Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold322
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: 1390506
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 9
Found at i:282968 original size:13 final size:13
Alignment explanation
Indices: 282950--282974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282940 ATAATGCACA
282950 GTATCGATACATT
1 GTATCGATACATT
282963 GTATCGATACAT
1 GTATCGATACAT
282975 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:283107 original size:33 final size:32
Alignment explanation
Indices: 283045--283108 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
283035 CTTAACTGTT
* *
283045 TGTATCGATACACACAAGATGTATTGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
283077 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
283109 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:289195 original size:13 final size:13
Alignment explanation
Indices: 289177--289201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
289167 CAGCATTCTC
289177 TGTATCGATACAT
1 TGTATCGATACAT
289190 TGTATCGATACA
1 TGTATCGATACA
289202 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:289671 original size:20 final size:22
Alignment explanation
Indices: 289646--289688 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
289636 AGCACTCACT
*
289646 AGGTCGCGACC-GGCA-CCCCC
1 AGGTCGCAACCGGGCAGCCCCC
289666 AGGTCGCAACCGGGCAGCCCCC
1 AGGTCGCAACCGGGCAGCCCCC
289688 A
1 A
289689 CACTCACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.19, C:0.47, G:0.30, T:0.05
Consensus pattern (22 bp):
AGGTCGCAACCGGGCAGCCCCC
Found at i:291602 original size:13 final size:13
Alignment explanation
Indices: 291584--291608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291574 ATAATGCACA
291584 GTATCGATACATT
1 GTATCGATACATT
291597 GTATCGATACAT
1 GTATCGATACAT
291609 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:291621 original size:20 final size:21
Alignment explanation
Indices: 291596--291648 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
291586 ATCGATACAT
*
291596 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
291616 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
291637 TGTATCGATACA
1 TGTATCGATACA
291649 GATGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:291726 original size:13 final size:13
Alignment explanation
Indices: 291708--291733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291698 TACACACAAG
291708 ATGTATCGATACA
1 ATGTATCGATACA
291721 ATGTATCGATACA
1 ATGTATCGATACA
291734 TCCCAAAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:291750 original size:33 final size:32
Alignment explanation
Indices: 291690--291753 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
291680 CTTAACTGTT
*
291690 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
291722 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
291754 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:298899 original size:19 final size:19
Alignment explanation
Indices: 298872--298927 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
298862 TGTATCGATA
* *
298872 CATTATATCGATACATGTT
1 CATTGTATCGATACATGCT
* **
298891 CATTGTATCAATACACACT
1 CATTGTATCGATACATGCT
298910 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
298928 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:298990 original size:13 final size:13
Alignment explanation
Indices: 298972--299002 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
298962 CAATACATGG
*
298972 TACATTGTATTGA
1 TACATTGTATCGA
298985 TACATTGTATCGA
1 TACATTGTATCGA
298998 TACAT
1 TACAT
299003 AGTGGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:300637 original size:12 final size:12
Alignment explanation
Indices: 300601--300638 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
300591 AACCATTAAA
*
300601 GATGATGAAGAT
1 GATGATGAAGTT
*
300613 GATGATGATGTT
1 GATGATGAAGTT
300625 GATGATGAAGTT
1 GATGATGAAGTT
300637 GA
1 GA
300639 CTCGGATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (12 bp):
GATGATGAAGTT
Found at i:302130 original size:20 final size:21
Alignment explanation
Indices: 302100--302140 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
302090 GCTTTGTATC
302100 CATACATTGTATCGATACATG
1 CATACATTGTATCGATACATG
302121 CATA-ATTGTATCGATACATG
1 CATACATTGTATCGATACATG
302141 AAACTGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (21 bp):
CATACATTGTATCGATACATG
Found at i:303836 original size:15 final size:15
Alignment explanation
Indices: 303816--303850 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
303806 AACCATCAAA
303816 GATGATGAAGATAAT
1 GATGATGAAGATAAT
* *
303831 GATGATGATGCTAAT
1 GATGATGAAGATAAT
303846 GATGA
1 GATGA
303851 AGTTGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:306990 original size:17 final size:16
Alignment explanation
Indices: 306951--306981 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
306941 AAAGGCTTTC
306951 AAAAT-TTTTAATAAA
1 AAAATGTTTTAATAAA
306966 AAAATGTTTTAATAAA
1 AAAATGTTTTAATAAA
306982 GGAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATGTTTTAATAAA
Found at i:308341 original size:20 final size:21
Alignment explanation
Indices: 308316--308355 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
308306 ATTTTTTAGA
308316 ATGTATCGATACAT-TGAAAG
1 ATGTATCGATACATCTGAAAG
308336 ATGTATCGATACATCTGAAA
1 ATGTATCGATACATCTGAAA
308356 AAACCCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATCTGAAAG
Found at i:310936 original size:19 final size:20
Alignment explanation
Indices: 310912--310967 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
310902 TGTATCGATA
* *
310912 CATTGTATCAATACATG-TT
1 CATTGTATCGATACATGCAT
310931 CATTGTATCGATACATGCAT
1 CATTGTATCGATACATGCAT
*
310951 AATTGTATCGATACATG
1 CATTGTATCGATACATG
310968 AAACTAGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
CATTGTATCGATACATGCAT
Found at i:311040 original size:33 final size:32
Alignment explanation
Indices: 310998--311060 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
310988 TACCACTGTT
310998 TGTATCGATACATG-GCACATTGTATCGATATAA
1 TGTATCGATACATGAG-A-ATTGTATCGATATAA
311031 TGTATCGATACATGAAGAATTGTATCGATA
1 TGTATCGATACATG-AGAATTGTATCGATA
311061 CATTATCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATATAA
Found at i:314083 original size:52 final size:50
Alignment explanation
Indices: 314020--314221 Score: 208
Period size: 52 Copynumber: 3.9 Consensus size: 50
314010 GAAATAATGA
* *
314020 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGGAAATAAAATAG
* * * *
314071 AAGTTGGAGTATCCTCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACTAGG
1 -GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAA-TA-G
* * *
314125 GGTTGGAGTATCCCCGATTGT-AGAAAATTAGTGTTTTAGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTGGAAATAAAAT-AG
* *** *
314176 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAA
314222 GCCGGGGTTG
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
51 41 0.32
52 54 0.43
53 31 0.24
54 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATAG
Found at i:314218 original size:51 final size:51
Alignment explanation
Indices: 314020--314238 Score: 201
Period size: 51 Copynumber: 4.2 Consensus size: 51
314010 GAAATAATGA
* * * *
314020 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAAT-AG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTG-TTTTGGAAATAAAATCAG
* * * * * *
314071 AAGTTGGAGTATCCTCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAA-CTAGG
1 -GGTTGGAGTATCCCCGATT-ATGAGAAATTAGTGTTTTGGAAATAAAATC-A-G
* *
314125 GGTTGGAGTATCCCCGATTGT-AGAAAATTAGTGTTTTAGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGAG-AAATTAGTGTTTTGGAAATAAAATCAG
* * * ** *
314176 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCAG
314227 GGTTGGAGTATC
1 GGTTGGAGTATC
314239 TCCTCGGAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
51 54 0.39
52 54 0.39
53 31 0.22
