGACACATTTTAT
4109647 A
1 A
4109648 CCGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (22 bp):
AAAAAGTATCGACACATTTTAT
Found at i:4110020 original size:179 final size:182
Alignment explanation
Indices: 4109642--4110141 Score: 820
Period size: 180 Copynumber: 2.8 Consensus size: 182
4109632 ATCGACACAT
4109642 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
1 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
4109707 CGACACTTTTTTAAATGGTATCGAC-C-TTTTTCTTCCAATCTGAACAT-AAGTACCGACACAAT
66 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
4109769 ATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGTATT
131 ATTAG-AAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
4109822 TTTATACCGGTTATATTAC-AAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
1 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
4109886 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
66 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
4109951 ATTAGAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
131 ATTAGAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
4110003 TTTATACCGG-T-TATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTTCAA
1 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGTAAA
* * *
4110066 --TCGACAC-TTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGACAC
63 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
*
4110128 AATATTAAAAGTGT
128 AATATTAGAAGTGT
4110142 GAAAACTTTG
Statistics
Matches: 304, Mismatches: 9, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
179 76 0.25
180 122 0.40
181 82 0.27
182 20 0.07
183 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (182 bp):
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
Found at i:4111334 original size:3 final size:3
Alignment explanation
Indices: 4111326--4111399 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
4111316 ACTTGTTTGG
* * * **
4111326 ATC ATC ATC -TC ATC ATC ATC ATC ATT ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
4111373 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
4111400 GTCAGCTTCA
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:4113322 original size:193 final size:197
Alignment explanation
Indices: 4112847--4114364 Score: 2625
Period size: 194 Copynumber: 7.9 Consensus size: 197
4112837 TATTTAAATT
4112847 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
4112912 TAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTGGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4112976 ATCGACACTTTTTATATATGGATCGA-AC-TTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
4113039 AAA
195 AAA
4113042 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4113106 TAATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT-GG
4113170 GATCGACACTTTT-TATATGGATCGACAC-TT-TGGGTGCACC-TGTTTCCATTCATTCTGGGAA
130 GATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
4113231 AAA
195 AAA
4113234 AGTATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
* *
4113298 TAATTGTACCAGTTAGAGTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4113362 ATCGACACTTTTATATATGGATCGACACTTTA-GGGTGCACCTTGTTTCCATTCATTCTGGGAAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4113426 AA
196 AA
*
4113428 AGTATCGACACAAAC-ATA-TAGTGTTGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4113491 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4113556 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCA-TCATTCTGGGAAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4113620 AA
196 AA
4113622 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4113687 TAATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4113751 ATCGACACTTTT-TATATGGATCGACACTTTATGGG-GCACCTTG--TCCATTCATTCT-GGAAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4113811 AA
196 AA
4113813 AGTATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4113877 TAATTGTACCGGTTAGATTGAAAAATTACATATT--ATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
4113939 ATCGACACTTTTATATATGGATCGACACTTTA-GGGTGTACCTTGTTTCCATTCATTCTGGG-AA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4114002 AA
196 AA
*
4114004 AGTATCGACACAAACTATATT-GTGTCGACACATTA-TTAGATATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4114067 T-ATTGTACC-GTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTT-GG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4114128 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCA-TCTGGGGAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCT-GGGAA
4114192 AAA
195 AAA
4114195 A-TATCGACACAAACTATATTAGTGTCG--ACATTA-TTAGACATATTCTCTCATAAAACC-GTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
4114255 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGAT-A-ATTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
4114317 ATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
4114365 GGCCATATTG
Statistics
Matches: 1276, Mismatches: 14, Indels: 71
0.94 0.01 0.05
Matches are distributed among these distances:
188 50 0.04
189 176 0.14
190 190 0.15
191 182 0.14
192 90 0.07
193 181 0.14
194 193 0.15
195 162 0.13
196 52 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (197 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
