Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 41
Found at i:3442016 original size:17 final size:19
Alignment explanation
Indices: 3441979--3442018 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
3441969 TATTAATAAG
3441979 AAAATATATAAAAACTATA
1 AAAATATATAAAAACTATA
*
3441998 AAAATA-ATAAATA-TATA
1 AAAATATATAAAAACTATA
3442015 AAAA
1 AAAA
3442019 AATTGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATATATAAAAACTATA
Found at i:3442539 original size:16 final size:17
Alignment explanation
Indices: 3442509--3442541 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3442499 AATTTTTAAG
3442509 AAAATATATTAATTTAT
1 AAAATATATTAATTTAT
*
3442526 AAAA-ATATTTATTTAT
1 AAAATATATTAATTTAT
3442542 TTAGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATATTAATTTAT
Found at i:3444031 original size:16 final size:17
Alignment explanation
Indices: 3444001--3444033 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3443991 AATTTTTAAG
3444001 AAAATATATTAATTTAT
1 AAAATATATTAATTTAT
*
3444018 AAAA-ATATTTATTTAT
1 AAAATATATTAATTTAT
3444034 TTAGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATATATTAATTTAT
Found at i:3445705 original size:22 final size:22
Alignment explanation
Indices: 3445676--3445730 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3445666 ATCTACACTC
*
3445676 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
3445698 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3445720 TTCAAAGATGA
1 TTCAAAGATGA
3445731 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3447169 original size:76 final size:76
Alignment explanation
Indices: 3446407--3447152 Score: 1393
Period size: 76 Copynumber: 9.8 Consensus size: 76
3446397 CTATTTCCCA
*
3446407 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3446472 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3446483 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3446548 AGCCTTAGGGT
66 AGCCTTAGGGT
3446559 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3446624 AGCCTTAAGGT
66 AGCCTTAGGGT
*
3446635 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3446700 AGCCTTAGGGT
66 AGCCTTAGGGT
3446711 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
**
3446776 AGCCTTAAAGT
66 AGCCTTAGGGT
3446787 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3446852 AGCCTTAAGGT
66 AGCCTTAGGGT
*
3446863 CATCTGTAAGTCCTTCAGTGCATTATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3446928 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3446939 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3447004 AGCCTTAAGGT
66 AGCCTTAGGGT
3447015 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3447080 AGCCTTATGGT
66 AGCCTTAGGGT
3447091 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT
3447153 TAAACCCTCG
Statistics
Matches: 655, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 655 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3447325 original size:3 final size:3
Alignment explanation
Indices: 3447319--3447363 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3447309 ATTTTTTTTT
* *
3447319 TTA TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3447364 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3448831 original size:16 final size:18
Alignment explanation
Indices: 3448810--3448842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3448800 ATATTTCTAA
3448810 ATAAA-TAA-ATATTTTT
1 ATAAATTAATATATTTTT
3448826 ATAAATTAATATATTTT
1 ATAAATTAATATATTTT
3448843 CTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAAATTAATATATTTTT
Found at i:3455239 original size:13 final size:13
Alignment explanation
Indices: 3455221--3455249 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3455211 AAAGCAAATG
3455221 AGATTGTTCTATT
1 AGATTGTTCTATT
3455234 AGATTGTTCTATT
1 AGATTGTTCTATT
3455247 AGA
1 AGA
3455250 AAATACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (13 bp):
AGATTGTTCTATT
Found at i:3459535 original size:17 final size:15
Alignment explanation
Indices: 3459488--3459539 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 15
3459478 TGAGTAATTT
3459488 TAAATAAAA--TAAA
1 TAAATAAAATTTAAA
3459501 TAAATAAAATTT-AA
1 TAAATAAAATTTAAA
3459515 -AAATAAAATATGTAAA
1 TAAATAAAAT-T-TAAA
3459531 TAAATAAAA
1 TAAATAAAA
3459540 GGGTAAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 18 0.55
14 3 0.09
15 2 0.06
16 2 0.06
17 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
TAAATAAAATTTAAA
Found at i:3460565 original size:13 final size:12
Alignment explanation
Indices: 3460520--3460567 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3460510 GAGCACTGAC
*
3460520 TGGGTTTGAGAT
1 TGGGTTTGAGGT
*
3460532 TGGGTTTGGGGT
1 TGGGTTTGAGGT
*
3460544 TAGGATTTGAGGT
1 T-GGGTTTGAGGT
3460557 TGGCGTTTGAG
1 TGG-GTTTGAG
3460568 ATTATGGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.12, C:0.02, G:0.46, T:0.40
Consensus pattern (12 bp):
TGGGTTTGAGGT
Found at i:3463514 original size:28 final size:29
Alignment explanation
Indices: 3463464--3463518 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
3463454 GAAGGAAAAA
3463464 TTATGAATATGATGAACATGTTTTTACCC
1 TTATGAATATGATGAACATGTTTTTACCC
3463493 TTATGAATATG-TGAACATGTTTTTAC
1 TTATGAATATGATGAACATGTTTTTAC
3463519 AGAAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (29 bp):
TTATGAATATGATGAACATGTTTTTACCC
Found at i:3465872 original size:20 final size:19
Alignment explanation
Indices: 3465827--3465872 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
3465817 AGTTTACCAA
3465827 AACAACATAAATTGTTCAC
1 AACAACATAAATTGTTCAC
3465846 AAGCAACATAAATTGTTCACC
1 AA-CAACATAAATTGTTCA-C
3465867 AACAAC
1 AACAAC
3465873 TAGTTAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (19 bp):
AACAACATAAATTGTTCAC
Found at i:3468287 original size:34 final size:36
Alignment explanation
Indices: 3468246--3468313 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
3468236 TCGTTGTTGA
3468246 TTTTTT-TATCATGTATCTAGAGTTACAAGTAGGAT
1 TTTTTTATATCATGTATCTAGAGTTACAAGTAGGAT
*
3468281 TTTTTTATATCATGTATCTAGAGTTATAAGTAG
1 TTTTTTATATCATGTATCTAGAGTTACAAGTAG
3468314 TCCTCGGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (36 bp):
TTTTTTATATCATGTATCTAGAGTTACAAGTAGGAT
Found at i:3474560 original size:2 final size:2
Alignment explanation
Indices: 3474555--3474603 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3474545 TTAATTATTA
*
3474555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3474597 AT AT AT A
1 AT AT AT A
3474604 ATGATATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3478888 original size:5 final size:5
Alignment explanation
Indices: 3478878--3478958 Score: 162
Period size: 5 Copynumber: 16.2 Consensus size: 5
3478868 AAATAATGAG
3478878 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
3478928 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
3478959 GAGAAAATCG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 76 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:3479192 original size:20 final size:21
Alignment explanation
Indices: 3479167--3479218 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3479157 TTTTCCCAAT
*
3479167 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3479187 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3479208 TCGCAATGCGA
1 TCGCAATGCGA
3479219 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3479232 original size:20 final size:20
Alignment explanation
Indices: 3479207--3479280 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
3479197 AATTGGGAAA
3479207 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
3479227 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3479247 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
3479267 ATCGCAATGCGATA
1 ATCGCAATGCGATA
3479281 ATACAAAATC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3479292 original size:61 final size:61
Alignment explanation
Indices: 3479227--3479361 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
3479217 GATACTGACT
* ** *
3479227 ATCGCAATGCGATACTGACTATCGCAATGCGA-TACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATTACCAACTATCGCAACGCGAT-ATACAAA
