Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 23
Found at i:840920 original size:23 final size:22
Alignment explanation
Indices: 840894--840937 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
840884 CAAGATTTAA
840894 ATATATTTAAAAATATATGTTAT
1 ATATATTTAAAAATATA-GTTAT
840917 ATATATTTAAAAATATAGTTA
1 ATATATTTAAAAATATAGTTA
840938 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATATTTAAAAATATAGTTAT
Found at i:847303 original size:19 final size:19
Alignment explanation
Indices: 847259--847304 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
847249 CCTTAGCTGG
*
847259 CCTTCAAACTTGTTTCCCC
1 CCTTCAGACTTGTTTCCCC
*
847278 CCTTCAGACTTGTTTCCTC
1 CCTTCAGACTTGTTTCCCC
847297 CCTTCAGA
1 CCTTCAGA
847305 ACCAATCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.37
Consensus pattern (19 bp):
CCTTCAGACTTGTTTCCCC
Found at i:862976 original size:41 final size:41
Alignment explanation
Indices: 862872--863081 Score: 142
Period size: 41 Copynumber: 5.1 Consensus size: 41
862862 TTCAAGATTT
* * * *
862872 CAATTCAA-TCAAATTCGATCATGGCATCATGCAGTAATTCA
1 CAATTCAATTC-AATTAGATCATGGAAACATGCAATAATTCA
* * * * *
862913 CCATTCGATTCAATTCA-TTCATGGCAGCATGCAATAATTCA
1 CAATTCAATTCAATT-AGATCATGGAAACATGCAATAATTCA
* * * *
862954 CAATTCAACTT-AATTAGATCATGTAAGCATGCAATAATCCT
1 CAATTCAA-TTCAATTAGATCATGGAAACATGCAATAATTCA
* * *
862995 TAATTTCAATTTAATTCAG-TCATGGAAACATG-AATTTATTCA
1 CAA-TTCAATTCAATT-AGATCATGGAAACATGCAA-TAATTCA
** * * *
863037 CAAACCAATTCAATTAGATCATGGTAACATGTATTAATTCA
1 CAATTCAATTCAATTAGATCATGGAAACATGCAATAATTCA
863078 CAAT
1 CAAT
863082 CTGATTCAAT
Statistics
Matches: 132, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
40 3 0.02
41 96 0.73
42 31 0.23
43 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (41 bp):
CAATTCAATTCAATTAGATCATGGAAACATGCAATAATTCA
Found at i:864836 original size:22 final size:22
Alignment explanation
Indices: 864808--864873 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
864798 TGGGTCTTTT
864808 TTTTCAATTCAATTAATTTAAA
1 TTTTCAATTCAATTAATTTAAA
*
864830 TTTTCAATTCAATTAGATCTT-TA
1 TTTTCAATTCAATTA-AT-TTAAA
*
864853 -TTT-AATTCCATTAATTTAAA
1 TTTTCAATTCAATTAATTTAAA
864873 T
1 T
864874 CTCTATTCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 9 0.24
22 18 0.49
23 3 0.08
24 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTCAATTCAATTAATTTAAA
Found at i:871109 original size:27 final size:26
Alignment explanation
Indices: 871079--871145 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
871069 ATAATATATA
*
871079 AAAAATGTTAAAAAAAATTAAAAAAGG
1 AAAAATGTTAAAAAAAA-TAAAAAAAG
* * *
871106 AAAAATTTTTAAAAATAATAAAAAAAT
1 AAAAA-TGTTAAAAAAAATAAAAAAAG
*
871133 AAACATGTTAAAA
1 AAAAATGTTAAAA
871146 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 7 0.21
27 16 0.48
28 10 0.30
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAAATGTTAAAAAAAATAAAAAAAG
Found at i:871109 original size:28 final size:28
Alignment explanation
Indices: 871078--871131 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
871068 AATAATATAT
*
871078 AAAAAATGTTAAAAAAAATTAAAAAAGG
1 AAAAAATGTTAAAAAAAATAAAAAAAGG
* * *
871106 AAAAATTTTTAAAAATAATAAAAAAA
1 AAAAAATGTTAAAAAAAATAAAAAAA
871132 TAAACATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (28 bp):
AAAAAATGTTAAAAAAAATAAAAAAAGG
Found at i:871185 original size:16 final size:17
Alignment explanation
Indices: 871142--871184 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
871132 TAAACATGTT
*
871142 AAAATTAAAAGAAAACA
1 AAAAATAAAAGAAAACA
871159 AAAAATAAAAGAAATA-A
1 AAAAATAAAAGAAA-ACA
871176 AAAAATAAA
1 AAAAATAAA
871185 GGATCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAGAAAACA
Found at i:872306 original size:18 final size:18
Alignment explanation
Indices: 872285--872334 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
872275 AATTAAATAA
872285 ATAAATAATAATAAAACT
1 ATAAATAATAATAAAACT
*
872303 AT-AATAAATAATAATACT
1 ATAAAT-AATAATAAAACT
*
872321 -TATATAAT-ATAAAA
1 ATAAATAATAATAAAA
872335 AATAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.19
17 7 0.26
18 15 0.56
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATAAAACT
Found at i:872326 original size:21 final size:20
Alignment explanation
Indices: 872284--872425 Score: 89
Period size: 21 Copynumber: 6.8 Consensus size: 20
872274 AAATTAAATA
*
872284 AATAAATAATAATAAAACTAT
1 AATAAATAATAATAATA-TAT
*
872305 AATAAATAATAATACTTATAT
1 AATAAATAATAATA-ATATAT
872326 AATATAA-AA-AATAATATAT
1 AATA-AATAATAATAATATAT
872345 AATAAATGATATAATATATTCTATAT
1 AATAAAT-A-ATAATA-A---TATAT
* *
872371 AATAAAT-ATACTACTATAT
1 AATAAATAATAATAATATAT
*
872390 -ATATAA-AAT-ATAATATAA
1 AATA-AATAATAATAATATAT
872408 AATAAATATATATATAAT
1 AATAAATA-ATA-ATAAT
872426 GATGTCATTC
Statistics
Matches: 96, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
18 13 0.14
19 22 0.23
20 7 0.07
21 24 0.25
22 12 0.12
23 6 0.06
26 12 0.12
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (20 bp):
AATAAATAATAATAATATAT
Found at i:872341 original size:12 final size:13
Alignment explanation
Indices: 872270--872421 Score: 58
Period size: 12 Copynumber: 12.1 Consensus size: 13
872260 GACCTATTAA
872270 AAATAAATTAA-AT
1 AAATAAA-TAATAT
872283 AAATAAAT-A-AT
1 AAATAAATAATAT
*
872294 -AATAAA-ACTAT
1 AAATAAATAATAT
872305 -AATAAATAATAAT
1 AAATAAATAAT-AT
** *
872318 ACTTATATAATAT
1 AAATAAATAATAT
872331 AAA-AAATAATAT
1 AAATAAATAATAT
*
872343 ATAATAAATGATAT
1 A-AATAAATAATAT
* **
872357 -AATATATTCTAT
1 AAATAAATAATAT
872369 ATAATAAAT-ATACT
1 A-AATAAATAATA-T
* *
872383 -ACTATAT-ATAT
1 AAATAAATAATAT
*
872394 AAA-ATATAATAT
1 AAATAAATAATAT
872406 AAAATAAATATATAT
1 -AAATAAATA-ATAT
872421 A
1 A
872422 TAATGATGTC
Statistics
Matches: 106, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
10 6 0.06
11 16 0.15
12 34 0.32
13 19 0.18
14 27 0.25
15 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:872347 original size:33 final size:32
Alignment explanation
Indices: 872271--872362 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 32
872261 ACCTATTAAA
* *
872271 AATAAATTAAATAAAT-AAATAATAATAAAACTAT
1 AATAAA-T-AATAAATGATATAAT-ATAAAACAAT
*
872305 AATAAATAATAATACTTATATAATATAAAA-AAT
1 AATAAATAATAA-A-TGATATAATATAAAACAAT
*
872338 AATATATAATAAATGATATAATATA
1 AATAAATAATAAATGATATAATATA
872363 TTCTATATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
31 11 0.22
32 6 0.12
33 15 0.29
34 13 0.25
35 6 0.12
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (32 bp):
AATAAATAATAAATGATATAATATAAAACAAT
Found at i:872363 original size:7 final size:7
Alignment explanation
Indices: 872284--872425 Score: 66
Period size: 7 Copynumber: 20.4 Consensus size: 7
872274 AAATTAAATA
*
872284 AATAAAT
1 AATATAT
872291 AATA-AT
1 AATATAT
*
872297 AAAACTAT
1 AATA-TAT
*
872305 AATAAAT
1 AATATAT
872312 AATA-AT
1 AATATAT
*
872318 ACTTATAT
1 A-ATATAT
872326 AATATA-
1 AATATAT
*
872332 AA-AAAT
1 AATATAT
872338 AATATAT
1 AATATAT
872345 -A-ATA-
1 AATATAT
872349 AATGATAT
1 AAT-ATAT
872357 AATATAT
1 AATATAT
**
872364 TCTATAT
1 AATATAT
*
872371 AATAAAT
1 AATATAT
872378 -ATACTACT
1 AATA-TA-T
872386 ATATATAT
1 A-ATATAT
*
872394 AAAATAT
1 AATATAT
*
872401 AATATAA
1 AATATAT
*
872408 AATAAAT
1 AATATAT
872415 ATATATAT
1 A-ATATAT
872423 AAT
1 AAT
872426 GATGTCATTC
Statistics
Matches: 101, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
5 6 0.06
6 16 0.16
7 54 0.53
8 20 0.20
9 2 0.02
10 3 0.03
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (7 bp):
AATATAT
Found at i:872388 original size:26 final size:24
Alignment explanation
Indices: 872326--872421 Score: 86
Period size: 26 Copynumber: 3.9 Consensus size: 24
872316 ATACTTATAT
* *
872326 AATATAAAAAATA-ATATATAATA
1 AATATATAATATATATATATAATA
*
872349 AATGATATAATATATTCTATATAATA
1 AAT-ATATAATATA-TATATATAATA
* *
872375 AATATACTACTATATATATAAAATA
1 AATATA-TAATATATATATATAATA
* *
872400 TAATATAAAATAAATATATATA
1 -AATATATAATATATATATATA
872422 TAATGATGTC
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.05
24 8 0.14
25 23 0.40
26 24 0.41
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (24 bp):
AATATATAATATATATATATAATA
Found at i:882789 original size:32 final size:30
Alignment explanation
Indices: 882724--882828 Score: 97
Period size: 32 Copynumber: 3.4 Consensus size: 30
882714 ATAAATTAAG
* * *
882724 AAAATAAAAAAAATGTT-AAAAGAGAAAAT
1 AAAATAGAAAAAATGTTAAAAATAAAAAAT
*
882753 AAAATAGAAAAAATGTTTAACAATAATAATAA-
1 AAAATAGAAAAAATG-TTAAAAATAA-AA-AAT
* *
882785 AAAATTGAAGAACATGTTAAAAATAAAAAAT
1 AAAATAGAA-AAAATGTTAAAAATAAAAAAT
882816 ATAAATAGAAAAA
1 A-AAATAGAAAAA
882829 TAATAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
29 14 0.23
30 4 0.07
31 9 0.15
32 26 0.43
33 7 0.12
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAATAGAAAAAATGTTAAAAATAAAAAAT
Found at i:883663 original size:20 final size:21
Alignment explanation
Indices: 883625--883663 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
883615 AATCAAAATT
*
883625 AAAACAAAACATTTTATTGCA
1 AAAACAAAACATTTAATTGCA
*
883646 AAAATAAAACA-TTAATTG
1 AAAACAAAACATTTAATTG
883664 AAACATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAACAAAACATTTAATTGCA
Found at i:884292 original size:45 final size:46
Alignment explanation
Indices: 884171--884489 Score: 412
Period size: 46 Copynumber: 7.0 Consensus size: 46
884161 ATACAATGAG
* * * * * *
884171 TGGCA-CCTTTTATGTCGTTAATACACTGTTATGCATTTTCATTTG
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* *
884216 TGGCATCCTTTCATGTCGATAATTCACCGTTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* * * *
