Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008438.1 Hibiscus syriacus cultivar Beakdansim tig00111237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 406264
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:2319 original size:29 final size:29
Alignment explanation
Indices: 2262--2319 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2252 GTGTTGGCCG
*
2262 TAGGTCGCCATGCTTTCCGGTCGACCTAC
1 TAGGTCGCCATGCTTCCCGGTCGACCTAC
*
2291 TAGGTCGCCATGTCTTCCCGG-CGAGCTAC
1 TAGGTCGCCATG-CTTCCCGGTCGACCTAC
2320 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCTTCCCGGTCGACCTAC
Found at i:2381 original size:14 final size:14
Alignment explanation
Indices: 2362--2394 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2352 CGCTGGGCAT
2362 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2376 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2390 ACGAG
1 CCGAG
2395 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2460 original size:33 final size:33
Alignment explanation
Indices: 2386--2460 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
2376 CCGAGGCCAT
* * * *
2386 CCGAACGAGCTATGCGAGGGCATCCGAGAGTAA
1 CCGAGCGAGCTATGAGAGGGAATCCGAGAGGAA
2419 CCGAGCGAGCTATGAGAGGGAATCCGAG-GGAA
1 CCGAGCGAGCTATGAGAGGGAATCCGAGAGGAA
*
2451 GCCGGGCGAG
1 -CCGAGCGAG
2461 GGTAGGTCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.28, C:0.23, G:0.40, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGAGAGGGAATCCGAGAGGAA
Found at i:2497 original size:29 final size:29
Alignment explanation
Indices: 2464--2548 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
2454 GGGCGAGGGT
* *
2464 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGACGACCTACA
*
2493 AGGTCGCCCGGAGGGCATGACGACTTACA
1 AGGTCGCCCGGAGGGCATGACGACCTACA
2522 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGGGCATGACGACCTA
2549 TGTGTTGGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGACGACCTACA
Found at i:19825 original size:30 final size:30
Alignment explanation
Indices: 19791--19847 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
19781 CATAATTTTA
19791 TAAGTTTTATTAAAATTATTATTTTATCAG
1 TAAGTTTTATTAAAATTATTATTTTATCAG
*
19821 TAAGTTTTATTAAACTTATTATTTTAT
1 TAAGTTTTATTAAAATTATTATTTTAT
19848 GAGTGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (30 bp):
TAAGTTTTATTAAAATTATTATTTTATCAG
Found at i:25587 original size:31 final size:32
Alignment explanation
Indices: 25549--25612 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
25539 AATATTTTTT
25549 TTCTCATTGCAG-AGTCAATATCATAATTGCA
1 TTCTCATTGCAGAAGTCAATATCATAATTGCA
25580 TTCTCATTGCAGAAGTCAATATCATAATTGCA
1 TTCTCATTGCAGAAGTCAATATCATAATTGCA
25612 T
1 T
25613 GACGATTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (32 bp):
TTCTCATTGCAGAAGTCAATATCATAATTGCA
Found at i:31527 original size:7 final size:7
Alignment explanation
Indices: 31515--31543 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
31505 TCGGAACTCC
31515 CTTTAAA
1 CTTTAAA
31522 CTTTAAA
1 CTTTAAA
31529 CTTTAAA
1 CTTTAAA
31536 CTTTAAA
1 CTTTAAA
31543 C
1 C
31544 AGCACTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (7 bp):
CTTTAAA
Found at i:38211 original size:23 final size:23
Alignment explanation
Indices: 38167--38212 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38157 ACTATCAACT
* *
38167 ATTTGGCATTAAACATTTACACC
1 ATTTGACATTAAACATTCACACC
* *
38190 ATTTGACATTGAACGTTCACACC
1 ATTTGACATTAAACATTCACACC
38213 CTGATATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTTGACATTAAACATTCACACC
Found at i:40129 original size:19 final size:19
Alignment explanation
Indices: 40093--40131 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40083 TTTAATAAAA
*
40093 ATAATAATTATTAAAATAT
1 ATAATAATTAATAAAATAT
40112 ATAATAA-TAATAATAATAT
1 ATAATAATTAATAA-AATAT
40131 A
1 A
40132 ATGTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATTAATAAAATAT
Found at i:40198 original size:23 final size:23
Alignment explanation
Indices: 40148--40198 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
40138 TATTTTTTTA
* *
40148 GTATTACAATAATATATTAAATT
1 GTATTACAATAATATATGAAACT
* * *
40171 ATATTATAATAATATATGATACT
1 GTATTACAATAATATATGAAACT
40194 GTATT
1 GTATT
40199 TTTATATTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (23 bp):
GTATTACAATAATATATGAAACT
Found at i:40259 original size:22 final size:20
Alignment explanation
Indices: 40233--40285 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
40223 ATTAATTTAT
*
40233 TTATTAATTTCATAAAATAATA
1 TTATTAATAT-ATAAAAT-ATA
*
40255 TTATTAAATATATAAAATATT
1 TTATT-AATATATAAAATATA
40276 TTATTAATAT
1 TTATTAATAT
40286 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 12 0.43
23 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAATATATAAAATATA
Found at i:40286 original size:11 final size:11
Alignment explanation
Indices: 40270--40310 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
40260 AAATATATAA
40270 AATATTTTATT
1 AATATTTTATT
*
40281 AATATTTTTTT
1 AATATTTTATT
* *
40292 AATATTATAAT
1 AATATTTTATT
40303 AATATTTT
1 AATATTTT
40311 TATTTTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
AATATTTTATT
Found at i:40305 original size:22 final size:22
Alignment explanation
Indices: 40270--40311 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40260 AAATATATAA
* *
40270 AATATTTTATTAATATTTTTTT
1 AATATTATAATAATATTTTTTT
40292 AATATTATAATAATATTTTT
1 AATATTATAATAATATTTTT
40312 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTATAATAATATTTTTTT
Found at i:40521 original size:24 final size:26
Alignment explanation
Indices: 40494--40547 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
40484 ACTATTTCAA
40494 TATTTT-TA-AAATAATAATATTAAT
1 TATTTTCTAGAAATAATAATATTAAT
* *
40518 TATTTTCTAGTAAATAATATTATTTAT
1 TATTTTCTAG-AAATAATAATATTAAT
40545 TAT
1 TAT
40548 ACTTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 2 0.08
27 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTTTCTAGAAATAATAATATTAAT
Found at i:56291 original size:25 final size:25
Alignment explanation
Indices: 56263--56310 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
56253 TATATGGAAA
56263 CTTTATTCAAG-TTTTACATCCAATG
1 CTTTATTCAAGCTTTT-CATCCAATG
*
56288 CTTTATTTAAGCTTTTCATCCAA
1 CTTTATTCAAGCTTTTCATCCAA
56311 GGCATGCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (25 bp):
CTTTATTCAAGCTTTTCATCCAATG
Found at i:62937 original size:18 final size:18
Alignment explanation
Indices: 62914--62949 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62904 TCACGTAGAA
62914 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
62932 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
62950 CCTTAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:63064 original size:23 final size:23
Alignment explanation
Indices: 63031--63074 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
63021 ATTACATATA
*
63031 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
*
63054 TGTCCCAAAGGACCGCGTAGA
1 TGTCCCAAAGGACCACGTAGA
63075 CCATCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Found at i:65190 original size:26 final size:26
Alignment explanation
Indices: 65144--65198 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
65134 TTTCAAAAAA
* * *
65144 TAAAATAATAAAACCATTATATTATT
1 TAAAATAATAAAACAAGTATAATATT
65170 TAAAAT-ATAAAACTAAGTATAATATT
1 TAAAATAATAAAAC-AAGTATAATATT
65196 TAA
1 TAA
65199 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAATAATAAAACAAGTATAATATT
Found at i:68067 original size:89 final size:89
Alignment explanation
Indices: 67916--68094 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
67906 GATAGTGATG
*
67916 TAACATCCCAAACTATGGGTTAGTGACTTAATTGTAAAGTTTCAGAATTTGGTGATTAAAGTAGA
1 TAACATCCCAAACTATGGGTTAGTGACTTAATTATAAAGTTTCAGAATTTGGTGATTAAAGTAGA
67981 AGAATGGATTAGTTCAATGATTTA
66 AGAATGGATTAGTTCAATGATTTA
68005 TAACATCCCAAACTATGGGTTAGTGACTTAATTATAAAGTTTCAGAATTTGGTGATTAAAGTAGA
1 TAACATCCCAAACTATGGGTTAGTGACTTAATTATAAAGTTTCAGAATTTGGTGATTAAAGTAGA
68070 AGAATGGATTAGTTCAATGATTTA
66 AGAATGGATTAGTTCAATGATTTA
68094 T
1 T
68095 CTGAAAATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (89 bp):
TAACATCCCAAACTATGGGTTAGTGACTTAATTATAAAGTTTCAGAATTTGGTGATTAAAGTAGA
