Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 399999
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:4377 original size:21 final size:21
Alignment explanation
Indices: 4351--4391 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4341 AAGAGTTGCA
4351 AAATTATATAGT-CAAATTGAT
1 AAATTATATAGTGC-AATTGAT
*
4372 AAATTATGTAGTGCAATTGA
1 AAATTATATAGTGCAATTGA
4392 CAATTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (21 bp):
AAATTATATAGTGCAATTGAT
Found at i:4745 original size:42 final size:42
Alignment explanation
Indices: 4698--4780 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
4688 TATGTTTTAT
* *
4698 GATGTTTGACTATTTATTTATGCGGGTTTAGTTTATTAATTG
1 GATGTTTGACTATTAATTTATGCGGGCTTAGTTTATTAATTG
***
4740 GATGTTTGACTATTAATTTATGTTTGCTTAGTTTATTAATT
1 GATGTTTGACTATTAATTTATGCGGGCTTAGTTTATTAATT
4781 TCATTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (42 bp):
GATGTTTGACTATTAATTTATGCGGGCTTAGTTTATTAATTG
Found at i:13163 original size:15 final size:16
Alignment explanation
Indices: 13138--13167 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13128 AAAAAAACAG
13138 AAAAATAAATAAAAAC
1 AAAAATAAATAAAAAC
13154 AAAAAT-AATAAAAA
1 AAAAATAAATAAAAA
13168 GTCCTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAATAAATAAAAAC
Found at i:13163 original size:19 final size:18
Alignment explanation
Indices: 13130--13165 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13120 TCACCCAGAA
*
13130 AAAAACAGAAAAATAAAT
1 AAAAACAAAAAAATAAAT
13148 AAAAACAAAAATAATAAA
1 AAAAACAAAAA-AATAAA
13166 AAGTCCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAACAAAAAAATAAAT
Found at i:14515 original size:56 final size:52
Alignment explanation
Indices: 14462--14581 Score: 125
Period size: 53 Copynumber: 2.2 Consensus size: 52
14452 CATATTATTC
14462 ATTATATTATTTATATTATT-ATACATTTTGTTTATAAATTTTATTATAAATTATAT
1 ATTATATTATTTATATTATTCATACA-TTT-TTT-T--ATTTTATTATAAATTATAT
* * * * *
14518 ATTTTACTATATATATTATTCCTTACATTTTTTTATTTTATTATAAATTATGT
1 ATTATATTATTTATATTATT-CATACATTTTTTTATTTTATTATAAATTATAT
*
14571 ATTATTTTATT
1 ATTATATTATT
14582 ATTCATTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
53 25 0.47
55 1 0.02
56 20 0.38
57 3 0.06
58 4 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (52 bp):
ATTATATTATTTATATTATTCATACATTTTTTTATTTTATTATAAATTATAT
Found at i:25476 original size:16 final size:17
Alignment explanation
Indices: 25445--25477 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25435 TTCATAAGTA
25445 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
*
25462 TATATTAAT-ATTTCAT
1 TATATCAATCATTTCAT
25478 GCTCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:25823 original size:46 final size:46
Alignment explanation
Indices: 25758--25862 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
25748 TTATCTTTGA
* * * *
25758 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-TTTTCATGT
*
25804 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGT
*
25850 CACGTTG-CATGGT
1 CATGTTGCCATGGT
25863 CTTATTCATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 11 0.21
46 41 0.79
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGT
Found at i:25874 original size:29 final size:30
Alignment explanation
Indices: 25827--25892 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
25817 TATCTTTCAA
* *
25827 CCATGGTCTTATTCTTTTCATGTCACGTTG
1 CCATGGTCTTATTCATTTCATATCACGTTG
25857 -CATGGTCTTATTCATTTCATATCACGTTG
1 CCATGGTCTTATTCATTTCATATCACGTTG
25886 CCATGGT
1 CCATGGT
25893 ATCTTTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (30 bp):
CCATGGTCTTATTCATTTCATATCACGTTG
Found at i:25921 original size:75 final size:76
Alignment explanation
Indices: 25783--25938 Score: 217
Period size: 75 Copynumber: 2.1 Consensus size: 76
25773 TCTTTCAACT
* * ** *
25783 ATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCAT
1 ATGGTCTTACTCATTTTCTATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
*
25848 GTCACGTTG-C
66 ATCACGTTGCC
*
25858 ATGGTCTTATTCA-TTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
1 ATGGTCTTACTCATTTTC-TATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
*
25922 TATCAGGTTGCC
65 TATCACGTTGCC
25934 ATGGT
1 ATGGT
25939 ATCTTTCAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
74 4 0.06
75 61 0.86
76 6 0.08
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (76 bp):
ATGGTCTTACTCATTTTCTATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
ATCACGTTGCC
Found at i:25973 original size:46 final size:46
Alignment explanation
Indices: 25857--25973 Score: 207
Period size: 46 Copynumber: 2.5 Consensus size: 46
25847 TGTCACGTTG
** *
25857 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
25903 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
25949 CATGGTCTTACACATTTCATATCAG
1 CATGGTCTTACACATTTCATATCAG
25974 AGAGAACACT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
Found at i:26140 original size:58 final size:54
Alignment explanation
Indices: 26010--26141 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 54
26000 TTACTGTGGG
* * * *
26010 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGG
1 ATTACCAGTCCAGGCTAAATCCCCTGCAAGACAAACTCATAGAGTATTGTCGGA
* *
26064 ATTACCAATCCAGGCTAAATCCCCTGCAACGACAATTACTC-TAATGAG-ATTGGTCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAA-GACAA--ACTCAT-A-GAGTATT-GTCGGA
26122 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
26142 TCAGGCCCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
54 27 0.42
55 3 0.05
56 1 0.02
57 8 0.12
58 26 0.40
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (54 bp):
ATTACCAGTCCAGGCTAAATCCCCTGCAAGACAAACTCATAGAGTATTGTCGGA
Found at i:28155 original size:23 final size:22
Alignment explanation
Indices: 28107--28156 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 22
28097 AATATCTTAT
28107 TAAAATAT-TAATTAAATAATA
1 TAAAATATCTAATTAAATAATA
28128 T---ATATCTAATTAAATAATTA
1 TAAAATATCTAATTAAATAA-TA
28148 TAAAATATC
1 TAAAATATC
28157 AAAATATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 3 0.12
21 1 0.04
23 5 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAATATCTAATTAAATAATA
Found at i:31893 original size:47 final size:47
Alignment explanation
Indices: 31841--32293 Score: 674
Period size: 47 Copynumber: 9.6 Consensus size: 47
31831 GATAATTGTG
* *
31841 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
31888 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31935 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
31984 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
32033 ATGTGAAAGTGAATATATGTGATGAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
32080 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCTGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
32127 ATGTGAAAGTGTATATATGTGATGAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
32174 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
32221 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
* *
32268 ACGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
32294 TCCCGAAGGG
Statistics
Matches: 378, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
46 2 0.01
47 280 0.74
48 2 0.01
49 94 0.25
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:42026 original size:59 final size:61
Alignment explanation
Indices: 41955--42071 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
41945 ATCACTTTAA
* * * * *
41955 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTACAACATAAACATTAAATTAAATTTAATATTAAATCT
42014 TATTAAAATAATAAAATATTTATCTACAACATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTA-CTACAACATAAACATTAAATTAAATTTAATATTAA
42072 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTACAACATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:47211 original size:3 final size:3
Alignment explanation
Indices: 47205--47235 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
47195 ACACTACTAT
47205 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
47236 CTATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47258 original size:16 final size:16
Alignment explanation
Indices: 47147--47259 Score: 67
Period size: 16 Copynumber: 7.1 Consensus size: 16
47137 AGTAAAGTAA
47147 ATAATAATACTATATAT
1 ATAATAATA-TATATAT
47164 A-AA-AATATATATAT
1 ATAATAATATATATAT
* * * *
47178 GTATATAATAGAAATAC
1 ATA-ATAATATATATAT
* * *
47195 ACACTACTATATA-AT
1 ATAATAATATATATAT
47210 AATAATAATA-ATA-A-
1 -ATAATAATATATATAT
47224 ATAATAATAATACTATAT
1 ATAATAAT-ATA-TATAT
*
47242 ATAAAAATATATATAT
1 ATAATAATATATATAT
47258 AT
1 AT
47260 GTATATAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
13 8 0.11
14 8 0.11
15 11 0.15
16 24 0.33
17 14 0.19
18 7 0.10
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (16 bp):
ATAATAATATATATAT
Found at i:47275 original size:82 final size:83
Alignment explanation
Indices: 47121--47302 Score: 307
Period size: 82 Copynumber: 2.2 Consensus size: 83
47111 GGATATAATG
*
