Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008071.1 Hibiscus syriacus cultivar Beakdansim tig00110569_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: 1969971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 5 of 8
Found at i:920617 original size:12 final size:12
Alignment explanation
Indices: 920600--920624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
920590 ATATAATCCT
920600 GAAGAAGAAAAA
1 GAAGAAGAAAAA
920612 GAAGAAGAAAAA
1 GAAGAAGAAAAA
920624 G
1 G
920625 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:922939 original size:19 final size:19
Alignment explanation
Indices: 922917--923047 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
922907 GGAAATTATT
922917 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
922936 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
922950 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
922969 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
922983 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
923002 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
923016 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
923035 ATCACAACGCGAA
1 ATCGCAATGCGAA
923048 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:922959 original size:33 final size:33
Alignment explanation
Indices: 922917--923043 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
922907 GGAAATTATT
922917 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
922950 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
922982 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
923016 ATCGCAATGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
923044 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:923024 original size:66 final size:66
Alignment explanation
Indices: 922918--923050 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
922908 GAAATTATTA
* *
922918 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
922983 T
66 T
*
922984 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
923049 T
66 T
923050 T
1 T
923051 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
T
Found at i:923225 original size:14 final size:14
Alignment explanation
Indices: 923206--923242 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
923196 CATCAATTAA
923206 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
923220 ACAAATCACCTTTT
1 ACAAATCAACTTTT
923234 ACAAATCAA
1 ACAAATCAA
923243 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:924684 original size:42 final size:42
Alignment explanation
Indices: 924638--924721 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
924628 CGATGACAGT
* * *
924638 GGCCTCTAGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTACAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
924680 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTACAACGATAGGAGGGGACTCTCGAGGAATGATAGG
924722 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GGCCTCTACAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:926752 original size:20 final size:19
Alignment explanation
Indices: 926721--926781 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
926711 TCTTTTGGTT
926721 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
926740 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
926761 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
926780 GA
1 GA
926782 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:926803 original size:33 final size:33
Alignment explanation
Indices: 926746--926842 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
926736 ACGAGATAAT
*
926746 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
926780 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
926813 GACAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
926843 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 43 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:926876 original size:19 final size:19
Alignment explanation
Indices: 926843--926923 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
926833 AAAATCGCAA
**
926843 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
926862 TGCGATTTTTATTTCACGT
1 TGCGATTTTTATTTCGCGT
*
926881 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
926895 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
926915 TGCGATTTT
1 TGCGATTTT
926924 CATTCTCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.45
20 11 0.22
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:927464 original size:20 final size:20
Alignment explanation
Indices: 927439--927491 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
927429 GCGCTATGTA
927439 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
927459 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
927479 TATCTCGTTGCGA
1 AATCGCGTTGCGA
927492 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:927552 original size:41 final size:41
Alignment explanation
Indices: 927460--927554 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
927450 GAAAGTCAGA
* * * * ** *
927460 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
927501 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
927543 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
927555 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:928891 original size:2 final size:2
Alignment explanation
Indices: 928884--928943 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
928874 CACAATCTTG
928884 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
928926 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
928944 TAAGGGTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:931101 original size:2 final size:2
Alignment explanation
Indices: 931094--931120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
931084 AGGTAACATG
931094 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 T
931121 GTATGTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:941017 original size:3 final size:3
Alignment explanation
Indices: 941009--941046 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
940999 TATGGTCAAT
941009 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
941047 GTAGTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:942034 original size:3 final size:3
Alignment explanation
Indices: 942028--942063 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
942018 AATGATGATG
942028 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
942064 TCAAAAACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:946001 original size:13 final size:14
Alignment explanation
Indices: 945985--946034 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
945975 CACCAACTTA
945985 AAACCCT-AACTCT
1 AAACCCTAAACTCT
945998 AAACCCTAAAC-CTT
1 AAACCCTAAACTC-T
*
946012 AAACCTTAAACTCT
1 AAACCCTAAACTCT
*
946026 AAACACTAA
1 AAACCCTAA
946035 CTCAGAGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.26
14 22 0.71
15 1 0.03
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCCTAAACTCT
Found at i:947020 original size:21 final size:21
Alignment explanation
Indices: 946994--947046 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
946984 CACTTAGGGA
**
946994 ACCGATTCCCCATTAGGGGGT
1 ACCGATTCCCCACGAGGGGGT
947015 ACCGATTCCTCCCACGAGGGGGT
1 ACCGATT-C-CCCACGAGGGGGT
*
947038 ACCAATTCC
1 ACCGATTCC
947047 TCCCACGCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 2 0.07
23 17 0.63
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.21
Consensus pattern (21 bp):
ACCGATTCCCCACGAGGGGGT
Found at i:947034 original size:23 final size:23
Alignment explanation
Indices: 947008--947053 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
946998 ATTCCCCATT
*
947008 AGGGGGTACCGATTCCTCCCACG
1 AGGGGGTACCAATTCCTCCCACG
947031 AGGGGGTACCAATTCCTCCCACG
1 AGGGGGTACCAATTCCTCCCACG
947054 CTCCAAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (23 bp):
AGGGGGTACCAATTCCTCCCACG
Found at i:956531 original size:23 final size:23
Alignment explanation
Indices: 956501--956547 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
956491 CTCCATGGGT
956501 AGCCTCCAGATGCAGGTGTAAAC
