Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009621.1 Hibiscus syriacus cultivar Beakdansim tig00117010_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: 839111
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:245373 original size:19 final size:19
Alignment explanation
Indices: 245333--245422 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
245323 TCTGGAACTT
*
245333 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
245354 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
245373 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
245387 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
245406 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
245423 CCAAAAGACA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 30 0.53
21 11 0.19
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:245428 original size:19 final size:19
Alignment explanation
Indices: 245389--245428 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
245379 GCAACGAGAG
**
245389 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
245408 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
245427 AA
1 AA
245429 GACAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:245628 original size:94 final size:94
Alignment explanation
Indices: 245526--245901 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
245516 ATGGATTGCA
* * *
245526 TTAC-TTCAACCAAAACACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
245590 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
245619 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
245684 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
245713 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
245778 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
245807 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
245867 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
245897 TTACT
1 TTACT
245902 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
90 41 0.15
93 23 0.09
94 205 0.76
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:247540 original size:20 final size:19
Alignment explanation
Indices: 247495--247649 Score: 81
Period size: 19 Copynumber: 8.8 Consensus size: 19
247485 TCTTTTGGTT
247495 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
247514 GATAATGAAAATCGCAATGCG-
1 GA-AATGAAAATCGCAA--CGA
** *
247535 GAAATGACTATTGCAACGA
1 GAAATGAAAATCGCAACGA
* *
247554 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
**
247568 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
247587 G--A-G--AATTGCAACGC
1 GAAATGAAAATCGCAACGA
247601 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
247620 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
247634 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
247650 TGCGATTTTG
Statistics
Matches: 101, Mismatches: 16, Indels: 38
0.65 0.10 0.25
Matches are distributed among these distances:
14 28 0.28
16 6 0.06
17 6 0.06
18 2 0.02
19 30 0.30
20 25 0.25
21 2 0.02
22 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:247577 original size:33 final size:33
Alignment explanation
Indices: 247523--247649 Score: 173
Period size: 33 Copynumber: 3.8 Consensus size: 33
247513 AGATAATGAA
* *
247523 AATCGCAATGCGGAAATGACTATTGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
*
247557 AATCGCAATGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
* **
247590 AATTGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
247623 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
247650 TGCGATTTTG
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 76 0.87
34 11 0.13
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:247628 original size:14 final size:14
Alignment explanation
Indices: 247547--247632 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
247537 AATGACTATT
247547 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
247561 GCAATGCGAAATGACTATC
1 GCAA--CGAGA-GA--ATC
*
247580 GCAACGAGAGAATT
1 GCAACGAGAGAATC
*
247594 GCAACGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
247613 GCAACGAGAGAATC
1 GCAACGAGAGAATC
247627 GCAACG
1 GCAACG
247633 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
14 22 0.39
15 1 0.02
16 8 0.14
17 8 0.14
18 1 0.02
19 16 0.29
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.12
Consensus pattern (14 bp):
GCAACGAGAGAATC
Found at i:247733 original size:20 final size:19
Alignment explanation
Indices: 247666--247734 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
247656 TTTGTTTTTA
247666 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
247685 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
**
247699 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
247719 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
247735 CTCGAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 3 0.08
19 9 0.23
20 15 0.38
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:248099 original size:20 final size:21
Alignment explanation
Indices: 248076--248207 Score: 166
Period size: 20 Copynumber: 6.5 Consensus size: 21
248066 CGATAGTCAG
* *
248076 ATTCGCATTGCGATTT-CCTA
1 ATTCGCGTTGCGATTTACTTA
* * *
248096 ATTCGCATTGCGATTTTCCTA
1 ATTCGCGTTGCGATTTACTTA
248117 ATTCGCGTTGCGATTTACTTA
1 ATTCGCGTTGCGATTTACTTA
248138 A-TCGCGTTGCGATTTACTTA
1 ATTCGCGTTGCGATTTACTTA
248158 A-TCGCGTTGCGATTTACTTA
1 ATTCGCGTTGCGATTTACTTA
*
248178 A-TCGCGTTGCGATTTACGT-
1 ATTCGCGTTGCGATTTACTTA
*
248197 ATTCGCATTGC
1 ATTCGCGTTGC
248208 TAATTATGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.01
20 81 0.77
21 23 0.22
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (21 bp):
ATTCGCGTTGCGATTTACTTA
Found at i:248168 original size:61 final size:60
Alignment explanation
Indices: 248078--248207 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 60
248068 ATAGTCAGAT
*
248078 TCGCATTGCGATTTCCTAATTCGCATTGCGATTTTCCTAATTCGCGTTGCGATTTACTTAA
1 TCGCATTGCGATTTCCTAATTCGCATTGCGATTTACCTAA-TCGCGTTGCGATTTACTTAA
* * * * * *
248139 TCGCGTTGCGATTTACTTAA-TCGCGTTGCGATTTACTTAATCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTT-CCTAATTCGCATTGCGATTTACCTAATCGCGTTGCGATTTACTTAA
248199 TCGCATTGC
1 TCGCATTGC
248208 TAATTATGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
60 26 0.43
61 30 0.50
62 4 0.07
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (60 bp):
TCGCATTGCGATTTCCTAATTCGCATTGCGATTTACCTAATCGCGTTGCGATTTACTTAA
Found at i:248266 original size:20 final size:20
Alignment explanation
Indices: 248217--248272 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
248207 CTAATTATGA
**
248217 AAATCGCAACACGAATACGT
1 AAATCGCAATGCGAATACGT
248237 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
248257 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
248273 TAGGAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:248345 original size:20 final size:21
Alignment explanation
Indices: 248301--248352 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
248291 ATAGTCAGTA
*
248301 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
248322 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
248342 TCGCATTGCGA
1 TCGCATTGCGA
248353 ATTGTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:248394 original size:21 final size:22
Alignment explanation
Indices: 248342--248394 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
248332 ATTTACTTAT
248342 TCGCATTGCG-AATTGTGAAAA
1 TCGCATTGCGAAATTGTGAAAA
* **
248363 ACGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGTGAAAA
248384 TCGCATTGCGA
1 TCGCATTGCGA
248395 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGTGAAAA
Found at i:248453 original size:143 final size:142
Alignment explanation
Indices: 248158--248476 Score: 328
Period size: 143 Copynumber: 2.2 Consensus size: 142
248148 GATTTACTTA
** * * *
248158 ATCGCGTTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGCATTGCTAATTATGAAAATCG
1 ATCGCGTTGCGATTTACCAAATCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAAACG
* *
248223 CAACACGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATTGCATT
66 CAACACGAATACGAAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAACTGCATT
*
248288 GCGATAGTCAGT
131 GCGATAATCAGT
* * * *
248300 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGTGAAAAAC
1 ATCGCGTTGCGATTTACCAAA-TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAAAC
* ** * **
248365 GCAACGCGAAATTGGAAAATCGCATTGCG-ATA-GTCATAATCGCGTTGCGAATCT-GG-AAACT
65 GCAACACG-AATACGAAAATCGCAATGCGAATACGT-A-AATCGCAATGCGAAT-TAGGAAAACT
*
248426 G-ATTTGCGATAATGGAG-
126 GCA-TTGCGATAAT-CAGT
* * *
248443 ATCGCGTTGCGAATTAGC-GATCGCATTGCGATTT
1 ATCGCGTTGCGATTTACCAAATCGCATTGCGATTT
248477 TGTTGGTCAT
Statistics
Matches: 146, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
141 14 0.10
142 21 0.14
143 77 0.53
144 33 0.23
145 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (142 bp):
ATCGCGTTGCGATTTACCAAATCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAAACG
CAACACGAATACGAAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAACTGCATT
GCGATAATCAGT
Found at i:250571 original size:20 final size:21
Alignment explanation
Indices: 250548--250598 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
250538 CGCGAATATG
*
250548 TAAA-TCGCATTGCGATTTTC
1 TAAATTCGCATTACGATTTTC
*
250568 TAAATTCGCGTTACGATTTTC
1 TAAATTCGCATTACGATTTTC
*
250589 CAAATTCGCA
1 TAAATTCGCA
250599 ACGTGAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (21 bp):
TAAATTCGCATTACGATTTTC
Found at i:250619 original size:20 final size:20
Alignment explanation
Indices: 250594--250640 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
250584 TTTTCCAAAT
**
250594 TCGCAACGTGAATATGTAAA
1 TCGCAACGCCAATATGTAAA
* *
250614 TCGCAACGCCAATTTGTAAT
1 TCGCAACGCCAATATGTAAA
250634 TCGCAAC
1 TCGCAAC
250641 ACAAAAGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCCAATATGTAAA
Found at i:250654 original size:20 final size:20
Alignment explanation
Indices: 250631--250679 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
250621 GCCAATTTGT