AA
Found at i:4113575 original size:386 final size:392
Alignment explanation
Indices: 4112847--4114364 Score: 2617
Period size: 386 Copynumber: 3.9 Consensus size: 392
4112837 TATTTAAATT
4112847 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
4112912 TAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTGGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4112976 ATCGACACTTTTTATATATGGATCGA-AC-TTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
4113039 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CG
195 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCG
4113103 GTATAATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
259 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTT
4113167 GGGGATCGACACTTTT-TATATGGATCGACAC-TT-TGGGTGCACC-TGTTTCCATTCATTCTGG
323 -GGGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
4113228 GAAAAA
387 GAAAAA
4113234 AGTATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
* *
4113298 TAATTGTACCAGTTAGAGTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4113362 ATCGACACTTTTATATATGGATCGACACTTTA-GGGTGCACCTTGTTTCCATTCATTCTGGGAAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
*
4113426 AAAGTATCGACACAAAC-ATA-TAGTGTTGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAGTATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGG
4113489 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTG
4113554 GGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCA-TCATTCTGGGA
324 GGATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
4113618 AAAA
389 AAAA
4113622 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4113687 TAATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4113751 ATCGACACTTTT-TATATGGATCGACACTTTATGGG-GCACCTTG--TCCATTCATTCT-GGAAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4113811 AAAGTATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGT
196 AAAGTATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGT
4113876 ATAATTGTACCGGTTAGATTGAAAAATTACATATT--ATTATACTTTTGGGTTCGATGATTTGGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
*
4113939 ATCGACACTTTTATATATGGATCGACACTTTA-GGGTGTACCTTGTTTCCATTCATTCTGGG-AA
326 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
4114002 AA
391 AA
*
4114004 AGTATCGACACAAACTATATT-GTGTCGACACATTA-TTAGATATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4114067 T-ATTGTACC-GTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTT-GG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
4114128 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCA-TCTGGGGAA
131 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCT-GGGAA
4114192 AAAA-TATCGACACAAACTATATTAGTGTCG--ACATTATTAGACATATTCTCTCATAAAACC-G
195 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGG
*
4114253 TATAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGAT-AATTGG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGG
* *
4114316 GATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
325 GATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
4114365 GGCCATATTG
Statistics
Matches: 1092, Mismatches: 13, Indels: 59
0.94 0.01 0.05
Matches are distributed among these distances:
377 27 0.02
378 77 0.07
379 120 0.11
380 44 0.04
381 48 0.04
382 50 0.05
383 48 0.04
384 60 0.05
385 70 0.06
386 307 0.28
387 41 0.04
388 95 0.09
389 105 0.10
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (392 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
AAAGTATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAAA
AA
Found at i:4114691 original size:19 final size:19
Alignment explanation
Indices: 4114659--4114706 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4114649 TTATATTCAC
4114659 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
4114677 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
4114696 ATACAAAATTA
1 ATACAAAATTA
4114707 AGTCGACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:4114806 original size:183 final size:179
Alignment explanation
Indices: 4114464--4114825 Score: 672
Period size: 183 Copynumber: 2.0 Consensus size: 179
4114454 CTCATCTCAT
4114464 TCATAATTATATTCACATACAAAAATATAAATCGTATACAAAATATAAATCTTACAAATTAAGTC
1 TCATAATTATATTCACATACAAAAATATAAATCGTATACAAAATATAAATCTTACAAATTAAGTC
4114529 GACATTTACATCATTGCATTCTTTTGTTATTCTTATGTAATATGCAGCTTTTGTTATCTCCTGTC
66 GACATTTACATCATTGCATTCTTTTGTTATTCTTATGTAATATGCAGCTTTTGTTATCTCCTGTC
4114594 TTCGTTCATTTTGATTGTGGCTTACGAGATCGTTTAATACTCGCGATCG
131 TTCGTTCATTTTGATTGTGGCTTACGAGATCGTTTAATACTCGCGATCG
4114643 TCATAATTATATTCACATAC-AAAATATAAATCGTATACAAAATTATAAATCTTATACAAAATTA
1 TCATAATTATATTCACATACAAAAATATAAATCGTATACAAAA-TATAAATC-T-TAC-AAATTA
4114707 AGTCGACATTTACATCATTGCATTCTTTTGTTATTCTTATGTAATATTGCAGCTTTTGTTATCTC
62 AGTCGACATTTACATCATTGCATTCTTTTGTTATTCTTATGTAATA-TGCAGCTTTTGTTATCTC
4114772 CTGTCTTCGTTCATTTTGATTGTGGCTTACGAGATCGTTTAATACTCGCGATCG
126 CTGTCTTCGTTCATTTTGATTGTGGCTTACGAGATCGTTTAATACTCGCGATCG
4114826 ATCCCAGTCT
Statistics
Matches: 178, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
178 22 0.12
179 28 0.16
180 1 0.01
181 3 0.02
182 52 0.29
183 72 0.40