* * * * *
3479288 ATCGCAACT-AGATACTGACTTTCGCAACGCGATTTCCAACTATCGCAACGCGATTTACATA
1 ATCGCAA-TGCGATACTGACTATCGCAACGCGATTACCAACTATCGCAACGCGATATACAAA
3479349 ATCGCAATGCGAT
1 ATCGCAATGCGAT
3479362 TTTCAAAGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
60 1 0.02
61 42 0.69
62 18 0.30
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (61 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATTACCAACTATCGCAACGCGATATACAAA
Found at i:3479354 original size:20 final size:20
Alignment explanation
Indices: 3479309--3479363 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
3479299 ATACTGACTT
*
3479309 TCGCAACGCGATTTCCAACTA
1 TCGCAACGCGATTTACAAC-A
3479330 TCGCAACGCGATTTACATA-A
1 TCGCAACGCGATTTACA-ACA
*
3479350 TCGCAATGCGATTT
1 TCGCAACGCGATTT
3479364 TCAAAGCGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 14 0.45
21 16 0.52
22 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTTACAACA
Found at i:3479889 original size:20 final size:20
Alignment explanation
Indices: 3479835--3479893 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3479825 GCGATTCTCT
**
3479835 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
3479855 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
3479875 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
3479894 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3480084 original size:25 final size:24
Alignment explanation
Indices: 3480030--3480084 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3480020 TGTTTATTAT
* *
3480030 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3480054 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3480080 TGTTT
1 TGTTT
3480085 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3480948 original size:18 final size:18
Alignment explanation
Indices: 3480927--3480971 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3480917 TCCACTTCGG
*
3480927 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3480945 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3480963 GAGCCATCA
1 GAGCCATCA
3480972 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3481507 original size:19 final size:20
Alignment explanation
Indices: 3481453--3481519 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3481443 TAGTTTACTT
* *
3481453 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3481473 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3481493 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3481512 TCGCAACG
1 TCGCAACG
3481520 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3481515 original size:39 final size:32
Alignment explanation
Indices: 3481492--3481556 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
3481482 GGAAATGGCT
3481492 ATCGCAATGCGAAATGAAAATCGCAACGAC-AAA
1 ATCGCAATGCGAAATG-AAATCGCAACG-CGAAA
3481525 ATCGCAATGCGAAATGAAATCGCAACGCGAAA
1 ATCGCAATGCGAAATGAAATCGCAACGCGAAA
3481557 CACAAATCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 1 0.03
32 14 0.45
33 16 0.52
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGCGAAA
Found at i:3481604 original size:14 final size:14
Alignment explanation
Indices: 3481585--3481642 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3481575 TTTCATTTCG
3481585 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3481599 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3481615 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3481631 CGTTGCGATTTT
1 CGTTGCGATTTT
3481643 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3481615 original size:32 final size:33
Alignment explanation
Indices: 3481568--3481658 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3481558 ACAAATCGTA
*
3481568 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3481601 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3481633 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3481659 AGCCATTTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:3481693 original size:20 final size:19
Alignment explanation
Indices: 3481631--3481698 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
3481621 GCGATTTTGT
**
3481631 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
3481650 CATTGCGATAGCCATTTCTA
1 CGTTGCGATAGTCATTTC-G
3481670 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
3481690 CGTTGCGAT
1 CGTTGCGAT
3481699 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 21 0.54
21 4 0.10
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:3481797 original size:27 final size:28
Alignment explanation
Indices: 3481733--3481799 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
3481723 AACTATTCTT
* *
3481733 CTTCTGGAATGTTTATATATATGTTGTC
1 CTTCTGGAATGTTTATATATATGCTGTA
**
3481761 CTT-TTAAATGTTTATATA-AGTGCT-TA
1 CTTCTGGAATGTTTATATATA-TGCTGTA
3481787 CTTCTGGAATGTT
1 CTTCTGGAATGTT
3481800 ATCTGAGCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 5 0.16
27 23 0.74
28 3 0.10
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (28 bp):
CTTCTGGAATGTTTATATATATGCTGTA
Found at i:3483586 original size:14 final size:14
Alignment explanation
Indices: 3483567--3483602 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3483557 ATTGTTTAAT
3483567 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3483581 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3483595 TGATTTGT
1 TGATTTGT
3483603 TATATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3483710 original size:20 final size:20
Alignment explanation
Indices: 3483685--3483723 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3483675 ATGTTGAAGG
3483685 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
3483705 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
3483724 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:3483753 original size:19 final size:19
Alignment explanation
Indices: 3483729--3483793 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
3483719 GCAACGAGAG
3483729 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3483748 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3483767 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
3483781 AATCGCAATGCGA
1 AATCGCAATGCGA
3483794 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3483843 original size:19 final size:20
Alignment explanation
Indices: 3483819--3483868 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3483809 GCGATTTTGT
3483819 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
3483838 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3483858 CGTTGCGATAG
1 CGTTGCGATAG
3483869 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:3485080 original size:12 final size:12
Alignment explanation
Indices: 3485063--3485087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3485053 ATATAATCCT
3485063 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3485075 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3485087 G
1 G
3485088 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3487400 original size:19 final size:19
Alignment explanation
Indices: 3487378--3487442 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
3487368 GGAAATTACT
3487378 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3487397 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
3487411 ATCTCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3487430 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3487443 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3487470 original size:14 final size:14
Alignment explanation
Indices: 3487453--3487542 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3487443 TTTAATTTCG
3487453 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3487467 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3487486 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3487500 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3487519 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3487533 CGTTGCGATT
1 CGTTGCGATT