250631 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
250651 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
250671 AATTCGCAA
1 AATTCGCAA
250680 AGCGCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:250697 original size:19 final size:20
Alignment explanation
Indices: 250673--250713 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
250663 AAAAGTCAAA
*
250673 TTCGCAAAGCGCA-TTTATT
1 TTCGCAAAGCGAATTTTATT
*
250692 TTCGCAACGCGAATTTTATT
1 TTCGCAAAGCGAATTTTATT
250712 TT
1 TT
250714 TGAATTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (20 bp):
TTCGCAAAGCGAATTTTATT
Found at i:251225 original size:20 final size:20
Alignment explanation
Indices: 251202--251245 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
251192 ACTTAAATTT
251202 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
* *
251222 GCAACGCGAAACTGAAAATC
1 GCAACACGAAAATGAAAATC
251242 GCAA
1 GCAA
251246 AGCGATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.18, T:0.09
Consensus pattern (20 bp):
GCAACACGAAAATGAAAATC
Found at i:251250 original size:20 final size:20
Alignment explanation
Indices: 251208--251250 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
251198 ATTTGCAACA
*
251208 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAAAG
*
251228 CGAAACTGAAAATCGCAAAG
1 CGAAAATGAAAATCGCAAAG
251248 CGA
1 CGA
251251 TTTTAGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAAAG
Found at i:251269 original size:19 final size:18
Alignment explanation
Indices: 251247--251367 Score: 125
Period size: 19 Copynumber: 6.4 Consensus size: 18
251237 AAATCGCAAA
*
251247 GCGATTTTAGTTTCGCGTT
1 GCGATTTCA-TTTCGCGTT
*
251266 GCGATTTTCATTTCACGTT
1 GCGA-TTTCATTTCGCGTT
*
251285 GCTACTTTCATTTCGCGTT
1 GCGA-TTTCATTTCGCGTT
* *
251304 GCTACTTTCATTTCACGTT
1 GCGA-TTTCATTTCGCGTT
*
251323 GCTAATTTCATTTCGCGTT
1 GC-GATTTCATTTCGCGTT
*
251342 GCTACTTTCATTTCGCGTT
1 GCGA-TTTCATTTCGCGTT
251361 GCGATTT
1 GCGATTT
251368 TAAGTTTCAG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
18 4 0.04
19 80 0.90
20 5 0.06
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.47
Consensus pattern (18 bp):
GCGATTTCATTTCGCGTT
Found at i:251313 original size:38 final size:38
Alignment explanation
Indices: 251257--251362 Score: 176
Period size: 38 Copynumber: 2.8 Consensus size: 38
251247 GCGATTTTAG
* * *
251257 TTTCGCGTTGCGATTTTCATTTCACGTTGCTACTTTCA
1 TTTCGCGTTGCTACTTTCATTTCACGTTGCTAATTTCA
251295 TTTCGCGTTGCTACTTTCATTTCACGTTGCTAATTTCA
1 TTTCGCGTTGCTACTTTCATTTCACGTTGCTAATTTCA
*
251333 TTTCGCGTTGCTACTTTCATTTCGCGTTGC
1 TTTCGCGTTGCTACTTTCATTTCACGTTGC
251363 GATTTTAAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (38 bp):
TTTCGCGTTGCTACTTTCATTTCACGTTGCTAATTTCA
Found at i:253408 original size:21 final size:21
Alignment explanation
Indices: 253383--253465 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
253373 AAAGCACATG
253383 TCATCATTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCCCTA
* * *
253404 TCATCCTTCAAGAGGCTCCTC
1 TCATCATTCAAGAGGCCCCTA
* * * *
253425 CCACCATTCAAGAGGCCTCTG
1 TCATCATTCAAGAGGCCCCTA
* *
253446 TCATCGTTCAAGAGGTCCCT
1 TCATCATTCAAGAGGCCCCT
253466 CCCACCGTTC
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTA
Found at i:253434 original size:42 final size:42
Alignment explanation
Indices: 253387--253480 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
253377 CACATGTCAT
253387 CATTCAAGAGGCCCCTATCATCCTTCAAGAGG-CTCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCTTCAAGAGGTC-CCTCCCAC
* * *
253429 CATTCAAGAGGCCTCTGTCATCGTTCAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCTTCAAGAGGTCCCTCCCAC
* *
253471 CGTTCGAGAG
1 CATTCAAGAG
253481 CCCTACCCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
CATTCAAGAGGCCCCTATCATCCTTCAAGAGGTCCCTCCCAC
Found at i:253474 original size:21 final size:20
Alignment explanation
Indices: 253410--253484 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
253400 CCTATCATCC
*
253410 TTCAAGAGGCTCCTCCCACCA
1 TTCAAGAGGC-CCTCCCACCG
** *
253431 TTCAAGAGGCCTCTGTCATCG
1 TTCAAGAGGCC-CTCCCACCG
253452 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGG-CCCTCCCACCG
*
253473 TTCGAGA-GCCCT
1 TTCAAGAGGCCCT
253485 ACCCTTTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.09
20 2 0.05
21 36 0.82
22 2 0.05
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (20 bp):
TTCAAGAGGCCCTCCCACCG
Found at i:254701 original size:13 final size:14
Alignment explanation
Indices: 254676--254708 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
254666 AAATTGATGT
254676 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
254690 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
254703 ATTTGT
1 ATTTGT
254709 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:254771 original size:77 final size:78
Alignment explanation
Indices: 254676--254849 Score: 280
Period size: 78 Copynumber: 2.3 Consensus size: 78
254666 AAATTGATGT
254676 ATTTGTAAAAGTTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
1 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
254740 GCTTGTTTAATTG
66 GCTTGTTTAATTG
* * * ***
254753 ATTTGTAAAAGTTAATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTT
1 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
254818 GCTTGTTTAATTG
66 GCTTGTTTAATTG
254831 ATTT-TAAAAGTTGATTTGT
1 ATTTGTAAAAGTTGATTTGT
254850 TGTTTTAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 33 0.37
78 56 0.63
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (78 bp):
ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
GCTTGTTTAATTG
Found at i:254772 original size:14 final size:14
Alignment explanation
Indices: 254753--254786 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
254743 TGTTTAATTG
254753 ATTTGTAAAAGTTA
1 ATTTGTAAAAGTTA
*
254767 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTA
254781 ATTTGT
1 ATTTGT
254787 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTA
Found at i:254973 original size:20 final size:20
Alignment explanation
Indices: 254948--255022 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
254938 CGATGGTTGC
254948 GAAAGCCAAATTCGCAACGT
1 GAAAGCCAAATTCGCAACGT
254968 GAAAGCCAAATTCGCAACGT
1 GAAAGCCAAATTCGCAACGT
* *
254988 GAAATCCAAATTCGCAACGA
1 GAAAGCCAAATTCGCAACGT
* *
255008 GAAAGTCAACTTCGC
1 GAAAGCCAAATTCGC
255023 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (20 bp):
GAAAGCCAAATTCGCAACGT
Found at i:257617 original size:24 final size:24
Alignment explanation
Indices: 257583--257636 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
257573 CTGAAACATC
257583 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
* *
257607 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
257631 ATCAAA
1 ATCAAA
257637 TTTCAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:257647 original size:24 final size:24
Alignment explanation
Indices: 257596--257647 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
257586 AAAATCCGAG
***
257596 TATTGACCAATATCAAAGTCCGGG
1 TATTGACCAATATCAAAGTCCAAA
* *
257620 TATTGACCAATATCAAATTTCAAA
1 TATTGACCAATATCAAAGTCCAAA
257644 TATT
1 TATT
257648 AACTAGTACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (24 bp):
TATTGACCAATATCAAAGTCCAAA
Found at i:258655 original size:19 final size:20
Alignment explanation
Indices: 258574--258657 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
258564 CCCGTTGCAA
*
258574 AATT-AAAATTCGTGTTGCG
1 AATTCAAAATTCGAGTTGCG
*
258593 AATTCGAAAA-TCGAGTTGCT
1 AATTC-AAAATTCGAGTTGCG
* * *
258613 ACA-ACAAAATTCGCGTTGCA
1 A-ATTCAAAATTCGAGTTGCG
258633 AATTCAAAA-TCGAGTTGCG
1 AATTCAAAATTCGAGTTGCG
258652 AATTCA
1 AATTCA
258658 GTGTTGCGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 23 0.44
20 24 0.46
21 5 0.10
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (20 bp):
AATTCAAAATTCGAGTTGCG
Found at i:258690 original size:20 final size:20
Alignment explanation
Indices: 258662--258699 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
258652 AATTCAGTGT
* *
258662 TGCGGATTTGTAAATCGCAA
1 TGCGAATTTGGAAATCGCAA
258682 TGCGAATTTGGAAATCGC
1 TGCGAATTTGGAAATCGC
258700 GATTTATATA
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:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
TGCGAATTTGGAAATCGCAA
Found at i:260237 original size:3 final size:3
Alignment explanation
Indices: 260229--260738 Score: 949
Period size: 3 Copynumber: 171.0 Consensus size: 3
260219 TTGTCCCCAG
260229 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260277 CTC CTC CTC CTC CTC CTC CTC CTC CTC C-C CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260324 CTC CTC CTC CTC CTC CTC CTC C-C CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
260371 CTC CTC CTC CTC CTC CTC CGC CTC CTC CTC CTC CTC CTC CT- CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260418 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260466 CTC CTC CTCC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CT-C CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260512 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260560 CTC CTC CTC CTC CTC CTC CTCC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CT-C CTC CTC CTC CTC CTC CTC CTC CTC
260606 CTC CTC C-C CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
260653 CTC CTC CTC CTC CTC CTC CGC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260701 CTC CTC CT- CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
260739 TACTATCTCT
Statistics
Matches: 496, Mismatches: 4, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
2 10 0.02
3 480 0.97
4 6 0.01
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:264447 original size:3 final size:3
Alignment explanation
Indices: 264439--264474 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
264429 ATATAGCTTC
*
264439 CTA CTA CTA CTA CCA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
264475 TTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CTA
Found at i:264479 original size:3 final size:3
Alignment explanation
Indices: 264473--264583 Score: 215