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (179 bp):
TCATAATTATATTCACATACAAAAATATAAATCGTATACAAAATATAAATCTTACAAATTAAGTC
GACATTTACATCATTGCATTCTTTTGTTATTCTTATGTAATATGCAGCTTTTGTTATCTCCTGTC
TTCGTTCATTTTGATTGTGGCTTACGAGATCGTTTAATACTCGCGATCG
Found at i:4116522 original size:34 final size:34
Alignment explanation
Indices: 4116483--4116547 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
4116473 CATCTTAATC
*
4116483 ACCCCTTAACACCCCAACTTCTTTCACCACTTCA
1 ACCCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
4116517 ACCCCTCAACACCTCTACTTCTTTCACCACT
1 ACCCCTCAACACCCCAACTTCTTTCACCACT
4116548 CAATCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.25, C:0.48, G:0.00, T:0.28
Consensus pattern (34 bp):
ACCCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:4116621 original size:21 final size:21
Alignment explanation
Indices: 4116581--4116645 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
4116571 CCCCTTATTC
* *
4116581 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
4116602 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
4116623 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
4116644 CT
1 CT
4116646 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:4118868 original size:17 final size:18
Alignment explanation
Indices: 4118846--4118887 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
4118836 ATATATCCGG
4118846 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
4118863 TATCATTTGTTACCGGTTT
1 TATCA-TTGTTACCGGTTT
4118882 TATCAT
1 TATCAT
4118888 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:4118905 original size:20 final size:19
Alignment explanation
Indices: 4118851--4118896 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4118841 TCCGGTATCA
4118851 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
4118870 TGTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCAT-T
4118890 TTTTACC
1 TTTTACC
4118897 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:4118930 original size:28 final size:29
Alignment explanation
Indices: 4118876--4118934 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
4118866 CATTTGTTAC
4118876 CGGTTTTATCATATTTTTACCTGTTATAT
1 CGGTTTTATCATATTTTTACCTGTTATAT
4118905 CGGTTTTATCATA-TTTTACCTGTTATAT
1 CGGTTTTATCATATTTTTACCTGTTATAT
4118933 CG
1 CG
4118935 TTGTGGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (29 bp):
CGGTTTTATCATATTTTTACCTGTTATAT
Found at i:4118951 original size:30 final size:28
Alignment explanation
Indices: 4118876--4118951 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
4118866 CATTTGTTAC
*
4118876 CGGTTTTATCATATTTTTACCTGTTATAT
1 CGGTTTGATCATA-TTTTACCTGTTATAT
*
4118905 CGGTTTTATCATATTTTACCTGTTATAT
1 CGGTTTGATCATATTTTACCTGTTATAT
4118933 C-GTTGTGGATCGATATTTT
1 CGGTT-T-GATC-ATATTTT
4118952 TTTAAAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 3 0.07
28 17 0.40
29 16 0.37
30 7 0.16
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.53
Consensus pattern (28 bp):
CGGTTTGATCATATTTTACCTGTTATAT
Found at i:4119070 original size:20 final size:20
Alignment explanation
Indices: 4119044--4119089 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
4119034 CACTTTTAAA
4119044 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
4119063 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
4119084 TTTACC
1 TTTACC
4119090 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:4120067 original size:22 final size:23
Alignment explanation
Indices: 4120025--4120067 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4120015 CATTATACTT
4120025 ATCAAAATGTTTACAACATTATA
1 ATCAAAATGTTTACAACATTATA
4120048 ATCAAAAT-TTTATCAA-ATTA
1 ATCAAAATGTTTA-CAACATTA
4120068 GTATAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (23 bp):
ATCAAAATGTTTACAACATTATA
Found at i:4120095 original size:31 final size:31
Alignment explanation
Indices: 4120057--4120123 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
4120047 AATCAAAATT
*
4120057 TTATCAAATTAGTATAAAATGA-TCATTAAAC
1 TTATCAAATTAGTAAAAAATGATTC-TTAAAC
* *
4120088 TTATCAAATTATTAAAAAATGATTCTTAAAT
1 TTATCAAATTAGTAAAAAATGATTCTTAAAC
4120119 TTATC
1 TTATC
4120124 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (31 bp):
TTATCAAATTAGTAAAAAATGATTCTTAAAC
Found at i:4130035 original size:176 final size:177
Alignment explanation
Indices: 4129711--4130044 Score: 408
Period size: 176 Copynumber: 1.9 Consensus size: 177
4129701 TCTACAATAC
* * * * *
4129711 AATTCCTCCCAGTTTCGATTCGATTCAATATGATAAGATCGATGTTTTTTTATAAAAAAAATTAT
1 AATTCCTCCCAGTTTCGATTCGATTCAATATGAAAAGATCAATGTTTTTTCAAAAAAAAAAATAT
* * * *
4129776 TCGTGTTGGACCAGATTAAGTCCATTTCTTGATTTTGGATGAAAAATACACACTTGAAAAATAAT
66 TCGTGTTGGACCAGATCAAGTCCAGTTCTTGATTTTAGATGAAAAATACACACTCGAAAAATAAT
4129841 ATTAATTGATCTTT-TATATTTATAAAGATCGATTGGTGTTGGACAT
131 ATTAATTGATCTTTATATATTTATAAAGATCGATTGGTGTTGGACAT
* * * * *
4129887 AATTCCTTCGAGTTTTGATTCGATTCAATCTTAAAAGATCAATGTCTTTTTCAAAAAATAAAAAT
1 AATTCCTCCCAGTTTCGATTCGATTCAATATGAAAAGATCAATGT-TTTTTCAAAAAA-AAAAAT
* * * *
4129952 A-T-GTGTTGGGCCAGATCAAGTCGAGTTCTTG-TTTTCAGATGAAAAATACCCACTCG-AGAAT
64 ATTCGTGTTGGACCAGATCAAGTCCAGTTCTTGATTTT-AGATGAAAAATACACACTCGAAAAAT
* *