47121 ATAATAATAATATTGAAGTAAAGTAAATAATAATACTATATATAAAAATATATATATGTATATAA
1 ATAATAATAATAAT-AAGTAAAGTAAATAATAATACTATATATAAAAATATATATATGTATATAA
47186 TAGAAATACACACTACTAT
65 TAGAAATACACACTACTAT
47205 ATAATAATAATAATAA-TAAA-T-AATAATAATACTATATATAAAAATATATATATATGTATATA
1 ATAATAATAATAATAAGTAAAGTAAATAATAATACTATATAT-AAAA-ATATATATATGTATATA
47267 ATAGAAATACACACTACTAT
64 ATAGAAATACACACTACTAT
47287 ATAATAATAATAATAA
1 ATAATAATAATAATAA
47303 ATATAGAAAT
Statistics
Matches: 95, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
80 18 0.19
81 5 0.05
82 57 0.60
83 2 0.02
84 13 0.14
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (83 bp):
ATAATAATAATAATAAGTAAAGTAAATAATAATACTATATATAAAAATATATATATGTATATAAT
AGAAATACACACTACTAT
Found at i:47383 original size:14 final size:14
Alignment explanation
Indices: 47359--47393 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
47349 TAATAAAAAC
47359 AATACTATATATAAA
1 AATA-TATATATAAA
*
47374 TATATATATATAAA
1 AATATATATATAAA
47388 AATATA
1 AATATA
47394 CACTAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATATATATAAA
Found at i:47507 original size:12 final size:13
Alignment explanation
Indices: 47492--47546 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
47482 AATAGGGGTG
47492 ATAATAATA-ATA
1 ATAATAATACATA
47504 ATAATAATACA-A
1 ATAATAATACATA
*
47516 ACAATAATACAT-
1 ATAATAATACATA
*
47528 AT-ATATATATATA
1 ATAATA-ATACATA
47541 ATAATA
1 ATAATA
47547 GTAGTCAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.09
12 26 0.74
13 3 0.09
14 3 0.09
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATAATACATA
Found at i:47640 original size:21 final size:21
Alignment explanation
Indices: 47616--47684 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
47606 TGGAGAGGGT
47616 ATATATAATATAATAATAATA
1 ATATATAATATAATAATAATA
*
47637 ATATATACATGAGAAATAATAATA
1 ATATATA-AT-A-TAATAATAATA
* *
47661 ATAATATAA-ATAATAGTAAAA
1 AT-ATATAATATAATAATAATA
47682 ATA
1 ATA
47685 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 3 0.08
23 1 0.03
24 13 0.32
25 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (21 bp):
ATATATAATATAATAATAATA
Found at i:48273 original size:30 final size:30
Alignment explanation
Indices: 48199--48284 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
48189 ATTTGATGGT
* **
48199 GTAGGTGCAAGTGGAACACAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
48229 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
48259 GTAGGTGCAAGTGGGAGGCAAGGTGG
1 GTAGGTGCAAGTGGGAGGCAAGGTGG
48285 CTAGGGTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.26, C:0.08, G:0.50, T:0.16
Consensus pattern (30 bp):
GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
Found at i:48282 original size:18 final size:18
Alignment explanation
Indices: 48231--48283 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
48221 GTGGTGGAGT
48231 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
*
48249 AGGTG---GT-GGA-G-T
1 AGGTGCAAGTGGGAGGCA
48261 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
48279 AGGTG
1 AGGTG
48284 GCTAGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 5 0.19
13 1 0.04
14 3 0.11
15 4 0.15
16 3 0.11
17 1 0.04
18 10 0.37
ACGTcount: A:0.25, C:0.08, G:0.53, T:0.15
Consensus pattern (18 bp):
AGGTGCAAGTGGGAGGCA
Found at i:48431 original size:12 final size:13
Alignment explanation
Indices: 48402--48429 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48392 TTGGGTAGGA
48402 TTTAAGTTTGCTT
1 TTTAAGTTTGCTT
48415 TTTAAGTTTGCTT
1 TTTAAGTTTGCTT
48428 TT
1 TT
48430 AATTTGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (13 bp):
TTTAAGTTTGCTT
Found at i:51475 original size:11 final size:11
Alignment explanation
Indices: 51440--51477 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
51430 TTATGAATCA
51440 TATG-TTTTGG
1 TATGATTTTGG
51450 TATGA-TTTGG
1 TATGATTTTGG
*
51460 CATGATTTTGG
1 TATGATTTTGG
51471 TATGATT
1 TATGATT
51478 ATAAGCATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (11 bp):
TATGATTTTGG
Found at i:51492 original size:23 final size:21
Alignment explanation
Indices: 51445--51494 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
51435 AATCATATGT
* *
51445 TTTGGTATGATTTGGCATGAT
1 TTTGGTATGATTTAGCATGAA
51466 TTTGGTATGATTATAAGCATGAA
1 TTTGGTATGATT-T-AGCATGAA
51489 TTTGGT
1 TTTGGT
51495 TGTTTATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (21 bp):
TTTGGTATGATTTAGCATGAA
Found at i:53481 original size:31 final size:33
Alignment explanation
Indices: 53439--53499 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
53429 GACACTTTAG
*
53439 TAAAATATAATTT-TGAT-ATTTATTTAAAATTT
1 TAAAATATAATTTAT-ATCAATTATTTAAAATTT
53471 TAAAA-ATAATTTATATCAATTATTTAAAA
1 TAAAATATAATTTATATCAATTATTTAAAA
53500 GTATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (33 bp):
TAAAATATAATTTATATCAATTATTTAAAATTT
Found at i:54805 original size:21 final size:20
Alignment explanation
Indices: 54766--54805 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54756 AAGATGTCAA
* *
54766 AATATAATTTTACAATTATT
1 AATAAAATTTTAAAATTATT
54786 AATAAAATTTTATAAATTAT
1 AATAAAATTTTA-AAATTAT
54806 AAAAAGCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAAATTTTAAAATTATT
Found at i:66447 original size:41 final size:41
Alignment explanation
Indices: 66390--66468 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
66380 CATTTACTCG
* * *
66390 GATTCAGAATCAATGGCATAGTAACCTCAAGTACCAATCAA
1 GATTCAAAATCAATGGCATACTAACCTCAAGTAACAATCAA
66431 GATTCAAAATCAATGGCATACTAACCTCAAGTAACAAT
1 GATTCAAAATCAATGGCATACTAACCTCAAGTAACAAT
66469 AAAAAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.23
Consensus pattern (41 bp):
GATTCAAAATCAATGGCATACTAACCTCAAGTAACAATCAA
Found at i:67640 original size:9 final size:10
Alignment explanation
Indices: 67613--67654 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
67603 CATATCACAA
67613 AAATAAAAAT
1 AAATAAAAAT
67623 AAATAAAAAT
1 AAATAAAAAT
* *
67633 AAGT-AAAAC
1 AAATAAAAAT
67642 AAATAAAAAT
1 AAATAAAAAT
67652 AAA
1 AAA
67655 ATCTAACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:68857 original size:19 final size:18
Alignment explanation
Indices: 68829--68866 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
68819 TTGTCATGCT
68829 CGTGTAGCCCACACACACC
1 CGTGTAGCCCACACA-ACC
*
68848 CGTGTGGCCCACACAACC
1 CGTGTAGCCCACACAACC
68866 C
1 C
68867 AAAAATGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.11
Consensus pattern (18 bp):
CGTGTAGCCCACACAACC
Found at i:71267 original size:23 final size:22
Alignment explanation
Indices: 71218--71267 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
71208 TGTCATCTCC
* *
71218 TAAAAATTAATATATATAATTT
1 TAAAAATAAATAAATATAATTT
* *
71240 AAAAAATAAATAAATTATATTTT
1 TAAAAATAAATAAA-TATAATTT
71263 TAAAA
1 TAAAA
71268 GTTTCAAGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAAATAAATATAATTT
Found at i:73880 original size:60 final size:60
Alignment explanation
Indices: 73812--73931 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
73802 TGAAAGAGGA
73812 AGTTTAGTTCTCATAAGTAATGGTCTAGACATTAATCAGAAGCGTTCAATCAATAATTTC
1 AGTTTAGTTCTCATAAGTAATGGTCTAGACATTAATCAGAAGCGTTCAATCAATAATTTC
73872 AGTTTAGTTCTCATAAGTAATGGTCTAGACATTAATCAGAAGCGTTCAATCAATAATTTC
1 AGTTTAGTTCTCATAAGTAATGGTCTAGACATTAATCAGAAGCGTTCAATCAATAATTTC
73932 TCTAAACCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (60 bp):
AGTTTAGTTCTCATAAGTAATGGTCTAGACATTAATCAGAAGCGTTCAATCAATAATTTC
Found at i:83881 original size:13 final size:12
Alignment explanation
Indices: 83863--83901 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
83853 TTGTGTGTTC
83863 TTTATTTTTATTT
1 TTTA-TTTTATTT
83876 TTTATTTTATTT
1 TTTATTTTATTT
83888 TATTATTTTATTT
1 T-TTATTTTATTT
83901 T
1 T
83902 ATTTTTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:83883 original size:5 final size:5
Alignment explanation
Indices: 83863--83906 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
83853 TTGTGTGTTC
*
83863 TTTAT TTT-T ATT-T TTTAT TTTAT TTTA- -TTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
83907 TCTCAAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
4 6 0.18
5 25 0.74
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:83886 original size:18 final size:19
Alignment explanation
Indices: 83863--83907 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
83853 TTGTGTGTTC
83863 TTTATTTTTATT-TTTTAT
1 TTTATTTTTATTATTTTAT
83881 TTTA-TTTTATTATTTTAT
1 TTTATTTTTATTATTTTAT
83899 TTTATTTTT
1 TTTATTTTT
83908 CTCAAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.28
18 14 0.56
19 4 0.16
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTATTTTTATTATTTTAT
Found at i:83902 original size:13 final size:13
Alignment explanation
Indices: 83868--83904 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
83858 TGTTCTTTAT
83868 TTTTATTTT-TTA
1 TTTTATTTTATTA
83880 TTTTATTTTATTA
1 TTTTATTTTATTA
83893 TTTTATTTTATT
1 TTTTATTTTATT
