Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3257268 original size:28 final size:29
Alignment explanation
Indices: 3257227--3257281 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
3257217 TCGGGTCAAC
*
3257227 CCGGTTCAGACCGGTCAAACCGGTTCAGA
1 CCGGTTCAAACCGGTCAAACCGGTTCAGA
3257256 CCGG-TCAAACCGGTCAAACCGGTTCA
1 CCGGTTCAAACCGGTCAAACCGGTTCA
3257282 AAACTGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.16
Consensus pattern (29 bp):
CCGGTTCAAACCGGTCAAACCGGTTCAGA
Found at i:3257292 original size:10 final size:9
Alignment explanation
Indices: 3257220--3257298 Score: 77
Period size: 9 Copynumber: 8.3 Consensus size: 9
3257210 AGTCGGGTCG
*
3257220 GGTCAACCC
1 GGTCAAACC
*
3257229 GGTTCAGACC
1 GG-TCAAACC
3257239 GGTCAAACC
1 GGTCAAACC
*
3257248 GGTTCAGACC
1 GG-TCAAACC
3257258 GGTCAAACC
1 GGTCAAACC
3257267 GGTCAAACC
1 GGTCAAACC
*
3257276 GGTTCAAAACT
1 GG-TC-AAACC
*
3257287 GGTCAAATC
1 GGTCAAACC
3257296 GGT
1 GGT
3257299 TTTCCAGCAG
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
9 33 0.57
10 19 0.33
11 6 0.10
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3258045 original size:20 final size:20
Alignment explanation
Indices: 3258020--3258068 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3258010 GGTTGTTACA
* *
3258020 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
3258040 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
3258060 ATCGCAACG
1 ATCGCAACG
3258069 AGAGAACCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:3258088 original size:33 final size:33
Alignment explanation
Indices: 3258042--3258135 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
3258032 AATTGACTAT
* **
3258042 CGCAACGCGGAAATGACTATCGCAACGAGAGAAC
1 CGCAATGC-GAAATGAAAATCGCAACGAGAGAAC
* ** *
3258076 CGCAATGCGAAATGAAAATCACAACGATTGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAC
3258109 CGCAATGCGAAAATGAAAATCGCAACG
1 CGCAATGCG-AAATGAAAATCGCAACG
3258136 CAAAATTAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGAGAGAAC
Found at i:3258207 original size:33 final size:34
Alignment explanation
Indices: 3258150--3258251 Score: 188
Period size: 34 Copynumber: 3.0 Consensus size: 34
3258140 ATTAGTTTCG
3258150 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
3258184 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
3258217 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
3258251 C
1 C
3258252 TGTAACACCC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 32 0.49
34 33 0.51
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:3260438 original size:20 final size:20
Alignment explanation
Indices: 3260415--3260501 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
3260405 CTGAAACTTT
3260415 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
3260435 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
3260455 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** * *
3260475 CTATCGCAACGCG-ACATGA
1 AAATCGCAACACGAAAATGA
3260494 AAATCGCA
1 AAATCGCA
3260502 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 10 0.17
20 48 0.83
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:3260539 original size:20 final size:20
Alignment explanation
Indices: 3260514--3260562 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3260504 GCGATTCTCT
3260514 CGTTGCGATAGTCAGATTCG
1 CGTTGCGATAGTCAGATTCG
* **
3260534 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCAGATTCG
3260554 CGTTGCGAT
1 CGTTGCGAT
3260563 TCACTCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAGATTCG
Found at i:3261180 original size:20 final size:20
Alignment explanation
Indices: 3261156--3261284 Score: 168
Period size: 20 Copynumber: 6.4 Consensus size: 20
3261146 GTCAGATTCA
3261156 CATTGCGATTTACGTAATCG
1 CATTGCGATTTACGTAATCG
* *
3261176 TATTGCGATTTACGTATTCG
1 CATTGCGATTTACGTAATCG
3261196 CATTGCGATTTACGTAATCG
1 CATTGCGATTTACGTAATCG
* **
3261216 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTACGTAA-TCG
* *
3261237 CGTTGCGATTTACGTATTCG
1 CATTGCGATTTACGTAATCG
* *
3261257 CATTGCGATTTAAGTATTCG
1 CATTGCGATTTACGTAATCG
3261277 CATTGCGA
1 CATTGCGA
3261285 ATTAGGAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 79 0.84
21 15 0.16
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
CATTGCGATTTACGTAATCG
Found at i:3261305 original size:21 final size:21
Alignment explanation
Indices: 3261281--3261326 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3261271 TATTCGCATT
3261281 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
3261302 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3261323 GCGA
1 GCGA
3261327 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3261659 original size:20 final size:20
Alignment explanation
Indices: 3261623--3261660 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3261613 ATCCTATTCT
**
3261623 CTGATAATCTTTTATTTCCA
1 CTGATAATCTTACATTTCCA
3261643 CTGATAATCTTACATTTC
1 CTGATAATCTTACATTTC
3261661 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
CTGATAATCTTACATTTCCA
Found at i:3261969 original size:21 final size:21
Alignment explanation
Indices: 3261944--3262002 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3261934 CAACAATTAT
3261944 TTTCATAAAAAGATTAAATCA
1 TTTCATAAAAAGATTAAATCA
* * *
3261965 TTTCATTAAAAGAATAAGTCA
1 TTTCATAAAAAGATTAAATCA
* *
3261986 TTTAATCAAAAGATTAA
1 TTTCATAAAAAGATTAA
3262003 GTTCTTTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (21 bp):
TTTCATAAAAAGATTAAATCA
Found at i:3265164 original size:21 final size:21
Alignment explanation
Indices: 3265140--3265179 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3265130 CAAAAGGATA
3265140 AGTCCTTTAATCGAAAGGTTT
1 AGTCCTTTAATCGAAAGGTTT
*
3265161 AGTCCTTTCATCGAAAGGT
1 AGTCCTTTAATCGAAAGGT
3265180 CTTAACCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
AGTCCTTTAATCGAAAGGTTT
Found at i:3265191 original size:21 final size:21
Alignment explanation
Indices: 3265149--3265191 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3265139 AAGTCCTTTA
* *
3265149 ATCGAAAGGTTTAGTCCTTTC
1 ATCGAAAGGTTTAGACCCTTC
3265170 ATCGAAAGGTCTTA-ACCCTTC
1 ATCGAAAGGT-TTAGACCCTTC
3265191 A
1 A
3265192 ATCTATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (21 bp):
ATCGAAAGGTTTAGACCCTTC
Found at i:3268863 original size:20 final size:20
Alignment explanation
Indices: 3268838--3268879 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3268828 GGTAACGAAT
* *
3268838 TTGACAAAACCGATTGGAAA
1 TTGACAAAACCAATTGAAAA
3268858 TTGACAAAACCAATTGAAAA
1 TTGACAAAACCAATTGAAAA
3268878 TT
1 TT
3268880 AAAAAAGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (20 bp):
TTGACAAAACCAATTGAAAA
Found at i:3269424 original size:197 final size:196
Alignment explanation
Indices: 3268939--3269443 Score: 490
Period size: 197 Copynumber: 2.6 Consensus size: 196
3268929 GTTGAAATTT
* * * * * *
3268939 GTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGACTGTCGGA-ATGTAATAGAAAT-AA
1 GTATCGATACTTTTATAAGTATATGTACCAAAGTATCGTACTTTAGGATTTG-AAAAGAAATGAA
* * *
3269002 AAAAGGAAAGTGTATCGAAAGTATCGATACCTTACACACATGTATCGATACATGACAATATAACA
65 AAAAAGAAA-CGTCTCGAAAGTATCGATACCTTACACACATGTATCGATACATGACAATATAACA
* * * *** * *
3269067 TGTTGAAGTTTGAAAAAACTGGTTTCAATTTGACAAAACAGGTAAAGAGATGCCACAATGGTTGA
129 TGCTGAAATTTCAAAAAACCAATTTCAATATGACAAAACAGGTAAAGAGATACCACAATGGTTGA
*
3269132 CATTT
194 C--TG
* * * * *
3269137 GTATCAATAATTTTATAAGTATATGCACCAAAGTATAGGTACTTTAGGAATTT-AAAAGAATTGC
1 GTATCGATACTTTTATAAGTATATGTACCAAAGTAT-CGTACTTTAGG-ATTTGAAAAGAAATG-
* * * ** *
3269201 AATAATAG---CGCCTATAAAGTATCGATACCTTAGACACATGTATCGATACATGACAATATAAC
63 AAAAAAAGAAACGTCTCGAAAGTATCGATACCTTACACACATGTATCGATACATGACAATATAAC
* * * *
3269263 ATGCTGAAATTTCAAAAAACCAATTTCGATATGACAAAATC-GGTAAAGCGCTACCAGATAT-GT
128 ATGCTGAAATTTCAAAAAACCAATTTCAATATGACAAAA-CAGGTAAAGAGATACCACA-ATGGT
3269326 TGAC-G
191 TGACTG
* * *
3269331 GTATTGATACTTTTATAAGTATATGTATCAAAGTATCGATATTTTAGGATTTGAAAAGAAATGAA
1 GTATCGATACTTTTATAAGTATATGTACCAAAGTATCG-TACTTTAGGATTTGAAAAGAAATGAA
* *
3269396 AAAAAGAAAACGTCTCGAAA-TAATCGATACCTTACACAAAAGTATCGA
65 AAAAAG-AAACGTCTCGAAAGT-ATCGATACCTTACACACATGTATCGA
3269444 GACTTGAGTA
Statistics
Matches: 244, Mismatches: 49, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
193 11 0.05
194 48 0.20
196 1 0.00
197 128 0.52
198 35 0.14
199 14 0.06
200 1 0.00
201 6 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (196 bp):
GTATCGATACTTTTATAAGTATATGTACCAAAGTATCGTACTTTAGGATTTGAAAAGAAATGAAA
AAAAGAAACGTCTCGAAAGTATCGATACCTTACACACATGTATCGATACATGACAATATAACATG
CTGAAATTTCAAAAAACCAATTTCAATATGACAAAACAGGTAAAGAGATACCACAATGGTTGACT
G
Found at i:3271649 original size:12 final size:12
Alignment explanation
Indices: 3271632--3271662 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3271622 AAATTGATGG
3271632 AGTGGTGAAAGA
1 AGTGGTGAAAGA
3271644 AGTGGTGAAAGA
1 AGTGGTGAAAGA
3271656 AGTGGTG
1 AGTGGTG
3271663 GAATTGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.45, T:0.19
Consensus pattern (12 bp):
AGTGGTGAAAGA