Period size: 3 Copynumber: 37.3 Consensus size: 3
264463 CTACTACTAC
264473 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
264520 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
264568 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
264584 GTCCTTCGTT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 105 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:268384 original size:31 final size:31
Alignment explanation
Indices: 268299--268438 Score: 165
Period size: 31 Copynumber: 4.5 Consensus size: 31
268289 CAAAGAAACA
*
268299 TAAGTTTTGGTCACTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTAAATTATTGTTTTAT
* * * **
268330 TAATTTTTTGT-AGTTTATGTTATTGTTTTAT
1 TAAGTTTTGGTCA-CTTAAATTATTGTTTTAT
** *
268361 TAAGGCTTGGTCACTTAAATTATTATTTTAT
1 TAAGTTTTGGTCACTTAAATTATTGTTTTAT
*
268392 TAAATTTTGGTCACTTAAATTATTGTTTTAT
1 TAAGTTTTGGTCACTTAAATTATTGTTTTAT
*
268423 TAAGTTTTGGCCACTT
1 TAAGTTTTGGTCACTT
268439 GGACATTGAA
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
30 1 0.01
31 86 0.98
32 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTAAATTATTGTTTTAT
Found at i:271064 original size:17 final size:17
Alignment explanation
Indices: 271022--271064 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
271012 GCTTGTAGGG
*
271022 TATCGATAAGCAGATGA
1 TATCGATACGCAGATGA
271039 TATCGATACGCAGATGA
1 TATCGATACGCAGATGA
271056 TATCGATAC
1 TATCGATAC
271065 ACTGAACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (17 bp):
TATCGATACGCAGATGA
Found at i:271928 original size:17 final size:17
Alignment explanation
Indices: 271906--271939 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
271896 ATTTATTTAA
*
271906 GAATATGTATTCGGCTT
1 GAATATGTATTCAGCTT
271923 GAATATGTATTCAGCTT
1 GAATATGTATTCAGCTT
271940 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (17 bp):
GAATATGTATTCAGCTT
Found at i:273271 original size:15 final size:15
Alignment explanation
Indices: 273247--273276 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
273237 TGGGCAGTAT
273247 CCTGCAAAAAAAATC
1 CCTGCAAAAAAAATC
*
273262 CCTGCGAAAAAAATC
1 CCTGCAAAAAAAATC
273277 TCTGTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.10, T:0.13
Consensus pattern (15 bp):
CCTGCAAAAAAAATC
Found at i:274331 original size:25 final size:26
Alignment explanation
Indices: 274268--274332 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 26
274258 ACATATCGAT
*
274268 AAACTATTAAATATTTGAAAACAATAC
1 AAACAATT-AATATTTGAAAACAATAC
*
274295 AAACAGTT-ATATTT-AAAAC-ATAC
1 AAACAATTAATATTTGAAAACAATAC
*
274318 AAAATAATTAATATT
1 -AAACAATTAATATT
274333 GACCATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.12
24 11 0.34
25 11 0.34
27 6 0.19
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.32
Consensus pattern (26 bp):
AAACAATTAATATTTGAAAACAATAC
Found at i:274446 original size:22 final size:23
Alignment explanation
Indices: 274418--274464 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
274408 CATTGGCGAC
274418 GTCCAAAT-ATTACCTTAGCCAT
1 GTCCAAATAATTACCTTAGCCAT
274440 GTCCAAATAATTACCTTAGCCAT
1 GTCCAAATAATTACCTTAGCCAT
274463 GT
1 GT
274465 AAACAGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (23 bp):
GTCCAAATAATTACCTTAGCCAT
Found at i:275084 original size:43 final size:42
Alignment explanation
Indices: 275017--275326 Score: 323
Period size: 43 Copynumber: 7.2 Consensus size: 42
275007 TGAGAACCAA
* * *
275017 AAACGCCGCCATAGTTCAAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* ** *
275060 AAACGCCGCAAAAGGTCGATATCTATAGCAACGTTTTTAGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * *
275103 AAACACTGCAAAAAGTCAAGATCTATAGCGGCGTTTATGGAAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
*
275146 AAACGCCACAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGA-AC
* *
275190 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTAGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
275232 AAACGTCGTAAAAGGCCAGATCTATAGCGGCGTTTCTGAACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
** * * **
275275 AAACGCCGCAAAATATCATATCTATAGCAGTATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
275318 AAACGCCGC
1 AAACGCCGC
275327 TAATTACCAT
Statistics
Matches: 218, Mismatches: 47, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
42 35 0.16
43 166 0.76
44 17 0.08
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:275279 original size:129 final size:129
Alignment explanation
Indices: 275035--275326 Score: 367
Period size: 129 Copynumber: 2.3 Consensus size: 129
275025 CCATAGTTCA
* *
275035 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCGATATCTATAGCAACGTTTTTA
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCGAGATCTATAGCAACATTTTTA
* * * *
275099 GAACAAACACTGCAAAAAGTCAAGATCTATAGCGGCGTTTATGGAATAAACGCCACAAAAGGTC
66 GAACAAACACTGCAAAAAGGCAAGATCTATAGCGGCGTTTATGAAACAAACGCCACAAAAGATC
**
275163 GAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTT
1 -AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCGAGATCTATAGCAACATTTTT
* * * * * *
275227 AGAACAAAC-GT-CGTAAAAGGCCAGATCTATAGCGGCGTTTCTGAACACAAACGCCGCAAAATA
65 AGAACAAACACTGC-AAAAAGGCAAGATCTATAGCGGCGTTTATGAA-ACAAACGCCACAAAAGA
275290 TC
128 TC
* * **
275292 ATATCTATAGCAGTATTTTTGGATACAAACGCCGC
1 AGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
275327 TAATTACCAT
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
127 1 0.01
128 59 0.42
129 63 0.44
130 19 0.13
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (129 bp):
AGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCGAGATCTATAGCAACATTTTTA
GAACAAACACTGCAAAAAGGCAAGATCTATAGCGGCGTTTATGAAACAAACGCCACAAAAGATC
Found at i:276440 original size:16 final size:16
Alignment explanation
Indices: 276419--276449 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
276409 CCGATTACTA
276419 TCACCTAATGCAAAAC
1 TCACCTAATGCAAAAC
276435 TCACCTAATGCAAAA
1 TCACCTAATGCAAAA
276450 ATTTAGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (16 bp):
TCACCTAATGCAAAAC
Found at i:278741 original size:41 final size:41
Alignment explanation
Indices: 278668--279136 Score: 378
Period size: 41 Copynumber: 11.4 Consensus size: 41
278658 TTTGTAACAC
* * * * * *
278668 AAACGCCATTAAAATACGAGTTTTTCGTGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
278709 AAACGCCACTAAAGTACAAGTCTATAACGGCGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* * *
278752 AAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTA-AA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
278792 AAATGCCACTAAAGTACAAGTCTATAGCAGCGTTTATAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* *
278835 AAACTCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
278876 AAACGCCACTAAAGTATGAGT-TATAGCGGCGTTTTTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* **
278916 AAACGCCACTACAA-TACGAGT-TATAACAACGATTT-TATAAAAA
1 AAACGCCACTA-AAGTACGAGTCTATAGCGGCG-TTTGTAT---AA
* * * *
278959 AAATGCCACTAAAGTATGAGTCT-TAGAGGTGTTTGTATAAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AA
* * *
279000 AAACGCTCA-TAAAGTATGATTCTATAGCGGCGTTTGTGTAA
1 AAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
279041 AAATGCCACTATAGTACTAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * * * *
279082 AAATGCCACTAAAGTAAGA-TCTTTTGCGGCATTTTTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
279122 AAACGCCTCTAAAGT
1 AAACGCCACTAAAGT
279137 TAGATATTTT
Statistics
Matches: 346, Mismatches: 66, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
40 108 0.31
41 126 0.36
42 20 0.06
43 91 0.26
44 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:278807 original size:83 final size:83
Alignment explanation
Indices: 278652--279097 Score: 383
Period size: 83 Copynumber: 5.4 Consensus size: 83
278642 CTTTAAATTT
* * * * * * * * *
278652 GCGGCATTTGT-AACACAAACGCCATTAAAATACGAGTTTTTCGTGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAAACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-AAAAATGCC
278716 ACTAAAGTACAAGTCTATA
65 ACTAAAGTACAAGTCTATA
* * * *
278735 ACGGCGTTTGTAAACAAAAACGCCACGAAAGAACGAGTCTTTAGCGGCGTTTGTAAAAAATGCCA
1 GCGGCGTTTGTAAACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAAAAATGCCA
278800 CTAAAGTACAAGTCTATA
66 CTAAAGTACAAGTCTATA
* * * * *
278818 GCAGCGTTTATAAACAAAAACTCCACTAAAGTACGAGTCTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTAAACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-AAAAATGCC
**
278883 ACTAAAGTATGAGT-TATA
65 ACTAAAGTACAAGTCTATA
* * * ** *
278901 GCGGCGTTTTTATAC--AAACGCCACTACAA-TACGAGT-TATAACAACGATTTTATAAAAAAAA
1 GCGGCGTTTGTAAACAAAAACGCCACTA-AAGTACGAGTCTATAGCGGCG--TTTGT--AAAAAA
**
278962 TGCCACTAAAGTATGAGTCT-TA
61 TGCCACTAAAGTACAAGTCTATA
* * * * * *
278984 GAGGTGTTTGTATA-AAAAACGCTCA-TAAAGTATGATTCTATAGCGGCGTTTGTGTAAAAATGC
1 GCGGCGTTTGTAAACAAAAACGC-CACTAAAGTACGAGTCTATAGCGGCGTTTGT-AAAAAATGC
* * *
279047 CACTATAGTACTAGTCTTTA
64 CACTAAAGTACAAGTCTATA
* *
279067 GCGGCGTTTGTATAC--AAATGCCACTAAAGTA
1 GCGGCGTTTGTAAACAAAAACGCCACTAAAGTA
279098 AGATCTTTTG
Statistics
Matches: 298, Mismatches: 49, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
80 7 0.02
81 19 0.06
82 39 0.13
83 154 0.52
84 70 0.23
85 9 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (83 bp):
GCGGCGTTTGTAAACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAAAAATGCCA
CTAAAGTACAAGTCTATA
Found at i:279121 original size:40 final size:40
Alignment explanation
Indices: 279026--279157 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 40
279016 TGATTCTATA
* * * * *
279026 GCGGCGTTTGTGTAAAAATGCCACTATAGTACTAG-TCTTTA
1 GCGGCATTTGTATACAAATGCCACTAAAGTA--AGATCTTTT
*
279067 GCGGCGTTTGTATACAAATGCCACTAAAGTAAGATCTTTT
1 GCGGCATTTGTATACAAATGCCACTAAAGTAAGATCTTTT
* * * * *
279107 GCGGCATTTTTATACAAACGCCTCTAAAGTTAGATATTTT
1 GCGGCATTTGTATACAAATGCCACTAAAGTAAGATCTTTT
* *
279147 ACGGCGTTTGT
1 GCGGCATTTGT
279158 TCAAAAAACG
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.03
40 47 0.61
41 28 0.36
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (40 bp):
GCGGCATTTGTATACAAATGCCACTAAAGTAAGATCTTTT