83905 TTTCTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:90339 original size:16 final size:16
Alignment explanation
Indices: 90291--90340 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
90281 AAAAAAGGAC
90291 TTATAAATATT-TAAA
1 TTATAAATATTATAAA
* *
90306 -TATAATTAATTATGAA
1 TTATAAAT-ATTATAAA
*
90322 TTATAACTATTATAAA
1 TTATAAATATTATAAA
90338 TTA
1 TTA
90341 ATATGAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 6 0.21
15 3 0.11
16 13 0.46
17 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTATAAATATTATAAA
Found at i:90801 original size:17 final size:15
Alignment explanation
Indices: 90765--90811 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 15
90755 GGAGTCCCAT
90765 TTTTAA-AAATTAAA
1 TTTTAATAAATTAAA
90779 TTTTAATAAATTAAA
1 TTTTAATAAATTAAA
*
90794 TTAATTAATAAATAAAA
1 TT--TTAATAAATTAAA
90811 T
1 T
90812 AAAGTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.21
15 10 0.34
17 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTAATAAATTAAA
Found at i:97213 original size:22 final size:22
Alignment explanation
Indices: 97181--97223 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
97171 ATATTAGTGT
* *
97181 ACATTTTTATATGTACATATAC
1 ACATTTATATATATACATATAC
*
97203 ACATTTATATATATATATATA
1 ACATTTATATATATACATATA
97224 TATATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
ACATTTATATATATACATATAC
Found at i:97215 original size:2 final size:2
Alignment explanation
Indices: 97208--97236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
97198 TATACACATT
97208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97237 TACTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105660 original size:18 final size:18
Alignment explanation
Indices: 105637--105676 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
105627 ATCTTAAGTG
*
105637 CCTTAAGTATTGAAGCAA
1 CCTTAAGTATTAAAGCAA
105655 CCTTAAGTATTAAAGCAA
1 CCTTAAGTATTAAAGCAA
105673 CCTT
1 CCTT
105677 TACCCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (18 bp):
CCTTAAGTATTAAAGCAA
Found at i:106345 original size:18 final size:16
Alignment explanation
Indices: 106287--106360 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 16
106277 AATTTTTAAA
* *
106287 TAATTTTTATAATATTA
1 TAATTTTTAT-ATTTTT
106304 TAACTTTTTATATTTTT
1 TAA-TTTTTATATTTTT
106321 TAATTTTTATATTTCTT
1 TAATTTTTATATTT-TT
* **
106338 TAAATTTTA-AAATTT
1 TAATTTTTATATTTTT
106353 TAATTTTT
1 TAATTTTT
106361 TTTACATGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
15 9 0.18
16 13 0.27
17 20 0.41
18 7 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTTATATTTTT
Found at i:106346 original size:17 final size:16
Alignment explanation
Indices: 106309--106346 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
106299 TATTATAACT
*
106309 TTTTATATTTTTTAAT
1 TTTTATATTTTTTAAA
106325 TTTTATATTTCTTTAAA
1 TTTTATATTT-TTTAAA
106342 TTTTA
1 TTTTA
106347 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATATTTTTTAAA
Found at i:107047 original size:14 final size:14
Alignment explanation
Indices: 107028--107054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
107018 CTTGTTTCCG
107028 CTTTTTCTTTTTTC
1 CTTTTTCTTTTTTC
107042 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
107055 TTTTCAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
CTTTTTCTTTTTTC
Found at i:112841 original size:6 final size:6
Alignment explanation
Indices: 112830--112858 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
112820 ACATCCAATC
112830 AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
112859 TACCTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:116010 original size:70 final size:70
Alignment explanation
Indices: 115897--116037 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
115887 CAATACTGCT
115897 TTAATCAAGGTAAGTTTTCCACCTTGTCCAAGTAACTTAGCCTTCCACAAAGAGAGTTTGGATTT
1 TTAATCAAGGTAAGTTTTCCACCTTGTCCAAGTAACTTAGCCTTCCACAAAGAGAGTTTGGATTT
115962 AATTC
66 AATTC
115967 TTAATCAAGGTAAGTTTTCCACCTTGTCCAAGTAACTTAGCCTTCCACAAAGAGAGTTTGGATTT
1 TTAATCAAGGTAAGTTTTCCACCTTGTCCAAGTAACTTAGCCTTCCACAAAGAGAGTTTGGATTT
116032 AATTC
66 AATTC
116037 T
1 T
116038 ATCTATGATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (70 bp):
TTAATCAAGGTAAGTTTTCCACCTTGTCCAAGTAACTTAGCCTTCCACAAAGAGAGTTTGGATTT
AATTC
Found at i:123168 original size:23 final size:24
Alignment explanation
Indices: 123123--123169 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
123113 CATTTACTAA
123123 GCAATATCAGATATTCATGTATTAG
1 GCAATATCAGATATTCA-GTATTAG
*
123148 GCAATATCATATATTCA-TATTA
1 GCAATATCAGATATTCAGTATTA
123170 TTCTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (24 bp):
GCAATATCAGATATTCAGTATTAG
Found at i:128499 original size:21 final size:22
Alignment explanation
Indices: 128460--128516 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
128450 TCTTAACCTA
128460 AAATTTTTAATTCTAATTATTT
1 AAATTTTTAATTCTAATTATTT
128482 AAATATTTT-ATT-TAATTATTCT
1 AAAT-TTTTAATTCTAATTATT-T
*
128504 TAATTATTTAATT
1 AAATT-TTTAATT
128517 ATCTAATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 9 0.30
22 14 0.47
23 7 0.23
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTTTAATTCTAATTATTT
Found at i:128512 original size:23 final size:23
Alignment explanation
Indices: 128460--128501 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
128450 TCTTAACCTA
128460 AAAT-TTTTAATTCTAATTATTT
1 AAATATTTTAATTCTAATTATTT
128482 AAATATTTT-ATT-TAATTATT
1 AAATATTTTAATTCTAATTATT
128502 CTTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATATTTTAATTCTAATTATTT
Found at i:130268 original size:104 final size:104
Alignment explanation
Indices: 130088--130354 Score: 455
Period size: 104 Copynumber: 2.6 Consensus size: 104
130078 TAACCGTTAT
* **
130088 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
130153 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
130192 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
130257 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
130296 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
130355 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 153 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:130709 original size:29 final size:29
Alignment explanation
Indices: 130676--130739 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
130666 TAATCCACCA
130676 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
130705 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
130735 CCCAA
1 CCCAA
130740 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:130713 original size:30 final size:30
Alignment explanation
Indices: 130683--130739 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
130673 CCACCCAACT
130683 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
130712 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
130740 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:137744 original size:104 final size:104
Alignment explanation
Indices: 137564--137830 Score: 464
Period size: 104 Copynumber: 2.6 Consensus size: 104
137554 TAACCGTTAT
* *
137564 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
137629 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
137668 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
137733 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
137772 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
137831 TTATATACAA
Statistics
Matches: 155, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
104 154 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:138187 original size:29 final size:29
Alignment explanation
Indices: 138154--138217 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
138144 TAATCCACCA
138154 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
138183 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
138213 CCCAA
1 CCCAA
138218 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:138191 original size:30 final size:30
Alignment explanation
Indices: 138161--138217 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
138151 CCACCCAACT
138161 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
138190 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
138218 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:143448 original size:25 final size:25
Alignment explanation
Indices: 143419--143469 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
143409 AAATCTTAAT
143419 ACCTTTTTCCATGGAGATACTTTCA
1 ACCTTTTTCCATGGAGATACTTTCA
143444 ACCTTTTTCCATGGAGATACTTTCA
1 ACCTTTTTCCATGGAGATACTTTCA
143469 A
1 A
143470 AAATACTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (25 bp):
ACCTTTTTCCATGGAGATACTTTCA
Found at i:151532 original size:25 final size:25
Alignment explanation
Indices: 151484--151530 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
151474 CGCTGAATCG
*
151484 GGGAATCAGCACTTAGCAACCCCTC
1 GGGAATCAGCACTAAGCAACCCCTC
151509 GGGAATCAGCAC-AAGCAACCCC
1 GGGAATCAGCACTAAGCAACCCC
