Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1125009 original size:15 final size:17
Alignment explanation
Indices: 1124972--1125010 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1124962 AGACAGGTAT
1124972 ATATTA-AAATATAAAA
1 ATATTATAAATATAAAA
1124988 ATATTATAAATA-AAAA
1 ATATTATAAATATAAAA
1125004 AT-TTATA
1 ATATTATA
1125011 CATTTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATTATAAATATAAAA
Found at i:1128976 original size:21 final size:22
Alignment explanation
Indices: 1128950--1128995 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1128940 GGAATAGTGG
*
1128950 ATGGCCCC-AACATCATTGTAA
1 ATGGCCCCAAACATCACTGTAA
*
1128971 ATGGCCCCAAACATCACTGTGA
1 ATGGCCCCAAACATCACTGTAA
1128993 ATG
1 ATG
1128996 AGGGTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (22 bp):
ATGGCCCCAAACATCACTGTAA
Found at i:1132262 original size:19 final size:19
Alignment explanation
Indices: 1132238--1132276 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1132228 AATCACTGCC
1132238 CAGAGCAAATGAAAGCTAA
1 CAGAGCAAATGAAAGCTAA
1132257 CAGAGCAAATGAAAGCTAA
1 CAGAGCAAATGAAAGCTAA
1132276 C
1 C
1132277 CAAAACTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (19 bp):
CAGAGCAAATGAAAGCTAA
Found at i:1154109 original size:20 final size:20
Alignment explanation
Indices: 1154084--1154130 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1154074 CACGAAATGT
**
1154084 AAGATTATCAGTGGGAATAA
1 AAGATTATCAGTGAAAATAA
1154104 AAGATTATCAGTGAAAATAA
1 AAGATTATCAGTGAAAATAA
1154124 AAGATTA
1 AAGATTA
1154131 CCAGGGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (20 bp):
AAGATTATCAGTGAAAATAA
Found at i:1155385 original size:17 final size:17
Alignment explanation
Indices: 1155363--1155397 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1155353 AATGATTAGG
*
1155363 TGAATCATTTGTCATTC
1 TGAATCAATTGTCATTC
1155380 TGAATCAATTGTCATTC
1 TGAATCAATTGTCATTC
1155397 T
1 T
1155398 TTTAACTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (17 bp):
TGAATCAATTGTCATTC
Found at i:1170191 original size:22 final size:22
Alignment explanation
Indices: 1170166--1170215 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1170156 GATGTACCGA
1170166 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
1170188 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
*
1170210 AACGCG
1 ATCGCG
1170216 TTCGTACCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
ATCGCGATTTTGAAACGATCCG
Found at i:1176224 original size:2 final size:2
Alignment explanation
Indices: 1176217--1176245 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1176207 TTGGTTAATT
1176217 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 T
1176246 TATGGGATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1179224 original size:24 final size:25
Alignment explanation
Indices: 1179188--1179236 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1179178 ATATATATTT
*
1179188 TTAAATACTTTTTA-CATTAACTTA
1 TTAAATACTTTTTATAATTAACTTA
1179212 TTAAATA-TATTTTATAATTAACTTA
1 TTAAATACT-TTTTATAATTAACTTA
1179237 ATTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 12 0.55
25 9 0.41
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATACTTTTTATAATTAACTTA
Found at i:1179304 original size:32 final size:31
Alignment explanation
Indices: 1179266--1179348 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
1179256 TTATTTTTAA
1179266 TTTAAAAATATATATATTATT-TTATCTAAACT
1 TTTAAAAATATAT-T-TTATTATTATCTAAACT
* * * *
1179298 TTTAAAACTACATTTTATTATTATTTTAACT
1 TTTAAAAATATATTTTATTATTATCTAAACT
1179329 TTTCAAAGAATATATTTTAT
1 TTT-AAA-AATATATTTTAT
1179349 CTTAATTTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 5 0.12
31 13 0.31
32 14 0.33
33 10 0.24
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTAAAAATATATTTTATTATTATCTAAACT
Found at i:1179475 original size:27 final size:27
Alignment explanation
Indices: 1179440--1179503 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
1179430 CATAAATTAT
1179440 ATATTTTTAAATAAAAATAATAATAAA
1 ATATTTTTAAATAAAAATAATAATAAA
* **
1179467 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATAAAAATAATAATAAA
*
1179494 ATATATTTAA
1 ATATTTTTAA
1179504 TAACTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATAAAAATAATAATAAA
Found at i:1179519 original size:25 final size:26
Alignment explanation
Indices: 1179457--1179550 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 26
1179447 TAAATAAAAA
1179457 TAATA-ATAAAATATTTTTAAATTAAGT
1 TAATATATAAAATATTTTT-AA-TAAGT
* *
1179484 TAATA-ATAAAATATATTTAATAACT
1 TAATATATAAAATATTTTTAATAAGT
*
1179509 TAATATA-AAAATATTTTTTA-AAGT
1 TAATATATAAAATATTTTTAATAAGT
1179533 TAATATATATAAAATATT
1 T-A-ATATATAAAATATT
1179551 ATGAATTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.07
25 21 0.36
26 8 0.14
27 25 0.43
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATATAAAATATTTTTAATAAGT
Found at i:1179535 original size:24 final size:26
Alignment explanation
Indices: 1179457--1179550 Score: 90
Period size: 25 Copynumber: 3.7 Consensus size: 26
1179447 TAAATAAAAA
*
1179457 TAATA-ATAAAATATTTTTAAATTAAGT
1 TAATATATAAAATATATTT-AA-TAAGT
*
1179484 TAATA-ATAAAATATATTTAATAACT
1 TAATATATAAAATATATTTAATAAGT
* *
1179509 TAATATA-AAAATATTTTTTA-AAGT
1 TAATATATAAAATATATTTAATAAGT
1179533 TAATATATATAAA-ATATT
1 TAATATATA-AAATATATT
1179551 ATGAATTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.17
25 25 0.43
26 6 0.10
27 17 0.29
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATATAAAATATATTTAATAAGT
Found at i:1184051 original size:21 final size:21
Alignment explanation
Indices: 1184025--1184064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1184015 CCAGAACCCA
*
1184025 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1184046 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1184065 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1184094 original size:21 final size:23
Alignment explanation
Indices: 1184046--1184094 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1184036 ATTCCCCTGT
1184046 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
1184069 AGGGGGAATCGGTT-TCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
1184090 GGGGG
1 GGGGG
1184095 ATCGATTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 13 0.57
ACGTcount: A:0.18, C:0.20, G:0.41, T:0.20
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1184106 original size:19 final size:20
Alignment explanation
Indices: 1184047--1184106 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
1184037 TTCCCCTGTG
*
1184047 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AA
* *
1184070 GGGGGAATCGGTTTCCTCAA
1 GGGGGAATCGATTCCCTCAA
1184090 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1184107 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 2 0.06
22 2 0.06
23 13 0.38
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:1190568 original size:65 final size:65
Alignment explanation
Indices: 1190430--1190593 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 65
1190420 CCGTTGGACC
* * * * *
1190430 CTTAGTGCATCGATGCATAAAGTGCATTCAATG-TTTCAAACAAGCCCGAGTGTATCGATGCATG
1 CTTA-TGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATG
1190494 G
65 G
* * *
1190495 CTTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAATATGAGTGCATCGATGCATG
1 CTTATGCATCGATGCATAAAATGCATTCGATGTTTTCA-AACAAACACGAGTGCATCGATGCATG
1190559 G
65 G
*
1190560 -TATATGCATCGATGCATATAATGCATTCGATGTT
1 CT-TATGCATCGATGCATAAAATGCATTCGATGTT
1190594 CAATTTATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 27 0.31
65 57 0.66
66 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
CTTATGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATGG
Found at i:1195696 original size:20 final size:17
Alignment explanation
Indices: 1195673--1195712 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
1195663 ATTTTTAAAA
1195673 TATTAAAATAATTTATTTAT
1 TATTAAAAT--TTTATTT-T
1195693 TATTAAAATTTTATTTT
1 TATTAAAATTTTATTTT
1195710 TAT
1 TAT
1195713 AATTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAAATTTTATTTT
Found at i:1195890 original size:27 final size:27
Alignment explanation
Indices: 1195868--1195919 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1195858 AGATTATTAT
*
1195868 ATTATTAAT-ATATAAAAATATTATTC
1 ATTATCAATAATATAAAAATATTATTC
* *
1195894 ATTATCAATAATTTAATAATATTATT
1 ATTATCAATAATATAAAAATATTATT
1195920 TCTATGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTATCAATAATATAAAAATATTATTC
Found at i:1196067 original size:28 final size:27
Alignment explanation
Indices: 1195959--1196068 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 27
1195949 ATTATATATT
* *
1195959 TATTATATTATTAAAATAAAATATAATA
1 TATTATATTATTATAATATAATA-AATA
* **
1195987 TCTTATATTATTATAATATAATTGAT-
1 TATTATATTATTATAATATAATAAATA
* *
1196013 TATT-TATTAATATTAA-A-AATATA-A
1 TATTATATTATTA-TAATATAATAAATA
1196037 TATTATATTATTATAATATTAATAAATA
1 TATTATATTATTATAATA-TAATAAATA