4130013 AATAGTATAGTTGGTCTTTATATATTTATAAA
128 AATA-T-TAATTGATCTTTATATATTTATAAA
4130045 TAAGGGTAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
175 12 0.09
176 81 0.61
177 21 0.16
178 18 0.14
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (177 bp):
AATTCCTCCCAGTTTCGATTCGATTCAATATGAAAAGATCAATGTTTTTTCAAAAAAAAAAATAT
TCGTGTTGGACCAGATCAAGTCCAGTTCTTGATTTTAGATGAAAAATACACACTCGAAAAATAAT
ATTAATTGATCTTTATATATTTATAAAGATCGATTGGTGTTGGACAT
Found at i:4144066 original size:15 final size:14
Alignment explanation
Indices: 4144048--4144084 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
4144038 TCTTCTTAGA
4144048 TTCTTGTCCACCTCT
1 TTCTTGTCCACCT-T
4144063 TTCTTGTCCACCTT
1 TTCTTGTCCACCTT
*
4144077 TTTTTGTC
1 TTCTTGTC
4144085 ATTCTTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.05, C:0.32, G:0.08, T:0.54
Consensus pattern (14 bp):
TTCTTGTCCACCTT
Found at i:4145466 original size:18 final size:19
Alignment explanation
Indices: 4145411--4145474 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 19
4145401 CGAAACCGGT
4145411 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
*
4145430 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
4145447 TTTTTCGGTTCGGTTC-GG
1 TTTTTCGGTTCGGTTCGGG
4145465 TTTTTCGGTT
1 TTTTTCGGTT
4145475 TTTCAATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 12 0.31
19 11 0.28
20 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.52
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:4148846 original size:9 final size:9
Alignment explanation
Indices: 4148832--4148856 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4148822 AAATATGGAC
4148832 TTAATATAT
1 TTAATATAT
4148841 TTAATATAT
1 TTAATATAT
4148850 TTAATAT
1 TTAATAT
4148857 TTAATAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATATAT
Found at i:4152407 original size:30 final size:31
Alignment explanation
Indices: 4152373--4152432 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
4152363 GTTCTAAATC
* *
4152373 TATCTTTAATT-TT-TTTTAATATTTTAATTT
1 TATCTTAAATTATTATTTTAAT-TTTAAATTT
4152403 TATCTTAAATTATTATTTTAATTTTAAATT
1 TATCTTAAATTATTATTTTAATTTTAAATT
4152433 AATCGTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 9 0.35
32 7 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (31 bp):
TATCTTAAATTATTATTTTAATTTTAAATTT
Found at i:4152429 original size:19 final size:19
Alignment explanation
Indices: 4152378--4152433 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
4152368 AAATCTATCT
4152378 TTAATTTT-TTTTAATATT-
1 TTAATTTTATTTTAA-ATTA
*
4152396 TTAATTTTATCTTAAATTA
1 TTAATTTTATTTTAAATTA
4152415 TT-ATTTTAATTTTAAATTA
1 TTAATTTT-ATTTTAAATTA
4152434 ATCGTCGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAATTTTATTTTAAATTA
Found at i:4155613 original size:19 final size:19
Alignment explanation
Indices: 4155581--4155619 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4155571 GATATTATAT
*
4155581 TTTAAAAGAAAATAATTAA
1 TTTAAAAGAAAATAAATAA
* *
4155600 TTTAAAATATAATAAATAA
1 TTTAAAAGAAAATAAATAA
4155619 T
1 T
4155620 CGAATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TTTAAAAGAAAATAAATAA
Found at i:4157154 original size:24 final size:25
Alignment explanation
Indices: 4157109--4157157 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4157099 AAATGGTTAA
*
4157109 ACTTTTTTGTTTCTCAAGTAGTAAT
1 ACTTTTTTCTTTCTCAAGTAGTAAT
4157134 ACTTTTTTACTTT-TCAA-TAGTAAT
1 ACTTTTTT-CTTTCTCAAGTAGTAAT
4157158 GATTAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 12 0.55
26 3 0.14
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (25 bp):
ACTTTTTTCTTTCTCAAGTAGTAAT
Found at i:4162425 original size:16 final size:16
Alignment explanation
Indices: 4162400--4162448 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
4162390 CAGTTAGTAA
* *
4162400 TTAGCGGTTAGAAATG
1 TTAGAGGTTAGAAAAG
**
4162416 TTAGTTGTTAGAAAAG
1 TTAGAGGTTAGAAAAG
4162432 TTAGAGGTTAGAAAAG
1 TTAGAGGTTAGAAAAG
4162448 T
1 T
4162449 CCGCGCCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.33
Consensus pattern (16 bp):
TTAGAGGTTAGAAAAG
Found at i:4162426 original size:30 final size:32
Alignment explanation
Indices: 4162381--4162445 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
4162371 CAAATAAATA
* *
4162381 AAATGTTAGCAGTTAG-TAA-TTAGCGGTTAG
1 AAATGTTAGCAGTTAGAAAAGTTAGAGGTTAG
**
4162411 AAATGTTAGTTGTTAGAAAAGTTAGAGGTTAG
1 AAATGTTAGCAGTTAGAAAAGTTAGAGGTTAG
4162443 AAA
1 AAA
4162446 AGTCCGCGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 14 0.48
31 2 0.07
32 13 0.45
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (32 bp):
AAATGTTAGCAGTTAGAAAAGTTAGAGGTTAG
Found at i:4162598 original size:128 final size:123
Alignment explanation
Indices: 4162454--4162693 Score: 318
Period size: 123 Copynumber: 1.9 Consensus size: 123
4162444 AAAGTCCGCG
** *
4162454 CCATAATAATTTGGATCATACCCCAAATTTGGTCACCACAAAGTCGAATCAAATACAATAAATAA
1 CCATAATAATGCGGATCATACCCCAAATCTGGTCACCACAAAGTCGAATCAAAT--AAT--A-AA
* * * * *
4162519 ATAAATATATAAAAAATGGTTTAAATGCAATAAAATAAAAGTCAGTAGTTAACAGAATCTTAA
61 ATAAATAAATAAAAAATAGTTAAAATGCAACAAAATAAAAATCAGTAGTTAACAGAATCTTAA
*** *
4162582 CCATAATAATGCGGATCATACCCTGGATCTGGTCACCACAAAGTCGAATCGAATAATAAAATAAA