151531 CTTTCACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.32, C:0.36, G:0.21, T:0.11
Consensus pattern (25 bp):
GGGAATCAGCACTAAGCAACCCCTC
Found at i:151675 original size:102 final size:102
Alignment explanation
Indices: 151449--151711 Score: 324
Period size: 101 Copynumber: 2.6 Consensus size: 102
151439 GTAACCTTAT
* * ** *
151449 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACT-TAGCAACCCCTCGGGA
1 TGGTGGATATCGCACATAGCACCACCAATGAATCGCGGAATCAGCACTATAGCAACCCCTCGGGA
*
151513 ATCAGCACAAGCAACCCCCTTTCACATTTCAAAGATA
66 ATCAGCACAAGCAAACCCCTTTCACATTTCAAAGATA
* *
151550 TGGTGGATATCGCACTTAGCACCA-CAATGAA-C-CGGGATCAGCACTATAGCAACCCCTCGGGG
1 TGGTGGATATCGCACATAGCACCACCAATGAATCGCGGAATCAGCACTATAGCAACCCCTC--GG
*
151612 GAATCAGCACATAGCAAACCCTTTTCAACATTTCAAAGATA
64 GAATCAGCACA-AGCAAACCCCTTTC-ACATTTCAAAGATA
* *
151653 TTGT-GATCA-CGCACATAGCACCACCAATGAATCGGCGGAATCAGCAC-ACAGCAACCCCT
1 TGGTGGAT-ATCGCACATAGCACCACCAATGAATC-GCGGAATCAGCACTATAGCAACCCCT
151712 TTATATACAA
Statistics
Matches: 141, Mismatches: 11, Indels: 16
0.84 0.07 0.10
Matches are distributed among these distances:
98 11 0.08
99 13 0.09
100 5 0.04
101 36 0.26
102 28 0.20
103 25 0.18
104 1 0.01
105 11 0.08
106 11 0.08
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (102 bp):
TGGTGGATATCGCACATAGCACCACCAATGAATCGCGGAATCAGCACTATAGCAACCCCTCGGGA
ATCAGCACAAGCAAACCCCTTTCACATTTCAAAGATA
Found at i:163465 original size:50 final size:50
Alignment explanation
Indices: 163341--163589 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
163331 GATAATAACA
* * ** * *
163341 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
163392 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
163442 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
163492 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
163547 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
163590 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:163519 original size:100 final size:104
Alignment explanation
Indices: 163340--163589 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
163330 TGATAATAAC
**
163340 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
163405 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
163442 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
163505 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
163547 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
163590 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:163705 original size:13 final size:13
Alignment explanation
Indices: 163684--163715 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
163674 GCTTGGATCA
*
163684 TCATCAAATAAAT
1 TCATAAAATAAAT
163697 TCATAAAATAAAT
1 TCATAAAATAAAT
163710 TCATAA
1 TCATAA
163716 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:163962 original size:30 final size:30
Alignment explanation
Indices: 163927--163984 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
163917 CCTCGACTCT
*
163927 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
163957 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
163985 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:171921 original size:27 final size:27
Alignment explanation
Indices: 171890--172067 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
171880 TAAATTGTAC
171890 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
171917 TGCACTAAGTGTGCGAAATGA--ATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
171942 GATGCACTAAGTGTGCGAATTGACCATGC
1 -A-GCACTAAGTGTGCGATTTGACTATGT
*
171971 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
171999 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
172026 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
172053 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
172068 GACTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.03
27 99 0.77
28 23 0.18
29 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:172031 original size:82 final size:81
Alignment explanation
Indices: 171891--172046 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
171881 AAATTGTACA
* *
171891 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATGTGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAAGTGT
171956 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
**
171972 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT-A-GCACTAAG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGA--ACGTGATGCACTAAG
*
172035 TGTGCGAGTTGA
63 TGTGCGAATTGA
172047 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 15 0.22
82 48 0.72
83 1 0.01
84 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:172058 original size:82 final size:81
Alignment explanation
Indices: 171887--172067 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
171877 GATTAAATTG
* *
171887 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATGTGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAA
171952 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * **
171968 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT-A-GCAC
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGA--ACGTGATGCAC
* **
172031 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
172050 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
172068 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 17 0.20
82 63 0.75
83 1 0.01
84 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAACGTGATGCACTAA
GTGTGCGAATTGACCA
Found at i:189943 original size:7 final size:7
Alignment explanation
Indices: 189915--189999 Score: 71
Period size: 7 Copynumber: 12.1 Consensus size: 7
189905 AGTTGAGATT
*
189915 CCCCAAT
1 CCCCAAA
189922 CCCCAAA
1 CCCCAAA
* *
189929 CTCTAAA
1 CCCCAAA
189936 CCCCAAA
1 CCCCAAA
**
189943 CCATAAA
1 CCCCAAA
*
189950 CCCCAAC
1 CCCCAAA
189957 CCCCAAA
1 CCCCAAA
*
189964 CCTCAAA
1 CCCCAAA
*
189971 TCCCAAA
1 CCCCAAA
* *
189978 TCACAAA
1 CCCCAAA
189985 CCCCAAA
1 CCCCAAA
*
189992 CTCCAAA
1 CCCCAAA
189999 C
1 C
190000 GCACCACAAT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.42, C:0.48, G:0.00, T:0.09
Consensus pattern (7 bp):
CCCCAAA
Found at i:196916 original size:17 final size:16
Alignment explanation
Indices: 196860--196915 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
196850 GTTTATTTTC
196860 TTGTTTTCAATTTAGT
1 TTGTTTTCAATTTAGT
* *
196876 TTGTTTTCAGTTTTTGT
1 TTGTTTTCA-ATTTAGT
196893 TTGTTTTCAATTTAGT
1 TTGTTTTCAATTTAGT
196909 TTGTTTT
1 TTGTTTT
196916 TATTATTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.68
Consensus pattern (16 bp):
TTGTTTTCAATTTAGT
Found at i:198032 original size:16 final size:17
Alignment explanation
Indices: 198006--198050 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
197996 GTTTTATAGG
*
198006 TTTAGTTGTTTGTCTAT
1 TTTAGTTGTTTATCTAT
*
198023 TTTA-TTGTTTATTTAT
1 TTTAGTTGTTTATCTAT
*
198039 TTTAGTTATTTA
1 TTTAGTTGTTTA
198051 ATTCCCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.18, C:0.02, G:0.11, T:0.69
Consensus pattern (17 bp):
TTTAGTTGTTTATCTAT
Found at i:199387 original size:72 final size:72
Alignment explanation
Indices: 199307--199499 Score: 251
Period size: 72 Copynumber: 2.7 Consensus size: 72
199297 ATCGACACTG
* *** * *
199307 CTCACACAAGCTTTAGAGAATCGGTAACACATGTTGGATCTCAAGCTATTGGTAAAAAATGATTT
1 CTCACACAAGCTTCAGAGAATCCACAACACATGTTGGATCTCAAGCCATTGATAAAAAATGATTT
*
199372 AATGTTA
66 AATGCTA
* *
199379 CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCATTGATAAAGAATGATTT
1 CTCACACAAGCTTCAGAGAATCCACAACACATGTTGGATCTCAAGCCATTGATAAAAAATGATTT
* *
199444 GATGCTG
66 AATGCTA
* * **
199451 CTCACACAAGCTTCAAATAATCCACAACATGTGTTGGATCTCAAGCCAT
1 CTCACACAAGCTTCAGAGAATCCACAACACATGTTGGATCTCAAGCCAT
199500 AGATTATTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 107 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (72 bp):
CTCACACAAGCTTCAGAGAATCCACAACACATGTTGGATCTCAAGCCATTGATAAAAAATGATTT
AATGCTA
Found at i:200785 original size:8 final size:8
Alignment explanation
Indices: 200774--200805 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
200764 ATAATCTCAT
200774 AAATATTA
1 AAATATTA
200782 AAATATTA
1 AAATATTA
200790 AAATATTA
1 AAATATTA
200798 AAAT-TTA
1 AAATATTA
200805 A
1 A
200806 CAACAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATTA
Found at i:201541 original size:19 final size:18
Alignment explanation
Indices: 201519--201614 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 18
201509 TTTATATATT
201519 TTTTAGAAATTTTTTAAAA
1 TTTTAGAAATTTTTT-AAA
*
201538 TTTTA-AAA--TTTGAAA
1 TTTTAGAAATTTTTTAAA
* * *
201553 TTTTTATAAATATTTTGAA
1 -TTTTAGAAATTTTTTAAA
*
201572 TTTTAAAAATTATTTTAAA
1 TTTTAGAAATT-TTTTAAA
* *
201591 TTTTTGAAAATTATTTTGAA
1 TTTTAG-AAATT-TTTTAAA
201611 TTTT
1 TTTT
201615 TTTTTTGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 3 0.05
16 8 0.13
17 3 0.05
18 12 0.19
19 20 0.32
20 16 0.26
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTAGAAATTTTTTAAA
Found at i:201571 original size:20 final size:19