54 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCAG
Found at i:314319 original size:52 final size:50
Alignment explanation
Indices: 314252--314388 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 50
314242 TCGGAAATAA
* *
314252 CGGAGTTGGAGTATCCTCGATT-GTGAAAATTTGGTGTTTTTGGAAATAAAAT
1 CGGAGTTGGAGTATCCCCGATTAG-GAAAA-TTGGTG-TTTTGGAAATAAAAC
314304 CGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAAC
1 CGGAGTTGGAGTATCCCCGATT--AGGAAAATTGGTGTTTTGGAAATAAAAC
* * *
314356 CGGGGTTGGAGTATCCCTGATTATGAACAATTG
1 CGGAGTTGGAGTATCCCCGATTAGGAA-AATTG
314389 AGAAACTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
50 4 0.05
51 5 0.07
52 55 0.72
53 6 0.08
54 5 0.07
55 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (50 bp):
CGGAGTTGGAGTATCCCCGATTAGGAAAATTGGTGTTTTGGAAATAAAAC
Found at i:316753 original size:13 final size:13
Alignment explanation
Indices: 316735--316760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
316725 ACAAAGATCC
316735 ATGTATCGATACA
1 ATGTATCGATACA
316748 ATGTATCGATACA
1 ATGTATCGATACA
316761 TGGAATAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:316838 original size:19 final size:19
Alignment explanation
Indices: 316814--316875 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
316804 CGATACATTA
316814 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
316833 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
316846 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
316865 TATCGATACAA
1 TATCGATACAA
316876 ATCGCTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:316850 original size:32 final size:32
Alignment explanation
Indices: 316799--316874 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
316789 GCAATAGCTT
*
316799 TGTAGCGATACATTATATCGATACAACACTTA
1 TGTATCGATACATTATATCGATACAACACTTA
*
316831 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTATATCGATACAACACTTA
316863 TGTATCGATACA
1 TGTATCGATACA
316875 AATCGCTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTATATCGATACAACACTTA
Found at i:319439 original size:13 final size:13
Alignment explanation
Indices: 319421--319445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319411 AATATTCTAA
319421 GTATCGATACATT
1 GTATCGATACATT
319434 GTATCGATACAT
1 GTATCGATACAT
319446 CAATACATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:319469 original size:68 final size:68
Alignment explanation
Indices: 319354--319510 Score: 235
Period size: 68 Copynumber: 2.3 Consensus size: 68
319344 TTTTCAGAAT
** ** * *
319354 GTATCGATACATTAAAT-GATGTATCAATACATCTGGAAAACTTAGATGTATCGATACAATATTC
1 GTATCGATACATTGTATCGATACATCAATACATCTGAAAAACTCAGATGTATCGATACAATATTC
319418 TAA
66 TAA
* *
319421 GTATCGATACATTGTATCGATACATCAATACATTTGAAAAACTCAGATGTATCGATACAATGTTC
1 GTATCGATACATTGTATCGATACATCAATACATCTGAAAAACTCAGATGTATCGATACAATATTC
319486 TAA
66 TAA
319489 GTATCGATACATTGTATCGATA
1 GTATCGATACATTGTATCGATA
319511 TAAGGCTACT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 15 0.19
68 66 0.81
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (68 bp):
GTATCGATACATTGTATCGATACATCAATACATCTGAAAAACTCAGATGTATCGATACAATATTC
TAA
Found at i:320873 original size:20 final size:20
Alignment explanation
Indices: 320822--320914 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
320812 ACCCTTAAAA
* *
320822 GTATCGATACACAATT-CAAA
1 GTATCGATACA-TATTGCAAT
320842 GTATCGATACATATTGCAAT
1 GTATCGATACATATTGCAAT
***
320862 GTATCGATACATGA-AAAAGAT
1 GTATCGATACAT-ATTGCA-AT
*
320883 GTATCGATACATGTTGCAAT
1 GTATCGATACATATTGCAAT
320903 GTATCGATACAT
1 GTATCGATACAT
320915 GAAAAAGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 41 0.68
21 16 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACATATTGCAAT
Found at i:320886 original size:21 final size:21
Alignment explanation
Indices: 320860--320935 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
320850 ACATATTGCA
320860 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
320881 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
320901 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
320922 ATGTATCGATACAT
1 ATGTATCGATACAT
320936 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:320893 original size:41 final size:41
Alignment explanation
Indices: 320842--320935 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
320832 ACAATTCAAA
320842 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
*
320883 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
320924 GTATCGATACAT
1 GTATCGATACAT
320936 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
Found at i:320915 original size:20 final size:20
Alignment explanation
Indices: 320842--320915 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
320832 ACAATTCAAA
*
320842 GTATCGATACATATTGCAAT
1 GTATCGATACATGTTGCAAT
****
320862 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
320883 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
320903 GTATCGATACATG
1 GTATCGATACATG
320916 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:320992 original size:13 final size:13
Alignment explanation
Indices: 320974--320999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320964 TACAGCAAGT
320974 ATGTATCGATACA
1 ATGTATCGATACA
320987 ATGTATCGATACA
1 ATGTATCGATACA
321000 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:323251 original size:21 final size:21
Alignment explanation
Indices: 323218--323262 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
323208 TTGCAAGTTG
*
323218 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
323240 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
323260 AAA
1 AAA
323263 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:327099 original size:20 final size:21
Alignment explanation
Indices: 327030--327107 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
327020 AAATGTCCAA
*
327030 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
327050 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
327075 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
327095 TTGTATCGATACA
1 ATGTATCGATACA
327108 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:327114 original size:13 final size:13
Alignment explanation
Indices: 327096--327133 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
327086 CATTTTTCTT
327096 TGTATCGATACAA
1 TGTATCGATACAA
*
327109 TGTATCGATACAC
1 TGTATCGATACAA
327122 TGTATCGATACA
1 TGTATCGATACA
327134 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:329615 original size:20 final size:20
Alignment explanation
Indices: 329564--329656 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
329554 ACCCTTAAAA
* *
329564 GTATCGATACACAATT-CAAA
1 GTATCGATACA-TATTGCAAT
329584 GTATCGATACATATTGCAAT
1 GTATCGATACATATTGCAAT
***
329604 GTATCGATACATGA-AAAAGAT
1 GTATCGATACAT-ATTGCA-AT
*
329625 GTATCGATACATGTTGCAAT
1 GTATCGATACATATTGCAAT
329645 GTATCGATACAT
1 GTATCGATACAT
329657 GAAAAAGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 41 0.68
21 16 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACATATTGCAAT
Found at i:329628 original size:21 final size:21
Alignment explanation
Indices: 329602--329677 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
329592 ACATATTGCA
329602 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
329623 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
329643 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
329664 ATGTATCGATACAT
1 ATGTATCGATACAT
329678 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:329635 original size:41 final size:41
Alignment explanation
Indices: 329584--329677 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
329574 ACAATTCAAA
329584 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
*
329625 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
329666 GTATCGATACAT
1 GTATCGATACAT
329678 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
Found at i:329657 original size:20 final size:20
Alignment explanation