3487543 TTCATTTCGC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3487489 original size:33 final size:33
Alignment explanation
Indices: 3487438--3487560 Score: 219
Period size: 33 Copynumber: 3.7 Consensus size: 33
3487428 AAATCGCAAC
* *
3487438 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
3487471 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
3487504 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
3487537 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
3487561 AGTACTTTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:3487491 original size:19 final size:19
Alignment explanation
Indices: 3487467--3487560 Score: 91
Period size: 19 Copynumber: 5.5 Consensus size: 19
3487457 GCGATTCTCT
3487467 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3487486 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3487500 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3487519 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3487533 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3487552 CATTGCGAT
1 CGTTGCGAT
3487561 AGTACTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 20 0.33
16 6 0.10
17 6 0.10
19 28 0.47
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3487686 original size:14 final size:14
Alignment explanation
Indices: 3487667--3487703 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3487657 CATCAATTAA
3487667 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3487681 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3487695 ACAAATCAA
1 ACAAATCAA
3487704 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3489143 original size:42 final size:42
Alignment explanation
Indices: 3489097--3489260 Score: 175
Period size: 42 Copynumber: 3.9 Consensus size: 42
3489087 CGATGACAGT
* * *
3489097 GGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* *** * * * *
3489139 GGCCTCTTCAATGATAGGATTTGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
3489181 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
3489223 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3489261 CAGGCGAGTC
Statistics
Matches: 94, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 94 1.00
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3489199 original size:84 final size:84
Alignment explanation
Indices: 3489088--3489263 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
3489078 CATCTTCAAC
*
3489088 GATGACAGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
* *
3489153 TAGGATTTGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
3489172 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
3489237 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
3489256 GATGACAG
1 GATGACAG
3489264 GCGAGTCGGG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:3489656 original size:91 final size:90
Alignment explanation
Indices: 3489479--3489665 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 90
3489469 ATATTTCAAA
*
3489479 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
3489544 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
3489572 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
3489636 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
3489663 ACT
1 ACT
3489666 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.23
95 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:3489697 original size:18 final size:18
Alignment explanation
Indices: 3489674--3489719 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
3489664 CTAAGCAATC
3489674 TAAGTGAAATGGTTAATT
1 TAAGTGAAATGGTTAATT
3489692 TAAGTGAAATGGTTAATT
1 TAAGTGAAATGGTTAATT
3489710 TAAGTGAAAT
1 TAAGTGAAAT
3489720 TACGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (18 bp):
TAAGTGAAATGGTTAATT
Found at i:3489886 original size:63 final size:62
Alignment explanation
Indices: 3489836--3489968 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 62
3489826 GAAACCTCAC
* * *
3489836 CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCT
1 CACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG-ACCGACCTCCT
* *** *
3489899 CACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCT
1 CACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG-ACCGACCTCCT
3489962 CACGCAA
1 CACGCAA
3489969 GGCATTGACC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (62 bp):
CACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGACCGACCTCCT
Found at i:3489969 original size:63 final size:63
Alignment explanation
Indices: 3489850--3489980 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
3489840 TAAAGTAGAC
3489850 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
3489913 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
3489976 ACCTC
1 ACCTC
3489981 TTCACGTAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:3491484 original size:19 final size:18
Alignment explanation
Indices: 3491433--3491577 Score: 108
Period size: 19 Copynumber: 8.1 Consensus size: 18
3491423 TCTTTTGGTT
*
3491433 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
3491452 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
*
3491472 GAAATGATTATCGCAA--C
1 GAAATGA-AATCGCAACGC
*
3491489 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
3491505 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
*
3491524 GAAATGAAAATTGCAA--C
1 GAAATG-AAATCGCAACGC
* *
3491541 GAGA-G-AATCACAACGC
1 GAAATGAAATCGCAACGC
*
3491557 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
3491576 GA
1 GA
3491578 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 13 0.13
16 10 0.10
17 10 0.10
19 52 0.51
20 16 0.16
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:3491500 original size:33 final size:33
Alignment explanation
Indices: 3491458--3491522 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3491448 ACGAGATAAT
**
3491458 GAGAATCGCAACGCGAAATGATTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
3491491 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
3491523 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:3491517 original size:52 final size:52
Alignment explanation
Indices: 3491441--3491577 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 52
3491431 TTGAAATGAA
* * **
3491441 AATCGCAACGAGATAATGAGAATCGCAACGCGAAATGATTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
3491494 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATTGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
3491546 AATCACAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
3491578 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 65 0.84
53 12 0.16
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:3491595 original size:19 final size:19
Alignment explanation
Indices: 3491573--3491639 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
3491563 AAAATCGCAA
*
3491573 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
3491592 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
3491611 TGCGATAGTT-ATTTCCGCAT
1 TGCGAT-TTTGATTT-CGCGT
3491631 TGCGATTTT
1 TGCGATTTT
3491640 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 27 0.69
20 12 0.31
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3492267 original size:20 final size:20
Alignment explanation
Indices: 3492156--3492269 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
3492146 CGCTATGTAA
* * *
3492156 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
3492176 ATCACGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
3492196 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
3492217 ATCGCATTGCCATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
3492237 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3492257 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3492270 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.79
21 11 0.14
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:3492380 original size:21 final size:21
Alignment explanation
Indices: 3492340--3492380 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3492330 ACTGTAGACC