884262 TGACATCC-TTCATGCCTATAATGCATCGTTATGCATTTTCGTTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* *
884307 TGGCATCCTTTCATGCTGATAATGCACTGTTATGCATTTTC-TTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* * *
884352 TGGCATCCTTTCATGCCGATAATGCACCATTATACAATTTCATTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* * *
884398 TGGCATCCTTTTATGCCAATAATGCACCTTTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
* *
884444 TGGCATCGTTTCATGCCGATAATGCACCGTTATACA-TTTCATTTA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
884489 T
1 T
884490 TCATTCATTT
Statistics
Matches: 240, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
45 94 0.39
46 146 0.61
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (46 bp):
TGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTA
Found at i:884365 original size:91 final size:92
Alignment explanation
Indices: 884171--884489 Score: 398
Period size: 91 Copynumber: 3.5 Consensus size: 92
884161 ATACAATGAG
* * * * * * *
884171 TGGCA-CCTTTTATGTCGTTAATACACTGTTATGCATTTTCATTTGTGGCATCCTTTCATG-TCG
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCATTTATGGCATCCTTTCATGCT-G
* *
884234 ATAATTCACCGTTATGCATTTTCATTTA
65 ATAATGCACTGTTATGCATTTTCATTTA
* * * * *
884262 TGACATCC-TTCATGCCTATAATGCATCGTTATGCATTTTCGTTTATGGCATCCTTTCATGCTGA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCATTTATGGCATCCTTTCATGCTGA
884326 TAATGCACTGTTATGCATTTTC-TTTA
66 TAATGCACTGTTATGCATTTTCATTTA
* * * **
884352 TGGCATCCTTTCATGCCGATAATGCACCATTATACAATTTCATTTATGGCATCCTTTTATGCCAA
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCATTTATGGCATCCTTTCATGCTGA
884417 TAATGCACCT-TTATGCATTTTCATTTA
66 TAATGCA-CTGTTATGCATTTTCATTTA
*
884444 TGGCATCGTTTCATGCCGATAATGCACCGTTATACA-TTTCATTTAT
1 TGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCATTTAT
884490 TCATTCATTT
Statistics
Matches: 199, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
90 11 0.06
91 145 0.73
92 43 0.22
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (92 bp):
TGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCATTTATGGCATCCTTTCATGCTGA
TAATGCACTGTTATGCATTTTCATTTA
Found at i:884436 original size:137 final size:137
Alignment explanation
Indices: 884171--884489 Score: 428
Period size: 137 Copynumber: 2.3 Consensus size: 137
884161 ATACAATGAG
* * * * * *
884171 TGGCA-CCTTTTATGTCGTTAATACACTGTTATGCATTTTCATTTGTGGCATCCTTTCATGTCGA
1 TGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * * * *
884235 TAATTCACCGTTATGCATTTTCATTTATGACATCCTTCATGCCTATAATGCATCGTTATGCATTT
66 TAATGCACCATTATACAATTTCATTTATGACATCCTTCATGCCAATAATGCACCGTTATGCATTT
*
884300 TCGTTTA
131 TCATTTA
*
884307 TGGCATCCTTTCATGCTGATAATGCACTGTTATGCATTTTC-TTTATGGCATCCTTTCATGCCGA
1 TGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
884371 TAATGCACCATTATACAATTTCATTTATGGCATCCTTTTATGCCAATAATGCACCTTTATGCATT
66 TAATGCACCATTATACAATTTCATTTATGACATCC-TTCATGCCAATAATGCACCGTTATGCATT
884436 TTCATTTA
130 TTCATTTA
* * *
884444 TGGCATCGTTTCATGCCGATAATGCACCGTTATACA-TTTCATTTAT
1 TGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTTCATTTAT
884490 TCATTCATTT
Statistics
Matches: 159, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
136 60 0.38
137 99 0.62
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (137 bp):
TGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
TAATGCACCATTATACAATTTCATTTATGACATCCTTCATGCCAATAATGCACCGTTATGCATTT
TCATTTA
Found at i:886624 original size:47 final size:46
Alignment explanation
Indices: 886553--886641 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
886543 GACAAGTGTA
* *
886553 TTGGTAAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGGTAAAAATAAGCCTACAAGCTTATGGAA--TAAATGGTAAGTATT
*
886601 TTGGT-AAAATAAGCCTACAAGCTTATGGGATAAATGGTAAG
1 TTGGTAAAAATAAGCCTACAAGCTTATGGAATAAATGGTAAG
886642 AGATTTTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 11 0.29
47 22 0.58
48 5 0.13
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.31
Consensus pattern (46 bp):
TTGGTAAAAATAAGCCTACAAGCTTATGGAATAAATGGTAAGTATT
Found at i:887138 original size:13 final size:13
Alignment explanation
Indices: 887120--887167 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
887110 TGATTCCCCC
*
887120 ACTGTTCACGGGT
1 ACTGTTCACGGAT
* *
887133 ACTGTTCACTGTT
1 ACTGTTCACGGAT
887146 ACTGTTCACGGAT
1 ACTGTTCACGGAT
887159 ACTGTTCAC
1 ACTGTTCAC
887168 TATTCATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (13 bp):
ACTGTTCACGGAT
Found at i:888335 original size:14 final size:14
Alignment explanation
Indices: 888316--888403 Score: 58
Period size: 14 Copynumber: 6.1 Consensus size: 14
888306 AAATTAAATA
888316 AATAAATAGATAAT
1 AATAAATAGATAAT
*
888330 AATAAAAATATAAATAAT
1 AAT---AA-ATAGATAAT
*
888348 AATACATAGATAAT
1 AATAAATAGATAAT
888362 -ATAAA-A-ATAAT
1 AATAAATAGATAAT
*
888373 AATATAATAAATAAT
1 AATA-AATAGATAAT
888388 -ATAATATATGATAAT
1 AATAA-ATA-GATAAT
888403 A
1 A
888404 TATATATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
11 5 0.09
12 4 0.07
13 7 0.12
14 18 0.31
15 11 0.19
17 2 0.03
18 11 0.19
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (14 bp):
AATAAATAGATAAT
Found at i:888362 original size:32 final size:33
Alignment explanation
Indices: 888316--888525 Score: 121
Period size: 32 Copynumber: 6.1 Consensus size: 33
888306 AAATTAAATA
888316 AATAAATAGATAATAATAAAAAT-ATAA-ATAAT
1 AATAAATAGATAAT-ATAAAAATAATAATATAAT
*
888348 AATACATAGATAATATAAAAATAATAATATAAT
1 AATAAATAGATAATATAAAAATAATAATATAAT
* *
888381 AAATAATATA-AT-ATATGATAAT-ATATATATATAT
1 -AATAA-ATAGATAATATAAAAATAATA-ATATA-AT
* * **
888415 ACTATAT-GATAAATATATACTATAATATATATAA-
1 AATAAATAGAT-AATATA-AAAATAATA-ATATAAT
* *
888449 AATATATATTAGAAAATAATAATAATAATAATAATAAT
1 AATA-A-A-TAGATAAT-ATAAAAATAATAAT-ATAAT
* *
888487 ATATAAATATATAACTAT-ATAATAATATATATAAT
1 A-ATAAATAGATAA-TATAAAAATAATA-ATATAAT
888522 AATA
1 AATA
888526 TATACTATAT
Statistics
Matches: 141, Mismatches: 16, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
31 8 0.06
32 24 0.17
33 21 0.15
34 18 0.13
35 22 0.16
36 21 0.15
37 17 0.12
38 7 0.05
39 3 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (33 bp):
AATAAATAGATAATATAAAAATAATAATATAAT
Found at i:888387 original size:12 final size:12
Alignment explanation
Indices: 888312--888581 Score: 86
Period size: 12 Copynumber: 21.8 Consensus size: 12
888302 ACTGAAATTA
888312 AATA-AATAAAT
1 AATATAATAAAT
888323 AGATAATAATAAA-
1 A-AT-ATAATAAAT
888336 AATATAA-ATAAT
1 AATATAATA-AAT
* *
888348 AATA-CATAGAT
1 AATATAATAAAT
*
888359 AATATAAAAATAAT
1 AATAT-AATA-AAT
888373 AATATAATAAAT
1 AATATAATAAAT
888385 AATATAATATATGAT
1 AATATAATA-A--AT
888400 AATATATATATATAT
1 AATATA-ATA-A-AT
*
888415 ACTATATGATAAAT
1 A--ATATAATAAAT
*
888429 -ATATACT--AT
1 AATATAATAAAT
888438 AATATATATAAAAT
1 AATATA-AT-AAAT
888452 ATATATTAGA-AAAT
1 A-ATA-TA-ATAAAT
888466 AATAATAAT-AAT
1 AAT-ATAATAAAT
*
888478 AATAATAATATAT
1 AAT-ATAATAAAT
*
888491 AA-ATATATAACT
1 AATATA-ATAAAT
888503 -ATATAAT-AAT
1 AATATAATAAAT
888513 ATATATAAT-AAT
1 A-ATATAATAAAT
* *
888525 -ATATACTATAT
1 AATATAATAAAT
*
888536 AGTATAATAAACT
1 AATATAATAAA-T
*
888549 -ATATAACATAATT
1 AATAT-A-ATAAAT
*
888562 AATAT-ATATAT
1 AATATAATAAAT
*
888573 ATTATAATA
1 AATATAATA
888582 TATCCCAGAC
Statistics
Matches: 197, Mismatches: 26, Indels: 71
0.67 0.09 0.24
Matches are distributed among these distances:
9 2 0.01
10 14 0.07
11 36 0.18
12 64 0.32
13 19 0.10
14 32 0.16
15 15 0.08
16 11 0.06
17 4 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (12 bp):
AATATAATAAAT
Found at i:888406 original size:2 final size:2
Alignment explanation
Indices: 888374--888584 Score: 89
Period size: 2 Copynumber: 115.0 Consensus size: 2
888364 AAAAATAATA
*
888374 AT AT A- AT AA AT A- AT AT A- AT AT AT GAT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
* *
888413 AT ACT AT AT GAT AA AT AT AT ACT AT A- AT AT AT AT A- AA AT AT
1 AT A-T AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
888454 AT AT -T AG A- AA AT A- AT A- AT A- AT A- AT A- AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
888487 AT AT AA AT AT AT A- ACT AT AT A- AT A- AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
888525 AT AT ACT AT AT AGT AT A- AT AA ACT AT AT A- AC AT A- AT -T A-
1 AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
888563 AT AT AT AT AT AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
888585 CCCAGACGAA
Statistics
Matches: 162, Mismatches: 12, Indels: 70
0.66 0.05 0.29
Matches are distributed among these distances:
1 27 0.17
2 121 0.75
3 14 0.09
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (2 bp):
AT
Found at i:888526 original size:96 final size:100
Alignment explanation
Indices: 888367--888553 Score: 255
Period size: 99 Copynumber: 1.9 Consensus size: 100
888357 ATAATATAAA
* *
888367 AATAATAATATAATAAATAATATAATATATGATAATATATATATATATACTATATGATAAATATA
1 AATAATAATATAATAAATAATATAAAATATGATAATATATATATATATACTATATAATAAATATA
888432 TACTATA-A-TATATATAAAATATATATTAGAAAAT
66 TACTATATAGTATA-ATAAAATATATATTAGAAAAT
888466 AATAATAATAATAAT-AATAATATATAAATAT-ATAACTATATA-ATA-ATA-TATATAAT-AAT
1 AATAATAAT-ATAATAAATAATATA-AAATATGATAA-TATATATATATATACTATATAATAAAT
*
888525 ATATACTATATAGTATAATAAACTATATA
63 ATATACTATATAGTATAATAAAATATATA
888554 ACATAATTAA
Statistics
Matches: 80, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
96 13 0.16
97 19 0.24
98 7 0.09
99 25 0.31
100 16 0.20
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (100 bp):