Indices: 329584--329657 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
329574 ACAATTCAAA
*
329584 GTATCGATACATATTGCAAT
1 GTATCGATACATGTTGCAAT
****
329604 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
329625 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
329645 GTATCGATACATG
1 GTATCGATACATG
329658 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:329734 original size:13 final size:13
Alignment explanation
Indices: 329716--329741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329706 TACAGCAAGT
329716 ATGTATCGATACA
1 ATGTATCGATACA
329729 ATGTATCGATACA
1 ATGTATCGATACA
329742 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:332052 original size:19 final size:19
Alignment explanation
Indices: 332024--332076 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
332014 TGTATTCATA
* *
332024 CATTGTATCGATACATATT
1 CATTGTATCGATACACACT
* *
332043 CATTGAATCGACACACACT
1 CATTGTATCGATACACACT
332062 CAATTGTATCGATAC
1 C-ATTGTATCGATAC
332077 TTGAAACTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (19 bp):
CATTGTATCGATACACACT
Found at i:332153 original size:20 final size:20
Alignment explanation
Indices: 332130--332181 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
332120 ATGGTACATT
332130 GTATCGATACATAGTGAAAA
1 GTATCGATACATAGTGAAAA
332150 GTATCGATACATAGTGAAAA
1 GTATCGATACATAGTGAAAA
332170 GTATCGATACAT
1 GTATCGATACAT
332182 TGTCCTAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (20 bp):
GTATCGATACATAGTGAAAA
Found at i:334293 original size:13 final size:13
Alignment explanation
Indices: 334275--334300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
334265 CAATTTTTTG
334275 TGTATCGATACAT
1 TGTATCGATACAT
334288 TGTATCGATACAT
1 TGTATCGATACAT
334301 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:335040 original size:21 final size:21
Alignment explanation
Indices: 334999--335042 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
334989 CTCTCCTTTA
* *
334999 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
335020 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
335041 TC
1 TC
335043 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:336866 original size:13 final size:13
Alignment explanation
Indices: 336848--336886 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
336838 ATAATCACCC
336848 TGTATCGATACAA
1 TGTATCGATACAA
336861 TGTATCGATACAA
1 TGTATCGATACAA
336874 TGTATCGATACAA
1 TGTATCGATACAA
336887 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:338076 original size:15 final size:15
Alignment explanation
Indices: 338056--338086 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
338046 ATTTCGTTTG
*
338056 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
338071 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
338086 G
1 G
338087 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:339918 original size:21 final size:21
Alignment explanation
Indices: 339889--339933 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
339879 CAAGTTTTAT
*
339889 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
339909 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
339931 TTT
1 TTT
339934 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:350153 original size:20 final size:20
Alignment explanation
Indices: 350128--350169 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
350118 CAATCTGTTG
350128 CCTTTTCAGTGTTACCTCTA
1 CCTTTTCAGTGTTACCTCTA
*
350148 CCTTTTCAGTGTTACTTCTA
1 CCTTTTCAGTGTTACCTCTA
350168 CC
1 CC
350170 ATTTAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.31, G:0.10, T:0.45
Consensus pattern (20 bp):
CCTTTTCAGTGTTACCTCTA
Found at i:356916 original size:5 final size:5
Alignment explanation
Indices: 356906--356931 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
356896 TTAATTAGAA
356906 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
356932 GAGGAGTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:359790 original size:2 final size:2
Alignment explanation
Indices: 359785--359905 Score: 70
Period size: 2 Copynumber: 60.0 Consensus size: 2
359775 TTTGTGTATG
*
359785 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA TA CTA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * * *
359826 TGC TA TA TA TA TG CA CTT TT TA TA TA TA TA TA TA TA TA TG CA TA
1 T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
359870 T- TA TA TA TA CA CTGA -A GA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA
359906 CTAAAATTAT
Statistics
Matches: 91, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
1 4 0.04
2 83 0.91
3 3 0.03
4 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:361520 original size:20 final size:19
Alignment explanation
Indices: 361497--361569 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
361487 CACACCCAGA
*
361497 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
361517 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
361536 TGTATCGATACATG-GACAAT
1 TGTATCGATACATGTG-C-AT
361556 TGTATCGATACATG
1 TGTATCGATACATG
361570 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:361635 original size:13 final size:13
Alignment explanation
Indices: 361614--361671 Score: 80
Period size: 13 Copynumber: 4.4 Consensus size: 13
361604 CGATACATGG
*
361614 TACAATGTATCGA
1 TACATTGTATCGA
*
361627 TACATTGTATCGGG
1 TACATTGTATC-GA
*
361641 TACAATGTATCGA
1 TACATTGTATCGA
361654 TACATTGTATCGA
1 TACATTGTATCGA
361667 TACAT
1 TACAT
361672 GAAGAAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 28 0.72
14 11 0.28
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:361650 original size:27 final size:27
Alignment explanation
Indices: 361612--361665 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
361602 ATCGATACAT
361612 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
361639 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
361666 ATACATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
GGTACAATGTATCGATACATTGTATCG
Found at i:368428 original size:2 final size:2
Alignment explanation
Indices: 368423--368537 Score: 58
Period size: 2 Copynumber: 57.0 Consensus size: 2
368413 TTTGTGTATG
* *
368423 TA TA TA TA TA TA TA TA TA T- TA TG TA TA TA CTA -A TGC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA
* * * * * *
368465 TA TG CA CTT TT TA TA TA TA TA TA TA TA TA TG CA TA T- 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
* * *
368507 TA CA CTGA -A GA TA TA TA TA TA TA TA TG TA TA
1 TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA
368538 CTAAAATTAT
Statistics
Matches: 85, Mismatches: 19, Indels: 18
0.70 0.16 0.15
Matches are distributed among these distances:
1 4 0.05
2 77 0.91
3 3 0.04
4 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:370152 original size:20 final size:19
Alignment explanation
Indices: 370129--370201 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
370119 CACACCCAGA
*
370129 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
370149 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
370168 TGTATCGATACATG-GACAAT
1 TGTATCGATACATGTG-C-AT
370188 TGTATCGATACATG
1 TGTATCGATACATG
370202 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:370267 original size:13 final size:13
Alignment explanation
Indices: 370246--370303 Score: 80
Period size: 13 Copynumber: 4.4 Consensus size: 13
370236 CGATACATGG
*
370246 TACAATGTATCGA
1 TACATTGTATCGA
*
370259 TACATTGTATCGGG
1 TACATTGTATC-GA
*
370273 TACAATGTATCGA
1 TACATTGTATCGA
370286 TACATTGTATCGA
1 TACATTGTATCGA
370299 TACAT
1 TACAT
370304 GAAGAAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 28 0.72
14 11 0.28
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:370282 original size:27 final size:27
Alignment explanation
Indices: 370244--370297 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
370234 ATCGATACAT
370244 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
370271 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