1 AGCCTCCAGATGCAGGTGTAAAC
956524 AGCCTCCAGATGCAGGTGTAAAC
1 AGCCTCCAGATGCAGGTGTAAAC
956547 A
1 A
956548 AGTTGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AGCCTCCAGATGCAGGTGTAAAC
Found at i:960866 original size:42 final size:41
Alignment explanation
Indices: 960815--960942 Score: 110
Period size: 42 Copynumber: 3.3 Consensus size: 41
960805 AGGAGGAGGT
*
960815 GGCGGTCCACCGCCAGGAACTCCAGGTGGTGCTGGAGGGCCA
1 GGCGCTCCACCGCCAGG-ACTCCAGGTGGTGCTGGAGGGCCA
* * * *
960857 GGCGCTCCACC-CCCGG----GAGGTGGCGGTGGA-GG--A
1 GGCGCTCCACCGCCAGGACTCCAGGTGGTGCTGGAGGGCCA
* *
960890 GGCACTCCGCCGCCAGGAGCTCCAGGTGGTGCTGGAGGGCCA
1 GGCGCTCCACCGCCAGGA-CTCCAGGTGGTGCTGGAGGGCCA
*
960932 GGAGCTCCACC
1 GGCGCTCCACC
960943 CTCGAGAGGT
Statistics
Matches: 63, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
33 10 0.16
34 4 0.06
35 2 0.03
36 11 0.17
39 11 0.17
40 2 0.03
41 4 0.06
42 19 0.30
ACGTcount: A:0.15, C:0.33, G:0.41, T:0.11
Consensus pattern (41 bp):
GGCGCTCCACCGCCAGGACTCCAGGTGGTGCTGGAGGGCCA
Found at i:960878 original size:36 final size:36
Alignment explanation
Indices: 960838--960954 Score: 87
Period size: 36 Copynumber: 3.2 Consensus size: 36
960828 CAGGAACTCC
960838 AGGTGGTGCTGGAGGGCCAGGCGCTCCACCCCCGGG
1 AGGTGGTGCTGGAGGGCCAGGCGCTCCACCCCCGGG
* * * * *
960874 AGGTGGCGGTGGA-GG--AGGCACTCCGCCGCCAGGAG
1 AGGTGGTGCTGGAGGGCCAGGCGCTCCACC-CCCGG-G
* * *
960909 CTCCAGGTGGTGCTGGAGGGCCAGGAGCTCCACCCTCGAG
1 ----AGGTGGTGCTGGAGGGCCAGGCGCTCCACCCCCGGG
960949 AGGTGG
1 AGGTGG
960955 AGGTGGCGCT
Statistics
Matches: 59, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
33 10 0.17
34 4 0.07
35 3 0.05
36 17 0.29
39 11 0.19
40 3 0.05
41 2 0.03
42 9 0.15
ACGTcount: A:0.15, C:0.29, G:0.44, T:0.12
Consensus pattern (36 bp):
AGGTGGTGCTGGAGGGCCAGGCGCTCCACCCCCGGG
Found at i:960998 original size:45 final size:47
Alignment explanation
Indices: 960948--961068 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 47
960938 CCACCCTCGA
*
960948 GAGGTGGAGGTGGCGCTCCGCCCCCGAGAGGTGACGGTGAAGGTGGAGGTG
1 GAGGTGGAGGTGGCGCTCCGCCCCCGAGAGGTGACAGTGAA----GAGGTG
* ** *
960999 GAGGTGGAGGTGGCACTCCGCTTCCGAGAGGTGGCAGTG--GAGGTG
1 GAGGTGGAGGTGGCGCTCCGCCCCCGAGAGGTGACAGTGAAGAGGTG
* *
961044 GAGGTGGAGGAGGCGCTCCACCCCC
1 GAGGTGGAGGTGGCGCTCCGCCCCC
961069 AGGAGATGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
45 26 0.43
51 34 0.57
ACGTcount: A:0.16, C:0.22, G:0.48, T:0.14
Consensus pattern (47 bp):
GAGGTGGAGGTGGCGCTCCGCCCCCGAGAGGTGACAGTGAAGAGGTG
Found at i:961008 original size:51 final size:51
Alignment explanation
Indices: 960948--961053 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
960938 CCACCCTCGA
* *
960948 GAGGTGGAGGTGGCGCTCCGCCCCCGAGAGGTGACGGTGAAGGTGGAGGTG
1 GAGGTGGAGGTGGCACTCCGCCCCCGAGAGGTGACAGTGAAGGTGGAGGTG
** * *
960999 GAGGTGGAGGTGGCACTCCGCTTCCGAGAGGTGGCAGTGGAGGTGGAGGTG
1 GAGGTGGAGGTGGCACTCCGCCCCCGAGAGGTGACAGTGAAGGTGGAGGTG
961050 GAGG
1 GAGG
961054 AGGCGCTCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.16, C:0.17, G:0.52, T:0.15
Consensus pattern (51 bp):
GAGGTGGAGGTGGCACTCCGCCCCCGAGAGGTGACAGTGAAGGTGGAGGTG
Found at i:961079 original size:45 final size:45
Alignment explanation
Indices: 960990--961089 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
960980 GACGGTGAAG
* * ** *
960990 GTGGAGGTGGAGGTGGAGGTGGCACTCCGCTTCCGAGAGGTGGCA
1 GTGGAGGTGGAGGTGGAGGAGGCACTCCACCCCCGAGAGATGGCA
*
961035 GTGGAGGTGGAGGTGGAGGAGGCGCTCCACCCCC-AGGAGATGGCA
1 GTGGAGGTGGAGGTGGAGGAGGCACTCCACCCCCGA-GAGATGGCA
*
961080 ATGGAGGTGG
1 GTGGAGGTGG
961090 TGGACGAGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (45 bp):
GTGGAGGTGGAGGTGGAGGAGGCACTCCACCCCCGAGAGATGGCA
Found at i:966548 original size:60 final size:60
Alignment explanation
Indices: 966453--966567 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
966443 ATACTTAAAC
* * * * * *
966453 TATGACCTCTATTTTAAATTGATTCTTAGACTTTAAGATATTATAAATCAGTCCTCATAT
1 TATGACCTATATTCTAAATTGATCCTTAAACTTTAAAATACTATAAATCAGTCCTCATAT
* * *
966513 TATGATCTATATTCTAAATTGATCCTTAAATTTTAAAATACTATATATCAGTCCT
1 TATGACCTATATTCTAAATTGATCCTTAAACTTTAAAATACTATAAATCAGTCCT
966568 TAAACTATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (60 bp):
TATGACCTATATTCTAAATTGATCCTTAAACTTTAAAATACTATAAATCAGTCCTCATAT
Found at i:970754 original size:2 final size:2
Alignment explanation
Indices: 970747--970782 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
970737 TTATAAAATA
970747 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
970783 CTCAAATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971111 original size:60 final size:60
Alignment explanation
Indices: 970973--971112 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 60
970963 ACTTTTAAAC
*
970973 ATTTTAATTTCATCCCTAAACTATGACTATCATTCTAAATTAATCCTCAAACCTTCAAAAT
1 ATTTTAATTTCATCCC-AAACTATGACTATCATTCTAAATTAATCCCCAAACCTTCAAAAT
* * ** * ***
971034 -TTTTATTTTCATCCCCAAACTATGATCT-TCATTCTACATTGGTCCCCAAACTTTTTGAAT
1 ATTTTAATTTCAT-CCCAAACTATGA-CTATCATTCTAAATTAATCCCCAAACCTTCAAAAT
*
971094 ATTTCAATTTCATCCCAAA
1 ATTTTAATTTCATCCCAAA
971113 TTATATGTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
60 50 0.77
61 15 0.23
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (60 bp):
ATTTTAATTTCATCCCAAACTATGACTATCATTCTAAATTAATCCCCAAACCTTCAAAAT
Found at i:971400 original size:60 final size:58
Alignment explanation
Indices: 971232--971404 Score: 145
Period size: 60 Copynumber: 2.9 Consensus size: 58
971222 TTGAATAAAT
* * * *
971232 TTAGGGATGAAATTGAAAGATTCAAAAGTTTAGGGACTAATTTAAAATGA-AGATCATAG
1 TTAGGGATGAAATT-AAATATTTAAAAGTTTAAGGACAAATTTAAAATGAGAG-TCATAG
* * * * * *
971291 TTTGGGGAT-AAATTGGAATGTTTCAAAGTTTAAGGA-AAATTTTAGAATGAGAGTCATGG
1 -TTAGGGATGAAATT-AAATATTTAAAAGTTTAAGGACAAA-TTTAAAATGAGAGTCATAG
* * *
971350 TTAGAGGATGAAATTATAATATTTAAAAGTTTAATGACCAATTTGAAATGAGAGT
1 TTAG-GGATGAAATTA-AATATTTAAAAGTTTAAGGACAAATTTAAAATGAGAGT
971405 TGTAATTTGA
Statistics
Matches: 89, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
58 5 0.06
59 39 0.44
60 43 0.48
61 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
TTAGGGATGAAATTAAATATTTAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATAG
Found at i:993979 original size:30 final size:30
Alignment explanation
Indices: 993952--994012 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
993942 TTTCAGAAGA
*
993952 AGCTAACAAAACAGAGACAACCCCAGAAAC
1 AGCTAACAAAACAGAGACAACCACAGAAAC
* *
993982 AGCTAACGAAACAGAGGCAACCACAGAAAC
1 AGCTAACAAAACAGAGACAACCACAGAAAC
994012 A
1 A
994013 TCAAAGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.28, G:0.16, T:0.03
Consensus pattern (30 bp):
AGCTAACAAAACAGAGACAACCACAGAAAC
Found at i:998895 original size:16 final size:16
Alignment explanation
Indices: 998876--998909 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
998866 AAGCAATGCC
998876 AAAGAGAAGATACTGA
1 AAAGAGAAGATACTGA
998892 AAAGAGAAGATACTGA
1 AAAGAGAAGATACTGA
998908 AA
1 AA
998910 CTGAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAGAGAAGATACTGA
Found at i:999990 original size:20 final size:20
Alignment explanation
Indices: 999951--999990 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
999941 ATCAATCCAT
* *
999951 TTGACCAAATGATCGTTCCC
1 TTGACCAAAGGATCGATCCC
*
999971 TTGACCAAAGGATTGATCCC
1 TTGACCAAAGGATCGATCCC
999991 CTCGAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
TTGACCAAAGGATCGATCCC
Found at i:1000158 original size:21 final size:21
Alignment explanation
Indices: 1000068--1000165 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 21
1000058 AATCCATCGA
**
1000068 GAAAAATGATCGATCCCTTCC
1 GAAAAATGATCGATCCCTTTG
* *
1000089 GAAAAAGGATTGATCCCTTTG
1 GAAAAATGATCGATCCCTTTG
* * * * ****
1000110 GTATAACGGTCGAAATATTT-
1 GAAAAATGATCGATCCCTTTG
1000130 GAAAAATGATCGATCCCTTTG
1 GAAAAATGATCGATCCCTTTG
*
1000151 GTAAAATGATCGATC
1 GAAAAATGATCGATC
1000166 TATTATGCCT
Statistics
Matches: 54, Mismatches: 22, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
20 12 0.22
21 42 0.78
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (21 bp):
GAAAAATGATCGATCCCTTTG
Found at i:1000949 original size:21 final size:21
Alignment explanation