Found at i:284249 original size:29 final size:29
Alignment explanation
Indices: 284205--284358 Score: 177
Period size: 29 Copynumber: 5.3 Consensus size: 29
284195 ATTTTATATC
*
284205 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTCTTATA
* * *
284235 TTAA-TT-TAAATATATTTTATTCTTGTC
1 TTAACTTAAAAATATATTTTATTCTTATA
* * *
284262 TTACCCTAAAAATATATTTTATTCTTATT
1 TTAACTTAAAAATATATTTTATTCTTATA
* *
284291 TTAACTTAAAAATATATTTTAATCTTTATC
1 TTAACTTAAAAATATATTTTATTC-TTATA
*
284321 TTAATTTAAAAAATATATTTTATTCTTATA
1 TTAACTT-AAAAATATATTTTATTCTTATA
284351 TTAACTTA
1 TTAACTTA
284359 TTACATAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
27 20 0.19
28 3 0.03
29 40 0.39
30 24 0.23
31 16 0.16
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATA
Found at i:284274 original size:56 final size:59
Alignment explanation
Indices: 284192--284358 Score: 196
Period size: 60 Copynumber: 2.8 Consensus size: 59
284182 ACATATCAAA
* * * *
284192 TTAATTTTATATCTTAACATTAAAAATATATTTTATTTTTATATTAA-TT-TAAATATATT
1 TTAATCTT-TATCTTAAC-CTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
* * * *
284251 TTATTC-TTGTCTTACCCTAAAAATATATTTTATTCTTATTTTAACTTAAAAATATATT
1 TTAATCTTTATCTTAACCTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
**
284309 TTAATCTTTATCTTAATTTAAAAAATATATTTTATTCTTATATTAACTTA
1 TTAATCTTTATCTTAACCT-AAAAATATATTTTATTCTTATATTAACTTA
284359 TTACATAAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
56 25 0.28
57 9 0.10
58 15 0.17
59 12 0.13
60 29 0.32
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.54
Consensus pattern (59 bp):
TTAATCTTTATCTTAACCTAAAAATATATTTTATTCTTATATTAACTTAAAAATATATT
Found at i:286127 original size:14 final size:14
Alignment explanation
Indices: 286108--286134 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
286098 AAATATAACC
286108 AATAAAAAATGGTA
1 AATAAAAAATGGTA
286122 AATAAAAAATGGT
1 AATAAAAAATGGT
286135 TTATACATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (14 bp):
AATAAAAAATGGTA
Found at i:289065 original size:5 final size:5
Alignment explanation
Indices: 289055--289085 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
289045 GGAGTGTAAA
289055 CGAGT CGAGT CGAGT CGAGT CGAGTT CGAGT
1 CGAGT CGAGT CGAGT CGAGT CGAG-T CGAGT
289086 ATTGCTAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (5 bp):
CGAGT
Found at i:298541 original size:2 final size:2
Alignment explanation
Indices: 298530--298578 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
298520 CAGGGTCGTT
298530 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298571 TA TA TA TA
1 TA TA TA TA
298579 GGGATAGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:300173 original size:112 final size:112
Alignment explanation
Indices: 300040--300275 Score: 402
Period size: 112 Copynumber: 2.1 Consensus size: 112
300030 ACATGTACAA
*
300040 AAAGTATCGATACTTTCAACATATACGGTAG-TTCTTTACCGGTTTTGTCATAATGAAATTGGTT
1 AAAGTATCGATACTTTCAACATATACGGTAGCTT-TTTACCGGTTTTGTCATAATGAAACTGGTT
* *
300104 TTTTCATATTTTTACCTGTTATATTGTTATGTATTAATACATTTTTAT
65 TTGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* * *
300152 AAAGTATCGATATTTTCAACATATCCGGTAGCTTTTTACCTGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATACGGTAGCTTTTTACCGGTTTTGTCATAATGAAACTGGTTT
300217 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
300264 AAAGTATCGATA
1 AAAGTATCGATA
300276 ATTTATAGGT
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
112 115 0.98
113 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (112 bp):
AAAGTATCGATACTTTCAACATATACGGTAGCTTTTTACCGGTTTTGTCATAATGAAACTGGTTT
TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
Found at i:300561 original size:74 final size:73
Alignment explanation
Indices: 300361--301522 Score: 1429
Period size: 73 Copynumber: 15.9 Consensus size: 73
300351 CAACATATCT
* * * *
300361 GGTAAGTACTTTAATGTAATAGGCAGCGTCTATTATTTTTTACCGTTTACATTATTAGA-AACCT
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATT-TTTTTTACCGTTTACATTATTA-ACAACCT
300425 TCAAAAAAACC
64 TCAAAAAAA-C
* * * **
300436 GGTAGGTATTTTAATATAATAAGTAGCGCATA-TTTTTTTACCGTTTACATTATTAACAGTCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
300500 AAAAAAATC
66 AAAAAAA-C
* * * *
300509 AGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAATAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
300574 AAAAAAACC
66 AAAAAAA-C
* *
300583 GGTAGGTATTTTAATGTAATAGGTAGTGCC--TTTTTTTTACTGTTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
300646 AAAAAAAACC
66 -AAAAAAA-C
* *
300656 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAACATTTACATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
300720 AAAAAAACC
66 AAAAAAA-C
* * * *
300729 GATAGGTATTTTAATGAAATAAGTAGCGCCTA-TTTTTTTACCATTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
*
300793 AAAAAAATT
66 AAAAAAA-C
* ** *
300802 GGTAGGTATTTTAATGTAATAGATAGCATCTATTTTTTTTACCGTTTATATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
300866 AAAAAAAC
66 AAAAAAAC
* *
300874 TGGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAACAATCTT
1 -GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
300939 --AAAAAAC
65 CAAAAAAAC
* *
300946 GGTAGGTATTTTAATGTAATAGGTAGAGCCTA-TTTTTTTACCGTTTATATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
*
301009 AAAAAACC
66 AAAAAAAC
* * * ** *
301017 GATAGGTATTTTAATGTAATAAGCAGCGTTTATTTTTTTTACTGTTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
301082 AAAAAAAATC
66 -AAAAAAA-C
* * *
301092 TGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTT
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAACAACCTT
301157 CAAAAAAATC
65 CAAAAAAA-C
* * *
301167 GGTAGGTATTTTAATGTAATATGTAACGCCTATTGTTTTTACCGTTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
*
301232 AAAAAATC
66 AAAAAAAC
* * * * *
301240 GATAGGTATTTTAATATAATAGGTAGCACCTATTTTTTTTACCGTTTAAATTATTAACAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
301305 AAAAAAACC
66 AAAAAAA-C
* * * * * * *
301314 GATAGATATTTTAATGTAATAGATAGCCCCTATTTTTTTTATCATTTATATTATTAACAACCTT-
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
301378 -AAAAAAC
66 AAAAAAAC
** * * * *
301385 GGTAAATATTTTAATGTAATAGGTA--GCCTATTTTATTTTATCATTTACATTATTAGCAATCTT
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAACAACCTT
* *
301448 TAAACAAAC
65 CAAAAAAAC
* * * * *
301457 TGATAGGTATTTTAATGTAATATGT-GTCACCTATTTTTTTTACCGTTTATATTATTAACAATCT
1 -GGTAGGTATTTTAATGTAATAGGTAG-CGCCTATTTTTTTTACCGTTTACATTATTAACAACCT
301521 TC
64 TC
301523 CTAAAAATCA
Statistics
Matches: 952, Mismatches: 113, Indels: 45
0.86 0.10 0.04
Matches are distributed among these distances:
69 8 0.01
70 54 0.06
71 85 0.09
72 109 0.11
73 322 0.34
74 218 0.23
75 125 0.13
76 31 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (73 bp):
GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
AAAAAAAC
Found at i:300619 original size:147 final size:147
Alignment explanation
Indices: 300361--301531 Score: 1482
Period size: 147 Copynumber: 8.0 Consensus size: 147
300351 CAACATATCT
* * * **
300361 GGTAAGTACTTTAATGTAATAGGCAGCGTCTATTATTTTTTACCGTTTACATTATTAGA-AACCT
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATT-TTTTTTACCGTTTACATTATTA-ACAACCT
* * *
300425 TCAAAAAAACCGGTAGGTATTTTAATATAATAAGTAGCGCATA-TTTTTTTACCGTTTACATTAT
64 T-AAAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTAT
**
300489 TAACAGTCTTCAAAAAAATC
128 TAACAACCTTCAAAAAAATC
* *
300509 AGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAATAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTT-
* * * *
300574 AAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGTGCC--TTTTTTTTACTGTTTACATTATTA
65 AAAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
*
300637 ACAACCTTCAAAAAAAACC
130 ACAACCTTC-AAAAAAATC
* * *
300656 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAACATTTACATTATTAACAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTTA
* *
300721 AAAAAACCGATAGGTATTTTAATGAAATAAGTAGCGCCTA-TTTTTTTACCATTTACATTATTAA
66 AAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAA
*
300785 CAACCTTCAAAAAAATT
131 CAACCTTCAAAAAAATC
* * *
300802 GGTAGGTATTTTAATGTAATAGATAGCATCTATTTTTTTTACCGTTTATATTATTAACAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTTA
* *
300867 AAAAAACTGGTAGGTATTTTAATGTAAT-AGATAGCGCCTATTTTTTTTACCGTTTACATTATTA
66 AAAAAACCGATAGGTATTTTAATGTAATAAG-TAGCGCCTATTTTTTTTACCGTTTACATTATTA
*
300931 ACAATCTT--AAAAAA-C
130 ACAACCTTCAAAAAAATC
*
300946 GGTAGGTATTTTAATGTAATAGGTAG-AGCCTA-TTTTTTTACCGTTTATATTATTAACAACCTT
1 GGTAGGTATTTTAATGTAATAGGTAGCA-CCTATTTTTTTTACCGTTTACATTATTAACAACCTT
* ** *
301009 -AAAAAACCGATAGGTATTTTAATGTAATAAGCAGCGTTTATTTTTTTTACTGTTTACATTATTA
65 AAAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
301073 ACAACCTTCAAAAAAAATC
130 ACAACCTTC-AAAAAAATC
* * * *
301092 TGTAGGTATTTTAATGTAATAGATAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTT
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTA-TTTTTTTTACCGTTTACATTATTAACAACCTT
* * * * *
301157 CAAAAAAATCGGTAGGTATTTTAATGTAATATGTAACGCCTATTGTTTTTACCGTTTACATTATT
65 -AAAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATT
301222 AACAACCTTC-AAAAAATC
129 AACAACCTTCAAAAAAATC
* * *
301240 GATAGGTATTTTAATATAATAGGTAGCACCTATTTTTTTTACCGTTTAAATTATTAACAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTT-
* * * * *
301305 AAAAAAACCGATAGATATTTTAATGTAAT-AGATAGCCCCTATTTTTTTTATCATTTATATTATT
65 AAAAAAACCGATAGGTATTTTAATGTAATAAG-TAGCGCCTATTTTTTTTACCGTTTACATTATT
301369 AACAACCTT--AAAAAA-C
129 AACAACCTTCAAAAAAATC
** * * * *
301385 GGTAAATATTTTAATGTAATAGGTAG--CCTATTTTATTTTATCATTTACATTATTAGCAATCTT
1 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTT-TTTTACCGTTTACATTATTAACAA-CCT
* * * * *
301448 TAAACAAACTGATAGGTATTTTAATGTAATATGT-GTCACCTATTTTTTTTACCGTTTATATTAT
64 TAAAAAAACCGATAGGTATTTTAATGTAATAAGTAG-CGCCTATTTTTTTTACCGTTTACATTAT
* **
301512 TAACAATCTTCCTAAAAATC
128 TAACAACCTTCAAAAAAATC
301532 AATATATAGT
Statistics
Matches: 898, Mismatches: 99, Indels: 53
0.86 0.09 0.05
Matches are distributed among these distances:
142 62 0.07
143 43 0.05
144 109 0.12
145 41 0.05
