Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1257876 original size:24 final size:24
Alignment explanation
Indices: 1257840--1257887 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1257830 AAATATTTTC
1257840 TAAAATATCATATA-ATTATAAAAA
1 TAAAATATCATATATATT-TAAAAA
* *
1257864 TAAATTATGATATATATTTAAAAA
1 TAAAATATCATATATATTTAAAAA
1257888 AATTAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATATCATATATATTTAAAAA
Found at i:1263050 original size:2 final size:2
Alignment explanation
Indices: 1263043--1263084 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1263033 CATAAGCCTT
1263043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1263085 AAGTAGAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1263684 original size:2 final size:2
Alignment explanation
Indices: 1263677--1263739 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1263667 AAATGAGAAT
1263677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1263719 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1263740 GTATCAAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1272876 original size:44 final size:44
Alignment explanation
Indices: 1272813--1272900 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
1272803 AGATTCAATT
*
1272813 GAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACG
1 GAGAATTGATGATTGTTGATGATTTATCTCTTATGATTTAGACG
1272857 GAGAATTGATGATTGTTGATGATTTATCTCTTATGATTTAGACG
1 GAGAATTGATGATTGTTGATGATTTATCTCTTATGATTTAGACG
1272901 AAGATGTCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (44 bp):
GAGAATTGATGATTGTTGATGATTTATCTCTTATGATTTAGACG
Found at i:1272954 original size:118 final size:118
Alignment explanation
Indices: 1272810--1273257 Score: 745
Period size: 118 Copynumber: 3.8 Consensus size: 118
1272800 ACCAGATTCA
1272810 ATTGAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTTG
1 ATTGAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTTG
* *
1272875 ATGATTTATCTCTTATGATTTAGACGAAGATGTCTAATCGTGATAAGACGACG
66 ATGGTTTATCTCTTATGATTTAGACGAAGATGTATAATCGTGATAAGACGACG
* *
1272928 ATTGAGAATTGATGATTGTTGGTGGTTTATCTCTTATGATTTAGATGGAGAATTGATGATTGTTG
1 ATTGAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTTG
1272993 ATGGTTTATCTCTTATGATTTAGACGAAGATGTATAATCGTGATAAGACGACG
66 ATGGTTTATCTCTTATGATTTAGACGAAGATGTATAATCGTGATAAGACGACG
* * *
1273046 ATTGAGAATTGATGATTGTTGGTGGTTTATCTCTTATGATTTAGATGGAGAATTGATGATTGTTA
1 ATTGAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTTG
* *
1273111 ATGGTTTATCTCTTCTAATTTAGACGAAGAAT-TATAATCGTGATAAGACGACG
66 ATGGTTTATCTCTTATGATTTAGACGAAG-ATGTATAATCGTGATAAGACGACG
* * *
1273164 ATTGAGAATTGATGATTGTTGATGGTTTTATCTTTTATGATTTAGACGGAAAATTAATGATTGTT
1 ATTGAGAATTGATGATTGTTGATGG-TTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTT
* *
1273229 GATTGTTTATCTCTTTTGATTTAGACGAA
65 GATGGTTTATCTCTTATGATTTAGACGAA
1273258 TTATACCATG
Statistics
Matches: 312, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
118 250 0.80
119 62 0.20
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (118 bp):
ATTGAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGACGGAGAATTGATGATTGTTG
ATGGTTTATCTCTTATGATTTAGACGAAGATGTATAATCGTGATAAGACGACG
Found at i:1272998 original size:44 final size:44
Alignment explanation
Indices: 1272931--1273016 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
1272921 GACGACGATT
*
1272931 GAGAATTGATGATTGTTGGTGGTTTATCTCTTATGATTTAGATG
1 GAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGATG
1272975 GAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGA
1 GAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGA
1273017 CGAAGATGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (44 bp):
GAGAATTGATGATTGTTGATGGTTTATCTCTTATGATTTAGATG
Found at i:1273116 original size:44 final size:44
Alignment explanation
Indices: 1273049--1273143 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
1273039 GACGACGATT
** * *
1273049 GAGAATTGATGATTGTTGGTGGTTTATCTCTTATGATTTAGATG
1 GAGAATTGATGATTGTTAATGGTTTATCTCTTATAATTTAGACG
*
1273093 GAGAATTGATGATTGTTAATGGTTTATCTCTTCTAATTTAGACG
1 GAGAATTGATGATTGTTAATGGTTTATCTCTTATAATTTAGACG
*
1273137 AAGAATT
1 GAGAATT
1273144 ATAATCGTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.43
Consensus pattern (44 bp):
GAGAATTGATGATTGTTAATGGTTTATCTCTTATAATTTAGACG
Found at i:1273249 original size:44 final size:45
Alignment explanation
Indices: 1273170--1273255 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
1273160 GACGATTGAG
*
1273170 AATTGATGATTGTTGATGGTTTTATCTTTTATGATTTAGACGGAA
1 AATTAATGATTGTTGATGGTTTTATCTTTTATGATTTAGACGGAA
*
1273215 AATTAATGATTGTTGATTG-TTTATCTCTTT-TGATTTAGACG
1 AATTAATGATTGTTGATGGTTTTATCT-TTTATGATTTAGACG
1273256 AATTATACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 18 0.47
45 20 0.53
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (45 bp):
AATTAATGATTGTTGATGGTTTTATCTTTTATGATTTAGACGGAA
Found at i:1275218 original size:60 final size:60
Alignment explanation
Indices: 1275146--1275259 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1275136 GTCAGATGAC
* *
1275146 CATTTTATAACTTCTAATAGTCGAG-GGACTCAATAAAGTAACATCCTATAGTTGGGAGAT
1 CATTTTATAACTTCTAATAGT-GAGAGGACTCAACAAAGTAACACCCTATAGTTGGGAGAT
* * * **
1275206 CATTTTGTAACTTTTAATAGTTAGAGGACTCAACAAAGTAGTACCCTATAGTTG
1 CATTTTATAACTTCTAATAGTGAGAGGACTCAACAAAGTAACACCCTATAGTTG
1275260 AGGGACCGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTCTAATAGTGAGAGGACTCAACAAAGTAACACCCTATAGTTGGGAGAT
Found at i:1285818 original size:20 final size:21
Alignment explanation
Indices: 1285779--1285818 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1285769 TCTTTATAAA
* *
1285779 ATATTTTTTCTTTTCTCCTTC
1 ATATTTTTTCTCTTCCCCTTC
1285800 ATATTTTTT-TCTTCCCCTT
1 ATATTTTTTCTCTTCCCCTT
1285819 ATTTTCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (21 bp):
ATATTTTTTCTCTTCCCCTTC
Found at i:1291962 original size:24 final size:24
Alignment explanation
Indices: 1291929--1291974 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1291919 CCAACGCCCA
1291929 CCTAACCTCTCTTATAAATACCGC
1 CCTAACCTCTCTTATAAATACCGC
*
1291953 CCTAATCTCTCTTATAAATACC
1 CCTAACCTCTCTTATAAATACC
1291975 TTCAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (24 bp):
CCTAACCTCTCTTATAAATACCGC
Found at i:1292720 original size:32 final size:32
Alignment explanation
Indices: 1292639--1292835 Score: 150
Period size: 32 Copynumber: 6.3 Consensus size: 32
1292629 AAATTGGTGT
* * *
1292639 ATGATGTGTGC--ATGATCGTGATAAGTTTGA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
** * * * * *
1292669 ACAATGTTTTCATACGATCATGATACGTTCAA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
* *
1292701 ATGATGTGTGCATATGATCATGGTATGTTTGA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
* * * *
1292733 ATGATGTATGC--ATGATCGTGACATGTTTGA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
* * * *
1292763 ACGATGTTTTCATACGATCATGATATGTTCGA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
** *
1292795 ATGATGTGTGCATATGATCGCGATATGTTTGA
1 ATGATGTGTGCATATGATCATGATATGTTCGA
*
1292827 ACGATGTGT
1 ATGATGTGT
1292836 CTATTCTATA
Statistics
Matches: 126, Mismatches: 37, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
30 31 0.25
32 95 0.75
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (32 bp):
ATGATGTGTGCATATGATCATGATATGTTCGA
Found at i:1292769 original size:62 final size:63
Alignment explanation
Indices: 1292703--1292835 Score: 178
Period size: 62 Copynumber: 2.1 Consensus size: 63
1292693 ACGTTCAAAT
* * * *
1292703 GATGTGTGCATATGATCATGGTATGTTTGAATGATGTATGC-ATGATCGTGACATGTTTGAAC
1 GATGTGTGCATACGATCATGATATGTTCGAATGATGTATGCAATGATCGCGACATGTTTGAAC
* * * *
1292765 GATGTTTTCATACGATCATGATATGTTCGAATGATGTGTGCATATGATCGCGATATGTTTGAAC
1 GATGTGTGCATACGATCATGATATGTTCGAATGATGTATGCA-ATGATCGCGACATGTTTGAAC
1292829 GATGTGT
1 GATGTGT
1292836 CTATTCTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
62 35 0.58
64 25 0.42
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (63 bp):
GATGTGTGCATACGATCATGATATGTTCGAATGATGTATGCAATGATCGCGACATGTTTGAAC
Found at i:1292800 original size:94 final size:94
Alignment explanation
Indices: 1292639--1292833 Score: 300
Period size: 94 Copynumber: 2.1 Consensus size: 94
1292629 AAATTGGTGT
* *
1292639 ATGATGTGTGCATGATCGTGATAAGTTTGAACAATGTTTTCATACGATCATGATACGTTCAAATG
1 ATGATGTATGCATGATCGTGACAAGTTTGAACAATGTTTTCATACGATCATGATACGTTCAAATG
* *
1292704 ATGTGTGCATATGATCATGGTATGTTTGA
66 ATGTGTGCATATGATCACGATATGTTTGA
* * * *
1292733 ATGATGTATGCATGATCGTGACATGTTTGAACGATGTTTTCATACGATCATGATATGTTCGAATG
1 ATGATGTATGCATGATCGTGACAAGTTTGAACAATGTTTTCATACGATCATGATACGTTCAAATG
*
1292798 ATGTGTGCATATGATCGCGATATGTTTGA
66 ATGTGTGCATATGATCACGATATGTTTGA
*
1292827 ACGATGT