1196065 TATT
1 TATT
1196069 TAAATATTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
24 11 0.17
25 16 0.25
26 6 0.09
27 7 0.11
28 24 0.38
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTATATTATTATAATATAATAAATA
Found at i:1196075 original size:50 final size:50
Alignment explanation
Indices: 1195976--1196076 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 50
1195966 TTATTAAAAT
**
1195976 AAAATATAATATCTTATATTATTATAATATAATTGATTATTTATTAATATTA
1 AAAATATAATA-CTTATATTATTATAATATAATAAATTATTTA-TAATATTA
1196028 AAAATATAATA-TTATATTATTATAATATTAATAAATATATTTA-AATATT
1 AAAATATAATACTTATATTATTATAATA-TAATAAAT-TATTTATAATATT
1196077 TTAATAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
50 22 0.49
51 6 0.13
52 17 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (50 bp):
AAAATATAATACTTATATTATTATAATATAATAAATTATTTATAATATTA
Found at i:1203728 original size:30 final size:29
Alignment explanation
Indices: 1203694--1203767 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
1203684 ACTAAAAATT
1203694 TTATAAAATCACAAAAATT-AGAGGCCCTAA
1 TTATAAAAT-ACAAAAATTAAGA-GCCCTAA
* *
1203724 TTATACATATA-AAAAATTAAGAGTCCTAA
1 TTATA-AAATACAAAAATTAAGAGCCCTAA
1203753 TTA-AAAATACAAAAA
1 TTATAAAATACAAAAA
1203768 AAAACTGCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 4 0.11
28 6 0.16
29 16 0.42
30 9 0.24
31 3 0.08
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (29 bp):
TTATAAAATACAAAAATTAAGAGCCCTAA
Found at i:1204996 original size:21 final size:21
Alignment explanation
Indices: 1204972--1205017 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1204962 AAATCATAGA
1204972 ATATAAACACTAATAAAATAT
1 ATATAAACACTAATAAAATAT
* * * *
1204993 ATATAATCATTAATAATATTT
1 ATATAAACACTAATAAAATAT
1205014 ATAT
1 ATAT
1205018 GATAAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAAACACTAATAAAATAT
Found at i:1211671 original size:58 final size:59
Alignment explanation
Indices: 1211572--1211682 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 59
1211562 GGAATATACA
**
1211572 TATAGTTTGGGATGAAACTTAAACATTCAAAAGTTTGAGGACTAATTTAGAATAAATGT
1 TATAGTTTGGGATGAAACTTAAACATTCAAAAGTTCAAGGACTAATTTAGAATAAATGT
* ***
1211631 TATAGTTTGGGATGGAACTT-AGTGTTCAAAAGTTCAAGGACTAATTTAGAAT
1 TATAGTTTGGGATGAAACTTAAACATTCAAAAGTTCAAGGACTAATTTAGAAT
1211683 GATAGTCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 27 0.59
59 19 0.41
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (59 bp):
TATAGTTTGGGATGAAACTTAAACATTCAAAAGTTCAAGGACTAATTTAGAATAAATGT
Found at i:1221336 original size:61 final size:62
Alignment explanation
Indices: 1221230--1221346 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 62
1221220 CTCTAAAATT
1221230 TTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
1 TTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
1221292 TTATTTTAGTATAAAAGTAAC-TTTGAAGTGTTAAATTTATTTTCAACTTTGAAGT
1 TTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGT
1221347 ATTGAAGTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 34 0.62
62 21 0.38
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (62 bp):
TTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
Found at i:1223089 original size:3 final size:3
Alignment explanation
Indices: 1223077--1223117 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1223067 CCATCGGATC
*
1223077 ATT A-T ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1223118 TGGTGTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1224472 original size:15 final size:16
Alignment explanation
Indices: 1224444--1224473 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1224434 TAAAATTTTA
1224444 TTTATATCTATTAATT
1 TTTATATCTATTAATT
1224460 TTTATAT-TATTAAT
1 TTTATATCTATTAAT
1224474 ATATGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATATCTATTAATT
Found at i:1228729 original size:16 final size:14
Alignment explanation
Indices: 1228708--1228746 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1228698 ATTTAATCAC
1228708 ATATATCATTTCCATA
1 ATATATC-TTT-CATA
*
1228724 ATATATCTTTTATA
1 ATATATCTTTCATA
1228738 ATATATCTT
1 ATATATCTT
1228747 ATTATCACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
16 7 0.32
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATCTTTCATA
Found at i:1228738 original size:14 final size:15
Alignment explanation
Indices: 1228721--1228751 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1228711 TATCATTTCC
1228721 ATAATATATCTT-TT
1 ATAATATATCTTATT
1228735 ATAATATATCTTATT
1 ATAATATATCTTATT
1228750 AT
1 AT
1228752 CACCCATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATATATCTTATT
Found at i:1229286 original size:20 final size:22
Alignment explanation
Indices: 1229256--1229310 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
1229246 ATGTTTCAAG
*
1229256 GGTATTCGATACCATCCT-TTA-
1 GGTA-TCGATACCACCCTCTTAT
*
1229277 GGTATCGATACTACCCTCTTAT
1 GGTATCGATACCACCCTCTTAT
*
1229299 AGTATCGATACC
1 GGTATCGATACC
1229311 TCTTCAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.39
21 7 0.25
22 10 0.36
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTATCGATACCACCCTCTTAT
Found at i:1241044 original size:14 final size:14
Alignment explanation
Indices: 1241025--1241054 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1241015 GAATTACATC
1241025 TTCTGGAAAATATT
1 TTCTGGAAAATATT
*
1241039 TTCTGGAAAATGTT
1 TTCTGGAAAATATT
1241053 TT
1 TT
1241055 ATGGTGTTTG
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:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (14 bp):
TTCTGGAAAATATT
Found at i:1241182 original size:22 final size:22
Alignment explanation
Indices: 1241141--1241181 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1241131 AATATATAAA
1241141 TAATATTATTTATTATAAAACT
1 TAATATTATTTATTATAAAACT
*
1241163 TAATATTA-TTATTTTAAAA
1 TAATATTATTTATTATAAAA
1241182 ATATTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTATTTATTATAAAACT
Found at i:1241597 original size:22 final size:23
Alignment explanation
Indices: 1241580--1241634 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
1241570 ATTATTATAT
1241580 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* *
1241604 TATATTTT-AAAATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
1241626 TAATATTTT
1 T-ATATTTT
1241635 TATTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 9 0.32
24 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:1248783 original size:29 final size:29
Alignment explanation
Indices: 1248751--1248807 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1248741 ATTTAAAAAT
1248751 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
1248780 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
1248808 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:1249090 original size:2 final size:2
Alignment explanation
Indices: 1249083--1249112 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1249073 TTATTATTAT
*
1249083 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1249113 AATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1249121 original size:3 final size:3
Alignment explanation
Indices: 1249113--1249178 Score: 68
Period size: 3 Copynumber: 22.3 Consensus size: 3
1249103 TATTTATATA
*
1249113 AAT AAT AAT AAT AAT AAT GA- AAT AAT AATT AA- AGA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A-AT AAT -AAT AAT
1249158 AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
1249179 TTACAAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 5 0.09
3 44 0.80
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1249156 original size:19 final size:20
Alignment explanation
Indices: 1249110--1249178 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1249100 ATATATTTAT
1249110 ATAAATAATAA-TAATAATA
1 ATAAATAATAATTAATAATA
1249129 ATGAAATAATAATTAA-AGA-A
1 AT-AAATAATAATTAATA-ATA
1249149 ATAAATAATAA-TAATAATA
1 ATAAATAATAATTAATAATA
1249168 ATAAAATAATA
1 AT-AAATAATA
1249179 TTACAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.09
19 15 0.34
20 21 0.48
21 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
ATAAATAATAATTAATAATA
Found at i:1249186 original size:12 final size:11
Alignment explanation
Indices: 1249147--1249200 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
1249137 ATAATTAAAG
*
1249147 AAATAAATAATA
1 AAAT-AATATTA
*
1249159 ATAATAATAATA
1 A-AATAATATTA
1249171 AAATAATATTA
1 AAATAATATTA
1249182 CAAATAATGATTA
1 -AAATAAT-ATTA
1249195 AAATAA
1 AAATAA
1249201 AAGGAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
11 9 0.24
12 22 0.58
13 7 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AAATAATATTA
Found at i:1249187 original size:36 final size:38
Alignment explanation
Indices: 1249110--1249188 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
1249100 ATATATTTAT
* *
1249110 ATAAATAATAATAATAATAATGAAATAATAATTAAAGAA
1 ATAAATAATAATAATAATAATAAAATAATAATT-AACAA
1249149 ATAAATAATAATAATAATAATAAAATAAT-ATT-ACAA
1 ATAAATAATAATAATAATAATAAAATAATAATTAACAA