146 206 0.23
147 281 0.31
148 92 0.10
150 64 0.07
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (147 bp):
GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAACAACCTTA
AAAAAACCGATAGGTATTTTAATGTAATAAGTAGCGCCTATTTTTTTTACCGTTTACATTATTAA
CAACCTTCAAAAAAATC
Found at i:307563 original size:24 final size:24
Alignment explanation
Indices: 307536--307610 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
307526 TATATCAAAA
*
307536 ATCAAAACACAATTCAGGTCAAGT
1 ATCAAAACACAATCCAGGTCAAGT
* * * *
307560 ATCAGATCAGAATCCAGGTCATGT
1 ATCAAAACACAATCCAGGTCAAGT
* * * *
307584 ATCATATCAGAATCCATGTC-AGT
1 ATCAAAACACAATCCAGGTCAAGT
307607 ATCA
1 ATCA
307611 GATTAGAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 6 0.14
24 37 0.86
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAACACAATCCAGGTCAAGT
Found at i:307642 original size:24 final size:23
Alignment explanation
Indices: 307546--307647 Score: 78
Period size: 24 Copynumber: 4.3 Consensus size: 23
307536 ATCAAAACAC
*
307546 AATTCAGGTCAAGTATCAGATCAG
1 AATTCAAGTCAA-TATCAGATCAG
* * * *
307570 AATCCAGGTCATGTATCATATCAG
1 AATTCAAGTCA-ATATCAGATCAG
* * * *
307594 AATCCATGTCAGTATCAGATTAG
1 AATTCAAGTCAATATCAGATCAG
* *
307617 AATTCAAGTCATATATCATAACAG
1 AATTCAAGTCA-ATATCAGATCAG
307641 AATTCAA
1 AATTCAA
307648 ATCGGAAATC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 19 0.30
24 45 0.70
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (23 bp):
AATTCAAGTCAATATCAGATCAG
Found at i:312571 original size:17 final size:18
Alignment explanation
Indices: 312549--312586 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
312539 ACGTTGTATG
312549 ATTAAAAAT-GTTTAGAT
1 ATTAAAAATAGTTTAGAT
*
312566 ATTAAATATCAGTTTAGAT
1 ATTAAAAAT-AGTTTAGAT
312585 AT
1 AT
312587 AACACGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (18 bp):
ATTAAAAATAGTTTAGAT
Found at i:312900 original size:30 final size:31
Alignment explanation
Indices: 312821--312901 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 31
312811 CTAAATTATC
* * * *
312821 AGTTTTGTTCCATTTTAGTACTTAAACTTTT
1 AGTTTTTTTTCATTTTAATACTTAAACGTTT
* **
312852 A-ATTTTTTTCATAATAATACTTAAA-GTTT
1 AGTTTTTTTTCATTTTAATACTTAAACGTTT
312881 AGTTTTTTTTCATTTTAATAC
1 AGTTTTTTTTCATTTTAATAC
312902 CCCATTCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 4 0.10
30 34 0.87
31 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (31 bp):
AGTTTTTTTTCATTTTAATACTTAAACGTTT
Found at i:322485 original size:18 final size:19
Alignment explanation
Indices: 322452--322498 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
322442 TTAGTATTTT
322452 TATTTTAAAAATTATAATA
1 TATTTTAAAAATTATAATA
322471 TATTTTAAAAA-TATAATA
1 TATTTTAAAAATTATAATA
*
322489 CATTTTAAAA
1 TATTTTAAAA
322499 TTTTCTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTTAAAAATTATAATA
Found at i:322735 original size:21 final size:21
Alignment explanation
Indices: 322685--322735 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
322675 TATCATCATC
*
322685 CATAGTAGATTATCATGTCAA
1 CATAGTAGATTATCACGTCAA
*
322706 TATCA-TAGATTATCACGT-AA
1 CAT-AGTAGATTATCACGTCAA
322726 GCATAGTAGA
1 -CATAGTAGA
322736 CCGTCACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (21 bp):
CATAGTAGATTATCACGTCAA
Found at i:323399 original size:5 final size:5
Alignment explanation
Indices: 323391--323415 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
323381 AAATAAAGTC
323391 GAATT GAATT GAATT GAATT GAATT
1 GAATT GAATT GAATT GAATT GAATT
323416 TTCAAGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GAATT
Found at i:324196 original size:35 final size:36
Alignment explanation
Indices: 324112--324208 Score: 126
Period size: 35 Copynumber: 2.7 Consensus size: 36
324102 AATGGATTAT
* * *
324112 GAATTTGGGGTTGAGCATGTAATTGAAGTATTTTTG
1 GAATTTTGGGTTTAGAATGTAATTGAAGTATTTTTG
*
324148 GAA-TTTGAAGTTTAGAATGTAATTGAAGTA-TTTTG
1 GAATTTTG-GGTTTAGAATGTAATTGAAGTATTTTTG
*
324183 GAATTTTGGGTTTATAATGTAATTGA
1 GAATTTTGGGTTTAGAATGTAATTGA
324209 TGAAGGTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 27 0.51
36 26 0.49
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.43
Consensus pattern (36 bp):
GAATTTTGGGTTTAGAATGTAATTGAAGTATTTTTG
Found at i:325508 original size:37 final size:35
Alignment explanation
Indices: 325483--325660 Score: 122
Period size: 34 Copynumber: 5.1 Consensus size: 35
325473 ACAATACGTA
325483 AGTTTT-AAAGCATTTTGAAAATTATATAATATAT
1 AGTTTTGAAAGCATTTTGAAAATTATATAATATAT
*
325517 AGTTTTGAAATCATTTTG-AAA--ATATAATATAT
1 AGTTTTGAAAGCATTTTGAAAATTATATAATATAT
** *
325549 AGTTTAAAAAAAACATTTTGAAAAACTTATATAATAT-T
1 AGTTT--TGAAAGCATTTTG-AAAA-TTATATAATATAT
** * * *
325587 --TTTAAAAATCATTTTTGAAAACTATATGATATAT
1 AGTTTTGAAAGCA-TTTTGAAAATTATATAATATAT
* **
325621 AGTTTTGAAAACATGTTTTTTAAA--ATATAATATAT
1 AGTTTTGAAAGCA--TTTTGAAAATTATATAATATAT
325656 AGTTT
1 AGTTT
325661 AATTTTTTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
32 16 0.14
33 9 0.08
34 31 0.26
35 30 0.26
36 14 0.12
37 7 0.06
38 1 0.01
39 9 0.08
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
AGTTTTGAAAGCATTTTGAAAATTATATAATATAT
Found at i:325549 original size:34 final size:33
Alignment explanation
Indices: 325401--325660 Score: 145
Period size: 35 Copynumber: 7.3 Consensus size: 33
325391 TCCCATTTTT
* *
325401 TATATAG-TTTACAAACATTTTAAAAATATTTATA
1 TATATAGTTTTAAAAACATTTTGAAAATA--TATA
* *
325435 TTATATAGTTTTTTAAAAACGTTTTTGAAAGCTTATATA
1 -TATATAG--TTTTAAAAAC-ATTTTGAAA--ATATATA
* *
325474 CAATACGTAAGTTTT-AAAGCATTTTGAAAATTATATAA
1 -TATA--T-AGTTTTAAAAACATTTTGAAAA-TATAT-A
* *
325512 TATATAGTTTTGAAATCATTTTGAAAATATA-A
1 TATATAGTTTTAAAAACATTTTGAAAATATATA
*
325544 TATATAGTTTAAAAAAAACATTTTGAAAA-ACT-TA
1 TATATAGTTT--TAAAAACATTTTGAAAATA-TATA
*
325578 TATAATATTTTTAAAAATCATTTTTGAAAACTATATGA
1 TAT-ATAGTTTTAAAAA-CA-TTTTGAAAA-TATAT-A
* *
325616 TATATAGTTTTGAAAACATGTTTTTTAAAATATA-A
1 TATATAGTTTTAAAAACA---TTTTGAAAATATATA
325651 TATATAGTTT
1 TATATAGTTT
325661 AATTTTTTTT
Statistics
Matches: 181, Mismatches: 19, Indels: 50
0.72 0.08 0.20
Matches are distributed among these distances:
32 11 0.06
33 6 0.03
34 31 0.17
35 48 0.27
36 3 0.02
37 25 0.14
38 30 0.17
39 18 0.10
40 4 0.02
41 3 0.02
42 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (33 bp):
TATATAGTTTTAAAAACATTTTGAAAATATATA
Found at i:326528 original size:22 final size:22
Alignment explanation
Indices: 326503--326546 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
326493 CTTTATTTCA
*
326503 TTTTTATTTAATATTTTTTTTAT
1 TTTTTATAT-ATATTTTTTTTAT
*
326526 TTTTTATATCTATTTTTTTTA
1 TTTTTATATATATTTTTTTTA
326547 AAAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTATATATATTTTTTTTAT
Found at i:334172 original size:5 final size:5
Alignment explanation
Indices: 334159--334294 Score: 51
Period size: 5 Copynumber: 28.0 Consensus size: 5
334149 TTTAACATTT
* *
334159 TTTTA TTTT- GTTT- TTTTA TTATA TTTTA TTATT- TTTTA GTTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA -TTTTA TTTTA
* ** * * *
334207 CTCAA TTTTA -TTTA -TCTA TTTTA -TTTA TTTT- TTTTA TTATCA TTATA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA
*
334254 -TTAA TATTTA TTATTA TTTT- TTTTCA -TTTA TTTTTA TTTTA
1 TTTTA T-TTTA TT-TTA TTTTA TTTT-A TTTTA -TTTTA TTTTA
334295 CAATCTAACA
Statistics
Matches: 97, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
4 34 0.35
5 40 0.41
6 23 0.24
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:334174 original size:13 final size:13
Alignment explanation
Indices: 334155--334193 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
334145 TCATTTTAAC
334155 ATTTTTTTATTTT
1 ATTTTTTTATTTT
* *
334168 GTTTTTTTATTAT
1 ATTTTTTTATTTT
*
334181 ATTTTATTATTTT
1 ATTTTTTTATTTT
334194 TTAGTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:334227 original size:13 final size:13
Alignment explanation
Indices: 334211--334244 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
334201 TTTTTACTCA
334211 ATTTTATTTATCT
1 ATTTTATTTATCT
*
334224 ATTTTATTTATTT
1 ATTTTATTTATCT
*
334237 TTTTTATT
1 ATTTTATT
334245 ATCATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATTTATCT
Found at i:336066 original size:7 final size:7
Alignment explanation
Indices: 336031--336062 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
336021 TTTCATGCAT
336031 TTTTACA
1 TTTTACA
336038 TTTTACA
1 TTTTACA
336045 TTTTACA
1 TTTTACA
*
336052 TTTTGCA
1 TTTTACA
336059 TTTT
1 TTTT
336063 GCATATACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.62
Consensus pattern (7 bp):
TTTTACA
Found at i:337285 original size:6 final size:6
Alignment explanation
Indices: 337271--337344 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
337261 AGATTTAATC
* *
337271 AAAACA AAAAGA AAAAGA AAAA-A GAAAAGA AGGAA-A AAAAGAA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA A-AAAGA AAAAG-A AAAAGA
* *
337320 AAGAACA AAAATCA AAAAGA AAAAG
1 AA-AAGA AAAA-GA AAAAGA AAAAG
337345 GAACAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
5 3 0.05
6 33 0.59
7 20 0.36
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:337292 original size:7 final size:7
Alignment explanation
Indices: 337276--337343 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
337266 TAATCAAAAC
337276 AAAAAG-
1 AAAAAGA
337282 AAAAAGA
1 AAAAAGA
337289 AAAAAGA
1 AAAAAGA
337296 AAAGAAGGAA
1 AAA-AA-G-A
337306 AAAAAGA
1 AAAAAGA
337313 AAAAAGA
1 AAAAAGA
* *
337320 AAGAA-C
1 AAAAAGA
**
337326 AAAAATC
1 AAAAAGA
337333 AAAAAGA
1 AAAAAGA
337340 AAAA
1 AAAA
337344 GGAACAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
6 10 0.19
7 32 0.62
8 3 0.06
9 3 0.06
10 4 0.08
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:337330 original size:23 final size:24
Alignment explanation
Indices: 337282--337330 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
337272 AAACAAAAAG
**
337282 AAAAAGAAAAAAGAAAAGAAGGAA
1 AAAAAGAAAAAAGAAAAGAACAAA
337306 AAAAAGAAAAAAG-AAAGAACAAA
1 AAAAAGAAAAAAGAAAAGAACAAA
337329 AA
1 AA
337331 TCAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAAGAAAAGAACAAA
Found at i:337348 original size:23 final size:22
Alignment explanation
Indices: 337289--337353 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
337279 AAGAAAAAGA
*
337289 AAAAAGAAAAGAAGGAA-AAAAAG
1 AAAAAG-AAA-AAGGAACAAAAAC
*
337312 AAAAA-AGAAA-GAACAAAAATC
1 AAAAAGAAAAAGGAACAAAAA-C
337333 AAAAAGAAAAAGGAACAAAAA
1 AAAAAGAAAAAGGAACAAAAA
337354 AGCACATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 7 0.20
21 7 0.20
22 4 0.11
23 14 0.40
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAGGAACAAAAAC
Found at i:337985 original size:22 final size:22
Alignment explanation
Indices: 337954--338002 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
337944 CCCCATCAAT
* *
337954 CCTTTGAGCATCAAATACTAAA
1 CCTTTAAGCATCAAATACCAAA
*
337976 CCTTTAAGCATCAAATGCCAAA
1 CCTTTAAGCATCAAATACCAAA
337998 CCTTT
1 CCTTT
338003 GACCAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.29
Consensus pattern (22 bp):
CCTTTAAGCATCAAATACCAAA
Found at i:338439 original size:18 final size:18
Alignment explanation
Indices: 338416--338451 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
338406 TCAACATCAA
* *
338416 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
338434 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
338452 GGATTCAGCA
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:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:340142 original size:106 final size:106
Alignment explanation
Indices: 338969--340130 Score: 1955
Period size: 106 Copynumber: 11.0 Consensus size: 106
338959 GTGCCACTAG
* * *
338969 AGACAACACAAGTTCAACTTCACAACGAAGGGATCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
339034 CATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
339075 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATAACTGCTCAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AAACAACTTCTCAATT
*
339140 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
339182 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
339247 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
339288 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
339353 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
339394 AGACGACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTCGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
339459 CAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
339500 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
339565 TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
339606 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
339671 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
339712 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
339777 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
339818 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
339883 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
339924 AGACAACGTAAGTTTAACTTCATGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
339989 CAGAGCCAAGTTCAACTTCACAACGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * ** *
340030 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
340095 CAGAGCCAATTTCAACTTCACGACGAAGGATGTTGG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
340131 CCTTGAAACA
Statistics
Matches: 1003, Mismatches: 52, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
106 900 0.90
107 103 0.10
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:341646 original size:13 final size:13
Alignment explanation
Indices: 341627--341665 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
341617 TCATTTTAAC
341627 ATTTTTTTATTTT
1 ATTTTTTTATTTT
* *
341640 GTTTTTTTATTAT
1 ATTTTTTTATTTT
341653 ATTTTTTTATTTT
1 ATTTTTTTATTTT
341666 TTAGTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:341703 original size:13 final size:12
Alignment explanation
Indices: 341644--341764 Score: 52
Period size: 13 Copynumber: 9.4 Consensus size: 12
341634 TATTTTGTTT
*
341644 TTTTATTATATTT
1 TTTTATT-TATTA
*
341657 TTTTATTTTTTA
1 TTTTATTTATTA
* *
341669 GTTTTTTTTACTCAA
1 -TTTTATTTA-T-TA
*
341684 ATTTATTTATCTA
1 TTTTATTTAT-TA
*
341697 TTTTATTTATTT
1 TTTTATTTATTA
341709 TTTTATTATCATTA
1 TTTTATT-T-ATTA
341723 TATTAATATTTATTA
1 T-TT--TATTTATTA
341738 TTATT-TTT-TTCA
1 TT-TTATTTATT-A
341750 -TTTATTT-TTA
1 TTTTATTTATTA
341760 TTTTA
1 TTTTA
341765 CAATCTAACA
Statistics
Matches: 85, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.04
11 12 0.14
12 15 0.18
13 28 0.33
14 13 0.15
15 9 0.11
16 1 0.01
17 4 0.05
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:347012 original size:149 final size:148
Alignment explanation
Indices: 346736--347689 Score: 950
Period size: 149 Copynumber: 6.6 Consensus size: 148
346726 TAAATCATTT
*
346736 TATTTCACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACT
1 TATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * *
346800 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGA
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAGTGCTCGA
* *
346865 CCTGATATTAAAGCGCATTC
130 CGTGATATTAAAGCACA-TC
* * * *
346885 TATTTCACCCGACCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCATGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * *
346950 CCCTCTAGAAGCGCTCGACATGAACTCTGTCTACCCTGCTTACCCTACACGTTG-AGATGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAG-TGCTCGA
*
347014 CGTGA-A-T------C-TGG
130 CGTGATATTAAAGCACAT-C
* * * *
347025 GA---CACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * * *
347087 CCCTTTGGAAGCGCTCGGCATGCACTCTGTCT-CCTCTGCCTACTCTAAACGTTGAAGCGCTCGG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACC-CTGCCTACCCTACACGTTGAAGTGCTCGA
* *
347151 CGTGACATTAAGGCACATC
130 CGTGATATTAAAGCACATC
347170 TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * *
347235 CCCCTCTGGAAGCGCTCGGCAT-ATACTCTGTCTCCCCTGTCTACTCTTA-ACGTTGAAGTGCTC
65 CCCCTCTGGAAGCGCTCGGCATGA-ACTCTGTCTACCCTGCCTAC-CCTACACGTTGAAGTGCTC
* *
347298 GACGTGATGTTATAGCACATC
128 GACGTGATATTAAAGCACATC
*
347319 TTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
1 -TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACT
* * *
347384 CCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCT-CAACGTTGAAGTGCTCG
65 CCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTAC-ACGTTGAAGTGCTCG
347448 ACGTGATATT-------A--
129 ACGTGATATTAAAGCACATC
* * * * * *
347459 TA--ACACCCTGCCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCATGCCTACTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
* * * * * * *
347522 CCCACTGGAAGCGCTCGGCATGAACTTTGTC-CCCCTTCCAACTCTTA-ACAG-TGAAGCGCTCG
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTAC-CCTACAC-GTTGAAGTGCTCG
* *
347584 GCGTGA-A--AATAG--GA--
129 ACGTGATATTAA-AGCACATC
* * * * * * * *
347598 -A--T-ACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTATTC
1 TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
*
347659 CCCACTGGAAGCGCTCGGCATGAACTCTGTC
66 CCCTCTGGAAGCGCTCGGCATGAACTCTGTC
347690 CCCCTTCTAA
Statistics
Matches: 695, Mismatches: 77, Indels: 78
0.82 0.09 0.09
Matches are distributed among these distances:
135 1 0.00
136 28 0.04
137 275 0.40
138 4 0.01
139 4 0.01
140 1 0.00
141 1 0.00
142 1 0.00
145 1 0.00
146 2 0.00
147 1 0.00
148 3 0.00
149 369 0.53
150 4 0.01
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (148 bp):
TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTC
CCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTGAAGTGCTCGAC
GTGATATTAAAGCACATC
Found at i:347080 original size:46 final size:45
Alignment explanation
Indices: 346889--347087 Score: 115
Period size: 46 Copynumber: 4.4 Consensus size: 45
346879 GCATTCTATT
* * * *
346889 TCACCC-GACCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGG
1 TCACCCTG-CCTACTCCACACGTTAGAGCGCTCGACGTAA-ATCAGG
* * * * *
346935 TCATCATGCCTACTCC-C-C-TCTAGAAGCGCTCGACATGAACTC-TG
1 TCACCCTGCCTACTCCACACGT-TAG-AGCGCTCGACGT-AAATCAGG
* * * * *
346979 TCTACCCTGCTTAC-CCTACACGTT-GAGATGCTCGGCGTGAATCTGGG
1 TC-ACCCTGCCTACTCC-ACACGTTAGAG-CGCTCGACGTAAATC-AGG
*
347026 ACACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGG
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAA-ATCAGG
*
347072 TCATCCTGCCTACTCC
1 TCACCCTGCCTACTCC
347088 CCTTTGGAAG
Statistics
Matches: 112, Mismatches: 26, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
43 1 0.01
44 9 0.08
45 24 0.21
46 64 0.57
47 13 0.12
48 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (45 bp):
TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAATCAGG
Found at i:347139 original size:137 final size:137
Alignment explanation
Indices: 346897--347694 Score: 834
Period size: 137 Copynumber: 5.7 Consensus size: 137
346887 TTTCACCCGA
* * * *
346897 CCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCATGCCTACTCCCCTCTAGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * *
346962 GCTCGACATGAACTCTGTCTACCCTGCTTACCCTACACGTTG-AGATGCTCGGCGTGA-ATCTGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAG-TGCTCGGCGTGACAT-TGG
*
347025 GACACCCTG
129 AACACCCTG
* * *
347034 CCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTTTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * *
347099 GCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATT--GG
*
347164 CACATCTTATTTCACCCGG
129 ---A----A---CACCCTG
347183 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * *
347248 GCTCGGCAT-ATACTCTGTCTCCCCTGTCTACTCTTAACGTTGAAGTGCTCGACGTGATGTTATA
66 GCTCGGCATGA-ACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCT---CG-G-CG---T-
*** *
347312 GCACATCTTGTTTCACCCGG
121 G-ACA--TTGGAACACCCTG
347332 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * **
347397 GCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGACGTGATATTATAA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
347462 CACCCTG
131 CACCCTG
* * * * *
347469 CCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCATGCCTACTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * * * *
347534 GCTCGGCATGAACTTTGTC-CCCCTTCCAACTCTTAACAG-TGAAGCGCTCGGCGTGAAAATAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAAC-GTTGAAGTGCTCGGCGTG-ACATTGG