AATAATAATATAATAAATAATATAAAATATGATAATATATATATATATACTATATAATAAATATA
TACTATATAGTATAATAAAATATATATTAGAAAAT
Found at i:888565 original size:84 final size:82
Alignment explanation
Indices: 888339--888529 Score: 212
Period size: 84 Copynumber: 2.3 Consensus size: 82
888329 TAATAAAAAT
* *
888339 ATAAATAATAATACATAGATA-ATATAAAA-ATAATAATATAATA-AATAAT-ATAATATATGAT
1 ATAAAT-AT-ATACATA-ATATATATAAAATAT-ATAATAGAAAATAATAATAATAATA-AT-AT
* *
888400 AATATATATATATATACTATATG
60 AATATATAAATATATACTATATA
*
888423 ATAAATATATACTATAATATATATAAAATATATATTAGAAAATAATAATAATAATAATAATAATA
1 ATAAATATATAC-ATAATATATATAAAATATATAATAGAAAATAATAATAATAATAAT-ATAATA
888488 TATAAATATATAACTATATA
64 TATAAATATAT-ACTATATA
888508 ATAATATATATA-ATAATATATA
1 ATAA-ATATATACATAATATATA
888530 CTATATAGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
82 7 0.07
83 21 0.22
84 42 0.45
85 17 0.18
86 7 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (82 bp):
ATAAATATATACATAATATATATAAAATATATAATAGAAAATAATAATAATAATAATATAATATA
TAAATATATACTATATA
Found at i:888565 original size:96 final size:98
Alignment explanation
Indices: 888367--888579 Score: 235
Period size: 97 Copynumber: 2.2 Consensus size: 98
888357 ATAATATAAA
* *
888367 AATAATAATATAATAAATAATATAATATATGATAATATATATATATATACTATATGATAAATATA
1 AATAATAATATAATAAATAATATAAAATATGATAATATATATATATATACTATATAATAAATATA
*
888432 TACTATAATATATATAAAATATATATTAGAAAAT
66 TACTATAATATATATAAAATATATA-TACAAAAT
888466 AATAATAATAATAAT-AATAATATATAAATAT-ATAACTATATA-ATA-ATA-TATATAAT-AAT
1 AATAATAAT-ATAATAAATAATATA-AAATATGATAA-TATATATATATATACTATATAATAAAT
* *
888525 ATATACTAT-ATAGTATAATAAACTATATA-ACATAATT
63 ATATACTATAATA-TAT-ATAAAATATATATACA-AAAT
*
888562 AATATATATATATTATAA
1 AATA-ATA-ATATAATAA
888580 TATATCCCAG
Statistics
Matches: 99, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
95 5 0.05
96 22 0.22
97 25 0.25
98 6 0.06
99 25 0.25
100 16 0.16
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (98 bp):
AATAATAATATAATAAATAATATAAAATATGATAATATATATATATATACTATATAATAAATATA
TACTATAATATATATAAAATATATATACAAAAT
Found at i:888573 original size:84 final size:85
Alignment explanation
Indices: 888376--888584 Score: 200
Period size: 86 Copynumber: 2.4 Consensus size: 85
888366 AAATAATAAT
* * *
888376 ATAATAAATAATATAATATATGATAATATATATATATATACTATATGATAAATATATACTATAAT
1 ATAATAAATAAT-TAATATATAAT-ATATAAATATATATACTATATAATAAATATATAC-ATAAT
*
888441 ATATATAAAATATATATTAGAAA
63 ATATATAAAATATATAATAGAAA
888464 ATAAT-AATAA-TAATAATAATAATATATAAATATATA-ACTATATAATAATATATATA-ATAAT
1 ATAATAAATAATTAAT-AT-ATAATATATAAATATATATACTATATAATAA-ATATATACATAAT
*
888525 ATATACT-ATATAGTATAAT--AAA
63 ATATA-TAAAATA-TATAATAGAAA
*
888547 CTATATAACATAATTAATATAT-ATATATTATAATATAT
1 ATA-ATAA-ATAATTAATATATAATATA-TA-AATATAT
888585 CCCAGACGAA
Statistics
Matches: 104, Mismatches: 6, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
83 5 0.05
84 21 0.20
85 26 0.25
86 34 0.33
87 13 0.12
88 5 0.05
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (85 bp):
ATAATAAATAATTAATATATAATATATAAATATATATACTATATAATAAATATATACATAATATA
TATAAAATATATAATAGAAA
Found at i:888584 original size:12 final size:12
Alignment explanation
Indices: 888391--888584 Score: 99
Period size: 12 Copynumber: 16.3 Consensus size: 12
888381 AAATAATATA
*
888391 ATATATGATAAT
1 ATATATTATAAT
888403 ATATA-TATATAT
1 ATATATTATA-AT
*
888415 ACTATATGATAAAT
1 A-TATATTAT-AAT
*
888429 ATATACTATAAT
1 ATATATTATAAT
*
888441 ATATA-TAAAAT
1 ATATATTATAAT
* *
888452 ATATATTAGAAA
1 ATATATTATAAT
*
888464 ATA-ATAATAAT
1 ATATATTATAAT
888475 A-ATA--ATAAT
1 ATATATTATAAT
888484 A-ATA-TATAAAT
1 ATATATTAT-AAT
888495 ATATAACTATATAAT
1 ATAT-A-T-TATAAT
888510 A-ATATATATAAT
1 ATATAT-TATAAT
*
888522 A-ATA-TATACT
1 ATATATTATAAT
*
888532 ATATAGTATAAT
1 ATATATTATAAT
* *
888544 AAACTA-TATAAC
1 ATA-TATTATAAT
888556 ATA-ATTAATATAT
1 ATATATT-ATA-AT
888569 ATATATTATAAT
1 ATATATTATAAT
888581 ATAT
1 ATAT
888585 CCCAGACGAA
Statistics
Matches: 146, Mismatches: 16, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
9 9 0.06
10 10 0.07
11 28 0.19
12 60 0.41
13 21 0.14
14 10 0.07
15 5 0.03
16 3 0.02
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (12 bp):
ATATATTATAAT
Found at i:890763 original size:19 final size:20
Alignment explanation
Indices: 890722--890765 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
890712 TAAGTTTAAG
* *
890722 TATAATTTGAAAAATATATT
1 TATAATTTCAAAAATATAAT
890742 TATAATTTCAAAAATA-AAT
1 TATAATTTCAAAAATATAAT
890761 TATAA
1 TATAA
890766 AATTCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAATTTCAAAAATATAAT
Found at i:892423 original size:20 final size:20
Alignment explanation
Indices: 892398--892452 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
892388 GCGATTTTCC
*
892398 AAATTCGGAACTCGAAAGTA
1 AAATTCGGAACGCGAAAGTA
* *
892418 AAATTC-GCACGCGAAAGTC
1 AAATTCGGAACGCGAAAGTA
*
892437 AAATTCGCAACGCGAA
1 AAATTCGGAACGCGAA
892453 TTTGTAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
AAATTCGGAACGCGAAAGTA
Found at i:892434 original size:19 final size:20
Alignment explanation
Indices: 892398--892500 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
892388 GCGATTTTCC
* *
892398 AAATTCGGAACTCGAAAGTA
1 AAATTCGCAACGCGAAAGTA
*
892418 AAATTCGC-ACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTA
*
892437 AAATTCGCAACGCGAATTTGT-
1 AAATTCGCAACGCGAA--AGTA
* *
892458 AAA-TCGCAACAC-AGAAGTC
1 AAATTCGCAACGCGA-AAGTA
*
892477 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTA
892497 AAAT
1 AAAT
892501 GTTTTTACGC
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
18 2 0.03
19 21 0.30
20 40 0.58
21 4 0.06
22 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTA
Found at i:892653 original size:22 final size:22
Alignment explanation
Indices: 892628--892675 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
892618 CTACGGTGAC
892628 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
892650 ATCCGTCCCCATTTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
892672 ATCC
1 ATCC
892676 ATCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.42, G:0.12, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:892912 original size:13 final size:13
Alignment explanation
Indices: 892894--892920 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
892884 ATTTGTCTTT
892894 TTTTGTCTTTTTG
1 TTTTGTCTTTTTG
892907 TTTTGTCTTTTTG
1 TTTTGTCTTTTTG
892920 T
1 T
892921 CGAAGAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (13 bp):
TTTTGTCTTTTTG
Found at i:894728 original size:21 final size:21
Alignment explanation
Indices: 894704--894753 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
894694 GTTAAGGGAA
894704 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
* *
894725 TTACGTCATTAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
894746 TTACGTGA
1 TTACGTGA
894754 AGATAATGGT
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:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:894985 original size:4 final size:4
Alignment explanation
Indices: 894976--895021 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
894966 TTTTTCGGCA
* * * *
894976 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
895022 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:895184 original size:21 final size:21
Alignment explanation
Indices: 895161--895260 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
895151 GCCCGATGCA
*
895161 CCTATCATCATTCAAGAGGCA
1 CCTATCATCATTCAAGAGGCC
* *
895182 CCT-CCTATCGTTCAAGAGGCC
1 CCTATC-ATCATTCAAGAGGCC
*
895203 CCTATCATCA-TCGAAGAAGCC
1 CCTATCATCATTC-AAGAGGCC
** *
895224 CCTCCCACCATTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
* *
895245 CCTGTCATCGTTCAAG
1 CCTATCATCATTCAAG
895261 TGGTCTCGCC
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.05
21 55 0.90
22 3 0.05
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (21 bp):
CCTATCATCATTCAAGAGGCC
Found at i:895208 original size:42 final size:42
Alignment explanation
Indices: 895161--895260 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
895151 GCCCGATGCA
* * * *
895161 CCTATCATCATTCAAGAGGCACCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGCACCTCCCACCATTCAAGAGGCC
*
895203 CCTATCATCA-TCGAAGAAGCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATCATTC-AAGAAGCACCTCCCACCATTCAAGAGGCC
* *
895245 CCTGTCATCGTTCAAG
1 CCTATCATCATTCAAG
895261 TGGTCTCGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 2 0.04
42 45 0.92
43 2 0.04
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCACCTCCCACCATTCAAGAGGCC
Found at i:896679 original size:61 final size:66
Alignment explanation
Indices: 896596--896736 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
896586 TTTTACATTG
896596 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGG
896656 A
66 A
* ** * * *
896657 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
*
896721 TA
65 GA
896723 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
896737 GTTTCTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
61 26 0.39
62 4 0.06
63 1 0.01
64 6 0.09
66 30 0.45
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGG
A
Found at i:896894 original size:20 final size:20
Alignment explanation
Indices: 896865--896909 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
896855 GCAACGCGAT
*
896865 TTTCGGTTTGCGAATTTGAC
1 TTTCGATTTGCGAATTTGAC
896885 TTTCGATTTGCGAATTTGAC
1 TTTCGATTTGCGAATTTGAC
896905 TTTCG
1 TTTCG
896910 CAACGCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTCGATTTGCGAATTTGAC
Found at i:896948 original size:20 final size:20