370298 ATACATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
GGTACAATGTATCGATACATTGTATCG
Found at i:377060 original size:2 final size:2
Alignment explanation
Indices: 377055--377173 Score: 66
Period size: 2 Copynumber: 59.0 Consensus size: 2
377045 TTTGTGTATG
* *
377055 TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA TA CTA -A TGC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA
* * * * * *
377097 TA TA TA TG CA CTT TT TA TA TA TA TA TA TA TA TG CA TA T- TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
377139 TA TA CA CTGA -A GA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
377174 CTAAAATTAT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
1 4 0.04
2 81 0.91
3 3 0.03
4 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:378788 original size:20 final size:19
Alignment explanation
Indices: 378765--378837 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
378755 CACACCCAGA
*
378765 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
378785 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
378804 TGTATCGATACATG-GACAAT
1 TGTATCGATACATGTG-C-AT
378824 TGTATCGATACATG
1 TGTATCGATACATG
378838 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:378903 original size:13 final size:13
Alignment explanation
Indices: 378882--378939 Score: 80
Period size: 13 Copynumber: 4.4 Consensus size: 13
378872 CGATACATGG
*
378882 TACAATGTATCGA
1 TACATTGTATCGA
*
378895 TACATTGTATCGGG
1 TACATTGTATC-GA
*
378909 TACAATGTATCGA
1 TACATTGTATCGA
378922 TACATTGTATCGA
1 TACATTGTATCGA
378935 TACAT
1 TACAT
378940 GAAGAAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 28 0.72
14 11 0.28
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:378918 original size:27 final size:27
Alignment explanation
Indices: 378880--378933 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
378870 ATCGATACAT
378880 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
378907 GGTACAATGTATCGATACATTGTATCG
1 GGTACAATGTATCGATACATTGTATCG
378934 ATACATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
GGTACAATGTATCGATACATTGTATCG
Found at i:387594 original size:20 final size:19
Alignment explanation
Indices: 387547--387604 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
387537 TTTGTATCAA
387547 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
*
387566 TTCATTGTATCGATACATAG
1 TACATTGTATCGATACAT-G
387586 -ACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
387605 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:387670 original size:13 final size:13
Alignment explanation
Indices: 387649--387679 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
387639 CGATACATGG
*
387649 TACAATGTATCGA
1 TACATTGTATCGA
387662 TACATTGTATCGA
1 TACATTGTATCGA
387675 TACAT
1 TACAT
387680 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:388969 original size:22 final size:21
Alignment explanation
Indices: 388944--388985 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
388934 ATTTAAAATA
388944 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
388964 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
388985 A
1 A
388986 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:391058 original size:28 final size:28
Alignment explanation
Indices: 391026--391082 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
391016 ATAAAGCCTT
*
391026 AATCAAACTAACGAGCTTTACTTTAGTC
1 AATCAAACTAACGAGCCTTACTTTAGTC
391054 AATCAAACTAACGAGCCTTACTTTAGTC
1 AATCAAACTAACGAGCCTTACTTTAGTC
391082 A
1 A
391083 TAAGGCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (28 bp):
AATCAAACTAACGAGCCTTACTTTAGTC
Found at i:396427 original size:20 final size:20
Alignment explanation
Indices: 396361--396428 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
396351 CTAAGAAAGG
*
396361 TATTTTATTATAA-AATTTA
1 TATTTTATAATAATAATTTA
396380 TATTTTTATAAT-ATAATTATA
1 TA-TTTTATAATAATAATT-TA
396401 TATTTTATAATAATAATTGTA
1 TATTTTATAATAATAATT-TA
396422 -ATTTTAT
1 TATTTTAT
396429 TTTCTTAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.07
20 28 0.65
21 12 0.28
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TATTTTATAATAATAATTTA
Found at i:398312 original size:13 final size:13
Alignment explanation
Indices: 398294--398320 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
398284 ACATGCTGCT
398294 TTGTATCGATACA
1 TTGTATCGATACA
398307 TTGTATCGATACA
1 TTGTATCGATACA
398320 T
1 T
398321 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:398416 original size:20 final size:19
Alignment explanation
Indices: 398391--398443 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
398381 TATCACTATT
398391 TGTATCGATACATG-GTACAA
1 TGTATCGATACATGAG-A-AA
398411 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
398431 TGTATCGATACAT
1 TGTATCGATACAT
398444 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATGAGAAA
Found at i:399521 original size:19 final size:19
Alignment explanation
Indices: 399497--399589 Score: 102
Period size: 19 Copynumber: 5.5 Consensus size: 19
399487 ACAGTAACTA
399497 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
399516 TATCGATAC--AA----TG
1 TATCGATACATAAGTGTTG
399529 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
399548 TATCGATAC--AA----TG
1 TATCGATACATAAGTGTTG
399561 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
399580 TATCGATACA
1 TATCGATACA
399590 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.35
15 4 0.06
17 4 0.06
19 32 0.52
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (19 bp):
TATCGATACATAAGTGTTG
Found at i:399532 original size:13 final size:13
Alignment explanation
Indices: 399514--399603 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
399504 ACATAAGTGT
399514 TGTATCGATACAA
1 TGTATCGATACAA
399527 TGTATCGATACATAA
1 TGTATCGATAC--AA
399542 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
399559 TGTATCGATACATAA
1 TGTATCGATAC--AA
399574 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
399591 TGTATCGCTACAA
1 TGTATCGATACAA
399604 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:399538 original size:32 final size:32
Alignment explanation
Indices: 399497--399602 Score: 203
Period size: 32 Copynumber: 3.3 Consensus size: 32
399487 ACAGTAACTA
399497 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
399529 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
399561 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
399593 TATCGCTACA
1 TATCGATACA
399603 AAGCTACTGC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:402235 original size:76 final size:76
Alignment explanation
Indices: 402040--402224 Score: 282
Period size: 76 Copynumber: 2.4 Consensus size: 76
402030 TTTTCATCTC
* * * *
402040 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCTAACCCC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAAACCC
* *
402105 GTTATTTTCGA
66 GTTATTTCCAA
*
402116 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAAACCT
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAAACCC
402181 GTTATTTCCAA
66 GTTATTTCCAA
*
402192 GGGGATACTCCAACCTCGGCTTTT-TATCTAAAA
1 GGGGATACTCCAACCTCGG-TTTTATTTCTAAAA
402225 ATATTATTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 96 0.96
77 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (76 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAAACCC
GTTATTTCCAA
Found at i:402286 original size:28 final size:27
Alignment explanation
Indices: 402255--402318 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
402245 TCGGGCGTAT
**
402255 TCCAACCCTATTATTTCATCGGGGATAC
1 TCCAACCC-ATTATTTCAGAGGGGATAC
* *
402283 TCCAATCCCGTTATTTCCGAGGGGATAC
1 TCCAA-CCCATTATTTCAGAGGGGATAC
402311 TCCAACCC
1 TCCAACCC
402319 CGATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 25 0.81
29 3 0.10
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (27 bp):
TCCAACCCATTATTTCAGAGGGGATAC
Found at i:402361 original size:51 final size:51