1 ATGATGT
1292834 GTCTATTCTA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (94 bp):
ATGATGTATGCATGATCGTGACAAGTTTGAACAATGTTTTCATACGATCATGATACGTTCAAATG
ATGTGTGCATATGATCACGATATGTTTGA
Found at i:1293032 original size:43 final size:43
Alignment explanation
Indices: 1292946--1293032 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1292936 ACTAAACACA
**
1292946 TAATTTATCCTACATTTTATTATTATGGACTAAAACTGGTAGT
1 TAATTTATCCTACATTTTATTATTATGGACTAAAACTAATAGT
*
1292989 TAATTTATCCTACATTTTATTATTATTGACTAAAACTAATAGT
1 TAATTTATCCTACATTTTATTATTATGGACTAAAACTAATAGT
1293032 T
1 T
1293033 TATGTACTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (43 bp):
TAATTTATCCTACATTTTATTATTATGGACTAAAACTAATAGT
Found at i:1297652 original size:28 final size:28
Alignment explanation
Indices: 1297617--1297670 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
1297607 TTTATATTTT
1297617 ATTTGAATATATTTCA-ATTATTTATGTG
1 ATTTGAATATATTT-AGATTATTTATGTG
1297645 ATTTGAATATATTTAGATTATTTATG
1 ATTTGAATATATTTAGATTATTTATG
1297671 CGGTTGTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (28 bp):
ATTTGAATATATTTAGATTATTTATGTG
Found at i:1299039 original size:39 final size:39
Alignment explanation
Indices: 1298994--1299069 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
1298984 ATAACATCCG
* **
1298994 TTATGTTTGTAATCTTGACAAATGCGACCACAATCTTGT
1 TTATGTTCGTAATCTTGACAAACACGACCACAATCTTGT
*
1299033 TTATGTTCGTAATCTTGACAAACACGACCATAATCTT
1 TTATGTTCGTAATCTTGACAAACACGACCACAATCTT
1299070 ATTTGAATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (39 bp):
TTATGTTCGTAATCTTGACAAACACGACCACAATCTTGT
Found at i:1300839 original size:20 final size:20
Alignment explanation
Indices: 1300810--1300847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1300800 ATGGACTTTA
* *
1300810 TTAATTATAATTAAAATTAT
1 TTAATCATAATCAAAATTAT
1300830 TTAATCATAATCAAAATT
1 TTAATCATAATCAAAATT
1300848 TAATATTGGT
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:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATCATAATCAAAATTAT
Found at i:1301055 original size:15 final size:14
Alignment explanation
Indices: 1301029--1301062 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1301019 TACATTCATG
1301029 AATAAAAAATAAAT
1 AATAAAAAATAAAT
1301043 AATAAACAAATAAAT
1 AATAAA-AAATAAAT
*
1301058 CATAA
1 AATAA
1301063 GTGAACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAAATAAAT
Found at i:1301468 original size:2 final size:2
Alignment explanation
Indices: 1301461--1301511 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1301451 CTAGAACCAC
1301461 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
1301503 AT AT AT AT A
1 AT AT AT AT A
1301512 GTTGTTTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1303838 original size:2 final size:2
Alignment explanation
Indices: 1303831--1303859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1303821 TAAGAATTTG
1303831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1303860 ATTTTAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1308533 original size:8 final size:8
Alignment explanation
Indices: 1308520--1308550 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1308510 AAATGGATAA
1308520 GAAATGAC
1 GAAATGAC
1308528 GAAATGAC
1 GAAATGAC
*
1308536 GAAATAAC
1 GAAATGAC
1308544 GAAATGA
1 GAAATGA
1308551 AAGAGAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.23, T:0.13
Consensus pattern (8 bp):
GAAATGAC
Found at i:1313094 original size:20 final size:21
Alignment explanation
Indices: 1313071--1313116 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
1313061 TTTTATTTAA
1313071 TTATTATATTATTTAATT-TT
1 TTATTATATTATTTAATTATT
1313091 TTATTATATTATTTAATTATT
1 TTATTATATTATTTAATTATT
1313112 TTATT
1 TTATT
1313117 TTTTTACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTATATTATTTAATTATT
Found at i:1313101 original size:28 final size:28
Alignment explanation
Indices: 1313061--1313120 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
1313051 TTTGTTAGTA
1313061 TTTTATTTAATTA-TTATATTATTTAATT
1 TTTTATTTAATTATTTA-ATTATTTAATT
*
1313089 TTTTA-TTATATTATTTAATTATTTTATT
1 TTTTATTTA-ATTATTTAATTATTTAATT
1313117 TTTT
1 TTTT
1313121 TACAGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 23 0.79
29 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTTATTTAATTATTTAATTATTTAATT
Found at i:1314754 original size:16 final size:16
Alignment explanation
Indices: 1314733--1314766 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1314723 GGTATAAACA
*
1314733 TGTACAACTTATCATG
1 TGTACAAATTATCATG
1314749 TGTACAAATTATCATG
1 TGTACAAATTATCATG
1314765 TG
1 TG
1314767 CAATAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (16 bp):
TGTACAAATTATCATG
Found at i:1317856 original size:170 final size:171
Alignment explanation
Indices: 1317573--1317913 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 171
1317563 TATTTAAAAA
1317573 AGGTATATTTAACAAGAAAAGTCGCGTTAGCGTAGTTCCTAAACTGAAAATTTGTCGCTTACGTG
1 AGGTATATTTAACAAGAAAAGTCGCGTTAGCGTAGTTCCTAAACTGAAAATTTGTCGCTTACGTG
1317638 GAACGCTTTAATTGGCTGATTTTTAAACAAATACGGGGATTAAGCACGGAATAAAGGGATTAGTC
66 GAACGCTTTAATTGGCTGATTTTTAAACAAATACGGGGATTAAGCACGGAATAAAGGGATTAGTC
1317703 AAACTAATAGGTTTTGTAATTTCTTTGATAAAATTGTTCTT
131 AAACTAATAGGTTTTGTAATTTCTTTGATAAAATTGTTCTT
1317744 AGGTATATTTAACAAGAAAAGTCGCGTTAGCGTAGTTCCTAAACTG-AAATTTGTCGCTTACGTG
1 AGGTATATTTAACAAGAAAAGTCGCGTTAGCGTAGTTCCTAAACTGAAAATTTGTCGCTTACGTG
1317808 GAACGCTTTAATTGGCTGATTTTTAAACAAATACGGGGATTAAGCACGGAATAAAGGGATTAGTC
66 GAACGCTTTAATTGGCTGATTTTTAAACAAATACGGGGATTAAGCACGGAATAAAGGGATTAGTC
1317873 AAACTAATAGGTTTTGTAATTTCTTTGATAAAATTGTTCTT
131 AAACTAATAGGTTTTGTAATTTCTTTGATAAAATTGTTCTT
1317914 TAAGGATAAG
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 124 0.73
171 46 0.27
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (171 bp):
AGGTATATTTAACAAGAAAAGTCGCGTTAGCGTAGTTCCTAAACTGAAAATTTGTCGCTTACGTG
GAACGCTTTAATTGGCTGATTTTTAAACAAATACGGGGATTAAGCACGGAATAAAGGGATTAGTC
AAACTAATAGGTTTTGTAATTTCTTTGATAAAATTGTTCTT
Found at i:1320525 original size:21 final size:20
Alignment explanation
Indices: 1320467--1320526 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1320457 AATTATTAGA
*
1320467 ATAGTAGCTAAAAAATAATA-
1 ATAGTAG-TTAAAAATAATAG
* *
1320487 ATAGTTA-TTATAATTAATAG
1 ATAG-TAGTTAAAAATAATAG
1320507 AGTAGTAGTTAAAAATAATA
1 A-TAGTAGTTAAAAATAATA
1320527 TTTTTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.29
20 7 0.23
21 15 0.48
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
ATAGTAGTTAAAAATAATAG
Found at i:1320600 original size:2 final size:2
Alignment explanation
Indices: 1320595--1320663 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1320585 TTACTTTTTT
1320595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1320637 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
1320664 GTTTAGAATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1321613 original size:22 final size:22
Alignment explanation
Indices: 1321584--1321655 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
1321574 AATCTATAAA
1321584 AAAT-TAAAAATACTTGAAAAC
1 AAATATAAAAATACTTGAAAAC
*
1321605 AAATATAAATAATA-ATG-AAA-
1 AAATATAAA-AATACTTGAAAAC
*** *
1321625 GTTTTTAAAAATACTTGAAAAC
1 AAATATAAAAATACTTGAAAAC
1321647 AAATATAAA
1 AAATATAAA
1321656 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 10 0.28
22 11 0.31
23 4 0.11
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (22 bp):
AAATATAAAAATACTTGAAAAC
Found at i:1321656 original size:20 final size:20
Alignment explanation
Indices: 1321591--1321657 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1321581 AAAAAATTAA
1321591 AAATACTTGAAAACAAATAT
1 AAATACTTGAAAACAAATAT
* ***** *
1321611 AAATAATAATGAAAGTTTTTAA
1 AAATACT--TGAAAACAAATAT
1321633 AAATACTTGAAAACAAATAT
1 AAATACTTGAAAACAAATAT
1321653 AAATA
1 AAATA
1321658 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 14, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
20 18 0.58
22 13 0.42
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (20 bp):
AAATACTTGAAAACAAATAT
Found at i:1322714 original size:17 final size:18
Alignment explanation
Indices: 1322674--1322721 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1322664 TTAATAATAT
1322674 TTATTTAA-ATG-AAACAA
1 TTATTTAACATGTAAAC-A
1322691 TTA-TTAACATGTAAAC-
1 TTATTTAACATGTAAACA
1322707 TTATTTAACAT-TAAA
1 TTATTTAACATGTAAA
1322722 TATCCTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.39
17 13 0.46
18 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (18 bp):
TTATTTAACATGTAAACA
Found at i:1325571 original size:2 final size:2
Alignment explanation
Indices: 1325566--1325618 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1325556 GTATTGGTAT