Alignment explanation
Indices: 201546--201615 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
201536 AATTTTAAAA
201546 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTA-AAATTAT
*
201566 TTTGAATTTTAAAAATTAT
1 TTTGAATTTTTAAAATTAT
*
201585 TTTAAATTTTTGAAAATTAT
1 TTTGAATTTTT-AAAATTAT
201605 TTTGAATTTTT
1 TTTGAATTTTT
201616 TTTTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.07
19 19 0.43
20 22 0.50
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:214088 original size:12 final size:13
Alignment explanation
Indices: 214063--214093 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
214053 TTTCTGGGGT
214063 TAAAATTAAAGGG
1 TAAAATTAAAGGG
214076 TAAAATT-AAGGG
1 TAAAATTAAAGGG
214088 TAAAAT
1 TAAAAT
214094 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (13 bp):
TAAAATTAAAGGG
Found at i:216501 original size:23 final size:24
Alignment explanation
Indices: 216450--216506 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
216440 AATGATCATG
* *
216450 AATAAGTA-AATAAAAATTGAAGA
1 AATATGTAGAATAAAAATAGAAGA
*
216473 AATATG-AGAATAAAAATAGAATA
1 AATATGTAGAATAAAAATAGAAGA
*
216496 ATTATGTAGAA
1 AATATGTAGAA
216507 AACCACCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.82
24 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (24 bp):
AATATGTAGAATAAAAATAGAAGA
Found at i:218920 original size:29 final size:28
Alignment explanation
Indices: 218871--218925 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
218861 ACAATATATT
*
218871 AAAAACATATGTAAAGCATA-TAAAACG
1 AAAAACATATGTAAAGAATATTAAAACG
*
218898 AAAATACATATGTTAAATAATATTAAAA
1 AAAA-ACATATG-TAAAGAATATTAAAA
218926 TATTTACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 7 0.30
29 7 0.30
30 5 0.22
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (28 bp):
AAAAACATATGTAAAGAATATTAAAACG
Found at i:219102 original size:14 final size:12
Alignment explanation
Indices: 219073--219103 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
219063 AGATATATAC
219073 ATATATAACAAA
1 ATATATAACAAA
219085 ATATATAACAAA
1 ATATATAACAAA
219097 ATATATA
1 ATATATA
219104 CTATGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATATAACAAA
Found at i:219379 original size:3 final size:3
Alignment explanation
Indices: 219371--219412 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
219361 GTATATACAT
* *
219371 ATA ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
219413 TGAAAATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:220581 original size:17 final size:17
Alignment explanation
Indices: 220559--220592 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
220549 GACGGGTTAT
220559 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
220576 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
220593 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:231788 original size:3 final size:3
Alignment explanation
Indices: 231780--231809 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
231770 CCTTAGTTTG
231780 ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
231810 AAAGCTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:236648 original size:23 final size:23
Alignment explanation
Indices: 236616--236679 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
236606 AAAAATTTAT
* *
236616 TATAACTTTTTAATATTCTGAAA
1 TATAAATTTTAAATATTCTGAAA
* *
236639 TATAAATTTTAAATATTTTTAAA
1 TATAAATTTTAAATATTCTGAAA
* *
236662 TAATAAATATTAATTATT
1 T-ATAAATTTTAAATATT
236680 TATAAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (23 bp):
TATAAATTTTAAATATTCTGAAA
Found at i:236674 original size:24 final size:23
Alignment explanation
Indices: 236627--236685 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
236617 ATAACTTTTT
* * *
236627 AATATTCTGAAATATAAATTTTA
1 AATATTTTTAAATATAAATATTA
236650 AATATTTTTAAATAATAAATATTA
1 AATATTTTTAAAT-ATAAATATTA
* *
236674 ATTATTTATAAA
1 AATATTTTTAAA
236686 ATTTATTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATTTTTAAATATAAATATTA
Found at i:240404 original size:16 final size:15
Alignment explanation
Indices: 240385--240439 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
240375 AATGTATAAT
240385 TAATTTTGATTTTATA
1 TAATTTT-ATTTTATA
*
240401 TAATTTTA-TATATA
1 TAATTTTATTTTATA
* *
240415 TAATTTTTATTTAATT
1 TAA-TTTTATTTTATA
240431 TAATTTTAT
1 TAATTTTAT
240440 AAATTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 8 0.24
15 12 0.36
16 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTATA
Found at i:240416 original size:14 final size:14
Alignment explanation
Indices: 240397--240440 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
240387 ATTTTGATTT
240397 TATATAATTTTATA
1 TATATAATTTTATA
*
240411 TATATAATTTTTATT
1 TATATAA-TTTTATA
*
240426 TAATTTAATTTTATA
1 T-ATATAATTTTATA
240441 AATTATTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATAATTTTATA
Found at i:241400 original size:13 final size:13
Alignment explanation
Indices: 241382--241409 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
241372 TATTTTTAAA
241382 TTAGCATATATGT
1 TTAGCATATATGT
241395 TTAGCATATATGT
1 TTAGCATATATGT
241408 TT
1 TT
241410 TAAATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAGCATATATGT
Found at i:248118 original size:14 final size:14
Alignment explanation
Indices: 248101--248129 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
248091 TCTCCTTGAG
248101 AGTCGATTTTAACC
1 AGTCGATTTTAACC
248115 AGTCGATTTTAACC
1 AGTCGATTTTAACC
248129 A
1 A
248130 CAAAATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (14 bp):
AGTCGATTTTAACC
Found at i:251569 original size:39 final size:39
Alignment explanation
Indices: 251526--251600 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
251516 GTTAGTTTTG
* * *
251526 AGTTTAGGGGCTAAAATGAAAATATTTTGAAATTAAATA
1 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAAATA
251565 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAA
1 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAA
251601 CATGAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (39 bp):
AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAAATA
Found at i:258022 original size:608 final size:608
Alignment explanation
Indices: 256868--258084 Score: 2292
Period size: 608 Copynumber: 2.0 Consensus size: 608
256858 CACATAACTT
*
256868 TAAAAAATATTCAAAAAAAACCATGGCAAGTCCCTCAACCTTTAACATTTTTGCAAAGTAACCCC
1 TAAAAAAAATTCAAAAAAAACCATGGCAAGTCCCTCAACCTTTAACATTTTTGCAAAGTAACCCC
*
256933 TGGGCTAGCTAGATTAAGCTAAAACAAACTCAAAAACATAAAAATCATTAAAAACGGGCTTGAGT
66 TGGGCTAGCTAGATTAAGCTAAAACAAACTCAAAAACATAAAAATCATTAAAAACGGGCTTGAAT
256998 ACACTTATATGCACCAAAAGGAGCTTGGACGAACCTAACCCTCTTCTCTAATGGTGATTTTTAGT
131 ACACTTATATGCACCAAAAGGAGCTTGGACGAACCTAACCCTCTTCTCTAATGGTGATTTTTAGT
*
257063 GGGAGAGACCAAATGAAGAAGATGAAGCAAGTTTTGTTTTATTTGATTTAGGTTGTAATTATTCA
196 GGGAGAGACCAAATGAAGAAGATGAAGCAAGTTTTGTTTTATTAGATTTAGGTTGTAATTATTCA
257128 ATTACCATTTTAACCTTTAAAATCTATTAAAATTTCAATAAAACCTTATCCATGCACATACACTA
261 ATTACCATTTTAACCTTTAAAATCTATTAAAATTTCAATAAAACCTTATCCATGCACATACACTA
* *
257193 TCTCTTTAAATGGTATATTTACCATTCAAGTCATTTAGTGTAAGATTTCATAGCCATTGGAGCCC
326 TCTCTTTAAATGGTACATTTACCATTCAAGTCATTTAGTGTAAGATTTCACAGCCATTGGAGCCC
257258 TTTAACTAATAGAACTCAACTTTTACACTTTTTATGATTTAGTCCTTTTTACTTAATTAACTACT
391 TTTAACTAATAGAACTCAACTTTTACACTTTTTATGATTTAGTCCTTTTTACTTAATTAACTACT
*
257323 TAAACATCAAAATTTCTAAAAAAAATTTAACATGACCTTAATACAATCTTTTAAACATTAAATGA
456 TAAACATCAAAATTTCTAAAAAAAATTTAACACGACCTTAATACAATCTTTTAAACATTAAATGA
*
257388 ATAATAAAATAATAATTCACATGTCAGAATTGTGGTCTTGAAACTACTGTTTTCGACATCACTGA
521 ATAATAAAATAATAATTCACATGTCAGAATTGTGGTCTTGAAACTACTGTTTTCAACATCACTGA
257453 AAACGGGCTGTTATATAACATGC
586 AAACGGGCTGTTATATAACATGC
* *
257476 TAAAAAAAATTCAAAAACAACCATGGCAAGTCCCTCAACCTTTAACATTTTTGCAAAGTAACCCT
1 TAAAAAAAATTCAAAAAAAACCATGGCAAGTCCCTCAACCTTTAACATTTTTGCAAAGTAACCCC
257541 TGGGCTAGCTAGATTAAGCTAAAACAAACTCAAAAACATAAAAATCATTAAAAACGGGCTTGAAT
66 TGGGCTAGCTAGATTAAGCTAAAACAAACTCAAAAACATAAAAATCATTAAAAACGGGCTTGAAT
*
257606 ACACTTATATGCACCAAAAGGAGCTTGGCCGAACCTAACCCTCTTCTCTAATGGTGATTTTTAGT
131 ACACTTATATGCACCAAAAGGAGCTTGGACGAACCTAACCCTCTTCTCTAATGGTGATTTTTAGT
257671 GGGAGAGACCAAATGAAGAAGATGAAGCAAGTTTTGTTTTATTAGATTTAGGTTGTAATTATTCA
196 GGGAGAGACCAAATGAAGAAGATGAAGCAAGTTTTGTTTTATTAGATTTAGGTTGTAATTATTCA
*
257736 ATTACCATTTTAACCTTTAAAATCTATTAAAATTTCAATAAAACCTTATCCATGCACGTACACTA
261 ATTACCATTTTAACCTTTAAAATCTATTAAAATTTCAATAAAACCTTATCCATGCACATACACTA
257801 TCTCTTTAAATGGTACATTTACCATTCAAGTCATTTAGTGTAAGATTTCACAGCCATTGGA-CCC
326 TCTCTTTAAATGGTACATTTACCATTCAAGTCATTTAGTGTAAGATTTCACAGCCATTGGAGCCC
*
257865 ATTTAACTAATAGAATTCAACTTTTACACTTTTTATGATTTAGTCCTTTTTACTTAATTAACTAC
391 -TTTAACTAATAGAACTCAACTTTTACACTTTTTATGATTTAGTCCTTTTTACTTAATTAACTAC
*
257930 TTAAACATCAAAATTTCTAAAAAAAATTTAACACGACCTTAATACAATCTTTTCAACATTAAATG
455 TTAAACATCAAAATTTCTAAAAAAAATTTAACACGACCTTAATACAATCTTTTAAACATTAAATG
257995 AATAATAAAATAATAATTCACATGTCAGAATTGTGGTCTTGAAACTACTGTTTTCAACATCACTG