Alignment explanation
Indices: 896872--896948 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
896862 GATTTTCGGT
896872 TTGCGAATTTGACTTTCG-A
1 TTGCGAATTTGACTTTCGCA
896891 TTTGCGAATTTGACTTTCGCA
1 -TTGCGAATTTGACTTTCGCA
* * *
896912 --ACG--CTT-A-TTTTGCA
1 TTGCGAATTTGACTTTCGCA
896926 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTTTCGCA
896946 TTG
1 TTG
896949 ATCGCAACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.14
15 1 0.02
16 4 0.09
18 4 0.09
19 1 0.02
20 27 0.61
21 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCA
Found at i:897175 original size:39 final size:39
Alignment explanation
Indices: 897121--897207 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
897111 CTCAGTTGTA
897121 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
897160 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
897199 GATTTTGAT
1 GATTTTGAT
897208 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:897975 original size:25 final size:25
Alignment explanation
Indices: 897941--897990 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
897931 ATTATTTTTC
* *
897941 CAAATAATGTACTCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
897966 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
897991 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:898094 original size:34 final size:39
Alignment explanation
Indices: 898056--898142 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
898046 TGTTGAAGGT
*
898056 AAATTCGCAACGCGAAA-T-AA-GCG-T-TGCGATAGTC
1 AAATTCGCAACGCGAAAGTAAATGCGCTACGCGATAGTC
* *
898090 AAATTTGCAACGCGAAAGTCAAATTCGCTACGCGATAGTC
1 AAATTCGCAACGCGAAAGT-AAATGCGCTACGCGATAGTC
898130 AAATTCGCAACGC
1 AAATTCGCAACGC
898143 TTATTTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
34 16 0.37
35 1 0.02
37 2 0.05
38 2 0.05
39 1 0.02
40 21 0.49
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (39 bp):
AAATTCGCAACGCGAAAGTAAATGCGCTACGCGATAGTC
Found at i:898104 original size:20 final size:20
Alignment explanation
Indices: 898081--898142 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
898071 AATAAGCGTT
*
898081 GCGATAGTCAAATTTGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
898101 GCGAAAGTCAAATTCGCTAC
1 GCGATAGTCAAATTCGCAAC
898121 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
898141 GC
1 GC
898143 TTATTTGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:898180 original size:20 final size:20
Alignment explanation
Indices: 898151--898259 Score: 104
Period size: 20 Copynumber: 5.8 Consensus size: 20
898141 GCTTATTTGT
898151 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
* *
898171 GTTTCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGC
** * *
898191 --AACG--CTT-A-TTTCAC
1 GTTGCGAATTTGACTTTCGC
*
898205 GTTGCGAATTTGACTTTCGT
1 GTTGCGAATTTGACTTTCGC
*
898225 GTTGCGAATTTGACTTTCTC
1 GTTGCGAATTTGACTTTCGC
898245 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
898260 ACCGCAACGC
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
14 4 0.06
15 1 0.01
16 4 0.06
18 4 0.06
19 1 0.01
20 55 0.80
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:898213 original size:34 final size:34
Alignment explanation
Indices: 898165--898298 Score: 124
Period size: 34 Copynumber: 3.8 Consensus size: 34
898155 CGAATTTGAC
*
898165 TTTCGCGTTTCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
* * *** *
898199 TTTCACGTTGCGAATTTGACTTTCGTGTTGCGAATTTGA
1 TTTCGCGTTGCGAATTTGACTATC--GCAACG--CTT-A
* *
898238 CTTTCTCGTTGCGAATTTGACTACCGCAACGCTTA
1 -TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
*
898273 TTTCGCGTTGCGAATTTGACTTTCGC
1 TTTCGCGTTGCGAATTTGACTATCGC
898299 GTTGATCGCA
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
34 44 0.57
35 1 0.01
36 5 0.06
38 5 0.06
39 1 0.01
40 21 0.27
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
Found at i:898223 original size:54 final size:53
Alignment explanation
Indices: 898134--898239 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 53
898124 ATAGTCAAAT
** *
898134 TCGCAACGCTTATTTGTGTTGCGAATTTGACTTTCGCGTTTCGAATTTGACTA
1 TCGCAACGCTTATTTACGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
*
898187 TCGCAACGCTTATTTCACGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACT
1 TCGCAACGCTTATTT-ACGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACT
898240 TTCTCGTTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 15 0.31
54 33 0.69
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (53 bp):
TCGCAACGCTTATTTACGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
Found at i:898270 original size:74 final size:74
Alignment explanation
Indices: 898149--898302 Score: 263
Period size: 74 Copynumber: 2.1 Consensus size: 74
898139 ACGCTTATTT
* *
898149 GTGTTGCGAATTTGACTTTCGCGTTTCGAATTTGACTATCGCAACGCTTATTTCACGTTGCGAAT
1 GTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTACCGCAACGCTTATTTCACGTTGCGAAT
898214 TTGACTTTC
66 TTGACTTTC
* *
898223 GTGTTGCGAATTTGACTTTCTCGTTGCGAATTTGACTACCGCAACGCTTATTTCGCGTTGCGAAT
1 GTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTACCGCAACGCTTATTTCACGTTGCGAAT
898288 TTGACTTTC
66 TTGACTTTC
*
898297 GCGTTG
1 GTGTTG
898303 ATCGCAACAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (74 bp):
GTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTACCGCAACGCTTATTTCACGTTGCGAAT
TTGACTTTC
Found at i:898594 original size:18 final size:18
Alignment explanation
Indices: 898571--898606 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
898561 AAGCCGGTTG
*
898571 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
898589 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
898607 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:900883 original size:24 final size:24
Alignment explanation
Indices: 900856--900909 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
900846 CCATCACATC
900856 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
900880 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
900904 ATCAAA
1 ATCAAA
900910 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:901056 original size:12 final size:12
Alignment explanation
Indices: 901035--901068 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
901025 GGTTGTGGGT
*
901035 TTTGAGATTGTG
1 TTTGATATTGTG
901047 TTTGATATTGTG
1 TTTGATATTGTG
*
901059 TTTGGTATTG
1 TTTGATATTG
901069 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:901851 original size:20 final size:20
Alignment explanation
Indices: 901815--901985 Score: 93
Period size: 19 Copynumber: 8.6 Consensus size: 20
901805 ACTAAAACCT
*
901815 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
901834 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
*
901853 GTTGCGAATTTGGAATATCGC
1 GTTGCGAATTTGAAAT-TCGC
*** *
901874 AACGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
901895 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * * * *
901915 ATTACGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* * *
901935 GTTGCGAAATTGGAATTCAC
1 GTTGCGAATTTGAAATTCGC
*
901955 GTTGCGAATTTGAGA-TCGC
1 GTTGCGAATTTGAAATTCGC
901974 GTTGCGAATTTG
1 GTTGCGAATTTG
901986 TTGGTCATTT
Statistics
Matches: 114, Mismatches: 28, Indels: 20
0.70 0.17 0.12
Matches are distributed among these distances:
18 1 0.01
19 48 0.42
20 38 0.33
21 19 0.17
22 7 0.06
23 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:901882 original size:21 final size:21
Alignment explanation
Indices: 901856--901901 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
901846 AAATTCAGTT
*
901856 GCGAATTTGGAATATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
901877 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
901898 GCGA
1 GCGA
901902 TTTACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:906040 original size:17 final size:18
Alignment explanation
Indices: 906018--906054 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
906008 AGGGTTAACC
906018 TTAGGGATTT-GAGATTT
1 TTAGGGATTTAGAGATTT
*
906035 TTAGGGATTTAGAGCTTT
1 TTAGGGATTTAGAGATTT
906053 TT
1 TT
906055 TGTAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (18 bp):
TTAGGGATTTAGAGATTT
Found at i:913367 original size:29 final size:30
Alignment explanation
Indices: 913321--913380 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
913311 AATTTTTGGA
* *
913321 AAAAATATGTAATATATATTATATAGTTTTT
1 AAAAATATATAATATATATTAAATA-TTTTT
913352 AAAAATATAT-AT-TATATTAAATATTTTT
1 AAAAATATATAATATATATTAAATATTTTT
913380 A
1 A
913381 TTTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 10 0.37
30 2 0.07
31 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAAATATATAATATATATTAAATATTTTT
Found at i:916265 original size:51 final size:50
Alignment explanation
Indices: 916202--916323 Score: 142
Period size: 50 Copynumber: 2.4 Consensus size: 50
916192 AATAATTTGC
* * * *
916202 TTCACTATTCTTCTGTGAAGGCTGAAGTTGCA-TGACTTGAAT-ATAATCT-AT
1 TTCACTACTCTTCCGTGAAGACTGAA--TG-ATTGACTT-AATGAGAATCTAAT
*
916253 TTCACTACTCTTCCGTGAAAACTGAATGATTGACTTAATGAGAATCTAAT
1 TTCACTACTCTTCCGTGAAGACTGAATGATTGACTTAATGAGAATCTAAT
916303 TTCACTACTCTTCCGTGAAGA
1 TTCACTACTCTTCCGTGAAGA
916324 TCAGACTCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
48 4 0.06
49 14 0.23
50 22 0.35
51 22 0.35
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (50 bp):
TTCACTACTCTTCCGTGAAGACTGAATGATTGACTTAATGAGAATCTAAT
Found at i:916548 original size:44 final size:44
Alignment explanation
Indices: 916484--916821 Score: 382
Period size: 44 Copynumber: 7.7 Consensus size: 44