1 CCATAATAATGCGGATCATACCCCAAATCTGGTCACCACAAAGTCGAATCAAATAATAAAATAAA
*
4162647 TAAATAAACAATAGTTAAAATGCAACAAAATAAAAATCAGTAGTTAA
66 TAAATAAAAAATAGTTAAAATGCAACAAAATAAAAATCAGTAGTTAA
4162694 TATGTAATAA
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
123 48 0.48
124 1 0.01
126 3 0.03
128 47 0.47
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (123 bp):
CCATAATAATGCGGATCATACCCCAAATCTGGTCACCACAAAGTCGAATCAAATAATAAAATAAA
TAAATAAAAAATAGTTAAAATGCAACAAAATAAAAATCAGTAGTTAACAGAATCTTAA
Found at i:4162693 original size:29 final size:29
Alignment explanation
Indices: 4162644--4162726 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
4162634 ATAATAAAAT
* *
4162644 AAATAAATAAACAATAGTTAAAATGCAACA
1 AAATAAA-AATCAGTAGTTAAAATGCAACA
* * *
4162674 AAATAAAAATCAGTAGTTAATATGTAATA
1 AAATAAAAATCAGTAGTTAAAATGCAACA
* *
4162703 AAATAAAAGTTAGTAGTTAGAAAT
1 AAATAAAAATCAGTAGTTA-AAAT
4162727 ATATAACATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 34 0.77
30 10 0.23
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.27
Consensus pattern (29 bp):
AAATAAAAATCAGTAGTTAAAATGCAACA
Found at i:4162732 original size:29 final size:29
Alignment explanation
Indices: 4162636--4162729 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
4162626 CGAATCGAAT
* * *
4162636 AATAAAAT-AAATAAATAAACAATAGTTAA
1 AATATAATAAAATAAA-AATCAGTAGTTAA
** *
4162665 AATGCAACAAAATAAAAATCAGTAGTTAA
1 AATATAATAAAATAAAAATCAGTAGTTAA
* * * *
4162694 TATGTAATAAAATAAAAGTTAGTAGTTAGA
1 AATATAATAAAATAAAAATCAGTAGTTA-A
4162724 AATATA
1 AATATA
4162730 TAACATAGCA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 39 0.76
30 12 0.24
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.27
Consensus pattern (29 bp):
AATATAATAAAATAAAAATCAGTAGTTAA
Found at i:4164209 original size:135 final size:136
Alignment explanation
Indices: 4163922--4164327 Score: 490
Period size: 138 Copynumber: 3.0 Consensus size: 136
4163912 GTAAATAGAA
* * * * *
4163922 ATAACATGGTTCCTATGCGATGAAGACGACTGGTTATCTAAGGATGACACTGCTCCTACGTGATG
1 ATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGG-TGACACAGCTCCTACGTGATG
* ** * * * * *
4163987 AGGATATCTGGTCGGTATATGATACGGTTACTACGTGATGAGGACGTATTGGTCATCTTTATGGA
65 AGGAGATCTGGTCGGTGGATGA-ACAGTTCCTACGTGATGAGGACG-ACTGGCCATCTTTAGGGA
*
4164052 TAAATGGTG
128 TAAATGATG
** * * *
4164061 ATAACACAATTCCTACGTGATGAGGACGATTGGTTATCTAAGGTGACACAACTCCTACGTGATAA
1 ATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTGACACAGCTCCTACGTGATGA
*
4164126 GGAGATCTGGTCGGTGGATG-ACAGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGGATAA
66 GGAGATCTGGTCGGTGGATGAACAGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
4164190 ATGATG
131 ATGATG
* * * * *
4164196 ATAACACGGTTCCTACGTGATGAGGATGACTGGTTATCTAAGTTTGACACGGCTCATATGTGATG
1 ATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAG-GTGACACAGCTCCTACGTGATG
* * * * *
4164261 ATGAGATCTGGTTGGTGGATGACACAGTTCCTACGTGATGAGGATGACTGACCATATTTAGGGAT
65 AGGAGATCTGGTCGGTGGATGA-ACAGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGAT
4164326 AA
129 AA
4164328 TTTGTTTTAA
Statistics
Matches: 228, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
135 60 0.26
136 56 0.25
138 76 0.33
139 36 0.16
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (136 bp):
ATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTGACACAGCTCCTACGTGATGA
GGAGATCTGGTCGGTGGATGAACAGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
ATGATG
Found at i:4164369 original size:36 final size:36
Alignment explanation
Indices: 4164329--4164424 Score: 147
Period size: 36 Copynumber: 2.7 Consensus size: 36
4164319 TAGGGATAAT
* * ** *
4164329 TTGTTTTAAGAGAAACTGTCTCAAGAGAGATAAAAC
1 TTGTTTCAAGGGAAACAATCTCAAGAGAAATAAAAC
4164365 TTGTTTCAAGGGAAACAATCTCAAGAGAAATAAAAC
1 TTGTTTCAAGGGAAACAATCTCAAGAGAAATAAAAC
4164401 TTGTTTCAAGGGAAACAATCTCAA
1 TTGTTTCAAGGGAAACAATCTCAA
4164425 TGTTTGTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACAATCTCAAGAGAAATAAAAC
Found at i:4164547 original size:36 final size:35
Alignment explanation
Indices: 4164497--4164612 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 35
4164487 AAAATTTGTA
4164497 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-T
* ** * ****
4164533 TGTTTCAAGGGAAACAATCTCAA-A-TGTTTTAA-
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
4164565 -GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-T
4164600 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
4164613 ACAATATCAA
Statistics
Matches: 59, Mismatches: 16, Indels: 11
0.69 0.19 0.13
Matches are distributed among these distances:
31 19 0.32
32 1 0.02
33 3 0.05
34 3 0.05
35 5 0.08
36 28 0.47
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:4164659 original size:132 final size:131
Alignment explanation
Indices: 4164366--4164819 Score: 510
Period size: 132 Copynumber: 3.4 Consensus size: 131
4164356 AGATAAAACT
* ** * *
4164366 TGTTTCAAGGGAAACAATCTCAAGAGAAATAAAACTTGTTTCAAGGGAAACAATCTC-AATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATGTTT
* * *
4164430 GT-GTTTCAAGAGAAACTGTCTAAAGGGAGAC-AAACTTGTTTCAAGAGAAACAATATCAAAATT
66 -TAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGA-AAACAATATCAAAGTT
4164493 TGTA
129 T-TA