AGAATGGATTAGTTCAATGATTTA
Found at i:68838 original size:64 final size:64
Alignment explanation
Indices: 68765--68988 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
68755 TGTTTGAATG
* * **
68765 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
68828 A
64 A
* * * **
68829 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCTAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** ** * ** *
68893 GGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
68957 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
68989 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 122 0.93
65 8 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:69536 original size:31 final size:31
Alignment explanation
Indices: 69498--69750 Score: 416
Period size: 31 Copynumber: 8.2 Consensus size: 31
69488 AGAGTCGAGG
69498 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
69529 GTTTACATATATTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
69560 ATTTACATATGTTTAAAGACACATATGAGCA
1 GTTTACATATGTTTAAAGGCACATATGAACA
69591 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
69622 TTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
69653 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
69684 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
69715 GTCTACATATGTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
69746 GTTTA
1 GTTTA
69751 TATTGTGACC
Statistics
Matches: 203, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 203 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:69662 original size:15 final size:15
Alignment explanation
Indices: 69642--69725 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
69632 GTTTAAAGGC
69642 ACATATGAACAGTCT
1 ACATATGAACAGTCT
*
69657 ACATATGTTTAA-AGGC-
1 ACATATG---AACAGTCT
*
69673 ACATATGAACAGTTT
1 ACATATGAACAGTCT
* *
69688 ATATATGTTTAA-AGGC-
1 ACATATG---AACAGTCT
69704 ACATATGAACAGTCT
1 ACATATGAACAGTCT
69719 ACATATG
1 ACATATG
69726 TTTAAAGGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 20 0.39
16 13 0.25
17 5 0.10
18 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (15 bp):
ACATATGAACAGTCT
Found at i:73206 original size:21 final size:21
Alignment explanation
Indices: 73177--73218 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
73167 ATTTGAATAT
* *
73177 TATGGAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
73198 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
73219 CCCATTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:73280 original size:21 final size:21
Alignment explanation
Indices: 73247--73286 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
73237 TTTTTATAGA
*
73247 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
73269 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
73287 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:76450 original size:20 final size:20
Alignment explanation
Indices: 76425--76518 Score: 96
Period size: 20 Copynumber: 5.0 Consensus size: 20
76415 ATCAGATTGT
76425 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
76445 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
76465 CCAGGGGGTATC-GATT--CC
1 CCAGGGGGTA-CAGATTCCCC
*
76483 CC---GGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
76500 CCA-GGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
76519 GGGTACAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
14 1 0.02
15 8 0.13
17 4 0.06
18 4 0.06
19 12 0.19
20 33 0.52
21 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:76507 original size:34 final size:35
Alignment explanation
Indices: 76450--76535 Score: 156
Period size: 34 Copynumber: 2.5 Consensus size: 35
76440 TCCCCCCAGG
76450 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
76485 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
76519 GGGTACAGATTCCCCCC
1 GGGAACAGATTCCCCCC
76536 TGTATGGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 32 0.64
35 18 0.36
ACGTcount: A:0.20, C:0.36, G:0.27, T:0.17
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:76529 original size:15 final size:15
Alignment explanation
Indices: 76477--76533 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
76467 AGGGGGTATC
*
76477 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
76492 GATTCCCCCCAGGGGTATC-
1 GATT--CCCC--GGGTA-CA
76511 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
76526 GATTCCCC
1 GATTCCCC
76534 CCTGTATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:76673 original size:21 final size:21
Alignment explanation
Indices: 76647--76688 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
76637 ATTTGAATAT
* *
76647 TATGAAGGGGTATCGATTCCC
1 TATGAAAGGGTACCGATTCCC
76668 TATGAAAGGGTACCGATTCCC
1 TATGAAAGGGTACCGATTCCC
76689 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAAGGGTACCGATTCCC
Found at i:77027 original size:34 final size:32
Alignment explanation
Indices: 76971--77040 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 32
76961 TTTTGTAAAG
* *
76971 GGGAAATGTTCTAGCTAGTCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAGTCCCG-G-AAAAACTA
*
77005 GGGAAAGGTTCTAGTTTA-TCCCGGAAAAACTA
1 GGGAAAGGTTCTAG-CTAGTCCCGGAAAAACTA
77037 GGGA
1 GGGA
77041 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 18 0.56
35 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAGTCCCGGAAAAACTA
Found at i:79711 original size:10 final size:11
Alignment explanation
Indices: 79689--79718 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
79679 CAAATATTGA
79689 TTAAAATAATT
1 TTAAAATAATT
79700 TTAAAA-AATT
1 TTAAAATAATT
79710 TTAAAATAA
1 TTAAAATAA
79719 AATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:80124 original size:12 final size:12
Alignment explanation
Indices: 80109--80143 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
80099 CGATTCTCGG
80109 CCCAATACCCGA
1 CCCAATACCCGA
*
80121 CCCAATACCCGG
1 CCCAATACCCGA
*
80133 CCCAAAACCCG
1 CCCAATACCCG
80144 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.51, G:0.11, T:0.06
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:90657 original size:18 final size:19
Alignment explanation
Indices: 90634--90679 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
90624 GCTCGACTCA
*
90634 AACTCGAAAT-CCTGAAGC
1 AACTCGAAATAACTGAAGC
*
90652 AACTCGAATTAACTGAAGC
1 AACTCGAAATAACTGAAGC
90671 AACTCGAAA
1 AACTCGAAA
90680 AAGGCTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (19 bp):
AACTCGAAATAACTGAAGC
Found at i:105501 original size:22 final size:22
Alignment explanation
Indices: 105473--105516 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
105463 GATGCATAAC
105473 ATAGAATATATCAGAATTCAGA
1 ATAGAATATATCAGAATTCAGA
105495 ATAGAATATATCAGAATTCAGA
1 ATAGAATATATCAGAATTCAGA
105517 CTGAAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (22 bp):
ATAGAATATATCAGAATTCAGA
Found at i:105639 original size:5 final size:6
Alignment explanation
Indices: 105628--105654 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
105618 ATAAATATTA
105628 TATTTT TATTTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TAT
105655 CATTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:110772 original size:19 final size:19
Alignment explanation
Indices: 110717--110773 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
110707 ATCATATAAT
110717 TTTATTAATTTA-A-AGAA
1 TTTATTAATTTACAGAGAA
* * *
110734 -ATATTAATTAATC-GATAA
1 TTTATTAATTTA-CAGAGAA
110752 TTTATTAATTTACAGAGAA
1 TTTATTAATTTACAGAGAA
110771 TTT
1 TTT
110774 TTTCGATTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 9 0.31
18 4 0.14
19 16 0.55
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTATTAATTTACAGAGAA
Found at i:112599 original size:12 final size:12
Alignment explanation
Indices: 112584--112621 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
112574 GTTATTTAAA
112584 CGGGTATTGGGC
1 CGGGTATTGGGC
*
112596 CGGGTATTGGGT
1 CGGGTATTGGGC
112608 CGGGTATTGGGC
1 CGGGTATTGGGC
112620 CG
1 CG
112622 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:112611 original size:24 final size:24
Alignment explanation
Indices: 112584--112638 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
112574 GTTATTTAAA
* * *
112584 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