520 AATAATAAAATAATAATTCACATGTCAGAATTGTGGTCTTGAAACTACTGTTTTCAACATCACTG
*
258060 AAAACGGGCTGTTATATAGCATGC
585 AAAACGGGCTGTTATATAACATGC
258084 T
1 T
258085 CATTAAATAA
Statistics
Matches: 594, Mismatches: 14, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
607 3 0.01
608 591 0.99
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (608 bp):
TAAAAAAAATTCAAAAAAAACCATGGCAAGTCCCTCAACCTTTAACATTTTTGCAAAGTAACCCC
TGGGCTAGCTAGATTAAGCTAAAACAAACTCAAAAACATAAAAATCATTAAAAACGGGCTTGAAT
ACACTTATATGCACCAAAAGGAGCTTGGACGAACCTAACCCTCTTCTCTAATGGTGATTTTTAGT
GGGAGAGACCAAATGAAGAAGATGAAGCAAGTTTTGTTTTATTAGATTTAGGTTGTAATTATTCA
ATTACCATTTTAACCTTTAAAATCTATTAAAATTTCAATAAAACCTTATCCATGCACATACACTA
TCTCTTTAAATGGTACATTTACCATTCAAGTCATTTAGTGTAAGATTTCACAGCCATTGGAGCCC
TTTAACTAATAGAACTCAACTTTTACACTTTTTATGATTTAGTCCTTTTTACTTAATTAACTACT
TAAACATCAAAATTTCTAAAAAAAATTTAACACGACCTTAATACAATCTTTTAAACATTAAATGA
ATAATAAAATAATAATTCACATGTCAGAATTGTGGTCTTGAAACTACTGTTTTCAACATCACTGA
AAACGGGCTGTTATATAACATGC
Found at i:259727 original size:40 final size:40
Alignment explanation
Indices: 259682--259825 Score: 130
Period size: 40 Copynumber: 3.6 Consensus size: 40
259672 GATTTGGATA
* *
259682 TATATATGGCACTTAGTATGCGGTTC-GAGATAG-TTTCGGC
1 TATATATGGCACTTAGTGTGCGATTCGGA-ATAGCTTT-GGC
* *
259722 TATATATGGCATTTAGTGTGTGATTCGGAATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGATTCGGAATAGCTTTGGC
* ** * *
259762 TATATATAGCACTTAGTGTGCGAGACCGAGATAGCTTTAGC
1 TATATATGGCACTTAGTGTGCGATTCGGA-ATAGCTTTGGC
* * * *
259803 AATGTAAGGCACTTAATGTGCGA
1 TATATATGGCACTTAGTGTGCGA
259826 GATTATAATA
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 52 0.61
41 33 0.39
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGATTCGGAATAGCTTTGGC
Found at i:263075 original size:40 final size:40
Alignment explanation
Indices: 262914--263068 Score: 258
Period size: 40 Copynumber: 3.9 Consensus size: 40
262904 ATTCGGATTG
262914 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
262953 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
262993 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
263033 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
263069 AGCTATATCC
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 13 0.12
40 93 0.88
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:270998 original size:40 final size:40
Alignment explanation
Indices: 270798--270984 Score: 297
Period size: 40 Copynumber: 4.7 Consensus size: 40
270788 ATTCGGATTG
270798 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
270837 TTATCCGGGCTAAGTCCCGAAGGCATTT-TGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
270876 ATAACCGAGCCAAGTCCTGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
270916 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
270956 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
270985 AGTGAGTAGC
Statistics
Matches: 134, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 45 0.34
40 89 0.66
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:277184 original size:39 final size:38
Alignment explanation
Indices: 277130--277204 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
277120 CTAATCCTCA
*
277130 ATTTCAATTTCAAACATACTAAATACAATTTCAATTTTG
1 ATTTCAATTTCAAACATACCAAATACAATTT-AATTTTG
277169 ATTTCAATTTCAAACATACCAAATACAATTTAATTT
1 ATTTCAATTTCAAACATACCAAATACAATTTAATTT
277205 CATAACTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.40
Consensus pattern (38 bp):
ATTTCAATTTCAAACATACCAAATACAATTTAATTTTG
Found at i:281419 original size:26 final size:25
Alignment explanation
Indices: 281252--281579 Score: 161
Period size: 25 Copynumber: 13.2 Consensus size: 25
281242 CATGTATTAA
*
281252 AAAATAGTTTAAAATAAATATTATAT
1 AAAA-AGTTTAAAATAAATAATATAT
* *
281278 AATAAA-TTTAAAGTAAGTAATATAT
1 AA-AAAGTTTAAAATAAATAATATAT
* * *
281303 AAAATAG-TT-AAA-AAATAACACAA
1 AAAA-AGTTTAAAATAAATAATATAT
* * **
281326 AAAAATATTTAAAATAAACAATGCA-
1 AAAAA-GTTTAAAATAAATAATATAT
*
281351 AAATAA-TTTAAAATAACT-A-ATAT
1 AAA-AAGTTTAAAATAAATAATATAT
*
281374 AAAAGGTTTAAAATAAATAATATAT
1 AAAAAGTTTAAAATAAATAATATAT
* * **
281399 AAAATAGTTTAAACTACAT-A-AGGT
1 AAAA-AGTTTAAAATAAATAATATAT
281423 --AAAGTTTAAAATAAATAATGTATAT
1 AAAAAGTTTAAAATAAATAA--TATAT
* *
281448 AAAAA-CTCAAAATAAATAATATGAT
1 AAAAAGTTTAAAATAAATAATAT-AT
* *
281473 AAAACAATTTAAAACAAATACCATATAT
1 AAAA-AGTTTAAAATAAATA--ATATAT
**
281501 AAAAAAACTTAAAATAAATAATA-AT
1 -AAAAAGTTTAAAATAAATAATATAT
*
281526 AAAACAGTTCAAAATAAAT-AT-TAT
1 AAAA-AGTTTAAAATAAATAATATAT
* * *
281550 -GAAAGATTTATAATAAATAAAATA-
1 AAAAAG-TTTAAAATAAATAATATAT
281574 AAAAAG
1 AAAAAG
281580 AAAACAAAAA
Statistics
Matches: 229, Mismatches: 42, Indels: 63
0.69 0.13 0.19
Matches are distributed among these distances:
21 12 0.05
22 8 0.03
23 38 0.17
24 31 0.14
25 63 0.28
26 39 0.17
27 15 0.07
28 15 0.07
29 8 0.03
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAAAGTTTAAAATAAATAATATAT
Found at i:281492 original size:53 final size:52
Alignment explanation
Indices: 281427--281545 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 52
281417 TAAGGTAAAG
* *
281427 TTTAAAATAAATA-ATGTATATAAAAACTCAAAATAAATAATATGATAAAACAA
1 TTTAAAATAAATACATATATAAAAAAACTCAAAATAAATAATA--ATAAAACAA
* * *
281480 TTTAAAACAAATACCATATATAAAAAAACTTAAAATAAATAATAATAAAACAG
1 TTTAAAATAAATA-CATATATAAAAAAACTCAAAATAAATAATAATAAAACAA
*
281533 TTCAAAATAAATA
1 TTTAAAATAAATA
281546 TTATGAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 31 0.54
55 26 0.46
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.27
Consensus pattern (52 bp):
TTTAAAATAAATACATATATAAAAAAACTCAAAATAAATAATAATAAAACAA
Found at i:281512 original size:28 final size:26
Alignment explanation
Indices: 281428--281529 Score: 116
Period size: 28 Copynumber: 3.8 Consensus size: 26
281418 AAGGTAAAGT
* *
281428 TTAAAATAAATAATGTATATAAAAAC
1 TTAAAATAAATAATATATAAAAAAAC
* * *
281454 TCAAAATAAATAATATGATAAAACAAT
1 TTAAAATAAATAATAT-ATAAAAAAAC
*
281481 TTAAAACAAATACCATATATAAAAAAAC
1 TTAAAATAAATA--ATATATAAAAAAAC
281509 TTAAAATAAATAATA-ATAAAA
1 TTAAAATAAATAATATATAAAA
281530 CAGTTCAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.10
26 17 0.27
27 17 0.27
28 19 0.30
29 4 0.06
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAAAAAC
Found at i:281614 original size:22 final size:21
Alignment explanation
Indices: 281585--281626 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
281575 AAAAGAAAAC
281585 AAAAAAGAAT-ACAATATAATG
1 AAAAAAG-ATGACAATATAATG
281606 AAAATAAGATGACAATATAAT
1 AAAA-AAGATGACAATATAAT
281627 AATGCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAAAGATGACAATATAATG
Found at i:282611 original size:20 final size:20
Alignment explanation
Indices: 282588--282626 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
282578 TGGATCATTA
282588 GTTTTGGGTTTGTAATTTTG
1 GTTTTGGGTTTGTAATTTTG
282608 GTTTTGGGTTTGTAATTTT
1 GTTTTGGGTTTGTAATTTT
282627 AAACTGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (20 bp):
GTTTTGGGTTTGTAATTTTG
Found at i:283004 original size:51 final size:50
Alignment explanation
Indices: 282924--283252 Score: 224
Period size: 51 Copynumber: 6.8 Consensus size: 50
282914 GAGATAAGAC
* * * *
282924 TTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGGGATAAGGTTTGTGGT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GTTTGTGGT
* * *
282975 TTGTAGCTTCAATCTGCCCCACTGCAACTTTAGGGAGATAAG---AT--T
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTGTGGT
*** * * * * * *
283020 CACTATCTTCAGTCTGCTCCACTGTAAATTCAGAGAGATAA------GAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTGTGGT
* * * * *
283064 TTGTAACTTCAACCTGCTCTACTGCAACTTTAGGAAGATAAGGTTTGTGGT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GTTTGTGGT
* *
283115 TTGTAGCTTCAATCTGC-CCTACTGTAACTTCAGGGAGATAAGATT-T-G-
1 TTGTAGCTTCAATCTGCTCC-ACTGCAACTTCAGGGAGATAAGTTTGTGGT
* * * * * *
283162 --CTATCTTCAGTTTACTCCACTGCAACTTCAGGGAGATAAGATTTGTGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-TTTGTGGT
**
283211 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAATGAGATAAG
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
283253 ATTCGCTATC
Statistics
Matches: 209, Mismatches: 52, Indels: 34
0.71 0.18 0.12
Matches are distributed among these distances:
44 30 0.14
45 63 0.30
46 4 0.02
47 2 0.01
48 1 0.00
49 1 0.00
50 5 0.02
51 103 0.49
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (50 bp):
TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGTTTGTGGT
Found at i:283016 original size:140 final size:139
Alignment explanation
Indices: 282853--283207 Score: 530
Period size: 140 Copynumber: 2.5 Consensus size: 139
282843 TCAGTCCATT
* *
282853 CCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCTAGGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGCAAATTC-AGGAGA
* * **
282918 TAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGCT
65 TAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGCT
282983 TCAATCTGCC
130 TCAATCTGCC