1325566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1325608 TA TA TA TA TA T
1 TA TA TA TA TA T
1325619 GCATACACGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1330278 original size:24 final size:25
Alignment explanation
Indices: 1330222--1330291 Score: 97
Period size: 24 Copynumber: 2.8 Consensus size: 25
1330212 TTAAATGGGT
* *
1330222 TTTAGTTTAATTAATTAAACTTAGGAG
1 TTTAGTTGAGTTAA-TAAACTTA-GAG
1330249 TTTAGTTGAGTTAATAAACTT-GAG
1 TTTAGTTGAGTTAATAAACTTAGAG
1330273 TTTAGTTGAGTTAATAAAC
1 TTTAGTTGAGTTAATAAAC
1330292 ATACTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.54
26 7 0.17
27 12 0.29
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (25 bp):
TTTAGTTGAGTTAATAAACTTAGAG
Found at i:1331028 original size:60 final size:60
Alignment explanation
Indices: 1330954--1331075 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
1330944 GTCCCCGACA
* * ** *
1330954 ATAGGTTGATGCTTTATTGAGTTTCTTGACTATTAAAAATTACAAAATGATCATTTGACT
1 ATAGGGTGATGCTTTAGTGAGTCCCTTGACTATTAAAAATTACAAAATGATCACTTGACT
* * * * * *
1331014 ATAGGGTGTTGCTTTGGTGAGTCCCTTGACTTTTAAAAGTTACAAAATTATCACTTGTCT
1 ATAGGGTGATGCTTTAGTGAGTCCCTTGACTATTAAAAATTACAAAATGATCACTTGACT
1331074 AT
1 AT
1331076 TCATATGTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (60 bp):
ATAGGGTGATGCTTTAGTGAGTCCCTTGACTATTAAAAATTACAAAATGATCACTTGACT
Found at i:1336915 original size:33 final size:34
Alignment explanation
Indices: 1336877--1336959 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 34
1336867 CGAATAATAT
* *
1336877 GAGTTCGAACAATGTTATTTGCACGTGT-GGTCA
1 GAGTTCGAACAATGTTATTTGCACATGTACGTCA
** **
1336910 GAGTTCGAACAATGTCGTTTGCACATGTACGTGT
1 GAGTTCGAACAATGTTATTTGCACATGTACGTCA
1336944 GAGTTCGAACAATGTT
1 GAGTTCGAACAATGTT
1336960 GTCTGTACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (34 bp):
GAGTTCGAACAATGTTATTTGCACATGTACGTCA
Found at i:1340472 original size:28 final size:27
Alignment explanation
Indices: 1340428--1340483 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1340418 GCTTTATTAA
*
1340428 GTCCCTCGATTATTAAAAGTTACAAAAT
1 GTCCCTCGACTATT-AAAGTTACAAAAT
1340456 GTCCCTTCGACTA-TAAAGTTACAAAAT
1 GTCCC-TCGACTATTAAAGTTACAAAAT
1340483 G
1 G
1340484 GTCACCTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 14 0.54
28 6 0.23
29 6 0.23
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (27 bp):
GTCCCTCGACTATTAAAGTTACAAAAT
Found at i:1341471 original size:42 final size:44
Alignment explanation
Indices: 1341418--1341507 Score: 141
Period size: 42 Copynumber: 2.1 Consensus size: 44
1341408 AAGTAAATAA
*
1341418 ATAACATCATTAAGTCTCAATAAGTCTAAA-ATAAAT-AACATC-
1 ATAACAACATTAAGTCTCAATAAGTCTAAATA-AAATCAACATCG
1341460 ATAACAACATTAAGTCTCAATAAGTCTAAATAAAATCAACATCG
1 ATAACAACATTAAGTCTCAATAAGTCTAAATAAAATCAACATCG
1341504 ATAA
1 ATAA
1341508 TATTCAATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
42 33 0.75
43 7 0.16
44 4 0.09
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.27
Consensus pattern (44 bp):
ATAACAACATTAAGTCTCAATAAGTCTAAATAAAATCAACATCG
Found at i:1342599 original size:22 final size:21
Alignment explanation
Indices: 1342574--1342618 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
1342564 AAAGGATGTC
1342574 TTTTTTAGAATTGTTCTATCTT
1 TTTTTTAGAATTGTTCTAT-TT
1342596 TTTTTTAGAATTGTTCTATTT
1 TTTTTTAGAATTGTTCTATTT
1342617 TT
1 TT
1342619 CATGATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTTTTAGAATTGTTCTATTT
Found at i:1345545 original size:67 final size:67
Alignment explanation
Indices: 1345408--1345603 Score: 166
Period size: 67 Copynumber: 2.9 Consensus size: 67
1345398 AAGATTTCAT
* * * *
1345408 GTGGACATTTGCCTACCTTAAATGAACCATGAATCTATTATTATTAAAGGAAAATTTAGATTTGA
1 GTGGACATTTGCCTACCTTAAATGAACCATGAATCTATCATTAGTAAAAGAAAATTTAAATTTGA
1345473 AG
66 AG
* * * * * * *
1345475 GTGGACGTTTGTCTATCTTGAAATGAACCATGAGTCTATCA-TCGTAAAAGAATATTTAAATTTT
1 GTGGACATTTGCCTACCTT-AAATGAACCATGAATCTATCATTAGTAAAAGAAAATTTAAATTTG
1345539 AAG
65 AAG
* * ** * * * *
1345542 GTGGGCACTTATCTA-TTCTAAATGAACTATAAAT-TCATCATTA-TAAAAGAAAATTCAAATTT
1 GTGGACATTTGCCTACCT-TAAATGAACCATGAATCT-ATCATTAGTAAAAGAAAATTTAAATTT
1345604 TAGGATGATC
Statistics
Matches: 103, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
65 1 0.01
66 34 0.33
67 49 0.48
68 19 0.18
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (67 bp):
GTGGACATTTGCCTACCTTAAATGAACCATGAATCTATCATTAGTAAAAGAAAATTTAAATTTGA
AG
Found at i:1349306 original size:18 final size:18
Alignment explanation
Indices: 1349261--1349306 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1349251 ACCGGTTACA
*
1349261 ACCCGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
1349279 ACCCGACCCGATCTGTTG
1 ACCCGACCCGACCCGTTG
1349297 ACCCGACCCG
1 ACCCGACCCG
1349307 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.48, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1353403 original size:24 final size:25
Alignment explanation
Indices: 1353347--1353416 Score: 97
Period size: 24 Copynumber: 2.8 Consensus size: 25
1353337 TTAAATGGGT
* *
1353347 TTTAGTTTAATTAATTAAACTTAGGAG
1 TTTAGTTGAGTTAA-TAAACTTA-GAG
1353374 TTTAGTTGAGTTAATAAACTT-GAG
1 TTTAGTTGAGTTAATAAACTTAGAG
1353398 TTTAGTTGAGTTAATAAAC
1 TTTAGTTGAGTTAATAAAC
1353417 ATACTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.54
26 7 0.17
27 12 0.29
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (25 bp):
TTTAGTTGAGTTAATAAACTTAGAG
Found at i:1355065 original size:16 final size:16
Alignment explanation
Indices: 1355044--1355077 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1355034 TTACTATTCA
*
1355044 CGTGAATAGTGAAATT
1 CGTGAATAGTAAAATT
1355060 CGTGAATAGTAAAATT
1 CGTGAATAGTAAAATT
1355076 CG
1 CG
1355078 GTCGGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (16 bp):
CGTGAATAGTAAAATT
Found at i:1362223 original size:34 final size:34
Alignment explanation
Indices: 1362180--1362295 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 34
1362170 ATAAACAAGT
1362180 AAATAAATAACACCATTAAGTCTCAATAAGTCTA
1 AAATAAATAACACCATTAAGTCTCAATAAGTCTA
*
1362214 AAATAAATAACATCATAACAACATTAAGTCTCAATAAGTCCA
1 AAATAAAT-A-A-C---AC--CATTAAGTCTCAATAAGTCTA
1362256 AAATAAATAACACCATTAAGTCTCAATAAGTCT-
1 AAATAAATAACACCATTAAGTCTCAATAAGTCTA
1362289 AAATAAA
1 AAATAAA
1362296 ATCAACATCG
Statistics
Matches: 72, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
33 7 0.10
34 27 0.38
35 1 0.01
36 3 0.04
37 1 0.01
39 1 0.01
40 3 0.04
41 1 0.01
42 28 0.39
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (34 bp):
AAATAAATAACACCATTAAGTCTCAATAAGTCTA
Found at i:1362239 original size:42 final size:42
Alignment explanation
Indices: 1362186--1362267 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1362176 AAGTAAATAA
* *
1362186 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAATAACATC
1 ATAACAACATTAAGTCTCAATAAGTCCAAAATAAATAACATC
1362228 ATAACAACATTAAGTCTCAATAAGTCCAAAATAAATAACA
1 ATAACAACATTAAGTCTCAATAAGTCCAAAATAAATAACA
1362268 CCATTAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.24
Consensus pattern (42 bp):
ATAACAACATTAAGTCTCAATAAGTCCAAAATAAATAACATC
Found at i:1363324 original size:26 final size:25
Alignment explanation
Indices: 1363291--1363339 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
1363281 AAAGGATGTC
1363291 TTTTTTAGAATTGTTCTATCTTTTTT
1 TTTTTTAGAATTGTTCTAT-TTTTTT
1363317 TTTTTTAGAATTGTTCTATTTTT
1 TTTTTTAGAATTGTTCTATTTTT
1363340 CATGATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTTTTAGAATTGTTCTATTTTTTT
Found at i:1363348 original size:26 final size:26
Alignment explanation
Indices: 1363293--1363348 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1363283 AGGATGTCTT
* **
1363293 TTTTAGAATTGTTCTATCTTTTTTTT
1 TTTTAGAATTGTTCTATCTTTTATGA
1363319 TTTTAGAATTGTTCTAT-TTTTCATGA
1 TTTTAGAATTGTTCTATCTTTT-ATGA
1363345 TTTT
1 TTTT
1363349 TGTAAGCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.66
Consensus pattern (26 bp):
TTTTAGAATTGTTCTATCTTTTATGA
Found at i:1365913 original size:32 final size:32
Alignment explanation
Indices: 1365877--1365942 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
1365867 TTCTATTTTT
*
1365877 TTGAGCATTTTCCC-TTTTTTATGAATCCCTAA
1 TTGAGCA-TTTCCCATTTTTTATAAATCCCTAA
1365909 TTGAGCATTTCCCATTTTTTATAAATCCCTAA
1 TTGAGCATTTCCCATTTTTTATAAATCCCTAA
1365941 TT
1 TT
1365943 ATGCTTGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (32 bp):
TTGAGCATTTCCCATTTTTTATAAATCCCTAA
Found at i:1372318 original size:21 final size:21
Alignment explanation
Indices: 1372283--1372332 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1372273 AGGATCAAAT
*
1372283 TCGTCGTGTGCATGAGCGTGC
1 TCGTCTTGTGCATGAGCGTGC
* * *