Indices: 1000907--1000949 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1000897 TTTCTGGGCT
*
1000907 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1000928 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1000949 A
1 A
1000950 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1001002 original size:20 final size:20
Alignment explanation
Indices: 1000977--1001014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1000967 GAACGCTAGA
*
1000977 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1000997 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1001015 TAATAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1001668 original size:103 final size:103
Alignment explanation
Indices: 1001484--1001701 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
1001474 GTAGAGGGTC
* * * *
1001484 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
1001549 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
1001587 TATGTGGTCCTTCGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1001652 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
1001690 TATGTGGTCCTT
1 TATGTGGTCCTT
1001702 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1001751 original size:23 final size:23
Alignment explanation
Indices: 1001718--1001785 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1001708 ATTATTATAT
1001718 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
1001741 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTACGGTGCAATTCTACGC
*
1001764 GGCACTTA-GGTGCAATTATACG
1 GGCAC-TACGGTGCAATTCTACG
1001786 AGCTGTGATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1021024 original size:20 final size:19
Alignment explanation
Indices: 1020971--1021024 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1020961 ACAATATTGA
*
1020971 TATAATTTTTTATTATAAC
1 TATAATTTTTTAATATAAC
** *
1020990 TATATATTTCATAATATCAC
1 TATA-ATTTTTTAATATAAC
1021010 TATTAATTTTTTAAT
1 TA-TAATTTTTTAAT
1021025 GATTCATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATTTTTTAATATAAC
Found at i:1027132 original size:2 final size:2
Alignment explanation
Indices: 1027127--1027165 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1027117 CTATTACAAG
* * *
1027127 TA TA TA CA TA GA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1027166 TAAAATATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1029423 original size:105 final size:105
Alignment explanation
Indices: 1029036--1029879 Score: 1474
Period size: 105 Copynumber: 8.0 Consensus size: 105
1029026 GTTGTGAAGT
* * *
1029036 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1029101 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
1029142 TGAAATTGAGAAGTTGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1029207 CTGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1029248 TGAAATGGAG-AATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1029312 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1029352 TGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1029417 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTG-AAATTGGCTC
* *
1029458 TGAGATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1029523 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1029563 TGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1029628 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1029668 TGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
1029733 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1029773 TGACATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
1029838 TGGAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1029878 TG
1 TG
1029880 GGTAAAACCT
Statistics
Matches: 701, Mismatches: 34, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
104 97 0.14
105 397 0.57
106 207 0.30
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:1029753 original size:421 final size:415
Alignment explanation
Indices: 1028981--1029886 Score: 1497
Period size: 421 Copynumber: 2.2 Consensus size: 415
1028971 AGTGACATCC
*
1028981 TCGTCGTGAAGTTGAACTGGTAC--TGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAA---
1 TCGTCGTGAAGTTGAACT--TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* *
1029041 --T-TGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
64 GCTCTGGGAAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
1029103 GGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
129 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAGATGTTTGGTGACA
* *
1029168 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTTGTTGTGA
194 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
1029233 AGTTGAAATTGGCTCTGAAATGGAGAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
259 AGTTGAAATTGGCTCTGAAATGGAGAATGTTCGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
1029298 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
324 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGAGA
1029363 AATGTTCGTTGACAACCAGCGGTCCCT
389 AATGTTCGTTGACAACCAGCGGTCCCT
1029390 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAATTGG
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG-AAATTGG
1029455 CTCTGAGATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
65 CTCTG-G---GA-AAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1029520 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAA-ATGTTTGGT
125 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAGATGTTTGGT
*
1029584 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
190 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTT
* *
1029649 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTG
255 GTGAAGTTGAAATTGGCTCTGAAATGGAG-AATGTTCGGTGACAACCAGCGGTCCCTTCGTCGTG
*
1029714 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGACAT
319 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAAT
*
1029779 TGAGAAATGTTTGTTGACAACCAGCGGTCCCT
384 TGAGAAATGTTCGTTGACAACCAGCGGTCCCT
* *
1029811 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGC
1 TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1029876 TCTGGGTAAAA
66 TCTGGG-AAAA
1029887 CCTGCAAAGA
Statistics
Matches: 463, Mismatches: 18, Indels: 25
0.92 0.04 0.05
Matches are distributed among these distances:
407 3 0.01
409 51 0.11
410 3 0.01
415 1 0.00
416 6 0.01
417 2 0.00
419 1 0.00
420 111 0.24
421 285 0.62
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (415 bp):
TCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC
TCTGGGAAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAGATGTTTGGTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATGGAGAATGTTCGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGAGAAA
TGTTCGTTGACAACCAGCGGTCCCT
Found at i:1041831 original size:62 final size:63
Alignment explanation
Indices: 1041707--1041831 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
1041697 AAGGGAATTA
*
1041707 AACCGATTTGGGGACCAAATTAAACGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * * * *
1041770 AACCGGTTTGGGGACCAAATTGAATGTTTTTCAGAACATAGGGAGCC-AAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1041832 CTTTTAACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 15 0.27
63 41 0.73
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:1046956 original size:12 final size:12
Alignment explanation
Indices: 1046939--1046963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1046929 AAAATCAAAA
1046939 AGAATTATTGTT
1 AGAATTATTGTT
1046951 AGAATTATTGTT
1 AGAATTATTGTT
1046963 A
1 A
1046964 TTCTTGAGAA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
AGAATTATTGTT
Found at i:1047144 original size:2 final size:2
Alignment explanation
Indices: 1047139--1047178 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1047129 ACACACACAC
1047139 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
1047179 TTATTTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1047509 original size:18 final size:16
Alignment explanation
Indices: 1047472--1047518 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1047462 TCACATTCAA
*
1047472 ATTTTATTTAAAAATT
1 ATTTTATTTAAAAAAT
*
1047488 ATTTTA---AAATAAT
1 ATTTTATTTAAAAAAT