**
3492340 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3492361 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3492381 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3492528 original size:5 final size:5
Alignment explanation
Indices: 3492518--3492584 Score: 134
Period size: 5 Copynumber: 13.4 Consensus size: 5
3492508 CGATTTTCTC
3492518 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
3492568 TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TA
3492585 AATTGTGGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 62 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3493343 original size:42 final size:42
Alignment explanation
Indices: 3493161--3493477 Score: 319
Period size: 43 Copynumber: 7.5 Consensus size: 42
3493151 TATCGTGATA
* *
3493161 TTTTTTGAACAAACGCCGCAAAAGGTCGATATCTATAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCG
** * ** *
3493204 TTTTCAGAACAAACGCCGCAAAAGGTTGAGATCTATAGTAGTG
1 TTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCG
* ** * *
3493247 TTTTTGGAAAAAATACCGCAAAAGGTCGATATCTATAGCGGTG
1 TTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCG
* * * * * **
3493290 TTTTCGAAACAAACGTCACAAAAGGTCAGATCTATAGTGGAA
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* *
3493332 TTTTTGGAACAAACGCCGCAAAAGGTCAGATTTATAGCGGTG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* * *
3493374 TTTTTGGAACAAACACCACAAAAAGTCAGATCTATAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
** * * *
3493416 TTTTTGGATACAAATACCGCAAAAAGTCATATCTATAGCGGCA
1 TTTTTGGA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
*
3493459 TTTTTTGAACAAACGCCGC
1 TTTTTGGAACAAACGCCGC
3493478 TAATTATTCT
Statistics
Matches: 224, Mismatches: 47, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
42 100 0.45
43 123 0.55
44 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
Found at i:3497932 original size:63 final size:64
Alignment explanation
Indices: 3497794--3497912 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 64
3497784 ATTGTTCAAG
* * * **
3497794 GTGTATCGATGCACATGAAGTGCATCGATGC-CTCTTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
*
3497857 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAAT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT
3497913 AGGATTTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 45 0.92
64 4 0.08
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:3498627 original size:23 final size:23
Alignment explanation
Indices: 3498601--3498667 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
3498591 CAATCTTATA
*
3498601 TGGCACTACGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
* *
3498624 TGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
* *
3498647 TGGCACTTCGATGCATTTATA
1 TGGCACTTCGGTGCAATTATA
3498668 TGAGCTGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:3499317 original size:23 final size:23
Alignment explanation
Indices: 3499291--3499362 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
3499281 ACAGCTCATA
*
3499291 GCACCGAAGTGCCACGAAGAATT
1 GCACCGAAGTGCCGCGAAGAATT
3499314 GCACCGAAGTGCCGC-ATAGAATT
1 GCACCGAAGTGCCGCGA-AGAATT
*
3499337 GCACCGAAGTGCCGCGTAGAATT
1 GCACCGAAGTGCCGCGAAGAATT
3499360 GCA
1 GCA
3499363 TATTCATGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 44 0.98
ACGTcount: A:0.31, C:0.26, G:0.28, T:0.15
Consensus pattern (23 bp):
GCACCGAAGTGCCGCGAAGAATT
Found at i:3505971 original size:23 final size:23
Alignment explanation
Indices: 3505929--3505980 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
3505919 TCATATAAAC
3505929 GCACCGAAGTGCCACATAGAATT
1 GCACCGAAGTGCCACATAGAATT
* * *
3505952 GCACCGAAGTGTCGCGTAGAATT
1 GCACCGAAGTGCCACATAGAATT
*
3505975 ACACCG
1 GCACCG
3505981 TAGTCCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
GCACCGAAGTGCCACATAGAATT
Found at i:3506254 original size:31 final size:30
Alignment explanation
Indices: 3506210--3506269 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3506200 TATTGTATAG
*
3506210 ACATATAATTTCCA-TACCTTTATCACATAA
1 ACATATAATTTCCATTA-CTTTACCACATAA
*
3506240 ACATATCATGTTCCATTACTTTACCACATA
1 ACATATAAT-TTCCATTACTTTACCACATA
3506270 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 16 0.62
32 2 0.08
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATTACTTTACCACATAA
Found at i:3508884 original size:23 final size:23
Alignment explanation
Indices: 3508858--3508918 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3508848 GCTCATTGAA
3508858 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3508881 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3508904 TACACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3508919 TATAAGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3509184 original size:31 final size:30
Alignment explanation
Indices: 3509140--3509199 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3509130 TATTGTATAG
*
3509140 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
3509170 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
3509200 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:3509638 original size:63 final size:64
Alignment explanation
Indices: 3509562--3509698 Score: 154
Period size: 63 Copynumber: 2.2 Consensus size: 64
3509552 GCACCACACC
* * *
3509562 ATGCAACGATGCATAAAT-CCTATTCGATGTTTATA-TTT-AAGGAGATGCATCAATGCACTCCT
1 ATGCATCGATGCATAAATGCC-ATTCGATGTTTATATTTTAAAAGAG-TGCATCAATGCACTCCA
3509624 T
64 T
** * * *
3509625 ATGCATCGATGCATTGATGGCATTCGATGTTTATATTTTAAAAGAGTGCATCGATGCACTTCAT
1 ATGCATCGATGCATAAATGCCATTCGATGTTTATATTTTAAAAGAGTGCATCAATGCACTCCAT
*
3509689 GTGCATCGAT
1 ATGCATCGAT
3509699 ACATCTTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 29 0.47
64 28 0.45
65 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCATAAATGCCATTCGATGTTTATATTTTAAAAGAGTGCATCAATGCACTCCAT
Found at i:3510240 original size:13 final size:14
Alignment explanation
Indices: 3510222--3510251 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3510212 TCTTCACGGG
3510222 GAAGAAGAAGAA-A
1 GAAGAAGAAGAAGA
3510235 GAAGAAGAAGAAGA
1 GAAGAAGAAGAAGA
3510249 GAA
1 GAA
3510252 ATCTGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAGAAGA
Found at i:3511809 original size:23 final size:23
Alignment explanation
Indices: 3511791--3511851 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
3511781 CTCGTATAAA
3511791 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3511814 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3511837 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3511852 TATAAGATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3512118 original size:31 final size:30
Alignment explanation
Indices: 3512074--3512133 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3512064 TATTGTATAG
*
3512074 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
3512104 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
3512134 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:3514738 original size:23 final size:23
Alignment explanation
Indices: 3514712--3514757 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3514702 CACCACAGCT
*
3514712 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
3514735 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3514758 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3517339 original size:30 final size:30
Alignment explanation
Indices: 3517303--3517375 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3517293 CCCGAAGAAC
3517303 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3517333 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3517363 CTATTCATAGGTC
1 CTATCCAGAGGTC
3517376 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3521309 original size:610 final size:610
Alignment explanation
Indices: 3520147--3521362 Score: 2036
Period size: 610 Copynumber: 2.0 Consensus size: 610
3520137 TTCTTTACTA
3520147 GCTCTATTCTTTTCAAACATATTTCATCTTTACTTTGCAATTCTCTTATTCGTTCCAACCATGCT
1 GCTCTATTCTTTTCAAACATATTTCATCTTTACTTTGCAATTCTCTTATTCGTTCCAACCATGCT
* *
3520212 GGTTTACGTCTTAACTCTGCACATAGACCACCGTCTTCAGTCAAAGATAACCTTGCATCCATAGC
