Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_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: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2584326 original size:38 final size:38
Alignment explanation
Indices: 2584275--2584351 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
2584265 TCTCAATTGC
** *
2584275 AACATAAATGCTCATCTTCCATTTCAGTTTCTTAATGG
1 AACATAAATGCTCATCTTCCACGTCAGCTTCTTAATGG
2584313 AACATAAATGCTCATCTTCCACGTCAGCTTCTTAATGG
1 AACATAAATGCTCATCTTCCACGTCAGCTTCTTAATGG
2584351 A
1 A
2584352 GTGTTGGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (38 bp):
AACATAAATGCTCATCTTCCACGTCAGCTTCTTAATGG
Found at i:2594244 original size:47 final size:45
Alignment explanation
Indices: 2594150--2594275 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
2594140 GTAACCATGC
* * *
2594150 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
2594194 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
2594241 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
2594276 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:2595854 original size:6 final size:6
Alignment explanation
Indices: 2595843--2595885 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
2595833 AAGACCTATG
* * *
2595843 GGTCAT GGTCAT GGTCAT GGTTAT GGTTAT GGTCAC GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
2595886 ATACAAGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (6 bp):
GGTCAT
Found at i:2602593 original size:18 final size:18
Alignment explanation
Indices: 2602570--2602614 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2602560 TATTTTGATT
2602570 AATGAACTAACATTATTC
1 AATGAACTAACATTATTC
*
2602588 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
2602606 AATGAACTA
1 AATGAACTA
2602615 GATGCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:2604935 original size:48 final size:48
Alignment explanation
Indices: 2604856--2605001 Score: 147
Period size: 48 Copynumber: 3.0 Consensus size: 48
2604846 CGATCGATCT
* **
2604856 TGTATTAGTGCAATTATGCACTCCTAAATTAGTGAAATTGTGCACTCC
1 TGTATTAGTGCATTTATGCACTCCTGTATTAGTGAAATTGTGCACTCC
* * *
2604904 TGTATTACTGCATTTATGCACTCCCGTATTAGT-ACCAA-TGTGCACTCT
1 TGTATTAGTGCATTTATGCACTCCTGTATTAGTGA--AATTGTGCACTCC
* * *
2604952 TGAATTAGTGCATTCT-TGCATTCCTGTATTAGTG-CATTCGTGCACTCC
1 TGTATTAGTGCATT-TATGCACTCCTGTATTAGTGAAATT-GTGCACTCC
2605000 TG
1 TG
2605002 ATTCTAGTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
46 1 0.01
47 2 0.03
48 74 0.93
49 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (48 bp):
TGTATTAGTGCATTTATGCACTCCTGTATTAGTGAAATTGTGCACTCC
Found at i:2604971 original size:24 final size:24
Alignment explanation
Indices: 2604859--2605025 Score: 115
Period size: 24 Copynumber: 6.9 Consensus size: 24
2604849 TCGATCTTGT
* *
2604859 ATTAGTGCAATT-ATGCACTCCTAA
1 ATTAGTGC-ATTCGTGCACTCCTGA
* *
2604883 ATTAGTGAAATT-GTGCACTCCTGT
1 ATTAGTG-CATTCGTGCACTCCTGA
* ** * *
2604907 ATTACTGCATTTATGCACTCCCGT
1 ATTAGTGCATTCGTGCACTCCTGA
* * *
2604931 ATTAGTACCAAT-GTGCACTCTTGA
1 ATTAGT-GCATTCGTGCACTCCTGA
* * *
2604955 ATTAGTGCATTCTTGCATTCCTGT
1 ATTAGTGCATTCGTGCACTCCTGA
2604979 ATTAGTGCATTCGTGCACTCCTGA
1 ATTAGTGCATTCGTGCACTCCTGA
* * *
2605003 TTCTAGTACATTCGTGTACTCCT
1 AT-TAGTGCATTCGTGCACTCCT
2605026 ATAATAGTAC
Statistics
Matches: 111, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
23 6 0.05
24 84 0.76
25 21 0.19
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (24 bp):
ATTAGTGCATTCGTGCACTCCTGA
Found at i:2605150 original size:24 final size:24
Alignment explanation
Indices: 2605006--2605143 Score: 131
Period size: 24 Copynumber: 5.8 Consensus size: 24
2604996 CTCCTGATTC
*
2605006 TAGTA-CATTCGTGTACTCCTATAA
1 TAGTACCATT-GTGTACTCCTATAT
2605030 TAGTACCATTGTGTACTCCTATAAT
1 TAGTACCATTGTGTACTCCTAT-AT
*
2605055 T-GTACCATTGTGTACTTCTATAT
1 TAGTACCATTGTGTACTCCTATAT
* * *
2605078 TAGTA-CATTCGTGTATTCTTGTAT
1 TAGTACCATT-GTGTACTCCTATAT
* ***
2605102 TAGT-GCAGTTGCACACTCCTATAT
1 TAGTACCA-TTGTGTACTCCTATAT
2605126 TAGTACCATTGTGTACTC
1 TAGTACCATTGTGTACTC
2605144 TTGTATTTGG
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
23 7 0.08
24 74 0.81
25 10 0.11
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (24 bp):
TAGTACCATTGTGTACTCCTATAT
Found at i:2606422 original size:67 final size:64
Alignment explanation
Indices: 2606274--2606422 Score: 169
Period size: 64 Copynumber: 2.3 Consensus size: 64
2606264 ATTATCTATG
* *
2606274 TAAATTTGAATATTAAAAGATAATTATATACTTTTGAATATTTCAAATTAAAATAATATTTGTT
1 TAAATTTGAATATTAAAAGACAATTATATACTTTTGAATATTTCAAATTAAAATAATATATGTT
* * *
2606338 TAAGTTTGAATAGTAAAA-ACAGTGTATAT-CTTTTGAATATTTC-AATTAAAAGATATTATTAT
1 TAAATTTGAATATTAAAAGACAAT-TATATACTTTTGAATATTTCAAATT-AAA-ATA--A-TAT
2606400 ATGTT
60 ATGTT
*
2606405 TAAAATTGAATATTAAAA
1 TAAATTTGAATATTAAAA
2606423 TATATCTAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
62 4 0.06
63 20 0.28
64 24 0.34
66 1 0.01
67 22 0.31
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (64 bp):
TAAATTTGAATATTAAAAGACAATTATATACTTTTGAATATTTCAAATTAAAATAATATATGTT
Found at i:2618120 original size:60 final size:60
Alignment explanation
Indices: 2618009--2618125 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
2617999 TGCAGGGTAG
* * * * *
2618009 GGCACAACCTTATGTGTCATATCCGGATTAGAATTAGAGTGTAAACCTAGTGTAGGTGGT
1 GGCACAACCTTATGTGCCATATCCGAATTAGAACTAAAGTGTAAACCTAGTGCAGGTGGT
* * *
2618069 GGCACGAA-CTTATGTGCCATATCCGAATTAGCACTAAAGTGTAAGCTTAGTGCAGGT
1 GGCAC-AACCTTATGTGCCATATCCGAATTAGAACTAAAGTGTAAACCTAGTGCAGGT
2618126 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (60 bp):
GGCACAACCTTATGTGCCATATCCGAATTAGAACTAAAGTGTAAACCTAGTGCAGGTGGT
Found at i:2625234 original size:30 final size:31
Alignment explanation
Indices: 2625189--2625248 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2625179 CATAGCTTTA
* **
2625189 TATTATGTTTACATATTTTTTAGAT-TCATT
1 TATTACGTTTACATATCATTTAGATATCATT
*
2625219 TATTACGTTTTCATATCATTTAGATATCAT
1 TATTACGTTTACATATCATTTAGATATCAT
2625249 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (31 bp):
TATTACGTTTACATATCATTTAGATATCATT