Found at i:3272259 original size:20 final size:20
Alignment explanation
Indices: 3272234--3272276 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3272224 TCTAAAAGAC
*
3272234 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
3272254 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATATAGATG
3272274 CAT
1 CAT
3272277 ATGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:3282623 original size:20 final size:20
Alignment explanation
Indices: 3282598--3282640 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3282588 TCTAAAAGAC
*
3282598 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
3282618 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATATAGATG
3282638 CAT
1 CAT
3282641 ATGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:3285556 original size:18 final size:18
Alignment explanation
Indices: 3285518--3285565 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3285508 GATGTAAGCC
** *
3285518 AAATTTTGTATATGAATG
1 AAATTTTGTATGCGAAAG
3285536 AAATTTTGTATGCGAAAG
1 AAATTTTGTATGCGAAAG
*
3285554 AAATTATGTATG
1 AAATTTTGTATG
3285566 TAATGACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (18 bp):
AAATTTTGTATGCGAAAG
Found at i:3286687 original size:64 final size:64
Alignment explanation
Indices: 3286619--3286775 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
3286609 TTGAAGGTGT
** * *
3286619 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
3286681 GC
63 GC
* * *
3286683 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* *
3286747 ACCGATGCATCAGTAATGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
3286776 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
64 72 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:3287130 original size:18 final size:18
Alignment explanation
Indices: 3287095--3287130 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3287085 AAAATGGGTA
* *
3287095 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
3287113 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
3287131 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:3288308 original size:18 final size:18
Alignment explanation
Indices: 3288281--3288350 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
3288271 TTAAGGAGTA
*
3288281 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
3288299 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
* *
3288321 GTCCTTCGGGATATAGTG
1 GTCCTACGGGACATAGTG
3288339 GTCCTACGGGAC
1 GTCCTACGGGAC
3288351 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 25 0.58
20 4 0.09
22 14 0.33
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:3291659 original size:18 final size:17
Alignment explanation
Indices: 3291605--3291653 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3291595 TTGGACCCTT
* *
3291605 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3291623 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3291641 AGTGCATTCGATG
1 AGTGCA-TCGATG
3291654 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3291758 original size:65 final size:64
Alignment explanation
Indices: 3291625--3291780 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 64
3291615 TGCACTAAGA
* * * *
3291625 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGACGTTTCAAAATACCTAGAGTACATCGATGCATGGCTG
*
3291689 GTGCATCGATGCATCAAATGCATTCGACGTTTTCATAAA-ATCCT-TAGTACATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGACG-TTTCA-AAATA-CCTAGAGTACATCGATGCATGGC
*
3291751 TAT
63 T-G
* * *
3291754 GTGCATCGAAGCATGAAATACATTCGA
1 GTGCATCGATGCATCAAATGCATTCGA
3291781 TGTTCAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
64 28 0.35
65 46 0.58
66 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGACGTTTCAAAATACCTAGAGTACATCGATGCATGGCTG
Found at i:3292787 original size:20 final size:21
Alignment explanation
Indices: 3292762--3292803 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3292752 AAATAATTTG
3292762 CACGCA-AAAAAGTATCGATA
1 CACGCATAAAAAGTATCGATA
* *
3292782 CACGCATAACAAGTATCTATA
1 CACGCATAAAAAGTATCGATA
3292803 C
1 C
3292804 TTATAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (21 bp):
CACGCATAAAAAGTATCGATA
Found at i:3293319 original size:179 final size:178
Alignment explanation
Indices: 3293019--3293353 Score: 523
Period size: 179 Copynumber: 1.9 Consensus size: 178
3293009 TTTGAAATAT
* *
3293019 TTTAAAGTAATAGGTAATTTTACAATGAAAACGGTAAAAGTCTACTAGTTTAATGATAATAGGCG
1 TTTAAAGTAATAGGTAAATTTACAATGAAAACGGTAAAAATCTACTAGTTTAATGATAATAGGCG
*
3293084 TAAACATAAAGTATCTATACTTTTTGTATAGGTTGCGATACTTTTAGTCCAGTATGTTTCTCTAA
66 TAAACATAAAGTATCTATACTCTTTGTATAGGTTGCGATACTTTTAGTCCAGTATGTTTCTC-AA
* * *
3293149 CAATTTGCACGTAGAAAATATCGATACTTATAATTTCGAAACCGATTAC
130 CAATTTGCAAGCACAAAATATCGATACTTATAATTTCGAAACCGATTAC
* * *
3293198 TTTAAAGTAATAGGTAAATTTACAGTGTAAACTGTAAAAATCTAC-AGATTTAATGATAATAGGC
1 TTTAAAGTAATAGGTAAATTTACAATGAAAACGGTAAAAATCTACTAG-TTTAATGATAATAGGC
3293262 GTAAACATAAAGTAT-TGATACTCTTTGTATAGGTAT-CGATACTTTTAGTCCAGTATGTTTCTC
65 GTAAACATAAAGTATCT-ATACTCTTTGTATAGGT-TGCGATACTTTTAGTCCAGTATGTTTCTC
*
3293325 AACAATTTGCAAGCACAAAGTATCGATAC
128 AACAATTTGCAAGCACAAAATATCGATAC
3293354 ATGTATAACA
Statistics
Matches: 143, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
178 28 0.20
179 114 0.80
180 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (178 bp):
TTTAAAGTAATAGGTAAATTTACAATGAAAACGGTAAAAATCTACTAGTTTAATGATAATAGGCG
TAAACATAAAGTATCTATACTCTTTGTATAGGTTGCGATACTTTTAGTCCAGTATGTTTCTCAAC
AATTTGCAAGCACAAAATATCGATACTTATAATTTCGAAACCGATTAC
Found at i:3293507 original size:199 final size:199
Alignment explanation
Indices: 3293167--3293705 Score: 742
Period size: 200 Copynumber: 2.7 Consensus size: 199
3293157 ACGTAGAAAA
* *
3293167 TATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAGTGTAAACTG
1 TATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACCG
* *
3293232 TAAAAATCTACAGATTTAATGATAATAGGCGTAAACATAAAGTATTGATACTCTTTGTATAGGTA
66 TAAAAATCTACAGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACT-TTTGTATAGGTA
* * *
3293297 TCGATACTTTTAGTCCAGTATGTTTCTC-AACAATTTGCAAGCACAAAGTATCGATACATGTATA
130 TCGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCAAGCACAAAGTATCGATACACGTATA
3293361 ACAAG
195 ACAAG
* * * *
3293366 TATCGATACTTATAATTTCGAAACCGATTACTTAAAAGTTATAGGTAAATTTACATTGTCAACCG
1 TATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACCG
* * * * * * *
3293431 TAAAAGTCTACCGGTTTAATGATAATAAGCGTAAACATAGAGCATCGTTACGTTTTGTTTAGGTA
66 TAAAAATCTACAGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-TTTTGTATAGGTA
* * * *
3293496 TCAATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCATGCAGAAAGTATCGATACACGTATC
130 TCGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCAAGCACAAAGTATCGATACACGTATA
3293561 ACAAG
195 ACAAG
* ** * * *
3293566 CATATATACTGT-TAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAACTTACAATGTAAACG
1 TATCGATACT-TATAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACC
* *
3293630 GTAAAATTCTACTGGTTTAATGATAATAGGCG-ATAACATAAAGTATCGATACTTTTTGTATAGG
65 GTAAAAATCTACAGGTTTAATGATAATAGGCGTA-AACATAAAGTATCGATAC-TTTTGTATAGG
3293694 TATCGATACTTT
128 TATCGATACTTT
3293706 AGATCTAAAC
Statistics
Matches: 296, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
199 140 0.47
200 155 0.52
201 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (199 bp):
TATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACCG
TAAAAATCTACAGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTGTATAGGTAT
CGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCAAGCACAAAGTATCGATACACGTATAA
CAAG
Found at i:3294224 original size:18 final size:18
Alignment explanation
Indices: 3294201--3294261 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
3294191 GACGCAGTTT
**
3294201 TTCTCAACCAAAACCTTC
1 TTCTCAACCAAAGTCTTC
* *
3294219 TTCTCAACCAAGGTCATC
1 TTCTCAACCAAAGTCTTC
*
3294237 TTATCAACCAAAGTCTTC
1 TTCTCAACCAAAGTCTTC
3294255 TTCTCAA
1 TTCTCAA
3294262 GTAAGGGCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (18 bp):
TTCTCAACCAAAGTCTTC
Found at i:3296023 original size:21 final size:20
Alignment explanation
Indices: 3295977--3296023 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3295967 TAAAATGGAA
* *
3295977 GTTTTGAAAATTTGAAGTCT
1 GTTTTGAAAATTTGAAATAT
3295997 GATTTTGAAAGATTTGAAATAT
1 G-TTTTGAAA-ATTTGAAATAT
3296019 GTTTT
1 GTTTT
3296024 TGATTGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (20 bp):
GTTTTGAAAATTTGAAATAT
Found at i:3296024 original size:22 final size:21
Alignment explanation
Indices: 3295978--3296026 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
3295968 AAAATGGAAG
* *
3295978 TTTTGAAAATTTGAAGTCTGA
1 TTTTGAAAATTTGAAATATGA
*
3295999 TTTTGAAAGATTTGAAATATGT
1 TTTTGAAA-ATTTGAAATATGA
3296021 TTTTGA
1 TTTTGA
3296027 TTGTTCAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (21 bp):
TTTTGAAAATTTGAAATATGA
Found at i:3296743 original size:19 final size:18
Alignment explanation
Indices: 3296696--3296749 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