916474 AAAAAATTCG
* *
916484 TTCCACTACTC-TCTCGTGGAGTTTAGATTTATGATTTAATTTAC
1 TTCCACTACTCTTC-CGTGGAGTTTAGATTTATGATTGAATTTGC
* * * *
916528 TTCCACTACTCTTCCATGGAGTTCAGATTTATGATTCAATTTTC
1 TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
916572 TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
1 TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
* * * *
916616 TTACACTACTCTTCCGTGGAGTTCATATTTATTATTGAATTTGC
1 TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
*
916660 TTCCACTACTCTTTCGTGGAGTTT-GATTTGA-GA-TGAATTTGC
1 TTCCACTACTCTTCCGTGGAGTTTAGATTT-ATGATTGAATTTGC
* * * *
916702 TTCCACTACTCTTTCTTGGAGTTCAGATTTATGATTGAATTTTC
1 TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
* * * * *** *
916746 TTCCACTACTCTTTCGTGGAGTTTGATACTTTGCTAAAAAAATATG-
1 TTCCACTACTCTTCCGTGGAGTTT-AGA-TTT-ATGATTGAATTTGC
916792 TTCCACTACTCTTCCGTGGAGTTT-GATTTA
1 TTCCACTACTCTTCCGTGGAGTTTAGATTTA
916822 AGATGACCCA
Statistics
Matches: 253, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
42 32 0.13
43 15 0.06
44 170 0.67
45 4 0.02
46 26 0.10
47 6 0.02
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (44 bp):
TTCCACTACTCTTCCGTGGAGTTTAGATTTATGATTGAATTTGC
Found at i:916860 original size:20 final size:20
Alignment explanation
Indices: 916838--916946 Score: 173
Period size: 20 Copynumber: 5.5 Consensus size: 20
916828 CCCAAGGAAT
*
916838 TTTACAAATGACCCGAAGGT
1 TTTACAAATGACCCGAAGGC
916858 TTTACAAATGACCCGAAGGC
1 TTTACAAATGACCCGAAGGC
* *
916878 TTTACAAATTACCCGAATGC
1 TTTACAAATGACCCGAAGGC
916898 TTTACAAATGACCCGAAGGC
1 TTTACAAATGACCCGAAGGC
* *
916918 TTTACAAATGACTCGGAGGC
1 TTTACAAATGACCCGAAGGC
916938 TTTACAAAT
1 TTTACAAAT
916947 TTGTGGGAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
TTTACAAATGACCCGAAGGC
Found at i:923320 original size:11 final size:11
Alignment explanation
Indices: 923306--923331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
923296 AAATTTTGGC
923306 TTTTTTTTGTT
1 TTTTTTTTGTT
923317 TTTTTTTTGTT
1 TTTTTTTTGTT
923328 TTTT
1 TTTT
923332 GAAAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:930203 original size:21 final size:23
Alignment explanation
Indices: 930179--930224 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
930169 ATCGGGGCTG
930179 TATAAATAATAATAT-T-TATAA
1 TATAAATAATAATATGTATATAA
* *
930200 TATAATTAATATTATGTATATAA
1 TATAAATAATAATATGTATATAA
930223 TA
1 TA
930225 ACGTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAAATAATAATATGTATATAA
Found at i:930225 original size:21 final size:19
Alignment explanation
Indices: 930177--930225 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
930167 TAATCGGGGC
930177 TGTATA-AATAATAATATT
1 TGTATATAATAATAATATT
*
930195 TATA-AT-ATAATTAATATT
1 TGTATATAATAA-TAATATT
930213 ATGTATATAATAA
1 -TGTATATAATAA
930226 CGTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 3 0.12
20 2 0.08
21 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
TGTATATAATAATAATATT
Found at i:956566 original size:54 final size:54
Alignment explanation
Indices: 956484--956587 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
956474 TACTAGAAGA
* ** * * *
956484 AACATGTCCAATATTACTGAGAATCCATTTATCTAGATCCGAATTAAAGACGCT
1 AACATGCCCAATATTACAAAGAAGCCATTTATCTAGATCCAAATAAAAGACGCT
*
956538 AACATGCCCAATATTACAAAGAGGCCATTTATCTAGATCCAAATAAAAGA
1 AACATGCCCAATATTACAAAGAAGCCATTTATCTAGATCCAAATAAAAGA
956588 TGTTTTTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.26
Consensus pattern (54 bp):
AACATGCCCAATATTACAAAGAAGCCATTTATCTAGATCCAAATAAAAGACGCT
Found at i:956705 original size:15 final size:15
Alignment explanation
Indices: 956682--956713 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
956672 TTTTTAAATA
*
956682 GTTCTCGAGTAGTGG
1 GTTCCCGAGTAGTGG
956697 GTTCCCGAGTAGTGG
1 GTTCCCGAGTAGTGG
956712 GT
1 GT
956714 CTCAGGTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.16, G:0.41, T:0.31
Consensus pattern (15 bp):
GTTCCCGAGTAGTGG
Found at i:959753 original size:19 final size:19
Alignment explanation
Indices: 959729--959777 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
959719 ATGCAATGGA
* *
959729 CTATGAATTTGAAATTACG
1 CTATGAATTTGAAAATAAG
*
959748 CTATGAATCTGAAAATAAG
1 CTATGAATTTGAAAATAAG
*
959767 TTATGAATTTG
1 CTATGAATTTG
959778 GATATAAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (19 bp):
CTATGAATTTGAAAATAAG
Found at i:959847 original size:13 final size:12
Alignment explanation
Indices: 959829--959890 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 12
959819 GTATCGGTTA
959829 TGAAAATGAGATG
1 TGAAAATGA-ATG
959842 TGAAAATGAATG
1 TGAAAATGAATG
* *
959854 TGAAAGTGAAAG
1 TGAAAATGAATG
*
959866 ATGAAAATGAAATA
1 -TGAAAATG-AATG
959880 TGAAATATGAA
1 TGAAA-ATGAA
959891 AGTTTGAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
12 13 0.32
13 23 0.56
14 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.23
Consensus pattern (12 bp):
TGAAAATGAATG
Found at i:959882 original size:7 final size:7
Alignment explanation
Indices: 959827--959891 Score: 50
Period size: 7 Copynumber: 10.0 Consensus size: 7
959817 AGGTATCGGT
959827 TATGAAA
1 TATGAAA
*
959834 -ATGAGA
1 TATGAAA
*
959840 TGTGAAA
1 TATGAAA
959847 -ATG-AA
1 TATGAAA
*
959852 TGTGAAA
1 TATGAAA
*
959859 -GTGAAA
1 TATGAAA
*
959865 GATGAAA
1 TATGAAA
959872 -ATGAAA
1 TATGAAA
959878 TATGAAA
1 TATGAAA
959885 TATGAAA
1 TATGAAA
959892 GTTTGAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 2 0.04
6 21 0.45
7 24 0.51
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (7 bp):
TATGAAA
Found at i:967881 original size:22 final size:23
Alignment explanation
Indices: 967856--967899 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
967846 AAAATTAAAA
*
967856 TAATATTTTC-AATCTATTATTT
1 TAATATTTGCAAATCTATTATTT
*
967878 TAATATTTGCAAATTTATTATT
1 TAATATTTGCAAATCTATTATT
967900 CAACCCCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATATTTGCAAATCTATTATTT
Found at i:971611 original size:16 final size:17
Alignment explanation
Indices: 971581--971613 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
971571 GTACGATCGA
*
971581 GTTATAACTCTATTTTG
1 GTTATAACTCAATTTTG
971598 GTTAT-ACTCAATTTTG
1 GTTATAACTCAATTTTG
971614 ATTCCACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (17 bp):
GTTATAACTCAATTTTG
Found at i:978734 original size:24 final size:25
Alignment explanation
Indices: 978707--978762 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
978697 TATAATGATA
*
978707 ATTTTTTTTATTATTAT-ATACTTC
1 ATTTTTTTTATTATTATAATAATTC
*
978731 A-TTTCTTTATTATTATAATAATTC
1 ATTTTTTTTATTATTATAATAATTC
*
978755 ATTGTTTT
1 ATTTTTTT
978763 GTGACGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 14 0.54
24 8 0.31
25 4 0.15
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTTTTTATTATTATAATAATTC
Found at i:978743 original size:23 final size:24
Alignment explanation
Indices: 978713--978757 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
978703 GATAATTTTT
*
978713 TTTATTATTAT-ATACTTCATTTC
1 TTTATTATTATAATAATTCATTTC
978736 TTTATTATTATAATAATTCATT
1 TTTATTATTATAATAATTCATT
978758 GTTTTGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTATTATAATAATTCATTTC
Found at i:989180 original size:16 final size:18
Alignment explanation
Indices: 989158--989198 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
989148 ACTCTTAATC
989158 TATTTTAAAA-ATTTTAA
1 TATTTTAAAATATTTTAA
989175 -ATTTTAAAATATTTTAA
1 TATTTTAAAATATTTTAA
989192 TATTTTA
1 TATTTTA
989199 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTAAAATATTTTAA
Found at i:991598 original size:94 final size:93
Alignment explanation
Indices: 991405--991606 Score: 205
Period size: 94 Copynumber: 2.1 Consensus size: 93
991395 AAGAAATGTG
* * *
991405 GTATTGATACCATGGTAAGGGTATCGATACCAGTAAACATCAAATCTAATTTGAGTATAGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAGT-AACATCAAAGCTAATTTGAGTATAGATACA
* *
991470 TAGAGGGGGTATCGGTACCATAGCATAGGG
65 TAGAGGGGGTATCGATACCATA-CATAGGA
* * * * *
991500 GTATCGATACCATGGTGAGTGTATCGATACCAGCT-ATATCGAAGCTAATTTCG-GTATTGATAC
1 GTATCGATACCATGGTAAGGGTATCGATACCAG-TAACATCAAAGCTAATTT-GAGTATAGATAC
*
991563 AT-GAAGGGGGTATCGATACCCTA-ATAAGGTA
64 ATAG-AGGGGGTATCGATACCATACAT-AGG-A
*
991594 GTATCAATACCAT
1 GTATCGATACCAT
991607 AAGCAGGGAT
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
92 2 0.02
93 4 0.04
94 52 0.58
95 31 0.34
96 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (93 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAGTAACATCAAAGCTAATTTGAGTATAGATACAT
AGAGGGGGTATCGATACCATACATAGGA
Found at i:992700 original size:45 final size:45
Alignment explanation
Indices: 992091--992669 Score: 789
Period size: 45 Copynumber: 12.9 Consensus size: 45
992081 AAAGGATGCC
* **
992091 ATAGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
992136 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
992181 AGAGTTGAAATGCATATGGGTGTATTATCAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
992226 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATATT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
992271 ATGGTTGAAATGTATACGGGTACATTATCAACAGAAAAGCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
992316 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * **
992361 AGAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
992406 ATGGTTGAAATGTATATGGGTACCTTATCAACAGAAAAGCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
992451 TTAGTTTAAATGTATATGGGTAAATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * **
992496 AGAGTTGAAATGCATATGGGTGTATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
992541 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
992586 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
992631 AGAGTTGAAATGCATATTGGTGCATTATCAACAGAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
992670 ATGTTATAGT
Statistics
Matches: 464, Mismatches: 70, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 464 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:994225 original size:17 final size:17
Alignment explanation
Indices: 994172--994237 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
994162 GAAATATAAT
*
994172 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
994188 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
994204 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
994221 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
994237 T
1 T
994238 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:994523 original size:18 final size:18
Alignment explanation
Indices: 994502--994540 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
994492 GCATATTATA
*
994502 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
994520 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
994538 CTC
1 CTC
994541 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:996138 original size:22 final size:22
Alignment explanation
Indices: 996116--996198 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
996106 AGAACCCCAG
* * *
996116 GGGGGTATCGATTCCCCTACAG
1 GGGGGAATCGATTCCCCTTCAA
*
996138 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
996161 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
**
996183 GGGGTTATCGATTCCC
1 GGGGGAATCGATTCCC
996199 TCTGCACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 32 0.60
23 21 0.40
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:996164 original size:23 final size:22
Alignment explanation
Indices: 996116--996186 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
996106 AGAACCCCAG
* * * *
996116 GGGGGTATCGATTCCCCTACAG
1 GGGGGAATCGGTTCCCCTTCAA
996138 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTC-AA
996161 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTCAA
996183 GGGG
1 GGGG
996187 TTATCGATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 23 0.52
23 21 0.48
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAA
Found at i:1003547 original size:21 final size:21
Alignment explanation
Indices: 1003521--1003567 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1003511 CAAAAGTAAT
1003521 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
1003542 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
1003563 AAGGT
1 AAGGT
1003568 CGAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AAGGTTGATAATATTGAAAAG
Found at i:1004443 original size:2 final size:2
Alignment explanation
Indices: 1004436--1004497 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
1004426 TGTCAGGAAG
* * * * * *
1004436 AT AT AT AT AT AT AT AT AT AC AC AC AC AC AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1004478 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1004498 GACTTTTATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1004797 original size:2 final size:2
Alignment explanation
Indices: 1004790--1004831 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1004780 GTTTTTAGCA
1004790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1004832 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1007357 original size:7 final size:7
Alignment explanation
Indices: 1007345--1007398 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
1007335 ATCAAAGAAA
1007345 GTCAACG
1 GTCAACG
1007352 GTCAACG
1 GTCAACG
*
1007359 GTC-ACT
1 GTCAACG
1007365 GTCAACG
1 GTCAACG
1007372 GTCAACG
1 GTCAACG
1007379 GTC-A-G
1 GTCAACG
1007384 GTC-A-G
1 GTCAACG
1007389 GTCAACG
1 GTCAACG
1007396 GTC
1 GTC
1007399 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 9 0.21
6 7 0.17
7 26 0.62
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1007370 original size:20 final size:19
Alignment explanation
Indices: 1007345--1007403 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
1007335 ATCAAAGAAA
*
1007345 GTCAACGGTCAACGGTCACT
1 GTCAACGGTCAACGGTCA-G
1007365 GTCAACGGTCAACGGTCAG
1 GTCAACGGTCAACGGTCAG
*
1007384 GTC-A-GGTCAACGGTCGG
1 GTCAACGGTCAACGGTCAG
1007401 GTC
1 GTC
1007404 GGGTCAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.41
18 1 0.03
19 3 0.08
20 18 0.49
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (19 bp):
GTCAACGGTCAACGGTCAG
Found at i:1007393 original size:17 final size:17
Alignment explanation
Indices: 1007371--1007438 Score: 91
Period size: 17 Copynumber: 4.0 Consensus size: 17
1007361 CACTGTCAAC
*
1007371 GGTCAACGGTCAGGTCA
1 GGTCAACGGTCGGGTCA
*
1007388 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
* *
1007405 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCA
*
1007422 GGTCAACAGTCGGGTCA
1 GGTCAACGGTCGGGTCA
1007439 ACCCGGTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:1007458 original size:19 final size:20
Alignment explanation
Indices: 1007434--1007504 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
1007424 TCAACAGTCG
*
1007434 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1007453 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1007472 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1007492 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1007505 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1007471 original size:10 final size:10
Alignment explanation
Indices: 1007436--1007504 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1007426 AACAGTCGGG
*
1007436 TCAACCCGGT
1 TCAAACCGGT
*
1007446 TCAGACCGG-
1 TCAAACCGGT
1007455 TCAAACCGGT
1 TCAAACCGGT
*
1007465 TCGAACCGG-
1 TCAAACCGGT
1007474 TCAAACCGGT
1 TCAAACCGGT
*
1007484 TCAAAACTGG-
1 TC-AAACCGGT
1007494 TCAAACCGGT
1 TCAAACCGGT
1007504 T
1 T
1007505 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1009297 original size:20 final size:20
Alignment explanation
Indices: 1009272--1009325 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1009262 CATAACATAG
1009272 GGGTATCGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
1009292 GGGTATCGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
* *
1009312 GCGTATCCATACCA
1 GGGTATCGATACCA
1009326 GGCTATATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCATGGTGA
Found at i:1011642 original size:20 final size:20
Alignment explanation
Indices: 1011617--1011670 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1011607 CATAACATAG
1011617 GGGTATCGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
*
1011637 GGGTATTGATACCATGGTGA
1 GGGTATCGATACCATGGTGA
1011657 GGGTATCGATACCA
1 GGGTATCGATACCA
1011671 GGCTATATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATGGTGA
Found at i:1011742 original size:22 final size:21
Alignment explanation
Indices: 1011717--1011766 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1011707 AGGGGGCATT
1011717 GATACCCTAA-TAGGGTAGTATC
1 GATACCCTAAGTAGGG--GTATC
*
1011739 GATACCATAAGTAGGGGTATC
1 GATACCCTAAGTAGGGGTATC
*
1011760 GAAACCC
1 GATACCC
1011767 AAGGGCTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
GATACCCTAAGTAGGGGTATC
Found at i:1011760 original size:21 final size:21
Alignment explanation
Indices: 1011717--1011761 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1011707 AGGGGGCATT
*
1011717 GATACCCTAATAGGGTAGTATC
1 GATACCATAATAGGG-AGTATC
1011739 GATACCATAAGTAGGG-GTATC
1 GATACCATAA-TAGGGAGTATC
1011760 GA
1 GA
1011762 AACCCAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATACCATAATAGGGAGTATC
Found at i:1012283 original size:45 final size:45
Alignment explanation
Indices: 1012231--1012635 Score: 497
Period size: 45 Copynumber: 9.0 Consensus size: 45
1012221 AAAGGATGCC
** * **
1012231 ATAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1012276 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
1012321 AGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
1012366 ATGGTTGAAATGTATATGGGTATATTATTAACAGAAATGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* **
1012411 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1012456 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** * * *
1012501 AGAGTTGAAATACATGTGGG-AGTATTATCAATAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTA-CATTATCAACAGAAAAGTATACT
* * *
1012546 ATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
1012591 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1012636 CACTACAACA
Statistics
Matches: 306, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.00
45 304 0.99
46 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:1012824 original size:43 final size:43
Alignment explanation
Indices: 1012765--1013115 Score: 175
Period size: 43 Copynumber: 8.2 Consensus size: 43
1012755 TGAGAACAAA
* *
1012765 AAACGCCGCAATAGGTCAATATCTATTA-CGGCATTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATCTA-TAGCGGCATTTTTGGAAC
* ** *
1012808 AAACGCCGCAAAAGGTCGATATCTATAGCGGTGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGAAC
* * * * * *
1012851 AAACGCCGCAAAAAGT-TATGATATATAGCGGCGTTTCT--AAA
1 AAACGCCGCAAAAGGTCAAT-ATCTATAGCGGCATTTTTGGAAC
* * * * *
1012892 AGAATGCCGCAAAAAGTC-AGATCTATAGTGGCGTTTTTGGATAC
1 A-AACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
* * * *
1012936 AAACGCCGCAAAAGAT-AAGACCTATA-CTGGCATTTTTAGAAC
1 AAACGCCGCAAAAGGTCAATATCTATAGC-GGCATTTTTGGAAC