1372304 TTGTCTTGTGGATGAGTGTGC
1 TCGTCTTGTGCATGAGCGTGC
1372325 TCGTCTTG
1 TCGTCTTG
1372333 CGAACGAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.18, G:0.36, T:0.38
Consensus pattern (21 bp):
TCGTCTTGTGCATGAGCGTGC
Found at i:1382735 original size:21 final size:22
Alignment explanation
Indices: 1382705--1382745 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1382695 AATTTAGTTT
*
1382705 AAAATGATTAATTAATTAATCA
1 AAAATGATTAAATAATTAATCA
*
1382727 AAAAT-ATTAAATATTTAAT
1 AAAATGATTAAATAATTAAT
1382746 ATATTATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATGATTAAATAATTAATCA
Found at i:1385994 original size:160 final size:161
Alignment explanation
Indices: 1385706--1386506 Score: 1080
Period size: 160 Copynumber: 5.0 Consensus size: 161
1385696 TCTGTTTTCT
* * *
1385706 TGGTGGATCCTGCACTTGCTTTCAAGGTAAATTTGAGTTTTCAT-TGTTATACACACGAATTCGG
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATG--ATACACACGAATTCGG
* * * * *
1385770 TCATCGAAGCTATGTTATTCAGACTCGAGTGTGAGCGTCAAATACGAGTTTT-AGACGGTTTAAA
64 TCATCGAAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAA
*
1385834 TCGGTTATGAATGTCTTTTGTTTTGACAATGTA
129 TCGGTTATGAATGTCTTTTGTTTTGACAATGTG
* * * * *
1385867 TGGTACATCATGCTCTTGTTTTCAAGGTAAATTTGAGTTTCCATATGACACACAAGAATTCGGTC
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTCGGTC
* **
1385932 ATCGAAGCTATGTTAGTTT-GACTCAAGAGTGAGCGTCAGATACGA-TTTTCCGATTATTTAAAT
66 ATCGAAGCTATGTTA-TTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAAT
*
1385995 TGGTTATGAATGTCTTTTGTTTTGACAATGTG
130 CGGTTATGAATGTCTTTTGTTTTGACAATGTG
* * *
1386027 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATCTGAGTTTTCATATGATACACACAAATTCGATC
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTCGGTC
* * * *
1386092 ATCGAAGCTATGTTATTTAGACTC-GGTGTGAGTGTTAGATACGAGTTTT-CAACGATTTAAATC
66 ATCGAAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAATC
*
1386155 GGTTATGAATGTCTTTTGTTTTGACAACGTG
131 GGTTATGAATGTCTTTTGTTTTGACAATGTG
*
1386186 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGTGTTTTCATTATGATAC-CACGAATTCGGT
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCA-TATGATACACACGAATTCGGT
* * * *
1386250 CATCGAAGCTATGTTATTTAGACTCGAGTGTGAGCATCAAATATGAGTTTTCC-ACGATTTAAAT
65 CATCGAAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAAT
1386314 CGGTTATGAATGTCTTTTGTTTTGACAATGTG
130 CGGTTATGAATGTCTTTTGTTTTGACAATGTG
* * * * *
1386346 TTGTAGATCATGCTCTTTCTTTCAAGGAAAATTTGACTTTTCATAATGATACACACGAATTCGAT
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCAT-ATGATACACACGAATTCGGT
* * * * * * *
1386411 CATCGAAGCTATGTTATTTAGACTCGATTATGAGTGTCGGATACGA-TTTTCCGGCGATTTAGAT
65 CATCGAAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAAT
** *
1386475 CGGTTACCAATGTCTTTTGTTTTTACAATGTG
130 CGGTTATGAATGTCTTTTGTTTTGACAATGTG
1386507 CATTGTTTCT
Statistics
Matches: 565, Mismatches: 64, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
159 140 0.25
160 294 0.52
161 129 0.23
162 2 0.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (161 bp):
TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTCGGTC
ATCGAAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACGAGTTTTCCGACGATTTAAATC
GGTTATGAATGTCTTTTGTTTTGACAATGTG
Found at i:1386389 original size:319 final size:320
Alignment explanation
Indices: 1385706--1386502 Score: 1113
Period size: 319 Copynumber: 2.5 Consensus size: 320
1385696 TCTGTTTTCT
* * * *
1385706 TGGTGGATCCTGCACTTGCTTTCAAGGTAAATTTGAGTTTTCAT-TGTTATACACACGAATTCGG
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATG--ATACACACGAATTCGA
* * * *
1385770 TCATCGAAGCTATGTTATTCAGACTCGAGTGTGAGCGTCAAATACGAGTTTT-AGACGGTTTAAA
64 TCATCGAAGCTATGTTATTTAGACTCGAGTGTGAGTGTCAGATACGAGTTTTCA-ACGATTTAAA
* *
1385834 TCGGTTATGAATGTCTTTTGTTTTGACAATGTATGGTACATCATGCTCTTGTTTTCAAGGTAAAT
128 TCGGTTATGAATGTCTTTTGTTTTGACAACGTATGGTACATCATGCTCTTGCTTTCAAGGTAAAT
1385899 TTGAGTTTCCATATGACACACAAGAATTCGGTCATCGAAGCTATGTTAGTTTGACTCAAGAGTGA
193 TTGAGTTTCCATATGACACACAAGAATTCGGTCATCGAAGCTATGTTAGTTTGACTCAAGAGTGA
* * ** *
1385964 GCGTCAGATACGATTTTCCGATTATTTAAATTGGTTATGAATGTCTTTTGTTTTGACAATGTG
258 GCATCAAATACGATTTTCCGACGATTTAAATCGGTTATGAATGTCTTTTGTTTTGACAATGTG
* *
1386027 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATCTGAGTTTTCATATGATACACACAAATTCGATC
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTCGATC
*
1386092 ATCGAAGCTATGTTATTTAGACTCG-GTGTGAGTGTTAGATACGAGTTTTCAACGATTTAAATCG
66 ATCGAAGCTATGTTATTTAGACTCGAGTGTGAGTGTCAGATACGAGTTTTCAACGATTTAAATCG
* *
1386156 GTTATGAATGTCTTTTGTTTTGACAACGTGTGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTG
131 GTTATGAATGTCTTTTGTTTTGACAACGTATGGTACATCATGCTCTTGCTTTCAAGGTAAATTTG
* * * * * *
1386221 TGTTTTCATTATGATAC-CACGAATTCGGTCATCGAAGCTATGTTA-TTTAGACTCGAGTGTGAG
196 AGTTTCCA-TATGACACACAAGAATTCGGTCATCGAAGCTATGTTAGTTT-GACTCAAGAGTGAG
*
1386284 CATCAAATATGAGTTTTCC-ACGATTTAAATCGGTTATGAATGTCTTTTGTTTTGACAATGTG
259 CATCAAATACGA-TTTTCCGACGATTTAAATCGGTTATGAATGTCTTTTGTTTTGACAATGTG
* * * *
1386346 TTGTAGATCATGCTCTTTCTTTCAAGGAAAATTTGACTTTTCATAATGATACACACGAATTCGAT
1 TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCAT-ATGATACACACGAATTCGAT
* * * ** *
1386411 CATCGAAGCTATGTTATTTAGACTCGATTATGAGTGTCGGATACGA-TTTTCCGGCGATTTAGAT
65 CATCGAAGCTATGTTATTTAGACTCGAGTGTGAGTGTCAGATACGAGTTTT-CAACGATTTAAAT
** *
1386475 CGGTTACCAATGTCTTTTGTTTTTACAA
129 CGGTTATGAATGTCTTTTGTTTTGACAA
1386503 TGTGCATTGT
Statistics
Matches: 425, Mismatches: 43, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
318 3 0.01
319 227 0.53
320 103 0.24
321 90 0.21
322 2 0.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (320 bp):
TGGTAGATCATGCTCTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTCGATC
ATCGAAGCTATGTTATTTAGACTCGAGTGTGAGTGTCAGATACGAGTTTTCAACGATTTAAATCG
GTTATGAATGTCTTTTGTTTTGACAACGTATGGTACATCATGCTCTTGCTTTCAAGGTAAATTTG
AGTTTCCATATGACACACAAGAATTCGGTCATCGAAGCTATGTTAGTTTGACTCAAGAGTGAGCA
TCAAATACGATTTTCCGACGATTTAAATCGGTTATGAATGTCTTTTGTTTTGACAATGTG
Found at i:1386709 original size:198 final size:200
Alignment explanation
Indices: 1386348--1386709 Score: 523
Period size: 198 Copynumber: 1.8 Consensus size: 200
1386338 ACAATGTGTT
* * *
1386348 GTAGATCATGCTCTTTCTTTCAAGGAAAATTTGACTTTTCATAATGATACACACGAATTCGATCA
1 GTAGATCATGCACTTGCTTTCAAGGAAAACTTGACTTTTCATAATGATACACACGAATTCGATCA
* * * *
1386413 TCGAAGCTATGTTATTTAGACTCGATTATGAGTGTCGGATACGATTTTCCGGCGATTTAGATCGG
66 TCGAAGCTATGTTATTTAGACTCGAGTATGAGTGTCAGATACGATTTTCCGACGATTTAAATCGG
* *
1386478 TTACCAATGTCTTTTGTTTTTACAATGTGCATTGTTTCTGCTAGTCCTAGTTTCTACTTCTGTTT
131 TTACCAACGTCTTTTGTTTTGACAATGTGCATTGTTTCTGCTAGTCCTAGTTTCTACTTCTGTTT
1386543 TCTTA
196 TCTTA
* * *
1386548 GTAGATCATGCACTTGGTTTCAAGGTAAACTTGAGTTTTCAT-ATGATACACACGAATTCGATCA
1 GTAGATCATGCACTTGCTTTCAAGGAAAACTTGACTTTTCATAATGATACACACGAATTCGATCA
* * * *
1386612 TCGAAGTTATGTTTTTTAGACT-GAGTGTGAGTGTCAGATACGAGTTTT-CGATGATTTAAATCG
66 TCGAAGCTATGTTATTTAGACTCGAGTATGAGTGTCAGATACGA-TTTTCCGACGATTTAAATCG
** *
1386675 GTTATGAACGTCTTTTGTTTTGACAATTTGCATTG
130 GTTACCAACGTCTTTTGTTTTGACAATGTGCATTG
1386710 CTAAAAAGGG
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
198 60 0.42
199 46 0.32
200 36 0.25
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (200 bp):
GTAGATCATGCACTTGCTTTCAAGGAAAACTTGACTTTTCATAATGATACACACGAATTCGATCA
TCGAAGCTATGTTATTTAGACTCGAGTATGAGTGTCAGATACGATTTTCCGACGATTTAAATCGG
TTACCAACGTCTTTTGTTTTGACAATGTGCATTGTTTCTGCTAGTCCTAGTTTCTACTTCTGTTT
TCTTA
Found at i:1390296 original size:2 final size:2
Alignment explanation
Indices: 1390289--1390315 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1390279 TTTTAGTATT
1390289 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
1390316 TGTGTTTTTA
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:1398220 original size:20 final size:20
Alignment explanation
Indices: 1398195--1398287 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1398185 TTTTCCCAAT
1398195 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1398215 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1398235 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1398256 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1398277 TCGCAATGCGA
1 TCGCAATGCGA
1398288 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1398237 original size:41 final size:41
Alignment explanation
Indices: 1398192--1398287 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1398182 CGATTTTCCC
1398192 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1398233 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1398274 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1398288 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1398241 original size:21 final size:20
Alignment explanation