112608 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
112632 CGGGTAT
1 CGGGTAT
112639 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:112782 original size:13 final size:13
Alignment explanation
Indices: 112738--112769 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
112728 TTTAATATTT
112738 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
112751 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
112764 ATCGGG
1 ATCGGG
112770 TAATCGGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.53, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:115006 original size:42 final size:42
Alignment explanation
Indices: 114947--115041 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
114937 ATGGTTTGTG
* * *
114947 TTTGAGGTTTGGGTGTTAAAATCTAGGGTTAGTGTGTTGTTA
1 TTTGAGGTTTAGATGTTAAAATCTAGGATTAGTGTGTTGTTA
* * *
114989 TTTGAGGTTTAGATGTTACAATTTAGGATTTGTGTGTTGTTA
1 TTTGAGGTTTAGATGTTAAAATCTAGGATTAGTGTGTTGTTA
*
115031 TGTGAGGTTTA
1 TTTGAGGTTTA
115042 AGGTTTGGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (42 bp):
TTTGAGGTTTAGATGTTAAAATCTAGGATTAGTGTGTTGTTA
Found at i:115358 original size:29 final size:29
Alignment explanation
Indices: 115316--115371 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
115306 TAACGGTAGA
115316 AAACATCATATATGAAACCGAAAATTTTT
1 AAACATCATATATGAAACCGAAAATTTTT
* * * *
115345 AAACATTATGTATGAAACTGAGAATTT
1 AAACATCATATATGAAACCGAAAATTT
115372 AGTATGCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (29 bp):
AAACATCATATATGAAACCGAAAATTTTT
Found at i:121082 original size:2 final size:2
Alignment explanation
Indices: 121075--121113 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
121065 TCTCATATTC
121075 TA TA TA TA TA 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 TA TA TA TA TA T
121114 GTGTGTGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122532 original size:24 final size:25
Alignment explanation
Indices: 122494--122542 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
122484 AAAAAATAAA
122494 TATATAATAATAAGGACAATTTGGT
1 TATATAATAATAAGGACAATTTGGT
*
122519 TATAT-ATAATAAGGATAATTTGGT
1 TATATAATAATAAGGACAATTTGGT
122543 CAAATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (25 bp):
TATATAATAATAAGGACAATTTGGT
Found at i:122549 original size:24 final size:24
Alignment explanation
Indices: 122500--122550 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
122490 TAAATATATA
* *
122500 ATAATAAGGACAATTTGGTTATAT
1 ATAATAAGGACAATTTGGTCAAAT
*
122524 ATAATAAGGATAATTTGGTCAAAT
1 ATAATAAGGACAATTTGGTCAAAT
122548 ATA
1 ATA
122551 CATTCTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (24 bp):
ATAATAAGGACAATTTGGTCAAAT
Found at i:122650 original size:15 final size:16
Alignment explanation
Indices: 122630--122662 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
122620 CAAAATACAA
122630 TATTCCC-AGTAATCT
1 TATTCCCTAGTAATCT
*
122645 TATTCCCTTGTAATCT
1 TATTCCCTAGTAATCT
122661 TA
1 TA
122663 CATTCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TATTCCCTAGTAATCT
Found at i:130918 original size:46 final size:46
Alignment explanation
Indices: 130848--130946 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
130838 AATATTGTAA
* *
130848 ATAAATAAATATTAATAAAATATATTTATATAAT-TAA-AAATAATG
1 ATAAATAAATAATAATAAAATATATATATA-AATATAAGAAATAATG
*
130893 ATAAATAGAATAATAATAAATTATATATATAAATGATAATGAAATAATG
1 ATAAATA-AATAATAATAAAATATATATATAAAT-ATAA-GAAATAATG
130942 ATAAA
1 ATAAA
130947 AAAAATTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
45 10 0.22
46 20 0.43
47 3 0.07
49 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (46 bp):
ATAAATAAATAATAATAAAATATATATATAAATATAAGAAATAATG
Found at i:132390 original size:3 final size:3
Alignment explanation
Indices: 132384--132448 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
132374 AATAATTATT
*
132384 TAA TAA TAA T-A TAA T-A TAA TAA T-A TAA TAA TATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
**
132427 TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
132449 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 44 0.85
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:132405 original size:16 final size:18
Alignment explanation
Indices: 132373--132448 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 18
132363 TTTGGGCTTG
*
132373 TAATAATTAT-TTAATAA
1 TAATAATAATATTAATAA
132390 TAAT-ATAATA-TAATAA
1 TAATAATAATATTAATAA
132406 T-ATAATAATATTTAATAA
1 TAATAATAATA-TTAATAA
*
132424 TAATAATAATAATT-TTAA
1 TAATAATAAT-ATTAATAA
132442 TAATAAT
1 TAATAAT
132449 TTAAGTAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.04
16 17 0.33
17 4 0.08
18 17 0.33
19 10 0.20
20 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATATTAATAA
Found at i:132426 original size:24 final size:23
Alignment explanation
Indices: 132373--132448 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
132363 TTTGGGCTTG
* *
132373 TAATAATTATTTAATAATAATATAA
1 TAATAA-TATATAATAAT-ATTTAA
132398 T-ATAATAATATAATAATATTTAA
1 TAATAAT-ATATAATAATATTTAA
132421 TAATAATA-ATAATAAT-TTTAA
1 TAATAATATATAATAATATTTAA
132442 TAATAAT
1 TAATAAT
132449 TTAAGTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 12 0.26
22 8 0.17
23 8 0.17
24 18 0.38
25 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATATATAATAATATTTAA
Found at i:132440 original size:21 final size:21
Alignment explanation
Indices: 132384--132448 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
132374 AATAATTATT
* *
132384 TAATAATAATATAATATAATAA
1 TAATAATAATTTTA-ATAATAA
132406 T-ATAATAATATTTAATAATAA
1 TAATAATAAT-TTTAATAATAA
132427 TAATAATAATTTTAATAATAA
1 TAATAATAATTTTAATAATAA
132448 T
1 T
132449 TTAAGTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 28 0.72
22 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATAATTTTAATAATAA
Found at i:133172 original size:305 final size:304
Alignment explanation
Indices: 132621--133222 Score: 1123
Period size: 305 Copynumber: 2.0 Consensus size: 304
132611 TGCACTAAAG
132621 GGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACA
1 GGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACA
*
132686 GATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
66 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
132751 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
131 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
132816 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
196 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
132881 TTTTTTGGAAACATCATGCACTGCATGACTTACAGATGACCCTAA
261 -TTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAA
* * * *
132926 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGCAGGACTTATA
1 GGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACA
*
132991 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTG
66 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
133056 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
131 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
133121 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
196 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
133186 TTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
261 TTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
133223 TAGGAAATAG
Statistics
Matches: 289, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
304 36 0.12
305 253 0.88
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (304 bp):
GGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACA
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAA
Found at i:133249 original size:76 final size:76
Alignment explanation
Indices: 132621--133222 Score: 1123
Period size: 76 Copynumber: 7.9 Consensus size: 76
132611 TGCACTAAAG
* *
132621 GGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
132686 GATGACCCTAA
66 GATGACCCTAA
*
132697 GGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
132762 GATGACCCTAA
66 GATGACCCTAA
*
132773 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
132838 GATGACCCTAA
66 GATGACCCTAA
*
132849 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGCATGACTTAC
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGCAGGACTTAC
132914 AGATGACCCTAA