3296686 ATTATTCAGT
*
3296696 GTGCATCGATGCACACAA
1 GTGCATCGATGCACCCAA
*
3296714 GAAGCCATCGATGCACCCATA
1 G-TG-CATCGATGCACCCA-A
*
3296735 GTGCATCGATACACC
1 GTGCATCGATGCACC
3296750 TAAAGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 14 0.48
21 2 0.07
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.17
Consensus pattern (18 bp):
GTGCATCGATGCACCCAA
Found at i:3297670 original size:18 final size:18
Alignment explanation
Indices: 3297647--3297744 Score: 135
Period size: 18 Copynumber: 5.4 Consensus size: 18
3297637 GGCATGGTCA
*
3297647 TCGGGAGATAGTGGTCCT
1 TCGGGACATAGTGGTCCT
*
3297665 TCGGGAGATAGTGGTCCT
1 TCGGGACATAGTGGTCCT
3297683 TCGGGACATAGTGGTCCT
1 TCGGGACATAGTGGTCCT
*
3297701 TCGGGACACAGTGGTCCT
1 TCGGGACATAGTGGTCCT
* *
3297719 TCGGGATATAGT-GTTCT
1 TCGGGACATAGTGGTCCT
3297736 TACGGGACA
1 T-CGGGACA
3297745 AATTCTATGC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
17 5 0.07
18 68 0.93
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (18 bp):
TCGGGACATAGTGGTCCT
Found at i:3299076 original size:13 final size:13
Alignment explanation
Indices: 3299058--3299082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3299048 GATCGGATTT
3299058 TTTTAACCGGTTA
1 TTTTAACCGGTTA
3299071 TTTTAACCGGTT
1 TTTTAACCGGTT
3299083 TTGGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:3299126 original size:12 final size:12
Alignment explanation
Indices: 3299111--3299156 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3299101 CGGTTTTTTT
*
3299111 ACCGGATAAAAA
1 ACCGGTTAAAAA
3299123 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
3299138 ACCGGTTAAAAA
1 ACCGGTTAAAAA
3299150 ACCGGTT
1 ACCGGTT
3299157 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:3299138 original size:15 final size:13
Alignment explanation
Indices: 3299117--3299157 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
3299107 TTTTACCGGA
3299117 TAAAAAACCGGTT
1 TAAAAAACCGGTT
3299130 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
3299144 TAAAAAACCGGTT
1 TAAAAAACCGGTT
3299157 T
1 T
3299158 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:3301452 original size:21 final size:21
Alignment explanation
Indices: 3301428--3301469 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3301418 AGTTTATTTT
3301428 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
3301449 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
3301470 AACTTGGAAG
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:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:3301507 original size:33 final size:33
Alignment explanation
Indices: 3301464--3301567 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
3301454 TTTGTTTCAA
3301464 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
3301497 TTATCAAACTTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
3301530 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3301562 TTATCG
1 TTATCG
3301568 TAAACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3301528 original size:17 final size:17
Alignment explanation
Indices: 3301476--3301528 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3301466 ATCGAACTTG
3301476 GAAGTTTTTAAGTATTT
1 GAAGTTTTTAAGTATTT
*
3301493 GAA-TTTATCAA--ACTTT
1 GAAGTTT-TTAAGTA-TTT
3301509 GAAGTTTTTAAGTATTT
1 GAAGTTTTTAAGTATTT
3301526 GAA
1 GAA
3301529 TTTATCGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 1 0.03
16 12 0.41
17 15 0.52
18 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (17 bp):
GAAGTTTTTAAGTATTT
Found at i:3303837 original size:19 final size:21
Alignment explanation
Indices: 3303798--3303837 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3303788 TGCACGCACA
3303798 AAGTATCGATACATGTATAAT
1 AAGTATCGATACATGTATAAT
3303819 AAGTATCGATAC-T-TATAAT
1 AAGTATCGATACATGTATAAT
3303838 TCTGAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (21 bp):
AAGTATCGATACATGTATAAT
Found at i:3304207 original size:168 final size:169
Alignment explanation
Indices: 3303899--3304219 Score: 409
Period size: 169 Copynumber: 1.9 Consensus size: 169
3303889 AAAATCTATT
* *
3303899 GGTTTAATGATAATAGGTGTAAACATAACGTATCAATACTTATTATATAGTATCGATACTTTTAT
1 GGTTTAATGATAATAGGTGTAAACATAACGTATCAATACTTATTATATAGTATAGATACTTTTAG
* * * * *
3303964 TCTAGTATGCATCTCAAACAAATTGCAGGCAAAAAAAAATTGATACACATGTATAAAGTATTGAT
66 TCCAGTATACATCTCAAACAAATTGCACGCAAAAAAAAATCGATACACATGTATAAAGTATCGAT
*
3304029 ATGCGGAATTTAGAAACCGATTAACGTTAAAAGTCTACC
131 ACGCGGAATTTAGAAACCGATTAACGTTAAAAGTCTACC
** *
3304068 GGTTTAATGATAATAGGTGTAAACATCAA-GTATTGATACGTT-TTGTATATGTATA-AGTACTT
1 GGTTTAATGATAATAGGTGTAAACAT-AACGTATCAATAC-TTATTATATA-GTATAGA-TACTT
* * * **
3304130 TTAGTCCAGTATACTTCTC-AACAATTTGCACGC-ACAAAGTATCGATACACATGTATAAAGTAT
62 TTAGTCCAGTATACATCTCAAACAAATTGCACGCAAAAAAAAATCGATACACATGTATAAAGTAT
* *
3304193 CGATACGTGGAATTTCGAAACCGATTA
127 CGATACGCGGAATTTAGAAACCGATTA
3304220 CTTTAAAGTT
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
168 49 0.38
169 53 0.41
170 28 0.22
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (169 bp):
GGTTTAATGATAATAGGTGTAAACATAACGTATCAATACTTATTATATAGTATAGATACTTTTAG
TCCAGTATACATCTCAAACAAATTGCACGCAAAAAAAAATCGATACACATGTATAAAGTATCGAT
ACGCGGAATTTAGAAACCGATTAACGTTAAAAGTCTACC
Found at i:3304879 original size:20 final size:20
Alignment explanation
Indices: 3304832--3304909 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
3304822 TACAGGTAAT
*
3304832 AAATTTGACAAAACTTA-TTGG
1 AAATTTGACAAAAC-CAGTT-G
3304853 AAA-TTGACAAAACCAGTTG
1 AAATTTGACAAAACCAGTTG
* *
3304872 AAATTTGACAAAACCAATTT
1 AAATTTGACAAAACCAGTTG
* *
3304892 CAATTTGAGAAAACCAGT
1 AAATTTGACAAAACCAGT
3304910 AAAGAGCTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 5 0.10
20 41 0.84
21 3 0.06
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (20 bp):
AAATTTGACAAAACCAGTTG
Found at i:3304905 original size:40 final size:40
Alignment explanation
Indices: 3304832--3304909 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
3304822 TACAGGTAAT
** *
3304832 AAATTTGACAAAACTTATTGGAAATTGACAAAACCAGTTG
1 AAATTTGACAAAACCAATTGCAAATTGACAAAACCAGTTG
* * *
3304872 AAATTTGACAAAACCAATTTCAATTTGAGAAAACCAGT
1 AAATTTGACAAAACCAATTGCAAATTGACAAAACCAGT
3304910 AAAGAGCTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (40 bp):
AAATTTGACAAAACCAATTGCAAATTGACAAAACCAGTTG
Found at i:3305298 original size:20 final size:20
Alignment explanation
Indices: 3305273--3305342 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3305263 TGTTGAAATT
3305273 TGACAAAACCAATTTCAATA
1 TGACAAAACCAATTTCAATA
*
3305293 TGACAAAACCGATTTCAATA
1 TGACAAAACCAATTTCAATA
* * *
3305313 TGAAAAAATCAGTTTCAATA
1 TGACAAAACCAATTTCAATA
3305333 TGACAAAACC
1 TGACAAAACC
3305343 GGTAAAGCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.24
Consensus pattern (20 bp):
TGACAAAACCAATTTCAATA
Found at i:3305299 original size:197 final size:198
Alignment explanation
Indices: 3304868--3305303 Score: 527
Period size: 199 Copynumber: 2.2 Consensus size: 198
3304858 GACAAAACCA
* * * * ** *
3304868 GTTGAAATTTGACAAAACCAATTTCAATTTGAGAAAACCAGTAAAGAGCTGCTGGAATTATTGAA
1 GTTGAAATTTGACAAAACCAATTTCAATTTGACAAAACCGGTAAAGAGATACCAGAATGATTGAA
* * * *
3304933 ATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTGTAGGAATTTAAAAGAAA
66 ATTTGTATCAATACGTTTATAACTATATGCACCAAAGTATCAGTACTGTAGGAATTTAAAAGAAA
* ** * * *
3304998 TAAAAAAGGAAGATGTTTCGACAGTATCGATACCTTACACACATGTATTGATACAGGACAATATA
131 TAAAAAA-GAAGACGCCTAGAAAGTATCGATACCTTACACACATGTATCGATACAGGACAATATA
3305063 ACAG
195 ACAG
*
3305067 GTT-AAAGTTTGACAAAACCAATTTCAATTTGACAAAACCGGTAAAGAGATACCAGAATGGTTGA
1 GTTGAAA-TTTGACAAAACCAATTTCAATTTGACAAAACCGGTAAAGAGATACCAGAATGATTGA
* * * *
3305131 CATTTTTATCAATACTTTTATAACTATATGCACCAAAGTATCAGTACTTTAGGAATTTAAAAGAA
65 AATTTGTATCAATACGTTTATAACTATATGCACCAAAGTATCAGTACTGTAGGAATTTAAAAGAA
* * * * * * * * *
3305196 TTGCAATAA-TAG-CGCCTATAAAGTATCGATATCTTAGACACATGTATCGATACATGACTATAT
130 AT-AAAAAAGAAGACGCCTAGAAAGTATCGATACCTTACACACATGTATCGATACAGGACAATAT
*
3305259 AACAT
194 AACAG
*
3305264 GTTGAAATTTGACAAAACCAATTTCAATATGACAAAACCG
1 GTTGAAATTTGACAAAACCAATTTCAATTTGACAAAACCG
3305304 ATTTCAATAT
Statistics
Matches: 201, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
197 79 0.39
198 8 0.04
199 110 0.55
200 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (198 bp):
GTTGAAATTTGACAAAACCAATTTCAATTTGACAAAACCGGTAAAGAGATACCAGAATGATTGAA
ATTTGTATCAATACGTTTATAACTATATGCACCAAAGTATCAGTACTGTAGGAATTTAAAAGAAA
TAAAAAAGAAGACGCCTAGAAAGTATCGATACCTTACACACATGTATCGATACAGGACAATATAA
CAG
Found at i:3309224 original size:64 final size:63
Alignment explanation
Indices: 3309139--3309299 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
3309129 TTGTTTAAGG
* * * * *
3309139 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCAAATAGGATTTA
* * *
3309203 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCAAATAGGATTTA
*
3309267 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
3309300 ACCTCCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCAAATAGGATTTA
Found at i:3309925 original size:23 final size:23
Alignment explanation
Indices: 3309891--3309953 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
3309881 ATTATTATAT
3309891 GGCACTGC-GGTGCAATTCTACGC
1 GGCACT-CAGGTGCAATTCTACGC
**
3309914 GGCACTCAGGTGCAATTCTACTT
1 GGCACTCAGGTGCAATTCTACGC
*
3309937 GGCACTTAGGTGCAATT
1 GGCACTCAGGTGCAATT
3309954 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCAGGTGCAATTCTACGC
Found at i:3310993 original size:23 final size:22
Alignment explanation
Indices: 3310959--3311021 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
3310949 ATTATTATAT
3310959 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
**
3310982 GGCACTCAGGTGCAATTCTACTT
1 GGCACT-AGGTGCAATTCTACGC
3311005 GGCACTTAGGTGCAATT
1 GGCAC-TAGGTGCAATT
3311022 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:3317877 original size:23 final size:23
Alignment explanation
Indices: 3317843--3317905 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3317833 ATTATTATAT
3317843 GGCAC-TACGGTGCAATTCTACGC
1 GGCACTTA-GGTGCAATTCTACGC
* *
3317866 GGCACTTAGGTGCAATTCTATGT
1 GGCACTTAGGTGCAATTCTACGC
3317889 GGCACTTAGGTGCAATT
1 GGCACTTAGGTGCAATT
3317906 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:3317910 original size:23 final size:23
Alignment explanation
Indices: 3317833--3317910 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
3317823 CCTTATGGAC
*
3317833 ATTATTATATGGCAC-TACGGTGCA
1 ATTA-TATGTGGCACTTA-GGTGCA
* * *
3317857 ATTCTACGCGGCACTTAGGTGCA
1 ATTATATGTGGCACTTAGGTGCA
*
3317880 ATTCTATGTGGCACTTAGGTGCA
1 ATTATATGTGGCACTTAGGTGCA
3317903 ATTATATG
1 ATTATATG
3317911 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 41 0.89
24 5 0.11
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTTAGGTGCA
Found at i:3323175 original size:224 final size:226
Alignment explanation
Indices: 3322661--3323264 Score: 835
Period size: 225 Copynumber: 2.7 Consensus size: 226
3322651 ATGTGCACAG
*
3322661 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACTTATTTTGTTATCGTTAGATTTCTA
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACTTATTTTGTTATCGTCAGATTTCTA
* * *
3322726 AGGTCC-CATTAGCTTTAAACATGCGCTACTTATTACATTAAATAAACACTACTTGTTATGTTAT
66 AGG-CCTCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAACACTACTTGATATGTTAT
* * *
3322790 TATGGTTGAT-ATGTTTCCAATAGTTAACCTATTTTGTTATCGTCGAATTTCTAAGGCTCTATCA
130 TATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCTCCATCA
*
3322854 GCTTAAACTTTGGTAACATTTTAGGCGCTACC
195 GCTTAAACTTTGGTAACATTTTAGACGCTACC
* * * * * *
3322886 TAATATATTGATAATACTAATAACAAATTAAGTAATTAACTTATTTTGTTATCATCGGGTTTCTA
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACTTATTTTGTTATCGTCAGATTTCTA
* * * *
3322951 AGGCCTCATCAGCTTTAAACAGGTGCTACCTATTACATTAAATAAACGCTACTTGGTATGTTATT
66 AGGCCTCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAACACTACTTGATATGTTATT
* * * *
3323016 A-GGTTGATAATGTTTTCAATAATTAACTTATTTTGTTATCGT-GGATTTATAAGGCTCCATCGG
131 ATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCTCCATCAG
3323079 CTTAAACTTTGGTAACATTTTAGACGCTACC
196 CTTAAACTTTGGTAACATTTTAGACGCTACC
* * * *
3323110 TAATATGTTGATAATATTGATAATAAATCAAGTAATTAACCTATTTTGTTAACGTCAGATTTCTA
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACTTATTTTGTTATCGTCAGATTTCTA
* * * * *
3323175 AGG-CTCCATCAGCTTTAAA-ATGCGCTACCTATTACGTTACATAAGCATTACCT-ATATGTTAT
66 AGGCCT-CATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAACACTACTTGATATGTTAT
* * *
3323237 TATGATTGATAATGTTTCTAGTAATTAA
130 TATGGTTGATAATGTTTCCAATAATTAA
3323265 TCGGTTATGT
Statistics
Matches: 331, Mismatches: 44, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
222 10 0.03
223 49 0.15
224 127 0.38
225 145 0.44
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (226 bp):
TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACTTATTTTGTTATCGTCAGATTTCTA
AGGCCTCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAACACTACTTGATATGTTATT
ATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGAATTTATAAGGCTCCATCAG
CTTAAACTTTGGTAACATTTTAGACGCTACC
Found at i:3330101 original size:18 final size:18
Alignment explanation
Indices: 3330061--3330107 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3330051 CTACGATCAT
*
3330061 TATAAATTTATTTATAAA
1 TATATATTTATTTATAAA
* *
3330079 TATATTTTTATTTA-AAC
1 TATATATTTATTTATAAA
3330096 TGATATATTTAT
1 T-ATATATTTAT
3330108 ATAGTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TATATATTTATTTATAAA
Found at i:3331875 original size:17 final size:18
Alignment explanation
Indices: 3331838--3331878 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3331828 ATATTTTGTA
*
3331838 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
3331856 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
3331873 TTTACT
1 TTTACT
3331879 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:3333924 original size:3 final size:3
Alignment explanation
Indices: 3333916--3333941 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3333906 ACCTGCTCAG
3333916 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
3333942 TGATGGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:3334148 original size:26 final size:24
Alignment explanation
Indices: 3334077--3334149 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 24
3334067 TTATATTTGT
3334077 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
3334102 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
3334124 ATACTTACTTTATTTTGTTAAATTTA
1 AT--TTACTTTATTTTGTTAAATTTA
3334150 TTGGACTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
22 4 0.11
23 10 0.26
24 5 0.13
25 7 0.18
26 12 0.32
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:3337834 original size:50 final size:50
Alignment explanation
Indices: 3337727--3337849 Score: 124
Period size: 50 Copynumber: 2.4 Consensus size: 50
3337717 GCCTACACAG
* * * *
3337727 ATATAGCGCGGTTCAAGGGGCGCGCTATACCCCATGTGTAACTCAGTCAGC
1 ATATAGCGCGGTGC-AGGGGCGCGCTATACCCCACGTGGAACTCAATCAGC
* **
3337778 AAATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGCGC-CAAATCAGC
1 ATATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGAACTC-AATCAGC
* *
3337828 GTATAGCACGG-GTCAGGGGCGC
1 ATATAGCGCGGTG-CAGGGGCGC
3337850 ACTTTACTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.03
50 46 0.77
51 12 0.20
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (50 bp):
ATATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGAACTCAATCAGC
Found at i:3338081 original size:22 final size:22
Alignment explanation
Indices: 3338039--3338081 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3338029 TTTACTTTAT
*
3338039 TATATTTTAGTCATTTTAATTC
1 TATATTTTAATCATTTTAATTC
3338061 TATATTTTAAT-ATTTTGAATT
1 TATATTTTAATCATTTT-AATT
3338082 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TATATTTTAATCATTTTAATTC
Found at i:3342445 original size:2 final size:2
Alignment explanation
Indices: 3342438--3342467 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3342428 GAAAATTTAA
3342438 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
3342468 CAAGAGCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3345204 original size:22 final size:21
Alignment explanation
Indices: 3345177--3345222 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3345167 AGAGTGTTTA
*
3345177 ATATATACTAAGTTTTTAGGGT
1 ATATATACTAAG-TTTTAGGAT
* *
3345199 ATATATATTGAGTTTTAGGAT
1 ATATATACTAAGTTTTAGGAT
3345220 ATA
1 ATA
3345223 AAAAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (21 bp):
ATATATACTAAGTTTTAGGAT
Found at i:3372563 original size:61 final size:61
Alignment explanation
Indices: 3372493--3372640 Score: 180
Period size: 61 Copynumber: 2.5 Consensus size: 61
3372483 GGAATGTTCA
*
3372493 AAAAGTTTGAGGACTAATTTAAAATGAATA-TTATAGTTTAGGGATGAAATTAAAATAAATC
1 AAAAGTTTGAGGACTAATTTAAAATGAATAGTCATAGTTTAGGGATGAAATTAAAAT-AATC
* * * *
3372554 AAAACTTTGA-GAGCTAATTTAGAAT-TATAGTCATAGTTTAGGGATGAAATTAAAATATTC
1 AAAAGTTTGAGGA-CTAATTTAAAATGAATAGTCATAGTTTAGGGATGAAATTAAAATAATC
*
3372614 AAAAGTTT-AGGA-TCAATCTAAAATGAA
1 AAAAGTTTGAGGACT-AATTTAAAATGAA
3372641 GGTCATACTT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
58 1 0.01
59 9 0.12
60 18 0.25
61 45 0.62
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (61 bp):
AAAAGTTTGAGGACTAATTTAAAATGAATAGTCATAGTTTAGGGATGAAATTAAAATAATC
Found at i:3378433 original size:17 final size:17
Alignment explanation
Indices: 3378411--3378443 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3378401 TGTTATTCCT
3378411 AGAGTTCCTAAGTTCAC
1 AGAGTTCCTAAGTTCAC
3378428 AGAGTTCCTAAGTTCA
1 AGAGTTCCTAAGTTCA
3378444 ATCACATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (17 bp):
AGAGTTCCTAAGTTCAC
Found at i:3390296 original size:34 final size:35
Alignment explanation
Indices: 3390232--3390303 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
3390222 CTAGTAATTT
3390232 AAGTTTTGTTTTATGATATCAAAAAAACAATATTA
1 AAGTTTTGTTTTATGATATCAAAAAAACAATATTA
3390267 AAGTTTTGTTTTATGATATC-AAAAAACAATATTA