Indices: 1398195--1398287 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1398185 TTTTCCCAAT
*
1398195 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1398215 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1398235 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1398256 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1398277 TCGCAATGCGA
1 TCGCAATGCGA
1398288 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1398301 original size:20 final size:20
Alignment explanation
Indices: 1398276--1398370 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1398266 AATTGGGAAA
*
1398276 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1398296 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1398317 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1398337 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1398357 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1398371 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1398350 original size:41 final size:41
Alignment explanation
Indices: 1398273--1398350 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1398263 GCGAATTGGG
* * **
1398273 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
1398314 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
1398351 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:1400221 original size:18 final size:18
Alignment explanation
Indices: 1400200--1400244 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1400190 TCCACTTCGG
*
1400200 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1400218 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1400236 GAGCCATCA
1 GAGCCATCA
1400245 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1400742 original size:20 final size:20
Alignment explanation
Indices: 1400717--1400762 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1400707 TAGTTTACTT
1400717 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
1400737 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
1400757 TCGCAA
1 TCGCAA
1400763 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:1400771 original size:19 final size:20
Alignment explanation
Indices: 1400728--1400783 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1400718 CGCAACACGA
1400728 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
1400748 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
1400767 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1400784 ACAAAAGCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:1400794 original size:14 final size:14
Alignment explanation
Indices: 1400772--1400861 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
1400762 ATGCGAAATG
1400772 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1400786 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
1400802 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1400818 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1400834 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1400850 AAAATCGCAACG
1 AAAATCGCAACG
1400862 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1400814 original size:32 final size:32
Alignment explanation
Indices: 1400756--1400866 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
1400746 AGAAATGGCT
*
1400756 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
1400789 AGCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1400821 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1400853 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1400867 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 61 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1400895 original size:19 final size:19
Alignment explanation
Indices: 1400873--1401012 Score: 130
Period size: 19 Copynumber: 7.6 Consensus size: 19
1400863 GAAACACAAA
*
1400873 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1400892 TCGCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
1400910 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
1400926 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
1400943 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
1400962 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1400982 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1401002 TCGTGTTGCGA
1 TCGCGTTGCGA
1401013 AAGTAAACTA
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.08
15 3 0.03
16 2 0.02
17 2 0.02
18 21 0.21
19 36 0.36
20 29 0.29
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1400973 original size:20 final size:19
Alignment explanation
Indices: 1400939--1400993 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1400929 TTGCGATTTT
*
1400939 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1400958 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1400978 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1400994 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1401010 original size:39 final size:37
Alignment explanation
Indices: 1400873--1401012 Score: 128
Period size: 39 Copynumber: 3.8 Consensus size: 37
1400863 GAAACACAAA
1400873 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
* *
1400910 TCGCGTTGCGA-TTT--TGT--CGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGA-TTTCATT
*** *
1400943 TCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTT-CGCGTTGCGAT-TTCATT
* * *
1400982 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCATTGCGATTTTCA-TTTCGCGTTGCGA
1401013 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
32 8 0.10
33 17 0.21
34 2 0.03
36 5 0.06
37 10 0.12
38 1 0.01
39 34 0.43
40 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (37 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
Found at i:1402881 original size:14 final size:14
Alignment explanation
Indices: 1402862--1402897 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1402852 ATTGTTTAAT
1402862 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1402876 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1402890 TGATTTGT
1 TGATTTGT
1402898 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1403023 original size:14 final size:15
Alignment explanation
Indices: 1403004--1403080 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
1402994 CGAAATGGCT
1403004 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
1403018 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
1403036 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
1403055 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
1403069 ATCGCAATGCGA
1 ATCGCAA-GCGA
1403081 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:1403036 original size:19 final size:19
Alignment explanation
Indices: 1403014--1403080 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
1403004 ATCGCAACGA
1403014 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1403033 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1403051 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1403065 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1403081 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1404243 original size:24 final size:24
Alignment explanation
Indices: 1404187--1404245 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1404177 AGTCAGTATT
* *
1404187 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
1404211 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
1404235 CGAATTTTGAT
1 CGAAATTTGAT
1404246 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:1404437 original size:12 final size:12
Alignment explanation
Indices: 1404420--1404444 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1404410 ATATAATCCT
1404420 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1404432 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1404444 G
1 G
1404445 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:1406795 original size:19 final size:19
Alignment explanation
Indices: 1406740--1406836 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1406730 GGAAATTACT
1406740 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1406758 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1406772 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1406791 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1406805 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1406824 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1406837 TTTAATTTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 21
0.69 0.08 0.24
Matches are distributed among these distances:
13 1 0.02
14 18 0.30
15 1 0.02
16 6 0.10
17 2 0.03
18 9 0.15
19 24 0.39
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1406798 original size:33 final size:33