65 AGATGACCCTAA
* *
132926 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGCAGGACTTATA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
132991 GATGACCCTAA
66 GATGACCCTAA
*
133002 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
133067 GATGACCCTAA
66 GATGACCCTAA
133078 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
133143 GATGACCCTAA
66 GATGACCCTAA
133154 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
133219 GATG
66 GATG
133223 TAGGAAATAG
Statistics
Matches: 511, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
76 437 0.86
77 74 0.14
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (76 bp):
GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
GATGACCCTAA
Found at i:133904 original size:22 final size:22
Alignment explanation
Indices: 133879--133933 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
133869 AATAAAGCTT
*
133879 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
133901 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
133923 TCATCTTTGAA
1 TCATCTTTGAA
133934 TAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:136694 original size:114 final size:114
Alignment explanation
Indices: 136494--136713 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
136484 GATCATGCAG
* * * *
136494 TTCATCTTTCAATTCCAATTATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAAA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAAATCAGATAACTCAAAAA
136559 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
* * * *
136608 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAAATCAGATAACTCAAAAA
*
136673 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTA
136714 CGAGAACGTG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAAATCAGATAACTCAAAAA
ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
Found at i:140850 original size:36 final size:36
Alignment explanation
Indices: 140773--140862 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
140763 GTAAATGCGA
* *
140773 AAATGCATAA-ATGCAAAAATAAGAATGCAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
140809 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
140845 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
140863 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:143214 original size:17 final size:19
Alignment explanation
Indices: 143192--143227 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
143182 TTAATATCTG
143192 AATAAAA-TAA-AAAAATT
1 AATAAAAGTAATAAAAATT
143209 AATAAAAGTAATAAAAATT
1 AATAAAAGTAATAAAAATT
143228 TGAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AATAAAAGTAATAAAAATT
Found at i:145536 original size:11 final size:11
Alignment explanation
Indices: 145520--145581 Score: 61
Period size: 11 Copynumber: 5.3 Consensus size: 11
145510 TTTGGGCTTG
*
145520 TAATAATTATT
1 TAATAATAATT
145531 TAATAATAATAT
1 TAATAATAAT-T
* *
145543 AATATATATAATA
1 TA-ATA-ATAATT
145556 TAATAATAATTT
1 TAATAATAA-TT
145568 TAATAATAATT
1 TAATAATAATT
145579 TAA
1 TAA
145582 GTAAAATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 18 0.43
12 15 0.36
13 4 0.10
14 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATAATAATT
Found at i:145571 original size:17 final size:18
Alignment explanation
Indices: 145520--145577 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
145510 TTTGGGCTTG
*
145520 TAATAATTA-TTTAATAA
1 TAATAATAATTTTAATAA
145537 TAAT-ATAATATATATAAT-A
1 TAATAATAAT-T-T-TAATAA
145556 TAATAATAATTTTAATAA
1 TAATAATAATTTTAATAA
145574 TAAT
1 TAAT
145578 TTAAGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 7 0.21
19 7 0.21
20 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATAATAATTTTAATAA
Found at i:152247 original size:54 final size:54
Alignment explanation
Indices: 152165--152330 Score: 242
Period size: 54 Copynumber: 3.1 Consensus size: 54
152155 TCCATCGCCA
*
152165 CCGGAACTTGGACCAGAGTTGGTGACAGCGTCAACGAGTGCATTTCCTTGTCCT
1 CCGGAACTTGGACCAGAGTTGGTGACAGCGTCAACGAATGCATTTCCTTGTCCT
* * *
152219 CCGGAACTTGGACCAGAGTTGATGACAGCATCAACCAATGCATTTCCTTGTCCT
1 CCGGAACTTGGACCAGAGTTGGTGACAGCGTCAACGAATGCATTTCCTTGTCCT
* * * ** *
152273 CCGGAACTTGGACCTGAGTTGGTGACAGTGTCGACGAATGCATGACCTTTTCCT
1 CCGGAACTTGGACCAGAGTTGGTGACAGCGTCAACGAATGCATTTCCTTGTCCT
152327 CCGG
1 CCGG
152331 TCTTGATTCC
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (54 bp):
CCGGAACTTGGACCAGAGTTGGTGACAGCGTCAACGAATGCATTTCCTTGTCCT
Found at i:155412 original size:70 final size:70
Alignment explanation
Indices: 155296--155441 Score: 258
Period size: 70 Copynumber: 2.1 Consensus size: 70
155286 TGGGACTTCA
*
155296 ATCTTGATGCTTAAGTAAAGATTGTACTAGTAATATTCCATGGGGAACACAACAGGACTAATACG
1 ATCTTGATGCTAAAGTAAAGATTGTACTAGTAATATTCCATGGGGAACACAACAGGACTAATACG
155361 ACAAT
66 ACAAT
*
155366 ATCTTGATGCTAAAGTAAAGATTGTACTAGTAATTATTCCAT-GGGAACACAACATGACTAATAC
1 ATCTTGATGCTAAAGTAAAGATTGTACTAGTAA-TATTCCATGGGGAACACAACAGGACTAATAC
155430 GACAAT
65 GACAAT
155436 ATCTTG
1 ATCTTG
155442 TTGTCAGGTA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
70 65 0.89
71 8 0.11
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (70 bp):
ATCTTGATGCTAAAGTAAAGATTGTACTAGTAATATTCCATGGGGAACACAACAGGACTAATACG
ACAAT
Found at i:156822 original size:28 final size:28
Alignment explanation
Indices: 156786--156844 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
156776 TAAGGATAAA
* *
156786 TTACTCTTAAAGTCACTTTATTCTGCGT
1 TTACACTTAAAGTCACTTTATTCTGAGT
156814 TTACACTTAAAGTCACTTTATTCTGAGT
1 TTACACTTAAAGTCACTTTATTCTGAGT
156842 TTA
1 TTA
156845 GTAATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (28 bp):
TTACACTTAAAGTCACTTTATTCTGAGT
Found at i:168133 original size:21 final size:21
Alignment explanation
Indices: 168109--168158 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
168099 TCCAGATTCA
*
168109 CAACGCGAACATCGATTATCG
1 CAACGCGAACATCGACTATCG
*
168130 CAACGCGAACTTCGACTATCG
1 CAACGCGAACATCGACTATCG
*
168151 CAATGCGA
1 CAACGCGA
168159 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCG
Found at i:168178 original size:19 final size:19
Alignment explanation
Indices: 168162--168307 Score: 148
Period size: 19 Copynumber: 7.3 Consensus size: 19
168152 AATGCGATTT
*
168162 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
168181 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
168200 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
168223 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
168242 TCCAAGTTCGTTGAGATAG
1 TCCAAGTTCGTTGCGATAG
* *
168261 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
168284 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
168303 TCCAA
1 TCCAA
168308 AATCGCATCA
Statistics
Matches: 105, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
19 58 0.55
21 31 0.30
23 16 0.15
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:168247 original size:61 final size:61
Alignment explanation
Indices: 168154--168307 Score: 285
Period size: 61 Copynumber: 2.6 Consensus size: 61
168144 ACTATCGCAA
*
168154 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGT
168213 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGT
168274 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
168308 AATCGCATCA
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
59 5 0.05
60 2 0.02
61 85 0.92
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (61 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGT
Found at i:169204 original size:42 final size:42
Alignment explanation
Indices: 169135--169238 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
169125 ACCAGTCGTT
* *
169135 GCGAACTTGGACTATCGCAACGAATTTGTAATAAATCGCAAC
1 GCGAACTTGGACTATCGCAACAAATTTGGAATAAATCGCAAC
* *
169177 GCGAGCTTGAACTATCGCAACAAATTTGGAATAAATCGCAAC
1 GCGAACTTGGACTATCGCAACAAATTTGGAATAAATCGCAAC
169219 GCGAACTTGGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
169239 TGTGATAGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
GCGAACTTGGACTATCGCAACAAATTTGGAATAAATCGCAAC
Found at i:169235 original size:21 final size:20
Alignment explanation
Indices: 169135--169238 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
169125 ACCAGTCGTT
169135 GCGAACTTGGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
* * *