1 AAGTTTTGTTTTATGATATCAAAAAAACAATATTA
3390301 AAG
1 AAG
3390304 CTTTCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 17 0.46
35 20 0.54
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (35 bp):
AAGTTTTGTTTTATGATATCAAAAAAACAATATTA
Found at i:3397658 original size:11 final size:10
Alignment explanation
Indices: 3397637--3397691 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
3397627 TCATTTTTTT
3397637 TAAAAATCAA
1 TAAAAATCAA
3397647 TAAAAATGCAA
1 TAAAAAT-CAA
3397658 TAAAAAT--A
1 TAAAAATCAA
*
3397666 -AAAAATGAA
1 TAAAAATCAA
*
3397675 TAAAATTCAA
1 TAAAAATCAA
3397685 TAAAAAT
1 TAAAAAT
3397692 ATAATGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 1 0.03
10 20 0.53
11 10 0.26
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:3397667 original size:27 final size:26
Alignment explanation
Indices: 3397637--3397692 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
3397627 TCATTTTTTT
3397637 TAAAAATCAATAAAAATGCAATAAAAA
1 TAAAAATCAAT-AAAATGCAATAAAAA
* *
3397664 TAAAAAATGAATAAAATTCAATAAAAA
1 T-AAAAATCAATAAAATGCAATAAAAA
3397691 TA
1 TA
3397693 TAATGTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 16 0.62
28 9 0.35
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (26 bp):
TAAAAATCAATAAAATGCAATAAAAA
Found at i:3397840 original size:14 final size:14
Alignment explanation
Indices: 3397818--3397847 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3397808 TTAATTGTTG
3397818 TTAAAAAATAATAA
1 TTAAAAAATAATAA
*
3397832 TTAATAAATAATAA
1 TTAAAAAATAATAA
3397846 TT
1 TT
3397848 CATTTGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATAATAA
Found at i:3400275 original size:2 final size:2
Alignment explanation
Indices: 3400268--3400295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3400258 TGTAACCAGG
3400268 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
3400296 GTATTCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3402373 original size:3 final size:3
Alignment explanation
Indices: 3402365--3402392 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3402355 GCAGCTTTTG
3402365 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3402393 AATCCCTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3409818 original size:23 final size:23
Alignment explanation
Indices: 3409756--3409819 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3409746 GAATAAAAAT
* *
3409756 AAATAAATAATTATA-TATTTATA
1 AAATTAAT-ATTATATTATTTAAA
* *
3409779 AAATTAATAGTAGATTATTTAAA
1 AAATTAATATTATATTATTTAAA
3409802 AAATTAA-ATTTATATTAT
1 AAATTAATA-TTATATTAT
3409820 CTATTCATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 5 0.15
23 28 0.85
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
AAATTAATATTATATTATTTAAA
Found at i:3410903 original size:26 final size:24
Alignment explanation
Indices: 3410841--3410903 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
3410831 CGATTTAATC
3410841 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
* *
3410865 AAAATATAT-TTATTAACATTTCTT
1 AAAATATATATTATTAAAATAT-TT
*
3410889 ATAATATAATATTAT
1 AAAATAT-ATATTAT
3410904 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 10 0.31
24 15 0.47
25 3 0.09
26 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:3410914 original size:23 final size:23
Alignment explanation
Indices: 3410888--3410962 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 23
3410878 TAACATTTCT
3410888 TATAATATAATATTATATTTTTA
1 TATAATATAATATTATATTTTTA
* *
3410911 TATAATAAAATAATCA-ATTATATTA
1 TATAATATAAT-ATTATATT-T-TTA
3410936 TAATAATATAAGATATTATATTTTTA
1 T-ATAATAT-A-ATATTATATTTTTA
3410962 T
1 T
3410963 TTTAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
23 13 0.32
24 4 0.10
25 4 0.10
26 10 0.24
27 5 0.12
28 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TATAATATAATATTATATTTTTA
Found at i:3411058 original size:19 final size:19
Alignment explanation
Indices: 3411034--3411102 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
3411024 ATATTATTAA
3411034 ATTATTAATAATGAATAAT
1 ATTATTAATAATGAATAAT
* *
3411053 ATTATTTAT-AT-ATTTAAT
1 ATTATTAATAATGA-ATAAT
*
3411071 ATTAATATAATAATCGAATAAA
1 ATT-AT-TAATAAT-GAATAAT
3411093 ATT-TTAATAA
1 ATTATTAATAA
3411103 AGATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.23
19 16 0.41
20 4 0.10
21 2 0.05
22 6 0.15
23 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTATTAATAATGAATAAT
Found at i:3411077 original size:27 final size:27
Alignment explanation
Indices: 3410997--3411082 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
3410987 AATAAAATTT
* *
3410997 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
3411024 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
3411051 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
3411080 ATA
1 ATA
3411083 ATCGAATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:3411220 original size:33 final size:29
Alignment explanation
Indices: 3411181--3411251 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 29
3411171 AATATAATTT
3411181 ATAATATTTTTATTTCAATAAAA-TATAACAA
1 ATAATATTTTTA-TT-AATAAAATTATAA-AA
3411212 TATTAATATTTTTATTAATAAAATTATAAAA
1 -A-TAATATTTTTATTAATAAAATTATAAAA
3411243 ATAATATTT
1 ATAATATTT
3411252 AATAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
29 8 0.22
30 1 0.03
31 9 0.24
32 8 0.22
33 11 0.30
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:3417249 original size:23 final size:21
Alignment explanation
Indices: 3417209--3417250 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3417199 ATATATATAT
*
3417209 ATATTTATTTTTATAAATAAA
1 ATATTTATTTTTAGAAATAAA
3417230 ATATTTATTTAATTAGAAATA
1 ATATTTATTT--TTAGAAATA
3417251 TCAGAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAA
Found at i:3417563 original size:3 final size:3
Alignment explanation
Indices: 3417498--3417551 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3417488 CTAATATGAA
3417498 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3417546 AAT AAT
1 AAT AAT
3417552 TAAAGTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3417858 original size:66 final size:65
Alignment explanation
Indices: 3417788--3417928 Score: 153
Period size: 66 Copynumber: 2.1 Consensus size: 65
3417778 GATTTTAACA
* * *
3417788 CTAAATATTAATAGGGGACAAAAATAAAT-TTAATAAAATTATAAGGGACTAATCATAA-A-ATT
1 CTAAATATTAAT-CGGGACAAAAATAAATATTAATAAAA-CATAAGGGACTAA--AAAAGATATT
3417850 TACC
62 TACC
** * *
3417854 CTAAATTATTAATCGGGATTAAAATAAATATTATTAAAACCTAAGGGACTAAAAAAGATATTTAC
1 CTAAA-TATTAATCGGGACAAAAATAAATATTAATAAAACATAAGGGACTAAAAAAGATATTTAC
3417919 C
65 C
3417920 CTAAATATT
1 CTAAATATT
3417929 TAAGATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
64 3 0.05
65 5 0.08
66 41 0.64
67 15 0.23
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (65 bp):
CTAAATATTAATCGGGACAAAAATAAATATTAATAAAACATAAGGGACTAAAAAAGATATTTACC
Found at i:3418077 original size:63 final size:64
Alignment explanation
Indices: 3417940--3418057 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 64
3417930 AAGATATATG
** * *
3417940 GTGACTAAATTATAAATAAAATAAAATTTGAATATTGAATTAAAACATATGAAAATATATTGCA
1 GTGACTAAATTATAAATAAAATAAAATTAAAAGATAGAATTAAAACATATGAAAATATATTGCA
* *
3418004 GTGACTAAATTAT-AATAAAATAAACTTAAAAGATAGAATTAAAACGTAT-AAAAT
1 GTGACTAAATTATAAATAAAATAAAATTAAAAGATAGAATTAAAACATATGAAAAT
3418058 TTGATTTTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
62 5 0.10
63 30 0.62
64 13 0.27
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (64 bp):
GTGACTAAATTATAAATAAAATAAAATTAAAAGATAGAATTAAAACATATGAAAATATATTGCA
Found at i:3424624 original size:2 final size:2
Alignment explanation
Indices: 3424589--3424616 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3424579 TTATCCTTTC
3424589 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
3424617 TCATATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3424897 original size:12 final size:13
Alignment explanation
Indices: 3424843--3424897 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
3424833 TGTGATGAGT
*
3424843 ATAAAATAAAAAA
1 ATAAAATTAAAAA
3424856 ATAAAATT-AAAA
1 ATAAAATTAAAAA
*
3424868 ATAATAATTAAAGTA
1 ATAA-AATTAAA-AA
3424883 AT-AAATTAAAAA
1 ATAAAATTAAAAA
3424895 ATA
1 ATA
3424898 TTGAAACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.31
13 18 0.51
14 3 0.09
15 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
ATAAAATTAAAAA
Found at i:3426166 original size:23 final size:21
Alignment explanation
Indices: 3426123--3426173 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 21
3426113 CTTCTGGATC
3426123 TGGGCCTTCGGGTTTGTAAA-
1 TGGGCCTTCGGGTTTGTAAAT
3426143 TGGGCCTTCGGGTCCCTTGTAAAT
1 TGGGCCTTCGGGT---TTGTAAAT
3426167 TGGGCCT
1 TGGGCCT
3426174 GTAATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.48
23 7 0.26
24 7 0.26
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.33
Consensus pattern (21 bp):
TGGGCCTTCGGGTTTGTAAAT
Found at i:3426206 original size:3 final size:3
Alignment explanation
Indices: 3426200--3426249 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