Alignment explanation
Indices: 1406740--1406832 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1406730 GGAAATTACT
1406740 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1406772 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1406805 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1406833 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 16 0.27
33 43 0.73
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1406854 original size:19 final size:20
Alignment explanation
Indices: 1406832--1406874 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1406822 AAATCGCAAC
1406832 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1406851 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1406871 GCGA
1 GCGA
1406875 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1406859 original size:14 final size:14
Alignment explanation
Indices: 1406860--1406893 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1406850 TGCGATTTTC
1406860 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1406874 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1406888 ATTTTC
1 ATTTTC
1406894 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1407034 original size:14 final size:14
Alignment explanation
Indices: 1407015--1407051 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1407005 CATCAATTAA
1407015 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1407029 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1407043 ACAAATCAA
1 ACAAATCAA
1407052 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:1408474 original size:21 final size:21
Alignment explanation
Indices: 1408408--1408474 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1408398 GTGAATCGGG
*
1408408 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1408428 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1408450 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1408471 CTCT
1 CTCT
1408475 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1408493 original size:42 final size:41
Alignment explanation
Indices: 1408408--1408530 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1408398 GTGAATCGGG
* * * * *
1408408 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1408450 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1408492 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1408531 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1410618 original size:19 final size:19
Alignment explanation
Indices: 1410532--1410683 Score: 170
Period size: 19 Copynumber: 8.1 Consensus size: 19
1410522 TCTTTTGGTT
*
1410532 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1410551 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1410571 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1410589 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1410605 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
1410625 GAAATTAAAATCGTAACGC
1 GAAATGAAAATCGCAACGC
1410644 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1410663 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1410682 GA
1 GA
1410684 TTTTGGTTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 52 0.46
20 44 0.39
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1410618 original size:33 final size:34
Alignment explanation
Indices: 1410557--1410621 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1410547 ACGAGATAAT
**
1410557 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
1410591 GAGAATCGCAACGC-GAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGGAAATGAAAATCGCAAC
1410622 CGCGAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
Found at i:1410648 original size:39 final size:38
Alignment explanation
Indices: 1410532--1410683 Score: 170
Period size: 39 Copynumber: 4.1 Consensus size: 38
1410522 TCTTTTGGTT
* *
1410532 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
1410571 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
1410605 GAAATGAAAATCGCAACCGCGAAATTAAAATCGTAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
1410644 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1410682 GA
1 GA
1410684 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
33 14 0.15
34 14 0.15
35 1 0.01
36 2 0.02
38 23 0.24
39 27 0.28
40 14 0.15
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1411342 original size:20 final size:20
Alignment explanation
Indices: 1411257--1411350 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1411247 CGCTAAGTAA
*
1411257 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
1411277 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1411297 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1411318 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1411338 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1411351 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1411369 original size:41 final size:41
Alignment explanation
Indices: 1411339--1411434 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
1411329 ATAGTCAGTA
* * *
1411339 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1411380 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1411421 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1411435 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1411383 original size:20 final size:20
Alignment explanation
Indices: 1411339--1411431 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1411329 ATAGTCAGTA
* **
1411339 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1411360 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1411380 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
1411401 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1411421 TCGCATTGCGA
1 TCGCATTGCGA
1411432 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1415829 original size:14 final size:14
Alignment explanation
Indices: 1415807--1415836 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1415797 GATCATATAA
1415807 ATGACCACTTAACT
1 ATGACCACTTAACT
*
1415821 ATGATCACTTAACT
1 ATGACCACTTAACT
1415835 AT
1 AT
1415837 TTAATTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (14 bp):
ATGACCACTTAACT
Found at i:1418958 original size:14 final size:14
Alignment explanation
Indices: 1418939--1418975 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
1418929 ATATGTTAAT
*
1418939 AATATAATTTTTTG
1 AATATAATTTTTTC
1418953 AATAT-A-TTTTTC
1 AATATAATTTTTTC
1418965 AATATAATTTT
1 AATATAATTTT
1418976 AAAATGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 10 0.50
13 2 0.10
14 8 0.40
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (14 bp):
AATATAATTTTTTC
Found at i:1422262 original size:20 final size:20
Alignment explanation
Indices: 1422234--1422386 Score: 103
Period size: 20 Copynumber: 7.5 Consensus size: 20
1422224 TCCAGATTCC
1422234 CAATGCGATTCTGACTATCG
1 CAATGCGATTCTGACTATCG
* ** *
1422254 CATTGCGATT-TTTCAAATTCG
1 CAATGCGATTCTGAC-TA-TCG
* *
1422275 CATTGCGATTTTCCGACTATCG
1 CAATGCGA--TTCTGACTATCG
* * *
1422297 CAATGCGAATATGTA-AATCG
1 CAATGCGATTCTG-ACTATCG
* *
1422317 CAATGCGAGTATGACTATCG
1 CAATGCGATTCTGACTATCG
*
1422337 CAATGCGATTCTGACTGTCG
1 CAATGCGATTCTGACTATCG
* * *
1422357 CAACGTGATGCTGACTATCG
1 CAATGCGATTCTGACTATCG
*
1422377 CATTGCGATT
1 CAATGCGATT
1422387 TTCAAAGCGC
Statistics
Matches: 100, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
19 3 0.03
20 71 0.71
21 12 0.12
22 10 0.10
23 3 0.03
24 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (20 bp):
CAATGCGATTCTGACTATCG
Found at i:1422586 original size:22 final size:22
Alignment explanation
Indices: 1422535--1422587 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1422525 CACTCTCTAA
* * *
1422535 GGCGACATCTGTCCCCATCTTC
1 GGCGAAATCAGTCCCCATCTCC
* *
1422557 GACAAAATCAGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
1422579 GGCGAAATC
1 GGCGAAATC
1422588 TGTCTATCTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GGCGAAATCAGTCCCCATCTCC
Found at i:1423077 original size:20 final size:20
Alignment explanation
Indices: 1422973--1423079 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
1422963 AGAATCGCAA
*
1422973 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1422992 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1423011 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
* ** *
1423031 TACGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1423051 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1423071 TGCGATTTT
1 TGCGATTTT
1423080 AAGTTTCAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 26 0.34
20 50 0.66
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1424050 original size:17 final size:18