1047501 ATTTTATTTAAAAAAT
1 ATTTTATTTAAAAAAT
1047517 AT
1 AT
1047519 ATACGTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTATTTAAAAAAT
Found at i:1052318 original size:5 final size:5
Alignment explanation
Indices: 1052304--1052339 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1052294 ACAAATTCAA
* *
1052304 AAAAG AAAGG AAAGG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1052340 GACGACGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1076065 original size:25 final size:26
Alignment explanation
Indices: 1076000--1076065 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
1075990 TGATCGATCC
*
1076000 TAAATAATACAAAAATTAACTCGACGA
1 TAAATAATATAAAAATTAACTCGAC-A
* * *
1076027 CATAATAATTTAAAAATTGACTCGA-A
1 TA-AATAATATAAAAATTAACTCGACA
1076053 TAAATAATATAAA
1 TAAATAATATAAA
1076066 TGGGGAGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 10 0.31
26 2 0.06
27 1 0.03
28 19 0.59
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (26 bp):
TAAATAATATAAAAATTAACTCGACA
Found at i:1079987 original size:22 final size:23
Alignment explanation
Indices: 1079959--1080003 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1079949 TGTTAGTTGT
1079959 CGAACAT-TAAATAAATGTTAAA
1 CGAACATATAAATAAATGTTAAA
**
1079981 CGAACATATTTATAAATGTTAAA
1 CGAACATATAAATAAATGTTAAA
1080004 AGAAAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (23 bp):
CGAACATATAAATAAATGTTAAA
Found at i:1081578 original size:21 final size:21
Alignment explanation
Indices: 1081554--1081614 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1081544 AACTTTGAAA
1081554 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1081575 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1081589 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1081610 AAATG
1 AAATG
1081615 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1081660 original size:36 final size:36
Alignment explanation
Indices: 1081546--1081665 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
1081536 TGGTAACCAA
1081546 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1081583 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1081618 CTTTGAAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1081655 -GTTGAAAAATG
1 CTTTGAAAAATG
1081666 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1082105 original size:16 final size:16
Alignment explanation
Indices: 1082072--1082105 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1082062 TTACTATTCA
**
1082072 CGTGAATAGTGAGTTT
1 CGTGAATAGTGAAATT
1082088 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1082104 CG
1 CG
1082106 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1084149 original size:21 final size:20
Alignment explanation
Indices: 1084125--1084188 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1084115 AACTTTGAAA
1084125 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1084146 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1084160 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1084181 AAATGTTT
1 AAATGTTT
1084189 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1084163 original size:35 final size:36
Alignment explanation
Indices: 1084117--1084238 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
1084107 TGGTAACCAA
1084117 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1084154 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1084189 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
1084226 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
1084239 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1090922 original size:2 final size:2
Alignment explanation
Indices: 1090915--1090942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1090905 TAATTTCTTC
1090915 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1090943 CTTGGAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1095127 original size:31 final size:31
Alignment explanation
Indices: 1095073--1095132 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1095063 AAAATTAAAG
* * * * *
1095073 TTTAGATATTAAAATATATCAAAATTGATAA
1 TTTAAATATTAAAACAAACCAAAAATGATAA
1095104 TTTAAATATTAAAACAAACCAAAAATGAT
1 TTTAAATATTAAAACAAACCAAAAATGAT
1095133 GGTTTAGGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (31 bp):
TTTAAATATTAAAACAAACCAAAAATGATAA
Found at i:1099004 original size:17 final size:17
Alignment explanation
Indices: 1098975--1099007 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1098965 GTATTTATTC
1098975 ATATAAAATATAATATA
1 ATATAAAATATAATATA
1098992 ATATGAAAA-ATAATAT
1 ATAT-AAAATATAATAT
1099008 TGTAATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:1099197 original size:32 final size:32
Alignment explanation
Indices: 1099125--1099187 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1099115 TTCCACCTCA
* *
1099125 TAAAATTATAAAATAATTAATATACTAAATAT
1 TAAAAATATAAAATAATTAATACACTAAATAT
1099157 TAAAAATATAAAATAATTTAACTACAC-AAAT
1 TAAAAATATAAAATAA-TTAA-TACACTAAAT
1099188 TTATCAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 15 0.56
33 8 0.30
34 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (32 bp):
TAAAAATATAAAATAATTAATACACTAAATAT
Found at i:1101142 original size:31 final size:31
Alignment explanation
Indices: 1101107--1101176 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1101097 TAAATTTCAC
* *
1101107 ATAAAATAATAATTCGA-TCTTTATATTTTAG
1 ATAAAATAATAAGTCGATTC-TTAGATTTTAG
* * *
1101138 ATAAAATATTAAGTCTATTCTTAGATTTTCG
1 ATAAAATAATAAGTCGATTCTTAGATTTTAG
1101169 ATAAAATA
1 ATAAAATA
1101177 CTGATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
ATAAAATAATAAGTCGATTCTTAGATTTTAG
Found at i:1102430 original size:22 final size:21
Alignment explanation
Indices: 1102405--1102460 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1102395 TCTCTATTTT
*
1102405 TTTAAATTATTTCATCTTAATA
1 TTTAAATAATTT-ATCTTAATA
* *
1102427 TTTAAATAATTTATTTTAATC
1 TTTAAATAATTTATCTTAATA
* *
1102448 TTAAAATATTTTA
1 TTTAAATAATTTA
1102461 AATTTAGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATAATTTATCTTAATA
Found at i:1102605 original size:16 final size:16
Alignment explanation
Indices: 1102586--1102620 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1102576 AAATTTTATG
*
1102586 TTTTTTCTATGTGGAT
1 TTTTTTCTATGTGAAT
1102602 TTTTTTCTATGTGAAT
1 TTTTTTCTATGTGAAT
1102618 TTT
1 TTT
1102621 ACGAACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.66
Consensus pattern (16 bp):
TTTTTTCTATGTGAAT
Found at i:1105998 original size:49 final size:47
Alignment explanation
Indices: 1105941--1106032 Score: 130
Period size: 49 Copynumber: 1.9 Consensus size: 47
1105931 CCATGGCTGA
1105941 CAAAATTCTGGGTTCAAAAAGTCCTACATAAGGCTATAACAATGATTGG
1 CAAAATTCTGGGTTCAAAAAGTCCT--ATAAGGCTATAACAATGATTGG
* * * *
1105990 CAAAATTCTGGTTTCAAGAAGTCCTATGAGGCTGTAACAATGA
1 CAAAATTCTGGGTTCAAAAAGTCCTATAAGGCTATAACAATGA
1106033 AGAAAAAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 16 0.41
49 23 0.59
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (47 bp):
CAAAATTCTGGGTTCAAAAAGTCCTATAAGGCTATAACAATGATTGG
Found at i:1109516 original size:29 final size:29
Alignment explanation
Indices: 1109474--1109534 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1109464 ATAGGACGCT
***
1109474 ATGCAATCCAGGCGACCTTGGAGGTCGCC
1 ATGCAATCCAGGCGACCTCCAAGGTCGCC
*
1109503 ATGCAATCCGGGCGACCTCCAAGGTCGCC
1 ATGCAATCCAGGCGACCTCCAAGGTCGCC
1109532 ATG
1 ATG
1109535 GCATTCGGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.16
Consensus pattern (29 bp):
ATGCAATCCAGGCGACCTCCAAGGTCGCC
Found at i:1109638 original size:25 final size:25
Alignment explanation
Indices: 1109610--1109683 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
1109600 CATGGGGGAG
1109610 GGGATGCATGCTGTGCATGGGACGT
1 GGGATGCATGCTGTGCATGGGACGT
* *
1109635 GGGA---A--CTGTGCAT-GGCCAT
1 GGGATGCATGCTGTGCATGGGACGT
*
1109654 GCAGATGCATGCTGTGCATGGGACGT
1 G-GGATGCATGCTGTGCATGGGACGT
1109680 GGGA
1 GGGA
1109684 ACTGTGCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 5 0.14
20 10 0.28
22 1 0.03
23 1 0.03
25 14 0.39
26 5 0.14
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.22