Found at i:2626180 original size:19 final size:19
Alignment explanation
Indices: 2626156--2626192 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2626146 CGGCCAAGAG
2626156 CATGTATATGCATTAAAAT
1 CATGTATATGCATTAAAAT
* *
2626175 CATGTATTTTCATTAAAA
1 CATGTATATGCATTAAAA
2626193 AGAATTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (19 bp):
CATGTATATGCATTAAAAT
Found at i:2628411 original size:16 final size:15
Alignment explanation
Indices: 2628386--2628419 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2628376 CTACAATTTC
*
2628386 TTAATATAGTTAGTA
1 TTAATATAGTTAATA
2628401 TTAATTATAGTTAATA
1 TTAA-TATAGTTAATA
2628417 TTA
1 TTA
2628420 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
TTAATATAGTTAATA
Found at i:2636838 original size:7 final size:6
Alignment explanation
Indices: 2636819--2636862 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2636809 GTTTTGCAAC
*
2636819 AAAAAG AAAAAG AAAGAAG AAAAA- CAAAAG AGAAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG A-AAAAG AAAAAG A
2636863 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 17 0.52
7 12 0.36
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2636838 original size:13 final size:12
Alignment explanation
Indices: 2636819--2636862 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2636809 GTTTTGCAAC
2636819 AAAAAGAAAAAG
1 AAAAAGAAAAAG
2636831 AAAGAAGAAAAA-
1 AAA-AAGAAAAAG
*
2636843 CAAAAGAGAAAAG
1 AAAAAGA-AAAAG
2636856 AAAAAGA
1 AAAAAGA
2636863 CTCCTACATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 9 0.33
13 14 0.52
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:2638694 original size:29 final size:32
Alignment explanation
Indices: 2638626--2638694 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 32
2638616 TTGGTTGTAA
* *
2638626 CTTATC-TTCATCATTCTCTTTACTTCATTTC
1 CTTATCTTTCATCATTCTCTCTACTTCATTAC
2638657 CTT-TGCTTTCATCATT-TC-CTA-TTCATTAC
1 CTTAT-CTTTCATCATTCTCTCTACTTCATTAC
2638686 CTTATCTTT
1 CTTATCTTT
2638695 TCTTATCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
29 14 0.42
30 4 0.12
31 6 0.18
32 9 0.27
ACGTcount: A:0.16, C:0.28, G:0.01, T:0.55
Consensus pattern (32 bp):
CTTATCTTTCATCATTCTCTCTACTTCATTAC
Found at i:2643985 original size:20 final size:20
Alignment explanation
Indices: 2643957--2644005 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2643947 TAAGAATAAT
*
2643957 TATGTCTTTATGACGTGTTC
1 TATGCCTTTATGACGTGTTC
* *
2643977 TATGCCTTTTTGATGTGTTC
1 TATGCCTTTATGACGTGTTC
2643997 TATGCCTTT
1 TATGCCTTT
2644006 GTGGCATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.53
Consensus pattern (20 bp):
TATGCCTTTATGACGTGTTC
Found at i:2644015 original size:20 final size:20
Alignment explanation
Indices: 2643957--2644015 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
2643947 TAAGAATAAT
* * *
2643957 TATGTCTTTATGACGTGTTC
1 TATGCCTTTGTGACATGTTC
* **
2643977 TATGCCTTTTTGATGTGTTC
1 TATGCCTTTGTGACATGTTC
*
2643997 TATGCCTTTGTGGCATGTT
1 TATGCCTTTGTGACATGTT
2644016 TATCGCTGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.51
Consensus pattern (20 bp):
TATGCCTTTGTGACATGTTC
Found at i:2644051 original size:23 final size:23
Alignment explanation
Indices: 2644001--2644051 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2643991 GTGTTCTATG
* *
2644001 CCTTTGTGGCATGTTTATCGCTG
1 CCTTTGTGGCACGTTTATCGCTA
* *
2644024 TCTTTGTGGCACGTTTATCTCTA
1 CCTTTGTGGCACGTTTATCGCTA
2644047 CCTTT
1 CCTTT
2644052 TGATGGCTTA
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:0.10, C:0.24, G:0.20, T:0.47
Consensus pattern (23 bp):
CCTTTGTGGCACGTTTATCGCTA
Found at i:2656349 original size:20 final size:20
Alignment explanation
Indices: 2656300--2656351 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2656290 TAAGAATAAT
* *
2656300 TATGTCTTTATGACGTGTTC
1 TATGCCTTTGTGACGTGTTC
2656320 TATGCCTTTGTGACGTGTTC
1 TATGCCTTTGTGACGTGTTC
2656340 TATGCCTTTGTG
1 TATGCCTTTGTG
2656352 GCATGTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TATGCCTTTGTGACGTGTTC
Found at i:2656358 original size:20 final size:20
Alignment explanation
Indices: 2656300--2656358 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2656290 TAAGAATAAT
* * *
2656300 TATGTCTTTATGACGTGTTC
1 TATGCCTTTGTGACATGTTC
*
2656320 TATGCCTTTGTGACGTGTTC
1 TATGCCTTTGTGACATGTTC
*
2656340 TATGCCTTTGTGGCATGTT
1 TATGCCTTTGTGACATGTT
2656359 TATCTCTGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (20 bp):
TATGCCTTTGTGACATGTTC
Found at i:2656371 original size:23 final size:23
Alignment explanation
Indices: 2656345--2656388 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2656335 TGTTCTATGC
*
2656345 CTTTGTGGCATGTTTATCTCTGT
1 CTTTGTGGCACGTTTATCTCTGT
2656368 CTTTGTGGCACGTTTATCTCT
1 CTTTGTGGCACGTTTATCTCT
2656389 ACCTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.50
Consensus pattern (23 bp):
CTTTGTGGCACGTTTATCTCTGT
Found at i:2656394 original size:23 final size:23
Alignment explanation
Indices: 2656344--2656394 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2656334 GTGTTCTATG
* *
2656344 CCTTTGTGGCATGTTTATCTCTG
1 CCTTTGTGGCACGTTTATCTCTA
*
2656367 TCTTTGTGGCACGTTTATCTCTA
1 CCTTTGTGGCACGTTTATCTCTA
2656390 CCTTT
1 CCTTT
2656395 TGATAGCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.49
Consensus pattern (23 bp):
CCTTTGTGGCACGTTTATCTCTA
Found at i:2667217 original size:14 final size:14
Alignment explanation
Indices: 2667198--2667228 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2667188 CTCTATCAAA
*
2667198 ACCCTAATCTTACT
1 ACCCTAATATTACT
2667212 ACCCTAATATTACT
1 ACCCTAATATTACT
2667226 ACC
1 ACC
2667229 TATACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (14 bp):
ACCCTAATATTACT
Found at i:2669244 original size:44 final size:44
Alignment explanation
Indices: 2668980--2669244 Score: 395
Period size: 44 Copynumber: 6.0 Consensus size: 44
2668970 CCATTTAATC
* * * *
2668980 CATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTAAATC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-TAATTT
* * ** * *