1249185 ATAA
1 ATAA
1249189 TGATTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 7 0.18
38 3 0.08
39 28 0.74
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (38 bp):
ATAAATAATAATAATAATAATAAAATAATAATTAACAA
Found at i:1250330 original size:3 final size:3
Alignment explanation
Indices: 1250317--1250370 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
1250307 ATTATTTATT
*
1250317 TAA TTA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1250363 TAA TAA TA
1 TAA TAA TA
1250371 TATATGAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1250572 original size:46 final size:45
Alignment explanation
Indices: 1250501--1250600 Score: 164
Period size: 46 Copynumber: 2.2 Consensus size: 45
1250491 GGAAATGTTA
* *
1250501 AAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGGTTTTG
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAA-GGCTTTG
*
1250547 AAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
1250592 AAAACATCA
1 AAAACATCA
1250601 AAAAGCTCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 15 0.29
46 36 0.71
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
Found at i:1250668 original size:76 final size:76
Alignment explanation
Indices: 1250533--1250805 Score: 467
Period size: 76 Copynumber: 3.6 Consensus size: 76
1250523 TTACAGATGA
* *
1250533 CCCGAAGG-GTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1250597 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
1250608 CCTGAAGGTTTTTTGGAAACATCTTGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1250673 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1250684 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1250749 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1250760 CCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1250806 TGGGAAATAG
Statistics
Matches: 188, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
75 7 0.04
76 181 0.96
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:1251055 original size:184 final size:184
Alignment explanation
Indices: 1250746--1251353 Score: 1171
Period size: 184 Copynumber: 3.3 Consensus size: 184
1250736 AGGCTTTGAA
*
1250746 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1250811 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
1250876 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
* *
1250930 AACATCAAAAATCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
*
1250995 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCATACTTTTTAACAATTTCATTTTAGA
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
1251060 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
1251114 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1251179 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
66 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
1251244 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
*
1251298 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACA
1251354 TATGACCCTA
Statistics
Matches: 416, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 416 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (184 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAATTTCATTTTAGA
AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
Found at i:1251424 original size:76 final size:76
Alignment explanation
Indices: 1251298--1251585 Score: 540
Period size: 76 Copynumber: 3.8 Consensus size: 76
1251288 TCAAAATAAC
* *
1251298 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACATATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1251363 AAGGCTTTGAA
66 AAGGCTTTGAA
1251374 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1251439 AAGGCTTTGAA
66 AAGGCTTTGAA
1251450 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1251515 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1251526 AACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCAGTGTAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1251586 TGGGAAATAG
Statistics
Matches: 208, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 208 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1252296 original size:23 final size:23
Alignment explanation
Indices: 1252261--1252313 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1252251 CATAAAGCTT
1252261 TCATC-TTTAAAAAGAGAATCTA
1 TCATCTTTTAAAAAGAGAATCTA
1252283 TCATCTTTTAAAAAGAGAATCTA
1 TCATCTTTTAAAAAGAGAATCTA
1252306 TCATCTTT
1 TCATCTTT
1252314 GAAGAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
TCATCTTTTAAAAAGAGAATCTA
Found at i:1259922 original size:12 final size:12
Alignment explanation
Indices: 1259907--1259956 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
1259897 GTAAAAATGA
1259907 AAATGTAAATAC
1 AAATGTAAATAC
*
1259919 AAATGTAAAAAATGC
1 AAATGT---AAATAC
*
1259934 AAATGTAAATGC
1 AAATGTAAATAC
1259946 AAATGTAAATA
1 AAATGTAAATA
1259957 TGTGAATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 22 0.67
15 11 0.33
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:1259937 original size:27 final size:27
Alignment explanation
Indices: 1259895--1259954 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
1259885 AAATGTAATT
1259895 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGTAAATACAA
* *
1259921 ATGTAAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAAATGAAAATGTAAATACAA
1259948 ATGTAAA
1 ATGTAAA
1259955 TATGTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.23
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGTAAATACAA
Found at i:1260048 original size:7 final size:7
Alignment explanation
Indices: 1260014--1260055 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1260004 ATAAAAGTAT
1260014 AAATGCA
1 AAATGCA
* *
1260021 CAATGAA
1 AAATGCA
1260028 AAATGCA
1 AAATGCA
1260035 AAGATGCA
1 AA-ATGCA
1260043 AAATGC-
1 AAATGCA
1260049 AAATGCA
1 AAATGCA
1260056 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1262121 original size:29 final size:28
Alignment explanation
Indices: 1262077--1262132 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1262067 ATTTCAAAAT
1262077 TATATTATGAAAAAAATATTAATTTATA
1 TATATTATGAAAAAAATATTAATTTATA
*
1262105 TATATTTAT-AAATAAAATATTTATTTAT
1 TATA-TTATGAAA-AAAATATTAATTTAT
1262133 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TATATTATGAAAAAAATATTAATTTATA
Found at i:1262419 original size:18 final size:16
Alignment explanation
Indices: 1262388--1262422 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1262378 ATAAATAAAA
1262388 ATATTATTTATTATAT
1 ATATTATTTATTATAT
1262404 ATATATATTTATT-TAT
1 ATAT-TATTTATTATAT
1262420 ATA
1 ATA
1262423 AATAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATTATAT
Found at i:1262438 original size:3 final size:3
Alignment explanation
Indices: 1262423--1262489 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
1262413 TATTTATATA
* * **
1262423 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
*
1262466 AAA AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1262490 TTGCAAATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:1262451 original size:11 final size:11
Alignment explanation
Indices: 1262422--1262489 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
1262412 TTATTTATAT
*
1262422 AAATAATAAAA
1 AAATAATAATA
*
1262433 ATAATAATAATG
1 A-AATAATAATA
1262445 AAATAATAATTA
1 AAATAATAA-TA
** *
1262457 AAGCAATAAAA
1 AAATAATAATA
1262468 AAATAATAATA
1 AAATAATAATA
1262479 ATAA-AATAATA
1 A-AATAATAATA
1262490 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 26 0.58
12 19 0.42
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1263791 original size:3 final size:3
Alignment explanation
Indices: 1263785--1263825 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
1263775 ATTATTTATT
1263785 TAA TAA TAA TAA TATA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
1263826 TGAAAGTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1271719 original size:55 final size:55
Alignment explanation
Indices: 1271660--1271982 Score: 538
Period size: 55 Copynumber: 5.9 Consensus size: 55
1271650 ACCAATACGA
*
1271660 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAT
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* *
1271715 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGTCCATATAG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* *
1271770 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCAAACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* *
1271825 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAATGCCCATACAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* * *
1271880 AAATTCATAAACGTATTATGAATTTCTTAGTTTTGCACACAAATTGCCCATACAT
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* *
1271935 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACGCATAGTGCC
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
1271983 ATTTGGTGAT
Statistics