169155 -CGAATTTGTAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
* *
169176 CGCGAGCTTGAACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* * *
169197 -CAAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
169218 CGCGAACTTGGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
169239 TGTGATAGTC
Statistics
Matches: 61, Mismatches: 15, Indels: 15
0.67 0.16 0.16
Matches are distributed among these distances:
19 16 0.26
21 28 0.46
23 17 0.28
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
GCGAACTTGGACTATCGCAA
Found at i:169266 original size:21 final size:21
Alignment explanation
Indices: 169242--169285 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
169232 ATCGCAATGT
169242 GATAGTCAAAGTTCGCGTTGC
1 GATAGTCAAAGTTCGCGTTGC
* *
169263 GATAGTCCAATTTCGCGTTGC
1 GATAGTCAAAGTTCGCGTTGC
169284 GA
1 GA
169286 ATCTGGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (21 bp):
GATAGTCAAAGTTCGCGTTGC
Found at i:169971 original size:20 final size:21
Alignment explanation
Indices: 169932--169971 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
169922 AATTTTAAGT
* *
169932 TATTTAAAAATAAATCTTATA
1 TATTAAAAAATAAATATTATA
169953 TATTAAAAAAT-AATATTAT
1 TATTAAAAAATAAATATTAT
169972 GGTCTCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTAAAAAATAAATATTATA
Found at i:175268 original size:3 final size:3
Alignment explanation
Indices: 175260--175284 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
175250 ATAAATAAGC
175260 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
175285 CAATTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:185737 original size:15 final size:16
Alignment explanation
Indices: 185709--185740 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
185699 AAAATCTTTC
185709 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
185725 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
185740 T
1 T
185741 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:188460 original size:17 final size:17
Alignment explanation
Indices: 188435--188469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
188425 TGAAAATTTT
188435 ATATGATTTTAAATTATC
1 ATATGATTTTAAA-TATC
188453 ATAT-ATTTTAAATATC
1 ATATGATTTTAAATATC
188469 A
1 A
188470 ACTTTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATGATTTTAAATATC
Found at i:189088 original size:20 final size:20
Alignment explanation
Indices: 189036--189089 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
189026 AACTTAATAT
*
189036 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
189058 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
189078 TATTATTTTTAT
1 TATTATTTTTAT
189090 AATTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:189232 original size:23 final size:23
Alignment explanation
Indices: 189183--189233 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
189173 GTGTTATATT
**
189183 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
189206 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
189229 ATATT
1 ATATT
189234 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:189289 original size:19 final size:19
Alignment explanation
Indices: 189221--189301 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
189211 TTAAATATCT
189221 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
189240 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
189259 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
189279 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
189297 -TATTA
1 TTATTA
189302 TTTCTATGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:189453 original size:10 final size:10
Alignment explanation
Indices: 189412--189457 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
189402 ATTTTATTAT
189412 AATATTAA-A
1 AATATTAATA
189421 AATA-TAATA
1 AATATTAATA
189430 TAATATTATTATA
1 -AATATTA--ATA
189443 AATATTAATA
1 AATATTAATA
189453 AATAT
1 AATAT
189458 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:189460 original size:21 final size:22
Alignment explanation
Indices: 189413--189469 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
189403 TTTTATTATA
*
189413 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
189434 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
189456 ATATTTTAAATATT
1 ATATTATAAATATT
189470 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:189474 original size:23 final size:21
Alignment explanation
Indices: 189420--189469 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
189410 ATAATATTAA
*
189420 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
189442 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
189463 AAATATT
1 AAATATT
189470 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:191864 original size:215 final size:216
Alignment explanation
Indices: 191489--191885 Score: 638
Period size: 215 Copynumber: 1.8 Consensus size: 216
191479 TAGTGTAATG
*
191489 ATTATTAGGATCATGTCTCCCGGTGAGGAGGATGTATGATTATTATTATTATTATTATTGTATTA
1 ATTATTAGGATCATGTCTCCC-G-GAGGAGGATGTATGATGATTATTATTATTATTATTGTATTA
* * *
191554 TATCAATAGGTGACGAGAAAGTAAGATTCGAACATTAATAAACTACTAATAAATTATCGAGTTAA
64 TATCAATAGGTGACAAGAAAGTAAGATCCAAACATTAATAAACTACTAATAAATTATCGAGTTAA
191619 AATTAATAAAATGATTCTTAATTCTTTGTTATGATTATGATACTTACATATTTTATGACTTTAGC
129 AATTAATAAAATGATTCTTAATTCTTTGTTATGATTATGATACTTACATATTTTATGACTTTAGC
191684 CTTAGCGAAGATGAATGATGATT
194 CTTAGCGAAGATGAATGATGATT
191707 ATTATTAGGATCATGTCTCCC-GAGGAGGATGTATGATGATTATTATTATTATTGATAT-T-TTA
1 ATTATTAGGATCATGTCTCCCGGAGGAGGATGTATGATGATTATTATTATTATT-AT-TGTATTA
* * * * *
191769 TATCAATATGTGACAAGAAGGTGAGATCCAAATATTCATAAACTACTAATAAATTATCGAGTTAA
64 TATCAATAGGTGACAAGAAAGTAAGATCCAAACATTAATAAACTACTAATAAATTATCGAGTTAA
* *
191834 AATTAATAAAATGATTCTTAATTTTTTGTTATGATTATGATGCTTACATATT
129 AATTAATAAAATGATTCTTAATTCTTTGTTATGATTATGATACTTACATATT
191886 AAAAGTATGA
Statistics
Matches: 166, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
215 141 0.85
216 3 0.02
217 1 0.01
218 21 0.13
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (216 bp):
ATTATTAGGATCATGTCTCCCGGAGGAGGATGTATGATGATTATTATTATTATTATTGTATTATA
TCAATAGGTGACAAGAAAGTAAGATCCAAACATTAATAAACTACTAATAAATTATCGAGTTAAAA
TTAATAAAATGATTCTTAATTCTTTGTTATGATTATGATACTTACATATTTTATGACTTTAGCCT
TAGCGAAGATGAATGATGATT
Found at i:194422 original size:24 final size:24
Alignment explanation
Indices: 194394--194446 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
194384 TTGTAAATGC
194394 TAAACGAAAATATTCGTGAACATA
1 TAAACGAAAATATTCGTGAACATA
194418 TAAACGAAAATATTCGTGAACATA
1 TAAACGAAAATATTCGTGAACATA
194442 TAAAC
1 TAAAC
194447 TAATACGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (24 bp):
TAAACGAAAATATTCGTGAACATA
Found at i:194479 original size:23 final size:24
Alignment explanation
Indices: 194435--194479 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
194425 AAATATTCGT
* *
194435 GAACATATAAACTAATACGTTTAC
1 GAACATATAAACGAACACGTTTAC
*
194459 GAACAT-TAAACGAACATGTTT
1 GAACATATAAACGAACACGTTT
194480 GCGAGCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (24 bp):
GAACATATAAACGAACACGTTTAC
Found at i:197853 original size:12 final size:12
Alignment explanation
Indices: 197834--197863 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
197824 GAAAATTAGA
197834 AAAATAAAAAAT
1 AAAATAAAAAAT
*
197846 ATAATAAAAAAT
1 AAAATAAAAAAT
197858 AAAATA
1 AAAATA
197864 CAGGTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:203327 original size:156 final size:157
Alignment explanation
Indices: 203043--203356 Score: 621
Period size: 156 Copynumber: 2.0 Consensus size: 157
203033 ACAAATAGGC
203043 CCCAGACATCAAAAGAAAGTAGTGTTTTCGTACGAGAGTTGGTAATGGAAGAGGAGCCTCCAGAG
1 CCCAGACATCAAAAGAAAGTAGTGTTTTCGTACGAGAGTTGGTAATGGAAGAGGAGCCTCCAGAG
203108 GAACAGCTTATATGGGCAGGAGCTAACACTGATAGGTAAAAAGTAGTGAAATTGTTTGAAGTTTG
66 GAACAGCTTATATGGGCAGGAGCTAACACTGATAGGTAAAAAGTAGTGAAATTGTTTGAAGTTTG
203173 ATTAGCGTGACTCGTTTTGG-TTATGG
131 ATTAGCGTGACTCGTTTTGGTTTATGG
203199 CCCAGACATCAAAAGAAAGTAGTGTTTTCGTACGAGAGTTGGTAATGGAAGAGGAGCCTCCAGAG
1 CCCAGACATCAAAAGAAAGTAGTGTTTTCGTACGAGAGTTGGTAATGGAAGAGGAGCCTCCAGAG
203264 GAACAGCTTATATGGGCAGGAGCTAACACTGATAGGTAAAAAGTAGTGAAATTGTTTGAAGTTTG