2669025 CCTAAGCTCGTAAGTTTATTTTACCAATATACTTACCGTTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
2669069 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
2669113 TATAAGCTCGTAAGTTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
2669157 CATAAGCTCGTAAGCTTATTTCACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
2669201 CATAAGCTCGTAAGCTTATTTTACTAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
2669245 GCATCAATGA
Statistics
Matches: 201, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
44 167 0.83
45 34 0.17
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:2669565 original size:59 final size:59
Alignment explanation
Indices: 2669502--2669818 Score: 255
Period size: 59 Copynumber: 5.4 Consensus size: 59
2669492 ATACTGTTAG
* * * * *
2669502 TATGATTTCCTTATCCTTGTAACACCCTTAGTGCTTTTTCTGGAAATCCATACACTCAT
1 TATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * * *
2669561 TATGATTCCCTTA-CCATTTTAGCA-CATATAATGCCCTATCTGGAAATCCATATATTCAA
1 TATGATTTCCTTATCC-TTTTAGCACCCT-TAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * * * * *
2669620 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATACATACTCTCAG
1 TATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * * *
2669679 TATGATTTCCTTATCATTTTAGCA-CATACAGTGCTCCATATGGAAATCCATACACTCAG
1 TATGATTTCCTTATCCTTTTAGCACCCT-TAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * * * * * *
2669738 TATGATTTTCATATCATTTTAGCA-CATATAGTTCTCCATATAGAAATCCATACACTCAG
1 TATGATTTCCTTATCCTTTTAGCACCCT-TAGTGCTCTATCTGGAAATCCATACACTCAA
*
2669797 TATGATTTCCTTATCATTTTAG
1 TATGATTTCCTTATCCTTTTAG
2669819 TGCTCCATAT
Statistics
Matches: 217, Mismatches: 36, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
58 5 0.02
59 210 0.97
60 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (59 bp):
TATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
Found at i:2669630 original size:118 final size:117
Alignment explanation
Indices: 2669440--2669818 Score: 368
Period size: 118 Copynumber: 3.2 Consensus size: 117
2669430 ATACCATTAA
* * *
2669440 TATGATTCCTTTACCATTGTTTTAGCACATGAAGTGCCCTATATGAAAATCCATACTGTT-AGTA
1 TATGATTCCCTTACCA---TTTTAGCACAT-AAGTGCCCTATATGGAAATCCATA-TATTCAGTA
* * * *** * * *
2669504 TGATTTCCTTATCCTTGTAACACCCTTAGTGCTTTTTCTGGAAATCCATACACTCAT
61 TGATTTCCTTATCATTGTAACACACTCAGTGCTCCATATGGAAATACATACACTCAG
* * *
2669561 TATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGAT
1 TATGATTCCCTTACCATTTTAGCACATA-AGTGCCCTATATGGAAATCCATATATTCAGTATGAT
* * *
2669626 TTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATACATACTCTCAG
65 TTCCTTATCATTGTAACACACTCAGTGCTCCATATGGAAATACATACACTCAG
* * * *
2669679 TATGATTTCCTTATCATTTTAGCACATACAGTGCTCC-ATATGGAAATCCATACACTCAGTATGA
1 TATGATTCCCTTACCATTTTAGCACATA-AGTGC-CCTATATGGAAATCCATATATTCAGTATGA
* * * * * * * *
2669743 TTTTCATATCATTTTAGCACA-TATAGTTCTCCATATAGAAATCCATACACTCAG
64 TTTCCTTATCATTGTAACACACT-CAGTGCTCCATATGGAAATACATACACTCAG
* *
2669797 TATGATTTCCTTATCATTTTAG
1 TATGATTCCCTTACCATTTTAG
2669819 TGCTCCATAT
Statistics
Matches: 221, Mismatches: 33, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
117 5 0.02
118 199 0.90
119 2 0.01
121 15 0.07
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (117 bp):
TATGATTCCCTTACCATTTTAGCACATAAGTGCCCTATATGGAAATCCATATATTCAGTATGATT
TCCTTATCATTGTAACACACTCAGTGCTCCATATGGAAATACATACACTCAG
Found at i:2669725 original size:177 final size:168
Alignment explanation
Indices: 2669542--2669880 Score: 421
Period size: 177 Copynumber: 2.0 Consensus size: 168
2669532 GTGCTTTTTC
* * * *
2669542 TGGAAATCCATACACTCATTATGATTCCCTTACCATTTTAGCACATATAATGC-CCTATCTGGAA
1 TGGAAATCCATACACTCAGTATGATTCCCATACCATTTTAGCACATATAATGCTCC-ATATAGAA
* *
2669606 ATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATACAT
65 ATCCATACACTCAATATGATTTCCTTATCA-TTT-------T-AGTGCTCCATATGGAAATACAT
* *
2669671 AC-TCTCAGTATGATTTCCTTATCATTTTAGCACATACAGTGCTCCATA
121 ACAT-TCAATAAGATTTCCTTATCATTTTAGCACATACAGTGCTCCATA
** * * *
2669719 TGGAAATCCATACACTCAGTATGATTTTCATATCATTTTAGCACATATAGTTCTCCATATAGAAA
1 TGGAAATCCATACACTCAGTATGATTCCCATACCATTTTAGCACATATAATGCTCCATATAGAAA
* *
2669784 TCCATACACTCAGTATGATTTCCTTATCATTTTAGTGCTCCATATGGAAATTCATACATTCAATA
66 TCCATACACTCAATATGATTTCCTTATCATTTTAGTGCTCCATATGGAAATACATACATTCAATA
*
2669849 AGATTTCCTTATCATTTTAGCACATATAGTGC
131 AGATTTCCTTATCATTTTAGCACATACAGTGC
2669881 CATTTCGTAA
Statistics
Matches: 144, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
168 58 0.40
169 2 0.01
176 3 0.02
177 79 0.55
178 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (168 bp):
TGGAAATCCATACACTCAGTATGATTCCCATACCATTTTAGCACATATAATGCTCCATATAGAAA
TCCATACACTCAATATGATTTCCTTATCATTTTAGTGCTCCATATGGAAATACATACATTCAATA
AGATTTCCTTATCATTTTAGCACATACAGTGCTCCATA
Found at i:2669854 original size:50 final size:50
Alignment explanation
Indices: 2669766--2669868 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 50
2669756 TTAGCACATA
* * *
2669766 TAGTTCTCCATATAGAAATCCATACACTCAGTATGATTTCCTTATCATTT
1 TAGTGCTCCATATAGAAATCCATACACTCAATAAGATTTCCTTATCATTT
* * *
2669816 TAGTGCTCCATATGGAAATTCATACATTCAATAAGATTTCCTTATCATTT
1 TAGTGCTCCATATAGAAATCCATACACTCAATAAGATTTCCTTATCATTT
2669866 TAG
1 TAG
2669869 CACATATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (50 bp):
TAGTGCTCCATATAGAAATCCATACACTCAATAAGATTTCCTTATCATTT
Found at i:2672546 original size:22 final size:22
Alignment explanation
Indices: 2672518--2672561 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2672508 GCCATTACTT
2672518 CTTTGAACCCATACCCAAACTC
1 CTTTGAACCCATACCCAAACTC
2672540 CTTTGAACCCATACCCAAACTC
1 CTTTGAACCCATACCCAAACTC
2672562 TTTTTATCTA
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:0.32, C:0.41, G:0.05, T:0.23
Consensus pattern (22 bp):
CTTTGAACCCATACCCAAACTC
Found at i:2673867 original size:2 final size:2
Alignment explanation
Indices: 2673860--2673896 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2673850 CTATAAAAAC
2673860 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 T
2673897 GTAATCTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2674329 original size:8 final size:8
Alignment explanation