*
347597 AATACCCTG
129 AACACCCTG
* * * * * * * *
347606 CCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTATTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
347671 GCTCGGCATGAACTCTGTC-CCCCT
66 GCTCGGCATGAACTCTGTCTCCCCT
347695 TCTAACTTTT
Statistics
Matches: 567, Mismatches: 64, Indels: 60
0.82 0.09 0.09
Matches are distributed among these distances:
136 29 0.05
137 284 0.50
138 4 0.01
139 4 0.01
140 1 0.00
141 1 0.00
144 1 0.00
146 3 0.01
149 228 0.40
152 2 0.00
153 1 0.00
154 1 0.00
157 1 0.00
158 1 0.00
159 4 0.01
161 2 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (137 bp):
CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGACATTGGAA
CACCCTG
Found at i:347265 original size:286 final size:282
Alignment explanation
Indices: 346741--347720 Score: 1085
Period size: 286 Copynumber: 3.4 Consensus size: 282
346731 CATTTTATTT
346741 CACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
1 CACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * *
346805 CTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGACCTGA
65 CTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGACGTGA
* * *
346870 TATTAAAGCGCATTCTATTTCACCCGACCTACTCTACACGTTAGGGCGCTCGGCGTAAGACCAGG
130 -ATT-AAGC-CATT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGG
* * * *
346935 TCATCATGCCTACTCCCCTCTAGAAGCGCTCGACATGAACTCTGTCTACCCTGCTTAC-CCTACA
191 TCATCATGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCTTACTCTTA-A
*
346999 CGTTG-AGATGCTCGGCGTGAATCTGGGA
255 CGTTGAAG-TGCTCGGCGTGAATCTGGAA
* * *
347027 CACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTT
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * *
347092 TGGAAGCGCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAC
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGACGTGA-
347157 ATTAAGGCACATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
130 ATTAA-GC-CAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
*
347222 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCAT-ATACTCTGTCTCCCCTG-TCTACTCTTAA
192 CATCATGCCTACTCCCCTCTGGAAGCGCTCGGCATGA-ACTCTGTCTCCCCTGCT-TACTCTTAA
* ***
347285 CGTTGAAGTGCTCGACGTGATGTTATAGCACATCTTGTTT
255 CGTTGAAGTGCT---CG-G-CG---T-G-A-ATC-TGGAA
*
347325 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTC
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * *
347390 TGGAAGCGCTCGGCATGTACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGTGCTCGACGTG-A
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGACGTGAA
** * * * *
347454 -T-----A-TTATAACACCCTGCCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATC
131 TTAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATC
* * * **
347512 ATGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTTTGTC-CCCCTTCCAACTCTTAACAG-TG
196 ATGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCTTACTCTTAAC-GTTG
* **
347575 AAGCGCTCGGCGTGAAAATAGGAA
260 AAGTGCTCGGCGTGAATCT-GGAA
* * * * * * * * *
347599 TACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTATTCCCCAC
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * * *
347664 TGGAAGCGCTCGGCATGAACTCTGTC-CCCCT-TCTAACTTTTAATGTTGAAGCGCTCG
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCT-ACTCTAAACGTTGAAGCGCTCG
347721 GCGAAATTCC
Statistics
Matches: 600, Mismatches: 70, Indels: 61
0.82 0.10 0.08
Matches are distributed among these distances:
272 2 0.00
273 24 0.04
274 82 0.14
275 1 0.00
276 1 0.00
277 1 0.00
280 1 0.00
281 1 0.00
282 2 0.00
285 26 0.04
286 317 0.53
287 8 0.01
288 1 0.00
289 2 0.00
290 1 0.00
291 1 0.00
294 1 0.00
295 2 0.00
296 2 0.00
297 3 0.00
298 121 0.20
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (282 bp):
CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTAAACGTTGAAGCGCTCGACGTGAA
TTAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATC
ATGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCTTACTCTTAACGTTGA
AGTGCTCGGCGTGAATCTGGAA
Found at i:348733 original size:52 final size:52
Alignment explanation
Indices: 348639--348755 Score: 146
Period size: 52 Copynumber: 2.2 Consensus size: 52
348629 ATGATAAATA
* * * * *
348639 AATTTTAGGATGGACATCATCAATAAAATAATTCATAATCGAAG-AAATTTC
1 AATTTCAGGGTGGACACCATCAATAAAATAAATCACAATCGAAGAAAATTTC
* * *
348690 ATATTTCAGGGTGGACACCATCAATAAAATAAATGACATTCGAAGAAAATTTG
1 A-ATTTCAGGGTGGACACCATCAATAAAATAAATCACAATCGAAGAAAATTTC
348743 AATTTCAGGGTGG
1 AATTTCAGGGTGG
348756 GCACGTACCC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 1 0.02
52 48 0.86
53 7 0.12
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (52 bp):
AATTTCAGGGTGGACACCATCAATAAAATAAATCACAATCGAAGAAAATTTC
Found at i:349189 original size:17 final size:18
Alignment explanation
Indices: 349164--349208 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
349154 ACTATTTCAA
*
349164 AATTTAAAAATCAACTTA-
1 AATTTAAAAA-CAAATTAT
349182 AA-TTAAAAACAAATTAT
1 AATTTAAAAACAAATTAT
349199 AATTTAAAAA
1 AATTTAAAAA
349209 GTATCCCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTTAAAAACAAATTAT
Found at i:349205 original size:18 final size:18
Alignment explanation
Indices: 349163--349208 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
349153 AACTATTTCA
*
349163 AAATTTAAAAATCAACTT
1 AAATTTAAAAATCAAATT
349181 AAA-TTAAAAA-CAAATT
1 AAATTTAAAAATCAAATT
349197 ATAATTTAAAAA
1 A-AATTTAAAAA
349209 GTATCCCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 10 0.40
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTTAAAAATCAAATT
Found at i:352391 original size:15 final size:16
Alignment explanation
Indices: 352355--352393 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
352345 AGAGCCTCTA
352355 AATCATTCAACATTTG
1 AATCATTCAACATTTG
* *
352371 AATCATTCAGCGTTT-
1 AATCATTCAACATTTG
352386 AATCATTC
1 AATCATTC
352394 TGAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (16 bp):
AATCATTCAACATTTG
Found at i:354665 original size:10 final size:10
Alignment explanation
Indices: 354650--354691 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
354640 GGACCGGCTG
354650 AAAACCGGAA
1 AAAACCGGAA
*
354660 AAAACC-GAG
1 AAAACCGGAA
*
354669 AAAACCGAAA
1 AAAACCGGAA
*
354679 AAAACGGGAA
1 AAAACCGGAA
354689 AAA
1 AAA
354692 TAACCAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.64, C:0.17, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:355780 original size:20 final size:19
Alignment explanation
Indices: 355755--355797 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
355745 TTAAGTATTT
355755 ATTTATATTTT-TTATTAATA
1 ATTTAT-TTTTATTATTAA-A
*
355775 ATTTATTTTTATTTTTAAA
1 ATTTATTTTTATTATTAAA
355794 ATTT
1 ATTT
355798 TATAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATTTTTATTATTAAA
Found at i:368270 original size:23 final size:21
Alignment explanation
Indices: 368244--368289 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
368234 TTATATTTTC
368244 AATTTTGTAAATAAAAATTATAT
1 AATTTTGTAAA-AAAAA-TATAT
* *
368267 AATTTTTTAAAGAAAATATAT
1 AATTTTGTAAAAAAAATATAT
368288 AA
1 AA
368290 ATATTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
AATTTTGTAAAAAAAATATAT
Found at i:368483 original size:20 final size:20
Alignment explanation
Indices: 368447--368484 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
368437 ATCCTATTAT
**
368447 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
368467 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
368485 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:372022 original size:12 final size:12
Alignment explanation
Indices: 372005--372036 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
371995 GGTTATTAAA
372005 CGGGTATAGGGC
1 CGGGTATAGGGC
*
372017 CGGGTATAGGGT
1 CGGGTATAGGGC
372029 CGGGTATA
1 CGGGTATA
372037 TATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.47, T:0.22
Consensus pattern (12 bp):
CGGGTATAGGGC
Found at i:372040 original size:2 final size:2
Alignment explanation
Indices: 372033--372093 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
372023 TAGGGTCGGG
* * * *
372033 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
372073 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
372094 TAATTTAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:372235 original size:35 final size:35
Alignment explanation
Indices: 372196--372263 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
372186 CCATCCCGTC
*
372196 CCCGTCTCCGTTTAACATAAACGGTTTTTCCCCAT
1 CCCGTCCCCGTTTAACATAAACGGTTTTTCCCCAT
372231 CCCGTCCCCGTTTAACATAAACGGTTTTTCCCC
1 CCCGTCCCCGTTTAACATAAACGGTTTTTCCCC
372264 GTCTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.32
Consensus pattern (35 bp):
CCCGTCCCCGTTTAACATAAACGGTTTTTCCCCAT
Found at i:374515 original size:21 final size:21
Alignment explanation
Indices: 374489--374532 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
374479 AAAAATATTA
*
374489 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
*
374510 AAAAATAATAATTTTTTAAAT
1 AAAAATAATAATATTTTAAAT
374531 AA
1 AA
374533 TTTTTTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:378421 original size:16 final size:16
Alignment explanation
Indices: 378400--378431 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
378390 ACTATTCACA
*
378400 TGAATAGTGAATTTTG
1 TGAATAGTGAAATTTG
378416 TGAATAGTGAAATTTG
1 TGAATAGTGAAATTTG
378432 GTCGGTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (16 bp):
TGAATAGTGAAATTTG
Found at i:378787 original size:12 final size:12
Alignment explanation
Indices: 378770--378798 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
378760 AAAAGACCAC
378770 GGCGGGTCTTAT
1 GGCGGGTCTTAT
378782 GGCGGGTCTTAT
1 GGCGGGTCTTAT
378794 GGCGG
1 GGCGG
378799 CTCTCTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.48, T:0.28
Consensus pattern (12 bp):
GGCGGGTCTTAT
Found at i:383879 original size:29 final size:29
Alignment explanation
Indices: 383821--383883 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
383811 AAAAATGTAG
*
383821 TAAAAATGAATAAAATAAAGAAGGTGAAA
1 TAAAAATGAATAAAATAAAGAAGGTAAAA