66 GGTTTAAGTCTTAACTCTGCACATAGACCACCGTCTCCAGTCAAAGATAACCTTGCATCCATAGC
* * *
3520277 TCGTAAAGCTGCAAATGTCTTTCTACTCAAAGCATCTGCTACCACGTTAGCATTTCTGGGATGAT
131 TCGTAAAGCTGCAAACGTCTTTCTACTCAAAGCATCTACTACCACGTTAGCATTTCCGGGATGAT
3520342 AGTCAATTATTATATCATAATCTCTCAAAAACTCAACCCATCTCCTTTGTCTCAAATTAAGCTCT
196 AGTCAATTATTATATCATAATCTCTCAAAAACTCAACCCATCTCCTTTGTCTCAAATTAAGCTCT
* *
3520407 TTTTGAGTCATCAGGTATTTCAAGCTCTTATGATCCGTATATAAATAACATCGTTCTCCATACAG
261 TTTTGAGTCATCAGATATTTCAAGCTCTTATGATCCGTATACAAATAACATCGTTCTCCATACAG
* * * * * *
3520472 ATAATAATGACAAATCTTGAGGGCGAATACCACTGTAGCCATTTCCAAATCATAGGTGGGGTAAT
326 ATAATAACGACAAATCTTGAGAGCGAACACCACTGCAACCATTTCCAAATCATAGGTGGGATAAT
* * *
3520537 TCTTTTCATGTGGTTTCAACTACCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACA
391 TCTTTTCATATGATTTCAACTACCTCGATGCATACGCTACCACCTTCCCTTCTTGAATTAATACA
*
3520602 CACCCCAACCCGTTATAGGACGCGTCACTGTATACGACAAAATTCTTGCCAGATTCCGGTTGAAC
456 CACCCCAACCCGTTATAGGACGCATCACTGTATACGACAAAATTCTTGCCAGATTCCGGTTGAAC
* * * *
3520667 CAATATAGGAGTTTATGTCAGAATCCTCTTTAAAGCTTTAAAACTTTCTTGACATTCAGAAGTCC
521 CAATACAGGAGTTTATGTCAGAATCATCTTTAAAGCTTCAAAACTTCCTTGACATTCAGAAGTCC
*
3520732 AAACAAACGGTACATTCTTTCACAT
586 AAAAAAACGGTACATTCTTTCACAT
*
3520757 GCTCTATTCTTTTCAAACATATTTCATCTTTACTTTGCAATTCTCTTATTCGTTCCAACCATGTT
1 GCTCTATTCTTTTCAAACATATTTCATCTTTACTTTGCAATTCTCTTATTCGTTCCAACCATGCT
* * * *
3520822 GGTTTAAGTTTTATCTCTGCACATAGACCATCGTCTCCAGTCAAAGATAACCTTGCGTCCATAGC
66 GGTTTAAGTCTTAACTCTGCACATAGACCACCGTCTCCAGTCAAAGATAACCTTGCATCCATAGC
3520887 TCGTAAAGCTGCAAACGTCTTTCTACTCAAAGCATCTACTACCACGTTAGCATTTCCGGGATGAT
131 TCGTAAAGCTGCAAACGTCTTTCTACTCAAAGCATCTACTACCACGTTAGCATTTCCGGGATGAT
* *
3520952 AGTCAATTATTATATCATAATCTCTTAAAAACTCAACCCATCTCCTTTGTCTTAAATTAAGCTCT
196 AGTCAATTATTATATCATAATCTCTCAAAAACTCAACCCATCTCCTTTGTCTCAAATTAAGCTCT
3521017 TTTTGAGTCATCAGATATTTCAAGCTCTTATGATCCGTATACAAATAACATCGTTCTCCATACAG
261 TTTTGAGTCATCAGATATTTCAAGCTCTTATGATCCGTATACAAATAACATCGTTCTCCATACAG
* * * * *
3521082 ATAATGACGCCAAATCTTGAGAGCGAACACCACTGCAACCATTTCTAAATCGTGGGTGGGATAAT
326 ATAATAACGACAAATCTTGAGAGCGAACACCACTGCAACCATTTCCAAATCATAGGTGGGATAAT
**
3521147 TCTTTTCATATGATTTCAACTGTCTCGATGCATACGCTACCACCTTCCCTTCTTGAATTAATACA
391 TCTTTTCATATGATTTCAACTACCTCGATGCATACGCTACCACCTTCCCTTCTTGAATTAATACA
* * * *
3521212 CACCCCAACCCGTTATGGGACGCATCACTGTATACGAGAAAATTCTTGCCAGATTCTGGTTGAAT
456 CACCCCAACCCGTTATAGGACGCATCACTGTATACGACAAAATTCTTGCCAGATTCCGGTTGAAC
* *
3521277 CAATACAGGAGTTTCTGTCAGAATTATCTTTAAAGCTTCAAAACTTCCTTGACATTCAGAAGTCC
521 CAATACAGGAGTTTATGTCAGAATCATCTTTAAAGCTTCAAAACTTCCTTGACATTCAGAAGTCC
* *
3521342 AAAAAAAGGGTATATTCTTTC
586 AAAAAAACGGTACATTCTTTC
3521363 TCTTCAGCTT
Statistics
Matches: 562, Mismatches: 44, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
610 562 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (610 bp):
GCTCTATTCTTTTCAAACATATTTCATCTTTACTTTGCAATTCTCTTATTCGTTCCAACCATGCT
GGTTTAAGTCTTAACTCTGCACATAGACCACCGTCTCCAGTCAAAGATAACCTTGCATCCATAGC
TCGTAAAGCTGCAAACGTCTTTCTACTCAAAGCATCTACTACCACGTTAGCATTTCCGGGATGAT
AGTCAATTATTATATCATAATCTCTCAAAAACTCAACCCATCTCCTTTGTCTCAAATTAAGCTCT
TTTTGAGTCATCAGATATTTCAAGCTCTTATGATCCGTATACAAATAACATCGTTCTCCATACAG
ATAATAACGACAAATCTTGAGAGCGAACACCACTGCAACCATTTCCAAATCATAGGTGGGATAAT
TCTTTTCATATGATTTCAACTACCTCGATGCATACGCTACCACCTTCCCTTCTTGAATTAATACA
CACCCCAACCCGTTATAGGACGCATCACTGTATACGACAAAATTCTTGCCAGATTCCGGTTGAAC
CAATACAGGAGTTTATGTCAGAATCATCTTTAAAGCTTCAAAACTTCCTTGACATTCAGAAGTCC
AAAAAAACGGTACATTCTTTCACAT
Found at i:3525000 original size:31 final size:30
Alignment explanation
Indices: 3524956--3525015 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
3524946 TATTGTATAG
3524956 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
3524986 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
3525016 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:3530898 original size:31 final size:31
Alignment explanation
Indices: 3530860--3530950 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
3530850 CAATTTAAGG
3530860 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
3530891 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
* *
3530922 CAAAAT-GTATTTGGAATT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
3530951 TTCAATATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.19
30 10 0.17
31 37 0.64
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:3531043 original size:19 final size:19
Alignment explanation
Indices: 3531016--3531082 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
3531006 AATGTTTTTA
* *
3531016 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
3531035 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
3531054 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
3531073 TGAACAGTAA
1 TGAACAGTAA
3531083 CCCGAGGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:3531214 original size:21 final size:21
Alignment explanation
Indices: 3531188--3531229 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3531178 ATTTGAATAT
3531188 TATGAAGGGGTA-TCGATTCCC
1 TATGAAGGGGTACT-GATTCCC
3531209 TATGAAGGGGTACTGATTCCC
1 TATGAAGGGGTACTGATTCCC
3531230 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACTGATTCCC
Found at i:3531296 original size:20 final size:22
Alignment explanation
Indices: 3531258--3531297 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3531248 TTTGAGTAGA
3531258 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
3531280 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3531298 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3532717 original size:63 final size:65
Alignment explanation
Indices: 3532611--3532771 Score: 181
Period size: 63 Copynumber: 2.5 Consensus size: 65
3532601 ATTGTTCAAG
* * * **
3532611 GTGTATCGATGCACATGAAGTGCATCGATGC-CTCTTTTAAAATAAAAACATCGAAT-GCCA-TC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAG-CATTC
3532673 A
65 A
* * *
3532674 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAGCATTCA
*
3532738 -TGTATCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
3532772 GTCAAAGGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
62 2 0.02
63 76 0.89
64 7 0.08
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (65 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAGCATTCA
Found at i:3533466 original size:23 final size:23
Alignment explanation
Indices: 3533413--3533473 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3533403 CAATCTTATA
* *
3533413 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3533436 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3533459 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
3533474 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3544257 original size:81 final size:80
Alignment explanation
Indices: 3544022--3544301 Score: 284
Period size: 82 Copynumber: 3.4 Consensus size: 80
3544012 GTGTTTAGCG
* * *
3544022 GCGTTTGTT-AAAAAACGCCACTATAGATTAATCCTATTGCGGCGTTTGTAAAAAAAACGCCGCT
1 GCGTTTGTTAAAAAAACGCCACTATAGATGAA-CCTATTGTGGCGTTTGT-ATAAAAACGCCGCT
*
3544086 AAAGTACTACTCTTTTAC
64 AAAGTACTA-TTTTTTAC
* * * *
3544104 GACGCTTT-TTGAAAAAATGCCAC-ATAGATGAACCATATTGTAGCGTTTGTATAAAAACGCTGC
1 G-CG-TTTGTTAAAAAAACGCCACTATAGATGAACC-TATTGTGGCGTTTGTATAAAAACGCCGC
*
3544167 TAAATTACTATTTTTTCAC
63 TAAAGTACTATTTTTT-AC
* * *
3544186 TGCGTTTGTT-AAGAAACGCCACTATGGATGAACCTATTGTGGCGTTTGTATAAAAATGCCGCTC
1 -GCGTTTGTTAAAAAAACGCCACTATAGATGAACCTATTGTGGCGTTTGTATAAAAACGCCGCT-
3544250 AAA-TACTATTATATTGTA-
64 AAAGTACTATT-T-TT-TAC
* *
3544268 GCATTTGTTAAAGAAACGCCACTATAGATGAACC
1 GCGTTTGTTAAAAAAACGCCACTATAGATGAACC
3544302 CAATTACGGC
Statistics
Matches: 169, Mismatches: 16, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
81 59 0.35
82 66 0.39
83 29 0.17
84 15 0.09
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (80 bp):
GCGTTTGTTAAAAAAACGCCACTATAGATGAACCTATTGTGGCGTTTGTATAAAAACGCCGCTAA
AGTACTATTTTTTAC
Found at i:3553329 original size:13 final size:13
Alignment explanation
Indices: 3553311--3553336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3553301 TTTTTAACTA
3553311 TCACAACGAATTT
1 TCACAACGAATTT