Indices: 2674316--2674392 Score: 54
Period size: 8 Copynumber: 9.9 Consensus size: 8
2674306 TATTAATATT
2674316 TATAATAA
1 TATAATAA
*
2674324 TATAATAT
1 TATAATAA
2674332 TATAATAA
1 TATAATAA
* *
2674340 AATACTCAA
1 TATAAT-AA
*
2674349 T-T-ATAT
1 TATAATAA
2674355 TATAATAA
1 TATAATAA
*
2674363 AATAATCAA
1 TATAAT-AA
*
2674372 T-T-ATAT
1 TATAATAA
2674378 TATAATAA
1 TATAATAA
2674386 TATAATA
1 TATAATA
2674393 TTTTATATTT
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
6 4 0.08
7 5 0.10
8 38 0.75
9 4 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAATAA
Found at i:2674401 original size:23 final size:23
Alignment explanation
Indices: 2674328--2674391 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
2674318 TAATAATATA
*
2674328 ATATTATAATAAAATACTCAATT
1 ATATTATAATAAAATAATCAATT
2674351 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAATT
*
2674374 ATATTATAATAATATAAT
1 ATATTATAATAAAATAAT
2674392 ATTTTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAATT
Found at i:2676844 original size:17 final size:17
Alignment explanation
Indices: 2676808--2676877 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
2676798 AGTATGTTGT
2676808 TTCATTCAA-TAAACCTAG
1 TTCATT-AATTAAA-CTAG
*
2676826 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
2676843 TTTATTCATTAAAACTGG
1 TTCATTAATT-AAACTAG
*
2676861 TTCATTAATCAAACTAG
1 TTCATTAATTAAACTAG
2676878 ATCTTTTAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 19 0.46
18 22 0.54
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:2676864 original size:35 final size:36
Alignment explanation
Indices: 2676806--2676877 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
2676796 TAAGTATGTT
* *
2676806 GTTTCATTCAATAAACCTAGTTCACTAATTAAACTA
1 GTTTCATTCAATAAAACTAGTTCACTAATCAAACTA
* * *
2676842 GTTT-ATTCATTAAAACTGGTTCATTAATCAAACTA
1 GTTTCATTCAATAAAACTAGTTCACTAATCAAACTA
2676877 G
1 G
2676878 ATCTTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (36 bp):
GTTTCATTCAATAAAACTAGTTCACTAATCAAACTA
Found at i:2679808 original size:47 final size:45
Alignment explanation
Indices: 2679733--2679858 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
2679723 TATAAAATCT
* *
2679733 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
2679778 CTTACCATTTAAATTCCATAAGCTTATAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
** *
2679825 CTTGTCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
2679859 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 23 0.33
45 10 0.14
46 2 0.03
47 35 0.50
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:2680018 original size:40 final size:40
Alignment explanation
Indices: 2679963--2680044 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2679953 ACCATAGTGC
* *
2679963 TACACATAAGGTCGTGCCCGCCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2680003 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2680043 TA
1 TA
2680045 TAAACCTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:2686537 original size:47 final size:44
Alignment explanation
Indices: 2686478--2686587 Score: 130
Period size: 47 Copynumber: 2.4 Consensus size: 44
2686468 ATTTATCCCG
*
2686478 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCCA
1 TAAGCTCATAAGCTTATTTTACCAAAATACTTACCA-TT--ATTCCA
* * * * *
2686525 TAAGCTCATAAGCTTATTTTTCCAATATACTTGCCATTATTTCG
1 TAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTATTCCA
*
2686569 TAAACTCATAAGCTTATTT
1 TAAGCTCATAAGCTTATTT
2686588 GCATGGTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
44 22 0.39
46 2 0.04
47 32 0.57
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
TAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTATTCCA
Found at i:2688946 original size:7 final size:7
Alignment explanation
Indices: 2688934--2688970 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2688924 AGATAAAAGC
2688934 TATGTGA
1 TATGTGA
2688941 TATGTGA
1 TATGTGA
2688948 TATGTGA
1 TATGTGA
*
2688955 TATGAGA
1 TATGTGA
*
2688962 TATATGA
1 TATGTGA
2688969 TA
1 TA
2688971 ATAAGATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (7 bp):
TATGTGA
Found at i:2688951 original size:14 final size:14
Alignment explanation
Indices: 2688934--2688980 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
2688924 AGATAAAAGC
*
2688934 TATGTGATATGTGA
1 TATGTGATATGAGA
2688948 TATGTGATATGAGA
1 TATGTGATATGAGA
* *
2688962 TATATGATAATAAGA
1 TATGTGAT-ATGAGA
2688977 TATG
1 TATG
2688981 AGATCCATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (14 bp):
TATGTGATATGAGA
Found at i:2703677 original size:14 final size:14
Alignment explanation
Indices: 2703658--2703699 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2703648 AGTGCTTCAA
2703658 CTTTTCTTTCTTTT
1 CTTTTCTTTCTTTT
2703672 CTTTTCTTTCTTTTT
1 CTTTTCTTTC-TTTT
*
2703687 GTTTTC-TTCTTTT
1 CTTTTCTTTCTTTT
2703700 GAGTTCTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 13 0.50
15 9 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTCTTTT
Found at i:2703753 original size:12 final size:12
Alignment explanation
Indices: 2703736--2703775 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
2703726 ATTTTGATTT
2703736 CTTTCACTTGCA
1 CTTTCACTTGCA
2703748 CTTTCACTTGCA
1 CTTTCACTTGCA
*
2703760 CCTTCACTTGCA
1 CTTTCACTTGCA
2703772 CTTT
1 CTTT
2703776 TTTTTTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.15, C:0.35, G:0.07, T:0.42
Consensus pattern (12 bp):
CTTTCACTTGCA
Found at i:2704004 original size:6 final size:6
Alignment explanation
Indices: 2703989--2704034 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
2703979 GGATAATTAA
2703989 GAAA-G GAAATG GAAATG GAAATG GAAATG GAAA-- GAAAT- GAAATG
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
2704033 GA
1 GA
2704035 TAGAAATGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.11
5 9 0.24
6 25 0.66
ACGTcount: A:0.54, C:0.00, G:0.33, T:0.13
Consensus pattern (6 bp):
GAAATG
Found at i:2705485 original size:17 final size:17
Alignment explanation
Indices: 2705442--2705485 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 17