66 GAACAGCTTATATGGGCAGGAGCTAACACTGATAGGTAAAAAGTAGTGAAATTGTTTGAAGTTTG
203329 ATTAGCGTGACTCGTTTTGGTTTATGG
131 ATTAGCGTGACTCGTTTTGGTTTATGG
203356 C
1 C
203357 TTTAGCTATA
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 150 0.96
157 7 0.04
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (157 bp):
CCCAGACATCAAAAGAAAGTAGTGTTTTCGTACGAGAGTTGGTAATGGAAGAGGAGCCTCCAGAG
GAACAGCTTATATGGGCAGGAGCTAACACTGATAGGTAAAAAGTAGTGAAATTGTTTGAAGTTTG
ATTAGCGTGACTCGTTTTGGTTTATGG
Found at i:204206 original size:2 final size:2
Alignment explanation
Indices: 204201--204237 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
204191 ATTAATTTAA
*
204201 AT AT AT AT AT AT AT AT AT AT AT AT AT CT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
204238 CTACTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:210336 original size:16 final size:16
Alignment explanation
Indices: 210315--210349 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
210305 ACAGAACCTC
*
210315 TAAATTATTCAACATT
1 TAAATTATCCAACATT
*
210331 TAAATTATCCAACGTT
1 TAAATTATCCAACATT
210347 TAA
1 TAA
210350 TCATTCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (16 bp):
TAAATTATCCAACATT
Found at i:218993 original size:7 final size:7
Alignment explanation
Indices: 218981--219005 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
218971 TAAAAAAATA
218981 ATTTTAT
1 ATTTTAT
218988 ATTTTAT
1 ATTTTAT
218995 ATTTTAT
1 ATTTTAT
219002 ATTT
1 ATTT
219006 GTGACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTAT
Found at i:221003 original size:42 final size:42
Alignment explanation
Indices: 220957--221115 Score: 255
Period size: 42 Copynumber: 3.8 Consensus size: 42
220947 TGGCGGCAGA
* * * * *
220957 GGGGGAGGTATGGGCAATGGAGGAAGTGGTGGTTTTGGAGGT
1 GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGTTTCGGTGGT
*
220999 GGGGGAGGTGTTGGCAGTGGCGGAAGTGGTGGTTTCGGTGGT
1 GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGTTTCGGTGGT
*
221041 GGGGGAGGTGTTGGCAGTGGCGGAAGTGGTGGTTTCGGTGGT
1 GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGTTTCGGTGGT
221083 GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGT
1 GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGT
221116 GGGGGAGTTG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.13, C:0.05, G:0.57, T:0.25
Consensus pattern (42 bp):
GGGGGAGGTGTTGGCAGTGGAGGAAGTGGTGGTTTCGGTGGT
Found at i:221072 original size:33 final size:33
Alignment explanation
Indices: 221035--221145 Score: 93
Period size: 42 Copynumber: 3.2 Consensus size: 33
221025 TGGTGGTTTC
*
221035 GGTGGTGGGGGAGGTGTTGGCAGTGGCGGAAGTGGT
1 GGTGGTGGGGGAGGTGTTGGCAGTGGAGGAA---GT
221071 GGTTTCGGTGGTGGGGGAGGTGTTGGCAGTGGAGGAAGT
1 GG--T--G--GTGGGGGAGGTGTTGGCAGTGGAGGAAGT
* *
221110 GGTGGTGGGGGA---GTTGGCAATGGGGGAAGT
1 GGTGGTGGGGGAGGTGTTGGCAGTGGAGGAAGT
221140 GGTGGT
1 GGTGGT
221146 TTCGGGGGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
30 22 0.33
33 8 0.12
35 1 0.02
36 2 0.03
37 1 0.02
38 1 0.02
39 4 0.06
40 1 0.02
42 26 0.39
ACGTcount: A:0.13, C:0.05, G:0.59, T:0.23
Consensus pattern (33 bp):
GGTGGTGGGGGAGGTGTTGGCAGTGGAGGAAGT
Found at i:221112 original size:30 final size:30
Alignment explanation
Indices: 221078--221145 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
221068 GGTGGTTTCG
* *
221078 GTGGTGG-GGGAGGTGTTGGCAGTGGAGGAA
1 GTGGTGGTGGG-GGAGTTGGCAATGGAGGAA
*
221108 GTGGTGGTGGGGGAGTTGGCAATGGGGGAA
1 GTGGTGGTGGGGGAGTTGGCAATGGAGGAA
221138 GTGGTGGT
1 GTGGTGGT
221146 TTCGGGGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.15, C:0.03, G:0.60, T:0.22
Consensus pattern (30 bp):
GTGGTGGTGGGGGAGTTGGCAATGGAGGAA
Found at i:221112 original size:72 final size:72
Alignment explanation
Indices: 221036--221187 Score: 216
Period size: 72 Copynumber: 2.1 Consensus size: 72
221026 GGTGGTTTCG
* * * * *
221036 GTGGTGG-GGGAGGTGTTGGCAGTGGCGGAAGTGGTGGTTTCGGTGGTGGGGGAGGTGTTGGCAG
1 GTGGTGGTGGG-GGAGTTGGCAATGGCGGAAGTGGTGGTTTCGGGGGTGGGGGAGGTGTTAGAAG
221100 TGGAGGAA
65 TGGAGGAA
* *
221108 GTGGTGGTGGGGGAGTTGGCAATGGGGGAAGTGGTGGTTTCGGGGGTGGGGGAGGTTTTAGAAGT
1 GTGGTGGTGGGGGAGTTGGCAATGGCGGAAGTGGTGGTTTCGGGGGTGGGGGAGGTGTTAGAAGT
*
221173 GGGGGAA
66 GGAGGAA
221180 GTGGTGGT
1 GTGGTGGT
221188 TTCGGTGGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 68 0.96
73 3 0.04
ACGTcount: A:0.13, C:0.04, G:0.59, T:0.24
Consensus pattern (72 bp):
GTGGTGGTGGGGGAGTTGGCAATGGCGGAAGTGGTGGTTTCGGGGGTGGGGGAGGTGTTAGAAGT
GGAGGAA
Found at i:221198 original size:24 final size:24
Alignment explanation
Indices: 221130--221198 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
221120 GAGTTGGCAA
*
221130 TGGGGGAAGTGGTGGTTTCGGGGG
1 TGGGGGAAGTGGTGGTTTCGGAGG
* *
221154 TGGGGG-A--GGT--TTT-AGAAG
1 TGGGGGAAGTGGTGGTTTCGGAGG
*
221172 TGGGGGAAGTGGTGGTTTCGGTGG
1 TGGGGGAAGTGGTGGTTTCGGAGG
221196 TGG
1 TGG
221199 CGGCGACGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
21 6 0.18
23 4 0.12
24 11 0.33
ACGTcount: A:0.12, C:0.03, G:0.58, T:0.28
Consensus pattern (24 bp):
TGGGGGAAGTGGTGGTTTCGGAGG
Found at i:228202 original size:15 final size:15
Alignment explanation
Indices: 228182--228210 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
228172 TAAAAAAATA
228182 ATATTTATTTTATTT
1 ATATTTATTTTATTT
228197 ATATTTATTTTATT
1 ATATTTATTTTATT
228211 CTTGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATATTTATTTTATTT
Found at i:241386 original size:19 final size:19
Alignment explanation
Indices: 241339--241402 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 19
241329 TCAATAATTT
241339 ATTATATAAATTAATAATAAAAA
1 ATTATATAAA--AATAAT--AAA
241362 AGTTATATAAAAATAATAAA
1 A-TTATATAAAAATAATAAA
*
241382 ATTATTTAACAAA-AATAAA
1 ATTATATAA-AAATAATAAA
241401 AT
1 AT
241403 ATACAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 15 0.39
20 7 0.18
22 6 0.16
23 1 0.03
24 9 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATTATATAAAAATAATAAA
Found at i:244549 original size:271 final size:268
Alignment explanation
Indices: 244043--244578 Score: 865
Period size: 271 Copynumber: 2.0 Consensus size: 268
244033 AGTTAAAAAA
* *
244043 GCCAAATGTCTGAGGAGAGACTGGCTTAATGCAATTCTTTAATAAGGGAAAATGGATGAATATAC
1 GCCAAATGTCTGAGGAGAGACTGGCTAAATGCAATTCTTTAATAAGGGAAAATGGATGAAGATAC
* * *
244108 TAGAATGAAAAGAGAGAACTTAAACTGCATGCCTACTCTGCATATCAGGGGCACCTGAGAGACAT
66 TAGAATGAAAAAAGAGAACTTAAACTGCATGCCTACTCTGCATATCAAGGGCACCTGAGAGACAC
* * *
244173 TCAGTTCAGTAGATTGTGATTTCAAATTAAGAATGGAAGTTAAAAGGGCCAAATGTCTGTGAGGA
131 TCAGTTCAGTAGAATGTGATTTCAAATTAAGAATGGAAGTTAAAAGGGCCAAATGTCTGAGAGAA
** **
244238 GAGACTGGCGTATCAGTTGCTGATCTTCTTGCTTTAAGGAATGAGTCAGGGGGCGTTCATTATAT
196 GAGACTGGCGTATCAGTTGCTGATCTTCTTGCACTAAGGAATGAGTCA-GACGCGTTCATTATAT
244303 ATGGAAAGG
260 ATGGAAAGG
* *
244312 GCCAAATGTCTGAGAGAAGAGACTGGCTAAATGCAGTTCTTTAATAAGGGAAAATGGATGACGAT
1 GCCAAATGTCTGAG-G-AGAGACTGGCTAAATGCAATTCTTTAATAAGGGAAAATGGATGAAGAT
* *
244377 ATTAGAATGAAAAAAGGGAACTTAAACTGCATGCCTACTCTGCATATCAAGGGCACCTGAGAGAC
64 ACTAGAATGAAAAAAGAGAACTTAAACTGCATGCCTACTCTGCATATCAAGGGCACCTGAGAGAC
*
244442 ACTGAGTTCAGTAGAATGTGATTTCAAATTAAGAATGGAAGTTAAAAGGGCCAAATGTCTGAGAG
129 ACTCAGTTCAGTAGAATGTGATTTCAAATTAAGAATGGAAGTTAAAAGGGCCAAATGTCTGAGAG
* *
244507 AAGAGACTGGCTTATTAGTTGCTGATCTTCTTGCACTAAGGAATGAGTCAGACGCGTTCATTATA
194 AAGAGACTGGCGTATCAGTTGCTGATCTTCTTGCACTAAGGAATGAGTCAGACGCGTTCATTATA
*
244572 TTTGGAA
259 TATGGAA
244579 CAATCTGATC
Statistics
Matches: 245, Mismatches: 20, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
269 14 0.06
270 20 0.08
271 211 0.86
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (268 bp):
GCCAAATGTCTGAGGAGAGACTGGCTAAATGCAATTCTTTAATAAGGGAAAATGGATGAAGATAC
TAGAATGAAAAAAGAGAACTTAAACTGCATGCCTACTCTGCATATCAAGGGCACCTGAGAGACAC
TCAGTTCAGTAGAATGTGATTTCAAATTAAGAATGGAAGTTAAAAGGGCCAAATGTCTGAGAGAA
GAGACTGGCGTATCAGTTGCTGATCTTCTTGCACTAAGGAATGAGTCAGACGCGTTCATTATATA
TGGAAAGG
Found at i:244804 original size:129 final size:128
Alignment explanation
Indices: 244563--244811 Score: 331
Period size: 129 Copynumber: 1.9 Consensus size: 128
244553 GTCAGACGCG
* * * * * *
244563 TTCATTATATTTGGAACAATCTGATCAAATTAGAGGCAAGCAGAGTTTTCATACAATGTGCCATA
1 TTCACTATATCTGGAACAATCAGATCAAATTAAAGGCAAGCAGAGTTTCCAGACAATGTGCCATA
** * *
244628 GAAATAGCGATGGTTGAAAGATTTTAATCTGACAAAGGAGAAACAGGGGGAAATAATAGTTGCA