3553324 TCACAACGAATTT
1 TCACAACGAATTT
3553337 GGAAAATCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TCACAACGAATTT
Found at i:3564824 original size:35 final size:35
Alignment explanation
Indices: 3564772--3564840 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
3564762 ACGGGGACGA
* * *
3564772 GGAAAAAATCGTATATGTTAAACGGGGACGGGGAT
1 GGAAAAAACCGTATATGTTAAACAGGGACAGGGAT
*
3564807 GGAAAAAACCGTTTATGTTAAACAGGGACAGGGA
1 GGAAAAAACCGTATATGTTAAACAGGGACAGGGA
3564841 CGGGTTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (35 bp):
GGAAAAAACCGTATATGTTAAACAGGGACAGGGAT
Found at i:3565883 original size:16 final size:16
Alignment explanation
Indices: 3565851--3565884 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3565841 TGATATCTTG
3565851 TTAAATATGATAATTT
1 TTAAATATGATAATTT
*
3565867 TTAAA-ATGTTAATTT
1 TTAAATATGATAATTT
3565882 TTA
1 TTA
3565885 GGGTAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAATATGATAATTT
Found at i:3574539 original size:21 final size:21
Alignment explanation
Indices: 3574501--3574551 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3574491 ACATAGTATT
3574501 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
3574521 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
3574542 ACATATAGAA
1 AAATA-AGAA
3574552 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:3574729 original size:2 final size:2
Alignment explanation
Indices: 3574722--3574748 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3574712 GTATACTTAA
3574722 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3574749 CTAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3576285 original size:106 final size:107
Alignment explanation
Indices: 3576093--3576324 Score: 322
Period size: 106 Copynumber: 2.2 Consensus size: 107
3576083 ATCTTCTGTC
* * * * * ** *
3576093 GTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTGTTTTGTTTACAGTCAGCCGTCTCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
*
3576158 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCAAT
66 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
*
3576200 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* * * **
3576264 TGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCT
66 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
3576306 GTGAAGTTGAAATTGGCTC
1 GTGAAGTTGAAATTGGCTC
3576325 TAGCTAAAAC
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 80 0.73
107 30 0.27
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
Found at i:3576770 original size:31 final size:31
Alignment explanation
Indices: 3576735--3576862 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 31
3576725 GGGAAATAAA
3576735 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
3576766 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
*
3576802 CTCAAA-GGTTTTGTGTTTCAAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
3576833 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACG-ATTTTGTGTTTCAAGAGAAAC
3576863 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
30 3 0.04
31 25 0.33
32 3 0.04
33 20 0.26
35 2 0.03
36 19 0.25
37 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:3576770 original size:67 final size:67
Alignment explanation
Indices: 3576638--3576829 Score: 240
Period size: 67 Copynumber: 2.8 Consensus size: 67
3576628 GTCTTAAAAA
* * * * * * *
3576638 AGACATAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
3576703 AGGG
64 AGGG
* * * *
3576707 AGACAAAATTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
1 AGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
3576772 GG
66 GG
* * *
3576774 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTGTGTTTCAAGAGAAAC
3576830 ATTTTCAAAG
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
67 74 0.69
68 3 0.03
69 30 0.28
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:3576889 original size:36 final size:33
Alignment explanation
Indices: 3576784--3576898 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
3576774 AGACGAAATT
* *
3576784 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
3576815 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
3576848 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
3576884 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
3576899 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:3576988 original size:37 final size:37
Alignment explanation
Indices: 3576937--3577110 Score: 154
Period size: 37 Copynumber: 4.9 Consensus size: 37
3576927 CAAGGATTGA
** *
3576937 TGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
3576974 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
3577010 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
3577038 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
3577076 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
3577111 GCATTTCAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
28 2 0.02
29 14 0.13
30 3 0.03
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 17 0.16
37 62 0.58
38 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:3577044 original size:102 final size:102
Alignment explanation
Indices: 3576936--3577202 Score: 464
Period size: 102 Copynumber: 2.6 Consensus size: 102
3576926 TCAAGGATTG
3576936 ATGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
1 ATGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
3577001 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
66 GACAAAATGCATTTCAAGGGAAATGTTTTCAATGTTT
*
3577038 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
1 ATGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
3577103 GACAAAATGCATTTCAAGGGAAATGTTTTCAATGTTT
66 GACAAAATGCATTTCAAGGGAAATGTTTTCAATGTTT
* *
3577140 ATGTTT-AAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAACTATCTCAA
1 ATGTTTCAAA-AGAAACTGTCTCAAGGGAGACAAAA-TTT-TGTTTCAAGGGAAACTATCTCAA
3577203 ACGAGATAAA
Statistics
Matches: 157, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
101 2 0.01
102 130 0.83
103 3 0.02
104 22 0.14
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
ATGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAATGCATTTCAAGGGAAATGTTTTCAATGTTT
Found at i:3578720 original size:183 final size:183
Alignment explanation
Indices: 3578412--3578761 Score: 646
Period size: 183 Copynumber: 1.9 Consensus size: 183
3578402 GGTTTAACTA
3578412 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATTGCCA
* **
3578477 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
3578542 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
* *
3578595 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATTGCCA
*
3578660 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
3578725 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
3578762 CGGATTTAAT
Statistics
Matches: 161, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:3581666 original size:17 final size:18
Alignment explanation
Indices: 3581644--3581677 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3581634 ATCCTACCCC
3581644 ACATGATATCTA-CCCGA
1 ACATGATATCTATCCCGA
*
3581661 ACATGATCTCTATCCCG
1 ACATGATATCTATCCCG
3581678 CATGCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (18 bp):
ACATGATATCTATCCCGA
Found at i:3582710 original size:21 final size:21
Alignment explanation
Indices: 3582672--3582722 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3582662 ACATAGTATT
3582672 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
3582692 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
3582713 ACATATAGAA
1 AAATA-AGAA
3582723 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:3584190 original size:50 final size:50
Alignment explanation
Indices: 3584130--3584242 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
3584120 TTAGTAGGAA
* * *
3584130 AGCGCGCCCCCTG-CACCGCCCTATA-TGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGTC-CCGCCATATACAG-TGATCTGGCGCCACGTGGGTAT
* *
3584180 AGCGCACCCCCTGTCCCGCGATATACAGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGTCCCGCCATATACAGTGATCTGGCGCCACGTGGGTAT