Matches: 250, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 250 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (55 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
Found at i:1276601 original size:31 final size:31
Alignment explanation
Indices: 1276566--1276684 Score: 179
Period size: 31 Copynumber: 3.9 Consensus size: 31
1276556 TAATAATCTA
1276566 TCCATATGTCCCGAAGAACATAGGTAATATG
1 TCCATATGTCCCGAAGAACATAGGTAATATG
*
1276597 TCCATATGTCCCGAAGAACATAGGTAATTTG
1 TCCATATGTCCCGAAGAACATAGGTAATATG
*
1276628 TCCATATGTCCCGAATAACATAGGTAA-ACTG
1 TCCATATGTCCCGAAGAACATAGGTAATA-TG
* *
1276659 T-CATATGTCCCGAAAAACATAAGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
1276685 CCCTCAACTC
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.28
31 59 0.72
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAATATG
Found at i:1280426 original size:3 final size:3
Alignment explanation
Indices: 1280418--1280457 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
1280408 TTCAGATTTC
*
1280418 TCT TCT TCT TCTT TCT TCT CCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TCT TC-T TCT TCT TCT TCT TC-T TCT TCT TCT TC
1280458 ACCATTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1280443 original size:16 final size:16
Alignment explanation
Indices: 1280422--1280457 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1280412 GATTTCTCTT
1280422 CTTCTTCTTTCTTCTC
1 CTTCTTCTTTCTTCTC
*
1280438 CTTCTTCTTTCTTCTT
1 CTTCTTCTTTCTTCTC
1280454 CTTC
1 CTTC
1280458 ACCATTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTCTTCTTTCTTCTC
Found at i:1280457 original size:13 final size:13
Alignment explanation
Indices: 1280418--1280456 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1280408 TTCAGATTTC
1280418 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
*
1280431 TCTTCTCCTTC-T
1 TCTTCTTCTTCTT
1280443 TCTTTCTTCTTCTT
1 TC-TTCTTCTTCTT
1280457 CACCATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 3 0.14
13 18 0.82
14 1 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:1281105 original size:63 final size:64
Alignment explanation
Indices: 1280995--1281114 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 64
1280985 AACATAAAGA
* **
1280995 GCATCGATGCACTCTTTTAAAATACAAACATCGAATGTCATTAATGCATCA-ATGCATAAGGAGT
1 GCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATTAATGCAT-AGATGCATAAGGAGT
* * *
1281059 GCATCGATGCACCCCCTT-AAATATAAACATCGAATAG-GATTTATGCATAGATGCAT
1 GCATCGATGCACCCCCTTAAAATACAAACATCGAAT-GTCATTAATGCATAGATGCAT
1281115 GGTGTGGTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
62 1 0.02
63 31 0.65
64 16 0.33
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (64 bp):
GCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATTAATGCATAGATGCATAAGGAGT
Found at i:1281489 original size:31 final size:30
Alignment explanation
Indices: 1281451--1281510 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1281441 TTATATAATC
1281451 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
1281482 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
1281511 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:1289467 original size:15 final size:15
Alignment explanation
Indices: 1289447--1289479 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1289437 GAGGGCGCGA
1289447 GAGCCGAACACTCAC
1 GAGCCGAACACTCAC
1289462 GAGCCGAACACTCAC
1 GAGCCGAACACTCAC
1289477 GAG
1 GAG
1289480 GAGTCAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.06
Consensus pattern (15 bp):
GAGCCGAACACTCAC
Found at i:1291347 original size:224 final size:225
Alignment explanation
Indices: 1290946--1291373 Score: 646
Period size: 224 Copynumber: 1.9 Consensus size: 225
1290936 CTCTAATGAT
* * ** * * *
1290946 TTTTCCTGGTGTATGCTTTGTAACTTTCCATTTATATGGATCATATTCGCTTCAAAAACCATGAA
1 TTTTCCTGGTGTAGGCTCTACAACTTGCCATTTATATGGATCATATTCGCATCAAAAACCACGAA
* * * *
1291011 ATCTTAGACCGAGAAACTAAGTATAATGACAATCTTTGAGACGAATTATGATTTGTTATTGTAGC
66 AGCTTAGACAGAGAAACTAAGTATAATGACAATCTTTGAGACGAATTATGATTTGTTACTATAGC
* *
1291076 TAACAAGCAGTGCCTCCTTATGGCTATGAGGAAGCCTTTCTTTTGGCATAA-CATACTTGCTACA
131 TAACAAGCAGTGCCTCCTTATGGCTATGAGGAAGCATTTCCTTTGGCA-AAGCATACTTGCTACA
* *
1291140 GTATTCTGATTGTATTTTGATCTCCACTGAG
195 ATACTCTGATTGTATTTTGATCTCCACTGAG
*
1291171 TTTTCCTGGTGTAGGCTCTACAACTTGCCATTTATATGGATCCTATT-GCATCAAAAACCACGAA
1 TTTTCCTGGTGTAGGCTCTACAACTTGCCATTTATATGGATCATATTCGCATCAAAAACCACGAA
*
1291235 AGCTTAGACAGAGAAACTAAGTATAATGACAGTCTTTGAGACGAATTATGATTTGTTACTATAGC
66 AGCTTAGACAGAGAAACTAAGTATAATGACAATCTTTGAGACGAATTATGATTTGTTACTATAGC
* *
1291300 TAACATGCAGTGTCTCCTTATGGCTAT-AGGGAAGCATTTCCTTTGGCAAAGCATACTTGCTACA
131 TAACAAGCAGTGCCTCCTTATGGCTATGA-GGAAGCATTTCCTTTGGCAAAGCATACTTGCTACA
1291364 ATACTCTGAT
195 ATACTCTGAT
1291374 CTGGTTTTCA
Statistics
Matches: 182, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
223 3 0.02
224 138 0.76
225 41 0.23
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (225 bp):
TTTTCCTGGTGTAGGCTCTACAACTTGCCATTTATATGGATCATATTCGCATCAAAAACCACGAA
AGCTTAGACAGAGAAACTAAGTATAATGACAATCTTTGAGACGAATTATGATTTGTTACTATAGC
TAACAAGCAGTGCCTCCTTATGGCTATGAGGAAGCATTTCCTTTGGCAAAGCATACTTGCTACAA
TACTCTGATTGTATTTTGATCTCCACTGAG
Found at i:1297388 original size:15 final size:15
Alignment explanation
Indices: 1297368--1297397 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1297358 TAAGTCCTGG
1297368 AGGGTTTGTTTCTGC
1 AGGGTTTGTTTCTGC
1297383 AGGGTTTGTTTCTGC
1 AGGGTTTGTTTCTGC
1297398 TCTAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (15 bp):
AGGGTTTGTTTCTGC
Found at i:1299042 original size:17 final size:17
Alignment explanation
Indices: 1299022--1299058 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1299012 GAGTTATAAG
*
1299022 TTGCCCTTTTTTAATTC
1 TTGCCCTTTTTAAATTC
1299039 TTGCCCTTTTTAAATTC
1 TTGCCCTTTTTAAATTC
1299056 TTG
1 TTG
1299059 TACAGTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.57
Consensus pattern (17 bp):
TTGCCCTTTTTAAATTC
Found at i:1300090 original size:24 final size:24
Alignment explanation
Indices: 1300063--1300126 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1300053 ATTCTCATGG
*
1300063 ACAATATGATGTGGAGTCTAGTAA
1 ACAAAATGATGTGGAGTCTAGTAA
* * **
1300087 ACAAAATAATATGGAGTCTAGTGG
1 ACAAAATGATGTGGAGTCTAGTAA
*
1300111 ACAAGATGATGTGGAG
1 ACAAAATGATGTGGAG
1300127 CCCATGATGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (24 bp):
ACAAAATGATGTGGAGTCTAGTAA
Found at i:1303765 original size:2 final size:2
Alignment explanation
Indices: 1303749--1303806 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
1303739 TAAGTTAATG
*
1303749 TA TA TA TT TA T- 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
*
1303790 TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1303807 GTATGTATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1303815 original size:8 final size:8
Alignment explanation
Indices: 1303760--1303817 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
1303750 ATATATTTAT
*
1303760 TATATATA
1 TATATATG
*
1303768 TATATATA
1 TATATATG
*
1303776 TATATATA
1 TATATATG
1303784 TATATATG
1 TATATATG
*
1303792 TATATATA
1 TATATATG
1303800 TATATATG
1 TATATATG
*
1303808 TATGTATG
1 TATATATG
1303816 TA
1 TA
1303818 ACGTTGAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:1308406 original size:29 final size:29
Alignment explanation
Indices: 1308373--1308434 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1308363 AAATAAACAT
1308373 ATTAGGGTAAATTATACATAGACCACCCA
1 ATTAGGGTAAATTATACATAGACCACCCA
1308402 ATTAGGGTAAATTATACATAGACCACCCA
1 ATTAGGGTAAATTATACATAGACCACCCA
1308431 ATTA
1 ATTA
1308435 TAGCCCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (29 bp):
ATTAGGGTAAATTATACATAGACCACCCA
Found at i:1309473 original size:14 final size:14
Alignment explanation
Indices: 1309454--1309496 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1309444 AATAGGGATA
1309454 ATAAATATTAGTTG
1 ATAAATATTAGTTG
**
1309468 ATAAATA-TAGAAG
1 ATAAATATTAGTTG
*
1309481 ATCAATATTAGTTG
1 ATAAATATTAGTTG
1309495 AT
1 AT
1309497 TTAAGTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (14 bp):
ATAAATATTAGTTG
Found at i:1311909 original size:15 final size:16
Alignment explanation
Indices: 1311885--1311924 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1311875 AATCATATTT
1311885 AATAAT-AAATTTTAA
1 AATAATAAAATTTTAA
1311900 AAT-ATAAAA-TTTAA
1 AATAATAAAATTTTAA
1311914 AATAATAAAAT
1 AATAATAAAAT
1311925 CCCTAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATAAAATTTTAA
Found at i:1311912 original size:14 final size:15
Alignment explanation
Indices: 1311885--1311924 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
1311875 AATCATATTT
*
1311885 AATAATAAATTTTAA
1 AATAATAAAATTTAA
1311900 AAT-ATAAAATTTAA
1 AATAATAAAATTTAA
1311914 AATAATAAAAT
1 AATAATAAAAT
1311925 CCCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATAAAATTTAA
Found at i:1313625 original size:2 final size:2
Alignment explanation
Indices: 1313618--1313655 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1313608 TTTCAAAGAA