2705432 CCTTCATTTC
*
2705442 CCCTTTTCTCTCTTTAT
1 CCCTTTTCTCTCTTCAT
2705459 ---TTTTCT-TCTTCAT
1 CCCTTTTCTCTCTTCAT
2705472 CCCTTTTCTCTCTT
1 CCCTTTTCTCTCTT
2705486 TCTTCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 8
0.71 0.03 0.26
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
16 6 0.27
17 4 0.18
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (17 bp):
CCCTTTTCTCTCTTCAT
Found at i:2705501 original size:30 final size:30
Alignment explanation
Indices: 2705442--2705503 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
2705432 CCTTCATTTC
* *
2705442 CCCTTTTCTCTCTTTATTTTTCTTCTTCAT
1 CCCTTTTCTCTCTTTATTCTTATTCTTCAT
* *
2705472 CCCTTTTCTCTCTTTCTTCTTATTTTTCAT
1 CCCTTTTCTCTCTTTATTCTTATTCTTCAT
2705502 CC
1 CC
2705504 TCTATTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (30 bp):
CCCTTTTCTCTCTTTATTCTTATTCTTCAT
Found at i:2705526 original size:14 final size:14
Alignment explanation
Indices: 2705509--2705547 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2705499 CATCCTCTAT
*
2705509 TTTCCATTTTCTTA
1 TTTCCATTTTCTCA
**
2705523 TTTCCATCCTCTCA
1 TTTCCATTTTCTCA
2705537 TTTCCATTTTC
1 TTTCCATTTTC
2705548 GCATCCTCTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTCCATTTTCTCA
Found at i:2705540 original size:28 final size:29
Alignment explanation
Indices: 2705488--2705547 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
2705478 TCTCTCTTTC
*
2705488 TTCTTATTTTTCATCCTCTATTTTCCATT
1 TTCTTATTTTCCATCCTCTATTTTCCATT
2705517 TTCTTA-TTTCCATCCTCTCA-TTTCCATT
1 TTCTTATTTTCCATCCTCT-ATTTTCCATT
2705545 TTC
1 TTC
2705548 GCATCCTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.58
Consensus pattern (29 bp):
TTCTTATTTTCCATCCTCTATTTTCCATT
Found at i:2705552 original size:22 final size:21
Alignment explanation
Indices: 2705523--2705564 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
2705513 CATTTTCTTA
2705523 TTTCCATCCTCTCATTTCCAT
1 TTTCCATCCTCTCATTTCCAT
2705544 TTTCGCATCCTCTCATTTCCA
1 TTTC-CATCCTCTCATTTCCA
2705565 ATTTACGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.14, C:0.38, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTCCATCCTCTCATTTCCAT
Found at i:2708171 original size:2 final size:2
Alignment explanation
Indices: 2708164--2708211 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2708154 GATTACAACC
2708164 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
2708206 AT AT AT
1 AT AT AT
2708212 GAATTTTTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2709561 original size:21 final size:22
Alignment explanation
Indices: 2709514--2709566 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2709504 ATTATTAAAA
2709514 ATTTTGAATTATTTAAGTTATT
1 ATTTTGAATTATTTAAGTTATT
* *
2709536 A-TTTGAGTTATTTGAGTT-TT
1 ATTTTGAATTATTTAAGTTATT
2709556 ATTTTGTAATT
1 ATTTTG-AATT
2709567 TGATTCGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
ATTTTGAATTATTTAAGTTATT
Found at i:2711101 original size:34 final size:35
Alignment explanation
Indices: 2711041--2711129 Score: 135
Period size: 34 Copynumber: 2.5 Consensus size: 35
2711031 GATTGCCCAG
2711041 AGGGAACAGATTTCCCCCCCAGGGGGTATCGATTCCC
1 AGGGAACAGA-TT-CCCCCCAGGGGGTATCGATTCCC
*
2711078 CGGGAACAGATTCCCCCCA-GGGGTATCGATTCCC
1 AGGGAACAGATTCCCCCCAGGGGGTATCGATTCCC
*
2711112 AGGGTACAGATTCCCCCC
1 AGGGAACAGATTCCCCCC
2711130 TGCATGGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 31 0.63
35 7 0.14
36 2 0.04
37 9 0.18
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (35 bp):
AGGGAACAGATTCCCCCCAGGGGGTATCGATTCCC
Found at i:2711278 original size:20 final size:21
Alignment explanation
Indices: 2711242--2711282 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2711232 ATTTGAATAT
*
2711242 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2711263 TATGAA-GGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2711283 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2711344 original size:21 final size:21
Alignment explanation
Indices: 2711311--2711350 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2711301 TTTTTGTAGA
*
2711311 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2711333 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2711351 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:2711604 original size:34 final size:32
Alignment explanation
Indices: 2711565--2711634 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2711555 TTTTGTAAAG
* * *
2711565 GGGAAAGGTTCTAGCTTATCCCATGTAAAAGCTA
1 GGGAAAGATTCTAGCTTAGCCCA-G-AAAAACTA
*
2711599 GGGAAAGATTCTAGTTTAGCCCAGAAAAACTA
1 GGGAAAGATTCTAGCTTAGCCCAGAAAAACTA
2711631 GGGA
1 GGGA
2711635 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (32 bp):
GGGAAAGATTCTAGCTTAGCCCAGAAAAACTA
Found at i:2713978 original size:33 final size:34
Alignment explanation
Indices: 2713916--2713999 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 34
2713906 ATTGCCCAGA
2713916 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
* *
2713951 GGGAACATATTCCCCCA-TGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
*
2713984 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
2714000 TGCATGGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 29 0.64
34 6 0.13
35 10 0.22
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:2713994 original size:15 final size:15
Alignment explanation
Indices: 2713943--2713998 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2713933 AGGGGGTATC
*
2713943 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
*
2713958 TATTCCCCCATGGGTATC-
1 GATT-CCCC--GGGTA-CA
2713976 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
2713991 GATTCCCC
1 GATTCCCC
2713999 CTGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 16 0.48
16 4 0.12
17 4 0.12
18 7 0.21
19 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.21, T:0.23
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:2714148 original size:20 final size:21
Alignment explanation
Indices: 2714112--2714152 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2714102 ATTTGAATAT
*