Alignment explanation
Indices: 1424018--1424051 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1424008 TTCCAAAATT
*
1424018 ACAATTAACTATTATTTA
1 ACAATTAACTAATATTTA
1424036 ACAATT-ACTAATATTT
1 ACAATTAACTAATATTT
1424052 GTTATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
ACAATTAACTAATATTTA
Found at i:1424667 original size:18 final size:18
Alignment explanation
Indices: 1424644--1424693 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1424634 TTTACTCGTA
1424644 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1424662 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1424680 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1424694 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1424866 original size:20 final size:20
Alignment explanation
Indices: 1424841--1424928 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
1424831 TAGTTTACTT
*
1424841 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1424861 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1424881 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
** *
1424901 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAAAATGACTA
1424921 TCGCAACG
1 TCGCAACG
1424929 AAAAAATCGC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1424998 original size:20 final size:19
Alignment explanation
Indices: 1424973--1425037 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
1424963 GAATCTCTCA
1424973 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTC-AATTCGCG
*
1424993 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCA-ATTCGCG
* *
1425013 TTGTGATAGTC-ATTCGTG
1 TTGCGATAGTCAATTCGCG
1425031 TTGCGAT
1 TTGCGAT
1425038 TTTAAGTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 11 0.28
19 1 0.03
20 27 0.69
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (19 bp):
TTGCGATAGTCAATTCGCG
Found at i:1425568 original size:18 final size:20
Alignment explanation
Indices: 1425529--1425570 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1425519 CTCACCTGTC
1425529 ATCGTTCAAGAGGGTTCCCCT
1 ATCGTTCAAGAGGG-TCCCCT
1425550 ATCGTTCAAGA-GG-CCCCT
1 ATCGTTCAAGAGGGTCCCCT
1425568 ATC
1 ATC
1425571 ATCCCTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGTTCAAGAGGGTCCCCT
Found at i:1425602 original size:21 final size:21
Alignment explanation
Indices: 1425578--1425634 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
1425568 ATCATCCCTA
1425578 AAGAGTCCCCTCCCACCGTTC
1 AAGAGTCCCCTCCCACCGTTC
* * * * *
1425599 AAGAGGCCACTGCCATCGTTG
1 AAGAGTCCCCTCCCACCGTTC
1425620 AAGAGAT-CCCTCCCA
1 AAGAG-TCCCCTCCCA
1425635 ACATTCTAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.39, G:0.19, T:0.18
Consensus pattern (21 bp):
AAGAGTCCCCTCCCACCGTTC
Found at i:1425985 original size:12 final size:12
Alignment explanation
Indices: 1425968--1426002 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1425958 GGAGGGTAAG
1425968 TCTTATATTTCT
1 TCTTATATTTCT
1425980 TCTTATATTTCT
1 TCTTATATTTCT
1425992 TCTTATATTTC
1 TCTTATATTTC
1426003 ATTTTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTATATTTCT
Found at i:1427081 original size:14 final size:14
Alignment explanation
Indices: 1427044--1427105 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1427034 TTGCTTGTTT
*
1427044 AATTGATTTATAAA
1 AATTGATTTGTAAA
1427058 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1427072 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1427087 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1427101 TAATT
1 -AATT
1427106 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1427257 original size:20 final size:20
Alignment explanation
Indices: 1427204--1427257 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1427194 AGGTACACTT
* **
1427204 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
1427224 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
1427244 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
1427258 TCAATTCGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:1427304 original size:20 final size:20
Alignment explanation
Indices: 1427251--1427475 Score: 243
Period size: 20 Copynumber: 11.7 Consensus size: 20
1427241 AAATCGCAAC
* *
1427251 GCGAAAGTC-AATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
1427270 GCGATAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1427289 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1427309 GCGATAGTCAAA-TAGCCGTT
1 GCGATAGTCAAATTCG-CGTT
1427329 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
1427349 GCGATAGACAAATTAGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
1427369 GCGATAGTTATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
1427389 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
1427409 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* *
1427423 ACGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1427443 GCGATAGTTAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1427463 GCGATATTCAAAT
1 GCGATAGTCAAAT
1427476 GAATGTGTAA
Statistics
Matches: 171, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
14 10 0.06
16 1 0.01
18 1 0.01
19 27 0.16
20 130 0.76
21 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:1427698 original size:140 final size:140
Alignment explanation
Indices: 1427446--1427715 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
1427436 TCGCGTTGCG
* *
1427446 ATAGTTAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
1427511 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1427576 AATACACATA
131 AATACACATA
1427586 ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1427651 TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1427716 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1427798 original size:18 final size:18
Alignment explanation
Indices: 1427775--1427809 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1427765 AAGCCGGTTG
*
1427775 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1427793 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1427810 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1430979 original size:20 final size:20
Alignment explanation
Indices: 1430956--1431022 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1430946 AATCGCGTTA
*
1430956 CGATAGTTAGATTCGCATTG
1 CGATAGTTATATTCGCATTG
* *
1430976 CGATAGTCATAATCGCATTG
1 CGATAGTTATATTCGCATTG
*
1430996 TGAT--TTACATATTCGCATTG
1 CGATAGTT--ATATTCGCATTG
1431016 CGATAGT
1 CGATAGT
1431023 CGGAAAATCG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 1 0.03
20 34 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (20 bp):
CGATAGTTATATTCGCATTG
Found at i:1434981 original size:25 final size:21
Alignment explanation
Indices: 1434934--1434989 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1434924 TAAACGTTCT
1434934 TCGATCGAATTAATTCGGTGA
1 TCGATCGAATTAATTCGGTGA
*
1434955 TCGATCGAATTAATTTGGT-A
1 TCGATCGAATTAATTCGGTGA
1434975 GTCGATCGAATTAAT
1 -TCGATCGAATTAAT
1434990 CGAATTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGATCGAATTAATTCGGTGA
Found at i:1435335 original size:21 final size:21
Alignment explanation
Indices: 1435311--1435358 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1435301 TAAATTATTG
*
1435311 TTAATTTAA-TCATTCTAATTT
1 TTAATTAAATTCA-TCTAATTT
*
1435332 TTAA-TAAATTCATCTTATTT
1 TTAATTAAATTCATCTAATTT
1435352 TTAATTA
1 TTAATTA
1435359 TATATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATTAAATTCATCTAATTT
Found at i:1436976 original size:13 final size:13
Alignment explanation
Indices: 1436958--1436982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1436948 AGCCATTAGT
1436958 TTCATAATTAATA
1 TTCATAATTAATA
1436971 TTCATAATTAAT
1 TTCATAATTAAT
1436983 GTGACATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATAATTAATA
Found at i:1443151 original size:22 final size:21
Alignment explanation
Indices: 1443109--1443148 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1443099 GAGTTTATTT
*
1443109 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1443130 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1443149 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1453653 original size:42 final size:44
Alignment explanation
Indices: 1453580--1453672 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 44
1453570 AACCCAAATA
1453580 TATTAATATTTTAAAATAATTAAAATAATATATTTTATAATTATT
1 TATTAATATTTTAAAATAATTAAAATAATATATTTTATAA-TATT
* * * *
1453625 TATT-ATA-TTTAAAAT-GTTAAATTTATATATTTTGTAATATT
1 TATTAATATTTTAAAATAATTAAAATAATATATTTTATAATATT
1453666 T-TTAATA
1 TATTAATA
1453673 ATTAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
40 2 0.05
41 8 0.19
42 18 0.42
43 8 0.19