1313618 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
1313656 TAAGTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1315438 original size:2 final size:2
Alignment explanation
Indices: 1315431--1315488 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1315421 AATTATAACA
* *
1315431 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AG 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
1315473 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1315489 CTTTCAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1317631 original size:21 final size:21
Alignment explanation
Indices: 1317592--1317632 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1317582 AACGTAATAA
*
1317592 CACAAAAATAGTAGCCCAAAT
1 CACAAAAATAGTAGACCAAAT
1317613 CACAAATAATAGT-GACCAAA
1 CACAAA-AATAGTAGACCAAA
1317633 ATGCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.15
Consensus pattern (21 bp):
CACAAAAATAGTAGACCAAAT
Found at i:1319772 original size:236 final size:235
Alignment explanation
Indices: 1319339--1319851 Score: 775
Period size: 236 Copynumber: 2.2 Consensus size: 235
1319329 GGTCTAACAT
*
1319339 ATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTATTTCAAGAAAAATCAA
1 ATGGCCCGAAGAACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTATTTCAAGAAAAATCAA
* *
1319404 TTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTATCATTTTCGAAAATCATGTGAAA
66 CTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTATCATTTTCGAAAATCATATGAAA
* * * *
1319469 ACATCCTGCTCGAAGGTCTTATGGATGCTCGAATGACTTATCATCTTGCTTGAAACACTTATAGA
131 ACATCCTGCTCGAAGGTCTTATGGATGCCCGAAAGACTTATCATCTTGCTCGAAAAACTTATAGA
1319534 TGACCTAAAGAATTTAAGAATCATGCTCG-AGACTTACTG
196 TGACCTAAAGAATTTAAGAATCATGCTCGAAGACTTACTG
*
1319573 ATGGCACGAAGAACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATC
1 ATGGCCCGAAGAACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTA--TTTCAAGAAAAATC
*
1319638 AACTTTCAGAAAAGA-TT-AATGAGAAACTTTGGAAATCGCTTTCTCATTTTCGAAAATCATATG
64 AACTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCG-TTTATCATTTTCGAAAATCATATG
*
1319701 AAAACATTCTGC-CGGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAAACTT
128 AAAACATCCTGCTC-GAAGGTCTTATGGAT-GCCCGAAAGACTTATCATCTTGCTCGAAAAACTT
* * * *
1319765 ATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGGCTTACTG
191 ATAGATGACCTAAAGAATTTAAGAATCATGCTCG-AAGACTTACTG
* *
1319811 ATGGCCCGAAGAACTTACTCA-TCAAGAAACTCTTGAAAATC
1 ATGGCCCGAAGAACTTACTAAGT-AAGAAACT-TTGGAAATC
1319852 AAGCTTAGTT
Statistics
Matches: 253, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
234 69 0.27
235 50 0.20
236 89 0.35
237 1 0.00
238 36 0.14
239 8 0.03
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (235 bp):
ATGGCCCGAAGAACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTATTTCAAGAAAAATCAA
CTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTATCATTTTCGAAAATCATATGAAA
ACATCCTGCTCGAAGGTCTTATGGATGCCCGAAAGACTTATCATCTTGCTCGAAAAACTTATAGA
TGACCTAAAGAATTTAAGAATCATGCTCGAAGACTTACTG
Found at i:1319834 original size:42 final size:41
Alignment explanation
Indices: 1319721--1319834 Score: 97
Period size: 42 Copynumber: 2.7 Consensus size: 41
1319711 GCCGGAAGGT
* *
1319721 CTTATGGATGGCCCGAA-AGACTTATCATCTTGCTCGAAAAA
1 CTTATAGATGGCCCGAAGA-ACTTATCATCATGCTCGAAAAA
* * * * * **
1319762 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGG
1 CTTATAGATGGCCCGAAGAACTT-ATCATCATGCTCGAAAAA
1319804 CTTACT-GATGGCCCGAAGAACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGAACTTA-TCATCA
1319835 AGAAACTCTT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
41 18 0.33
42 36 0.65
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGAACTTATCATCATGCTCGAAAAA
Found at i:1320006 original size:53 final size:52
Alignment explanation
Indices: 1319887--1320822 Score: 695
Period size: 53 Copynumber: 17.7 Consensus size: 52
1319877 TTATAGTTAT
* * * *
1319887 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTAATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTT-CAAATTCATTTGAAAA
1319941 CATCAAGAAACCCCTGAAAATCATGCTTAGTTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCATTTGAAAA
1319994 CATCAAGAAACCCCTGAAAATCATGCTTAGTTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCATTTGAAAA
* * * * ** *
1320047 CATTAATAAACCCCTAAAAATTAGGCTTAACTTCTTTCAAATTTATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCATTTGAAAA
* ** *
1320100 CATCAAGAAACCCCTGAAAATCAAGGTTAGCCTCTTTCAAATTCATTT-AATA
1 CATCAAGAAACCCCTGAAAATC-AGCTTAGTTTCTTTCAAATTCATTTGAAAA
* * *
1320152 CATCAAGAAACCCCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCATTTGAAAA
* * * *
1320205 CATCAAGAAACCCTTAAAAATTAGACTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAG-CTTAGTTTCTTTCAAATTCATTTGAAAA
* * * *
1320258 CATAAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCATTTGAAAA
* ** *
1320311 CATCAAGAAACCCCTAAAAATCAAGCTTAAATTCTTTCAAATTTATTTGAAAA
1 CATCAAGAAACCCCTGAAAATC-AGCTTAGTTTCTTTCAAATTCATTTGAAAA
* * * * *
1320364 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTTTTTTTATTATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAA-TCAGCTTAG-TTTCTTTCA-AATTCATTTGAAAA
* * * * * *
1320419 TATC-ATAAACCTCTAAAAATTAAGCTTAG---CTTT----TTCCTTTGAAAA
1 CATCAAGAAACCCCTGAAAA-TCAGCTTAGTTTCTTTCAAATTCATTTGAAAA
* * * *
1320464 CATCAAGAAACCCCTGAAAACCATGCTTAGCTTCTTTAAAATTCATCATG----
1 CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAATTCAT-TTGAAAA
* * * * *
1320514 --TCAAGAAACCTCTGAAAATCAGACTT-GATTTCTTTGAAAGCTAATTTAAAAA
1 CATCAAGAAACCCCTGAAAATCAG-CTTAG-TTTCTTTCAAA-TTCATTTGAAAA
** * **
1320566 TCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACACATTTGAAAA
1 -CATCAAGAAACCCCTGAAAATCAG-CTTAGTTTCTTT-CAAATTCATTTGAAAA
** ** * * * * *
1320621 TTGTCAAGAAACTTCTGAAAATAAGGCTTAGTTTCTTTAAAAGCTCGTTTAAAAA
1 -CATCAAGAAACCCCTGAAAATCA-GCTTAGTTTCTTTCAAA-TTCATTTGAAAA
* ** * * *
1320676 TGATCAAGAAACTTCTGAAAATCGAACTTAGTTTCTTTAAAAACTCATTT-AAAA
1 -CATCAAGAAACCCCTGAAAATC-AGCTTAGTTTCTTT-CAAATTCATTTGAAAA
* ** * * * *
1320730 TCATCAGGAATA-TTCTGAAAATCAGACTTATTTTCTTTGAAAGCTCATTTAAAAA
1 -CATCAAGAA-ACCCCTGAAAATCAG-CTTAGTTTCTTTCAAA-TTCATTTGAAAA
* * **
1320785 TAATCAAGAAACTTCC-GAAAATTGGACTTAGTTTCTTT
1 -CATCAAGAAAC-CCCTGAAAATCAG-CTTAGTTTCTTT
1320823 AAAAAATTGC
Statistics
Matches: 751, Mismatches: 90, Indels: 81
0.81 0.10 0.09
Matches are distributed among these distances:
45 15 0.02
46 18 0.02
47 2 0.00
48 32 0.04
49 7 0.01
50 3 0.00
51 1 0.00
52 46 0.06
53 332 0.44
54 115 0.15
55 168 0.22
56 12 0.02
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (52 bp):
CATCAAGAAACCCCTGAAAATCAGCTTAGTTTCTTTCAAATTCATTTGAAAA
Found at i:1320075 original size:106 final size:106
Alignment explanation
Indices: 1319887--1320509 Score: 798
Period size: 106 Copynumber: 5.9 Consensus size: 106
1319877 TTATAGTTAT
* * *
1319887 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTAATTTGAAAACATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTT-CAAATTCATTTGAAAACATCAAGAAAC
* * * *
1319952 CCCTGAAAATCATGCTTAGTTTCTTTCAAATTCATTTGAAAA
65 CCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
1319994 CATCAAGAAACCCCTGAAAATCATGCTTAGTTTCTTTCAAATTCATTTGAAAACATTAATAAACC
1 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
* *
1320059 CCTAAAAATTAGGCTTAACTTCTTTCAAATTTATTTGAAAA
66 CCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * *
1320100 CATCAAGAAACCCCTGAAAATCAAGGTTAGCCTCTTTCAAATTCATTT-AATACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
*
1320164 CCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAA
66 CCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * *
1320205 CATCAAGAAACCCTTAAAAAT-TAGACTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAAG-CTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAAC
1320269 CCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
65 CCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
** *
1320311 CATCAAGAAACCCCTAAAAATCAAGCTTAAATTCTTTCAAATTTATTTGAAAACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
* * * *
1320376 CCTAAAAATTAAGCTTAGCTTTTTTTTATTATTCATTTGAAAA
66 CCTAAAAATTAGGCTTAGC-TTCTTTCA-AATTCATTTGAAAA
* * * *
1320419 TATC-ATAAACCTCTAAAAATTAAGCTTAGCTT-TTTC-----C-TTTGAAAACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
* ** * *
1320476 CCTGAAAACCATGCTTAGCTTCTTTAAAATTCAT
66 CCTAAAAATTAGGCTTAGCTTCTTTCAAATTCAT
1320510 CATGTCAAGA
Statistics
Matches: 456, Mismatches: 55, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
98 6 0.01
99 6 0.01
100 35 0.08
104 2 0.00
105 91 0.20
106 235 0.52
107 65 0.14
108 16 0.04
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (106 bp):
CATCAAGAAACCCCTAAAAATCAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACC
CCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
Found at i:1320253 original size:211 final size:212
Alignment explanation
Indices: 1319887--1320509 Score: 795
Period size: 211 Copynumber: 3.0 Consensus size: 212
1319877 TTATAGTTAT
*