*
4164497 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATGTTT
4164562 TAAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGAAAACAATATCAAAGTT
66 T-AGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAA-GAAAACAATATCAAAGTT
4164627 TT-
129 TTA
* * * * * *
4164629 TGTTTCAAGAGAAATTGTATCAAGCA-AGACAAAATTTATTTCGAGGGAAACAAACTCAAA-GAT
1 TGTTTCAAGAGAAACTGTCTCAAG-AGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATG-T
* * * *
4164692 TTTACGTTTCAAGAGAAAATGT-TCCAAGAGAGACAAAATTTTGCTTCAA-ATGAAACAATCTCA
64 TTTA-GTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA-CTTGTTTCAAGA--AAACAATATCA
*
4164755 ATGTTCTTA
124 AAGTT-TTA
* * * * *
4164764 CGTTTCAAGAGAAACTATCTCAAAAGAGACACAACTTGTTTCAAGAGAAACAATCT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCT
4164820 TACAGGTTTT
Statistics
Matches: 278, Mismatches: 30, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
131 56 0.20
132 94 0.34
133 51 0.18
134 32 0.12
135 45 0.16
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (131 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATGTTT
TAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAAAACAATATCAAAGTTTT
A
Found at i:4164804 original size:200 final size:198
Alignment explanation
Indices: 4164367--4164817 Score: 570
Period size: 198 Copynumber: 2.3 Consensus size: 198
4164357 GATAAAACTT
* * * * * * *
4164367 GTTTCAAGGGAAACAATCTCAAGAGAAATAAAACTTGTTTCAAGGGAAACAATCTCAATGTTTGT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGAAAACAATATCAAAGTTTGT
* ** *
4164432 GTTTCAAGAGAAACTGTCTAAAGGGAGACAAACTTGTTTCAAGAGAAACAATATCAAAATTTGTA
66 GTTTCAAGAGAAACTGTATAAAGCAAGACAAACTTATTTCAAGAGAAACAATATCAAAATTTGTA
* * * *
4164497 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
131 CGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGCTTCAAAGGAAACAATCTCAAATGTTT
4164562 TAA
196 TAA
* *
4164565 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGAAAACAATATCAAAGTTTTT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGAAAACAATATCAAAGTTTGT
* * * * *
4164630 GTTTCAAGAGAAATTGTATCAAGCAAGACAAAATTTATTTCGAGGGAAACAA-ACTCAAAGATTT
66 GTTTCAAGAGAAACTGTATAAAGCAAGAC-AAACTTATTTCAAGAGAAACAATA-TCAAA-ATTT
*
4164694 -TACGTTTCAAGAGAAAATGT-TCCAAGAGAGACAAAATTTTGCTTCAAATGAAACAATCTC-AA
128 GTACGTTTCAAGAGAAAATGTCT-CAAGAGAGACAAAA-TTTGCTTCAAAGGAAACAATCTCAAA
*
4164756 TGTTCTTAC
191 TGTT-TTAA
* *
4164765 GTTTCAAGAGAAACTATCTCAAAAGAGACACAACTTGTTTCAA-GAGAAACAAT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGA-AAACAAT
4164818 CTTACAGGTT
Statistics
Matches: 219, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
198 82 0.37
199 63 0.29
200 74 0.34
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (198 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGAAAACAATATCAAAGTTTGT
GTTTCAAGAGAAACTGTATAAAGCAAGACAAACTTATTTCAAGAGAAACAATATCAAAATTTGTA
CGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGCTTCAAAGGAAACAATCTCAAATGTTT
TAA
Found at i:4164845 original size:67 final size:66
Alignment explanation
Indices: 4164366--4164845 Score: 488
Period size: 67 Copynumber: 7.2 Consensus size: 66
4164356 AGATAAAACT
* ** * * *
4164366 TGTTTCAAGGGAAACAATCTCAAGAGAAATAAAACTTGTTTCAAGGGAAACAATCTCAATG-TTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAATGTTTT
*
4164430 G
66 A
* * * **
4164431 TGTTTCAAGAGAAACTGTCTAAAGGGAGAC-AAACTTGTTTCAAGAGAAACAATATCAAAATTTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAATGTTT-
4164495 TA
65 TA
* *
4164497 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTC-AATGTTT
4164562 TA
65 TA
* * *
4164564 AGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAG-GAAAACAATATCAAAGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAG-AAACAATCTCAATGTTT
4164628 T-
65 TA
* * * * * * * *
4164629 TGTTTCAAGAGAAATTGTATCAAGCA-AGACAAAATTTATTTCGAGGGAAACAAACTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAG-AGAGACAAAACTTGTTTCAAGAGAAACAATCTCAATG-TT
4164693 TTA
64 TTA
* * * *
4164696 CGTTTCAAGAGAAAATGT-TCCAAGAGAGACAAAATTTTGCTTCAA-ATGAAACAATCTCAATGT
1 TGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA-CTTGTTTCAAGA-GAAACAATCTCAATGT
4164759 TCTTA
63 T-TTA
* * * * * *
4164764 CGTTTCAAGAGAAACTATCTCAAAAGAGACACAACTTGTTTCAAGAGAAACAATCTTACAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCA-ATGTTT
4164829 TA
65 TA
* *
4164831 TGTTTTAAGTGAAAC
1 TGTTTCAAGAGAAAC
4164846 AATTTCCAAA
Statistics
Matches: 348, Mismatches: 50, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
64 26 0.07
65 74 0.21
66 45 0.13
67 141 0.41
68 61 0.18
69 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAATGTTTT
A
Found at i:4165710 original size:23 final size:23
Alignment explanation
Indices: 4165677--4165741 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
4165667 CTTATATGGA
4165677 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * * *
4165700 ACTTCGATGCAATTCTACGTGGT
1 ACTTCGGTGCATTTCTACGCGGC
*
4165723 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
4165742 AGCTATGGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:4169621 original size:2 final size:2
Alignment explanation
Indices: 4169614--4169652 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4169604 TTTATTTATG