Consensus pattern (25 bp):
GGGATGCATGCTGTGCATGGGACGT
Found at i:1109645 original size:20 final size:20
Alignment explanation
Indices: 1109620--1109694 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1109610 GGGATGCATG
1109620 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
* * *
1109640 CTGTGCATGGCCATGCAGAT-GCATG
1 CTGTGCATGG-GA--C-G-TGGGA-A
1109665 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
1109685 CTGTGCATGG
1 CTGTGCATGG
1109695 CCATGCACGT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 21 0.50
21 4 0.10
22 1 0.02
23 1 0.02
24 4 0.10
25 11 0.26
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.23
Consensus pattern (20 bp):
CTGTGCATGGGACGTGGGAA
Found at i:1109662 original size:45 final size:45
Alignment explanation
Indices: 1109612--1109701 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1109602 TGGGGGAGGG
1109612 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1109657 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1109702 CGTCGAACGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (45 bp):
GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
Found at i:1110210 original size:21 final size:21
Alignment explanation
Indices: 1110185--1110228 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1110175 AATCTAGTTA
1110185 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1110206 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1110227 AT
1 AT
1110229 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1110238 original size:28 final size:30
Alignment explanation
Indices: 1110205--1110267 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1110195 TAGTATAAAT
*
1110205 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1110233 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1110263 TATTA
1 TATTA
1110268 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:1110810 original size:20 final size:21
Alignment explanation
Indices: 1110766--1110810 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1110756 AAATATTGTG
**
1110766 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
1110787 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
1110807 TTTA
1 TTTA
1110811 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:1111100 original size:26 final size:25
Alignment explanation
Indices: 1111071--1111129 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1111061 AAATCATATT
*
1111071 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1111097 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1111123 ATTATTA
1 ATTATTA
1111130 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1114041 original size:26 final size:26
Alignment explanation
Indices: 1114015--1114242 Score: 183
Period size: 26 Copynumber: 9.2 Consensus size: 26
1114005 GATGATTTAG
*
1114015 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1114041 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1114067 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1114093 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * *
1114116 TATTTA-ATGAT-TTGATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
1114139 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
1114165 TAATGATTTTATAATAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
1114190 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1114214 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
1114239 TAAT
1 TAAT
1114243 TATTACTAAT
Statistics
Matches: 163, Mismatches: 26, Indels: 27
0.75 0.12 0.12
Matches are distributed among these distances:
21 4 0.02
22 3 0.02
23 15 0.09
24 22 0.13
25 30 0.18
26 88 0.54
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:1114122 original size:19 final size:20
Alignment explanation
Indices: 1114093--1114147 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 20
1114083 ATCATTATAA
1114093 AAATGATTTAATAATGATTT
1 AAATGATTTAATAATGATTT
1114113 AAAT-A-TT--TAATGATTT
1 AAATGATTTAATAATGATTT
*
1114129 -GATGATTTAATAATGATTT
1 AAATGATTTAATAATGATTT
1114148 GATAATAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 2 0.07
18 2 0.07
19 10 0.33
20 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (20 bp):
AAATGATTTAATAATGATTT
Found at i:1114148 original size:19 final size:19
Alignment explanation
Indices: 1114095--1114150 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1114085 CATTATAAAA
1114095 ATGATTTAATAATGATTT-
1 ATGATTTAATAATGATTTG
*
1114113 A-AATATT--TAATGATTTG
1 ATGAT-TTAATAATGATTTG
1114130 ATGATTTAATAATGATTTG
1 ATGATTTAATAATGATTTG
1114149 AT
1 AT
1114151 AATAATCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (19 bp):
ATGATTTAATAATGATTTG
Found at i:1114179 original size:124 final size:123
Alignment explanation
Indices: 1113957--1114226 Score: 436
Period size: 124 Copynumber: 2.2 Consensus size: 123
1113947 ATGTATTTAT
*
1113957 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAATAATGAT
*
1114022 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATT-TAATAATGATTTAGTAA
1114081 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAATAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAATAATGAT
* * * * *
1114146 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
* *
1114204 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
1114227 CTAATGATTT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 102 0.74
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (123 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAATAATGAT
TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
Found at i:1114211 original size:35 final size:37
Alignment explanation
Indices: 1114172--1114264 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 37
1114162 TAATAATGAT
* * *
1114172 TTTATAATAATTATTTAGT-T-ATTATTTAGTAATTA
1 TTTATAATAATTATTTAATATAATGATTTAATAATTA
*
1114207 TTTATAATAATGATTTAATACTAATGATTTAATAATTA
1 TTTATAATAATTATTTAATA-TAATGATTTAATAATTA
*
1114245 -TTACTAATAATTATATAATA
1 TTTA-TAATAATTATTTAATA
1114265 CTAACAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
35 17 0.35
37 4 0.08
38 27 0.56
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (37 bp):
TTTATAATAATTATTTAATATAATGATTTAATAATTA
Found at i:1114218 original size:49 final size:48
Alignment explanation
Indices: 1114015--1114264 Score: 138
Period size: 49 Copynumber: 5.0 Consensus size: 48
1114005 GATGATTTAG
* * * *
1114015 TAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAA
1 TAATGATTTAATAATAATGATT-TAATAATTA-TT-ACTAATAAT--TTATAA
* * * *
1114067 TAATGATTTAGTAATAATCATTATAAAAATGATT--TAATAATGATT-T-A
1 TAATGATTTAATAATAATGATT-TAATAATTATTACTAATAAT--TTATAA
* * *
1114114 -AAT-ATTTAATGATTTGATGATTTAATAATGATTTGA-TAATAATCATTATAA
1 TAATGATTTAAT-A-ATAATGATTTAATAATTA-TT-ACTAATAAT--TTATAA
* * * * * *
1114165 TAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
1 TAATGATTTAATAATAATGATTTAATAATTA-TTACTAATAATTTATAA
*
1114214 TAATGATTTAATACTAATGATTTAATAATTATTACTAATAATTATATAA
1 TAATGATTTAATAATAATGATTTAATAATTATTACTAATAATT-TATAA
1114263 TA
1 TA
1114265 CTAACAAATG
Statistics
Matches: 161, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
45 6 0.04
46 12 0.07
47 9 0.06
48 11 0.07
49 59 0.37
50 2 0.01
51 24 0.15
52 32 0.20
53 6 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (48 bp):
TAATGATTTAATAATAATGATTTAATAATTATTACTAATAATTTATAA
Found at i:1114233 original size:14 final size:14
Alignment explanation
Indices: 1114015--1114242 Score: 114
Period size: 14 Copynumber: 17.1 Consensus size: 14
1114005 GATGATTTAG
*
1114015 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
1114029 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
1114041 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1114055 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1114067 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
1114081 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1114093 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
1114104 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
1114120 TAATGATTTGATGATTTAA
1 TAATGATTT-A--A--TAA
*