66 GAAATAGAAATGGTTGAAAGAATTTAATCTGACAAAGAAGAAACA-GGGGAAATAATAGTTGCA
*
244692 TTCACTATATCTGGAACAATCAGATCAAATTAAAGGCAAGCAGAGTTTCCAGACTCTATGTGCCA
1 TTCACTATATCTGGAACAATCAGATCAAATTAAAGGCAAGCAGAGTTTCCAGA--CAATGTGCCA
* * *
244757 TAGAAATAGAAATGGTTGAATGAATTT-AT-TGAGAAAGAAGAAGCAGGGGAAATAA
64 TAGAAATAGAAATGGTTGAAAGAATTTAATCTGACAAAGAAGAAACAGGGGAAATAA
244812 AAGAGTTAGC
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
128 10 0.10
129 60 0.58
130 2 0.02
131 32 0.31
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (128 bp):
TTCACTATATCTGGAACAATCAGATCAAATTAAAGGCAAGCAGAGTTTCCAGACAATGTGCCATA
GAAATAGAAATGGTTGAAAGAATTTAATCTGACAAAGAAGAAACAGGGGAAATAATAGTTGCA
Found at i:247415 original size:30 final size:30
Alignment explanation
Indices: 247370--247426 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
247360 GGTGATTGTT
* *
247370 ATAGATCTTCAGGAGCACATGGCGACCTTC
1 ATAGATCTCCAGGAGCACACGGCGACCTTC
*
247400 ATAGGTCTCCAGGAGCACACGGCGACC
1 ATAGATCTCCAGGAGCACACGGCGACC
247427 GGCGACCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (30 bp):
ATAGATCTCCAGGAGCACACGGCGACCTTC
Found at i:256060 original size:30 final size:31
Alignment explanation
Indices: 255994--256069 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
255984 AATTAGGGCG
* *
255994 ATTTTTCTGATATATCATCGATGAACAGTAT
1 ATTTTTCTGATCTAACATCGATGAACAGTAT
* * *
256025 A-TTTTCTGATCTAACATCGGT-AATATTAT
1 ATTTTTCTGATCTAACATCGATGAACAGTAT
256054 ATTTTTC-GATCTAACA
1 ATTTTTCTGATCTAACA
256070 CCCTTAGTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 16 0.41
30 22 0.56
31 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (31 bp):
ATTTTTCTGATCTAACATCGATGAACAGTAT
Found at i:256186 original size:51 final size:51
Alignment explanation
Indices: 256089--256209 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 51
256079 GTAAAGCGTG
* * * *
256089 CCCCCTGCACCGCACTATACGATGATTTGGCGCCACGTGGGGTATAGCGCA
1 CCCCCTGCACCGCGCTATACGATGATCTGGCGACACGTGGGATATAGCGCA
* * *
256140 CCCCCTGCACCGCGCTATACGGTGATCTGGCATACACGT-GGATATAGCGCG
1 CCCCCTGCACCGCGCTATACGATGATCTGGC-GACACGTGGGATATAGCGCA
* * *
256191 GCCCCTGCAGCGTGCTATA
1 CCCCCTGCACCGCGCTATA
256210 TGCCACGTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 54 0.92
52 5 0.08
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.20
Consensus pattern (51 bp):
CCCCCTGCACCGCGCTATACGATGATCTGGCGACACGTGGGATATAGCGCA
Found at i:256513 original size:13 final size:13
Alignment explanation
Indices: 256487--256540 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
256477 TTAAAGGTAA
*
256487 TTTTGTTATAATTT
1 TTTTATTAT-ATTT
256501 TTTTATTATATTT
1 TTTTATTATATTT
*
256514 ATTTATTAT-TTT
1 TTTTATTATATTT
**
256526 TTAAATTATATTT
1 TTTTATTATATTT
256539 TT
1 TT
256541 GTGTTTGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 9 0.26
13 17 0.50
14 8 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTATTATATTT
Found at i:256533 original size:25 final size:24
Alignment explanation
Indices: 256492--256538 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
256482 GGTAATTTTG
*
256492 TTATAATTTTTTTATTATATTTAT
1 TTATAATTTTTTAATTATATTTAT
*
256516 TTATTATTTTTTAAATTATATTT
1 TTATAATTTTTT-AATTATATTT
256539 TTGTGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATAATTTTTTAATTATATTTAT
Found at i:259886 original size:26 final size:25
Alignment explanation
Indices: 259857--259928 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 25
259847 AAAATCCAAC
*
259857 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA-AATT
*
259883 AAA-TGAGA-AATAATAAA--AAAATT
1 AAATTTA-ACAA-AATAAAGTAAAATT
259906 ACAATTTAACAAAATAAAGTAAA
1 A-AATTTAACAAAATAAAGTAAA
259929 TACAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
23 4 0.11
24 11 0.31
25 8 0.22
26 13 0.36
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (25 bp):
AAATTTAACAAAATAAAGTAAAATT
Found at i:262163 original size:110 final size:111
Alignment explanation
Indices: 261969--262185 Score: 373
Period size: 110 Copynumber: 2.0 Consensus size: 111
261959 ACAAAAATTG
* * * *
261969 ATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTAAAT
1 ATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAACAATTTAAATTAAAA
* *
262034 TAACACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATACTTA
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATACTTA
262080 ATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAACAATTTAAATTAAAA
1 ATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAACAATTTAAATTAAAA
262144 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATA
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATA
262186 TATGATTTCC
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 68 0.68
111 32 0.32
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (111 bp):
ATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAACAATTTAAATTAAAA
TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATACTTA
Found at i:269407 original size:3 final size:3
Alignment explanation
Indices: 269401--269456 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
269391 CTCATGCCTA
269401 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
269447 TAT TA- TAT TA
1 TAT TAT TAT TA
269457 AGCTAAGTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 44 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:269432 original size:14 final size:14
Alignment explanation
Indices: 269401--269456 Score: 87
Period size: 14 Copynumber: 3.9 Consensus size: 14
269391 CTCATGCCTA
269401 TATTATTATTATTAT
1 TATTATTA-TATTAT
269416 TATTATTAT-TATAT
1 TATTATTATAT-TAT
269430 TATTATTATATTAT
1 TATTATTATATTAT
269444 TATTATTATATTA
1 TATTATTATATTA
269457 AGCTAAGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.03
14 29 0.74
15 9 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:269456 original size:11 final size:11
Alignment explanation
Indices: 269404--269449 Score: 83
Period size: 11 Copynumber: 4.1 Consensus size: 11
269394 ATGCCTATAT
269404 TATTATTATTA
1 TATTATTATTA
269415 TTATTATTATTA
1 -TATTATTATTA
269427 TATTATTATTA
1 TATTATTATTA
269438 TATTATTATTA
1 TATTATTATTA
269449 T
1 T
269450 TATATTAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 23 0.68
12 11 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:271822 original size:290 final size:290
Alignment explanation
Indices: 271302--272143 Score: 1616
Period size: 290 Copynumber: 2.9 Consensus size: 290
271292 GGCTATATCT
271302 CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
1 CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
271367 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
66 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
* *
271432 AATATTTTGTTAATGAGATTTCCCTAGCTACTTCACAAATAAGATCCACATAAACTCATGTCCAT
131 AATATTTTGTGAATGAGATTTCCCTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
271497 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
196 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
271562 TTGCTATATCTCGATTCCATTGGCAGAAGC
261 TTGCTATATCTCGATTCCATTGGCAGAAGC
* *
271592 CGAAATATCTAAATATTGTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
1 CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
*
271657 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTGATTAAGCAATATTATACTTTCATA
66 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
271722 AATATTTTGTGAATGAGATTTCCCTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
131 AATATTTTGTGAATGAGATTTCCCTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
271787 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
196 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
271852 TTGCTATATCTCGATTCCATTGGCAGAAGC
261 TTGCTATATCTCGATTCCATTGGCAGAAGC
271882 CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAG--AGGATTAATGAGAGAT
1 CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
271945 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
66 TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
*
272010 AATATTTTGTGAATGAGATTTCCTTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
131 AATATTTTGTGAATGAGATTTCCCTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
272075 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