3584230 AGCGCGCCCCCTG
1 AGCGCGCCCCCTG
3584243 ATCCGCGCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 53 0.96
51 2 0.04
ACGTcount: A:0.15, C:0.37, G:0.28, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGTCCCGCCATATACAGTGATCTGGCGCCACGTGGGTAT
Found at i:3584249 original size:50 final size:50
Alignment explanation
Indices: 3584158--3584255 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
3584148 CCCTATATGC
*
3584158 TGATTTGGCGCCACGTGGGTATAGCGCACCCCCTGTCCCGCGATATACAG
1 TGATCTGGCGCCACGTGGGTATAGCGCACCCCCTGTCCCGCGATATACAG
* *
3584208 TGATCTGGCGCCACGTGGGTATAGCGCGCCCCCTGAT-CCGCGCTATAC
1 TGATCTGGCGCCACGTGGGTATAGCGCACCCCCTG-TCCCGCGATATAC
3584256 CTGGATATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.16, C:0.34, G:0.29, T:0.21
Consensus pattern (50 bp):
TGATCTGGCGCCACGTGGGTATAGCGCACCCCCTGTCCCGCGATATACAG
Found at i:3584457 original size:13 final size:14
Alignment explanation
Indices: 3584429--3584457 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3584419 ATATTTTATA
3584429 ATATTTTTACTATT
1 ATATTTTTACTATT
3584443 ATATTTTTACT-TT
1 ATATTTTTACTATT
3584456 AT
1 AT
3584458 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:3584726 original size:111 final size:111
Alignment explanation
Indices: 3584532--3584755 Score: 376
Period size: 111 Copynumber: 2.0 Consensus size: 111
3584522 TAGAAATCAT
* *
3584532 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* *
3584597 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
* * *
3584643 ATATCTCGACACTTTGTTGATACAGTAACATTTTAACGTTTTTATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
*
3584708 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
3584754 AT
1 AT
3584756 TTTGTAATTA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACAGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
Found at i:3597088 original size:23 final size:23
Alignment explanation
Indices: 3597041--3597090 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3597031 AATAACATAT
**
3597041 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
3597064 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
3597087 TAGG
1 TAGG
3597091 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:3597145 original size:23 final size:23
Alignment explanation
Indices: 3597119--3597166 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3597109 ATCAAGTACA
3597119 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
3597142 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
3597165 AT
1 AT
3597167 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:3597151 original size:87 final size:87
Alignment explanation
Indices: 3597005--3597166 Score: 306
Period size: 87 Copynumber: 1.9 Consensus size: 87
3596995 ATGTTATATT
*
3597005 ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
3597070 GCGCTTATATAATAAAATAGGC
66 GCGCTTATATAATAAAATAGGC
*
3597092 ATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
3597157 GCGCTTATAT
66 GCGCTTATAT
3597167 TGACCTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAGGC
Found at i:3597550 original size:20 final size:21
Alignment explanation
Indices: 3597527--3597568 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3597517 ATCGATACAA
*
3597527 TTATAT-AAGTGTCGATACTT
1 TTATATGAAGTGTCAATACTT
*
3597547 TTATGTGAAGTGTCAATACTT
1 TTATATGAAGTGTCAATACTT
3597568 T
1 T
3597569 CGATAGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (21 bp):
TTATATGAAGTGTCAATACTT
Found at i:3597947 original size:182 final size:181
Alignment explanation
Indices: 3597623--3598042 Score: 553
Period size: 182 Copynumber: 2.3 Consensus size: 181
3597613 TACGCGTACT
* * * * * *
3597623 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGTTTTACCGGTTTTGTTATTTCGATACCG
1 TATTAACGTATCGACACTTTCAATATATCCGGTAGC-TTTTACCGGTTTTATCATTTCGATACCG
* * *
3597688 GTTTTGTCATATTCTTACTTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCTACACT
65 GTTTTGTCATATTCATACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACT
*
3597753 TTATACGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
130 GTATACGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
3597805 TATTAACGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCG-TGACC
1 TATTAACGTATCGACACTTTCAATATATCCGGTAGCT-TTTACCGGTTTTATCATTTCGAT-ACC
* *
3597869 GGTTTTGTCATACTT-ATACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
64 GGTTTTGTCATA-TTCATACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACA
* * *
3597933 CTGTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
128 CTGTATACGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
* * * *
3597987 T-TTAAATC-TAATCAATACTTTCGATATATCCAGTAG-TGATTTACCGGTTTTATCAT
1 TATT-AA-CGT-ATCGACACTTTCAATATATCCGGTAGCT--TTTACCGGTTTTATCAT
3598043 ATTTTTACAT
Statistics
Matches: 211, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
181 4 0.02
182 165 0.78
183 42 0.20
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (181 bp):
TATTAACGTATCGACACTTTCAATATATCCGGTAGCTTTTACCGGTTTTATCATTTCGATACCGG
TTTTGTCATATTCATACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTG
TATACGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
Found at i:3601487 original size:15 final size:14
Alignment explanation
Indices: 3601459--3601488 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3601449 GTTAAATCTG
3601459 AAAATAATATAATA
1 AAAATAATATAATA
3601473 AAAATAATGATAATA
1 AAAATAAT-ATAATA
3601488 A
1 A
3601489 TATTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAATAATATAATA
Found at i:3601968 original size:37 final size:37
Alignment explanation
Indices: 3601921--3602017 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
3601911 TATTTGTATT
* * *
3601921 TTAATTAAATATAAATTCATAAATAATATAGTT-GTAC
1 TTAATCAAATATAAATTCATAAATAAAATA-TTCATAC
* * *
3601958 TTAATCAAATATAAATTTATGAATAAAATATTCATAT
1 TTAATCAAATATAAATTCATAAATAAAATATTCATAC
*
3601995 TTCAATCGAATATAAATTCATAA
1 TT-AATCAAATATAAATTCATAA
3602018 TTTTAATAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 2 0.04
37 30 0.61
38 17 0.35
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (37 bp):
TTAATCAAATATAAATTCATAAATAAAATATTCATAC
Found at i:3602005 original size:24 final size:25
Alignment explanation
Indices: 3601978--3602035 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
3601968 ATAAATTTAT
*
3601978 GAATAAAATATTCAT-ATTTCAATC
1 GAATAAAATATTCATAATTTCAATA
* *
3602002 GAATATAA-ATTCATAATTTTAATA
1 GAATAAAATATTCATAATTTCAATA
3602026 GAATATAAAT
1 GAATA-AAAT
3602036 CTTAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 6 0.22
24 19 0.70
25 2 0.07
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (25 bp):
GAATAAAATATTCATAATTTCAATA
Found at i:3603593 original size:2 final size:2
Alignment explanation
Indices: 3603586--3603693 Score: 93
Period size: 2 Copynumber: 57.0 Consensus size: 2
3603576 TTGGGCCGGG
*
3603586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
3603628 T- TA AA TA TA TA AA TA TA TA T- TT TT TA TT TA AA T- TA AA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3603667 TA T- TA -A TA T- 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
3603694 AATAATTAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
1 6 0.07
2 79 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3604280 original size:21 final size:21
Alignment explanation
Indices: 3604247--3604293 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
3604237 TTTATTTTTT
3604247 AAATAATATTAAATTGAGTTATAA
1 AAATAATA--AAATTGAGTT-TAA
3604271 AAATAATAAAATTGAGTTTAA
1 AAATAATAAAATTGAGTTTAA
3604292 AA
1 AA
3604294 GAACAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
24 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATAATAAAATTGAGTTTAA
Found at i:3604301 original size:20 final size:22
Alignment explanation
Indices: 3604257--3604302 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
3604247 AAATAATATT
* *
3604257 AAATTGAGTTATAAAAATAATA
1 AAATTGAGTTATAAAAAGAACA
3604279 AAATTGAGTT-T-AAAAGAACA
1 AAATTGAGTTATAAAAAGAACA
3604299 AAAT
1 AAAT
3604303 CAGGTCATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