3426190 TATTATTATT
*
3426200 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3426247 TAA
1 TAA
3426250 AATGGGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3427101 original size:42 final size:41
Alignment explanation
Indices: 3427018--3427114 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 41
3427008 AGGTCTTATG
* * * *
3427018 GATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTACA
1 GATGACCCGAAGGATTTAGCATCATGCTCGAAAGACTTACA
*
3427059 GATGACCCGAAGGATTTAAGCATCATGCTCTAAAGACTTACA
1 GATGACCCGAAGGATTT-AGCATCATGCTCGAAAGACTTACA
*
3427101 GGTGACCCGAAGGA
1 GATGACCCGAAGGA
3427115 CTTACGAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (41 bp):
GATGACCCGAAGGATTTAGCATCATGCTCGAAAGACTTACA
Found at i:3427356 original size:260 final size:264
Alignment explanation
Indices: 3426798--3427644 Score: 1206
Period size: 265 Copynumber: 3.2 Consensus size: 264
3426788 CTTATGGATA
* * * * * *
3426798 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACATATAGATGGCCTGAAGGACTTACAAATTAAG
1 ACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAG
* *
3426863 AAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAAGAACCCTTTTGTTAGGTTTAGCTTCATTTAA
66 AAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTTTGTTAGGCTTAGCTTCATTTAA
*
3426928 CAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAA
131 CAACTCTTTTGAGATAATTAGGAAACCCCTTAAAA-TAGGCTTAGTTTTTAAAATCTCATTTGAA
* *
3426993 AATATCCTGCATTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTAC
195 AACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTAC
3427058 AGATG
260 AGATG
* * * *
3427063 ACCCGAAGGATTTAAGCATCATGCTCTAAAGACTTACAGGTGACCCGAAGGACTTACGAATCAAG
1 ACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAG
* * * *
3427128 AAACCTTCAAAAGCTTAGTTT-TATAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTA
66 AAACCCTCGAAAGCTTAGTTTCT-TAGTTGTCAAAGAACCCCTTTGTTAGGCTTAGCTTCATTTA
* *
3427192 ACAACTCTTTTGAGATAATTAGGAAA-CCC-T-GAA-AGGTTTAGTTTTTAAAATCTCATTTGAA
130 ACAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATAGGCTTAGTTTTTAAAATCTCATTTGAA
*
3427253 AGCAT-CTAGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTA
195 AACATCCT-GCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTA
3427317 CAGATG
259 CAGATG
** * * *
3427323 ACCCGAAATATTTAAACATCATGCTTGAAAGACTTACAGATGGCTCAAAGGACTTACGAATCAAG
1 ACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAG
* * * *
3427388 AAACCCTCGAAAGCTTACTTTCTTATTTGTCAATGAACCCCTTTATTAGGCTTAGCTTCATTTAA
66 AAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTTTGTTAGGCTTAGCTTCATTTAA
* * *
3427453 CAACTCTTTTAAGATAATTAGAAAACCCCTTAAAATTAGGCTTAGTTTTTAATATCTCATTTGAA
131 CAACTCTTTTGAGATAATTAGGAAACCCCTTAAAA-TAGGCTTAGTTTTTAAAATCTCATTTGAA
* *
3427518 AACATCCTGCACTGAAGGTCTTATGGAT-AGCCTGAAGGAC-TTATTATCTTGCTCGAAAGGCTT
195 AACATCCTGCACTGAAGGTCTTATGGATGA-CCCGAAGG-CTTTATCATCTTGCTCGAAAGGCTT
*
3427581 ATAGATG
258 ACAGATG
* * **
3427588 ACCCGAAGGATTTAAAACATCATGCTCAAAAGAATTACAGATGGCCTTAAGGACTTA
1 ACCCGAAGGATTT-AAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTA
3427645 TAAATTCGGG
Statistics
Matches: 517, Mismatches: 53, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
259 2 0.00
260 225 0.44
261 4 0.01
262 3 0.01
263 3 0.01
264 5 0.01
265 235 0.45
266 40 0.08
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (264 bp):
ACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAG
AAACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTTTGTTAGGCTTAGCTTCATTTAA
CAACTCTTTTGAGATAATTAGGAAACCCCTTAAAATAGGCTTAGTTTTTAAAATCTCATTTGAAA
ACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTTGCTCGAAAGGCTTACA
GATG
Found at i:3428769 original size:54 final size:54
Alignment explanation
Indices: 3428669--3428776 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
3428659 TTAATCACTG
* * * * *
3428669 GTTCATAAAACATTTGATAACACATTCATCATTTCCCGTGGTTTCTGCTCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCCATAGCTTCTGCCCAGAT
* * * *
3428723 GTTCGTAAAACATTTTACAACACATTCATCCTTTCCTATAGCTTCTGCCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCCATAGCTTCTGCCCAGAT
3428777 TTCTCAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCATTTCCCATAGCTTCTGCCCAGAT
Found at i:3430402 original size:12 final size:12
Alignment explanation
Indices: 3430385--3430414 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3430375 TTTTCTTTTC
3430385 TTTTTCATCTCT
1 TTTTTCATCTCT
*
3430397 TTTTTCATCTTT
1 TTTTTCATCTCT
3430409 TTTTTC
1 TTTTTC
3430415 TTTTTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTCATCTCT
Found at i:3430408 original size:31 final size:29
Alignment explanation
Indices: 3430373--3430431 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
3430363 TGATTCAATT
3430373 TCTTTTCTTTTC-TTTTTCATCTCTTTTTTCA
1 TCTTTT-TTTTCTTTTTTC-T-TCTTTTTTCA
3430404 TCTTTTTTTTCTTTTTTCTTCTTTTTTC
1 TCTTTTTTTTCTTTTTTCTTCTTTTTTC
3430432 TGATGAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.33
30 6 0.22
31 12 0.44
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (29 bp):
TCTTTTTTTTCTTTTTTCTTCTTTTTTCA
Found at i:3430418 original size:19 final size:19
Alignment explanation
Indices: 3430394--3430430 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3430384 CTTTTTCATC
3430394 TCTTTTTTCATCTTTTTTT
1 TCTTTTTTCATCTTTTTTT
*
3430413 TCTTTTTTCTTCTTTTTT
1 TCTTTTTTCATCTTTTTT
3430431 CTGATGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TCTTTTTTCATCTTTTTTT
Found at i:3430431 original size:10 final size:10
Alignment explanation
Indices: 3430372--3430432 Score: 65
Period size: 10 Copynumber: 6.1 Consensus size: 10
3430362 TTGATTCAAT
3430372 TTCTTTTCTT-
1 TTCTTTT-TTC
3430382 TTC-TTTTTC
1 TTCTTTTTTC
3430391 ATCTCTTTTTTC
1 -T-TCTTTTTTC
*
3430403 ATCTTTTTT-
1 TTCTTTTTTC
3430412 TTCTTTTTTC
1 TTCTTTTTTC
3430422 TTCTTTTTTC
1 TTCTTTTTTC
3430432 T
1 T
3430433 GATGAATGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 2 0.05
9 11 0.25
10 23 0.52
11 2 0.05
12 6 0.14
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:3443026 original size:17 final size:16
Alignment explanation
Indices: 3443004--3443037 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3442994 GTAAAACAGT
3443004 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3443021 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3443037 A
1 A
3443038 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3447294 original size:34 final size:30
Alignment explanation
Indices: 3447256--3447324 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
3447246 TTGATATAAC
3447256 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
3447290 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
3447319 AATTTA
1 AATTTA
3447325 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:3447335 original size:29 final size:30
Alignment explanation
Indices: 3447265--3447324 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3447255 CAATTTAAGG
3447265 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3447296 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3447325 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3447664 original size:74 final size:73
Alignment explanation
Indices: 3447541--3447731 Score: 292
Period size: 74 Copynumber: 2.5 Consensus size: 73
3447531 TTTATTTAGT
* *
3447541 ATGGTATCGATACCCTCATATATGGTACCGATACCCCTATGAACATTTTGGTTCCGAGAAATAAC
1 ATGGTACCGATACCC-CCTATA-GGTACC-ATACCCCTATGAACATTTTGGTTCCGAGAAATAAC
3447606 AGAATGCTCGG
63 AGAATGCTCGG
3447617 ATGGTACCGATACCCCCTATAGGGTACCATACCCCTATGAACATTTTGGTTCCGAGAAATAACAG
1 ATGGTACCGATACCCCCTATA-GGTACCATACCCCTATGAACATTTTGGTTCCGAGAAATAACAG
3447682 AATGCTCGG
65 AATGCTCGG
* *
3447691 ATGGTACCGATACCCCCTAGTAGGTATCGATACCCCCATGA
1 ATGGTACCGATACCCCCTA-TAGGTA-CCATACCCCTATGA
3447732 TATGGTATCG
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
74 69 0.64
75 25 0.23
76 14 0.13
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (73 bp):
ATGGTACCGATACCCCCTATAGGTACCATACCCCTATGAACATTTTGGTTCCGAGAAATAACAGA
ATGCTCGG
Found at i:3447721 original size:20 final size:21
Alignment explanation
Indices: 3447693--3447768 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
3447683 ATGCTCGGAT
3447693 GGTACCGATACCCCCTA-GTA
1 GGTACCGATACCCCCTACGTA
* *
3447713 GGTATCGATACCCCC-ATGATA
1 GGTACCGATACCCCCTACG-TA
* * *
3447734 TGGTATCGATACCCCTTACTTA
1 -GGTACCGATACCCCCTACGTA
3447756 GGTACCGATACCC
1 GGTACCGATACCC
3447769 TCAGGCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 14 0.30
22 16 0.34
23 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (21 bp):
GGTACCGATACCCCCTACGTA
Found at i:3447741 original size:22 final size:21
Alignment explanation
Indices: 3447691--3447748 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
3447681 GAATGCTCGG
*
3447691 ATGGTACCGATACCCCCTAGT
1 ATGGTATCGATACCCCCTAGT
3447712 A-GGTATCGATACCCCC-ATGAT
1 ATGGTATCGATACCCCCTA-G-T
3447733 ATGGTATCGATACCCC
1 ATGGTATCGATACCCC
3447749 TTACTTAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 15 0.45