1114139 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1114153 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1114165 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
1114179 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
1114191 T-ATTATTTAGTAA
1 TAATGATTTAATAA
1114204 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
1114214 TAATGATTTAATAC
1 TAATGATTTAATAA
1114228 TAATGATTTAATAA
1 TAATGATTTAATAA
1114242 T
1 T
1114243 TATTACTAAT
Statistics
Matches: 169, Mismatches: 24, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
10 4 0.02
11 22 0.13
12 40 0.24
13 19 0.11
14 59 0.35
15 2 0.01
16 11 0.07
18 1 0.01
19 9 0.05
20 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:1114384 original size:17 final size:17
Alignment explanation
Indices: 1114359--1114391 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1114349 ACTAAATATT
*
1114359 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1114376 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1114392 AAAATCATTG
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:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1115548 original size:14 final size:14
Alignment explanation
Indices: 1115515--1115548 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1115505 TTTTAATCAA
*
1115515 AATAAATATTTTTT
1 AATAAATATTTTAT
1115529 AATAAATATTTTAT
1 AATAAATATTTTAT
*
1115543 ATTAAA
1 AATAAA
1115549 ATAGAGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATAAATATTTTAT
Found at i:1116565 original size:15 final size:14
Alignment explanation
Indices: 1116542--1116572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1116532 TACAACACTA
1116542 AACTTTAATATAAT
1 AACTTTAATATAAT
1116556 AACTTATAATATAAT
1 AACTT-TAATATAAT
1116571 AA
1 AA
1116573 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1116580 original size:16 final size:16
Alignment explanation
Indices: 1116547--1116593 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1116537 CACTAAACTT
*
1116547 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1116562 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1116578 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1116594 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1116714 original size:32 final size:34
Alignment explanation
Indices: 1116634--1116715 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
1116624 CTAAACCCTT
*
1116634 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
1116667 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
1116700 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
1116716 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:1116833 original size:46 final size:48
Alignment explanation
Indices: 1116756--1116847 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
1116746 CAACAAACAA
*
1116756 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATT-AATAATTTTTTTT
*
1116805 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTT
1116848 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 10 0.24
46 13 0.32
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTTTT
Found at i:1116858 original size:47 final size:48
Alignment explanation
Indices: 1116756--1116860 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 48
1116746 CAACAAACAA
* *
1116756 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
*
1116805 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT--CT
1116852 ATATAACTA
1 ATATAACTA
1116861 TCAAACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 10 0.20
46 13 0.25
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
Found at i:1116916 original size:41 final size:40
Alignment explanation
Indices: 1116828--1116916 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1116818 TTAACAAAAC
* *
1116828 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1116869 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
1116910 AAACTAA
1 AAACTAA
1116917 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:1117081 original size:21 final size:21
Alignment explanation
Indices: 1117051--1117103 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1117041 CCCTTTCTTC
*
1117051 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1117072 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1117093 TTCTTTCTTTC
1 TTCTTTCTTTC
1117104 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:1117094 original size:17 final size:16
Alignment explanation
Indices: 1117074--1117105 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1117064 TTCTCCCTTT
1117074 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1117091 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1117106 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1117138 original size:23 final size:23
Alignment explanation
Indices: 1117108--1117153 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1117098 TCTTTCTCGG
1117108 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1117131 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1117154 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:1117300 original size:27 final size:27
Alignment explanation
Indices: 1117265--1117317 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1117255 GTACCAATAA
1117265 TCAAATGGTTCACATGCATGCATTGGC
1 TCAAATGGTTCACATGCATGCATTGGC
1117292 TCAAATGGTTCACATGCATGCATTGG
1 TCAAATGGTTCACATGCATGCATTGG
1117318 GAGCTGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (27 bp):
TCAAATGGTTCACATGCATGCATTGGC
Found at i:1117427 original size:29 final size:29
Alignment explanation
Indices: 1117395--1117529 Score: 236
Period size: 29 Copynumber: 4.7 Consensus size: 29
1117385 GGAATGACGT
1117395 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
1117424 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
1117453 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
1117482 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
* *
1117511 CTAGG-CTGCATGGCGACCT
1 C-GGGACTACATGGCGACCT
1117530 CTCTATTCAT
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 101 0.98
30 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (29 bp):
CGGGACTACATGGCGACCTACAAGGTCGC
Found at i:1117613 original size:70 final size:70
Alignment explanation
Indices: 1117528--1117670 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 70
1117518 GCATGGCGAC
1117528 CTCTCTATTCATGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGTTGCATGCTCCCC
1 CTCTCTATTCATGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGTTGCATGCTCCCC
1117593 ATTGG
66 ATTGG
* *
1117598 CTCTCTATTCCTGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGTTGCATGCTCCTC
1 CTCTCTATTCATGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGTTGCATGCTCCCC
1117663 ATTGG
66 ATTGG
1117668 CTC
1 CTC
1117671 GTATGGCTCG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.12, C:0.32, G:0.21, T:0.35
Consensus pattern (70 bp):
CTCTCTATTCATGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGTTGCATGCTCCCC
ATTGG
Found at i:1117644 original size:11 final size:11
Alignment explanation
Indices: 1117630--1117694 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
1117620 CATTGGCTCG
1117630 TATGGCTCGTA
1 TATGGCTCGTA
1117641 TATGGCTCGT-
1 TATGGCTCGTA
*
1117651 TGCAT-GCTCCTCA
1 T--ATGGCTCGT-A
1117664 T-TGGCTCG--
1 TATGGCTCGTA
1117672 TATGGCTCGTA
1 TATGGCTCGTA
*
1117683 TATAGCTCGTA
1 TATGGCTCGTA
1117694 T
1 T
1117695 GTCACCCTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
8 1 0.02
9 7 0.16
10 2 0.05
11 30 0.70
12 2 0.05
13 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (11 bp):
TATGGCTCGTA
Found at i:1117668 original size:42 final size:42
Alignment explanation
Indices: 1117609--1117692 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1117599 TCTCTATTCC
*
1117609 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATAGCTCGT
*
1117651 TGCATGCTCCTCATTGGCTCGTATGGCTCGTATATAGCTCGT
1 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATAGCTCGT
1117693 ATGTCACCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.35
Consensus pattern (42 bp):
TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATAGCTCGT
Found at i:1117706 original size:13 final size:13
Alignment explanation
Indices: 1117688--1117722 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1117678 TCGTATATAG
1117688 CTCGTATGTCACC
1 CTCGTATGTCACC
*
1117701 CTCGTATGACACC
1 CTCGTATGTCACC
1117714 C-CGTATGTC
1 CTCGTATGTC
1117723 GCCTGGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.17, C:0.37, G:0.17, T:0.29
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:1118274 original size:3 final size:3
Alignment explanation
Indices: 1118266--1118292 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1118256 TATTTAAATC
1118266 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1118293 AAAACAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1120506 original size:14 final size:14
Alignment explanation
Indices: 1120456--1120511 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1120446 CGTTCGTAAA
1120456 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
1120470 CATTCGGTTATG-T
1 CGTTCGGTTATGTT
*
1120483 -G--CGTTTATGTT
1 CGTTCGGTTATGTT
1120494 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1120508 CGTT
1 CGTT
1120512 TATGTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.21
11 1 0.03
12 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1120528 original size:24 final size:24
Alignment explanation
Indices: 1120457--1120531 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
1120447 GTTCGTAAAC
*
1120457 GTTCGGTTATGTTCATTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
* *
1120481 GTGCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
**
1120505 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
1120529 GTT
1 GTT
1120532 TAACCCAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGGTTAT
Found at i:1121640 original size:16 final size:16
Alignment explanation
Indices: 1121616--1121671 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
1121606 ACGTTTATGG
1121616 TCGTTTATGTTCGTGT
1 TCGTTTATGTTCGTGT
* *
1121632 TCATTTATGTTCATGT
1 TCGTTTATGTTCGTGT
*
1121648 TCGTTTATGTTCGAGT
1 TCGTTTATGTTCGTGT
1121664 TCGTTTAT
1 TCGTTTAT
1121672 TTATTAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (16 bp):
TCGTTTATGTTCGTGT
Found at i:1121757 original size:16 final size:16
Alignment explanation
Indices: 1121736--1121766 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1121726 AAAAAAATTA
1121736 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
1121752 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
1121767 TTATTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:1129777 original size:14 final size:13
Alignment explanation
Indices: 1129758--1129831 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
1129748 TTTAGATTTT
1129758 TTAAAATTATATTA
1 TTAAAA-TATATTA
1129772 TTAAAACTATATTA
1 TTAAAA-TATATTA
*
1129786 --AAAATAAATTA
1 TTAAAATATATTA
*
1129797 TTAATAATTATAAATTT
1 TTAA-AA-TAT--ATTA
*
1129814 TTAAAATATATTT
1 TTAAAATATATTA
1129827 TTAAA
1 TTAAA
1129832 TGTAATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.12
12 4 0.08
13 11 0.22
14 15 0.30
15 5 0.10
16 2 0.04
17 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAATATATTA
Found at i:1130224 original size:15 final size:13
Alignment explanation
Indices: 1130206--1130261 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 13
1130196 TATCTTTTAA
1130206 TTTTTTATTAAAG
1 TTTTTTATTAAAG
*
1130219 TTTTTTATTAAGTTATT
1 TTTTTTATTAA---A-G
1130236 TTTTATTATTAAAG
1 TTTT-TTATTAAAG
1130250 TTTTTTATTAAA
1 TTTTTTATTAAA
1130262 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 19 0.53
14 4 0.11
15 1 0.03
16 1 0.03
17 4 0.11
18 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (13 bp):
TTTTTTATTAAAG
Found at i:1130248 original size:31 final size:31
Alignment explanation
Indices: 1130206--1130273 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1130196 TATCTTTTAA
**
1130206 TTTT-TTATTAAAGTTTTTTATTAAGTTATT
1 TTTTATTATTAAAGTTTTTTATTAAAATATT
1130236 TTTTATTATTAAAGTTTTTTATTAAAATATT
1 TTTTATTATTAAAGTTTTTTATTAAAATATT
1130267 TTTTATT
1 TTTTATT
1130274 TATTTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.66
Consensus pattern (31 bp):
TTTTATTATTAAAGTTTTTTATTAAAATATT
Found at i:1130269 original size:16 final size:15
Alignment explanation
Indices: 1130205--1130273 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
1130195 TTATCTTTTA
1130205 ATTTTTTATT-AAA-
1 ATTTTTTATTAAAAT
* **
1130218 GTTTTTTATTAAGTT
1 ATTTTTTATTAAAAT
1130233 ATTTTTTATTATTAAA-
1 ATTTTTTATTA--AAAT
*
1130249 GTTTTTTATTAAAAT
1 ATTTTTTATTAAAAT
1130264 ATTTTTTATT
1 ATTTTTTATT
1130274 TATTTTTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
13 9 0.21
14 4 0.09
15 19 0.44
16 10 0.23
17 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
ATTTTTTATTAAAAT
Found at i:1130281 original size:28 final size:28
Alignment explanation
Indices: 1130205--1130281 Score: 66
Period size: 31 Copynumber: 2.6 Consensus size: 28
1130195 TTATCTTTTA
* ** **
1130205 ATTTTTTATTAAAGTTTTTTATTAAGTT
1 ATTTTTTATTTATTTTTTTTATTAAAAT
1130233 ATTTTTTA-TTATTAAAGTTTTTTATTAAAAT
1 ATTTTTTATTTATT----TTTTTTATTAAAAT
1130264 ATTTTTTATTTATTTTTT
1 ATTTTTTATTTATTTTTT
1130282 CAACATGGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
27 2 0.05
28 12 0.31
31 20 0.51
32 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (28 bp):
ATTTTTTATTTATTTTTTTTATTAAAAT
Found at i:1130769 original size:33 final size:33
Alignment explanation
Indices: 1130700--1130791 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
1130690 TGATTTAAAA
*
1130700 TAATAGGTAGTGAGTTTTTTAGTGAGATTTTATT
1 TAATAGGTAGTGAGTTTTTTAGTG-GATATTATT
* * *
1130734 TAATGGGTAGTGA-ATTTTTAGTGGATAATTGTT
1 TAATAGGTAGTGAGTTTTTTAGTGGAT-ATTATT
1130767 TAATAGGTAGTGAGTTTTTTAGTGG
1 TAATAGGTAGTGAGTTTTTTAGTGG
1130792 GATCAAAAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
32 3 0.06
33 25 0.50
34 22 0.44
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (33 bp):
TAATAGGTAGTGAGTTTTTTAGTGGATATTATT
Found at i:1138757 original size:60 final size:60
Alignment explanation
Indices: 1138687--1138799 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
1138677 GTACCCTGAC
* *
1138687 TATATAACACTACTTTATTGAGTCTCCTGACTATTAAAAATTATAAAATGATCCCTCGAT
1 TATATAACACTACTTTATTGAGTCTCCCGACTATTAAAAATTACAAAATGATCCCTCGAT
* * * *
1138747 TATATGACACTATTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATC
1 TATATAACACTACTTTATTGAGTCTCCCGACTATTAAAAATTACAAAATGATC
1138800 ACTAGACTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (60 bp):
TATATAACACTACTTTATTGAGTCTCCCGACTATTAAAAATTACAAAATGATCCCTCGAT
Found at i:1144323 original size:2 final size:2
Alignment explanation
Indices: 1144316--1144346 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1144306 AAATAAAAAG
1144316 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1144347 TGTCTGTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1145582 original size:36 final size:37
Alignment explanation
Indices: 1145515--1145584 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1145505 TTTTTATATT
1145515 TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
* *
1145552 TTTAATTTTTTAAAGAAAA-TATATAAATATTTT
1 TTTAATTTTGTAAAAAAAATTATATAAATATTTT
1145585 TCAACTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
Found at i:1148771 original size:97 final size:96
Alignment explanation
Indices: 1148594--1148776 Score: 226
Period size: 97 Copynumber: 1.9 Consensus size: 96
1148584 AAAATTTTGT
* * *
1148594 ATAATACAGTTTAGAAAGAAAAAAAACATTTTGAATGATATTATAATATATGGTATATAATAATA
1 ATAATACAGTTTAGAAAGAAAAAAAACATTTTGAATGATATTATAATATA--GTACACAACAATA
* *
1148659 TTAAAATATATATTTTTAAAACCTTTTCTGAAA
64 TTAAAATAAATATTTTAAAAACCTTTTCTGAAA
* ** *
1148692 ATAATATAGTTTAGAAAG-AAAAAAACATTTTGAATGATATTATAATATA-TACACAACCTTTTT
1 ATAATACAGTTTAGAAAGAAAAAAAACATTTTGAATGATATTATAATATAGTACACAACAATATT
1148755 GAAAATGAAATAATTTTAAAAA
66 -AAAAT-AAAT-ATTTTAAAAA
1148777 ATATTTTGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
94 8 0.11
95 5 0.07
96 3 0.04
97 40 0.55
98 17 0.23
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (96 bp):