4169614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4169653 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4171472 original size:2 final size:2
Alignment explanation
Indices: 4171465--4171503 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4171455 TAAGTACTAT
4171465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4171504 CCATTCTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4171621 original size:24 final size:24
Alignment explanation
Indices: 4171594--4171639 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4171584 TTCCATTTTG
4171594 TTTTATTCATTTTAC-TTTTTTACT
1 TTTTATT-ATTTTACATTTTTTACT
*
4171618 TTTTATTATTTTTCATTTTTTA
1 TTTTATTATTTTACATTTTTTA
4171640 TGATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATTATTTTACATTTTTTACT
Found at i:4171621 original size:46 final size:44
Alignment explanation
Indices: 4171548--4171636 Score: 101
Period size: 46 Copynumber: 2.0 Consensus size: 44
4171538 GTTTTGGTTT
4171548 TTTTATTCAATTCTATTTTTCAATTTTTTATT-TTTATTCCATTTTG
1 TTTTATTCAATTCTATTTTTCAA-TTTTTATTATTT-TT-CATTTTG
* * *
4171594 TTTTATTC-ATTTTACTTTTTTACTTTTTATTATTTTTCATTTT
1 TTTTATTCAATTCTA-TTTTTCAATTTTTATTATTTTTCATTTT
4171637 TTATGATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
44 6 0.16
45 15 0.39
46 17 0.45
ACGTcount: A:0.18, C:0.10, G:0.01, T:0.71
Consensus pattern (44 bp):
TTTTATTCAATTCTATTTTTCAATTTTTATTATTTTTCATTTTG
Found at i:4171636 original size:15 final size:14
Alignment explanation
Indices: 4171573--4171636 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
4171563 TTTTTCAATT
4171573 TTTTATTTTTATTCCA
1 TTTTATTTTT-TT-CA
* *
4171589 TTTTGTTTTATTCA
1 TTTTATTTTTTTCA
* *
4171603 TTTTACTTTTTTACT
1 TTTTA-TTTTTTTCA
4171618 TTTTATTATTTTTCA
1 TTTTATT-TTTTTCA
4171633 TTTT
1 TTTT
4171637 TTATGATGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 8 0.21
15 22 0.58
16 8 0.21
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTATTTTTTTCA
Found at i:4174988 original size:4 final size:4
Alignment explanation
Indices: 4174981--4175007 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4174971 TATATATATG
4174981 GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GAT
4175008 TTAAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:4175722 original size:29 final size:29
Alignment explanation
Indices: 4175679--4175765 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
4175669 AATTTTGACC
* * *
4175679 AGTGACTAAAATGTAAGTTTTGAAAGTTT
1 AGTGACTAAAGTGTAACTTTTAAAAGTTT
4175708 AGTGACTAAAGTGTAACTTTTAAAAGTTT
1 AGTGACTAAAGTGTAACTTTTAAAAGTTT
* * *
4175737 AGAGACCAAAAGTGTAATTTTTAAAAGTT
1 AGTGA-CTAAAGTGTAACTTTTAAAAGTT
4175766 GTATATTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.59
30 21 0.41
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (29 bp):
AGTGACTAAAGTGTAACTTTTAAAAGTTT
Found at i:4175751 original size:30 final size:29
Alignment explanation
Indices: 4175686--4175765 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 29
4175676 ACCAGTGACT
* * *
4175686 AAAA-TGTAAGTTTTGAAAGTTTAGTGAC
1 AAAAGTGTAACTTTTAAAAGTTTAGAGAC
*
4175714 TAAAGTGTAACTTTTAAAAGTTTAGAGACC
1 AAAAGTGTAACTTTTAAAAGTTTAGAGA-C
*
4175744 AAAAGTGTAATTTTTAAAAGTT
1 AAAAGTGTAACTTTTAAAAGTT
4175766 GTATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 3 0.07
29 20 0.45
30 21 0.48
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (29 bp):
AAAAGTGTAACTTTTAAAAGTTTAGAGAC
Found at i:4177902 original size:36 final size:36
Alignment explanation
Indices: 4177861--4177963 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
4177851 TTTTATCTAT
*
4177861 TATCAGCTTTGATACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
4177897 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
* * *
4177933 TATTAGCTTTGGTACATTCGTGTATTAATGT
1 TATCAGCTTTGGTACATTCATGTATCAATGT
4177964 CCAGCACCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
Found at i:4183406 original size:32 final size:32
Alignment explanation
Indices: 4183370--4183465 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
4183360 TTGACATATA
*
4183370 TCGAAAATCAACTGATCCGATATTGACTCGAC
1 TCGAAAATCAACTGATCCGATATTGACACGAC
* * *
4183402 TCG-AAATCTAAAC-GATTCGATATTAACCCGAC
1 TCGAAAATC--AACTGATCCGATATTGACACGAC
* *
4183434 CCAAAAATCAACTGATCCGATATTGACACGAC
1 TCGAAAATCAACTGATCCGATATTGACACGAC
4183466 CCGATATTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
31 8 0.15
32 36 0.69
33 8 0.15
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (32 bp):
TCGAAAATCAACTGATCCGATATTGACACGAC
Found at i:4184709 original size:14 final size:14
Alignment explanation
Indices: 4184690--4184740 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
4184680 TCTTATACAT
4184690 ATACATATGCATAC
1 ATACATATGCATAC
4184704 ATACATATGCATAC
1 ATACATATGCATAC
*
4184718 ATGCATA--CAT--
1 ATACATATGCATAC
4184728 ATACATATGCATA
1 ATACATATGCATA
4184741 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 6 0.19
12 6 0.19
14 20 0.62
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (14 bp):
ATACATATGCATAC
Found at i:4184743 original size:14 final size:14
Alignment explanation
Indices: 4184688--4184749 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