21 3 0.09
22 14 0.42
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTAGT
Found at i:3448568 original size:21 final size:20
Alignment explanation
Indices: 3448482--3448639 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
3448472 AAATGACCAA
**
3448482 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3448501 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3448521 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3448541 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3448562 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3448583 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3448603 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3448624 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3448640 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3448668 original size:20 final size:20
Alignment explanation
Indices: 3448606--3448835 Score: 214
Period size: 20 Copynumber: 11.5 Consensus size: 20
3448596 CGATTTTCCA
* ** *
3448606 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3448626 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
3448646 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
3448666 AAATCGCTACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3448686 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3448706 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3448726 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3448746 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3448766 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3448786 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3448806 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3448826 AAATCACAAC
1 AAATCGCAAC
3448836 ACTGAAATTT
Statistics
Matches: 172, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 168 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3449756 original size:12 final size:12
Alignment explanation
Indices: 3449739--3449763 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3449729 ATATAATCCT
3449739 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3449751 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3449763 G
1 G
3449764 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3452062 original size:19 final size:19
Alignment explanation
Indices: 3452040--3452411 Score: 384
Period size: 19 Copynumber: 21.4 Consensus size: 19
3452030 CGGAAATTAC
*
3452040 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3452059 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3452073 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3452093 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3452107 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452126 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3452145 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3452159 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452178 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3452197 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3452211 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452230 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3452249 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
3452263 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452282 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3452301 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3452315 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452334 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3452353 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
3452367 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3452386 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
3452404 AATCGCAA
1 AATCGCAA
3452412 CGAGAGAATC
Statistics
Matches: 297, Mismatches: 20, Indels: 73
0.76 0.05 0.19
Matches are distributed among these distances:
14 71 0.24
15 8 0.03
16 9 0.03
17 8 0.03
18 18 0.06
19 170 0.57
20 13 0.04
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3452155 original size:52 final size:52
Alignment explanation
Indices: 3452068--3452433 Score: 689
Period size: 52 Copynumber: 7.0 Consensus size: 52
3452058 AAATCCCAAC
3452068 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3452121 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3452173 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3452225 ATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3452277 ATGAAAATCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3452329 ATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3452381 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3452432 AT
1 AT
3452434 TATAAACGCA
Statistics
Matches: 307, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
51 30 0.10
52 261 0.85
53 16 0.05
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3452488 original size:19 final size:19
Alignment explanation
Indices: 3452458--3452501 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3452448 GATTCTCTCG
3452458 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3452476 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3452495 TTGCGAT
1 TTGCGAT
3452502 AGTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3452507 original size:19 final size:19
Alignment explanation
Indices: 3452466--3452509 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3452456 CGTTGCGATT
**
3452466 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
3452485 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
3452504 TCATTT
1 TCATTT
3452510 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:3452627 original size:14 final size:14
Alignment explanation
Indices: 3452608--3452644 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3452598 CATCAATTAC
3452608 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3452622 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3452636 ACAAATCAA
1 ACAAATCAA
3452645 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3454626 original size:33 final size:33
Alignment explanation
Indices: 3454580--3454672 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3454570 GCGAAACCAA
* *
3454580 AATCGCAACGCGAAATGAAAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3454613 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3454646 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3454673 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3454637 original size:19 final size:19
Alignment explanation
Indices: 3454543--3454677 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3454533 TAGTTTACTT
* *
3454543 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3454563 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3454582 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3454601 TCGCAA--CGACAT---AA
1 TCGCAACGCGAAATGAAAA
*
3454615 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3454634 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3454648 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3454667 TCGCAATGCGA
1 TCGCAACGCGA
3454678 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3454651 original size:14 final size:14
Alignment explanation
Indices: 3454599--3454655 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3454589 GCGAAATGAA
* *
3454599 AATCGCAACGACAT
1 AATCGCAACGAAAG
3454613 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3454630 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3454646 AATCGCAACG
1 AATCGCAACG
3454656 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3454695 original size:19 final size:19
Alignment explanation
Indices: 3454673--3454801 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3454663 AAAATCGCAA
3454673 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3454692 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3454706 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3454725 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3454739 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3454758 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3454777 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3454797 TGCGA
1 TGCGA
3454802 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3454715 original size:33 final size:33
Alignment explanation
Indices: 3454673--3454764 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3454663 AAAATCGCAA
3454673 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3454706 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3454739 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3454765 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3455008 original size:93 final size:93
Alignment explanation
Indices: 3454849--3455503 Score: 1294
Period size: 93 Copynumber: 7.1 Consensus size: 93
3454839 ATGGATTGCA