ATAATACAGTTTAGAAAGAAAAAAAACATTTTGAATGATATTATAATATAGTACACAACAATATT
AAAATAAATATTTTAAAAACCTTTTCTGAAA
Found at i:1150588 original size:3 final size:3
Alignment explanation
Indices: 1150574--1150614 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1150564 TGTTCTATAT
* *
1150574 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1150615 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1151938 original size:3 final size:3
Alignment explanation
Indices: 1151927--1151982 Score: 94
Period size: 3 Copynumber: 18.0 Consensus size: 3
1151917 AACAACAAAC
1151927 TAT TCAT TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
1151974 TAT TAT TAT
1 TAT TAT TAT
1151983 AGGTTAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1153328 original size:14 final size:14
Alignment explanation
Indices: 1153309--1153336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1153299 ACACATCAAT
1153309 AGATATTTTATCTC
1 AGATATTTTATCTC
1153323 AGATATTTTATCTC
1 AGATATTTTATCTC
1153337 TTTATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
AGATATTTTATCTC
Found at i:1155406 original size:3 final size:3
Alignment explanation
Indices: 1155398--1155486 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
1155388 AATGTGTAAT
*
1155398 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1155446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1155487 GGGGTTAAAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1157442 original size:4 final size:4
Alignment explanation
Indices: 1157435--1157459 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1157425 TATAACTAAC
1157435 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
1157460 AAACGCGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1165157 original size:26 final size:28
Alignment explanation
Indices: 1165112--1165167 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
1165102 TTAAATGGTA
1165112 ATAATTTTTTCAAAAATATATAAA-ATTT
1 ATAATTTTTTCAAAAATATA-AAATATTT
*
1165140 ATAA-TTTTT-AAAATTATAAAATATTT
1 ATAATTTTTTCAAAAATATAAAATATTT
1165166 AT
1 AT
1165168 TATCATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 14 0.54
27 5 0.19
28 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAATTTTTTCAAAAATATAAAATATTT
Found at i:1165486 original size:26 final size:26
Alignment explanation
Indices: 1165447--1165496 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1165437 AAGAATTTTT
**
1165447 TTTTTCAAAATATATGAAATTTATAA
1 TTTTTCAAAATATAAAAAATTTATAA
1165473 TTTTT-AAAAGTATAAAAAATTTAT
1 TTTTTCAAAA-TATAAAAAATTTAT
1165497 TATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTTTCAAAATATAAAAAATTTATAA
Found at i:1166278 original size:2 final size:2
Alignment explanation
Indices: 1166273--1166309 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1166263 TCTCTCTCTC
1166273 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
1166310 CTTTGCCTTA
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:1174907 original size:23 final size:23
Alignment explanation
Indices: 1174864--1174908 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1174854 ATATATTAGG
**
1174864 TAGCGCTTATATAATGTAATAGA
1 TAGCGCTTATATAATAAAATAGA
1174887 TAGCGCTTATATAATAAAATAG
1 TAGCGCTTATATAATAAAATAG
1174909 GTTAATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGA
Found at i:1175065 original size:23 final size:23
Alignment explanation
Indices: 1175022--1175068 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1175012 ACATATTAGA
**
1175022 TAGCGCTTATATAACGTAATAGG
1 TAGCGCTTATATAACAAAATAGG
*
1175045 TAGCGCTTATATAATAAAATAGG
1 TAGCGCTTATATAACAAAATAGG
1175068 T
1 T
1175069 TAATTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (23 bp):
TAGCGCTTATATAACAAAATAGG
Found at i:1175125 original size:158 final size:157
Alignment explanation
Indices: 1174838--1175333 Score: 718
Period size: 158 Copynumber: 3.2 Consensus size: 157
1174828 AACCGAAAAT
** * * *
1174838 ATTATCAAATACAATAATATATTAGGTAGCGCTTATATAATGTAATAGATAGCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
* *
1174903 AAATAGGTTAATTACTTAATTTGTTATTATAACATATTAGGTAAACACCTAAAATGTTACCAAGG
66 AAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
*
1174968 ATAACATAACCGGTTAATTACTAGAAAT
131 ATAACATAACCGGTTAATTACT-GAAAC
* *
1174996 ATTATTAAGCACAATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
* *
1175061 AAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTATCAAGG
66 AAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
1175126 ATAACATAACCGGTTAATTACTGTAAAC
131 ATAACATAACCGGTTAATTACTG-AAAC
* * * * *
1175154 ATTATCAAGCTCAATAACATATTAGGTGGCGCTCATATAACGTAATAAGTAACGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
* * *
1175219 AAATATGTTAATTACTTAATTTGTTATTACAAC-----A--TAAACGCTTAAAATGTTACCAATG
66 AAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
1175277 ATAACATAACCGGTTAATTACTGGAAAC
131 ATAACATAACCGGTTAATTACT-GAAAC
* *
1175305 ATTATTAAGCATAATAACATATTAGGTAG
1 ATTATCAAGCACAATAACATATTAGGTAG
1175334 TTCTTATGTA
Statistics
Matches: 308, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
151 72 0.23
152 1 0.00
153 1 0.00
157 1 0.00
158 233 0.76
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (157 bp):
ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
AAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
ATAACATAACCGGTTAATTACTGAAAC
Found at i:1175557 original size:73 final size:74
Alignment explanation
Indices: 1175420--1175668 Score: 394
Period size: 73 Copynumber: 3.4 Consensus size: 74
1175410 AAAATTTAAA
* *
1175420 CTACCTATTACATTAAAATACCTACCG-TTTTTTTTAAGGTTGTTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTTTAATGTTGCTAATAATGTAAACGGTAAAAA
1175484 AAATAGGCG
66 AAATAGGCG
1175493 CTACCTATTACATTAAAATACCTACCGATTTTTTTTAATGTTGCTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTTTAATGTTGCTAATAATGTAAACGGTAAAAA
*
1175558 AAATA-GTG
66 AAATAGGCG
* * *
1175566 CTACCTATTACATTAAAATACCTACCGATTTTTTTGAATATTGCTAATAATGTAAACGAGAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTTTAATGTTGCTAATAATGTAAACG-G-TAAA
*
1175631 AAAAATAGGCA
64 AAAAATAGGCG
*
1175642 CTACCTATTACATTAAACTACCTACCG
1 CTACCTATTACATTAAAATACCTACCG
1175669 GATATGTTGA
Statistics
Matches: 163, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
73 85 0.52
74 41 0.25
75 10 0.06
76 27 0.17
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (74 bp):
CTACCTATTACATTAAAATACCTACCGATTTTTTTTAATGTTGCTAATAATGTAAACGGTAAAAA
AAATAGGCG
Found at i:1176169 original size:114 final size:112
Alignment explanation
Indices: 1175749--1176319 Score: 874
Period size: 112 Copynumber: 5.1 Consensus size: 112
1175739 TAGCGCATAT
*
1175749 AAAGTATCGATACTTTATAAAAATATATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
1175814 ACCAGTTTCATTATGATAAAACCGGTAAAGAGCTACCTAATATGTTG
66 ACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * *
1175861 AAAATATCAATACTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAAATAT-AAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGT-AAAAATATGACAA
*
1175925 AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTGCCTGATATGTTG
65 AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * *
1175973 AAAGTATCGATACTTTATAAAAATATATCAATACTTTATAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
1176038 ACCAGTTTTATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* *
1176085 AAAGTATCGATCCTTTATATAAAAATGTATCGATACTTTACAATATAACAGTTAAAAATATGACA
1 AAAGTATCGATAC-TT-TATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
* * *
1176150 AAACCATTTTCATTATGACAAAACTGGTAAAGAGCTACTTGATATGTTG
64 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
** *
1176199 AAAGTATATATATTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
1 AAAGTATCGATA--CTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
* * * *
1176264 AAACCAATTTCATTATAACAAATCCGGTAAAGAGCTACTTGATATGTTG
64 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
1176313 AAAGTAT
1 AAAGTAT
1176320 ATATATTTTT
Statistics
Matches: 418, Mismatches: 35, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
111 8 0.02
112 201 0.48
113 10 0.02
114 197 0.47
115 2 0.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
Done.