* *
282993 CCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAAATTCAGAGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGCAAATTCAG-GAGA
* *
283058 TAAGATTTGTAACTTCAACCTGCTCTACTGCAACTTTAGGAAGATAAGGTTTGTGGTTTGTAGCT
65 TAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGCT
283123 TCAATCTGCC
130 TCAATCTGCC
* * ** * * *
283133 CTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTACTCCACTGCAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGCAAATTCA-GGAGA
283198 TAAGATTTGT
65 TAAGATTTGT
283208 GATTTGTAGC
Statistics
Matches: 194, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
139 2 0.01
140 191 0.98
141 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (139 bp):
CCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGCAAATTCAGGAGAT
AAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGCTT
CAATCTGCC
Found at i:283058 original size:45 final size:45
Alignment explanation
Indices: 282852--283384 Score: 197
Period size: 45 Copynumber: 11.6 Consensus size: 45
282842 TTCAGTCCAT
* * * *
282852 TCCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGC
1 TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * *
282897 TCCACTGCAAATTCTA-GGAGATAAGACTT--GTAACTTCAACCTGC
1 TCCACTGCAAATTC-AGGGAGATAAGA-TTCACTATCTTCAATCTGC
* * * * *** *
282941 TCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
1 TCCACTGCAAATTCAGGGAGATAA-G---AT--TCACTATCTTCAATCTGC
* * * *
282992 CCCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGTCTGC
1 TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * ** * *
283037 TCCACTGTAAATTCAGAGAGATAAGATT-TGTAACTTCAACCTGC
1 TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * * * * *** *
283081 TCTACTGCAACTTTAGGAAGATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
1 TCCACTGCAAATTCAGGGAGATAA-G---AT--TCACTATCTTCAATCTGC
* * ** * * *
283132 -CCTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTAC
1 TCC-ACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * * *
283177 TCCACTGCAACTTCAGGGAGATAAGATTTGTGATTTGTAGCTTCAATCTGC
1 TCCACTGCAAATTCAGGGAGATAAGA--T-TCA---CTATCTTCAATCTGC
* ** * *
283228 TCCACTGCAACTTCAATGAGATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * * * * * * **
283273 TCCATTGCAACTTTAGGGAGACAAGACTT--GTAACTTCAACCCAC
1 TCCACTGCAAATTCAGGGAGATAAGA-TTCACTATCTTCAATCTGC
* * * *
283317 TCCACTGCAACTTCAGGGAGATAAGGTTTACTA---T-GATCTGC
1 TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
* * *
283358 TCTACTGCAACTTCAGAGAGATAAGAT
1 TCCACTGCAAATTCAGGGAGATAAGAT
283385 CTGTTATTTA
Statistics
Matches: 368, Mismatches: 91, Indels: 62
0.71 0.17 0.12
Matches are distributed among these distances:
41 27 0.07
42 1 0.00
43 3 0.01
44 89 0.24
45 130 0.35
46 6 0.02
47 4 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 99 0.27
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
TCCACTGCAAATTCAGGGAGATAAGATTCACTATCTTCAATCTGC
Found at i:283216 original size:96 final size:96
Alignment explanation
Indices: 282852--283476 Score: 383
Period size: 96 Copynumber: 6.7 Consensus size: 96
282842 TTCAGTCCAT
* * * ** * *
282852 TCCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCTA-GGA
1 TCCACTGTAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTT-TAGGGA
* *
282916 GATAAGACTTGT-A-----A-CTTCAACCTGC
65 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * * *
282941 TCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGCTTCAATCTGCCCCACTGCAACTTT
1 TCCACTGTAACTTCAGAGAGATAA-GATT-T-G---CTATCTTCAGTCTGCTCCACTGCAACTTT
* * * *
283006 AGGGAGATAAGA--T-TCA---CTATCTTCAGTCTGC
60 AGGGAGATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * ** * *
283037 TCCACTGTAAATTCAGAGAGATAAGATTTG-TAACTTCAACCTGCTCTACTGCAACTTTAGGAAG
1 TCCACTGTAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
* *
283101 ATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
66 ATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * *
283132 -CCTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTACTCCACTGCAACTTCAGGGA
1 TCC-ACTGTAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGA
283196 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
65 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * *
283228 TCCACTGCAACTTCA-ATGAGATAAGATTCGCTATCTTCAGTCTGCTCCATTGCAACTTTAGGGA
1 TCCACTGTAACTTCAGA-GAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGA
* * * **
283292 GACAAGACTTGT-A-----A-CTTCAACCCAC
65 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * * * *
283317 TCCACTGCAACTTCAGGGAGATAAGGTTTACTA---TGA-TCTGCTCTACTGCAACTTCAGAGAG
1 TCCACTGTAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
* * * * *
283378 ATAAGATCTGTTATTTATACCTTCAATCTGT
66 ATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * * * * * *
283409 TCCATTGTAATTTCAGGGAGA-AGAGATTTG-TAGCTTCAATCTACTCCGCTGAAACTTCAAGGA
1 TCCACTGTAACTTCAGAGAGATA-AGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGA
283472 GATAA
65 GATAA
283477 AAATTGTGGC
Statistics
Matches: 421, Mismatches: 81, Indels: 62
0.75 0.14 0.11
Matches are distributed among these distances:
85 29 0.07
86 3 0.01
89 91 0.22
90 4 0.01
91 5 0.01
92 32 0.08
93 3 0.01
94 7 0.02
95 97 0.23
96 148 0.35
97 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (96 bp):
TCCACTGTAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
ATAAGATTTGTGATTTGTAGCTTCAATCTGC
Found at i:283473 original size:44 final size:44
Alignment explanation
Indices: 283420--283562 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 44
283410 CCATTGTAAT
*
283420 TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAAC
1 TTCAAGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAAC
* * * * ** ** *
283464 TTCAAGGAGATA-AAAATTGTGGCTTCGAGA-C-GCTCCAATGCCAT
1 TTCAAGGAGA-AGAGATTTGTAGCTTC-A-ATCTACTCCGCTGAAAC
* * * *
283508 TTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCTGCTGGAAC
1 TTCAAGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAAC
283552 TTCAAGGAGAA
1 TTCAAGGAGAA
283563 ACAAATTGTT
Statistics
Matches: 70, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
42 1 0.01
43 2 0.03
44 63 0.90
45 3 0.04
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TTCAAGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAAC
Found at i:283665 original size:131 final size:130
Alignment explanation
Indices: 283549--283800 Score: 305
Period size: 131 Copynumber: 1.9 Consensus size: 130
283539 ACTCTGCTGG
* *
283549 AACT-TCAAGGAGAAACAAAT-TGTTGAT-TTCAACCTACTCCACTACTGC-TTAGGGAGATAGG
1 AACTCTCAAGGAGAAA-AAATCTG-TAATATTCAACCTACTCCACTACTGCTTTAGAGAGATAGG
* * *
283610 ATGGTGGCTTAAATCTGCTCCACTATTGGTTAGGGAGACAAGATTCGCCATCTTCGATCTGCTCC
64 ATGGTGACTTAAATCTGCTCCACTACTGGTTAGGGAGACAAGATTCGCCATCTTCGATCTACTCC
283675 AC
129 AC
* * * * * * *
283677 AACTGCTTAGGGAGATAAGATCTGTAATATTCAGCCTACTCTAGTACTGCTTTAGAGAGATAGGA
1 AACT-CTCAAGGAGAAAAAATCTGTAATATTCAACCTACTCCACTACTGCTTTAGAGAGATAGGA
* * * *
283742 TGGTGACTTAAATCTGTTCCACTACTGGTTAGGGAGACAAGATTTGCCGTCTTTGATCT
65 TGGTGACTTAAATCTGCTCCACTACTGGTTAGGGAGACAAGATTCGCCATCTTCGATCT
283801 GTTCCACAGC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
128 4 0.04
129 6 0.06
130 28 0.27
131 66 0.63
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (130 bp):
AACTCTCAAGGAGAAAAAATCTGTAATATTCAACCTACTCCACTACTGCTTTAGAGAGATAGGAT
GGTGACTTAAATCTGCTCCACTACTGGTTAGGGAGACAAGATTCGCCATCTTCGATCTACTCCAC
Found at i:287857 original size:24 final size:24
Alignment explanation
Indices: 287811--287860 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
287801 GTGAAAGTTT
*
287811 AATGCAAATGATGCAATGCAATGC
1 AATGCAAATGATGCAACGCAATGC
*
287835 AATGCAAATGCATGGAACG-AATGC
1 AATGCAAATG-ATGCAACGCAATGC
287859 AA
1 AA
287861 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (24 bp):
AATGCAAATGATGCAACGCAATGC
Found at i:289916 original size:24 final size:24
Alignment explanation
Indices: 289853--289938 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 24
289843 ACATAAAAGG
289853 TTTAAAATAAATACCAT-AAAAGCAA
1 TTTAAAATAAATA--ATAAAAAGCAA
*
289878 TTTAAAGTAAATAATACAAAA-CAA
1 TTTAAAATAAATAATA-AAAAGCAA
* *
289902 TTTAAAATCATTAATAAAAAG---
1 TTTAAAATAAATAATAAAAAGCAA
*
289923 TCTAAAATAAATAATA
1 TTTAAAATAAATAATA
289939 TGTAAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 13 0.25
23 6 0.12
24 16 0.31
25 16 0.31
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (24 bp):
TTTAAAATAAATAATAAAAAGCAA
Found at i:290383 original size:26 final size:26
Alignment explanation
Indices: 290218--290394 Score: 115
Period size: 25 Copynumber: 7.2 Consensus size: 26
290208 ATGTATTAAA
* *
290218 AAAATAGTTTAAAATAAATATTACAT
1 AAAATAGTTTAAAATAAATAATATAT
* * *
290244 AAAA-AATTTAAAGTAAGTAATATAT
1 AAAATAGTTTAAAATAAATAATATAT
* *
290269 AAAATAG-TT-AAA-AAATAACACA-
1 AAAATAGTTTAAAATAAATAATATAT
** **
290291 AAAATA-TTTAAAAT-AAGCA-ATGC
1 AAAATAGTTTAAAATAAATAATATAT
* *
290314 AAAACAGTTTAAAAT-AATTA-ATAT
1 AAAATAGTTTAAAATAAATAATATAT
*
290338 AAAA-GGTTTAAAATAAATAATATAT
1 AAAATAGTTTAAAATAAATAATATAT
* * *
290363 AAAATAGTTTAAACTACATAATGTAT