Alignment explanation
Indices: 402303--402422 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 51
402293 TTATTTCCGA
**
402303 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAA-TTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCT-CACAATC
*
402354 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
*
402405 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
402423 TTATTTCATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 59 0.94
52 4 0.06
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:402489 original size:31 final size:28
Alignment explanation
Indices: 402406--402478 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
402396 CTCACAATCA
***
402406 GGGATACTCCAACCCCGTTATTTCATCG
1 GGGATACTCCAACCCCGTTATTTCCGAG
402434 GGGATACTCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
*
402462 GGGATACTCTAACCCCG
1 GGGATACTCCAACCCCG
402479 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAG
Found at i:402554 original size:158 final size:158
Alignment explanation
Indices: 402255--402580 Score: 402
Period size: 158 Copynumber: 2.1 Consensus size: 158
402245 TCGGGCGTAT
** *
402255 TCCAACCCTATTATTTCATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCC
1 TCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC
* ** * **
402320 GATTTTATTTTTAAAACACCAATTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAA
66 GACTTTATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAACCCCGACCTTATTTCCAA
402385 AACACCAATTTCTCACAATCAGGGATAC
131 AACACCAATTTCTCACAATCAGGGATAC
*
402413 TCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCC
1 TCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC
* * *** ** * *
402478 GGCTTTATTTCCAAAATATTGATT-TCTCACAATCGGGGATACTTTAACCCCGGCCTTATTTCTA
66 GACTTTATTTCCAAAACACCAATTCTC-CACAATCGGGGATACTCCAACCCCGACCTTATTTCCA
* *** * *
402542 AAATATTGATTTCTCATAATCGGGGATAC
130 AAACACCAATTTCTCACAATCAGGGATAC
*
402571 TCCAATCCCG
1 TCCAACCCCG
402581 ATTTTATTTT
Statistics
Matches: 141, Mismatches: 26, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
157 2 0.01
158 139 0.99
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (158 bp):
TCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC
GACTTTATTTCCAAAACACCAATTCTCCACAATCGGGGATACTCCAACCCCGACCTTATTTCCAA
AACACCAATTTCTCACAATCAGGGATAC
Found at i:402588 original size:51 final size:51
Alignment explanation
Indices: 402461--402631 Score: 200
Period size: 51 Copynumber: 3.4 Consensus size: 51
402451 TTATTTCCGA
* * *
402461 GGGGATACTCTAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCATAATC
** *
402512 GGGGATACTTTAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCATAATC
* ** * * *
402563 GGGGATACTCCAATCCCGATTTTATTTTTAAAACATCGATTT-TCTATAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTC-ATAATC
* *
402614 AGGGATACTCCAGCCCCG
1 GGGGATACTCCAACCCCG
402632 TTGTTATCTC
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 2 0.02
51 101 0.98
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCATAATC
Found at i:405905 original size:13 final size:13
Alignment explanation
Indices: 405887--405912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
405877 CAATTTTTGG
405887 TGTATCGATACAT
1 TGTATCGATACAT
405900 TGTATCGATACAT
1 TGTATCGATACAT
405913 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:405924 original size:32 final size:33
Alignment explanation
Indices: 405867--405930 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
405857 TACAAGCCAA
**
405867 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
405900 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
405931 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:405937 original size:19 final size:18
Alignment explanation
Indices: 405867--405937 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
405857 TACAAGCCAA
405867 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
405887 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
405900 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
405919 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
405938 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:406652 original size:21 final size:21
Alignment explanation
Indices: 406609--406654 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
406599 TAATTCACGC
* *
406609 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
406630 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
406651 ATTC
1 ATTC
406655 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:407807 original size:13 final size:13
Alignment explanation
Indices: 407789--407813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407779 ACTTAAGTAA
407789 TGTATCGATACAT
1 TGTATCGATACAT
407802 TGTATCGATACA
1 TGTATCGATACA
407814 ATCTAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:409403 original size:84 final size:84
Alignment explanation
Indices: 409248--409412 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
409238 CATTTTCCAC
* * * *
409248 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
409313 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
409332 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
409394 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
409413 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:411483 original size:13 final size:13
Alignment explanation
Indices: 411465--411490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
411455 CAATTTTTGG
411465 TGTATCGATACAT
1 TGTATCGATACAT
411478 TGTATCGATACAT
1 TGTATCGATACAT
411491 AGTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:411502 original size:32 final size:33
Alignment explanation
Indices: 411445--411508 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
411435 TACAAGCCAA
**
411445 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATAGTTGGTGTATCGATACAT
411478 TGTATCGATAC-ATAGTTGGTGTATCGATACA
1 TGTATCGATACAATAGTTGGTGTATCGATACA
411509 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATAGTTGGTGTATCGATACAT
Found at i:411515 original size:19 final size:18
Alignment explanation
Indices: 411445--411512 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
411435 TACAAGCCAA
*
411445 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--GTTGG
411465 TGTATCGATAC-A--T--
1 TGTATCGATACAAGTTGG
411478 TGTATCGATACATAGTTGG
1 TGTATCGATACA-AGTTGG
411497 TGTATCGATACAAGTT
1 TGTATCGATACAAGTT
411513 TGGCTACTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 4 0.10
19 13 0.31
20 11 0.26
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (18 bp):
TGTATCGATACAAGTTGG
Found at i:414571 original size:5 final size:5
Alignment explanation
Indices: 414561--414590 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
414551 TAGTTAGAAA
414561 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
414591 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:414608 original size:5 final size:6
Alignment explanation
Indices: 414560--414625 Score: 52
Period size: 5 Copynumber: 11.3 Consensus size: 6
414550 CTAGTTAGAA
*
414560 AAAATT -AAATT -AAATT -AAATT -AAATT AAATTTTT AAAAATT AAAA-T
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAA--ATT -AAAATT AAAATT
*
414606 AAAATT AAAATT AATATT AA
1 AAAATT AAAATT AAAATT AA
414626 TTGACTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
5 25 0.48
6 20 0.38
7 2 0.04
8 2 0.04
9 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AAAATT
Found at i:414982 original size:166 final size:165
Alignment explanation
Indices: 414757--415094 Score: 416
Period size: 166 Copynumber: 2.0 Consensus size: 165
414747 TAAAACTCAT
* * * *
414757 AAAATAAATTAATTTTTCAAAACTGATTCAATAGGAATTTGATGACAATATTAGATGAATTTTAA
1 AAAATAAATGAATTTTTCAAAACTGATTAAATAGGAATTAGATAACAATATTAGATGAATTTTAA
* ** *
414822 AAATTTT-AAATAGAGAAAAATCCCCCCAAAAACATTTATGGAA-TAAAAAACTTGATTTTTCGA
66 AAATTTTAAAATA-AGAAAAATCCCCCCAAAAACATTTA-CGAAGTAAAAAACTCCATATTTC-A
414885 AAAAAAGAA-AATTTCAAAGAAAAAATGAAAAACATATG