1319887 CATCAAGAAACCCCTAAAAATC-AGGCTTAGCTTCTTTAAAAATTAATTTGAAAACATCAAGAAA
1 CATCAAGAAACCCCTAAAAATCAAGG-TTAGCTTCTTT-CAAATTAATTTGAAAACATCAAGAAA
* * * * * *
1319951 CCCCTGAAAATCATGCTTAGTTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATC
64 CCCCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCTTAAAAATT
* * *
1320016 ATG-CTTAGTTTCTTTCAAATTCATTTGAAAACATTAATAAACCCCTAAAAATTAGGCTTAACTT
129 A-GACTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAACCCCTAAAAATTAGGCTTAACTT
*
1320080 CTTTCAAATTTATTTGAAAA
193 CTTTCAAATTCATTTGAAAA
* * * *
1320100 CATCAAGAAACCCCTGAAAATCAAGGTTAGCCTCTTTCAAATTCATTT-AATACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATCAAGGTTAGCTTCTTTCAAATTAATTTGAAAACATCAAGAAACC
1320164 CCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCTTAAAAATTAG
66 CCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCTTAAAAATTAG
*
1320229 ACTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAACCCCTAAAAATTAGGCTTAGCTTCTT
131 ACTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAACCCCTAAAAATTAGGCTTAACTTCTT
1320294 TCAAATTCATTTGAAAA
196 TCAAATTCATTTGAAAA
* ** *
1320311 CATCAAGAAACCCCTAAAAATCAAGCTTAAATTCTTTCAAATTTATTTGAAAACATCAAGAAACC
1 CATCAAGAAACCCCTAAAAATCAAGGTTAGCTTCTTTCAAATTAATTTGAAAACATCAAGAAACC
* * * * * *
1320376 CCTAAAAATTAAGCTTAGCTTTTTTTTATTATTCATTTGAAAATATC-ATAAA-CCTCTAAAAAT
66 CCTAAAAATTATGCTTAGC-TTCTTTCA-AATTCATTTGAAAACATCAAGAAACCCT-TAAAAAT
* * ** * *
1320439 TA-AGCTTAGCTT-TTTC-----C-TTTGAAAACATCAAGAAACCCCTGAAAACCATGCTTAGCT
128 TAGA-CTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAACCCCTAAAAATTAGGCTTAACT
*
1320496 TCTTTAAAATTCAT
192 TCTTTCAAATTCAT
1320510 CATGTCAAGA
Statistics
Matches: 368, Mismatches: 35, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
206 48 0.13
207 1 0.00
210 1 0.00
211 191 0.52
212 50 0.14
213 58 0.16
214 19 0.05
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (212 bp):
CATCAAGAAACCCCTAAAAATCAAGGTTAGCTTCTTTCAAATTAATTTGAAAACATCAAGAAACC
CCTAAAAATTATGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCTTAAAAATTAG
ACTTAGCTTCTTTCAAATTCATTTGAAAACATAAAGAAACCCCTAAAAATTAGGCTTAACTTCTT
TCAAATTCATTTGAAAA
Found at i:1320587 original size:55 final size:55
Alignment explanation
Indices: 1320514--1320826 Score: 391
Period size: 55 Copynumber: 5.7 Consensus size: 55
1320504 ATTCATCATG
* * *
1320514 TCAAGAAACCTCTGAAAATCAGACTT-GATTTCTTTGAAAGCTAATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAG-TTTCTTTAAAAGCTCATTTAAAAATCA
* * * **
1320569 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACACATTTGAAAATTG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
1320624 TCAAGAAACTTCTGAAAATAAGGCTTAGTTTCTTTAAAAGCTCGTTTAAAAATGA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
*
1320679 TCAAGAAACTTCTGAAAATC-GAACTTAGTTTCTTTAAAAACTCATTT-AAAATCA
1 TCAAGAAACTTCTGAAAATCAG-ACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
1320733 TCAGGAATA-TTCTGAAAATCAGACTTATTTTCTTTGAAAGCTCATTTAAAAATAA
1 TCAAGAA-ACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* **
1320788 TCAAGAAACTTCCGAAAATTGGACTTAGTTTCTTTAAAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA
1320827 AATTGCATTA
Statistics
Matches: 220, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
54 47 0.21
55 172 0.78
56 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
Found at i:1322743 original size:4 final size:4
Alignment explanation
Indices: 1322727--1322783 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
1322717 TGAATTATTT
* * *
1322727 TTTC TTT- TTTC TTTC TTTA TTTT TTTC TTATTC TTTC TTTC TTTTC TCTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -T-TTC TTTC TTTC -TTTC TTTC
1322777 TTTC TTT
1 TTTC TTT
1322784 TATGTTTCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
3 3 0.07
4 32 0.73
5 6 0.14
6 3 0.07
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1322743 original size:11 final size:11
Alignment explanation
Indices: 1322727--1322784 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 11
1322717 TGAATTATTT
1322727 TTTCTTTTTTC
1 TTTCTTTTTTC
*
1322738 TTTCTTTATTTT
1 TTTCTTT-TTTC
1322750 TTTCTTATTCTTTC
1 TTTC-T-TT-TTTC
1322764 TTTCTTTTCTCTC
1 TTTCTTTT-T-TC
1322777 TTTCTTTT
1 TTTCTTTT
1322785 ATGTTTCTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.21
12 10 0.26
13 12 0.31
14 9 0.23
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:1322746 original size:22 final size:22
Alignment explanation
Indices: 1322724--1322771 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1322714 TCTTGAATTA
*
1322724 TTTTTTCTTTTTTCTTTCTTTAT
1 TTTTTTC-TTATTCTTTCTTTAT
*
1322747 TTTTTTCTTATTCTTTCTTTCT
1 TTTTTTCTTATTCTTTCTTTAT
1322769 TTT
1 TTT
1322772 CTCTCTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTCTTATTCTTTCTTTAT
Found at i:1324165 original size:22 final size:20
Alignment explanation
Indices: 1324132--1324197 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 20
1324122 TACGATGTAT
1324132 AGATGCTAATGCAAAATTGCAA
1 AGATGC-AATGCAAAA-TGCAA
1324154 AGATGCACATGCAAAGATGCAA
1 AGATGCA-ATGCAAA-ATGCAA
* *
1324176 AAATGGGAATGCAAAATGCAA
1 AGAT-GCAATGCAAAATGCAA
1324197 A
1 A
1324198 ATGTAAATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.21
22 28 0.72
23 3 0.08
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (20 bp):
AGATGCAATGCAAAATGCAA
Found at i:1325112 original size:20 final size:20
Alignment explanation
Indices: 1325087--1325177 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
1325077 GATTTTCCAT
* *
1325087 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1325107 AATCGCCAACGCGAACACATA
1 AATCG-CAACGCGAACACATA
* *
1325128 AATCGCAACGCG-TC-CGTA
1 AATCGCAACGCGAACACATA
* * *
1325146 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1325166 AATCGCAACGCG
1 AATCGCAACGCG
1325178 TATGGGTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.23
19 1 0.02
20 30 0.49
21 16 0.26
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1325180 original size:20 final size:20
Alignment explanation
Indices: 1325126--1325454 Score: 434
Period size: 20 Copynumber: 16.6 Consensus size: 20
1325116 CGCGAACACA
1325126 TAAATCGCAACGCG--TCCG
1 TAAATCGCAACGCGTATCCG
*
1325144 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
1325164 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
1325184 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1325204 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
1325224 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
1325244 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
1325264 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1325284 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
1325304 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1325324 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
1325344 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1325364 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1325384 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1325404 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1325424 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1325444 TAAATCACAAC
1 TAAATCGCAAC
1325455 ACTGAAATTT
Statistics
Matches: 274, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
18 13 0.05
19 2 0.01
20 258 0.94
21 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1326158 original size:24 final size:24
Alignment explanation
Indices: 1326119--1326165 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1326109 AAATTTGGTC
1326119 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1326143 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1326166 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1326358 original size:12 final size:12
Alignment explanation
Indices: 1326341--1326365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1326331 ATATAATCCT
1326341 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1326353 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1326365 G
1 G
1326366 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:1328025 original size:14 final size:14
Alignment explanation
Indices: 1328006--1328095 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1327996 TTGAAATGAA
1328006 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1328020 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1328037 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1328053 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1328072 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1328086 AATCGCAACG
1 AATCGCAACG
1328096 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1328043 original size:33 final size:33
Alignment explanation
Indices: 1327998--1328112 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1327988 TCTTTTGGTT
1327998 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1328031 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1328064 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1328097 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1328113 TGCGATTTGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1328044 original size:19 final size:18