** *
383850 TAAAAATGAATGCAATAAAGTAGAG-AAAA
1 TAAAAATGAATAAAATAAAGAAG-GTAAAA
383879 TAAAA
1 TAAAA
383884 CAGATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.17
Consensus pattern (29 bp):
TAAAAATGAATAAAATAAAGAAGGTAAAA
Found at i:384035 original size:16 final size:17
Alignment explanation
Indices: 384014--384055 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
384004 ATACAAAAAT
*
384014 AAAAATAGAAGATA-AA
1 AAAAATAAAAGATATAA
384030 AAAAATAAAAGATATAA
1 AAAAATAAAAGATATAA
*
384047 AATAATAAA
1 AAAAATAAA
384056 TATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAAATAAAAGATATAA
Found at i:384060 original size:16 final size:17
Alignment explanation
Indices: 384041--384102 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
384031 AAAATAAAAG
384041 ATATA-AAATAATAAAT
1 ATATATAAATAATAAAT
384057 ATATATAACAT-AT-AAT
1 ATATATAA-ATAATAAAT
384073 -TATAGT-AATAA-AAAT
1 ATATA-TAAATAATAAAT
384088 ATATATAAATAATAA
1 ATATATAAATAATAA
384103 TGATATATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 18 0.47
17 6 0.16
18 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
ATATATAAATAATAAAT
Found at i:384136 original size:2 final size:2
Alignment explanation
Indices: 384129--384156 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
384119 ATTAAAAGTC
384129 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
384157 ACGATAGAAT
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):
TA
Found at i:385770 original size:110 final size:110
Alignment explanation
Indices: 385637--385843 Score: 333
Period size: 110 Copynumber: 1.9 Consensus size: 110
385627 GCTCTGGAAA
* * *
385637 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAATCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* *
385702 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
66 TCCCTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * *
385747 TTGTTTGTTGACAATCAGTCGCCCATTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAATCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
*
385812 TCCCTCGCTATGAAGTTGAAATTGGCTCTGAA
66 TCCCTCGCTATGAAGTTGAAATTGACTCTGAA
385844 ACTGGGAAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 88 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (110 bp):
TTGTTTGTTGACAATCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
TCCCTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
Found at i:386909 original size:9 final size:9
Alignment explanation
Indices: 386883--386912 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
386873 TTTTTTGTTC
*
386883 TTTTTTCAC
1 TTTTTTCAA
386892 TTTTTTCAA
1 TTTTTTCAA
386901 TTTTTTCAA
1 TTTTTTCAA
386910 TTT
1 TTT
386913 AGGGTGCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTTCAA
Found at i:386970 original size:11 final size:10
Alignment explanation
Indices: 386950--386974 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
386940 AACGTTTTCA
386950 TTTTTGTTTT
1 TTTTTGTTTT
386960 TTTTTGTTTT
1 TTTTTGTTTT
386970 TTTTT
1 TTTTT
386975 ACTTAGGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:399382 original size:29 final size:29
Alignment explanation
Indices: 399324--399386 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
399314 AAAAATGTAG
* *
399324 TAAAAATGAATTAAATAAAGAAGGTGAAA
1 TAAAAATGAATGAAATAAAGAAGGTAAAA
* *
399353 TAAAAATGAATGCAATAAAGTAGAG-AAAA
1 TAAAAATGAATGAAATAAAGAAG-GTAAAA
399382 TAAAA
1 TAAAA
399387 CAGATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.16, T:0.19
Consensus pattern (29 bp):
TAAAAATGAATGAAATAAAGAAGGTAAAA
Found at i:399540 original size:2 final size:2
Alignment explanation
Indices: 399533--399567 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
399523 AATGAAGATA
*
399533 AT AT AT AT AT AT AT AT AT CT 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 A
399568 AGAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:400771 original size:3 final size:3
Alignment explanation
Indices: 400763--400806 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
400753 GGCAGCAAAA
* * * *
400763 AAT AAT AAT GAT AAT GAT GAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
400807 ATACAATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:402659 original size:19 final size:19
Alignment explanation
Indices: 402635--402705 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
402625 GAATGCAATT
*
402635 AGTGCATCGATGCATAAGG
1 AGTGCATCAATGCATAAGG
402654 AGTGCATCAATGCATAAGG
1 AGTGCATCAATGCATAAGG
*
402673 AGTGCATCAATGCATAAGT
1 AGTGCATCAATGCATAAGG
*
402692 AGTGCATCGATGCA
1 AGTGCATCAATGCA
402706 CCTGCTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.23
Consensus pattern (19 bp):
AGTGCATCAATGCATAAGG
Found at i:421411 original size:20 final size:20
Alignment explanation
Indices: 421382--421434 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
421372 GCAGCCTTCG
* **
421382 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAAAAGGA
421402 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAAAAGGA
* *
421422 TACATCGTTGCAC
1 TGCATCGATGCAC
421435 TAATTGCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAAAAGGA
Found at i:421563 original size:21 final size:21
Alignment explanation
Indices: 421537--421613 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
421527 CTAGTGCAGG
421537 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
421558 TGCATGGATGCACTGCAAGGA
1 TGCATGGATGCACTGCAGGGA
*
421579 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
421600 TGCATGGATGCACT
1 TGCATGGATGCACT
421614 TTGACACCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:424981 original size:21 final size:21
Alignment explanation
Indices: 424957--425019 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
424947 CTAGCTGTTG
*
424957 CAACCTTCG-TGCATGGATGCA
1 CAACCTT-GATGCATCGATGCA
**
424978 CAA-CAGGATGCATCGATGCA
1 CAACCTTGATGCATCGATGCA
424998 CAACCTTGATGCATCGATGCA
1 CAACCTTGATGCATCGATGCA
425019 C
1 C
425020 TAATTGCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.43
21 19 0.54
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (21 bp):
CAACCTTGATGCATCGATGCA
Found at i:425119 original size:21 final size:21
Alignment explanation
Indices: 425093--425138 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
425083 TGCGTGGATA
425093 CACTGC-AGGGATGCATAGATG
1 CACTGCAAGGG-TGCATAGATG
*
425114 CACTGCAAGGGTGCATGGATG
1 CACTGCAAGGGTGCATAGATG
425135 CACT
1 CACT
425139 TTGACACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.20
Consensus pattern (21 bp):
CACTGCAAGGGTGCATAGATG
Found at i:425239 original size:29 final size:29
Alignment explanation
Indices: 425218--425275 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
425208 AAACTTTGAA
425218 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
425247 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
425276 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:425265 original size:30 final size:30
Alignment explanation
Indices: 425218--425277 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
425208 AAACTTTGAA
425218 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
425247 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
425278 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:428195 original size:28 final size:28
Alignment explanation
Indices: 428164--428224 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
428154 ATCTTTTTAA
428164 ATTTATTTAAAATAAATAATATAAAA-AT
1 ATTTATTTAAAATAAA-AATATAAAATAT
*
428192 ATTTTTTTAAAATAAAAATATAAAATAT
1 ATTTATTTAAAATAAAAATATAAAATAT
428220 ATTTA
1 ATTTA
428225 AATCAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTATTTAAAATAAAAATATAAAATAT
Found at i:445895 original size:35 final size:35
Alignment explanation
Indices: 445856--445928 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
445846 AATACCTTAT
445856 TTTA-GGGTTTAGAATGTAATTAAAGTATTTTAGAA
1 TTTAGGGGTTT-GAATGTAATTAAAGTATTTTAGAA
* * *
445891 TTTAGGGGTTTTAATGTAATTAAAGTGTTTTGGAA
1 TTTAGGGGTTTGAATGTAATTAAAGTATTTTAGAA
445926 TTT
1 TTT
445929 GGAACATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 28 0.82
36 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.47
Consensus pattern (35 bp):
TTTAGGGGTTTGAATGTAATTAAAGTATTTTAGAA
Found at i:447843 original size:19 final size:19
Alignment explanation
Indices: 447819--447864 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
447809 AGAGAAGCGA
447819 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
447838 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
447857 AAAAGGAA
1 AAAAGGAA
447865 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.13
Consensus pattern (19 bp):
AAAAGGAAATTCGAGATCG
Found at i:447878 original size:18 final size:19
Alignment explanation
Indices: 447819--447892 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
447809 AGAGAAGCGA
**
447819 AAAAGGAAATTCGA-GATCG
1 AAAAGGAAATT-GAGGATTT
**
447838 AAAAGGAAATTCGA-GATCG
1 AAAAGGAAATT-GAGGATTT
*
447857 AAAAGGAATTTG-GGATTT
1 AAAAGGAAATTGAGGATTT
*
447875 AAAATGAAATTGAGGATT
1 AAAAGGAAATTGAGGATT
447893 ATGTTGCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 14 0.29
19 34 0.71
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (19 bp):
AAAAGGAAATTGAGGATTT
Found at i:460572 original size:3 final size:3
Alignment explanation
Indices: 460564--460620 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
460554 TCATTTCGTT
** ** **
460564 TTA TTA TTA TTA TTA TTA AAA TTA AAA TTA AAA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
460610 TTA TTA TTA TT
1 TTA TTA TTA TT
460621 TAATAAAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:462350 original size:13 final size:16
Alignment explanation
Indices: 462332--462373 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
462322 CCATTTTCTG
462332 ATATTTTAAA-TA-A-
1 ATATTTTAAATTATAT
462345 ATATTTTAAATTATAT
1 ATATTTTAAATTATAT
462361 ATATTTT-AATTAT
1 ATATTTTAAATTAT
462374 TTTTAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 7 0.27
16 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTTAAATTATAT
Done.