128 AAAAAAGAAGAATTTC-AAGAAAAAATGAAAAACATATG
* * * * *
414923 AAAATATATGAATTTTTCAAAACTGATTAAATAATG-ATTAGATAATAGTATTTGATGAATTTTA
1 AAAATAAATGAATTTTTCAAAACTGATTAAAT-AGGAATTAGATAACAATATTAGATGAATTTTA
* * * *
414987 AAAATTTTAAAATAAGAAAAATCCCTCCAAAAATATTTACGAAGTAGAAAACTCCATATTTCAGA
65 AAAATTTTAAAATAAGAAAAATCCCCCCAAAAACATTTACGAAGTAAAAAACTCCATATTTCAAA
* **
415052 AATAGAAGAATTTCAAGAAAAAATGAAAAATTTAT-
130 AAAAGAAGAATTTCAAGAAAAAATGAAAAACATATG
415087 AAAATAAA
1 AAAATAAA
415095 ATAAAATTTT
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
164 7 0.05
165 30 0.20
166 103 0.70
167 7 0.05
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (165 bp):
AAAATAAATGAATTTTTCAAAACTGATTAAATAGGAATTAGATAACAATATTAGATGAATTTTAA
AAATTTTAAAATAAGAAAAATCCCCCCAAAAACATTTACGAAGTAAAAAACTCCATATTTCAAAA
AAAGAAGAATTTCAAGAAAAAATGAAAAACATATG
Found at i:415109 original size:20 final size:21
Alignment explanation
Indices: 415071--415109 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
415061 ATTTCAAGAA
415071 AAAATGAAAAATTTATAAAAT
1 AAAATGAAAAATTTATAAAAT
* *
415092 AAAAT-AAAATTTTTTAAA
1 AAAATGAAAAATTTATAAA
415110 CTAATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATGAAAAATTTATAAAAT
Found at i:418879 original size:3 final size:3
Alignment explanation
Indices: 418871--418896 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
418861 AGTATTTCTC
418871 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
418897 AATGATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:430915 original size:13 final size:13
Alignment explanation
Indices: 430889--430922 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
430879 CTATTTTATC
*
430889 TTTTTTCT-TTTT
1 TTTTTTCTCTCTT
430901 TTTTTTCTCTCTT
1 TTTTTTCTCTCTT
430914 TTTTTTCTC
1 TTTTTTCTC
430923 CCTTGCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTCTCTT
Found at i:431926 original size:168 final size:167
Alignment explanation
Indices: 431598--432055 Score: 645
Period size: 168 Copynumber: 2.7 Consensus size: 167
431588 CATGAAAATG
* * * * * *
431598 ACTGTTTTACTATAATTTAAATGATCATCTTTGATGAATTTTAAAAATTATAAACTAAGAAAAAT
1 ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAATTATAAACCAAGAAAAAT
* * * *
431663 CCTTCTGAAAATAATTAC-GGAGTAGAAAACTTCGTATTTCGAAAACATGAGAATTTCAAGGAAC
66 CC-CCTGAAAATAATTACTGGAGTAGAAAACTCCGTATTTAGAAAACAAGAGAATTTCAAGGAAC
431727 AAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
130 AAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
*
431765 ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAGTTATAAACCAAGAAAAAT
1 ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAATTATAAACCAAGAAAAAT
* *
431830 CTCCCTGAAAATAATTACTGGAGTAGAAAACTCCGTATTTAGAAAATAAGAGAATTTTAAGGAAC
66 C-CCCTGAAAATAATTACTGGAGTAGAAAACTCCGTATTTAGAAAACAAGAGAATTTCAAGGAAC
431895 AAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
130 AAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
* * * *
431933 ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTGTAAACCAAGAAAGAT
1 ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAATTATAAACCAAGAAAAAT
** * * * *
431998 CCCCCAAAAACAATTA-TAGAGTAGAAAACT-C-TATATTATGAAAACAGGAAAATTTCAA
66 CCCCTGAAAATAATTACTGGAGTAGAAAACTCCGTAT-TTA-GAAAACAAGAGAATTTCAA
432056 TGAAAAATTA
Statistics
Matches: 261, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
164 3 0.01
165 4 0.02
166 28 0.11
167 85 0.33
168 141 0.54
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (167 bp):
ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAATTATAAACCAAGAAAAAT
CCCCTGAAAATAATTACTGGAGTAGAAAACTCCGTATTTAGAAAACAAGAGAATTTCAAGGAACA
AAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
Found at i:432082 original size:157 final size:164
Alignment explanation
Indices: 431598--432121 Score: 523
Period size: 168 Copynumber: 3.2 Consensus size: 164
431588 CATGAAAATG
* * * * * * * *
431598 ACTGTTTTACTATAATTTAAATGATCATCTTTGATGAATTTTAAAAATTATAAACTAAGAAAAAT
1 ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTATAAACCAAGAAAAAT
* ** * * * * * *
431663 C-CTTCTGAAAATAATTAC-GGAGTAGAAAACTTCGTATTTCGAAAACATGAGAATTTCAAGGAA
66 CTC-CCCAAAAACAATTACTAGAGTAGAAAACTCCGTATTTAGAAAACAAGAAAATTTCAAGGAA
431726 CAAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
130 CAAAATGAAAAA--CAT-AAAA-GAATGAATTTTTCAAA
* * *
431765 ACTGATTTACTATGATTTAAATGATGATATTTGATGAGTTTTAAAAGTTATAAACCAAGAAAAAT
1 ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTATAAACCAAGAAAAAT
** * * * * *
431830 CTCCCTGAAAATAATTACTGGAGTAGAAAACTCCGTATTTAGAAAATAAGAGAATTTTAAGGAAC
66 CTCCCCAAAAACAATTACTAGAGTAGAAAACTCCGTATTTAGAAAACAAGAAAATTTCAAGGAAC
431895 AAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
131 AAAATGAAAAA--CAT-AAAA-GAATGAATTTTTCAAA
* *
431933 ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTGTAAACCAAGAAAGAT
1 ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTATAAACCAAGAAAAAT
* *
431998 C-CCCCAAAAACAATTA-TAGAGTAGAAAACT-C-TATATTATGAAAACAGGAAAATTTCAATG-
66 CTCCCCAAAAACAATTACTAGAGTAGAAAACTCCGTAT-TTA-GAAAACAAGAAAATTTCAAGGA
* * **
432058 A-AAAATTAAGGAA-AT-AAA-AA-GAATTTTTTGAA
129 ACAAAATGAA-AAACATAAAAGAATGAATTTTTCAAA
* *
432090 ACTGATTTATTGTGAGTTAAATGATGATATTT
1 ACTGATTTATTATGATTTAAATGATGATATTT
432122 AAAGAATTTT
Statistics
Matches: 319, Mismatches: 33, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
157 40 0.13
158 2 0.01
160 3 0.01
162 2 0.01
164 10 0.03
165 7 0.02
166 29 0.09
167 85 0.27
168 141 0.44
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.32
Consensus pattern (164 bp):
ACTGATTTATTATGATTTAAATGATGATATTTGATGAGTTATAAAAATTATAAACCAAGAAAAAT
CTCCCCAAAAACAATTACTAGAGTAGAAAACTCCGTATTTAGAAAACAAGAAAATTTCAAGGAAC
AAAATGAAAAACATAAAAGAATGAATTTTTCAAA
Found at i:433567 original size:230 final size:228
Alignment explanation
Indices: 433158--433593 Score: 588
Period size: 228 Copynumber: 1.9 Consensus size: 228
433148 GTTGAGAATG
* * * * *
433158 TGGAATCCAAACTTCTCTTTCACAGGAATTCTAAATTCTAGAATAACTTGGATTGCATACCAGCT
1 TGGAATCCAAACATCCCTTTCACAGAAATTCTAAATTCTAAAATAAATTGGATTGCATACCAGCT
* * * *
433223 TTAGATTAGTGTTAGGTTGTCATTGGCTTGATTTTGTCATATCAGTGATTGACTAACTCAAATTA
66 TTAGATTAGTATCAGGTTGTCATTGACTTGATTTTGTCATATCAGTGATTGACTAACTCAAAGTA
*
433288 TATTCCTCTCATTTTATAAATGGTTAATGATTTTCATAATGGGTGTACTCATTTTCA-TGTGTAC
131 TATTCCTCTCATTTTATAAATGGTTAATGATTTTCATAATGGGTGTACTCATTTTCACAG-GTAC
433352 ATTAGAAACATTCCCCCCTGTCCTTTTATAAATA
195 ATTAGAAACATTCCCCCCTGTCCTTTTATAAATA
* * * **
433386 TGGAATCCAAACATCCCTCTTC-CAGAAATTCTAAATTTTAAAATAAATTTGATTGCTTACTGGC
1 TGGAATCCAAACATCCCT-TTCACAGAAATTCTAAATTCTAAAATAAATTGGATTGCATACCAGC
* * * * *
433450 TTTAGATTAGTATCGGGTTGTCATTGACTTGATTTTTTTATATCTGTGTGATTGACTGACTCAAA
65 TTTAGATTAGTATCAGGTTGTCATTGACTTGATTTTGTCATATC--AGTGATTGACTAACTCAAA
* * * * *
433515 GTCTATTCCTTTCTTTTTTTTAATGGTTAATGATTTTCATAATGGGTGTACTCATTTTCACAGGT
128 GTATATTCCTCTCATTTTATAAATGGTTAATGATTTTCATAATGGGTGTACTCATTTTCACAGGT
*
433580 ATATTAGAAACATT
193 ACATTAGAAACATT
433594 TCTCATACAA
Statistics
Matches: 178, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
228 88 0.49
229 3 0.02
230 86 0.48
231 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (228 bp):
TGGAATCCAAACATCCCTTTCACAGAAATTCTAAATTCTAAAATAAATTGGATTGCATACCAGCT
TTAGATTAGTATCAGGTTGTCATTGACTTGATTTTGTCATATCAGTGATTGACTAACTCAAAGTA
TATTCCTCTCATTTTATAAATGGTTAATGATTTTCATAATGGGTGTACTCATTTTCACAGGTACA
TTAGAAACATTCCCCCCTGTCCTTTTATAAATA
Found at i:435372 original size:6 final size:6
Alignment explanation
Indices: 435361--435388 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
435351 AACTTGATAT
435361 TTAAAA TTAAAA TTAAAA TTAAAA TTAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAA
435389 TTGAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:435519 original size:32 final size:31
Alignment explanation
Indices: 435437--435520 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 31
435427 TTTTTAACAT
* *
435437 TCAAGTTAAATTAAGAATTAAAATTAATTTA
1 TCAAATTAAATTAAAAATTAAAATTAATTTA
* * *
435468 TAAAATATAAAATATAAAATT-AATTTAATTATAA