3454849 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3454914 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3454942 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455007 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455035 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455100 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455128 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455193 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455221 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455285 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455313 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455378 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455406 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3455471 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3455499 TTACT
1 TTACT
3455504 AAGCAATCTA
Statistics
Matches: 560, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.16
93 468 0.84
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3455354 original size:278 final size:279
Alignment explanation
Indices: 3454849--3455503 Score: 1294
Period size: 278 Copynumber: 2.4 Consensus size: 279
3454839 ATGGATTGCA
3454849 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3454914 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
3454979 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
3455044 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
3455109 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
3455128 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3455193 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
3455257 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
3455322 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
3455387 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
3455406 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3455471 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
3455504 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
278 263 0.70
279 112 0.30
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:3457179 original size:14 final size:14
Alignment explanation
Indices: 3457160--3457249 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3457150 TTGAAATGAA
3457160 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3457174 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3457193 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3457207 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3457226 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3457240 AATCGCAACG
1 AATCGCAACG
3457250 CGAAATTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3457192 original size:33 final size:33
Alignment explanation
Indices: 3457152--3457266 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
3457142 TCTTTTGGTT
3457152 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3457185 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3457218 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3457251 GAAATTAAAATCGCAA
1 GAAATGAAAATCGCAA
3457267 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3457198 original size:19 final size:19
Alignment explanation
Indices: 3457174--3457271 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
3457164 GCAACGAGAG
3457174 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3457193 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3457207 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3457226 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
3457240 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
*
3457259 AATCGCAATGCGA
1 AATCGCAACGCGA
3457272 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3457289 original size:19 final size:19
Alignment explanation
Indices: 3457267--3457325 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
3457257 AAAATCGCAA
3457267 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3457286 TGCGA---T--TATCTCGT
1 TGCGATTTTGGTTTCGCGT
3457300 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3457319 TGTGATT
1 TGCGATT
3457326 CTCTCGTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 11 0.37
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.08, C:0.15, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3457309 original size:33 final size:33
Alignment explanation
Indices: 3457267--3457341 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
3457257 AAAATCGCAA
3457267 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
* *
3457300 TGCGATTTTGGTTTCGCGTTGTGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
3457333 TGCGATTTT
1 TGCGATTTT
3457342 CATTTCTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
Found at i:3457380 original size:41 final size:41
Alignment explanation
Indices: 3457323--3457400 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
3457313 TCGCGTTGTG
*
3457323 ATTCTCTCGTTGCGATTTTCATTTCTCTCCTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCCTTGCGACAGTC
*
3457364 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCCTTGCGAC
3457401 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.27, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCCTTGCGACAGTC
Found at i:3457385 original size:20 final size:21
Alignment explanation
Indices: 3457324--3457399 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3457314 CGCGTTGTGA
3457324 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
3457345 TTCTCTCCTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3457365 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3457386 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3457400 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.26, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3457521 original size:33 final size:33
Alignment explanation
Indices: 3457479--3457549 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3457469 AATACTAACT
*
3457479 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3457512 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3457545 TGAAA
1 TGAAA
3457550 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3457783 original size:22 final size:22
Alignment explanation
Indices: 3457731--3457785 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3457721 TGGTTGTGAG
** *
3457731 GGATTTCGCCGGATATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3457753 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3457775 GGATTTCTTCG
1 GGATTTCTTCG
3457786 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3457957 original size:20 final size:20
Alignment explanation
Indices: 3457932--3458086 Score: 195
Period size: 20 Copynumber: 7.7 Consensus size: 20
3457922 CTTTAAATAT
3457932 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3457952 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3457974 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3457993 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3458013 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3458033 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3458053 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
3458073 CAAGTTGCGATTTA
1 CGCGTTGCGATTTA
3458087 TGTGTTCACG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 98 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3458080 original size:40 final size:40
Alignment explanation
Indices: 3457934--3458125 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 40
3457924 TTAAATATCG
* * *
3457934 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTA-T
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGA-TACA
* *
3457975 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
* **
3458015 CATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
** * *
3458055 CGTTGCGATTTACGGATACAAGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACA
* ** *
3458095 CGTTGCGATTTTCATATTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTT
3458126 TGGAAAATCG
Statistics
Matches: 127, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 96 0.76
41 29 0.23
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
Found at i:3458099 original size:20 final size:20
Alignment explanation
Indices: 3457934--3458105 Score: 177
Period size: 20 Copynumber: 8.6 Consensus size: 20
3457924 TTAAATATCG
*
3457934 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* * *
3457954 CGTTGCGATTTTATGTATTA-T
1 CGTTGCGA-TTTACGGA-TACA
*
3457975 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* *
3457995 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACA
* ** *
3458015 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACA
3458035 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACA
3458055 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACA
* * *
3458075 AGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACG-GATACA
3458095 CGTTGCGATTT
1 CGTTGCGATTT
3458106 TCATATTCGC
Statistics
Matches: 129, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 110 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACA
Done.