2714112 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2714133 TATGAA-GGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2714153 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2714474 original size:34 final size:32
Alignment explanation
Indices: 2714435--2714504 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2714425 TTTTGTAAAG
* * *
2714435 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2714469 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2714501 GGGA
1 GGGA
2714505 GTTTGTACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2715461 original size:43 final size:44
Alignment explanation
Indices: 2715332--2715463 Score: 158
Period size: 47 Copynumber: 2.9 Consensus size: 44
2715322 AAAATAATAT
*
2715332 AAAATCTCTTACCATTTATCTCATAAGCTCTTAAGCTTATTTTACC
1 AAAAT-TCTTACCATTTAT-TCATAAGCTCCTAAGCTTATTTTACC
* * *
2715378 AAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATC
1 AAAATTCTTACCATTT--ATT-CATAAGCTCCTAAGCTTATTTTACC
* *
2715425 AATATTCTTGCCA-TTATTCATAAGCTCCTAAGCTTATTT
1 AAAATTCTTACCATTTATTCATAAGCTCCTAAGCTTATTT
2715464 GCATACTTAC
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
43 20 0.26
44 3 0.04
45 10 0.13
46 8 0.11
47 35 0.46
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (44 bp):
AAAATTCTTACCATTTATTCATAAGCTCCTAAGCTTATTTTACC
Found at i:2717988 original size:7 final size:7
Alignment explanation
Indices: 2717975--2718015 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2717965 GGATATTGTC
2717975 TATGGTA
1 TATGGTA
*
2717982 AATGGTA
1 TATGGTA
*
2717989 TATGGTT
1 TATGGTA
2717996 TATGGTA
1 TATGGTA
*
2718003 TATGGTT
1 TATGGTA
2718010 TATGGT
1 TATGGT
2718016 TTATTAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (7 bp):
TATGGTA
Found at i:2717999 original size:21 final size:21
Alignment explanation
Indices: 2717975--2718019 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2717965 GGATATTGTC
2717975 TATGGTAAATGGTATATGGTT
1 TATGGTAAATGGTATATGGTT
* *
2717996 TATGGTATATGGTTTATGGTT
1 TATGGTAAATGGTATATGGTT
2718017 TAT
1 TAT
2718020 TAGTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (21 bp):
TATGGTAAATGGTATATGGTT
Found at i:2718009 original size:14 final size:14
Alignment explanation
Indices: 2717983--2718015 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2717973 TCTATGGTAA
2717983 ATGGTATATGGTTT
1 ATGGTATATGGTTT
2717997 ATGGTATATGGTTT
1 ATGGTATATGGTTT
2718011 ATGGT
1 ATGGT
2718016 TTATTAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
ATGGTATATGGTTT
Found at i:2718016 original size:7 final size:7
Alignment explanation
Indices: 2717983--2718019 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2717973 TCTATGGTAA
*
2717983 ATGGTAT
1 ATGGTTT
2717990 ATGGTTT
1 ATGGTTT
*
2717997 ATGGTAT
1 ATGGTTT
2718004 ATGGTTT
1 ATGGTTT
2718011 ATGGTTT
1 ATGGTTT
2718018 AT
1 AT
2718020 TAGTTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (7 bp):
ATGGTTT
Found at i:2728016 original size:44 final size:45
Alignment explanation
Indices: 2727976--2728062 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
2727966 GTTATGGAAT
*
2727976 AATGGCAAGTGTATTGGTAAAAAAAGCTTACGAGCTTATGGTACA
1 AATGGCAAGTATATTGGTAAAAAAAGCTTACGAGCTTATGGTACA
* * *
2728021 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGT
1 AATGGCAAGTATATTGGTAAAAAAAGCTTACGAGCTTATGGT
2728063 TAATAAATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (45 bp):
AATGGCAAGTATATTGGTAAAAAAAGCTTACGAGCTTATGGTACA
Found at i:2735604 original size:64 final size:61
Alignment explanation
Indices: 2735535--2735714 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 61
2735525 TGGGACACTT
* *
2735535 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATATCCTG
1 AGTGCATCGATGCA-T--GGATGCATCGATGCATAAAATGCATTCGATGTTTG-AAAATATCCAG
* * *
2735600 -GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAG
1 AGTGCATCGATGCATGG---ATGCATCGATGCATAAAATGCATTCGATG-TTTGAAAATATCCAG
* **
2735664 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGCATCGATGCAT-G-GA-TGCATCGATGCATAAAATGCATTCGATGTT
2735715 CAATTAATTC
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
61 2 0.02
63 1 0.01
64 50 0.51
65 43 0.44
66 1 0.01
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (61 bp):
AGTGCATCGATGCATGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATCCAG
Found at i:2735686 original size:19 final size:19
Alignment explanation
Indices: 2735662--2735712 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2735652 GAAAATATTC
2735662 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2735681 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2735700 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2735713 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2735688 original size:65 final size:65
Alignment explanation
Indices: 2735556--2735714 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 65
2735546 GCACTAAGGA
* ***
2735556 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATATCCTGGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATATCCAGGTGCATCGATGCATGGAGAG
* *
2735620 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATATCCAG-GTGCATCGATGCATGGAGA
2735684 G
65 G
* **
2735685 TGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
2735715 CAATTAATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATATCCAGGTGCATCGATGCATGGAGAG
Found at i:2735754 original size:65 final size:64
Alignment explanation
Indices: 2735556--2735763 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
2735546 GCACTAAGGA
* * * * *
2735556 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATATCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
2735619 G
64 G
* * * **
2735620 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAG
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
* *
2735685 TGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGAC
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGAC
2735747 TG
63 TG
2735749 CTGCATCGGTGCATG
1 -TGCATCGGTGCATG
2735764 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 53 0.43
65 61 0.49
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