Alignment explanation
Indices: 1328005--1328117 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1327995 GTTGAAATGA
1328005 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1328020 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1328037 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1328053 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1328070 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1328086 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1328103 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1328118 TTTGGTTTCG
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1328147 original size:14 final size:14
Alignment explanation
Indices: 1328128--1328182 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1328118 TTTGGTTTCG
1328128 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1328142 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1328161 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1328175 CGTTGCGA
1 CGTTGCGA
1328183 CAGTCATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1328345 original size:33 final size:33
Alignment explanation
Indices: 1328303--1328373 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1328293 AATACTAACT
*
1328303 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1328336 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1328369 TGAAA
1 TGAAA
1328374 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1328608 original size:23 final size:22
Alignment explanation
Indices: 1328555--1328610 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1328545 TGGTTGTGAG
**
1328555 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1328577 GGAAATCTTCGGAGATGGGGAAC
1 GGATTTCTTCGGAGATGGGG-AC
1328600 GGATTTCTTCG
1 GGATTTCTTCG
1328611 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.21, C:0.16, G:0.39, T:0.23
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1328781 original size:20 final size:20
Alignment explanation
Indices: 1328756--1328949 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1328746 CTTTAAATAT
1328756 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1328776 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1328798 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1328817 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1328837 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1328857 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1328877 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1328897 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1328917 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1328937 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1328950 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1328943 original size:60 final size:60
Alignment explanation
Indices: 1328756--1328949 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1328746 CTTTAAATAT
**
1328756 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1328817 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1328877 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1328937 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1328950 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1328966 original size:21 final size:20
Alignment explanation
Indices: 1328942--1329018 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1328932 ATATTCGCGT
1328942 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1328963 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1328983 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1329005 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1329019 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1329029 original size:20 final size:20
Alignment explanation
Indices: 1329004--1329055 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1328994 AAGAATCGCG
*
1329004 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1329024 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1329044 TTGCGATTCTGG
1 TTGCGATTCTGG
1329056 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1329995 original size:17 final size:18
Alignment explanation
Indices: 1329950--1329995 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1329940 ATATATAAAG
*
1329950 ATAAAACAAATAAAAATA
1 ATAAAAGAAATAAAAATA
1329968 ATAAAAG-AATAAAAA-A
1 ATAAAAGAAATAAAAATA
* *
1329984 TTGAAAGAAATA
1 ATAAAAGAAATA
1329996 CAAAGAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 12 0.50
18 6 0.25
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (18 bp):
ATAAAAGAAATAAAAATA
Found at i:1331150 original size:27 final size:25
Alignment explanation
Indices: 1331120--1331182 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
1331110 ATAGTGATTT
*
1331120 AAATGCATAAATTAAA-AATACAACACA
1 AAATACATAAA-TAAATAATA-AA-ACA
* *
1331147 AAATTCATGAATAAATAATAAAACA
1 AAATACATAAATAAATAATAAAACA
1331172 AAATACATAAA
1 AAATACATAAA
1331183 GTGACTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 12 0.39
26 6 0.19
27 13 0.42
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (25 bp):
AAATACATAAATAAATAATAAAACA
Found at i:1347700 original size:34 final size:35
Alignment explanation
Indices: 1347638--1347710 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 35
1347628 TAAACAAGCG
1347638 CCACCCTTATATTCCTTGCCCCCACCAATCATCTT
1 CCACCCTTATATTCCTTGCCCCCACCAATCATCTT
*
1347673 CCACCCTTCTATTCCTTG-CCCCACCAATCATCTT
1 CCACCCTTATATTCCTTGCCCCCACCAATCATCTT
1347707 CCAC
1 CCAC
1347711 AGAGCAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 20 0.54
35 17 0.46
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.30
Consensus pattern (35 bp):
CCACCCTTATATTCCTTGCCCCCACCAATCATCTT
Found at i:1349839 original size:48 final size:48
Alignment explanation
Indices: 1349787--1349884 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
1349777 TAATCAAACT
* *
1349787 TTAGGGCATGGAATCGGCACTGATATCTAACATTTGTACAAACAATTA
1 TTAGGGCATGGAATCGGCAATGATATCTAACATCTGTACAAACAATTA
*
1349835 TTAGGGCATGGAATCGGCAATGATATCTAATATCTGTACAAACAATTA
1 TTAGGGCATGGAATCGGCAATGATATCTAACATCTGTACAAACAATTA
1349883 TT
1 TT
1349885 TGTAAAAGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (48 bp):
TTAGGGCATGGAATCGGCAATGATATCTAACATCTGTACAAACAATTA
Found at i:1352472 original size:68 final size:68
Alignment explanation
Indices: 1352363--1352496 Score: 223
Period size: 68 Copynumber: 2.0 Consensus size: 68
1352353 TTGTTGATTA
* *
1352363 CTAATAATTTGCCCCACTTTGCAGCAATGTTTTTAAAAGTATCCCAATTCCAAGCGTGAAAGGAA
1 CTAATAATTTGCCCCACTTTGCAGAAATGTTTTTAAAAGTATCACAATTCCAAGCGTGAAAGGAA
1352428 TTG
66 TTG
** *
1352431 CTAATAATTTGCCCCACTTTGTGGAAATGTTTTTGAAAGTATCACAATTCCAAGCGTGAAAGGAA
1 CTAATAATTTGCCCCACTTTGCAGAAATGTTTTTAAAAGTATCACAATTCCAAGCGTGAAAGGAA
1352496 T
66 T
1352497 ACCTTCGCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (68 bp):
CTAATAATTTGCCCCACTTTGCAGAAATGTTTTTAAAAGTATCACAATTCCAAGCGTGAAAGGAA
TTG
Found at i:1354013 original size:33 final size:33
Alignment explanation
Indices: 1353965--1354027 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1353955 CGCAAAGGAT
* *
1353965 GCATCCACCGTGTCTGATGCATCAGACCTTTGA
1 GCATCCACCGCGTCTGATGCAGCAGACCTTTGA
* * *
1353998 GCATCCACTGCGTCTGTTTCAGCAGACCTT
1 GCATCCACCGCGTCTGATGCAGCAGACCTT
1354028 CGAGGTCGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.29
Consensus pattern (33 bp):
GCATCCACCGCGTCTGATGCAGCAGACCTTTGA
Found at i:1354337 original size:24 final size:24
Alignment explanation
Indices: 1354310--1354356 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1354300 GTTCGTGAAC
1354310 GTTCAGTTATATTCGTTTATGTTT
1 GTTCAGTTATATTCGTTTATGTTT
* *
1354334 GTTCGGTTATGTTCGTTTATGTT
1 GTTCAGTTATATTCGTTTATGTT
1354357 CATTCATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.09, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCAGTTATATTCGTTTATGTTT
Found at i:1354367 original size:24 final size:24
Alignment explanation
Indices: 1354311--1354370 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1354301 TTCGTGAACG
* **
1354311 TTCAGTTATATTCGTTTATGTTTG
1 TTCAGTTATGTTCGTTTATGTTCA
*
1354335 TTCGGTTATGTTCGTTTATGTTCA
1 TTCAGTTATGTTCGTTTATGTTCA
*
1354359 TTCATTTATGTT
1 TTCAGTTATGTT
1354371 TAATCCAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.58
Consensus pattern (24 bp):
TTCAGTTATGTTCGTTTATGTTCA
Found at i:1355047 original size:16 final size:16
Alignment explanation
Indices: 1355028--1355108 Score: 126
Period size: 16 Copynumber: 5.1 Consensus size: 16
1355018 CCAATGTTTA
1355028 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1355044 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1355060 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
1355076 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