44 3 0.07
45 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (44 bp):
TATTAATATTTTAAAATAATTAAAATAATATATTTTATAATATT
Found at i:1453682 original size:18 final size:17
Alignment explanation
Indices: 1453661--1453696 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1453651 ATATTTTGTA
1453661 ATATTTTTAATAATTAAT
1 ATATTTTTAATAA-TAAT
1453679 ATATTTTTAATAATAAT
1 ATATTTTTAATAATAAT
1453696 A
1 A
1453697 ATAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTTTAATAATAAT
Found at i:1465042 original size:39 final size:39
Alignment explanation
Indices: 1464996--1465091 Score: 117
Period size: 37 Copynumber: 2.5 Consensus size: 39
1464986 ATACTTGAAT
**
1464996 TTTTTTTTTCATTTTAGTAT-TTCTCATTAAAAATTTT-A
1 TTTTTTTTTCATTTTAGTATCTTCT-ACCAAAAATTTTAA
*
1465034 TTTATTTTT-ATTTTAGTATCTTCTACCAAAAATTTTAA
1 TTTTTTTTTCATTTTAGTATCTTCTACCAAAAATTTTAA
* *
1465072 TTTTTGTTTCATTTTTGTAT
1 TTTTTTTTTCATTTTAGTAT
1465092 ACCGCTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.41
38 20 0.41
39 9 0.18
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (39 bp):
TTTTTTTTTCATTTTAGTATCTTCTACCAAAAATTTTAA
Found at i:1474831 original size:21 final size:21
Alignment explanation
Indices: 1474807--1474846 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1474797 TTTATTTTAT
1474807 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1474828 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1474847 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1474894 original size:33 final size:33
Alignment explanation
Indices: 1474841--1474939 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1474831 TTTGTTTCAA
1474841 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1474873 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * * *
1474906 TTATCAAACTTGTAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1474939 T
1 T
1474940 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1474968 original size:13 final size:13
Alignment explanation
Indices: 1474950--1474979 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1474940 ATGTTGAGTT
1474950 AATTAAGTATTTA
1 AATTAAGTATTTA
*
1474963 AATTAAGTATTTG
1 AATTAAGTATTTA
1474976 AATT
1 AATT
1474980 TATCGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (13 bp):
AATTAAGTATTTA
Found at i:1475201 original size:21 final size:21
Alignment explanation
Indices: 1475175--1475231 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1475165 TGGAGCGTGG
*
1475175 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
1475196 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1475217 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
1475232 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:1475423 original size:15 final size:15
Alignment explanation
Indices: 1475398--1475453 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1475388 ATCTGGAATA
*
1475398 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1475413 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1475428 TAAAAAATCCGGTTTTT
1 T-TAAAA-CCGGTTTTT
1475445 TTAAAACCG
1 TTAAAACCG
1475454 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 17 0.50
16 7 0.21
17 10 0.29
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1477617 original size:32 final size:32
Alignment explanation
Indices: 1477576--1477637 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1477566 TAAAGATGTG
1477576 ATCAAATGCAAATTAAGAGAAATTTAACAACA
1 ATCAAATGCAAATTAAGAGAAATTTAACAACA
*
1477608 ATCAAATGCAAATTAGGAGAAATTTAACAA
1 ATCAAATGCAAATTAAGAGAAATTTAACAA
1477638 TAATGAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (32 bp):
ATCAAATGCAAATTAAGAGAAATTTAACAACA
Found at i:1480174 original size:45 final size:45
Alignment explanation
Indices: 1480125--1480339 Score: 306
Period size: 45 Copynumber: 4.8 Consensus size: 45
1480115 CACCTATATG
* * *
1480125 CATTTCAATTATAACATTC-TTTCATGCCTTTTATACAATATTATA
1 CATTTCATTTATGACA-TCATTTCATGCCTTTTATACACTATTATA
* * * *
1480170 CATTTCATTTCTGGCATCCTTTCATGCCTTTTATACACTATCATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
* *
1480215 CATTTCATTTATGACATCTTTTCATTCCTTTTATACACTATTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
*
1480260 CATTTCATTTATGACATCATTTCATGCCTTTTATGCACTATTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
* *
1480305 CATTTCATTTATGGCATCATTTCATTCCTTTTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATA
1480340 TTCTGTTTAC
Statistics
Matches: 152, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
44 2 0.01
45 150 0.99
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.48
Consensus pattern (45 bp):
CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
Found at i:1480361 original size:135 final size:135
Alignment explanation
Indices: 1480125--1480374 Score: 333
Period size: 135 Copynumber: 1.9 Consensus size: 135
1480115 CACCTATATG
* *
1480125 CATTTCAATTATAACATTCTTTCATGCCTTTTATACAATATTATACATTTCATTTCTGGCATCCT
1 CATTTCAATTATAACATTCTTTCATGCCTTTTATACAATATTATACATTTCATTTATGGCATCAT
* *
1480190 TTCATGCCTTTTATACACTATCATACATTTCATTTATGACATCTTTTCATTCCTTTTATACACTA
66 TTCATGCCTTTTATACACTATCATACATTTCATTTATAACATCTATTCATTCCTTTTATACACTA
1480255 TTATA
131 TTATA
* * * *
1480260 CATTTCATTTATGACA-TCATTTCATGCCTTTTATGCACTATTATACATTTCATTTATGGCATCA
1 CATTTCAATTATAACATTC-TTTCATGCCTTTTATACAATATTATACATTTCATTTATGGCATCA
* ** * * * *
1480324 TTTCATTCCTTTTATATTCTGT-TTACGTTTTCCTTTATAACATCTATTCAT
65 TTTCATGCCTTTTATACACTATCATAC-ATTTCATTTATAACATCTATTCAT
1480375 ACTAATTATG
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
134 5 0.05
135 93 0.95
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (135 bp):
CATTTCAATTATAACATTCTTTCATGCCTTTTATACAATATTATACATTTCATTTATGGCATCAT
TTCATGCCTTTTATACACTATCATACATTTCATTTATAACATCTATTCATTCCTTTTATACACTA
TTATA
Found at i:1480384 original size:90 final size:90
Alignment explanation
Indices: 1480112--1480386 Score: 263
Period size: 90 Copynumber: 3.1 Consensus size: 90
1480102 CATGCTTATA
* * * * *
1480112 ATGCACCTAT-ATGCATTTCAATTATAACATTC-TTTCATGCCTTTTATACAATATTATACATTT
1 ATGCA-CTATCATACATTTCATTTATGACA-TCATTTCATTCCTTTTATACACTATTATACATTT
* ** * * *
1480175 CATTTCTGGCATCCTTTCATGCCTTTT
64 CATTTATAACATCATTTCATGACTATT
* *
1480202 ATACACTATCATACATTTCATTTATGACATCTTTTCATTCCTTTTATACACTATTATACATTTCA
1 ATGCACTATCATACATTTCATTTATGACATCATTTCATTCCTTTTATACACTATTATACATTTCA
* * *
1480267 TTTATGACATCATTTCATGCCTTTT
66 TTTATAACATCATTTCATGACTATT
* * ** * *
1480292 ATGCACTATTATACATTTCATTTATGGCATCATTTCATTCCTTTTATATTCTGTT-TACGTTTTC
1 ATGCACTATCATACATTTCATTTATGACATCATTTCATTCCTTTTATACACTATTATAC-ATTTC
*
1480356 CTTTATAACATC-TATTCAT-ACTAATT
65 ATTTATAACATCAT-TTCATGACT-ATT
1480382 ATGCA
1 ATGCA
1480387 TCGTTGTACA
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
89 12 0.08
90 147 0.92
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (90 bp):
ATGCACTATCATACATTTCATTTATGACATCATTTCATTCCTTTTATACACTATTATACATTTCA
TTTATAACATCATTTCATGACTATT
Found at i:1480624 original size:68 final size:68
Alignment explanation
Indices: 1480536--1480716 Score: 274
Period size: 68 Copynumber: 2.7 Consensus size: 68
1480526 TTAGCTGTTT
* *
1480536 ATCTAACTGGCATAATTGACACATTTTTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG-CA
1 ATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTAGGCCTCAAAAGAACTTAGTC-
1480600 TTTC
65 TTTC
* *
1480604 ATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAAGCACTTAGTCT
1 ATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTAGGCCTCAAAAGAACTTAGTCT
1480669 TTC
66 TTC
* * * *
1480672 ATCTAACTGACATAATTGACACATTCATGCCAATTGCACAGTTAG
1 ATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTAG
1480717 ATCATTATTC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
68 103 0.99
69 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (68 bp):
ATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTAGGCCTCAAAAGAACTTAGTCT
TTC
Found at i:1481003 original size:55 final size:55
Alignment explanation
Indices: 1480883--1481040 Score: 221
Period size: 55 Copynumber: 2.9 Consensus size: 55
1480873 ACACGTAGTA
* ** *
1480883 CCTATACGG-TAGTTCATCGACTCATGATGAATTATGTGG-GTTGCACACATCGTG
1 CCTATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATCGTG
*
1480937 CCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATCGTG
1 CCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATCGTG
* * *
1480992 CCTATATGGTTATTCATAAACTTATGATGAATTCCGTGGATTTGCACAC
1 CCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACAC
1481041 TTAGTGCCGA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
54 32 0.34
55 61 0.66
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (55 bp):
CCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATCGTG
Done.