Found at i:2736140 original size:30 final size:31
Alignment explanation
Indices: 2736092--2736170 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 31
2736082 ATTGATTTTG
2736092 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
2736123 AAAAACTTACT-CCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
2736153 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
2736171 TTTGTTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 26 0.60
31 17 0.40
ACGTcount: A:0.32, C:0.34, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:2740620 original size:22 final size:21
Alignment explanation
Indices: 2740594--2740640 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
2740584 AAGGTCAAAA
*
2740594 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
2740616 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
2740636 ATCAA
1 ATCAA
2740641 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:2742842 original size:19 final size:19
Alignment explanation
Indices: 2742818--2742868 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2742808 GAAAATATTC
2742818 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2742837 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2742856 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2742869 TTCATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2742910 original size:65 final size:66
Alignment explanation
Indices: 2742710--2742919 Score: 195
Period size: 65 Copynumber: 3.2 Consensus size: 66
2742700 GTTCACTAAG
* * * *** * *
2742710 GATGCATCGATGCATAAAATGCATTCGATG-TTTGAAAA-ATAGCCTCGTTCATCGATGCATGGC
1 GATGCATCGGTGCATGAAATGCATTCGATGTTTTGAAAATAT-TCAGAGTGCATCGATGCATGGA
2742773 TT
65 TT
* *
2742775 G-TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-
1 GATGCATCGGTGCATGAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAT
2742838 -
66 T
* * *
2742838 GAGTGCATCGGTGCATGGAATGCATTCGATGTTCATT-TAATTCA-TC-GA-TGCATCGATGCAT
1 GA-TGCATCGGTGCATGAAATGCATTCGATGTT--TTGAAAAT-ATTCAGAGTGCATCGATGCAT
2742899 GGATT
62 GGATT
2742904 GATGCATCGGTGCATG
1 GATGCATCGGTGCATG
2742920 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 43 0.35
65 68 0.55
66 9 0.07
67 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (66 bp):
GATGCATCGGTGCATGAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAT
T
Found at i:2764169 original size:16 final size:16
Alignment explanation
Indices: 2764148--2764191 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
2764138 ATTGAAAAAT
2764148 AAAGAAAGTAAAATTA
1 AAAGAAAGTAAAATTA
2764164 AAAGAAAGTAAAATTA
1 AAAGAAAGTAAAATTA
*
2764180 AAAGAATGTAAA
1 AAAGAAAGTAAA
2764192 CTTGAAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (16 bp):
AAAGAAAGTAAAATTA
Found at i:2764929 original size:22 final size:23
Alignment explanation
Indices: 2764901--2764945 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2764891 CTAAAAACAG
* *
2764901 TAAAAATACTGAA-GATAATTCC
1 TAAAAATAATAAATGATAATTCC
2764923 TAAAAATAATAAATGATAATTCC
1 TAAAAATAATAAATGATAATTCC
2764946 CTTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (23 bp):
TAAAAATAATAAATGATAATTCC
Found at i:2766551 original size:150 final size:150
Alignment explanation
Indices: 2766277--2766554 Score: 351
Period size: 150 Copynumber: 1.9 Consensus size: 150
2766267 TATTTCAAAC
** *
2766277 ACTAACTCGATGTGGTGATAGATTCTATGTTCCATATTTGCATAGGATAGGTAGTCATCCCCCTT
1 ACTAACTCGATGTGGTGATAGATTCTACATTCCATATTTGCATAGGATAGGTAGGCATCCCCCTT
* * * * *
2766342 TAAACCTTCCCTTATAAAATATGCTTACCTTACTAGTTGTCTAGCATACGTTATGTCTTTGAATT
66 TAAACCTTCCATTATAAAATATGCTTACCTTACTAATTGTCTAACAGACATTATGTCTTTGAATT
2766407 GTTAATGTAAGAAATGACAT
131 GTTAATGTAAGAAATGACAT
* ** * *
2766427 ACTAACTTGATGTGGTGATAGATTCTACATTTGATATTTGTATAGGATAGGTAGGCGTCCCCCTT
1 ACTAACTCGATGTGGTGATAGATTCTACATTCCATATTTGCATAGGATAGGTAGGCATCCCCCTT
* * * * * * * *
2766492 TGAACCTTTCATTTTGAAATATGTTTACCTTACTAATTGTAC-AATAGACATTCTTTCTTTGAA
66 TAAACCTTCCATTATAAAATATGCTTACCTTACTAATTGT-CTAACAGACATTATGTCTTTGAA
2766555 CTGTCCTATC
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
150 105 0.99
151 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (150 bp):
ACTAACTCGATGTGGTGATAGATTCTACATTCCATATTTGCATAGGATAGGTAGGCATCCCCCTT
TAAACCTTCCATTATAAAATATGCTTACCTTACTAATTGTCTAACAGACATTATGTCTTTGAATT
GTTAATGTAAGAAATGACAT
Found at i:2766571 original size:17 final size:17
Alignment explanation
Indices: 2766549--2766581 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2766539 ACATTCTTTC
*
2766549 TTTGAACTGTCCTATCG
1 TTTGAACTATCCTATCG
2766566 TTTGAACTATCCTATC
1 TTTGAACTATCCTATC
2766582 ATTGGTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTGAACTATCCTATCG
Found at i:2767950 original size:20 final size:20
Alignment explanation
Indices: 2767921--2767958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2767911 TCGGCTAAGG
*
2767921 CATGAGTCTTAATTAAAAGA
1 CATGAATCTTAATTAAAAGA
*
2767941 CATGAATCTTCATTAAAA
1 CATGAATCTTAATTAAAA
2767959 ATATGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (20 bp):
CATGAATCTTAATTAAAAGA
Found at i:2782904 original size:31 final size:29
Alignment explanation
Indices: 2782861--2782934 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
2782851 CATCATGATT
2782861 CATTTT-GAAGACACATACAACTTAGTGGAG
1 CATTTTGGAAGACACATAC--CTTAGTGGAG
* *
2782891 CATTTTGGAAGACAAATACCTTGGTGGAG
1 CATTTTGGAAGACACATACCTTAGTGGAG
*
2782920 CA-TTTGGGAGACACA
1 CATTTTGGAAGACACA
2782935 AACAGCTCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.28
29 11 0.28
30 6 0.15
31 11 0.28
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (29 bp):
CATTTTGGAAGACACATACCTTAGTGGAG
Found at i:2782920 original size:29 final size:30
Alignment explanation
Indices: 2782861--2782932 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
2782851 CATCATGATT
*
2782861 CATTTT-GAAGACACATACAACTTAGTGGAG
1 CATTTTGGAAGACAAATAC-ACTTAGTGGAG
*
2782891 CATTTTGGAAGACAAATAC-CTTGGTGGAG
1 CATTTTGGAAGACAAATACACTTAGTGGAG
*
2782920 CA-TTTGGGAGACA
1 CATTTTGGAAGACA
2782933 CAAACAGCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.26