4184678 AATCTTATAC
4184688 ATATACATATGCAT
1 ATATACATATGCAT
*
4184702 ACATACATATGCAT
1 ATATACATATGCAT
* *
4184716 ACATGCATA--C--
1 ATATACATATGCAT
4184726 ATATACATATGCAT
1 ATATACATATGCAT
*
4184740 ATATATATAT
1 ATATACATAT
4184750 ATATATATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.18
12 2 0.05
14 30 0.77
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (14 bp):
ATATACATATGCAT
Found at i:4184753 original size:24 final size:24
Alignment explanation
Indices: 4184704--4184754 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4184694 ATATGCATAC
*
4184704 ATACATATGCATACATGCATACAT
1 ATACATATGCATACATACATACAT
* * *
4184728 ATACATATGCATATATATATATAT
1 ATACATATGCATACATACATACAT
4184752 ATA
1 ATA
4184755 TATGATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (24 bp):
ATACATATGCATACATACATACAT
Found at i:4188017 original size:24 final size:24
Alignment explanation
Indices: 4187985--4188032 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4187975 TCGAACCTGA
4187985 AATACCTAGGAATACAATTATCAT
1 AATACCTAGGAATACAATTATCAT
4188009 AATACCTAGGAATACAATTATCAT
1 AATACCTAGGAATACAATTATCAT
4188033 TTTAACCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (24 bp):
AATACCTAGGAATACAATTATCAT
Found at i:4190381 original size:30 final size:30
Alignment explanation
Indices: 4190347--4190404 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
4190337 CACAAATCAA
4190347 TCACTAACGTTAACGTTTGTTACAAAATAG
1 TCACTAACGTTAACGTTTGTTACAAAATAG
* *
4190377 TCACTAATGTTATCGTTTGTTACAAAAT
1 TCACTAACGTTAACGTTTGTTACAAAAT
4190405 GATCATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (30 bp):
TCACTAACGTTAACGTTTGTTACAAAATAG
Found at i:4190798 original size:30 final size:30
Alignment explanation
Indices: 4190687--4190789 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
4190677 TAACCGTTAT
* *
4190687 TAACGTTGAGTGACCATTTTTTAGCAAACGA
1 TAACGTT-AGTGACCATTTTATAACAAACGA
*
4190718 TAACGTTAGTGACCATTTTATAACAAATGA
1 TAACGTTAGTGACCATTTTATAACAAACGA
*
4190748 TAATGTTAGTGACCATTTTATAACAAACGA
1 TAACGTTAGTGACCATTTTATAACAAACGA
4190778 TAACGTTAGTGA
1 TAACGTTAGTGA
4190790 TAAATTTATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
30 59 0.89
31 7 0.11
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (30 bp):
TAACGTTAGTGACCATTTTATAACAAACGA
Found at i:4210971 original size:6 final size:6
Alignment explanation
Indices: 4210950--4210990 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
4210940 TAGTATTAGA
4210950 AAATATT AAA-AT AAATAT AAATAT AAATAT AAATATT AAAT
1 AAATA-T AAATAT AAATAT AAATAT AAATAT AAATA-T AAAT
4210991 TGATCTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.12
6 20 0.62
7 8 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:4212539 original size:23 final size:23
Alignment explanation
Indices: 4212512--4212565 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
4212502 AAAACTACCA
4212512 AAAGACATAGAAAAACATGTCAC
1 AAAGACATAGAAAAACATGTCAC
* * **
4212535 AAAGACAGAGATAAATGTGTCAC
1 AAAGACATAGAAAAACATGTCAC
*
4212558 AAATACAT
1 AAAGACAT
4212566 GATTATTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.17
Consensus pattern (23 bp):
AAAGACATAGAAAAACATGTCAC
Found at i:4213285 original size:15 final size:16
Alignment explanation
Indices: 4213249--4213288 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4213239 GAAAATAATT
*
4213249 CAAACTGAAATGAACC
1 CAAACTGAAATCAACC
4213265 CAAACTGAAA-CAACC
1 CAAACTGAAATCAACC
*
4213280 CGAACTGAA
1 CAAACTGAA
4213289 TTTAACCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.50, C:0.28, G:0.12, T:0.10
Consensus pattern (16 bp):
CAAACTGAAATCAACC
Found at i:4213335 original size:17 final size:17
Alignment explanation
Indices: 4213251--4213335 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 17
4213241 AAATAATTCA
* *
4213251 AACTGAAATG-AACCCA
1 AACTGAAAAGCAACCCG
4213267 AACTG-AAA-CAACCCG
1 AACTGAAAAGCAACCCG
*** *
4213282 AACTG-AATTTAACCTG
1 AACTGAAAAGCAACCCG
* *
4213298 AACCGAAAAGTAACCCG
1 AACTGAAAAGCAACCCG
*
4213315 AACTGAAAAGCATCCCG
1 AACTGAAAAGCAACCCG
4213332 AACT
1 AACT
4213336 AAATTTAACT
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
15 14 0.26
16 14 0.26
17 26 0.48
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14
Consensus pattern (17 bp):
AACTGAAAAGCAACCCG
Found at i:4217406 original size:15 final size:15
Alignment explanation
Indices: 4217386--4217419 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4217376 AAATAGAGAT
4217386 AAAATAAAAGTAATA
1 AAAATAAAAGTAATA
4217401 AAAATAAAAGTAATA
1 AAAATAAAAGTAATA
4217416 AAAA
1 AAAA
4217420 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATAAAAGTAATA
Found at i:4217439 original size:24 final size:24
Alignment explanation
Indices: 4217387--4217450 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
4217377 AATAGAGATA
*
4217387 AAATAAAAGTAAT-AAAAATAAAAG
1 AAATAAAA-AAATAAAAAATAAAAG
*
4217411 TAATAAAAAAATAAAAAAT-AAAG
1 AAATAAAAAAATAAAAAATAAAAG
*
4217434 CAAATAAACAGAATAAA
1 -AAATAAA-AAAATAAA
4217451 GAAAATAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 7 0.21
24 19 0.58
25 7 0.21
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (24 bp):
AAATAAAAAAATAAAAAATAAAAG
Done.