* ** * * * * * * *
1012978 AAACGTCGTTATAGGTCTA-ACCTTTTGCGGCGTTTTTAGACAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
* * * * * * *
1013021 AAACGCCGCAAAAGGT-TAGACCTATAACGTCGTTTTTGAACAC
1 AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGA-AC
* * *
1013064 AAACGCCGCAAAAAGTC-AGA-CTTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATC-TATAGCGGCATTTTTGGA-AC
1013107 AAACGCCGC
1 AAACGCCGC
1013116 TAATTACCTT
Statistics
Matches: 244, Mismatches: 49, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
41 18 0.07
42 51 0.21
43 173 0.71
44 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCTATAGCGGCATTTTTGGAAC
Found at i:1015598 original size:80 final size:79
Alignment explanation
Indices: 1015489--1015642 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 79
1015479 GGAATCCCTG
* * * *
1015489 CAAGTAATATGAAGGACTAAACTTCTCAATTTACATTCAGGTCAAATTGATAACAGATATTTACA
1 CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTA-A
*
1015554 GACCACTGCTAATTA
65 GACAACTGCTAATTA
* *
1015569 CAAGTAAAATGAAGGACTAAACTTCTCAATTTTCATTCAGATCAAATTTAAAACAAATATTTAAG
1 CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTAAG
1015634 ACAACTGCT
66 ACAACTGCT
1015643 CATTGAAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
79 10 0.15
80 57 0.85
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (79 bp):
CAAGTAAAATGAAGGACTAAACTTCTCAATTTACATTCAGATCAAATTGAAAACAAATATTTAAG
ACAACTGCTAATTA
Found at i:1017848 original size:41 final size:42
Alignment explanation
Indices: 1017791--1017970 Score: 201
Period size: 41 Copynumber: 4.4 Consensus size: 42
1017781 GAGGATTGGC
* *
1017791 AACGCCACTATAGTAC-ATGTTTATAACAGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
1017832 AACGCCACTATAGTAC-ATGTGTATAACGGCATTTGTATAAA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
1017873 AACGCCACTAAAGTACAAT-TCTATAGCGACGTTTGTAT-AA
1 AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
* * *
1017913 AACTGCCACTAAATTACGA-GTCTT-TAGCGGCGTTTGTATAAA
1 AAC-GCCACTAAAGTACAATGT-TTATAACGGCGTTTGTATAAA
1017955 AACGCCACTAAAGTAC
1 AACGCCACTAAAGTAC
1017971 TACTCTTTTG
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
40 5 0.04
41 108 0.89
42 8 0.07
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (42 bp):
AACGCCACTAAAGTACAATGTTTATAACGGCGTTTGTATAAA
Found at i:1017997 original size:41 final size:40
Alignment explanation
Indices: 1017819--1018006 Score: 162
Period size: 41 Copynumber: 4.5 Consensus size: 40
1017809 GTTTATAACA
* ** * * *
1017819 GCGTTTGTATAAAAACGCCACTATAGTACATGTGTATAACG
1 GCGTTTGT-TAAAAACGCCACTAAAGTACAACTCTTTAGCG
* * *
1017860 GCATTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCG
1 GCGTTTGT-TAAAAACGCCACTAAAGTACAACTCTTTAGCG
* * * *
1017901 ACGTTTG-TATAAAACTGCCACTAAATTACGAGTCTTTAGCG
1 GCGTTTGTTA-AAAAC-GCCACTAAAGTACAACTCTTTAGCG
* *
1017942 GCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCG
1 GCGTTTGT-TAAAAACGCCACTAAAGTACAACTCTTTAGCG
*
1017983 GCGTTTGTTGAAAAAATGCCACTA
1 GCGTTTGTT--AAAAACGCCACTA
1018007 TCGATGAACC
Statistics
Matches: 123, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.02
40 6 0.05
41 96 0.78
42 17 0.14
43 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (40 bp):
GCGTTTGTTAAAAACGCCACTAAAGTACAACTCTTTAGCG
Found at i:1019568 original size:21 final size:21
Alignment explanation
Indices: 1019542--1019588 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1019532 CAAAAGTAAT
1019542 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
1019563 AAGGTTGATAATATTGAAAAG
1 AAGGTTGATAATATTGAAAAG
1019584 AAGGT
1 AAGGT
1019589 CGAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AAGGTTGATAATATTGAAAAG
Found at i:1020464 original size:2 final size:2
Alignment explanation
Indices: 1020457--1020510 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1020447 TGTCAGGAAG
1020457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1020499 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1020511 GACTTTTATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1022971 original size:22 final size:21
Alignment explanation
Indices: 1022946--1022995 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1022936 AGGGGGCATT
1022946 GATACCCTAA-TAGGGTAGTATC
1 GATACCCTAAGTAGGG--GTATC
*
1022968 GATACCATAAGTAGGGGTATC
1 GATACCCTAAGTAGGGGTATC
*
1022989 GAAACCC
1 GATACCC
1022996 AAGGGCCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
GATACCCTAAGTAGGGGTATC
Found at i:1022989 original size:21 final size:21
Alignment explanation
Indices: 1022946--1022990 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1022936 AGGGGGCATT
*
1022946 GATACCCTAATAGGGTAGTATC
1 GATACCATAATAGGG-AGTATC
1022968 GATACCATAAGTAGGG-GTATC
1 GATACCATAA-TAGGGAGTATC
1022989 GA
1 GA
1022991 AACCCAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GATACCATAATAGGGAGTATC
Found at i:1023512 original size:45 final size:45
Alignment explanation
Indices: 1023460--1023901 Score: 571
Period size: 45 Copynumber: 9.8 Consensus size: 45
1023450 AAAGGATGCC
** * **
1023460 ATAGTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
1023505 TTAGTTGAAAGGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
1023550 AGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
1023595 ATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* **
1023640 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1023685 TTAGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * **
1023730 AGAGTTGAAATGCATGTGGGTGTATTATCAACAG-AAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1023774 ATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
1023819 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
1023864 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAA
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAA
1023902 AATGTTATTG
Statistics
Matches: 342, Mismatches: 54, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
44 35 0.10
45 307 0.90
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:1023873 original size:179 final size:180
Alignment explanation
Indices: 1023463--1023901 Score: 727
Period size: 179 Copynumber: 2.4 Consensus size: 180
1023453 GGATGCCATA
** * *
1023463 GTTGAAATGTATATGTATACATTGTCAACAGAAAAACATACTTTAGTTGAAAGGTATATGGGTAC
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTAC
1023528 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATA
66 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATA
* * *
1023593 CTATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATG
131 CTATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
1023643 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTAC
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTAC
* *
1023708 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATGTGGGTGTATTATCAACA-GAAAGTATA
66 ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATA
1023772 CTATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
131 CTATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
** ** * *
1023822 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGC
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTAC
*
1023887 ATTATCAACAGAAAA
66 ATTATCAACATAAAA
1023902 AATGTTATTG
Statistics
Matches: 243, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
179 128 0.53
180 115 0.47
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (180 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTAC
ATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATA
CTATGGTTGAAATGTATATGAGTACATTATCAACAAAAAAGTATACTATG
Found at i:1027067 original size:15 final size:15
Alignment explanation
Indices: 1027047--1027077 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1027037 GGTGCCTATT
1027047 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
1027062 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
1027077 A
1 A
1027078 ACCGGTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Found at i:1034722 original size:9 final size:9
Alignment explanation
Indices: 1034710--1034734 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1034700 ACATATATAA
1034710 ATCATATTC
1 ATCATATTC
1034719 ATCATATTC
1 ATCATATTC
1034728 ATCATAT
1 ATCATAT
1034735 AATAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (9 bp):
ATCATATTC
Found at i:1043679 original size:2 final size:2
Alignment explanation
Indices: 1043672--1043705 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1043662 CCTATAAATC
1043672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1043706 TATTCTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1047705 original size:26 final size:26
Alignment explanation
Indices: 1047669--1047727 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
1047659 TTATGCAAAT
* *
1047669 GTTCTGCATTAGATTTTGTTCAACTA
1 GTTCTGTATTAGACTTTGTTCAACTA
1047695 GTTCTGTATTAGACTTTGTTCAACTA
1 GTTCTGTATTAGACTTTGTTCAACTA
1047721 GTTCTGT
1 GTTCTGT
1047728 TATTTTATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (26 bp):
GTTCTGTATTAGACTTTGTTCAACTA
Found at i:1048408 original size:221 final size:222
Alignment explanation
Indices: 1048012--1048455 Score: 872
Period size: 221 Copynumber: 2.0 Consensus size: 222
1048002 AATTGTTGAT
1048012 ATAATATCTTTCAAAAATGTTTTTATTAACTATATTATCATATCAATCTGAAAAATTGTAGTAAC
1 ATAATATCTTTCAAAAATGTTTTTATTAACTATATTATCATATCAATCTGAAAAATTGTAGTAAC
1048077 ATGTTAGACAGCTGCTACATCACAATGATTTTCGTTTCCTTCTCCCATTGACATTCTCTTTTGAC
66 ATGTTAGACAGCTGCTACATCACAATGATTTTCGTTTCCTTCTCCCATTGACATTCTCTTTTGAC
1048142 AGTGGTCCGGTGTTGGTTATGGTTTTGGAGAAGGAAGATGCCATTGCTCATTGGCGAGATTTGAT