29 11 0.29
30 6 0.16
31 11 0.29
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (30 bp):
CATTTTGGAAGACAAATACACTTAGTGGAG
Found at i:2797009 original size:19 final size:19
Alignment explanation
Indices: 2796985--2797044 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
2796975 TTGGAGTGCA
**
2796985 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAAGAAG
2797004 AAAAGAAGAGAAAAAGAAG
1 AAAAGAAGAGAAAAAGAAG
2797023 AAAAGAAGA-AAAGAA-AAG
1 AAAAGAAGAGAAA-AAGAAG
2797041 AAAA
1 AAAA
2797045 TGAGAAGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 10 0.26
19 28 0.74
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAGAAAAAGAAG
Found at i:2797032 original size:27 final size:29
Alignment explanation
Indices: 2796984--2797044 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
2796974 ATTGGAGTGC
*
2796984 AAAAAGAAGAGAAAAATCAGAAAAGAAGAG
1 AAAAAGAAGAGAAAAA-CAGAAAAGAAAAG
*
2797014 AAAAAGAAGA-AAAGA-AGAAAAGAAAAG
1 AAAAAGAAGAGAAAAACAGAAAAGAAAAG
2797041 AAAA
1 AAAA
2797045 TGAGAAGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.52
29 4 0.14
30 10 0.34
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (29 bp):
AAAAAGAAGAGAAAAACAGAAAAGAAAAG
Found at i:2807389 original size:22 final size:20
Alignment explanation
Indices: 2807363--2807407 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
2807353 GTTGCGGAAT
2807363 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAA-A
*
2807385 TGATGGTGTTGATGATGAAA
1 TGATGGTCTTGATGATGAAA
2807405 TGA
1 TGA
2807408 AGATGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (20 bp):
TGATGGTCTTGATGATGAAA
Found at i:2814589 original size:10 final size:10
Alignment explanation
Indices: 2814574--2814603 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2814564 CAACATGGGC
2814574 AGCTGAAAGT
1 AGCTGAAAGT
2814584 AGCTGAAAGT
1 AGCTGAAAGT
*
2814594 AGCTAAAAGT
1 AGCTGAAAGT
2814604 GATGTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (10 bp):
AGCTGAAAGT
Found at i:2827048 original size:15 final size:14
Alignment explanation
Indices: 2827028--2827058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2827018 ACTTAAAAAA
2827028 AAAAGAAAAGCAAAG
1 AAAAGAAAAG-AAAG
2827043 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
2827057 AA
1 AA
2827059 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:2837867 original size:11 final size:11
Alignment explanation
Indices: 2837851--2837907 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
2837841 TTTTTTGAAA
2837851 TTTTGGTTTTT
1 TTTTGGTTTTT
*
2837862 TTTTGGATTTT
1 TTTTGGTTTTT
*
2837873 TTTTGG-CTTT
1 TTTTGGTTTTT
*
2837883 TTTTGTTTTTT
1 TTTTGGTTTTT
*
2837894 TTTTTGTTTTT
1 TTTTGGTTTTT
2837905 TTT
1 TTT
2837908 AAAAAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.82
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:2837883 original size:22 final size:21
Alignment explanation
Indices: 2837851--2837907 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2837841 TTTTTTGAAA
2837851 TTTTGGTTTTTTTTTGGATTTT
1 TTTTGG-TTTTTTTTGGATTTT
* **
2837873 TTTTGGCTTTTTTTGTTTTTT
1 TTTTGGTTTTTTTTGGATTTT
*
2837894 TTTTTGTTTTTTTT
1 TTTTGGTTTTTTTT
2837908 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.82
Consensus pattern (21 bp):
TTTTGGTTTTTTTTGGATTTT
Found at i:2837895 original size:12 final size:12
Alignment explanation
Indices: 2837880--2837907 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2837870 TTTTTTTGGC
2837880 TTTTTTTGTTTT
1 TTTTTTTGTTTT
2837892 TTTTTTTGTTTT
1 TTTTTTTGTTTT
2837904 TTTT
1 TTTT
2837908 AAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:2842781 original size:26 final size:26
Alignment explanation
Indices: 2842745--2842796 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2842735 GTTACTAGTT
*
2842745 ATGTAGCTAACATATAACTTAGCAAG
1 ATGTAGCTAACAGATAACTTAGCAAG
2842771 ATGTAGCTAACAGATAACTTAGCAAG
1 ATGTAGCTAACAGATAACTTAGCAAG
2842797 TACACATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (26 bp):
ATGTAGCTAACAGATAACTTAGCAAG
Found at i:2854406 original size:19 final size:20
Alignment explanation
Indices: 2854368--2854410 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2854358 GAAACCCCTT
*
2854368 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
2854388 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
2854407 TGAA
1 TGAA
2854411 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:2856668 original size:23 final size:24
Alignment explanation
Indices: 2856640--2856693 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
2856630 AAAATCAGCA
2856640 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
2856663 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
2856687 AAGAAAA
1 AAGAAAA
2856694 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:2856698 original size:24 final size:23
Alignment explanation
Indices: 2856640--2856699 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
2856630 AAAATCAGCA
2856640 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
2856663 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
2856687 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
2856700 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:2863282 original size:33 final size:33
Alignment explanation
Indices: 2863203--2863306 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2863193 ATACAATCTG
* *
2863203 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2863239 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2863272 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2863305 TC
1 TC
2863307 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2868929 original size:33 final size:33
Alignment explanation
Indices: 2868850--2868953 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2868840 ATACAATCTG
* *
2868850 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2868886 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2868919 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2868952 TC
1 TC
2868954 ATTCATCACA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Done.