1 AAAATAGTTTAAAATAAATAATATAT
290389 ATAAAT
1 A-AAAT
290395 TTAAAGTACG
Statistics
Matches: 116, Mismatches: 25, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
22 9 0.08
23 27 0.23
24 23 0.20
25 30 0.26
26 23 0.20
27 4 0.03
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAATAGTTTAAAATAAATAATATAT
Found at i:290443 original size:26 final size:25
Alignment explanation
Indices: 290406--290562 Score: 126
Period size: 28 Copynumber: 6.2 Consensus size: 25
290396 TAAAGTACGT
* *
290406 AAAAGTTTAAAATAAATAATGTATA
1 AAAAATTTAAAATAAATAATATATA
*
290431 TAAAATTTCAAAATAAATAATATGATA
1 AAAAATTT-AAAATAAATAATAT-ATA
*
290458 AAACAATTTAAAACAAATACCATATATAA
1 AAA-AATTTAAAATAAATA--ATATAT-A
*
290487 AAAAACTTAAAATAAATAATA-ATA
1 AAAAATTTAAAATAAATAATATATA
* * *
290511 AAACAGTTCAAAATAAAT-AT-TATG
1 AAA-AATTTAAAATAAATAATATATA
* *
290535 AAAGATTTATAATAAATAA-A-ATA
1 AAAAATTTAAAATAAATAATATATA
290558 AAAAA
1 AAAAA
290563 GAAAACAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
23 16 0.15
24 12 0.11
25 19 0.18
26 16 0.15
27 14 0.13
28 20 0.19
29 8 0.08
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAAATTTAAAATAAATAATATATA
Found at i:290470 original size:53 final size:52
Alignment explanation
Indices: 290411--290529 Score: 134
Period size: 53 Copynumber: 2.2 Consensus size: 52
290401 TACGTAAAAG
* * *
290411 TTTAAAATAAATA-ATGTAT-ATAAAATTTCAAAATAAATAATATGATAAAACAA
1 TTTAAAATAAATACATATATAAAAAAACTT-AAAATAAATAATA--ATAAAACAA
* *
290464 TTTAAAACAAATACCATATATAAAAAAACTTAAAATAAATAATAATAAAACAG
1 TTTAAAATAAATA-CATATATAAAAAAACTTAAAATAAATAATAATAAAACAA
*
290517 TTCAAAATAAATA
1 TTTAAAATAAATA
290530 TTATGAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
53 31 0.55
55 18 0.32
56 7 0.12
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.29
Consensus pattern (52 bp):
TTTAAAATAAATACATATATAAAAAAACTTAAAATAAATAATAATAAAACAA
Found at i:290486 original size:28 final size:26
Alignment explanation
Indices: 290411--290562 Score: 125
Period size: 25 Copynumber: 5.9 Consensus size: 26
290401 TACGTAAAAG
* *
290411 TTTAAAATAAATAATGTATATAA-AA
1 TTTAAAATAAATAATATATAAAACAA
290436 TTTCAAAATAAATAATATGATAAAACAA
1 TTT-AAAATAAATAATAT-ATAAAACAA
* *
290464 TTTAAAACAAATACCATATATAAAAAAA
1 TTTAAAATAAATA--ATATATAAAACAA
* *
290492 CTTAAAATAAATAATA-ATAAAACAG
1 TTTAAAATAAATAATATATAAAACAA
* * *
290517 TTCAAAATAAAT-AT-TATGAAA-GA
1 TTTAAAATAAATAATATATAAAACAA
* * *
290540 TTTATAATAAATAAAATAAAAAA
1 TTTAAAATAAATAATATATAAAA
290563 GAAAACAAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
23 10 0.10
24 8 0.08
25 25 0.25
26 16 0.16
27 14 0.14
28 24 0.24
29 4 0.04
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.29
Consensus pattern (26 bp):
TTTAAAATAAATAATATATAAAACAA
Found at i:290598 original size:22 final size:21
Alignment explanation
Indices: 290569--290610 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
290559 AAAAGAAAAC
290569 AAAAAAGA-ATACAATATAATG
1 AAAAAAGATA-ACAATATAATG
290590 AAAATAAGATAACAATATAAT
1 AAAA-AAGATAACAATATAAT
290611 AATGTAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 14 0.74
23 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAAAGATAACAATATAATG
Found at i:292514 original size:10 final size:10
Alignment explanation
Indices: 292499--292525 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
292489 GTAGAAGAAA
292499 AATAAAATAG
1 AATAAAATAG
292509 AATAAAATAG
1 AATAAAATAG
292519 AATAAAA
1 AATAAAA
292526 GAGGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
AATAAAATAG
Found at i:299464 original size:19 final size:19
Alignment explanation
Indices: 299440--299533 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 19
299430 AAAATTATTA
299440 TTTTATAAAATTTTAAATT
1 TTTTATAAAATTTTAAATT
** *
299459 TTTTATATATTTTTTAGATT
1 TTTTATA-AAATTTTAAATT
*
299479 TTTT-TAAAATTTATAATTT
1 TTTTATAAAATTT-TAAATT
299498 TTTTAAATACAAATTTTAGAA-T
1 TTTT--ATA-AAATTTTA-AATT
299520 TTTTATAAATATTT
1 TTTTATAAA-ATTT
299534 AGAATTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.07
19 19 0.32
20 20 0.34
22 9 0.15
23 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTAAATT
Found at i:299551 original size:19 final size:19
Alignment explanation
Indices: 299508--299552 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
299498 TTTTAAATAC
*
299508 AAAT-TTTAGAATTTTTAT
1 AAATATTTAGAATTTTTAA
299526 AAATATTTAGAA-TTTTAA
1 AAATATTTAGAATTTTTAA
299544 AAATTATTT
1 AAA-TATTT
299553 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
AAATATTTAGAATTTTTAA
Found at i:300899 original size:23 final size:25
Alignment explanation
Indices: 300873--300919 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
300863 TATCATTCAT
*
300873 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
300896 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
300920 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:301240 original size:46 final size:46
Alignment explanation
Indices: 301180--301445 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
301170 TTTGACGTGA
* * * * * *
301180 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
301226 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
301272 TGCCATGGTATCTTTCAACTATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
301318 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
301356 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
301402 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
301446 AGAGCACACT
Statistics
Matches: 197, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
38 33 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 150 0.76
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:301364 original size:38 final size:39
Alignment explanation
Indices: 301311--301435 Score: 180
Period size: 38 Copynumber: 3.1 Consensus size: 39
301301 CACATCTCAT
301311 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
301350 A-CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C
301393 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 --ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
301434 AT
1 AT
301436 TTCATATCAG
Statistics
Matches: 78, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
38 33 0.42
39 3 0.04
40 3 0.04
41 1 0.01
43 1 0.01
44 3 0.04
45 1 0.01
46 33 0.42
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (39 bp):
ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:301411 original size:84 final size:84
Alignment explanation
Indices: 301270--301434 Score: 312
Period size: 84 Copynumber: 2.0 Consensus size: 84
301260 TTCATGTCAC
*
301270 GTTGCCATGGTATCTTTCAACTATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
301335 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
*
301354 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
301419 ACCATGGTCTTACACA
66 ACCATGGTCTTACACA
301435 TTTCATATCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:301684 original size:62 final size:62
Alignment explanation
Indices: 301575--301728 Score: 211
Period size: 62 Copynumber: 2.5 Consensus size: 62
301565 ACCTTAATTC
* * * *
301575 GGATC-CCCGTCCGGGCTAAATCCATTTTACACGTATTTTTCAAGAGGGCTATATCAAAATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCAAGAGGGCTATATCAAAATA
** * **
301636 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATTAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCAAGAGGGCTATATCAAAATA
*
301698 GGATCACCCATCCGGGCTAGATCCTTTTTAC
1 GGATCACCCGTCCGGGCTAGATCCTTTTTAC
301729 CGTCAACTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 5 0.06
62 77 0.94
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (62 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCAAGAGGGCTATATCAAAATA
Found at i:312371 original size:18 final size:18
Alignment explanation
Indices: 312341--312384 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
312331 CAATAAAATT
*
312341 ATAA-AAAAGAATTCAAA
1 ATAATAAAAGAATTAAAA
*
312358 ATAATAAAATAATTAAAA
1 ATAATAAAAGAATTAAAA
*
312376 ATTATAAAA
1 ATAATAAAA
312385 ATTGTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAATAAAAGAATTAAAA
Found at i:326854 original size:20 final size:21
Alignment explanation
Indices: 326831--326890 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
326821 GAAAAAAATT
*
326831 AAATCCAA-ATTAAAATACTA
1 AAATTCAAGATTAAAATACTA
* *
326851 AAATTCAAGA-TAAAATCCTG
1 AAATTCAAGATTAAAATACTA
*
326871 AAATTCAAGATAAAAATACT
1 AAATTCAAGATTAAAATACT
326891 GATGTGGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (21 bp):
AAATTCAAGATTAAAATACTA
Found at i:326892 original size:21 final size:20
Alignment explanation
Indices: 326841--326892 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
326831 AAATCCAAAT
*
326841 TAAAATACTAAAATTCAAGA
1 TAAAATACTGAAATTCAAGA
*
326861 TAAAATCCTGAAATTCAAGA
1 TAAAATACTGAAATTCAAGA
326881 TAAAAATACTGA
1 T-AAAATACTGA
326893 TGTGGCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.25
Consensus pattern (20 bp):
TAAAATACTGAAATTCAAGA
Done.