131 AGTGGTCCGGTGTTGGTTATGGTTTTGGAGAAGGAAGATGCCATTGCTCATTGGCGAGATTTGAT
1048207 TGGACCCACCGATGCTGGCAAGGCCAA
196 TGGACCCACCGATGCTGGCAAGGCCAA
1048234 ATAATATCTTTC-AAAATGTTTTTATTAACTATATTATCATATCAATCTGAAAAATTGTAGTAAC
1 ATAATATCTTTCAAAAATGTTTTTATTAACTATATTATCATATCAATCTGAAAAATTGTAGTAAC
*
1048298 ATGTTAGACAGCTGCTACATCACAATTATTTTCGTTTCCTTCTCCCATTGACATTCTCTTTTGAC
66 ATGTTAGACAGCTGCTACATCACAATGATTTTCGTTTCCTTCTCCCATTGACATTCTCTTTTGAC
1048363 AGTGGTCCGGTGTTGGTTATGGTTTTGGAGAAGGAAGATGCCATTGCTCATTGGCGAGATTTGAT
131 AGTGGTCCGGTGTTGGTTATGGTTTTGGAGAAGGAAGATGCCATTGCTCATTGGCGAGATTTGAT
1048428 TGGACCCACCGATGCTGGCAAGGCCAA
196 TGGACCCACCGATGCTGGCAAGGCCAA
1048455 A
1 A
1048456 ATTTCTCACC
Statistics
Matches: 221, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
221 209 0.95
222 12 0.05
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (222 bp):
ATAATATCTTTCAAAAATGTTTTTATTAACTATATTATCATATCAATCTGAAAAATTGTAGTAAC
ATGTTAGACAGCTGCTACATCACAATGATTTTCGTTTCCTTCTCCCATTGACATTCTCTTTTGAC
AGTGGTCCGGTGTTGGTTATGGTTTTGGAGAAGGAAGATGCCATTGCTCATTGGCGAGATTTGAT
TGGACCCACCGATGCTGGCAAGGCCAA
Found at i:1051231 original size:50 final size:50
Alignment explanation
Indices: 1051171--1051275 Score: 201
Period size: 50 Copynumber: 2.1 Consensus size: 50
1051161 GCTCATAAAC
1051171 TAAGTATGCTAGTAGAAGTAGTAATAAGAAGTAAATATGTTCATGATTCA
1 TAAGTATGCTAGTAGAAGTAGTAATAAGAAGTAAATATGTTCATGATTCA
*
1051221 TAAGTATGCTAGTAGAAGTAGTAATAAGAAGTAAATATTTTCATGATTCA
1 TAAGTATGCTAGTAGAAGTAGTAATAAGAAGTAAATATGTTCATGATTCA
1051271 TAAGT
1 TAAGT
1051276 CCGAAGCAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (50 bp):
TAAGTATGCTAGTAGAAGTAGTAATAAGAAGTAAATATGTTCATGATTCA
Found at i:1059235 original size:12 final size:12
Alignment explanation
Indices: 1059218--1059242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1059208 AATTTTTTGC
1059218 AAATGAAAGCTT
1 AAATGAAAGCTT
1059230 AAATGAAAGCTT
1 AAATGAAAGCTT
1059242 A
1 A
1059243 GAAAGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AAATGAAAGCTT
Found at i:1063225 original size:40 final size:40
Alignment explanation
Indices: 1063169--1063250 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
1063159 TGCAGGTTTA
* *
1063169 TAATACACTTCAGTGTATATGGT-GGGCACGAGCTTATGTG
1 TAATACACTTCAGTGTATATGGTAGGAC-CGACCTTATGTG
*
1063209 TAATACACTTCGGTGTATATGGTAGGACCGACCTTATGTG
1 TAATACACTTCAGTGTATATGGTAGGACCGACCTTATGTG
1063249 TA
1 TA
1063251 GCACTACGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCAGTGTATATGGTAGGACCGACCTTATGTG
Found at i:1063536 original size:46 final size:46
Alignment explanation
Indices: 1063354--1063614 Score: 388
Period size: 45 Copynumber: 5.8 Consensus size: 46
1063344 GTTACCATGC
* * *
1063354 AAATAAACTTACGAGCTTAT-GAAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* * *
1063398 TAATAAGCTTACGAGTTTATGG-ATTAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
*
1063443 AAATAAGCTTACAAGCTTATGGAATT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1063488 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* * *
1063534 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTTTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
*
1063580 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAG
1063615 AGATTTTATA
Statistics
Matches: 199, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
44 19 0.10
45 91 0.46
46 89 0.45
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
Found at i:1063552 original size:91 final size:90
Alignment explanation
Indices: 1063354--1063614 Score: 391
Period size: 91 Copynumber: 2.9 Consensus size: 90
1063344 GTTACCATGC
* * * * *
1063354 AAATAAACTTACGAGCTTAT-GAAATAATGGCAAGTATATTGGTATAATAAGCTTACGAGTTTAT
1 AAATAAGCTTACGAGCTTATGGAATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1063418 GGATTAAATGGTAAGTATATGGGTA
66 GGATTAAATGGTAAGTATATGGGTA
*
1063443 AAATAAGCTTACAAGCTTATGGAATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
*
1063508 GGAATTAAATGGTAAGTATATTGGTA
66 GG-ATTAAATGGTAAGTATATGGGTA
* * *
1063534 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTTTTTTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGAATT-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1063599 TGGGA-TAAATGGTAAG
65 T-GGATTAAATGGTAAG
1063615 AGATTTTATA
Statistics
Matches: 157, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
89 18 0.11
90 42 0.27
91 57 0.36
92 38 0.24
93 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
GGATTAAATGGTAAGTATATGGGTA
Found at i:1069455 original size:24 final size:22
Alignment explanation
Indices: 1069415--1069458 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
1069405 CAAATATACA
*
1069415 TTTATGAGATTTATGTTTGAGC
1 TTTATGACATTTATGTTTGAGC
1069437 TTTATAGACATTTGATGTTTGA
1 TTTAT-GACATTT-ATGTTTGA
1069459 CACAAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (22 bp):
TTTATGACATTTATGTTTGAGC
Found at i:1072209 original size:21 final size:19
Alignment explanation
Indices: 1072172--1072260 Score: 115
Period size: 21 Copynumber: 4.5 Consensus size: 19
1072162 TGAAAATATT
1072172 GATACTCTTGGAAAGTATC
1 GATACTCTTGGAAAGTATC
*
1072191 GATACTATTGGTTAAAGTATC
1 GATACTCTTGG--AAAGTATC
1072212 GATACTCTTGGGAAACGTATC
1 GATACTCTT-GGAAA-GTATC
*
1072233 TATACTCTTGGAAAGTATC
1 GATACTCTTGGAAAGTATC
*
1072252 AATACTCTT
1 GATACTCTT
1072261 AGCCTAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
19 23 0.37
20 8 0.13
21 29 0.47
22 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
GATACTCTTGGAAAGTATC
Found at i:1072248 original size:40 final size:38
Alignment explanation
Indices: 1072163--1072260 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 38
1072153 TTTTTTTGCT
* *
1072163 GAAAATATTGATACTCTTGGAAAGTATCGATACTATTG
1 GAAAGTATCGATACTCTTGGAAAGTATCGATACTATTG
* *
1072201 GTTAAAGTATCGATACTCTTGGGAAACGTATCTATACTCTTG
1 G--AAAGTATCGATACTCTT-GGAAA-GTATCGATACTATTG
*
1072243 GAAAGTATCAATACTCTT
1 GAAAGTATCGATACTCTT
1072261 AGCCTAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
38 1 0.02
40 31 0.61
41 5 0.10
42 14 0.27
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (38 bp):
GAAAGTATCGATACTCTTGGAAAGTATCGATACTATTG
Found at i:1077269 original size:16 final size:16
Alignment explanation
Indices: 1077248--1077278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1077238 ATAATGAATC
*
1077248 ATATTTTTATGATATG
1 ATATTTTTATAATATG
1077264 ATATTTTTATAATAT
1 ATATTTTTATAATAT
1077279 CAGTTACCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATATTTTTATAATATG
Found at i:1079776 original size:29 final size:31
Alignment explanation
Indices: 1079735--1079793 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
1079725 CTTTGATTCT
*
1079735 AAACTTTTCCAAATTTTATACTTTGGTCACC
1 AAACTTTTCCAAAATTTATACTTTGGTCACC
**
1079766 AAAC-TTT-CAAAATTTATGTTTTGGTCAC
1 AAACTTTTCCAAAATTTATACTTTGGTCAC
1079794 TAACCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.72
30 3 0.12
31 4 0.16
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (31 bp):
AAACTTTTCCAAAATTTATACTTTGGTCACC
Found at i:1084320 original size:20 final size:20
Alignment explanation
Indices: 1084297--1084346 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1084287 AAGTTCTATC
* *
1084297 CTTATGGACCATCCTTAACT
1 CTTACGGACCATCATTAACT
*
1084317 CTTACGGACCATCATTAGCT
1 CTTACGGACCATCATTAACT
1084337 CTTACGGACC
1 CTTACGGACC
1084347 TTAATCAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (20 bp):
CTTACGGACCATCATTAACT
Found at i:1084474 original size:19 final size:19
Alignment explanation
Indices: 1084450--1084596 Score: 143
Period size: 19 Copynumber: 7.5 Consensus size: 19
1084440 TTGTGTTGCT
*
1084450 GAAAGTCTCGATACTCTTG
1 GAAAGTATCGATACTCTTG
*
1084469 GAAAGTTTTC-ATACTCTTGG
1 GAAAG-TATCGATACTCTT-G
* *
1084489 GTAAATTATCGCTACTCTTG
1 G-AAAGTATCGATACTCTTG
*
1084509 GAAAGTATCGATACACTTGG
1 GAAAGTATCGATACTCTT-G
*
1084529 GAAAAGTATCCATACTCTTG
1 G-AAAGTATCGATACTCTTG
*
1084549 GAAAGTATCGATACACTTGG
1 GAAAGTATCGATACTCTT-G
* * *
1084569 GAAAATATCAATATTCTTG
1 GAAAGTATCGATACTCTTG
1084588 GAAAGTATC
1 GAAAGTATC
1084597 AATATTATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
19 51 0.49
20 29 0.28
21 25 0.24
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (19 bp):
GAAAGTATCGATACTCTTG
Found at i:1084528 original size:40 final size:38
Alignment explanation
Indices: 1084461--1084596 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 38
1084451 AAAGTCTCGA
* * *
1084461 TACTCTTGGAAAGTTTTC-ATACTCTTGGGTAAATTATCGC
1 TACTCTTGGAAAG-TATCGATACACTTGGG-AAAATATC-C
1084501 TACTCTTGGAAAGTATCGATACACTTGGGAAAAGTATCC
1 TACTCTTGGAAAGTATCGATACACTTGGGAAAA-TATCC
*
1084540 ATACTCTTGGAAAGTATCGATACACTTGGGAAAATATCAA
1 -TACTCTTGGAAAGTATCGATACACTTGGGAAAATATC-C
*
1084580 TATTCTTGGAAAGTATC
1 TACTCTTGGAAAGTATC
1084597 AATATTATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
39 27 0.31
40 60 0.69
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (38 bp):
TACTCTTGGAAAGTATCGATACACTTGGGAAAATATCC
Found at i:1090070 original size:18 final size:18
Alignment explanation
Indices: 1090044--1090107 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
1090034 GAAATTCCAG
*
1090044 AATATTGAAGTGAGTATC
1 AATACTGAAGTGAGTATC
1090062 AATACTGAAGTGAGTATC
1 AATACTGAAGTGAGTATC
* *
1090080 GATACCATAGAAGAGAAGTATC
1 AATA-C-T-GAAGTG-AGTATC
1090102 AATACT
1 AATACT
1090108 ATAGGAGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 20 0.53
19 1 0.03
20 2 0.05
21 6 0.16
22 9 0.24
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (18 bp):
AATACTGAAGTGAGTATC
Done.