1355092 TGCTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1355108 T
1 T
1355109 TTATTTATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.07, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1355444 original size:96 final size:96
Alignment explanation
Indices: 1355275--1355450 Score: 291
Period size: 96 Copynumber: 1.8 Consensus size: 96
1355265 CTATCCACCA
* *
1355275 CGTCTGTTGCAGCAGATCTTCGAGGTCGCCTGGGCTGAGACGGGGTTTGGGGTGCCATGATTAGA
1 CGTCTGTTGCAGCAGACCTTCGAGGTCGCCTGGGCTGAGACGGGGGTTGGGGTGCCATGATTAGA
1355340 TCGAAACTTTCACTGCAAAGTGCAACGACCG
66 TCGAAACTTTCACTGCAAAGTGCAACGACCG
*
1355371 CGTCTGTTGCAGCAGACCTTCGAGGTCGCTTGGGCTGAGACGGGGGTTGGGGTGCCATGGA-TAG
1 CGTCTGTTGCAGCAGACCTTCGAGGTCGCCTGGGCTGAGACGGGGGTTGGGGTGCCAT-GATTAG
* *
1355435 ATTGGAACTTTCACTG
65 ATCGAAACTTTCACTG
1355451 AAAAATGTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
96 72 0.97
97 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.25
Consensus pattern (96 bp):
CGTCTGTTGCAGCAGACCTTCGAGGTCGCCTGGGCTGAGACGGGGGTTGGGGTGCCATGATTAGA
TCGAAACTTTCACTGCAAAGTGCAACGACCG
Found at i:1358342 original size:2 final size:2
Alignment explanation
Indices: 1358335--1358366 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1358325 GTTGGGTGGC
1358335 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
1358367 GTTTAGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1359527 original size:200 final size:199
Alignment explanation
Indices: 1359169--1359528 Score: 465
Period size: 200 Copynumber: 1.8 Consensus size: 199
1359159 AGTTGAGACC
* * * *
1359169 AATATCGACACATACGAGATATTGTAAGCGGCTAAAAATCGTATTGAAAATGATTCCAAAGCTTG
1 AATATCGACACATACGAGACATTATAAGCGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTTG
* * *
1359234 TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTGGAGGGGTATTTATGGGTAG
66 TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTATGGGAAG
*
1359299 TTAATCCAAAAATTTCGTAATTTATAAGATCAAAGGCATAATATTATAAATTATCTTTCAACTGA
131 TTAATCCAAAAATTTCATAATTTATAAGATCAAAGGCATAATATTATAAATTATCTTTCAACTGA
1359364 TGGT
196 TGGT
* * * * *
1359368 AATATCGATACATACGAGACATTATAAGTTGGCTACAAATCGCGTGGAAAATGGTTCCAAAGCTT
1 AATATCGACACATACGAGACATTATAAG-CGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTT
* * * * *
1359433 GCTTTTGTGCATGAAGAAGAAGCT-AAAATGGTT-GGTAGGCATTTTCGAGGAGTATTT-TGGGG
65 G-TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTAT-GGG
* ** *
1359495 AATTTAATCTGGAAATTTTCATAATTTATAAGAT
128 AAGTTAATC-CAAAAATTTCATAATTTATAAGAT
1359529 TAGAATCGTA
Statistics
Matches: 135, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
198 1 0.01
199 55 0.41
200 60 0.44
201 19 0.14
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (199 bp):
AATATCGACACATACGAGACATTATAAGCGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTTG
TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTATGGGAAG
TTAATCCAAAAATTTCATAATTTATAAGATCAAAGGCATAATATTATAAATTATCTTTCAACTGA
TGGT
Found at i:1359573 original size:200 final size:199
Alignment explanation
Indices: 1359169--1359595 Score: 452
Period size: 200 Copynumber: 2.1 Consensus size: 199
1359159 AGTTGAGACC
* * * *
1359169 AATATCGACACATACGAGATATTGTAAGCGGCTAAAAATCGTATTGAAAATGATTCCAAAGCTTG
1 AATATCGACACATACGAGACATTATAAGCGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTTG
* * *
1359234 TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTGGAGGGGTATTTATGGGTAG
66 TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTATGGGAAG
* * *
1359299 TTAATCCAAAAATTTCGTAATTTATAAGATCAAAGGCATAATATTATAAATTATCTTTCAACTGA
131 TTAATCCAAAAATTTCATAATTTATAAGATCAAAGGCATAATATTATAAATTATATTCCAACTGA
1359364 TGGT
196 TGGT
* * * * *
1359368 AATATCGATACATACGAGACATTATAAGTTGGCTACAAATCGCGTGGAAAATGGTTCCAAAGCTT
1 AATATCGACACATACGAGACATTATAAG-CGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTT
* * * * *
1359433 GCTTTTGTGCATGAAGAAGAAGCT-AAAATGGTT-GGTAGGCATTTTCGAGGAGTATTT-TGGGG
65 G-TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTAT-GGG
* ** * * * * * *
1359495 AATTTAATCTGGAAATTTTCATAATTTATAAGATTAGAA-TCGTAGTATTAGT-ACTTATATTCC
128 AAGTTAATC-CAAAAATTTCATAATTTATAAGATCA-AAGGCATAATATTA-TAAATTATATTCC
* *
1359558 AATTTA-GGCT
190 AACTGATGG-T
* *
1359568 AATATCGGCATATACGAGACATTATAAG
1 AATATCGACACATACGAGACATTATAAG
1359596 AGGTGCAAAA
Statistics
Matches: 187, Mismatches: 34, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
198 1 0.01
199 57 0.30
200 107 0.57
201 22 0.12
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (199 bp):
AATATCGACACATACGAGACATTATAAGCGGCTAAAAATCGCATGGAAAATGATTCCAAAGCTTG
TTTTGTGCATAAAGAAAAAACTAAAAATGGTTCGATAGGCATATTCGAGGAGTATTTATGGGAAG
TTAATCCAAAAATTTCATAATTTATAAGATCAAAGGCATAATATTATAAATTATATTCCAACTGA
TGGT
Found at i:1362165 original size:23 final size:23
Alignment explanation
Indices: 1362147--1362207 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1362137 CTCATATAAA
*
1362147 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1362170 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1362193 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1362208 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1363820 original size:63 final size:63
Alignment explanation
Indices: 1363709--1363867 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 63
1363699 TAATGGAGGC
* * ** * *
1363709 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGTATTTGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
** **
1363772 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* *
1363835 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
1363868 CTTCAACAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 79 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:1363859 original size:19 final size:20
Alignment explanation
Indices: 1363835--1363872 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1363825 ATTTAAATTA
1363835 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
1363854 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
1363873 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:1367700 original size:23 final size:23
Alignment explanation
Indices: 1367674--1367734 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1367664 CTCATATAAA
*
1367674 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1367697 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1367720 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1367735 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1369344 original size:63 final size:63
Alignment explanation
Indices: 1369237--1369395 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
1369227 TAATGGAGGC
* * ** *
1369237 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGTATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
** **
1369300 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* *
1369363 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
1369396 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 80 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:1369387 original size:19 final size:20
Alignment explanation
Indices: 1369363--1369400 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1369353 ATTTAAATTA
1369363 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
1369382 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
1369401 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:1370638 original size:18 final size:18
Alignment explanation
Indices: 1370617--1370661 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1370607 CGAATATAAT
1370617 ATTTAAATCAAATACAAA
1 ATTTAAATCAAATACAAA
* * *
1370635 ATTTCAATCTAATATAAA
1 ATTTAAATCAAATACAAA
1370653 ATCTTAAAT
1 AT-TTAAAT
1370662 TTCATTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTAAATCAAATACAAA
Found at i:1372598 original size:19 final size:20
Alignment explanation
Indices: 1372574--1372612 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1372564 CATTATGAGA
1372574 TGGGGGTATCGGTAC-CTCC
1 TGGGGGTATCGGTACTCTCC
1372593 TGGGGGTATCGGTACTCTCC
1 TGGGGGTATCGGTACTCTCC
1372613 GAGCAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.10, C:0.26, G:0.36, T:0.28
Consensus pattern (20 bp):
TGGGGGTATCGGTACTCTCC
Found at i:1372690 original size:19 final size:20
Alignment explanation
Indices: 1372648--1372687 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1372638 AAATCTTACA
* *
1372648 TGGGGGTATTGGTACCCTCT
1 TGGGGATATCGGTACCCTCT
1372668 TGGGGATATCGGTACCCTCT
1 TGGGGATATCGGTACCCTCT
1372688 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.33, T:0.33
Consensus pattern (20 bp):
TGGGGATATCGGTACCCTCT
Found at i:1378702 original size:21 final size:21
Alignment explanation
Indices: 1378678--1378717 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1378668 AAGACTATTT
1378678 TCATTTTTATATTTTGAAACA
1 TCATTTTTATATTTTGAAACA
1378699 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
1378718 ATAAAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Done.