AAATTGAGTTATAAAAAGAACA
Found at i:3606823 original size:31 final size:30
Alignment explanation
Indices: 3606788--3606889 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 30
3606778 AGTAATTTTA
*
3606788 AATTTAACTTTTAAACTTTATATAAAATACT
1 AATTTAACTTTTAAACTTTAGATAAAATA-T
*
3606819 AATTTAAATTTTAAACTTTAGATAAAATAGT
1 AATTTAACTTTTAAACTTTAGATAAAATA-T
3606850 AATTTAA-TCTTTAAACTTTAGATAAAATAT
1 AATTTAACT-TTTAAACTTTAGATAAAATAT
*
3606880 ATTTTAACTT
1 AATTTAACTT
3606890 CTGATCTGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
30 9 0.14
31 56 0.86
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (30 bp):
AATTTAACTTTTAAACTTTAGATAAAATAT
Found at i:3617329 original size:3 final size:3
Alignment explanation
Indices: 3617321--3617349 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3617311 AGATTACTCT
3617321 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3617350 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3627472 original size:15 final size:15
Alignment explanation
Indices: 3627452--3627480 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3627442 GGACCCCTAT
3627452 ATCCCGAAGGACTAC
1 ATCCCGAAGGACTAC
3627467 ATCCCGAAGGACTA
1 ATCCCGAAGGACTA
3627481 TTATACCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (15 bp):
ATCCCGAAGGACTAC
Found at i:3627629 original size:23 final size:26
Alignment explanation
Indices: 3627592--3627660 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
3627582 TTCTCTTATG
3627592 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
3627616 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
3627641 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
3627661 AAAATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:3627642 original size:12 final size:12
Alignment explanation
Indices: 3627625--3627660 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3627615 TATCATGTTC
3627625 TCATATCACATG
1 TCATATCACATG
*
3627637 TCATATCACATA
1 TCATATCACATG
3627649 TCATATCACATG
1 TCATATCACATG
3627661 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:3628076 original size:64 final size:63
Alignment explanation
Indices: 3627968--3628151 Score: 235
Period size: 64 Copynumber: 2.9 Consensus size: 63
3627958 TAATGAAGGT
* * ** * **
3627968 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
3628032 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* *
3628096 AGGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
3628152 TTAAAAGAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 98 0.93
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:3628167 original size:64 final size:64
Alignment explanation
Indices: 3628035--3628193 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 64
3628025 TGCTGGGATG
* ** *
3628035 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGAGG
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATAAGAGA
** *
3628099 CATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAGAGT
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAATAAGAG-
3628162 A
64 A
** *
3628163 CATCGATGCACTACCAATGCATCGATACACC
1 CATCGATGCACTACTTATGCATCGATGCACC
3628194 TTCAAACAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.04
64 72 0.89
65 6 0.07
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATAAGAGA
Found at i:3637294 original size:49 final size:49
Alignment explanation
Indices: 3637222--3637319 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
3637212 AAATGCAATC
3637222 ATATGTCAATATCAGAATGGATGTGTGGTGGACTAGGAAGGACACTGTT
1 ATATGTCAATATCAGAATGGATGTGTGGTGGACTAGGAAGGACACTGTT
*
3637271 ATATGTGAATATCAGAATGGATGTGTGGTGGACTAGGAAGGACACTGTT
1 ATATGTCAATATCAGAATGGATGTGTGGTGGACTAGGAAGGACACTGTT
3637320 TGAAATGAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.29
Consensus pattern (49 bp):
ATATGTCAATATCAGAATGGATGTGTGGTGGACTAGGAAGGACACTGTT
Found at i:3648676 original size:28 final size:28
Alignment explanation
Indices: 3648604--3648663 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
3648594 AGAGAATAAG
3648604 AAAAAAAATGAAAATATGTTTTAAGTAT
1 AAAAAAAATGAAAATATGTTTTAAGTAT
3648632 AAAAAAAATGAAAATATGTTTTAAGTAT
1 AAAAAAAATGAAAATATGTTTTAAGTAT
3648660 AAAA
1 AAAA
3648664 TTATTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (28 bp):
AAAAAAAATGAAAATATGTTTTAAGTAT
Found at i:3656162 original size:21 final size:21
Alignment explanation
Indices: 3656138--3656198 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3656128 CAAACTTTAC
3656138 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
3656159 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
3656174 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
3656195 CAAA
1 CAAA
3656199 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:3656173 original size:36 final size:35
Alignment explanation
Indices: 3656129--3656199 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
3656119 AACATCTACC
3656129 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
3656164 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
3656200 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:3661705 original size:20 final size:21
Alignment explanation
Indices: 3661666--3661708 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
3661656 GATATACAAT
*
3661666 TATTTATATAACATAAATAATA
1 TATTTATAAAACAT-AATAATA
3661688 TATTTATAAAACAT-ATAATA
1 TATTTATAAAACATAATAATA
3661708 T
1 T
3661709 TAATATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTTATAAAACATAATAATA
Found at i:3661720 original size:19 final size:18
Alignment explanation
Indices: 3661687--3661722 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3661677 CATAAATAAT
*
3661687 ATATTTATAAAACATATA
1 ATATTAATAAAACATATA
3661705 ATATTAATATAAACATAT
1 ATATTAATA-AAACATAT
3661723 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAATAAAACATATA
Found at i:3665081 original size:17 final size:17
Alignment explanation
Indices: 3665055--3665095 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3665045 ATATATATAT
* *
3665055 ATATATATAATTTTAAA
1 ATATAAATAATTGTAAA
3665072 ATATAAATAATTGTAAA
1 ATATAAATAATTGTAAA
3665089 ATTATAA
1 A-TATAA
3665096 CAGTTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATATAAATAATTGTAAA
Found at i:3669298 original size:64 final size:64
Alignment explanation
Indices: 3669230--3669349 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 64
3669220 TGTTCAAGGT
* * *
3669230 GTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCAAATGCCATCAGG
1 GTATCGATGCACAAGAAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATGCCATCAGG
* * * *
3669294 GTATCGATGCACAAGTAGTGCATCGATGCATTCCCTTAAAATACAAACATCGAATG
1 GTATCGATGCACAAGAAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATG
3669350 AGATTTATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (64 bp):
GTATCGATGCACAAGAAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATGCCATCAGG
Found at i:3669366 original size:64 final size:64
Alignment explanation
Indices: 3669228--3669388 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
3669218 ATTGTTCAAG
* * * * *
3669228 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCAAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATGACATCA
* * * * * *
3669292 GGGTATCGATGCACAAGTAGTGCATCGATGCATTCCCTTAAAATACAAACATCGAATGAGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATGACA-TCA
* *
3669357 -TGTACCGATGCA-TAGATAGTGCATCGATGCAC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCAC
3669389 CTGTCAAGGG
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.03
64 76 0.95
65 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCAAATGACATCA
Found at i:3670065 original size:23 final size:23
Alignment explanation
Indices: 3670033--3670099 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
3670023 ATCTTATATA
*
3670033 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
3670056 GCACTTCGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
3670079 GCACTTCGGTGCAATTCTACG
1 GCACTTCGGTGCAATTCTACG
3670100 AGCTGTCGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Done.