1 TCAAAT-TAAATTA-AAAATTAAAATTAATT-T-A
435502 TCAAATTAAATTAAAAATT
1 TCAAATTAAATTAAAAATT
435521 TATAAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
31 4 0.10
32 20 0.48
33 12 0.29
34 6 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (31 bp):
TCAAATTAAATTAAAAATTAAAATTAATTTA
Found at i:435583 original size:17 final size:15
Alignment explanation
Indices: 435561--435620 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
435551 ACACATATAT
435561 AAAATATAATTTAATTA
1 AAAATAT-A-TTAATTA
*
435578 AAAATATATTAA-AA
1 AAAATATATTAATTA
435592 ATAAATATAATTAATATA
1 A-AAATAT-ATTAAT-TA
435610 TAAAATATATT
1 -AAAATATATT
435621 TAAAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 2 0.06
15 10 0.28
16 6 0.17
17 10 0.28
18 7 0.19
19 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATATTAATTA
Found at i:435596 original size:33 final size:34
Alignment explanation
Indices: 435562--435627 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 34
435552 CACATATATA
435562 AAATATAATTTAAT-TA-AAAATATA-TTAAAAAT
1 AAATATAA-TTAATATATAAAATATATTTAAAAAT
435594 AAATATAATTAATATATAAAATATATTTAAAAAT
1 AAATATAATTAATATATAAAATATATTTAAAAAT
435628 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 5 0.16
32 10 0.32
33 8 0.26
34 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATATAATTAATATATAAAATATATTTAAAAAT
Found at i:435638 original size:5 final size:5
Alignment explanation
Indices: 435628--435667 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
435618 ATTTAAAAAT
435628 TTAAA TTAAA TTAAA TTAAA TTAAA TT-AA TTAAA TATAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T-TAAA
435668 ATACATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:436093 original size:5 final size:5
Alignment explanation
Indices: 436083--436119 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
436073 AACGCCTATG
*
436083 TATAA TATAA TATAT TATAA -ATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
436120 CCATCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:436835 original size:33 final size:32
Alignment explanation
Indices: 436781--436892 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
436771 ATATAACTAG
436781 TATAAATATATTATTATATAAAAATTTATATAA
1 TATAAATATATTATTATAT-AAAATTTATATAA
436814 TATAAAT-TATTAATT-TAATAAAATTTATATAAAA
1 TATAAATATATT-ATTAT-ATAAAATTTATAT--AA
* **
436848 TATATAATATATTAAATATGATAAAAAATATACTAA
1 TATA-AATATATT-ATTAT-ATAAAATTTATA-TAA
436884 TA-AAATATA
1 TATAAATATA
436893 AAAATATTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
32 16 0.24
33 12 0.18
34 12 0.18
35 4 0.06
36 11 0.16
37 11 0.16
38 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
TATAAATATATTATTATATAAAATTTATATAA
Found at i:437366 original size:42 final size:42
Alignment explanation
Indices: 437307--437388 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
437297 TAAGATTTTT
* *
437307 GAGTAAAGTGGGTAGGCTGTAGTTTGTCAAGAAACCAAGCAA
1 GAGTAAAGTAGGTAGGCTGTAGTTTGCCAAGAAACCAAGCAA
*
437349 GAGTAAAGTAGGTAGGCTGTAGTTTGCCAAGAAACTAAGC
1 GAGTAAAGTAGGTAGGCTGTAGTTTGCCAAGAAACCAAGC
437389 CAAATGCTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.22
Consensus pattern (42 bp):
GAGTAAAGTAGGTAGGCTGTAGTTTGCCAAGAAACCAAGCAA
Found at i:439308 original size:12 final size:12
Alignment explanation
Indices: 439291--439315 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
439281 GAGAAGAAAG
439291 AGAAAATAAAAA
1 AGAAAATAAAAA
439303 AGAAAATAAAAA
1 AGAAAATAAAAA
439315 A
1 A
439316 TAACACAAAT
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AGAAAATAAAAA
Found at i:442140 original size:33 final size:33
Alignment explanation
Indices: 442084--442148 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
442074 GTTGGAAGCA
* *
442084 ATGTATCGATACAATTCATCATGTATTGATACG
1 ATGTATCGATACAATTCACCATGTATCGATACG
*
442117 ATGTATCGATATAATGT-ACCATGTATCGATAC
1 ATGTATCGATACAAT-TCACCATGTATCGATAC
442149 AAACAGTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACAATTCACCATGTATCGATACG
Found at i:442204 original size:20 final size:20
Alignment explanation
Indices: 442179--442232 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
442169 CTGTCAGTTT
**
442179 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
442199 CATGTATTGATAC-ATTGAA
1 CATGTATCGATACAATTGAA
442218 CATGTATCGATACAA
1 CATGTATCGATACAA
442233 AGCATAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:443956 original size:26 final size:26
Alignment explanation
Indices: 443926--443985 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
443916 AACATTAGAC
443926 CAATATTTAATCCCATTGATTAGGAT
1 CAATATTTAATCCCATTGATTAGGAT
443952 CAATATTTAATCCCATTGATTAGGAT
1 CAATATTTAATCCCATTGATTAGGAT
*
443978 TAATATTT
1 CAATATTT
443986 GCCTAACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (26 bp):
CAATATTTAATCCCATTGATTAGGAT
Found at i:445324 original size:111 final size:110
Alignment explanation
Indices: 445090--445413 Score: 343
Period size: 109 Copynumber: 2.9 Consensus size: 110
445080 TTAGCCTAAC
* * ** * *
445090 ATAATTAAATAAACTAGGTCTAAAATAAATTAATTAATATGCACATAGGCTTATTTTGTCTAATA
1 ATAATTAAATAAA-TAGGCCT-AAATAAATTAATTAATAAGCATGTAGACTTATTTTATCTAATA
* * * * * *
445155 TATATTTTTGATAAGGCTTGGCGTGAAATTAAATGATTTATGACGCAAT
64 TAT-TTTTTTATAAGACTTGGCCTTAAATTAAAT-AATTATGACCCAAT
* *
445204 ATAATTAAATGAAATAGGCCTAAATAAATTAATTAAATAAGCATGTAGACCTA-TTTATCTATTA
1 ATAATTAAAT-AAATAGGCCTAAATAAATTAATT-AATAAGCATGTAGACTTATTTTATCTAATA
*
445268 TATTTTTTTATAAGATTTGGCCTTAAATTAAATAATTATGACCCAAT
64 TATTTTTTTATAAGACTTGGCCTTAAATTAAATAATTATGACCCAAT
* * *
445315 ATAAGTAAATAAAATAGGCCCAAATAAATTAA-T--TAAGCATGTGTGACTTATTTTATCTAATA
1 ATAATTAAAT-AAATAGGCCTAAATAAATTAATTAATAAGCATGT-AGACTTATTTTATCTAATA
* * *
445377 TATATTTTTATATA-ACTTGGGCTTAAATTAAAAAATT
64 TATTTTTTTATA-AGACTTGGCCTTAAATTAAATAATT
445414 TAAGACCTTG
Statistics
Matches: 180, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
107 9 0.05
108 5 0.03
109 41 0.23
110 2 0.01
111 41 0.23
112 25 0.14
113 25 0.14
114 29 0.16
115 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (110 bp):
ATAATTAAATAAATAGGCCTAAATAAATTAATTAATAAGCATGTAGACTTATTTTATCTAATATA
TTTTTTTATAAGACTTGGCCTTAAATTAAATAATTATGACCCAAT
Found at i:446103 original size:36 final size:36
Alignment explanation
Indices: 446063--446422 Score: 254
Period size: 36 Copynumber: 10.1 Consensus size: 36
446053 TTTAGAAGTT
** *
446063 ATATCCTTAAGAAAGGCTTTAAAAGTTTTTAATGAA
1 ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
* *
446099 ATAT-CTTAAGGAGAGG-TTTCGG-AGGTTTT--TGAA
1 ATATCCTTAA-GAAAGGCTTT-GGAAGTTTTTGATGAA
* *
446132 ATATCCTTAAGAAAGGCTTCGGAAGTTTTTAATGAA
1 ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
* * * *
446168 ACATCATCAAGAGAA-GCTTTGGAAGTTTTTGATGGA
1 ATATCCTTAAGA-AAGGCTTTGGAAGTTTTTGATGAA
* * * * *
446204 ACATCCTCTAA-AAAGACTTCGGAAGTCTTTAATGAA
1 ATATCCT-TAAGAAAGGCTTTGGAAGTTTTTGATGAA
* ** * * * * *
446240 ATGTCCCCAAGAAACGTTTTGG-AGGTTTTGCTAAA
1 ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
* ** *
446275 ATATCCTTAA-AAGAAGCTTTAAAAGTTTTTAATGAA
1 ATATCCTTAAGAA-AGGCTTTGGAAGTTTTTGATGAA
* * *
446311 ACAT-CTTCAAGAAGGGCTTTGGAGGTTTTTGATGAA
1 ATATCCTT-AAGAAAGGCTTTGGAAGTTTTTGATGAA
* * *
446347 ACATCCTCAAGAAAAGCTTTGGAAGTTTTTGATGAA
1 ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
* * * *
446383 ATATCCTTAAAAAAGGCTTTGAAACTTTTTGATAAA
1 ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
446419 ATAT
1 ATAT
446423 TTTTAATGAA
Statistics
Matches: 246, Mismatches: 62, Indels: 32
0.72 0.18 0.09
Matches are distributed among these distances:
33 15 0.06
34 15 0.06
35 41 0.17
36 167 0.68
37 8 0.03
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
ATATCCTTAAGAAAGGCTTTGGAAGTTTTTGATGAA
Found at i:446153 original size:33 final size:33
Alignment explanation
Indices: 446063--446161 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 33
446053 TTTAGAAGTT
*** *
446063 ATATCCTTAAGAAAGGCTTTAAAAGTTTTTAATGAA
1 ATATCCTTAAGAAAGGC-TTCGGAGGTTTT--TGAA