196 TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
272140 TTGC
261 TTGC
272144 AGCTCCAAAT
Statistics
Matches: 543, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
288 213 0.39
290 330 0.61
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (290 bp):
CGAAATATCTAAATCTTTTTTTGTTTGGTCATTTCAGAAAAGAAGAGAAAGGATTAATGAGAGAT
TGAGACTTTTACAGAGCCTTGTCCCAAACGGAACTAAGGTAATTAAGCAATATTATACTTTCATA
AATATTTTGTGAATGAGATTTCCCTAGCTACTTCACAATTAAGATCCACATAAACTCATGTCCAT
TGATGATGATAATACAGGTTGATATCAGCACGATGCTTGAAGATGCCATTCATTATGTGAAGTTC
TTGCTATATCTCGATTCCATTGGCAGAAGC
Found at i:273917 original size:23 final size:23
Alignment explanation
Indices: 273887--273932 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
273877 ATACGGACCT
273887 TGGATGATAGCCACTAATTGACG
1 TGGATGATAGCCACTAATTGACG
273910 TGGATGATAGCCACTAATTGACG
1 TGGATGATAGCCACTAATTGACG
273933 GAGGAAGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGATGATAGCCACTAATTGACG
Found at i:275943 original size:65 final size:65
Alignment explanation
Indices: 275862--275991 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
275852 GTAACAAAAA
275862 ATGATGCTCTATGGGTTCGGTTCATTCTAGCGAAATACAAATGCCATGAGAGGATACCAAGGGAG
1 ATGATGCTCTATGGGTTCGGTTCATTCTAGCGAAATACAAATGCCATGAGAGGATACCAAGGGAG
275927 ATGATGCTCTATGGGTTCGGTTCATTCTAGCGAAATACAAATGCCATGAGAGGATACCAAGGGAG
1 ATGATGCTCTATGGGTTCGGTTCATTCTAGCGAAATACAAATGCCATGAGAGGATACCAAGGGAG
275992 TTAAAGAACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (65 bp):
ATGATGCTCTATGGGTTCGGTTCATTCTAGCGAAATACAAATGCCATGAGAGGATACCAAGGGAG
Found at i:276859 original size:3 final size:3
Alignment explanation
Indices: 276853--276896 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
276843 ATCATTAAAT
*
276853 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
276897 TAACCTACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:277115 original size:17 final size:18
Alignment explanation
Indices: 277089--277122 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
277079 AAGGCAAGGA
*
277089 AGCCATACGTG-GAGGGG
1 AGCCAGACGTGAGAGGGG
277106 AGCCAGACGTGAGAGGG
1 AGCCAGACGTGAGAGGG
277123 AGAAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.18, G:0.47, T:0.09
Consensus pattern (18 bp):
AGCCAGACGTGAGAGGGG
Found at i:279332 original size:35 final size:35
Alignment explanation
Indices: 279286--279355 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
279276 TTCATTTAGG
279286 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
279321 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
279356 CCTACACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:279357 original size:20 final size:20
Alignment explanation
Indices: 279285--279348 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
279275 TTTCATTTAG
279285 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
*
279305 GGGGGAATCTG-T---TCCC-
1 GGGGGAATC-GATACCCCCCA
279321 -GGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
279340 GGGGGAATC
1 GGGGGAATC
279349 TGTTCCCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
17 3 0.09
18 3 0.09
20 18 0.51
21 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.14
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:284957 original size:3 final size:3
Alignment explanation
Indices: 284949--285005 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
284939 TTATATATAT
** *
284949 TTA TTA TTA TCG TTA TTT TTA TTA TTTA TTA TTA TTA -TA TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA
*
284995 TCA TTA TTA TT
1 TTA TTA TTA TT
285006 TACATATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:288943 original size:31 final size:32
Alignment explanation
Indices: 288907--288968 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
288897 ATTTTACATG
288907 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
288938 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
288969 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:289505 original size:21 final size:20
Alignment explanation
Indices: 289467--289506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
289457 ATCAACGTTT
*
289467 TTTGCATCTGCATTTGCATC
1 TTTGCATCTGCATATGCATC
289487 TTTGCATCTTGCATATGCAT
1 TTTGCATC-TGCATATGCAT
289507 TTCATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTGCATCTGCATATGCATC
Found at i:292050 original size:4 final size:4
Alignment explanation
Indices: 292041--292202 Score: 301
Period size: 4 Copynumber: 41.0 Consensus size: 4
292031 AAAAGTATAC
*
292041 ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
292089 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
292137 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
292185 ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT
292203 GATACATAAA
Statistics
Matches: 154, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.01
4 152 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:292849 original size:105 final size:102
Alignment explanation
Indices: 292662--292900 Score: 295
Period size: 105 Copynumber: 2.3 Consensus size: 102
292652 TGAGAATTTT
** * *
292662 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
292727 TAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
292767 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* *
292832 TT-AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
292869 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
292901 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 4 0.03
105 77 0.65
106 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:292891 original size:36 final size:36
Alignment explanation
Indices: 292846--292930 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
292836 ACAAAGTTGA
**
292846 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
292882 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
292918 TCTCATTTGAGAC
1 TCTCACTTGAGAC
292931 TATATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:292962 original size:34 final size:36
Alignment explanation
Indices: 292864--292965 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 36
292854 GAGATCGTTT
* *
292864 TCTC-AAAAACAAACTTT-GTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAA-TTTCATCTCGCTTGAGACAATA
** ** *
292899 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTCATCTCGCTTGAGACAATA
*
292935 TCT-T-AAAGCAAATTTCATCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTCATCTCGCTTGAGACA
292966 TCATTTTCTC
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
34 21 0.38
35 8 0.15
36 26 0.47
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTCATCTCGCTTGAGACAATA
Found at i:293255 original size:29 final size:29
Alignment explanation
Indices: 293213--293310 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 29
293203 TTTCTCTTGA
293213 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
293242 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *
293271 AAATATCTTTGAG-TTGTTTCTTTTG-A-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
293297 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
293311 CTATTTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
26 12 0.19
27 1 0.02
28 11 0.17
29 39 0.62
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:293325 original size:26 final size:27
Alignment explanation
Indices: 293275--293354 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
293265 TTGAATAAAT
* *
293275 ATCTTTGAGT-TGTTTCTTTTGAAAA-A
1 ATCTTTGAGTCTATTTATTTT-AAAACA
293301 ATCTTTGAGTCTATTTATTTTAAAACA
1 ATCTTTGAGTCTATTTATTTTAAAACA
** *
293328 AAGTTT-TGTCTATTTATTTTAAAACA
1 ATCTTTGAGTCTATTTATTTTAAAACA
293354 A
1 A
293355 AGTTTTGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 34 0.72
27 13 0.28
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.49
Consensus pattern (27 bp):
ATCTTTGAGTCTATTTATTTTAAAACA
Found at i:293355 original size:26 final size:26
Alignment explanation
Indices: 293309--293364 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
293299 AAATCTTTGA
293309 GTCTATTTATTTTAAAACAAAGTTTT
1 GTCTATTTATTTTAAAACAAAGTTTT
293335 GTCTATTTATTTTAAAACAAAGTTTT
1 GTCTATTTATTTTAAAACAAAGTTTT
293361 GTCT
1 GTCT
293365 CTCTTGAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (26 bp):
GTCTATTTATTTTAAAACAAAGTTTT
Done.