* *
446099 ATAT-CTTAAGGAGAGGTTTCGGAGGTTTTTGAA
1 ATATCCTTAA-GAAAGGCTTCGGAGGTTTTTGAA
*
446132 ATATCCTTAAGAAAGGCTTCGGAAGTTTTT
1 ATATCCTTAAGAAAGGCTTCGGAGGTTTTT
446162 AATGAAACAT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
33 25 0.48
34 5 0.10
35 13 0.25
36 9 0.17
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (33 bp):
ATATCCTTAAGAAAGGCTTCGGAGGTTTTTGAA
Found at i:446315 original size:107 final size:108
Alignment explanation
Indices: 446179--446412 Score: 249
Period size: 107 Copynumber: 2.2 Consensus size: 108
446169 CATCATCAAG
* * * **
446179 AGAAGCTTTGGAAGTTTTTGATGGAACATCCTCTAA-AAAGACTTCGGAAGTCTTTAATGAAATG
1 AGAAGCTTTGAAAGTTTTTAATGAAACATCCTC-AAGAAAGACTTCGGAAGTCTTTAATGAAACA
* * *
446243 TCCCCAAGAAACGTTTTGG-AGGTTTTGCTAAAATATCCTTAAA
65 TCCCCAAGAAAAGCTTTGGAAGGTTTTGATAAAATATCCTTAAA
* * * * * * * *
446286 AGAAGCTTTAAAAGTTTTTAATGAAACATCTTCAAGAAGGGCTTTGGAGGTTTTTGATGAAACAT
1 AGAAGCTTTGAAAGTTTTTAATGAAACATCCTCAAGAAAGACTTCGGAAGTCTTTAATGAAACAT
* * *
446351 CCTCAAGAAAAGCTTTGGAAGTTTTTGATGAAATATCCTTAAA
66 CCCCAAGAAAAGCTTTGGAAGGTTTTGATAAAATATCCTTAAA
*
446394 A-AAGGCTTTGAAACTTTTT
1 AGAA-GCTTTGAAAGTTTTT
446413 GATAAAATAT
Statistics
Matches: 103, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
106 2 0.02
107 66 0.64
108 35 0.34
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (108 bp):
AGAAGCTTTGAAAGTTTTTAATGAAACATCCTCAAGAAAGACTTCGGAAGTCTTTAATGAAACAT
CCCCAAGAAAAGCTTTGGAAGGTTTTGATAAAATATCCTTAAA
Found at i:446462 original size:50 final size:50
Alignment explanation
Indices: 446372--446467 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
446362 GCTTTGGAAG
* * * * *
446372 TTTTTGATGAAATATCCTTAAAAAAGGCTTTGAAACTTTTTGATAAAATA
1 TTTTTAATGAAACATCCTCAAAAAAGGATTTGAAACTTTTTAATAAAATA
* *
446422 TTTTTAATGAAACATCCTCAAGAGAGGATTTGGAAA-TTTTTAATAA
1 TTTTTAATGAAACATCCTCAAAAAAGGATTT-GAAACTTTTTAATAA
446468 CCGAGGTCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 34 0.89
51 4 0.11
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (50 bp):
TTTTTAATGAAACATCCTCAAAAAAGGATTTGAAACTTTTTAATAAAATA
Found at i:447682 original size:20 final size:21
Alignment explanation
Indices: 447657--447707 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
447647 TTACAATTTA
*
447657 TATTGATACATGACT-GAATG
1 TATTGATACATGACTAAAATG
* *
447677 TATTGATATATGCCTAAAATG
1 TATTGATACATGACTAAAATG
*
447698 TATCGATACA
1 TATTGATACA
447708 AAACCACCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (21 bp):
TATTGATACATGACTAAAATG
Found at i:447818 original size:74 final size:74
Alignment explanation
Indices: 447732--447915 Score: 291
Period size: 74 Copynumber: 2.5 Consensus size: 74
447722 ATTGCCAAAG
* * * *
447732 AAATGTATCGATACATGCTTATAATTGTATTGATACATTTCTTATTGTATCGATACATTCTGGGT
1 AAATGTATCGATACATGCTTACAATCGTATCGATACATTTCTCATTGTATCGATACATTCTGGGT
447797 TTTTGACCC
66 TTTTGACCC
*
447806 AAATGTATCGATACACGCTTACAATCGTATCGATACATTTCTCATTGTATCGATACATTCTGGGT
1 AAATGTATCGATACATGCTTACAATCGTATCGATACATTTCTCATTGTATCGATACATTCTGGGT
447871 TTTTGACCC
66 TTTTGACCC
* *
447880 AAATGTATCGATACATTCTT-CAA-CGTATCAATACAT
1 AAATGTATCGATACATGCTTACAATCGTATCGATACAT
447916 GCAGGCAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 12 0.12
73 3 0.03
74 87 0.85
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (74 bp):
AAATGTATCGATACATGCTTACAATCGTATCGATACATTTCTCATTGTATCGATACATTCTGGGT
TTTTGACCC
Found at i:455972 original size:21 final size:20
Alignment explanation
Indices: 455926--455978 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
455916 GTAGCTAAAC
**
455926 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
455946 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
455966 TTGTATCGATACA
1 TTGTATCGATACA
455979 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:462157 original size:13 final size:13
Alignment explanation
Indices: 462139--462177 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
462129 ACATTTTTCT
462139 TTGTATCGATACA
1 TTGTATCGATACA
462152 TTGTATCGATACA
1 TTGTATCGATACA
*
462165 CTGTATCGATACA
1 TTGTATCGATACA
462178 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:464757 original size:13 final size:13
Alignment explanation
Indices: 464739--464764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464729 TACACCAAGT
464739 ATGTATCGATACA
1 ATGTATCGATACA
464752 ATGTATCGATACA
1 ATGTATCGATACA
464765 CCAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:464783 original size:34 final size:32
Alignment explanation
Indices: 464721--464785 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
464711 TAGCCAAACT
**
464721 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
464753 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
464786 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:471926 original size:12 final size:11
Alignment explanation
Indices: 471907--471948 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
471897 CATCCTTCGT
*
471907 AAAAAAAAACA
1 AAAAAAAAATA
471918 AACAAAAAAATA
1 AA-AAAAAAATA
471930 AAAATAAAAATA
1 AAAA-AAAAATA
471942 AAAAAAA
1 AAAAAAA
471949 GAAAGGTCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:473734 original size:130 final size:130
Alignment explanation
Indices: 473497--473866 Score: 480
Period size: 130 Copynumber: 2.9 Consensus size: 130
473487 CATGACTTCG
* * *
473497 TGACACCTCATCTTTTTAAACCCACACAAGTTGGTGGCATCC-TTCTCAAAAGCCCACACAAGTA
1 TGACACTTCATCTTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTT
* * * *
473561 GGTGGTATCCTTTT-TTTCAAAGCCCACAACTCCGTGGCACCTTCCTTCTAAAGTCTATAACTCT
66 GGTGGCAT-CTTTTCTTTCAAAGCCCATAACTCCGTGGCACCTTCCTTCTAAAGTCCACAACTCT
473625 A
130 A
***
473626 T-AGCACTTCATCTTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCTTGCACAAGT
1 TGA-CACTTCATCTTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGT
*
473690 TGATGGCATCTTTTCTTTCAAAGCCCATAACTCCGTGGCACCTTCCTTCTAAAGTCCACAACTCT
65 TGGTGGCATCTTTTCTTTCAAAGCCCATAACTCCGTGGCACCTTCCTTCTAAAGTCCACAACTCT
*
473755 G
130 A
* * * * *
473756 TGACACTTCATCCTTTTAAGCTCACACAAGTCGGTGGCATCCTTTCTCCAAAGCCCACATAAGTT
1 TGACACTTCATCTTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTT
* * ** *
473821 GGTGGCAACCTTTTC--TCAAAGCCTATAACTTTGTGGCATCTTCCTT
66 GGTGGC-ATCTTTTCTTTCAAAGCCCATAACTCCGTGGCACCTTCCTT
473867 TCAAAAACCA
Statistics
Matches: 210, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
128 1 0.00
129 70 0.33
130 131 0.62
131 8 0.04
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.31
Consensus pattern (130 bp):
TGACACTTCATCTTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTT
GGTGGCATCTTTTCTTTCAAAGCCCATAACTCCGTGGCACCTTCCTTCTAAAGTCCACAACTCTA
Found at i:473833 original size:33 final size:33
Alignment explanation
Indices: 473773--473843 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
473763 TCATCCTTTT
* *
473773 AAGCTCACACAAGTCGGTGGCATCC-TTTCTCCA
1 AAGCCCACACAAGTCGGTGGCAACCTTTTCT-CA
* *
473806 AAGCCCACATAAGTTGGTGGCAACCTTTTCTCA
1 AAGCCCACACAAGTCGGTGGCAACCTTTTCTCA
473839 AAGCC
1 AAGCC
473844 TATAACTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (33 bp):
AAGCCCACACAAGTCGGTGGCAACCTTTTCTCA
Found at i:474154 original size:52 final size:52
Alignment explanation
Indices: 474082--474277 Score: 232
Period size: 52 Copynumber: 3.8 Consensus size: 52
474072 TTCCATTTTA
* * * *
474082 AAGTCTAATGTCGCTAGCCCTGAATCAGCATATTAGCACTC-TCTTCATCTTT
1 AAGTCCAATGTCGATGGCCCTGAATCAGCACATTAGCACTCATC-TCATCTTT
* * * * *
474134 AAGTCCAATGTCGTTGGCCCTAAATTAGCACATTGGCACCCATCTCATCTTT
1 AAGTCCAATGTCGATGGCCCTGAATCAGCACATTAGCACTCATCTCATCTTT
* * * *
474186 AAGTCCAATGTCGATGGCCTTGAATCAACACATTGGCACTCATCTCATTTTT
1 AAGTCCAATGTCGATGGCCCTGAATCAGCACATTAGCACTCATCTCATCTTT
* **
474238 AAGTCCAATGTCGATGGCCTTGAATTGGCACATTAGCACT
1 AAGTCCAATGTCGATGGCCCTGAATCAGCACATTAGCACT
474278 TTTGTCATCT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
52 122 0.98
53 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (52 bp):
AAGTCCAATGTCGATGGCCCTGAATCAGCACATTAGCACTCATCTCATCTTT
Done.